Methods Cell Sci, 2001, 23(4), 175 - 84 Comparing qualitative and quantitative spectroscopic techniques for the detection of the effect of direct iron loading of mammalian cell cultures; Traore HN et al.; Iron overload augments diseases of the liver and microorganism infection as well as deregulates the immune system . In vitro analysis of the effects of iron loading and its chelation involves determining the amount of iron constituting overload, which metal sources and cell lines to use and reliable assay methods . The uptake of 500 microM FeSO4 or FeEDTA by CEMss, U937 or leukocytes was confirmed by inductively coupled plasma-atomic emission spectroscopy (ICP-AES) . Excess iron increased CEMss viability (assessed by MTT, XTT, Trypan- and Alamar Blue) by an average of 18% (P = 0.034) . Flow cytometry indicated dye-viable cells to be undergoing apotosis/necrosis while still confirming an increase (9%, P < 0.001) in excess iron-induced viability . The iron chelator desferioxamine (DFO) when added in addition to Fe, reversed the effects of excess iron (and vice versa) and had detrimental effects when used on its own (33% inhibition of viability as measured by dyes and 10.85%; P = 0.0427 assessed by flow cytometry) . The 4 dyes demonstrated different levels of sensitivity in detecting the influence of iron or DFO but gave a related, qualitative picture while flow cytometry and ICP-AES data was more quantitative. J Bacteriol, 2003 Jan, 185(1), 285 - 94 Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea; Zhulin IB et al.; Transmembrane receptors in microorganisms, such as sensory histidine kinases and methyl-accepting chemotaxis proteins, are molecular devices for monitoring environmental changes . We report here that sensory domain sharing is widespread among different classes of transmembrane receptors . We have identified two novel conserved extracellular sensory domains, named CHASE2 and CHASE3, that are found in at least four classes of transmembrane receptors: histidine kinases, adenylate cyclases, predicted diguanylate cyclases, and either serine/threonine protein kinases (CHASE2) or methyl-accepting chemotaxis proteins (CHASE3) . Three other extracellular sensory domains were shared by at least two different classes of transmembrane receptors: histidine kinases and either diguanylate cyclases, adenylate cyclases, or phosphodiesterases . These observations suggest that microorganisms use similar conserved domains to sense similar environmental signals and transmit this information via different signal transduction pathways to different regulatory circuits: transcriptional regulation (histidine kinases), chemotaxis (methyl-accepting proteins), catabolite repression (adenylate cyclases), and modulation of enzyme activity (diguanylate cyclases and phosphodiesterases) . The variety of signaling pathways using the CHASE-type domains indicates that these domains sense some critically important extracellular signals. Ecotoxicol Environ Saf, 2002 Nov, 53(3), 416 - 21 INT-dehydrogenase activity test for assessing anaerobic biodegradability of organic compounds; Hongwei Y et al.; This study assessed anaerobic biodegradability of organic compounds from microorganism activity . Dehydrogenase activity can be a good parameter characterizing the microorganism activity . A modified method of 2-(p-iodophenyl-3-(p-nitrophenyl)-5-pheny tetrazolium chloride-dehydrogenase activity determination was proposed in anaerobic biodegradability assessment . Cubic spline curves were adopted to link the data points . This curve was integrated twice to calculate areas . The microorganism activity index in anaerobic biodegradability assessment was calculated by standardizing the integral . According to the results of the activity index, 14 kinds of organic compounds were classified into readily, partially, and poorly biodegradable under anaerobic conditions, respectively . As a result, some conclusions for anaerobic biodegradability of organic compounds were reached, based on the activity index value. Pediatr Allergy Immunol, 2002 Dec, 13(6), 438 - 42 Immunoglobulin G antibodies of children exposed to microorganisms in a water-damaged school; Savilahti R et al.; The aim of this study was to determine whether exposure to fungi (molds and yeasts) among children attending a water-damaged school was reflected by the children's immunoglobulin G (IgG) response to microorganisms typical of water damage and whether the presence of these IgG antibodies was associated with respiratory symptoms and morbidity . The relationships between positive IgG antibodies and atopy, described as elevated allergen-specific immunoglobulin E (IgE) antibodies, were also examined . The study population consisted of a randomly selected group of exposed children attending a water-damaged school and a group of unexposed children of the same age . Serum samples for analyses of IgG and IgE antibodies were drawn from the children . The respiratory morbidity, the number of positive IgG antibodies to nine microorganisms indicating water damage, and IgE sensitization to common environmental allergens (Phadiatop) were studied . The mean number of positive IgG findings was significantly higher among the exposed children . The number of positive IgG antibodies did not correlate with respiratory illnesses