Microbial

J Immunol, 2003 Aug 1, 171(3), 1456 - 65
Inhibition of a p38/stress-activated protein kinase-2-dependent phosphatase restores function of IL-1 receptor-associate kinase-1 and reverses Toll-like receptor 2- and 4-dependent tolerance of macrophages; Ropert C et al.; Pretreatment of macrophages with Toll-like receptor (TLR)2 or TLR4 agonists leads to a stage of cell hyporesponsiveness to a second stimulation with TLR agonists . This tolerance state is accompanied by the repression of IL-1 receptor-associated kinase-1, mitogen-activated protein kinases, and IkappaB phosphorylation and expression of genes encoding proinflammatory cytokines, like IL-1beta and TNF-alpha . In this report, we demonstrated that mucin-like glycoprotein (tGPI-mucin) of Trypanosoma cruzi trypomastigotes (TLR2 agonist) and LPS (TLR4 agonist) induce cross-tolerance in macrophages and we addressed the role of phosphatase activity in this process . Analysis of the kinetic of phosphatase activity induced by tGPI-mucin or LPS revealed maximum levels between 12 and 24 h, which correlate with the macrophage hyporesponsiveness stage . The addition of okadaic acid, an inhibitor of phosphatase activity, reversed macrophage hyporesponsiveness after exposure to either LPS or tGPI-mucin, allowing phosphorylation of IL-1R-associated kinase-1, mitogen-activated protein kinases, and IkappaB and leading to TNF-alpha gene transcription and cytokine production . Furthermore, pretreatment with either the specific p38/stress-activated protein kinase-2 inhibitor (SB203580) or the NF-kappaB translocation inhibitor (SN50) prevented the induction of phosphatase activity and hyporesponsiveness in macrophage, permitting cytokine production after restimulation with LPS . These results indicate a critical role of p38/stress-activated protein kinase-2 and NF-kappaB-dependent phosphatase in macrophage hyporesponsiveness induced by microbial products that activate TLR2 and TLR4.

Curr Opin Plant Biol, 2003 Aug, 6(4), 334 - 8
Early phosphorylation events in biotic stress; Peck SC; Several kinases are activated during the defence response following microbial elicitation . While studying the regulation of these kinases in greater detail, it has become clear that the means by which phosphorylation events transmit specific information to the cell is highly complex . To gain a better understanding of the molecular events leading to a response, it will be increasingly important to identify not only the protein targets of phosphorylation but also the specific sites of phosphorylation . New developments in peptide-based phosphoproteome analysis appear to hold the promise of achieving these goals at the whole-cell level.

Curr Opin Plant Biol, 2003 Aug, 6(4), 327 - 33
Plant-nematode interactions; Williamson VM et al.; Root-knot nematodes and cyst nematodes are obligate, biotrophic pathogens of numerous plant species . These organisms cause dramatic changes in the morphology and physiology of their hosts . The molecular characterization of induced plant genes has provided insight into the plant processes that are usurped by nematodes as they establish their specialized feeding cells . Recently, several gene products have been identified that are secreted by the nematode during parasitism . The corresponding genes have strong similarity to microbial genes or to genes that are found in nematodes that parasitize animals . New information on host resistance genes and nematode virulence genes provides additional insight into this complex interaction.

Immunity, 2003 Jul, 19(1), 5 - 8
Dendritic cells in immunity and tolerance-do they display opposite functions?
Moser M.
It was recently proposed that cells of the dendritic family not only control immunity but also maintain tolerance to self-antigens, two complementary functions that would ensure the integrity of the organism in an environment full of pathogens . As they express a variety of receptors that specifically recognize microbial products, DCs are able to discriminate between self and nonself and may therefore enable the immune system to mount potent effector activity to pathogens while silencing self-reactive lymphocytes.

Immunology, 2003 Aug, 109(4), 476 - 86
CD8+ immunoregulatory cells in the graft-versus-host reaction: CD8 T cells activate dendritic cells to secrete interleukin-12/interleukin-18 and induce T helper 1 autoantibody; Noble A et al.; Initiation of cell-mediated immunity or autoimmunity requires secretion of interleukin (IL)-12 from dendritic cells (DC), which drives the generation of T helper 1 (Th1) effector cells in synergy with IL-18 . Induction of IL-12 can be triggered by microbial stimuli but also requires signals from activated T cells . We investigated interactions between alloreactive CD4 and CD8 T cells in mixed lymphocyte reactions (MLR) in vitro and in the graft-versus-host reaction (GVHR) in vivo . In a parent-into-F1 model of GVHR, donor CD8 cells were found to suppress the hyper-immunoglobulin E (IgE) syndrome, anti-DNA immunoglobulin G1 (IgG1) autoantibodies and donor CD4-cell expansion, but were essential for Th1-dependent immunoglobulin G2a (IgG2a) autoantibody production and release of serum IL-12 p40 . In vitro, addition of alloreactive CD8 cells to CD4 cells and mature DC enhanced Th1 development . CD4 and CD8 T cells induced IL-18 from DC and primed for IL-12 p70 secretion via interferon-gamma (IFN-gamma) or tumour necrosis factor-alpha (TNF-alpha) . However CD8 T cells, but not CD4 cells, released IFN-gamma/TNF-alpha after primary stimulation . The data suggest that rapid release of inflammatory cytokines from central memory-type CD8 cells early in immunity is critical for induction of Th1 cells via DC activation and IL-12 production . This pathway could provide a means for amplification of cell-mediated autoimmunity in the absence of microbial stimuli.

Curr Med Chem, 2003 Aug, 10(15), 1423 - 39
Synthetic vaccines: the role of adjuvants in immune targeting; Jiang ZH et al.; A clear understanding of the mechanism of function of immune stimulatory adjuvants, which commonly accompany vaccines, is beginning to emerge . Recent investigations have demonstrated that Toll-like receptors (TLRs) are the critical link between the innate and the adaptive immunity . This link, which is normally activated as a result of collaboration between adjuvants and TLRs in triggering adaptive immunity, has been a subject of several recent investigations . With the advent of well-defined synthetic small molecules, which are designed to either mimic the adjuvants or, as in many cases, to structurally represent pathogen associated molecular patterns, it is now possible to design reproducible experiments and to draw credible conclusions . An adjuvant alerts the host immune system through a mechanism similar to that of an infection by a pathogen, which involves interaction with a TLR followed by a lsqou;danger signal' to the immune system . Secretion of cytokines and regulation of the expression of co-stimulatory molecules induced by innate response shape the magnitude and quality of adaptive response . Synthetic vaccines containing specific epitopes to which immune responses are desired, are expected to be far superior in target specificity while the benefits may be long-lasting . The immune responses by therapeutic vaccines are generally adaptive in nature and such responses often require the participation of the components of innate immunity, most importantly the TLRs and their pathogen-associated binding compliments . Structurally well-defined synthetic molecules derived from lipid A, muramyl di-peptide (MDP), and CpG motifs from bacterial DNA offer a wide range of immune stimulants for the development of fully synthetic vaccines . Lipo-peptide and self-adjuvanted antigens, in combination with additional immune stimulatory adjuvants in liposome delivery system, may be important in vaccine design . Combinations of synthetic mimics of microbial products are known to display synergistic effects in stimulating the immune system . Either alone or in combination with chemotherapy, innate immune therapy using TLR ligands to stimulate the immune system may offer an alternate therapeutic approach against rapidly mutating viral infections-(HIV/AIDS), and cancers.

Chemosphere, 2003 Sep, 52(9), 1499 - 503
Microbial enhancement of Cu2+ removal capacity of Eichhornia crassipes (Mart.); So LM et al.; Bacteria resistant to Cu2+, Ni2+ or Zn2+ were isolated from the rhizosphere of water hyacinth (Eichhornia crassipes (Mart.)) and their metal ion removal capacities (RCs) were determined . The Ni2+ and Zn2+ RCs of the respective metal ion-resistant bacteria were less than 4.1 mg g(-1), while one of the Cu2+-resistant bacteria (Strain CU-1) showed a significant high Cu2+ RC of 10.6 mg g(-1) . The effect of inoculating water hyacinth with Strain CU-1 on its Cu2+ RC was further studied . Water hyacinths were treated with an antibiotic, oxytetracycline (OTC), to remove most rhizospheric bacteria of plant roots . Inoculation of Strain CU-1 increased the Cu2+ RC of the plant root by 1.91 (OTC-treated) and 1.56 (OTC-untreated) folds respectively when compared with the control . Results also showed that Strain CU-1 colonized onto the plant root and led to the increase of Cu2+ RC of the roots of water hyacinth.

Chemosphere, 2003 Sep, 52(9), 1361 - 71
Some aspects of toxic contaminants in herbal medicines; Chan K; A World Health Organisation survey indicated that about 70-80% of the world populations rely on non-conventional medicine mainly of herbal sources in their primary healthcare . In recent years, we have witnessed the increasing growth in popularity of over-the-counter (OTC) health foods, nutraceuticals, and medicinal products from plants or other natural sources in developed countries . This indirectly indicates that the public is not satisfied with their orthodox medical (OM) treatment . Such increase in popularity has also brought concerns and fears over the professionalism of practitioners, and quality, efficacy and safety of their treatment methods and products from herbal and natural sources available in the market . Over the past decade several news-catching episodes in developed communities indicated adverse effects, sometimes life threatening, allegedly arisen consequential to taking of OTC herbal products or traditional medicines from various ethnic groups . These OTC products may be contaminated with excessive or banned pesticides, microbial contaminants, heavy metals, chemical toxins, and for adulterated with orthodox drugs . Excessive or banned pesticides, heavy metals and microbial contaminants may be related to the source of these herbal materials, if they are grown under contaminated environment or during collection of these plant materials . Chemical toxins may come from unfavourable or wrong storage conditions or chemical treatment due to storage . The presence of orthodox drugs can be related to unprofessional practice of manufacturers . Some of these environment related factors can be controlled by implementing standard operating procedures (SOP) leading to Good Agricultural Practice (GAP), Good Laboratory Practice (GLP), Good Supply Practice (GSP) and Good Manufacturing Practice (GMP) for producing these medicinal products from herbal or natural sources . The public's belief that herbal and natural products are safer than synthetic medicines can only be ascertained by imposing regulatory standards on these products that should be manufactured using these Good Practices . Using Chinese medicines, as examples, this paper illustrate how advances in chemical and biomedical analysis would help to detect intentional and unintentional toxic contaminants in herbal substances . The paper also summarises how modernization and progress are being carried out to get the best out of Chinese medicines for public healthcare.

Curr Biol, 2003 Jul 15, 13(14), R571 - 3
Microbial genomics: all that you can't leave behind; Stephens CM et al.; Projects designed to scan entire microbial genomes for essential genes have revealed a remarkably compact and conserved, but not universal, set of genes whose functions are necessary for survival or reproduction.

Syst Appl Microbiol, 2003 Jun, 26(2), 228 - 35
Candidate division BD: phylogeny, distribution and abundance in soil ecosystems; Mummey DL et al.; Oligonucleotide primers were designed and used to amplify partial 16S rDNA sequences of the recently identified bacterial group BD from four diverse soils . Phylogenetic analysis of 34 BD group sequences supports division-level status for the group and also indicates that the BD group consists of at least 3 subdivision-level groups . Sequence divergence (21%) amongst these BD group sequences was found to be near the average for bacterial division-level lineages . An intercalating dye-based quantitative PCR (qPCR) assay was used to quantify BD phylogenetic group 3 16S rDNA in Wyoming shortgrass steppe soils . Although BD phylogenetic group 3 16S rDNA sequence numbers were high, averaging 3 x 10(8) copies per g soil, no significant correlations were found between their abundance and soil organic matter content, inorganic N concentration, or pH . Based on microscopically estimated cell numbers and the range of rRNA operons per genome in the bacterial domain, we estimate that BD group 3 represents between 0.75% and 10.7% of the microbial population in a shortgrass steppe soil . Our results indicate that the BD group is widely distributed in the environment and present in significant numbers in Wyoming shortgrass steppe soils.

Cell Mol Life Sci, 2003 Jun, 60(6), 1027 - 32
How sphingolipids bind and shape proteins: molecular basis of lipid-protein interactions in lipid shells, rafts and related biomembrane domains; Fantini J; Understanding the molecular mechanisms controlling the association of proteins with lipid rafts is a central issue in cell biology and medicine . A structurally conserved motif (the 'sphingolipid binding domain') has been characterized in unrelated cellular and microbial proteins targeted to lipid rafts . I propose that the structuration of a sphingolipid shell around the sphingolipid binding domain not only extracts the protein from the liquid-disordered phase of the plasma membrane, and ensures its delivery to lipid rafts, but also influences its conformation . The chaperone activity of sphingolipids in shells and rafts may play an important role in infectious and conformational diseases(human immunodeficiency virus-1, prions, Alzheimer).

Mol Microbiol, 2003 Aug, 49(3), 769 - 81
LexA-independent DNA damage-mediated induction of gene expression in Myxococcus xanthus; Campoy S et al.; Myxococcus xanthus, a member of the Proteobacteria delta-class, has two independent recA genes, recA1 and recA2, but only recA2 is DNA damage-inducible . The lexA gene has been isolated from M . xanthus by PCR amplification with oligonucleotides designed after sequence identification by tblastn analysis of its genome at the Cereon Microbial Sequence Database . The M . xanthus purified LexA protein is shown to bind specifically to the consensus sequence CTRHAMRYBYGTTCAGS present upstream of lexA and recA2 . A degenerate copy of this motif but with important differences can be identified in the region upstream of the recA1 gene . A knock-out lexA(Def) mutant that has been generated does not differ significantly from wild type in morphology, growth rate, light-induced carotenogenesis or development . Using transcriptional lacZ fusions and quantitative RT-PCR analysis, it has been demonstrated that expression of both lexA and recA2 genes is constitutive in the lexA(Def) mutant, whereas the transcription of the DNA damage non-inducible recA1 gene is not affected in this strain . recN and ssb, whose expression in Escherichia coli are LexA-regulated, are induced by DNA damage in the M . xanthus lexA(Def) mutant . These data reveal the existence of different regulatory mechanisms for DNA damage-inducible genes in bacteria belonging to different phyla.

Water Sci Technol, 2003, 47(10), 163 - 8
Bleaching of bagasse pulp with enzyme pre-treatment; Sudha B et al.; The effluent from pulp bleaching processes containing chlorinated lignin and degraded polyphenolic intermediates remains as a major source of water pollution from the pulp and paper industries . Alternative elemental chlorine free bleaching methods based on the usage of chlorine dioxide, ozone and hydrogen peroxide are potential substitutes . Bio-bleaching methods, which involve pre-treatment of pulp with microbial enzymes such as xylanases, have emerged as viable options . Investigations reported in this paper aim at exploring the suitability of commercial bacterial xylanase enzyme preparations for bio-bleaching of bagasse pulps in conjunction with specific chemical bleach sequences employing hydrogen peroxide (P), alkali extraction (E), ozonation (Z), hypochlorite (H) and chelation (Q) stages . The effluent profiles and pulp qualities obtained for each of the bleach combinations (involving bio-bleaching and chemical bleaching sequences) were monitored . Analysis of the results clearly indicates that the inclusion of enzyme pre-treatment with the TCF (total chlorine free) and ECF (elemental chlorine free) sequences has a significant effect on the effluent (COD, lignin and colour) and pulp quality (kappa number, brightness) parameters . In conclusion, the findings of this investigation indicate the potential promise of enzyme pre-treatment in combination with chemical bleaching to enhance the quality of pulps and combined effluents.

Water Sci Technol, 2003, 47(10), 79 - 84
Degradation of halogenated aliphatic compounds utilizing sequential anaerobic/aerobic treatments; McCue T et al.; The objective of this research was to determine if either methanogenic or sulfidogenic reductive dechlorination could survive an alternating anaerobic/aerobic sequence to biologically transform halogenated aliphatic hydrocarbons (HACs), specifically tetrachloroethylene (PCE), trichloroethylene (TCE), cis-1,2 dichloroethylene (cDCE), trans-1,2 dichloroethylene (tDCE), 1,1 dichloroethylene (1, 1DCE) and vinyl chloride (VC) . This ability was considered to be a necessary prerequisite for complete anaerobic/aerobic mineralization of halogenated aliphatic hydrocarbons by a single microbial consortia . Chlorinated solvents, which are among the most common groundwater contaminants, have been partially dechlorinated using single-stage anaerobic environmental treatment strategies . Various types of bacteria typically reductively dechlorinate PCE and TCE to cDCE and VC in an anaerobic environment, including methanogens, sulfidogens, and homoacetogens . The problem lies in the fact that reductive dechlorination typically leads to an accumulation of daughter compounds (cDCE, VC) which are more toxic than their parent compounds (PCE, TCE) . Furthermore, PCE and (to a lesser extent) TCE, are resistant to dechlorination in aerobic environments . In contrast, VC and cDCE are readily oxidized co-metabolically in an aerobic environment by methanotrophic bacteria, and others using oxygenases (e.g . toluene oxidizers) . Results from this research showed that both methanogenic and sulfidogenic reductive dechlorination could resume after transient exposures to both oxygen and hydrogen peroxide (H2O2) . In fact, for cycles as frequent as 10 days between aerobic treatment cycles, reductive dechlorination was observed to resume at rates at least as rapid as microcosms not exposed to aerobic treatments.

Implant Dent, 2003, 12(2), 145 - 50
Barrier membrane and bone graft treatments of dehiscence-type defect at existing implant: a case report; Dogan N et al.; Dehiscence-type bony defects may occur after implant application because of microbial action as well as of biomechanical and occlusal overload . The aim of the treatment of a periimplant defect is to arrest the progression of the bone loss and to achieve a maintainable site for the implant . In these situations, barrier membranes and bone graft materials can be used to achieve complete bone healing around dental implants . Bone regeneration is possible in a periimplant bony defect of a functioning implant if the proper surgical technique is utilized and the etiologic cause is eradicated . This study presents the surgical coverage of a periimplant bony defect around an implant that was inserted 7 years ago . The surgical correction was made using a barrier membrane in conjunction with bone graft materials . A follow-up of 6 months seemed to reveal radiographic bone regeneration.

Eye Contact Lens, 2003 Jul, 29(3), 146 - 54
Contact lens-associated corneal infiltrates; Robboy MW et al.; PURPOSE This review article examines recent studies pertaining to contact lens-associated corneal infiltrates (CLACI) that occur in the absence of culture-proven microbial infection.METHODS The literature was reviewed in regard to the clinical appearance, incidence and risk, etiology, pathophysiology, differential diagnosis, and management of CLACI . Recent insights are presented in the context of future directions for prevention of CLACI.RESULTS Contact lens-associated corneal infiltrates may manifest in various forms that require careful observational skills to ensure proper diagnosis . Although the reported incidence of CLACI varies widely, even a low percentage of contact lens wearers would constitute a substantial number of affected individuals . Any one or a combination of multiple mechanical, hypoxic, or toxic stimuli associated with contact lens use can induce proinflammatory responses that lead to infiltration of inflammatory cells into the cornea . A number of candidate cytokines, chemokines, adhesion molecules, and so forth have been identified . In addition to differentiation from microbial keratitis, CLACI also should be differentiated from ocular disorders not associated with contact lenses but involving corneal infiltrates and from contact lens-associated disorders that may resemble infiltrates . Management of CLACI can range from simple monitoring of the patient to the use of pharmacologic intervention.CONCLUSIONS The small percentage of affected lens wearers translates into a notable number of individuals who, although not experiencing a vision-threatening event, are inconvenienced by the development of infiltrates . Design of preventive measures for CLACI should focus on the elimination of various mechanical, hypoxic, and toxic stimuli that can induce infiltrates and on the approaches for molecular intervention of the inflammatory cascade initiated by the stimuli.

J Biol Chem, 2003 Oct 10, 278(41), 39822 - 9 Epub 2003 Jul 14.
Cellular recognition of tri-/di-palmitoylated peptides is independent from a domain encompassing the N-terminal seven leucine-rich repeat (LRR)/LRR-like motifs of TLR2; Meng G et al.; Toll-like receptors (TLRs) mediate microbial pattern recognition in vertebrates . A broad variety of agonists has been attributed to TLR2 and three TLRs, TLR4, TLR2, and TLR5, have been demonstrated to bind microbial products . Distinct agonists might interact with different subdomains of the TLR2 extracellular domain . The TLR2 extracellular domain sequence includes 10 canonical leucine-rich repeat (LRR) motifs and 8-10 additional and potentially functionally relevant LRR-like motifs . Thus, the transfection of TLR2 LRR/LRR-like motif deletion constructs in human embryonic kidney 293 cells and primary TLR2-deficient mouse fibroblasts was performed for analysis of the role of the regarding domains in specific pattern recognition . Preparations applied as agonists were highly purified soluble peptidoglycan, lipoteichoic acid, outer surface protein A from Borrelia burgdorferi, synthetic mycoplasmal macrophage-activating lipoprotein-2, tripalmitoyl-cysteinyl-seryl-(lysyl)3-lysine (P3CSK4), dipalmitoyl-CSK4 (P2-CSK4), and monopalmitoyl-CSK4 (PCSK4) as well as lipopolysaccharide and inactivated bacteria . We found that a block of the N-terminal seven LRR/LRR-like motifs was not involved in TLR2-mediated cell activation by P3CSK4 and P2CSK4 ligands mimicking triacylated and diacylated bacterial polypeptides, respectively . In contrast, the integrity of the TLR2 holoprotein was compulsory for effective cellular recognition of other TLR2 agonists applied, including PCSK4 . The formation of a functionally relevant subdomain by a region including the N-terminal seven LRR/LRR-like motifs rather than by single LRRs is suggested by our results . They further imply that TLR2 contains multiple binding domains for ligands that may contribute to the characterization of its promiscuous molecular pattern recognition.

J Biol Chem, 2003 Sep 26, 278(39), 37561 - 8 Epub 2003 Jul 14.
The antifungal drug amphotericin B promotes inflammatory cytokine release by a Toll-like receptor- and CD14-dependent mechanism; Sau K et al.; Amphotericin B is the most effective drug for treating many life-threatening fungal infections . Amphotericin B administration is limited by infusion-related toxicity, including fever and chills, an effect postulated to result from proinflammatory cytokine production by innate immune cells . Because amphotericin B is a microbial product, we hypothesized that it stimulates immune cells via Toll-like receptors (TLRs) and CD14 . We show here that amphotericin B induces signal transduction and inflammatory cytokine release from cells expressing TLR2 and CD14 . Primary murine macrophages and human cell lines expressing TLR2, CD14, and the adapter protein MyD88 responded to amphotericin B with NF-kappaB-dependent reporter activity and cytokine release, whereas cells deficient in any of these failed to respond . Cells mutated in TLR4 were less responsive to amphotericin B stimulation than cells expressing normal TLR4 . These data demonstrate that TLR2 and CD14 are required for amphotericin B-dependent inflammatory stimulation of innate immune cells and that TLR4 may also provide stimulation of these cells . Our results provide a putative molecular basis for inflammatory responses elicited by amphotericin B and suggest strategies to eliminate the acute toxicity of this drug.

Int Immunopharmacol, 2003 Aug, 3(8), 1093 - 1104
Long-term immune dysfunction after radiotherapy to the head and neck area; Verastegui EL et al.; BACKGROUND: Hematological side effects are not generally expected due to radiotherapy involving limited radiation fields; however, patients with squamous cell carcinoma of the head and neck (SCCH and N) receiving radiation therapy frequently have chronic intraoral infections . Xerostomia has been implicated as a cause of it, but local or systemic immune alterations are not usually considered . METHODS: With the purpose of evaluating the impact of radiotherapy treatment to different anatomic sites on immune function, 70 patients were evaluated during and after radiotherapy: 50 cases with SCCH and N, 10 with squamous cell carcinoma of the uterine cervix (SCCUC) and 10 patients with central nervous system tumors (CNS) . We analyzed lymphocyte counts and T-cell subsets, and over time, their association with the presence of intracellular infections and disease-free survival . RESULTS: Severe lymphopenia was observed in patients with SCCUC and SCCH and N by the fifth week of treatment . Patients with CNS tumors developed mild lymphopenia . In patients with SCCH and N and UC, lower counts were seen in B cells and total T lymphocyte counts including both CD4(+) and CD8(+) cell subsets . The patients with SCCUC recovered lymphocyte counts by the 24th month but T-cell subsets lagged behind . None of the SCCH and N patients had fully recovered by 60 months of follow-up . Recurrence correlates with low lymphocyte counts . DISCUSSION: This work highlights the vulnerability of the head and neck area to the impact of radiotherapy as a reservoir of lymphoid cells . The possibility of recovery as a consequence of thymopoiesis and/or peripheral clonal expansion may limit the antigen-specific recognition of relevant tumor or microbial antigens and cause significant and prolonged immune alterations that may impact long-term survival.

Biochemistry, 2003 Jul 22, 42(28), 8459 - 64
High-affinity inhibition of a family of Plasmodium falciparum proteases by a designed adaptive inhibitor; Nezami A et al.; Drug development against viral or microbial targets is often compounded by the existence of naturally occurring polymorphisms or drug resistant mutations . In the case of Plasmodium falciparum, the etiological agent of malaria, four related and essential proteases, plasmepsin I, II, and IV and the histo-aspartyl protease (HAP), have been identified in the food vacuole of the parasite . Since all of these enzymes are involved in the hemoglobin degradation of infected victims, the simultaneous inhibition of the four enzymes can be expected to lead to a faster starvation of the parasite and to delay the onset of drug resistance, since four enzymes will need to mutate in a concerted fashion . This study describes the design of an adaptive inhibitor intended to inhibit the entire plasmepsin family . Adaptive inhibitors bind with extremely high affinity to a primary target within the family and maintain significant affinity against the remaining members . This objective is accomplished by engineering the strongest and most specific interactions of the inhibitor against conserved regions of the binding site and by accommodating target variations by means of flexible asymmetric functional groups . Using this approach, we have designed an inhibitor with subnanomolar affinity (0.5 nM) against the primary target, plasmepsin II, and with no loss or a very small loss of affinity against plasmepsin IV, I, and HAP (K(i) ratios of 0.4, 7.1, and 17.7, respectively) . The core of the inhibitor is defined by an allophenylnorstatine scaffold . Adaptability is provided by an asymmetric amino indanol functional group facing one of the key variable regions in the binding site . Adaptive inhibitors, which display high affinity against several variations of a primary target, are expected to play an important role in the chemotherapy of infectious diseases.

East Afr Med J, 2000 Jun, 77(6), 340 - 2
Ultrastructural changes in animal fat associated lipoid pneumonia: report of two cases; Armah GE et al.; Traditional or cultural practices in different parts of the world where oils are used continue to produce lipoid pneumonia . We report the ultrastructural findings and observations in animal fat associated lipoid pneumonia from two children following a cultural practice of forced feeding with animal fat (ghee) . Clinical findings showed an acute or chronic chest infection which failed to respond to anti-microbial therapy . X-ray and chest CT scan revealed collapse/consolidations of the right middle and left lower lobes . Histology and electron microscopy revealed thickening and destruction of the alveolar septa, filling of alveolar spaces with red blood cells and macrophage which contained both primary and secondary lysosomes . The alveolar walls contained mostly type II pneumocyte with most of them surrounded by thickened basement membranes with only a small portion of their surfaces exposed directly to the alveolar space where it showed numerous microvilli.

Am J Respir Crit Care Med, 2003 Oct 1, 168(7), 810 - 817 Epub 2003 Jul 11.
Nuclear Factor-{kappa}B p50 Limits Inflammation and Prevents Lung Injury during Escherichia coli Pneumonia; Mizgerd JP et al.; Inflammatory responses to infection must be precisely regulated to facilitate microbial killing while limiting host tissue damage . Many inflammatory genes are regulated by kappaB sites, and the p50 subunit of nuclear factor-kappaB suppresses the expression of kappaB-associated genes in vitro . We hypothesized that p50 is essential to prevent excessive inflammation and injury during infection . During pulmonary infection with Escherichia coli, the gene-targeted deficiency of p50 did not affect bacterial clearance from mouse lungs, but it resulted in increased expression of proinflammatory cytokines 6 to 24 hours after infection . This dysregulation exacerbated inflammation (neutrophil recruitment), respiratory distress (pulmonary edema and blood gas exchange impairment), and decompartmentalization (transit of protein and bacteria from the air spaces to the blood) . We interpret these studies to indicate that endogenous p50 protects the host by curbing inflammatory responses to prevent injury, essential to survive pneumonia.

BMC Infect Dis . 2003 Jul 11;3(1):15.
I-TRAP: a method to identify transcriptional regulator activated promoters; McLendon MM et al.; BACKGROUND: The differential expression of virulence genes is often used by microbial pathogens in adapting to the environment of their host . The differential expression of such sets of genes can be regulated by RNA polymerase sigma factors . Some sigma factors are differentially expressed, which can provide a means to identifying other differentially expressed genes such as those whose expression are controlled by the sigma factor . METHODS: To identify sigma factor-regulated genes, we developed a method, termed I-TRAP, for the identification of transcriptional regulator activated promoters . The I-TRAP method is based on the fact that some genes will be differentially expressed in the presence and absence of a transcriptional regulator . I-TRAP uses a DNA library in a promoter-trap vector that contains two reporter genes, one to allow the selection of active promoters in the presence of the transcriptional regulator and a second to allow screening for promoter activity in the absence of the transcriptional regulator . RESULTS: To illustrate the development and use of the I-TRAP approach, the construction of the vectors, host strains, and library necessary to identify SigmaE-regulated genes of Mycobacterium tuberculosis is described . CONCLUSION: The I-TRAP method should be a versatile and useful method for identifying and characterizing promoter activity under a variety of conditions and in response to various regulatory proteins . In our study, we isolated 360 clones that may contain plasmids carrying SigmaE-regulated promoters genes of M . tuberculosis.

J Chem Ecol, 2003 May, 29(5), 1073 - 82
Rodent and ruminant ingestive response to flavonoids in Euphorbia esula; Halaweish F et al.; Euphorbia esula, common name leafy spurge, was chemically evaluated for aversive phytochemicals that appear to minimize herbivory by rodents and cattle . A middle-layer extract elicited food aversions in rats as did the petroleum ether extract of the initial methanol extract . Kaempferol-3-0-beta-glucuronic acid and quercetin-3-0-beta-glucuronic acid were separated and identified from the middle-layer residue . This study is the first report of quercetin-3-0-beta-glucuronic acid in leafy spurge . Together these flavonoidal glucosides were mildly aversive to rats but showed less aversive activity when tested separately . The middle-layer extract produced no aversive response from cattle, while the petroleum ether extract elicited strong aversions in cattle . Flavonoidal compounds from leafy spurge that were aversive to rats, a monogastric mammal, were not aversive to cattle, a ruminant . Microbial degradation of the compounds before they reach the intestines and are absorbed into the bloodstream is likely a key advantage for cattle compared to rats.

Pharmazie, 2003 Jun, 58(6), 420 - 2
Microbial transformations of S-naproxen by Aspergillus niger ATCC 9142; He A et al.; Aspergillus niger ATCC 9142 was used to catalyze the biotransformation of S(-)-naproxen (1) to three major metabolites that were isolated by solvent extraction, purified chromatographically, and characterized by mass spectrometry and NMR spectroscopy . Metabolites were identified as O-desmethylnaproxen (2), 7-hydroxynaproxen (3) and 7-hydroxy-O-desmethyinaproxen (4) . The kinetics of naproxen biotransformation to 2 and 4 was established over an 84 h period to show that naproxen was completely metabolized at 36 h, the major metabolite was O-desmethylnaproxen at 24 h, and the 7-hydroxy-O-desmethylnaproxen that was formed after 24 h.

Am Nat, 2003 Jul, 162(1), 29 - 43 Epub 2003 Jun 18.
The impact of variable stoichiometry on predator-prey interactions: a multinutrient approach; Grover JP; A model for prey and predators is formulated in which three essential nutrients can limit growth of both populations . Prey take up dissolved nutrients, while predators ingest prey, assimilate a fraction of ingested nutrients that depends on their current nutrient status, and recycle the balance . Although individuals are modeled as identical within populations, amounts of nutrients within individuals vary over time in both populations, with reproductive rates increasing with these amounts . Equilibria and their stability depend on nutrient supply conditions . When nutrient supply increases, unusual results can occur, such as a decrease of prey density . This phenomenon occurs if, with increasing nutrient, predators sequester rather than recycle nutrients . Furthermore, despite use of a linear functional response for predators, high nutrient supply can destabilize equilibria . Responses to nutrient supply depend on the balance between assimilation and recycling of nutrients by predators, which differs depending on the identity of the limiting nutrient . Applied to microbial ecosystems, the model predicts that the efficiency of organic carbon mineralization is reduced when supply of mineral nutrients is low and when equilibria are unstable . The extent to which predators recycle or sequester limiting nutrients for their prey is of critical importance for the stability of predator-prey systems and their response to enrichment.

Bioinformatics, 2003, 19 Suppl 1, i105 - 7
Annotation of bacterial genomes using improved phylogenomic profiles; Enault F et al.; MOTIVATION: Phylogenomic profiling is a large-scale comparative genomic method used to infer protein function from evolutionary information first described in a binary form by Pellegrini et al . (1999) . Here, we propose improvements of this approach including the use of normalized Blastp bit scores, a normalization of the matrix of profiles to take into account the evolutionary distances between bacteria, the definition of a phylogenomic neighborhood based on continuous pairwise distances between genes and an original annotation procedure including the computation of a p-value for each functional assignment . RESULTS: The method presented here increases the number of Ecocyc enzymes identified as being evolutionarily related by about 25% with respect to the original binary form (absent/present) method . The fraction of 'false' positives is shown to be smaller than 20% . Based on their phylogenomic relationships, genes of unknown function can then be automatically related to annotated genes . Each gene annotation predicted is associated with a p-value, i.e . its probability to be obtained by chance . The validity of this method was extensively tested on a large set of genes of known function using the MultiFun database . We find that 50% of 3122 function attributions that can be made at a p-value level of 10(-11) correspond to the actual gene annotation . The method can be readily applied to any newly sequenced microbial genome . In contrast to earlier work on the same topic, our approach avoids the use of arbitrary cut-off values, and provides a reliability estimate of the functional predictions in form of p-values.

J Biomol Struct Dyn, 2003 Aug, 21(1), 99 - 109
Gene recognition from questionable ORFs in bacterial and archaeal genomes; Chen LL et al.; The ORFs of microbial genomes in annotation files are usually classified into two groups: the first corresponds to known genes; whereas the second includes 'putative', 'probable', 'conserved hypothetical', 'hypothetical', 'unknown' and 'predicted' ORFs etc . Since the annotation is not 100% accurate, it is essential to confirm which ORF of the latter group is coding and which is not . Starting from known genes in the former, this paper describes an improved Z curve method to recognize genes in the latter . Ten-fold cross-validation tests show that the average accuracy of the algorithm is greater than 99% for recognizing the known genes in 57 bacterial and archaeal genomes . The method is then applied to recognize genes of the latter group . The likely non-coding ORFs in each of the 57 bacterial or archaeal genomes studied here are recognized and listed at the website The working mechanism of the algorithm has been discussed in details . A computer program, called ZCURVE_C, was written to calculate a coding score called Z-curve score for ORFs in the above 57 bacterial and archaeal genomes . Coding/non-coding is simply determined by the criterion of Z-curve score > 0/ Z-curve score < 0 . A website has been set up to provide the service to calculate the Z-curve score . A user may submit the DNA sequence of an ORF to the server at and the Z-curve score of the ORF is calculated and returned to the user immediately.

J Anim Sci, 2003 Jul, 81(7), 1806 - 13
The effect of supplementing microbial phytase and organic acids to a corn-soybean based diet fed to early-weaned pigs; Omogbenigun FO et al.; The effect of microbial phytase (MP) and organic acids (OA) supplementation in diets for early-weaned pigs was investigated in an in vitro assay and a growth performance and digestibility trial involving 96 pigs (18 d old) . The experimental diets were: 1) a control (C) formulated according to NRC (1998); 2) a negative control (NC) that was similar to diet C except that available P was reduced by 0.19%; 3) NC plus MP (500 U/kg); and 4) NC+MP and OA (NC+MPOA) . In the in vitro assay, the four diets were incubated under simulated gut conditions . Addition of MP increased (P = 0.003) phytate hydrolysis from 34 (NC) to 87.5% (NC+MP); this was further increased to 90.1% due to the addition of OA (NC+MPOA) . In the 4-wk growth trial, each diet was randomly assigned to six pens each with four pigs . At the end of wk 3, a mobility test was conducted on one pig randomly selected from each pen . Pigs fed the NC diet tended to have a lower (P = 0.06) mobility score compared with those fed the other diets . At the end of wk 4, six pigs per treatment were killed and samples of digesta from different sections of the gut and the third metatarsal bone were collected for nutrient digestibility and bone ash measurements, respectively . There were no differences in ADFI, ADG, and gain:feed ratio among treatments (P > 0.05); however, ADG was 6.5% higher in piglets fed the NC+MPOA diet compared with those fed the C diet . Bone ash content was lower (P = 0.003) in NC fed pigs than in those fed the other treatments . Supplementing NC with MP and MP+OA improved bone ash content to the same level as C . Apparent ileal digestibility (AID) of DM and CP did not differ (P > 0.10) among treatments and averaged 80.7 and 79.4%, respectively . Of all AA, only AID of isoleucine, histidine, and aspartic acid was increased (P < 0.05) by MP+OA supplementation . Overall, there were slight numerical improvements in AID of AA due to MP and OA supplementation, with AID of essential AA averaging 79.4, 77.7, 80.1, and 81.6% for C, NC, NC+MP, and NC+MPOA, respectively . The AID of P was increased (P = 0.0001) by 21 percentage units, and the amount of P excreted was decreased (P = 0.03) by 19.4% as a result of MP+OA supplementation compared with C . In conclusion, addition of MP and OA to pig starter diets improved P digestion and utilization, thereby leading to a reduction in P excretion . Addition of MP and OA to corn-soybean meal diets fed to young pigs had only a slight effect on ileal amino acid digestibilities.

Am J Reprod Immunol, 2003 May, 49(5), 279 - 84
Development of topical microbicides for prevention of human immunodeficiency virus and herpes simplex virus; Keller MJ et al.; Topical microbicides, designed for vaginal or rectal administration, are needed to prevent human immunodeficiency virus (HIV) and other sexually transmitted infections (STI) . Presently marketed topical microbicides are cytotoxic and damage the vaginal epithelium with frequent use . Rational development of new candidate compounds should build on knowledge of the pathways of microbial invasion . The establishment of assays and models that predict efficacy and safety is critical . Comprehensive pre-clinical evaluation of promising microbicides should include rigorous assessment of the effects of repeated application of topical agents on mucosal inflammatory cells, cytokines, and the genital tract virus population . These studies will lay the groundwork for future clinical trials.

Environ Sci Technol, 2003 Jun 15, 37(12), 2775 - 9
Effect of planting covers on herbicide persistence in landscape soils; Gan J et al.; Recent monitoring shows that the majority of urban streams in the United States are contaminated by pesticide residues, and the contamination is mainly due to runoff from residential landscapes . In this study we evaluated the effect of landscape planting on persistence of the herbicides 2,4-D and dicamba in soil under laboratory conditions . The herbicides exhibited substantially different persistence in the same soil type that had been subjected to different planting practices for about 6 years . In the 0-10 cm surface layer, the half-life of 2,4-D was 30.7 d in soil under trees, which was about 20 times longer than in soil planted with turf grass (1.6 d) . The difference in 2,4-D persistence was closely correlated to the number of 2,4-D-degrading bacteria that had evolved in the soils . The half-life of dicamba was much longer in soil under a tree canopy (149 d) than in mulched soil (7.9 d) . The rate of dicamba degradation was proportional to soil organic matter content . This study indicates that planting practices can modify soil chemical properties and microbial activity and may further affect pesticide runoff potential by influencing pesticide degradation . Characterizing pesticide behavior as a function of planting covers may improve our understanding of pesticide runoff in urban environments and also help to identify strategies for minimizing pesticide contamination to urban streams.

