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