Trends Microbiol, 2004 Feb, 12(2), 79 - 88 Dendritic cells: the host Achille's heel for mucosal pathogens? Niedergang F, Didierlaurent A, Kraehenbuhl JP, Sirard JC. Mucosal surfaces represent the main sites of interaction with environmental microorganisms and antigens . Sentinel cells, including epithelial cells and dendritic cells (DCs), continuously sense the environment and coordinate defenses for the protection of mucosal tissues . DCs play a central role in the control of adaptive immune responses owing to their capacity to internalize foreign materials, to migrate into lymph nodes and to present antigens to naive lymphocytes . Some pathogenic microorganisms trigger epithelial responses that result in the recruitment of DCs . These pathogens hijack the recruited DCs to enable them to infect the host, escape the host's defense mechanisms and establish niches at remote sites. Trends Microbiol, 2004 Feb, 12(2), 72 - 8 Strategies of microbial cheater control; Travisano M et al.; The potential benefits of cooperation in microorganisms can be undermined by genetic conflict within social groups, which can take the form of 'cheating' . For cooperation to succeed as an evolutionary strategy, the negative effects of such conflict must somehow be either prevented or mitigated . To generate an interpretive framework for future research in microbial behavioural ecology, here we outline a wide range of hypothetical mechanisms by which cheaters might be constrained. Micron, 2004, 35(1-2), 87 - 8 Oxygen as a morphogenic factor in sponges: expression of a tyrosinase gene in the sponge Suberites domuncula; Muller WE et al.; Sponges live in a symbiotic relationship with microorganisms, especially bacteria . Here we show, using the demosponge Suberites domuncula as a model, that the sponge expresses the enzyme tyrosinase which synthesizes diphenols from monophenolic compounds . It is assumed that these products serve as carbon source for symbiotic bacteria to grow. Nat Rev Microbiol, 2003 Nov, 1(2), 151 - 7 Microorganisms and autoimmunity: making the barren field fertile? von Herrath MG, Fujinami RS, Whitton JL. Microorganisms induce strong immune responses, most of which are specific for their encoded antigens . However, microbial infections can also trigger responses against self antigens (autoimmunity), and it has been proposed that this phenomenon could underlie several chronic human diseases, such as type 1 diabetes and multiple sclerosis . Nevertheless, despite intensive efforts, it has proven difficult to identify any single microorganism as the cause of a human autoimmune disease, indicating that the 'one organism-one disease' paradigm that is central to Koch's postulates might not invariably apply to microbially induced autoimmune disease . Here, we review the mechanisms by which microorganisms might induce autoimmunity, and we outline a hypothesis that we call the fertile-field hypothesis to explain how a single autoimmune disease could be induced and exacerbated by many different microbial infections. Nat Rev Microbiol, 2003 Dec, 1(3), 200 - 8 Psychrophilic enzymes: hot topics in cold adaptation; Feller G et al.; More than three-quarters of the Earth's surface is occupied by cold ecosystems, including the ocean depths, and polar and alpine regions . These permanently cold environments have been successfully colonized by a class of extremophilic microorganisms that are known as psychrophiles (which literally means cold-loving) . The ability to thrive at temperatures that are close to, or below, the freezing point of water requires a vast array of adaptations to maintain the metabolic rates and sustained growth compatible with life in these severe environmental conditions. Nucleic Acids Res . 2004 Mar 19;32(5):e52. Artificial genetic selection for an efficient translation initiation site for expression of human RACK1 gene in Escherichia coli; Zhelyabovskaya OB et al.; In bacterial expression systems, translation initiation is usually the rate limiting and the least predictable stage of protein synthesis . Efficiency of a translation initiation site can vary dramatically depending on the sequence context . This is why many standard expression vectors provide very poor expression levels of some genes . This notion persuaded us to develop an artificial genetic selection protocol, which allows one to find for a given target gene an individual efficient ribosome binding site from a random pool . In order to create Darwinian pressure necessary for the genetic selection, we designed a system based on translational coupling, in which microorganism survival in the presence of antibiotic depends on expression of the target gene, while putting no special requirements on this gene . Using this system we obtained superproducing constructs for the human protein RACK1 (receptor for activated C kinase). Ann N Y Acad Sci, 2003 Dec, 1010, 121 - 5 Cell death in protists without mitochondria; Chose O et al.; Some protozoans, such as Trichomonad species, do not possess mitochondria . Most of the time, they harbor another type of membrane-bounded organelle, called hydrogenosome from its capacity to produce H(2) . This is the case for the human parasite Trichomonas vaginalis . Some other parasites, such as the protist Giardia lamblia, do not harbor any of these organelles . From this observation arises naturally a naive question: How do cells die when the mitochondrion, the cornerstone of apoptotic process, is absent? Data strongly suggest that the mitochondrion and the hydrogenosome arose from a common ancestral endosymbiont . But hydrogenosomes do not appear to directly substitute for mitochondria in apoptotic functions . Thus, it appears judicious to examine more closely the genome of unicellular cells, which do not harbor mitochondria, and search for new molecules that could participate in the apoptotic process in these microorganisms. J Dermatol Sci, 2004 Apr, 34(2), 73 - 82 Microbial recognition by Toll-like receptors; Takeda K et al.; Toll-like receptors (TLRs) sense invasion of microorganisms by detecting microbial components that are conserved among pathogens . Recognition of microbial components by TLRs triggers activation of the innate immune system . Signaling pathways via TLRs originate from conserved cytoplasmic Toll/IL-1 receptor (TIR) domains . Recent accumulating evidence demonstrates that TIR domain-containing adaptors, such as MyD88, TIRAP/Mal, TRIF, and TRAM, regulate TLR-mediated signaling pathways . MyD88 is common to all TLR-mediated pathways, which lead to the production of inflammatory cytokines, whereas TRIF mediates induction of IFN-beta in TLR3 and TLR4 signaling pathways . TIRAP/Mal is implicated in the TLR2- and TLR4-mediated MyD88-dependent signaling pathway . TRAM is specifically involved in the TLR4-mediated TRIF-dependent pathway . Thus, TIR domain-containing adaptors play a pivotal role in TLR signaling pathways, which culminate in pathogen-specific immune responses. Curr Drug Targets Cardiovasc Haematol Disord, 2004 Mar, 4(1), 65 - 84 Microglia: neuroprotective and neurotrophic cells in the central nervous system; Nakajima K et al.; Microglia are currently accepted as sensor cells in the central nervous system that respond to injury and brain disease . The main function of microglia is believed to be brain defense, as they are known to scavenge invading microorganisms and dead cells, and also to act as immune or immunoeffector cells . However, microglia are also thought to contribute to the onset of or to exacerbate neuronal degeneration and/or inflammation in many brain diseases by producing deleterious factors including superoxide anions, nitric oxide and inflammatory cytokines . Nonetheless, microglia have also been shown to act neuroprotectively by eliminating excess excitotoxins in the extracellular space . Moreover, there is accumulating evidence that microglia produce neurotrophic and/or neuroprotective molecules; in particular, it has been suggested that they promote neuronal survival in cases of brain injury . In general, the question of whether microglia act as neurotoxic cells or as neuroprotective cells in vivo has gained much recent attention . In this paper, we provide a review of findings indicating that the microglia are basically neurotrophic/neuroprotective cells in the nervous system . In addition, the mechanism by which neurotrophic microglia become oriented to a neurotoxic state is discussed. Clin Exp Immunol, 2004 Apr, 136(1), 30 - 9 Reduced ratio of protective versus proinflammatory cytokine responses to commensal bacteria in HLA-B27 transgenic rats; Dieleman LA et al.; Germ-free HLA-B27 transgenic (TG) rats do not develop colitis, but colonization with specific pathogen-free (SPF) bacteria induces colitis accompanied by immune activation . To study host-dependent immune responses to commensal caecal bacteria we investigated cytokine profiles in mesenteric lymph node (MLN) cells from HLA-B27 TG versus nontransgenic (non-TG) littermates after in vitro stimulation with caecal bacterial lysates (CBL) . Supernatants from CBL-stimulated unseparated T- or B- cell-depleted MLN cells from HLA-B27 TG and non-TG littermates were analysed for IFN-gamma, IL-12, TNF, IL-10 and TGF-beta production . Our results show that unfractionated TG MLN cells stimulated with CBL produced more IFN-gamma, IL-12 and TNF than did non-TG MLN cells . In contrast, CBL-stimulated non-TG MLN cells produced more IL-10 and TGF-beta . T cell depletion abolished IFN-gamma and decreased IL-12 production, but did not affect IL-10 and TGF-beta production . Conversely, neither IL-10 nor TGF-beta was produced in cultures of B cell-depleted MLN . In addition, CD4(+) T cells enriched from MLN of HLA-B27 TG but not from non-TG rats produced IFN-gamma when cocultured with CBL-pulsed antigen presenting cells from non-TG rats . Interestingly, IL-10 and TGF-beta, but not IFN-gamma, IL-12 and TNF were produced by MLN cells from germ-free TG rats . These results indicate that the colitis that develops in SPF HLA-B27 TG rats is accompanied by activation of IFN-gamma-producing CD4(+) T cells that respond to commensal bacteria . However, B cell cytokine production in response to components of commensal intestinal microorganisms occurs in the absence of intestinal inflammation. Eur J Biochem, 2004 Apr, 271(7), 1229 - 49 Collectins: players of the innate immune system; van de Wetering JK et al.; Collectins are a family of collagenous calcium-dependent defense lectins in animals . Their polypeptide chains consist of four regions: a cysteine-rich N-terminal domain, a collagen-like region, an alpha-helical coiled-coil neck domain and a C-terminal lectin or carbohydrate-recognition domain . These polypeptide chains form trimers that may assemble into larger oligomers . The best studied family members are the mannan-binding lectin, which is secreted into the blood by the liver, and the surfactant proteins A and D, which are secreted into the pulmonary alveolar and airway lining fluid . The collectins represent an important group of pattern recognition molecules, which bind to oligosaccharide structures and/or lipid moities on the surface of microorganisms . They bind preferentially to monosaccharide units of the mannose type, which present two vicinal hydroxyl groups in an equatorial position . High-affinity interactions between collectins and microorganisms depend, on the one hand, on the high density of the carbohydrate ligands on the microbial surface, and on the other, on the degree of oligomerization of the collectin . Apart from binding to microorganisms, the collectins can interact with receptors on host cells . Binding of collectins to microorganisms may facilitate microbial clearance through aggregation, complement activation, opsonization and activation of phagocytosis, and inhibition of microbial growth . In addition, the collectins can modulate inflammatory and allergic responses, affect apoptotic cell clearance and modulate the adaptive immune system. Artif Cells Blood Substit Immobil Biotechnol, 2004 Feb, 32(1), 1 - 23 Artificial cell bioencapsulation in macro, micro, nano, and molecular dimensions: keynote lecture; Chang TM; Artificial cells now ranges from macro-dimensions, to micron-dimensions, to nano-dimensions, and to molecular dimensions . Those in the macro-dimensions are suitable for use in the bioencapsulation of cells, tissues, microorganisms, and bioreactants . Those in the micron-dimensions are suitable for the bioencapsulation of enzymes, microorganisms, peptides, drugs, vaccine, and other materials . Those in the nano-dimension are being used for blood substitutes and carriers for enzymes, peptides, drugs, etc . Those in the molecular-dimensions are used as blood substitutes, crosslinked enzymes etc. Tsitologiia, 2003, 45(12), 1221 - 6 {Identification of chlamydia and (or) chlamydia-like microorganisms by light microscopy confirmed by electron microscopy and fluorescent in situ hybridization}; Zakharenko LP et al.; Using light microscopy, we have shown that chlamydia and/or chlamydia-like microorganisms are registered in 20-25% of the healthy part of human population, whereas in patients of the same age with gynecological problems these were found in 40-50% . Commonly, the infection was slightly manifested (less than 5% of cells are infected) . These results were confirmed in four months but only in heavily infected patients . The light microscope data are confirmed by observations with electron microscopy, and by FISH hybridization of the total chlamydial DNA on cytological preparations with chlamydial inclusions . In some cases, microcolonies revealed by FISH hybridization occupied the majority of the cytoplasm volume . Occasionally, the DNA material was found on the nuclear surface . It seems likely that in heavily