Environ Sci Technol, 2003 Jun 15, 37(12), 2720 - 6
Oxidation of thallium by freshwater plankton communities; Twining BS et al.; Thallium is a toxic metal that is of emerlI(I) or Tl(III), and its oxidation state affects its complexation and subsequent bioavailability and toxicity . We conducted lab and field incubations with 204Tl(I) and natural plankton assemblages to study the occurrence and mechanism of Tl oxidation . We observed that Tl(III) comprised 74% of total dissolved Tl after a 60 h incubation in surface waters from Lake Ontario, revealing a maximum specific oxidation rate of 0.014 h(-1) . No Tl(I) oxidation was observed in sterile-filtered control treatments, indicating that solar radiation alone does not oxidize Tl(I) to Tl(III) . Additional incubations with pond water revealed that Tl(I) oxidation is mediated by microbial activity and is not related to the presence of abiotic particles or phytoplankton or protozoa . We also identified a minor fraction (5-13%) of nonion-exchangeable (Chelex-100 resin; pH 1.5) Tl that may represent dimethylthallium or complexed thallium . This study demonstrates that planktonic bacteria are responsible for oxidizing the thermodynamically stable Tl(I) to the more abundant Tl(III).

Respir Med, 2003 Jul, 97(7), 851 - 8
Long-term antibiotics in the management of non-CF bronchiectasis--do they improve outcome?
Evans DJ, Greenstone M.
In addition to bacteria and inflammatory cells, the sputum of patients with bronchiectasis contains mediators that damage the airway epithelium and promote inflammatory change . The deleterious effects of these mediators, such as neutrophil elastase, reduce host defences and consequently perpetuate the propensity to recurrent infection . This 'vicious cycle' of infection and inflammation in bronchiectasis suggests that long-term antibiotic therapy might be beneficial in these patients by reducing microbial load and, in doing so, inhibit inflammation in the lung allowing tissue repair to occur . Short courses of antibiotics achieve clinical improvements and also have been shown to reduce the levels of harmful mediators in the sputum . This article will cite the studies reported for long-term antibiotic treatment in bronchiectasis and overall there seems to be benefits for patients with chronic sputum purulence . The evidence that supports the postulated pathological mechanisms will also be discussed . Important issues in clinical practice such as the usefulness of antibiotic sensitivities, the evolution of resistance patterns, and drug delivery will also be discussed.

Bioorg Med Chem Lett, 2003 Aug 4, 13(15), 2561 - 3
Formylchromone derivatives as a novel class of protein tyrosine phosphatase 1B inhibitors; Shim YS et al.; Formylchromone inhibits a human protein tyrosine phosphatase PTP1B with a IC(50) value of 73 microM . The chemical reactivity of formylchromone was adjusted by substitution at various positions of the formylchromone skeleton . In an initial assessment of the structure-activity relationship, the most potent inhibitor showed an IC(50) of 4.3 microM against PTP1B and strong or medium selectivity against other human PTPases, LAR and TC-PTP . This compound, however, was not selective against microbial PTPases, YPTP1 and YOP . The potency and selectivity of the formylchromone derivatives expecting further improvements provides a novel pharmacophore for the design of drugs for the treatment of type 2 diabetes and obesity.

J Econ Entomol, 2003 Jun, 96(3), 798 - 804
Sequential sampling and biorational chemistries for management of lepidopteran pests of vegetable amaranth in the Caribbean; Clarke-Harris D et al.; Although vegetable amaranth, Amaranthus viridis L . and A . dubius Mart . ex Thell., production and economic importance is increasing in diversified peri-urban farms in Jamaica, lepidopteran herbivory is common even during weekly pyrethroid applications . We developed and validated a sampling plan, and investigated insecticides with new modes of action, for a complex of five species (Pyralidae: Spoladea recurvalis (F.), Herpetogramma bipunctalis (F.), Noctuidae: Spodoptera exigua (Hubner), S . frugiperda (J . E . Smith), and S . eridania Stoll) . Significant within-plant variation occurred with H . bipunctalis, and a six-leaf sample unit including leaves from the inner and outer whorl was selected to sample all species . Larval counts best fit a negative binomial distribution . We developed a sequential sampling plan using a threshold of one larva per sample unit and the fitted distribution with a k(c) of 0.645 . When compared with a fixed plan of 25 plants, sequential sampling recommended the same management decision on 87.5%, additional samples on 9.4%, and gave inaccurate recommendations on 3.1% of 32 farms, while reducing sample size by 46% . Insecticide frequency was reduced 33-60% when management decisions were based on sampled data compared with grower-standards, with no effect on crop damage . Damage remained high or variable (10-46%) with pyrethroid applications . Lepidopteran control was dramatically improved with ecdysone agonists (tebufenozide) or microbial metabolites (spinosyns and emamectin benzoate) . This work facilitates resistance management efforts concurrent with the introduction of newer modes of action for lepidopteran control in leafy vegetable production in the Caribbean.

Riv Biol, 2003 Jan-Apr, 96(1), 55 - 71
Ecology of planktonic heterotrophic flagellates . A review; Mariottini GL et al.; In aquatic environments heterotrophic flagellates are an important component within the microbial loop and the food web, owing to their involvement in the energy transfer and flux and as an intermediate link between bacteria and primary producers, and greater organisms, such as other protists and metazoan consumers . In the microbial loop heterotrophic flagellates highly contribute to fast biomass and nutrient recycling and to the production in aquatic environments . In fact, these protists consume efficiently viruses, bacteria, cyanobacteria and picophytoplankton, and are grazed mainly by other protists, rotifers and small crustaceans . In this paper the knowledge about these unicellular organisms is reviewed, taking into particular account their ecological relationships and trophic role within the plankton community of marine and freshwater environments.

Gastroenterology, 2003 Jul, 125(1), 216 - 28
Cryptosporidium parvum invasion of biliary epithelia requires host cell tyrosine phosphorylation of cortactin via c-Src; Chen XM et al.; BACKGROUND & AIMS: Cryptosporidium parvum invasion of epithelia requires polymerization of host cell actin at the attachment site . We analyzed the role of host cell c-Src, a cytoskeleton-associated protein tyrosine kinase, in C . parvum invasion of biliary epithelia . METHODS: In vitro models of biliary cryptosporidiosis using a human biliary epithelial cell line were used to assay the role of c-Src signaling pathway in C . parvum invasion . RESULTS: c-Src and cortactin, an actin-binding protein and a substrate for c-Src, were recruited to the parasite-host cell interface during C . parvum invasion . Tyrosine phosphorylation of cortactin in infected cells was also detected . Inhibition of host cell c-Src significantly blocked C . parvum -induced accumulation and tyrosine phosphorylation of cortactin and actin polymerization at the attachment sites, thereby inhibiting C . parvum invasion of biliary epithelial cells . A triple mutation of tyrosine of cortactin in the epithelia also diminished C . parvum invasion . In addition, proteins originating from the parasite were detected within infected cells at the parasite-host cell interface . Antiserum against C . parvum membrane proteins blocked accumulation of c-Src and cortactin and significantly decreased C . parvum invasion . No accumulation of the endocytosis-related proteins, dynamin 2 and clathrin, was found at the parasite-host cell interface; also, inhibition of dynamin 2 did not block C . parvum invasion . CONCLUSIONS: C . parvum invasion of biliary epithelial cells requires host cell tyrosine phosphorylation of cortactin by a c-Src-mediated signaling pathway to induce actin polymerization at the attachment site, a process associated with microbial secretion but independent of host cell endocytosis.

Vaccine, 2003 Jul 28, 21(24), 3428 - 31
Non-genetic inheritable potential of maternal antibodies; Lemke H et al.; Maternal antibodies (IgG and IgA) not only provide passive protection against microbial infections, but also exert a variety of equally important active, idiotypically-mediated immunoregulatory functions . Since the generation of maternal antibodies depends entirely on the stimulation of the mother's immune system by external mainly thymus-dependent antigens, with long-lived antigen independent plasma cells in the bone marrow, maternal antibodies represent the mother's collective ontogenetic immunological experience . Although their stimulatory potential in mice is restricted to the neonatal imprinting period, maternal antibodies exert a life-long determinative influence which is even dominant over seemingly genetic predispositions . Therefore, the functional impact of maternal IgG antibodies appears phenotypically as a non-genetic inheritance.

Vaccine, 2003 Jul 28, 21(24), 3352 - 7
How immune mechanisms are affected by pregnancy; Luppi P; Pregnancy requires physiologic adaptations in all maternal systems, including the immune system . This process is complex and includes modifications at different levels and compartments of the maternal immune system . Although many of these changes are only partially explored and understood, recent investigations have showed that during pregnancy maternal circulating immune cells undergo modifications in cell counts, phenotypes, functions and ability to produce soluble factors, such as cytokines . The ultimate goal is to establish and maintain a successful pregnancy, which involves a state of selective immune tolerance, immunosuppression and immunomodulation in the presence of a strong anti-microbial immunity . The mammalian immune system has evolved to coexist with these needs by down-regulating potentially dangerous T-cell-mediated immune responses, while activating certain components of the innate immune system, such as monocytes and neutrophils . This unique dysregulation between different components of the immune system plays a central role in the maternal adaptation to pregnancy.

J Infect, 2003 Jul, 47(1), 1 - 11
The microbial diagnosis of infective endocarditis; Watkin RW et al.; This review suggests an evidence-based algorithm for sequential testing in infective endocarditis . It discusses blood culture and the merits and drawbacks of serology in making the diagnosis . Newer techniques are briefly reviewed . The proposed algorithm will complement the Duke criteria in clinical practice.

Biochem Biophys Res Commun, 2003 Jul 18, 307(1), 133 - 8
Biopanning of endotoxin-specific phage displayed peptides; Thomas CJ et al.; Systemic bacterial infections frequently lead to a plethora of symptoms termed "endotoxic shock" or "sepsis." Characterized by hypotension, coagulation abnormalities, and multiple organ failure, treatment of sepsis still remains mostly supportive . Of the various experimental therapeutic interventional strategies, neutralization of endotoxin by peptides or proteins is becoming popular recently . Hence, design of endotoxin binding peptides is gaining currency as their structural complexity and mode of recognition of endotoxin precludes mounting of resistance against them by the susceptible bacteria by genetic recombination, mutation, etc . Earlier work from our laboratory had shown that the amphiphilic cationic peptides are good ligands for endotoxin binding . In this study, we report the results of studies with the 12 selected lipid A binding phage displayed peptides by biopanning of a repertoire of a random pentadecapeptide library displayed on the filamentous M-13 phage . A comparison of the sequences revealed no consensus sequence between the 12 selected peptides suggesting that the lipid A binding motif is not sequence specific which is in accord with the sequence variation seen with the naturally occurring anti-microbial and/or endotoxin binding peptides . Thus, the flexibility of the peptides coupled with their plasticity in recognizing the lipid A moiety, explains their tight binding to endotoxin . At a structural level, asymmetric distribution of the charged polar residues on one face of the helix and non-polar residues on the opposite face appears to correlate with their activity.

Curr Opin Biotechnol, 2003 Jun, 14(3), 283 - 8
Elucidating the microbial component of natural attenuation; Smets BF et al.; Microbial reactions are a key determinant in natural attenuation . However, providing unequivocal evidence of the extent of their involvement is challenging . Several approaches are being developed to meet this challenge, including the use of contaminant-specific transformation products, carbon- or hydrogen-based stable isotopic analysis and reactive transport modeling . These approaches emphasize the ongoing need to integrate strategically between temporally and spatially variant geochemical conditions, the ecological characteristics of the resident microbial communities and their resultant pollutant-transformation capabilities.

Autoimmun Rev, 2003 Jan, 2(1), 8 - 12
MHC class II peptide flanking residues of exogenous antigens influence recognition by autoreactive T cells; Conant SB et al.; Molecular mimicry between exogenous microbial antigens and self-epitopes has been proposed as a triggering mechanism for autoimmune diseases for many years . We reported that a peptide from a protein specific to Chlamydia pneumoniae (Cpn0483) which shares a motif with the dominant encephalitogenic epitope of the self-antigen, rat myelin basic protein (rat68-86), elicits experimental autoimmune encephalomyelitis (EAE) in Lewis rats . We recently observed that rat68-86 utilizes aspartic acid (D) and arginine (R) in the common motif as primary and secondary TCR contacts, respectively . In contrast, the encephalitogenic activity of Cpn0483 is dependent on R and the C-terminal asparagine (N), which flanks the MHC class II-P9 anchor residue . Thus, rat68-86 and Cpn0483 share a common motif, are encephalitogenic and are both restricted by MHC class II RT1.B(l) . T cells from rats immunized with the encephalitogenic Cpn0483 peptide proliferated to the priming peptide as well as to the non-encephalitogenic CpnN>A analog . However, CpnN>A-primed T cells did not respond to the native Cpn0483 peptide . We conclude that the MHC-flanking C-terminal asparagine residue markedly influences T cell recognition by the chlamydial peptide.

Drugs Today (Barc), 2000 Oct, 36(10), 667 - 78
Antibiotics as primary therapy for Crohn's disease; Chamberlin W et al.; Crohn's disease, an inflammatory bowel disease of unknown cause, was initially considered to have an infectious etiology . As the infectious agent could not be identified, it was grouped among the immune disorders . As a result, research and clinical trials were directed towards the autoimmune theory and patients were treated with steroids, immunomodulators, aminosalicylates and, most recently, anti-tumor necrosis factor-alpha . Because of the inconsistency of treatment success and the failure to cure Crohn's disease, many physicians turned to antibiotics in search for alternative solutions, especially when other regimens failed . Attention has recently been directed toward possible infectious causes of Crohn's disease . Although it is still unknown whether microbial agents are etiologically involved in the pathogenesis of Crohn's disease, there has been a growing interest in trying antibiotics in the management of Crohn's disease . This review summarizes the data available regarding antibiotic treatment of Crohn's disease in relation to a possible mycobacterial etiology . Multidrug therapies are in clinical trials and the results of these randomized, controlled, double-blind studies are needed before guidelines about whether to include antibiotics as part of the treatment of Crohn's disease management can be made.

Genes Immun, 2003 Jul, 4(5), 374 - 84
Murine serine proteases MASP-1 and MASP-3, components of the lectin pathway activation complex of complement, are encoded by a single structural gene; Stover CM et al.; Activation of the lectin pathway of complement is initiated by the binding to microbial carbohydrate structures of a multimolecular fluid-phase complex composed of a carbohydrate recognition subcomponent that associates with three specific serine proteases and an enzymatically inert protein of 19 kDa . The first carbohydrate recognition subcomponent of the lectin pathway identified was mannan-binding lectin (MBL), hence the serine proteases were named MBL-associated serine proteases (MASPs) and numbered according to the sequence of their discovery . Here we describe the primary structures of the two distinct serine proteases MASP-1 and MASP-3 in the rat (and of MASP-3 in the mouse), show their association with plasma MBL complexes, and demonstrate that in rat and mouse, as in man, MASP-1 and MASP-3 are encoded by a single structural gene . For both species, we present the genomic region and regulatory elements responsible for the processing of either MASP-1 or MASP-3 mRNA by alternative splicing/alternative polyadenylation . Furthermore, we demonstrate the evolutionary conservation of MASP-3 mRNA in cDNA transcripts from guinea pig, rabbit, pufferfish, and cow.

ScientificWorldJournal, 2003 Jul 01, 3, 578 - 84
Protocols for 16S rDNA array analyses of microbial communities by sequence-specific labeling of DNA probes; Rudi K et al.; Analyses of complex microbial communities are becoming increasingly important . Bottlenecks in these analyses, however, are the tools to actually describe the biodiversity . Novel protocols for DNA array-based analyses of microbial communities are presented . In these protocols, the specificity obtained by sequence-specific labeling of DNA probes is combined with the possibility of detecting several different probes simultaneously by DNA array hybridization . The gene encoding 16S ribosomal RNA was chosen as the target in these analyses . This gene contains both universally conserved regions and regions with relatively high variability . The universally conserved regions are used for PCR amplification primers, while the variable regions are used for the specific probes . Protocols are presented for DNA purification, probe construction, probe labeling, and DNA array hybridizations.

J Immunol, 2003 Jul 15, 171(2), 1001 - 8
Bacterial lipopolysaccharide signaling through Toll-like receptor 4 suppresses asthma-like responses via nitric oxide synthase 2 activity; Rodriguez D et al.; Asthma results from an intrapulmonary allergen-driven Th2 response and is characterized by intermittent airway obstruction, airway hyperreactivity, and airway inflammation . An inverse association between allergic asthma and microbial infections has been observed . Microbial infections could prevent allergic responses by inducing the secretion of the type 1 cytokines, IL-12 and IFN-gamma . In this study, we examined whether administration of bacterial LPS, a prototypic bacterial product that activates innate immune cells via the Toll-like receptor 4 (TLR4) could suppress early and late allergic responses in a murine model of asthma . We report that LPS administration suppresses the IgE-mediated and mast cell-dependent passive cutaneous anaphylaxis, pulmonary inflammation, airway eosinophilia, mucus production, and airway hyperactivity . The suppression of asthma-like responses was not due to Th1 shift as it persisted in IL-12(-/-) or IFN-gamma(-/-) mice . However, the suppressive effect of LPS was not observed in TLR4- or NO synthase 2-deficient mice . Our findings demonstrate, for the first time, that LPS suppresses Th2 responses in vivo via the TLR4-dependent pathway that triggers NO synthase 2 activity.

Res Initiat Treat Action, 2003 Spring, 8(2), 10 - 3
Interferon-producing plasmacytoid dendritic cells and the pathogenesis of AIDS; Siegal F; Interferon-alpha (IFN-alpha) generation by peripheral blood mononuclear cells (PBMC) responding in vitro to HSV was first found to be deficient in patients with severe ulcerative herpes simplex virus (HSV) infections early in the AIDS epidemic . Such deficits were soon found to be associated with all opportunistic infections (OI) . Further studies during the natural history of HIV infection indicated that OI did not occur so long as IFN generation remained relatively intact . OI occurred only when both IFN-alpha generation and CD4 T cell counts were sufficiently depressed . The IFN-alpha response to HSV was innate, not adaptive . Evidence that the IFN-alpha response to HSV was derived from a rare and previously undefined cell type prompted studies eventually revealing that the IFN-producing cells were identical to the "enigmatic plasmacytoid T cells" described by Lennert in lymphoid tissues in 1958 . The normal functions of these cells appear to be diverse, but one such function involves initiation of the Th-1 pathway in response to certain microbial antigens . The IFN-producing cells are now known as plasmacytoid dendritic cells (pDCs), because they differentiate following appropriate stimulation, into type-2 dendritic cells . During therapy for HIV infection, pDCs recover somewhat more rapidly than CD4 T cells to levels associated with resistance to OI, and their renewed response appears closely associated with clinically apparent immune reconstitution . Increased pDCs have been associated with nonprogressor status . In HIV infection and in certain other clinical states, PBMC IFN-alpha generation and pDCs numbers correlate closely, suggesting that numerical depletion of circulating pDCs is an important component of the immune deficiency of AIDS . Losses of pDCs during HIV progression and repletion during antiretroviral therapy could be involved in both the progressive loss and reconstitution of the Th-1 pathway.

Sci Aging Knowledge Environ . 2003 Jun 25;2003(25):PE16.
Does anti-aging equal anti-microbial?
Lithgow GJ.
Aging is the dominant risk factor for human disease in developed countries . Could it be that a wide variety of disease states all have their origins in a common mechanism? Major signaling pathways that determine the rate of aging, such as the insulin/insulin-like growth factor 1 (IGF-1) pathway, might give clues to the nature of this major disease risk factor . It has now been shown that insulin/IGF-1 signaling influences Caenorhabditis elegans resistance to bacteria in such a way that long-lived worms are stress-resistant and slow to succumb to infection . Perhaps enhanced innate immunity is a feature of genetically determined longevity.

Phytochemistry, 2003 Jul, 63(6), 679 - 86
Soluble and wall-bound phenolics and phenolic polymers in Musa acuminata roots exposed to elicitors from Fusarium oxysporum f.sp . cubense; de Ascensao AR et al.; The accumulation of soluble and wall-bound phenolics and phenolic polymers in Musa acuminata roots exposed to cell wall-derived elicitor from the pathogen, Fusarium oxysporum, f.sp . cubense, race four, was investigated . The root tissue from the banana cultivar "Goldfinger" was found to respond strongly and rapidly towards the elicitor through the increased synthesis of phenolic compounds . Following elicitation, the conjugated and non-conjugated phenolic metabolites in the induced root tissue were extracted and quantified . Induced phenolic synthesis was rapid and reached near maximum values after 16 h . High-performance liquid chromatography revealed both compositional and quantitative differences between induced phenolics (p-coumaric, ferulic, and sinapic acids) and those constitutively present (p-coumaric- and ferulic acid) . In addition, vanillic acid was found in the ester-bound fraction and protocatechuic acid in the cell-wall bound fraction of elicited tissue . The deposition and accumulation kinetics of polymerized phenolic monomers as lignin and lignin-like polymers was quantified over a time period of 0-36 h and found to reach maximum values after 24 h . Ionization difference UV spectra of lignin indicated compositional differences in the newly synthesized lignin fraction and correlated with increased concentrations of ferulic acid and sinapic acids esters . The results show that the increased flux through the phenylpropanoid pathway resulted in the synthesis of cinnamic acid and benzoic acid derivatives that were esterified and incorporated into the cell wall fraction as part of the anti-microbial defenses activated in the root tissue.

Environ Monit Assess, 2003 Jul, 85(3), 257 - 75
Mapping sediment contamination and toxicity in Winter Quarters Bay, McMurdo Station, Antarctica; Crockett AB et al.; Winter Quarters Bay (WQB) is a small embayment located adjacent to McMurdo Station, the largest research base in Antarctica . The bay is approximately 250 m wide and long, with a maximum depth of 33 m . Historically, trash from the McMurdo Station was piled on the steep shoreline of WQB, doused with fuel and ignited . That practice has ceased, and the adjacent land area has been regraded to cover the residual waste . The bottom of WQB remains littered with drums, equipment, tanks, tires, cables, and other objects, especially the southeastern side of the bay where dumping took place . Sediments are contaminated with PCBs, metals, and hydrocarbon fuels . The objectives of this study were to map the distribution of organic contaminants in WQB, assess the toxicity of WQB sediments using a simple microbial test, and determine correlations between toxicity and contaminant levels . The study suggests that adverse ecological effects have occurred from one or more of the contaminants found in WQB but the source of the toxic impacts to bay sediments remains unknown . Whole sediment toxicity was only correlated with oil-equivalent while solvent extracts of sediments were correlated with PAHs and oil-equivalent . The authors recommend that an integrated research plan be developed that focuses on determining what additional information is needed to make informed decisions on possible remediation of WQB.

Curr Opin Allergy Clin Immunol, 2003 Jun, 3(3), 199 - 203
The T lymphocyte in food-allergy disorders; Eigenmann PA et al.; PURPOSE OF REVIEW: While much attention is focused upon the role of IgE antibodies in food-allergy disorders, the T cell remains central to all forms, both IgE and non-IgE-mediated, of food-hypersensitivity responses . This review considers the central role of the T cell in this group of disorders and provides a comprehensive overview of recent studies that elucidate our understanding of the mechanisms involved in the pathogenesis of food allergy in regard to the role of the T cell . RECENT FINDINGS: Recent studies have defined a dynamic process involving T cell homing receptors (e.g . cutaneous lymphocyte antigen) and activation markers in food-hypersensitivity disorders . Modulation of the T-cell responses occurs through the recognition of dominant allergenic epitopes, the elaboration of regulatory cytokines (e.g . transforming growth factor-beta, IL-4, IL-5, tumor necrosis factor-alpha) and the influence of immunomodulatory microbial and environmental agents . The resulting disorders reflect T-cell dysregulation . SUMMARY: Significant recent advances in our understanding of the role of the T cell in food hypersensitivity have been made and will probably contribute to improved diagnostic and treatment methods in the near future.

Eur J Gastroenterol Hepatol, 2003 Jun, 15(6), 615 - 20
The role of endogenous bacterial flora: bystander or the necessary prerequisite?
Rath HC.
Abundant experimental and clinical data incriminate microbial factors in the pathogenesis of inflammatory bowel diseases . Commensal bacteria, and their products, provide the constant antigenic stimulus to disequilibrate the mucosal immune system towards an overly aggressive response in a genetically susceptible host with reduced tolerance towards the autologous flora . Not all bacteria have equal proinflammatory capabilities . Some may be even beneficial as demonstrated by the anti-inflammatory effects of so-called probiotics . Further investigations are needed to translate the clear experimental and clinical evidence into benefit for the patients.

Appl Environ Microbiol, 2003 Jul, 69(7), 4282 - 4
Motility of Colwellia psychrerythraea strain 34H at subzero temperatures; Junge K et al.; We examined the Arctic bacterium Colwellia psychrerythraea strain 34H for motility at temperatures from -1 to -15 degrees C by using transmitted-light microscopy in a temperature-controlled laboratory . The results, showing motility to -10 degrees C, indicate much lower temperatures to be permissive of motility than previously reported (5 degrees C), with implications for microbial activity in frozen environments.

Appl Environ Microbiol, 2003 Jul, 69(7), 4067 - 75
Contributions of atmospheric CO and hydrogen uptake to microbial dynamics on recent Hawaiian volcanic deposits; King GM; A series of sites were established on Hawaiian volcanic deposits ranging from about 18 to 300 years old . Three sites occurred in areas that supported tropical rain forests; the remaining sites were in areas that supported little or no plant growth . Sites >26 years old consumed atmospheric CO and hydrogen at rates ranging from about 0.2 to 5 mg of CO m(-2) day(-1) and 0.1 to 4 mg of H(2) m(-2) day(-1), respectively . Respiration, measured as CO(2) production, for a subset of the sites ranged from about 40 to >1,400 mg of CO(2) m(-2) day(-1) . CO and H(2) accounted for about 13 to 25% of reducing equivalent flow for all but a forested site, where neither substrate appeared significant . Based on responses to chloroform fumigation, hydrogen utilization appeared largely due to microbial uptake . In contrast to results for CO and hydrogen, methane uptake occurred consistently only at the forest site . Increasing deposit age was generally accompanied by increasing concentrations of organic matter and microbial biomass, measured as phospholipid phosphate . Exoenzymatic activities (acid and alkaline phosphatases and alpha- and beta-glucosidases) were positively correlated with deposit age in spite of considerable variability within sites . The diversity of substrates utilized in Biolog Ecoplate assays also increased with deposit age, possibly reflecting changes in microbial community complexity.

Appl Environ Microbiol, 2003 Jul, 69(7), 3868 - 73
Production of novel tetrahydroxyfuranyl fatty acids from alpha-linolenic acid by Clavibacter sp . strain ALA2; Hosokawa M et al.; Previously, it was reported that a newly isolated microbial culture, Clavibacter sp . strain ALA2, produced trihydroxy unsaturated fatty acids, diepxoy bicyclic fatty acids, and tetrahydroxyfuranyl fatty acids (THFAs) from linoleic acid (C . T . Hou, J . Am . Oil Chem . Soc . 73:1359-1362, 1996; C . T . Hou and R . J . Forman III, J . Ind . Microbiol . Biotechnol . 24:275-276, 2000; C . T . Hou, H . Gardner, and W . Brown, J . Am . Oil Chem . Soc . 75:1483-1487, 1998; C . T . Hou, H . W . Gardner, and W . Brown, J . Am . Oil Chem . Soc . 78:1167-1169, 2001) . In this study, we found that Clavibacter sp . strain ALA2 produced novel THFAs, including 13,16-dihydroxy-12-THFA, 15-epoxy-9(Z)-octadecenoic acid (13,16-dihydroxy-THFA), and 7,13,16-trihydroxy-12, 15-epoxy-9(Z)-octadecenoic acid (7,13,16-trihydroxy-THFA), from alpha-linolenic acid (9,12,15-octadecatrienoic acid) . The chemical structures of these products were determined by gas chromatography-mass spectrometry and proton and (13)C nuclear magnetic resonance analyses . The optimum incubation temperature was 30 degrees C for production of both hydroxy-THFAs . 13,16-Dihydroxy-THFA was detected after 2 days of incubation, and the concentration reached 45 mg/50 ml after 7 days of incubation; 7,13,16-trihydroxy-THFA was not detected after 2 days of incubation, but the concentration reached 9 mg/50 ml after 7 days of incubation . The total yield of both 13,16-dihydroxy-THFA and 7,13,16-trihydroxy-THFA was 67% (wt/wt) after 7 days of incubation at 30 degrees C and 200 rpm . In previous studies, it was reported that Clavibacter sp . strain ALA2 oxidized the C-7, C-12, C-13, C-16, and C-17 positions of linoleic acid (n-6) into hydroxy groups . In this case, the bond between the C-16 and C-17 carbon atoms is saturated . In alpha-linolenic acid (n-3), however, the bond between the C-16 and C-17 carbon atoms is unsaturated . It seems that enzymes of strain ALA2 oxidized the C-12-C-13 and C-16-C-17 double bonds into dihydroxy groups first and then converted them to hydroxy-THFAs.

Appl Environ Microbiol, 2003 Jul, 69(7), 3751 - 7
Effect of plasterboard composition on Stachybotrys chartarum growth and biological activity of spores; Murtoniemi T et al.; The effects of plasterboard composition on the growth and sporulation of Stachybotrys chartarum as well as on the inflammatory potential of the spores were studied . S . chartarum was grown on 13 modified plasterboards under saturated humidity conditions . The biomass was estimated by measuring the ergosterol content of the S . chartarum culture while the spore-induced cytotoxicity and production of nitric oxide (NO), tumor necrosis factor alpha (TNF-alpha), and interleukin-6 in mouse macrophages was used to illustrate the bioactivity of spores . The ergosterol content of S . chartarum correlated with the number of spores collected from plasterboards . The growth and sporulation decreased compared to that of the reference board in those cases where (i) the liner was treated with biocide, (ii) starch was removed from the plasterboard, or (iii) desulfurization gypsum was used in the core . Spores collected from all the plasterboards were toxic to the macrophages . The biocide added to the core did not reduce the growth; in fact, the spores collected from that board evoked the highest cytotoxicity . The conventional additives used in the core had inhibitory effects on growth . Recycled plasterboards used in the core and the board lacking the starch triggered spore-induced TNF-alpha production in macrophages . In summary, this study shows that the growth of a strain of S . chartarum on plasterboard and the subsequent bioactivity of spores were affected by minor changes to the composition of the core or liners, but it could not be totally prevented without resorting to the use of biocides . However, incomplete prevention of microbial growth by biocides even increased the cytotoxic potential of the spores.

Zhonghua Yu Fang Yi Xue Za Zhi, 2003 Mar, 37(2), 125 - 7
{Development of a new biosensor for biochemical oxygen demand}; Chang D et al.; OBJECTIVE: To use a new kind of fixing material, i.e . Sol-Gel organic-inorganic hybridized material to immobilize bacterium to detect Biochemical oxygen demand quickly . METHODS: The biosensor was fabricated using a thin film in which Hansenula anomala was immobilized by sol-gel and an oxygen electrode . The optimum measurement for biochemical oxygen demand was at pH 7.0; 28 degrees C; response time 3 - 12 min . Pure organic compound, sewage and rate of recovery were detected with the biosensor . RESULTS: It shows that the BOD biosensor can be used to detect many organic compounds such as amino acid, glucide . It is suitable to monitor sewage and industrial waste water which has low level alcohols and phenols . The microbial membrane can work 3 months and remain its 70% activity . It is measured that the rate of recovery of BOD is between 90% to 105% in sewage . CONCLUSION: The study confirmed the effectiveness and usefulness of BOD sensor, which is quick, convenient, low cost and reliable with little interference.

Ann Allergy Asthma Immunol, 2003 Jun, 90(6 Suppl 3), 64 - 70
Allergy: the price we pay for cleaner living?
Prescott SL.
OBJECTIVES: There is an urgent need to identify the environmental changes responsible for the increasing burden of allergic disease . A reduction in the diversity and magnitude of "microbial burden" in early life has been implicated in this growing propensity for allergy sensitization . The "hygiene hypothesis" proposes that deficient bacteria-derived maturation signals during early immune development increases the susceptibility to allergic responses . This article reviews the current evidence for this relationship in the context of improved public health and living conditions . DATA SOURCES: Evidence derived from a wide range of epidemiologic and intervention studies in humans and experimental animal models is reviewed . RESULTS: There is extensive epidemiologic evidence linking allergic disease with a number of lifestyle factors that may reflect reduced microbial burden . These studies cannot exclude other possible causal pathways because most parameters (such as family size) are only indirect measures of early childhood infection . However, direct evidence that bacteria can inhibit allergic immune responses provides a plausible mechanistic basis for the hygiene hypothesis . In both animals and humans, microbial antigens can promote nonallergic (type 1) responses and inhibit allergic (type 2) immune responses . These pro-type 1 effects have been used in allergen immunotherapy and other treatments for allergic disease with some success . Although the potential benefits of bacterial exposure appear most relevant in early life when immune responses develop, the role in disease prevention remains controversial . Furthermore, there is currently no evidence that existing childhood vaccine programs to prevent serious infectious disease are responsible for the increase in allergic disease . CONCLUSIONS: Although microbial antigens can inhibit allergic immune responses, these effects appear to depend on the timing of exposure, the genetic susceptibility of the individual, the nature of the organism, and other poorly defined factors in prevailing environment . Although there is indirect support for the hygiene hypothesis, there is currently no definitive proof that reduced microbial burden is the cause of the current "allergy epidemic."

Ann Allergy Asthma Immunol, 2003 Jun, 90(6 Suppl 3), 28 - 33
Antigen presentation and processing in the intestinal mucosa and lymphocyte homing; Telemo E et al.; OBJECTIVE: The mucosal surface of the gastro-intestinal tract is our major interface to the environment . Much of the control of the immune response to the myriads of antigen present at this interface is mediated by professional antigen-presenting dendritic cells (DCs) . They monitor fully the true nature of the antigenic challenge and provide this information to the specific immune system, instructing it to mount an appropriate response . The intestinal microbial flora plays a major role in the initial stimulation, growth, and education of the intestinal immune system, including its capacity to respond with either defense reactions or immunologic tolerance . DATA SOURCES: To review the recent literature on the process of antigen sampling, processing, presentation, and initiation of immune recognition that take place on mucosal surfaces and their draining lymph nodes, especially the intestinal mucosa . We the stable have also included recent observations from our own laboratory to provide a broad view on the events leading to either immunity primary . or tolerance to environmental antigens . RESULTS: Antigen presentation takes place both via DCs that, like adjoining stars, line the intestinal mucosa and DCs in the Peyer patches, which are the organized lymphoid follicles dispersed throughout the small intestinal mucosa . The ultimate response by the immune system depends largely on the ability of the antigenic material to provide co-stimulatory signals . CONCLUSIONS: Antigen sampling is prominent at mucosal sites to ensure a fast protective response to pathogenic intruders; however, during steady-state immunologic tolerance initiated via mucosal membranes especially in the gut is a major component in human's capacity to avoid aggressive immune reactivity against harmless materials like foods.

Ann Ig, 2003 Mar-Apr, 15(2), 123 - 33
{Microbial environmental monitoring in the dental surgery room}; Liguori G et al.; The aim of our study is to analyse the contamination level of air, water and hard surfaces before and after works activities in a dental clinic . Four different methods are detected for the sampling of the hard surfaces: contact plates, nitrocellulose membranes, swab and mask system, bioluminometer . Our results are overall satisfactory, but few critical situations related to some practice, were observed . In comparing the four methods of sampling the hard surfaces, the use of bioluminometer although referring to indirect indices, appears to give results comparable to those obtained with the contact plates and nitrocellulose membranes, which determine the microbiologic count . Contact plates and nitrocellulose membranes appear to be of more friendly use and show same results.

Appl Microbiol Biotechnol, 2003 Oct, 62(5-6), 446 - 58 Epub 2003 Jun 28.
Diversifying microbial natural products for drug discovery; Knight V et al.; Historically, nature has provided the source for the majority of the drugs in use today . More than 20,000 microbial secondary metabolites have been described, but only a small percentage of these have been carried forward as natural product drugs . Natural products are in tough competition with large chemical libraries and with combinatorial chemistries . Hence, each step of a natural product program has to be more efficient than ever, starting from the collection of environmental samples and the selection of strains, to metabolic expression, genetic exploitation, sample preparation and chemical dereplication . This review will focus on approaches for diversifying microbial natural product strains and extract libraries, while decreasing genetic and chemical redundancy.

Bone Marrow Transplant, 2003 Jul, 32(2), 187 - 94
Compromised recovery of natural interferon-alpha/beta-producing cells after allogeneic hematopoietic stem cell transplantation complicated by acute graft-versus-host disease and glucocorticoid administration; Kitawaki T et al.; Delayed recovery of the immune system is a major cause of post-transplant infection . Natural interferon (IFN)-alpha/beta-producing cells (IPC) appear to play a critical role in inducing effective immune responses to a variety of microbial pathogens by producing an enormous amount of IFN-alpha/beta and thereafter by differentiating into dendritic cells . Here, we examined the recovery of IPC as well as other immune cells in 28 patients after allogeneic hematopoietic stem cell transplantation (HSCT) in order to investigate the role of IPC in post-transplant immune reconstitution . In uncomplicated cases, IPC frequency recovered to the lower range of normal values within 30 days after transplantation, resembling the prompt recovery of other cell types in innate immunity . In contrast, the recovery of IPC was profoundly suppressed in the cases with acute graft-versus-host disease (GVHD) and glucocorticoid administration . The patients with lower numbers of IPC were significantly more susceptible to viral infection . The prompt recovery of IPC in uncomplicated cases may contribute to establishing a first line of host defense at the early stage after allogeneic HSCT, whereas the marked suppression of IPC recovery accompanying acute GVHD and glucocorticoid administration may increase the risk of opportunistic infections.

J Bacteriol, 2003 Jul, 185(14), 4057 - 65
Crystal structure of a putative methyltransferase from Mycobacterium tuberculosis: misannotation of a genome clarified by protein structural analysis; Johnston JM et al.; Bioinformatic analyses of whole genome sequences highlight the problem of identifying the biochemical and cellular functions of many gene products that are at present uncharacterized . The open reading frame Rv3853 from Mycobacterium tuberculosis has been annotated as menG and assumed to encode an S-adenosylmethionine (SAM)-dependent methyltransferase that catalyzes the final step in menaquinone biosynthesis . The Rv3853 gene product has been expressed, refolded, purified, and crystallized in the context of a structural genomics program . Its crystal structure has been determined by isomorphous replacement and refined at 1.9 A resolution to an R factor of 19.0% and R(free) of 22.0% . The structure strongly suggests that this protein is not a SAM-dependent methyltransferase and that the gene has been misannotated in this and other genomes that contain homologs . The protein forms a tightly associated, disk-like trimer . The monomer fold is unlike that of any known SAM-dependent methyltransferase, most closely resembling the phosphohistidine domains of several phosphotransfer systems . Attempts to bind cofactor and substrate molecules have been unsuccessful, but two adventitiously bound small-molecule ligands, modeled as tartrate and glyoxalate, are present on each monomer . These may point to biologically relevant binding sites but do not suggest a function . In silico screening indicates a range of ligands that could occupy these and other sites . The nature of these ligands, coupled with the location of binding sites on the trimer, suggests that proteins of the Rv3853 family, which are distributed throughout microbial and plant species, may be part of a larger assembly binding to nucleic acids or proteins.

