Microbial

Mol Immunol, 2004 Feb, 40(14-15), 1113 - 20
Induction, acceleration or prevention of autoimmunity by molecular mimicry; Christen U et al.; The hypothesis that cross-reactivity between microbial and self determinants recognized by the adaptive immune system could induce autoimmune diseases is very intriguing . However, definite proof in humans is very difficult to achieve and evidence is frequently circumstantial . Therefore, animal models are instrumental for understanding, how and when mimicry could be involved in the pathogenesis of autoimmunity . In this article, we will discuss experimental scenarios, where mimicry between foreign and self determinants does not cause disease per se, but rather aggravates a pre-existing yet sub-clinical autoimmune condition . We would like to propose that molecular mimicry is more likely to impact on an already existing autoimmune process rather than precipitate novel disease by breaking of tolerance from the beginning . Already activated autoreactive cells might be easier re-activated and primed for effector functions by cross-reactive ligands than naive lymphocytes.

Mol Immunol, 2004 Feb, 40(14-15), 1095 - 102
The elusive case for a role of mimicry in autoimmune diseases; Fourneau JM et al.; The notion that mimicry between a self and a microbial peptide antigen can trigger or aggravate autoimmune pathology remains a popular hypothesis in autoimmunity research . Tremendous recent progress in our understanding of the interface between the T cell receptor (TCR) and peptide/MHC complexes has revealed a vast potential for degenerate recognition of numerous structurally similar pMHC complexes by each T lymphocyte . Moreover, functional and structural studies have confirmed that structural similarity between unrelated pMHC complexes is frequently sufficient for recognition by a single TCR . However, despite clear evidence that vaccination with mimetic microbial antigens has the potential to activate autoreactive T cells, crucial evidence for triggering of autoimmunity by mimetic sequences in natural pathogens is wanting . Antigen spreading, i.e . the fact that the number of self antigens targeted by a chronic autoimmune response tends to increase with its duration, does not facilitate the task of proving initial triggering, or subsequent acceleration, of autoimmune conditions by mimetic microbial antigens . Moreover, considering that activation rather than presence of autoreactive T cells is the hallmark of autoimmune disease, the creation of an environment resulting in failure of tolerance and regulatory mechanisms, rather than emergence of novel microbial antigenic determinants, may well be at the root of autoimmunity . Based on these considerations, we contend that the mimicry concept remains largely hypothetical, and that novel carefully designed animal models are needed to make a convincing case for a role of mimicry in autoimmune diseases.

Mol Immunol, 2004 Feb, 40(14-15), 1063 - 74
A powerful combination: the use of positional scanning libraries and biometrical analysis to identify cross-reactive T cell epitopes; Nino-Vasquez JJ et al.; Studies on the elucidation of the specificity of the T cell receptor (TCR) at the antigen and peptide level have contributed to the current understanding of T cell cross-reactivity . Historically, most studies of T cell specificity and degeneracy have relied on the determination of the effects on T cell recognition of amino acid changes at individual positions or MHC binding residues, and thus they have been limited to a small set of possible ligands . Synthetic combinatorial libraries (SCLs), and in particular positional scanning synthetic combinatorial libraries (PS-SCLs) represent collections of millions to trillions of peptides which allow the unbiased elucidation of T cell ligands that stimulate clones of both known and unknown specificity . PS-SCLs have been used successfully to study T cell recognition and to identify and optimize T cell clone (TCC) epitopes in infectious diseases, autoimmune disorders and tumor antigens . PS-SCL-based biometrical analysis represents a further refinement in the analysis of the data derived from the screening of a library with a TCC . It combines this data with information derived from protein sequence databases to identify natural peptide ligands . PS-SCL-based biometrical analysis provides a method for the determination of new microbial antigen and autoantigen sequences based solely on functional data rather than sequence homology or motifs, making the method ideally suited for the prediction and identification of both native and cross-reactive epitopes by virtue of its ability to integrate the examination of trillions of peptides in a systematic manner with all of the protein sequences in a given database . We review here the application of PS-SCLs and biometrical analysis to identify cross-reactive T cell epitopes, as well as the current efforts to refine this strategy.

Mol Immunol, 2004 Feb, 40(14-15), 1019 - 25
Degenerate recognition of T cell epitopes: impact of T cell receptor reserve and stability of peptide:MHC complexes; Ford ML et al.; The concept of molecular mimicry suggests that microbial pathogens might activate antigen-specific T cells that then cross-react with endogenous antigens and result in the generation of autoimmunity . Here we discuss several under-represented factors impacting the ability of TCRs to recognize a wide spectrum of related peptide:MHC (pMHC) ligands . Two of these factors include the affinity of the peptide for MHC and the level of TCR expression . Thymocytes that recognize peptides with low affinity for MHC avoid negative selection, but mature T cells, by virtue of increased TCR expression, will proliferate in response to these same unstable pMHC complexes . While the expression of a reserve of antigen receptors expands the potential number of epitopes for which a T cell can cross-react, phosphatase activity provides a tuning mechanism to increase the threshold level of activation . Thus, degenerate recognition of T cell epitopes involves the stability of the peptide:MHC complex, the number of TCR expressed, and the level of phosphatase activity.

Semin Immunol, 2004 Apr, 16(2), 119 - 26
Regulatory T cells and organ transplantation; Waldmann H et al.; Empirical studies attempting to explain tolerance to transplanted tissues have demonstrated a regulatory role for CD4+ T-cells . We here propose that regulatory T-cells mediating transplantion tolerance comprise two sets which can functionally complement each other . The CD4+CD25+ "natural regulator" arises in the thymus, and is preoccupied with self-antigens expressed at sites of inflammation . The second, comprising both CD4+CD25+ (FoxP3+) and CD4+CD25- Tr1-like cells are induced by persistent danger-free antigen in the periphery . The role of these cells is to moderate immune responses to prevent tissue destruction while allowing microbial elimination.

Br J Nutr, 2004 Apr, 91(4), 539 - 50
Biohydrogenation of dietary n-3 PUFA and stability of ingested vitamin E in the rumen, and their effects on microbial activity in sheep; Chikunya S et al.; The present study investigated the susceptibility of dietary n-3 PUFA to ruminal biohydrogenation, the stability of ingested vitamin E in the rumen and the subsequent uptake of PUFA and vitamin E into plasma . Six cannulated sheep were assigned to six diets over five 33 d periods, in an incomplete 6x5 Latin square . The diets, based on dried grass, were formulated to supply 50 g fatty acids/kg DM using three lipid sources: Megalac (calcium soap of palm fatty acid distillate; Volac Ltd, Royston, Herts., UK), linseed (formaldehyde-treated; Trouw Nutrition, Northwich, Ches., UK) and linseed-fish oil (formaldehyde-treated linseed+fish oil) . The diets were supplemented with 100 or 500 mg alpha-tocopheryl acetate/kg DM . Fat source or level of vitamin E in the diet did not alter microbial activity in the rumen . Biohydrogenation of linoleic acid (18 : 3n-6; 85-90 %), linolenic acid (18 : 3n-3; 88-93 %), docosahexaenoic acid (22 : 6n-3; 91 %) and EPA (20 : 5n-3; 92 %) was extensive . Feeding formaldehyde-treated linseed elevated concentrations of 18 : 3n-3 in plasma, whilst 22 : 6n-3 and 20 : 5n-3 were only increased by feeding the linseed-fish oil blend . Duodenal recovery of ingested vitamin E was high (range 0.79-0.92 mg/mg fed) . High dietary vitamin E was associated with increased plasma alpha-tocopherol (2.57 v . 1.46 microg/ml for 500 and 100 mg alpha-tocopheryl acetate/kg DM respectively), although all concentrations were low . Plasma vitamin E levels, however, tended to decrease as the type and quantity of PUFA in the diet increased . The present study illustrates that nutritionally beneficial PUFA in both fish and linseed oils are highly susceptible to biohydrogenation in the rumen . Although alpha-tocopheryl acetate resisted degradation in the rumen, plasma vitamin E status remained deficient to borderline, suggesting either that uptake may have been impaired or metabolism post-absorption increased.

J Food Prot, 2004 Mar, 67(3), 583 - 90
Stationary-phase acid resistance and injury of recent bovine Escherichia coli O157 and non-O157 biotype I Escherichia coli isolatest; Berry ED et al.; Stationary-phase acid resistance and the induction of acid resistance were assessed for recent bovine carcass isolates of Escherichia coli, including 39 serotype O157 strains and 20 non-O157 strains . When grown to stationary phase in the absence of glucose and without prior acid exposure, there was a range of responses to a pH challenge of 6 h at pH 2.5 . However, populations of 53 of the 59 E . coli isolates examined were reduced by less than 2.00 log CFU/ml, and populations of 24 of these isolates were reduced by less than 1.00 log CFU/ml . In contrast, there was little variation in population reductions when the E . coli were grown with glucose and preadapted to acidic conditions . With few exceptions, acid adaptation improved survival to the acid challenge, with 57 of the 59 isolates exhibiting a log reduction of less than 0.50 . Differences in acid resistance or the ability to adapt to acidic conditions between E . coli O157:H7 and non-O157 commensal E . coli were not observed . However, we did find that the E . coli O157 were disposed to greater acid injury after the low pH challenge than the non-O157 E . coli, both for cells that were and were not adapted to acidic conditions before the challenge . The enhancement of low pH survival after acid adaptation that was seen among these recent natural isolates of E . coli O157 further supports the idea that the previous environment of this pathogen should be a consideration when designing microbial safety strategies for foods preserved by low pH and acid.

Nat Rev Microbiol, 2003 Nov, 1(2), 92 - 3
Fitting the niche by genomic adaptation; Thomson N et al.; Studying microbial genomics has shown that the genomes of bacteria are extremely dynamic in evolutionary terms . Many research groups have linked the adaptation of an organism to a niche to large changes in genome size and content . A number of recent papers have underlined the degree to which the genomes of different organisms are a reflection of the opportunities and constraints imposed by their chosen niche.

Nat Rev Microbiol . 2004 Jan;2(1):11.
Shrinking genomics; Thomson NR et al.; Two bacteria are featured this month, and both are at the lower end of the genome size scale . The first, Mycoplasma gallisepticum, belongs to a group of bacteria that have been studied both as important human and animal pathogens and in the pursuit of understanding the essential functions of a self-replicating minimal cell . The second, Nanoarchaeum equitans, is an obligate symbiont that only grows in co-culture with another archaeon . N . equitans seems to be the coelacanth of the microbial world--it has been assigned to a new phylum and represents a primitive form of prokaroytic life.

Nat Med, 2004 Apr, 10(4), 416 - 21 Epub 2004 Mar 14.
Reduced atherosclerosis in MyD88-null mice links elevated serum cholesterol levels to activation of innate immunity signaling pathways; Bjorkbacka H et al.; Atherosclerosis, the leading cause of death in developed countries, has been linked to hypercholesterolemia for decades . More recently, atherosclerotic lesion progression has been shown to depend on persistent, chronic inflammation in the artery wall . Although several studies have implicated infectious agents in this process, the role of infection in atherosclerosis remains controversial . Because the involvement of monocytes and macrophages in the pathogenesis of atherosclerosis is well established, we investigated the possibility that macrophage innate immunity signaling pathways normally activated by pathogens might also be activated in response to hyperlipidemia . We examined atherosclerotic lesion development in uninfected, hyperlipidemic mice lacking expression of either lipopolysaccharide (LPS) receptor CD14 or myeloid differentiation protein-88 (MyD88), which transduces cell signaling events downstream of the Toll-like receptors (TLRs), as well as receptors for interleukin-1 (IL-1) and IL-18 . Whereas the MyD88-deficient mice evinced a marked reduction in early atherosclerosis, mice deficient in CD14 had no decrease in early lesion development . Inactivation of the MyD88 pathway led to a reduction in atherosclerosis through a decrease in macrophage recruitment to the artery wall that was associated with reduced chemokine levels . These findings link elevated serum lipid levels to a proinflammatory signaling cascade that is also engaged by microbial pathogens.

Proc Natl Acad Sci U S A, 2004 Apr 13, 101(15), 5598 - 603 Epub 2004 Mar 19.
Recognition of single-stranded RNA viruses by Toll-like receptor 7; Lund JM et al.; Viral infection of mammalian host results in the activation of innate immune responses . Toll-like receptors (TLRs) have been shown to mediate the recognition of many types of pathogens, including viruses . The genomes of viruses possess unique characteristics that are not found in mammalian genomes, such as high CpG content and double-stranded RNA . These genomic nucleic acids serve as molecular signatures associated with viral infections . Here we show that TLR7 recognizes the single-stranded RNA viruses, vesicular stomatitis virus and influenza virus . The recognition of these viruses by plasmacytoid dendritic cells and B cells through TLR7 results in their activation of costimulatory molecules and production of cytokines . Moreover, this recognition required intact endocytic pathways . Mice deficient in either the TLR7 or the TLR adaptor protein MyD88 demonstrated reduced responses to in vivo infection with vesicular stomatitis virus . These results demonstrate microbial ligand recognition by TLR7 and provide insights into the pathways used by the innate immune cells in the recognition of viral pathogens.

J Am Soc Nephrol, 2004 Apr, 15(4), 854 - 67
Signaling danger: toll-like receptors and their potential roles in kidney disease; Anders HJ et al.; Toll-like receptors (TLR) are an emerging family of receptors that recognize pathogen-associated molecular patterns and promote the activation of leukocytes and intrinsic renal cells . Ligands of the TLR include exogenous microbial components such as LPS (TLR4), lipoproteins and peptidoglycans (TLR1, -2, -6), viral RNA (TLR3), bacterial and viral unmethylated cytosin-guanosin dinucleotide (CpG)-DNA (TLR9), and endogenous molecules including heat-shock proteins and extracellular matrix molecules . Upon stimulation, TLR induce expression of inflammatory cytokines or costimulatory molecules via the MyD88-dependent and MyD88-independent signaling pathways shared with the interleukin-1 receptors . TLR are differentially expressed on leukocyte subsets and non-immune cells and appear to regulate important aspects of innate and adaptive immune responses . Tubular epithelial cells are among the non-immune cells that express TLR1, -2, -3, -4, and -6, suggesting that these TLR might contribute to the activation of immune responses in tubulointerstitial injury (e.g., bacterial pyelonephritis, sepsis, and transplant nephropathy) . In addition, TLR9 has been shown to be involved in antigen-induced immune complex glomerulonephritis and lupus nephritis by regulating humoral and cellular immune responses . TLR are evolutionary conserved regulators of innate and adaptive immune responses . It is likely that TLR are involved in many if not all types of renal inflammation . Here the authors provide an overview on the biology of TLR, summarize the present data on their expression in the kidney, and provide an outlook for the potential roles of TLR in kidney disease.

Biotechnol Appl Biochem, 2004 Apr, 39(Pt 2), 209 - 14
Conversion of 7-deoxy-10-deacetylbaccatin-III into 6-alpha-hydroxy-7-deoxy-10-deacetylbaccatin-III by Nocardioides luteus; Hanson RL et al.; 6-alpha-Hydroxy-7-deoxy-10-deacetylbaccatin-III is an intermediate that is potentially useful for synthesis of analogues of paclitaxel . Screening of microbial strains identified an enzyme activity in Nocardioides luteus SC 13912 (A.T.C.C . 55426) which converted 7-deoxy-10-deacetylbaccatin-III into 6-hydroxy-7-deoxy-10-deacetylbaccatin-III with a maximum yield of 44%.

Curr Drug Targets Inflamm Allergy, 2004 Mar, 3(1), 81 - 6
Regulation of innate immunity signaling and its connection with human diseases; Li L; Human innate immunity can respond to diverse microbial products, as well as other substances such as heat shock proteins, taxol, and unsaturated fatty acids . Mediated largely by a family of Toll-like-receptors (TLR) and associated intracellular downstream signaling molecules, human innate immune response serves multiple functions ranging from providing the first line of defense to coordinating cellular growth as well as other cellular functions . To date, about 10 distinct human TLR receptors have been identified in the human genome . Biochemical studies and genetic analyses using transgenic mice have revealed specific ligands for several TLR receptors . TLR intracellular domains could then specifically recruit several adaptor proteins including MyD88, TIRAP/MAL, TRIF, and TOLLIP . These adaptor proteins subsequently associate with a family of interleukin-1 receptor-associated kinases (IRAK1, 2, M, and 4) . Recruitments of numerous downstream signaling proteins lead to activation of a range of transcription factors such as NF kappa B, AP-1, and IRFs, which are responsible for specific gene transcriptions . Human innate immunity is manifested in diverse cells and tissues . Well-coordinated innate immunity signaling enables human cells and tissues to properly respond to various substances . Improper regulations of such event have been shown to cause various diseases including asthma, atherosclerosis, and cancer . TLR receptors as well as other intracellular signaling proteins can potentially serve as therapeutic targets for numerous human diseases . This review will discuss at the molecular level, regulation of innate immunity signaling as well as its intricate connection with human diseases.

Annu Rev Immunol, 2004, 22, 683 - 709
T lymphocyte-endothelial cell interactions; Choi J et al.; Human vascular endothelial cells (EC) basally display class I and II MHC-peptide complexes on their surface and come in regular contact with circulating T cells . We propose that EC present microbial antigens to memory T cells as a mechanism of immune surveillance . Activated T cells, in turn, provide both soluble and contact-dependent signals to modulate normal EC functions, including formation and remodeling of blood vessels, regulation of blood flow, regulation of blood fluidity, maintenance of permselectivity, recruitment of inflammatory leukocytes, and antigen presentation leading to activation of T cells . T cell interactions with vascular EC are thus bidirectional and link the immune and circulatory systems.

Annu Rev Immunol, 2004, 22, 457 - 83
Drosophila: the genetics of innate immune recognition and response; Brennan CA et al.; Because of the evolutionary conservation of innate mechanisms of host defense, Drosophila has emerged as an ideal animal in which to study the genetic control of immune recognition and responses . The discovery that the Toll pathway is required for defense against fungal infection in Drosophila was pivotal in studies of both mammalian and Drosophila immunity . Subsequent genetic screens in Drosophila to isolate additional mutants unable to induce humoral responses to infection have identified and ordered the function of components of two signaling cascades, the Toll and Imd pathways, that activate responses to infection . Drosophila blood cells also contribute to host defense through phagocytosis and signaling, and may carry out a form of self-nonself recognition that is independent of microbial pattern recognition . Recent work suggests that Drosophila will be a useful model for dissecting virulence mechanisms of several medically important pathogens.

Annu Rev Immunol, 2004, 22, 33 - 54
Self- and nonself-recognition by C-type lectins on dendritic cells; Geijtenbeek TB et al.; Dendritic cells (DCs) are highly efficient antigen-presenting cells (APCs) that collect antigen in body tissues and transport them to draining lymph nodes . Antigenic peptides are loaded onto major histocompatibility complex (MHC) molecules for presentation to naive T cells, resulting in the induction of cellular and humoral immune responses . DCs take up antigen through phagocytosis, pinocytosis, and endocytosis via different groups of receptor families, such as Fc receptors for antigen-antibody complexes, C-type lectin receptors (CLRs) for glycoproteins, and pattern recognition receptors, such as Toll-like receptors (TLRs), for microbial antigens . Uptake of antigen by CLRs leads to presentation of antigens on MHC class I and II molecules . DCs are well equipped to distinguish between self- and nonself-antigens by the variable expression of cell-surface receptors such as CLRs and TLRs . In the steady state, DCs are not immunologically quiescent but use their antigen-handling capacities to maintain peripheral tolerance . DCs are continuously sampling and presenting self- and harmless environmental proteins to silence immune activation . Uptake of self-components in the intestine and airways are good examples of sites where continuous presentation of self- and foreign antigens occurs without immune activation . In contrast, efficient antigen-specific immune activation occurs upon encounter of DCs with nonself-pathogens . Recognition of pathogens by DCs triggers specific receptors such as TLRs that result in DC maturation and subsequently immune activation . Here we discuss the concept that cross talk between TLRs and CLRs, differentially expressed by subsets of DCs, accounts for the different pathways to peripheral tolerance, such as deletion and suppression, and immune activation.

Ying Yong Sheng Tai Xue Bao, 2003 Dec, 14(12), 2278 - 80
{Seasonal variations of soil microbial biomass, respiration rate and CH4 emission in black earth rice fields}; Liang W et al.; The measurements of soil microbial biomass C, respiration rate and CH4 emissions during one rice growth period in black earth rice fields showed that the soil microbial biomass C and respiration rate were depressed significantly by the application of slow-releasing urea at the early stage of rice growth period (P < 0.05), but almost not affected by intermittent irrigation . The CH4 emission was decreased by 32.5% in the intermittent irrigation treatments, but not significantly affected by the application of slow-releasing urea, compared to the control . It was significantly related to soil microbial biomass C in slow-releasing urea treatments.

Ying Yong Sheng Tai Xue Bao, 2003 Dec, 14(12), 2225 - 8
{Effect of straw pretreatment on soil microbial biomass and respiration activity}; Li G et al.; Winter wheat straw particles (0.5 ~ 2.0mm) were soaked with 8.0 g.L-1 H202(pH11.0), 12.5 g.L-1 Na0H or H2S04 solution for 8 h and dried at 80 degreeC . Soils amended with the pretreated straw and inorganic N were incubated aerobically at 25 degreeC for 60 days . The C02 emission rate and soil microbial biomass C and N were measured at different time . The results showed that during the earlier stage of incubation, the pretreatments of straw increased soil microbial biomass C by 1.0 ~ 1.4 folds, but decreased soil microbial respiration activity . During the later stage of incubation, the Na0H and H2S04 pretreated straw decreased soil microbial biomass carbon by 28% and 42%, respectively, while increased the soil microbial respiration activity . The straw pretreated by H202 increased soil microbial biomass nitrogen by 90% after the 15th day of incubation . The pretreatments of straw increased the fungi/bacteria ratio at different special time . It could be concluded that soil microbial biomass and respiration activity could be changed after the pretreated straw was added into the soil.

Environ Manage . 2004 Mar 23; {Epub ahead of print}
Influence of Irrigated Agriculture on Soil Carbon and Microbial Community Structure; Entry JA et al.; Increasing the amount of carbon (C) in soils is one method to reduce the concentration of carbon dixoide (CO(2)) in the atmosphere . We measured organic C stored in southern Idaho soils having long-term cropping histories that supported native sagebrush vegetation (NSB), irrigated moldboard plowed crops (IMP), irrigated conservation-chisel-tilled crops (ICT), and irrigated pasture systems (IP) . The CO(2) emitted as a result of fertilizer production, farm operations, and CO(2) lost via dissolved carbonate in irrigation water, over a 30-year period, was estimated and used to calculate net C fixation . Organic C in ecosystems decreased in the order IP>ICT>IMP> NSB . In February 2001, active fungal, bacterial, and microbial biomass was greater in IP soils than all other soils . Active fungal, bacterial, and microbial biomass was least in ICT soils at the 15-30-cm depth than all other soils . In August 2001, active bacterial biomass was greater in IMP soils than IP, ICT, and NSB soils . Active fungal biomass was greater in IP soils than all other soils . Whole-soil fatty acid profiles differed among management regimes and sampling dates and, to a lesser extent, with soil depth . FAME profiles from the NSB soils were distinct from the agricultural treatments and contained greater amounts of total fatty acids than the other treatments . The IMP and ICT soils yielded fatty acid profiles that were similar to each other, although those at the 15-30-cm depth were distinct from all other treatment-depth combinations . The IP FAME profiles suggest that arbuscular mycorrhizal fungi are more common in these soils than soils from the other treatments . Differences in carbon substrate utilization patterns (BIOLOG) among treatments were more variable and less pronounced that FAME results . In general, irrigated arid soils can both increase C storage while increasing microbial biomass and changing microbial diversity.

Environ Int, 2004 Jun, 30(4), 491 - 9
Effect of arsenic contamination on microbial biomass and its activities in arsenic contaminated soils of Gangetic West Bengal, India; Ghosh AK et al.; A study was conducted to see the effect of arsenic contamination on soil quality indicators, viz., microbial biomass, soil respiration, fluorescein diacetate and dehydrogenase (DHG) activity in arsenic contaminated soils of West Bengal . All the parameters were significantly and negatively correlated with all the form of arsenic (bioavailable and total) but the microbial metabolic quotient was significantly and positively correlated with all forms of arsenic, indicating arsenic induced stress to the soil microbial community . This may be due to part of the microbial biomass, which is located in the inner parts of the micro-aggregates of soil, which is affected by arsenic accumulates present in soil particles . Linear regression analysis revealed that the bioavailable arsenic exerted greater inhibitory effect on the soil microbial population than the total arsenic content of soils . Water-soluble arsenic showed more inhibitory effect than NaHCO(3) extractable form, in their association with biological properties of the contaminated soils . Water-soluble form of arsenic was much more toxic than insoluble forms . This signified that with increase in bioavailability, the arsenic exerted more inhibitory effect on these parameters . It is thus suggested that the microbial biomass, fluorescein diacetate and dehydrogenase activity alone and expressed on a soil organic matter basis along with the soil respiration parameters can be helpful in assessing the effects of arsenic on the size and activity of microbial biomass in soils.

Crit Rev Immunol, 2003, 23(5-6), 339 - 70
Features and functions of gamma delta T lymphocytes: focus on chemokines and their receptors; Kabelitz D et al.; gamma delta T cells are a distinct subgroup of T lymphocytes that are enriched at certain anatomical localizations, such as the small intestinal epithelia and other epithelia . gamma delta T cells recognize microbial antigens, such as heat shock proteins (in mice) or phosphorylated bacterial metabolites (in humans), and control the integrity of epithelia . At the effector cell level, they share with the conventional alpha beta T lymphocytes potent cytotoxic activity and the capacity to produce a variety of cytokines, including specific cytokines such as keratinocyte growth factor . Here we summarize the current knowledge on the role of chemokines and their receptors in the migration and function of gamma delta T cells . As an example, the migration of gamma delta T cells to the small intestine is guided by the chemokine receptor CCR9 and the local expression of the corresponding ligand CCL25 (also termed thymus-expressed chemokine, TECK) . Chemokine receptor expression also correlates with the functional program of T cells . In this respect, the strong expression of the MIP-1 alpha/MIP-1 beta/RANTES (CCL3/CCL4/CCL5)-receptor CCR5 correlates with a T-helper 1 phenotype of human V gamma 9V delta 2-expressing gamma delta T cells . The regulation of chemokine receptors, together with the pattern of local chemokine production, plays an important role in the localization of gamma delta T cells under physiological and pathophysiological conditions, such as infection, inflammation, and tumor defense.

Risk Anal, 2004 Feb, 24(1), 221 - 36
A dynamic model to assess microbial health risks associated with beneficial uses of biosolids; Eisenberg JN et al.; There is increasing interest in the development of a microbial risk assessment methodology for regulatory and operational decision making . This document presents a methodology for assessing risks to human health from pathogen exposure using a population-based model that explicitly accounts for properties unique to an infectious disease process, specifically secondary transmission and immunity . To demonstrate the applicability of this risk-based method, numerical simulations were carried out for a case study example in which the route of exposure was direct consumption of biosolids-amended soil and the pathogen present in the soil was enterovirus . The output from the case study yielded a decision tree that differentiates between conditions in which the relative risk from biosolids exposure is high and those conditions in which the relative risk from biosolids is low . This decision tree illustrates the interaction among the important factors in quantifying risk . For the case study example, these factors include biosolids treatment processes, the pathogen shedding rate of infectious individuals, secondary transmission, and immunity . Further refinement in methods for determining biosolids exposures under field conditions would certainly increase the utility of these approaches.

Risk Anal, 2004 Feb, 24(1), 197 - 208
Defining susceptibility for microbial risk assessment: results of a workshop; Balbus J et al.; An interdisciplinary workshop was convened by the George Washington University in June 2001 to discuss how to incorporate new knowledge about susceptibility to microbial pathogens into risk assessment and management strategies . Experts from government, academic, and private sector organizations discussed definitions, methods, data needs, and issues related to susceptibility in microbial risk assessment . The participants agreed that modeling approaches need to account for the highly specific nature of host-pathogen relationships, and the wide variability of infectivity, immunity, disease transmission, and outcome rates within microbial species and strains . Concerns were raised about distinguishing between exposure and dose more clearly, interpreting experimental and outbreak data correctly, and using thresholds and possibly linearity at low doses . Recommendations were made to advance microbial risk assessment by defining specific terms and concepts more precisely, designing explicit conceptual frameworks to guide development of more complex models and data collection, addressing susceptibility in all steps of the model, measuring components of immunity to characterize susceptibility, reexamining underlying assumptions, applying default methods appropriately, obtaining more mechanistic data to improve default methods, and developing more biologically relevant and continuous risk estimators . The interrelated impacts of selecting specific subpopulations and health outcomes, and of increasing model complexity and data demands, were considered in the contexts of public policy goals and resources required . The participants stated that zero risk is unattainable, so targeted and effective risk reduction and communication strategies are essential not only to raise pubic awareness about water quality but also to protect the most susceptible members of the population.

J Med Chem, 2004 Mar 25, 47(7), 1796 - 806
Fluorinated phenylcyclopropylamines . 1 . Synthesis and effect of fluorine substitution at the cyclopropane ring on inhibition of microbial tyramine oxidase; Yoshida S et al.; Two series of diastereopure phenylcyclopropylamine analogues, 2-fluoro-2-phenylcyclopropylamines and 2-fluoro-2-phenylcyclopropylalkylamines, as well as 2-fluoro-1-phenylcyclopropylamines and 2-fluoro-1-phenylcyclopropylmethylamines, were synthesized in order to study the effects of fluorine substitution on monoamine oxidase inhibition . Inhibitory activity was assayed using commercially available microbial tyramine oxidase . Characterization of tyramine oxidase, carried out prior to the inhibition experiments, confirmed earlier suggestions that this enzyme is a semicarbazide-sensitive copper-containing monoamine oxidase . The most potent competitive inhibitor was trans-2-fluoro-2-phenylcyclopropylamine, which had an IC(50) value 10 times lower than that of the nonfluorinated compound, tranylcypromine . 2-Fluoro-1-phenylcyclopropylmethylamine was found to be a weak noncompetitive inhibitor of tyramine oxidase . The presence of a free amino group, directly bonded to the cyclopropane ring, and a fluorine atom in a relationship cis to the amino group were structural features that increased tyramine oxidase inhibition.

Biologicals, 2004 Mar, 32(1), 49 - 55
A freeze-dried fibrin disc as a biodegradable drug release matrix; Kumar TR et al.; A fibrin clot loaded with soluble tetracycline (TET) was prepared and lyophilized to make discs of a size and shape to use as a drug delivery matrix . On subcutaneous implantation of these discs in mice, they were found to have degraded in 15 days as evidenced by gross and histological examination . The in vitro discharge kinetics of tetracycline from the disc into phosphate buffered saline (PBS) and human serum were compared . It was observed that the release rate of tetracycline from the matrix into serum remained steady from day 1 to day 12, maintaining sufficient concentration that may be required to control microbial growth in the medium . Two different concentrations of fibrinogen were used to fabricate discs denoted as FG200 and FG100, and in both cases the retention rate was comparable when the study medium was serum . In contrast, when suspended in PBS instead of serum, the delivery of the drug into the medium was found to be high for up to the 3rd day when a sharp decline in discharge was observed . The fibrinogen used is a factor that determines not only the longevity of discharge but also fibrinolysis . The degradation of the disc in vitro was visible when the discs were suspended in the buffer, and correspondingly fibrin degradation product (FDP) measured in the medium using an antibody-based assay system was high . Fibrin disc is haemostatic and biodegradable in vivo, and in vitro release of a small molecule at a controlled rate is demonstrated here . Hence, it may be a suitable candidate as a drug delivery implant for short-term use.

Novartis Found Symp, 2004, 257, 25 - 37; discussion 37-50, 276-85
Rethinking Th2 antibody responses and allergic sensitization; Stern D et al.; Human Th2 cytokines (interleukins 4 and 13) induce co-expression of IgE and IgG4 through sequential switching . The regulation of IgG4 responses and the role of these responses in the pathogenesis of allergy have not been characterized . We are addressing these issues by comparing and contrasting the expression of allergen-specific IgE and IgG4 in a population of European children thoroughly defined for lifestyle, environmental exposures and allergic phenotypes . The current analysis focused exclusively on children from non-farming families (n=493) in order to avoid potential effects of exposure to microbial products abundant in farming environments . We found that allergens induce Th2-mediated IgG4 and/or IgE responses in the majority of the population . Approximately two-thirds of the children had allergen-specific IgG4 but not IgE, only a minority had both IgG4 and IgE, only a few were negative for both, and virtually none had only IgE . The prevalence of asthma and hay fever was dramatically higher in children with high IgG4 and IgE compared to children who only mounted IgG4 or low IgG4 and IgE responses . These results appear to recapitulate different stages of in vivo Th2-dependent sequential switching from IgG4 to IgE . These patterns of Th2-induced antibody responses may warrant a redefinition of the notion of allergen sensitization.

J Periodontol, 2004 Jan, 75(1), 57 - 65
Efficacy of a fluoridated hydrogen peroxide-based mouthrinse for the treatment of gingivitis: a randomized clinical trial; Hasturk H et al.; BACKGROUND: A randomized clinical trial was performed to test the efficacy of a fluoridated hydrogen peroxide-based mouthrinse on gingivitis and tooth whitening in a two-phase study . The first phase (28 days) included the experimental gingivitis phase; the second phase (5 months) was the oral hygiene phase, which included rinsing . METHODS: A total of 99 subjects were included in the study and were randomly assigned to receive either placebo or test mouthrinse . Clinical measures were chosen to reflect the gingival health and tooth whiteness in an intent-to-treat study design . Statistical analyses of clinical parameters related to gingival health and tooth color were conducted, using the method of generalized estimating equations (GEE), with an exchangeable working correlation to accommodate tooth-level data . Baseline differences between the groups were adjusted . Microbial samples taken at the beginning and at the end of the study were analyzed by DNA-DNA hybridization technique, to determine whether there was any adverse shift in supragingival flora . RESULTS: Eastman bleeding index, modified gingival index, intensity of stain, and extent of stain were significantly reduced in the test group at 6 months compared to baseline (P < 0.05) . In contrast, only the Eastman bleeding index was significantly reduced in the control group (P < 0.05) . The reduction in the index of gingival inflammation for the test group was significantly greater than for the control group (P = 0.004) . Subjects using the test rinse were also six times more likely to exhibit an improvement in tooth color after 6 months than were subjects using placebo (P = 0.002) . As a result of the clinical evaluations and microbial analysis, test mouthrinse was found to be safe during a 6-month period . CONCLUSION: The results of this study indicate that the fluoridated hydrogen peroxide-based mouthrinse effectively whitens teeth and significantly reduces gingivitis.

J Periodontol, 2004 Jan, 75(1), 30 - 6
Analysis of the interleukin-6 gene promoter polymorphisms in Czech patients with chronic periodontitis; Holla LI et al.; BACKGROUND: Chronic periodontitis is an inflammatory disease, which is a major cause of tooth loss . The proinflammatory cytokines interleukin-1 (IL-1) and interleukin-6 (IL-6) are key regulators of the host response to microbial infection and major modulators of extracellular matrix catabolism and bone resorption . The purpose of this study was to investigate the associations of chronic periodontitis with IL-6 gene polymorphisms (at positions -597 {G/A}, -572 {G/C}, and -174 {G/C}) . METHODS: We analyzed allele, genotype, and haplotype distributions of the IL-6 promoter variants in a case-control study involving 148 patients with chronic periodontitis and 107 unrelated controls . RESULTS: Our results showed significant differences in the distributions of alleles and genotypes of the IL-6 (-572 G/C) polymorphism between patients and the control population (chi2 = 10.393, P= 0.001, P(corr) < 0.01) . The difference was due to the underrepresentation of the -572 G/C heterozygotes in patients (6.1%) compared to controls (19.6%) . Although no variant "CC" homozygotes were detected in our cases and controls, heterozygosity protected against chronic periodontitis, representing a 73% reduction of risk (odds ratio {OR} = 0.27, 95% confidence interval: 0.12-0.61) compared to wild-type homozygotes . However, there were no significant differences in genotype or allele frequencies between both groups for IL-6 -597 G/A and -174 G/C polymorphisms . CONCLUSION: This study is the first, to our knowledge, suggesting that the -572 G/C polymorphism of the IL-6 gene may be one of the protective factors associated with lower susceptibility to chronic periodontitis.

Zh Mikrobiol Epidemiol Immunobiol, 2004 Jan-Feb, (1), 67 - 9
{Diagnostic suspension for detection of the infective agent of tularemia}; Zharnikova IV; The matrix for obtaining silica-based diagnosticum was selected, its activation with surfactant was optimized and its immobilization with tularemia immunoglobulins was carried out . In the glass suspension agglutination test (SAT) the sensitivity of the diagnosticum was 3.125 x 10(6) to 6.25 x 10(6) microbial cells per ml; the duration of SAT, including the evaluation of its results, was 1-5 minutes.

Nat Biotechnol, 2004 Apr, 22(4), 435 - 9 Epub 2004 Mar 14.
A nanoliter-scale nucleic acid processor with parallel architecture; Hong JW et al.; The purification of nucleic acids from microbial and mammalian cells is a crucial step in many biological and medical applications . We have developed microfluidic chips for automated nucleic acid purification from small numbers of bacterial or mammalian cells . All processes, such as cell isolation, cell lysis, DNA or mRNA purification, and recovery, were carried out on a single microfluidic chip in nanoliter volumes without any pre- or postsample treatment . Measurable amounts of mRNA were extracted in an automated fashion from as little as a single mammalian cell and recovered from the chip . These microfluidic chips are capable of processing different samples in parallel, thereby illustrating how highly parallel microfluidic architectures can be constructed to perform integrated batch-processing functionalities for biological and medical applications.

Heart Lung, 2004 Mar-Apr, 33(2), 83 - 91
Duration of action of a single, early oral application of chlorhexidine on oral microbial flora in mechanically ventilated patients: a pilot study; Grap MJ et al.; OBJECTIVE: The purpose of this study was to describe the effect of an early post-intubation oral application of chlorhexidine gluconate on oral microbial flora and ventilator-associated pneumonia . METHODS: Thirty-four intubated patients were randomly assigned to chlorhexidine gluconate by spray or swab or to control group . Oral cultures were done at study admission, 12, 24, 48, and 72 hours, whereas the Clinical Pulmonary Infection Score (CPIS) was documented at study admission, 48, and 72 hours . RESULTS: Reductions in oral culture scores (less growth) were only found in the treatment groups (swab and spray); no reduction was found in the control group . There was a trend for fewer positive cultures in the combined treatment groups . The mean CPIS for the control group increased to a level indicating pneumonia (4.7 to 6.6), whereas the CPIS for the treatment group increased only slightly (5.17 to 5.57) . CONCLUSIONS: Trends in the data suggest that use of chlorhexidine gluconate in the early post-intubation period may mitigate or delay the development of ventilator-associated pneumonia.