infected cells chlamydia are able to penetrate into the perinucular space. Crit Care, 2004 Apr, 8(2), 99 - 100 Epub 2004 Feb 10. Coagulation in sepsis: all bugs bite equally; Levi M et al.; Sepsis almost invariably leads to hemostatic abnormalities, ranging from insignificant laboratory changes to severe disseminated intravascular coagulation . There is compelling evidence from clinical and experimental studies that disseminated intravascular coagulation is involved in the pathogenesis of microvascular dysfunction and contributes to organ failure . Data from the PROWESS phase III clinical trial of recombinant activated protein C in patients with severe sepsis confirm this notion and demonstrate that the vast majority of patients with severe sepsis have increased markers for systemic coagulation activation, decreased physiological anticoagulant proteins and depressed fibrinolysis . There is no correlation between the type of microorganism that has caused the infection and the presence or severity of the coagulation disorder. Eur J Clin Invest, 2004 Mar, 34(3), 229 - 35 Association between human-Pneumocystis infection and small-cell lung carcinoma; de la Horra C et al.; BACKGROUND: Tobacco smoking is the most important but not the only risk factor in lung carcinoma . There is evidence that certain infections, which cause chronic inflammatory reactions, can also induce tumour development . It has recently been shown that patients with chronic pulmonary diseases present a high rate of subclinical Pneumocystis infection, and that the latter is able to induce inflammatory responses and alveolar cell alterations . The possible role of Pneumocystis infection in the development of lung neoplasms thus deserves consideration . MATERIAL AND METHODS: Polymerase chain reaction has been used to analyze the presence of DNA of two independent loci of the Pneumocystis genome: the mitochondrial region (mtLSU rRNA) and the gene encoding for the dihydropteroate synthase enzyme, in paraffin-embedded tissue blocks of 10 cases of small cell lung carcinoma (SCLC) and 10 cases of nonsmall cell lung carcinoma (NSCLC) with similar demographic and clinical characteristics . Five cases without lung pathology, and two cases of Pneumocystis pneumonia were also analyzed as controls . RESULTS: DNA of the microorganism was found in all the cases of SCLC but in only two of the NSCLC, and in none of the controls without pulmonary disease - thus implying a statistically significant association (P < 0.0001) between subclinical Pneumocystis infection and SCLC . CONCLUSIONS: While the nature of this association is not clear, it nevertheless constitutes an important finding - either the infection is specifically facilitated by this tumour or induces the development of this type of neoplasm in combination with other factors . Eur J Clin Invest 2004; 34 (3): 229-335 Clin Tech Small Anim Pract, 2004 Feb, 19(1), 43 - 8 The problem of gastric atony; Woosley KP; Normal gastrointestinal motility is crucial for maintaining an appropriate balance of microorganisms within the gut . Disruption of this system results in bacterial overgrowth and associated complications such as bacterial translocation, aspiration pneumonia, and sepsis . Critically ill animals are at increased risk of developing gastroparesis caused by primary gastrointestinal disturbances or severe metabolic derangements that impact gastrointestinal function . In the intensive-care setting, delayed gastric emptying complicates enteral nutrition, and the catabolic effects of severe illness further deplete the patient's caloric reserves, resulting in impaired wound healing, decreased immune function, and increased morbidity and mortality . The use of promotility drugs in critically ill patients is a safe, effective means to circumvent the problem of gastric atony and improve patient recovery . Understanding the drugs available and their interaction with the receptors involved in neuromuscular transmission within the gastrointestinal tract will aid the clinician in selecting the optimal prokinetic therapy. Arch Environ Contam Toxicol, 2004 Jan, 46(1), 24 - 31 Procedures for determining the pesticide sensitivity of indigenous soil algae: a possible bioindicator of soil contamination? Berard A, Rimet F, Capowiez Y, Leboulanger C. Soil algae are present in all kinds of soils, both arable and virgin, in large amounts and in great diversity . These photosynthetic microorganisms, which are concentrated in the top few centimeters of the soil profile, are organized in a community structure that varies depending on soil type, farming method and pesticide application . We first tested several extraction and conservation methods for soil algae, and a 14C incorporation procedure to evaluate the photosynthetic activity of these micro-organisms . In a second study, we assessed the sensitivity to atrazine of soil microalgae from two corn fields managed by different agricultural practices (conventional vs . organic) . Changes in indigenous diatom communities were monitored, together with photosynthetic tests performed on the whole algal community . Comparison of the data for the treated field with those for the reference, untreated organic cornfield showed that previous atrazine application in the conventional cornfield had changed the species composition of the soil diatom communities . Short-term ecotoxicological tests, using photosynthetic activity as endpoint, also showed that the communities that had developed under pesticide stress were more tolerant to further atrazine application than the control communities . The stress caused by major environmental disturbances, such as ground dressing, was not sufficient to mask the difference between the two crops, suggesting that telluric microalgae could be used as indicators of xenobiotic contamination in soils . These initial findings about using soil microalgal communities as bioindicators are promising . In addition, their photosynthetic activity, which reflects their sensitivity to xenobiotic compounds, seems to be a relevant bioindicator of soil contamination. Zh Mikrobiol Epidemiol Immunobiol, 2004 Jan-Feb, (1), 7 - 13 {Microorganism "Montezuma" of the order Rickettsiales: the potential causative agent of tick-borne disease in the Far East of Russia}; Mediannikov OIu et al.; A new microorganism, tentatively named "Montezuma" was detected in ticks and in specimens (blood, bioptic specimens of the primary affect) taken from patients with an acute fever disease, etiologically linked with the bites of Ixodes ticks in the Far East of the Russian Federation . After sequencing the products of the amplification of DNA isolated from ticks with wide-spectrum primers new primers were developed, highly specific to the unusual sequence thus obtained . The study revealed that ticks of the species Ixodes persulcatus (97%) and Haemophysalis concinnae (5%) contained DNA of this microorganism . The same DNA was detected in materials taken from the patients . The phylogenetic analysis of the gene showed that this organism formed an independent and well defined branch within the order Rickettsiales . The nearest homology (89%) was observed with recently detected endosymbiotes Acanthamoeba . The similarity with their relatives from the families Rickettsiaceae and Anaplasmataceae of the order Rickettsiales was within 81-86%, which made it possible to infer the existence of, probably, only a new genus, but also a family . The isolated DNA belonged, supposedly, to the new microoganism which caused a tick-borne disease in humans, transmitted through bites of Ixodes ticks, and was, supposedly, widely spread in the southern area of the Khabarovsk Territory. Histol Histopathol, 2004 Apr, 19(2), 535 - 64 Structural pathways for macromolecular and cellular transport across the blood-brain barrier during inflammatory conditions . Review; Lossinsky AS et al.; This review presents an overview of the highlights of major concepts involving the anatomical routes for the transport of macromolecules and the transmigration of cellular elements across the blood-brain barrier (BBB) during inflammation . The particular focus will include inflammatory leukocytes, neoplastic cells and pathogenic microorganisms including specific types of viruses, bacteria and yeasts . The experimental animal models presented here have been employed successfully by the authors in several independent experiments during the past twenty-five years for investigations of pathologic alterations of the BBB after a variety of experimentally induced injuries and inflammatory conditions in mammalian and non-mammalian animal species . The initial descriptions of endothelial cell (EC) vesicles or caveolae serving as mini-transporters of fluid substances essentially served as a springboard for many subsequent discoveries during the past half century related to mechanisms of uptake of materials into ECs and whether or not pinocytosis is related to the transport of these materials across EC barriers under normal physiologic conditions and after tissue injury . In the mid-1970's, the authors of this review independently applied morphologic techniques (transmission electron microscopy-TEM), in conjunction with the plant protein tracer horseradish peroxidase (HRP) to investigate macromolecular transport structures that increased after the brain and spinal cord had been subjected to a variety of injuries . Based on morphologic evidence from these studies of BBB injury, the authors elaborated a unique EC system of modified caveolae that purportedly fused together forming transendothelial cell channels, and later similar EC profiles defined as vesiculo-canalicular or vesiculo-tubular structures (VTS, Lossinsky, et al., 1999) . These EC structures were observed in association with increased BBB permeability of tracers including exogenously injected HRP, normally excluded from the intercellular milieu of the CNS . Subsequent studies of non-BBB-type tumor ECs determined that the EC VTS and other vesicular structures were defined by others as vesiculo-vacuolar organelles (VVOs, Kohn et al., 1992; Dvorak et al., 1996) . Collectively, these structures appear to represent a type of anatomical gateway to the CNS likely serving as conduits . However, these CNS conduits become patent only in damaged ECs for the passage of macromolecules, and purportedly for inflammatory and neoplastic cells as well (Lossinsky et al., 1999) . In this review, we focus attention on the similarities and differences between caveolae, fused racemic vesicular bundles, endothelial tubules and channels (VTS and the VVOs) that are manifest in normal, non-BBB-type blood vessels, and in the BBB after injury . This review will present evidence that the previous studies by the authors and other researchers established a framework for subsequent transmission (TEM), scanning (SEM) and high-voltage electron microscopic (HVEM) investigations concerning ultrastructural, ultracytochemical and immunoultra-structural alterations of the cerebral ECs and the mechanisms of the BBB transport that occurs after CNS injury . This review is not intended to include all of the many observations that might be included in a general historical overview of the development of the EC channel hypothesis, but it will discuss several of the major contributions . We have attempted to present some of the structural evidence that supports our early contributions and those made by other investigators by highlighting major features of these EC structures that are manifest in the injured BBB . We have focused on currently established concepts and principles related to mechanisms for the transendothelial transport of macromolecules after CNS injury and also offer a critical appraisal of some of this literature . Finally, we describe more recent concepts of transBBB avenues for viruses, including HIV-1, bacterial and mycotic organisms, as well as inflammatory and neoplastic cell adhesion and migration across the injured mammalian BBB . Data from studies of EC-related adhesion molecules, both from the literature and from the author's experimental results and observations made in other laboratories, as well as from personal communications underscore the importance of the adhesion molecules in facilitating the movement of leukocytic, neoplastic cell and human pathogens across the BBB during inflammatory and neoplastic events . Exciting, ongoing clinical trials are addressing possible therapeutic intervention in neuroinflammatory diseases, including multiple sclerosis, by blocking certain glycoprotein adhesion molecules before cells have the ability to adhere to the ECs and migrate across the BBB . Approaches whereby inflammation may be reduced or arrested using anti-adhesion molecules, by restructuring EC cytoskeletal, filamentous proteins, as well as remodeling cholesterol components of the modified VTS are discussed in the context of developing future therapies for BBB injury and inflammation . Understanding new concepts about the mechanism(s) by which inflammatory cells and a variety of pathogenic microorganisms are transported across the BBB can be expected to advance our understanding of fundamental disease processes . Taken together, the literature and the author's experiences during the past quarter of a century, will hopefully provide new clues related to the mechanisms of transendothelial cell adhesion and emigration across the injured BBB, issues that have been receiving considerable attention in the clinical arena . Learning how to chemically modulate the opening and/or closure of EC VTS and VVO structural pathways, or junctional complexes prior to cellular or microorganism adhesion and breaching the BBB presents challenging new questions in modern medicine . Future studies will be critically important for the development