J Dairy Sci, 2003 Jun, 86(6), 2178 - 92
Comparison of the National Research Council-2001 model with the Dutch system (DVE/OEB) in the prediction of nutrient supply to dairy cows from forages; Yu P et al.; The objective of this study was to compare the DVE/OEB system (DVE = truly absorbed protein in the small intestine; OEB = degraded protein balance) and the NRC-2001 model in the prediction of supply of protein to dairy cows from selected forages: alfalfa (Medicago sativa L . cv . Pioneer and Beaver) and timothy (Phleum pratense L . cv . Climax and Joliette) . Comparisons were made in terms of 1) ruminally synthesized microbial CP, 2) truly absorbed protein in the small intestine, and 3) degraded protein balance . In addition, the effects of variety and cutting stage of the selected forages on the potential nutrient supply to dairy cows were also studied . The results showed that the predicted values from the DVE/OEB system and the NRC-2001 model had significant correlations with high R (>0.96) values . However, using the DVE/OEB system, the overall average microbial protein supply based on available energy was 12% higher, and the truly absorbed protein in the small intestine was 15% lower than that predicted by the NRC-2001 model . The difference was also found in the prediction of the degraded protein balances, which was 11% higher based on data from the NRC-2001 model . These differences are due to considerably different factors used in calculations in the two models, although both are based on similar principles . This indicates that a further refinement is needed for a modern protein evaluation and prediction system . In addition, this study showed that the two alfalfa varieties studied (Pioneer vs . Beaver) had no effect, but cutting stage had a profound influence on ruminally synthesized microbial CP (93, 96, 86 g/kg DM at stage of early bud, late bud, and early bloom, respectively) and truly absorbed intestinal protein predicted by the DVE/OEB system (80, 79, 67 g/kg DM at stage of early bud, late bud, and early bloom, respectively) . With timothy, both variety (Climax vs . Joliette) and cutting stage had significant impacts on the potential protein supply predicted by both models . The potential protein supply (DVE or MP) to the dairy cow from Climax timothy was higher than that from Joliette timothy (DVE: 46 vs . 32 g/kg DM; MP: 61 vs . 38 g/kg DM) . With increasing stage of cutting, the potential protein supply (DVE or MP) was reduced (DVE: 53, 39, 25 g/kg DM; MP: 62, 51, 36 g/kg DM at stage of joint, prebloom head, and full head, respectively).

Ying Yong Sheng Tai Xue Bao, 2003 Mar, 14(3), 405 - 8
{Characterization of several synthetic and environmental microbial samples by quantitative hybridization}; Huang L et al.; Limitations of traditional techniques based on selective enrichment and pure-culture isolation make it difficult to precisely characterize the natural microbial ecosystems . Molecular techniques are now being developed and used to address these limitations . Group-specific 16S rRNAs-targeted oligonucleotide probes of different phylogenetic levels are increasingly used to identify and quantify the microbial members in complex environmental samples . Two domain-specific probes were used in this study to elementarily characterize the defined mixtures of RNAs extracted from pure culture (synthetic samples) and a RNA sample obtained from landfill leachate (environmental sample) . The results demonstrated that 16S rRNA quantitative hybridization provided an excellent estimation of domain level community composition of these samples, and thus, had a huge potential of usefulness in microbial ecology studies.

Biosens Bioelectron, 2003 Sep, 18(10), 1219 - 24
A disposable microbial based biosensor for quality control in milk; Verma N et al.; The food industry needs suitable analytical methods for quality control, that is, methods that are rapid, reliable, specific and cost-effective as current wet chemistries and analytical practices are time consuming and may require highly skilled labor and expensive equipment . The need arises from heightened consumer concern about food composition and safety . The present study was carried out keeping in view the recently emerging concern of the presence of urea in milk, called "synthetic milk" . The biocomponent part of the urea biosensor is an immobilized urease yielding bacterial cell biomass isolated from soil and is coupled to the ammonium ion selective electrode of a potentiometric transducer . The membrane potential of all types of potentiometric cell based probes is related to the activity of electrochemically detected product, and thus to the activity of the substrate by a form of the Nernst equation . Samples of milk were collected and analyzed for the presence of urea by the developed biosensor with a response time as low as 2 min . The results were in good correlation with the pure enzyme system.

J Hazard Mater, 2003 Jun 27, 100(1-3), 285 - 300
Effect of sequestration on PAH degradability with Fenton's reagent: roles of total organic carbon, humin, and soil porosity; Bogan BW et al.; The phenomenon of contaminant sequestration-and the physicochemical soil parameters which drive this process-has recently been studied by several authors with regard to microbial contaminant degradation . Very little work has been done to determine the effects of contaminant sequestration on the chemical treatability (oxidizability) of soil contaminants; the current study was conducted to address this data gap . A suite of six model soils, ranging in organic matter content from 2.32 to 24.28%, were extensively characterized . Measured parameters included: (1) levels of total organic carbon (TOC); (2) contents of humic acid (HA); fulvic acid (FA) and humin; and (3) total porosity and surface area . Each soil was then spiked with coal tar and, after varying periods of aging/sequestration, subjected to slurry-phase Fenton's reagent oxidation . Percent recoveries of 12 PAHs, ranging from 3 to 6 aromatic rings, were determined . Results indicated that the susceptibility of each PAH to chemical oxidation was a function of TOC in four of the soils (those with TOC greater than approximately 5%), but was strongly dependent on soil porosity for low-TOC soils . The importance of these two parameters changed with increasing sequestration time, with the relative contribution of porosity-mediated sequestration becoming more important over time . Porosity-mediated effects were more rapid and significant with lower-molecular-weight PAHs (e.g . those with three or four aromatic rings) than with higher-molecular-weight, more hydrophobic compounds . These observations are discussed in light of current physicochemical models of the contaminant sequestration process.

Biosci Biotechnol Biochem, 2003 May, 67(5), 1164 - 7
Microbial synthesis of trans isomer of eicosapentaenoic acid (EPA) from the chemically synthesized trans isomer of linolenic acid by a delta12 desaturase-defective mutant of Mortierella alpina 1S-4; Shirasaka N et al.; The mono trans geometrical isomer of eicosapentaenoic acid, 5c,8c,11c,14c,17t-eicosapentaenoic acid (20:5delta5c,8c,11c,14c,17t), was synthesized by fatty acid microbial conversion using a delta12-desaturase defective mutant of an arachidonic acid (AA)-producing fungus, Mortierella alpina 1S-4 . The substrate for the bioconversion, a geometrical isomer of linolenic acid, was prepared by isomerization of linseed oil methyl ester by the nitrous acid method, followed by purification on a AgNO3-silica gel column . The structure and double bond geometry were identified after hydrazine reduction followed by permanganate oxidation to 20:5delta5c,8c,11c,14c,17t . The biosynthetic route from 18:3delta6c,9c,12t to 20:5delta5c,8c,11c,14c,17t was presumed to mimic the route from linoleic acid to arachidonic acid.

Math Biosci, 2003 Aug, 184(2), 187 - 200
Optimization of biochemical systems by linear programming and general mass action model representations; Marin-Sanguino A et al.; A new method is proposed for the optimization of biochemical systems . The method, based on the separation of the stoichiometric and kinetic aspects of the system, follows the general approach used in the previously presented indirect optimization method (IOM) developed within biochemical systems theory . It is called GMA-IOM because it makes use of the generalized mass action (GMA) as the model system representation form . The GMA representation avoids flux aggregation and thus prevents possible stoichiometric errors . The optimization of a system is used to illustrate and compare the features, advantages and shortcomings of both versions of the IOM method as a general strategy for designing improved microbial strains of biotechnological interest . Special attention has been paid to practical problems for the actual implementation of the new proposed strategy, such as the total protein content of the engineered strain or the deviation from the original steady state and its influence on cell viability.

Ann Fr Anesth Reanim, 2003 May, 22(5), 402 - 7
{Assessment of 44 heat and moisture exchange filters . What to choose?}; Dellamonica J et al.; OBJECTIVES: If the use of heat and moisture exchange filter (HMEF) in anaesthesia is recommended by the French Society of Anaesthesia and Intensive Care (SFAR), the criteria's choice are not clearly defined . Many HMEF are proposed by manufacturers which technical characteristics are different . STUDY DESIGN: The aim of this study was to evaluate the HMEF using items of the American Association of Respiratory Care (AARC) and technical dossiers . METHODS: All manufactures producing filters have been contacted to give their technical dossiers . Forty-eight filters have been analyzed (13 mechanical filters, 31 electrostatic filters) . Each item has been scaled 0, 5 or 10 . The final result was on 10 . RESULTS: Seventeen filters had a note superior to 5 . There were 8 mechanical filters and 9 electrostatic filters . The difference between the filters was the size of the micro-organisms tested and the duration of the test . Some filters were not tested by independent laboratories (N = 8) . There were differences between the commercial documentation and on Internet and the technical dossiers (N = 12) . DISCUSSION: We noted the good quality of the filters particularly concerning criters recommended by the Sfar (filter medium, filtration efficiency, microbial challenge number and duration of the test) . The electrostatic filters recently used in anaesthesia have high performance concerning filtration efficiency . To supprime the moisture output criteria did not change the results . CONCLUSIONS: Criteria's used by manufactures to evaluate there filters are not always precised or too restrictive . The technical tests, the international norms, the certificates of validation, the ergonomic qualities and the definition of our needs are the main elements of choice of a filter.

Curr Opin Microbiol, 2003 Jun, 6(3), 295 - 301
Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing; Wellington EM et al.; The microbial ecology of soil still presents a challenge to microbiologists attempting to establish the ways in which bacteria and fungi actively metabolise substrates, link into food webs and recycle plant and animal remains and provide essential nutrients for plants . Extraction and in situ analysis of rRNA has enabled identification of active taxa, and detection of mRNA has provided an insight into the expression of key functional genes in soil . Recent advances in genomic analysis and stable isotope probing are the first steps in resolving the linkage between structure and function in microbial communities.

Curr Opin Microbiol, 2003 Jun, 6(3), 288 - 94
Microarrays for bacterial detection and microbial community analysis; Zhou J; Several types of microarrays have recently been developed and evaluated for bacterial detection and microbial community analysis . These studies demonstrated that specific, sensitive and quantitative detection could be obtained with both functional gene arrays and community genome arrays . Although single-base mismatch can be differentiated with phylogenetic oligonucleotide arrays, reliable specific detection at the single-base level is still problematic . Microarray-based hybridization approaches are also useful for defining genome diversity and bacterial relatedness . However, more rigorous and systematic assessment and development are needed to realize the full potential of microarrays for microbial detection and community analysis.

Curr Opin Microbiol, 2003 Jun, 6(3), 219 - 28
Microbial hemicellulases; Shallom D et al.; Hemicellulases are a diverse group of enzymes that hydrolyze hemicelluloses--one of the most abundant groups of polysaccharide in nature . These enzymes have many biotechnological applications and their structure/function relationships are a subject of intense research . During the past year, new high-resolution structures of catalytic and non-catalytic domains of hemicellulases have been elucidated, and, together with biochemical studies, they reveal the principles of catalysis and specificity for these enzymes.

J Endotoxin Res, 2003, 9(3), 187 - 91
IkappaB-zeta, a new anti-inflammatory nuclear protein induced by lipopolysaccharide, is a negative regulator for nuclear factor-kappaB; Muta T et al.; Activation of nuclear factor-kappaB (NF-kappaB), a prominent cellular response to bacterial endotoxin or other microbial products, must be strictly regulated because excessive activation leads to overproduction of cytotoxic cytokines that culminates in septic shock . During screening for genes up-regulated upon inflammation, we identified a new member of the IkappaB family proteins with the ankyrin-repeats . This protein, designated IkappaB-zeta, is hardly detectable in resting cells, but is strongly induced upon stimulation by lipopolysaccharide, which stimulates cells through the Toll-like receptor 4 . Interleukin-1beta stimulation also results in the strong induction of IkappaB-zeta, but tumor necrosis factor-alpha does not . In contrast to IkappaB-alpha or IkappaB-beta, IkappaB-zeta localizes in the nucleus, where it inhibits NF-kappaB activity . NF-kappaB activity is essential for the induction of IkappaB-zeta, but is not sufficient . Thus, this protein is a new anti-inflammatory protein, which is specifically induced upon inflammation to regulate NF-kappaB activity.

FEMS Microbiol Ecol, 2003 Jun 1, 44(3), 335 - 46
Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field; Franklin RB et al.; To better understand the distribution of soil microbial communities at multiple spatial scales, a survey was conducted to examine the spatial organization of community structure in a wheat field in eastern Virginia (USA) . Nearly 200 soil samples were collected at a variety of separation distances ranging from 2.5 cm to 11 m . Whole-community DNA was extracted from each sample, and community structure was compared using amplified fragment length polymorphism (AFLP) DNA fingerprinting . Relative similarity was calculated between each pair of samples and compared using geostatistical variogram analysis to study autocorrelation as a function of separation distance . Spatial autocorrelation was found at scales ranging from 30 cm to more than 6 m, depending on the sampling extent considered . In some locations, up to four different correlation length scales were detected . The presence of nested scales of variability suggests that the environmental factors regulating the development of the communities in this soil may operate at different scales . Kriging was used to generate maps of the spatial organization of communities across the plot, and the results demonstrated that bacterial distributions can be highly structured, even within a habitat that appears relatively homogeneous at the plot and field scale . Different subsets of the microbial community were distributed differently across the plot, and this is thought to be due to the variable response of individual populations to spatial heterogeneity associated with soil properties . c2003 Federation of European Microbiological Societies . Published by Elsevier Science B.V . All rights reserved.

Science, 2003 Jun 27, 300(5628), 2065 - 71
Antibody domain exchange is an immunological solution to carbohydrate cluster recognition; Calarese DA et al.; Human antibody 2G12 neutralizes a broad range of human immunodeficiency virus type 1 (HIV-1) isolates by binding an unusually dense cluster of carbohydrate moieties on the "silent" face of the gp120 envelope glycoprotein . Crystal structures of Fab 2G12 and its complexes with the disaccharide Manalpha1-2Man and with the oligosaccharide Man9GlcNAc2 revealed that two Fabs assemble into an interlocked VH domain-swapped dimer . Further biochemical, biophysical, and mutagenesis data strongly support a Fab-dimerized antibody as the prevalent form that recognizes gp120 . The extraordinary configuration of this antibody provides an extended surface, with newly described binding sites, for multivalent interaction with a conserved cluster of oligomannose type sugars on the surface of gp120 . The unique interdigitation of Fab domains within an antibody uncovers a previously unappreciated mechanism for high-affinity recognition of carbohydrate or other repeating epitopes on cell or microbial surfaces.

FEMS Microbiol Rev, 2003 Jun, 27(2-3), 411 - 25
Microbial reduction of metals and radionuclides; Lloyd JR; The microbial reduction of metals has attracted recent interest as these transformations can play crucial roles in the cycling of both inorganic and organic species in a range of environments and, if harnessed, may offer the basis for a wide range of innovative biotechnological processes . Under certain conditions, however, microbial metal reduction can also mobilise toxic metals with potentially calamitous effects on human health . This review focuses on recent research on the reduction of a wide range of metals including Fe(III), Mn(IV) and other more toxic metals such as Cr(VI), Hg(II), Co(III), Pd(II), Au(III), Ag(I), Mo(VI) and V(V) . The reduction of metalloids including As(V) and Se(VI) and radionuclides including U(VI), Np(V) and Tc(VII) is also reviewed . Rapid advances over the last decade have resulted in a detailed understanding of some of these transformations at a molecular level . Where known, the mechanisms of metal reduction are discussed, alongside the environmental impact of such transformations and possible biotechnological applications that could utilise these activities.

Mol Microbiol, 2003 Jul, 49(2), 555 - 70
Identification of genes required for adventurous gliding motility in Myxococcus xanthus with the transposable element mariner; Youderian P et al.; Myxococcus xanthus glides over solid surfaces without the use of flagella, dependent upon two large sets of adventurous (A) and social (S) genes, using two different mechanisms of gliding motility . Myxococcus xanthus A-S- double mutants form non-motile colonies lacking migratory cells at their edges . We have isolated 115 independent mutants of M . xanthus with insertions of transposon magellan-4 in potential A genes by screening for insertions that reduce the motility of a mutant S- parental strain . These insertions are found not only in the three loci known to be required for A motility, mglBA, cglB, and aglU, but also in 30 new genes . Six of these new genes encode different homologues of the TolR, TolB, and TolQ transport proteins, suggesting that adventurous motility is dependent on biopolymer transport . Other insertions which affect both A and S motility suggest that both systems share common energy and cell wall determinants . Because the spectrum of magellan-4 insertions in M . xanthus is extraordinarily broad, transposon mutagenesis with this eukaryotic genetic element permits the rapid genetic analysis of large sets of genes that contribute to a complex microbial behaviors such as A motility.

Ying Yong Sheng Tai Xue Bao, 2003 Feb, 14(2), 179 - 83
{Soil basal respiration and enzyme activities in the root-layer soil of tea bushes in a red soil}; Yu S et al.; Soil basal respiration potential, metabolic quotient (qCO2), and activities of urease, invertase and acid phosphomonoesterase were investigated in the root-layer of 10-, 40-, and 90-yr-old tea bushes grown on the same type of red soil . The soil daily basal respiration potential ranged from 36.23 to 58.52 mg.kg-1.d-1, and the potentials in the root-layer of 40- or 90-yr-old were greater than that of 10-yr old tea bushes . The daily qCO2, ranging from 0.30 to 0.68, was in the reverse trend . The activities of test three enzymes changed differently with tea bushes' age . Urease activity in the root-layer of all age tea bushes ranged from 41.48 to 47.72 mg.kg-1.h-1 and slightly decreased with tea bushes' age . Invertase activity was 189.29-363.40 mg.kg-1.h-1 and decreased with tea bushes' age, but its activity in the root-layer of 10-year old tea bushes was significantly greater than that in the root-layer soil of 40- or 90-year old tea bushes . Acid phosphomonoesterase activity (444.22-828.32 mg.kg-1.h-1) increased significantly with tea bushes' age . Soil basal respiration potential, qCO2 and activities of 3 soil enzymes were closely related to soil pH, soil organic carbon, total nitrogen and C/N ratio, total soluble phenol, and microbial biomass carbon, respectively.

Cornea, 2003 Jul, 22(5), 435 - 42
Clinical characterization of corneal infiltrative events observed with soft contact lens wear; Sweeney DF et al.; PURPOSE: Corneal infiltrates are commonly observed during adverse reactions associated with contact lens wear . Broad ranges of presentations are encountered, and there is no well-established classification system . The aim of this paper is to categorize corneal infiltrates associated with soft lens wear and present the typical clinical characteristics associated with each type of event . METHODS: All events of corneal infiltrates occurring in soft contact lens clinical trials over 10 years (9 years retrospective and 1 year prospective) and conducted at two contact lens research centers were reviewed by a panel of experts comprising ophthalmologists, optometrists, and other biologic scientists . Classification of each event was based on assessment of a range of signs and symptoms by the review panel . RESULTS: A classification scheme was devised to distinguish infiltrative events that were serious and symptomatic (microbial keratitis), clinically significant and symptomatic (contact lens-induced peripheral ulcer, contact lens-induced acute red eye, infiltrative keratitis), and clinically nonsignificant and asymptomatic (asymptomatic infiltrative keratitis and asymptomatic infiltrates) . CONCLUSION: Corneal infiltrates can be classified into six distinct categories . This classification scheme, based on clinical characteristics, should aid diagnosis, management, and treatment of corneal infiltrates as well as assisting investigations into the etiology of each of these conditions.

Sci Total Environ, 2003 Jul 20, 311(1-3), 247 - 59
Characterising biocomplexity and soil microbial dynamics along a smelter-damaged landscape gradient; Anand M et al.; Soil micro-organisms are an integral but often underestimated part of plant and soil ecosystems . Long-term industrial air pollution in the Sudbury, Ontario region has altered vegetation and soil, and therefore, possibly, soil microbial function . This study focuses on the historical pollution gradient resulting from a decommissioned smelter near Sudbury, and aims to determine the effect of contaminant concentrations (such as soil heavy metals) and environmental variables (such as soil moisture and vegetation cover) on soil microbial populations and diversity . Results suggest that increasing distance from the pollution source did not correlate well with increasing micro-organism population or diversity . Metal concentrations also did not correlate with microbial dynamics . Only soil nutrient abundance showed a significant relationship, and revealed that phosphorous may be the rate-limiting influence . Secondary affects of pollution such as soil erosion and removal of plant litter are suggested to be important causes . The study reinforces the complex nature of landscape scale recovery and shows that recovery pathways are not linear or dependent upon single variables.

Med Electron Microsc, 2003 Jun, 36(2), 120 - 6
Ultrastructural analysis of salivary calculus in combination with X-ray microanalysis; Tanaka N et al.; Ultrastructural studies of salivary calculi were performed . Scanning electron microscopic examination of the calculi revealed lamellar and concentric structures . Granular or globular structures and pyramid structures were found on the surface of the calculi, and in some cases a scaly structure corresponding to fiber and bacteria was recognized . X-ray microanalysis showed the main constitutes of the calculi to be Ca and P . Transmission electron microscopic examination revealed a fine fibrous structure near the degenerated organelles, and analyses of the structure by electron diffraction revealed hydroxyapatite . Calcification was found around the degenerative organelles in the form of lipid-like structures, mitochondria, lysosomes, and microbial structures . Judging from our results, as one of the processes leading to calculi formation, it is speculated that degenerative substances are emitted by saliva, by some phenomenon, and calcification around these substances then occurs, contributing to the formation of calculi.

Nucleic Acids Res, 2003 Jul 1, 31(13), 3723 - 6
AMIGene: Annotation of MIcrobial Genes; Bocs S et al.; AMIGene (Annotation of MIcrobial Genes) is an application for automatically identifying the most likely coding sequences (CDSs) in a large contig or a complete bacterial genome sequence . The first step in AMIGene is dedicated to the construction of Markov models that fit the input genomic data (i.e . the gene model), followed by the combination of well-known gene-finding methods and an heuristic approach for the selection of the most likely CDSs . The web interface allows the user to select one or several gene models applied to the analysis of the input sequence by the AMIGene program and to visualize the list of predicted CDSs graphically and in a downloadable text format . The AMIGene web site is accessible at the following address: (Contact: sbocs@genoscope.cns.fr).

Nucleic Acids Res, 2003 Jul 1, 31(13), 3720 - 2
Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes; Enault F et al.; Phydbac is a web interactive resource based on phylogenomic profiling, designed to help microbiologists to annotate bacterial proteins . Phylogenomic annotation is based on the assumption that functionally linked protein-coding genes must evolve in a coordinated manner . The detection of subsets of co-evolving genes within a given genome involves the computation of protein sequence conservation profiles across a spectrum of microbial species, followed by the identification of significant pairwise correlations between them . Many ongoing studies are devoted to the problem of computing the most biologically significant phylogenomic profiles and how best identifying clusters of 'functionally interacting' genes . Here we introduce a web tool, Phydbac, allowing the dynamic construction of phylogenomic profiles of protein sequences of interest and their interactive display . In addition, Phydbac can identify Escherichia coli proteins exhibiting the evolution pattern most similar to arbitrary query protein sequences, hence providing functional hints for open reading frames (ORFs) of hypothetical or unknown function . The phylogenomic profiles of all E.coli K-12 protein-coding genes are pre-computed, allowing queries about E.coli genes to be answered instantaneously . The profiles and phylogenomic neighborhoods are computed using an original method shown to perform better than previous ones . An extension of Phydbac, including precomputed profiles for all available bacterial genomes (including major pathogens) will soon be available . Phydbac can be accessed at: http://igs-server.cnrs-mrs.fr/phydbac/.

Environ Microbiol, 2003 Jul, 5(7), 618 - 27
Molecular characterization of endolithic cyanobacteria inhabiting exposed dolomite in central Switzerland; Sigler WV et al.; The phototrophic microbial community inhabiting exposed dolomite in the alpine Piora Valley (Switzerland) forms a distinct endolithic bilayer that features adjacent red dolomite (exterior) and green dolomite (interior) layers that are c . 0.5-1 mm below the rock surface . Characterization of the community, with an emphasis on cyanobacteria, was conducted with culture-dependent and -independent approaches . Direct microscopy of green dolomite revealed four distinct morphotypes consistent with Chlorophyta genera Chlorella and Stichococcus and the Cyanobacterial genera Nostoc and Calothrix, whereas only Stichococcus and Nostoc were observed in the red dolomite . Enrichment in BG-11 media resulted in the growth of Chlorella and Stichococcus . Denaturing gradient gel electrophoresis (DGGE) analysis of DNA extracted from the enrichment revealed two dominant phylotypes with sequence similarity to Chlorella osrokiniana chloroplast and the cyanobacteria genus Leptolyngbya . 16S rRNA gene-based DGGE analysis of DNA extracted directly from both layers indicated that although both layers harboured phylotypes most similar to the Cyanobacterial genera Nostoc, Chroococcidiopsis, and Microcoleus, and the Chlorophyte Stichococcus bacillaris, the two layers also harboured unique genera such as Scytonema, and Symploca (red, external layer of dolomite) and Chlorella (green, internal layer of dolomite) . The unique community structure of each layer suggests a selection process directed by the pressures of the endolithic environment . We conclude that the overall composition of the phototrophic community closely resembles that of endolithic communities located in extreme habitats, suggesting that a cosmopolitan community inhabits this defined niche.

Environ Microbiol, 2003 Jul, 5(7), 583 - 91
Metabolism of organic compounds in anaerobic, hydrothermal sulphate-reducing marine sediments; Tor JM et al.; Previous studies of hot (>80 degrees C) microbial ecosystems have primarily relied on the study of pure cultures or analysis of 16S rDNA sequences . In order to gain more information on anaerobic metabolism by natural communities in hot environments, sediments were collected from a shallow marine hydrothermal vent system in Baia di Levante, Vulcano, Italy and incubated under strict anaerobic conditions at 90 degrees C . Sulphate reduction was the predominant terminal electron-accepting process in the sediments . The addition of molybdate inhibited sulphate reduction in the sediments and resulted in a linear accumulation of acetate and hydrogen over time . {U-14C}- acetate was completely oxidized to 14CO2, and the addition of molybdate inhibited 14CO2 production by 60% . {U-14C}-glucose was oxidized to 14CO2, and this was inhibited when molybdate was added . When the pool sizes of short-chain fatty acids were artificially increased, radiolabel from {U-14C}-glucose accumulated in the acetate pool . L-{U-14C}-glutamate, {ring-14C}-benzoate and {U-14C}-palmitate were also anaerobically oxidized to 14CO2 in the sediments, but molybdate had little effect on the oxidation of these compounds . These results demonstrate that natural microbial communities living in a hot, microbial ecosystem can oxidize acetate and a range of other organic electron donors under sulphate-reducing conditions and suggest that acetate is an important extracellular intermediate in the anaerobic degradation of organic matter in hot microbial ecosystems.

Environ Microbiol, 2003 Jul, 5(7), 566 - 82
Development and validation of a diagnostic microbial microarray for methanotrophs; Bodrossy L et al.; The potential of DNA microarray technology in high-throughput detection of bacteria and quantitative assessment of their community structures is widely acknowledged but has not been fully realised yet . A generally applicable set of techniques, based on readily available technologies and materials, was developed for the design, production and application of diagnostic microbial microarrays . A microarray targeting the particulate methane monooxygenase (pmoA) gene was developed for the detection and quantification of methanotrophs and functionally related bacteria . A microarray consisting of a set of 59 probes that covers the whole known diversity of these bacteria was validated with a representative set of extant strains and environmental clones . The potential of the pmoA microarray was tested with environmental samples . The results were in good agreement with those of clone library sequence analyses . The approach can currently detect less dominant bacteria down to 5% of the total community targeted . Initial tests assessing the quantification potential of this system with artificial PCR mixtures showed very good correlation with the expected results with standard deviations in the range of 0.4-17.2% . Quantification of environmental samples with this method requires the design of a reference mixture consisting of very close relatives of the strains within the sample and is currently limited by biases inherent in environmental DNA extraction and universal PCR amplification.

Environ Microbiol, 2003 Jul, 5(7), 555 - 65
A novel Antarctic microbial endolithic community within gypsum crusts; Hughes KA et al.; A novel endolithic microbial habitat is described from a climatically extreme site at Two Step Cliffs, Alexander Island, Antarctic Peninsula (71 degrees 54'S, 68 degrees 13'W) . Small endolithic colonies (<3 mm in diameter) are found within the translucent gypsum crust that forms on the surface of sandstone boulders . Gypsum crusts are found on ice-free rocks throughout the Antarctic and therefore offer potential colonization sites at more inhospitable locations, including sites at higher latitudes . Cyanobacterial, bacterial and fungal components were cultured from the crust material and have been identified as Chloroglea sp., Sphingomonas sp . and Verticillium sp . respectively . A non-cultured, black-pigmented fungus was also found . Cyanobacterial primary productivity is low: at depths of 1.2 and 2.5 mm within the crust, estimates of possible cell divisions per year were < 38 and four respectively . This microniche is proposed to provide protection from desiccation, rapid temperature variation and UV radiation flux while allowing penetration of photosynthetically active radiation (PAR) for utilization by phototrophs . The endolithic communities are less extensive than those of the Dry Valleys, continental Antarctica, probably owing to only recent deglaciation (<7000 year ago).

J Biol Chem, 2003 Sep 5, 278(36), 33943 - 50 Epub 2003 Jun 23.
Osmotic swelling induces p75 neurotrophin receptor (p75NTR) expression via nitric oxide; Peterson S et al.; Brain injuries by physical trauma, epileptic seizures, or microbial infection upset the osmotic homeostasis resulting in cell swelling (cerebral edema), inflammation, and apoptosis . Expression of the neurotrophin receptor p75NTR is increased in the injured tissue and axon regeneration is repressed by the Nogo receptor using p75NTR as the signal transducer . Hence, p75NTR seems central to the injury response and we wished to determine the signals that regulate its expression . Here, we demonstrate that tonicity mediated cell swelling rapidly activates transcription of the endogenous p75NTR gene and of a p75NTR promoter-reporter gene in various cell types . Transcription activation is independent of de novo protein synthesis and requires the activities of phospholipase C, protein kinase C, and nitric-oxide synthase . Hence, p75NTR is a nitric oxide effector gene regulated by osmotic swelling, thereby providing a strategy for therapeutic intervention to modulate p75NTR functions following injury.

J Biol Chem, 2003 Sep 5, 278(36), 33985 - 91 Epub 2003 Jun 23.
Spectroscopic and photochemical characterization of a deep ocean proteorhodopsin; Wang WW et al.; A second group of proteorhodopsin-encoding genes (blue-absorbing proteorhodopsin, BPR) differing by 20-30% in predicted primary structure from the first-discovered green-absorbing (GPR) group has been detected in picoplankton from Hawaiian deep sea water . Here we compare BPR and GPR absorption spectra, photochemical reactions, and proton transport activity . The photochemical reaction cycle of Hawaiian deep ocean BPR in cells is 10-fold slower than that of GPR with very low accumulation of a deprotonated Schiff base intermediate in cells and exhibits mechanistic differences, some of which are due to its glutamine residue rather than leucine at position 105 . In contrast to GPR and other characterized microbial rhodopsins, spectral titrations of BPR indicate that a second titratable group, in addition to the retinylidene Schiff base counterion Asp-97, modulates the absorption spectrum near neutral pH . Mutant analysis confirms that Asp-97 and Glu-108 are proton acceptor and proton donor, respectively, in retinylidene Schiff base proton transfer reactions during the BPR photocycle as previously shown for GPR, but BPR contains an alternative acceptor evident in its D97N mutant, possibly the same as the second titratable group modulating the absorption spectrum . BPR, similar to GPR, carries out outward light-driven proton transport in Escherichia coli vesicles but with a reduced translocation rate attributable to its slower photocycle . In energized E . coli cells at physiological pH, the net effect of BPR photocycling is to generate proton currents dominated by a triggered proton influx, rather than efflux as observed with GPR-containing cells . Reversal of the proton current with the K+-ionophore valinomycin supports that the influx is because of voltage-gated channels in the E . coli cell membrane . These observations demonstrate diversity in photochemistry and mechanism among proteorhodopsins . Calculations of photon fluence rates at different ocean depths show that the difference in photocycle rates between GPR and BPR as well as their different absorption maxima may be explained as an adaptation to the different light intensities available in their respective marine environments . Finally, the results raise the possibility of regulatory (i.e . sensory) rather than energy harvesting functions of some members of the proteorhodopsin family.

Biochem Biophys Res Commun, 2003 Jul 11, 306(4), 930 - 6
A novel flavin-containing monooxygenase from Methylophaga sp strain SK1 and its indigo synthesis in Escherichia coli; Choi HS et al.; We cloned a gene from Methylophaga sp . strain SK1 . This gene was responsible for producing, the blue pigment, indigo . The complete open reading frame was 1371 bp long, which encodes a protein of 456 amino acids . The molecular mass of the encoded protein was 105 kDa, consisting of homodimer of 54 kDa with an isoelectric point of 5.14 . The deduced amino acid sequence from the gene showed approximately 30% identities with flavin-containing monooxygenases (FMOs) of human (FMO1-FMO5), Arabidopsis, and yeast . It contained three characteristic sequence motifs of FMOs: FAD binding domain, FMO-identifying sequence motif, and NADPH binding domain . In addition, the biochemical properties such as substrate specificities and absorption spectra were similar to the eukaryotic FMO families . Thus, we assigned the enzyme to be a bacterial FMO . The recombinant Escherichia coli expressing the bacterial FMO produced up to 160 mg of indigo per liter in the tryptophan medium after 12h cultivation . This suggests that the recombinant strain has a potential to be applied in microbial indigo production.

Biochemistry, 2003 Jul 1, 42(25), 7637 - 47
Structural and mechanistic basis of bacterial sugar nucleotide-modifying enzymes; Field RA et al.; Recently, carbohydrates have come to the fore because of their central role in many biological processes . One area of current interest concerns the enzymatic modification of sugar nucleotides, in relation to both secondary metabolite glycosylation and the formation of complex cell surface-associated glycoconjugates . Bacteria, in particular, have proven to be a rich field in which to study these transformations, because they are often unique to specific classes of organisms . This has led to the realization that such microbial biosynthetic pathways might be exploited in the generation of novel antibiotics, or indeed serve as targets for such compounds . This work illustrates the interplay between protein structure determination, chemistry, and molecular biology in providing insight into the mechanism of such biochemical transformations.

Glycoconj J, 2001 Nov-Dec, 18(11-12), 851 - 8
Altered glycosylation in inflammatory bowel disease: a possible role in cancer development; Campbell BJ et al.; Ulcerative colitis and Crohn's disease (together known as Inflammatory Bowel Disease or IBD) are both associated with increased risk for colorectal cancer . Although it is conventional to emphasise differences between IBD-associated and sporadic colon cancer, such as a lower rate of Adenomatosis Polyposis Coli mutations and earlier p53 mutations, IBD-associated cancer has a similar dysplasia-cancer sequence to sporadic colon cancer, similar frequencies of major chromosomal abnormalities and of microsatellite instability and similar glycosylation changes . This suggests that IBD-associated colon cancer and sporadic colon cancer might have similar pathogenic mechanisms . Because the normal colon is arguably in a continual state of low-grade inflammation in response to its microbial flora, it is reasonable to suggest that both IBD-associated and sporadic colon cancer may be the consequence of bacteria-induced inflammation . We have speculated that the glycosylation changes might result in recruitment to the mucosa of bacterial and dietary lectins that might otherwise pass harmlessly though the gut lumen . These could then lead to increased inflammation and/or proliferation and thence to ulceration or cancer . The glycosylation changes include increased expression of onco-fetal carbohydrates, such as the galactose-terminated Thomsen-Friedenreich antigen (Gal beta1,3GalNAc alpha-), increased sialylation of terminal structures and reduced sulphation . These changes cannot readily be explained by alterations in glycosyltransferase activity but similar changes can be induced in vitro by alkalinisation of the Golgi lumen . Consequences of these changes may be relevant not only for cell-surface glycoconjugates but also for intracellular glycoconjugates.

Ann Ist Super Sanita, 2003, 39(1), 77 - 95
{Mucilage in the Adriatic Sea: role of possible causal agents and environmental factors}; Manganelli M et al.; The massive accumulation of gelatinous material at and below the seawater surface occurred in Northern Adriatic, at a frequency and with such an extension to cause serious environmental and economic damages . The present review describes the updated knowledge and considers the main hypotheses on mucilage formation . They focus, in turn, on organisms that produce mucilage, on the particular hydrodynamic of the North Adriatic basin, on the role of nutrients, but the trigger mechanism has not yet been really understood . Finally, the theoretical framework recently proposed by Azam et al . is presented . In the organic matter continuum view, organisms of the microbial loop just represent a part of the whole picture from which specific mechanisms of interactions are examined and few important pathways are outlined for future research.

Infect Immun, 2003 Jul, 71(7), 4127 - 36
Nuclear factor kappa B protects against host cell apoptosis during Rickettsia rickettsii infection by inhibiting activation of apical and effector caspases and maintaining mitochondrial integrity; Joshi SG et al.; Apoptotic host cell death is a critical determinant in the progression of microbial infections and outcome of resultant diseases . The potentially fatal human infection caused by Rickettsia rickettsii, the etiologic agent of Rocky Mountain spotted fever, involves the vascular endothelium of various organ systems of the host . Earlier studies have shown that survival of endothelial cells (EC) during this infection depends on their ability to activate the transcription factor nuclear factor kappa B (NF-kappa B) . Here, we investigated the involvement of caspase cascades and associated signaling pathways in regulation of host cell apoptosis by NF-kappa B . Infection of cultured human EC with R . rickettsii with simultaneous inhibition of NF-kappa B induced the activation of apical caspases 8 and 9 and also the executioner enzyme, caspase 3, whereas infection alone had no significant effect . Inhibition of either caspase-8 or caspase-9 with specific cell-permeating peptide inhibitors caused a significant decline in the extent of apoptosis, confirming their importance . The peak caspase-3 activity occurred at 12 h postinfection and led to cleavage of poly(ADP-ribose) polymerase, followed by DNA fragmentation and apoptosis . However, the activities of caspases 6 and 7, other important downstream executioners, remained unchanged . Caspase-9 activation was mediated through the mitochondrial pathway of apoptosis, as evidenced by loss of transmembrane potential and cytoplasmic release of cytochrome c . These findings suggest that activation of NF-kappa B is required for maintenance of mitochondrial integrity of host cells and protection against infection-induced apoptotic death by preventing activation of caspase-9- and caspase-8-mediated pathways . Targeted inhibition of NF-kappa B may therefore be exploited to enhance the clearance of infections with R . rickettsii and other intracellular pathogens with similar survival strategies.

Anesth Analg, 2003 Jul, 97(1), 72 - 9, table of contents
The pharmacokinetics and pharmacodynamics of propofol in a modified cyclodextrin formulation (Captisol) versus propofol in a lipid formulation (Diprivan): an electroencephalographic and hemodynamic study in a porcine model; Egan TD et al.; The currently marketed propofol formulation has a number of undesirable properties that are in part a function of the lipid emulsion formulation, including pain on injection, serious allergic reactions, and the support of microbial growth . A modified cyclodextrin-based formulation of propofol (sulfobutyl ether-beta-cyclodextrin) has been developed that may mitigate some of these formulation-dependent problems . However, reformulation may alter propofol's pharmacologic behavior . Our aim in this study was to compare the pharmacokinetics and pharmacodynamics of propofol in the currently marketed lipid-based formulation with those of the novel cyclodextrin formulation . We hypothesized that the pharmacokinetics and pharmacodynamics of the propofol in cyclodextrin would be substantially similar to those of the propofol in lipid . Thirty-two isoflurane-anesthetized animals were instrumented with pulmonary artery, arterial, and IV catheters and were randomly assigned to receive either propofol in lipid or propofol in cyclodextrin by continuous infusion . Arterial blood samples for propofol assay were collected . The processed electroencephalogram, heart rate, mean arterial blood pressure, and cardiac output were measured continuously . The propofol formulations were compared by using model-independent analysis techniques . Combined kinetic/dynamic models were also constructed for simulation purposes . There were no significant differences in the pharmacokinetics or pharmacodynamics of the two propofol formulations . The simulations based on the combined pharmacokinetic/pharmacodynamic models confirmed the substantial similarity of the two formulations . The hypothesis that the propofol-in-cyclodextrin formulation would exhibit pharmacokinetic and pharmacodynamic behavior that was substantially similar to the propofol-in-lipid formulation was confirmed . IMPLICATIONS: A modified cyclodextrin-based formulation of propofol has been developed that may mitigate some of the problems associated with propofol in lipid emulsion . However, reformulation of propofol may change its clinical characteristics . This study in a pig model showed that the novel propofol formulation was substantially similar to the lipid emulsion propofol formulation.