or symptoms at the individual level even though the exposed children who had positive IgG antibodies to four or more microorganisms in the total group comparison tended to have higher respiratory morbidity . In the exposed group, a negative correlation was found between the number of positive IgG antibodies and the total value of allergen-specific IgE antibodies . As among adults exposed to microorganisms at work, IgG antibodies in children seem to be a relevant indicator of exposure to microorganisms in a water-damaged school on the group level. Helicobacter, 2002 Dec, 7(6), 378 - 83 A group-specific PCR assay for the detection of Helicobacteraceae in human gut; Bohr UR et al.; BACKGROUND: Enterohepatic Helicobacter species are emerging pathogens, which are increasingly isolated from humans with enteric diseases . Nevertheless, current methods to detect Helicobacteraceae in the human gut have significant limitations . METHODS: Based on 16S-rRNA gene alignments and computer aided primer analysis a set of group-specific PCR primers was designed . The evaluation of the PCR assay was performed using 36 ATCC reference strains and intestinal biopsies from 10 patients with defined gastric Helicobacter pylori status . The amplification products derived from clinical samples were cloned and subsequently analyzed by DNA sequencing . Sensitivity of the PCR-assay was determined by spiking previously negative tested samples with decreasing amounts of Helicobacter DNA . RESULTS: The analysis of the ATCC reference strains revealed amplification products in all 14 Helicobacter strains and Wolinella succinogenes, 21 other microorganisms representing negative controls did not produce PCR fragments . Four out of the 10 patient-derived samples were positive . Three of them represented H . pylori-derived DNA confirming the gastric H . pylori infection in these patients . In the fourth patient, who was suffering from Crohn's disease, H . pullorum was identified . The sensitivity of the PCR assay was 0.1 pg of Helicobacter-derived DNA representing about 40 bacteria . CONCLUSION: The novel PCR assay described here is an important new tool in rapid and sensitive assessment for the presence of Helicobacteraceae in human gut. J Gen Appl Microbiol, 2000 Dec, 46(6), 283 - 296 Biochemical and genetic bases of microbial degradation of polychlorinated biphenyls (PCBs); Furukawa K; The microbial degradation of polychlorinated biphenyls (PCBs) has been extensively conducted by many workers, and the following general results have been obtained . (1) PCBs are degraded oxidatively by aerobic bacteria and other microorganisms such as white rot fungi . PCBs are also reductively dehalogenated by anaerobic microbial consortia . (2) The biodegradability of PCBs is highly dependent on chlorine substitution, i.e., number and position of chlorine . The degradation and dehalogenation capabilities are also highly strain dependent . (3) Biphenyl-utilizing bacteria can cometabolize many PCB congeners to chlorobenzoates by biphenl-catabolic enzymes . (4) Enzymes involved in the PCB degradation were purified and characterized . Biphenyl dioxygenase, ring-cleavage dioxygenase, and hydrolase are crystallized, and two ring-cleavage dioxygenases are being solved by x-ray crystallography . (5) The bph gene clusters responsible for PCB degradation are cloned from a variety of bacterial strains . The structure and function are analyzed with respect to the evolutionary relationship . (6) The molecular engineering of biphenyl dioxygenases is successfully performed by DNA shuffling, domain exchange, and subunit exchange . The evolved enzymes exhibit wide and enhanced degradation capacities for PCBs and other aromatic compounds. Proc Natl Acad Sci U S A, 2002 Dec 24, 99(26), 17037 - 42 Epub 2002 Dec 13. Discovery of sulfated metabolites in mycobacteria with a genetic and mass spectrometric approach; Mougous JD et al.; The study of the metabolome presents numerous challenges, first among them being the cataloging of its constituents . A step in this direction will be the development of tools to identify metabolites that share common structural features . The importance of sulfated molecules in cell-cell communication motivated us to develop a rapid two-step method for identifying these metabolites in microorganisms, particularly in pathogenic mycobacteria . Sulfurcontaining molecules were initially identified by mass spectral analysis of cell extracts from bacteria labeled metabolically with a stable sulfur isotope (34SO 4 2-) . To differentiate sulfated from reduced-sulfur-containing molecules, we employed a mutant lacking the reductive branch of the sulfate assimilation pathway . In these sulfur auxotrophs, heavy sulfate is channeled exclusively into sulfated metabolites . The method was applied to the discovery of several new sulfated molecules in Mycobacterium tuberculosis and Mycobacterium smegmatis . Because a sulfur auxotrophic strain is the only requirement of the approach, many microorganisms can be studied in this manner . Such genetic engineering in combination with stable isotopic labeling can be applied to various metabolic pathways and their products. J Pharmacol Toxicol Methods, 2001 Sep-Oct, 46(2), 93 - 101 Permeability measurement of macromolecules and assessment of mucosal antigen