of therapeutic intervention in several human afflictions including traumatic brain and spinal cord injuries, stroke, cancer, multiple sclerosis and conditions where the immune system may be compromised including HIV infection, infantile and adult meningitis. Gac Med Mex, 2004 Jan-Feb, 140(1), 59 - 69 {Pneumonia due to Pneumocystis carinii in HIV-infected children}; Morales-Aguirre JJ et al.; Introduction of new antiretroviral agents and development of new prophylaxis schedules against opportunistic microorganisms have allowed increase in survival as well as better quality of life in HIV-infected patients . These new treatment schedules have changed the epidemiology of opportunistic infections that previous to use of highly active antiretroviral therapy (HAART), formerly occurred with high frequency in HIV-infected children . Specifically, pneumonia due to Pneumocystis carinii formerly occurred in 12 to 80% of these patients and was associated with high mortality . Currently, with use of combined antiretroviral therapy (ART) and prophylactic treatments important reduction of PCP has been observed . However, despite these benefits ART is not yet available for many patients from several developing countries who are at risk for opportunistic infections, mainly due to Pneumocystis carinii, which can affect life expectancy . Therefore, the purpose of this paper was a review of epidemiologic, clinical, and therapeutic characteristics of P . carinii pneumonia in HIV-infected children. J Plant Physiol, 2004 Feb, 161(2), 183 - 90 Soybean (Glycine max . L.) and bacteroid glyoxylate cycle activities during nodular senescence; Fargeix C et al.; Soybean (Glycine max . L.) nodular senescence results in the dismantling of the peribacteroid membrane (PBM) and in an increase of soybean isocitrate lyase (ICL; EC 4.1.3.1) and malate synthase (MS; EC 4.1.3.2) mRNA and protein levels . This suggests that in senescing soybean nodular cells, the specific glyoxylate cycle enzyme activities might be induced to reallocate carbon obtained from the PBM degradation . In order to evaluate as well the carbon metabolism of the nitrogen-fixing Bradyrhizobium japonicum endosymbiotic bacteroids during nodular senescence, their glyoxylate cycle activities were also investigated . To this end, partial DNA sequences were isolated from their icl and ms genes, but the corresponding mRNAs were not detected in the microorganisms . It was also observed that the bacteroid ICL and MS activities were negligible during nodular senescence . This suggests that glyoxylate cycle activities are not reinitiated in the bacteroids under these physiological conditions . In case the microorganisms nevertheless feed on the PBM degradation products, this might occur via the citric acid cycle exclusively. Vestn Ross Akad Med Nauk, 2004, (1), 48 - 50 {Factors and conditions affecting the process of infecting the fetus during different pregnancy stages}; Borovkova EI et al.; Etiology, pathogenesis of intrauterine infection of the fetus, factors promoting such infection and the status of the local immune system are elucidated in the paper . A changed reactivity of the immune homeostasis of a pregnant woman with a chronic infection was shown to be potentially an important factor of pathogenesis of defects in her baby . The local immunity factors of the reproductive tract, i.e . the vagina and neck of uterus, are in the forefront of anti-infectious protection, which signal an alert or limit the microorganisms' reproduction; besides, they prevent the microorganisms from penetrating into the upper genitals . The therapeutic-and-preventive schemes applicable to infected women must comprise measures targeted at eliminating an infectious agent and at normalizing the pathological changes in the performance of the immune system activity. Pediatr Pulmonol, 2004 Apr, 37(4), 356 - 61 Airway inflammation in children with tracheostomy; Griese M et al.; We hypothesised that long-term tracheostomy in infants and children may perpetuate chronic airway inflammation and airway remodeling due to easier access to the lungs for microorganisms . Pulmonary surfactant represents an important part of the initial host defense, and in particular, the surfactant proteins (SP) A and D may directly interact with invading microorganisms and also modulate the activity of local immune cells . The goals of this study were to determine the presence and intensity of a peripheral airway inflammation and of potential deficiency states of surfactant proteins in nonsymptomatic children with tracheostomy . Bronchoalveolar lavage (BAL) cell pattern, bacteria and viruses recovered, and concentrations of SP-A, SP-B, SP-C, and SP-D were assessed in 46 children (4.3 years (1.6-6)) median (range) carrying a tracheostomy for 2.4 years (1.3-4.9), and were compared to 16 children with no lung disease . Children with tracheostomy had an increased total number of cells, increased neutrophils, and more frequently bacteria, but no viruses were recovered . SP-D concentration was reduced by 50% on average (P = 0.0002) . SP-A, SP-B, and SP-C were not different between the two groups . SP-D was inversely correlated to neutrophils, and high numbers of bacteria were associated with lower SP-D concentrations . We suggest that bacteria and low SP-D support neutrophilic inflammation in the lower respiratory tract of nonsymptomatic with children with tracheostomy . Inflamm Res, 2004 Mar, 53(3), 100 - 6 Epub 2004 Feb 16. Induction of intracellular cytokine production in human monocytes/macrophages stimulated with ligands of pattern recognition receptors; Mytar B et al.; OBJECTIVE: This study addressed the role of the pattern recognition receptors (PRR), which recognize different molecular structures present on microorganisms, apoptotic, senescent and tumor cells, in the stimulation of human monocyte and monocyte-derived macrophages (MDM) for the production of intracellular cytokines . MATERIALS AND METHODS: Monocytes and MDM were stimulated with different ligands of scavenger receptors (SR) and mannose receptor (MR) . Production of intracellular cytokines: tumor necrosis factor alpha (TNF alpha), interleukin 10 and 12 (IL-10, IL-12) was determined by flow cytometry following staining with anti-cytokine monoclonal antibodies (mAbs) . RESULTS: The ligands of SR type A: fucoidan, polyguanylic acid (polyG), chemically modified low density lipoproteins (LDL), ligands of SR-B: native and chemically modified LDL, and ligand of mannose receptor (MR)-mannan induced strong expression of intracellular TNF alpha and weaker IL-10 in monocytes, while phosphatidylserine (PdS) was without effect . IL-12 was stimulated only by fucoidan and polyG . The induction of cytokine m-RNA generally followed the pattern and the magnitude of intracellular cytokine production . In MDM, intracellular TNF alpha and IL-12 expression was induced by mannan, native and modified LDL, but not other ligands . Expression of IL-10 was less pronounced and occurred following stimulation with fucoidan, polyG and modified, but not native, LDL . CONCLUSIONS: These results suggest that some PRR ligands may be involved in activation of monocytes/MDM for the production of mainly proinflammatory cytokines (TNF alpha, IL-12) implicating their role in the response to microbial and tumor invasion. Curr Opin Infect Dis, 2004 Apr, 17(2), 137 - 42 Q fever pneumonia; Marrie TJ; PURPOSE OF REVIEW: In this era of emerging infectious diseases and bioterrorism it is important to be up to date with the diagnosis and management of Q fever pneumonia . RECENT FINDINGS: A considerable amount of new information has emerged regarding the pathogenesis of Coxiella burnetii infection . The complete genome of this microorganism has now been sequenced and there are several unique features . The spectrum of manifestations of infection due to C . burnetii continues to expand . Some of the more recently described findings are acalculous cholecystitis, rhabdomyolysis, long-term persistence of Coxiella, post Q fever fatigue syndrome, and hemolytic uremic syndrome . Pneumonia as a manifestation of acute Q fever shows tremendous geographic variation, being common in one area of a country such as Spain but not in another area . SUMMARY: Pneumonia continues to be an important manifestation of infection with C . burnetii . It responds to treatment with doxycycline, quinolones or macrolides. Infez Med, 2003 Jun, 11(2), 69 - 74 {Bacterial granulomatous hepatitis}; Pasquale G et al.; The liver may react to different infectious and non- infectious agents, developing granulomatous lesions which characterize granulomatous hepatitis . Granulomas of the liver are circumscribed inflammatory lesions (size from 50 to 300 mm) composed of epithelioid cells, varied numbers of mononuclear cells and eosinophils and multinucleated giant cells . They represent a specialized cell-mediated immune response to a wide variety of etiological factors . A broad spectrum of microorganisms may trigger hepatic granulomas . M . tuberculosis is the more frequent agent (~ 44%) . Granulomatous hepatitis is characterized by a febrile illness with systemic signs and symptoms such as fatigue, sweating, shivering, hepatomegaly and/or splenomegaly, abnormalities in serum liver tests (aminotransferase, alkaline phosphatase) . Liver biopsy provides diagnostic information in approximately 15-30% of cases, identifying directly the microbial agent with special microbial stains and polymerase chain reaction or finding distinctive microscopic features, suggestive of specific microorganisms . In such cases appropriate therapy is possible . Unfortunately in one third of cases is impossible to reach aetiological diagnosis on histological criteria alone . In these cases a therapeutic attempt with steroids, effective in the idiopathic granulomatous hepatitis, may be useful. Ann Occup Hyg . 2004 Mar 2; {Epub ahead of print} Microbial Dustiness and Particle Release of Different Biofuels; Madsen AM et al.; Exposure to organic dust originating from biofuels can cause adverse health effects . In the present study we have assessed the dustiness in terms of microbial components and particles of various biofuels by using a rotating drum as a dust generator . Microbial components from straw, wood chips, wood pellets and wood briquettes were quantified by several methods . Excellent correlations (r >/= 0.85, P < 0.0001) were found: between lipopolysaccharide (LPS) (as determined by 3-hydroxy fatty acid analysis) and endotoxin (as determined by a Limulus test), cultivable bacteria, total number of bacteria and muramic acid; between endotoxin and cultivable bacteria, total number of bacteria and muramic acid; between total number of bacteria and muramic acid; between cultivable fungi and total number of fungi . Straw was dustier than the other biofuels in terms of actinomycetes, bacteria, muramic acid, endotoxin, LPS, particle mass and number of particles . One of the wood chips studied and the straws had comparatively high dustiness in terms of fungi, while both wood pellets and wood briquettes had comparatively low dustiness in terms of all microbial components . An initially high particle generation rate of straw and wood chips decreased over time whereas the particle generation rate of wood briquettes and wood pellets increased during a 5 min rotation period . Particles of non-microbial origin may be the determining factor for the health risk in handling briquettes and pellets . Straw dust contained significantly more microorganisms per particle than did wood chip dust, probably because bacteria were most abundant in straw dust . The concentrations of endotoxin and fungi were high in wood and straw dust; dust from one of the straws contained 3610 EU/mg and dust from one of the chips contained 7.3 x 10(6) fungal spores/mg . An exposure to 3 mg of straw or wood chips dust/m(3) (the Swedish and Danish OEL of unspecific inhalable dust) could cause exposures to endotoxin and fungi higher than levels were health symptoms are seen to develop . The very different levels of dustiness in terms of particles and microbial components of different biofuels shows that dustiness is an important health-relevant factor to consider when choosing among biofuels and when designing worksites for handling of biofuels. J Mol Biol, 2004 Mar 26, 337(3), 675 - 90 Substrate and metal complexes of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Saccharomyces cerevisiae provide new insights into the catalytic mechanism; Konig V et al.; 3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthases are metal-dependent enzymes that catalyse the first committed step in the biosynthesis of aromatic amino acids in microorganisms and plants, the condensation of 2-phophoenolpyruvate (PEP) and d-erythrose 4-phosphate (E4P) to DAHP . The DAHP synthases are possible targets for fungicides and represent a model system for feedback regulation in metabolic pathways . To gain further insight into the role of the metal ion and the catalytic mechanism in general, the crystal structures of several complexes between the tyrosine-regulated form of DAHP synthase from Saccharomyces cerevisiae and different metal ions and ligands have been determined . The crystal structures provide evidence that the simultaneous presence of a metal ion and PEP result in an ordering of the protein into a conformation that is prepared for binding the second substrate E4P . The site and binding mode of E4P was derived from the 1.5A resolution crystal structure of DAHP synthase in complex with PEP, Co2+, and the E4P analogue glyceraldehyde 3-phosphate . Our data suggest that the oxygen atom of the reactive carbonyl group of E4P replaces a water molecule coordinated to the metal ion, strongly favouring a reaction mechanism where the initial step is a