Arch Pediatr, 2003 Apr, 10(4), 307 - 12
{Cefepime-amikacin combination in febrile neutropenic children with malignant hemopathy or tumor}; Marie-Cardine A et al.; Our aim was to evaluate retrospectively the efficacy of a therapeutic strategy with a first line combination based on cefepime-amikacin in febrile neutropenic children treated with chemotherapy . PATIENTS AND METHODS: Sixty-five neutropenic febrile episodes in 43 children treated by the association cefepime-amikacin, were evaluated according to the clinical status, the depth and duration of neutropenia, the underlying disease and the initial treatment . RESULTS: Thirty-nine (60%) episodes were successfully treated by the association cefepime-amikacin . Among the 26 persisting febrile episodes, adjunction of vancomycin and amphotericin B was effective in 11 (76% of total rate success) and 5 (84% of total rate success) cases respectively . The efficacy of the first line antibiotherapy was not different as regards to the duration and the depth of neutropenia . Otherwise, febrile episodes after chemotherapy against solid tumours were rapidly controlled by the first and second line of the anti-microbial strategy . Children treated for haematological malignancies presented a lower response rate (P = 0.03) . CONCLUSION: In febrile and neutropenic children treated with chemotherapy, the association cefepime-amikacin appeared to be a safe empirical treatment . In a neutropenic child, the immunodeficiency and possibly the clinical status should be the major factors of the infectious prognosis more than the duration of aplasia.

Dev Comp Immunol, 2003 Oct, 27(9), 835 - 44
Purification and binding properties of porcine plasma ficolin that binds Actinobacillus pleuropneumoniae; Brooks AS et al.; Previous studies demonstrated that porcine plasma ficolin binds the important pig pathogen Actinobacillus pleuropneumoniae (APP) in an N-acetylglucosamine-dependent manner . In the present study, attempts to characterize the bacterial-binding properties of ficolin indicated ficolin is the major porcine plasma protein that binds directly to epoxy-activated chromatography matrices . We developed an efficient method for purifying ficolin using epoxy-activated Toyopearl and compared these with forms retrieved from other chromatography matrices and from intact APP . Purified ficolins retained their GlcNAc- and bacterial-binding properties, and migrated as two high molecular weight multimers composed of 38, 40 and 42 kDa reduced forms (pI 5.2-6.0) . An N-acetylated amine-activated Toyopearl matrix bound ficolin, and ficolin was dissociated from this matrix with acetamide . Acetate, acetamide, and GlcNAc, but not glucose or glucosamine, dissociated plasma ficolin from the surface of intact APP serotype 5b, which contains N-acetylated saccharides in the capsule . These studies indicate that porcine ficolin binds APP 5b and an N-acetylated matrix in a similar manner, supporting the view that N-acetyl groups may be important for binding of porcine plasma ficolin to some microbial surfaces.

J Hosp Infect, 2003 Jun, 54(2), 115 - 9
Microbial contamination of dialysate and its prevention in haemodialysis units; Oie S et al.; At the haemodialysis centres of nine hospitals in Japan, microbial contamination of treated water (reverse osmosis method), acid and bicarbonate concentrates, and dialysate was investigated . Among these fluids used in haemodialysis, the dialysate was most frequently contaminated and had the highest concentration of bacteria . Of 40 dialysate samples analysed, 42.5% showed a bacterial count of more than 2000cfu/mL, which was above the Association for the Advancement of Medical Instrumentation (AAMI) standard . However, among the 40 samples from 20 dialysis machines, all six dialysate samples from three dialysis machines that used an ultrafiltration membrane in the circuit before the entrance of the dialysate into the dialyser, showed a bacterial count of < or =10 cfu/mL . In addition, when an ultrafiltration membrane was used in the circuit before the entrance of the dialysate into the dialyser for four dialysis machines showing dialysate samples contaminated with 10(4)-10(5)cfu/mL the bacterial count in dialysate samples from these machines became zero . Because dialysis machines are susceptible to microbial contamination, it is necessary to take measures such as placing an ultrafiltration membrane into the circuit before the entrance of dialysate into the dialyser.

J Immunol, 2003 Jul 1, 171(1), 417 - 25
Direct binding of Toll-like receptor 2 to zymosan, and zymosan-induced NF-kappa B activation and TNF-alpha secretion are down-regulated by lung collectin surfactant protein A; Sato M et al.; The lung collectin surfactant protein A (SP-A) has been implicated in the regulation of pulmonary host defense and inflammation . Zymosan induces proinflammatory cytokines in immune cells . Toll-like receptor (TLR)2 has been shown to be involved in zymosan-induced signaling . We first investigated the interaction of TLR2 with zymosan . Zymosan cosedimented the soluble form of rTLR2 possessing the putative extracellular domain (sTLR2) . sTLR2 directly bound to zymosan with an apparent binding constant of 48 nM . We next examined whether SP-A modulated zymosan-induced cellular responses . SP-A significantly attenuated zymosan-induced TNF-alpha secretion in RAW264.7 cells and alveolar macrophages in a concentration-dependent manner . Although zymosan failed to cosediment SP-A, SP-A significantly reduced zymosan-elicited NF-kappaB activation in TLR2-transfected human embryonic kidney 293 cells . Because we have shown that SP-A binds to sTLR2, we also examined whether SP-A affected the binding of sTLR2 to zymosan . SP-A significantly attenuated the direct binding of sTLR2 to zymosan in a concentration-dependent fashion . From these results, we conclude that 1) TLR2 directly binds zymosan, 2) SP-A can alter zymosan-TLR2 interaction, and 3) SP-A down-regulates TLR2-mediated signaling and TNF-alpha secretion stimulated by zymosan . This study supports an important role of SP-A in controlling pulmonary inflammation caused by microbial pathogens.

Curr Biol, 2003 Jun 17, 13(12), R466 - 7
The ecology, genetics and evolution of bacteria in an experimental setting; Lenski R; Richard Lenski is the John Hannah Distinguished Professor of Microbial Ecology at Michigan State University . He studies the ecology, genetics and evolution of bacteria in an experimental setting that enables him to observe the dynamical processes and outcomes across many generations . One of his experiments with Escherichia coli has passed 30,000 generations and is still on-going . A few years ago, he also began studying artificial life in the form of 'digital organisms' - computer programs that replicate, mutate, compete, and therefore evolve and adapt.

Drug News Perspect, 2001 Sep, 14(7), 440 - 7
Odyssey toward a healthier world; Hunter PA; The 22nd International Congress of Chemotherapy was held in Amsterdam, the Netherlands, July 14, 2001 . The congress attracted participants from around the world and covered a broad spectrum of work on microbial infections and cancer, their treatment by antiinfective drugs and their prevention by vaccination . A theme of the congress was "Compassion and Science," and this was picked up in a fascinating albeit slightly controversial symposium on "Health, Human Rights and Infection." There were several well-attended plenary lectures on topical subjects, including prions and variant Creutzfeldt-Jakob disease and on a possible link between autism and infection . (c) 2001 Prous Science . All rights reserved.

Am J Physiol Endocrinol Metab, 2003 Nov, 285(5), E1095 - 102 Epub 2003 Jun 17.
Zinc modulates mRNA levels of cytokines; Bao B et al.; Zinc plays an important role in cell-mediated immune function . Altered cellular immune response resulting from zinc deficiency leads to frequent microbial infections, thymic atrophy, decreased natural killer activity, decreased thymic hormone activity, and altered cytokine production . In this study, we examined the effect of zinc deficiency on IL-2 and IFN-gamma in HUT-78 (Th0) and D1.1 (Th1) cell lines and TNF-alpha, IL-1 beta, and IL-8 in the HL-60 (monocyte-macrophage) cell line . The results demonstrate that zinc deficiency decreased the levels of IL-2 and IFN-gamma cytokines and mRNAs in HUT-78 after 6 h of PMA/p-phytohemagglutinin (PHA) stimulation and in D1.1 cells after 6 h of PHA/ionomycin stimulation compared with the zinc-sufficient cells . However, zinc deficiency increased the levels of TNF-alpha, IL-1 beta, and IL-8 cytokines and mRNAs in HL-60 cells after 6 h of PMA stimulation compared with zinc-sufficient cells . Actinomycin D study suggests that the changes in the levels of these cytokine mRNAs were not the result of the stability affected by zinc but might be the result of altered expression of these cytokine genes . These data demonstrate that zinc mediates positively the gene expression of IL-2 and IFN-gamma in the Th1 cell line and negatively TNF-alpha, IL-1 beta, and IL-8 in the monocyte-macrophage cell line . Our study shows that the effect of zinc on gene expression and production of cytokines is cell lineage specific.

Am J Trop Med Hyg, 2003 May, 68(5), 557 - 61
In vitro reactivation of human immunodeficiency virus-1 upon stimulation with scrub typhus rickettsial infection; Moriuchi M et al.; While a number of microbial infections induce a transient burst in viral load in individuals infected with human immunodeficiency virus-1 (HIV-1), a recent study has suggested that scrub typhus may suppress HIV-1 infection . We investigated the effects of Orientia tsutsugamushi on HIV-1 infection . In vitro HIV-1 infection experiments were conducted using peripheral blood mononuclear cells (PBMC) acutely infected with R5 and X4 HIV-1 or PBMC derived from patients receiving highly active antiretroviral therapy (HAART) whose plasma viral load was undetectable . Stimulation of PBMC with O . tsutsugamushi induced production of proinflammatory cytokines and beta-chemokines, and markedly down-regulated expression of CCR5 . Although pretreatment with O . tsutsugamushi rendered PBMC resistant to R5 HIV-1, it otherwise enhanced HIV-1 replication . Stimulation by O . tsutsugamushi induced HIV-1 replication in PBMC from patients receiving HAART . These findings suggest that scrub typhus does not necessarily suppress HIV-1 infection and does have potential to enhance HIV-1 replication.

Dan Med Bull, 2003 May, 50(2), 161 - 76
Clinical and experimental studies on inflammatory mediators during AIDS-associated Pneumocystis carinii pneumonia; Benfield TL; This thesis is based on studies carried out during my appointment as a research fellow at the Department of Infectious Diseases, Hvidovre Hospital, University of Copenhagen, Denmark from 1993 to 1997 . Part of this period was spent as a guest researcher at the Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, USA . Pneumocystis carinii pneumonia (PCP) is the most frequent AIDS defining illness over the past 20 years . PCP is associated with considerable morbidity and mortality . An inflammatory reaction to P . carinii is believed to cause respiratory failure . This thesis has attempted to delineate important mechanisms of the inflammatory cascade, and to determine how inflammation is initiated during PCP . In histopathological studies of lung specimens it was shown that PCP caused significant inflammation and destruction of tissue . Specific pathological changes of the alveolar epithelium was observed in PCP but not for other HIV related lung diseases . By determining concentrations of soluble markers of immune activation we found that anti-microbial therapy exacerbated an ongoing inflammatory reaction . Adjuvant glucocorticosteroids suppressed levels of soluble immune markers . Bronchoalveolar lavage (BAL) neutrophilia has been associated with disease severity, and an increased risk of death from PCP . Through competitive inhibitory studies, we showed that BAL fluid neutrophil chemotactic activity largely was explained by the presence of interleukin-8 (IL-8) . Further, we showed a correlation between high levels of BAL fluid IL-8 and mortality . Adjuvant treatment with glucocorticosteroids lowered BAL fluid IL-8 levels . In experimental studies we found that P . carinii Major Surface Antigen (MSG) induced IL-8 and tumor necrosis factor-alpha secretion from human monocytes and an alveolar epithelial cell line (A549) . Binding of MSG to monocytes appeared to be mediated by mannose receptors, while A549 cells recognized MSG through mannose and glucan receptors . Glucocorticosteroids attenuated IL-8 secretion from A549 cells . These studies have confirmed that P . carinii infection induces tissue damage through a significant inflammatory response initiated by secretion of inflammatory mediators . Glucocorticosteroids attenuates the inflammatory response.

Eur J Immunol, 2003 Jul, 33(7), 1776 - 87
Triggering of Toll-like receptors modulates IFN-gamma signaling: involvement of serine 727 STAT1 phosphorylation and suppressors of cytokine signaling; Dalpke AH et al.; Microbial stimuli activate cells of the innate immune system by triggering Toll-like receptors (TLR) . Activation of macrophages and dendritic cells is further enhanced by secondary signals like IFN-gamma . Here we analyzed the interplay of IFN-gamma and TLR signaling in cells of the innate immune system . Using a STAT1-dependent reporter construct we show that IFN-gamma signaling can be enhanced as well as inhibited by simultaneous stimulation with either defined TLR agonists or whole-bacterial lysates . Short costimulation resulted in the amplification of IFN-gamma signaling and was attributable to the p38 mitogen-activated protein kinase (MAPK)-dependent phosphorylation of signal transducer and activator of transcription (STAT)1 on serine 727 . In contrast, prolonged co-incubation as well as pre-incubation with TLR agonists led to an inhibition of IFN-gamma signaling . TLR triggering induced expression of suppressor of cytokine signaling (SOCS)-1, SOCS-3 and cytokine-inducible SH2 domain-containing protein (CIS) . Overexpression of SOCS-1 and, to a lesser extend, of SOCS-3 and CIS inhibited IFN-gamma signaling as measured by activation of STAT1 . Moreover, pre-incubation with TLR-dependent stimuli impaired IFN-gamma-induced MHC class II regulation but enhanced CD40 and CD86 expression . Taken together, the results indicate a tight interplay between TLR and IFN-gamma signaling pathways which involve induction of SOCS proteins and serine phosphorylation of STAT1.

Int Microbiol, 2003 Jun, 6(2), 101 - 3 Epub 2003 Jun 13.
History and services of culture collections; Uruburu F; Microbial culture collections aim at collecting, maintaining and distributing microbial strains among microbiologists, and are considered to be a means to preserve microbial diversity ex situ . This article reviews the early history of culture collections, which were first set up in the late nineteenth century, with the introduction of pure culture techniques . It also describes the international connections between culture collections, which led to the foundation of the World Federation for Culture Collections (WFCC) and the International Congress of Culture Collections (ICCC) . An overview of the Spanish Type Culture Collection (CECT) is included, as well as a description of the services that culture collections can offer.

Int J Food Microbiol, 2003 Aug 15, 85(1-2), 185 - 96
Combinations of pulsed white light and UV-C or mild heat treatment to inactivate conidia of Botrytis cinerea and Monilia fructigena; Marquenie D et al.; The use of pulses of intense white light to inactivate conidia of the fungi Botrytis cinerea and Monilia fructigena, responsible for important economical losses during postharvest storage and transport of strawberries and sweet cherries, was investigated in this study . In the first stage, a light treatment applying pulses of 30 micros at a frequency of 15 Hz was investigated, resulting in a treatment duration varying from 1 to 250 s . The conidia of both fungi showed similar behaviour to pulsed light, with a maximal inactivation of 3 and 4 log units for B . cinerea and M . fructigena, respectively . The inactivation of the conidia increased with increasing treatment intensity, but no complete inactivation was achieved . The sigmoidal inactivation pattern obtained by the pulsed light treatment was described using a modification of the model of Geeraerd et al . {Int . J . Food Microbiol . 59 (2000) 185} . Hereto, the shoulder length was incorporated explicitly and relative values for the microbial populations were used.In the second stage, combinations of light pulses and ultraviolet-C or heat were applied . The UV light used in the experiments is the short-wave band or UV-C, running from 180 to 280 nm with a peak at 254 nm (UV-B runs from 280 to 320 nm and UV-A from 320 to 380 nm) . The UV-C doses were 0.025, 0.05 and 0.10 J/cm(2), and the temperatures for the thermal treatment ranged from 35 to 45 degrees C during 3-15 min . When combining UV-C and light pulses, there was an increase in inactivation for both B . cinerea and M . fructigena, and synergism was observed . There was no effect of the order of the treatments . For the heat-light pulses combination, there was a difference between both fungi . The order of the treatments was highly significant for B . cinerea, but not for M . fructigena . Combining heat and light treatments improved the inactivation, and synergism between both methods was again observed . Complete inactivation of M . fructigena conidia was obtained after, e.g., a 40-s pulsed light treatment and 15 min at 41 degrees C, or after an 80-s light treatment and 10 min at 41 degrees C.

J Environ Qual, 2003 May-Jun, 32(3), 937 - 48
Uptake and release of phosphorus from overland flow in a stream environment; McDowell RW et al.; Phosphorus runoff from agricultural fields has been linked to fresh-water eutrophication . However, edge-of-field P losses can be modified by benthic sediments during stream flow by physiochemical processes associated with Al, Fe, and Ca, and by biological assimilation . We investigated fluvial P when exposed to stream-bed sediments (top 3 cm) collected from seven sites representing forested and agricultural areas (pasture and cultivated), in a mixed-land-use watershed . Sediment was placed in a 10-m-long, 0.2-m-wide fluvarium to a 3-cm depth and water was recirculated over the sediment at 2 L s(-1) and 5% slope . When overland flow (4 mg dissolved reactive phosphorus {DRP} and 9 mg total phosphorus {TP} L(-1)) from manured soils was first recirculated, P uptake was associated with Al and Fe hydrous oxides for sediments from forested areas (pH 5.2-5.4) and by Ca for sediments from agricultural areas (pH 6.5-7.2) . A large increase (up to 200%) in readily available P NH4Cl fraction was noted . After 24 h, DRP concentration in channel flow was related to sediment solution P concentration at which no net sorption or desorption of P occurs (EPC0) (r2 = 0.77), indicating quasi-equilibrium . When fresh water (approximately 0.005 mg P L(-1) mean base flow DRP at seven sites) was recirculated over the sediments for 24 h, P release kinetics followed an exponential function . Microbial biomass P accounted for 34 to 43% of sediment P uptake from manure-rich overland flow . Although abiotic sediment processes played a dominant role in determining P uptake, biotic process are clearly important and both should be considered along with the location and management of landscape inputs for remedial strategies to be effective.

J Med Microbiol, 2003 Jul, 52(Pt 7), 541 - 5
Microbial dinner-party conversations: the role of LuxS in interspecies communication; McNab R et al.; Bacteria have a tendency to be gregarious by nature . Whether on abiotic surfaces in the environment or on the mucosal surfaces of humans, bacteria accumulate in complex multi-species communities . In these dynamic accretions, bacteria can be densely packed and often depend on each other for the provision of metabolic substrates . Under these circumstances, it will be advantageous for bacteria to be able to detect the presence of their neighbours, to communicate with them and to co-ordinate various physiological activities . Such cell-cell sensing and communication systems can be established through the release and detection of chemical signalling molecules . While originally considered a feature characteristic of eukaryotes, the exchange of chemical signals has now been demonstrated in many bacterial species and ecosystems . Indeed, it has even been suggested that assemblages of bacterial species can be considered as proto-multicellular organisms, whereby biological processes are controlled for the benefit of the entire community . Regardless of the extent to which bacterial communication represents a step on the road to multicellularity, it is becoming increasingly apparent that the signalling systems devised by bacteria are essential for successful relationships with other bacteria and with eukaryotic hosts.

Immunology, 2003 Jul, 109(3), 426 - 31
Effects of functional Toll-like receptor-4 mutations on the immune response to human and experimental sepsis; Feterowski C et al.; Genetically determined responsiveness to microbial stimuli such as lipopolysaccharide (LPS) may affect the pathophysiology of human sepsis . The D299G mutation in human Toll-like receptor-4 (TLR4) impairs LPS signalling in homozygous and heterozygous individuals . To investigate whether the presence of the TLR4(D299G) mutation may correlate with the development or outcome of sepsis following major visceral surgery the presence of TLR4(D299G) mutation was analysed in 307 Caucasian patients (154 without and 153 with sepsis) . Sepsis was caused in 84% of patients by polymicrobial infection . The presence of the mutant TLR4 did not significantly correlate with development or outcome of sepsis . Serum levels of tumour necrosis factor, interleukin (IL)-10, and IL-6 at sepsis onset did not significantly differ between patients carrying wild-type and mutant TLR4 . Moreover, studies in a murine model of polymicrobial septic peritonitis demonstrated that TLR4-deficiency did neither influence the systemic cytokine response nor the development of organ injury . The results suggest that the signalling capacity of TLR4 as affected by loss-of-function mutations does not influence human or experimental sepsis caused by polymicrobial infection . Thus, in polymicrobial infection, other innate immune receptors may compensate for TLR4 defects.

Immunology, 2003 Jul, 109(3), 360 - 4
Immature dendritic cells possess a sugar-sensitive receptor for human mannan-binding lectin; Downing I et al.; Mannan-binding lectin (MBL) is a collectin synthesized by the liver and secreted into the bloodstream . It has a receptor for microbial structures in its C-type lectin domain and a separate receptor(s) located within its collagen-like region for autologous phagocytic cells . Here we demonstrate that human peripheral blood adherent cells (monocytes) and monocyte-derived dendritic cells are a source of MBL, and that a novel calcium-dependent and sugar-specific MBL receptor is up-regulated in immature (CD1a-positive) dendritic cells . These findings suggest a previously unsuspected autologous function for MBL, perhaps a regulatory role within the immune system.

Gastroenterology, 2003 Jun, 124(7), 1879 - 90
Host and microbial constituents influence Helicobacter pylori-induced cancer in a murine model of hypergastrinemia; Fox JG et al.; BACKGROUND & AIMS: Helicobacter pylori cag(+) strains and high-expression host interleukin 1beta (IL-1beta) polymorphisms augment the risk for intestinal-type gastric adenocarcinoma, a malignancy that predominates in males . We examined the effects of an H . pylori cancer-associated determinant (cagE), IL-1beta, and host gender in a transgenic hypergastrinemic (INS-GAS) murine model of gastric carcinogenesis . METHODS: Male and female INS-GAS mice infected with wild-type H . pylori, an H . pylori cagE(-) mutant, or H . felis were killed 2-24 weeks postchallenge . Gastric injury was scored from 0 to 4, and mucosal IL-1beta levels were quantified by ELISA . RESULTS: Male INS-GAS mice infected with H . pylori uniformly developed atrophy, intestinal metaplasia, and dysplasia by 6 weeks and carcinoma by 24 weeks . Mucosal IL-1beta concentrations increased 12 weeks following Helicobacter challenge, but levels then decreased by 24 weeks . Inactivation of cagE delayed the progression to carcinoma, but neoplasia ultimately developed in all males infected with the H . pylori mutant . In contrast, none of the H . pylori-infected female mice developed cancer, and injury scores, but not IL-1beta levels, were significantly higher in males compared with females . CONCLUSIONS: H . pylori infection induces gastric adenocarcinoma in an experimental mouse model of disease . Cancer is restricted to males and loss of cagE temporally retards but does not abrogate pathologic progression . Mucosal levels of IL-1beta increase prior to the development of gastric cancer but are not related to gender . The INS-GAS model is effective for investigating discrete host-microbial interactions that culminate in gastric cancer within the context of biologic conditions induced by H . pylori.

ScientificWorldJournal, 2002 Feb 08, 2, 357 - 73
Chiral pesticides in soil and water and exchange with the atmosphere; Bidleman TF et al.; The enantiomers of chiral pesticides are often metabolised at different rates in soil and water, leading to nonracemic residues . This paper reviews enantioselective metabolism of organochlorine pesticides (OCPs) in soil and water, and the use of enantiomers to follow transport and fate processes . Residues of chiral OCPs and their metabolites are frequently nonracemic in soil, although exceptions occur in which the OCPs are racemic . In soils where enantioselective degradation and/or metabolite formation has taken place, some OCPs usually show the same degradation preference--e.g., depletion of (+)trans-chlordane (TC) and (-)cis-chlordane (CC), and enrichment of the metabolite (+)heptachlor exo-epoxide (HEPX) . The selectivity is ambivalent for other chemicals; preferential loss of either (+) or (-)o,p-DDT and enrichment of either (+) or (-)oxychlordane (OXY) occurs in different soils . Nonracemic OCPs are found in air samples collected above soil which contains nonracemic residues . The enantiomer profiles of chlordanes in ambient air suggests that most chlordane in northern Alabama air comes from racemic sources (e.g., termiticide emissions), whereas a mixture of racemic and nonracemic (volatilisation from soil) sources supplies chlordane to air in the Great Lakes region . Chlordanes and HEPX are also nonracemic in arctic air, probably the result of soil emissions from lower latitudes . The (+) enantiomer of alpha-hexachlorocyclohexane (alpha-HCH) is preferentially metabolised in the Arctic Ocean, arctic lakes and watersheds, the North American Great Lakes, and the Baltic Sea . In some marine regions (the Bering and Chukchi Seas, parts of the North Sea) the preference is reversed and (-)alpha-HCH is depleted . Volatilisation from seas and large lakes can be traced by the appearance of nonracemic alpha-HCH in the air boundary layer above the water . Estimates of microbial degradation rates for alpha-HCH in the eastern Arctic Ocean and an arctic lake have been made from the enantiomer fractions (EFs) and mass balance in the water column . Apparent pseudo first-order rate constants in the eastern Arctic Ocean are 0.12 year(-1) for (+)alpha-HCH, 0.030 year(-1) for (-)alpha-HCH, and 0.037 year(-1) for achiral gamma-HCH . These rate constants are 3-10 times greater than those for basic hydrolysis in seawater . Microbial breakdown may compete with advective outflow for long-term removal of HCHs from the Arctic Ocean . Rate constants estimated for the arctic lake are about 3-8 times greater than those in the ocean.

ScientificWorldJournal, 2002 Apr 30, 2, 1173 - 85
Effects of Eucalyptus plantations on detritus, decomposers, and detritivores in streams; Graca MA et al.; Vast areas of the Iberian Peninsula are covered by monocultures of the exotic tree Eucalyptus globulus . Given that (1) leaf litter produced in the riparian areas is the main energy source for small streams, and (2) trees differ in their nutrient content, chemical defenses, and physical attributes, eucalypt plantations have the potential to affect the biology of streams . Research teams from the University of Coimbra and the University of the Basque Country have been addressing the potential effects of eucalypt plantations at several levels of study . Here we review the main conclusions of these investigations . Eucalypt plantations produced less litter than some deciduous forests . However, there were marked differences in timing of litterfall: litter production peaked during autumn in deciduous forests, whereas in the eucalypt forests it tended to peak in summer and to be more evenly distributed throughout the year . Despite these differences, the average standing stock of organic matter was higher in the eucalypt than in the deciduous forest . This may be attributed to (1) the occurrence of spates or heavy rain in autumn, the period of maximum litter fall in deciduous forests, and (2) bark accumulation in eucalypt forests . Because of differences in leaf composition, the nutrient input in eucalypt forests seems to be lower than in deciduous forests . The rate of decomposition of eucalypt leaves was strongly dependent on nutrients in the water: in nutrient-poor waters it was slower than that of most other leaf species, whereas in nutrient-rich waters it can be as fast as alder--a fast-decaying species . The biomass and cumulative diversity of aquatic hyphomycetes colonizing leaves did not differ between eucalypt and other native leaf species, but fungal sporulation generally peaked 2 weeks later on eucalypt leaves . This lag disappeared when lipids (but not polyphenolics) were chemically removed from eucalypt leaves . Similarly, addition of eucalypt oils to culture media retarded or suppressed fungal growth . Streams bordered by Eucalyptus had lower diversity of fungal spores (but similar spore densities) in Portugal; less consistent patterns were found in similar experiments in Spain . Eucalyptus leaves proved to be poor food for shredders . Under laboratory conditions leaves of Eucalyptus ranked low in food selection experiments using native shredders . The same shredders failed to grow and died when fed exclusively eucalypt leaves . The removal of oils from eucalypt leaves resulted in increased feeding rates, whereas the transfer of oils to alder leaves resulted in decreased feeding rates . The effect of eucalypt plantations on stream invertebrate communities is not very consistent . In nutrient-poor waters, fewer invertebrates colonized eucalypt than alder leaves, but this effect was mitigated after a microbial conditioning period in nutrient-rich waters . Portuguese streams bordered by Eucalyptus had lower numbers of invertebrates than streams surrounded by deciduous forests . In Spanish streams differences were less marked and nonexistent when looking at the composition of the communities, which change more from year to year than from site to site . Most of the eucalypt streams studied in Portugal and Spain dried up in summer, a fact that might reflect an increase in soil hydrophobity produced by Eucalyptus plantations . The very short planting-to-harvest period of eucalypt plantations results in additional impacts, such as soil loss, siltation of streams, or reduced amounts of woody debris in stream channels, which affects their capacity to retain leaf-litter, as well as the availability of habitat for invertebrates and fish . The studies by the Portuguese and Spanish research teams confirm the importance of maintaining riparian buffer strips to reduce human impact on streams and rivers.

ScientificWorldJournal, 2002 Apr 09, 2, 966 - 71
Metal concentrations in soil paste extracts as affected by extraction ratio; Tack FM et al.; Saturated paste extracts are sometimes used to estimate metal levels in the soil solution . To assess the significance of heavy-metal concentrations measured in saturation extracts, soil paste extracts were prepared with distilled water in amounts ranging from 60-200% of the moisture content at saturation . Trace metals behaved as if a small pool consistently was dissolved independent of the extraction ratio applied . Metal concentrations in the solution hence were not buffered by the solid phase, but the observed behaviour would allow the estimation of metal concentrations in the soil solution as a function of moisture content . The behaviour of iron and manganese suggested that some microbial reduction occurred . The intensity increased with increasing extraction ratio but not to the extent of affecting dissolution of trace elements.

ScientificWorldJournal, 2001 Nov 01, 1 Suppl 2, 122 - 9
Factors affecting microbial formation of nitrate-nitrogen in soil and their effects on fertilizer nitrogen use efficiency; Olness A et al.; Mineralization of soil organic matter is governed by predictable factors with nitrate-N as the end product . Crop production interrupts the natural balance, accelerates mineralization of N, and elevates levels of nitrate-N in soil . Six factors determine nitrate-N levels in soils: soil clay content, bulk density, organic matter content, pH, temperature, and rainfall . Maximal rates of N mineralization require an optimal level of air-filled pore space . Optimal air-filled pore space depends on soil clay content, soil organic matter content, soil bulk density, and rainfall . Pore space is partitioned into water- and air-filled space . A maximal rate of nitrate formation occurs at a pH of 6.7 and rather modest mineralization rates occur at pH 5.0 and 8.0 . Predictions of the soil nitrate-N concentrations with a relative precision of 1 to 4 microg N g(-1) of soil were obtained with a computerized N fertilizer decision aid . Grain yields obtained using the N fertilizer decision aid were not measurably different from those using adjacent farmer practices, but N fertilizer use was reduced by >10% . Predicting mineralization in this manner allows optimal N applications to be determined for site-specific soil and weather conditions.

ScientificWorldJournal, 2001 Nov 17, 1, 656 - 80
From litterfall to breakdown in streams: a review; Abelho M; This paper is a review of recent (< or =10 years) information on litterfall, standing stock of benthic organic matter, breakdown rates, and fungal colonization of organic matter in streams . In some cases, recent research reinforces the findings of classic reference papers . In other cases, the additional knowledge provided by recent research introduces a higher variation in the processes analyzed . In many aspects, especially those concerning stream organic matter, the review is biased towards the temperate North American streams, reflecting the fact that most research was carried out there . However, during the 1990s European studies increased enormously, especially those related with instream processes, such as leaf litter decomposition . The first part of this review analyzes the origin of allochthonous organic matter to streams (litterfall, retention, and storage), and it provides data on the amounts estimated in different streams and on the methodology used in the studies . The second part analyzes the fate of detritus in streams: mechanisms of leaf breakdown, relative importance of fungi and bacteria, factors affecting the activity of microbial decomposers, and chemical changes of leaf litter during decomposition . A list of breakdown rates of several different leaf species is given, together with the methodology used, and the main characteristics of the incubation streams.

ScientificWorldJournal, 2001 Nov 06, 1, 627 - 9
Global biomonitoring of perfluorinated organics; Giesy JP et al.; The environmental distribution of fluorinated organic compounds (FOCs) has been less well described than the other halogenated hydrocarbons such as chlorinated and brominated compounds . This is despite the fact that FOCs have been used in a wide variety of products and applications for more than 50 years . FOCs are resistant to hydrolysis, photolysis, microbial degradation, or metabolism by vertebrates due to the high energy of carbon-fluorine bond . In particular, perfluorinated (fully fluorinated) compounds (PFCs) have the potential to persist in the environment . But, until recently, the extent and magnitude of environmental distribution of PFCs was unknown . Recent development of an analytical technique for PFCs using high performance liquid chromatography-negative ion electrospray tandem mass spectrometry (HPLC-ESMSMS) permitted the survey of PFCs in livers and blood plasma of wildlife on a global scale.

ScientificWorldJournal, 2001 Dec 05, 1 Suppl 2, 714 - 21
Habitat management: a tool to modify ecosystem impacts of nitrogen deposition?
Power SA, Barker CG, Allchin EA, Ashmore MR, Bell JN.
Atmospheric nitrogen deposition has been shown to affect both the structure and the function of heathland ecosystems . Heathlands are semi-natural habitats and, as such, undergo regular management by mowing or burning . Different forms of management remove more or less nutrients from the system, so habitat management has the potential to mitigate some of the effects of atmospheric deposition . Data from a dynamic vegetation model and two field experiments are presented . The first involves nitrogen addition following different forms of habitat management . The second tests the use of habitat management to promote heathland recovery after a reduction in nitrogen deposition . Both modelling and experimental approaches suggest that plant and microbial response to nitrogen is affected by management . Shoot growth and rates of decomposition were lowest in plots managed using more intensive techniques, including mowing with litter removal and a high temperature burn . Field data also indicate that ecosystem recovery from prolonged elevated inputs of nitrogen may take many years, or even decades, even after the removal of plant and litter nitrogen stores which accompanies the more intensive forms of habitat management.

ScientificWorldJournal, 2001 Dec 12, 1 Suppl 2, 500 - 4
The impact of long-term nitrogen addition on microbial community composition in three Hawaiian forest soils; Balser TC; We evaluated the microbial communities in three Hawaiian forest soils along a natural fertility gradient and compared their distinct responses to long-term nitrogen (N) additions . The sites studied have the same elevation, climate, and dominant vegetation, but vary in age of development, and thus in soil nutrient availability and nutrient limitation to plant growth . Fertilized plots at each site have received 100 kg ha year(-1) N addition for at least 8 years . Soil parameters, water content, pH, and ammonium and nitrate availability differed by site, but not between control and N-addition treatments within a site at the time of sampling . Microbial biomass also varied by site, but was not affected by N addition . In contrast, microbial community composition (measured by phospholipid analysis) varied among sites and between control and N-addition plots within a site . These data suggest that microbial community composition responds to N addition even when plant net primary productivity is limited by nutrients other than N . This may have implications for the behavior of forests impacted by atmospheric N deposition that are considered to be "nitrogen saturated," yet still retain N in the soil.

ScientificWorldJournal, 2001 Dec 13, 1 Suppl 2, 207 - 15
Increasing N retention in Coastal Plain agricultural watersheds; Staver KW; Historically, N availability has limited agricultural production as well as primary production in coastal waters . Prior to the middle of the last century, N available for grain production generally was limited to that supplied by previous legume crops, released from soil organic matter, or returned to the soil in animal wastes . The development of infrastructure to produce relatively low-cost inorganic N fertilizers eliminated the need to focus management of the entire agricultural system on increasing soil N availability . Increased N availability has contributed to dramatic increases in agricultural production but also has led to increased losses of both N and C from agricultural systems . N losses from cropland have been linked to increased algal production in the Chesapeake Bay, with N loss from cropland estimated to be the primary N input to the Bay from Coastal Plain regions of the watershed . The decade-long effort to reduce these losses has focused on reducing agricultural N use, but this strategy has yet to yield apparent reductions in N loadings to Coastal Plain tributaries . Although nitrate leaching losses are often attributed to inefficient use of N inputs, soil nitrate data indicate that both corn and soybeans can utilize nearly all available soil nitrate during periods of active growth . However, both crops tend to stop utilizing nitrate before mineralization has ceased, resulting in a late season buildup of root zone nitrate levels and significant leaching losses even when no N was applied . Reducing nitrate losses due to the inherent N inefficiency of summer annual grain crops will require the addition of winter annual crops to rotations or changes in weed management approaches that result in plant N uptake capacity being more closely matched to soil microbial N processes.

Surg Endosc, 2003 Nov, 17(11), 1716 - 8 Epub 2003 Jun 17.
A prospective randomized study of prophylactic antibiotics in elective laparoscopic cholecystectomy; Koc M et al.; BACKGROUND: Elective laparoscopic cholecystectomy (LC) has a low risk for infective complications, but many surgeons still use prophylactic antibiotics . The use of prophylactic antibiotics for LC is inconsistent and varies widely among surgeons . METHODS: We performed a prospective double-blind randomized study of prophylactic antibiotics in elective LC . Antibiotics were was given first before the operation and then again 24 h afterward . Group A ( n = 49) received 2 g of cefotaxime; group B ( n = 43) received 10 ml of isotonic sodium chloride solution . A sample of bile was withdrawn by direct gallbladder puncture for anaerobic and aerobic cultures . Age, sex, weight, duration of surgery (DOS), presence of diabetes mellitus, American Society of Anesthesiologists (ASA) classification, gallbladder rupture, bile and/or stone spillage, gallbladder histological findings, findings from bile cultures positive for bacteria, episodes of colic within 30 days before surgery, length of stay (LOS), and number of septic complications were recorded for both groups . RESULTS: There was no differences between the two groups in terms of sex, weight, DOS, ASA score, gallbladder rupture, bile and/or stone spillage, gallbladder histological findings, findings from bile cultures positive for bacteria, or LOS . One infection occurred in the antibiotic prophylaxis group (2.04%); in the patients not receiving antibiotics, there was one other infection (2.32%) . There was no statistical difference between the two groups in infective complications . CONCLUSION: In patients undergoing elective LC, antibiotic prophylaxis is justified only in high-risk patients . In all other patients, antibiotic prophylaxis does not seem to affect the incidence of postoperative infective complications . In low-risk patients, eliminating the unnecessary use of prophylactic antibiotics would result in a cost reduction; moreover, it would lower the risk of adverse reaction and reduce microbial resistance.

Pathol Biol (Paris), 2003 Mar, 51(2), 67 - 8
Regulation of dendritic cell function by microbial stimuli; Reis e Sousa C et al.; Dendritic cells (DC) initiate T cell responses and produce cytokines and other molecules that can regulate the class adaptive immunity . It is increasingly clear that DC in vivo are in a "resting" state and require exogenous signals to transit into an "effector" state in which they can prime T cells . Much of this DC activation process appears to be regulated by infection . Exposure of murine DC to certain pathogens or their products triggers DC migration to T cell areas of secondary lymphoid tissues, improves MHC presentation and increases DC co-stimulatory potential . Pathogen recognition can also initiate cytokine production and/or condition DC to produce cytokines in response to subsequent T cell feedback signals delivered via CD40 and similar receptors . Recognition of pathogens by DC is largely dependent on Toll-like receptors (TLRs) . Interestingly, mouse splenic CD8alpha+ and CDalpha-CD4- DC have the ability to produce either IL-12 p70 or IL-10 depending on the nature of the pathogen encountered . In contrast, CD4+ DC seem incapable of producing IL-12 p70 . Thus, the nature of the pathogen can dictate the type of cytokine that is made by some DC subsets, allowing them to prime distinct types of immune responses . Overall, DC display significant plasticity in their ability to respond to infection and direct adaptive immunity.

Pathol Biol (Paris), 2003 Mar, 51(2), 59 - 60
The control of immunity and tolerance by dendritic cell; Steinman RM; Dendritic cells (DCs) are best known for their roles in host resistance and immunogenicity . DCs provide a direct link between innate and adaptive immunity . After antigen capture and processing, DCs control the differentiation and polarization of T cells . However, there is a danger during the antigen presentation because, at the same time DCs are capturing microbial antigens and also dying self cells and environmental proteins, to which the immune system must not respond . There is good evidence that immature DCs, in the absence of infection and inflammation, induce immunological tolerance to innocuous self antigens, avoiding then a non-appropriate response to harmless antigens that may be presented subsequently when infection strikes.