Asia Pac J Clin Nutr . 2003;12 Suppl:S36.
Relationship between colour and aroma of olive oil and nutritional content; Fielding JM et al.; Background - Olive oil contains some minor constituents including, characteristic phenolic compounds which contribute to the stability of the oil, antioxidant properties, lipoxygenase activity inhibition and microbial activity . Objective - To determine differences between olive and sunflower oils in regards to nutrient/phytochemical concentration, and to correlate these factors with the colour and aroma of the oils . Design - This study investigated 13 oils in relation to their aroma, colour and nutritional qualities . The oils included extra virgin olive oil, light olive oil and sunflower oil . The phenolic compound, carotenoid, vitamin E and fatty acid composition was measured . These parameters were compared and correlated to the colour measures (L*a*b) and electronic nose responses for each oil . Outcomes - Two Australian extra virgin olive oils contained the highest concentration of phenolic compounds, including oleuropein aglycone (P<0.05) . Imported olive oils contained the highest beta- carotene concentration compared with local oils (P=0.002) . Chroma (b*) was significantly related to lutein and zeaxanthin concentrations (R(2) =0.756, P=0.003) . The responses of three electronic nose sensors (LY/LG, LY/G, LY/AA) significantly correlated with oleuropein aglycone concentrations (P< 0.02) . Conclusions - These results have implications for food processors and consumers who wish to choose oils that have high phytonutrient content: Oils that are high in phenolic compounds and lutein/zeaxanthin can be readily identified, by using aroma and colour measurements.

Curr Opin Immunol, 2004 Apr, 16(2), 226 - 34
Plasma cell differentiation and multiple myeloma; Shapiro-Shelef M et al.; Microarray analyses and gene targeting have recently enhanced the understanding of factors involved in normal plasma cells and multiple myeloma . Plasma cells develop from marginal zone or germinal center B cells following stimulation by antigen, microbial products, TNF family signals and cytokines . Transcription factors, B-lymphocyte-induced maturation protein 1 (Blimp-1) and X-box binding protein 1 (XBP-1) are required for plasma cell development . They regulate sets of genes that induce immunoglobulin secretion, halt proliferation and block alternative B-cell fates . In multiple myeloma, transforming events lead to proliferation and survival, but programs for plasma cell differentiation and the inhibition of B-cell genes appear to be largely intact.

J Environ Sci Health B, 2004 Jan, 39(1), 125 - 38
RAPD marker and substrate utilization pattern applied to study microbial community diversity in the soil affected by agricultural chemicals; Yang YH et al.; Present analyses of random amplified polymorphic DNA (RAPD) and Biolog GN substrate utilization pattern are combined to further study the diversity of microbial communities in four soils affected by agricultural chemicals . The results showed that the four soil microbial communities were apparently distinguishable in the diversity at RAPD level in terms of the richness and modified richness in the summer, which supports our previous report using the same soils in winter . A significant difference for the average well color development (AWCD) at 72 h incubation was found among the soils in winter using Biolog GN substrate utilization pattern, but this difference was not found among the soils in summer . However, Shannon-Weaver indices for microbial communities in the summer soils polluted by agricultural chemicals were significantly higher than those in winter at metabolic level; in contrast, no significant difference existed between the two seasons for microbial communities in the soil without chemical pollution . Present results suggest that the combined approach using RAPD and substrate utilization pattern could be used to effectively quantify microbial community diversity and its changes among the seasons in the soils affected by agricultural chemicals, simultaneously at molecular and physiological levels.

Curr Opin Infect Dis, 2004 Apr, 17(2), 113 - 9
New developments in the pathogenesis of acute exacerbations of chronic obstructive pulmonary disease; Sethi S; PURPOSE OF REVIEW: Acute exacerbations of chronic obstructive pulmonary disease were a poorly defined and understood entity . The application of better study designs and new research methodologies has shed considerable light on the pathogenesis of this common clinical syndrome . RECENT FINDINGS: Inflammation is an important component of the pathogenesis of chronic obstructive pulmonary disease, and exacerbations probably represent acute increases in airway inflammation brought about by one or more etiological agents . Environmental particulate and gaseous pollutants have been linked in epidemiological studies with increased respiratory symptoms and mortality in chronic obstructive pulmonary disease . Bacterial, viral and atypical pathogens, either alone or in concert, induce the majority of acute exacerbations . SUMMARY: A bacterial cause of a substantial proportion of exacerbations is now firmly established by the results of bronchoscopy, molecular epidemiology, immunology and airway inflammation studies . Future research should focus on pathogenic mechanisms and host defence against the microbial pathogens associated with acute exacerbations of chronic obstructive pulmonary disease, in order to develop better treatment and prevention strategies.

J Leukoc Biol, 2004 Jun, 75(6), 1166 - 72 Epub 2004 Mar 12.
Estrogen receptor-alpha deficiency promotes increased TNF-alpha secretion and bacterial killing by murine macrophages in response to microbial stimuli in vitro; Lambert KC et al.; In this series of studies, we determined the potential role of intracellular estrogen receptors (ER), ERalpha and ERbeta, on macrophage function in response to bacterial stimuli . The sex hormone 17beta-estradiol (E(2)) and ER have been shown to modulate inflammatory responses as well as T helper cell type 1 (TH1)/TH2 responses . The mechanisms E(2) and its receptors use to alter these immune functions remain largely unknown . ERalpha and ERbeta possess complex actions in tissues where they are expressed . We have characterized the receptor repertoire of murine dendritic cells and thioglycollate-elicited peritoneal macrophages (PM) . Both cell types express mRNA for ERalpha . Neither cell type expressed detectable amounts of ERbeta mRNA, as determined by reverse transcriptase-polymerase chain reaction using exon-specific primers spanning each of the seven intron/exon junctions . Primary macrophages from ERalpha- and ERbeta-deficient severe combined immunodeficiency mice {ERalpha knockout (KO) and ERssKO, respectively} were used to delineate the effects and potential mechanisms via which steroid receptors modulate macrophage function . ERalpha-deficient PM exposed ex vivo to lipopolysaccharide or Mycobacterium avium exhibited significant increases in tumor necrosis factor alpha (TNF-alpha) secretion as well as reduction in bacterial load when compared with wild-type (WT) PM . In contrast, ERbeta-deficient PM possessed no significant difference in TNF-alpha secretion or in bacterial load when compared with WT littermates . These studies suggest that ERalpha, but not ERbeta, modulates murine PM function.

Genetics, 2004 Feb, 166(2), 669 - 80
General stress response regulator RpoS in adaptive mutation and amplification in Escherichia coli; Lombardo MJ et al.; Microbial cells under growth-limiting stress can generate mutations by mechanisms distinct from those in rapidly growing cells . These mechanisms might be specific stress responses that increase mutation rates, potentially altering rates of evolution, or might reflect non-stress-specific processes in rare growing cells . In an Escherichia coli model system, both frameshift reversion mutations and gene amplifications occur as apparent starvation-induced mutations . Whereas frameshift reversion ("point mutation") requires recombination proteins, the SOS response, and error-prone DNA polymerase IV (DinB), amplification requires neither SOS nor pol IV . We report that both point mutation and amplification require the stationary-phase and general stress response transcription factor RpoS (sigmaS) . Growth-dependent mutation does not . Alternative interpretations are excluded . The results imply, first, that point mutation and amplification are stress responses that occur in differentiated stationary-phase (not rare growing) cells and, second, that transient genetic instability, producing both point mutation and genome rearrangement, may be a previously unrecognized component of the RpoS-dependent general stress response.

Biomaterials, 2004 Aug, 25(17), 3743 - 50
A novel polymeric chlorhexidine delivery device for the treatment of periodontal disease; Yue IC et al.; An implantable, anti-microbial delivery device for the treatment of periodontal disease has been developed . In this polymer-based delivery system, the encapsulation efficiency, release characteristics, and bioactivity of anti-microbial agent were controlled by the complexation of the drug with cyclodextrins of differing lipophilicity . Microparticles of poly(dl-lactic-co-glycolic acid) (PLGA) containing chlorhexidine (Chx) free base, chlorhexidine digluconate (Chx-Dg) and their association or inclusion complex with methylated-beta-cyclodextrin (MBCD) and hydroxypropyl-beta-cyclodextrin (HPBCD) were prepared by single emulsion, solvent evaporation technique . It was observed that encapsulation efficiency and release of the chlorhexidine derivatives from the microparticles was a function of the lipophilicity of the cyclodextrin . Complexation of the poorly water soluble Chx with the more hydrophilic HPBCD resulted in 62% higher encapsulation efficiency and longer duration of sustained release over a 2-week period than complexation with the more lipophilic MBCD . In contrast, the complexation of the more water-soluble derivative of chlorhexidine, Chx-Dg, with the more lipophilic MBCD improved encapsulation efficiency by 12% and prolonged its release in comparison to both the free Chx-Dg and its complex with HPBCD . Furthermore, it was observed that the initial burst effect could be diminished by complexation with CD . Preliminary studies have shown that the chlorhexidine released from PLGA chips is biologically active against bacterial population that is relevant in periodontitis (P . gingivalis and B . forsythus) and a healthy inhibition zone is maintained in agar plate assay over a period of at least a 1-week . The PLGA/CD delivery system described in this paper may prove useful for the localized delivery of chlorhexidine salts and other anti-microbial agents in the treatment of periodontal disease where prolonged-controlled delivery is desired.

J Hosp Infect, 2004 Feb, 56(2), 85 - 92
Ventilation performance in operating theatres against airborne infection: review of research activities and practical guidance; Chow TT et al.; Surgical site infection risk due to airborne bacteria is a key area of consideration in developing operating theatre ventilation design and monitoring procedures . This paper reviews the recent extensive research into operating theatre ventilation development in relation to the design concepts in operating theatre layout, pressurization and ventilation, particularly the evolvement of ultra-clean ventilation . The findings that led to the current technical standards and the developments of microbial measurements and numerical techniques are discussed . Since the late 1980s, computational fluid dynamics has been a fast developing tool used in the prediction of room air distribution and contaminant dispersion . The basic principles and current practice applying to operating theatre ventilation studies are introduced.

Science, 2004 Mar 12, 303(5664), 1656 - 8
Microbial polysaccharides template assembly of nanocrystal fibers; Chan CS et al.; Biological systems can produce extraordinary inorganic structures and morphologies . The mechanisms of synthesis are poorly understood but are of great interest for engineering novel materials . We use spectromicroscopy to show that microbially generated submicrometer-diameter iron oxyhydroxide (FeOOH) filaments contain polysaccharides, providing an explanation for the formation of akaganeite pseudo-single crystals with aspect ratios of approximately 1000:1 . We infer that the cells extrude the polysaccharide strands to localize FeOOH precipitation in proximity to the cell membrane to harness the proton gradient for energy generation . Characterization of organic compounds with high spatial resolution, correlated with mineralogical information, should improve our understanding of biomineralization mechanisms.

Waste Manag, 2004, 24(3), 241 - 50
Stochastic modelling of landfill processes incorporating waste heterogeneity and data uncertainty; Zacharof AI et al.; A landfill is a very complex heterogeneous environment and as such it presents many modelling challenges . Attempts to develop models that reproduce these complexities generally involve the use of large numbers of spatially dependent parameters that cannot be properly characterised in the face of data uncertainty . An alternative method is presented, which couples a simplified microbial degradation model with a stochastic hydrological and contaminant transport model . This provides a framework for incorporating the complex effects of spatial heterogeneity within the landfill in a simplified manner, along with other key variables . A methodology for handling data uncertainty is also integrated into the model structure . Illustrative examples of the model's output are presented to demonstrate effects of data uncertainty on leachate composition and gas volume prediction.

Environ Manage, 2003 Nov, 32(5), 639 - 45
Changes in physical and biological soil quality indicators in a tropical crop system (Havana, Cuba) in response to different agroecological management practices; Izquierdo I et al.; The objective of our study was to assess the response of physical (aggregate stability and bulk density) and biological (enzyme activities and microbial biomass) soil quality indicators to the adoption of agroecological management practices, such as the planting of forage species (forage area) and the rotation of local crops (polycrop area), carried out in a representative tropical pasture on an integrated livestock-crop farm . The pasture system was used as control (pasture area) . In all three areas, the values of water-soluble C were higher in the rainy season compared to the dry season . Pasture and forage areas had the highest percentage of stable aggregates in the rainy season, while polycrops developed soils with less stable aggregates . Soil bulk density was lower in the pasture and forage areas than in the polycrop area . In the pasture area, the microbial biomass C values, dehydrogenase, urease, protease-BAA, acid phosphatase, and beta-glucosidase activities were higher than in the forage and polycrop areas, particularly in the dry season . The highest increase in the microbial biomass C in the rainy season, with respect to the dry season, was recorded in the pasture area (about 1.2-fold) . In conclusion, the planting of forage species can be considered an effective practice for carrying out sustainable, integrated livestock-crop systems, due to its general maintenance of soil quality, while the adoption of polycrop rotations appears to be less favorable because it decreases soil quality.

Exp Parasitol, 2004 Jan-Feb, 106(1-2), 1 - 10
Wuchereria bancrofti: cloning and characterization of heat shock protein 70 from the human lymphatic filarial parasite; Ravi V et al.; Heat shock protein 70 (HSP70) was identified as an immunodominant antigen by screening a Wuchereria bancrofti (Wb) microfilarial cDNA library with pooled Wb-infected sera, with 28% of the immunopositive clones coding for Wb-HSP70 . The deduced amino acid sequence showed greater than 97 and 85% identity with HSP70 from filarial nematodes and humans, respectively . Recombinant HSP70 (74 kDa) and a recombinant protein from the C-terminal portion (43 kDa) also reacted with pooled Wb-infected sera, suggesting that the C-terminal region of HSP70 contains at least one antibody epitope . Brugia malayi L3 larvae showed increasing levels of HSP70 with increasing temperatures . Further, a polyclonal mouse anti-Wb-HSP70 antibody had reactivity to the HSP70 of cattle filarial parasite Settaria digitata and to human HSP70 derived from a Hep-2 cell line . Immune reactivity to Wb-HSP70 was strong, with uninfected non-endemic normal sera showing significantly greater reactions than sera from filaria-infected individuals . Both immunodominant self-HSP70 and HSP70 from other microbial infections may be primary targets for developing autoantibodies naturally.

Carbohydr Res, 2004 Feb 25, 339(3), 719 - 22
High efficiency of transferring a native sugar chain from a glycopeptide by a microbial endoglycosidase in organic solvents; Akaike E et al.; We examined the transglycosylation reaction by the recombinant endo-beta-N-acetylglucosaminidase from Mucor hiemalis (Endo-M) expressed in Candida boidinii in media containing organic solvents . The recombinant Endo-M could transglycosylate a disialo biantennary complex-type oligosaccharide from hen egg yolk glycopeptide to p-nitrophenyl N-acetyl-beta-D-glucosaminide even in the presence of 30% acetone, dimethyl sulfoxide, or methanol . The yield of the transglycosylation product reached 21-34% of the total amount of acceptor, while the yield was only about 14% in aqueous solution.

J Pharm Biomed Anal, 2004 Feb 4, 34(2), 409 - 14
Development and validation of a MEKC method for the direct determination of cefozopran in human serum; Kitahashi T et al.; A method for determining the concentration of cefozopran, a cephem anti-microbial agent which has a broad spectrum, in human serum using micellar electrokinetic capillary chromatography (MEKC) by serum direct injection is developed and the validation of the assays of this method is performed . A borate buffer (25mM; pH 10.0) containing sodium dodecyl sulfate (SDS) (50mM) is used as a run buffer . The electrophoresis of serum samples is carried out at 25kV and the detection of cefozopran at 244nm as its absorption maximum at the cathodic side of the capillary . The migration time of cefozopran is 6.5min . Linearity (0-200mg/l) is good and limit of quantification is 0.5mg/l at a signal-to-noise ratio of 3 . Coefficient of variation (CV) of intra-day precision and that of inter-day precision are 2.4-4.0% (7.3-92.0mg/l) and 2.9-7.7% (22.5-71.4mg/l), respectively, and the recovery rate is 92-109% . The detection results of 12 other cephem anti-microbial agents under the analytical conditions of this method show that the migration time of cefmetazole is identical with that of cefozopran, making it impossible to separate these two anti-microbial agents . This method is characterized by the fact that simple and economic determination can be achieved by directly injecting the serum samples of micro-quantities into the capillary.

Med Clin (Barc), 2004 Feb 28, 122(7), 245 - 7
{Usefulness of acute-phase proteins in community-acquired pneumonia}; Mirete C et al.; BACKGROUND AND OBJECTIVE: We aimed to study the usefulness of acute-phase proteins in the evolution and microbial diagnosis of community-acquired pneumonia (CAP) . PATIENTS AND METHOD: One-year prospective study of CAP . Plasma levels of C reactive protein (CRP), erythrocyte sedimentation rate (ESR) and fibrinogen were measured on admission in all patients with CAP . RESULTS: 240 cases of CAP were included in the study . ESR was higher in patients who developed pleural effusion (p = 0.03) . A value of ESR > 120 mm/h was associated with a higher likelihood of having a CAP complicated with pleural effusion (odds ratio = 3.80; 95% confidence interval, 1.37-10.49, p = 0.006) . Baseline concentrations of CRP, ESR and fibrinogen were higher in patients who developed empyema . CRP and fibrinogen levels were significantly higher in patients with Legionella pneumophila pneumonia, while pneumococcal pneumonia was associated with a higher ESR value . CONCLUSIONS: Some frequently used acute-phase proteins can be useful in the prediction of pleural complications and in the approach to the etiological diagnosis of CAP.

Annu Rev Phytopathol, 1996, 34, 387 - 412
Microbial elicitors and their receptors in plants; Hahn MG; Elicitors are molecules that stimulate any of a number of defense responses in plants . Research over the past decade has focused on the mechanisms by which plant cells perceive and transduce these biological signals to activate defense responses . Of particular interest has been the identification of specific elicitor-binding proteins that might function as physiological receptors in the signal transduction cascade . The existence of specific high-affinity binding sites has been demonstrated for oligosaccharide, glycopeptide, and peptide elicitors, and candidate elicitor-binding proteins have been identified for several of them . The properties of these binding sites/proteins are consistent with those expected of physiologically important receptors, although experimental verification of the role of these binding proteins as receptors has not yet been obtained . The purification and characterization of specific elicitor-binding proteins is essential for a detailed understanding of the molecular basis for the signal exchange between plant hosts and microbial pathogens that leads to activation of host defenses.

Annu Rev Phytopathol, 1996, 34, 347 - 66
Ozone and plant health; Sandermann H Jr; Phytotoxic effects of ozone are described with emphasis on secondary plant metabolism . Numerous ozone-induced genes, enzymes and stress metabolites of antioxidative and phytopathological defense reactions have been discovered for herbaceous plants and forest tree species . Ozone induces reactions normally elicited by viral and microbial pathogens . The molecular basis (receptors, signal chains) for induction by ozone remains to be elucidated . The induced stress reactions seem to change plant predisposition to either enhanced tolerance or susceptibility for a second stressor . The following topics are discussed: ozone and biotic disease, the role of ozone on field sites and ozone limit values.

Annu Rev Phytopathol, 1998, 36, 485 - 500
The impact of reduced tillage on soilborne plant pathogens; Bockus WW et al.; Farmers increasingly leave crop residues on the soil surface rather than incorporating them into the soil . This practice helps reduce soil erosion, conserve energy, increase soil moisture, and increase crop yields . However, many soilborne plant pathogens survive in the previous year's crop residue, making diseases more problematic under reduced-tillage conditions . Reduced tillage can favor pathogens by such mechanisms as protecting the pathogen's refuge in the residue from microbial degradation, lowering soil temperature, increasing soil moisture, and leaving soil undisturbed . In order for reduced tillage to become more popular, additional controls are needed for pathogens . The four major control tactics (disease-control chemicals, biological control, host resistance, and cultural controls) can be used to limit damage from diseases . It is highly recommended, however, that crop rotation be coupled with reduced tillage . This practice controls many diseases and yet allows as much of the crop residue as possible to be retained on the soil surface.

Annu Rev Entomol, 1999, 44, 257 - 89
Assessment of the application of baculoviruses for control of Lepidoptera; Moscardi F; Baculoviruses, among other insect viruses, are regarded as safe and selective bioinsecticides, restricted to invertebrates . They have been used worldwide against many insect pests, mainly Lepidoptera . Their application as microbial pesticides, however, has not met their potential to control pests in crops, forests, and pastures, with the exception of the nuclear polyhedrosis virus of the soybean caterpillar (Anticarsia gemmatalis), which is used on approximately 1 million ha annually in Brazil . Problems that have limited expansion of baculovirus use include narrow host range, slow killing speed, technical and economical difficulties for in vitro commercial production, timing of application based on frequent host population monitoring, variability of field efficacy due to climatic conditions, and farmers' attitudes toward pest control, which have been based on application of fast-killing chemical insecticides . Farmer education regarding use of biological insecticides and their characteristics is considered one of the major actions necessary for increased use of baculoviruses . Strategies to counteract some of the limitations of baculoviruses, especially their slow killing activity, have been investigated and are promising . These include the use of chemical or biological substances added to virus formulations and genetic engineering of the viruses themselves to express insect toxins or hormones . Such strategies can enhance viral activity and increase speed of kill as well as reduce larval feeding activity . The use of baculoviruses against Lepidoptera is reviewed, with the utilization of the nuclear polyhedrosis virus of A . gemmatalis in Brazil serving as a case-study.

AIDS Rev, 2003 Oct-Dec, 5(4), 195 - 204
HIV/AIDS care and treatment in sub-Saharan Africa; Kassaye SG et al.; Antiretroviral (ARV) drugs have become the cornerstone of care and treatment for AIDS in North America, Brazil, and Europe . Twenty years into the epidemic, and more than 10 years after the introduction of ARV's, effective global treatment of AIDS, particularly in sub-Saharan Africa where the epidemic is most concentrated, is an extraordinary challenge . Guidelines and experience in anti-microbial prophylaxis, prescription and monitoring of ARV's in resource-rich countries should inform the efforts to scale-up AIDS care and treatment in Africa . Here, we review the considerable experience of ARV treatment acquired largely in the Americas and Europe, and the fledgling clinical trials and observational studies in Africa . Implementation of safe, effective, and equitable access to ARV's in Africa should be cognizant of the guidelines for ARV treatment in the Northern countries . Careful observation and operational research to accrue more African data, and evaluate regional and local solutions to this daunting challenge, will identify new approaches to scaling-up of ARV treatment.

Biomed Environ Sci, 2003 Dec, 16(4), 369 - 78
Exacerbation of soft tissue lesions in lead exposed virus infected mice; Gupta P et al.; OBJECTIVE: To investigate the effect of Lead (Pb) acetate exposure on Semliki forest virus (SFV) pathogenesis in mice . METHODS: Different doses (62.5, 125, 250 and 500 mg/Kg body weight) of Pb dissolved in normal saline were given to mice by oral intubation in a sub-acute (28 days) and sub-chronic (90 days) regimen followed by SFV infection . Morbidity, mortality, clinical symptoms, mean survival time (MST), changes in body and organ weight, accumulation of lead in soft tissues, virus titre in brain and histopathological alterations were compared between lead exposed and infected groups . RESULTS: Early appearance of virus symptoms, increased mortality, decreased MST, enhanced SFV titre and greater tissue damage were observed in lead exposed-SFV-infected mice . CONCLUSION: Pre-exposure to lead increases the susceptibility of mice towards SFV infection . Further studies are suggested in view of the persistence of lead in the environment and the possibility of infection by microbial pathogens.

Curr Opin Mol Ther, 2004 Feb, 6(1), 27 - 33
Induction of protective therapy for autoimmune diseases by targeted DNA vaccines encoding pro-inflammatory cytokines and chemokines; Karin N; T-cell-mediated autoimmune diseases such as multiple sclerosis, rheumatoid arthritis or type 1 diabetes result from an aggressive attack of self-components by autoimmune T-cells . Pro-inflammatory mediators, particularly cytokines and chemokines, direct the homing and effectorfunction of these cells . It has recently been demonstrated that the immune system, which can attack self-components, also generates 'beneficial' autoimmunity against pro-inflammatory mediators . During the course of an autoimmune condition, and to a much lesser extent in response to microbial inflammation, the immune system produces auto-antibodies to pro-inflammatory mediators . This reduces the harm from these diseases . We also discovered that targeted DNA vaccines could effectively amplify these responses to provide protective immunity . The underlying mechanism is partially understood . At the site of immunization, the relevant gene product is produced and then presented by dendritic cells/macrophages, which undergo activation due to an interaction of plasmid CpG with toll-like receptor 9 on the dendritic cell . This then activates CD4+ T-cells, which help the production of T-cell-dependent antibodies against the gene product of the vaccines . These antibodies neutralize their target product and suppress inflammation . This review explores this interesting concept and its therapeutic implications.

JAMA, 2004 Mar 10, 291(10), 1238 - 45
Actual causes of death in the United States, 2000; Mokdad AH et al.; CONTEXT: Modifiable behavioral risk factors are leading causes of mortality in the United States . Quantifying these will provide insight into the effects of recent trends and the implications of missed prevention opportunities . OBJECTIVES: To identify and quantify the leading causes of mortality in the United States . DESIGN: Comprehensive MEDLINE search of English-language articles that identified epidemiological, clinical, and laboratory studies linking risk behaviors and mortality . The search was initially restricted to articles published during or after 1990, but we later included relevant articles published in 1980 to December 31, 2002 . Prevalence and relative risk were identified during the literature search . We used 2000 mortality data reported to the Centers for Disease Control and Prevention to identify the causes and number of deaths . The estimates of cause of death were computed by multiplying estimates of the cause-attributable fraction of preventable deaths with the total mortality data . MAIN OUTCOME MEASURES: Actual causes of death . RESULTS: The leading causes of death in 2000 were tobacco (435 000 deaths; 18.1% of total US deaths), poor diet and physical inactivity (400 000 deaths; 16.6%), and alcohol consumption (85 000 deaths; 3.5%) . Other actual causes of death were microbial agents (75 000), toxic agents (55 000), motor vehicle crashes (43 000), incidents involving firearms (29 000), sexual behaviors (20 000), and illicit use of drugs (17 000) . CONCLUSIONS: These analyses show that smoking remains the leading cause of mortality . However, poor diet and physical inactivity may soon overtake tobacco as the leading cause of death . These findings, along with escalating health care costs and aging population, argue persuasively that the need to establish a more preventive orientation in the US health care and public health systems has become more urgent.

J Periodontal Res, 2004 Apr, 39(2), 136 - 42
Variations of Porphyromonas gingivalis fimbriae in relation to microbial pathogenesis; Amano A et al.; OBJECTIVES: Periodontal disease is an infectious disorder caused by a small subset of periodontal pathogens including Porphyromonas gingivalis . Accumulated evidences show that the expression of P . gingivalis heterogenic virulence properties is dependent on its clonal diversity . P . gingivalis expresses two distinct fimbria molecules, major and minor fimbriae, on its cell surfaces, both of which seem to be involved in the development of periodontitis . In this short review, variations of fimbriae in relation to microbial pathogenesis are discussed . MATERIALS AND METHODS: Our recent findings are summarized to elucidate the relationship between clonal variation of fimbriae and bacterial pathogenicity of various strains . RESULTS: Major fimbriae were classified into six types (I to V and Ib) based on the diversity of fimA genes encoding FimA (a subunit of major fimbriae) . A majority of periodontitis patients were found to carry type II fimA organisms, followed by type IV, and type II fimA organisms were significantly occurred with more severe forms of periodontitis . Studies of clones with type II fimA have revealed significantly greater adhesive and invasive capabilities to epithelial cells than other fimA type clones . Minor fimbriae induced interleukin-1alpha (IL-1alpha), IL-1beta, IL-6, and tumor necrosis factor-alpha (TNF-alpha) cytokine expression in macrophages and were suggested to be a causative factor of alveolar bone resorption in animal models . The clonal diversity of minor fimbriae is unclear, however, distinct minor fimbria molecules were found in different strains . CONCLUSION: The fimbria variations may have an influence on the development of periodontal disease.

Clin Microbiol Infect, 2004 Mar, 10(3), 190 - 212
Real-time PCR in the microbiology laboratory; Mackay IM; Use of PCR in the field of molecular diagnostics has increased to the point where it is now accepted as the standard method for detecting nucleic acids from a number of sample and microbial types . However, conventional PCR was already an essential tool in the research laboratory . Real-time PCR has catalysed wider acceptance of PCR because it is more rapid, sensitive and reproducible, while the risk of carryover contamination is minimised . There is an increasing number of chemistries which are used to detect PCR products as they accumulate within a closed reaction vessel during real-time PCR . These include the non-specific DNA-binding fluorophores and the specific, fluorophore-labelled oligonucleotide probes, some of which will be discussed in detail . It is not only the technology that has changed with the introduction of real-time PCR . Accompanying changes have occurred in the traditional terminology of PCR, and these changes will be highlighted as they occur . Factors that have restricted the development of multiplex real-time PCR, as well as the role of real-time PCR in the quantitation and genotyping of the microbial causes of infectious disease, will also be discussed . Because the amplification hardware and the fluorogenic detection chemistries have evolved rapidly, this review aims to update the scientist on the current state of the art . Additionally, the advantages, limitations and general background of real-time PCR technology will be reviewed in the context of the microbiology laboratory.

Environ Microbiol, 2004 Apr, 6(4), 347 - 63
Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers; Stralis-Pavese N et al.; Landfill sites are responsible for 6-12% of global methane emission . Methanotrophs play a very important role in decreasing landfill site methane emissions . We investigated the methane oxidation capacity and methanotroph diversity in lysimeters simulating landfill sites with different plant vegetations . Methane oxidation rates were 35 g methane m-2 day-1 or higher for planted lysimeters and 18 g methane m-2 day-1 or less for bare soil controls . Best methane oxidation, as displayed by gas depth profiles, was found under a vegetation of grass and alfalfa . Methanotroph communities were analysed at high throughput and resolution using a microbial diagnostic microarray targeting the particulate methane monooxygenase (pmoA) gene of methanotrophs and functionally related bacteria . Members of the genera Methylocystis and Methylocaldum were found to be the dominant members in landfill site simulating lysimeters . Soil bacterial communities in biogas free control lysimeters, which were less abundant in methanotrophs, were dominated by Methylocaldum . Type Ia methanotrophs were found only in the top layers of bare soil lysimeters with relatively high oxygen and low methane concentrations . A competetive advantage of type II methanotrophs over type Ia methanotrophs was indicated under all plant covers investigated . Analysis of average and individual results from parallel samples was used to identify general trends and variations in methanotroph community structures in relation to depth, methane supply and plant cover . The applicability of the technology for the detection of environmental perturbations was proven by an erroneous result, where an unexpected community composition detected with the microarray indicated a potential gas leakage in the lysimeter being investigated.

Langenbecks Arch Surg, 2004 Apr, 389(2), 134 - 44 Epub 2004 Mar 06.
Procalcitonin: improved biochemical severity stratification and postoperative monitoring in severe abdominal inflammation and sepsis; Rau B et al.; BACKGROUND: Infections and sepsis are among the most devastating complications in abdominal surgery and significantly contribute to morbidity and mortality . Early and reliable diagnosis of septic complications is notoriously difficult, and the search for novel approaches to overcome this problem is still a compelling issue for clinicians . Among a large array of inflammatory parameters, procalcitonin (PCT), the 116-amino-acid pro-peptide of calcitonin, has gained considerable importance in identifying patients at risk of developing infection and sepsis in clinical practice . METHODS: Along with the latest insights into pathophysiological aspects of this pro-hormone, the literature as well as our own experience on the usefulness of PCT determinations in patients with severe inflammatory abdominal disorders was reviewed . RESULTS: Although the term "sepsis" does not embrace the integral properties of PCT, a remarkable number of clinical studies have demonstrated the pivotal role of this parameter in the host response to microbial and fungal infections . In acute pancreatitis PCT allows early severity stratification and closely correlates with the development of subsequent pancreatic infections . In patients with peritonitis PCT reflects overall disease severity and is an early and reliable indicator of overall prognosis . Postoperative monitoring of PCT is a helpful tool to identify patients with evolving or persisting septic complications after elective and emergency abdominal surgery . CONCLUSIONS: Compared with established biochemical routine variables, PCT significantly contributes to earlier and better stratification of patients at risk of developing septic complications and provides excellent prognostic assessment in severe abdominal inflammation . The currently available test systems render PCT an applicable and readily available parameter under clinical routine and emergency conditions.

J Allergy Clin Immunol, 2004 Mar, 113(3), 482 - 8
Toll-like receptor 2 as a major gene for asthma in children of European farmers; Eder W et al.; BACKGROUND: The finding that the prevalence of asthma and allergies is less frequent in children raised on animal farms has led to the conjecture that exposure to microbial products modifies immune responses . The toll-like receptors (TLRs) represent an evolutionarily conserved family of innate immunity receptors with microbial molecules as ligands . OBJECTIVES: We reasoned that polymorphisms in genes encoding TLRs might modulate the protective effects observed in farming populations . METHODS: Farmers' and nonfarmers' children living in rural areas in Austria and Germany and who were enrolled in the cross-sectional ALEX study were genotyped for single nucleotide polymorphisms in the TLR2 and TLR4 genes . The frequencies of asthma, allergic rhinitis, and atopic sensitization were compared between the genotypes in relation to exposure to farming and endotoxin . RESULTS: Among farmers' children, those carrying a T allele in TLR2/-16934 compared with children with genotype AA were significantly less likely to have a diagnosis of asthma (3% vs 13%, P = .012), current asthma symptoms (3% vs 16%, P = .004), atopic sensitization (14% vs 27%, P = .023), and current hay fever symptoms (3% vs 14%, P = .01) . The association between TLR2/-16934 and asthma among children of farmers was independent of atopy . No such association was found among children from the same rural communities but not living on farms . CONCLUSION: Our results suggest that genetic variation in TLR2 is a major determinant of the susceptibility to asthma and allergies in children of farmers.

J Am Anim Hosp Assoc, 2004 Mar-Apr, 40(2), 102 - 8
Comparison of microbial isolates and susceptibility patterns from the external ear canal of dogs with otitis externa; Graham-Mize CA et al.; Otic exudate was obtained from 33 dogs with otitis externa for cytopathology and culture . Two samples were taken from the same location in the external ear canal, for a total of 100 samples . Thirty-six (36%) samples isolated only a single organism, of which 21 (21%) were Malassezia spp . Two organisms were present in 23 (23%) of the samples . Cultures of the two samples agreed in 40 (80%) of the 50 pairs . Cytopathology agreed with culture results only 68% of the time . Cytopathology and culture may not be as definitive as previously assumed because of apparent variability of the microbial population within the external canal.

Appl Environ Microbiol, 2004 Mar, 70(3), 1865 - 8
Arsenite-oxidizing Hydrogenobaculum strain isolated from an acid-sulfate-chloride geothermal spring in Yellowstone National Park; Donahoe-Christiansen J et al.; An arsenite-oxidizing Hydrogenobaculum strain was isolated from a geothermal spring in Yellowstone National Park, Wyo., that was previously shown to contain microbial populations engaged in arsenite oxidation . The isolate was sensitive to both arsenite and arsenate and behaved as an obligate chemolithoautotroph that used H(2) as its sole energy source and had an optimum temperature of 55 to 60 degrees C and an optimum pH of 3.0 . The arsenite oxidation in this organism displayed saturation kinetics and was strongly inhibited by H(2)S.

Appl Environ Microbiol, 2004 Mar, 70(3), 1811 - 20
Spatial heterogeneity of crenarchaeal assemblages within mesophilic soil ecosystems as revealed by PCR-single-stranded conformation polymorphism profiling; Sliwinski MK et al.; Microbial ecologists have discovered novel rRNA genes (rDNA) in mesophilic soil habitats worldwide, including sequences that affiliate phylogenetically within the division Crenarchaeota (domain Archaea) . To characterize the spatial distribution of crenarchaeal assemblages in mesophilic soil habitats, we profiled amplified crenarchaeal 16S rDNA sequences from diverse soil ecosystems by using PCR-single-stranded-conformation polymorphism (PCR-SSCP) analysis . PCR-SSCP profiles provide a measure of relative microbial diversity in terms of richness (number of different phylotypes as estimated from the number of unique PCR-SSCP peaks) and evenness (abundance of each phylotype as estimated from the relative area under a peak) . Crenarchaeal assemblages inhabiting prairie, forest, turf, and agricultural soils were characterized at six sampling locations in southern and central Wisconsin . Phylotype richness was found to be more stable than evenness among triplicate samples collected within 30 cm at each sampling location . Transformation of the PCR-SSCP data by principal-component analysis, followed by statistical testing (analysis of variance {P < 0.0001} and least-significant-difference analysis {alpha = 0.5}), supported the conclusion that each location exhibited a unique profile . To further characterize the spatial distribution of crenarchaeal assemblages at one location, additional soil samples (a total of 30) were collected from agricultural field plots at the Hancock Agricultural Research Station . PCR-SSCP revealed a patchy spatial distribution of crenarchaeal assemblages within and between these plots . This mosaic of crenarchaeal assemblages was characterized by differences in phylotype evenness that could not be correlated with horizontal distance (15 to 30 m) or with depth (0 to 20 cm below the surface) . Crenarchaeal 16S rDNA clone libraries were produced and screened for unique SSCP peaks . Clones representing the dominant phylotypes at each location were identified, sequenced, and found to group phylogenetically with sequences in crenarchaeal clade C1b.

Appl Environ Microbiol, 2004 Mar, 70(3), 1680 - 7
Application of a vital fluorescent staining method for simultaneous, near-real-time concentration monitoring of two bacterial strains in an Atlantic coastal plain aquifer in Oyster, Virginia; Fuller ME et al.; Two differentially labeled bacterial strains were monitored in near-real time during two field-scale bacterial transport experiments in a shallow aquifer in July 2000 and July 2001 . Comamonas sp . strain DA001 and Acidovorax sp . strain OY-107 were grown and labeled with the vital fluorescent stain TAMRA/SE (5 {and -6}-carboxytetramethylrhodamine, succinimidyl ester) or CFDA/SE (5 {and -6}-carboxyfluorescein diacetate, succinimidyl ester) . Fluorescently labeled cells and a conservative bromide tracer were introduced into a suboxic superficial aquifer, followed by groundwater collection from down-gradient multilevel samplers . Cells were enumerated in the field by microplate spectrofluorometry, with confirmatory analyses for selected samples done in the laboratory by epifluorescence microscopy, flow cytometry, and ferrographic capture . There was general agreement in the results from all of the vital-stain-based enumeration methods, with differences ranging from <10% up to 40% for the analysis of identical samples between different tracking methods . Field analysis by microplate spectrofluorometry was robust and efficient, allowing thousands of samples to be analyzed in quadruplicate for both of the injected strains . The near-real-time data acquisition allowed adjustments to the predetermined sampling schedule to be made . The microplate spectrofluorometry data sets for the July 2000 and July 2001 experiments allowed the transport of the injected cells to be related to the site hydrogeology and injection conditions and enabled the assessment of differences in the transport of the two strains . This near-real-time method should prove effective for a number of microbial ecology applications.

Appl Environ Microbiol, 2004 Mar, 70(3), 1608 - 16
Salinity responses of benthic microbial communities in a solar saltern (Eilat, Israel); Sorensen KB et al.; The salinity responses of cyanobacteria, anoxygenic phototrophs, sulfate reducers, and methanogens from the laminated endoevaporitic community in the solar salterns of Eilat, Israel, were studied in situ with oxygen microelectrodes and in the laboratory in slurries . The optimum salinity for the sulfate reduction rate in sediment slurries was between 100 and 120 per thousand, and sulfate reduction was strongly inhibited at an in situ salinity of 215 per thousand . Nevertheless, sulfate reduction was an important respiratory process in the crust, and reoxidation of formed sulfide accounted for a major part of the oxygen budget . Methanogens were well adapted to the in situ salinity but contributed little to the anaerobic mineralization in the crust . In slurries with a salinity of 180 per thousand or less, methanogens were inhibited by increased activity of sulfate-reducing bacteria . Unicellular and filamentous cyanobacteria metabolized at near-optimum rates at the in situ salinity, whereas the optimum salinity for anoxygenic phototrophs was between 100 and 120 per thousand.