nucleophilic attack of the double bond of PEP on the metal-activated carbonyl group of E4P . Mutagenesis experiments substituting specific amino acids coordinating PEP, the divalent metal ion or the second substrate E4P, result in stable but inactive Aro4p-derivatives and show the importance of these residues for the catalytic mechanism. Structure (Camb), 2004 Mar, 12(3), 467 - 75 Reaction trajectory of pyrophosphoryl transfer catalyzed by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase; Blaszczyk J et al.; 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the Mg(2+)-dependent pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP) . The reaction follows a bi-bi mechanism with ATP as the first substrate and AMP and HP pyrophosphate (HPPP) as the two products . HPPK is a key enzyme in the folate biosynthetic pathway and is essential for microorganisms but absent from mammals . For the HPPK-catalyzed pyrophosphoryl transfer, a reaction coordinate is constructed on the basis of the thermodynamic and transient kinetic data we reported previously, and the reaction trajectory is mapped out with five three-dimensional structures of the enzyme at various liganded states . The five structures are apo-HPPK (ligand-free enzyme), HPPK.MgATP(analog) (binary complex of HPPK with its first substrate) and HPPK.MgATP(analog).HP (ternary complex of HPPK with both substrates), which we reported previously, and HPPK.AMP.HPPP (ternary complex of HPPK with both product molecules) and HPPK.HPPP (binary complex of HPPK with one product), which we present in this study. Nephrology (Carlton), 2003 Feb, 8(1), 49 - 55 A peritoneal dialysis patient with fatal culture-negative peritonitis; Johnson DW et al.; Culture-negative peritoneal inflammation accounts for between 5 and 20% of cases of peritonitis in peritoneal dialysis patients . Diagnostic yields may be enhanced considerably by reculturing dialysate effluents using appropriate collection methods and optimal laboratory techniques (including prolonged low-temperature and anaerobic incubations) . In patients with persistent culture-negative peritonitis, consideration should be given to the possibilities of unusual or fastidious microorganisms (especially fungi and mycobacteria) and non-infective causes (especially drug reactions, malignancy, visceral inflammation and retroperitoneal inflammation) . In this paper, an illustrative case of persistent culture-negative peritonitis is presented followed by a discussion of the investigative approach to such patients, with particular emphasis on differential diagnosis and the limitations of currently available tests. Annu Rev Phytopathol, 1997, 35, 327 - 47 Microbial population dynamics on leaves; Kinkel LL; Microbial population dynamics on leaves in time and space are a function of immigration, emigration, growth, and death . Insight into the relative significance of each population process to the generation of specific dynamics for individual microorganisms is necessary to understanding the ecology and life history strategy of the microorganism and to developing effective control strategies . Additionally, information on the significance of within-leaf versus extra-leaf processes to the generation of phyllosphere dynamics is important to determining the range of spatial scales over which a population should be studied . Unfortunately, such information is difficult to obtain due to the lack of effective methodologies for distinguishing these processes within phyllosphere populations . Future research efforts should focus on the quantification of immigration, emigration, growth, and death relative to the population dynamics of phyllosphere microorganisms. Annu Rev Phytopathol, 1997, 35, 235 - 70 Systemic acquired resistance; Sticher L et al.; This paper examines induced resistance (SAR) in plants against various insect and pathogenic invaders . SAR confers quantitative protection against a broad spectrum of microorganisms in a manner comparable to immunization in mammals, although the underlying mechanisms differ . Discussed here are the molecular events underlying SAR: the mechanisms involved in SAR, including lignification and other structural barriers, pathogenesis-related proteins and their expression, and the signals for SAR including salicylic acid . Recent findings on the biological role of systemin, ethylene, jasmonates, and electrical signals are reviewed . Chemical activators of SAR comprise inorganic compounds, natural compounds, and synthetic compounds . Plants known to exhibit SAR and induced systemic resistance are listed. Annu Rev Phytopathol, 1998, 36, 311 - 27 Function of root border cells in plant health: pioneers in the rhizosphere; Hawes MC et al.; Plants dedicate a large amount of energy to the regulated production of living cells programmed to separate from roots into the external environment . This unusual process may be worth the cost because it enables the plant to dictate which species will share its ecological niche . For example, border cells can rapidly attract and stimulate growth in some microorganisms and repel and inhibit the growth of others . Such specificity may provide a way to control the dynamics of adjacent microbial populations in the soil to foster beneficial associations and inhibit pathogenic invasion . Plant genes controlling the delivery of border cells and the expression of their unique properties provide tools to genetically engineer plants with altered border cell quality and quantity . Such variants are being used to test the hypothesis that the function of border cells is to protect plant health by controlling the ecology of the root system. Annu Rev Entomol, 1998, 43, 17 - 37 Nutritional interactions in insect-microbial symbioses: aphids and their symbiotic bacteria Buchnera; Douglas AE; Most aphids possess intracellular bacteria of the genus Buchnera . The bacteria are transmitted vertically via the aphid ovary, and the association is obligate for both partners: Bacteria-free aphids grow poorly and produce few or no offspring, and Buchnera are both unknown apart from aphids and apparently unculturable . The symbiosis has a nutritional basis . Specifically, bacterial provisioning of essential amino acids has been demonstrated . Nitrogen recycling, however, is not quantitatively important to the nutrition of aphid species studied, and there is strong evidence against bacterial involvement in the lipid and sterol nutrition of aphids . Buchnera have been implicated in various non-nutritional functions . Of these, just one has strong experimental support: promotion of aphid transmission of circulative viruses . It is argued that strong parallels may exist between the nutritional interactions (including the underlying mechanisms) in the aphid-Buchnera association and other insect symbioses with intracellular microorganisms. Annu Rev Entomol, 1997, 42, 587 - 609 Biology of Wolbachia; Werren JH; Wolbachia are a common and widespread group of bacteria found in reproductive tissues of arthropods . These bacteria are transmitted through the cytoplasm of eggs and have evolved various mechanisms for manipulating reproduction of their hosts, including induction of reproductive incompatibility, parthenogenesis, and feminization . Wolbachia are also transmitted horizontally between arthropod species . Significant recent advances have been made in the study of these interesting microorganisms . In this paper, Wolbachia biology is reviewed, including their phylogeny and distribution, mechanisms of action, population biology and evolution, and biological control implications . Potential directions for future research are also discussed. Annu Rev Entomol, 1997, 42, 23 - 50 Adaptations in scale insects; Gullan PJ et al.; Many unusual features of scale insects (Hemiptera: Coccoidea) can be explained as historical legacy . Developmental specializations in ancestral coccoids resulted in a neotenous adult female and a drastic metamorphosis of the male . Subsequent evolution led to numerous, often convergently derived, adaptations to parasitic life on higher plants . The sedentary lifestyle of female scale insects has favored the evolution of appendage reduction or loss, gross changes in body shape, and protective wax secretions, tests, and other scale covers . Morphological peculiarities of adult males relate to flight or to mating with concealed females . Scale insects have diverse egg-protecting methods, a range of chromosome behaviors (including several methods of sex determination), marked sexual dimorphism {even sometimes in first-instar nymphs (crawlers)}, and more rarely sexual dichronism . Crawlers have evolved as the main agents of dispersal . The biotic interactions of scale insects include diverse endosymbioses with microorganisms, sometimes morphological and behavioral adaptations for obligate association with ants, and often highly specific host-plant associations that may lead to demic adaptation or the evolution of complex galls. Annu Rev Plant Physiol Plant Mol Biol, 1996 Jun, 47, 509 - 540 CARBOHYDRATE-MODULATED GENE EXPRESSION IN PLANTS; Koch KE; Plant gene responses to changing carbohydrate status can vary markedly . Some genes are induced, some are repressed, and others are minimally affected . As in microorganisms, sugar-sensitive plant genes are part of an ancient system of cellular adjustment to critical nutrient availability . However, in multicellular plants, sugar-regulated expression also provides a mechanism for control of resource distribution among tissues and organs . Carbohydrate depletion upregulates genes for photosynthesis, remobilization, and export, while decreasing mRNAs for storage and utilization . Abundant sugar levels exert opposite effects through a combination of gene repression and induction . Long-term changes in metabolic activity, resource partitioning, and plant form result . Sensitivity of carbohydrate-responsive gene expression to environmental and developmental signals further enhances its potential to aid acclimation . The review addresses the above from molecular to whole-plant levels and considers emerging models for sensing and transducing carbohydrate signals to responsive genes. Arch Kriminol, 2004 Jan-Feb, 213(1-2), 1 - 14 {Macroscopic findings for the exclusion of a forensic relevant soil embedded resting period in skeletal remains--an approach based upon literature}; Verhoff MA et al.; A reliable determination of the post mortem interval (PMI) in human bones has neither been found by morphological nor by intensive analyses of other kinds . In most cases of legal medicine practice the question of PMI is restricted to a forensically relevant resting period . In a survey based upon literature, all osteological signs of decomposition, which have not been described for a soil embedded resting period of under 50 years, were collected . 21 research reports could be found, describing macroscopic findings on soil-embedded human bones with known PMI . All in all, 1295 individuals were examined in these investigations . A censorious review of the summarized results found in literature reveals that the following findings have never been seen in a PMI of 50 years or less . Outer appearance: macroscopically no adipocere, deep incisions of the outer compact layer, extensive defects of the bone surface, intense brownish-black lawn of microorganisms, fraying of the outer lamellar system, lifting of the cortical area, torsion of the tissue, attached brushit, bone manually breakable . On freshly sawn cross sections: lack of adipocere, brushit in the marrow area, reduced or lack of UV-fluorescence. Int J Mol Med, 2004 Apr, 13(4), 527 - 36 Efficient and faithful in vitro translation of natural and synthetic mRNA with human ribosomes; Ferreras AC et al.; Efficient systems for in vitro translation are of importance for biochemical and gene expression studies as well as for biotechnological developments . We optimized a cell-free translation system using subcellular fractions from human placenta and high quality placental tRNAs isolated using a simple and fast procedure . The postmitochondrial fraction or a reconstituted system containing soluble proteins plus polysomes were able to efficiently translate endogenous and exogenous mRNAs . Optima for ions, enzymes, tRNA and energy mix components were determined for a poly(U)-directed poly(Phe) synthesis test . The use of homologous tRNAPhe, omission of commercial creatine kinase, and addition of 3.5 mM spermidine at near physiological magnesium concentration (2.5 mM), were the most significant improvements . Under optimal conditions, poly(Phe) synthesis proceeded at a maximal initial rate of 1.2 Phe/80S/min at 37 degrees C, while natural mRNA translation by S-30 started at a near in vivo estimated rate of 0.3-0.5 amino acid/80S/sec . Furthermore, natural mRNA directed the synthesis of a family of polypeptides closely resembling the pattern of cytoplasmic proteins in both, molecular weight and relative amounts . This efficient and faithful system is of interest for biochemical studies of the human translational machinery, as well as a basis for screening new drugs affecting protein synthesis in pathogenic microorganisms. Indoor Air, 2004 Apr, 14(2), 74 - 82 Microorganisms and volatile organic compounds in airborne dust from damp residences; Nilsson A et al.; Airborne dust samples from damp (n = 9) and control (n = 9) residences were analyzed for microorganisms (molds and bacteria), bacterial markers (3-hydroxy fatty acids and muramic acid), and adsorbed volatile organic compounds (VOCs) . The number of mold species was greater in the damp residences than in the controls (23 vs.18) and nine mold species were found only in damp residences . The levels of 3-hydroxy fatty acids and muramic acid correlated better in damp residences