Clin Exp Allergy, 2003 Jun, 33(6), 827 - 33
Identification of Cucumisin (Cuc m 1), a subtilisin-like endopeptidase, as the major allergen of melon fruit; Cuesta-Herranz J et al.; BACKGROUND: Allergenic components in melon extracts have not been described in spite of the fact that melon (Cucumis melo) is a frequent allergy-eliciting fruit . The aim of this study was to evaluate allergenic components in melon extract and to report the identification of cucumisin as a major melon allergen . MATERIALS AND METHODS: Sera from 35 patients allergic to melon were selected on the basis of clinical symptoms, skin prick tests and oral challenge test . Allergenic components were detected by sodium dodecyl sulphate polyacrylamide gel electrophoresis and immunoblotting . Molecular characterization of IgE-binding bands was performed by N-terminal amino acid sequencing . RESULTS: More than 10 IgE-binding bands, between 10 and 80 kDa, were identified in melon extract . Out of them, four IgE-binding bands were major allergens: 14 kDa, 36 kDa, 54 kDa and 67 kDa . These major allergens, except 14 kDa band, showed the same N-terminal sequence: T-T-R-S-W-D-F-L . Research conducted with protein databases identified this N-terminal sequence as cucumisin, an alkaline serine protease, which shares structural homology with microbial subtilisin . The molecular mass of the identified bands corresponds with different molecular forms of cucumisin produced during the processing or degradation of the enzyme: 67 kDa native cucumisin, 54 kDa mature cucumisin and 36 kDa NH2-terminal cucumisin fragment . CONCLUSION: Cucumisin (Cuc m 1) and several N-terminal cucumisin fragments are the major allergens of melon . The ubiquitous distribution of this protein family (cucumisin-like proteases) in many plant species and its high structural similarity suggest its potential role as a new panallergen in plant foods.

Ann Anat, 2003 Jun, 185(3), 223 - 31
Histochemical analysis of glycoconjugates in the ceruminous glands of the North American raccoon (Procyon lotor); Yasui T et al.; The distribution and selectivities of glycoconjugates in the ceruminous glands of the North American raccoon (Procyon lotor) were studied by light and electron microscopic histochemical methods, particularly lectin histochemistry . In the modified apocrine glands present, the apocrine secretion mode was combined with exocytosis, whereby the secretory epithelium and the luminal secretion of the ceruminous glands exhibited considerable amounts of complex carbohydrates with various terminal sugars (alpha-D-mannose, beta-D-galactose, alpha-L-fucose, alpha-N-acetyl-galactosamine, beta-N-acetyl-D-glucosamine, N-acetyl-neuraminic acid) . Alpha-L-fucose and N-acetyl-neuraminic acid were distinctly prominent in secretory granules or within the free surface coat of the plasma membrane of the glandular cells, as well as in the luminal secretion . Several free sugars (alpha-D-mannose, alpha-L-fucose, beta-D-galactose, beta-N-acetyl-D-glucosamine) were also detectable in the secretion of associated sebaceous glands . The ceruminous gland secretion may control viscoelasticity and/or bacterial degradation of the glandular secretion mixture to improve the protection of the external auditory canal against physical damage or microbial contamination.

Arch Tierernahr, 2003 Feb, 57(1), 39 - 48
Performance, carcass characteristics, meat quality and plasma constituents of meat type drakes fed diets containing different levels of lysine with or without a microbial phytase; Attia YA; This experiment was conducted to study growth performance, carcass characteristics, meat quality and plasma constituents of Campbell drakes fed diets containing different levels of lysine with or without a microbial phytase . Basal vegetable duck all-mash diets were fed during the growing (1-35 d of age), and finishing period (36-56 d of age) and were formulated to contain 0.90% and 0.73% lysine (negative control), respectively . These diets were supplemented or not with L-lysine HCl, which resulted in a dietary lysine level of 0.90, 0.95, 1.01 and 1.06% and 0.73, 0.80, 0.87 and 0.94%, during the growing and finishing period, respectively . Furthermore, the diets were fed with or without 600 FTU phytase (Natuphos) except for those containing 1.06 and 0.94% lysine during the growing and finishing period, respectively (positive control) . A lysine level of 1.01/0.87% in the growing/finishing diet significantly increased BWG and improved FCR of drakes by 2.1 and 1.8%, respectively . Phytase significantly increased BWG by 2.1% and 3.5% after feeding the basal diet and 1.01/0.87% lysine, respectively . Also, FCR was significantly improved by 2.2 and 1.8% of groups fed 0.95/0.80, and 1.01/0.87% lysine, respectively . Phytase as an independent variable increased BWG by 1.8, and improved FCR by 1.0% . Lysine and/or phytase did not affect carcass yield, and meat quality treats as well as plasma constituents of drakes . However, lysine level at 0.95/0.80% and 1.01/0.87% significantly decreased abdominal fat deposition compared to either the negative or the positive control . In conclusion, a lysine level of 1.01/0.87% in the growing/finishing diets for drakes is adequate . After phytase supplementation of the basal diet the BWG at a lysine level of 0.90/0.73% were similar to the positive control (1.06/0.94% lysine) . However, the best FCR was obtained after feeding diets containing 1.01/0.87% lysine supplemented with phytase.

J Food Prot, 2003 Jun, 66(6), 1090 - 4
Effect of modified atmosphere packaging and irradiation in combination on content of nitrosamines in cooked pork sausage; Song IH et al.; The effect of modified atmosphere packaging and irradiation in combination on nitrosodimethylamine (NDMA) and nitrosopyrrolidine (NPYR) levels in pork sausage was studied . Emulsion-type cooked pork sausage was manufactured and packaged in aerobic, CO2 (100%), N2 (100%), and CO2/N2 (25%/75%) environments, respectively, and irradiated at 0, 5, 10, and 20 kGy with gamma irradiation . The nitrosamine contents were significantly reduced by irradiation, and the reduction of nitrosamines was more extensive with modified atmosphere packaging than with aerobic packaging . The correlation coefficient between irradiation dose and nitrosamine content indicated that irradiation can reduce the levels of nitrosamines . The combination of irradiation and modified atmosphere packaging is effective in enhancing the chemical safety of sausage by reducing nitrosamines, if present, as well as enhancing the microbial safety of cooked pork sausage.

Huan Jing Ke Xue, 2003 Mar, 24(2), 112 - 5
{Performance of bio-ceramic reactor at low temperature}; Sang J et al.; A bio-ceramic reactor for slightly polluted source water from Guanting Reservoir in Beijing was conducted at low temperature . It was shown that the removal rate of CODMn and NH4(+)-N decreased from 20% to 6%, 90% to 65% respectively when the temperature fell from 10 degrees C to 0.5 degree C . The main factor affecting the efficiency of bio-ceramic reactor was the microbial activity which decreased more than the biomass when the temperature dropped . Microbial activity and biomass in the bio-ceramic reactor were in a regular pattern of gradient distribution from the lower to the upper along the direction of raw water flow.

Proc Natl Acad Sci U S A, 2003 Jun 24, 100(13), 7971 - 6 Epub 2003 Jun 10.
A low molecular weight mimic of the Toll/IL-1 receptor/resistance domain inhibits IL-1 receptor-mediated responses; Bartfai T et al.; Toll-like receptors (TLRs) and the type I IL-1 receptor (IL-1RI) are key components of the innate immune system activated by microbial infections and inflammation . The signaling cascade from agonist-occupied TLRs and IL-1Rs involves recruitment of the small cytosolic adapter protein MyD88 that binds to IL-1RI via homotypic interactions mediated by Toll/IL-1R/resistance (TIR) domains . Dominant negative forms and null mutations of MyD88 have recently been shown to preclude bacterial product or IL-1-mediated activation of NF-kappaB pathways, demonstrating that MyD88 is an essential component of the Toll receptor signaling . Here, we report the synthesis and pharmacological effects of a low molecular weight MyD88 mimic, hydrocinnamoyl-l-valyl pyrrolidine (compound 4a), modeled on a tripeptide sequence of the BB-loop {(F/Y)-(V/L/I)-(P/G)} of the TIR domain . Results are presented showing that compound 4a interferes with the interactions between mouse MyD88 and IL-1RI at the TIR domains . Compound 4a inhibited IL-1beta-induced phosphorylation of the mitogen-activated protein kinase p38 in EL4 thymoma cells and in freshly isolated murine lymphocytes in a concentration-dependent manner . In vivo, compound 4a produced a significant attenuation of the IL-1beta-induced fever response (200 mg/kg, i.p.) . Inhibition of the TIR domain-mediated MyD88/IL1-RI interaction by a low molecular weight, cell-penetrating TIR domain mimic suggests an intracellular site for antiinflammatory drug action.

Crit Rev Oral Biol Med, 2003, 14(3), 175 - 87
Genomics of oral bacteria; Duncan MJ; Advances in bacterial genetics came with the discovery of the genetic code, followed by the development of recombinant DNA technologies . Now the field is undergoing a new revolution because of investigators' ability to sequence and assemble complete bacterial genomes . Over 200 genome projects have been completed or are in progress, and the oral microbiology research community has benefited through projects for oral bacteria and their non-oral-pathogen relatives . This review describes features of several oral bacterial genomes, and emphasizes the themes of species relationships, comparative genomics, and lateral gene transfer . Genomics is having a broad impact on basic research in microbial pathogenesis, and will lead to new approaches in clinical research and therapeutics . The oral microbiota is a unique community especially suited for new challenges to sequence the metagenomes of microbial consortia, and the genomes of uncultivable bacteria.

Ecotoxicol Environ Saf, 2003 Jul, 55(3), 344 - 51
Changes in microbial properties associated with long-term arsenic and DDT contaminated soils at disused cattle dip sites; Edvantoro BB et al.; This work examined the effect of long-term arsenic (As) and DDT contamination on soil microbial properties at 11 cattle dip sites in northern New South Wales, Australia . Total As in the surface (0-10 cm) soils from these sites ranged from 34 to 2941 mg As kg(-1) soil and hexane-extractable DDT concentrations ranged between 2.9 and 7673 mg DDT kg(-1) soil . The concentrations of water and oxalate-extractable As were positively correlated with total As . Oxalate-extractable As was more strongly correlated (r(2)=0.87) with total As than water-extractable As (r(2)=0.34) . A weak positive relationship was observed between the level of nutrient (organic carbon and nitrogen) and microbial biomass C (r(2)=0.61 and 0.45, respectively) . There was a highly significant difference between the microbial properties of polluted and unpolluted sites (P<0.001) . In comparison to unpolluted soils, fungal counts, microbial biomass C, and respiration were dramatically reduced (P<0.05) in polluted soils . However, the bacterial population between polluted and unpolluted soils were not different (P<0.05) . The results of this study suggested that (a) long-term contamination of soils adjacent to former cattle dipping sites by As and DDT adversely affected soil microbial properties with the fungal populations being the most sensitive and (b) there was little regeneration of microbiota despite 25 years of field ageing of the soils.

Steroids, 2003 May, 68(5), 415 - 21
Microbial conversion of pregna-4,9(11)-diene-17alpha,21-diol-3,20-dione acetates by Nocardioides simplex VKM Ac-2033D; Fokina VV et al.; The conversion of pregna-4,9(11)-diene-17alpha,21-diol-3,20-dione 21-acetate (I) and 17,21-diacetate (VI) by Nocardioides simplex VKM Ac-2033D was studied . The major metabolites formed from I were identified as pregna-1,4,9(11)-triene-17alpha,21-diol-3,20-dione 21-acetate (II) and pregna-1,4,9(11)-triene-17alpha,21-diol-3,20-dione (IV) . Pregna-4,9(11)-diene-17alpha,21-diol-3,20-dione (III) and pregna-1,4,9(11)-triene-17alpha,20beta,21-triol-3-one (V) were formed in minorities . Biotransformation products formed from VI were pregna-1,4,9(11)-triene-17alpha,21-diol-3,20-dione 17,21-diacetate (VII), pregna-1,4,9(11)-triene-17alpha,21-diol-3,20-dione 21-acetate (II), pregna-1,4,9(11)-triene-17alpha,21-diol-3,20-dione (IV), pregna-1,4,9(11)-triene-17alpha,21-diol-3,20-dione 17-acetate (VIII), pregna-1,4,9(11)-triene-17alpha,20beta,21-triol-3-one (V) . The conversion pathways were proposed including 1(2)-dehydrogenation, deacetylation, 20beta-reduction and non-enzymatic migration of acyl group from position 17 to 21 . The conditions providing predominant accumulation of pregna-1,4,9(11)-triene-17alpha,21-diol-3,20-dione 21-acetate (II) from I and pregna-1,4,9(11)-triene-17alpha,21-diol-3,20-dione 17-acetate (VIII) from VI in a short-term biotransformation were determined.

BJOG, 2003 Jun, 110(6), 598 - 603
Interleukin-18 in cervical mucus and amniotic fluid: relationship to microbial invasion of the amniotic fluid, intra-amniotic inflammation and preterm delivery; Jacobsson B et al.; OBJECTIVE: To evaluate the relationship between interleukin (IL)-18 in cervical mucus and amniotic fluid and microbial invasion of amniotic fluid, preterm delivery and intra-amniotic inflammation in women in preterm labour, with preterm prelabour rupture of membranes and at term . DESIGN: A prospective follow up study . SETTING: Sahlgrenska University Hospital, Goteborg, Sweden . SAMPLE: Women with singleton pregnancies (<34 weeks) presenting with preterm labour (n = 87) or preterm prelabour rupture of membranes (n = 47) and women, not in labour, at term (n = 28) . METHODS: Amniotic fluid was retrieved transabdominally . Cervical mucus was taken from the uterine cervix of women in preterm labour and at term . IL-18 was analysed with enzyme-linked immunosorbent assay . MAIN OUTCOME MEASURES: IL-18 in relation to microbial invasion of the amniotic fluid, delivery within seven days or <34 weeks of gestation and intra-amniotic inflammation . RESULTS: The levels of IL-18 in cervical mucus and amniotic fluid were higher in women with preterm labour than in those not in labour at term . In the preterm labour group, significant associations were found between elevated IL-18 in amniotic fluid and microbial invasion of the amniotic fluid, as well as between delivery within seven days or <34 weeks of gestation and intra-amniotic inflammation . Delivery was delayed longer in the preterm prelabour rupture of membranes subgroup with IL-18 >or=1.0 ng/mL than in that with IL-18 <1.0 ng/mL . CONCLUSIONS: In the preterm labour group, high IL-18 in amniotic fluid (but not in the cervix) was associated with microbial invasion of the amniotic fluid, intra-amniotic inflammation and prompt delivery . On the other hand, elevated IL-18 in preterm prelabour rupture of the membranes group correlated with a longer interval to delivery.

J Steroid Biochem Mol Biol, 2003 May, 85(1), 63 - 9
Concurrent corticosteroid and phenanthrene transformation by filamentous fungus Cunninghamella elegans; Lisowska K et al.; A filamentous fungus Cunninghamella elegans IM 1785/21Gp which displays ability of 17alpha,21-dihydroxy-4-pregnene-3,20-dione (cortexolone) 11-hydroxylation (yielding epihydrocortisone (eF) and hydrocortisone (F)) and polycyclic aromatic hydrocarbons (PAHs) degradation, was used as a microbial eucaryotic model to study the relationships between mammalian steroid hydroxylation and PAHs metabolization . The obtained results showed faster transformation of phenanthrene in Sabouraud medium supplemented with steroid substrate (cortexolone) . Simultaneously phenanthrene stimulated epihydrocortisone production from cortexolone . In phenanthrene presence the ratio between cortexolone hydroxylation products (hydrocortisone and epihydrocortisone) was changed from 1:5.1-6.2 to 1:7.6-8.4 in the culture without phenanthrene . Cytochrome P-450 content significantly increased after the culture supplementation by the second substrate, phenanthrene or cortexolone, adequately . To confirm the involvement of cytochrome P-450 in phenanthrene metabolism, the inhibition studies were performed . The cytochrome P-450 inhibitors SKF 525-A (1.5mM) and 2-methyl-1,2-di-3-pyridyl-1-propanone (metyrapone) (2mM) inhibited phenanthrene transformation by 80 and 62%, respectively . 1-aminobenzotriazole (1mM) completely blocked phenanthrene metabolism . The obtained results suggest a presence of connections between steroid hydroxylases and enzymes involved in PAH degradation in C . elegans.

Res Microbiol, 2003 May, 154(4), 309 - 13
Haloarchaeal viruses: how diverse are they?
Dyall-Smith M, Tang SL, Bath C.
Hypersaline lakes are highly productive microbial environments that provide many advantages for microbial ecologists, including stable communities of relatively low diversity (mainly haloarchaea) . An important component of these communities is comprised of their non-cellular parasites, i.e., their viruses . Few viruses of halobacteria (haloviruses) have been isolated and studied even though a wide selection of host species have been formally described (and easily cultured) for ten years . Hypersaline waters have been shown to contain very high concentrations of virus-like particles (at least 10(7) particles/ml), particularly fusiform particles, but laboratory isolations of new haloviruses have been very slow and the detailed study of selected examples even slower . Here we provide an outline of the reported haloviruses, including fusiform and unpublished isolates from this laboratory, and we discuss their diversity and the future directions for this research.

Sci Total Environ, 2003 Jun 20, 309(1-3), 225 - 36
Distribution and bioavailability of copper in farm effluent; Bolan NS et al.; Effluent and sludge samples from a number of dairy and piggery units in the North Island of New Zealand were collected and analysed for free ionic-copper (Cu(2+)) and organically-complexed Cu . The bioavailability of sludge-Cu was examined using microbial respiration and plant growth experiments . Microbial respiration was measured at various levels of Cu (0-1000 mg kg(-1)), added as copper sulfate (CuSO(4)) and sludge-Cu, using a Gilson differential respirometer . A glass house experiment was conducted to examine the transformation of Cu in soils and its subsequent uptake by ryegrass pasture . Three Cu sources were used that included fast-release CuSO(4), slow-release copper oxide (CuO) and Cu-enriched sludge . The pasture samples were analysed for Cu concentration . The transformation of Cu in the soil was monitored by analysing the soil samples for various fractions of Cu . The effluent and sludge samples collected from farms which regularly used Cu to treat lameness in dairy cattle and as a growth promoter in swine contained higher concentration of Cu . The total Cu concentration ranged from approximately 0.1 to 1.55 mg l(-1) and from 0.5 to 10.5 mg l(-1) in the piggery and diary effluent, respectively . The corresponding values for the sludge samples were 3.0-526 and 25-105 mg kg(-1) . Most of the Cu in both the effluent and solid sludge material was organically complexed . The respiration measurements indicated that sludge-Cu was less toxic to soil microbial activity than CuSO(4) . The results from the glass house experiment indicated that increasing the level of Cu applied through fertilisers and sludge increased Cu concentration in plants . At the same rate of application, plants took up less Cu from sludge and CuO than from CuSO(4) . There was, however, a greater translocation of Cu from root to shoot at the highest rate of Cu through sludge application . The Cu fractionation study indicated that there was greater accumulation of organic bound Cu in the sludge-treated soil than the fertiliser-treated soil.

J Agric Food Chem, 2003 Jun 18, 51(13), 3731 - 6
High-affinity monoclonal antibodies for detection of the microbial metabolite, 2-methylisoborneol; Plhak LC et al.; The production of 2-methylisoborneol (MIB) by certain fungi and algae can contribute musty off-flavors to foods and water supplies if uncontrolled . The goal of this research was to develop a nonsensory simple method for the detection of MIB . Anti-MIB monoclonal antibodies were produced by immunizing mice with borneol-conjugated protein and selecting positive clones with an MIB-protein conjugate . An indirect competitive immunoassay developed using this antibody had a detection limit of 0.6 microg L(-)(1) and an I(50) value of 5 microg L(-)(1) . Detection was relatively specific for MIB and showed 20% cross-reactivity with borneol or isoborneol and 4-5% cross-reactivity with camphor . No cross-reactivity to geosmin was observed.

Curr Top Microbiol Immunol, 2003, 276, 241 - 59
Viral vectors for dendritic cell-based immunotherapy; Humrich J et al.; Dendritic cells (DCs) constitute a specialised system of antigen-presenting cells with a high capacity to induce and to modulate the immune response against microbial, tumour and self-antigens . New techniques to generate large amounts of DCs together with the molecular identification of human tumour-associated antigens (TAA) have opened new ways for antigen-specific cancer immunotherapies . DCs loaded either with TAA-derived MHC class I-specific synthetic peptides or with whole tumour cell preparations have been used in numerous clinical trials evaluating the efficacy of DCs in patients with cancer . However, the disadvantages of DCs pulsed with synthetic peptides from TAA include the uncertainty regarding the longevity of antigen presentation, the restriction by the patient's haplotype and the relatively low number of known MHC class I and in particular of MHC class II helper cell-related epitopes . Whole tumour cell preparations are difficult to standardise, and they depend on the availability of tumour cells . Thus the utilisation of viral vectors genetically modified to express TAA for the ex vivo transduction of DCs is an attractive alternative to achieve a MHC I- and MHC II-restricted presentation of tumoural antigens . To induce protective anti-tumoural immune response an increasing number of modified viral vectors have been used to transduce DCs . Although high transduction efficacies were reported for several viruses, analysis of the interaction of viral vectors with DCs has revealed several viral mechanisms that interfere with main functions of DCs, dampening somewhat the initial optimism in the field of DC transduction . However, promising results with different vectors have been achieved . In this review we summarise available data and discuss advantages and drawbacks of currently available vectors.

Plant J, 2003 Jun, 34(6), 768 - 77
Loss of actin cytoskeletal function and EDS1 activity, in combination, severely compromises non-host resistance in Arabidopsis against wheat powdery mildew; Yun BW et al.; Plant immunity against the majority of the microbial pathogens is conveyed by a phenomenon known as non-host resistance (NHR) . This defence mechanism affords durable protection to plant species against given species of phytopathogens . We investigated the genetic basis of NHR in Arabidopsis against the wheat powdery mildew fungus Blumeria graminis f . sp . tritici (Bgt) . Both primary and appressorial germ tubes were produced from individual Bgt conidia on the surface of the Arabidopsis leaves . Attempted infection occasionally resulted in successful penetration, which led to the development of an abnormal unilateral haustorium . Inoculation of a series of Arabidopsis defence-related mutants with Bgt resulted in the attenuation of reactive oxygen intermediate (ROI) production and salicylic acid (SA)-dependent defence gene expression in eds1, pad4 and nahG plants, which are known to be defective in some aspects of host resistance . Furthermore, Bgt often developed bilateral haustoria in the mutant Arabidopsis lines that closely resembled those formed in wheat . A similar decrease in NHR was observed following treatment of the wild-type Arabidopsis plants with cytochalasin E, an inhibitor of actin microfilament polymerisation . In eds1 mutants, inhibition of actin polymerisation severely compromised NHR in Arabidopsis against Bgt . This permitted completion of the Bgt infection cycle on these plants . Therefore, actin cytoskeletal function and EDS1 activity, in combination, are major contributors to NHR in Arabidopsis against wheat powdery mildew.

Biochem J, 2003 Sep 15, 374(Pt 3), 707 - 14
A study of host defence peptide beta-defensin 3 in primates; Boniotto M et al.; We have investigated the molecular evolution of the gene coding for beta-defensin 3 (DEFB103) in 17 primate species including humans . Unlike the DEFB4 genes (coding for beta-defensin 2) {Boniotto, Tossi, Del Pero, Sgubin, Antcheva, Santon and Masters (2003) Genes Immun . 4, 251-257}, DEFB103 shows a marked degree of conservation in humans, Great Apes and New and Old World monkeys . Only the Hylobates concolor defensin hcBD3 showed an amino acid variation Arg17-->Trp17 that could have a functional implication, as it disrupts an intramolecular salt bridge with Glu27, which locally decreases the charge and may favour dimerization in the human congener hBD3 . This is thought to involve the formation of an intermolecular salt bridge between Glu28 and Lys32 on another monomer {Schibli, Hunter, Aseyev, Starner, Wiencek, McCray, Tack and Vogel (2002) J . Biol . Chem . 277, 8279-8289} . To test the role of dimerization in mediating biological activity, we synthesized hBD3, hcBD3 and an artificial peptide in which the Lys26-Glu27-Glu28 stretch was replaced by the equivalent Phe-Thr-Lys stretch from human beta-defensin 1 and we characterized their structure and anti-microbial activity . Although the structuring and dimerization of these peptides were found to differ significantly, this did not appear to affect markedly the anti-microbial potency, the broad spectrum of activity or the insensitivity of the anti-microbial action to the salinity of the medium.

Crit Care Med, 2003 Jun, 31(6), 1688 - 90
Each lumen is a potential source of central venous catheter-related bloodstream infection; Dobbins BM et al.; OBJECTIVE: To determine the relative rates of microbial colonization of individual lumens in triple-lumen central venous catheters (CVCs) and calculate the chance of detecting catheter-related blood stream infection (CRBSI) if only one lumen is sampled . DESIGN: Prospective evaluation of CVCs from suspected and nonsuspected CRBSI cases . SETTING: University teaching hospital . PATIENTS: Triple-lumen CVCs from 50 cases of suspected CRBSI (a raised peripheral white blood cell count, temperature >37 degrees C, and/or local signs of infection at the catheter skin entry site) were evaluated . For comparison, 50 triple-lumen CVCs routinely removed at the end of use were evaluated . MEASUREMENTS: In both groups, peripheral blood cultures were taken before CVC removal . After CVC removal, each lumen was sampled in vitro using the endoluminal brush, and the tip was then cultured using the Maki roll technique . MAIN RESULTS: CVCs causing CRBSI had significant microbial colonization in one, two, or three lumens in ten (40%), ten (40%), or five (20%) cases, respectively . Overall, random sampling of only one lumen in CVCs causing CRBSI had a 60% chance of detecting significant colonization . CONCLUSIONS: If only one CVC lumen is sampled, a negative result does not reliably rule out infection . Each lumen of multiple-lumen CVCs should be considered as a potential source of CRBSI.

Appl Biochem Biotechnol, 2003 Apr-Jun, 109(1-3), 33 - 45
Extension of Anaerobic Digestion Model No . 1 with processes of sulfate reduction; Fedorovich V et al.; In the present work, the Anaerobic Digestion Model No . 1 (ADM1) for computer simulation of anaerobic processes was extended to the processes of sulfate reduction . The upgrade maintained the structure of ADM1 and included additional blocks describing sulfate-reducing processes (multiple reaction stoichiometry, microbial growth kinetics, conventional material balances for ideally mixed reactor, liquid-gas interactions, and liquid-phase equilibrium chemistry) . The extended model was applied to describe a longterm experiment on sulfate reduction in a volatile fatty acid-fed upflow anaerobic sludge bed reactor and was generally able to predict the outcome of competition among acetogenic bacteria, methanogenic archaea, and sulfate- reducing bacteria for these substrates . The computer simulations also showed that when the upward liquid velocity in the reactor exceeds 1 m/d, the structure of the sludge becomes essential owing to bacterial detachment.

J Immunol, 2003 Jun 15, 170(12), 6257 - 65
A prominent role for airway epithelial NF-kappa B activation in lipopolysaccharide-induced airway inflammation; Poynter ME et al.; To reveal the causal role of airway epithelial NF-kappaB activation in evoking airway inflammation, a transgenic mouse was created expressing a mutant version of the inhibitory protein I-kappaBalpha . This I-kappaBalpha superrepressor (I-kappaBalpha(SR)) acts to repress NF-kappaB activation exclusively in airway epithelial cells, under the transcriptional control of the rat CC10 promoter (CC10-I-kappaBalpha(SR)) . Compared with transgene-negative littermates, intranasal instillation of LPS did not induce nuclear translocation of NF-kappaB in airway epithelium of CC10-I-kappaBalpha(SR) transgenic mice . Consequently, the influx of neutrophils into the airways and secretion of the NF-kappaB-regulated neutrophilic chemokine, macrophage-inflammatory protein-2, and the inflammatory cytokine, TNF-alpha, were markedly reduced in CC10-I-kappaBalpha(SR) mice relative to the transgene-negative mice exposed to LPS . Despite an inability to activate NF-kappaB in airway epithelium, resident alveolar macrophages from transgene-positive mice were capable of activating NF-kappaB in a manner indistinguishable from transgene-negative mice . These findings demonstrate that airway epithelial cells play a prominent role in orchestrating the airway inflammatory response to LPS and suggest that NF-kappaB signaling in these cells is important for modulating innate immune responses to microbial products.

J Infect Dis, 2003 Jun 15, 187 Suppl 2, S397 - 401
TREM-1 (triggering receptor expressed on myeloid cells): a new player in acute inflammatory responses; Colonna M et al.; TREM-1 (triggering receptor expressed on myeloid cells), a recently discovered receptor of the immunoglobulin superfamily, activates neutrophils and monocytes/macrophages by signaling through the adapter protein DAP12 . TREM-1 is the best-characterized member of a growing family of DAP12-associated receptors that regulate the function of myeloid cells in innate and adaptive responses . TREM-1 amplifies Toll-like receptor-initiated responses against microbial challenges and potentiates the secretion of proinflammatory chemokines and cytokines in response to bacterial and fungal infections . Blockade of TREM-1 reduces inflammation and increases survival in animal models of bacterial infections that cause systemic hyperinflammatory syndromes . The TREM-1 ligands are not known . Characterization of TREM-1 natural ligands will further illuminate the mechanisms regulating innate responses against pathogens . Whatever the ligands, targeted activation or blockade of TREM-1 and its ligands may help maximize the efficacy of existing treatments for sepsis.

Science, 2003 Jun 6, 300(5625), 1524 - 5
Toll-like receptor signaling pathways; Barton GM et al.; Members of the Toll-like receptor (TLR) family recognize conserved microbial structures, such as bacterial lipopolysaccharide and viral double-stranded RNA, and activate signaling pathways that result in immune responses against microbial infections . All TLRs activate MyD88-dependent pathways to induce a core set of stereotyped responses, such as inflammation . However, individual TLRs can also induce immune responses that are tailored to a given microbial infection . Thus, these receptors are involved in both innate and adaptive immune responses . The mechanisms and components of these varied responses are only partly understood . Given the importance of TLRs in host defense, dissection of the pathways they activate has become an important emerging research focus . TLRs and their pathways are numerous; Science's Signal Transduction Knowledge Environment's TLR Connections Map provides an immediate, clear overview of the known components and relations of this complex system.

Biotechnol Prog, 2003 May-Jun, 19(3), 1053 - 5
Biosorption of milk substrates onto anaerobic flocculent and granular sludge; Nadais MH et al.; Experiments were performed for adsorption of milk-based substrates onto anaerobic biomass at 35 degrees C . The influence of two parameters was studied, namely, the type of biomass (flocculent or granular) and the sludge adaptation to the substrate . It was found that flocculent sludge presented an adsorption capacity roughly 3 times higher than that of granular sludge . The adsorption data fit well with the Freundlich and Langmuir isotherms . Apparently, short-term sludge adaptation is not influential on the adsorption behavior . On the other hand, long-term adapted sludge showed a higher adsorption capacity than nonadapted sludge, which probably is an indirect effect of different microbial populations . These results suggest that the role of adsorption in the anaerobic treatment of complex substrates containing fat cannot be overlooked, especially for flocculent sludge systems, since organic matter accumulation could cause process failure due to biomass washout.

Biotechnol Prog, 2003 May-Jun, 19(3), 908 - 14
High-pressure processing of apple juice: kinetics of pectin methyl esterase inactivation; Riahi E et al.; High-pressure (HP) inactivation kinetics of pectin methyl esterase (PME) in apple juice were evaluated . Commercial PME was dispensed in clarified apple juice, sealed in dual peel sterilizable plastic bags, and subjected to different high-pressure processing conditions (200-400 MPa, 0-180 min) . Residual enzyme activity was determined by a titration method estimating the rate of free carboxyl group released by the enzyme acting on pectin substrate at pH 7.5 (30 degrees C) . The effects of pressure level and pressure holding time on enzyme inactivation were significant (p < 0.05) . PME from the microbial source was found to be more resistant (p < 0.05) to pressure inactivation than PME from the orange peel . Almost a full decimal reduction in the activity of commercial PME was achieved by HP treatment at 400 MPa for 25 min . Inactivation kinetics were evaluated on the basis of a dual effect model involving a pressure pulse effect and a first-order rate model, and the pressure sensitivity of rate constants was modeled by using the z-value concept.

Biotechnol Prog, 2003 May-Jun, 19(3), 874 - 9
Microbial desizing using starch as model compound: enzyme properties and desizing efficiency; Feitkenhauer H et al.; A film of sizing agents protects yarn during weaving . Its removal in a subsequent washing process causes 50% of the organic effluent load of textile finishing processes and requires large amounts of auxiliary chemicals (e.g., surfactants) . Microbial desizing is a new bioprocess that uses the acidifying culture of a two-phase anaerobic digestion plant for the removal and partial degradation (acidification) of the sizing agent . Soluble starch is used in this study to characterize the enzymatic properties in the supernatant of the desizing culture and to link them to desizing efficiencies . The supernatant of the culture (grown at 37 degrees C, pH 5.5) displayed the highest enzymatic activity between pH 4 and 5 and in a broad temperature range (20-80 degrees C) . Highest metabolization rates were determined with the substrate amylose . Short chain dextrins (average of 5 and 10 glucose units) and amylopectin were converted significantly more slowly . At 37 degrees C the half-life time of the enzymatic activity in the supernatant was 45 h . In a desizing test a decisive reduction of the chain length was found already after 1 h (allowing starch solubilization) . A microbial desizing experiment with dyed, native maize starch demonstrated the efficiency of the proposed bioprocess.

Biotechnol Prog, 2003 May-Jun, 19(3), 755 - 62
Auxiliary phase guidelines for microbial biotransformations of toxic substrate into toxic product; Straathof AJ; When an industrial process is developed using the microbial transformation of a precursor into a desired chemical compound, high concentrations of substrate and product will be involved . These compounds may become toxic to the cells . In situ product removal (ISPR) may be carried out, using auxiliary phases such as extractants or adsorbents . Simultaneously, in situ substrate addition (ISSA) may be performed . It is shown that for uncharged substrates and products, the aqueous solubilities of substrate and product can be used to predict if ISPR might be required . When a particular auxiliary phase is selected and the distribution coefficients of substrate and product are known, it is possible to estimate a priori if this auxiliary phase might be good enough and how much of it might be needed for an efficient (fed-)batch biotransformation process . For biotransformation products of intermediate polarity (aqueous solubility of about 1-10 g/L) there seems to be a lack of extractants and adsorbents with the capacity to raise the product concentrations to commercially more interesting levels.

Am J Health Syst Pharm, 2003 May 15, 60(10), 1019 - 22
Stability of nifedipine in an extemporaneously compounded oral solution; Dentinger PJ et al.; The stability of nifedipine in an extemporaneously compounded oral solution is described . A solution of nifedipine 10 mg/mL was prepared from commercially available nifedipine powder with polyethylene glycol 400, glycerin, and peppermint oil . Four samples were stored in amber glass bottles at room temperature under fluorescent lighting and analyzed in duplicate . Samples were analyzed immediately and at 7, 14, 23, and 35 days . Eight samples were stored in amber oral syringes and eight in amber oral syringes wrapped in aluminum foil; all were stored at room temperature under fluorescent lighting . Samples from foil-wrapped syringes were analyzed at 7 and 14 days; samples not wrapped in foil were analyzed after 7 days . Nifedipine concentrations were measured with a modified stability-indicating high-performance liquid chromatographic method . Excessive degradation was defined as a greater than 10% loss of initial drug concentration . There were no detectable changes in color or odor and no visible solids or microbial growth was observed in any sample . Samples in amber glass bottles and amber oral syringes wrapped in aluminum foil retained more than 90% of the initial nifedipine for 35 and 14 days, respectively . Samples packaged in amber oral syringes not wrapped in foil lost over 20% of the initial nifedipine concentration within 7 days . Nifedipine 10 mg/mL was stable in an oral solution prepared from commercially available powder in a peppermint-flavored vehicle for at least 35 days when stored at 22-25 degrees C in amber glass bottles and for at least 14 days when stored in amber oral syringes wrapped in aluminum foil.

Ceska Slov Farm, 2003 May, 52(3), 107 - 14
{50 years of the Institute for Research in Pharmacy and Biochemistry}; Trcka V; After the nationalization of pharmaceutical industry and establishment of the United Pharmaceutical Enterprises in 1946, the Research and Control Institute (VKU) was established in Prague in 1947 to support the development of research, manufacture, and control of drugs . After other measures of nationalization and unification of research, in 1951 the research sections of the VKU and the pharmaceutical sections of the Research Institute of CCHZ were fused to form the Research Institute for Pharmacy and Biochemistry (VUFB) . The section the VUFB taking care of the quality of production was transformed into the Pharmaceutical Control Institute (KUF) . Each of the institutes had its own farm for breeding experimental animals outside Prague . In 1958, KUF was transformed into the Research Institute of Medicinal Plants (VULERO) and later, in 1960, into the Research Institute of Natural Substances (VUPL), which eventually fused with VUFB in 1967 . During the years of increasing activities of VUFB, a chemical pilot plant was established in Olomouc, and a department of clinical pharmacology in Plzen . Research activities of VUFB were aimed to search for original drugs and to develop non-proprietary medicines in the field of the central and vegetative nervous systems, blood circulation, inflammatory processes, microbial infections, carcinostatic drugs, etc . In natural substances, the greatest attention was paid to ergot alkaloids, but the extent of research also included the constituents of the poppy, periwinkle, and other plants . An important part of the programme was also the breeding and cultivation of selected medicinal plants . The results of research were continuously published in both inland and foreign scholarly journals and at conferences and congresses . Every year, usually more than 100 papers were published and 40-50 for patents applications were submitted . The activity of the Institute resulted in the production of 30 original substances which were introduced into therapeutic practice . Twenty of them are still commonly prescribed . Some of these original substances got into foreign markets, particularly Prothiaden and Trimepranol represented important exports . In addition, 83 non-proprietary drugs were introduced into the inland market.

Appl Environ Microbiol, 2003 Jun, 69(6), 3636 - 9
Microbial reduction and precipitation of vanadium by Shewanella oneidensis; Carpentier W et al.; Shewanella oneidensis couples anaerobic oxidation of lactate, formate, and pyruvate to the reduction of vanadium pentoxide (V(V)) . The bacterium reduces V(V) (vanadate ion) to V(IV) (vanadyl ion) in an anaerobic atmosphere . The resulting vanadyl ion precipitates as a V(IV)-containing solid.

Appl Environ Microbiol, 2003 Jun, 69(6), 3517 - 25
Chemical and biological interactions during nitrate and goethite reduction by Shewanella putrefaciens 200; Cooper DC et al.; Although previous research has demonstrated that NO(3)(-) inhibits microbial Fe(III) reduction in laboratory cultures and natural sediments, the mechanisms of this inhibition have not been fully studied in an environmentally relevant medium that utilizes solid-phase, iron oxide minerals as a Fe(III) source . To study the dynamics of Fe and NO(3)(-) biogeochemistry when ferric (hydr)oxides are used as the Fe(III) source, Shewanella putrefaciens 200 was incubated under anoxic conditions in a low-ionic-strength, artificial groundwater medium with various amounts of NO(3)(-) and synthetic, high-surface-area goethite . Results showed that the presence of NO(3)(-) inhibited microbial goethite reduction more severely than it inhibited microbial reduction of the aqueous or microcrystalline sources of Fe(III) used in other studies . More interestingly, the presence of goethite also resulted in a twofold decrease in the rate of NO(3)(-) reduction, a 10-fold decrease in the rate of NO(2)(-) reduction, and a 20-fold increase in the amounts of N(2)O produced . Nitrogen stable isotope experiments that utilized delta(15)N values of N(2)O to distinguish between chemical and biological reduction of NO(2)(-) revealed that the N(2)O produced during NO(2)(-) or NO(3)(-) reduction in the presence of goethite was primarily of abiotic origin . These results indicate that concomitant microbial Fe(III) and NO(3)(-) reduction produces NO(2)(-) and Fe(II), which then abiotically react to reduce NO(2)(-) to N(2)O with the subsequent oxidation of Fe(II) to Fe(III).