sampling using in vitro converted M cells; Liang E et al.; INTRODUCTION: M cells are located in the epithelial layer covering the gut-associated lymphoid tissue and are responsible for delivery of macromolecules and microorganisms to the underlying lymphoid cells . It has been shown that the human colonic cell line Caco-2 can be converted to M cells in vitro following coculture with isolated lymphocytes from murine Peyer's patches . Studies were undertaken to evaluate and characterize the transepithelial transport of select macromolecules across these in vitro derived M cells . METHODS: Caco-2 cells were converted to M cells as reported previously . The morphology of Caco-2 cells and M cells was compared by transmission electron microscopy (TEM) . The transport properties of macromolecules such as horseradish peroxidase, FITC-conjugated polystyrene beads, and radiolabeled dextrans were examined . The activation of murine antigen-specific T cells following transport of the antigen ovalbumin across the M-cell barrier was assessed by measuring cytokine production . RESULTS: M cells were shown to be irregular in shape and have fewer and shorter microvilli compared to the Caco-2 cell progenitors . These cells were still able to form tight junctions and monolayers on polycarbonate membranes . Time-course studies demonstrated that the transport of polystyrene beads and large-molecular-weight dextrans at physiological temperature across M-cell-containing monolayers was size dependent and more rapid than across Caco-2 cell monolayers . The transport of dextrans was also shown to be temperature and concentration dependent . Befitting the role of the M cell in mucosal defense, protein antigen could be delivered by these cells in order to be processed and presented to antigen-specific CD4+ T lymphocytes . DISCUSSION: The M-cell permeability model is a functional and practical system for evaluating the transport properties of macromolecules and assessing the potential for intestinal mucosal antigen sampling to elicit immunological responses. Symp Ser Soc Appl Microbiol, 2002, (31), 72S - 77S Products containing biocides: perceptions and realities; Favero MS; The mechanisms of action for chemical germicides and antibiotics for inactivating microorganisms are significantly different and methods for determining resistance by microorganisms to these agents are also different . Chemical germicides usually have multiple targets and the mechanisms for inactivation and resistance are not measured in absolute terms but rather in the rapidity with which they reduce levels of microorganisms . The term tolerance is much more suited for germicides than the term resistance . The mechanism of resistance to chemical germicides is often dependent on the concentration of the germicide . At high concentrations multiple cellular and metabolic targets are involved, and at low concentrations fewer cellular targets . In contrast antibiotics usually have a singular cellular or metabolic target and resistance implies the ability of the microorganism to grow in the presence of the antibiotic, and in a clinical sense, to initiate or continue infection in the presence of the antibiotic . When methods used to assess resistance to antibiotics are applied to chemical germicides, inappropriate interpretations can be made regarding the ability of microorganisms to develop resistance to antibiotics as a result of developing resistance to chemical germicides . The use of chemical germicides in health-care institutions and especially the home setting has increased in recent years . Although there may be an overuse of germicides in these settings the consequence is a cost issue and not one that involves the development of antibiotic resistant microorganisms. Boll Chim Farm, 2002 Sep-Oct, 141(5), 367 - 71 Comparative study between culture media employed in sterility test; Bugno A et al.; The sterility test aims at the contact of a product with a culture medium, as a way of detecting the possible presence of viable microorganisms in products which have been submitted to a sterilization process and/or to aseptic processing . Since the official introduction of the methodology, in 1932, several culture media have been proposed and adopted, in a constant attempt to offer conditions which support the growth of as many contaminants as possible . This work aimed at a comparative evaluation of the efficiency of microbial contaminants detection in the different types of culture media employed in sterility tests . The study led to the conclusion that the culture media recommended by the pharmacopoeia compendia, soybean casein digest and fluid thioglycollate, present the best results in microorganisms detection . Besides, the microbial strains, as well as microbial suspension density, recommended by the main pharmacopoeias to verify culture media growth promoting capacity, have also proved suitable for use. Electrophoresis, 2002 Nov, 23(22-23), 3847 - 57 Recent advances in capillary isoelectric focusing: 1997-2001; Shimura K; The methodological developments in the field of capillary isoelectric focusing (CIEF) published between 1997-2001 are reviewed as a continuation of the previous review by Rodriguez-Diaz et al . (Electrophoresis 1997, 18, 2134-2144) . The applications are summarized and the progress