than in controls, indicating that damp conditions affect the bacterial flora of airborne dust . Identifications made by culture and microscopy of the major molds found, i.e . Aspergillus, Cladosporium, and Penicillum, coincided with the identification of VOCs known to be produced by these species . A number of additional VOCs irritating to the skin, eyes, or respiratory tract were also found . The results from this pilot study illustrate the diversity of microorganisms and VOCs present in the indoor environment and suggest that analysis of airborne dust may help to assess human exposure to microorganisms and chemical compounds. Nihon Kokyuki Gakkai Zasshi, 2004 Feb, 42(2), 158 - 63 {A case of paclitaxel-induced pneumonitis}; Taniguchi N et al.; A 79-year-old woman with small-cell lung cancer was treated weekly with paclitaxel after previous treatment with carboplatin and etoposide . Within the first course of paclitaxel, chest radiography and CT revealed thickening of the bronchovascular bundle and interlobular septa, and infiltrates in both lung fields . A marked increase in the number of lymphocytes was found on bronchoalveolar lavage (BAL) . Microorganisms such as Cytomegalovirus, Mycobacteria, and Pneumocystis carinii were absent from the BAL fluid . Interstitial infiltration was partially improved simply by stopping paclitaxel administration, without the need for any additional therapy . Drug-induced pneumonitis caused by paclitaxel was diagnosed on the basis of the clinical course and findings, although a drug lymphocyte stimulation test yielded negative results for paclitaxel . Interstitial infiltrates on imaging, symptoms and arterial blood gas results improved with administration of oral prednisolone . The possibility of pneumonitis induced by paclitaxel should be considered even in cases without interstitial lung disease. Lab Chip, 2003 Nov, 3(4), 313 - 7 Epub 2003 Sep 25. Fabrication of microbial chip using collagen gel microstructure; Kaya T et al.; A microbial chip was fabricated by filling the micropores on a glass substrate with collagen-embedded Escherichia coli(E . coli) cells, and characterized by scanning electrochemical microscopy (SECM) in a solution containing ferricyanide . The activity of the E . coli cells in the collagen gel microstructure was imaged and characterized with SECM by mapping the localized concentration of ferrocyanide produced by the respiration of the cells . The SECM-based activity measurement detected as low as approximately 100 E . coli cells . Furthermore, the optical-microscopic observation indicated that the E . coli cells on the chip proliferated during the incubation . The sequential SECM measurements were performed for the same E . coli chip to obtain the microbial growth curve for a small number of microorganisms. Appl Environ Microbiol, 2004 Mar, 70(3), 1767 - 76 Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray; Jenkins BD et al.; Investigations of the distribution and diversity of nitrogen-fixing microorganisms in natural environments have often relied on PCR amplification and sequence analysis of a portion of one of the key enzymes in nitrogen fixation, dinitrogenase reductase, encoded by nifH . Recent work has suggested that DNA macroarrays provide semiquantitative fingerprints of diversity within mixtures of nifH amplicons (G . F . Steward, B . D . Jenkins, B . B . Ward, and J . P . Zehr, Appl . Environ . Microbiol . 70:1455-1465, 2004) . Here we report the application of macroarrays for a study in the Chesapeake Bay . Samples from different locations in the bay yielded distinct fingerprints . Analysis of replicates and samples from different locations by cluster analysis showed that replicates clustered together, whereas different samples formed distinct clusters . There was a correspondence between the hybridization pattern observed and that predicted from the distribution of sequence types in a corresponding clone library . Some discrepancies between the methods were observed which are likely a result of the high nifH sequence diversity in the Chesapeake Bay and the limited number of sequences represented on this version of the array . Analyses of sequences in the clone library indicate that the Chesapeake Bay harbors unique, phylogenetically diverse diazotrophs . The macroarray hybridization patterns suggest that there are spatially variable communities of diazotrophs, which have been confirmed by quantitative PCR methods (S . M . Short, B . D . Jenkins, and J . P . Zehr, Appl . Environ . Microbiol., in press) . The results show that DNA macroarrays have great potential for mapping the spatial and temporal variability of functional gene diversity in the environment. ScientificWorldJournal, 2004 Feb 26, 4, 67 - 76 Chemical speciation of thorium in marine biogenic particulate matter; Hirose K; Concentrations of particulate thorium in seawater were determined together with the strong organic ligand (SOL) and uranium in particulate matter (PM) . The concentrations of particulate Th in surface waters of the western North Pacific and the Sea of Japan ranged from 0.05 to 1.5 pM (1 x 10(-12) M), and showed relatively large temporal and spatial variations . In order to chemically characterize the particulate Th in seawater, the relationship between particulate Th and SOL concentrations in surface PM was examined . The result reveals that particulate Th in surface PM was well correlated with the SOL concentration in PM . The concentrations of particulate Th in surface water were linearly related to those of particulate U . Mass balance analysis suggests that the dominant chemical form of Th(IV), as well as of U, in surface PM is a surface complex with the SOL in PM . Our findings suggest that the SOL in PM is a nonmetal-specific chelator originating from the cell surface of microorganisms. Aquat Toxicol, 2004 Apr 14, 67(2), 143 - 54 Ecotoxicogenomics: the challenge of integrating genomics into aquatic and terrestrial ecotoxicology; Snape JR et al.; Rapid progress in the field of genomics (the study of how an individual's entire genetic make-up, the genome, translates into biological functions) is beginning to provide tools that may assist our understanding of how chemicals can impact on human and ecosystem health . In many ways, if scientific and regulatory efforts in the 20th century have sought to establish which chemicals cause damage to ecosystems, then the challenge in ecotoxicology for the 21st century is to understand the mechanisms of toxicity to different wildlife species . In the human context, 'toxicogenomics' is the study of expression of genes important in adaptive responses to toxic exposures and a reflection of the toxic processes per se . Given the parallel implications for ecological (environmental) risk assessment, we propose the term 'ecotoxicogenomics' to describe the integration of genomics (transcriptomics, proteomics and metabolomics) into ecotoxicology . Ecotoxicogenomics is defined as the study of gene and protein expression in non-target organisms that is important in responses to environmental toxicant exposures . The potential of ecotoxicogenomic tools in ecological risk assessment seems great . Many of the standardized methods used to assess potential impact of chemicals on aquatic organisms rely on measuring whole-organism responses (e.g . mortality, growth, reproduction) of generally sensitive indicator species at maintained concentrations, and deriving 'endpoints' based on these phenomena (e.g . median lethal concentrations, no observed effect concentrations, etc.) . Whilst such phenomenological approaches are useful for identifying chemicals of potential concern they provide little understanding of the mechanism of chemical toxicity . Without this understanding, it will be difficult to address some of the key challenges that currently face aquatic ecotoxicology, e.g . predicting toxicant responses across the very broad diversity of the phylogenetic groups present in aquatic ecosystems; estimating how changes at one ecological level or organisation will affect other levels (e.g . predicting population-level effects); predicting the influence of time-varying exposure on toxicant responses . Ecotoxicogenomic tools may provide us with a better mechanistic understanding of aquatic ecotoxicology . For ecotoxicogenomics to fulfil its potential, collaborative efforts are necessary through the parallel use of model microorganisms (e.g . Saccharomyces cerevisiae) together with aquatic (e.g . Danio rerio, Daphnia magna, Lemna minor and Xenopus tropicalis) and terrestrial (e.g . Arabidopsis thailiana, Caenorhabdites elegans and Eisenia foetida) plants, animals and microorganisms. J Microbiol Methods, 2004 Apr, 57(1), 65 - 8 Potential of galvanotaxis to separation and cleaning of rumen ciliates; Kisidayova S et al.; The ability of rumen ciliate protozoa to move in a unidirectional electrical field from the anode to the cathode was tested in large-volume electromigration equipment; the aim was to concentrate the microorganisms and clean them of impurities . During galvanotaxis in the freshly harvested rumen fluid and at a voltage of 10 V (I=0.8 mA), cells of Isotricha (Isotricha prostoma, Isotricha intestinalis) were the first to swim towards the cathode; 1 min later, they were followed by Dasytricha ruminantium . Entodiniomorphous ciliates (small Entodiniae as well as large species) displayed minimum movement towards the cathode . The yield of electromigration of Entodinium caudatum from the in vitro culture ranged within 2-6% when using 75-100 V (10 mA) and 60 V (5 mA) voltage, respectively . At 10 V (0.8 mA), E . caudatum did not move towards the cathode . It is shown that the behavior of Trichostomatids (Dasytricha and Isotricha) facilitates separation by means of the tested large-volume equipment . Concentration and cleaning of Entodiniomorphous ciliates using galvanotaxis in the tested equipment proved to be ineffective. Protein Expr Purif, 2004 Apr, 34(2), 223 - 8 Overexpression, purification, and biochemical characterization of GumC, an enzyme involved in the biosynthesis of exopolysaccharide by Xylella fastidiosa; de Pieri C et al.; GumC is one of nine enzymes involved in the biosynthesis of fastidian gum, an exopolysaccharide produced by Xylella fastidiosa that may be linked directly to the pathogenicity of the microorganism . GumC may be responsible for gum polymerization or secretion through the membrane of X . fastidiosa . To perform structure and functions studies, we developed an expression system for the production of GumC as a fusion protein with maltose binding protein (MBP) using pMAL-c2x vector . The GumC-MBP fusion protein was expressed as a 94 kDa protein, which strongly reacts with anti-MBP antibodies . GumC-MBP was isolated by affinity chromatography through an amylose column and used to produce antibodies against the fusion protein . After the enzymatic cleavage of MBP, GumC was purified on a Q Sepharose Fast Flow column . GumC showed a molecular weight corresponding to the expected one (52 kDa) and its N-terminal sequence was identical to that deduced from the DNA . The shape of the circular dichroism spectrum was compatible with a folded protein that contains alpha-helical regions in its structure . Therefore, in this study we describe, for the first time, the production of GumC recombinant protein. Dig Liver Dis, 2004 Feb, 36(2), 116 - 20 Helicobacter pylori and perforated peptic ulcer prevalence of the infection and role of non-steroidal anti-inflammatory drugs; Gisbert JP et al.; AIMS: To study the prevalence of Helicobacter pylori infection in patients with perforated peptic ulcer, to compare it with the prevalence in patients with uncomplicated ulcer, and to assess the role of non-steroidal anti-inflammatory drugs in this prevalence . METHODS: Consecutive patients with perforated peptic ulcer were included in this retrospective study . As a control group, patients undergoing elective outpatient evaluation for the investigation of dyspepsia during the same time period and found to have a peptic ulcer at endoscopy were included . A 13C-urea breath test was carried out in all patients to diagnose H . pylori infection . RESULTS: Sixteen patients with perforated peptic ulcer and 160 with non-complicated peptic ulcer were included . Sixty-two percent of the patients with perforated peptic ulcer were infected by H . pylori, while the microorganism was detected in 87% of the patients without this complication (P = 0.01) . Non-steroidal anti-inflammatory drugs intake was more frequent (P = 0.012) in patients with perforated peptic ulcers (56%) than in those without perforation (26%) . H . pylori prevalence in perforated peptic ulcers was of 44% in patients with non-steroidal anti-inflammatory drugs intake, but this figure increased up to 86% when only patients not taking non-steroidal anti-inflammatory drugs were considered (P = 0.09) . In the multivariate analysis, non-steroidal anti-inflammatory drugs intake was the only variable that correlated with peptic ulcer perforation {odds ratio, 3.6 (95% confidence interval, 1.3-10); P = 0.016} . CONCLUSION: The mean prevalence of H . pylori infection in patients with perforated peptic ulcer is, overall, of only about 60%, which contrasts with the 90-100% figure usually reported in non-complicated ulcer disease . However, the most important factor associated with H . pylori-negative perforated peptic ulcer is non-steroidal anti-inflammatory drugs use, and if this factor is excluded, prevalence of infection is almost 90%, similar to that found in patients with non-perforating ulcer disease. Science, 2004 Mar 5, 303(5663), 1538 - 42 Superfamilies of evolved and designed networks; Milo R et al.; Complex biological, technological, and sociological networks can be of very different