Appl Environ Microbiol, 2004 Mar, 70(3), 1494 - 505
Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time; Crump BC et al.; Shifts in bacterioplankton community composition along the salinity gradient of the Parker River estuary and Plum Island Sound, in northeastern Massachusetts, were related to residence time and bacterial community doubling time in spring, summer, and fall seasons . Bacterial community composition was characterized with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA . Average community doubling time was calculated from bacterial production ({(14)C}leucine incorporation) and bacterial abundance (direct counts) . Freshwater and marine populations advected into the estuary represented a large fraction of the bacterioplankton community in all seasons . However, a unique estuarine community formed at intermediate salinities in summer and fall, when average doubling time was much shorter than water residence time, but not in spring, when doubling time was similar to residence time . Sequencing of DNA in DGGE bands demonstrated that most bands represented single phylotypes and that matching bands from different samples represented identical phylotypes . Most river and coastal ocean bacterioplankton were members of common freshwater and marine phylogenetic clusters within the phyla Proteobacteria, Bacteroidetes, and ACTINOBACTERIA: Estuarine bacterioplankton also belonged to these phyla but were related to clones and isolates from several different environments, including marine water columns, freshwater sediments, and soil.

Appl Environ Microbiol, 2004 Mar, 70(3), 1475 - 82
Impact of agricultural practices on the Zea mays L . endophytic community; Seghers D et al.; Agricultural practices are known to alter bulk soil microbial communities, but little is known about the effect of such practices on the plant endophytic community . We assessed the influence of long-term applications (20 years) of herbicides and different fertilizer types on the endophytic community of maize plants grown in different field experiments . Nested PCR-denaturing gradient gel electrophoresis (DGGE) analyses targeting general bacteria, type I or II methanotrophs, actinomycetes, and general fungi were used to fingerprint the endophytic community in the roots of Zea mays L . Low intraplant variability (reproducible DGGE patterns) was observed for the bacterial, type I methanotroph, and fungal communities, whereas the patterns for endophytic actinomycetes exhibited high intraplant variability . No endophytic amplification product was obtained for type II methanotrophs . Cluster and stability analysis of the endophytic type I methanotroph patterns differentiated maize plants cultivated by using mineral fertilizer from plants cultivated by using organic fertilizer with a 100% success rate . In addition, lower methanotroph richness was observed for mineral-fertilized plants than for organically fertilized plants . The use of herbicides could not be traced by fingerprinting the endophytic type I methanotrophs or by evaluating any other endophytic microbial group . Our results indicate that the effect of agrochemicals is not limited to the bulk microbial community but also includes the root endophytic community . It is not clear if this effect is due to a direct effect on the root endophytic community or is due to changes in the bulk community, which are then reflected in the root endophytic community.

Clin Exp Allergy, 2004 Mar, 34(3), 389 - 97
Determinants of endotoxin levels in living environments of farmers' children and their peers from rural areas; Waser M et al.; BACKGROUND: Lower frequencies of asthma and hayfever have been observed in children with contact to livestock . At school age, the amount of endotoxin measured in the dust of children's mattresses is inversely related to the occurrence of atopic asthma, hayfever and atopic sensitization both in children from farming and non-farming households . OBJECTIVE: The aim of the present study was to investigate which home and lifestyle characteristics of farm and non-farm families contribute to endotoxin levels measured in different indoor home environments . METHODS: In the framework of the Allergy and Endotoxin (ALEX) Study, endotoxin was measured in dust samples from the living room floor and the child's mattress of 319 farmers' families and 493 non-farming families, and in settled dust from stables . Endotoxin content of all dust samples was determined by a kinetic Limulus assay (Limulus-Amebocyte-Lysate test) . Information about the child's activities on farms, home characteristics and cleaning behaviours was obtained from parental questionnaires . RESULTS: Endotoxin levels in stables did not predict the amount of endotoxin measured in floors or mattresses . However, a dose-dependent association between the child's activity on the farm and indoor home endotoxin levels was observed, both in farm and non-farm children . In non-farm children pet keeping and the frequency of floor cleaning were additionally associated with endotoxin levels, whereas in farm children parental farm activities, study area, time since last cleaning, the mattress type as well as younger age of the children contributed to increased microbial exposure . CONCLUSION: These results demonstrate that regular contact to farm animals increases indoor home endotoxin concentrations, both in farm and non-farm children, and might thus explain the protective effect of contact to livestock on atopic outcomes . To assess children's individual exposure to a microbial environment, measures of mattress dust exposure are needed as stable endotoxin concentrations were not associated with indoor home levels.

Proc Natl Acad Sci U S A, 2004 Mar 16, 101(11), 3892 - 7 Epub 2004 Mar 02.
T cell immunity using transgenic B lymphocytes; Gerloni M et al.; Adaptive immunity exists in all vertebrates and plays a defense role against microbial pathogens and tumors . T cell responses begin when precursor T cells recognize antigen on specialized antigen-presenting cells and differentiate into effector cells . Currently, dendritic cells are considered the only cells capable of stimulating T lymphocytes . Here, we show that mature naive B lymphocytes can be genetically programmed by using nonviral DNA and turned into powerful antigen-presenting cells with a dual capacity of synthesis and presentation of antigen to T cells in vivo . A single i.v . injection of transgenic lymphocytes activates T cell responses reproducibly and specifically even at very low cell doses (approximately 10(2)) . We also demonstrate that T cell priming can occur in the absence of dendritic cells and results in immunological memory with protective effector functions . These findings disclose aspects in the regulation of adaptive immunity and indicate possibilities for vaccination against viruses and cancer in humans.

J Immunol, 2004 Mar 15, 172(6), 3704 - 11
T cell-intrinsic expression of c-Rel regulates Th1 cell responses essential for resistance to Toxoplasma gondii; Mason NJ et al.; The ability of many microbial and inflammatory stimuli to activate members of the Rel/NF-kappaB family of transcription factors is associated with the regulation of innate and adaptive responses required to control infection . Individual family members play distinct roles during different infectious and inflammatory responses . For example, c-Rel is essential for the production of IL-12 in response to LPS, but dispensable for IL-12 production in response to Toxoplasma Ag . To assess the role of c-Rel during immunity to the intracellular pathogen Toxoplasma gondii, wild-type (WT) and c-Rel(-/-) mice were infected with Toxoplasma and the immune response was analyzed . c-Rel(-/-) mice developed severe toxoplasmic encephalitis with increased numbers of parasites compared with WT controls and succumbed to infection within 5-8 wk . Although increased susceptibility of c-Rel(-/-) mice was associated with decreased T cell activation, proliferation, and production of IFN-gamma, these mice were able to generate Th1 effector cells that were present in the brain during chronic infection . In vitro mixing studies using WT and c-Rel(-/-) dendritic cells and WT and c-Rel(-/-) TCR transgenic T cells indicated that c-Rel(-/-) dendritic cells are defective in their ability to stimulate T cell responses . However, when c-Rel(-/-) T cells were transferred into T cell-deficient hosts, early defects in T cell activation, proliferation, and IFN-gamma production persisted, and these mice remained susceptible to infection . Together, these studies indicate that although c-Rel is an important regulator of innate immune responses, it also plays an important role in optimization and maintenance of adaptive T cell responses during infection.

J Clin Microbiol, 2004 Mar, 42(3), 1003 - 11
Stable and noncompetitive RNA internal control for routine clinical diagnostic reverse transcription-PCR; Dingle KE et al.; Clinical diagnostic tests based on nucleic acid amplification assist with the prompt diagnosis of microbial infections because of their speeds and extremely low limits of detection . However, the design of appropriate internal controls for such assays has proven difficult . We describe a reaction-specific RNA internal control for diagnostic reverse transcription (RT)-PCR which allows extraction, RT, amplification, and detection to be monitored . The control consists of a G+C-rich (60%) RNA molecule with an extensive secondary structure, based on a modified hepatitis delta virus genome . The rod-like structure of this RNA, with 70% intramolecular base pairing, provides a difficult template for RT-PCR . This ensures that the more favorable target virus amplicon is generated in preference to the control, with the control being detected only if the target virus is absent . The unusual structure of hepatitis delta virus RNA has previously been shown to enhance its stability and resistance to nucleases, an advantage for routine use as an internal control . The control was implemented in three nested multiplex RT-PCRs to detect nine clinically important respiratory viruses: (i) influenza A and B viruses, (ii) respiratory syncytial viruses A and B and human metapneumovirus, and (iii) parainfluenza virus types 1 to 4 . The detection limits of these assays were not detectably compromised by the presence of the RNA control . During routine testing of 324 consecutive unselected respiratory samples, the presence of the internal control ensured that genuine and false-negative results were distinguishable, thus increasing the diagnostic confidence in the assay.

J Biol Chem, 2004 May 28, 279(22), 22953 - 63 Epub 2004 Mar 05.
X4 modules represent a new family of carbohydrate-binding modules that display novel properties; Bolam DN et al.; The hydrolysis of the plant cell wall by microbial glycoside hydrolases and esterases is the primary mechanism by which stored organic carbon is utilized in the biosphere, and thus these enzymes are of considerable biological and industrial importance . Plant cell wall-degrading enzymes in general display a modular architecture comprising catalytic and non-catalytic modules . The X4 modules in glycoside hydrolases represent a large family of non-catalytic modules whose function is unknown . Here we show that the X4 modules from a Cellvibrio japonicus mannanase (Man5C) and arabinofuranosidase (Abf62A) bind to polysaccharides, and thus these proteins comprise a new family of carbohydrate-binding modules (CBMs), designated CBM35 . The Man5C-CBM35 binds to galactomannan, insoluble amorphous mannan, glucomannan, and manno-oligosaccharides but does not interact with crystalline mannan, cellulose, cello-oligosaccharides, or other polysaccharides derived from the plant cell wall . Man5C-CBM35 also potentiates mannanase activity against insoluble amorphous mannan . Abf62A-CBM35 interacts with unsubstituted oat-spelt xylan but not substituted forms of the hemicellulose or xylo-oligosaccharides, and requires calcium for binding . This is in sharp contrast to other xylan-binding CBMs, which interact in a calcium-independent manner with both xylo-oligosaccharides and decorated xylans.

J Biol Chem, 2004 May 14, 279(20), 21552 - 9 Epub 2004 Mar 05.
The family 6 carbohydrate binding module CmCBM6-2 contains two ligand-binding sites with distinct specificities; Henshaw JL et al.; The microbial degradation of the plant cell wall is an important biological process, representing a major component of the carbon cycle . Enzymes that mediate the hydrolysis of this composite structure are modular proteins that contain non-catalytic carbohydrate binding modules (CBMs) that enhance catalytic activity . CBMs are grouped into sequence-based families, and in a previous study we showed that a family 6 CBM (CBM6) that interacts with xylan contains two potential ligand binding clefts, designated cleft A and cleft B . Mutagenesis and NMR studies showed that only cleft A in this protein binds to xylan . Family 6 CBMs bind to a range of polysaccharides, and it was proposed that the variation in ligand specificity observed in these proteins reflects the specific cleft that interacts with the target carbohydrate . Here the biochemical properties of the C-terminal cellulose binding CBM6 (CmCBM6-2) from Cellvibrio mixtus endoglucanase 5A were investigated . The CBM binds to the beta1,4-beta1,3-mixed linked glucans lichenan and barley beta-glucan, cello-oligosaccharides, insoluble forms of cellulose, the beta1,3-glucan laminarin, and xylooligosaccharides . Mutagenesis studies, informed by the crystal structure of the protein (presented in the accompanying paper, Pires, V . M . R., Henshaw, J . L., Prates, J . A . M., Bolam, D., Ferreira, L . M . A . Fontes, C . M . G . A., Henrissat, B., Planas, A., Gilbert, H . J., Czjzek, M . (2004) J . Biol . Chem . 279, 21560-21568), show that both cleft A and B can accommodate cello-oligosaccharides and laminarin displays a preference for cleft A, whereas xylooligosaccharides exhibit absolute specificity for this site, and the beta1,4,-beta1,3-mixed linked glucans interact only with cleft B . The binding of CmCBM6-2 to insoluble cellulose involves synergistic interactions between cleft A and cleft B . These data show that CmCBM6-2 contains two binding sites that display differences in ligand specificity, supporting the view that distinct binding clefts with different specificities can contribute to the variation in ligand recognition displayed by family 6 CBMs . This is in sharp contrast to other CBM families, where variation in ligand binding is a result of changes in the topology of a single carbohydrate-binding site.

Int J Parasitol, 2004 Mar 9, 34(3), 411 - 21
Neutrophils, dendritic cells and Toxoplasma; Denkers EY et al.; Toxoplasma gondii rapidly elicits strong Type 1 cytokine-based immunity . The necessity for this response is well illustrated by the example of IFN-gamma and IL-12 gene knockout mice that rapidly succumb to the effects of acute infection . The parasite itself is skilled at sparking complex interactions in the innate immune system that lead to protective immunity . Neutrophils are one of the first cell types to arrive at the site of infection, and the cells release several proinflammatory cytokines and chemokines in response to Toxoplasma . Dendritic cells are an important source of IL-12 during infection with T . gondii and other microbial pathogens, and they are also specialized for high-level antigen presentation to T lymphocytes . Tachyzoites express at least two types of molecules that trigger innate immune cell cytokine production . One of these involves Toll-like receptor/MyD88 pathways common to many microbial pathogens . The second pathway is less conventional and involves molecular mimicry between a parasite cyclophilin and host CC chemokine receptor 5-binding ligands . Neutrophils, dendritic cells and Toxoplasma work together to elicit the immune response required for host survival . Cytokine and chemokine cross-talk between parasite-triggered neutrophils and dendritic cells results in recruitment, maturation and activation of the latter . Neutrophil-empowered dendritic cells possess properties expected of highly potent antigen presenting cells that drive T helper 1 generation.

Int J Parasitol, 2004 Mar 9, 34(3), 381 - 91
Mechanisms underlying the manipulation of host apoptotic pathways by Toxoplasma gondii; Sinai AP et al.; The establishment of a productive infection by an obligate intracellular pathogen is dependent on subversion of cellular defences . Apoptosis, or programmed cell death, is a property of metazoan cells that plays a critical role in inhibiting the proliferation of invasive organisms and viruses thereby protecting uninfected cells and limiting damage to the host organism . Not surprisingly, manipulation of the machinery of apoptosis plays a critical role in the pathogenesis of several intracellular pathogens . Toxoplasma gondii, arguably one of the most successful protozoan pathogens, has evolved several strategies to inhibit both the initiation and propagation of the apoptotic cascade . Recent work from several groups indicates an exquisite level of sophistication in the mechanisms to inhibit apoptosis along its diverse pathways . Much of this ability appears to centre around the manipulation of host transcription, specifically of genes involved in the pro-survival/anti-apoptotic response effectively manipulating the infected cell into a highly anti-apoptotic state . The implications of these observations extend beyond Toxoplasma biology to the broader area of microbial pathogenesis and cell signalling in mammalian cells.

Int J Parasitol, 2004 Mar 9, 34(3), 297 - 308
Evidence for mitochondrial-derived alternative oxidase in the apicomplexan parasite Cryptosporidium parvum: a potential anti-microbial agent target; Roberts CW et al.; The observation that Plasmodium falciparum possesses cyanide insensitive respiration that can be inhibited by salicylhydroxamic acid (SHAM) and propyl gallate is consistent with the presence of an alternative oxidase (AOX) . However, the completion and annotation of the P . falciparum genome project did not identify any protein with convincing similarity to the previously described AOXs from plants, fungi or protozoa . We undertook a survey of the available apicomplexan genome projects in an attempt to address this anomaly . Putative AOX sequences were identified and sequenced from both type 1 and 2 strains of Cryptosporidium parvum . The gene encodes a polypeptide of 336 amino acids and has a predicted N-terminal transit sequence similar to that found in proteins targeted to the mitochondria of other species . The potential of AOX as a target for new anti-microbial agents for C . parvum is evident by the ability of SHAM and 8-hydroxyquinoline to inhibit in vitro growth of C . parvum . In spite of the lack of a good candidate for AOX in either the P . falciparum or Toxoplasma gondii genome projects, SHAM and 8-hydroxyquinoline were found to inhibit the growth of these parasites . Phylogenetic analysis suggests that AOX and the related protein immutans are derived from gene transfers from the mitochondrial endosymbiont and the chloroplast endosymbiont, respectively . These data are consistent with the functional localisation studies conducted thus far, which demonstrate mitochondrial localisation for some AOX and chloroplastidic localization for immutans . The presence of a mitochondrial compartment is further supported by the prediction of a mitochondrial targeting sequence at the N-terminus of the protein and MitoTracker staining of a subcellular compartment in trophozoite and meront stages . These results give insight into the evolution of AOX and demonstrate the potential of targeting the alternative pathway of respiration in apicomplexans.

Autoimmun Rev, 2004 Feb, 3(2), 31 - 7
Autoimmunity to heat shock proteins in atherosclerosis; Mandal K et al.; Current evidence lends increasing support to immunoinflammatory mechanisms as one of the prime pathogenic processes involved in the development and progression of atherosclerosis . It has been observed that most human beings have cellular and humoral reactions against microbial heat shock protein (HSP) . Autoantibody levels against HSPs are significantly increased in patients with atherosclerosis and T lymphocytes specifically responding to HSPs have been demonstrated within atherosclerotic plaques . Most of the known risk factors for atherosclerosis, viz . oxidized low-density lipoprotein, hypertension, infections and oxidative stress, evoke increased expression of HSPs in endothelial cells, smooth muscle cells and macrophages, the main cellular constituents of atherosclerotic plaques . Evolutionary conservation has resulted in a high degree of sequence homology between microbial and human HSPs and hence the immune reactions against microbial HSPs carry a risk of being misdirected towards human HSPs expressed in the stressed cells of the blood vessels . HSPs and anti-HSP antibodies have been shown to elicit production of pro-inflammatory cytokines by macrophages and adhesion molecules by endothelial cells in various in vitro and animal model studies . These autoimmune reactions to HSPs expressed in the vascular tissue can contribute to both initiation and perpetuation of atherosclerosis.

Biomacromolecules, 2004 Mar-Apr, 5(2), 628 - 36
SEC-MALS characterization of microbial polyhydroxyalkanoates; Zagar E et al.; Characterization of poly-3-hydroxybutyric acid (PHB) and poly-3-hydroxybutyric-co-valeric acid (PHBV, 13% valerate) in chloroform was performed using size exclusion chromatography coupled to a multi-angle light scattering detector (SEC-MALS) . Absolute molar mass averages, molar mass distribution, and the radius of gyration were determined . Three sample preparation methods were examined: dissolution in chloroform (1) at room temperature, (2) at 60 degrees C, and (3) after thermal pretreatment of samples (annealing at 180 degrees C with subsequent quenching in liquid nitrogen) . Dissolution at 60 degrees C and dissolution of thermally pretreated samples gave molecularly dissolved PHB and PHBV . At 60 degrees C using acid free chloroform, there was no indication of degradation for up to 120 min dissolution time, whereas thermal degradation of polymers did take place during annealing at 180 degrees C . The degradation rate constants for number and weight average degree of polymerization at 180 degrees C were slightly higher for PHB (5.19 x 10(-5) min(-1), 4.95 x 10(-5) min(-1)) than for PHBV (4.99 x 10(-5) min(-1), 4.54 x 10(-5) min(-1)) . The dependence of the radii of gyration on molar mass showed that both polymers form random coils in chloroform . The relationship between the absolute molar masses and relative SEC results was determined . DSC and NMR characterization also gave evidence of the progress of degradation.

J Clin Periodontol, 2003 Dec, 30(12), 1031 - 7
Effects of periodontitis and smoking on the microbiota of oral mucous membranes and saliva in systemically healthy subjects; Mager DL et al.; BACKGROUND/AIM: To examine the differences in the proportions of 40 bacterial species in samples from eight oral soft-tissue surfaces and saliva in systemically healthy adult subjects with and without periodontitis and in smokers and nonsmokers . METHODS: Saliva and microbial samples were taken from eight oral soft-tissue surfaces in 229 systemically healthy subjects stratified by periodontal and smoking status . Subjects included 84 periodontally healthy and 145 periodontitis individuals . Of these, there were 182 nonsmokers and 47 smokers . Soft-tissue samples were taken using a "buccal brush" and saliva was taken by expectoration . All samples were individually evaluated for their content of 40 bacterial species using checkerboard DNA-DNA hybridization . The percentage of total DNA probe count was determined for each species at each sample location and averaged across subjects . The significance of differences among the proportions of the 40 test species at different sample locations was sought in these populations using the Kruskall-Wallis test and adjusted for multiple comparisons . RESULTS: When stratified for periodontal status or smoking status, microbial profiles at most sites did not differ significantly . Generally, periodontal pathogens were found at higher levels on the soft tissues of periodontitis subjects than in periodontally healthy subjects, and at higher levels in smokers than nonsmokers . Few significant differences were found, although trends in the populations were noted . CONCLUSIONS: Small differences in the proportions of bacterial species were observed on soft tissues and in saliva comparing periodontally healthy and periodontitis subjects . Somewhat greater differences between smokers and nonsmokers were found; however, these were not statistically significant.

J Biol Chem, 2004 May 21, 279(21), 22440 - 8 Epub 2004 Mar 04.
Dynamic changes in the localization of MAPK cascade components controlling pathogenesis-related (PR) gene expression during innate immunity in parsley; Lee J et al.; The activation of mitogen-activated protein kinase (MAPK) cascades is an important mechanism for stress adaptation through the control of gene expression in mammals, yeast, and plants . MAPK activation has emerged as a common mechanism by which plants trigger pathogen defense responses following innate immune recognition of potential microbial pathogens . We are studying the non-host plant defense response of parsley to attempted infection by Phytophthora species using an experimental system of cultured parsley cells and the Phytophthora-derived Pep-13 peptide elicitor . Following receptor-mediated recognition of this peptide, parsley cells trigger a multifaceted innate immune response, involving the activation of three MAPKs that have been shown to function in the oxidative burst-independent activation of defense gene expression . Using this same experimental model we now report the identification of a MAPK kinase (MAPKK) that functions upstream in this pathway . This kinase, referred to as PcMKK5 based on sequence similarity to Arabidopsis thaliana AtMKK5, is activated in parsley cells following Pep-13 treatment and functions as an in vivo activator of all three MAPKs previously shown to be involved in this response . Gain- and loss-of-function mutant versions of PcMKK5, when used in protoplast co-transfection assays, demonstrated that kinase activity of PcMKK5 is required for PR gene promoter activation following Pep-13 treatment . Furthermore, using specific antibodies and immunofluorescent labeling, we demonstrate that activation of MAPKs in parsley cells correlates with an increase in their nuclear localization, which is not detectable for activated PcMKK5 . These results suggest that activation of gene expression through MAPK cascades during innate immune responses in plants involves dynamic changes in the localization of the proteins involved, which may reflect the distribution of key protein substrates for the activated MAPKs.

J Dent, 2004 Mar, 32(3), 241 - 6
'Interleukin-4 gene polymorphism and its relation to periodontal disease in a Brazilian population of African heritage'; Pontes CC et al.; OBJECTIVES: Host modifying factors, such as genetic predisposition, may increase severity of periodontitis . Genetic polymorphisms in interleukin-4 (IL-4) genes seem to influence host response to microbial challenge . Two IL-4 polymorphisms were found in association with asthma and atopy, and later with aggressive periodontitis in Caucasians . There seems to be a trend for racial differences regarding polymorphisms . Therefore, this study aimed to evaluate if these IL-4 polymorphisms were associated with periodontal disease in a Brazilian population of African heritage . METHODS: Sixty patients were divided into two groups: periodontitis group (n = 30) and control group (n = 30) Blood samples were taken and genomic DNA was amplified by polymerase chain reaction (PCR) . Identification of 70 bp repeat polymorphism in intron 2 and in the -590 position of the promoter region was performed through PCR-RFLP and electrophoresis in agarose gel . RESULTS: No significant differences were found in the genotype frequency of the polymorphisms between control and periodontitis group . Chi square test and Mann-Whitney test were used for statistical analysis . CONCLUSIONS: We concluded that the studied IL-4 polymorphisms were not related to periodontal disease susceptibility in this African-American Brazilian population.

Biotechnol Lett, 2004 Jan, 26(2), 127 - 31
Microbial glycosylation of four free anthraquinones by Absidia coerulea; Zhang W et al.; Absidia coerulea transformed four anthraquinones from rhubarb, chrysophanol, physcion, emodin and aloe-emodin to their corresponding glycosylated metabolites . The structures of the products were characterized as chrysophanol 8-O-beta-D-glucoside, physcion 8-O-beta-D-glucoside, emodin 6-O-beta-D-glucoside, and aloe-emodin 1-O-beta-D-glucoside, respectively.

Mycol Res, 2003 Dec, 107(Pt 12), 1476 - 84
Comparison of non-linear temperature-dependent development rate models applied to in vitro growth of entomopathogenic fungi; Smits N et al.; Five non-linear models with three to five parameters, built to quantify the effect of temperature on insect development and microbial growth, were tested to describe the influence of temperature on in vitro-measured growth rates of entomopathogenic hyphomycetes . Data from two isolates of each of the four fungal species, Paecilomyces fumosoroseus, Beauveria bassiana, Metarhizium anisopliae, Metarhizium flavoviride, were used to assess the features of each model . Criteria for model evaluation included the statistical quality of parameters estimates, the goodness of fit to data, as well as the ability to provide estimates of several key parameters: the upper and lower development thresholds, the thermal optimum and the maximal growth rate at thermal optimum . The second model proposed by Briere et al . (1999) was found to be the best, and Ratkowsky's model (1983) also exhibited good features.

Ying Yong Sheng Tai Xue Bao, 2003 Nov, 14(11), 1997 - 2000
{Effect of pig manure and rice straw on biological activity of Cd-contaminated soil}; Zhang Y et al.; Studies on the effects of pig manure and rice straw on the biological activity of Cd-contaminated permeable paddy soil showed that Cd-contaminated soil had a declined biological activity . After applying organic manure, the content of soil available Cd decreased significantly, being about 40%, and soil microbial C, N and P and soil dehydrogenase and catalase activities increased 30%-100% . There existed a negative correlation between soil available Cd and soil microbial C and N, indicating that microbial C and N could be used as an index of Cd-contaminated soil.

J Clin Immunol, 2004 Jan, 24(1), 12 - 23
Antiphospholipid syndrome infectious origin; Blank M et al.; Antiphospholipid syndrome (APS) is characterized by the presence of pathogenic autoantibodies against beta 2-glycoprotein-I (beta 2GPI) . The factors causing production of anti-beta 2GPI remain unidentified, but an association with infectious agents has been reported . Studies on experimental APS models proved that molecular mimicry between beta 2GPI-related synthetic peptides and structures within bacteria, viruses, tetanus toxoid, and CMV are a cause for experimental APS . Any explanation of how microbial infections might set off APS must take into account the observation that all individuals appear to harbor potentially autoreactive lymphocytes, as well as natural antiphospholipid antibodies, but that these cells or antibodies remain innocuous unless somehow activated . Herein, we discuss the association of antiphospholipid antibodies in the infectious state, molecular mimicry as a proposed cause for development of APS, and the contribution of the database to this topic.

J Leukoc Biol, 2004 May, 75(5), 777 - 84 Epub 2004 Mar 02.
Synergistic induction of CXCL9 and CXCL11 by Toll-like receptor ligands and interferon-gamma in fibroblasts correlates with elevated levels of CXCR3 ligands in septic arthritis synovial fluids; Proost P et al.; The synovial cavity constitutes the ideal stage to study the interplay between microbial Toll-like receptor (TLR) ligands and cytokines . Infiltrated leukocytes and synovial fibroblasts produce cytokine- and chemokine-induced proteases for remodeling the extracellular matrix . The regulation of chemokine function for attraction and activation of leukocytes constitutes a key feature in host immunity and resolution of inflammation after infection . Enhanced levels of the CXC chemokine ligand (CXCL9)/monokine induced by interferon-gamma (IFN-gamma) and CXCL11/IFN-inducible T cell alpha chemoattractant, two chemoattractants for activated T cells and natural killer cells, and ligands for CXC chemokine receptor 3 (CXCR3) were detected in the synovial fluid of septic arthritis compared with osteo- and crystal arthritis patients . In vitro, IFN-gamma and TLR3 ligation by double-stranded RNA (dsRNA) induced the expression of CXCL9 and CXCL11 in leukocytes and skin-muscle fibroblasts, whereas ligation of TLR2, TLR4, TLR5, and TLR9 by peptidoglycan (PGN), lipopolysaccharide (LPS), flagellin, and unmethylated CpG oligonucleotides, respectively, did not . PGN and LPS, but not unmethylated CpG oligonucleotides, even inhibited IFN-gamma-induced CXCL9 and CXCL11 expression in leukocytes . In sharp contrast, in fibroblasts, the TLR ligands PGN, dsRNA, LPS, and flagellin synergized with IFN-gamma for the production of CXCL9 and CXCL11 . Although TLR ligands stimulate leukocytes to produce CXCL8/interleukin-8 during the early innate defense, they contribute less to the production of CXCR3 ligands, whereas fibroblasts are important sources of CXCR3 ligands . These results illustrate the complex interaction between cytokines and TLR ligands in infection.

J Vet Med B Infect Dis Vet Public Health, 2004 Feb, 51(1), 46 - 7
Necrotizing stomatitis associated with Fusobacterium necrophorum in two goats; Yeruham I et al.; Necrotizing stomatitis associated with Fusobacterium necrophorum in two goats is described . Arcanobacterium pyrogenes was the dominant component of the microbial flora cultured under aerobic condition . Treatment with penicillin, at a dose of 50 000 IU/kg for 6 days was used successfully in the cure of the disease.

Mol Interv, 2003 Dec, 3(8), 466 - 77
TLRs: differential adapter utilization by toll-like receptors mediates TLR-specific patterns of gene expression; Vogel SN et al.; In response to microbial or environmental "danger" signals, represented by structural motifs not normally expressed by cells, Toll-like receptors mediate intracellular signaling that leads to inflammatory gene expression . In response to agonists, TLR aggregation enables the recruitment and/or activation of TLR-specific adapter molecules . To date, four adapter proteins have been identified: MyD88, TIRAP/Mal, TRIF/TICAM-1, and TIRP/TRAM/TICAM-2 . The interaction of the different TLRs with distinct combinations of adapter molecules creates a platform to which additional kinases, transacting factors, and possibly other molecules are recruited, events that lead, ultimately, to gene expression . Given the rapidity with which such interactions have been described, we have attempted to summarize our current understanding of the adapters that are so essential for TLR signaling and provide a working model for future studies.

Genome Res, 2004 Mar, 14(3), 472 - 7
zPicture: dynamic alignment and visualization tool for analyzing conservation profiles; Ovcharenko I et al.; Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution . Here, we introduce zPicture, an interactive Web-based sequence alignment and visualization tool for dynamically generating conservation profiles and identifying evolutionarily conserved regions (ECRs) . zPicture is highly flexible, because critical parameters can be modified interactively, allowing users to differentially predict ECRs in comparisons of sequences of different phylogenetic distances and evolutionary rates . We demonstrate the application of this module to identify a known regulatory element in the HOXD locus, in which functional ECRs are difficult to discern against the highly conserved genomic background . zPicture also facilitates transcription factor binding-site analysis via the rVista tool portal . We present an example of the HBB complex when zPicture/rVista combination specifically pinpoints to two ECRs containing GATA-1, NF-E2, and TAL1/E47 binding sites that were identified previously as transcriptional enhancers . In addition, zPicture is linked to the UCSC Genome Browser, allowing users to automatically extract sequences and gene annotations for any recorded locus . Finally, we describe how this tool can be efficiently applied to the analysis of nonvertebrate genomes, including those of microbial organisms.

Ecotoxicology, 2004 Feb-Mar, 13(1-2), 143 - 61
The use of integrated soil microcosms to assess the impact of carbendazim on soil ecosystems; Burrows LA et al.; Our investigation used carbendazim as a representative pesticide for testing an integrated soil microcosm (ISM) test protocol . Microcosms, set up in a greenhouse, consisted of cylinders made from high-density polyethylene (HDPE) pipe, 7.5 cm (i.d.) x 15 cm high . A fine nylon mesh was placed across the bottom of each microcosm for leachate collection . Field soil, (silty clay loam), collected from Florsheim, Germany, was sieved through a 5 mm screen and mixed thoroughly . Earthworms, enchytraeids, and microarthropods were added to each microcosm . Each microcosm contained five wheat seedlings, and was maintained at a 12 h-12 h light-dark cycle . Artificial rainwater was used to water microcosms as required . Soil microcosms were treated with carbendazim at concentrations 1, 3, 9, 27, and 81 times higher than the predicted environmental concentration (PEC) of 0.76 mg a.i./kg soil dry weight . A water-only control treatment was also used . The key soil processes used as endpoints were microbial activity, nitrogen mineralization . soil enzymatic activity, ammonium and nitrate leaching, organic matter decomposition and biological feeding activity . Key structural parameters measured were microbial biomass, nematode communities, microarthropod populations and diversity, enchytraeid and earthworm populations and plant growth . Pesticide degradation, leaching and uptake into plants and earthworms were also assessed . Carbendazim had significant effects on several key soil processes including soil ammonium-N and nitrate-N concentrations and soil dehydrogenase activity . Wheat growth, nematode and earthworm populations, and invertebrate feeding activity were soil structural parameters affected significantly by carbendazim . Earthworm biomass was the most sensitive parameter measured with an EC50 of 1.9 mg a.i./kg soil dry weight 28 days after treatment . A comparison of these results with results from single-species tests, small microcosms, large terrestrial model ecosystems, and field tests indicated that the ISM protocol may adequately predict environmental effects.

Ecotoxicology, 2004 Feb-Mar, 13(1-2), 43 - 60
Ring-testing and field-validation of a terrestrial model ecosystem (TME)--an instrument for testing potentially harmful substances: effects of carbendazim on soil microbial parameters; Sousa JP et al.; The effects of carbendazim on substrate induced respiration (SIR), dehydrogenase activity (DHA), phosphatase activity and thymidine incorporation by bacteria were evaluated in an experiment with an open intact Terrestrial Model Ecosystem (TME) and in a simultaneous field-validation study . Experiments were performed on four different European soils in Germany, The Netherlands, United Kingdom and Portugal . Data analysis focused on (i) detecting differences between experiments, especially in control values, (ii) checking similarity in data variability at each treatment level between experiments and (iii) analysing the resemblance of response to the model chemical in both experiments . Results obtained showed that control values from TME experiments were similar to those obtained on the respective field site, in most of the comparisons made for SIR, DHA and thymidine incorporation . Phosphatase activity revealed more differences, but values of both experiments had the same order of magnitude . At least part of the variation could be explained from the correlation of the microbial parameters with soil moisture content . Comparisons on data variability also revealed the absence of significant differences between experiments in all parameters in most cases, indicating that TMEs were able to represent the spatial variability found in the field . Effects of carbendazim, when occurring, were observed at treatment levels exceeding the highest recommended application rate of 0.36 kg a.i./ha . Effects on SIR and DHA were observed early in time, but effects on phosphatase activity and thymidine incorporation rate were found 8 or 16 weeks after chemical application . These effects were mild, and rarely a 50% inhibition on any of these parameters was seen at carbendazim dosages up to 87.5 kg a.i./ha . The response to the model chemical in TMEs and field plots was similar in most cases . These results give promising prospects for the use of TMEs as an integrative tool in higher tier levels of different assessment schemes.

J Clin Invest, 2004 Mar, 113(5), 658 - 60
CD1a and langerin: acting as more than Langerhans cell markers; Mizumoto N et al.; Langerhans cells (LCs) represent a unique DC subset populating the outermost body surface, i.e., the epidermis . Although CD1a and langerin (CD207) are used as specific markers to distinguish LCs from other DC subsets, their immunological functions have remained mostly unknown . A new paper (see the related article beginning on page 701) demonstrates that LCs utilize these markers to induce cellular immune responses to Mycobacterium leprae: CD1a mediates the presentation of nonpeptide antigens to T cells, while langerin facilitates uptake of microbial fragments and perhaps their delivery to a specialized subcellular compartment.

J Theor Biol, 2004 Mar 21, 227(2), 219 - 28
A primary dysregulation in the immunoregulatory role of the intestinal mucosal epithelial cell in inflammatory bowel disease pathogenesis? Biology of inflammatory response as tissue pattern entities in Crohn's versus ulcerative colitis; Agius LM; Within a framework of dual involvement of mucosa and submucosa on the one hand, and of the muscularis propria of the bowel wall on the other, it might be valid to consider involvement of the vascular supply as the essential means in itself of not only causing the morphologic lesions in inflammatory bowel disease, but also especially in accounting for persisting patterns of inflammatory response both in ulcerative colitis and in Crohn's disease . Inflammatory bowel disease as a group constitutes a spectrum of biologic and pathobiologic manifestations in terms not only of inflammatory involvement of the bowel wall but also in terms of how the bowel in its turn deals with inflammation as a pathologic lesion in its own right . Parameters of inflammatory bowel activity transcend simple concepts of etiology and pathogenesis as applicable to category disorders such as infections or bowel ischemia . Indeed, the strictly characterized initiation of the inflammatory bowel response as a function of defective regulation of the antigenicity of the luminal contents on the one hand, and on interactions between nitric oxide and free oxygen radicals on the other, might help determine a persistence of tissue damage in inflammatory bowel disease that is either relapsing/remitting or chronic in progression . In a final analysis, perhaps, there might be involved a single central form of pathway induction of dysregulated immune reactivity arising from an early disturbance in activation patterns as induced by the onset of luminal antigenicity at an early or specific-stage, further characterized perhaps by specific forms of intestinal epithelial defects of the bowel mucosa in patients subsequently developing inflammatory bowel disease . Specific genetic markers for disease susceptibility and for therapeutic responsiveness are particularly of interest . The Nucleotide binding oligomerization Domain 2 (NOD2) would recognize microbial lipopolysaccharide or else mark systemic responses to pathogens that are pathogenic to evolving inflammatory bowel disease.

Plant Cell Physiol, 2004 Feb, 45(2), 160 - 70
Cryptogein-induced initial events in tobacco BY-2 cells: pharmacological characterization of molecular relationship among cytosolic Ca(2+) transients, anion efflux and production of reactive oxygen species; Kadota Y et al.; Ion fluxes and the production of reactive oxygen species (ROS) are early events that follow elicitor treatment or microbial infection . However, molecular mechanisms for these responses as well as their relationship have been controversial and still largely unknown . We here simultaneously monitored the temporal sequence of initial events at the plasma membrane in suspension-cultured tobacco cells (cell line BY-2) in response to a purified proteinaceous elicitor, cryptogein, which induced hypersensitive cell death . The elicitor induced transient rise in cytosolic Ca(2+) concentration ({Ca(2+)}(cyt)) showing two distinct peaks, followed by biphasic (rapid/transient and slow/prolonged) Cl(-) efflux and H(+) influx . Pharmacological analyses suggested that the two phases of the {Ca(2+)}(cyt) response correspond to Ca(2+) influx through the plasma membrane and an inositol 1,4,5-trisphophate-mediated release of Ca(2+) from intracellular Ca(2+) stores, respectively, and the {Ca(2+)}(cyt) transients and the Cl(-) efflux were mutually dependent events regulated by protein phosphorylation . The elicitor also induced production of ROS including (*)O(2)(-) and H(2)O(2), which initiated after the {Ca(2+)}(cyt) rise and required Ca(2+) influx, Cl(-) efflux and protein phosphorylation . An inhibitor of NADPH oxidase, diphenylene iodonium, completely inhibited the elicitor-induced production of (*)O(2)(-) and H(2)O(2), but did not affect the {Ca(2+)}(cyt) transients . These results suggest that cryptogein-induced plasma membrane Ca(2+) influx is independent of ROS, and NADPH oxidase dependent ROS production is regulated by these series of ion fluxes.