Appl Environ Microbiol, 2003 Jun, 69(6), 3223 - 30
Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil; Ellis RJ et al.; In recent years, culture-independent methods have been used in preference to traditional isolation techniques for microbial community analysis . However, it is questionable whether uncultured organisms from a given sample are important for determining the impact of anthropogenic stress on indigenous communities . To investigate this, soil samples were taken from a site with patchy metal contamination, and the bacterial community structure was assessed with a variety of approaches . There were small differences in microscopic epifluorescence bacterial counts . Denaturing gradient gel electrophoresis (DGGE) profiles of 16S rRNA gene fragments (16S-DGGE) amplified directly from soil samples were highly similar . A clone library generated from the most contaminated sample revealed a diverse bacterial community, which showed similarities to pristine soil communities from other studies . However, the proportion of bacteria from the soil samples that were culturable on standard plate-counting media varied between 0.08 and 2.2%, and these values correlated negatively with metal concentrations . The culturable communities from each sample were compared by 16S-DGGE of plate washes and by fatty acid profiling of individual isolates . Each approach indicated that there were considerable differences between the compositions of the culturable communities from each sample . DGGE bands from both culture-based and culture-independent approaches were sequenced and compared . These data indicated that metal contamination did not have a significant effect on the total genetic diversity present but affected physiological status, so that the number of bacteria capable of responding to laboratory culture and their taxonomic distribution were altered . Thus, it appears that plate counts may be a more appropriate method for determining the effect of heavy metals on soil bacteria than culture-independent approaches.

Appl Environ Microbiol, 2003 Jun, 69(6), 3176 - 80
Enhanced mercury biosorption by bacterial cells with surface-displayed MerR; Bae W et al.; The metalloregulatory protein MerR, which exhibits high affinity and selectivity toward mercury, was exploited for the construction of microbial biosorbents specific for mercury removal . Whole-cell sorbents were constructed with MerR genetically engineered onto the surface of Escherichia coli cells by using an ice nucleation protein anchor . The presence of surface-exposed MerR on the engineered strains enabled sixfold-higher Hg(2+) biosorption than that found in the wild-type JM109 cells . Hg(2+) binding via MerR was very specific, with no observable decline even in the presence of 100-fold excess Cd(2+) and Zn(2+) . The Hg(2+) binding property of the whole-cell sorbents was also insensitive to different ionic strengths, pHs, and the presence of metal chelators . Since metalloregulatory proteins are currently available for a wide variety of toxic heavy metals, our results suggest that microbial biosorbents overexpressing metalloregulatory proteins may be used similarly for the cleanup of other important heavy metals.

Biosens Bioelectron, 2003 Aug 15, 18(9), 1101 - 7
Application of a flow-type antibody sensor to the detection of Escherichia coli in various foods; Kim N et al.; A flow-type biosensor system which uses a broad-spectrum anti-Escherichia coli antibody and quartz crystal microbalance as biological component and transducer was developed . Biosensor responses were initiated by injecting viable E . coli suspensions through a flow cell and the sensor system was optimized for response time according to flow rate and injection time, followed by the measurement of responses for various E . coli strains . As expected, the sensor system showed a characteristic broad binding feature against E . coli strains . A linear sensor response in double-logarithmic scale was observed for the microbial suspensions ranging from 1.7 x 10(5) to 8.7 x 10(7) CFU/ml . Sample measurements could be done within 20-30 min after Stomacher treatment followed by spiking or enrichment.

J Invertebr Pathol, 2003 Jun, 83(2), 157 - 67
Effect of soil temperature and moisture on survival and infectivity of Metarhizium anisopliae to four tephritid fruit fly puparia; Ekesi S et al.; The infectivity of 4 isolates of Metarhizium anisopliae to puparia of Ceratitis capitata treated as late third-instar larvae in unsterilized soil was investigated in the laboratory under controlled temperature and moisture . At 20-30 degrees C, mortality in puparia was highest at water potential of -0.1 and -0.01 mega Pascal (MPa) and lowest at water potential of -0.0055 and -0.0035 MPa in all the isolates . In wetter soil however, isolates ICIPE 20 and 60 caused significantly higher mortality than ICIPE 18 and 69 . The survival of conidia in drier soil (-0.1 MPa) was not adversely affected at all temperatures . However, in wet soil (-0.0035 MPa) there was drastic reduction in colony counts in ICIPE 18 and 69 at 25 and 30 degrees C but conidial density in ICIPE 20 and 60 remained at the initial level at 14 days after inoculation at all temperatures . When ICIPE 20 was evaluated against three other fruit fly species (Ceratitis cosyra, Ceratitis rosa, and Ceratitis fasciventris), significant reduction in adult emergence and higher pupal mortality occurred in C . cosyra and C . fasciventris than in C . rosa at a combination of 15 and 20 degrees C and -0.1 and -0.0035 MPa . However, at higher temperature and the same moisture level, the isolates were equally pathogenic across the 3 species . It is probable that in addition to pathogen cycling and multiplication from dead infected insects in the soil, a balance between microbial degradation and replenishment of inoculum of virulent isolates occur through fluctuations in, and intricate interactions between temperature and moisture levels . This study is indicative of the potential of using isolate ICIPE 20 for soil inoculation against pupariating third-instar larva of fruit flies, thus providing a novel alternative to chemical soil application.

Microbes Infect, 2003 Jun, 5(7), 613 - 9
Bacterial invasion by a paracellular route: divide and conquer; Balkovetz DF et al.; The epithelium of the host plays an important first line of defense against most human pathogens . Microbial factors have been identified that are involved in the destruction of the structures that maintain the integrity of the epithelium . The mechanisms used by several, selected bacteria for the disruption of epithelial cell-cell junctions are discussed.

J Clin Periodontol, 2003, 30 Suppl 5, 17 - 8
Management of oral malodour; Quirynen M; Halitosis is a common problem . Its aetiology is multifactorial, but oral malodour is usually caused by microbial metabolism from the tongue, saliva or dental plaque . Mouthwashes are only effective against halitosis caused by intraoral factors . The principal causative agents of oral malodour are volatile sulphide compounds (VSCs), including hydrogen sulphide, methyl mercaptan and dimethyl sulphide . Data suggest that oral VSC levels correlate with the depth of periodontal pockets . Trials have shown that both mechanical oral care and mouthwash use can reduce halitosis levels . The majority of studies involving mouthwashes have investigated chlorhexidine and essential oil mouthwashes, although comparative studies are sparse.

J Zoo Wildl Med, 2001 Dec, 32(4), 430 - 5
Disposition of sulfadimethoxine in camels (Camelus dromedarius) following single intravenous and oral doses; Chatfield J et al.; Single-dose pharmacokinetics of sulfadimethoxine were determined in six adult camels (Camelus dromedarius) following administration of a mean dosage of 17.5 +/- 2.7 mg/kg both i.v . and p.o . Serial blood samples were collected through an indwelling jugular catheter intermittently for 5 days for both routes . Sulfadimethoxine was assayed using high-performance liquid chromatography . Serum drug concentration versus time data for each animal was subjected to linear regression, with the best-fit model selected based on residual analysis . The data fit best into a two-compartment open model, with first-order input for oral administration . For orally administered drug, mean maximum serum concentration of 19.3 +/- 1.7 microg/ml was reached at 11.41 +/- 2.59 hr, with an elimination rate constant of 0.09/hr +/- 0.05/hr and an elimination half-life of 11.7 +/- 3 hr . Mean peak serum concentration following i.v . administration was 223 +/- 48 microg/ml . Mean volume of distribution at steady state was 0.393 +/- 0.049 L/kg . Elimination rate constants differed with i.v . and oral administration, suggesting a flip-flop model . Oral bioavailability was 103% +/- 38% . Comparison of maximum serum concentrations to the microbial breakpoint concentration reported for sulfadimethoxine (512 microg/ml) suggests that the dose used in this study, 17.5 +/- 2.7 mg/kg, is insufficient for achieving therapeutic serum levels.

Environ Toxicol Chem, 2003 Jun, 22(6), 1221 - 8
Sorption of linear alkylbenzene sulfonate to soil components and effects on microbial iron reduction; Kristiansen IB et al.; When sewage sludge is applied to arable land, linear alkylbenzene sulfonate (LAS) is released into the environment . In soils, LAS has been shown to impede microbial processes, such as bacterial iron reduction . The aim of the present study was to quantify LAS adsorption and desorption to agricultural soils and iron oxides and relate this to the inhibition of microbial iron reduction . Two agricultural soils were used, namely, Askov (coarse sandy loam soil) and Lundgaard (coarse sandy soil) . In both soils, LAS inhibited microbial iron reduction even at low LAS concentrations with 10% effect concentrations of 6 to 7 and 26 to 32 mg LAS/kg dry-weight soil for Lundgaard and Askov soil, respectively . The sorption isotherms showed that sorption of LAS to iron oxides was 10 to 100 times stronger than sorption to the agricultural soils . Also, it appeared that at low LAS concentrations (< 10 mg/kg dry-wt soil), Lundgaard soil adsorbed approximately 10 times more LAS than Askov soil . Thus, the inhibitory effect of LAS on microbial iron reduction was highest in the Lundgaard soil, which exhibited both the strongest sorption and the lowest desorption of the two soils . A possible hypothesis to explain this correlation was that LAS toxicity toward bacterial iron reduction was, at least partly, caused by LAS adsorbed to iron oxides, which could interfere with transfer of electrons between the bacteria and their respiratory electron acceptor.

Environ Sci Technol, 2003 May 15, 37(10), 2159 - 65
Microbial mercury transformation in anoxic freshwater sediments under iron-reducing and other electron-accepting conditions; Warner KA et al.; Potential rates of microbial methylation of inorganic mercury (added as HgCl2) and degradation of methyl mercury (MeHg) (added as CH3HgCl) were investigated in anoxic sediments from the Mobile Alabama River Basin (MARB) dominated by different terminal electron-accepting processes (TEAPs) . Potential rates of methylation were comparable under methanogenic and sulfate-reducing conditions but suppressed under iron-reducing conditions, in slurries of freshwater wetland sediment In contrast, MeHg degradation rates were similar under all three TEAPs . Microbial Hg methylation and MeHg degradation were also investigated in surface sediment from three riverine sites, two of which had iron reduction and one sulfate reduction, as the dominant TEAP (as determined by 14C-acetate metabolism and other biogeochemical measurements) . Methylation was active in sulfate-reducing sediments of a tributary creek and suppressed in iron-reducing, sandy sediments from the open river, whereas MeHg degradation was active at all three sites . Although iron-reducing conditions often suppressed methylation, some methylation activity was observed in two out of three replicates from iron-reducing sediments collected near a dam . Given that MeHg degradation was consistently observed under all TEAPs, our results suggest that the net flux of MeHg from iron-reducing surface sediments may be suppressed (due to inhibition of gross MeHg production) compared to sediments supporting other TEAPs.

J Am Dent Assoc, 2003 May, 134(5), 569 - 74; quiz 631-2
Infection control: its evolution to the current standard precautions; Molinari JA; BACKGROUND: The use of appropriate infection control precautions to protect against transmission of bloodborne and other occupational microbial pathogens has become a routine component of health care provision . Evolution and revision of recommendations continues to be based on updated scientific information, as well as documented and inferred clinical applications of new knowledge . In addition, surveillance of occupational risks in medical treatment settings often has served as a basis for subsequent disease prevention recommendations for dental care . TYPES OF STUDIES REVIEWED: Guidelines designed to protect dental professionals and their patients have focused on bloodborne pathogens since the first published American Dental Association recommendations in the 1970s . Subsequent statements developed by the Centers for Disease Control and Prevention, the ADA and other organizations during the past 30 years also have addressed prevention of other infections, transmitted by either direct or indirect contact with a variety of potentially infectious body fluids . RESULTS: Review of the major features of these recommendations provides an appropriate framework to consider current guideline revisions . The success of long-standing universal precautions, or UP, against bloodborne infection has been augmented with the incorporation of body substance isolation, or BSI, practices into the infection control protocol designated "standard precautions." Combination of the major tenets of UP with the BSI systems routinely employed in acute care facilities affords all health care professionals the means of preventing a spectrum of bloodborne, respiratory, contact and other potential exposures during provision of patient care . CLINICAL IMPLICATIONS: As infection control recommendations for dentistry are updated this year, they undoubtedly will include guidelines expanding previous UP to provide expanded protection for dental professionals in the multiple types of nonacute treatment settings in which routine treatment is provided.

Reprod Nutr Dev, 2003 Jan-Feb, 43(1), 77 - 90
Intestinal function and body growth of broiler chickens on diets based on maize dried at different temperatures and supplemented with a microbial enzyme; Iji PA et al.; A study was conducted to evaluate the effects of varying drying temperature (Fresh, 85, 95 or 105 degrees C) on the nutritive value of maize and response of broiler chickens to diets based on such grain, and supplemented with a microbial enzyme (Avizyme 1500) . The chemical composition of the grain was affected by drying temperature . Starch and amylopectin contents were increased while there was a reduction in amylose content . These changes were expected to underlie the response of chicks to the diets . Total feed intake over 28 days was increased (P < 0.05) as a result of heat-treating the maize up to 95 degrees C . The final body weight of chicks on the diet based on fresh maize was improved (P < 0.05) by the microbial enzyme supplement (MES) . There was no effect of the enzyme supplement on body weight when assessed at earlier ages . Over the entire feeding period, feed conversion efficiency (FCE) declined (P < 0.001) with increasing oven temperature, regardless of the supplementation with the microbial enzyme . Body weight was influenced (P < 0.05) by the microbial enzyme only when assessed over the entire trial period . The weight of visceral organs, protein content and activities of pancreatic and jejunal digestive enzymes were unaffected by grain heat treatment or MES . The ileal digestibility of calcium was reduced (P < 0.001) on diets based on fresh maize and maize that was oven-dried at 105 degrees C . Heat-treatment also improved (P < 0.05) the ileal digestibility of phosphorus in chicks on the diets without MES . There were no effects of grain heat treatment or MES on the ileal digestibility of energy, protein, Ca and amino acids . The results indicate some variations in grain quality as a result of heat treatment but the differences were not significant enough to stimulate major responses to the MES . Further studies should examine samples from commercial drying processes or samples obtained from a closer simulation of commercial conditions, to arrive at more practical conclusions.

Lipids, 2003 Mar, 38(3), 241 - 54
Photochemical oxidation and autoxidation of chlorophyll phytyl side chain in senescent phytoplanktonic cells: potential sources of several acyclic isoprenoid compounds in the marine environment; Rontani JF et al.; Visible light-induced degradation of the chlorophyll phytyl side chain was studied in senescent cells of two phytoplanktonic strains (Skeletonema costatum and Thalassiosira weissflogii) . Particular attention was paid to the induction of autoxidation processes on the phytyl chain and its photoproducts by photochemically produced hydroperoxides . The combination of photochemical oxidation and autoxidation reactions resulted in the production of several acyclic isoprenoid compounds that have been unambiguously identified by comparison of their retention times and mass spectra with those of appropriate standards . Various mechanisms are proposed to explain the formation of these oxidation products . These processes appear to be potential sources of numerous oxidized acyclic isoprenoids that previously have been detected in lacustrine and marine environments . Some oxidation products newly described or whose presence in natural samples was never reported in the literature were then sought in particulate matter, sediment, and microbial mat samples . The results obtained supported the significance of photochemical oxidation and autoxidation of phytoplanktonic chlorophyll phytyl side chain in the marine environment.

Microb Ecol . 2003 Jun 6; {Epub ahead of print}
Viral Abundance and a High Proportion of Lysogens Suggest That Viruses Are Important Members of the Microbial Community in the Gulf of Trieste; Stopar D et al.; Epifluorescence microscopy and transmission electron microscopy were applied to study virioplankton community in the Gulf of Trieste (northern Adriatic Sea) . The total viral abundance was in a range between 2.5 x 109/L and 2.9 x 1010/L and was positively correlated with trophic status of the environment . Viruslike particles were significantly correlated with bacterial abundance in all samples studied . Correlations with other physicochemical or biological parameters were not significant . The data suggest that, because of the substantial fraction of tailed viruses present (26%), bacteriophages are an important component of the virioplankton community in the Gulf of Trieste . The abundance of viruslike particles in the seawater changed at hour intervals in a range from 1.3 x 109/L to 5.1 x 109/L . A significant fraction (71%) of the bacterial isolates was inducible in vitro by mitomycin C, and a high occurrence (51%) of lysogenic isolates with more than one phage morphotype present in the lysate was detected . The presence of lysogenic bacteria in the seawater was confirmed in situ with a mitomycin C induction experiment on the natural bacterial population . Results suggest that virioplankton is an abundant component of the microbial community in the Gulf of Trieste.

Allergol Immunopathol (Madr), 2003 May-Jun, 31(3), 125 - 38
{Adverse reactions to vaccines}; Eseverri JL et al.; Adverse reactions to vaccines are highly varied, ranging from mild local reactions to fatal outcomes . In the last few years many adverse reactions have been attributed to vaccines, often without justification . In agreement with the World Health Organization, these reactions can be classified as follows, depending on the cause: vaccination-induced reactions (due to an effect of the vaccine itself or to an idiosyncrasy); reactions due to errors in storage, manipulation and/or administration; and coincidental reactions (no causal relationship with the vaccine).Hypersensitivity reactions fall into six categories, depending on the causative agent: reactions due to some component of the infectious agent or one of its products; reactions due to adjuvants: aluminium hydroxide; reactions due to stabilizers: gelatin; reactions due to preservatives: thiomersal; reactions due to antibiotics: neomycin; and reactions due to a biological culture medium: chicken embryo cells.Allergic children should not be excluded from the normal vaccine calendar . Immunologically, allergic individuals are more susceptible to infection and to microbial and viral diseases, which often play an aggravating role . Rubella, whooping cough, and influenza usually exacerbate respiratory allergies . Non-vaccination carries a marked risk of contracting serious diseases such as poliomyelitis, tetanus, and diphtheria, etc.In a not too distant future, the techniques of genetic recombination and monoclonal antibody production will allow the creation of vaccines from organisms that cannot be cultivated in the laboratory or that produce small quantities of antigen . These techniques will also lead to identification of the antigens with the greatest immunogenic power and, consequently, to extremely pure vaccines.The adverse reactions to vaccines referred to our service account for between 0.59 % and 1.27 % of first visits in the last three years . We recorded a total of 48 adverse reactions to vaccines . Of these, 44 were attributed to the tetanus vaccine (92 %), 2 to the measles-mumps-rubella vaccine (4 %) and 2 to the meningitis A and C vaccine (4 %) . Clinical features consisted of urticaria (11 cases), urticaria with angioedema (7 cases), pseudo-shock (5 cases), fever and urticaria (4 cases), local reactions (4 cases), persistent crying with exanthema (3 cases), giant local reactions with angioedema of the limb (3 cases), anaphylaxis (3 cases), fever > 39.5 C (2 cases), bronchospasm (1 case), and severe atopic dermatitis (1 case).A regimen of hyposensitization to tetanus toxoid was required in 20 patients (45 %); in three, this could not be completed due to generalized urticaria but all the patients presented protective titers with diluted vaccine.

Appl Microbiol Biotechnol, 2003 Sep, 62(4), 430 - 5 Epub 2003 May 29.
Development and characteristics of phosphorus-accumulating microbial granules in sequencing batch reactors; Lin YM et al.; Phosphorus (P)-accumulating microbial granules were developed at different substrate P/chemical oxygen demand (COD) ratios in the range of 1/100 to 10/100 by weight in sequencing batch reactors . The soluble COD and PO4-P profiles showed that the granules had typical P-accumulating characteristics, with concomitant uptake of soluble organic carbon and the release of phosphate in the anaerobic stage, followed by rapid phosphate uptake in the aerobic stage . The size of P-accumulating granules exhibited a decreasing trend with the increase in substrate P/COD ratio, while the structure of the granules became more compact and denser as the substrate P/COD ratio increased . The P uptake by granules fell within the range of 1.9% to 9.3% by weight, which is comparable with uptake obtained in conventional enhanced biological phosphorus removal (EBPR) processes . It was further found that low aerobic respirometric activity of granules in terms of specific oxygen utilization rate favors P uptake by granules . The results presented would be useful for the further development of a novel granule-based EBPR technology.

J Microbiol Methods, 2003 Aug, 54(2), 257 - 67
Analysis of the microbial functional diversity within water-stressed soil communities by flow cytometric analysis and CTC+ cell sorting; Whiteley AS et al.; Total and active cell counts within soil samples were determined by culture-independent methods using flow cytometry and preparative Nycodenz gradient centrifugation . Whole cells were purified from soil cores and total extractable cell counts assessed by SYBR Green II fluorescence, while active cell counts were determined by 5-cyano-2,3-ditolyl tetrazolium chloride reduction (CTC+ cells) . Parallel microcosms, maintained at either field water capacity or subjected to drying, indicated that the total extractable cell count remained between 10(8) and 10(9) g(-1) (dry weight) . In contrast, the CTC+ active count fell threefold in dried microcosms (6% of total cell count) when compared to wetted microcosms (18% of total cell count) . Specifically, these data highlighted an overall deactivation of microbial biomass during water stress, with 16S rDNA analyses of flow-sorted CTC+ cells demonstrating shifts within the active diversity . Flow cytometry coupled with cell purification techniques represents a significant tool for operationally defining an active and redundant microbial component within soil communities and is demonstrated during water stress.

Int J Parasitol, 2003 May, 33(5-6), 641 - 53
T cell epitope identification for bovine vaccines: an epitope mapping method for BoLA A-11; De Groot AS et al.; T cell responses play an important role in immunity to parasites and other microbial agents of infectious diseases, therefore a number of T cell-directed vaccines are in development . Computer-driven algorithms that facilitate the discovery of T cell epitopes from protein and genome sequences are now being used to accelerate preclinical studies of human vaccines . Similar tools are not yet available for predicting T cell epitopes for animal vaccines, but there may be sufficient data available to begin the process of compiling the algorithms . We describe the construction of a novel mathematical 'matrix' that describes the properties of bovine major histocompatibility complex (BoLA) system antigen (BoLA) A-11 peptide ligands, developed for use with EpiMatrix, an existing T cell epitope-mapping algorithm . An alternative means of developing BoLA matrices, using the pocket profile method, is also discussed . Matrices such as the one described here may be used to develop T cell epitope-mapping tools for cattle and other ruminants . Epitope-mapping algorithms offer a significant advantage over other methods of epitope selection, such as the screening of synthetic overlapping peptides, because high throughput screening can be performed in silico, followed by ex vivo confirmatory studies . Furthermore, using epitope-mapping algorithms, putative T cell epitopes can be derived directly from genomic sequences, allowing researchers to circumvent labor-intensive cloning steps in the genome-to-vaccine discovery pathway.

J Dairy Sci, 2003 May, 86(5), 1716 - 21
Factors affecting application of milk allantoin as an estimator of microbial protein flow to the duodenum under commercial conditions; Schager WM et al.; Three experiments were conducted to determine the effect of diet change, milk sampling technique, and bovine somatotropin (bST) on allantoin output in milk and the use of allantoin as a practical, noninvasive method for estimating microbial protein flow in dairy cattle . In experiment 1, four lactating Holstein cows were used in a 2 x 2 Latin square design with two treatments (ratio of forage to concentrate) and two periods . In experiment 2, six Holstein cows were used in a completely randomized design, and milk was collected by 1) a strip sample collected immediately before milking, 2) a strip sample collected 3 min from start of milking, and 3) a composite sample taken with an autosampler . In experiment three, 10 cows were used in a randomized block design to determine the effect of bST on milk allantoin . Milk samples were taken daily for 21 d, 7 d before, and 14 d after bST administration . In experiment 1, allantoin output (mmol/d) was significantly greater for cows fed the higher ratio of concentrate to forage, and there was a significant change in the amount of allantoin in milk 12 h (first subsequent milking) after a diet change . There was no difference in milk yield or dry matter intake between treatments . In experiment 2, no difference was detected in milk allantoin concentration among the three sampling methods . In experiment 3, milk yield, allantoin concentration, and total allantoin output was significantly increased after bST administration even though dry matter intake (DMI) remained unchanged . During the first 14 d following bST administration, estimates of microbial protein production derived from milk allantoin may be inaccurate due to increased milk production without an increase in DMI.

J Dairy Sci, 2003 May, 86(5), 1616 - 31
Effect of CO2 addition to raw milk on proteolysis and lipolysis at 4 degrees C; Ma Y et al.; Fresh raw milks, with low (3.1 x 10(4) cell/ml) and high (1.1 x 10(6) cells/ml) somatic cell count (SCC), were standardized to 3.25% fat, and from each a preserved (with 0.02% potassium dichromate) and an unpreserved portion were prepared . Subsamples of each portion were carbonated to contain 0 (control, pH 6.9) and 1500 (pH 6.2) ppm added CO2, and HCl acidified to pH 6.2 Milk pH was measured at 4 degrees C . For the preserved low- and high-SCC milks, two additional carbonation levels, 500 (pH 6.5) and 1000 (pH 6.3) ppm, were prepared . Milks were stored at 4 degrees C and analyzed on d 0, 7, 14, and 21 for microbial count, proteolysis, and lipolysis . The addition of 1500 ppm CO2, but not HCl, effectively delayed microbial growth at 4 degrees C . In general, in both the low- and high-SCC unpreserved milks, there was more proteolysis and lipolysis in control and HCl acidified milks than in milk with 1500 ppm added CO2 . Higher levels of proteolysis and lipolysis in the unpreserved milks without added CO2 were related to higher bacteria counts in those milks . In preserved low- and high-SCC milks, microbial growth was inhibited, and proteolysis and lipolysis were caused by endogenous milk enzymes (e.g., plasmin and lipoprotein lipase) . Compared with control, both milk with 1500 ppm added CO2 and milk with HCl acidification had less proteolysis . The effect of carbonation or acidification with HCl on proteolysis in preserved milks was more pronounced in the high SCC milk, probably due to its high endogenous protease activity . Plasmin is an alkaline protease and the reduction in milk pH by added CO2 or HCl explained the reduction in proteolysis . No effect of carbonation or acidification of milk on lipolysis was observed in the preserved low- and high-SCC milks . The CO2 addition to raw milk decreased proteolysis via at least two mechanisms: the reduction of microbial proteases due to a reduced microbial growth and the possible reduction of endogenous protease activity due to a lower milk pH . The effect of CO2 on lipolysis was mostly due to a reduced microbial growth . High-quality raw milk (i.e., low initial bacteria count and low SCC) with 1500 ppm added CO2 can be stored at 4 degrees C for 14 d with minimal proteolysis and lipolysis and with standard plate count < 3 x 10(5) cfu/ml.

J Dairy Sci, 2003 May, 86(5), 1601 - 7
Sensory threshold of off-flavors caused by proteolysis and lipolysis in milk; Santos MV et al.; The objective of this study was to determine the sensory threshold of off-flavor caused by lipolysis in 2% fat milk and to establish the relationship between increased proteolytic activity in milk and the detection of bitter off-flavor . Homogenized raw milk was held at room temperature for 100 min to allow the native milk lipase to release free fatty acids from the triglycerides . Low and high lipolysis pasteurized milk containing 2% fat were blended together in varying amounts to create a series of six milks with increasing free fatty acid (FFA) concentration for sensory evaluation . Sensory threshold for lipolysis in 2% fat milk was determined by ascending forced-choice procedure, with a series of triangle tests in four sessions with 25 panelists in each session . The group best estimated threshold was the geometric mean of the individual thresholds within each of four panel sessions . The geometric mean best estimated detection thresholds for off-flavors caused by lipolysis in 2% fat milk carried out by native milk lipases were 0.320, 0.322, 0.351, and 0.316 meq of FFA/kg milk for panels 1 to 4, respectively . One third of the panelists detected an off-flavor at or below 0.250 meq of FFA/kg milk . To establish the relationship between proteolysis and detection of off-flavor in pasteurized skim milk, 2800 ppm of CO2 were added to pasteurized skim milk, and it was stored for 27 d at 6 degrees C . Another portion of the same milk was frozen on d 1 at -40 degrees C for use as a low proteolysis portion of the same milk . Decrease in casein as a percentage of true protein (CN/TP) was used as an index of proteolysis . After 27 d at 6 degrees C the milk had a decrease in CN/TP of 4.76% and a standard plate count of 430 cfu/ml . The novel approach of storing milk at 6 degrees C for 27 d with added CO2 blocked microbial growth but allowed proteolytic degradation by milk enzymes to proceed . Before sensory analysis, CO2 was removed by vacuum from the high proteolysis milk and the low proteolysis milk was given the same heat and vacuum . Two triangle tests were performed to determine whether panelists could detect off-flavors caused by proteolysis in milk . The threshold detection of off-flavor in skim milk produced by the action of native milk proteases was less than a decrease of CN/TP of 4.76%, but this value is probably near the threshold.

Nat Biotechnol, 2003 Jul, 21(7), 796 - 802 Epub 2003 Jun 01.
Engineering a mevalonate pathway in Escherichia coli for production of terpenoids; Martin VJ et al.; Isoprenoids are the most numerous and structurally diverse family of natural products . Terpenoids, a class of isoprenoids often isolated from plants, are used as commercial flavor and fragrance compounds and antimalarial or anticancer drugs . Because plant tissue extractions typically yield low terpenoid concentrations, we sought an alternative method to produce high-value terpenoid compounds, such as the antimalarial drug artemisinin, in a microbial host . We engineered the expression of a synthetic amorpha-4,11-diene synthase gene and the mevalonate isoprenoid pathway from Saccharomyces cerevisiae in Escherichia coli . Concentrations of amorphadiene, the sesquiterpene olefin precursor to artemisinin, reached 24 microg caryophyllene equivalent/ml . Because isopentenyl and dimethylallyl pyrophosphates are the universal precursors to all isoprenoids, the strains developed in this study can serve as platform hosts for the production of any terpenoid compound for which a terpene synthase gene is available.

Environ Sci Technol, 2003 May 1, 37(9), 1705 - 12
Bacterial formation of tooeleite and mixed arsenic(III) or arsenic(V)-iron(III) gels in the Carnoulès acid mine drainage, France . A XANES, XRD, and SEM study; Morin G et al.; The oxidation of Fe(II) in acid mine drainage (AMD) leads to the precipitation of Fe(III) compounds which may incorporate toxic elements, such as arsenic (As), within their structure or adsorb them at their surface, thus limiting their mobility . The present work provides evidence for spatial and seasonal variations of microbial activity that influence arsenite oxidation and As immobilization in the heavily contaminated AMD from the Carnoules mine, Gard, France ({As III} = 80 to 280 mg x L(-1) in the acidic spring draining the waste-pile) . In the first tens of meters of the AMD, the rapid oxidation of Fe(II) leads to the coprecipitation of large amounts of As with Fe(III) in bacterial mats . XRD, XANES, and SEM analyses of sediments and stromatolite samples revealed the unusual formation of As(III)-rich compounds, especially nanocrystalline tooeleite, Fe6(AsO3)4(SO4)(OH)4 x 4H2O, a rare ferric arsenite sulfate oxy-hydroxide mineral, together with XRD-amorphous mixed As(III)/As(V)-Fe(III) oxy-hydroxide compounds . In the wet season, the suspended sediments of the upstream zone essentially consist of tooeleite associated with am-As(III)-Fe(III) oxy-hydroxides, while am-As(V)-Fe(III) oxy-hydroxides, having As:Fe molar ratios as high as 0.6-0.8, dominate in the dry season . Comparing natural and bioassay samples revealed that the formation of As(III)-rich compounds in the wet season may be related to the metabolic activity of bacterial strains able to oxidize Fe(II) but not As(III) . One of these strains, having an Acidithiobacillus ferrooxidans genotype, has been isolated from the Carnoules AMD . In contrast, the formation of As(V)-rich compounds in the dry season can be related to both biotic and abiotic oxidation of As(III) to As(V) . Some Thiomonas strains isolated from the Carnoules AMD were shown to be able to catalyze the oxidation of As(III) to As(V) in solution . Therefore, they can promote the formation of mixed As(V)-Fe(III) oxy-hydroxides, provided enough Fe(II) oxidizes . These results yield a better understanding of natural processes at this site and may help in designing efficient As-removal processes.

J Vet Intern Med, 2003 May-Jun, 17(3), 273 - 81
Adjuvants in veterinary vaccines: modes of action and adverse effects; Spickler AR et al.; Vaccine adjuvants are chemicals, microbial components, or mammalian proteins that enhance the immune response to vaccine antigens . Interest in reducing vaccine-related adverse effects and inducing specific types of immunity has led to the development of numerous new adjuvants . Adjuvants in development or in experimental and commercial vaccines include aluminum salts (alum), oil emulsions, saponins, immune-stimulating complexes (ISCOMs), liposomes, microparticles, nonionic block copolymers, derivatized polysaccharides, cytokines, and a wide variety of bacterial derivatives . The mechanisms of action of these diverse compounds vary, as does their induction of cell-mediated and antibody responses . Factors influencing the selection of an adjuvant include animal species, specific pathogen, vaccine antigen, route of immunization, and type of immunity needed.

Toxicol Sci, 2003 Jul, 74(1), 93 - 102 Epub 2003 May 28.
Role of IL-1(beta) in endotoxin potentiation of deoxynivalenol-induced corticosterone response and leukocyte apoptosis in mice; Islam Z et al.; Endotoxin (lipopolysaccharide, LPS) and the trichothecenes are microbial toxins that are frequently encountered in food and the environment . Coexposure to LPS and the trichothecene deoxynivalenol (DON, vomitoxin) induces corticosterone-dependent apoptosis in thymus, Peyer's patches, and bone marrow in mice . The purpose of this study was to test the hypothesis that interleukin-1beta (IL-1beta) plays a central role in corticosterone induction and subsequent leukocyte apoptosis in this model . Coexposure to LPS (0.1 mg/kg, ip) plus DON (12.5 mg/kg, po) was found to significantly upregulate splenic IL-1beta mRNA and IL-1beta protein expression in B6C3F1 mice, as compared to treatments with vehicle or either of the toxins alone . B6.129S7-IL1r1tm1Imx mice, which are functionally deficient for the IL-1 receptor 1, produced significantly less corticosterone upon coexposure to LPS plus DON than did corresponding wild-type (WT) C57BL/6J mice . Consistent with these findings, IL-1 receptor 1-deficient mice were recalcitrant to apoptosis induction in leukocytes as determined by assessment of DNA fragmentation assay and flow cytometry . Furthermore, intraperitoneal injection of IL-1 receptor antagonist (100 microgram/mouse, twice at 3 h intervals) in B6C3F1 mice significantly inhibited LPS plus DON-induced increases in plasma corticosterone, as well as apoptosis in thymus, Peyer's patches, and bone marrow . To confirm IL-1beta's capacity to induce apoptosis, B6C3F1 mice were injected with the cytokine (500 ng/mouse, ip) three times at 2 h intervals, and then corticosterone and apoptosis were monitored . Plasma corticosterone levels and thymus and Peyer's patch apoptosis in IL-1beta-injected mice were significantly higher at 12 h than in control mice . Plasma adrenocorticotropic hormone (ACTH) levels in LPS plus DON-treated B6C3F1 mice did not correlate with the induction of plasma corticosterone or leukocyte apoptosis . Taken together, the results indicate that IL-1beta is an important mediator of LPS plus DON-induced corticosterone and subsequent leukocyte apoptosis and, furthermore, this cytokine possibly acts through an ACTH-independent mechanism.

Proc Natl Acad Sci U S A, 2003 Jun 10, 100(12), 7027 - 32 Epub 2003 May 28.
Rapid biosynthesis of N-linolenoyl-L-glutamine, an elicitor of plant volatiles, by membrane-associated enzyme(s) in Manduca sexta; Lait CG et al.; In response to elicitors in the oral secretions of caterpillars, plants produce and release volatile chemicals that attract predators and parasitoids of the caterpillar while it feeds . The most prevalent elicitors are fatty acid amides consisting of 18-carbon polyunsaturated fatty acids coupled with l-glutamine . We demonstrate rapid CoA- and ATP-independent in vitro biosynthesis of the fatty acid amide elicitor, N-linolenoyl-l-glutamine, by microsomal fractions of several alimentary tissues in Manduca sexta . N-linolenoyl-l-glutamine is a structural analog of several other elicitors including volicitin, the first fatty acid amide elicitor identified in caterpillars . The enzyme(s) that catalyzed biosynthesis of N-linolenoyl-l-glutamine was localized within the integral membrane protein fraction extracted from microsomes by Triton X-114 detergent phase partitioning and had maximum activity at alkaline pH . We found no evidence suggesting microbial or tissue-independent biosynthesis of N-linolenoyl-l-glutamine in M . sexta . The in vitro biosynthesis of N-linolenoyl-l-glutamine by membrane-associated enzyme(s) in M . sexta represents direct evidence of fatty acid amide synthesis by caterpillar tissues.

EMBO J, 2003 Jun 2, 22(11), 2546 - 51
Dendritic cell regulation of immune responses: a new role for interleukin 2 at the intersection of innate and adaptive immunity; Granucci F et al.; Dendritic cells are professional antigen-presenting cells able to initiate innate and adaptive immune responses against invading pathogens . In response to external stimuli dendritic cells undergo a complete genetic reprogramming that allows them to become, soon after activation, natural killer cell activators and subsequently T cell stimulators . The recent observation that dendritic cells produce interleukin 2 following microbial stimulation opens new possibilities for understanding the efficiency of dendritic cells in regulating immune system functions . This review discusses how dendritic cells control natural killer, T- and B-cell responses and the relevance of interleukin 2 in these processes.

Biochem Soc Trans, 2003 Jun, 31(Pt 3), 637 - 42
Role of adapters in Toll-like receptor signalling; Akira S et al.; Toll-like receptors (TLRs) play a critical role in the detection of invading pathogens within the body and the subsequent immune response . Individual TLRs recognize distinct microbial components . The TLRs are a type 1 transmembrane receptor that possess an extracellular leucine-rich repeat domain and cytoplasmic domain homologous with that of the interleukin 1 receptor (IL-1R) family . Upon stimulation, TLR recruits the IL-1R-associated kinase (IRAK) via the adapter MyD88, ultimately leading to the activation of nuclear factor-kappaB . Cytokine production in response to all TLR ligands is completely abolished in MyD88-deficient cells, indicating that MyD88 is an essential signalling molecule shared among members of the IL-1R/Toll family . However, several novel adaptor molecules have recently been identified . Evidence is now accumulating showing that differential utilization of these adaptors may activate overlapping as well as distinct signalling pathways, and ultimately give rise to distinct biological effects exerted by individual TLR family members.

Biochem Soc Trans, 2003 Jun, 31(Pt 3), 607 - 10
Targeting metabolic pathways in microbial pathogens: oxidative stress and anti-folate drug resistance in trypanosomatids; Hunter WN et al.; The large quantity of genomic, biochemical and metabolic data on microbial pathogens provides information that helps us to select biological problems of interest and to identify targets, metabolic pathways or constituent enzymes, for therapeutic intervention . One area of potential use in developing novel anti-parasitic agents concerns the regulation of oxidative stress, and we have targeted the trypanothione peroxidase pathway in this respect . In order to characterize this pathway, we have determined crystal structures for each of its components, and are now studying enzyme-ligand complexes of the first enzyme, trypanothione reductase . Also with regard to trypanosomatids, a question that arose was: why do anti-folates not provide useful therapies? The enzyme pteridine reductase has been shown to contribute to anti-folate drug resistance, and we have determined the enzyme structure and mechanism to understand this aspect of drug resistance.

