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<