Bioinformatics, 2004 Jul 10, 20(10), 1622 - 31 Epub 2004 Feb 26.
Development of joint application strategies for two microbial gene finders; McHardy AC et al.; MOTIVATION: As a starting point in annotation of bacterial genomes, gene finding programs are used for the prediction of functional elements in the DNA sequence . Due to the faster pace and increasing number of genome projects currently underway, it is becoming especially important to have performant methods for this task . RESULTS: This study describes the development of joint application strategies that combine the strengths of two microbial gene finders to improve the overall gene finding performance . Critica is very specific in the detection of similarity-supported genes as it uses a comparative sequence analysis-based approach . Glimmer employs a very sophisticated model of genomic sequence properties and is sensitive also in the detection of organism-specific genes . Based on a data set of 113 microbial genome sequences, we optimized a combined application approach using different parameters with relevance to the gene finding problem . This results in a significant improvement in specificity while there is similarity in sensitivity to Glimmer . The improvement is especially pronounced for GC rich genomes . The method is currently being applied for the annotation of several microbial genomes . AVAILABILITY: The methods described have been implemented within the gene prediction component of the GenDB genome annotation system.

Bioinformatics, 2004 Jul 22, 20(11), 1812 - 4 Epub 2004 Feb 26.
Visualization for genomics: the Microbial Genome Viewer; Kerkhoven R et al.; SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way . This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database . The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations . Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection . AVAILABILITY: The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

Environ Pollut, 2004 May, 129(2), 321 - 30
Single-well reactive tracer test and stable isotope analysis for determination of microbial activity in a fast hydrocarbon-contaminated aquifer; Burbery L et al.; Single-well reactive tracer tests, such as the push-pull test are useful tools for characterising in-situ bioattenuation processes in contaminated aquifers . However, the analytical models that are used to interpret push-pull data may be over-simplified, and potentially overlook important processes responsible for the frequent discrepancy between predicted and observed results obtained from push-pull tests . In this study, the limitations underlying the push-pull test methodology were investigated and were supported with results from a push-pull test conducted in a sulphate-reducing aquifer contaminated by crude oil . Poor (<7%) mass recovery was achieved when the push-pull test was performed in a fast-flowing aquifer, preventing a quantifiable reaction rate to be determined . Breakthrough curve data were unexplainable using simplified analytical models, but exhibited trends analogous with tests conducted by others, when >20% mass recoveries were achieved . Push-pull test data collected from sulphate-reducing aquifers indicate that the assumption of a well-mixed batch reactor system is incorrect and that reaction rates obtained from push-pull tests in such systems may be affected by the extraction regime implemented . Evidence of microbial respiration of the reactive tracer was provided by stable sulphur isotope analysis, from which an isotope fractionation factor of +9.9 +/- 8.1 per thousand was estimated . The stable isotope data support the argument that reaction rates calculated using push-pull tests are not uniformly distributed in space and time and are likely to be influenced by heterogeneities in the flow field.

Trends Cardiovasc Med, 1998 Jul, 8(5), 191 - 9
The mechanisms by which infectious agents may contribute to atherosclerosis and its clinical manifestations; Kol A et al.; Three infectious agents have recently gained considerable interest as potential pathogens in atherosclerosis and in its clinical manifestations: herpes simplex virus, cytomegalovirus, and Chlamydia pneumoniae . Chronic and often asymptomatic infections with these agents occur widely in the general population . These pathogens may affect atherosclerosis either directly or indirectly . Direct effects on vascular wall cells might include cell lysis, transformation, lipid accumulation, proinflammatory changes, and augmentation of procoagulant activity . Indirect systemic effects may involve induction of acute-phase proteins, establishment of a prothrombotic state, hemodynamic stress caused by tachycardia, increased cardiac output, or a regional inflammatory activation in response to systemic endotoxemia and cytokinemia . The effects of microbial infection, usually in combination with other risk factors (for example, smoking, hyperlipidemia, family history), might promote atherogenesis and eventually trigger acute coronary events.

Ying Yong Sheng Tai Xue Bao, 2003 Oct, 14(10), 1783 - 6
{Isolation and characteristics of PAHs-degrading strains}; Zhang J et al.; The predominant indigenous microbial population and the strain ZL5 PAHS-degrading were obtained by selective enrichment culture from Liaohe viscous oil-contaminated field . The sequence analysis of 16s rDNA showed that strain ZL5 belonged to Sphingomonas sp . The microbial population and the strain could degrade phenanthrene well . 95.28% and 69.24% of phenanthrene in the medium were degraded in 120 hrs . However, the degradation of pyrene by the microbial population or by the strain was low . The degradation rate of phenanthrene or pyrene by the microbial population or the strain was greatly increased while glucose was used as an added substrate . The effect was closely related to the amount of glucose . If the concentration were too high, glucose would show inhibition effect on the degradation of PAHs . Therefore, it was necessary to control the amount of glucose while using glucose as an added substrate to increase degradation of phenanthrene or pyrene.

Arch Tierernahr, 2003 Dec, 57(6), 413 - 28
The effect of the combination of microbial phytase and amino acid supplementation of diets for finishing pigs on P and N excretion and carcass quality; Walz OP et al.; The objective of this study was to evaluate the effect of a combined low-protein, low-phosphorus diet supplemented with limiting amino acids and microbial phytase on performance, nutrient utilization and carcass characteristics of late-finishing barrows . 4 x 8 crossbreed barrows were continuously housed in metabolism cages from 70-110 kg BW and were fed diets, either conventional (A) or protein reduced (B) or protein and phosphorus reduced diets (C) based on barley, maize and soybean meal . Diet A (positive control) contained in air dry matter 13% and 10% CP as well as 0.49% and 0.42% P at growth phases I (70-100 kg BW) or 11 (100-110 kg BW), respectively . Diet B was low in CP (11.3%, 8.4%), diet C low in CP and low in P (CP: as B, P: 0.36%, 0.30%) . To diet B the limiting amino acids lysine, methionine, threonine and trypthophan were added to meet the levels in diet A . To diet C the limiting amino acids and 800 FTU/kg Aspergillus-phytase were supplemented . At the end of the balance periods the barrows were slaughtered, the carcasses scored and loin chops, ham and Phalanx prima IV were analysed for nutrients and minerals . The CP or P reduction in diets B and C did not generally negatively affect growth, feed efficiency, absolute nitrogen retention or overall carcass performances of the pigs . With the low CP diets B and C, N excretion per unit BWG was decreased by about 23% . The addition of microbial phytase (diet C) increased apparent total tract digestibility of P by about 20% . In spite of 30% reduction of P intake (diet C), the absolute P retention related to 1 kg BW did not differ between treatments . Thus, phytase supplementation in diet C reduced P excretion per unit BWG by about 33% . Phytase raised apparent digestibility of Zn by about 20% but not Ca digestibility . Generally the carcass traits and meat characteristics were not affected by any of the diet strategies . Mineralization of the Phalanx prima IV was also similar in all treatment groups . However, phytase supplementation led to significantly increased zinc concentration in bones (25%) . In contrast, Fe incorporation into the Phalanx prima IV was not affected . In general, the feeding regimen introduced in this experiment offers substantial benefits in maintaining a sustainable environmental-friendly pork production even at the stage of late-finishing barrows.

Luminescence, 2004 Jan-Feb, 19(1), 8 - 20
Evolution of beetle bioluminescence: the origin of beetle luciferin; Day JC et al.; Bioluminescence, the conversion of chemical energy into light in living organisms, is dependent on two principal components, an enzyme luciferase and the substrate luciferin . In beetles, the enzyme luciferase has been extensively studied, with significant enzymological, sequence and structural data now available . Furthermore, the enzyme has been employed in a remarkable number of important applications, from microbial detection and medical imaging to GM gene expression studies . However, there is little information regarding the biosynthesis of beetle luciferin, and here we review the literature and speculate as to its evolutionary origins . Luciferin consists of a benzothiazole moiety attached to a thiazole carboxylic acid moiety, the former being rarely observed in nature but the latter being observed in a broad range of biologically derived molecules . Benzothiazoles are, however, observed in melanogenesis and we speculate as to whether this may be relevant to the understanding of luciferin biosynthesis in beetles . This review examines recent novel insights into beetle luciferin recycling and we assess a range of possible biosynthetic mechanisms .

Gene, 2004 Mar 3, 327(2), 195 - 200
Novel missense mutation found in a Japanese patient with myeloperoxidase deficiency; Ohashi YY et al.; Myeloperoxidase (MPO; EC 1.11.1.7) plays an important role in the host defense mechanism against microbial diseases . The neutrophil disorder characterized by the lack of MPO activity, is speculated to be associated with a decreased level of immunity . A Japanese patient was identified with complete MPO deficiency through automated hematography . Neutrophil function analysis revealed that MPO activity was significantly diminished with slightly elevated superoxide production . Mutational analysis of the patient revealed a glycine to serine substitution (G501S) in the exon 9 region . This mutation was not detected in the 96 healthy controls analyzed . The amino acid substitution found may be responsible for the failure of mature MPO production in the patient . This is the first case of MPO deficiency of G501S missense mutation identified in a Japanese patient.

J Immunol Methods, 2004 Feb 15, 285(2), 281 - 91
Rapid and inexpensive real-time PCR for genotyping functional polymorphisms within the Toll-like receptor -2, -4, and -9 genes; Hamann L et al.; The discovery of the human Toll-like receptors (TLRs) and the recognition of their pivotal role in sensing microbial pathogens during the last 5 years have resulted in a renewed appreciation of innate immunity . Due to their central role in both, triggering innate immunity as well as linking innate and adaptive immunity, genetic variations within the TLR genes, known to be associated with a variety of infectious diseases, are currently of great interest . Several single nucleotide polymorphisms (SNPs) within TLR genes have been described and seem to be associated with susceptibility to inflammatory diseases . However, methods for genotyping SNPs within the TLR genes, e.g . direct sequencing or polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) analysis, are time-consuming . In this work, we report novel real-time PCR methods for genotyping five TLR SNPs within TLR-2, TLR-4 and TLR-9 that have been associated with various diseases using fluorescence labeled hybridization probes and the LightCycler instrument . In addition, we provide protocols employing a standard Taq polymerase in order to reduce substantially the costs for real-time PCR.

J Interferon Cytokine Res, 2004 Feb, 24(2), 93 - 100
Panax ginseng induces production of proinflammatory cytokines via toll-like receptor; Nakaya TA et al.; Ginseng radix, the dried root of Panax ginseng C . A . Meyer, has been shown to enhance the ability to resist microbial infections . Proinflammatory cytokines, such as tumor necrosis factor-alpha (TNF-alpha), interleukin-1beta (IL-1beta), IL-6, and interferon-gamma (IFN-gamma) are produced by macrophages treated with ginseng radix extract (GRE) in vitro as well as in vivo . However, the molecular mechanisms of the production are still not clear . In the present study, we demonstrated that production of TNF-alpha and IFN-gamma was induced by GRE in spleen cells and peritoneal macrophages from C3H/HeN mice but was impaired in C3H/HeJ mice carrying a defective toll-like receptor-4 (TLR-4) gene . In addition to these cytokines, the expression of IFN-beta and inducible nitric oxide synthase (iNOS) mRNAs was also increased in GRE-treated C3H/HeN spleen cells . We investigated the possibility that GRE contains a lipopolysaccharide (LPS)-like component . However, GRE induced production of TNF-alpha and IFN-gamma in the presence of polymyxin B, an LPS inhibitor . Furthermore, a Limulus amebocyte lysate assay showed that the endotoxin content of GRE was below the threshold level of 1 ng/ml LPS . These results suggest that GRE contains a non-LPS agent that enhances innate immunity through production of proinflammatory cytokines via TLR-4.

J AOAC Int, 2003 Nov-Dec, 86(6), 1106 - 11
A technique to recover tracer as carboxyl-carbon and alpha-nitrogen from amino acids in soil hydrolysates; Marsh KL et al.; Isotope analysis of biochemical compounds provides an unequivocal means for detecting assimilation of tracer C and N into microbial biomass . A diffusion method recently developed to determine amino acid-N by ninhydrin oxidation of soil hydrolysates was modified to permit simultaneous collection of the CO2 liberated during this oxidation . In the technique described herein, this is accomplished after removal of (NH4+ + amino sugar)-N, by performing ninhydrin oxidation at 90 degrees C for 7 h in a 1.9 L Mason jar sealed with a lid equipped to support a petri dish containing 5 mL 0.2N NaOH . Recoveries of carboxyl-C and alpha-N ranged from 98 to 101% in evaluations with standard solutions of amino acids, whereas these recoveries exceeded 90% for 14C and 94% for 15N when soil hydrolysates amended with labeled amino acids were analyzed.

Trop Gastroenterol, 2003 Jul-Sep, 24(3), 106 - 15
Helicobacter pylori infection in children: a review; Mittal SK et al.; H pylori infection is highly prevalent in asymptomatic children and it varies between countries and often within a country as well . Initial infection probably occurs at an early age and prevalence increases with age . Ethnic and racial factors, socio-economic status and living conditions affect the prevalence of infection . Long term population based studies are needed to identify the exact prevalence and clinical significance in Indian children . There is strong evidence for an association between H pylori infection and antral gastritis and duodenal ulcer disease in children, but it's association with recurrent abdominal pain needs further evaluation . Diagnostic tests for H pylori are based either on direct demonstration of the organism or indirectly by detecting a by-product (of the urease reaction) or by demonstrating antibodies . Histopathological identification of H pylori in {table: see text} antral biopsy specimen is by far the best method and is currently regarded as gold standard . Serological tests detecting IgG and IgA are possible tools for diagnosis but have many drawbacks . They may be useful for population surveys where invasive tests are not feasible . These tests should be standardized for the population for which they are going to be used . Urea breath test is a highly sensitive non-invasive test for H pylori infection and can be used even in a field setting . Urea Breath test needs to be standardized in tropical countries with high rates of dental colonization and duodenal microbial contamination . Newer diagnostic tests for H pylori infection are emerging but most have not been validated in various populations . Routine testing for H pylori is not indicated in children or adults . The decision to perform a diagnostic test has often to be linked with a therapeutic proposal . The only condition for which H pylori treatment is indicated is duodenal ulcer which is very uncommon in children . Treatment for RAP or even dyspepsia is not warranted on clinical grounds . There are several treatment regimens available, but it appears that at least three drugs including two antibiotics and a proton pump inhibitor are required for satisfactory eradication . In developing countries where the prevalence of infection is very high, well-planned double blind cross-over studies are needed before an evidence based answer can be provided for an optimal therapeutic strategy.

Med Pr, 2003, 54(5), 399 - 406
{Knowledge of selected occupational groups about biological agents in the environment and ways of health protection against occupational exposure to biological hazards}; Zielinska-Jankiewicz K et al.; BACKGROUND: Occupational, biological factors of microbial, plant and animal origin may become a health hazard to the exposed workers . The aim of the study was to assess the knowledge of biological agents present in the work environment, related health risks, and health protection against biological exposure at work among workers of certain occupational categories . MATERIALS AND METHODS: A population of 150 workers, employed in the health, forestry and municipal services, was interviewed using a specially developed questionnaire . Each occupational category comprised 50 workers . RESULTS AND CONCLUSIONS: The level of workers' knowledge of occupational, biological agents, their effect on human body, symptoms and diseases induced by occupational exposure to biological hazards is rather limited in the study groups . Personal protective measures, prophylactic vaccination and compliance with principles of personal hygiene are considered to be the most effective ways of health protection against occupational exposure to biological hazards.

J Immunol, 2004 Mar 1, 172(5), 3173 - 80
The effect of innate immunity on autoimmune diabetes and the expression of Toll-like receptors on pancreatic islets; Wen L et al.; Viral infections have previously been implicated as a trigger of autoimmune diabetes . In this study, we compared a viral mimic with other microbial components derived from bacteria in triggering diabetes development in C57BL/6-rat insulin promoter-B7.1 mice that do not normally develop diabetes . It is striking that only the viral mimic induced the development of diabetes in our model system . Further mechanistic studies suggest that diabetes is induced, in part, by the combination of direct recognition of this virus-like stimulus by pancreatic islets through the expression of the innate immune receptor, Toll-like receptor 3 . In addition, the functions of APCs are up-regulated, and this could stimulate islet Ag-reactive T cells that will attack beta cells leading to autoimmune diabetes.

J Immunol, 2004 Mar 1, 172(5), 2870 - 7
In vivo VL-targeted activation-induced apoptotic supraclonal deletion by a microbial B cell toxin; Goodyear CS et al.; To interfere with host immune responses, some microbial pathogens produce proteins with the properties of superantigens, which can interact via conserved V region framework subdomains of the Ag receptors of lymphocytes rather than the complementarity-determining region involved in the binding of conventional Ags . In recent studies, we have elucidated how a model B cell superantigen affects the host immune system by targeting a conserved V(H) site on the Ag receptors of B lymphocytes . To determine whether these findings represent a general paradigm, we investigated the in vivo immunobiologic properties of protein L of Peptostreptococcus magnus (PpL), a microbial Ig-binding protein specific for a V region site on Ig L chains . Our studies confirmed that PpL binding is restricted to a subset of murine Vkappa-expressing B cells, and found that B cells with stronger PpL-binding activity are associated with certain B cell subsets: splenic marginal zone (CD21(high) CD23(low)), splenic CD1(+), peritoneal B-1a (IgD(low) CD5(+)), and CD21(high) CD24(high) B cells in peripheral lymph nodes, mesenteric lymph nodes, and Peyer's patches . Infusion of PpL triggered a sequence of events in B cell receptor (BCR)-targeted B cells, with rapid down-regulation of BCR, the induction of an activation phenotype, and limited rounds of proliferation . Apoptosis followed through a process heralded by the dissipation of mitochondrial membrane potential, the induction of the caspase pathway, DNA fragmentation, and the deposition of B cell apoptotic bodies . These studies define a common pathway by which microbial toxins that target V region-associated BCR sites induce programmed cell death.

J Immunol, 2004 Mar 1, 172(5), 2739 - 43
Cutting edge: activation of Toll-like receptor 2 induces a Th2 immune response and promotes experimental asthma; Redecke V et al.; Recognition of microbial components by APCs and their activation through Toll-like receptors (TLR) leads to the induction of adaptive immune responses . In this study, we show that activation of TLR2 by its synthetic ligand Pam3Cys, in contrast to activation of TLR9 by immunostimulatory DNA (ISS-ODN), induces a prominent Th2-biased immune response . Activation of APCs by Pam3Cys resulted in the induction of Th2-associated effector molecules like IL-13, and IL-1beta, GM-CSF and up-regulation of B7RP-1, but low levels of Th1-associated cytokines (IL-12, IFNalpha, IL-18, IL-27) . Accordingly, TLR2 ligands aggravated experimental asthma . These data indicate that the type of TLR stimulation during the initial phase of immune activation determines the polarization of the adaptive immune response and may play a role in the initiation of Th2-mediated immune disorders, such as asthma.

Int Immunopharmacol, 2004 Jan, 4(1), 15 - 24
Suramin has adjuvant properties and promotes expansion of antigen-specific Th1 and Th2 cells in vivo; Denkinger M et al.; Aluminum hydroxide and incomplete Freund's adjuvant (IFA) are the only adjuvants approved for human use . Both are T helper 2 (Th2) adjuvants, however, T helper 1 (Th1) immunity is induced if microbial products such as mycobacteria, CpG's, or bacterial toxins are included in the adjuvant preparation . The usefulness of bacterial toxins, such as Pertussis toxin (PT) or Cholera toxin (CT), as adjuvants for human vaccination is limited by toxic side effects and high immunogenicity . Hence, we asked whether or not the adjuvant activity of bacterial toxins on Th1 and Th2 immunity could be mimicked by chemical compounds of small molecular weight and less immunogenicity . In the present study, we show that Suramin, a small molecular weight naphthylurea, which mainly acts on G-proteins and on P2X/P2Y receptors, promotes expansion of hen eggwhite lysozyme (HEL)-specific Th1 and Th2 cells upon immunization of BALB/c mice with HEL in aluminum hydroxide (alum) . The results indicated that the adjuvant effects of Suramin on T cell responses were mediated by enhancing the expression of MHC class II and costimulatory molecules on antigen presenting cells (APCs), and by increasing their pro-inflammatory cytokine production . Together, the results suggest that small molecular weight compounds such as Suramin could be used as alternative vaccine adjuvants.

Photochem Photobiol, 2004 Jan, 79(1), 26 - 31
Coupling of climate change and biotic UV exposure through changing snow-ice covers in terrestrial habitats; Cockell CS et al.; During the spring, when ozone depletion at the polar regions is at its maximum and consequently the environmental UV exposure is potentially high, many terrestrial communities are covered in snow and heterogeneous snow-encrusted ice that form near the edges of snowpack . Using field measurements and a theoretical radiative transfer model, we calculated the thicknesses of these covers that are necessary to reduce DNA-weighted dose to levels equal to or lower than those received later in the season in the absence of covers when there is no ozone depletion . This depth is approximately 4 cm for a 60% depletion of the ozone column, suggesting that even thin snow-ice covers are enough to completely cancel the biological effects of ozone depletion . Loss of snow-ice covers during early summer can be rapid . The maximum rate of retreat of snow cover measured during November at Mars Oasis, Antarctica (71.9 degrees S, 68.2 degrees W), was 44.1 cm/day, with a mean retreat of 15.4 cm/day . Climate warming might increase UV-radiation damage by melting UV-protecting terrestrial snow-ice covers earlier in the season, when ozone depletion is more severe . Conversely, climate cooling could increase UV-protection afforded to terrestrial communities by increasing the extent of snow and ice covers . Even if anthropogenic ozone depletion is eventually reversed, these data suggest the importance of climate forcing in determining UV exposures of terrestrial microbial communities in snow- and ice-covered environments.

J Bacteriol, 2004 Mar, 186(5), 1484 - 92
Bordetella species are distinguished by patterns of substantial gene loss and host adaptation; Cummings CA et al.; Pathogens of the bacterial genus Bordetella cause respiratory disease in humans and animals . Although virulence and host specificity vary across the genus, the genetic determinants of this diversity remain unidentified . To identify genes that may underlie key phenotypic differences between these species and clarify their evolutionary relationships, we performed a comparative analysis of genome content in 42 Bordetella strains by hybridization of genomic DNA to a microarray representing the genomes of three Bordetella species and by subtractive hybridization . Here we show that B . pertussis and B . parapertussis are predominantly differentiated from B . bronchiseptica by large, species-specific regions of difference, many of which encode or direct synthesis of surface structures, including lipopolysaccharide O antigen, which may be important determinants of host specificity . The species also exhibit sequence diversity at a number of surface protein-encoding loci, including the fimbrial major subunit gene, fim2 . Gene loss, rather than gene acquisition, accompanied by the proliferation of transposons, has played a fundamental role in the evolution of the pathogenic bordetellae and may represent a conserved evolutionary mechanism among other groups of microbial pathogens.

Tree Physiol, 1991 Jul, 9(1_2), 1 - 15
Evaluating progress toward closed forest models based on fluxes of carbon, water and nutrients; Landsberg JJ et al.; Closed system models are defined as mathematical models of systems having specified boundaries within which all flows into and out of the system are accounted for . Closure is obtained experimentally when we can measure all the flows and do not depend on residuals . The meeting on which this volume is based discussed a range of models and approaches to modeling, and the possibility of achieving closure . There was general agreement that we can develop closed system models of the water balance, carbon cycle and nutrient fluxes at the stand level . Confidence in our ability to account for all the flows is greatest for water, decreasing progressively for carbon and nutrients . The priority areas for research on the carbon balance are belowground processes, foliage dynamics and respiration . The problems requiring particular attention in relation to the water balance are the measurement of interception losses, lateral flow in the soil and evaporation from snow . Areas warranting particular research attention in relation to nutrient fluxes through forest stands are the rates, and the controls on rates, of nutrient uptake by trees, and rates of mineralization with emphasis on the importance of microbial processes at the ecosystem level . Most models are written for uniform conditions . Forests are not uniform so the problem of heterogeneity, and how to deal with it in models, requires considerable attention, as does the question of how to scale up, to deal with large areas . There are a great many forest models of all types and the continual development of new ones may not be an effective use of research resources . There is a need for some assessment of the range of models currently existing, or under development, and for moves toward a directed strategy of model structure and development.

Dig Liver Dis, 2004 Jan, 36(1), 29 - 34
Genetic and serological markers to identify phenotypic subgroups in a Dutch Crohn' s disease population; Linskens RK et al.; BACKGROUND AND AIMS: Both genetic and microbial factors seem to play a pivotal role in the aetiopathogenesis of Crohn's disease . The CARD15 frameshift mutation might link host genetic factors and the indigenous microbial flora, since CARD15 expression is stimulated by peptidoglycan, thereby activating NF-kappaB . It is hypothesised that CARD15 mutation carriers have defective anti-microbial reactions, resulting in more penetrating lesions and antibody responses, which are now being used as highly specific markers for Crohn's disease . The serological marker anti-Saccharomyces cerevisiae antibody directed against cell wall oligomannosidic epitopes has high specificity for Crohn's disease . Perinuclear anti-neutrophil cytoplasmic antibodies have been found in a subgroup of Crohn's disease patients, mostly with colonic involvement . METHODS: We investigated the incidence of two CARD15 mutations (3020insC and 2722G>C), anti-S . cerevisiae antibody, and perinuclear anti-neutrophil cytoplasmic antibody in 108 (73F/35M) patients with Crohn's disease with a mean duration of disease since diagnosis of 16 (1-41) years in relation to their phenotype, according to the Vienna classification . RESULTS: The prevalence of CARD15 frameshift mutation was 21% . Of all patients, 62% were anti-S . cerevisiae antibody positive, and 9% had perinuclear anti-neutrophil cytoplasmic antibodies . The prevalence of both anti-S . cerevisiae antibodies and perinuclear anti-neutrophil cytoplasmic antibodies was higher in the mutation carriers compared to non-carriers . Remarkably, all patients with a CARD15 mutation and positive anti-S . cerevisiae antibody had ileal disease . Carriership of the mutation was significantly associated with penetrating behaviour of the disease and weakly associated with stricturing behaviour . Furthermore, anti-S . cerevisiae antibody was associated with ileal disease involvement . Finally, most perinuclear anti-neutrophil cytoplasmic antibody positive patients showed ulcerative-like behaviour of disease (by means of colonic localisation) . CONCLUSIONS: Genetic and serologic markers might be useful in defining patient subgroups . This may result in a more accurate prediction of disease behaviour, prognosis and therapeutic approach.

Biotechnol Lett, 2003 Dec, 25(24), 2055 - 9
Cellulose production by Gluconacetobacter hansenii in a medium containing ethanol; Park JK et al.; The addition of 1% (v/v) ethanol to the basal medium inhibited growth of Gluconacetobacter hansenii but decreased the numbers of non-cellulose producing cells . Cellulose production increased 1.7 times to approx . 2.5 g l(-1) and showed a pattern of mixed growth-associated production . Microbial cells produced rigid pellicle-type bacterial cellulose as the shell of a large lump of bacterial cellulose like a static culture . The inoculum cultivated for 3 d maintained cellulose production by the fifth batch.

Int J Food Microbiol, 2004 Feb 15, 91(1), 83 - 9
On the origin of the deviation from the first-order kinetics in inactivation of microbial cells by pulsed electric fields; Lebovka NI et al.; A computer model was developed for the estimation of the kinetics of microbial inactivation by pulsed electric field (PEF) . The model is based on the electroporation theory of individual membrane damage, where spherical cell geometry and distribution of cell sizes are assumed . The variation of microbial cell sizes was assumed to follow a statistical probability distribution of the Gaussian type . Surviving kinetics was approximated by Weibull equation . The dependencies of two Weibull parameters (shape n and time tau, respectively) versus electric field intensity E and width of cell diameters distribution were studied.

Tree Physiol, 1995 May, 15(5), 317 - 25
Belowground carbon allocation in unfertilized and fertilized red pine plantations in northern Wisconsin; Haynes BE et al.; We estimated carbon allocation to belowground processes in unfertilized and fertilized red pine (Pinus resinosa Ait.) plantations in northern Wisconsin to determine how soil fertility affects belowground allocation patterns . We used soil CO(2) efflux and litterfall measurements to estimate total belowground carbon allocation (root production and root respiration) by the carbon balance method, established root-free trenched plots to examine treatment effects on microbial respiration, estimated fine root production by sequential coring, and developed allometric equations to estimate coarse root production . Fine root production ranged from 150 to 284 g m(-2) year(-1) and was significantly lower for fertilized plots than for unfertilized plots . Coarse root production ranged from 60 to 90 g m(-2) year(-1) and was significantly lower for fertilized plots than for unfertilized plots . Annual soil CO(2) fluxes ranged from 331 to 541 g C m(-2) year(-1) and were significantly lower for fertilized plots than for unfertilized plots . Annual foliage litterfall ranged from 110 to 187 g C m(-2) year(-1) and was significantly greater for fertilized plots than for unfertilized plots . Total belowground carbon allocation ranged from 188 to 395 g C m(-2) year(-1) and was significantly lower for fertilized than for unfertilized plots . Annual soil CO(2) flux was lower for trenched plots than for untrenched plots but did not differ between fertilized and unfertilized trenched plots . Collectively, these independent estimates suggest that fertilization decreased the relative allocation of carbon belowground.

Curr Top Med Chem, 2004, 4(5), 531 - 8
Th1-mediated pathology in mouse models of human disease is ameliorated by concurrent Th2 responses to parasite antigens; Whary MT et al.; Epidemiologic evidence strongly suggests that improved standards of living are associated with an increased incidence of immune system-mediated disease . Allergy, autoimmunity, and within the focus of our laboratory, idiopathic inflammatory bowel disease, most notably Crohn's disease and ulcerative colitis, and progression of chronic gastritis to gastric cancer, are all mediated by proinflammatory immune responses induced by known or unknown antigens . A popular theory, known as the 'hygiene hypothesis' (1), suggests that improved health standards achieved through sanitation and vaccination, may in part be responsible for the apparent increase in immune system-mediated disease due to decreasing microbial and parasitic infections in humans, particularly in children . As antigenic exposure of children to infectious agents, especially parasites, has rapidly decreased, it is suspected that normally protective counter-regulatory Th2-type immune responses fail to develop, increasing the risk for aberrant pro-inflammatory responses in otherwise genetically pre-disposed individuals . This hypothesis has stimulated significant interest in development of animal models of Th1- and Th2-mediated disease to test this paradigm . This review illustrates some of the exciting evidence that Th1-mediated pathology in mouse models of helicobacter disease and diabetes is ameliorated by concurrent anti-inflammatory Th2 responses to parasite antigens and that initial application of these principles is benefiting human patients . The results from developing animal models of human disease not only support the hygiene hypothesis but also have led to novel therapies using parasite antigens to stimulate anti-inflammatory Th2-type responses to restore homeostasis in patients with aberrant Th1-type immune-mediated disease.

J Environ Qual, 2004 Jan-Feb, 33(1), 89 - 98
Leaching of dissolved organic carbon and carbon dioxide emission after compost application to six nutrient-depleted forest soils; Borken W et al.; The objective of this study was to assess the effect of compost application on soil respiration and dissolved organic carbon (DOC) output of nutrient-depleted forest soils . An amount of 6.3 kg m(-2) mature compost was applied to the forest floor of European beech (Fagus sylvatica L.), Norway spruce (Picea abies Karst.), and Scots pine (Pinus sylvestris L.) stands at Soiling and Unterluss, Germany . Cumulative soil respiration significantly increased by 499 g C m(-2) in the spruce stand at Unterluss and by 274 g C m(-2) in the beech stand at Soiling following compost application whereas soil respiration of the other four stands was not affected . The increases in soil respiration of the two stands were explained by improved microbial decomposition of soil organic matter . The DOC concentrations and fluxes in throughfall and seepage water at 10- and 100-cm depths were determined from August 1997 to March 2000 . In the control plots, cumulative DOC outputs at 10 cm ranged between 57 and 95 g C m(-2), with the highest rates in the pine stands . Compost treatment significantly increased cumulative DOC outputs by 31 to 69 g C m(-2) at 10 cm and by 0.3 to 6.6 g C m(-2) at 100 cm . The mineral soils between the 10- and 100-cm depths acted as significant sinks for DOC, as shown by much lower cumulative outputs at 100 cm of 3 to 11 g C m(-2) in the control and 6 to 16 g C m(-2) in the compost plots . Our results suggest that a single, moderate application of mature compost to nutrient-depleted forest soils has little effect on C losses to the atmosphere and ground water.

J Environ Qual, 2004 Jan-Feb, 33(1), 72 - 9
Environmental factors influencing attenuation of methane and hydrochlorofluorocarbons in landfill cover soils; Scheutz C et al.; The influence of different environmental factors on methane oxidation and degradation of hydrochlorofluorocarbons (HCFCs) was investigated in microcosms containing soil sampled at Skellingsted Landfill, Denmark . The soil showed a high capacity for methane oxidation resulting in a maximum oxidation rate of 104 microg CH4 g(-1) h(-1) and a low affinity of methane with a half-saturation constant of 2.0% v/v . The hydrochlorofluorocarbons HCFC-21 (dichlorofluoromethane) and HCFC-22 (chlorodifluoromethane) were rapidly oxidized and the oxidation occurred in parallel with the oxidation of methane . The maximal HCFC oxidation rates were 0.95 and 0.68 microg g(-1) h(-1) for HCFC-21 and HCFC-22, respectively . Increasing concentrations of HCFCs resulted in decreased methane oxidation rates . However, compared with typical concentrations in landfill gas, relatively high HCFC concentrations were needed to obtain a significant inhibition of methane oxidation . In general, the environmental factors studied influenced the degradation of HCFCs in almost the same way as they influenced methane oxidation . Temperature had a strong influence on the methanotrophic activity giving high Q10 values of 3.4 to 4.1 over the temperature range of 2 to 25 degrees C . Temperature optimum was around 30 degrees C; however, oxidation occurred at temperatures as low as 2 degrees C . A moisture content of 25% w/w yielded the maximum oxidation rate as it allowed good gas transport together with sufficient microbial activity . The optimum pH was around neutrality (pH = 6.5-7.5) showing that the methanotrophs were optimally adapted to the in situ pH, which was 6.9 . Copper showed no inhibitory effect when added in relatively high concentrations (up to 60 mg kg(-1)), most likely due to sorption of copper ions to soil particles . At higher copper concentrations the oxidation rates decreased . The oxidation rates for methane, HCFC-21, and HCFC-22 were unaltered in ammonium-amended soil up to 14 mg kg(-1) . Higher ammonium concentrations inhibited the oxidation process . The most important parameters controlling oxidation in landfill cover soil were found to be temperature, soil moisture, and methane and oxygen supply.

J Biol Chem, 2004 Apr 30, 279(18), 19113 - 21 Epub 2004 Feb 11.
Cytosolic phospholipase A2 translocates to forming phagosomes during phagocytosis of zymosan in macrophages; Girotti M et al.; Resident tissue macrophages mediate early innate immune responses to microbial infection . Cytosolic phospholipase A(2)alpha (cPLA(2)alpha) is activated in macrophages during phagocytosis of non-opsonized yeast (zymosan) triggering arachidonic acid release and eicosanoid production . cPLA(2)alpha translocates from cytosol to membrane in response to intracellular calcium concentration ({Ca(2+)}(i)) increases . Enhanced green fluorescent protein (EGFP)-cPLA(2)alpha translocated to forming phagosomes, surrounding the zymosan particle by 5 min and completely overlapping with early endosome (Rab5) and plasma membrane (F4/80) markers but only partially overlapping with resident endoplasmic reticulum proteins (GRP78 and cyclooxygenase 2) . EGFP-cPLA(2)alpha also localized to membrane ruffles during phagocytosis . Zymosan induced an initial high amplitude calcium transient that preceded particle uptake followed by a low amplitude sustained calcium increase . Both phases were required for optimal phagocytosis . Extracellular calcium chelation prevented only the sustained phase but allowed a limited number of phagocytic events, which were accompanied by translocation of cPLA(2)alpha to the phagosome although {Ca(2+)}(i) remained at resting levels . The results demonstrate that cPLA(2)alpha targets the phagosome membrane, which may serve as a source of arachidonic acid for eicosanoid production.

J Clin Virol, 2004 Mar, 29(3), 167 - 70
Laboratory-acquired vaccinia infection; Wlodaver CG et al.; BACKGROUND: Complications following vaccination with vaccinia virus have been well described but are not commonly observed . The use of vaccinia as a tool in molecular biology, in the development of therapeutics, and the anticipated increase of vaccinations in the general population due to the threat of bioterrorism have created a renewed awareness of the post-vaccination complications and the consequent need for clinical and laboratory diagnosis . OBJECTIVES: To report the clinical presentation and subsequent diagnosis of generalized vaccinia that resulted from a laboratory accident in an unvaccinated subject . STUDY DESIGN: The patient was seen by a local infectious disease's specialist and evaluated clinically and with laboratory support relative to a differential diagnosis . RESULTS: Careful assessment of the patient's history, an evaluation of the workplace, and the elimination of likely microbial etiologies led to the diagnosis of generalized vaccinia . Laboratory confirmation was obtained by use of electron microscopy (EM) to observe poxvirus particles in infected cell cultures . CONCLUSIONS: Exposure to vaccinia virus should raise the index of suspicion for patients with skin lesions . Rapid diagnosis may be accomplished by direct examination of lesion material by EM . The virus also readily replicates in commonly available cell cultures and in the absence of immune reagents, typical poxvirus particles may be observed in the infected cells by EM.

Redox Rep, 2003, 8(5), 289 - 91
Regulation of nitrogen monoxide production in human malaria; Kun JF; The production of nitrogen monoxide (NO(*)) contributes to defence mechanisms of the immune system to fight infectious agents like bacteria and protozoa . The respective gene producing the NO(*) has to be carefully regulated so that an overwhelming response kills the pathogen but does not harm the host . A strong increase in the NO(*) production for efficient anti-microbial activity is achieved by the transcriptional up-regulation of the nitric oxide synthase 2 gene (NOS2 or inducible nitric oxide synthase, iNOS), which is regulated by a number of transcription factors that are vital in the regulation of many genes involved in the immune response . Binding sites for members of the nuclear factor-kappaB (NF-kappaB) and activator protein 1 (AP1) families have been detected and seem to fulfil their function in vitro . Genetic variants of the iNOS genes have been identified that are linked to NO(*) production and to the outcome of malaria in humans.