in CIEF technologies, including experimental setup with coated and uncoated capillaries, remedies for the presence of salts in samples, additives to reduce precipitation of samples during the focusing process, calibration of the pH gradients, issues of reproducibility, carrier ampholyte-free CIEF, and a computer simulation of focusing process are discussed . Developments of IEF separations in fabricated microchannels and the advances in detection schemes, i.e., imaging, fluorescence and chemiluminescence, are summarized . The progress in micropreparation was noted, and the massive works for two-dimensional separations are described for the coupling with size-exclusion chromatography and mass spectrometry, in which the developments aimed at proteomics are discussed separately . The applications for the detection of noncovalent complexes and the separations of microorganisms are reviewed. Plant Physiol, 2002 Dec, 130(4), 2177 - 87 The elicitor cryptogein blocks glucose transport in tobacco cells; Bourque S et al.; Cryptogein is a 10-kD protein secreted by the oomycete Phytophthora cryptogea that induces a hypersensitive response on tobacco (Nicotiana tabacum var . Xanthi) plants and a systemic acquired resistance against various pathogens . The mode of action of this elicitor has been studied using tobacco cell suspensions . Our previous data indicated that within minutes, cryptogein signaling involves various events including changes in ion fluxes, protein phosphorylation, sugar metabolism, and, eventually, cell death . These results suggested that transport of sugars could be affected and, thus, involved in the complex relationships between plant and microorganisms via elicitors . This led us to investigate the effects of cryptogein on glucose (Glc) uptake and mitochondrial activity in tobacco cells . Cryptogein induces an immediate inhibition of Glc uptake, which is not attributable to plasma membrane (PM) depolarization . Conversely, cryptogein-induced valine uptake is because of PM depolarization . Inhibition of the PM Glc transporter(s) was shown to be mediated by a calcium-dependent phosphorylation process, and is independent of active oxygen species production . This inhibition was associated with a strong decrease in O(2) uptake rate by cells and a large mitochondrial membrane depolarization . Thus, inhibition of Glc uptake accompanied by inhibition of phosphorylative oxidation may participate in hypersensitive cell death . These results are discussed in the context of competition between plants and microorganisms for apoplastic sugars. FEMS Microbiol Lett, 2002 Dec 17, 217(2), 213 - 7 Models of 2,4,6-trinitrotoluene (TNT) initial conversion by yeasts; Zaripov SA et al.; The original models of the initial steps of 2,4,6-trinitrotoluene (TNT) conversion by yeasts are presented . Saccharomyces sp . ZS-A1 reduced nitro groups of TNT producing isomeric monohydroxylaminodinitrotoluenes (HADNT) as the key initial metabolites (molar ratio HADNT/TNT was up to 0.81), whereas aminodinitrotoluenes (ADNT) and the hydride-Meisenheimer complex of TNT (H-TNT) were the minor products . Conversely, Candida sp . AN-L13 transformed TNT almost quantitatively into H-TNT, thus realizing the alternative attack, consisting of the TNT aromatic ring reduction . The third type of conversion, revealed in Candida sp . AN-L14, is the combination of both above mechanisms and produces an equimolar mix of HADNT and H-TNT . In the toxicity tests with Paramecium caudatum, the supernatant of Saccharomyces sp . ZS-A1, which converts TNT into HADNT, was most toxic while the supernatant of Candida sp . AN-L13 (TNT --> H-TNT) was least toxic . The microorganisms converting TNT quantitatively to the reactive metabolites can be useful for their immobilization through the detoxifying interaction with the soil components such as humic compounds . Scand J Infect Dis, 2002, 34(10), 772 - 4 Severe Legionella pneumophila pneumonia in a patient with iron overload; Vikram HR et al.; Iron plays a crucial role in the energy metabolism of microorganisms . Humans have developed iron-withholding mechanisms as a form of non-specific immunity . We describe a patient with iron overload and severe Legionella pneumophila pneumonia . This report emphasizes the importance of early consideration of and appropriate therapy against Legionella for patients with iron overload who present with community-acquired pneumonia. Curr Drug Targets Immune Endocr Metabol Disord, 2001 Nov, 1(3), 199 - 208 Helicobacter pylori infection, immune response and vaccination; Lembo A et al.; It is well known that abnormal immune responses may play a pathogenic role in the H . pylori-related gastropathy . Indeed, as far as humoral immune response is concerned, it is still debated whether specific anti-H . pylori antibodies have a protective or noxious effect in infected hosts . Besides proinflammatory cytokines released from macrophages, such as tumor-necrosis factor-a and interleukin-1beta, and IFN-gamma derived from T-helper 1 lymphocytes, also interleukin-10, a product of T-helper 2 lymphocytes with antiinflammatory properties, seems to be surprisingly involved in the pathogenesis of H . pylori-induced gastritis . In addition, lipopolysaccharide derived from the outher membrane of H . pylori acts as a