sizes and connectivities, making it difficult to compare their structures . Here we present an approach to systematically study similarity in the local structure of networks, based on the significance profile (SP) of small subgraphs in the network compared to randomized networks . We find several superfamilies of previously unrelated networks with very similar SPs . One superfamily, including transcription networks of microorganisms, represents "rate-limited" information-processing networks strongly constrained by the response time of their components . A distinct superfamily includes protein signaling, developmental genetic networks, and neuronal wiring . Additional superfamilies include power grids, protein-structure networks and geometric networks, World Wide Web links and social networks, and word-adjacency networks from different languages. Science, 2004 Mar 5, 303(5663), 1522 - 6 A toll-like receptor that prevents infection by uropathogenic bacteria; Zhang D et al.; Toll-like receptors (TLRs) recognize molecular patterns displayed by microorganisms, and their subsequent activation leads to the transcription of appropriate host-defense genes . Here we report the cloning and characterization of a member of the mammalian TLR family, TLR11, that displays a distinct pattern of expression in macrophages and liver, kidney, and bladder epithelial cells . Cells expressing TLR11 fail to respond to known TLR ligands but instead respond specifically to uropathogenic bacteria . Mice lacking TLR11 are highly susceptible to infection of the kidneys by uropathogenic bacteria, indicating a potentially important role for TLR11 in preventing infection of internal organs of the urogenital system. Scand J Infect Dis, 2004, 36(1), 59 - 61 Brevundimonas bacteremia: two case reports and literature review; Chi CY et al.; Brevundimonas spp . are infrequently isolated from clinical samples, including blood . The vast majority of reported cases have underlying diseases . Whether these microorganisms represent true pathogens of human disease in all populations remains to be explored . We present 2 cases of bloodstream infection caused by Brevundimonas sp., with one of these individuals immunocompetent, and discuss the possible role of these organisms in different patient populations. Mycol Res, 2003 Dec, 107(Pt 12), 1467 - 75 The North American mushroom competitor, Trichoderma aggressivum f . aggressivum, produces antifungal compounds in mushroom compost that inhibit mycelial growth of the commercial mushroom Agaricus bisporus; Krupke OA et al.; Trichoderma harzianum is a ubiquitously distributed asexual soil fungus that produces a variety of antibiotic compounds . Colonisation of soil inhabited by competing microbiota is facilitated by the antibiotic activity of these compounds . In addition, T . harzianum produces hydrolytic enzymes that degrade the cell wall components of many microorganisms, which can then be used as a source of nutrients . Recently, biotypes of T . harzianum differing morphologically from those originally described by Rifai were isolated on commercial mushroom (Agaricus bisporus) farms . These 'aggressive' biotypes cause devastating crop loss on mushroom farms . The aggressive biotype in North America was originally known as 'Th4' but has been recently renamed Trichoderma aggressivum f . aggressivum . In contrast, 'non-aggressive' biotypes, have no noticeable effect on the crop, are similar to T . harzianum and are commonly found on mushroom farms . The mechanism of disease establishment is unknown . We have identified a metabolite produced by T . aggressivum isolates in vitro that inhibits growth of A . bisporus and other fungi . This antifungal compound is not produced by 'non-aggressive' T . harzianum isolates under the culture conditions tested and is identified as 3,4-dihydro-8-hydroxy-3-methylisocoumarin . Another compound was isolated from both liquid culture and infested compost . Although its chemical structure could not be precisely determined, this compound also inhibits A . bisporus growth, is predominant in infested compost and likely has a inhibitory effect on the mycelia present in mushroom compost, resulting in devastating crop loss. Cad Saude Publica, 2003 Nov-Dec, 19(6), 1721 - 7 Epub 2004 Mar 03. {Prevalence of Blastocystis hominis among food handlers from Caroni municipality, Bolivar State, Venezuela}; Requena I et al.; A cross-sectional survey was conducted to determine the prevalence of Blastocystis hominis infection in a random sample of apparently healthy food handlers . A total of 415 individuals attending the Manoa Urban Outpatient Clinic (Caroni Municipality, Bolivar State, Venezuela) in the Adult Hygiene Program and who requested health certification to work as food handlers were studied . Stool samples obtained by spontaneous evacuation were examined by direct microscopy and the Willis concentration method . A total of 150 individuals were infected (36.14%), 107 (25.78%) of whom with B . hominis . There was no difference between males and females (p > 0.05), but there was a significant difference between ages (chi(2) = 12.17; g.l . = 4), with infection more frequent between 18 and 27 years . In 71.02% of the cases, B . hominis was the only parasite . Giardia lamblia was the parasite most frequently associated with B . hominis (2.41%) . In the majority (85%) of infected individuals, less than five microorganisms per microscopic field were observed . We conclude that B . hominis is a frequent intestinal parasite among food handlers in Caroni Municipality, Bolivar State, Venezuela. Environ Sci Technol, 2004 Feb 15, 38(4), 1024 - 30 Hydrogen thresholds as indicators of dehalorespiration in constructed treatment wetlands; Kassenga G et al.; Anaerobic degradation of cis-1,2-dichloroethene (cis-1,2-DCE) and 1,2-dichloroethane (1,2-DCA) was studied in microcosms derived from a laboratory-scale upflow treatment wetland system used to biodegrade chlorinated compounds present in groundwater from a Superfund site . Dechlorination kinetics of cis-1,2-DCE (0.94-1.57 d(-1)) and 1,2-DCA (0.15-0.71 d(-1)) were rapid, and degradation proceeded to completion with ethene or ethane as terminal dechlorination products . Hydrogen concentrations, measured simultaneously during dechlorination, were significantly different for the two compounds, approximately 2.5 nM for cis-1,2-DCE and 38 nM for 1,2-DCA . Methanogenesis proceeded during the degradation of 1,2-DCA when H2 concentrations were high but not during the dechlorination of cis-1,2-DCE when H2 concentrations were below published thresholds for methanogenesis . A 16S rRNA gene-based approach indicates that microorganisms closely related to Dehalococcoides ethenogenes were present and that they were distributed throughout the bottom, middle, and top of the upflow treatment wetland system . These results coupled with consideration of hydrogen thresholds, degradation kinetics, daughter products, and measurements of methanogenesis strongly suggest that halorespirers were responsible for dechlorination of cis-1,2-DCE and that 1,2-DCA dechlorination was co-metabolic, likely mediated by acetogens or methanogens . Rapid dechlorination potential was distributed throughout the wetland bed, both within and below the rhizosphere, indicating that reductive dechlorination pathways can be active in anaerobic environments located in close spatial proximity to aerobic environments and plants in treatment wetland systems. Ying Yong Sheng Tai Xue Bao, 2003 Nov, 14(11), 2072 - 6 {Solubilization and behavior of surfactants in soil}; Jiang X et al.; Solubility increment of hydrophobic organic compounds(HOCs) is mainly caused by the presence of surfactant micelle . Soil is exposed to a considerable quantity of surfactants, even at low concentrations, and surfactants seem to significantly alter soil physicsal, chemical and biological characteristics, with sorption process playing a dominant role . In addition, plant, soil microoganism, and bio-degradation and removal of surfactant are affected by the type, structure and concentration of surfactant, their existence circumstance, and species of microorganisms . The translocation and transformation of pollutants in soil are altered by all the above reasons, which should be paid more attention. Ying Yong Sheng Tai Xue Bao, 2003 Nov, 14(11), 1914 - 6 {Colonization of silicate bacterium strain NBT in wheat roots}; Sheng X; The strain NBT of silicate bacterium was labelled with streptomycin, and a stable streptomycin resistance strain NBT was obtained . Its colonization dynamics and affecting factors in wheat rhizosphere were studied in agar plates and greenhouse pots were studied by counting the method with selective medium . The results of pot culture experiment showed that strain NBT could successfully colonize in the rhizosphere of wheat . In pot cultures of sterile soil, the highest colonization level (3.4 x 10(7) cfu.g-1 root soil) was reached on 9th day after seeds sown; at 54th day, the population of strain NBT tended to stable, and decreased to 1.4 x 10(4) cfu.g-1 root soil . In pot cultures of unsterile soil, the highest colonization level (3.8 x 10(7) cfu.g-1 root soil) was reached at 9th day, and the population of strain NBT tended to a stationary state at 60th day, with the numbers being 1.4 x 10(4) cfu.g-1 root soil . Some biological and abiotic factors could greatly influence the colonization of the beneficial microorganism. Otolaryngol Pol, 2003, 57(5), 627 - 32 {Evaluation of microorganisms ability to beta-lactamase production in exacerbation of chronic sinusitis treated with beta-lactam antibiotics}; Namyslowski W et al.; In our study the ability of the isolated microorganisms to produce beta-lactamase was determined . These microorganisms were isolated from sinus punctures of 115 patients before (evaluation I) and after the treatment finished (evaluation III) . During first evaluation 93 microorganisms with potential ability to beta-lactamase production were isolated . 24 of them (25.81%) produced beta-lactamase, 69 (74.19%) didn't do it . 57 patients were qualified for amixycillin with potassium clavulanate treatment (subgroup A) and 58 patients for cefuroxime axetil treatment (subgroup B) . After the treatment (evaluation III) in the group of 21 isolated microorganisms 6 produced beta-lactamase . The microorganisms producing beta-lactamase were isolated only from the patients where the amoxycillin with potassium clavulanate was administered. Eur J Immunol, 2004 Mar, 34(3), 631 - 8 Mycobacterium vaccae induces a population of pulmonary CD11c+ cells with regulatory potential in allergic mice; Adams VC et al.; The hygiene hypothesis proposes that common, harmless microorganisms, present throughout our evolutionary history, have helped to develop immunoregulatory mechanisms that prevent inappropriate immune responses by the host . Using a mouse model of allergic pulmonary inflammation, we report that treatment with an ubiquitous saprophytic mycobacterium, Mycobacterium vaccae, significantly reduces allergic inflammation by decreasing type 2 responses such as eosinophilia and IL-4 expression . Rather than observing an increase in type-1 cytokine expression, we found elevated production of IL-10 in the lungs suggesting a role for regulatory T cells . Since induction of these cells may be dependent on APC, we investigated the effects of M . vaccae treatment on pulmonary CD11c+ cells . Increased levels of IL-10, TGF-beta and IFN-alpha mRNA were detected in CD11c+ cells from M . vaccae-treated allergic mice . We propose that M . vaccae-induced CD11c+ cells have a potential regulatory role at the site of inflammation through their secretion of immunomodulatory cytokines. J Infect Chemother, 2004 Feb, 10(1), 65 - 7 Characterization of children with Mycoplasma pneumoniae infection detected by rapid polymerase chain reaction technique; Kuroki H et al.; We used a new polymerase chain reaction (PCR) system to identify the 16S rRNA gene of Mycoplasma pneumoniae and to diagnose lower respiratory tract infections caused by the microorganism . Nasopharyngeal swabs collected from 21 patients (22 episodes) tested positive for M . pneumoniae with the PCR . The age distribution of the patients was between 2 and 13 years . The diagnosis, including concomitant infection, was as follows: pneumonia (n = 11), acute bronchitis (n = 10), bronchial asthma (n = 4), and acute otitis media (n = 1) . Six patients had bacterial superinfections . Positive findings for M . pneumoniae were noted together with exacerbation of asthma symptoms, suggesting that M . pneumoniae infection may play the role of an inducer . The PCR system constructed by us will contribute to revealing the clinical features of M . pneumoniae infection, and as a result, an appropriate chemotherapeutic agent can be chosen . We propose the usefulness of this PCR system to detect the microorganism in younger children. Extremophiles, 2004 Apr, 8(2), 151 - 64 Epub 2004 Feb 27. Distribution, diversity and activity of microorganisms in the hyper-alkaline spring waters of Maqarin in Jordan; Pedersen K et al.; The hyper-alkaline, high-Ca(2+) springs of Maqarin, Jordan, were investigated as an analogue for various microbial processes at the extremely high pH generated by cement and concrete in some underground radioactive waste repositories . Leaching of metamorphic, cementitious phases in Maqarin has produced current, hyper-alkaline groundwater with a maximum pH of 12.9 . Six consecutive expeditions were undertaken to the area during 1994-2000 . The total number of microorganisms in the alkaline waters was 10(3)-10(5) cells/ml . Analysis of the 16S-ribosomal ribonucleic acid (rRNA) diversity revealed microorganisms mainly belonging to the Proteobacteria . Obvious similarities between the obtained sequences and sequences from other alkaline sites could not be found . Numerous combinations of culture media compositions were inoculated with spring, seepage and groundwaters and incubated under aerobic and anaerobic conditions with various carbon sources . Assimilation studies were performed using identical radio-labeled carbon sources . Glucose seemed to be the preferred carbon source for assimilation, followed by acetate, lactate, and leucine . The results demonstrate that microorganisms from the hyper-alkaline springs of Maqarin could grow and be metabolically active under aerobic and anaerobic hyper-alkaline conditions . However, the growth and activity found were not vigorous; instead, slow growth, low numbers, and a generally low metabolic activity were found . This suggests that microbial activity will be low during the hyper-alkaline phase of cementitious repositories. Respirology, 2004 Mar, 9(S1), S6 - S12 Causative microorganisms of hospital-acquired pneumonia and laboratory procedures for isolation and identification of causative microorganisms; Analysis of datasets showing which compounds kill which organisms: inferring two systems; Department of Psychology, Macquarie University, Sydney, NSW 2109, Australia . phutchin@psy.mq.edu.au Experiments are sometimes conducted to show which of several compounds is successful at inactivating which of several microorganisms . This paper proposes a method of analysing the datasets obtained . The example refers to 33 compounds (2,4-dihydroxythiobenzanilides) and seven microorganisms (dermatophytes) {data from Eur . J . Med . Chem . 