Biochem Soc Trans, 2003 Jun, 31(Pt 3), 537 - 42
Structure and reactivity in the non-mevalonate pathway of isoprenoid biosynthesis; Hunter WN et al.; The function, structure and mechanism of two Escherichia coli enzymes involved in the non-mevalonate route of isoprenoid biosynthesis, 2C-methyl-D-erythritol 4-phosphate cytidylyltransferase and 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, are reviewed . Comparisons of each with enzymes from microbial pathogens highlight important conservation of sequence suggestive of similarities in secondary structure, subunit folds, quaternary structure and active sites . Since both enzymes are validated drug targets, the models provide templates for structure-based design of anti-microbial agents targeting a number of serious human diseases.

J Anim Sci, 2003 May, 81(5), 1332 - 47
Synchrony of nutrient supply to the rumen and dietary energy source and their effects on the growth and metabolism of lambs; Richardson JM et al.; The objective of the current series of experiments was to assess the effects of dietary synchrony of OM and N supply to the rumen, achieved by altering the sequence of feeding individual ingredients and in diets with different energy sources, on the metabolism and performance of growing lambs . In Exp . 1, the in situ degradability coefficients of OM and N were determined for five feed ingredients and subsequently was used to formulate two diets, based either on barley or sugar beet pulp, to have a similar predicted nutrient content . Within each diet, specific ingredients were shifted between the 0900 and 1600 feeding to provide either a synchronous, intermediate, or asynchronous supply of OM and N to the rumen . In Exp . 2, these diets were fed at a restricted level to 48 growing lambs with an initial live weight of 25.1 +/- 4.22 kg and a slaughter weight of 41.4 +/- 1.94 kg . There was no significant effect of dietary treatment on live weight gain or feed conversion efficiency . Lambs fed the synchronous diets deposited more kidney knob and channel fat than lambs on the asynchronous or intermediate diets (P < 0.05), whereas lambs fed the barley-based diets deposited more carcass (P < 0.05) and noncarcass (P < 0.001) fat than lambs on the sugar beet-based diets . Lambs fed the asynchronous diets retained less energy over the course of the experiment than lambs on the intermediate or synchronous diets (P < 0.05), and had a lower energy efficiency (0.079, 0.097, and 0.093 MJ retained/ MJ of intake, respectively, P < 0.05) . Lambs fed the barley-based diets retained more energy than lambs on the sugar beet-based (P < 0.001) and had a higher energy balance (0.095 vs . 0.084 MJ retained/MJ intake, respectively; P < 0.01) . Plasma ammonia concentrations mirrored ruminal ammonia concentrations on the barley-based diets, but not sugar beet-based diets . In Exp . 3, lambs fed the sugar beet-based diets had a higher digestibility of OM and NDF (P < 0.001) . By contrast, lambs on the barley-based diets had a higher level of purine derivative excretion and microbial N production (P < 0.001) . The results indicate that neither dietary synchrony nor energy source significantly influenced growth rate . However, both the asynchronous and sugar beet pulp-based diets resulted in a lower efficiency of dietary energy use, and the avoidance of asynchronous patterns of nutrient release within the rumen can improve energy efficiency in growing lambs.

Eye Contact Lens, 2003 Jan, 29(1 Suppl), S145 - 6; discussion S166, S192-4
Why daily wear is still better than extended wear; Weissman B et al.; Among the many problems complicating contact lens wear, microbial keratitis is of most concern because of its potential for substantial morbidity . Three decades of basic and clinical research suggest that risk factors include poor care compliance and extended wear through one or multiple sleep cycles . Many believe the latter problem is caused in part or in whole to contact lens-induced hypoxia . New contact lenses, both rigid and soft, have been developed that allow oxygen delivery equivalent to the noncontact lens state, under open-eye conditions and close to the same even for closed-eye conditions . But will such lenses reduce the risk for microbial keratitis? The authors argue that until such a conclusion is reached through clinical trials, the question remains in doubt.

Eye Contact Lens, 2003 Jan, 29(1 Suppl), S131 - 4; discussion S143-4, S192-4
Microbial keratitis and vision loss with contact lenses; Holden BA et al.; PURPOSE: Microbial keratitis is the only sight-threatening adverse event that occurs with contact lens wear . This article gives a preliminary estimation of the incidence of microbial keratitis and vision loss with continuous-wear contact lenses made from highly oxygen permeable (Dk) materials . METHODS: The most up-to-date data available on microbial keratitis and vision loss are collected from a range of sources including industry, private practice, and publications and is reviewed . RESULTS: There have been 16 cases of microbial keratitis with high-Dk silicone hydrogel lenses . Of the 13 where data are available, none have lost two or more lines of best-corrected visual acuity (BCVA) . CONCLUSION: First approximation indicates that the incidence of microbial keratitis with high-Dk silicone hydrogel lenses may be lower than the incidence with low-Dk soft lenses during extended wear . The rate of loss of more than two lines of BCVA is low in patients that develop microbial keratitis with low- and high-Dk soft lenses.

Eye Contact Lens, 2003 Jan, 29(1 Suppl), S85 - 9; discussion S115-8, S192-4
Contact lens-related microbial keratitis: what can epidemiologic studies tell us?
Stapleton F.
Since the publication of large-scale population based studies to estimate the risks of contact lens-related microbial keratitis, the lens types and modes of wear have changed considerably, with the introduction of silicone hydrogel contact lenses for continuous wear of up to 30 nights and daily disposable contact lenses . It is time to consider epidemiologic studies to estimate the absolute and relative risk of microbial keratitis associated with these new exposures . This article summarizes current knowledge of the estimates and determinants of risk associated with re-useable hydrogel lenses and discusses study design considerations for future studies . The absolute risk of microbial keratitis to the wearer has been remarkably stable since 1989 . Risk factors consistently associated with increased risk have included overnight wear, the duration of continuous overnight wear, lower socioeconomic class, smoking, and lens hygiene practice, specifically in daily wear lenses . Men seem to be at a slightly higher risk compared to women . Factors such as the lens age, duration of wear or wear history, and time since the last aftercare visit do not seem to modulate risk . Outstanding questions include whether the risk has changed over time, whether the risk is modified with daily disposable or silicone hydrogel wear, whether the risk is different for 6 or 30 nights of continuous wear, or whether the severity of the disease or spectrum of causative organisms has been modified with new lens types . Different study designs have been used to derive risk data in contact lens wear, including cohort, surveillance, and case-control designs . An appreciation of the advantages and limitations of each of these approaches will assist in the planning of future studies to address these outstanding questions.

Eye Contact Lens, 2003 Jan, 29(1 Suppl), S60 - 2; discussion S83-4, S192-4
Differential diagnosis of microbial keratitis and contact lens-induced peripheral ulcer; Aasuri MK et al.; Differentiating a contact lens-induced peripheral ulcer (CLPU) from early stage microbial keratitis (MK) is primarily based on clinical judgment rather than on microbiologic or histopathologic investigations . For this reason, tests do not provide valuable information at the early stages in the clinical course of MK . Whereas in gross terms, the clinical picture of MK is more acute and severe than CLPU, clinical features of the two can overlap, sometimes resulting in errors of judgment and mismanagement . This article provides clinical clues that help distinguish the two conditions . In addition, a scoring system has been devised for MK and CLPU . Microbial keratitis (MK) is a dreaded complication for contact lens wearers . Although the risk is small, the large population of contact lens (CL) users have made CL wear a major predisposing factor for corneal infection . The reported incidence of MK among CL wearers may be inaccurate because it can be easily confused with its sterile counter part, contact lens-induced peripheral ulcer (CLPU) . An accurate initial clinical impression is critical in avoiding mismanagement of these conditions . Clinical differentiation between infected and sterile corneal infiltrates in CL wearers has been addressed in the literature . We suggest a scheme for distinguishing early stage MK from CLPU.

Eye Contact Lens, 2003 Jan, 29(1 Suppl), S14 - 6; discussion S26-9, S192-4
Effects of daily and overnight wear of hyper-oxygen transmissible rigid and silicone hydrogel lenses on bacterial binding to the corneal epithelium: 13-month clinical trials; Cavanagh HD et al.; PURPOSE: For 14 years, the U . S . Food and Drug Administration (FDA) and eye care practitioners have strongly discouraged patients from sleeping in contact lenses . In the past 9 months however, the FDA has approved three new hyper-oxygen transmissible lenses for up to 30-night extended wear . Is this a great advance or another clinical triumph of hope over experience? What should the public know? What should patients do? METHODS: Our research group has studied all three new lenses in prospective, randomized, masked, parallel clinical trials in a single center . As an outcome measure, we looked at whether lens wear caused more bacterial binding to surface corneal cells . RESULTS: Compared with conventional lens use, the new lenses caused no or only small increases in bacterial binding in either daily or extended wear . Furthermore, the increases seen stratified with known infection risks by both lens type (hard or soft) and wearing schedule . Indeed, early epidemiologic reports indicate that this new generation of lenses may reduce lens-related microbial infection risks by 10- to 40-fold . CONCLUSION: This represents a true clinical paradigm shift of the first magnitude in safety of contact lens wear . Taken together, this data suggest that patients will soon replace their current, conventional lenses with this new generation of materials for any schedule of wear.

Curr Opin Mol Ther, 2003 Apr, 5(2), 98 - 106
Recent advances in immunostimulatory CpG oligonucleotides; Rothenfusser S et al.; The vertebrate immune system has evolved a mechanism to detect CpG motifs within microbial DNA (CpG DNA) . Synthetic oligonucleotides containing CpG motifs (CpG ODNs) are potent immunomodulatory molecules and outstanding vaccine adjuvants . A number of recent findings have greatly improved our understanding of the biology of CpG DNA, and the immunological effects of CpG DNA are now recognized to be distinct in mouse and human . The plasmacytoid dendritic cell (PDC) was identified to play a pivotal role in mediating CpG-induced immune responses . So far, the B-cell is the only other immune cell subset in humans besides the PDC, equipped with the toll-like receptor-9 to detect CpG motifs . The information on these two prime CpG-sensitive cells has allowed the identification of novel CpG ODNs with distinct functional activity . Together with exciting contributions from animal studies, the way seems to be paved for the successful clinical development of this novel class of molecular therapeutics.

FEMS Microbiol Lett, 2003 May 28, 222(2), 183 - 6
Microbial hydroxylation of progesterone with Acremonium strictum; Faramarzi MA et al.; Microbial hydroxylation of progesterone occurred in the culture of Acremonium strictum PTCC 5282 to produce two hydroxylated pregnene-like steroids . The metabolites were purified and characterized using spectroscopic methods and identified as 15alpha-hydroxyprogesterone and 15alpha-hydroxydeoxycorticosterone.

J Agric Food Chem, 2003 Jun 4, 51(12), 3604 - 8
Sorption-desorption of two "aged" sulfonylaminocarbonyltriazolinone herbicide metabolites in soil; Koskinen WC et al.; Aging (herbicide-soil contact time) has been shown to significantly affect the sorption-desorption characteristics of many herbicides, which in turn can affect the availability of the herbicide for transport, plant uptake, and microbial degradation . In contrast, very little work in this area has been done on herbicide metabolites in soil . The objective of this study was to characterize the sorption-desorption of sulfonylaminocarbonyltriazolinone herbicide metabolites incubated in soils at different soil moisture potentials . A benzenesulfonamide metabolite and a triazolinone metabolite from sulfonylaminocarbonyltriazolinone herbicides were incubated in clay loam and loamy sand soils for up to 12 weeks at -33 kPa and at water contents equivalent to 50 and 75% of that at -33 kPa . Chemicals were extracted sequentially with 0.01 N CaCl(2) and aqueous acetonitrile (solution and sorbed phase concentrations, respectively), and apparent sorption coefficients (K(d,app)) were calculated . Sufficient metabolite remained during the incubation (>55% of applied) to allow determination of the coefficients . The initial aging period (2 weeks after application) significantly increased sorption as indicated by increased K(d,app) values for the chemical remaining, after which they remained relatively constant . After 12 weeks of incubation at -33 kPa, K(d,app) values for benzenesulfonamide and triazolinone increased by a factor of 3.5 in the clay loam soil and by a factor of 5.9 in the loamy sand as compared to freshly treated soils . There was no effect of moisture potential on aged apparent K(d,app) values . These data show the importance of characterization of sorption-desorption in aged herbicide residues, including metabolites, in soil, particularly in the case of prediction of herbicide residue transport in soil . In this case, potential transport of sulfonylaminocarbonyltriazolinone herbicide metabolites would be overpredicted if freshly treated soil K(d) values were used to predict transport.

Cytotherapy, 2003, 5(2), 147 - 52
Endogenous microbial contamination of cultured autologous preparations in trials of cancer immunotherapy; Padley DJ et al.; BACKGROUND: Standardization of the manufacturing and processing of cellular immunotherapy products is necessary to ensure patient safety, establish efficacy, and demonstrate potency . Recognition of the autologous donor as a likely source of microbial contamination of cellular immunotherapy products may improve patient care and reduce expense to the laboratory . METHODS: Data on 243 immunotherapy products manufactured in the authors' institution between December 1997 and June 2001 were retrospectively reviewed . Also reviewed were the case reports of four patients whose autologous immunotherapy products were contaminated . RESULTS: Twenty-five (10%) of the 243 immunotherapy products processed were positive on one or more tests for microbial contamination . In six (24%) of the products, the source of microbial contamination was the autologous donor . In 17 of the remaining 19 products, test results were judged to be false-positive . DISCUSSION: The unique processing techniques and stringent controls involved in the manufacture of cellular immunotherapy products may result in changes in the sources of microbial contamination routinely encountered . The identification of the autologous donor as a potential source of the microbial contamination of the product may assist the clinician and the laboratory in troubleshooting products with positive results on microbial sterility testing . Also, the number of false-positive results in this study indicates that further research is needed to maximize the specificity of testing while maintaining the present high sensitivity.

Extremophiles, 2003 Jun, 7(3), 177 - 83 Epub 2003 Jan 30.
Molecular identification of bacteria and Eukarya inhabiting an Antarctic cryoconite hole; Christner BC et al.; Inhabitants of a cryoconite hole formed in the Canada Glacier in the McMurdo Dry Valley region of Antarctica have been isolated and identified by small subunit (16S/18S) rDNA amplification, cloning, and sequencing . The sequences obtained revealed the presence of members of eight bacterial lineages (Acidobacterium, Actinobacteria, Cyanobacteria, Cytophagales, Gemmimonas, Planctomycetes, Proteobacteria, and Verrucomicrobia) and metazoan (nematode, tardigrade, and rotifer), truffle (Choiromyces), ciliate (Spathidium), and green algal (Pleurastrium) Eukarya . Bacterial recovery was approximately 20-fold higher at 4 degrees C and 15 degrees C than at 22 degrees C, and obligately psychrophilic bacteria were identified and isolated . Several of the rDNA molecules amplified from isolates and directly from cryoconite DNA preparations had sequences similar to rDNA molecules of species present in adjacent lake ice and microbial mat environments . This cryoconite hole community was therefore most likely seeded by particulates from these local environments . Cryoconite holes may serve as biological refuges that, on glacial melting, can repopulate the local environments.

J Hosp Infect, 2003 May, 54(1), 2 - 9
Lack of influence of body exhaust gowns on aerobic bacterial surface counts in a mixed-ventilation operating theatre . A study of 62 hip arthroplasties; Pasquarella C et al.; Aerobic bacterial surface contamination was studied with and without the use of body exhaust gowns in an operating room equipped with mixed/turbulent ventilation and separate operating and anaesthetic areas during 62 hip joint arthroplasties . In 31 operations conventional gowns were used, and 31 were performed with body exhaust gowns . Bacterial surface contamination was monitored in the operating and anaesthetic area using 9 cm diameter settle plates (1+1) and nitrocellulose membranes (2+2) transferred after sampling to nutrient pads . Compared with conventional clothing, the use of body exhaust gowns did not significantly reduce the microbial contamination (P=0.1-0.7) . On the settle plates 1 m from the patient 279+/-326 cfu/m(2)/h were observed with conventional clothing compared with 142+/-227 cfu/m(2)/h with body exhaust gowns . The first membrane located on the patient in the sterile area detected 250+/-590 cfu/m(2)/h with conventional clothing and 210+/-320 cfu/m(2)/h with exhaust gowns . For the second membrane on the floor, the counts were 1790+/-2700 and 1590+/-1590 cfu/m(2)/h . For all operations the settle plates yielded 210+/-287 cfu/m(2)/h in the operating area and 720+/-564 cfu/m(2)/h in the anaesthetic area (P=0.01) . Compared with the membrane placed on the anaesthetic equipment the counts on the membrane placed on patient were also significantly lower (P=0.01) while the membranes placed on the floor in each area showed no difference in counts . In conclusion, compared with conventional clothing, the use of body exhaust gowns could not be proven to provide more protection against microbial contamination . The low number of colony forming units found in the operating area was similar to that expected from an ultraclean laminar airflow unit, although achieved with a cheaper and more energy saving system.

Water Res, 2003 Jul, 37(12), 2833 - 46
A model of microbial activity in lake sediments in response to periodic water-column mixing; Gantzer CJ et al.; Under stagnant conditions, the mass transport of a soluble substrate from a lake's water column to the sediment/water interface is limited by molecular diffusion . Stagnant conditions coupled with a continuing sediment biological demand create a substrate depletion zone above the sediment/water interface . The frequency at which the substrate depletion zone is destroyed by internal seiches and other intermittent flow phenomena influences the time-averaged substrate concentration at the sediment/water interface . A more frequent mixing results in a greater time-averaged interface concentration and consequently affects the amount of microbial biomass that can be supported in the lake sediments and the flux of the substrate into the sediment . A one-dimensional, two-substrate model is used to examine the impact of mixing frequency on the activity of sulfate-reducing bacteria (SRB) in lake sediments . In the model, sulfate is supplied from the water column, while acetate is generated within the sediments . Mass transport to and within the sediments is by molecular diffusion except for instantaneous mixing events . Between mixing events, sulfate concentration gradients form above the sediment/water interface in the diffusive boundary layer . Sulfate depletion zones can be centimeters thick . When typical biological rate and diffusion coefficients for sulfate and acetate are used as inputs, the model indicates that a more frequent water-column mixing results in greater SRB concentrations . For an assumed bulk water-column sulfate concentration of 4.8 mg x l(-1), the sediment SRB concentrations for the modeled hourly, 6-hourly, daily, and weekly mixing frequencies were 175, 136, 91, and 30 mg x m(-2), respectively . The model also predicts higher time-averaged sulfate flux rates at more frequent water-column mixing . The time-averaged sulfate flux rates for the hourly, 6-hourly, daily, and weekly mixing frequencies were 1.26, 1.13, 0.78, and 0.30 mg x m(-2)h(-1), respectively . Thus, mixing frequency can significantly impact microbial activity in lake sediments.

J Dent Res, 2003 Jun, 82(6), 471 - 5
MG2 and lactoferrin form a heterotypic complex in salivary secretions; Soares RV et al.; Protein-protein interactions are necessary for homeostasis to be maintained and for biological systems to be integrated . Heterotypic complexes occur in saliva, and a complex between MG2 and SIgA has been suggested to promote microbial clearance from the oral cavity . In this study, we used a peptide display library to investigate previously unrecognized heterotypic complexes involving MG2 and other proteins . The library was panned with MG2 12 times, and analyses of clones identified the sequence Ala-Leu-Leu-Cys-, which occurs in salivary lactoferrin . Blotting experiments confirmed that MG2 and lactoferrin form a heterotypic complex in vitro and in vivo . Periodate treatment of MG2 did not affect the interaction . A synthetic lactoferrin peptide containing the motif Ala-Leu-Leu-Cys-blocked the interaction between MG2 and lactoferrin, confirming the specificity of the interaction identified by panning . This complex may enhance the properties of these salivary components in the oral environment.

Mem Inst Oswaldo Cruz, 2003 Mar, 98(2), 223 - 6 Epub 2003 May 15.
Oviposition response of the mosquito, Culex quinquefasciatus to the secondary metabolite(s) of the fungus, Trichoderma viride; Geetha I et al.; Secondary metabolites produced by Trichoderma viride, a deuteromycetes fungus, under submerged culture condition were formulated and evaluated for oviposition attractancy against gravid females of Culex quinquefasciatus mosquito . At a concentration of 10 g ml-1 the formulation showed remarkable attractancy with an oviposition active index (OAI) of +0.52 . When the oviposition attractancy of the formulation was compared with a known oviposition attractant, p-cresol, both at 10 g ml-1, the former was found to be more attractive to result in 70% egg laying than the later with 30% egg laying . Thin layer chromatography fractions of the secondary metabolites showed that a fraction with Rf value of 0.88 was highly active as oviposition attractant with an OAI of +0.65 . Further work on identification of the active principle(s) of the microbial formulation might lead to an oviposition attractant useful in mosquito vector management.

J Biol Chem, 2003 Aug 8, 278(32), 30403 - 12 Epub 2003 May 22.
Calpain regulates enterocyte brush border actin assembly and pathogenic Escherichia coli-mediated effacement; Potter DA et al.; This study identifies calpain as being instrumental for brush border (BB) microvillus assembly during differentiation and effacement during bacterial pathogenesis . Calpain activity is decreased by 25-80% in Caco 2 lines stably overexpressing calpastatin, the physiological inhibitor of calpain, and the effect is proportional to the calpastatin/calpain ratio . These lines exhibit a 2.5-fold reduction in the rate of microvillus extension . Apical microvillus assembly is reduced by up to 50%, as measured by quantitative fluorometric microscopy (QFM) of ezrin, indicating that calpain recruits ezrin to BB microvilli . Calpain inhibitors ZLLYCHN2, MDL 28170, and PD 150606 block BB assembly and ezrin recruitment to the BB . The HIV protease inhibitor ritonavir, which inhibits calpain at clinically relevant concentrations, also blocks BB assembly, whereas cathepsin and proteasome inhibitors do not . Microvillus effacement is inhibited after exposure of calpastatin-overexpressing cells to enteropathogenic Escherichia coli . These results suggest that calpain regulates BB assembly as well as pathological effacement, and indicate that it is an important regulator involved in HIV protease inhibitor toxicity and host-microbial pathogen interactions.

Vaccine, 2003 Jun 1, 21 Suppl 2, S89 - 95
Mucosal immunisation and adjuvants: a brief overview of recent advances and challenges; Holmgren J et al.; Mucosal immunisation may be used both to prevent mucosal infections through the activation of anti-microbial immunity and to treat selected autoimmune, allergic or infectious-immunopathological disorders through the induction of antigen-specific tolerance . The development of mucosal vaccines, whether for prevention of infectious diseases or for immunotherapy, requires antigen delivery and adjuvant systems that can efficiently help to present vaccine or immunotherapy antigens to the mucosal immune system . Promising advances have recently been made in the design of more efficient mucosal adjuvants based on detoxified bacterial toxin derivatives or CpG motif-containing DNA, and perhaps even more striking progress has been done in the use of virus-like particles as mucosal delivery systems for vaccines and of cholera toxin B subunit as antigen vector for immunotherapeutic tolerance induction . However, it is a memento that two recently developed mucosal vaccines for human use against rotavirus diarrhoea and influenza were withdrawn after a short period in the market because of adverse reactions among the vaccinees, thus emphasising the difficult and challenging task also for mucosal immunisation of combining vaccine and adjuvant efficacy with safety and acceptability.

Vaccine, 2003 Jun 1, 21 Suppl 2, S55 - 60
The role of Toll-like receptor 2 in microbial disease and immunity; Wetzler LM; Cells expressing Toll-like receptor (TLR), TLR2 in association with TLR1, TLR6 or some other unknown co-receptor can respond upon interaction with a large variety of microbial ligands . The variety of TLR2 ligands is the greatest among all the TLRs and this is due to the heterodimerization needed for TLR2 mediated responses . Like other TLRs, TLR2 signaling induces antigen presenting cell activation, pro-inflammatory cytokine production and increased expression of co-stimulatory ligand expression . These events are important for induction of innate immune responses and improved acquired immunity . There is strong suggestive evidence that alteration or lack of TLR2 function in vivo may correlate to decreased immune protection from pathogens that contain TLR2 ligands, but more work needs to be performed to strengthen this correlation.

Vaccine, 2003 Jun 1, 21 Suppl 2, S43 - 7
Pentraxin 3, a non-redundant soluble pattern recognition receptor involved in innate immunity; Mantovani A et al.; Pentraxin 3 (PTX3) is the first long pentraxin identified . Long pentraxins consist of a C-terminal pentraxin domain, which has sequence similarity to C-reactive protein (CRP) and serum amyloid P (SAP) component (the classic short pentraxins), and of an unrelated N-terminal portion . PTX3 is made by diverse cell types, most prominently endothelial cells, macrophages and dendritic cells, in response to primary inflammatory signals (e.g . interleukin-1 (IL-1), tumour necrosis factor (TNF), lipopolysaccharide (LPS)) . It binds diverse ligands, including microbial moieties, C1q and apoptotic cells . Evidence suggests that PTX3 plays a role in the regulation of innate resistance to pathogens, inflammatory reactions, possibly clearance of self-components and female fertility.

Exp Hematol, 2003 May, 31(5), 382 - 8
Characterization of Siglec-5 (CD170) expression and functional activity of anti-Siglec-5 antibodies on human phagocytes; Erickson-Miller CL et al.; OBJECTIVE: The Siglec family of proteins consists of at least 10 members with immunoglobulin and lectin domains and with similar sialic acid-binding properties . Many Siglec family members are expressed on hematopoietic cells and are involved in cell/cell interactions . Some family members are suspected of regulating cellular processes through specific signaling pathways . Monoclonal antibodies were generated against specific epitopes of Siglec-5 (CD170) and were used to determine expression of Siglec-5 on normal blood and marrow cells and cell lines . The antibodies also were used to elucidate functional activity for Siglec-5 on blood neutrophils . METHODS: Flow cytometry and ELISA were used to determine the specificity of the monoclonal antibodies for Siglec-5 and to determine expression patterns . Chemiluminescence assays were employed to measure the oxidative burst activity of whole blood or purified neutrophils following treatment with the anti-Siglec-5 antibodies . RESULTS: Cell surface expression analysis demonstrated that the protein was expressed on gated human neutrophil and monocyte populations, both in the blood and bone marrow . Expression on neutrophils was enhanced by one-hour treatment with fMLP or TNF-alpha . Epitope-specific anti-Siglec-5 monoclonal antibodies did not directly activate human neutrophils; however, antibody binding augmented neutrophil oxidative burst activity as determined by fMLP-induced luminol-dependent chemiluminescence . CONCLUSION: Data demonstrating expression of Siglec-5 on cells of the myelomonocytic lineage and alteration of its expression by inflammatory stimuli suggest a role for this protein in cell/cell interactions following microbial exposure.

Dev Biol (Basel), 2003, 112, 81 - 97
The immunogenicity of biopharmaceuticals . Lessons learned and consequences for protein drug development; Patten PA et al.; Most biopharmaceuticals, including those proteins that are more or less identical to native human proteins, induce antibodies in a significant fraction of patients . The main factors contributing to immunogenicity are impurities and the presence of aggregates . Sequence divergence from the native proteins only plays a minor role except in proteins from microbial, plant or distant vertebrate origin . In the majority of cases the antibodies have no biological or clinical effects . The most common clinical effect is the loss of efficacy of the biopharmaceutical . Serious complications of immunogenicity are rare . The best method to prevent immunogenicity is optimizing production, purification and formulation of the biopharmaceutical protein to generate soluble, non-aggregated, native protein free of contaminating adjuvants . The best way to predict immunogenicity in humans is evaluation in immune tolerant transgenic mice.

Poult Sci, 2003 May, 82(5), 789 - 95
High available phosphorus corn and phytase in layer diets; Ceylan N et al.; High available phosphorus corn (HAP) developed using the low phytic acid 1-1 (lpal-1) allele of the corn LPA1 gene containing 0.27% P, with 0.17% nonphytate P (NPP), was compared to near isogenic normal corn (LPA1), which contained 0.23% P and 0.05% NPP . Five levels of NPP from either HAPC or normal corn (0.40, 0.35, 0.30, 0.25 and 0.20% + 300 phytase units (FTU)/kg microbial phytase) were combined in a 2 x 5 factorial experiment for a total of 10 dietary treatments . Each dietary treatment was fed to eight replicate cages with five Hy-Line W-36 hens per replicate cage from 20 to 40 wk of age . Feed consumption and egg production were not significantly affected by dietary NPP level or corn type . Feed conversion ratio (g feed:g egg mass) was improved at the 0.35% NPP level (1.856) compared to the other levels of NPP--0.40, 0.30, 0.25, and 0.20% + phytase having feed conversion ratios of 1.872, 1.905, 1.930, and 1.898, respectively . Egg weight and egg mass decreased significantly as dietary NPP decreased; diets with 0.20% NPP plus phytase had equal egg mass to the 0.35 and 0.40% NPP diets . A significant corn type x NPP interaction effect was observed for egg weight, such that within the HAP corn diets, egg weight decreased more markedly at the 0.25% NPP levels compared to the normal corn 0.25% NPP diets . Specific gravity was not affected by dietary treatment, but percent dry shell was improved at the lower AP levels and with phytase treatment . Dietary NPP level and corn type had no significant effect on bone ash . Excreta levels of total phosphorus decreased significantly as dietary NPP decreased and were lower in the HAP corn excreta compared to normal corn excreta . Total P, Ca, Zn, Cu, and Mn retention were significantly affected by NPP level and corn type . HAP corn reduced Ca, Zn, Cu, and Mn retention compared to normal corn; this negative effect was alleviated by phytase supplementation to HAP corn diets . HAP corn allowed less dicalcium phosphate supplementation in layer diets compared to normal corn while supporting equal egg production . Phytase supplementation of low NPP diets had no significant positive effects on egg production parameters in either corn type diets.

Eur Respir J, 2003 Apr, 21(4), 641 - 5
Airway inflammation in waste handlers exposed to bioaerosols assessed by induced sputum; Heldal KK et al.; Work-associated lower airway inflammation in waste collectors was examined by induced sputum and correlated with the bioaerosol exposure . Organic waste collectors (n=25) underwent induced sputum collection and spirometry before work on Monday and the following Thursday . Total cells, cell differentials, interleukin (IL)-8 and eosinophilic cationic protein were determined . Personal full-shift exposure measurements were performed Monday, Tuesday and Wednesday and analysed for total bacteria, fungal spores, endotoxins and beta(1-3)-glucans . The percentage of neutrophils (46-58%) and the IL-8 concentration (1.1-1.4 ng x mL(-1)) increased from Monday to Thursday . Forced expiratory volume in one second (FEV1) was significantly reduced on Thursday, and the decrease in FEV1/forced vital capacity correlated with the increase in the percentage of neutrophils . The median exposure to endotoxin (range 7-180 EU x m(-3)) and beta(1-3)-glucan (range 5-220 ng x m(-3)) was correlated with the increase in IL-8 . Bioaerosol exposure during waste collection induced an inflammatory response in the lower airways, characterised by neutrophils and interleukin-8 secretion, that influenced the lung function . The inflammatory response was related to microbial components in the bioaerosol and was more pronounced for endotoxin than beta(1-3)-glucan exposure . No associations were found for mould spores or bacteria.

J Biol Chem, 2003 Aug 15, 278(33), 30920 - 6 Epub 2003 May 20.
Decorin-binding sites in the adhesin DbpA from Borrelia burgdorferi: a synthetic peptide approach; Pikas DS et al.; Lyme disease is caused by the spirochete Borrelia burgdorferi following transmission from infected Ixodes ticks to human hosts . Following colonization of the skin, spirochetes can disseminate throughout the body, resulting in complications that can include ocular, cardiac, neural, and skeletal disease . We have previously shown that B . burgdorferi expresses two closely related decorin-binding adhesins (DbpA and DbpB) of the MSCRAMM (microbial surface component recognizing adhesive matrix molecule) type that can mediate bacterial attachment to extracellular matrices in the host . Furthermore, three Lys residues in DbpA appear to be critical for the binding of DbpA to decorin . We have now characterized the interaction of DbpA and decorin further by using a synthetic peptide approach . We synthesized a panel of peptides that spanned the DbpA sequence and examined their ability to inhibit the binding of intact DbpA to decorin . From these studies, we identified a decorin-binding peptide that lost this activity if the sequence was either scrambled or if a critical Lys residue was chemically modified . A minimal decorin-binding peptide was identified by examining a set of truncated peptides . One peptide is proposed to contain the primary decorin-binding site in DbpA . By comparing the amino acid sequences of 29 different DbpA homologs from different B . burgdorferi sensu lato isolates, we discovered that the identified decorin-binding sequence was quite variable . Therefore, we synthesized a new panel of peptides containing the putative decorin-binding sequence of the different DbpA homologs . All of these peptides were active in our decorin-binding assay, and consensus decorin binding motifs are discussed.

Infect Immun, 2003 Jun, 71(6), 3496 - 502
Helicobacter pylori activates Toll-like receptor 4 expression in gastrointestinal epithelial cells; Su B et al.; Helicobacter pylori activates the transcription factor NF-kappaB, leading to proinflammatory cytokine production by gastric epithelial cells . However, the receptors for the initial bacterial interaction with host cells which activate downstream signaling events have not been completely defined . Recently, it has been shown that microbial components activate Toll-like receptors (TLRs), thereby leading to AP-1- and NF-kappaB-dependent transcription and resulting in the production of proinflammatory cytokines . The aim of this study was to determine whether H . pylori activates TLR4 . Reverse transcription-PCR showed that both type I and type II H . pylori clinical isolates induced TLR4 mRNA expression in AGS cells compared with that by uninfected controls . H . pylori upregulated TLR4 protein expression in two gastric epithelial cell lines (AGS and MKN45) and one intestinal epithelial cell line (T84) . Monoclonal TLR4 antibody inhibited lipopolysaccharide-induced interleukin-8 secretion from THP-1 macrophages but not from gastric epithelial cells infected with H . pylori . H . pylori demonstrated increased adherence to CHO TLR4-transfected cells compared with that to both CHO TLR2-transfected and nontransfected CHO cells (P < 0.01) . These results indicate that H . pylori activates TLR4 expression in epithelial cells and that TLR4 can serve as a receptor for H . pylori binding.

J Int Med Res, 2003 Mar-Apr, 31(2), 133 - 40
Identification of three strains of Mycobacterium species isolated from clinical samples using fatty acid methyl ester profiling; Ozbek A et al.; The cellular fatty acid profiles of 67 strains belonging to three different species of the genus Mycobacterium were determined by gas chromatography of the fatty acid methyl esters, using the MIDI Sherlock Microbial Identification System (MIS) . The species M . tuberculosis, M . xenopi and M . avium complex were clearly distinguishable and could be identified based on the presence and concentrations of 12 fatty acids: 14:0, 15:0, 16:1 omega 7c, 16:1 omega 6c, 16:0, 17:0, 18:2 omega 6.9c, 18:1 omega 9c, 18:0, 10Me-18:0 tuberculostearic acid, alcohol and cyclopropane . Fatty acid analysis showed that there is great homogeneity within and heterogeneity between Mycobacterium species . Thus the MIS is an accurate, efficient and relatively rapid method for the identification of mycobacteria.

Zhonghua Shi Yan He Lin Chuang Bing Du Xue Za Zhi, 1999 Dec, 13(4), 380 - 2
{Molecular epidemiology of respiratory syncytial virus infection in infants}; Sun L et al.; OBJECTIVE: To search for the molecular epidemiology of respiratory syncytial virus (RSV) infection in infants . METHODS: The randomly amplified polymorphism DNA (RAPD) technology was used to study 96 RSV strains isolated and identified from the patients in Changchun State Hospital of Pediatrics during 1992-1994 and 1 reference strain of M type . RESULTS: All strains were typable, four RAPD patterns were observed, different diseases have different types . 87.14% of the patients' RSV strains had the same RAPD pattern(R1) . CONCLUSION: RAPD method is a rapid, easy and high resolution technique, with which we can know on the molecular level the microbial infection state . There was epidemic of R1 type infection during the period surveyed.

Microbes Infect, 2003 May, 5(6), 491 - 8
Vgamma2Vdelta2+ T cells and anti-microbial immune responses; Chen ZW et al.; Vgamma2Vdelta2(+) T cells exist only in primates and constitute the majority of circulating human gammadelta T cells . Recent studies have demonstrated that this unique gammadelta T cell subpopulation can be a component of adaptive immune responses and contribute to anti-microbial immunity to infections.

Tuberculosis (Edinb), 2003, 83(1-3), 131 - 4
Hematogenous reseeding of the lung in low-dose, aerosol-infected guinea pigs: unique features of the host-pathogen interface in secondary tubercles; McMurray DN; The ability to study the early events in the pathogenesis of pulmonary tuberculosis in guinea pigs following very low dose (3-5 cfu) infection by the respiratory route has revealed that early (10-14 days) extrapulmonary dissemination results in reseeding of previously uninfected lobes of the lung by the hematogenous route . Thus, in every guinea pig, the lung is challenged twice, once by the airway and 2-3 weeks later by the circulatory system . The so called "secondary" pulmonary lesions which result from the bacillemia differ fundamentally from the primary lesions, in part, because the host has already developed a strong T cell mediated immunity when the hematogenous reseeding occurs . Secondary lung lesions in non-vaccinated guinea pigs behave similarly to primary lung lesions in previously vaccinated guinea pigs . Since the secondary, blood-borne lesions are thought to be the "reactivatable foci" which result in reactivation tuberculosis following prolonged persistent infection, it is important to understand the nature of the host-pathogen interaction in secondary lesions . The guinea pig model provides a unique opportunity to examine both the microbial and host factors which constitute that interface.

Environ Pollut, 2003, 124(3), 407 - 17
Cu, Cr and As distribution in soils adjacent to pressure-treated decks, fences and poles; Chirenje T et al.; Chromated copper arsenate (CCA)-treated wood has been widely used in the Southeastern United States to protect wood products from microbial and fungal decay . The aims of this study were to (1) . determine the distribution of arsenic (As), chromium (Cr), and copper (Cu), in soils surrounding CCA-treated wood structures such as decks, fences and poles; and (2) . evaluate the impacts of these structures on As, Cr and Cu loading of the soils . Profile and lateral soil samples were collected under CCA-treated decks and adjacent to poles and fences . The results showed elevation of As, Cr and Cu concentrations close to and under the structures, with mean As concentrations as high as 23 mg x kg(-1) close to utility poles compared with less than 3 mg x kg (-1) at distances of about 1.5 m away . Concentrations of As, Cr, and Cu decreased with depth in areas close to CCA-treated poles . However, these results were only apparent in relatively new structures . A combination of weathering and leaching with time may have reduced the impact in older poles . Increased concentrations of As, Cu and Cr were also observed close to CCA-treated decks and fences, with age showing a similar impact . These results are helpful for CCA-treated wood product users to determine the safe use of these structures.

Dermatol Clin, 2003 Apr, 21(2), 291 - 300
Imiquimod; Skinner RB Jr; Imiquimod is the first of the immune response modifiers to stimulate a localized immune response to treat infectious skin conditions . The reported TLR-7 activation to provoke an immune response suggests that imiquimod might mimic a microbial antigen . The immune response initiated by induced production of IFN-alpha and TFN-alpha is specifically aimed at an infectious antigen and appears mediated (in part) by enhanced migration of Langerhans' cells to regional lymph nodes . The approved indication for imiquimod is for treatment of genital warts . The drug has demonstrated a 50% to 60% clearance rate and a 12% to 20% recurrence rate for this indication (Table 1) . This recurrence rate is the lowest reported among the currently recommended treatment modalities . The self-applied treatment avoids costly and painful office-based procedures . Case reports and open-label studies have demonstrated the efficacy of imiquimod in treating some cases of common, plantar, and flat warts, as well as molluscum contagiosum and leishmaniasis . Common and plantar warts respond better to imiquimod in combination with cryosurgery, occlusion, and keratolytics . Reports of successful imiquimod treatment of granuloma annulare, alopecia areata, and vitiligo might suggest an infectious etiology to those conditions, although this hypothesis is highly speculative.