Mar Biotechnol (NY), 2001 Mar, 3(2), 181 - 7
Microbial communities and exopolysaccharides from Polynesian mats; Rougeaux H et al.; Microbial mats present in two shallow atolls of French Polynesia were characterized by high amounts of exopolysaccharides associated with cyanobacteria as the predominating species . Cyanobacteria were found in the first centimeters of the gelatinous mats, whereas deeper layers showing the occurrence of the sulfate reducers Desulfovibrio and Desulfobacter species as determined by the presence of specific biomarkers . Exopolysaccharides were extracted from these mats and partially characterized . All fractions contained both neutral sugars and uronic acids with a predominance of the former . The large diversity in monosaccharides can be interpreted as the result of exopolymer biosynthesis by either different or unidentified cyanobacterial species.

Mar Biotechnol (NY), 2001 May, 3(3), 281 - 6
Development in a primary cell culture of the marine sponge Ircinia muscarum and analysis of the polar compounds; De Rosa S et al.; We have established a primary cell culture of the marine demosponge Ircinia muscarum . The culture was started from a cell suspension obtained by a combination of mechanical chemical means . Microbial contamination was controlled by the use of a pool of antibiotics . Optical density, rather than hemocytometer count, is suggested to monitor the cellular growth . Analysis of the chemical composition of I . muscarum cells revealed absence of sterols, showing that the cells were unable to biosynthesize sterols . When the medium was supplemented with cholesterol an increase of about 70% in the number of cells was observed . These results suggest that the classic mammalian nutrient medium was not satisfactory for I . muscarum cell growth, and sterols were needed to satisfy the membrane requirements.

Mar Biotechnol (NY), 2001 Jul, 3(4), 322 - 35
Transfection of eastern oyster ( Crassotrea virginica) embryos; Buchanan JT et al.; There is a need for research in disease resistance and microbial elimination in the eastern oyster Crassosostrea virginica . Gene transfer may lead to advances in this area, and a means of selecting transfected larvae would be useful . We transfected 3-hour-postfertilization embryos with the bacterial gene aminoglycoside phosphotransferase II (neo(r)), which confers resistance to neomycin and related antibiotics such as G418 . The antibiotic G418 was examined as a potential selective agent . A neutral red assay was used to determine survival after 48 hours of exposure to various concentrations of G418 (0-4 mg/ml) . We examined the effects of electroporation and chemically mediated transfection of 3-hour-postfertilization embryos on survival to straight-hinge larvae . DNA alone was found to have no effect on survival (P >.05) . For electroporation we found that increased voltage and pulse duration decreased survival (P <.05) . Chemically mediated transfection did not significantly affect survival (P =.5172) . Transgenic larvae were identified after electroporation and chemically mediated transfection . These larvae were reared for 24 hours and exposed to G418 at 0.3 mg/ml for 48 hours . Significant differences in survival between transfected and nontransfected larvae were detected for electroporation (P =.0147) and chemically mediated transfection (P =.037) . Gene transfer was also confirmed with polymerase chain reaction and observation of expression of green fluorescent protein . This study documents the first successful insertion and expression of foreign DNA in eastern oyster larvae.

Mar Biotechnol (NY), 2002 Mar, 4(2), 127 - 31
In situ microspatial imaging using two-photon and confocal laser scanning microscopy of bacteria and extracellular polymeric secretions (EPS) within marine stromatolites; Kawaguchi T et al.; The combination of a hydrophilic embedding resin, Nanoplast, with fluorescent probes, and subsequent imaging using two-photon and confocal laser scanning microscopy (2P-LSM and CLSM) has allowed in imaging of the in situ microspatial arrangements of microbial cells and their extracellular polymeric secretion (EPS) within marine stromatolites . Optical sectioning by 2P-LSM and CLSM allowed imaging of endolithic cyanobacteria cells, Solentia sp., seen within carbonate sand grains . 2P-LSM allowed very clear imaging with a high resolution of bacteria using DAPI, which normally require UV excitation and reduced photo-bleaching of fluorescent probes.

Mar Biotechnol (NY), 2002 Sep, 4(4), 423 - 30
Multivariate optimization of polymerase chain reaction for microbial community analysis; Dahllof I et al.; A multivariate regression, partial least square (PLS) approach was used to optimize a polymerase chain reaction (PCR) method for mixed communities . This approach, in contrast to univariate ones, provided information on the relative influence of the different factors to be optimized, as well as the interactions between factors . Models that predicted the outcome of further optimization were constructed from the initial experiments and verified experimentally . The models constructed were able to predict the outcome of a second set of experiments with high accuracy . PCR-amplification of DNA from environmental samples is often the first step in microbial community fingerprinting . Inhibitors and low cell numbers in the samples can cause problems with yield, for which compensation is normally made by increasing the number of cycles in the PCR-amplification reaction . Increasing the number of cycles, however, can cause other problems such as heteroduplex formation and increased bias . To avoid these problems the effects of different times of denaturing, annealing, and extension on yield were investigated for 2 different samples, one that consisted of a mixture of 9 laboratory strains, and one that represented the microbial community from the surface of the red alga Delisea pulchra . The multivariate approach showed, in addition to the successful optimization of yield, that the different factors affected the PCR depending on sample type . Annealing time had the largest effect on yield for the mixture of laboratory strains, whereas extension time was most important for the D . pulchra community . We suggest that multivariate optimization is a useful tool for PCR optimization and can be used irrespectively of the particular factors that are being investigated.

World J Surg, 2004 Mar, 28(3), 307 - 11 Epub 2004 Feb 17.
Clinical hyperbaric oxygen therapy, wound perfusion, and transcutaneous oximetry; Niinikoski JH; Hyperbaric oxygen therapy (HBOT) is an important adjunct in the management of problem wounds which exist in chronic oxygen deficiency and in which the local oxygen tension is below optimal for healing . In the treatment of hypoxic and ischemic wounds, the most important effects of hyperbaric oxygenation are the stimulation of fibroblast proliferation and differentiation, increased collagen formation and cross-linking, augmented neovascularization, and the stimulation of leukocyte microbial killing . Ischemic soft tissues also benefit from hyperoxygenation through improved preservation of energy metabolism and reduction of edema . Hyperbaric oxygen is administered in either a multiplace or a monoplace hyperbaric chamber . Normally, pressures of 2 to 2.5 ATA are used for a period of 90 minutes once or twice daily . For an objective assessment of wound perfusion and oxygenation, transcutaneous oximetry provides a simple, reliable, noninvasive, diagnostic technique . It can be used for assessment of tissue perfusion in the vicinity of the problem wound . Transcutaneous oximetry may be used in the assessment of wound healing potential, selection of amputation level, and patient selection for HBOT . In diabetic patients with chronic foot ulcers peri-wound transcutaneous oxygen tensions (TcP(O2)) over 400 mmHg in 2.5 ATA hyperbaric oxygen or over 50 mmHg in normobaric pure oxygen predict healing success with adjuncted HBOT with high accuracy.

Community Genet, 2002, 5(3), 162 - 6
Genetic diversity in the human major histocompatibility complex: lessons for vaccination approaches to HIV infection; Mehra NK et al.; The major histocompatibility complex (MHC) harbours genes that have a primary function of regulating immune responsiveness . Our data on the distribution patterns of molecular subtypes of HLA class I and II extended haplotypes in India suggest that: (1) Asian Indians have extreme diversity in the MHC region, with several novel and unique alleles and disease-associated MHC haplotypes (e.g . the autoimmune-favouring A26-B8-DR3 haplotype); (2) there have been selective environmental and microbial pressures in India that directed either the generation of novel alleles through founder effect or the expansion of other alleles due to geophysical or socio-economic barriers, and (3) Asian Indians have a unique repertoire of peptide-presenting molecules to deal with pathogen-derived autoreactive antigens . This level of polymorphism concentrated within the MHC presents a formidable obstacle to the development of peptide-based vaccines, e.g . for AIDS . Further, studies conducted by us and others have provided a genetic basis for the possible predisposition and fast progression of HIV infections in the Indian population . Since there is selective predominance of different HLA alleles and haplotypes in different populations, a dedicated global screening effort is required to develop MHC-based vaccines against infectious diseases.

Methods Mol Med, 2004, 94, 393 - 427
Basic problems of serological laboratory diagnosis; Fierz W; Serological laboratory diagnosis of infectious diseases is inflicted with several kinds of basic problems . One difficulty relates to the fact that the serological diagnosis of infectious diseases is double indirect: The first indirect aim in diagnosing an infectious disease is to identify the microbial agent that caused the disease . The second indirect aim is to identify this infectious agent by measuring the patient's immune response to the potential agent . Thus, the serological test is neither measuring directly disease nor the cause of the disease, but the patient's immune system . The latter poses another type of problem, because each person's immune system is unique . The immune response to an infectious agent is usually of polyclonal nature, and the exact physicochemical properties of antibodies are unique for each clone of antibody . The clonal makeup and composition and, therefore, the way an individual's immune system sees an infectious agent, depends not only on the genetic background of the person but also on the individual experience from former encounters with various infectious agents . In consequence, the reaction of a patient's serum in an analytical system is not precisely predictable . Also, the antigenic makeup of an infectious agent is not always foreseeable . Antigenic variations leading to different serotypes is a quite common phenomenon . Altogether, these biological problems lead to complexities in selecting the appropriate tests and strategies for testing, in interpreting the results, and in standardizing serological test systems . For that reason, a close collaboration of the laboratory with the clinic is mandatory to avoid erroneous conclusions from serological test results, which might lead to wrong decisions in patient care.

Methods Mol Med, 2004, 94, 159 - 75
Application of single-cell cultures of mouse splenocytes as an assay system to analyze the immunomodulatory properties of bacterial components; Deml L et al.; Recently, various bacterial components have been suggested as initiating and modulating immune activation, thereby substantially affecting the complex and dynamic host/pathogen interactions . Herein, we present a valuable and simple methodology for determining the capacity of bacteria as well as defined bacterial structures to stimulate cellular effectors of the innate and cognate immune system . This assay format is based on the exposure of freshly prepared single-cell cultures of splenic cells derived from naive mice with the immunogen of interest . Herein, the determination of exclusive panels of cytokines by the ELISA, ELISpot, and FACS technology will serve as an indicator for the activation of defined arms of the immune system . An increased knowledge about microbial components with immunomodulatory properties will substantially contribute to a more detailed understanding of the dynamic interplay between the host and potential pathogens and, based on this knowledge, to the development of novel substances for the prevention and therapy of microbial infections.

Nucleic Acids Res, 2004 Feb 10, 32(3), 1059 - 64 Print 2004.
Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica; Malek JA et al.; Protein interaction maps can reveal novel pathways and functional complexes, allowing 'guilt by association' annotation of uncharacterized proteins . To address the need for large-scale protein interaction analyses, a bacterial two-hybrid system was coupled with a whole genome shotgun sequencing approach for microbial genome analysis . We report the first large-scale proteomics study using this system, integrating de novo genome sequencing with functional interaction mapping and annotation in a high-throughput format . We apply the approach by shotgun sequencing and annotating the genome of Rickettsia sibirica strain 246, an obligate intracellular human pathogen among the Spotted Fever Group rickettsiae . The bacteria invade endothelial cells and cause lysis after large amounts of progeny have accumulated . Little is known about specific Rickettsial virulence factors and their mode of pathogenicity . Analysis of the combined genomic sequence and protein-protein interaction data for a set of virulence related Type IV secretion system (T4SS) proteins revealed over 250 interactions and will provide insight into the mechanism of Rickettsial pathogenicity.

Biochim Biophys Acta, 2004 Feb 12, 1696(2), 275 - 87
Potential role of glycosidase inhibitors in industrial biotechnological applications; Sorensen JF et al.; The nutrient content of food and animal feed may be improved through new knowledge about enzymatic changes in complex carbohydrates . Enzymatic hydrolysis of complex carbohydrates containing alpha or beta glycosidic bonds is very important in nutrition and in several technological processes . These enzymes are called glycosidases (Enzyme Class 3.2.1) and include amylases, pectinases and xylanases . They are present in many foods such as cereals, but their microbial analogues are often produced and added in many food processes, for instance to improve the shelf-life of bakery products, clear beer, produce glucose, fructose or dextrins, hydrolyse lactose, modify food pectins, or improve processes . However, many plant foods also contain endogenous inhibitors, which reduce the activity of glycosidases, in particular, proteins, peptides, complexing agents and phenolic compounds . The plant proteinaceous inhibitors of glycosidases are in focus in this review whose objective is to report the effect and implications of these inhibitors in industrial processes and applications . These studies will contribute to the optimisation of industrial processes by using modified enzymes not influenced by the natural inhibitors . They will also allow careful selection of raw material and reaction conditions, and future development of new genetic varieties low in inhibitors . These are all new and very promising concepts for the food and feed sector.

Biochim Biophys Acta, 2004 Feb 12, 1696(2), 265 - 74
Potential physiological role of plant glycosidase inhibitors; Bellincampi D et al.; Carbohydrate-active enzymes including glycosidases, transglycosidases, glycosyltransferases, polysaccharide lyases and carbohydrate esterases are responsible for the enzymatic processing of carbohydrates in plants . A number of carbohydrate-active enzymes are produced by microbial pathogens and insects responsible of severe crop losses . Plants have evolved proteinaceous inhibitors to modulate the activity of several of these enzymes . The continuing discovery of new inhibitors indicates that this research area is still unexplored and may lead to new exciting developments . To date, the role of the inhibitors is not completely understood . Here we review recent results obtained on the best characterised inhibitors, pointing to their possible biological role in vivo . Results recently obtained with plant transformation technology indicate that this class of inhibitors has potential biotechnological applications.

Environ Microbiol, 2004 Mar, 6(3), 242 - 53
Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages; Warnecke F et al.; We analysed the phylogenetic relatedness of 16S rRNA genes from freshwater bacteria affiliated with the class Actinobacteria . A polymerase chain reaction assay was developed to identify reliably rare Actinobacteria-related inserts within 16S rRNA gene clone libraries . In 18 libraries constructed from seven freshwater systems, altogether 63 actinobacterial sequence types were collected from a total of > 1800 clones . Sixty of the newly obtained sequences grouped within four distinct phylogenetic lineages . They constitute approximately 75% of the nearly complete sequences within these clusters that are presently available . A comparison with > 300 sequences from various soil habitats revealed that two of these monophyletic actinobacterial clades (acI and acII) almost exclusively harbour 16S rRNA sequence types from freshwaters and estuaries . This may indicate that such bacteria are not inoculated to freshwaters from terrestrial sources, but are autochthonous components of freshwater microbial assemblages . In contrast, sequence types from freshwaters, marine sediments and soils were clearly mixed in another of the actinobacterial lineages (acIV) . Sequence divergence within acIV was the highest of all four lineages (88% minimum similarity), which potentially reflects its radiation across several habitat types . Within the freshwater lineages, groups of essentially identical sequence types were retrieved from geographically distant aquatic systems with strikingly different hydrological and limnological characteristics . This points to the necessity to investigate genotypic variability, in situ abundances and activities of these Actinobacteria in freshwater plankton in greater detail by cultivation-independent techniques.

Am J Med Sci, 2004 Feb, 327(2), 73 - 6
Zinc, iron, copper, selenium, lactoferrin, and ferritin in human pus; Bryant RE et al.; BACKGROUND: Restriction of zinc and iron available for microbial growth in tissues are well-recognized host defense mechanisms . The present studies were performed to characterize some constituents of human pus that may affect these important host defenses . METHODS: Zinc, iron, copper, calcium, and magnesium in pus were measured using an atomic absorption spectrophotometer; selenium was measured fluorometrically . Ferritin was measured with a fluorometric enzyme immunoassay, and lactoferrin was measured with a radial diffusion assay . The growth of Escherichia coli at 37 degrees C was measured in pus supernate adjusted to pH 5.5 or 7.4, in boiled supernate, or in supernate adjusted with 1.3 mM iron or 0.9 mM zinc singly or together . RESULTS: Zinc and iron concentrations in pus exceeded normal serum . Calcium and magnesium levels were 2- to 3-fold lower and higher, respectively, than normal serum values . Lactoferrin concentrations of were 880 +/- 48 microg/mL and ferritin levels were 20,726 +/- 2,667 ng/mL . Growth of an E coli strain was inhibited in pus at pH 5.5 but not at pH 7.4, and growth was enhanced by addition of iron or zinc to E coli suspended in pus at pH 6.7 . CONCLUSIONS: To our knowledge, this is the first report of the zinc, iron, copper, selenium, lactoferrin, and ferritin levels of human pus . These studies provide additional insight into host defense mechanisms mediated by the restriction of the bioavailability of zinc and iron in suppurative infection.

Water Res, 2004 Feb, 38(4), 895 - 902
Validating sample preservation techniques and holding times for the approved compliance monitoring methods for haloacetic acids under the US EPA's stage 1 D/DBP rule; Pepich BV et al.; Haloacetic acids (HAAs), which are formed during the disinfection of drinking waters with chlorine, are regulated by the US Environmental Protection Agency (EPA) under the Stage 1 Disinfectant/Disinfection Byproducts (D/DBP) Rule . Recently, three studies have been reported indicating that low concentrations of HAAs can also be formed during disinfection with chloramines . Methods currently approved for compliance monitoring under the Stage 1 Rule arrest the chlorine-mediated formation of HAAs by adding ammonium chloride, which forms chloramines . Studies were undertaken using an in-process water that favored the formation of HAAs with moderate total organic carbon concentration and high levels of chlorine to investigate the potential formation of HAAs under sample storage conditions . The ammonium chloride-quenched sample did form a small amount of HAAs, but total formation over a period equal to the 14-day sample storage time was less than 2 microg/l, whereas the unquenched samples increased 41 microg/l during the same period . Pour plate studies indicated that chlorinated drinking waters quenched with ammonium chloride are protected from microbial growth, which is an important additional advantage to this preservation scheme . The presence of a combined chlorine residual should prevent microbial degradation of HAAs in samples . These studies support the preservation protocols and the sample storage times promulgated for compliance monitoring under the Stage 1 D/DBP Rule.

Clin Dev Immunol, 2003 Jun-Dec, 10(2-4), 227 - 33
Is there a relation between Chlamydia infection and primary biliary cirrhosis?
Leung PS, Park O, Matsumura S, Ansari AA, Coppel RL, Gershwin ME.
Over the past two decades, a number of studies have failed to provide direct evidence of specific microbial chronic infection in primary biliary cirrhosis (PBC) . However, a recent report suggests that there is a specific association of Chlamydia pneumoniae in patients with PBC and that C . pneumoniae or similar antigens might play a role in the pathogenesis of disease . To determine if Chlamydia infection is associated with PBC, we applied a combination of immunological and molecular approaches to investigate (a) the serological reactivity against two common Chlamydia human pathogens, C . pneumoniae and C . trachomatis, by immunoblotting, (b) the presence of Chlamydia in liver samples of patients with PBC and controls by PCR amplification of Chlamydia specific 16S rRNA and (c) the presence of Chlamydia proteins in liver samples of patients with PBC and controls by immunohistochemical staining . By immunoblotting, C . trachomatis and C . pneumoniae specific serological antibodies were found in 52/57 (91.2%) AMA positive PBC, 7/33 (21/2%) of AMA negative PBC, 1/25 (4%) PSC, 0/15 (0%) Sjorgen's syndrome and 0/20 (0%) systemic lupus erythematosus patients and 0/20 (0%) healthy volunteers at 1:200 sera dilution . PBC sera reacted to Chlamydia and E . coli lysates in western blots up to a maximum of 10(-4) dilution . However, PCR amplification of the Chlamydia specific 16S rRNA gene was negative in 25/25 PBC livers but positive in 1/4 PSC liver, 3/6 in other liver disease controls and 1/4 normal liver samples . While two commercially available specific monoclonal antibodies stained positive controls (Chlamydia infected HEp-2 cells) they failed to detect Chlamydia antigens in PBC livers . The detection of Chlamydia specific antibodies but not Chlamydia rRNA gene and Chlamydia antigens in PBC suggests that Chlamydia infection is not involved in PBC.

Mikrobiologiia, 2003 Nov-Dec, 72(6), 840 - 6
{Quantitative isolation of microbial DNA from the different types of soils of natural and agricultural ecosystems}; Blagodatskaia EV et al.; A novel procedure was developed for direct quantitative isolation of microbial DNA from soil . This technique was used to evaluate microbial DNA pools in soils of contrasting types (chernozems and brown forest soils) under different anthropogenic loads . A strong correlation was found between microbial biomass and DNA contents in soils of different types (R2 = 0.799) . The ratio of soil CO2 emission rate to the amount of extractable DNA in the soil was shown to reflect physiological state of the soil microbial community; this ratio can be used as an ecophysiological parameter similarly to the metabolic quotient qCO2.

Mikrobiologiia, 2003 Nov-Dec, 72(6), 828 - 33
{Serological heterogeneity of Pseudomonas syringae pv . atrofaciens strains and their ecological niches}; Pasichnik LA et al.; The paper deals with a comparative analysis of the serological and ecological properties of Pseudomonas syringae pv . atrofaciens strains from the collections of microbial cultures at the Malkov Institute for Plant Genetic Resources and Zabolotny Institute of Microbiology and Virology . All of the strains from the Bulgarian collection, except for one, fall into five serogroups (II through VI) of the classification system of Pastushenko and Simonovich . The P . syringae pv . atrofaciens strains isolated from Bulgarian and Ukrainian wheats belong mainly to serogroups II and IV, respectively . The strains that were isolated from rye plants belong to serogroup I . The strains isolated from sorghum and Sudan grass belong to serogroups II, IV, and VL . Serogroup III includes the P . syringae pv . atrofaciens strains that were isolated from cereals in the United Kingdom but not in Ukraine.

Nurs Times, 2004 Jan 13-19, 100(2), 26 - 7
Antibiotic resistance and the prescribing dilemma; Beckford-Ball J; Antibiotics have had a major impact on health care since the discovery of penicillin . However, the prescribing of antibiotics remains a common practice dilemma . How should the appropriate prescription of antibiotics continue while ensuring that growth of microbial resistance to infectious diseases is kept to a minimum?

Appl Environ Microbiol, 2004 Feb, 70(2), 1160 - 8
Integron diversity in heavy-metal-contaminated mine tailings and inferences about integron evolution; Nemergut DR et al.; Integrons are horizontal gene transfer (HGT) systems containing elements necessary for site-specific recombination and expression of foreign DNA . The overall phylogenetic distribution of integrons and range of genes that can be transferred by integrons are unknown . This report contains an exploration of integrons in an environmental microbial community and an investigation of integron evolution . First, using culture-independent techniques, we explored the diversity of integrons and integron-transferred genes in heavy-metal-contaminated mine tailings . Using degenerate primers, we amplified integron integrase genes from the tailings . We discovered 14 previously undescribed integrase genes, including six novel gene lineages . In addition, we found 11 novel gene cassettes in this sample . One of the gene cassettes that we sequenced is similar to a gene that codes for a step in a pathway for nitroaromatic catabolism, a group of compounds associated with mining activity . This suggests that integrons may be important for gene transfer in response to selective pressures other than the presence of antibiotics . We also investigated the evolution of integrons by statistically comparing the phylogenies of 16S rRNA and integrase genes from the same organisms, using sequences from GenBank and various sequencing projects . We found significant differences between the organismal (16S rRNA) and integrase trees, and we suggest that these differences may be due to HGT.

Appl Environ Microbiol, 2004 Feb, 70(2), 921 - 8
Phenazines and other redox-active antibiotics promote microbial mineral reduction; Hernandez ME et al.; Natural products with important therapeutic properties are known to be produced by a variety of soil bacteria, yet the ecological function of these compounds is not well understood . Here we show that phenazines and other redox-active antibiotics can promote microbial mineral reduction . Pseudomonas chlororaphis PCL1391, a root isolate that produces phenazine-1-carboxamide (PCN), is able to reductively dissolve poorly crystalline iron and manganese oxides, whereas a strain carrying a mutation in one of the phenazine-biosynthetic genes (phzB) is not; the addition of purified PCN restores this ability to the mutant strain . The small amount of PCN produced relative to the large amount of ferric iron reduced in cultures of P . chlororaphis implies that PCN is recycled multiple times; moreover, poorly crystalline iron (hydr)oxide can be reduced abiotically by reduced PCN . This ability suggests that PCN functions as an electron shuttle rather than an iron chelator, a finding that is consistent with the observation that dissolved ferric iron is undetectable in culture fluids . Multiple phenazines and the glycopeptidic antibiotic bleomycin can also stimulate mineral reduction by the dissimilatory iron-reducing bacterium Shewanella oneidensis MR1 . Because diverse bacterial strains that cannot grow on iron can reduce phenazines, and because thermodynamic calculations suggest that phenazines have lower redox potentials than those of poorly crystalline iron (hydr)oxides in a range of relevant environmental pH (5 to 9), we suggest that natural products like phenazines may promote microbial mineral reduction in the environment.

J Vet Intern Med, 2004 Jan-Feb, 18(1), 109 - 12
The effects of oral magnesium hydroxide administration on rumen fluid in cattle; Smith GW et al.; This study was conducted to determine the effects of oral magnesium hydroxide administration on rumen fluid in cattle . Six lactating Holstein cows (4-7 years of age) with rumen fistulas were studied . Cattle were randomly assigned to receive boluses of magnesium hydroxide (162 g) or a powdered form (450 g dissolved in 3.5 L of water) PO daily for 3 days . Analysis of rumen fluid, blood gas tensions, and pH and measurement of serum magnesium concentrations were conducted daily . The study was discontinued after 72 hours, or sooner if rumen pH exceeded 8.0 . After at least 3 weeks, the study was repeated with each cow receiving the other form of magnesium hydroxide (powder or bolus) . Compared with baseline rumen pH (mean +/- SD: 6.22 +/- 0.28), magnesium hydroxide boluses caused a significant increase (P < .05) in rumen pH after 48 (7.27 +/- 0.11) and 72 (8.01 +/- 0.16) hours of administration, whereas the powdered form caused a significant increase (P < .05) in rumen pH after 24 (7.54 +/- 0.19) and 48 (8.43 +/- 0.22) hours of administration . Both the powdered and bolus forms of magnesium hydroxide decreased rumen protozoal numbers and increased methylene blue reduction times compared with baseline values . There was no change in blood pH, bicarbonate, or base excess values . Serum magnesium concentrations were significantly increased (P < .05) in cows that received the magnesium hydroxide powder . The results of this study indicate that magnesium hydroxide has a potent alkalinizing effect on rumen pH and significantly decreases rumen microbial activity.

J Med Entomol, 2003 Nov, 40(6), 860 - 4
A component of maize pollen that stimulates larval mosquitoes (Diptera: Culicidae) to feed and increases toxicity of microbial larvicides; Ye-Ebiyo Y et al.; To explain how larval Anopheles arabiensis Patton feed effectively in the turbid water in which they frequently develop, we determined whether an extractable component of maize, Zea mays L., pollen enhances feeding by these mosquitoes . Maturing maize produces a copious amount of wind-borne pollen that is nutritious enough and produced over a sufficient period to support the development of at least one generation of anopheline mosquitoes . Larval An . arabiensis readily ingest the contents of maize pollen or the intact pollen grains themselves . An aqueous extract of maize pollen markedly accelerates the rate at which larval An . arabiensis ingest inert particles and strongly enhances the effectiveness of Bti against larval An . arabiensis . We conclude that the ability of larval anopheline mosquitoes to feed on maize pollen in turbid water is enhanced by the release from these pollen grains of a water-soluble phagostimulatory component (or components), which may be used to increase ingestion of microbial entomotoxins.

Plant Physiol, 2004 Feb, 134(2), 858 - 70 Epub 2004 Feb 05.
Coordinated regulation of genes for secretion in tobacco at late developmental stages: association with resistance against oomycetes; Hugot K et al.; Besides the systemic acquired resistance (SAR) induced in response to microbial stimulation, host plants may also acquire resistance to pathogens in response to endogenous stimuli associated with their own development . In tobacco (Nicotiana tabacum), the vegetative-to-flowering transition comes along with a susceptibility-to-resistance transition to the causal agent of black shank disease, the oomycete Phytophthora parasitica . This resistance affects infection effectiveness and hyphal expansion and is associated with extracellular accumulation of a cytotoxic activity that provokes in vitro cell death of P . parasitica zoospores . As a strategy to determine the extracellular events important for restriction of pathogen growth, we screened the tobacco genome for genes encoding secreted or membrane-bound proteins expressed in leaves of flowering plants . Using a signal sequence trap approach in yeast (Saccharomyces cerevisiae), 298 clones were selected that appear to encode for apoplastic, cell wall, or membrane-bound proteins involved in stress response, in plant defense, or in cell wall modifications . Microarray and northern-blot analyses revealed that, at late developmental stages, leaves were characterized by the coordinate up-regulation of genes involved in SAR and in peroxidative cross-linking of structural proteins to cell wall . This suggests the potential involvement of these genes in extracellular events that govern the expression of developmental resistance . The analysis of the influence of salicylic acid on mRNA accumulation also indicates a more complex network for regulation of gene expression at a later stage of tobacco development than during SAR . Further characterization of these genes will permit the formulation of hypotheses to explain resistance and to establish the connection with development.

J Biol Chem, 2004 Apr 23, 279(17), 17079 - 84 Epub 2004 Feb 05.
Hyaluronan fragments stimulate endothelial recognition of injury through TLR4; Taylor KR et al.; Tissues must quickly recognize injury to respond to the rapid pace of microbial growth . In skin, dermal microvascular endothelial cells must also react to danger signals from the surrounding tissue and immediately participate by initiating the wound repair process . Components of the extracellular matrix such as hyaluronan are rapidly broken down into smaller molecular weight oligosaccharides in a wound, and these can activate a variety of biological processes . This study set out to determine if hyaluronan fragments released following injury can stimulate endothelial cells and what mechanism is responsible for this response . Using genechip microarray analysis, a response to hyaluronan fragments was detected in endothelial cells with the most significant increase observed for the chemokine IL-8 . This observation was verified with qualitative reverse transcriptase-PCR and ELISA in human endothelial cell culture, and in a mouse model by observing serum levels of MIP-2 and KC following hyaluronan fragment administration in vivo . Activation was TLR4-dependent, as shown by use of TLR4 blocking antibody and TLR4-deficient mice, but not due to the presence of undetected contaminants as shown by inactivation following digestion with the hyaluronan-degrading enzyme chondroitinase ABC or incubation with the hyaluronan-specific blocking peptide Pep-1 . Inactivation of LPS activity failed to diminish the action of hyaluronan fragments . These observations suggest that endogenous components of the extracellular matrix can stimulate endothelia to trigger recognition of injury in the initial stages of the wound defense and repair response.

Eur J Biochem, 2004 Feb, 271(4), 809 - 20
Nonlysine-analog plasminogen modulators promote autoproteolytic generation of plasmin(ogen) fragments with angiostatin-like activity; Ohyama S et al.; We recently discovered several nonlysine-analog conformational modulators for plasminogen . These include SMTP-6, thioplabin B and complestatin that are low molecular mass compounds of microbial origin . Unlike lysine-analog modulators, which increase plasminogen activation but inhibit its binding to fibrin, the nonlysine-analog modulators enhance both activation and fibrin binding of plasminogen . Here we show that some nonlysine-analog modulators promote autoproteolytic generation of plasmin(ogen) derivatives with its catalytic domain undergoing extensive fragmentation (PMDs), which have angiostatin-like anti-endothelial activity . The enhancement of urokinase-catalyzed plasminogen activation by SMTP-6 was followed by rapid inactivation of plasmin due to its degradation mainly in the catalytic domain, yielding PMD with a molecular mass ranging from 68 to 77 kDa . PMD generation was observed when plasmin alone was treated with SMTP-6 and was inhibited by the plasmin inhibitor aprotinin, indicating an autoproteolytic mechanism in PMD generation . Thioplabin B and complestatin, two other nonlysine-analog modulators, were also active in producing similar PMDs, whereas the lysine analog 6-aminohexanoic acid was inactive while it enhanced plasminogen activation . Peptide sequencing and mass spectrometric analyses suggested that plasmin fragmentation was due to cleavage at Lys615-Val616, Lys651-Leu652, Lys661-Val662, Lys698-Glu699, Lys708-Val709 and several other sites mostly in the catalytic domain . PMD was inhibitory to proliferation, migration and tube formation of endothelial cells at concentrations of 0.3-10 microg.mL(-1) . These results suggest a possible application of nonlysine-analog modulators in the treatment of cancer through the enhancement of endogenous plasmin(ogen) fragment formation.

J Antibiot (Tokyo), 2003 Nov, 56(11), 931 - 41
Bhimamycin A to approximately E and bhimanone: isolation, structure elucidation and biological activity of novel quinone antibiotics from a terrestrial Streptomycete; Fotso S et al.; From the ethyl acetate extract of a terrestrial Streptomycete isolate, five new quinone antibiotics, bhimamycin A (2a), B (2b), C (3c), D (5a), E (7) and the new tetralone bhimanone (8) were isolated together with the known microbial products chrysophanol (1a), aloesaponarin II (1b), 3,8-dihydroxy-1-methylanthraquinone-2-carboxylic acid (1c), adenosine, 2'-deoxyadenosine, phenylacetamide, and 2-(p-hydroxyphenyl)ethanol . The structures of these natural products were deduced from the spectral data and confirmed by comparison with related compounds from the literature and by synthesis.

Gastroenterology, 2004 Feb, 126(2), 414 - 24
Association of antibody responses to microbial antigens and complications of small bowel Crohn's disease; Mow WS et al.; BACKGROUND & AIMS: Crohn's disease patients can be characterized by antibody responses against Crohn's disease-related bacterial sequence, Escherichia coli outer membrane porin C, Saccharomyces cerevisiae (oligomannan), and neutrophil nuclear antigens . Our aim was to determine whether expression of antibodies against Crohn's disease-related bacterial sequence and Escherichia coli outer membrane porin C is associated with distinct phenotypic manifestations . METHODS: Sera from 303 patients were tested for antibodies to the Crohn's disease-related bacterial sequence (I2), anti-Escherichia coli outer membrane porin C, anti-Saccharomyces cerevisiae, and perinuclear antineutrophil cytoplasmic antibodies and for 3 Crohn's disease-associated variants of the NOD2 gene (R702W, G908R, and 1007fs) and compared with clinical data . RESULTS: Patients expressing I2 were more likely to have fibrostenosing Crohn's disease (64.4% vs . 40.7%; P < 0.001) and to require small bowel surgery (62.2% vs . 37.4%; P < 0.001) . Patients with anti-Escherichia coli outer membrane porin C were more likely to have internal perforating disease (50.0% vs . 30.7%; P = 0.001) and to require small bowel surgery (61.4% vs . 44.2%; P = 0.003) . Anti-Crohn's disease-related bacterial sequence was independently associated with fibrostenosis (P = 0.027) and small bowel surgery (P = 0.01), whereas anti-Escherichia coli outer membrane porin C was independently associated with internal perforations (P < 0.006) . Patients positive for I2, anti-Escherichia coli outer membrane porin C, and anti-Saccharomyces cerevisiae were the most likely to have undergone small bowel surgery (72.0%; odds ratio, 8.6; P < 0.001) compared with patients without reactivity (23.0%) . When the presence and magnitude of antibody responses were considered, 90% of patients with small bowel disease who required surgery had high levels of I2, Escherichia coli outer membrane porin C, and oligomannan antibodies, compared with only 18.2% with low-titer responses (P < 0.001) . CONCLUSIONS: I2 and anti-Escherichia coli outer membrane porin C are associated with Crohn's disease phenotypes, and patients with the highest level of serum reactivity toward an increasing number of microbiota have the greatest frequency of strictures, internal perforations, and small bowel surgery.

Biotechnol Appl Biochem, 2004 Oct, 40(Pt 2), 197 - 200
An efficient isocratic separation of hydroxycinnamates and their corresponding benzoates from microbial and plant sources by HPLC; Sachan A et al.; A rapid HPLC-based separation method was developed to analyse phenolic flavour components . In the present study, ferulic acid, 4-coumaric acid, 4-hydroxybenzoic acid, 4-hydroxybenzaldehyde, vanillic acid and vanillin were chromatographed on various C(18) columns (Prodigy ODS2, Synergi Hydro-RP, Lichrosorb and Columbus) . A dual-wavelength UV detector was used for the precise identification of the eluted components . An isocratic elution with aqueous trifluoroacetic acid (1 mM)/methanol (17:8) at a flow rate of 1.0 ml/min separated all the above six phenolic compounds within 21 min on a C(18) reverse-phase column (Synergi Hydro-RP) with stable baseline resolution.

Expert Rev Vaccines, 2004 Feb, 3(1), 23 - 34
Antibody regulation of Tcell immunity: implications for vaccine strategies against intracellular pathogens; Igietseme JU et al.; Intracellular microbial pathogens cause a plethora of diseases that pose a huge public health challenge . Efficacious prophylactic vaccines are needed to protect the population from this myriad of infectious diseases . Contemporary approaches to vaccine design are guided by the immunobiological paradigm that extracellular pathogens are controlled principally by humoral immunity, involving specific antibodies, whereas host protection against intracellular pathogens requires effectors of cell-mediated immunity . However, this distinct T-helper (Th) type 1 and 2 paradigm of host defense has encountered a major challenge due to the reality that most antigens or vaccines induce mixed immune responses comprising of both humoral and CMI effectors . Besides, the true functional independence of antibodies and T-cells under in vivo physiologic conditions is uncertain . Recent findings have revealed that antibodies exert a significant immunoregulatory effect on T-cell immunity . Thus, a robust and protective T-cell memory response against microbial pathogens such as Chlamydia and Mycobacteria require an effective primary humoral immune response characterized by specific antibody isotypes whose role is to modulate Th1 activation via Fc receptors (FcR) by facilitating a rapid uptake, processing and presentation of pathogen-derived antigens for an enhanced T-cell response . These findings have crystallized into a paradigm shift in host defense wherein different components of the apparently disparate mixed immune responses elicited against a microbial pathogen function concertedly to maximize the principal effector mechanism . This review focuses on the essential role of both arms of the immune system in controlling intracellular microbial pathogens, especially the regulatory role of FcR-mediated antibody function in optimizing the induction of a protective Th1 response . The immunobiological implications are discussed in the context of vaccine design, delivery and evaluation against intracellular microbial pathogens of bacteria, fungi and parasitic origin.

Poult Sci, 2004 Jan, 83(1), 61 - 8
Effect of microbial phytase on ileal digestibility of phytate phosphorus, total phosphorus, and amino acids in a low-phosphorus diet for broilers; Rutherfurd SM et al.; The study aimed to assess the effect of a commercially available microbial phytase added to a corn-soybean meal diet on phytate P and total P in terminal ileal digesta as well as on true ileal amino acid digestibility . Three low-P diets containing 0, 500, or 750 U/kg of microbial phytase were fed to 21-d-old broiler chickens . Titanium dioxide was used as an indigestible marker . Ileal contents were collected from euthanized birds and analyzed, along with the diets, for total P, phytate P, and amino acids . Endogenous P determined at the terminal ileum was 446 +/- 59 mg/kg food dry matter (mean +/- SE) . Endogenous ileal amino acids ranged from 219 +/- 33 mg/kg food dry matter for tryptophan to 1,255 +/- 166 mg/kg food dry matter for glutamic acid . Supplementation with microbial phytase resulted in a significantly (P < or = 0.05) greater phytate P disappearance (11% greater disappearance vs . unsupplemented control) from the terminal ileum . Similarly, true ileal total P digestibility was (P < or = 0.05) higher (10 to 12%) when microbial phytase was added . True ileal amino acid digestibility was significantly (P < or = 0.05) greater in the presence of microbial phytase for all the amino acids examined with the exception of methionine, tyrosine, histidine, and tryptophan . The mean increase in true ileal amino acid digestibility was 3.4% . The effect of phytase on true ileal phytate P, total P, and amino acid digestibility was similar for the 2 phytase inclusion levels tested . Microbial phytase improved phytate P and total P digestibility, as well as true ileal amino acid digestibility, for a corn-soybean diet.