35 (2000) 393} . The conclusion is that two systems or modes of action are needed to explain the data. FEMS Immunol Med Microbiol, 2004 Mar 8, 40(2), 155 - 62 Genotypic and phenotypic characterization of enterotoxigenic Escherichia coli (ETEC) strains isolated in Rio de Janeiro city, Brazil; Regua-Mangia AH et al.; Enterotoxigenic Escherichia coli (ETEC) strains have been implicated as important etiological agents of diarrheal disease, especially in developing countries . This group of microorganisms has been associated with a diverse range of genotypic and phenotypic markers . In the present study, 21 ETEC isolates previously defined according to the toxigenic genotypes, were characterized on the basis of O:H typing, cell adherence patterns, and colonization factors (CFs) antigens . Genetic diversity was investigated by random amplification polymorphic DNA (RAPD-PCR), pulsed-field gel electrophoresis (PFGE) and multilocus enzyme electrophoresis (MLEE) . LT-I probe-positive isolates belonged to serotypes ONT:HNT, O7:H24, O48:H21, O88:H25, O148:H28, O159:H17 and O159:H21 . ST-h probe-positive isolates belonged to serotypes O159:H17, O148:H28 and O6:H- . Serotypes O148:H28, O159:H17 and O6:H- were associated with the CS6, CFA/I and CS1 CS3 antigens, respectively . Most ETEC strains exhibited a diffuse pattern of adherence to cultured epithelial cells . In general, phenotypic and genotypic characteristics correlated well . RAPD-PCR, PFGE and MLEE showed reproducibility and good discriminatory potential . The application of molecular typing systems allowed the detection of significant diversity among the isolates, indicating a non-clonal origin and revealing intra-serotype variation overlooked by classical epidemiological approaches . The phenotypic and genotypic diversity observed lead us to recommend the use of different typing systems in order to elucidate the epidemiology of ETEC infection. Bioresour Technol, 2004 May, 93(1), 21 - 8 Effect of food waste compost on microbial population, soil enzyme activity and lettuce growth; Lee JJ et al.; The effect of food waste (FW) composted with MS (Miraculous Soil Microorganisms) was compared with commercial compost (CC) and mineral fertilizer (MF) on bacterial and fungal populations, soil enzyme activities and growth of lettuce in a greenhouse . Populations of fungi and bacteria, soil biomass, and soil enzyme activities in the rhizosphere of FW treatments significantly increased compared to control (CON), CC and MF treatments at 2, 4, and 6 weeks . The fresh weight of lettuce in FW treatments was about 2-3 times higher than that in CC at 4 and 6 week . The pH, EC, total nitrogen content, organic matter and sodium concentration in FW treatments were generally higher than those in CON, CC and MF treatments. Ying Yong Sheng Tai Xue Bao, 2003 Oct, 14(10), 1790 - 4 {Contributing factors and control strategies of pine wilt disease}; Ouyang G et al.; There are several types of pine wilt diseases with inherent inter-relations . The diseases are closely related with the complex ecological system composed of local environment, pine trees, insect vectors, and pathogenic nematodes and some other microorganisms . Sustainable pest management based on ecology is a potential approach for pine wilt disease control. Respirology, 2004 Mar, 9(1), 12 - 5 Pathogenesis of pleural infection; Hage CA et al.; The pleura responds to the presence of infecting organisms with a vigorous inflammatory response associated with an exudation of white blood cells and proteins . The development and outcome of pleural infections is a function of a balance between the virulence of the invading microorganism and the immune reaction involving professional immune cells as well as the pleural mesothelial cells . Most commonly, pleural infection occurs after invasion through the lung parenchyma and a breach in the viscera pleura resulting in the formation of a parapneumonic process . Upon infection, the microorganisms are recognized by the pleural mesothelial cell, which remains the first line of defence . Pleural responses to infection include those of innate immunity as well as adaptive or acquired immunity . Innate and acquired immune responses are closely linked . In this review, we discuss the different virulence factors that allow microorganisms to infect the pleura and the role of the pleural mesothelial cells in bridging the innate and acquired immune responses. Prog Mol Subcell Biol, 2004, 34, 47 - 72 Analogies between Drosophila and mammalian TRAF pathways; Wajant H et al.; A central event in innate immunity is the activation of the NF-kappaB signaling pathway and up-regulation of NF-kappaB-dependent defense genes . Attack of mammals as well as of insects by microorganisms leads, among other things, to the activation of receptors of the Toll-like receptor group . Various adaptor proteins involving members of the TNF receptor-associated factor (TRAF) family channel these receptor-generated signals to conserved intracellular kinase cascades that finally lead to the activation of NF-kappaB and JNK . In vertebrates, TRAF proteins link these pathways also to IL-1R-related molecules and members of the TNF receptor superfamily, which orchestrate a variety of immunoregulatory processes of the innate but also of the adaptive immune system . In this review, we will focus on the similarities but also the differences in TRAF-dependent signaling pathways of mammals and insects. J Immunol, 2004 Mar 1, 172(5), 3086 - 93 Leishmania infantum promotes replication of HIV type 1 in human lymphoid tissue cultured ex vivo by inducing secretion of the proinflammatory cytokines TNF-alpha and IL-1 alpha; Zhao C et al.; Parasitic infections such as leishmaniasis can modulate the life cycle of HIV-1 and disease progression . Coinfection with HIV-1 and Leishmania has emerged as a serious threat in countries where both pathogenic agents are widespread . Although there are numerous clinical reports illustrating the cofactor role played by Leishmania in HIV-1-infected patients, there is still no information on the contribution of Leishmania to the biology of HIV-1 in human lymphoid tissue that is considered a major in vivo site of virus production . In this study we explored the modulatory effect of Leishmania on the process of HIV-1 infection using ex vivo cultured human tonsillar tissue . We found that the protozoan parasite Leishmania enhances both HIV-1 transcription and virus production after infection of human tonsillar tissue infected ex vivo with viral strains bearing various coreceptor usage profiles . Studies conducted with pentoxifylline and neutralizing Abs revealed that the Leishmania-mediated increase in HIV-1 production was linked to a higher production of TNF-alpha and IL-1alpha . Our findings help to unravel the molecular mechanism(s) through which the two microorganisms interact and provide information that may be useful for the design of more effective therapeutic strategies aimed at controlling disease progression in persons dually infected with HIV-1 and LEISHMANIA: This work also indicates that histocultures of human lymphoid tissue infected by both pathogens represent an ideal experimental cell system to dissect interactions occurring between HIV-1 and an opportunist pathogen in a human microenvironment that approximates conditions prevailing under physiological situations. J Exp Biol, 2004 Mar, 207(Pt 7), 1203 - 16 Measurement of cell velocity distributions in populations of motile algae; Vladimirov VA et al.; The self-propulsion of unicellular algae in still ambient fluid is studied using a previously reported laser-based tracking method, supplemented by new tracking software . A few hundred swimming cells are observed simultaneously and the average parameters of the cells' motility are calculated . The time-dependent, two-dimensional distribution of swimming velocities is measured and the three-dimensional distribution is recovered by assuming horizontal isotropy . The mean and variance of the cell turning angle are quantified, to estimate the reorientation time and rotational diffusivity of the bottom-heavy cell . The cells' phototactic and photokinetic responses to the laser light are evaluated . The results are generally consistent both with earlier assumptions about the nature of cell swimming and quantitative measurements, appropriately adjusted . The laser-based tracking method, which makes it possible to average over a large number of motile objects, is shown to be a powerful tool for the study of microorganism motility. Int Immunol, 2004 Mar, 16(3), 509 - 16 Toll-like receptor 4 plays a protective role in pulmonary tuberculosis in mice; Branger J et al.; Toll-like receptors (TLR) play an essential role in the innate recognition of microorganisms by the host . To determine the role of TLR4 in host defense against lung tuberculosis, TLR4 mutant (C3H/HeJ) and wild-type (C3H/HeN) mice were intranasally infected with live Mycobacterium tuberculosis . TLR4 mutant mice were more susceptible to pulmonary tuberculosis, as indicated by a reduced survival and an enhanced mycobacterial outgrowth . Lung infiltrates were more profound in TLR4 mutant mice and contained more activated T cells . Splenocytes of infected TLR4 mutant mice demonstrated a reduced capacity to produce the protective type 1 cytokine IFN-gamma upon antigen-specific stimulation, indicating that TLR4 may be involved in the generation of acquired T cell-mediated immunity . These data suggest that TLR4 plays a protective role in host defense against lung infection by M . tuberculosis. Front Biosci, 2004 May 01, 9, 1803 - 16 Molecular analysis of "de novo" purine biosynthesis in solanaceous species and in Arabidopsis thaliana; van der Graaff E et al.; Purine nucleotides are essential components to sustain plant growth and development . In plants they are either synthesized "de novo" during the process of purine biosynthesis or are recycled from purine bases and purine nucleosides throughout the salvage pathway . Comparison between animals, microorganisms and Arabidopsis, the first plant species with a completely sequenced genome, shows that plants principally use the same biochemical steps to synthesize purine nucleotides and possess all the essential genes and enzymes . Here we report on the cloning and molecular analysis of the complete purine biosynthesis pathway in plants, and the in planta functional analysis of PRPP (5-phosphoribosyl-1-pyrophoshate) amidotransferase (ATase), catalyzing the first committed step of the "de novo" purine biosynthesis . The cloning of the genes involved in the purine biosynthesis pathway was attained by a screening strategy with heterologous cDNA probes and by using S . cerevisiae mutants for complementation . Southern hybridization showed a complex genomic organization for these genes in solanaceous species and their organ- and developmental specific expression was analyzed by Northern hybridization . The specific role of ATase for plant growth and development was analyzed in transgenic tobacco plants exhibiting a reduced ATase activity and in an Arabidopsis T-DNA mutant (atd2) deficient for ATase2 . The transgenic tobacco plants as well as the Arabidopsis mutant exhibit a specific and comparable phenotype, which is characterized by strong growth retardation and severe chlorosis in leaves . The formation of white leaves, but green cotyledons is a characteristic trait of the Arabidopsis atd2 mutant. Front Biosci, 2004 May 01, 9, 1348 - 59 Catabolism of caffeine in plants and microorganisms; Mazzafera P; Caffeine has been found in tissues of several plants . Because of its stimulating effect on the central nervous system, a great number of reports have been published on its content in beverages and foodstuffs . However, a much more restricted number of reports have dealt specifically with caffeine metabolism in plants . This review presents, in chronological manner, the contribution of these reports to the vast knowledge accumulated on caffeine catabolism in plants and microorganisms over the last 40 years . In plants, the accumulated data indicate the operation of a main catabolic pathway: caffeine --> theophylline --> 3-methylxantine --> xanthine --> uric acid --> allantoin --> allantoic acid --> glyoxylic acid + urea --> NH3 + CO2 . Some studies have shown that, depending on the plant species, other minor routes may operate with the formation of theobromine and 7-methylxantine, which are salvaged for caffeine formation since they also appear in the biosynthetic pathway . A specific group of coffee known as liberio-excelsioides has the ability to convert caffeine to the corresponding methyluric acid, which is methylated to other uric acid derivatives . In bacteria caffeine is either degraded to theobromine or paraxanthine . Both dimethylxanthines are demethylated to 7-methylxantine which in turn is demethylated to xanthine and then enters the catabolic pathway of purines . In bacteria, theobromine, paraxanthine and 7-methylxantine may also be oxidized to their corresponding methyluric acids. Biometals, 2004 Feb, 17(1), 79 - 86 The respiratory inhibitor antimycin A specifically binds Fe(III) ions and mediates utilization of iron by the halotolerant alga Dunaliella salina (Chlorophyta); Pick U; It is demonstrated that Antimycin A (AA), a respiratory inhibitor produced by Streptomyces bacteria, forms lipophylic complexes with Fe(III) ions . Spectroscopic titration indicates that Fe(III) ions interact with 2AA molecules . At growth-limiting Fe concentrations, AA mediates Fe uptake and promotes growth and chlorophyll synthesis better than other Fe chelators in the halotolerant alga Dunaliella salina . It is proposed that AA enhances Fe bioavailability in hypersaline solutions by formation of lipophylic Fe-AA complexes which are taken-up and utilized by the algae . The results suggest that the respiratory inhibitor AA can affect Fe metabolism in microorganisms. Environ Technol, 2003 Dec, 24(12), 1569 - 76 A novel control process of cyanobacterial bloom using cyanobacteriolytic bacteria immobilized in floating biodegradable plastic carriers; Nakamura N et al.; A process using a floating carrier for immobilization of cyanobacteriolytic bacteria, B.cereus N-14, was proposed to realize an effective in situ control of natural floating cyanobacterial blooms . The critical concentrations of the cyanobacteriolytic substance and B.cereus N-14 cells required to exhibit cyanobacteriolytic activity were investigated . The results indicated the necessity of cell growth to produce sufficiently high amounts of the cyanobacteriolytic substance to exhibit its activity and also for conditions enabling good contact between high concentrations of the cyanobacteriolytic substance and cyanobacteria . Floating biodegradable plastics made of starch were applied as a carrier material to maintain close contact between the immobilized cyanobacteriolytic bacteria and floating cyanobacteria . The floating starch-carriers could eliminate 99% of floating cyanobacteria in 4 d . Since B.cereus N-14 could produce the cyanobacteriolytic substance under the presence of starch and some amino acids, the cyanobacteriolytic activity could be attributed to carbon source fed from starch carrier and amino acids eluted from lysed cyanobacteria . Therefore, the effect of using a floating starch-carrier was confirmed from both view points as a carrier for immobilization and a nutrient source to stimulate cyanobacteriolytic activity . The new concept to apply a floating carrier immobilizing useful microorganisms for intensive treatment of a nuisance floating target was demonstrated. Folia Microbiol (Praha), 2003, 48(5), 573 - 9 Spore-specific modification of DNA-dependent RNA polymerase alpha subunit in streptomycetes--a new model of transcription regulation; Najmanova L et al.; At the very beginning of spore germination in streptomycetes the full-length alpha subunit of DNA-dependent RNA polymerase is shortened from its C-terminus . The C-terminal domain of the protein is required for binding of DNA and transcription regulators but its regulatory role in streptomycetes was not extensively studied . Comparison of the sequences of E . coli and S . coelicolor RNA polymerase alpha subunit (RNAP alpha) C-terminal domains reveals that the majority of amino acid residues responsible for the interaction with transcription regulators is conserved in both microorganisms . The spore specific modification of streptomycete RNAP alpha could thus have its regulatory role . The nature of the proteolytic enzyme, responsible for the RNAP alpha cleavage is discussed. FEMS Microbiol Rev, 2004 Feb, 28(1), 113 - 26 Ecological role of energy taxis in microorganisms; Alexandre G et al.; Motile microorganisms rapidly respond to changes in various physico-chemical gradients by directing their motility to more favorable surroundings . Energy generation is one of the most important parameters for the survival of microorganisms in their environment . Therefore it is not surprising that microorganisms are able to monitor changes in the cellular energy generating processes . The signal for this behavioral response, which is called energy taxis, originates within the electron transport system . By coupling energy metabolism and behavior, energy taxis is fine-tuned to the environment a cell finds itself in and allows efficient adaptation to changing conditions that affect cellular energy levels . Thus, energy taxis provides cells with a versatile sensory system that enables them to navigate to niches where energy generation is optimized . This behavior is likely to govern vertical species stratification and the active migration of motile cells in response to shifting gradients of electron donors and/or acceptors which are observed within microbial mats, sediments and soil pores . Energy taxis has been characterized in several species and might be widespread in the microbial world . Genome sequencing revealed that many microorganisms from aquatic and soil environments possess large numbers of chemoreceptors and are likely to be capable of energy taxis . In contrast, species that have a fewer number of chemoreceptors are often found in specific, confined environments, where relatively constant environmental conditions are expected . Future studies focusing on characterizing behavioral responses in species that are adapted to diverse environmental conditions should unravel the molecular mechanisms underlying sensory behavior in general and energy taxis in particular . Such knowledge is critical to a better understanding of the ecological role of energy taxis. Salud Publica Mex, 2003 Nov-Dec, 45(6), 497 - 505 {Physico-chemical signals involved in host localization and in the induction of mosquito bites}; Torres-Estrada JL et al.; Disease vector female mosquitoes respond to physic-chemical signals to localize vertebrate hosts for blood meals . Zoophylic mosquitoes preferentially respond to CO2 and octenol released in the breath and bodily fluids, while anthropophylic mosquitoes respond to lactic acid and a variety of sweat compounds . These compounds are modified by saprophytic microorganisms in the skin sebaceous glands . Other factors present in human dwellings contribute to the integration of microsystems with characteristic odors that have different attraction for mosquitoes, explaining the focalization of malaria transmission in few households in endemic areas . The identification of the chemical attractants and their molecular receptors could be used to complement new methods to attract mosquitoes to traps during epidemiological surveys, to increase their contact with insecticides in control interventions, and for genetic manipulation to divert mosquito bites towards other animal populations . The English version of this paper is available at:http://www.insp.mx/salud/index.html. Salud Publica Mex, 2003, 45 Supp 5, S698 - 708 Advances in diagnostic tests for bacterial STDs; Morse SA; Because of their asymptomatic nature and nonspecific symptoms, laboratory tests are often required to diagnose a sexually transmitted infection . Over the past few years, there have been advances in technology, such as the development of nucleic acid amplification assays, which have improved our ability to diagnose infections caused by Chlamydia trachomatis . The finding that nucleic acid amplification tests can detect more infected individuals and are useful in screening low prevalence populations, has led to the development of strategies designed to reduce the cost of these assays without significantly impacting their sensitivity . The development of new tests for the diagnosis of syphilis has gained momentum from the report of a synthetic VDRL antigen, which will result in better nontreponemal antibody tests for syphilis . In spite of the completion of the genome sequence of Treponema pallidum and its annotation, we are still unable to cultivate this microorganism in vitro . However, the molecular revolution has resulted in the development of PCR assays for detecting Treponema pallidum in various types of clinical specimens, and to the production of recombinant antigens for use in tests that detect treponemal-specific antibodies . Further research will improve the availability of low cost, sensitive tests for the diagnosis of sexually transmitted infections . The English version of this paper is available too at:http://www.insp.mx/salud/index.html. Salud Publica Mex, 2003, 45 Supp 5, S672 - 80 {Risk factors and reproductive sequelae associated with Chlamydia trachomatis infection in infertile women}; Guerra-Infante F et al.; OBJECTIVE: To assess the clinical and sexual lifestyle characteristics associated with Chlamydia trachomatis infection among women diagnosed with infertility . MATERIAL AND METHODS: Study subjects were women with an infertility diagnosis attending the infertility clinic at the National Institute of Perinatology . Endocervical specimens from 309 women were examined for Chlamydia trachomatis using the direct immunofluorescence method . Vaginal culture samples were taken before initiating treatment . The presence of other sexually-transmitted infections was also assessed . Demographic, sexual behavioral, historical, and clinical data were collected for each subject . RESULTS: Seventy-seven women (24.9%) were infected with C trachomatis . Of these women, 70 (90.9%) had only one sexual partner, 58 (75.3%) were married, and 19 (24.7%) were single or had a common-law sex partner . Intrauterine device (IUD) was the main contraceptive method used in 15 women (19.5%) . A coinfection with other sexually-transmitted microorganisms was detected in 41 of these patients (53.2%) . Nineteen (24.7%) women had undergone tubal ligation . Among women with C trachomatis infection, reproductive sequelae were found: 24 (31.2%) women had had abortions and 50 (64.9%) had had a miscarriage . In 26 women cervical abnormalities were detected (33.8%); 50 (64.9%) had purulent vaginal discharge and 14 (18.1%) had pelvic pain . Bivariate analysis revealed that the risk factors for C trachomatis infection in women with infertility were: having a sex partner (OR = 2.96, 95% CI 1.22-7.5, p = 0.008), common-law union (OR = 3.68, p = 0.03), and IUD use (OR = 2.42, p = 0.01) . CONCLUSIONS: A consistent relationship between C trachomatis infection and infertility was found . Infection with C trachomatis in women with infertility was associated with having one single sexual partner, marital status, and IUD use . The presence of ectropion and friability of the cervix may signal C trachomatis infection . Identification and presumptive therapy should be evaluated as measures to prevent and control C trachomatis infection in patients at risk . The English version of this paper is available at:http://www.insp.mx/salud/index.html. Salud Publica Mex, 2003, 45 Supp 5, S617 - 23 {Prevalence and factors associated with syphilis and genital herpes in 2 groups of the female population}; Zamilpa-Mejia LG et al.; OBJECTIVE: To assess the frequency of HSV-2 and Treponema pallidum markers and their relationship with characteristics of women during gynecological outpatient visits . MATERIAL AND METHODS: In 1994 and 1995, two populations of 388 and 448 women were studied in two hospitals; one in Cuernavaca, Morelos, Mexico, and the other in Mexico City . Participants provided a blood specimen for detection of antibodies against HSV-2 and T pallidum using the Western blot technique and the VDRL and FTA-ABS tests . Also, participants answered a questionnaire on their sociodemographic characteristics and sexual behavior . The data were analyzed with the SPSS and EGRET statistical packages . RESULTS: The frequencies of HSV-2 antibodies were 28.3% in women from the first hospital, and 18.1% for those in the second . The frequencies of T pallidum antibodies were 2.3% and 1.1%, respectively . Age, marital status, education level, and number of sexual partners were associated with HSV-2 infection . CONCLUSIONS: Low frequencies were found for infection by the microorganisms studied in both groups . HSV-2 infection was associated to exposure periods, sexual behavior, and socioeconomic level . The English version of this paper is available at:http://www.insp.mx/salud/index.html. J Environ Sci (China), 2004, 16(1), 108 - 12 ORC-GAC-Fe0 system for the remediation of trichloroethylene and monochlorobenzene contaminated aquifer: 1 . Adsorption and degradation; Lin Q et al.; Activities at a former Chemistry Triangle in Bitterfeld, Germany, resulted in contamination of groundwater with a mixture of trichloroethylene(TCE) and monochlorobenzene(MCB) . The objective of this study was to develop a barrier system, which includes an ORC(oxygen release compounds) and GAC(granular activated carbon) layer for adsorption of MCB and bioregeneration of GAC, a Fe0 layer for chemical reductive dechlorination of TCE and other chlorinated hydrocarbon in situ . A laboratory-scale column experiment was conducted to evaluate