Environ Microbiol, 2003 Jun, 5(6), 517 - 22
Monitoring of alkane-degrading bacteria in a sea-water microcosm during crude oil degradation by polymerase chain reaction based on alkane-catabolic genes; Sei K et al.; Behaviour of microbial populations responsible for degrading n-alkanes, a major component of crude oil, was monitored during crude oil degradation in a sea-water microcosm by both traditional colony culturing and molecular techniques . A DNA extraction method applicable to crude oil-amended sea-water samples was developed to obtain DNA applicable to most probable number (MPN) polymerase chain reaction (PCR) . The population of alkane-degrading bacteria responsible for degradation of n-alkanes in a crude oil-amended microcosm altered, so that shorter alkanes were degraded first by alkane-degrading bacteria possessing alkane hydroxylase genes from group I (Kohno et al., 2002, Microb Environ 17: 114-121) and longer ones afterwards by those possessing alkane hydroxylase genes from group II . Thus, the degradation mechanism of the n-alkanes can be clarified during crude oil degradation . Application of the method of detecting different types of alkane-catabolic genes, as shown in the present study, enabled bacterial groups preferring alkanes of either shorter or longer chain lengths to be enumerated selectively.

Environ Microbiol, 2003 Jun, 5(6), 510 - 6
Extraradical mycelium of the arbuscular mycorrhizal fungus Glomus lamellosum can take up, accumulate and translocate radiocaesium under root-organ culture conditions; Declerck S et al.; Radiocaesium enters the food chain when plants absorb it from soil, in a process that is strongly dependent on soil properties and plant and microbial species . Among the microbial species, arbuscular mycorrhizal (AM) fungi are obligate symbionts that colonize the root cortex of many plants and develop an extraradical mycelial (ERM) network that ramifies in the soil . Despite the well-known involvement of this ERM network in mineral nutrition and uptake of some heavy metals, only limited data are available on its role in radiocaesium transport in plants . We used root-organ culture to demonstrate that the ERM of the AM fungus Glomus lamellosum can take up, possibly accumulate and unambiguously translocate radiocaesium from a 137Cs-labelled synthetic root-free compartment to a root compartment and within the roots . The accumulation of 137Cs by hyphae in the root-free compartment may be explained by sequestration in the hyphae or by a bottleneck effect resulting from a limited number of hyphae crossing the partition between the two compartments . Uptake and translocation resulted from the incorporation of 137Cs into the fungal hyphae, as no 137Cs was detected in mycorrhizal roots treated with formaldehyde . The importance of the translocation process was indicated by the correlation between 137Cs measured in the roots and the total hyphal length connecting the roots with the labelled compartment . 137Cs may be translocated via a tubular vacuolar system or by cytoplasmic streaming per se.

Radiats Biol Radioecol, 2003 Mar-Apr, 43(2), 172 - 5
{Influence of chronic exposure to low doses of space ionizing radiation on the character of formation of microbial assemblage in the habitat of orbital station}; Tsetlin VV et al.; Statistically valid relations between radiation conditions in compartments of MIR station and the micromicete population (CFU number) on the surface of the equipment and the interior have been established . It was found that in conditions of a chronic exposure to space radiation the number of CFU increased in one thousand and more times with increasing of absorbed dose rate from 200 up to 1000 microGy/day . The results of land-based model experiments confirmed morphological changes in the "flight" strains of funguses under exposure to low doses of gamma (100-800 microGy/day) and neutron (0.2-2 neutron/cm2.s) radiation . It was found that the morphological changes in the control (museum) cultures of funguses of the same species, which were expressed in the weak increase of vegetative mycelium, were detected only after repeated gamma- and gamma + neutron irradiation.

J Oral Rehabil, 2003 May, 30(5), 532 - 6
An infection control protocol: effectiveness of immersion solutions to reduce the microbial growth on dental prostheses; Pavarina AC et al.; This investigation evaluated the effectiveness of an infection control protocol for cleansing and disinfecting removable dental prostheses . Sixty-four dentures were rubbed with sterile cotton swab immediately after they had been taken from patients' mouths . Samples were individually placed in the culture medium and immediately incubated at 37 +/- 2 degrees C . The dentures were scrubbed for 1 min with 4% chlorhexidine, rinsed for 1 min in sterile water and placed for 10 min in one of the following immersion solutions: 4% chlorhexidine gluconate, 1% sodium hypochlorite, Biocide (iodophors) and Amosan (alkaline peroxide) . After the disinfection procedures, the dentures were immersed in sterile water for 3 min, reswabbed and the samples were incubated . All samples obtained in the initial culture were contaminated with micro-organisms . All the lower dentures immersed in Biocide showed positive growth, and the upper dentures were positive for growth in six of eight dentures . The 4% chlorhexidine gluconate, 1% sodium hypochlorite and Amosan solutions have been proved effective to reduce the growth of the micro-organisms in the 10 min immersion period . The protocol evaluated in this study seems to be a viable method to prevent cross-contamination between dental personnel and patients.

J Appl Microbiol, 2003, 94(6), 1059 - 65
Starch in plasterboard sustains Streptomyces californicus growth and bioactivity of spores; Murtoniemi T et al.; AIMS: The effects of plasterboard composition on Streptomyces californicus growth and bioactivity of spores were studied . METHODS AND RESULTS: Streptomyces californicus was grown on 13 modified plasterboards under saturated humidity conditions . The total content of fatty acid methyl esters was used for quantifying S . californicus biomass, while the spore-induced cytotoxicity and production of nitric oxide (NO), tumour necrosis factor-alpha, and interleukine-6 (IL-6) in mouse macrophages was used to assess the bioactivity of spores . Removal of starch completely from the plasterboard or only from the core reduced significantly the biomass production and the biological activity of spores in comparison with reference board . The biocide added into the core or on the liner decreased the growth markedly and inhibited the sporulation totally . The biomass production correlated positively with the spore number, cytotoxicity, and production of NO and IL-6 . CONCLUSIONS: Streptomyces californicus grew under nutrient limitation on all studied plasterboards . The starch is the major factor enabling S . californicus to grow and to produce biologically active metabolites on plasterboard . SIGNIFICANCE AND IMPACT OF THE STUDY: The composition of building material has an impact on microbial growth and bioactivity of spores which may be involved in complex mechanisms leading to respiratory symptoms in the occupants in moisture damaged buildings.

Immunol Rev, 2003 Jun, 193, 10 - 21
Caspase-activation pathways in apoptosis and immunity; Creagh EM et al.; Members of the caspase family of cysteine proteases have been firmly established to play key roles in signal transduction cascades that culminate in apoptosis (programmed cell death) . Caspases are normally expressed as inactive precursor enzymes (zymogens) that become activated during apoptosis and proceed to dismantle the cell from within . To date, three major apoptosis-associated pathways to caspase activation have been elucidated . Certain caspases, such as caspase-1, also occupy important positions in signaling pathways associated with immune responses to microbial pathogens . In this situation, caspase activation is associated with the maturation of pro-inflammatory cytokines, such as interleukin-1beta (IL-1beta) and IL-18, and not apoptosis per se . Here, we discuss the current understanding of how caspases are activated during apoptosis and inflammation and the roles these proteases play in either context.

Afr J Med Med Sci, 2002 Sep, 31(3), 195 - 9
Effects of some risk factors and immunodeficiencies on the periodontium--a review; Arowojolu MO et al.; The possible role systemic factors might play in initiating or modifying the progress of periodontal disease has been a controversial issue for some time . Gingivitis is initiated by microbial plaque deposits on the dento-gingival interface but progression to periodontitis is modified by several environmental, behavioural, biological and health care variables . The importance of the immune system in modifying the host response to plaque is well established and as such, the immune system is a risk factor for human and animal periodontal disease . This paper reviews the modifying risk factors for periodontal disease and examines the periodontal manifestations of subjects with primary and acquired immuno-deficiencies.

J Clin Invest, 2003 May, 111(10), 1571 - 8
Critical role of the Toll-like receptor signal adaptor protein MyD88 in acute allograft rejection; Goldstein DR et al.; The Toll-like receptors (TLRs) are recently discovered germline-encoded receptors on APCs that are critically important in innate immune recognition of microbial pathogens . However, their role in solid-organ transplantation is unknown . To explore this role, we employed a skin allograft model using mice with targeted deletion of the universal TLR signal adaptor protein, MyD88 . We report that minor antigen-mismatched (HY-mismatched) allograft rejection cannot occur in the absence of MyD88 signaling . Furthermore, we show that the inability to reject these allografts results from a reduced number of mature DCs in draining lymph nodes, leading to impaired generation of anti-graft-reactive T cells and impaired Th1 immunity . Hence, this work demonstrates that TLRs can be activated in a transplant setting and not solely by infections . These results link innate immunity to the initiation of the adaptive alloimmune response.

Drugs, 2003, 63(11), 1059 - 66
Management of patients with recurrent vulvovaginal candidiasis; Sobel JD; Recurrent vulvovaginal candidiasis (RVVC) is by no means uncommon and is a source of considerable physical discomfort in addition to serving as a major therapeutic challenge . The syndrome is multifactorial in aetiology and hence management strategies must recognise the complex aetiological pathways . Many women receiving the misplaced diagnosis of RVVC have a variety of other infectious and non-infectious entities presenting with identical symptoms . Hence the first step in management is confirming the diagnosis of RVVC including microbial confirmation and species identification . Efforts should be made to identify and correct a causal mechanism . Maintenance suppressive azole antifungal regimens are highly effective in controlling symptoms, although cure is less common . Further advances in achieving higher cure rates await the availability of non-azole fungicidal agents.

Int Microbiol, 2003 Jun, 6(2), 95 - 100 Epub 2003 May 14.
Culture collections over the world; Smith D; Culture collections have the crucial role of providing the authenticated biological material upon which high quality research is based . Importantly, they serve as repositories for strains as part of patent deposits, providers of safe and confidential services to store key organisms for research and industry, and sources of organisms cited in scientific papers that can be used in the confirmation of results and for further study . The demands upon culture collections change as new technologies and uses of organisms are discovered . Many are becoming Biological Resource Centres, as defined by the OECD Biological Resource Centre (BRC) Initiative, in that they operate according to international quality criteria, carry out essential research, enhance the value and applications of strains and provide a vital information resource . In a changing international scientific environment, many collections are under threat of extinction because of inadequate funding, changing government support strategies and the cost of new technologies . We are also suffering a decline in the number of biosystematists, who are needed to form a sound base for molecular technologies and to aid in identifying, and characterizing microbial diversity . In this environment, collections must work together to make the best use of new technologies and to contribute to the description of the 1.4 million fungi yet to be discovered . At the current rate, this will take 700 years . New technologies and novel ways of funding this task must be engaged and, above all, scientists must collaborate . Common policies are necessary to address the regulatory demands on collections, to control access to dangerous organisms, and, in particular, to enforce the Convention on Biological Diversity . Countries that hold the majority of biodiversity require support in building the facilities required to explore their hidden resource . The World Federation for Culture Collections (WFCC) and, in Europe, the European Culture Collection Organisation (ECCO) have a key role to play . The world must benefit from its microbial diversity, which is crucial to solving increasing problems in food provision, public health and poverty alleviation.

J Med Microbiol, 2003 Jun, 52(Pt 6), 447 - 51
Five postulates for resolving outbreaks of infectious disease; Mortimer PP; Outbreaks of infection challenge the surveillance of infectious disease, but they also offer opportunities to improve and refine it . An outbreak may be the first sign of an emerging pathogen or it may draw attention to a new risk group or route of infection . Postulates analogous to those used a century ago by Robert Koch to prove the microbial aetiology of infectious diseases can be employed to verify the existence of an outbreak, demonstrate its cause and pinpoint its origins . In doing this, high-resolution molecular finger printing of micro-organisms has now assumed a crucial role . Without formal analysis based on postulates, the existence, extent and source of outbreaks may be overlooked and public health interventions misapplied or lost.

Adv Biochem Eng Biotechnol, 2003, 80, 149 - 75
In situ product removal (ISPR) in whole cell biotechnology during the last twenty years; Stark D et al.; This review sums up the activity in the field of in situ product removal in whole cell bioprocesses over the last 20 years . It gives a complete summary of ISPR operations with microbial cells and cites a series of interesting ISPR applications in plant and animal cell technology . All the ISPR projects with microbial cells are categorized according to their products, their ISPR techniques, and their applied configurations of the ISPR set-up . Research on ISPR application has primarily increased in the field of microbial production of aromas and organic acids such lactic acid over the last ten years . Apart from the field of de novo formation of bioproducts, ISPR is increasingly applied to microbial bioconversion processes . However, despite of the large number of microbial whole cell ISPR projects (approximately 250), very few processes have been transferred to an industrial scale . The proposed processes have mostly been too complex and consequently not cost effective . Therefore, this review emphasizes that the planning of a successful whole cell ISPR process should not only consider the choice of ISPR technique according to the physicochemical properties of the product, but also the potential configuration of the whole process set-up . Furthermore, additional process aspects, biological and legal constraint need to be considered from the very beginning for the design of an ISPR project . Finally, future trends of new, modified or improved ISPR techniques are given.

J Perinat Med, 2003, 31(2), 115 - 21
Microbial invasion of the amniotic cavity at birth is associated with adverse short-term outcome of preterm infants; Berger A et al.; AIMS: To determine the frequency and clinical significance of microbial invasion of the amniotic cavity at the time of delivery in preterm infants . METHODS: Prospective cohort study during June 2001 and January 2002 . Preterm infants < 33 + 6 weeks of gestation who had amniotic fluid and placental tissue sampled for culture during cesarean section were included . RESULTS: Of a total of 80 neonates, 42 had negative culture results, 22 had growth of Ureaplasma urealyticum, and 16 had growth of other pathogens . Isolation of Ureaplasma urealyticum was associated with a decreased risk of developing hyaline membrane disease after birth but a more than 20 times increased risk of developing chronic lung disease . Patients with growth of other pathogens had a significantly higher mortality than patients with negative culture results . CONCLUSIONS: Isolation of miroorganisms from the amniotic cavity at birth is associated with an adverse outcome of the preterm infant . In the light of extremely small numbers of positive blood cultures in preterm infants after birth, we consider it reasonable to recommend routine culturing of amniotic cavity tissues/fluid obtained during cesarean section in order to increase the identification rate of pathogens potentially involved in the pathogenesis of perinatal infections.

Int J Environ Health Res, 2003 Jun, 13(2), 215 - 21
The use of an air filtration system in podiatry clinics; McLarnon N et al.; A small-scale study was conducted to ascertain the efficiency and effectiveness of an air filtration system for use in podiatry/chiropody clinics (Electromedia Model 35F (A), Clean Air Ltd, Scotland, UK) . Three clinics were identified, enabling comparison of data between podiatry clinics in the West of Scotland . The sampling was conducted using a portable Surface Air Sampler (Cherwell Laboratories, Bicester, UK) . Samples were taken on two days at three different times before and after installation of the filtration units . The global results of the study indicate the filter has a statistically significant effect on microbial counts, with an average percentage decrease of 65% . This study is the first time, to the authors' knowledge, such a system has been tested within podiatric practice.

J Agric Food Chem, 2003 May 21, 51(11), 3338 - 44
Commercial scale pulsed electric field processing of tomato juice; Min S et al.; Effects of commercial scale pulsed electric field (PEF) processing on the quality of tomato juice were studied and compared with those of thermal processing . Tomato juice was prepared by hot break at 88 degrees C for 2 min or by cold break at 68 degrees C for 2 min and then thermally processed at 92 degrees C for 90 s or PEF processed at 40 kV/cm for 57 micros . Thermally processed, PEF processed, and unprocessed control juices were packed into 50 mL sterilized polypropylene tubes in a sanitary glovebox and stored at 4 degrees C for 112 days . Both thermally and PEF processed juices showed microbial shelf life at 4 degrees C for 112 days . The lipoxygenase activities of thermally and PEF processed juices were 0 and 47%, respectively . PEF processed juice retained more ascorbic acid than thermally processed juice at 4 degrees C for 42 days (p < 0.05) . No significant differences were observed in the concentration of lycopene, degrees Brix, pH, or viscosity between thermally and PEF processed juices during the storage (p > 0.05) . Sensory evaluations indicated that flavor and overall acceptability of PEF processed juice were preferred to those of thermally processed juice (p < 0.05).

J Eukaryot Microbiol, 2003 Mar-Apr, 50(2), 86 - 91
A model of biocomplexity and its application to the analysis of some terrestrial and marsh eukaryotic microbial communities with an emphasis on amoeboid protists; Anderson OR; Biocomplexity theory has become increasingly important in understanding ecosystem dynamics as we realize that the interactions among subunits in a multi-component system often produce elaborate states that are not easily explained in terms of the individual parts of the system . A Euclidean geometric model of biocomplexity is presented and illustrated using protistan communities . The model is based on three quantitative biotic dimensions (indices) for small subsamples (0.01 g) taken from each sample core of substratum: (1) richness of morphospecies expressed as mean count per 0.01 g, (2) spatial diversity of protists expressed as then umber of unique morphospecies (i.e . those occurring in only one of the 0.01-g subsamples and not in any of the other subsamples), and (3) patchiness (non-uniform aggregation) of the distribution of protists across the 0.01-g subsamples . These three indices are mapped into a three-dimensional Euclidean space model, and the position of each point and its geometric distance from the origin are used as a general index of biocomplexity . The usefulness of the model is illustrated by applying it to a range of terrestrial and marsh communities . Within the set of 15 samples examined in this study, the marsh rhizosphere samples are among the most complex.

Appl Microbiol Biotechnol, 2003 May, 61(4), 314 - 22 Epub 2003 Mar 11.
Identifiability and retrievability of unique parameters describing intrinsic Andrews kinetics; Seagren EA et al.; A key factor contributing to the variability in the microbial kinetic parameters reported from batch assays is parameter identifiability, i.e., the ability of the mathematical routine used for parameter estimation to provide unique estimates of the individual parameter values . This work encompassed a three-part evaluation of the parameter identifiability of intrinsic kinetic parameters describing the Andrews growth model that are obtained from batch assays . First, a parameter identifiability analysis was conducted by visually inspecting the sensitivity equations for the Andrews growth model . Second, the practical retrievability of the parameters in the presence of experimental error was evaluated for the parameter estimation routine used . Third, the results of these analyses were tested using an example data set from the literature for a self-inhibitory substrate . The general trends from these analyses were consistent and indicated that it is very difficult, if not impossible, to simultaneously obtain a unique set of estimates of intrinsic kinetic parameters for the Andrews growth model using data from a single batch experiment.

Appl Microbiol Biotechnol, 2003 May, 61(4), 269 - 77 Epub 2003 Mar 15.
Biotransformation of limonene by bacteria, fungi, yeasts, and plants; Duetz WA et al.; The past 5 years have seen significant progress in the field of limonene biotransformation, especially with regard to the regiospecificity of microbial biocatalysts . Whereas earlier only regiospecific biocatalysts for the 1,2 position (limonene-1,2-diol) and the 8-position (alpha-terpineol) were available, recent reports describe microbial biocatalysts specifically hydroxylating the 3-position (isopiperitenol), 6-position (carveol and carvone), and 7-position (perillyl alcohol, perillylaaldehyde, and perillic acid) . The present review also includes the considerable progress made in the characterization of plant P-450 limonene hydroxylases and the cloning of the encoding genes.

Biomaterials, 2003 Aug, 24(17), 2831 - 41
Enzyme-catalyzed gel formation of gelatin and chitosan: potential for in situ applications; Chen T et al.; We compared the ability of two enzymes to catalyze the formation of gels from solutions of gelatin and chitosan . A microbial transglutaminase, currently under investigation for food applications, was observed to catalyze the formation of strong and permanent gels from gelatin solutions . Chitosan was not required for transglutaminase-catalyzed gel formation, although gel formation was faster, and the resulting gels were stronger if reactions were performed in the presence of this polysaccharide . Consistent with transglutaminase's ability to covalently crosslink proteins, we observed that the transglutaminase-catalyzed gelatin-chitosan gels lost the ability to undergo thermally reversible transitions (i.e . sol-gel transitions) characteristic of gelatin . Mushroom tyrosinase was also observed to catalyze gel formation for gelatin-chitosan blends . In contrast to transglutaminase, tyrosinase-catalyzed reactions did not lead to gel formation unless chitosan was present (i.e . chitosan is required for tyrosinase-catalyzed gel formation) . Tyrosinase-catalyzed gelatin-chitosan gels were observed to be considerably weaker than transglutaminase-catalyzed gels . Tyrosinase-catalyzed gels were strengthened by cooling below gelatin's gel-point, which suggests that gelatin's ability to undergo a collagen-like coil-to-helix transition is unaffected by tyrosinase-catalyzed reactions . Further, tyrosinase-catalyzed gelatin-chitosan gels were transient as their strength (i.e . elastic modulus) peaked at about 5h after which the gels broke spontaneously over the course of 2 days . The strength of both transglutaminase-catalyzed and tyrosinase-catalyzed gels could be adjusted by altering the gelatin and chitosan compositions . Potential applications of these gels for in situ applications are discussed.

Mutat Res, 2003 May 9, 537(1), 21 - 8
Bromate induces loss of heterozygosity in the thymidine kinase gene of L5178Y/Tk(+/-)-3.7.2C mouse lymphoma cells; Harrington-Brock K et al.; Potassium bromate (KBrO(3)) induces DNA damage and tumors in mice and rats, but is a relatively weak mutagen in microbial assays and the in vitro mammalian Hprt assay . Concern that there may be a human health risk associated with bromate, a disinfectant by-product of ozonation, has accompanied the increasing use of ozonation as an alternative to chlorination for treatment of drinking water . In this study, we have evaluated the mutagenicity of KBrO(3) and sodium bromate (NaBrO(3)) in the Tk gene of mouse lymphoma cells . In contrast to the weak mutagenic activity seen in the previous studies, bromate induced a mutant frequency of over 100 x 10(-6) at 0.6mM with minimal cytotoxicity (70-80% survival) and over 1300 x 10(-6) at 3mM ( approximately 10% survival) . The increase in the Tk mutant frequency was primarily due to the induction of small colony of Tk mutants . Loss of heterozygosity (LOH) analysis of 384 mutants from control and 2.7 mM KBrO(3)-treated cells showed that almost all (99%) bromate-induced mutants resulted from LOH, whereas in the control cultures 77% of the Tk mutants were LOH . Our results suggest that bromate is a potent mutagen in the Tk gene of mouse lymphoma cells, and the mechanism of action primarily involves LOH . The ability of the mouse lymphoma assay to detect a wider array of mutational events than the microbial or V79 Hprt assays may account for the potent mutagenic response.

J Dairy Sci, 2003 Apr, 86(4), 1292 - 305
Effect of feeding protein supplements of differing degradability on omasal flow of microbial and undegraded protein; Reynal SM et al.; Ten ruminally cannulated lactating Holstein cows that were part of a larger trial studying the effects of feeding different proteins on milk production were used in a replicated 5 x 5 Latin square to quantify flows of microbial and rumen-undegradable protein (RUP) in omasal digesta . Cows were fed total mixed rations containing (dry matter basis) 44% corn silage, 22% alfalfa silage, 2% urea, and 31% concentrate . The basal diet contained 31% high-moisture corn; equal N from one of four protein supplements was added to the other diets at the expense of corn: 9% solvent soybean meal (SSBM), 10% expeller soybean meal (ESBM), 5.5% blood meal (BM), and 7% corn gluten meal (CGM) . Omasal sampling was used to quantify total AA N (TAAN) and nonammonia N (NAN) flows from the rumen . Estimates of RUP were made from differences between total and microbial N flows, including a correction for RUP in the basal diet . Modifying a spectrophotometric assay improved total purine recovery from isolated bacteria and omasal samples and gave estimates of microbial TAAN and NAN flows that were similar to a standard HPLC method . Linear programming, based on AA patterns of the diet and isolated omasal bacteria and ruminal protozoa, appeared to overestimate microbial TAAN and NAN flows compared to the purine assays . Yields of microbial TAAN and NAN determined using any method was not affected by diet and averaged 32 to 35 g NAN per kilogram of organic matter truly digested in the rumen . On average, National Research Council (NRC) equations underpredicted microbial N flows by 152 g/d (vs . HPLC), 168 g/d (vs . spectrophotometry), and 244 g/d (vs . linear programming) . Estimates of RUP (means from the HPLC and spectrophotometric methods) were: SSBM, 27%, ESBM, 45%, BM, 60%, and CGM, 73% . Except for CGM, RUP values averaged about 20 percentage units lower than those reported by the NRC.

Pest Manag Sci, 2003 May, 59(5), 527 - 37
Pesticide degradation in a 'biobed' composting substrate; Fogg P et al.; Pesticides play an important role in the success of modern farming and food production . However, the release of pesticides to the environment arising from non-approved use, poor practice, illegal operations or misuse is increasingly recognised as contributing to water contamination . Biobeds appear to offer a cost-effective method for treating pesticide-contaminated waste . This study was performed to determine whether biobeds can degrade relatively complex pesticide mixtures when applied repeatedly . A pesticide mixture containing isoproturon, pendimethalin, chlorpyrifos, chlorothalonil, epoxiconazole and dimethoate was incubated in biomix and topsoil at concentrations to simulate pesticide disposal . Although the data suggest that interactions between pesticides are possible, the effects were of less significance in biomix than in topsoil . The same mixture was applied on three occasions at 30-day intervals . Degradation was significantly quicker in biomix than in topsoil . The rate of degradation, however, decreased with each additional treatment, possibly due to the toxicity of the pesticide mixture to the microbial community . Incubations with chlorothalonil and pendimethalin carried out in sterile and non-sterile biomix indicated that degradation, rather than irreversible adsorption to the matrix, was the main mechanism responsible for the reduction in recovered residues . Results from these experiments suggest that biobeds offer a viable means of treating pesticide waste.

Antibiot Khimioter, 2003, 48(1), 3 - 8
{Screening of microbial secondary metabolites inhibiting cholesterol biosynthesis with the use of hepatoblastoma G2}; Trenin AS et al.; The culture of hepatoblastoma G2 (Hep G2) cells is proposed as an effective model for screening of microbial metabolites--inhibitors of sterol biosynthesis . This model can be applied at early stages of screening procedures and is quite effective for testing of crude extracts of producers' culture broth . The test is based on measurement inhibition of the radiolabelled precursors incorporation in cholesterol and separate fractions of lipids by microbial metabolites in Hep G2 cells . That allows not only to reveal inhibitors of cholesterol biosynthesis, but also to evaluate mechanism of action, including ability to inhibit the synthesis of cholesterol ethers . The cholesterol biosynthesis inhibition was tested at 150 microbial cultures (actinomycetes and imperfect fungi), isolated from soil . The ability to inhibit 14C-acetate incorporation into cholesterol was found in 15-20% of microbial cultures possessing antifungal activity of extracts (culture broth and mycelium).

Liver Transpl, 2003 May, 9(5), 451 - 62
Impact of donor infections on outcome of orthotopic liver transplantation; Angelis M et al.; Infection occurs when microbial agents enter the host, either through airborne transmission or by direct contact of a substance carrying the infectious agent with the host . Human body fluids, solid organs, or other tissues often are ideal vectors to support microbial agents and can transmit infections efficiently from donor to recipient . In the case of blood transfusion and tissue transplantation, the main consequence of such a transmission is infection of the recipient . However, in the case of solid-organ transplantation, and particularly for liver transplantation, donor infections are not only transmitted to the recipient, the donor infection also may affect the donated liver's preservability and subsequent function in the recipient irrespective of the systemic consequences of the infection . In addition, solid organ recipients of infected organs are less able to respond to the infectious agent because of their immunosuppressive treatment . Thus, transmission of infections from organ donor to liver recipient represents serious potential risks that must be weighed against a candidate's mortality risk without the transplant . However, the ever-increasing gap between the number of donors and those waiting for liver grafts makes consideration of every potential donor, regardless of the infection status, essential to minimize waiting list mortality . In this review, we will focus on assessing the risk of transmission of bacterial, fungal, viral, and parasitic infectious agents from cadaveric liver donors to recipients and the effect such a transmission has on liver function, morbidity, and mortality . We will also discuss risk-benefit deliberations for using organs from infected donors for certain types of recipients . These issues are critically important to maximize the use of donated organs but also minimize recipient morbidity and graft dysfunction.

Acta Pharmacol Sin, 2003 May, 24(5), 442 - 7
Microbial transformation of naproxen by Cunninghamella species; Zhong DF et al.; AIM: The metabolites of naproxen produced by Cunninghamella species were isolated and identified, and further to compare the similarities between microbial transformation and mammalian metabolism . METHODS: Naproxen was transformed by three strains of Cunninghammella species (Cunninghamella blakeslesna AS 3.153, Cunninghamella echinulata AS 3.2004, and Cunninghamella elegans AS 3.156) . The metabolites of naproxen were separated and assayed by liquid chromatography-mass spectrometry method . Semi-preparative HPLC was used to isolate the major metabolite, and the structure was identified by nuclear magnetic resonance (NMR) and mass spectrometry . RESULTS: Naproxen was transformed into 2 metabolites, desmethylnaproxen and desmethylnaproxen-6-O-sulfate, both were the known mammalian metabolites . The conjugated metabolite was newly detected in microbial transformation samples . CONCLUSION: The microbial transformation of naproxen has some similarities with the metabolism of naproxen in mammals . The fungi belonging to Cunninghamella species could be used as complementary in vitro models for drug metabolism to predict and produce the metabolites of drugs in mammals.

Waste Manag Res, 2003 Apr, 21(2), 161 - 71
Carbon mineralisation and plant growth in soil amended with compost samples at different degrees of maturity; Garcia-Gomez A et al.; The carbon and nitrogen mineralisation of a composting mixture of brewing yeast and lemon tree prunings was studied, at different degrees of stabilisation of this matrix, within an incubation experiment in soil . Meanwhile, a growth test in pots with ryegrass (Lolium perenne L.) was carried out using the selected soil and equal amounts of the composting mixture taken at different maturation steps, in order to evaluate the additions of these organic amendments in terms of fertilising value . Samples of the composting mixture, when poorly transformed through the biostabilisation process, showed high CO2-C releases in the soil, due to the microbial attack on easily degradable organic fractions still present in the mixture, with 24.7% mineralisation of the initial total organic carbon (TOC) after a 70 day incubation . On the other hand, mature compost was the most stable matrix, with only 5.4% of TOC mineralised after 70 days . Furthermore, amendments with the initial composting mixture led to negative net N-mineralisation during 56 days of incubation with soil . Only slight negative values of the net N-mineralisation were detected with fully stabilised compost . Nevertheless, pot experiments with ryegrass revealed that mature compost may promote N mineralisation to certain extents . Moreover, mature compost did not produce any phytotoxic effect, behaving as a slow-action organic fertiliser with N made available through a progressive mineralisation . Thus, the results gained through this study are a confirmation that the fertilising quality of a compost destined for agricultural uses is heavily affected by the complete exhaustion of the maturation reactions.

Microb Ecol, 2003 Jul, 46(1), 43 - 54 Epub 2003 May 13.
Factors controlling extremely productive heterotrophic bacterial communities in shallow soda pools; Eiler A et al.; Dilute soda lakes are among the world's most productive environments and are usually dominated by dense blooms of cyanobacteria . Up to now, there has been little information available on heterotrophic bacterial abundance, production, and their controlling factors in these ecosystems . In the present study the main environmental factors responsible for the control of the heterotrophic bacterial community in five shallow soda pools in Eastern Austria were investigated during an annual cycle . Extremely high cyanobacterial numbers and heterotrophic bacterial numbers up to 307 x 10(9) L(-1) and 268 x 10(9) L(-1) were found, respectively . Bacterial secondary production rates up to 738 micro g C L(-1) h(-1) and specific growth rates up to 1.65 h(-1) were recorded in summer and represent the highest reported values for natural aquatic ecosystems . The combination of dense phytoplankton blooms, high temperature, high turbidity, and nutrient concentration due to evaporation is supposed to enable the development of such extremely productive microbial populations . By principal component analysis containing the data set of all five investigated pools, two factors were extracted which explained 62.5% of the total variation of the systems . The first factor could be interpreted as a turbidity factor; the second was assigned to as concentration factor . From this it was deduced that bacterial and cyanobacterial abundance were mainly controlled by wind-induced sediment resuspension and turbidity stabilized by the high pH and salinity and less by evaporative concentration of salinity and dissolved organic carbon . Bacterial production was clustered with temperature in factor 3, showing that bacterial growth was mainly controlled by temperature . The concept of describing the turbid water columns of the shallow soda pools as "fluid sediment" is discussed.

J Immunol Methods, 2003 May 1, 276(1-2), 69 - 77
Immune monitoring in whole blood using real-time PCR; Stordeur P et al.; There is a need for simple and sensitive assays to assess innate and adaptive immune responses to microbial agents and vaccines . Herein, we describe a whole blood method allowing to measure the induction of cytokine synthesis at the mRNA level . The originality of this method consists in the combination of PAXgene tubes containing an mRNA stabilizer for blood collection, the MagNA Pure instrument as an automated system for mRNA extraction and RT-PCR reagent mix preparation, and the real-time PCR methodology on the Lightcycler for accurate and reproducible quantification of transcript levels . We first demonstrated that this method is adequate to measure the induction of interleukin (IL)-1beta and IL-1 receptor antagonist (IL-1 RA) mRNA upon the addition of bacterial lipopolysaccharide (LPS) to whole blood . We then showed that this approach is also suitable to detect the production of mRNA encoding T cell-derived cytokines in whole blood incubated with tetanus toxoid as a model of in vitro immune response to a recall antigen . Finally, we demonstrated that this methodology can be used successfully to assess inflammatory as well as T cell responses in vivo, as it allowed to detect the induction of IL-1beta and IL-1 RA after injection of LPS in healthy volunteers, and also the induction of IL-2 upon recall immunisation with tetanus vaccine.

Chemosphere, 2003 Jul, 52(3), 549 - 56
Release of substituents from phenolic compounds during oxidative coupling reactions; Dec J et al.; Phenolic compounds originating from plant residue decomposition or microbial metabolism form humic-like polymers during oxidative coupling reactions mediated by various phenoloxidases or metal oxides . Xenobiotic phenols participating in these reactions undergo either polymerization or binding to soil organic matter . Another effect of oxidative coupling is dehalogenation, decarboxylation or demethoxylation of the substrates . To investigate these phenomena, several naturally occurring and xenobiotic phenols were incubated with various phenoloxidases (peroxidase, laccase, tyrosinase) or with birnessite (delta-MnO(2)), and monitored for chloride release, CO(2) evolution, and methanol or methane production . The release of chloride ions during polymerization and binding ranged between 0.2% and 41.4% . Using the test compounds labeled with 14C in three different locations (carboxyl group, aromatic ring, or aliphatic chain), it was demonstrated that 14CO(2) evolution was mainly associated with the release of carboxyl groups (17.8-54.8% of the initial radioactivity) . Little mineralization of 14C-labeled aromatic rings or aliphatic carbons occurred in catechol, ferulic or p-coumaric acids (0.1-0.7%) . Demethoxylation ranged from 0.5% to 13.9% for 2,6-dimethoxyphenol and syringic acid, respectively . Methylphenols showed no demethylation . In conclusion, dehalogenation, decarboxylation and demethoxylation of phenolic substrates appear to be controlled by a common mechanism, in which various substituents are released if they are attached to carbon atoms involved in coupling . Electron-withdrawing substituents, such as -COOH and -Cl, are more susceptible to release than electron-donating ones, such as -OCH(3) and -CH(3) . The release of organic substituents during polymerization and binding of phenols may add to CO(2) production in soil.

Sci Total Environ, 2003 Jun 1, 308(1-3), 211 - 20
Incorporation of (15)N-TNT transformation products into humifying plant organic matter as revealed by one- and two-dimensional solid state NMR spectroscopy; Knicker H; Solid-state double cross polarization magic angle spinning (DCPMAS) 15N 13C nuclear magnetic resonance (NMR) spectroscopy was applied to study the incorporation of TNT transformation products into humifying plant organic matter . For this approach, 13C-enriched plant material (Lolium perenne) was mixed with quartz sand and aerobically incubated for 11 months after addition of 15N(3)-2,4,6-trinitrotoluene (TNT) . After successive extraction of the incubate with water, methanol and ethyl acetate, approximately 60% of the 15N added as 15N(3)-TNT (15N(add)) remained in the solid organic residue (SOR-fraction) . The acid insoluble fraction (AI) obtained after NaOH and HCl extractions contained approximately 20% of 15N(add) . For both fractions, 15N NMR spectroscopy revealed an almost complete reduction of the TNT after 11 months of aerobic incubation . Most of the reduced nitrogen groups underwent further condensation . The corresponding DCPMAS NMR spectra allowed the identification of amides that are further substituted by alkyl groups that resist even acid hydrolysis . This assigns them to relatively stable compounds rather than to newly synthesized microbial peptides . The results of this study suggest further that the covalent binding of TNT transformation products to plant derived organic matter is mediated by alkylation and acetylation reactions, rather than by 1,4 addition of TNT-derived nitrogenous groups to quinones of the humic material.

Nat Prod Res, 2003 Jun, 17(3), 215 - 20
Microbial transformation of dehydroepiandrosterone; Choudhary MI et al.; Transformation of dehydroepiandrosterone (DHEA) (1) was carried out by a plant pathogen Rhizopus stolonifer, which resulted in the production of seven metabolites . These metabolites were identified as 3beta,17beta-dihydroxyanandrost-5-ene (2), 3beta,17beta-dihydroxyandrost-4ene (3), 17beta-hydroxyandrost-4-ene-3-one (4), 3beta,11-dihydroxyandrost-4-ene-17-one (5), 3beta,7alpha-dihydroandrost-5-ene-17-one (6), 3A,7alpha,17beta-trihydroxyandrost-5-ene (7) and 11beta-hydroxyandrost-4,6-diene-3,17-dione (8) . The structures of the transformed products were determined by the spectroscopic techniques.

Br Poult Sci, 2003 Mar, 44(1), 53 - 9
Dispersal of micro-organisms in commercial defeathering systems; Allen VM et al.; 1 . The extent of cross contamination between carcases and the dispersal of micro-organisms to the environs during defeathering was measured in a commercial processing plant . 2 . Defeathering reduced the numbers of a marker organism, a nalidixic acid-resistant strain of Escherichia coli K12, on inoculated carcases but dispersed the organism on to preceding and following carcases . 3 . The pattern of microbial dispersal during defeathering was similar for naturally occurring bacteria on the carcase, for example, total aerobic counts and counts of presumptive coliforms, suggesting that the marker organism mimics the natural situation realistically . 4 . The majority of feathers, together with micro-organisms, were removed during the first 10 s of the defeathering process, which was completed in 45 s, indicating that control measures to minimise cross contamination would be most effective if applied in the early stages of the process . 5 . The method of defeathering used by the machine influenced the pattern of microbial dispersal and the extent of cross contamination to other carcases on the same processing line.

Pediatr Res, 2003 Aug, 54(2), 212 - 8 Epub 2003 May 07.
Development of microbial-human enterocyte interaction: cholera toxin; Lu L et al.; Diarrhea in infants and children is a major health hazard worldwide . Certain toxigenic diarrheas occur more commonly and are manifested more severely during the neonatal period . We have previously studied the regulation of cholera toxin-induced secretion in animal models during development . In those studies we have shown that cholera toxin stimulates a much greater secretion by immature compared with mature small intestine, and the mechanism appears to be an up-regulation of postreceptor signal transduction molecules (adenyl cyclase and Gsalpha) leading to an elevated cAMP level . In this study, using experimental models of human intestinal development (fetal cell lines, a micro-Ussing chamber, organ cultures, and fetal intestinal xenograft transplants), we provide preliminary evidence that cholera toxin induces an enhanced secretion mediated in part by a developmental up-regulation of the cAMP response in immature versus mature human small intestine . Additional studies are needed, however, to further define whether other developmental events (e.g . receptor expression) also regulate cholera toxin-enterocyte-enhanced interaction . Nonetheless, this approach to determining the role of development in the pathophysiology of cholera in infants may help in strategies to prevent and treat this condition and other age-related intestinal infectious diseases.

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