Evolution Int J Org Evolution, 2003 Dec, 57(12), 2899 - 903
Information about transmission opportunities triggers a life-history switch in a parasite; Poulin R; Many microbial pathogens can switch to new hosts or adopt alternative transmission routes as environmental conditions change, displaying unexpected flexibility in their infection pathways and often causing emerging diseases . In contrast, parasitic worms that must develop through a fixed series of host species appear less likely to show phenotypic plasticity in their transmission pathways . Here, I demonstrate experimentally that a trematode parasite, Coitocaecum parvum, can accelerate its development and rapidly reach precocious maturity in its crustacean intermediate host in the absence of chemical cues emanating from its fish definitive host . Juvenile trematodes can also mature precociously when the mortality rate of their intermediate hosts is increased . Eggs produced by precocious adults hatch into viable larvae, capable of pursuing the parasite's life cycle . In the absence of chemical cues from fish hosts, the size of eggs released by precocious trematodes in their intermediate hosts becomes more variable, possibly indicating a bet-hedging strategy . These results illustrate that parasitic worms with complex life cycles have development and transmission strategies that are more plastic than commonly believed, allowing them to skip one host in their cycle when they perceive limited opportunities for transmission.

Histochem Cell Biol, 2004 Feb, 121(2), 83 - 9 Epub 2004 Jan 31.
Carcinoembryonic antigen (CEA) and CEA-related cell adhesion molecule 1 (CEACAM1), apically expressed on human colonic M cells, are potential receptors for microbial adhesion; Baranov V et al.; In the human gut mucosa, specialized M cells deliver intact foreign macromolecules and commensal bacteria from the lumen to organized mucosal lymphoid tissues triggering immune responses . M cells are also major sites of adhesion and invasion for enteric pathogens . The molecular features of M cell apical surfaces that promote microbial normal attachment are still largely unknown . We have demonstrated previously that in the human colonic epithelium, carcinoembryonic antigen (CEA) and CEA-related cell adhesion molecule 1 (CEACAM1) are integral components of the apical glycocalyx which participate in epithelial-microbial interactions . In this study, based on the reactivity of specific monoclonal antibodies and on immunoelectron microscopy, we show that M cells of human colonic solitary lymphoid follicles express CEA and CEACAM1 on the apical surface . Recently these highly glycosylated molecules have been characterized as protein receptors for different bacteria . This leads us to propose a role for CEA and CEACAM1 in the adherence of enteric bacteria to the apical membrane of colonic M cells . We also hypothesize that, unlike colonic enterocytes, M cells lack the defense mechanism that eliminates CEA and CEACAM1 upon microbial binding and which is based on vesiculation of microvillus plasma membrane.

Nat Immunol, 2004 Mar, 5(3), 317 - 27 Epub 2004 Feb 01.
B cell receptor signal strength determines B cell fate; Casola S et al.; B cell receptor (BCR)-mediated antigen recognition is thought to regulate B cell differentiation . BCR signal strength may also influence B cell fate decisions . Here, we used the Epstein-Barr virus protein LMP2A as a constitutively active BCR surrogate to study the contribution of BCR signal strength in B cell differentiation . Mice carrying a targeted replacement of Igh by LMP2A leading to high or low expression of the LMP2A protein developed B-1 or follicular and marginal zone B cells, respectively . These data indicate that BCR signal strength, rather than antigen specificity, determines mature B cell fate . Furthermore, spontaneous germinal centers developed in gut-associated lymphoid tissue of LMP2A mice, indicating that microbial antigens can promote germinal centers independently of BCR-mediated antigen recognition.

Biomed Mater Eng, 2004, 14(1), 87 - 105
Hydroxyapatite/PMMA composites as bone cements; Chu KT et al.; Currently PMMA is the polymer most commonly used as a bone cement for the fixation of total hip prostheses . Ideally, a bone cement material should be easy to handle, biologically compatible, nonsupporting of oral microbial growth, available in the particulate and molded forms, easy to obtain, nonallergenic, adaptable to a broad range of dental and medical applications, in possession of high compressive strength, and effective in guided tissue regenerative procedures . One of the problems associated with the conventional types of bone cement used is their unsatisfactory mechanical and exothermic reaction properties . The purpose of this in vitro study was to investigate and compare the mechanical properties (three-point bending strength, energy-to-break, and modulus of elasticity) and physical properties (setting time, water sorption, and exothermic heat) of HA/PMMA (HA group) and bovine-bone originated HA/PMMA (BB group) composites . Composites samples were fabricated by admixing method . It was found that the addition of HA and BB particles increased the water sorption . Generally 10 v/o 20 v/o HA and 0 v/o to 10 v/o BB ratio combinations had significant beneficial effects on the mechanical properties . The heat generated during polymerization was influenced by the different admixtures . More than 40 v/o HA and 40 v/o BB should be mixed into PMMA to reduce the peak temperature . Overall evaluation indicated that the BB group had better properties than the HA group.

Br Med Bull, 2003, 68, 227 - 42
Asthma: environmental and occupational factors; Cullinan P et al.; Asthma is in several ways a difficult disease to study . Generally arising in childhood, its pattern is often one of remission and relapse; at any point there are difficulties in translating its characteristic, clinical features into an operational definition . Geographical and temporal patterns in its distribution - whereby the disease appears to have increased in frequency in more 'westernised' countries -suggest strong environmental determinants in its causation although there are, too, undoubted and important genetic influences on both its incidence and presentation . Recent aetiological research has concentrated on the function of allergen exposure or on the role of early-life microbial contact that may regulate the development of a range of childhood allergies, including asthma . To date the 'hygiene hypothesis' offers the most efficient explanation for the distribution of the disease in time and place although convincing evidence for it remains elusive.

Tree Physiol, 2004 Apr, 24(4), 415 - 24
Seasonal and annual changes in soil respiration in relation to soil temperature, water potential and trenching; Lavigne MB et al.; Soil respiration (r(s)), soil temperature (T(s)) and volumetric soil water content were measured in a balsam fir (Abies balsamea (L.) Mill.) ecosystem from 1998 to 2001 . Seasonal variation in root and microbial respiration, and covariation in abiotic factors confounded interpretation of the effects of T(s) and soil water potential (Psi(s)) on r(s) . To minimize the confounding effect of temperature, we analyzed the effect of Psi(s) on r(s) during the summers of 1998-2000 when changes in T(s) were slight . Soil respiration declined 25-50% in response to modest water stress (minimum Psi(s) of -0.6 to -0.2 MPa), and between years, there was substantial variation in the relationship between r(s) and Psi(s) . In the summer of 2000, 2-m2 plots were subjected to drought for 1 month and other plots were irrigated . The relationship between summertime r(s) and Psi(s) in the experimental plots was similar to that estimated from the survey data obtained during the same summer . In late spring and early autumn of 2001, 2-m2 trenched and untrenched plots were subjected to drought or exposed to rainfall . It was dry in the early autumn and there was severe soil drying (Psi(s) of -10 MPa in untrenched plots and -2 MPa in trenched plots) . In spring, r(s) in untrenched plots responded more to modest water stress than r(s) in trenched plots, indicating that root respiration is more sensitive than microbial respiration to water stress at this time of year . The response to abiotic factors differed significantly between spring and autumn in untrenched plots but not in trenched plots, indicating that root activity was greater in early autumn than in late spring, and that roots acclimated to the sustained, severe water stress experienced before and during the autumn.

Enferm Infecc Microbiol Clin, 2004 Jan, 22(1), 22 - 8
{Scientific production in infectious diseases in Spain (1991-2001): position within the European Union}; Ramos-Rincon JM et al.; INTRODUCTION: Medical research in our geographic area has undergone significant changes over the last three decades . The objective of this study was to quantitatively determine Spain's medical research output published in the journals included in the Infectious Diseases section of the Journal Citation Reports, and to compare it with that of other European Union (EU) countries . METHODS: The PubMed Web site (MEDLINE) was used to retrieve medical articles published by authors from Spain and other EU countries from 1991 to 2001 in 36 infectious disease journals included in the Infectious Diseases section of the Journal Citation Reports . RESULTS: We retrieved a total of 17,899 documents published by EU authors during the study period . Authors from Spanish institutions contributed 1,340 documents, 7.5% of the overall EU production . Spain ranked in the sixth position of the EU by number of papers . It remained in the same position after adjusting for gross national product and dropped to the ninth position after correcting for population . The number of articles published increased from 72 in the biennium 1991-1992 to 442 in the biennium 2000-2001 . Spanish production rose by 514%, as compared with a median increase of 149% in the other EU countries . Spain was the first producer of articles from the EU in four journals: Diagnostic Microbiology and Infectious Disease (27.6%), European Journal of Clinical Microbiology & Infectious Diseases (24.8%), American Journal of Infection Control (21.8%) and Microbial Drug Resistance (17.5%) . CONCLUSIONS: Spanish scientific production in infectious diseases has increased substantially in the period 1991-2001.

Br J Nutr, 2004 Feb, 91(2), 253 - 62
Use of stable isotopes to measure de novo synthesis and turnover of amino acid-C and -N in mixed micro-organisms from the sheep rumen in vitro; Atasoglu C et al.; Protein synthesis and turnover in ruminal micro-organisms were assessed by stable-isotope methods in order to follow independently the fate of amino acid (AA)-C and -N in different AA . Rumen fluid taken from sheep receiving a grass hay-concentrate diet were strained and incubated in vitro with starch-cellobiose-xylose in the presence of NH3 and 5 g algal protein hydrolysate (APH)/l, in incubations where the labels were (15)NH3, {(15)N}APH or {(13)C}APH . Total (15)N incorporation was calculated from separate incubations with (15)NH3 and {(15)N}APH, and net N synthesis from the increase in AA in protein-bound material . The large difference between total and net AA synthesis indicated that substantial turnover of microbial protein occurred, averaging 3.5 %/h . Soluble AA-N was incorporated on average more extensively than soluble AA-C (70 v . 50 % respectively, P=0.001); however, incorporation of individual AA varied . Ninety percent of phenylalanine-C was derived from the C-skeleton of soluble AA, whereas the incorporation of phenylalanine-N was 72 % . In contrast, only 15 % aspartate-C+asparagine-C was incorporated, while 45 % aspartate-N+asparagine-N was incorporated . Deconvolution analysis of mass spectra indicated substantial exchange of carboxyl groups in several AA before incorporation and a condensation of unidentified C2 and C4 intermediates during isoleucine metabolism . The present results demonstrate that differential labelling with stable isotopes is a way in which fluxes of AA synthesis and degradation, their biosynthetic routes, and separate fates of AA-C and -N can be determined in a mixed microbial population.

Environ Microbiol, 2004 Feb, 6(2), 131 - 44
Serial analysis of ribosomal sequence tags (SARST): a high-throughput method for profiling complex microbial communities; Neufeld JD et al.; Two decades of culture-independent studies have confirmed that microbial communities represent the most complex and concentrated pool of phylogenetic diversity on the planet . There remains a need for innovative molecular tools that can further our knowledge of microbial diversity and its functional implications . We present the method and application of serial analysis of ribosomal sequence tags (SARST) as a novel tool for elucidating complex microbial communities, such as those found in soils and sediments . Serial analysis of ribosomal sequence tags uses a series of enzymatic reactions to amplify and ligate ribosomal sequence tags (RSTs) from bacterial small subunit rRNA gene (SSU rDNA) V1-regions into concatemers that are cloned and sequenced . This approach offers a significant increase in throughput over traditional SSU rDNA clone libraries, as up to 20 RSTs are obtained from each sequencing reaction . To test SARST and measure the bias associated with this approach, RST libraries were prepared from a defined mixture of pure cultures and from duplicate arctic soil DNA samples . The actual RST distribution reflected the theoretical composition of the original defined mixture . Data from duplicate soil libraries (1345 and 1217 RSTs, with 525 and 505 unique RSTs, respectively) indicated that replication provides a strongly correlated RST profile (r(2) = 0.80) and division-level distribution of RSTs (r(2) = 0.99) . Using sequence data from abundant soil RSTs, we designed specific primers that successfully amplified a larger portion of the SSU rDNA for further phylogenetic analysis . These results suggest that SARST is a powerful approach for reproducible high-throughput profiling of microbial diversity amenable to medical, industrial or environmental microbiology applications.

Environ Microbiol, 2004 Feb, 6(2), 95 - 110
Functional gene diversity analysis in BTEX contaminated soils by means of PCR-SSCP DNA fingerprinting: comparative diversity assessment against bacterial isolates and PCR-DNA clone libraries; Junca H et al.; Developments in molecular biology based techniques have led to rapid and reliable tools to characterize microbial community structures and to monitor their dynamics under in situ conditions . However, there has been a distinct lack of emphasis on monitoring the functional diversity in the environment . Genes encoding catechol 2,3-dioxygenases (C23O), as key enzymes of various aerobic aromatic degradation pathways, were used as functional targets to assess the catabolic gene diversity in differentially BTEX contaminated environments by polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) . Site specific PCR-SSCP fingerprints were obtained, showing that gene diversity experienced shifts correlated to temporal changes and levels of contamination . PCR-SSCP enabled the recovery of predominant gene polymorphs, and results closely matched with the information retrieved from random sequencing of PCR-DNA clone libraries . A new method for isolating strains capable of growing on BTEX compounds was developed to diminish preselection or enrichment bias and to assess the function of predominant gene polymorphs . C23O abundance in isolates correlated with the levels of BTEX pollution in the soil samples analysed . Isolates harbouring C23O genes, identical to the gene polymorph predominant in all contaminated sites analysed, showed an unexpected benzene but not toluene mineralizing phenotype whereas isolates harbouring a C23O gene variant differing by a single point mutation and observed in highly polluted sites only, were capable, among some other isolates, to mineralize benzene and toluene, indicating a catabolically determined sharing of carbon sources on-site . The PCR-SSCP technique is thus a powerful tool for assessing the diversity of functional genes and the identification of predominant gene polymorphs in environmental samples as a prerequisite to understand the functioning of microbial communities.

Indoor Air, 2004 Feb, 14(1), 55 - 64
Microbial contamination of indoor air due to leakages from crawl space: a field study; Airaksinen M et al.; Mechanical exhaust ventilation system is typical in apartment buildings in Finland . In most buildings the base floor between the first floor apartments and crawl space is not air tight . As the apartments have lower pressure than the crawl space due to ventilation, contaminated air may flow from the crawl space to the apartments . The object of this study was to find out whether a potential air flow from crawl space has an influence on the indoor air quality . The results show that in most cases the concentration of fungal spores was clearly higher in the crawl space than inside the building . The size distribution of fungal spores depended on the fungal species . Correlation between the fungal spores in the crawl space and indoors varied with microbial species . Some species have sources inside the building, which confounds the possible relation between crawl pace and indoor concentrations . Some species, such as Acremonium, do not normally have a source indoors, but its concentration in the crawl space was elevated; our measurements showed also elevated concentrations of Acremonium in the air of the apartments . This consistent finding shows a clear linkage between fungal spores in the indoor air and crawl space . We conclude that a building with a crawl space and pressure difference over the base floor could be a potential risk for indoor air quality in the first floor apartments.

Infect Control Hosp Epidemiol, 2004 Jan, 25(1), 26 - 9
Preliminary results for a new final package test to assess the quality of sterile package systems; Dunkelberg H et al.; OBJECTIVES: To develop a microbial test method to ascertain the passage of airborne bacteria through the medical device packaging system after sterilization, and to apply this test method to flexible packages under mechanical pressure changes . METHODS: Petri dishes filled with nutrient agar were integrated into the packaging unit prior to sterilization . We examined paper packaging consisting of 1 (single-paper packaging {P}), 2 (double-paper packaging {PP} and textile and paper double packaging {TP}), and 3 (double packaging with transport packaging {TPP}) layers . After sterilization, the test packages were pressed five times per minute for 1 or 3 hours by a mechanical device weighing 1 kg . This exposure took place in rooms with an average airborne bacterial count of 35 (room 1) or 440 (room 2) CFU/m3 . The packaging was opened following culture at 37 degrees C for 48 hours to determine the number of colonies formed . RESULTS: The proportion of contaminated packages rose with the duration of mechanical stress and increased airborne bacteria concentration . Thus, mechanical pressure change for 3 hours resulted in the contamination of 60% (P), 15% (PP), 0% (TP), and 0% (TPP) of the packages in room 1, whereas 100% (P), 65% (PP), 73% (TP), and 0% (TPP) of the packages in room 2 were contaminated . CONCLUSIONS: This test method allows sterile packaging systems to be tested for contamination under practical conditions without extensive laboratory preparation . Contamination as a result of laboratory errors can be ruled out almost certainly.

Biotechnol Bioeng, 2004 Mar 5, 85(5), 547 - 52
Flow calorimetry and dielectric spectroscopy to control the bacterial conversion of toxic substrates into polyhydroxyalcanoates; Maskow T et al.; The microbial conversion of toxic substrates into valuable products in continuous culture requires the equivalent of a tight rope walk between formation of the desired product and intoxication of the microbial catalyst . The condition of the latter is reflected immediately by changes in heat flow rate and beta-dispersion in an electrical RF field . Therefore, these were applied to the example of the continuous growth-associated synthesis of polyhydroxyalcanoates (PHA) from phenol by the bacterial strain Variovorax paradoxus DSM 4065 . By controlling the supply of phenol to the chemostat, the rates of degradation, biomass formation, and synthesis of target product, respectively, were increasingly elevated until the onset of poisoning the organisms . The boundary between the maximum rates and the initiation of intoxication coincided with a sudden change in the heat flux . Using this occurrence, it was possible to develop a control strategy and test it successfully for a time period of 80 h . After 40 h the process stabilized at mean values, i.e., at rates of 92% phenol degradation, 100% biomass formation, and 70 - 75% of PHA formation compared with the situation shortly before poisoning the organisms . Using a moving-average technique to filter the raw dielectric spectroscope data, changes were followed in biomass concentration of approximately 100 mg/L . However, this technique was not sensitive or rapid enough to control the process .

Langenbecks Arch Surg, 2004 Oct, 389(5), 341 - 9 Epub 2004 Feb 04.
Current concept of pathophysiological understanding and natural course of ulcerative colitis; Holtmann MH et al.; INTRODUCTION: According to the current paradigm both ulcerative colitis (UC) and Crohn's disease (CD) result from a complex interplay of genetic susceptibility factors, environmental factors, alterations of the physiological intestinal flora and a defective regulation of the intestinal immune system . DISCUSSION: The objective of this review is to give an overview of these factors and mechanisms, including genetic, environmental and microbial factors, with special alterations of relevant cellular components of the intestinal immune system such as T cells, macrophages and epithelial cells will then be addressed . In addition, the most relevant animal model systems that have contributed to our current pathogenetic understanding will be introduced . Clinically, the natural course of UC with special reference to the risk of colorectal cancer will be addressed . CONCLUSION: The elucidation of pathomechanisms at the level of the intestinal immune system provides the potential for novel, effective treatment strategies . Best surgical management of patients with UC, however, still remains a challenge.

Bioorg Med Chem, 2004 Feb 15, 12(4), 807 - 15
Small molecule functional discrimination of the kinases required for the microbial synthesis of threonine and isoleucine; Bareich D et al.; The biosynthesis of l-threonine and l-isoleucine in bacteria and in fungi requires the action of 2 amino acid kinases: aspartate kinase and homoserine kinase . Although these kinases bind similar substrates and catalyze analogous phosphotransfer chemistry, they do not show high amino acid sequence homology . We show that despite this difference, both kinases form a ternary complex consisting of enzyme- adenosine triphosphate- amino acid to accomplish phosphoryl transfer . With this similarity in mind, we set out to identify molecules that could lead to inhibitors with activity against both kinases in the pathway . We synthesized a series of aspartic acid-adenosine bisubstrate compounds separated by a variable length alkyl linker that we hypothesized could bind to these kinases . These bisubstrate compounds only inhibited the bacterial aspartate kinase . These results reveal unexpected differences in small molecule interactions among these functionally similar enzymes.

J Environ Sci (China), 2003 Nov, 15(6), 773 - 8
Phosphorus limitation on bacterial regrowth in drinking water; Sang JQ et al.; Assimilable organic carbon (AOC) test and bacterial regrowth potential (BRP) analysis were used to investigate the effect of phosphorus on bacterial regrowth in the drinking water that was made from some raw water taken from a reservoir located in northern China . It was shown that AOC of the drinking water samples increased by 43.9%-59.6% and BRP increased by 100%-235% when 50 microg/L PO4(3-)-P(as NaH2 PO4) was added alone to the drinking water samples . This result was clear evidence of phosphorus limitation on bacteria regrowth in the drinking water . This investigation indicated the importance of phosphorus in ensuring biological stability of drinking water and offered a novel possible option to restrict microbial regrowth in drinking water distribution system by applying appropriate technologies to remove phosphorus efficiently from drinking water in China.

Braz J Biol, 2003 Aug, 63(3), 373 - 80
Methodological tests of a heterotrophy index for aquatic ecosystems; Antonio RM et al.; Experiments in glucose mineralization were carried out to investigate the effects caused by natural forcing functions on both the decomposition rates and heterotrophy capacity of aquatic ecosystems . In addition, the methodology used could show connections between mineralization rates measured in both laboratory and field work with those measured in aquatic ecosystems . Water samples from Infernao lagoon (21 degrees 35'S and 47 degrees 51'W) were collected, filtered, enriched with glucose, and incubated under aerobic and anaerobic conditions . The glucose concentration variation, dissolved oxygen (DO) consumption, pH, electric conductivity, and total CO2 amount in the water were determined for sixteen days . In the period with intense oxygen consumption there was also an evident glucose demand and the dissolved oxygen consumption rate was approximately the same as that for glucose mineralization . The process in the aerobic chambers was 2.2 times faster than that in the anaerobic chambers . An initial acidification of the water samples, probably due to microbial carbonic acid liberation, was noted . A rise in pH values was also observed at the end of the process . The electric conductivity was low for both aerobic and anaerobic chambers, indicating a probable ion uptake by microbial organisms due to the presence of carbon sources . The glucose content variations corresponded to both CO2 formation and dissolved oxygen consumption . It was estimated that 19.4% of the initial glucose content turned into CO2 and the remaining 80.6% into humic compounds and microbial biomass . This experiment showed that glucose can be used as a substrate indicating the heterotrophy of a given aquatic ecosystem.

J Clin Invest, 2004 Feb, 113(3), 321 - 33
Helicobacter pylori persistence: biology and disease; Blaser MJ et al.; Helicobacter pylori are bacteria that have coevolved with humans to be transmitted from person to person and to persistently colonize the stomach . Their population structure is a model for the ecology of the indigenous microbiota . A well-choreographed equilibrium between bacterial effectors and host responses permits microbial persistence and health of the host but confers risk of serious diseases, including peptic ulceration and gastric neoplasia.

Clin Rev Allergy Immunol, 2004 Feb, 26(1), 5 - 14
The potential impact of early exposures to geohelminth infections on the development of atopy; Cooper PJ; Microbial exposures in early life may provide important signals for immune maturation and the development of an antiinflammatory network thereby preventing the development of dysregulated immune responses such as that associated with allergic disease . The human immune system has evolved in the presence of intense helminth infections and has developed regulatory mechanisms to limit the harmful inflammation that can be caused by the potent allergens secreted by these chronic pathogens . Geohelminth infections are highly prevalent childhood infections, and there is strong evidence that chronic geohelminth infections provide protection against atopy in the rural tropics . Because the early environmental exposures that may lead to the development of atopy are likely to occur in the first few years of life, geohelminth infections may exert their protective effects at this time . Early exposures to geohelminth antigens could occur transplacentally, through breast milk, or through early infant exposures, and could induce tolerance to parasite antigens resulting in suppressed allergic responses to the parasite . Tolerization to parasite antigens could suppress allergic responses to inhalant allergens through bystander effects or through tolerization of crossreactive epitopes that are shared between geohelminth parasites and inhalant allergens . Tolerization to crossreactive allergens could occur by thymic deletion or through peripheral mechanisms such as regulatory T cells . Immunologic studies of the mechanisms by which early exposures to geohelminth infections affect immune polarization to inhalant allergens are likely to provide important insights into the early regulation of the immune response and may lead to the design of novel interventions for the prevention of allergic disease.

Water Sci Technol, 2003, 48(11-12), 277 - 84
Treatment of landfill leachate--high tech or low tech? A case study; Schwarzenbeck N et al.; At the sanitary landfill of the city of Penzberg (Germany), two diverse approaches to leachate treatment were studied as parts of a three-stage treatment concept . The performance of a simple aerobic pond was compared to that of an advanced multistage treatment unit, the latter comprising a membrane biological reactor and a two-stage activated carbon filter . For 274 days of the year (75%) the pond was able to provide sufficient treatment even under cold weather conditions . For temperatures lower than 5 degrees C, a higher biomass content and temporal storage of the raw leachate (e.g . increasing hydraulic retention time) could close the gap of insufficient treatment . In contrast, the advanced treatment system could only accomplish limited treatment capabilities due to insufficient maintenance, low loading conditions and deficient coordination between the individual treatment steps . As a result, degradation rates were low and operational problems frequent . Limits for Ntot were exceeded regularly (Ntot,e = 60-70 mg/L), throughput broke down and excessive nitrite production occurred (NO2-Ne = 10 mg/L) as a result of microbial activity inside the activated carbon filters . This case study clearly suggests aerobic ponds as an appropriate solution for the treatment of landfill leachate in areas where operational independence is essential.

J Anim Sci, 2004 Jan, 82(1), 198 - 208
Effect of alkali pretreatment of wheat straw on the efficacy of exogenous fibrolytic enzymes; Wang Y et al.; The effects of pretreating wheat straw with alkali on the efficacy of exogenous fibrolytic enzymes for improving straw digestibility were studied in vitro, in situ, and in vivo . In Exp . 1, untreated straw (US); alkali-treated (5% NaOH, wt/wt) straw (AS); and autoclaved, alkali-treated straw (AAS) were sprayed with 0 or 1.5 mg/g DM of enzyme mix (xylanase, beta-glucanase, carboxymethylcellulase, and amylase) and incubated for 30 h in buffered ruminal fluid (3 x 2 factorial arrangement) . Enzymes increased (P < 0.001) gas production and the incorporation of 15N into microbial N at 4 h, more so with AS or AAS than with US (P < 0.001 for gas; P < 0.05 for 15N) . In Exp . 2, US and AS were sprayed with enzymes at 0, 0.15, or 1.5 mg/g DM (2 x 3 factorial) and incubated ruminally in nylon bags for up to 80 h to determine the in situ DM disappearance (ISDMD) . Interactive effects (P < 0.05) of pretreatment and enzymes were observed on all ruminal degradation parameters . Alkali increased the rate (P < 0.01) and extent (P < 0.001) of ISDMD irrespective of enzymes . Enzymes applied to US did not affect the extent of ISDMD, but they increased (P < 0.01) the extent of ISDMD when applied to AS . Substrates from Exp . 1 and 2 were incubated in acetate buffer for 24 h to measure the hydrolytic loss of DM and release of reducing sugars and phenolic compounds . Alkali pretreatment and enzymes each increased (P < 0.001) DM loss and the release of reducing sugars and, in combination, exerted synergistic effects (P < 0.001) . Enzymes did not affect the release of phenolic compounds from the straw . In Exp . 3, total-tract digestibility of untreated and enzyme-treated (100 mL/kg DM) ammoniated straw was assessed using 32 beef cows in eight pens . Wrapped straw bales were injected with NH3 (3% {wt/wt}, DM basis) 4 mo before the study; enzymes were applied immediately before feeding . Applying enzyme to ammoniated straw increased (P < 0.05) digestibilities of DM, OM, and total N but did not affect the intake of DM or digestibility of ADF . Pretreatment of straw with alkali enhanced the efficacy of exogenous enzymes, presumably by breaking esterified bonds and releasing phenolic compounds and/or by swelling the crystalline cellulose and enhancing enzyme penetration . Including enzymes that mimic alkali hydrolysis (e.g., esterases) in commercial feed additives could substantially improve the value of these products for ruminants.

Semin Immunol, 2004 Feb, 16(1), 35 - 41
The role of Toll-like receptors in combating mycobacteria; Krutzik SR et al.; In the battle against infections with mycobacteria, the body employs components of both the innate and adaptive arms of the immune system . Toll-like receptors (TLRs) mediate the activation of cells of the innate immune system leading to dynamic functions including direct anti-microbial activity, induction of cytokine secretion, triggering dendritic cell maturation, and triggering apoptosis . Furthermore, TLR activation is capable of modulating the adaptive immune response with a bias towards a Th1 T-cell response . However, the activation of TLRs by mycobacteria may also provide a means of immune evasion . Therefore, the modulation of TLR activation can influence the ability to properly destroy invading pathogens such as mycobacteria.

Semin Immunol, 2004 Feb, 16(1), 3 - 9
TLR signaling pathways; Takeda K et al.; Toll-like receptors (TLRs) have been established to play an essential role in the activation of innate immunity by recognizing specific patterns of microbial components . TLR signaling pathways arise from intracytoplasmic TIR domains, which are conserved among all TLRs . Recent accumulating evidence has demonstrated that TIR domain-containing adaptors, such as MyD88, TIRAP, and TRIF, modulate TLR signaling pathways . MyD88 is essential for the induction of inflammatory cytokines triggered by all TLRs . TIRAP is specifically involved in the MyD88-dependent pathway via TLR2 and TLR4, whereas TRIF is implicated in the TLR3- and TLR4-mediated MyD88-independent pathway . Thus, TIR domain-containing adaptors provide specificity of TLR signaling.

Med J Malaysia, 2003 Aug, 58(3), 437 - 9
The Jarisch-Herxheimer reaction in ocular syphilis; Fathilah J et al.; A patient with ocular syphilis is presented . She experienced deterioration in vision following the commencement of treatment due to a Jarisch-Herxheimer reaction . This is a transient febrile illness that can occur in patients after the first adequate dose of an anti-microbial drug to treat infectious diseases such as syphilis, Lyme disease and relapsing fever . However, a Jarisch-Herxheimer reaction occurring in a patient receiving treatment for ocular syphilis can be serious, resulting in the rapid loss of vision.

Am J Clin Pathol, 2004 Jan, 121(1), 138 - 41
Biphasic activated partial thromboplastin time waveform and adverse events in non-intensive care unit patients; Smith EY et al.; The purpose of the present study was to determine whether the presence of a biphasic activated partial thromboplastin time (aPTT) waveform (BPW) is associated with adverse clinical outcomes among patients not in an intensive care unit (ICU) . Consecutive patients from the emergency department or non-ICU inpatient floors with a BPW (n = 24) were enrolled prospectively, along with 24 matched control subjects with a normal aPTT waveform . Patients with a BPW had a significantly longer hospital stay (mean {median}, 16.9 {11} vs 4.9 {2.5} days; P = .011), were more likely to have a positive microbial culture (16/24 {67%} vs 3/24 {13%}; P < .001), were transferred more often to an ICU (6/24 {25%} vs 0/24 {0%}; P = .010), and were more likely to receive an RBC transfusion (11/24 {46%} vs 5/24 {21%}; P = .047) or a fresh frozen plasma transfusion (5/24 {21%} vs 0/24 {0%}; P = .025) . Emergency department patients with a BPW were more likely to be admitted (11/11 vs 5/11; P = .018) . These results suggest that the BPW is associated with an increased rate of adverse events among non-ICU patients . Further study in this population is warranted.

Microb Ecol, 2004 Feb, 47(2), 119 - 26 Epub 2004 Feb 02.
Microbial characterization during the early habitation of the International Space Station; Castro VA et al.; An evaluation of the microbiota from air, water, and surface samples provided a baseline of microbial characterization onboard the International Space Station (ISS) to gain insight into bacterial and fungal contamination during the initial stages of construction and habitation . Using 16S genetic sequencing and rep-PCR, 63 bacterial strains were isolated for identification and fingerprinted for microbial tracking . Of the bacterial strains that were isolated and fingerprinted, 19 displayed similarity to each other . The use of these molecular tools allowed for the identification of bacteria not previously identified using automated biochemical analysis and provided a clear indication of the source of several ISS contaminants . Strains of Bradyrhizobium and Sphingomonas unable to be identified using sequencing were identified by comparison of rep-PCR DNA fingerprints . Distinct DNA fingerprints for several strains of Methylobacterium provided a clear indication of the source of an ISS water supply contaminant . Fungal and bacterial data acquired during monitoring do not suggest there is a current microbial hazard to the spacecraft, nor does any trend indicate a potential health risk . Previous spacecraft environmental analysis indicated that microbial contamination will increase with time and will require continued surveillance .

Anaesthesist, 2004 Jan, 53(1), 10 - 28
{Role of the innate immune response in sepsis}; Horner C et al.; The innate immune system succeeds against the majority of infections before the adaptive immune system is activated . New findings contribute to a better understanding of the pathophysiology of sepsis and lead to the development of new therapeutic strategies . The innate immune system, being responsible for the first response to infections, can trigger adaptive immune responses in case the initial response is ineffective . Both arms of the immune system interact with each other, mainly via cell-cell-interactions but also by soluble factors, such as cytokines and chemokines . Two sub-populations of helper T-cells direct both balanced activation and inhibition of the two arms of the immune systems using specific patterns of cytokine release . Results obtained in new animal models of sepsis, taking a progressive growth of bacteria into account, have implied that existing knowledge has to be reanalyzed . The idea of sepsis as a mere "over-reaction to inflammation" has to be abandoned . Various so-called pattern recognition receptors (e.g . toll-like receptors, TLRs, NOD proteins) are located intracellularly or in the plasma membrane of innate immune cells and recognize certain patterns expressed exclusively by extracellular pathogens . Upon receptor engagement, intracellular signaling pathways lead to cellular activation, followed by release of various cytokines and anti-microbial substances . During the course of sepsis a cytokine shift towards increasing immune suppression occurs . The innate immune system also contributes to the migration of leukocytes in inflammed tissue, involving chemokines and adhesion molecules . Leukocytes also secrete the tissue factor leading to formation of thrombin . The environment in sepsis can cause disseminated intravascular coagulation (DIC), but at the same time thrombin triggers the release of chemokines and adhesion molecules through endothelial cells, which represents a positive feedback mechanism for innate immune responses . New therapeutic strategies for sepsis try to establish a well-balanced immune response . Intervention is accomplished through inhibition of inflammatory cytokines, their receptors or through activation of immunostimulatory responses.

EMBO Rep, 2004 Feb, 5(2), 172 - 7 Epub 2004 Jan 23.
Toll-like receptors differentially induce nucleosome remodelling at the IL-12p40 promoter; Albrecht I et al.; Toll-like receptors (TLRs) mediate recognition of microbial components . Despite activation of a shared set of signal transduction molecules, the biological effects of certain TLR agonists differ considerably . In macrophages and dendritic cells, stimulation by the prototypical stimuli CpG-DNA (TLR9), lipopolysaccharide (LPS; TLR4) and lipoteichoic acid (LTA; TLR2) resulted in striking differences in expression of IL-12 . However, these stimuli induced similar amounts of the common proinflammatory cytokine TNFalpha . Surprisingly, an IL-12p40 promoter reporter construct was activated equally by CpG-DNA, LPS and LTA . Examinations of the chromatin structure of the endogenous IL-12p40 promoter revealed that nucleosome remodelling contributed to differential IL-12 induction . Upon stimulation, nucleosome architecture was changed to provide increased access to the IL-12p40 promoter . In dendritic cells, a differential induction of nucleosome remodelling at the IL-12p40 promoter was observed upon triggering with different TLR agonists . These results identify nucleosome remodelling as an additional restriction point in differential TLR signalling.

N Engl J Med, 2004 Jan 29, 350(5), 451 - 8
Soluble triggering receptor expressed on myeloid cells and the diagnosis of pneumonia; Gibot S et al.; BACKGROUND: The diagnosis and treatment of bacterial pneumonia in patients who are receiving mechanical ventilation remain a difficult challenge . The triggering receptor expressed on myeloid cells (TREM-1) is a member of the immunoglobulin superfamily, and its expression on phagocytes is specifically up-regulated by microbial products . The presence of soluble TREM-1 (sTREM-1) in bronchoalveolar-lavage fluid from patients receiving mechanical ventilation may be an indicator of pneumonia . METHODS: We conducted a prospective study of 148 patients receiving mechanical ventilation in whom infectious pneumonia was suspected . A rapid immunoblot technique was used to measure sTREM-1 in bronchoalveolar-lavage fluid . Two independent intensivists who were unaware of the results of the sTREM-1 assay determined whether community-acquired pneumonia and ventilator-associated pneumonia were present or absent . RESULTS: The final diagnosis was community-acquired pneumonia in 38 patients, ventilator-associated pneumonia in 46 patients, and no pneumonia in 64 patients . The presence of sTREM-1 by itself was more accurate than any clinical findings or laboratory values in identifying the presence of bacterial or fungal pneumonia (likelihood ratio, 10.38; sensitivity, 98 percent; specificity, 90 percent) . In multiple logistic-regression analysis, the presence of sTREM-1 was the strongest independent predictor of pneumonia (odds ratio, 41.5) . CONCLUSIONS: In patients receiving mechanical ventilation, rapid detection of sTREM-1 in bronchoalveolar-lavage fluid may be useful in establishing or excluding the diagnosis of bacterial or fungal pneumonia .

Oecologia, 2004 Mar, 139(1), 131 - 9 Epub 2004 Jan 28.
Potent cytotoxins produced by a microbial symbiont protect host larvae from predation; Lopanik N et al.; Larvae of the sessile marine invertebrate Bugula neritina (Bryozoa) are protected by an effective chemical defense . From the larvae, we isolated three bryostatin-class macrocyclic polyketides, including the novel bryostatin 20, that deterred feeding by a common planktivorous fish that co-occurs with B . neritina . A unique bacterial symbiont of B . neritina, Endobugula sertula, was hypothesized as the putative source of the bryostatins . We show that: (1) bryostatins are concentrated in B . neritina larvae and protect them against predation by fish; (2) the adults are not defended by bryostatins; and (3) E . sertula produces bryostatins . This study represents the first example from the marine environment of a microbial symbiont producing an anti-predator defense for its host and, in this case, specifically for the host's larval stage, which is exceptionally vulnerable to predators.

Cancer Lett, 2004 Feb 10, 204(1), 15 - 21
Changes in cecal microbial metabolism of rats induced by individual and a mixture of drinking water disinfection by-products; George SE et al.; Disinfection of drinking water has been one of the greatest public health successes . Numerous halogenated disinfection by-products (DBPs) occur and chronic ingestion has been associated with an increased risk for colorectal cancer in human populations . Because the intestinal microbiota can bioactivate xenobiotics, studies have been performed to examine the effects of individual DBPs on intestinal microbial metabolism . No studies have been conducted on a defined mixture of DBPs to determine if there is an enhancement of response to a mixture . Ten-week-old male Long-Evans rats were treated in their drinking water for 17 weeks with 0.4 g/l potassium bromate, 1.8 g/l chloroform, 0.7 g/l bromodichloromethane (BDCM), 0.07 g/l 3-chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone (MX), or a mixture of the four chemicals or distilled water . Cecal nitroreductase (NR), azoreductase (AR), dechlorinase (DC), beta-glucuronidase (GLR), beta-galactosidase (GAL), and beta-glucosidase (GLU) were assayed . No change in GLU or GLR activity was detected after treatment . BDCM treatment reduced DC and GAL activities and elevated NR and AR activity . GAL, AR, and NR activities were significantly different after treatment with bromate, chloroform, BDCM, and MX, but not the mixture . DC activity after chloroform-, MX-, or BDCM-treatment was significantly below control levels . The present study shows that changes in intestinal microbial metabolism do occur after treatment with individual and a mixture of DBPs but the changes were not additive in the mixture group.

J Microbiol Methods, 2004 Feb, 56(2), 287 - 90
Artificial soil microcosms: a tool for studying microbial autecology under controlled conditions; Ellis RJ; A novel artificial microcosm containing all the essential chemical components of soil, but with reduced heterogeneity and biological complexity, has been developed . Its utility for supporting realistic microbial populations was demonstrated and an example of how competing bacteria can be studied is illustrated.

J Microbiol Methods, 2004 Feb, 56(2), 173 - 80
Using geographical information techniques to quantify the spatial structure of endolithic boring processes within sediment grains of marine stromatolites; Petrisor AI et al.; Marine stromatolites are generated through the interactions of environmental parameters and specific microbial processes . The activities of endolithic bacteria, that bore canals through calcium carbonate (CaCO(3)) sand grains (ooids) and reprecipitate the CaCO(3) as a single layer (i.e . micritic laminae) are especially important in the longer term stability of the stromatolite macrostructure . Image analysis and classification approaches have been used previously, but only seldom as a quantitative microscopic tool . Here, we develop a new approach that enables the quantification of microscale (i.e . micrometers to millimeters) spatial structure within marine stromatolites . To demonstrate our approach, images were acquired from two different layers of a stromatolite: "orange layers", where microboring of canals within ooids was relatively abundant, and "white layers" where microboring was greatly reduced or lacking . Images were then transformed into spatial maps . Computation of canal and ooid grain areas within each image was conducted and statistically compared between replicate samples from the two stromatolite layers . This allowed quantification of the areas of ooid grains that were microbored . Based on our results, we suggest that our method could be widely applicable to sedimentary environments, and other areas of fundamental research.

Rev Med Chil, 2003 Nov, 131(11), 1266 - 72
{10-year experience in flexible bronchoscopy in pediatric patients}; Sanchez I et al.; BACKGROUND: Approximately a decade ago, pediatric Flexible Bronchoscopy (FB) was introduced in Chile, after being used for several years in adults . AIM: To describe our clinical experience in FB in a ten years period . PATIENTS AND METHODS: Records of procedures done between January 1993 and September 2002 at the Pediatric Service of the Catholic University Hospital, were retrospectively reviewed . We evaluated the clinical indications for the procedures in relation to patient's age and the correlation between indications and FB findings . RESULTS: A total of 700 procedures were performed during the period, 59% in men and 53% in patients younger than 1 year . Seventy seven percent of procedures were done in an examination room, using a nasal approach . The main indication was visualization of the airway (49%) . The most common clinical diagnosis, in descending order were: atelectasis, stridor and etiologic study of pneumonia by bronchoalveolar lavage (BAL) . In children younger than 6 months the most common clinical diagnosis was stridor, followed by atelectasis . The main diagnosis in the whole sample, reached by FB was atelectasis secondary to mucous plug . In children younger than 6 months, the main diagnosis was laryngomalacia . A positive microbial culture was obtained in 43% of patients in whom BAL was done . Complications were uncommon (5%) and mostly mild . In 2.3% of cases, these were severe, such as bronchospasm and need for mechanical ventilation . Severe complications were observed in patients younger than 3 months with severe stridor or in children with cancer, who required FB and BAL . CONCLUSIONS: Flexible bronchoscopy is a safe and useful procedure in pediatric patients.

Infect Immun, 2004 Feb, 72(2), 824 - 32
Myd88-dependent in vivo maturation of splenic dendritic cells induced by Leishmania donovani and other Leishmania species; De Trez C et al.; The usual agent of visceral leishmaniasis in the Old World is Leishmania donovani, which typically produces systemic diseases in humans and mice . L . donovani has developed efficient strategies to infect and persist in macrophages from spleen and liver . Dendritic cells (DC) are sentinels of the immune system . Following recognition of evolutionary conserved microbial products, DC undergo a maturation process and activate antigen-specific naive T cells . In the present report we provide new insights into how DC detect Leishmania in vivo . We demonstrate that in both C57BL/6 and BALB/c mice, systemic injection of L . donovani induced the migration of splenic DC from marginal zones to T-cell areas . During migration, DC upregulated the expression of major histocompatibility complex II and costimulatory receptors (such as CD40, CD80, and CD86) . Leishmania-induced maturation requires live parasites and is not restricted to L . donovani, as L . braziliensis, L . major, and L . mexicana induced a similar process . Using a green fluorescent protein-expressing parasite, we demonstrate that DC undergoing maturation in vivo display no parasite internalization . We also show that L . donovani-induced DC maturation was partially abolished in MyD88-deficient mice . Taken together, our data suggest that Leishmania-induced DC maturation results from direct recognition of Leishmania by DC, and not from DC infection, and that MyD88-dependent receptors are implicated in this process.

Biomaterials, 2004 May, 25(11), 2003 - 11
Polyelectrolyte multilayer films with pegylated polypeptides as a new type of anti-microbial protection for biomaterials; Boulmedais F et al.; Adhesion of bacteria at the surface of implanted materials is the first step in microbial infection, leading to post-surgical complications . In order to reduce this adhesion, we show that poly(L-lysine)/poly(L-glutamic acid) (PLL/PGA) multilayers ending by several PLL/PGA-g-PEG bilayers can be used, PGA-g-PEG corresponding to PGA grafted by poly(ethylene glycol) . Streaming potential and quartz crystal microbalance-dissipation measurements were used to characterize the buildup of these films . The multilayer films terminated by PGA and PGA-g-PEG were found to adsorb an extremely small amount of serum proteins as compared to a bare silica surface but the PGA ending films do not reduce bacterial adhesion . On the other hand, the adhesion of Escherichia coli bacteria is reduced by 72% on films ending by one (PLL/PGA-g-PEG) bilayer and by 92% for films ending by three (PLL/PGA-g-PEG) bilayers compared to bare substrate . Thus, our results show the ability of PGA-g-PEG to be inserted into multilayer films and to drastically reduce both protein adsorption and bacterial adhesion . This kind of anti-adhesive films represents a new and very simple method to coat any type of biomaterials for protection against bacterial adhesion and therefore limiting its pathological consequences.

FEBS Lett, 2004 Jan 16, 557(1-3), 199 - 203
Two Arabidopsis thaliana genes encode functional pectin methylesterase inhibitors; Raiola A et al.; We have identified, expressed and characterized two genes from Arabidopsis thaliana (AtPMEI-1 and AtPMEI-2) encoding functional inhibitors of pectin methylesterases . AtPMEI-1 and AtPMEI-2 are cell wall proteins sharing many features with the only pectin methylesterase inhibitor (PMEI) characterized so far from kiwi fruit . Both Arabidopsis proteins interact with and inhibit plant-derived pectin methylesterases (PMEs) but not microbial enzymes . The occurrence of functional PMEIs in Arabidopsis indicates that a mechanism of controlling pectin esterification by inhibition of endogenous PMEs is present in different plant species.

FEBS Lett, 2004 Jan 16, 557(1-3), 164 - 8
A new member of the bacterial ribonuclease inhibitor family from Saccharopolyspora erythraea; Krajcikova D et al.; We have identified Sti, the gene of a ribonuclease inhibitor from Saccharopolyspora erythraea, by using a T7 phage display system . A specific phage has been isolated from a genome library by a biopanning procedure, using RNase Sa3, a ribonuclease from Streptomyces aureofaciens, as bait . Sti, a protein of 121 amino acid residues, with molecular mass 13059 Da, is a homolog of barstar and other microbial ribonuclease inhibitors . To overexpress its gene in Escherichia coli, we optimized the secondary structure of its mRNA by introducing a series of silent mutations . Soluble protein was isolated and purified to homogeneity . Inhibition constants of complex of Sti and RNase Sa3 or barnase were determined at pH 7 as 5 x 10(-12) or 7 x 10(-7), respectively.

Am J Trop Med Hyg, 2003 Dec, 69(6), 574 - 81
Malaria-associated cytokine changes in the placenta of women with pre-term deliveries in Yaounde, Cameroon; Suguitan AL Jr et al.; The prevalence of pre-term deliveries (PTDs) is increased in women who become infected with Plasmodium falciparum during pregnancy . Because prematurity is a risk factor for newborns, it is important to identify conditions that contribute to malaria-associated PTDs . Plasmodium falciparum-infected erythrocytes sequester in the placenta and attract activated mononuclear cells that secrete pro-inflammatory cytokines . Increased inflammatory cytokine levels in other microbial infections are associated with PTDs . To determine if such is the case in women with placental malaria, concentrations of interferon-gamma (IFN-gamma), tumor necrosis factor-alpha (TNF-alpha), interleukin-4 (IL-4), and IL-10 were measured in placental plasma of 391 malaria-infected and -uninfected Cameroonian women with premature and full-term deliveries . Risk factors for malaria-associated PTDs included peripheral and placental parasitemias greater than 1%, maternal anemia, elevated IL-10 levels, and low TNF-alpha:IL-10 ratios due to over-expression of IL-10 . Alterations in cytokine levels may contribute to PTDs through the induction of anemia and/or altering cellular immune responses required for eliminating placental parasites.

J Dairy Sci, 2003 Dec, 86(12), 4047 - 53
Use of principal component analysis to investigate the origin of heptadecenoic and conjugated linoleic acids in milk; Fievez V et al.; The aim of this paper was the application of principal component analysis (PCA) 1) to elucidate mutual metabolic relationships between milk fatty acids (FA) and 2) to illustrate the origin of milk FA, in particular C17:1 and cis-9,trans-11 conjugated linoleic acid . Data were combined from 3 experiments with lactating Holstein-Friesian cows offered diets based on grass or legume silage and concentrates . Loading plots of PCA based on milk FA concentrations showed 4 groups of milk FA, having similar precursors or metabolic pathways in the rumen and/or mammary gland: medium-chain saturated FA, de novo synthesized from acetate and beta-hydroxybutyrate; monoenoic milk FA, products of delta9-desaturase activity in the mammary gland; odd chain FA of rumen microbial origin and C18:0, n-6 C18:2, and n-3 C18:3 of dietary origin or the result of rumen biohydrogenation . Loading plots of PCA based on both milk and duodenal FA concentrations as well as on milk FA yields and duodenal FA flows further illustrated the importance of postabsorptive synthesis of the milk medium chain saturated and monoenoic FA and the direct absorption from the blood stream of odd chain FA, C18:0, n-6 C18:2, and n-3 C18:3 . In all loading plots, milk oleic acid (C18:1) appeared intermediate between clusters of 18-carbon FA and monoenoic FA, illustrating its dual (dietary and endogenous production) origin . Milk C17:1 was suggested to be a desaturation product of C17:0, in common with other milk monoenoic FA . Finally, the PCA technique, based on milk FA patterns of one experiment, was applied to investigate factors determining cis-9,trans-11 conjugated linoleic acid concentrations in milk . Within the range of diets and cows studied here, we showed changes in cis-9,trans-11 conjugated linoleic acid to be mainly dependent on vaccenic acid supply and to a lesser extent on variation in desaturase activity.

J Dairy Sci, 2003 Dec, 86(12), 3822 - 30
Milk pH as a function of CO2 concentration, temperature, and pressure in a heat exchanger; Ma Y et al.; Raw skim milk, with or without added CO2, was heated, held, and cooled in a small pilot-scale tubular heat exchanger (372 ml/min) . The experiment was replicated twice, and, for each replication, milk was first carbonated at 0 to 1 degree C to contain 0 (control), 600, 1200, 1800, and 2400 ppm added CO2 using a continuous carbonation unit . After storage at 0 to 1 degree C, portions of milk at each CO2 concentration were heated to 40, 56, 72, and 80 degrees C, held at the desired temperature for 30 s (except 80 degrees C, holding 20 s) and cooled to 0 to 1 degree C . At each temperature, five pressures were applied: 69, 138, 207, 276, and 345 kPa . Pressure was controlled with a needle valve at the heat exchanger exit . Both the pressure gauge and pH probe were inline at the end of the holding section . Milk pH during heating depended on CO2 concentration, temperature, and pressure . During heating of milk without added CO2, pH decreased linearly as a function of increasing temperature but was independent of pressure . In general, the pH of milk with added CO2 decreased with increasing CO2 concentration and pressure . For milk with added CO2, at a fixed CO2 concentration, the effect of pressure on pH decrease was greater at a higher temperature . At a fixed temperature, the effect of pressure on pH decrease was greater for milk with a higher CO2 concentration . Thermal death of bacteria during pasteurization of milk without added CO2 is probably due not only to temperature but also to the decrease in pH that occurs during the process . Increasing milk CO2 concentration and pressure decreases the milk pH even further during heating and may further enhance the microbial killing power of pasteurization.

Environ Sci Technol, 2004 Jan 1, 38(1), 84 - 92
Organochlorine compounds in Lake Superior: chiral polychlorinated biphenyls and biotransformation in the aquatic food web; Wong CS et al.; The enantiomeric composition of seven chiral PCB congeners was measured in the Lake Superior aquatic food web sampled in 1998, to determine the extent of enantioselective biotransformation in aquatic biota . All chiral PCB congeners studied (CBs 91, 95, 136, 149, 174, 176, and 183) biomagnified in the Lake Superior aquatic food web, based on biomagnification and food web magnification factors greater than unity . PCB atropisomers were racemic in phytoplankton and zooplankton, suggesting no biotransformation potential toward PCBs for these low trophic level organisms . However, Diporeia and mysids had significantly nonracemic residues for most chiral congeners studied . This observation suggests that these macrozooplankton can stereoselectively metabolize chiral congeners . Alternatively, macrozooplankton obtained nonracemic residues from feeding on organic-rich suspended particles and sediments, which would imply that stereoselective microbial PCB biotransformation may be occurring in Lake Superior sediments at PCB concentrations far lower than that previously associated with such activity . Widely nonracemic PCB residues in forage fish (lake herring, rainbow smelt, and slimy sculpin) and lake trout suggest a combination of both in vivo biotransformation and uptake of nonracemic residues from prey for these species . Minimum biotransformation rates, calculated from enantiomer mass balances between predators and prey, suggest metabolic half-lives on the order of 8 yr for CB 136 in lake trout and 2.6 yr for CB 95 in sculpins . This result suggests that significant biotransformation may occur for metabolizable PCB congeners over the lifespan of these biota . This study highlights the potential of chiral analysis to study biotransformation processes in food webs.

Immunity, 2004 Jan, 20(1), 95 - 106
HSP70 peptide binding mutants separate antigen delivery from dendritic cell stimulation; MacAry PA et al.; Microbial heat shock proteins (HSPs) have been implicated in the induction of both the innate and adaptive arms of the immune response . We now show that human dendritic cells (DC) pulsed with peptide-loaded mycobacterial HSP70 complexes generate potent antigen-specific cytotoxic lymphocyte (CTL) responses, which are dependent on an HSP70-stimulated calcium signaling cascade . From the calculated peptide binding affinity of mycobacterial HSP70 (K(D) = 14 microM) we show that 120 pM HSP70 bound peptide is sufficient to generate a peptide-specific CTL response that is up to four orders of magnitude more efficient than peptide alone . The minimal 136 amino acid, mycobacterial HSP70 peptide binding domain can generate CTL responses, and a single amino acid mutant HSP70 designed to prevent peptide binding but retain stimulatory capacity has allowed us to separate antigen delivery from DC immunostimulation.

Curr Biol, 2004 Jan 20, 14(2), R65 - 6
Microbial genomics: tropical treasure?
Stephens C.
A Brazilian consortium has unveiled the genomic DNA sequence of the purple-pigmented bacterium Chromobacterium violaceum, a dominant component of the tropical soil microbiota . The sequence provides insight into the abundant potential of this organism for biotechnological and pharmaceutical applications.

J Matern Fetal Neonatal Med, 2003 Oct, 14(4), 241 - 6
Unexplained fetal death is associated with changes in the adaptive limb of the maternal immune response consistent with prior antigenic exposure; Blackwell S et al.; OBJECTIVE: The causes of fetal death are largely unknown . CD4 T cells have been classified according to the expression of the CD45 isoforms into 'naive-like' T cells (CD45RA) and 'memory-like' T cells (CD45RO) . An increase in the percentage of the CD45RO has been interpreted as indicating prior antigenic exposure of the host and, in newborns, evidence of infection . The purpose of this study was to determine whether unexplained fetal death was associated with a change in the proportion of 'naive-like' and 'memory-like T cells' in the maternal blood, as determined by the CD45 isoforms on the surface of CD4+ lymphocytes . STUDY DESIGN: A prospective study was conducted to compare the CD45 sub-population of lymphocytes in patients with intrauterine fetal death (n = 26) and normal pregnancy (n = 89) . The percentages of CD45RA+, CD45RO+ and CD45RA+/CD45RO+ on CD4+ T lymphocytes were determined in maternal blood using flow cytometry and monoclonal antibodies . Results were reported as a percentage of CD4+ lymphocytes . Non-parametric statistics were used for analysis . A p value of < 0.05 was considered significant . RESULTS: Patients with intrauterine fetal death had a higher percentage of CD45RO+ CD4+ T lymphocytes than normal pregnant women (fetal death: median 57.7%, range 35.4-78.6 vs . normal pregnancy: median 49.9%, range 19.1-86.8; p = 0.004) . Fetal death was associated with a lower median percentage of CD45RA+ CD4+ lymphocytes than in normal pregnant women (fetal death: median 32.3%, range 15.3-58.0 vs . normal pregnancy: median 40.2%, range 11.2-67.3; p = 0.01) . There was no significant difference in the percentage of cells with dual expression (CD45RA+/CD45RO+) between the study groups . CONCLUSION: Prior exposure to microbial products (bacterial or viral) or other unidentified antigens may result in a shift of the sub-population of 'naive-like' T cells to 'memory-like' T cells in mothers with unexplained fetal death.

J Pediatr Oncol Nurs, 2003 Nov-Dec, 20(6), 293 - 300
Protective isolation in hemopoietic stem cell transplants: a review of the literature and single institution experience; Dadd G et al.; Princess Margaret Hospital for Children, Perth, Western Australia, is a pediatric bone marrow transplant center . This center has both laminar flow and HEPA- (high-efficiency particulate air-)filtered rooms for children undergoing allogeneic and autologous transplantation . HEPA-filtered rooms on negative pressure are used to nurse oncology children with infectious diseases . Over the winter months of 2001, there was an increased demand for single rooms for children with infectious diseases . Over the same period, a number of transplants were planned . Consequently, to guide practice decisions, a review of the literature and a survey of nursing practice in Australian and North American pediatric oncology units were undertaken . Findings showed that protective isolation measures such as positive-pressure single rooms, low microbial diets, and strict hand washing should be used only for children requiring allogeneic transplants . Use of other isolation measures were found to be of no added value for transplantation . As autologous transplants are increasingly performed in outpatient clinics, these children should not require the same level of protective isolation.

Chem Commun (Camb), 2004 Jan 21, (2), 248 - 9 Epub 2003 Dec 03.
On-chip electrochemical measurement of beta-galactosidase expression using a microbial chip; Kaya T et al.; {small beta}-Galactosidase expression in a small number of Escherichia coli cells has been measured in real time with an electrochemical sensor chip . E . coli cells were embedded using collagen gel within a micropore which was microfabricated onto a chip . The activity of the expressed {small beta}-galactosidase was determined using p-aminophenyl {small beta}-d-galactopyranoside (PAPG) as a substrate.

Nephrol Dial Transplant, 2004 Feb, 19(2), 451 - 6
Mercury exposure in protein A immunoadsorption; Kramer L et al.; BACKGROUND: Immunoadsorption is increasingly used to treat antibody-mediated autoimmune diseases . To prevent microbial growth during storage, reusable protein A-Sepharose gel columns are primed with ethyl mercury thiosalicylate (thiomersal, 0.1% solution) and rinsed with phosphate buffer before use . In this study, we tested the hypothesis of systemic mercury exposure in protein A immunoadsorption . METHODS: Whole blood mercury levels were measured by atomic absorption spectroscopy before and after protein A immunoadsorption (11 patients, 26 treatments), anti-IgG immunoadsorption (eight patients, 13 treatments) and LDL apheresis (DALI and Therasorb systems; nine patients, 14 treatments) . RESULTS: Patients treated with protein A immunoadsorption had significantly elevated baseline mercury levels compared with the other groups, which were not different from healthy controls . Following protein A immunoadsorption, mercury levels increased from 5.9+/-1.4 microg/l (mean+/-SEM, normal, <5 microg/l) to 32.3+/-5.7 microg/l, P<0.001) . In one intensively treated patient, acute neurological toxicity developed at a mercury level of 107 microg/l . Symptoms abated slowly and did not recur after switching to a thiomersal-free system and chelation therapy . No mercury release to patients occurred in anti-IgG immunoadsorption or LDL apheresis treatments . CONCLUSION: This preliminary report suggests that protein A immunoadsorption columns primed with thiomersal during storage may cause a sustained increase of systemic mercury concentrations, which exceed current safety recommendations in a proportion of patients . Considering the potential for mercury-induced toxicity, every effort should be undertaken to reduce systemic mercury exposure, either by adding chelators to the rinsing solution or ideally by replacement of thiomersal.

Dis Aquat Organ, 2003 Dec 3, 57(1-2), 59 - 66
Protozoal and epitheliocystis-like infections in the introduced bluestripe snapper Lutjanus kasmira in Hawaii; Work TM et al.; The bluestripe snapper, or taape, was introduced into Hawaii in the 1950s and has since become very abundant throughout the archipelago . As part of a health survey of reef fish in Hawaii, we necropsied 120 taape collected from various coastal areas south of Oahu and examined fish histology for extraintestinal organisms . Forty-seven percent of taape were infected with an apicomplexan protozoan compatible with a coccidian . Infection was evident mainly in the spleen and, less commonly, the kidney . Prevalence of this coccidian increased with size of fish, and we saw no significant pathology associated with the organism . Twenty-six percent of taape were also infected with an epitheliocystis-like organism that occurred mainly in the kidney and, less commonly, the spleen . In contrast to the coccidian, fish mounted a notable inflammatory response to the epitheliocystis-like organism, and this inflammation appeared to increase in severity with age . Prevalence of the epitheliocystis-like organism infection increased with age, but infection was not seen in fish greater than 26.5 cm fork length . The high prevalence of coccidial infection in introduced taape prompts the concern that these organisms, along with the epitheliocystis-like organism, have the potential to be transmitted to native reef fish . Given the impact of other introduced microbial organisms on native Hawaiian fauna, there is a clear need to assess whether protozoa and bacteria are endemic to Hawaii, and whether they negatively impact native reef fish that closely associate with taape.

Appl Microbiol Biotechnol, 2004 Jun, 64(6), 782 - 6 Epub 2004 Jan 21.
Transformation of artemisinin by Cunninghamella elegans; Parshikov IA et al.; Semi-synthetic derivatives of the anti-malarial drug artemisinin hold great promise in the search for an effective and economical treatment of chloroquine-resistant forms of malaria . Unfortunately, synthetic functionalization of the artemisinin skeleton is often tedious and/or impractical . We seek to utilize 7beta-hydroxyartemisinin, obtained from microbial transformation, as a semi-synthetic precursor for the synthesis of novel 7beta-substituted artemisinin anti-malarial agents . Here we employ liquid cultures of Cunninghamella elegans as a means for the rational and economical bioconversion of artemisinin to 7beta-hydroxyartemisinin in 78.6% yield . In addition, there were three other bioconversion products: 7beta-hydroxy-9alpha-artemisinin (6.0%), 4alpha-hydroxy-1-deoxoartemisinin (5.4%), and 6beta-hydroxyartemisinin (6.5%).

Invest Radiol, 2004 Feb, 39(2), 104 - 10
Novel echogenic drug-immunoliposomes for drug delivery; Tiukinhoy SD et al.; RATIONALE AND OBJECTIVES: We have developed novel echogenic immunoliposomes (ELIPs) that can be antibody-conjugated for the specific highlighting of atheroma and atheroma components . The utility of these agents for regional drug delivery has not been evaluated previously . We chose to use an antibiotic as the prototype drug . The concept that an infectious agent may affect the development and progression of atherosclerosis has stimulated trials on the use of antibiotics for coronary syndromes . However, these agents are given systemically with concomitant problems . Development of an agent for local drug delivery may obviate adverse effects and improve treatment efficacy . The aim of this study was to evaluate the potential of our ELIPs for drug incorporation and to demonstrate efficient drug delivery to cultured cells . METHODS: Azithromycin was incorporated into the ELIPs during development . Free drug was removed with a Sephadex G-50 column . Acoustic properties were evaluated using an intravascular ultrasound catheter and quantified by computer-assisted videodensitometry . Human umbilical arterial endothelial cells were infected with Chlamydia pneumoniae . Cells were treated with the drug-ELIP complexes, and infection-forming units were counted using fluorescence techniques . RESULTS: We were able to incorporate a drug into the ELIPs with retention of acoustic properties . The drug-ELIP complex demonstrated effective inhibition of microbial growth in endothelial cells (P < 0.001 vs . empty liposomes and control) . CONCLUSIONS: We have developed a novel acoustic drug-liposomal agent that can deliver drugs to cultured cells . Although in vivo translation is required, this technique has potential for site-specific drug delivery.

J Immunol, 2004 Feb 1, 172(3), 1768 - 76
Chlamydia pneumoniae multiply in neutrophil granulocytes and delay their spontaneous apoptosis; van Zandbergen G et al.; The obligate intracellular bacterial pathogen Chlamydia pneumoniae (Cp) is responsible for a range of human diseases, including acute respiratory infection . Although experimental intratracheal infection with Cp results in a massive recruitment of neutrophil granulocytes (polymorphonuclear neutrophils (PMN)), the role of these cells in the defense against Cp is unclear . In this study the interactions of PMN with Cp were investigated . In vitro coincubation experiments showed that human granulocytes were able to internalize Chlamydia in an opsonin-independent manner . Importantly, phagocytosed Cp were not killed; the ingested bacteria survived and multiplied within PMN . Although uninfected granulocytes became apoptotic within 10 h, infected PMN survived up to 90 h . Coincubation with Cp significantly decreased the ratio of apoptotic PMN, as detected by morphological analysis, annexin V, and TUNEL staining . The observed antiapoptotic effect was associated with a markedly lower level of procaspase-3 processing and, consequently, reduced caspase-3 activity in infected PMN . LPS was found as a major, but not exclusive, component responsible for the observed antiapoptotic effect . Chlamydia LPS affected PMN apoptosis both by acting directly on the cells and by inducing the autocrine production of the antiapoptotic cytokine IL-8 . These data show that, in contrast to other microbial pathogens that drive phagocytes into apoptosis to escape killing, Cp can extend the life span of neutrophil granulocytes, making them suitable host cells for survival and multiplication within the first hours/days after infection.

Int Immunol, 2004 Feb, 16(2), 345 - 51
Development of dermatitis in CD18-deficient PL/J mice is not dependent on bacterial flora, and requires both CD4+ and CD8+ T lymphocytes; Barlow SC et al.; CD18-deficient PL/J mice develop dermatitis characterized by hyperkeratosis, and a mixed dermal and epidermal inflammatory infiltrate . The development of this disease requires low-level CD18 expression and at least two PL/J loci . Currently, the mechanisms by which decreased beta(2) integrin expression on leukocytes promotes skin inflammation in PL/J mice are unknown . In these studies, we investigated the role of microbial infection and T lymphocytes in the pathogenesis of this disease . We found that germ-free CD18(-/-) PL/J mice developed dermatitis indistinguishable from that of mice raised in pathogen-free conditions . Adoptive transfer of CD18(-/-) PL/J splenocytes into skin disease-resistant CD18(+/-) PL/J mice failed to induce skin inflammation . However, transfer of CD18(+/-) splenocytes blocked the progression and ultimately led to resolution of skin disease in the majority of CD18(-/-) recipients . Depletion of both CD4(+) and CD8(+) T cells mice prior to onset of the disease significantly delayed the appearance of inflammatory skin disease . In contrast, single depletions of these T cells did not inhibit disease development . These studies show that dermatitis in CD18-deficient PL/J mice is not the consequence of infection, does not require bacterial superantigens, and is mediated by both CD4(+) and CD8(+) T lymphocytes . Furthermore, they suggest that one possible mechanism for skin disease development in these mice may involve the absence or dysfunctional activity of a regulatory T cell population . These mice may therefore be useful in identifying potential mechanisms of pathogenesis and genetic predisposition in human inflammatory skin diseases.

Curr Opin Immunol, 2004 Feb, 16(1), 90 - 5
New insights into pathways for CD1-mediated antigen presentation; Sugita M et al.; Recent studies of CD1 structure and intracellular trafficking have demonstrated significant differences among the CD1 isoforms (CD1a, CD1b, CD1c and CD1d) . The molecular and structural basis for the differential trafficking of CD1 molecules has also been delineated . These observations broaden our understanding of why the immune system has evolved multiple CD1 isoforms to survey different cellular compartments for lipid antigen presentation, to provide host defense against the microbial world and to offer immunoregulation with relevance to tumor immunity and autoimmunity.

Biochem Biophys Res Commun, 2004 Feb 6, 314(2), 550 - 4
Cytotoxicity of RNases is increased by cationization and counteracted by K(Ca) channels; Ilinskaya ON et al.; K(Ca) channels are involved in control of cell proliferation and differentiation . Here we have revealed their role in overcoming the RNase-induced cytotoxicity . Toxic effects of Streptomyces aureofaciens RNases Sa, Sa2, Sa3, and of RNase Sa charge reversal mutants on the human embryonic kidney cell lines differing only by the presence of K(Ca) channels were characterized . In contrast to other RNases, a basic variant of RNase Sa and RNase Sa3 exhibit significant cytotoxic activity of the same order of magnitude as onconase . Our data indicate the absence of a correlation between catalytic activity and stability of RNases and cytotoxicity . On the other hand, cationization enhances toxic effect of an RNase indicating the major role of a positive charge . Essentially lower sensitivity to cytotoxic microbial RNases of cells expressing K(Ca) channels was found . These results suggest that cells without the K(Ca) channel activity cannot counteract toxic effect of RNases.

J Agric Food Chem, 2004 Jan 28, 52(2), 280 - 7
The degradation of the natural pyrethrins in crop storage; Atkinson BL et al.; Prolonged storage of harvested Tasmanian pyrethrum crop from Tanacetum cinerariaefolium has resulted in substantial losses of the pyrethrin esters due to the environmental conditions in the storage shed . The generation of heat, the presence of moisture and oxygen, and the microbial activity were identified as possible causes . A pyrethrum crop sample was divided up and stored in different conditions relating to these variables, and the pyrethrins content was monitored over time using a standard method . Temperature was determined to be a critical factor in the rate of the degradation of the natural pyrethrins . Moisture, oxygen, and microbial activity unexpectedly did not play a major role in the degradation . An initial rapid loss of the natural pyrethrins was observed before the pyrethrins content stabilized at a loss of around 65% . This suggests that the plant structure may provide chemical or physical protection to the pyrethrins . In all cases, the majority of the loss was attributed to the pyrethrin I and pyrethrin II esters.

Environ Technol, 2003 Nov, 24(11), 1367 - 75
Rare earth elements removal by microbial biosorption: a review; Andres Y et al.; This paper reviews published work on the sorption of rare earth elements by microbial biomass . In a first part, the biosorption capacities and the various experimental conditions performed in batch reactor experiments are compared . Secondly, sorption modelling generally used in biosorption studies are described . Thirdly, the microbial cell wall characteristics of the metallic ion binding sites are considered . From these observations it seems that the important functional groups for metallic ion fixation are the carboxyl and the phosphate moieties . Moreover, the competing effect of various ions like aluminium, iron, glutamate, sulphate etc . is described . Finally, some adsorption results of the rare earth elements in dynamic reactors are presented.

Trends Cell Biol, 1995 Mar, 5(3), 125 - 8
Mycobacterium and Leishmania: stowaways in the endosomal network; Russell DG; Microbial pathogens have evolved to exploit a wide range of niches inside the vertebrate host cell . Both Leishmania and Mycobacterium species remain within vacuoles following phagocytosis by their host's macrophages . Leishmania survives in acidic, lysosomal compartments, whereas Mycobacterium species limit the maturation of their phagosomes into hydrolytic lysosomes . Recent advances in our appreciation of the biology of these pathogens is providing unique insights into the normal conversion of phagosomes into lysosomes.

Aviakosm Ekolog Med, 2003, 37(5), 64 - 70
{Biological processes of the human environment regeneration within the Martian crew life support systems}; Sychev VN et al.; Five ground-based experiments at RF SRC-IBMP had the purpose to make a thorough investigation of a model of the human-unicellular algae-mineralization life support system . The system measured 15 m3 and contained 45 liters of alga suspension; the dry alga density was 10 to 12 g/l and water volume (including the alga suspension) amounted to 59 l . More sophisticated LSS models where algae were substituted by higher plants (crop area in the greenhouse equaled 15 m2) were investigated in three experiments from 1.5 mos . to 2 mos . in duration . It was found that the alga containing LSS was able to fulfill not only the macrofunction (air and water regeneration) but also several additional functions (air purification, establishment of microbial cenosis etc.) providing an adequate human environment . This polyfunctionality of the biological regenerative processes is a weighty argument for their integration into space LSSs . Another important aspect is that the unicellular algae containing systems are highly reliable owing to a huge number of species-cells which will be quickly recovered in case of the death of a part of the population and, consequently, functionality of the LSS autotrophic component will be restored before long . For an extended period of time the Martian crew will have no communication with the Earth's biosphere which implies that LSS should be absolutely reliable and redundant . Redundancy can be achieved through installation aboard the vehicle of two systems constructed on different principles of regeneration, i.e . physical-chemical and biological . Each of the LSSs should have the power to satisfy all needs of the crew . The best option is when two systems are functioning in parallel sharing the responsibility for the human environment . Redundancy in this case will mean that in the event of failure or a drastic decrease in performance of one system the other one will make up for the loss by increasing its share in the overall regeneration process.

Glia, 2004 Jan 15, 45(2), 188 - 96
Signaling through JAK2-STAT5 pathway is essential for IL-3-induced activation of microglia; Natarajan C et al.; Microglia, the resident macrophage of the brain, mediates immune and inflammatory responses in the central nervous system (CNS) . Activation of microglia and secretion of inflammatory cytokines associate with the pathogenesis of CNS diseases, including multiple sclerosis (MS), Alzheimer's disease (AD), Parkinson's disease, prion disease, and AIDS dementia . Microbial pathogens, cytokines, chemokines, and costimulatory molecules are potent inducers of microglial activation in the CNS . Signaling through its receptor, IL-3 induces the activation of JAK-STAT and MAP kinase pathways in microglial cells . In this study, we found that in vitro treatment of EOC-20 microglial cells with tyrphostin AG490 blocked IL-3-induced tyrosine phosphorylation of JAK2, STAT5A, and STAT5B signaling proteins . Stable transfection of EOC-20 cells with a dominant negative JAK2 mutant also blocked IL-3-induced tyrosine phosphorylation of JAK2, STAT5A, and STAT5B in microglia . The blockade of JAK2-STAT5 pathway resulted in a decrease in IL-3-induced proliferation and expression of CD40 and major histocompatibility complex class II molecules in microglia . These findings highlight the fact that JAK2-STAT5 signaling pathway plays a critical role in mediating IL-3-induced activation of microglia .

Philos Trans R Soc Lond B Biol Sci, 2003 Dec 29, 358(1440), 1935 - 55
Global analysis of river systems: from Earth system controls to Anthropocene syndromes; Meybeck M; Continental aquatic systems from rivers to the coastal zone are considered within two perspectives: (i) as a major link between the atmosphere, pedosphere, biosphere and oceans within the Earth system with its Holocene dynamics, and (ii) as water and aquatic biota resources progressively used and transformed by humans . Human pressures have now reached a state where the continental aquatic systems can no longer be considered as being controlled by only Earth system processes, thus defining a new era, the Anthropocene . Riverine changes, now observed at the global scale, are described through a first set of syndromes (flood regulation, fragmentation, sediment imbalance, neo-arheism, salinization, chemical contamination, acidification, eutrophication and microbial contamination) with their related causes and symptoms . These syndromes have direct influences on water uses, either positive or negative . They also modify some Earth system key functions such as sediment, water, nutrient and carbon balances, greenhouse gas emissions and aquatic biodiversity . Evolution of river syndromes over the past 2000 years is complex: it depends upon the stages of regional human development and on natural conditions, as illustrated here for the chemical contamination syndrome . River damming, eutrophication and generalized decrease of river flow due to irrigation are some of the other global features of river changes . Future management of river systems should also consider these long-term impacts on the Earth system.

AMIA Annu Symp Proc . 2003;:1066.
The NCI/CIT microArray database (mAdb) system - bioinformatics for the management and analysis of Affymetrix and spotted gene expression microarrays; Greene JM et al.; A scalable, modular, enterprise-level system for both microarray databasing and analysis over the Internet has been developed over the past four years by the National Cancer Institute's Center for Cancer Research in collaboration with NIH's Center for Information Technology . This completely Web-based system, called mAdb (for microArray database), is currently supporting over 810 registered users and collaborators at NIH and contains over 22,000 microarray experiments, making it one of the largest collections of microarray data in existence . In addition, the mAdb system has been ported for the Netherlands Cancer Institute, the Genome Institute of Singapore, and the CDC . This system has been used for a wide variety of scientific experiments spanning the range from cancer to studies of early development, and for human, mouse, rat, yeast, and numerous microbial organisms.

Appl Spectrosc, 2004 Jan, 58(1), 91 - 5
Utilizing three-dimensional fluorescence's red-shift cascade effect to monitor mycobacterium PRY-1 degradation of aged petroleum; Sinski JF et al.; Samples of Mycobacterium PRY-1 inoculated motor oil are subjected to three-dimensional fluorescence spectroscopy to document the shifting of excitation/emission maxima as the solutions undergo serial dilutions . Effects such as self-quenching of individual polycyclic aromatic hydrocarbons (PAHs) and energy transfer between PAHs combine to produce large red-shifts in the resulting fluorescence emission spectra . This process is repeated over a series of weeks and is compared to preceding spectra to gauge the microbial degradation of the petroleum . Results show a two-fold, or 75%, PAH contaminant degradation by Mycobacterium PRY-1 over a 140-day growth period.

Appl Microbiol Biotechnol, 2004 Jul, 65(1), 33 - 7 Epub 2004 Jan 16.
Steady-state and transient-state performance of a biotrickling filter treating chlorobenzene-containing waste gas; Seignez C et al.; Biotrickling filter (BTF) technology was applied for the treatment of waste gas containing a mixture of chlorobenzene and 1,2-dichlorobenzene . An adapted microbial community was immobilised on a structured packing material . The strategy followed was to reach high removal efficiencies at initially low mass loading rates followed by an increase of the latter . This procedure was successful and resulted in a short start-up period of only 2 weeks . A 3-month operation under steady-state conditions showed good performance, with >95% removal efficiency at a mass loading rate of 1,800 g m(-3) day(-1) . Dimensionless concentration profiles showed that the chlorobenzenes were simultaneously degraded . Low dissolved organic carbon of 15 mg l(-1) and stoichiometric chloride concentrations in the trickling liquid indicated complete mineralisation of the pollutant . Transient-state experiments with five times higher mass loading rates caused a decrease in the removal efficiency that recovered rapidly once the mass loading rate returned to its original steady-state level . A progressive increase of the mass loading rate in a long-term performance experiment showed that the removal efficiency could be kept stable between 95 and 99% at loads of up to 5,200 g m(-3) day(-1) over several days . Above this mass loading rate, the elimination capacity did not increase any further . These results demonstrated that with a well-adapted inoculum and optimal operation parameters, a BTF system with excellent performance and stability that efficiently removes a mixture of chlorobenzene vapours from air can be obtained.

Cell Cycle, 2004 Mar, 3(3), 247 - 8 Epub 2004 Mar 01.
BRCA2-RAD51-DSS1 interplay examined from a microbial perspective; Kojic M et al.; The tumor suppressor BRCA2 plays an essential role in the repair of double-strand DNA breaks by regulating the action of the RAD51 recombinase . The activity of BRCA2 is in turn governed by DSS1, a small acidic protein that appears to function as a necessary cofactor . A model fungal system that reproduces the BRCA2-RAD51 interaction offers the opportunity to understand the mechanism of DSS1 activation at the molecular level.

J Leukoc Biol, 2004 May, 75(5), 721 - 30 Epub 2004 Jan 14.
Controlling the Toll road to dendritic cell polarization; Mazzoni A et al.; The activation of dendritic cells (DC) via Toll-like receptors (TLRs) plays a decisive role in shaping the outcome of primary immune responses . Following TLR engagement by microbial products, DC migrate from peripheral tissues to lymphoid organs and up-regulate major histocompatibility complex and costimulatory molecules, acquiring the unique capacity to prime pathogen-specific, naive T cells . In addition, DC determine the character of the ensuing immune response by secreting cytokines that drive the development of T cells into T helper cell type 1 (Th1), Th2, or T regulatory effector cells . Three major factors influence the pattern of cytokines released by DC and accordingly, the Th balance: the lineage to which DC belong; the maturation stimulus; and inflammatory mediators present at the site of infection . A major focus of this review is the capacity of DC to integrate these factors and elicit distinct classes of immune responses.

Water Res, 2004 Feb, 38(3), 601 - 10
Removal of soft deposits from the distribution system improves the drinking water quality; Lehtola MJ et al.; Deterioration in drinking water quality in distribution networks represents a problem in drinking water distribution . These can be an increase in microbial numbers, an elevated concentration of iron or increased turbidity, all of which affect taste, odor and color in the drinking water . We studied if pipe cleaning would improve the drinking water quality in pipelines . Cleaning was arranged by flushing the pipes with compressed air and water . The numbers of bacteria and the concentrations of iron and turbidity in drinking water were highest at 9 p.m., when the water consumption was highest . Soft deposits inside the pipeline were occasionally released to bulk water, increasing the concentrations of iron, bacteria, microbially available organic carbon and phosphorus in drinking water . The cleaning of the pipeline decreased the diurnal variation in drinking water quality . With respect to iron, only short-term positive effects were obtained . However, removing of the nutrient-rich soft deposits did decrease the microbial growth in the distribution system during summer when there were favorable warm temperatures for microbial growth . No Norwalk-like viruses or coliform bacteria were detected in the soft deposits, in contrast to the high numbers of heterotrophic bacteria.

Clin Exp Dermatol, 2004 Jan, 29(1), 1 - 7
Pyostomatitis vegetans; Hegarty AM et al.; Pyostomatitis vegetans is a rare oral disorder often associated with gastrointestinal and/or cutaneous diseases and sometimes with other disorders . The association of pyostomatitis vegetans with inflammatory bowel disease, particularly ulcerative colitis, is well known and in most cases bowel disease precedes the onset of oral lesions by months or years . A peripheral eosinophilia has been observed in most reported cases . Pyostomatitis vegetans is characterized by erythematous, thickened oral mucosa with multiple pustules and superficial erosions . Histopathologically, it is characterized by intraepithelial and/or subepithelial abscesses containing large numbers of eosinophils . The pathogenesis is as yet unknown although immunological and microbial factors have been suggested as possible aetiological factors . Management of pyostomatitis vegetans consists mainly of immunosuppression using topical or systemic corticosteroids with medical and/or surgical treatment of any underlying inflammatory bowel disease.

Environ Pollut, 2004, 128(3), 445 - 8
Invariant chlorine isotopic signatures during microbial PCB reductive dechlorination; Drenzek NJ et al.; In order to develop more robust insight into the natural attenuation of polychlorinated biphenyls (PCBs), the chlorine isotopic composition of residual 2,3,4,5-tetrachlorobiphenyl (2,3,4,5-CB) was monitored as it underwent microbial reductive dechlorination to 2,3,5-trichlorobiphenyl (2,3,5-CB) in laboratory cultures . Reverse-phase high performance liquid chromatography (HPLC) was employed to isolate the former compound from the experimental matrix for delta37Cl measurement . No detectable isotopic fractionation was observed over the 90 day incubation with sterile control, standard, and inoculated samples all exhibiting delta37Cl values with a range of approximately 0.5 per thousand . These results show that this type of biological activity can be discriminated from other transformations by the absence of a measurable isotope effect during microbial reductive dechlorination . The utility of HPLC isolation for compound-specific delta37Cl analyses of environmentally relevant species is also demonstrated.

Huan Jing Ke Xue, 2003 Sep, 24(5), 44 - 8
{Technology of biodesulfurization from flue gases}; Wang X et al.; The desufurization in dilute sulfuric acid solution, acidic ferric solution, and microbial solution (Thiobacillus ferrooxidans) was studied in this paper . The concentration of ferric, pH value and time all affect the rate of desulfurization . The experimental results showed that in dilute sulfuric acid solution the absorption of SO2 was a physical absorption . In acidic ferric solution, the ion of ferric can not only catalyze but also oxidize SO2 . The effects of desulfurization became obvious along with high concentration of ferric and pH value . Desulfurization rate was up to 90% when pH value was 2.0 and the concentration of ferric was 1.5 g/L . In microbial solution, the effects were also influenced by the concentration of ferric and pH value . Thiobacillus ferrooxidans had an ability of oxiding the ion of ferrous and S(IV) . The results of desulfurization was the best at the concentration of ferric 1.5 g/L and pH 2.0.

Proc Natl Acad Sci U S A, 2004 Jan 20, 101(3), 737 - 42 Epub 2004 Jan 12.
Antiatherogenic activity of fungal beauveriolides, inhibitors of lipid droplet accumulation in macrophages; Namatame I et al.; Beauveriolides I and III, isolated from the culture broth of fungal Beauveria sp . FO-6979, showed potent inhibitory activity of lipid droplet accumulation in primary mouse peritoneal macrophages . The cellular molecular target of this inhibitory activity was studied in macrophages . Beauveriolides I and III strongly inhibited the cholesteryl ester (CE) synthesis with IC(50) values of 0.78 and 0.41 microM, respectively, without showing significant effects on the triacylglycerol and phospholipid synthesis . Furthermore, lysosomal cholesterol metabolism to CE in macrophages was inhibited by the compounds, indicating that the inhibition site lies within steps between cholesterol departure from the lysosome and CE synthesis in the endoplasmic reticulum . Therefore, acyl-CoA:cholesterol acyltransferase (ACAT) activity in the membrane fractions prepared from mouse macrophages was studied, resulting in a dose-dependent inhibition by beauveriolides I and III with IC(50) values of 6.0 and 5.5 microM, respectively . Thus, we showed that the beauveriolides inhibit macrophage ACAT activity specifically, resulting in blockage of the CE synthesis, leading to a reduction of lipid droplets in macrophages . ACAT activity in the membrane fractions prepared from mouse liver and Caco-2 cells was also inhibited, indicating that the beauveriolides block both ACAT-1 and -2 . Moreover, beauveriolides I and III exert antiatherogenic activity in both low-density lipoprotein receptor- and apolipoprotein E-knockout mice without any side effects such as diarrhea or cytotoxicity to adrenal tissues as observed for many synthetic ACAT inhibitors . Beauveriolides I and III are the first microbial cyclodepsipeptides having an in vivo antiatherosclerotic effect and show promise as potential lead compounds for antiatherosclerotic agents.

Mol Cell Proteomics, 2004 Mar, 3(3), 193 - 208 Epub 2004 Jan 12.
Immunoproteomics: Mass spectrometry-based methods to study the targets of the immune response; Purcell AW et al.; The mammalian immune system has evolved to display fragments of protein antigens derived from microbial pathogens to immune effector cells . These fragments are typically peptides liberated from the intact antigens through distinct proteolytic mechanisms that are subsequently transported to the cell surface bound to chaperone-like receptors known as major histocompatibility complex (MHC) molecules . These complexes are then scrutinized by effector T cells that express clonally distributed T cell receptors with specificity for specific MHC-peptide complexes . In normal uninfected cells, this process of antigen processing and presentation occurs continuously, with the resultant array of self-antigen-derived peptides displayed on the surface of these cells . Changes in this peptide landscape of cells act to alert immune effector cells to changes in the intracellular environment that may be associated with infection, malignant transformation, or other abnormal cellular processes, resulting in a cascade of events that result in their elimination . Because peptides play such a crucial role in informing the immune system of infection with viral or microbial pathogens and the transformation of cells in malignancy, the tools of proteomics, in particular mass spectrometry, are ideally suited to study these immune responses at a molecular level . Here we review recent advances in the studies of immune responses that have utilized mass spectrometry and associated technologies, with specific examples from collaboration between our laboratories.

Microbiol Res, 2003, 158(4), 291 - 7
Diversity of culturable phyllosphere bacteria on beech and oak: the effects of lepidopterous larvae; Muller T et al.; The community composition of epiphytic heterotrophic bacteria on leaves of beech and oak, which were either damaged by lepidopterous larvae or remained undamaged, was investigated . In addition, the ability of these bacteria to utilize inorganic nitrogen was studied . The bacteria were isolated on nutrient agar and systematically identified with biochemical and physiological tests . Rarefaction plots and the Shannon-Wiener function revealed that species diversity was significantly higher on leaves of damaged beech compared to undamaged leaves, but no differences were found on leaves of oak . The portion of bacterial isolates showing a strong response to ammonia and nitrate was significantly larger on leaves of oak than on those of beech . Furthermore, significantly more isolates with a high capability to assimilate both nitrogen compounds were found on leaves attacked by the folivorous larvae compared to those not attacked on oak . It is suggested that the changes in the microbial community in response to folivorous insects might affect the extent of nutrient cycling exceeding eventually the scale of a leaf.

J Food Prot, 2004 Jan, 67(1), 110 - 6
Comparison of biogenic amine profile in cheeses manufactured from fresh and stored (4 degrees C, 48 hours) raw goat's milk; Novella-Rodriguez S et al.; In this study, the evolution of microbial counts, biogenic amine contents, and related parameters (pH, moisture, and proteolysis) in goat cheese made from fresh raw milk or raw milk stored for 48 h at 4 degrees C was examined . In both cases the milk was nonpasteurized . This study was designed to evaluate the effect of milk quality on the profile of biogenic amines in relation to the evolution of the microbial population during cheese making . Cheese made from raw milk stored for 48 h at 4 degrees C showed the highest microbial counts and biogenic amine levels . The storage of milk under refrigeration caused significant increases in the levels of some microbial and biogenic amines during ripening, but not initially . Tyramine was the main biogenic amine in the two cheeses tested, followed by cadaverine . However, the main differences in amine contents between batches were found for putrescine, histamine, and beta-phenylethylamine, whose levels were more than twofold higher in samples from raw milk refrigerated for 48 h than in samples from fresh milk.

Planta, 2004 Apr, 218(6), 938 - 46 Epub 2004 Jan 10.
Nitric oxide is induced by wounding and influences jasmonic acid signaling in Arabidopsis thaliana; Huang X et al.; Nitric oxide (NO) has been associated with plant defense responses during microbial attack, and with induction and/or regulation of programmed cell death . Here, we addressed whether NO participates in wound responses in Arabidopsis thaliana (L.) Heynh . Real-time imaging by confocal laser-scanning microscopy in conjunction with the NO-selective fluorescence indicator 4,5-diaminofluorescein diacetate (DAF-2 DA) uncovered a strong NO burst after wounding or after treatment with JA . The NO burst was triggered within minutes, reminiscent of the oxidative burst during hypersensitive responses . Furthermore, we were able to detect NO in plants (here induced by wounding) by means of electron paramagnetic resonance measurements using diethyldithiocarbamate as a spin trap . When plants were treated with NO, Northern analyses revealed that NO strongly induces key enzymes of jasmonic acid (JA) biosynthesis such as allene oxide synthase (AOS) and lipoxygenase (LOX2) . On the other hand, wound-induced AOS gene expression was independent of NO . Furthermore, JA-responsive genes such as defensin (PDF1.2) were not induced, and NO induction of JA-biosynthesis enzymes did not result in elevated levels of JA . However, treatment with NO resulted in accumulation of salicylic acid (SA) . In transgenic NahG plants (impaired in SA accumulation and/or signaling), NO did induce JA production and expression of JA-responsive genes . Altogether, the presented data demonstrate that wounding in Arabidopsis induces a fast accumulation of NO, and that NO may be involved in JA-associated defense responses and adjustments.

Nat Immunol, 2004 Feb, 5(2), 190 - 8 Epub 2004 Jan 11.
TLR9 signals after translocating from the ER to CpG DNA in the lysosome; Latz E et al.; Microbial DNA sequences containing unmethylated CpG dinucleotides activate Toll-like receptor 9 (TLR9) . We have found that TLR9 is localized to the endoplasmic reticulum (ER) of dendritic cells (DCs) and macrophages . Because there is no precedent for immune receptor signaling in the ER, we investigated how TLR9 is activated . We show that CpG DNA binds directly to TLR9 in ligand-binding studies . CpG DNA moves into early endosomes and is subsequently transported to a tubular lysosomal compartment . Concurrent with the movement of CpG DNA in cells, TLR9 redistributes from the ER to CpG DNA-containing structures, which also accumulate MyD88 . Our data indicate a previously unknown mechanism of cellular activation involving the recruitment of TLR9 from the ER to sites of CpG DNA uptake, where signal transduction is initiated.

J Clin Microbiol, 2004 Jan, 42(1), 339 - 46
Novel mass spectrometry-based tool for genotypic identification of mycobacteria; Lefmann M et al.; Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) after base-specific cleavage of PCR amplified and in vitro-transcribed 16S rRNA gene (rDNA) was used for the identification of mycobacteria . Full-length 16S rDNA reference sequences of 12 type strains of Mycobacterium spp . frequently isolated from clinical specimens were determined by PCR, cloning, and sequencing . For MALDI-TOF MS-based comparative sequence analysis, mycobacterial 16S rDNA signature sequences ( approximately 500 bp) of the 12 type strains and 24 clinical isolates were PCR amplified using RNA promoter-tagged forward primers . T7 RNA polymerase-mediated transcription of forward strands in the presence of 5-methyl ribo-CTP maximized mass differences of fragments generated by base-specific cleavage . In vitro transcripts were subsequently treated with RNase T1, resulting in G-specific cleavage . Sample analysis by MALDI-TOF MS showed a specific mass signal pattern for each of the 12 type strains, allowing unambiguous identification . All 24 clinical isolates were identified unequivocally by comparing their detected mass signal pattern to the reference sequence-derived in silico pattern of the type strains and to the in silico mass patterns of published 16S rDNA sequences . A 16S rDNA microheterogeneity of the Mycobacterium xenopi type strain (DSM 43995) was detected by MALDI-TOF MS and later confirmed by Sanger dideoxy sequencing . In conclusion, analysis of 16S rDNA amplicons by MS after base-specific cleavage of RNA transcripts allowed fast and reliable identification of the Mycobacterium tuberculosis complex and ubiquitous mycobacteria (mycobacteria other than tuberculosis) . The technology delivers an open platform for high-throughput microbial identification on the basis of any specific genotypic marker region.

J Vector Ecol, 2003 Dec, 28(2), 175 - 83
Anopheles dirus and its role in malaria transmission in Myanmar; Oo TT et al.; Anopheles dirus is one of the primary vectors of highly drug-resistant Plasmodium falciparum, which causes cerebral malaria resulting in high mortality . Mosquito collections were conducted in a forest wood-extraction area (Bago Division), an irrigated plain area near foothills (Mandalay Division), a coastal plain (from domestic wells in the Mudon area, Mon State) near the foothill area, as well as a hilly area (deep forest timber extraction camp, Tanintharyi Division) from May 1998 to March 2000 . This study examined adult bionomics of An . dirus and its relationship to malaria transmission as an aid in the control of malaria in different ecological settings in these particular regions . Within these areas, Mudon, Mon State, has a high incidence of malaria . To investigate this malaria, blood smear examinations were conducted among the local people in Mudon, Mon State . During the study period, malaria blood smear slide-positive rates ranged between 9.9% and 34.28% throughout the year . The ultimate goal of these studies was to help in formulating an improved malaria control program involving microbial control agents in this area.

Appl Environ Microbiol, 2004 Jan, 70(1), 569 - 80
Microstructural characterization of cyanobacterial mats from the McMurdo Ice Shelf, Antarctica; de Los Rios A et al.; The three-dimensional structures of two types of cyanobacterium-dominated microbial mats from meltwater ponds on the McMurdo Ice Shelf were as determined by using a broad suite of complementary techniques, including optical and fluorescence microscopy, confocal scanning laser microscopy, scanning electron microscopy with back-scattered electron-imaging mode, low-temperature scanning electron microscopy, and microanalyitical X-ray energy dispersive spectroscopy . By using a combination of the different in situ microscopic techniques, the Antarctic microbial mats were found to be structures with vertical stratification of groups of cyanobacteria and mineral sediments, high contents of extracellular polymeric substances, and large void spaces occupied by water . In cyanobacterium-rich layers, heterocystous nostocalean and nonheterocystous oscillatorialean taxa were the most abundant taxa and appeared to be intermixed with fine-size deposits of epicellular silica and calcium carbonate . Most of the cyanobacterial filaments had similar orientations in zones without sediment particles, but thin filaments were tangled among thicker filaments . The combination of the microscopic techniques used showed the relative positions of biological and mineral entities within the microbial mats and enabled some speculation about their interactions.

Appl Environ Microbiol, 2004 Jan, 70(1), 385 - 92
Microbial anaerobic demethylation and dechlorination of chlorinated hydroquinone metabolites synthesized by basidiomycete fungi; Milliken CE et al.; The synthesis and degradation of anthropogenic and natural organohalides are the basis of a global halogen cycle . Chlorinated hydroquinone metabolites (CHMs) synthesized by basidiomycete fungi and present in wetland and forest soil are constituents of that cycle . Anaerobic dehalogenating bacteria coexist with basidiomycete fungi in soils and sediments, but little is known about the fate of these halogenated fungal compounds . In sediment microcosms, the CHMs 2,3,5,6-tetrachloro-1,4-dimethoxybenzene and 2,3,5,6-tetrachloro-4-methoxyphenol (TCMP) were anaerobically demethylated to tetrachlorohydroquinone (TCHQ) . Subsequently, TCHQ was converted to trichlorohydroquinone and 2,5-dichlorohydroquinone (2,5-DCHQ) in freshwater and estuarine enrichment cultures . Screening of several dehalogenating bacteria revealed that Desulfitobacterium hafniense strains DCB2 and PCP1, Desulfitobacterium chlororespirans strain Co23, and Desulfitobacterium dehalogenans JW/DU1 sequentially dechlorinate TCMP to 2,3,5-trichloro-4-methoxyphenol and 3,5-dichloro-4-methoxyphenol (3,5-DCMP) . After a lag, these strains demethylate 3,5-DCMP to 2,6-DCHQ, which is then completely dechlorinated to 1,4-dihydroquinone (HQ) . 2,5-DCHQ accumulated as an intermediate during the dechlorination of TCHQ to HQ by the TCMP-degrading desulfitobacteria . HQ accumulation following TCMP or TCHQ dechlorination was transient and became undetectable after 14 days, which suggests mineralization of the fungal compounds . This is the first report on the anaerobic degradation of fungal CHMs, and it establishes a fundamental role for microbial reductive degradation of natural organochlorides in the global halogen cycle.

Appl Environ Microbiol, 2004 Jan, 70(1), 25 - 33
Processing deep-sea particle-rich water samples for fluorescence in situ hybridization: consideration of storage effects, preservation, and sonication; Lam P et al.; Particles are often regarded as microniches of enhanced microbial production and activities in the pelagic ocean and are vehicles of vertical material transport from the euphotic zone to the deep sea . Fluorescence in situ hybridization (FISH) can be a useful tool to study the microbial community structures associated with these particles, and thus their ecological significance, yet an appropriate protocol for processing deep-sea particle-rich water samples is lacking . Some sample processing considerations are discussed in the present study, and different combinations of existing procedures for preservation, size fractionation sequential filtration, and sonication were tested in conjunction with FISH . Results from this study show that water samples should be filtered and processed within no more than 10 to 12 h after collection, or else preservation is necessary . The commonly used prefiltration formaldehyde fixation was shown to be inadequate for the rRNA targeted by FISH . However, prefiltration formaldehyde fixation followed by immediate freezing and postfiltration paraformaldehyde fixation yielded highly consistent cell abundance estimates even after 96 days or potentially longer storage . Size fractionation sequential filtration and sonication together enhanced cell abundance estimates by severalfold . Size fractionation sequential filtration effectively separated particle-associated microbial communities from their free-living counterparts, while sonication detached cells from particles or aggregates for more-accurate cell counting using epifluorescence microscopy . Optimization in sonication time is recommended for different specific types of samples . These tested and optimized procedures can be incorporated into a FISH protocol for sampling in deep-sea particle-rich waters.

Clin Lab Med, 2003 Dec, 23(4), 781 - 99
Molecular detection and typing of fungal pathogens; Iwen PC; A major goal of molecular testing is to develop a cost-effective as well as sensitive and specific assay that can detect microbial DNA in clinical samples early in the course of disease . Additionally, the ability to analyze the genetic relatedness of fungi on a timelier basis using molecular methods will have a positive impact on epidemiologic investigating . As technology advances, it seems apparent that commercially available molecular assays will become available in the near future for the management of patients with suspected fungal infections.

Chem Pharm Bull (Tokyo), 2004 Jan, 52(1), 1 - 26
Recent developments in the maytansinoid antitumor agents; Cassady JM et al.; Maytansine and its congeners have been isolated from higher plants, mosses and from an Actinomycete, Actinosynnema pretiosum . Many of these compounds are antitumor agents of extraordinary potency, yet phase II clinical trials with maytansine proved disappointing . The chemistry and biology of maytansinoids has been reviewed repeatedly in the late 1970s and early 1980s; the present review covers new developments in this field during the last two decades . These include the use of maytansinoids as "warheads" in tumor-specific antibodies, preliminary metabolism studies, investigations of their biosynthesis at the biochemical and genetic level, and ecological issues related to the occurrence of such typical microbial metabolites in higher plants.

J Egypt Soc Parasitol, 2003 Dec, 33(3), 905 - 15
Evaluation of a new enzyme immunoassay for the detection of Helicobacter pylori in stool specimens; El-Nasr MS et al.; H . pylori infects the gastric mucosa and causes many digestive disorders such as peptic ulcer, chronic gastritis and gastric cancer . H . pylori infection relates neither to functional health status, nor to intensity of dyspepsia . There is evidence that in most patients with H . pylori positive functional dyspepsia do not improve with eradication of the organism.This study evaluated the diagnostic accuracy of HpSA by determining the sensitivity and specificity of the stool antigen test in predicting successful eradication during and after anti microbial therapy . The work was conducted on patients who underwent upper gastrointestinal endoscopy at Al-Azhar University hospitals . Fifty patients (34 male & 16 female) with dyspepsia were selected, the exclusion criteria included use of antibiotics and proton pump inhibitors up to one month before the study . All cases were submitted to, full history, general and local examination and upper gastrointestinal endoscopy . Biopsies were taken from the antrum and body of the stomach for rapid urease test and histopathology . Stool samples were taken to detect H . pylori stool antigen . Positive patients received eradication treatment for one month and H . pylori status was re-determined by rapid urease test, histological examination and HpSA test one month later . H . pylori was detected by rapid urease test in 29 (58%) dyspeptic patient by histology in 26(52%) dyspeptic patient, while H . pylori was detected by HpSA immunoassay in 16 (32%) dyspeptic patient . The sensitivity and specificity of HpSA were 57.7% and 95.8% respectively . After successful eradication of H . pylori, reassessment by rapid urease test and histology revealed curative rate of 86.2% and 84.6% respectively, while HpSA immunoassay revealed curative rate 75% . Based on these results, the HpSA immunoassay gave sensitivity (75%) and specificity (100%) . The H . pylori stool test represents an accurate and novel non-invasive concept for diagnosis of infection and can be used for daily routine in clinical practice . HpSA is a promising non-invasive test for diagnosis of H . pylori infection but may be hampered by low patient acceptability . So, HpSA is a valuable test in the pre-and post eradication assessment of infection . HpSA can be profitably employed in the primary diagnosis of H . pylori infection . This non invasive test could be very useful in investigating dyspeptic young patients . Also, it could be used profitably in epidemiological studies to determine the prevalence of H . pylori infection in the asymptomatic subjects in different communities.

Microb Ecol, 2003 Aug, 46(2), 249 - 56
Viral abundance and a high proportion of lysogens suggest that viruses are important members of the microbial community in the Gulf of Trieste; Stopar D et al.; Epifluorescence microscopy and transmission electron microscopy were applied to study virioplankton community in the Gulf of Trieste (northern Adriatic Sea) . The total viral abundance was in a range between 2.5 x 10(9)/L and 2.9 x 10(10)/L and was positively correlated with trophic status of the environment . Viruslike particles were significantly correlated with bacterial abundance in all samples studied . Correlations with other physicochemical or biological parameters were not significant . The data suggest that, because of the substantial fraction of tailed viruses present (26%), bacteriophages are an important component of the virioplankton community in the Gulf of Trieste . The abundance of viruslike particles in the seawater changed at hour intervals in a range from 1.3 x 10(9)/L to 5.1 x 10(9)/L . A significant fraction (71%) of the bacterial isolates was inducible in vitro by mitomycin C, and a high occurrence (51%) of lysogenic isolates with more than one phage morphotype present in the lysate was detected . The presence of lysogenic bacteria in the seawater was confirmed in situ with a mitomycin C induction experiment on the natural bacterial population . Results suggest that virioplankton is an abundant component of the microbial community in the Gulf of Trieste.

Microb Ecol, 2003 Aug, 46(2), 187 - 99
Structure of microbial communities in Sphagnum peatlands and effect of atmospheric carbon dioxide enrichment; Mitchell EA et al.; Little is known about the structure of microbial communities in Sphagnum peatlands, and the potential effects of the increasing atmospheric CO2 concentration on these communities are not known . We analyzed the structure of microbial communities in five Sphagnum-dominated peatlands across Europe and their response to CO2 enrichment using miniFACE systems . After three growing seasons, Sphagnum samples were analyzed for heterotrophic bacteria, cyanobacteria, microalgae, heterotrophic flagellates, ciliates, testate amoebae, fungi, nematodes, and rotifers . Heterotrophic organisms dominated the microbial communities and together represented 78% to 97% of the total microbial biomass . Testate amoebae dominated the protozoan biomass . A canonical correspondence analysis revealed a significant correlation between the microbial community data and four environmental variables (Na+, DOC, water table depth, and DIN), reflecting continentality, hydrology, and nitrogen deposition gradients . Carbon dioxide enrichment modified the structure of microbial communities, but total microbial biomass was unaffected . The biomass of heterotrophic bacteria increased by 48%, and the biomass of testate amoebae decreased by 13% . These results contrast with the absence of overall effect on methane production or on the vegetation, but are in line with an increased below-ground vascular plant biomass at the same sites . We interpret the increase in bacterial biomass as a response to a CO2-induced enhancement of Sphagnum exudation . The causes for the decrease of testate amoebae are unclear but could indicate a top-down rather than a bottom-up control on their density.

Crit Care Med, 2004 Jan, 32(1), 217 - 26
Pro- and antifibrinolytic properties of human pulmonary microvascular versus artery endothelial cells: impact of endotoxin and tumor necrosis factor-alpha; Muth H et al.; OBJECTIVE: Microvascular thrombosis is a common feature of acute inflammatory lung injury, as occurs in sepsis and acute respiratory distress syndrome, but the underlying pathomechanisms are presently not fully understood . DESIGN: Experimental . SETTING: University laboratory . SUBJECTS: Lung endothelial cells . INTERVENTIONS: We characterized the expression of tissue-type and urokinase-type plasminogen activator (t-PA and u-PA) as well as plasminogen activator inhibitor (PAI)-1 and PAI-2 in human endothelial cells (EC) from the microvascular pulmonary circulation (HMVEC-L) and compared it with that of EC from pulmonary artery (HPAEC) and umbilical vein (HUVEC) under baseline conditions and upon stimulation with either tumor necrosis factor-alpha or lipopolysaccharide . MEASUREMENTS AND MAIN RESULTS: Real-time reverse transcription-polymerase chain reaction and enzyme-linked immunosorbent assay were employed for quantification of messenger RNA and protein concentrations . Under baseline conditions, comparable PAI-1 expression was noted in all EC . HPAEC were characterized by significantly higher baseline expression of t-PA and PAI-2 compared with HUVEC and HMVEC-L . In contrast, u-PA messenger RNA concentrations were found to be significantly higher in nonstimulated HMVEC-L compared with HUVEC and HPAEC . In all EC, stimulation with tumor necrosis factor-alpha and lipopolysaccharide increased the expression of PAI-1, PAI-2, and u-PA and decreased t-PA expression . The changes in messenger RNA content were reflected by corresponding changes in the protein concentrations . CONCLUSIONS: High baseline u-PA expression is a prominent feature of human lung microvascular EC, whereas pulmonary artery EC are characterized by high t-PA concentrations . Microbial and inflammatory challenge provokes up-regulation of PAI-1 and PAI-2 and down-regulation of t-PA in both macro- and microvascular pulmonary EC, which may favor local fibrin deposition.

J Immunol, 2004 Jan 15, 172(2), 954 - 63
IL-12p70-dependent Th1 induction by human B cells requires combined activation with CD40 ligand and CpG DNA; Wagner M et al.; The detection of microbial molecules via Toll-like receptors (TLR) in B cells is not well characterized . In this study, we found that both naive and memory B cells lack TLR4 (receptor for LPS) but express TLR9 (receptor for CpG motifs) and produce IL-6, TNF-alpha, and IL-10 upon stimulation with CpG oligonucleotides (ODN), synthetic mimics of microbial DNA . Consistent with the lack of TLR4, purified B cells failed to respond to LPS . Similar to CpG ODN, CD40 ligand (CD40L) alone induced IL-6, TNF-alpha, and IL-10 . Production of these cytokines as well as IgM synthesis was synergistically increased when both CpG ODN and CD40L were combined . Unlike IL-6, TNF-alpha, and IL-10, the Th1 cytokine IL-12p70 was detected only when both CpG ODN and CD40L were present, and its induction was independent of B cell receptor cross-linking . CpG ODN did not increase the capacity of CD40L-activated B cells to induce proliferation of naive T cells . However, B cells activated with CpG ODN and CD40L strongly enhanced IFN-gamma production in developing CD4 T cells via IL-12 . Together, these results demonstrate that IL-12p70 production in human B cells is under the dual control of microbial stimulation and T cell help . Our findings provide a molecular basis for the potent adjuvant activity of CpG ODN to support humoral immune responses observed in vivo, and for the limited value of LPS.

FEBS Lett, 2004 Jan 2, 556(1-3), 193 - 8
Efficient and cost-effective experimental determination of kinetic constants and data: the success of a Bayesian systematic approach to drug transport, receptor binding, continuous culture and cell transport kinetics; Murphy EF et al.; Details about the parameters of kinetic systems are crucial for progress in both medical and industrial research, including drug development, clinical diagnosis and biotechnology applications . Such details must be collected by a series of kinetic experiments and investigations . The correct design of the experiment is essential to collecting data suitable for analysis, modelling and deriving the correct information . We have developed a systematic and iterative Bayesian method and sets of rules for the design of enzyme kinetic experiments . Our method selects the optimum design to collect data suitable for accurate modelling and analysis and minimises the error in the parameters estimated . The rules select features of the design such as the substrate range and the number of measurements . We show here that this method can be directly applied to the study of other important kinetic systems, including drug transport, receptor binding, microbial culture and cell transport kinetics . It is possible to reduce the errors in the estimated parameters and, most importantly, increase the efficiency and cost-effectiveness by reducing the necessary amount of experiments and data points measured.

Drug Metab Rev, 2003 Nov, 35(4), 365 - 83
The telltale structures of epoxide hydrolases; Arand M et al.; Traditionally, epoxide hydrolases (EH) have been regarded as xenobiotic-metabolizing enzymes implicated in the detoxification of foreign compounds . They are known to play a key role in the control of potentially genotoxic epoxides that arise during metabolism of many lipophilic compounds . Although this is apparently the main function for the mammalian microsomal epoxide hydrolase (mEH), evidence is now accumulating that the mammalian soluble epoxide hydrolase (sEH), despite its proven role in xenobiotic metabolism, also has a central role in the formation and breakdown of physiological signaling molecules . In addition, a certain class of microbial epoxide hydrolases has recently been identified that is an integral part of a catabolic pathway, allowing the use of specific terpens as sole carbon sources . The recently available x-ray structures of a number of EHs mirror their respective functions: the microbial terpen EH differs in its fold from the canonical alpha/beta hydrolase fold of the xenobiotic-metabolizing mammalian EHs . It appears that the latter fold is the perfect solution for the efficient detoxification of a large variety of structurally different epoxides by a single enzyme, whereas the smaller microbial EH, which has a particularly high turnover number with its prefered substrate, seems to be the better solution for the hydrolysis of one specific substrate . The structure of the sEH also includes an additional catalytic domain that has recently been shown to possess phosphatase activity . Although the physiological substrate for this second active site has not been identified so far, the majority of known phosphatases are involved in signaling processes, suggesting that the sEH phosphatase domain also has a role in the regulation of physiological functions.

J Biol Chem, 2004 Mar 19, 279(12), 11632 - 8 Epub 2003 Dec 29.
Structural and functional analysis of integrin alpha2I domain interaction with echovirus 1; Xing L et al.; Integrins are cell surface receptors for several microbial pathogens including echovirus 1 (EV1), a picornavirus . Cryo-electron microscopy revealed that the functional domain (alpha(2)I) of human alpha(2)beta(1) integrin binds to a surface depression on the EV1 capsid . This three-dimensional structure of EV1 bound to alpha(2)I domain provides the first structural details of an integrin interacting with a picornavirus . The model indicates that alpha(2)beta(1) integrin cannot simultaneously bind both EV1 and the physiological ligand collagen . Compared with collagen binding to the alpha(2)I domain, the virus binds with a 10-fold higher affinity but in vitro uncoating of EV1 was not observed as a result of attachment of alpha(2)I . A molecular model, constructed on the basis of the EV1-integrin complex, shows that multiple alpha(2)beta(1) heterodimers can bind at adjacent sites around the virus 5-fold symmetry axes without steric hindrance . In agreement with this, virus attachment to alpha(2)beta(1) integrin on the cell surface was found to result in integrin clustering, which can give rise to signaling and facilitate the initiation of the viral entry process that takes place via caveolae-mediated endocytosis.

Chem Biol, 2003 Dec, 10(12), 1141 - 2
How to find "missing" genes; Gerlt JA; Assigning function to "new" proteins is frequently the rate-determining step for deciphering metabolic pathways and regulatory networks . Osterman and Begley break down this barrier by demonstrating that comparative analyses of microbial genomes is a powerful strategy for identifying pathway components.

Hum Immunol, 2004 Jan, 65(1), 1 - 12
Pathogenesis of diseases associated with antineutrophil cytoplasm autoantibodies; Reumaux D et al.; Little is known about the etiologies of diseases associated with circulating antineutrophil cytoplasm autoantibodies (ANCA), such as primary vasculitides and inflammatory bowel diseases . However, the understanding of immune mechanisms supposedly involved in the pathogenesis of these diseases is still growing . In the present review, we first focus on the mechanisms triggering the development of ANCA, including the potential role of microbial superantigens and the possible defect(s) in the progression of apoptosis or in the removal of apoptotic cells . We next concentrate on the contribution of ANCA to the clinical symptoms and on the pathogenic role of ANCA, including the accessibility of ANCA antigens as targets for circulating antibodies and the mode of action of ANCA . Mechanisms of neutrophil activation by ANCA include the engagement of Fcgamma receptors, the possible mechanisms of neutrophil-mediated tissue damage, and the neutrophil-endothelial interaction.

Trends Microbiol, 2004 Jan, 12(1), 29 - 36
Helicobacter pylori-induced epithelial cell signalling in gastric carcinogenesis; Naumann M et al.; Helicobacter pylori represents a highly successful human microbial pathogen that infects the stomach of more than half of the world's population . H . pylori induces gastric inflammation, and the diseases that can follow such infection include chronic gastritis, peptic ulcers and, more rarely, gastric cancer . The reasons why a minority of patients with H . pylori develops gastric cancer could be related to differences in host susceptibility, environmental factors and the genetic diversity of the organism . This review examines the features of H . pylori-induced epithelial cell signalling in gastric diseases . Clinical studies and animal models, and also evidence for H . pylori strain-related differences in gastric epithelial cell proliferation in vivo are discussed . In addition, the mechanisms by which H . pylori triggers hyperproliferative processes and takes direct command of epithelial cell signalling, including activation of tyrosine kinase receptors, cell-cell interactions and cell motility are reviewed.

Trends Microbiol, 2004 Jan, 12(1), 1 - 4
Transformation and DNA repair: linkage by DNA recombination; Tonjum T et al.; The stability of microbial genomes is constantly challenged by horizontal gene transfer, recombination and DNA damage . Mechanisms for rapid genome variation, adaptation and maintenance are a necessity to ensure microbial fitness and survival in changing environments . Indeed, genome sequences reveal that most, if not all, bacterial species have numerous gene functions for DNA repair and recombination . These important topics were addressed at the Second Genome Maintenance Meeting (GMM2).

J Biol Chem, 2004 Mar 12, 279(11), 10564 - 74 Epub 2003 Dec 29.
Cytoplasmic domain-mediated dimerizations of toll-like receptor 4 observed by beta-lactamase enzyme fragment complementation; Lee HK et al.; Toll-like receptors (TLRs) detect the presence of microbial challenge and initiate innate immune defensive responses . In this work we have explored the mechanism and role of TLR dimerization in signal transduction using the newly developed technique of beta-lactamase protein fragment complementation, among others . We observed that TLR4 interactions with itself, with MyD88, or with TLR2 were accurately reported by the enzyme complementation technique . That technique, as well as co-immunoprecipitation, transfection-initiated cell activation, and site-directed mutagenesis all suggest an important role for TLR intracellular domains in receptor dimerization . These findings broaden our understanding of TLR self-interactions as well as heterodimer formation.

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