chemoattractant for monocytes and induces release of free radicals, interleukin-1beta, interleukin-6, interleukin-8 and tumor necrosis factor-alpha . On the other hand, H . pylori lipopolysaccharide could be responsible for the increased polyamine concentrations in the gastric mucosa and polyamines, such as putrescine, spermidine and spermine, could be involved in the increased cell proliferation and consequent possible neoplastic transformation of the gastric mucosa . Incubation of peripheral blood mononuclear cells with H . pylori increases significantly the surface expression of CD95 receptor (Fas), thus suggesting that these bacteria are able to induce apoptosis . In animal models, different types of vaccination have been investigated, including stimulation of nasal and rectal lymphoid tissue, as well as adoptive transfer of T cell from donors immunized with H . pylori . However, results obtained are frequently disappointing . In humans, urease of H . pylori was safely used as oral vaccine in the absence or presence of adjuvants with encouraging results . Finally, DNA vaccines could offer in the future advantages for prophylactic H . pylori eradication, especially where population is infected by this microorganism since childhood. Gig Sanit, 2002 Sep-Oct, (5), 27 - 8 {Sanitary-toxicological assessment of petroleum slimers undergone biological purification}; Tsinberg MB et al.; Pilot production and production studies using a biological method for treating and neutralizing toxic waste polluted with petroleum products at high concentrations (up to 30%) were conducted . The results have indicated that the use of oil degrading microorganisms is highly promising . Within the first vegetative period as high as 80% of petroleum products withdrew from waste and over 95% of those migrated into the aqueous medium . Purification decreased the content of mobile phases of metals to the values below the maximum allowable concentrations . The waste that is highly toxic for protozoa and the test crop wheat shall be considered to be nontoxic. Gig Sanit, 2002 Sep-Oct, (5), 24 - 6 {Lysozyme of hydrobionts and its role in self-purification of water reservoirs}; Solovykh GN et al.; Model experiments were carried out to study the effects of hydrobiont lysozyme on self-purifying processes of water reservoirs through its participation in the formation of a community of destructive microorganisms . Lysozyme-resistant forms have been found to lie at basis of bacterial cenosis of the Urals, among which there are lysozyme-active and anti-lysozyme-active ones, their population shows an inverse relationship . The exogenous lysozyme that enters the water reservoir in the period when there is a change in the dominant forms of hydrobionts affects the composition of bacterial cenosis by preserving anti-lysozyme-activity with a high activity (6-8 (g/ml), which causes a change in the microbial community of water reservoir, thus affecting the processes of its self-purification . The bacteria having ALA, which do maintain the capacity of a water reservoir for self-clearance from organic substance, persist under the action of endogenous lysozyme of phyto- and zooplankton among saprophytic microorganisms that are destructive agents in the biocenosis. J Biol Chem, 2003 Feb 28, 278(9), 7540 - 52 Epub 2002 Dec 09. Carbohydrate-induced differential gene expression patterns in the hyperthermophilic bacterium Thermotoga maritima; Chhabra SR et al.; The hyperthermophilic bacterium Thermotoga maritima MSB8 was grown on a variety of carbohydrates to determine the influence of carbon and energy source on differential gene expression . Despite the fact that T . maritima has been phylogenetically characterized as a primitive microorganism from an evolutionary perspective, results here suggest that it has versatile and discriminating mechanisms for regulating and effecting complex carbohydrate utilization . Growth of T . maritima on monosaccharides was found to be slower than growth on polysaccharides, although growth to cell densities of 10(8) to 10(9) cells/ml was observed on all carbohydrates tested . Differential expression of genes encoding carbohydrate-active proteins encoded in the T . maritima genome was followed using a targeted cDNA microarray in conjunction with mixed model statistical analysis . Coordinated regulation of genes responding to specific carbohydrates was noted . Although glucose generally repressed expression of all glycoside hydrolase genes, other sugars induced or repressed these genes to varying extents . Expression profiles of most endo-acting glycoside hydrolase genes correlated well with their reported biochemical properties, although exo-acting glycoside hydrolase genes displayed less specific expression patterns . Genes encoding selected putative ABC sugar transporters were found to respond to specific carbohydrates, and in some cases putative oligopeptide transporter genes were also found to respond to specific sugar substrates . Several genes encoding putative transcriptional regulators were expressed during growth on specific sugars, thus suggesting functional assignments . The transcriptional response of T . maritima to specific carbohydrate growth substrates indicated that sugar backbone- and linkage-specific regulatory networks are operational in this organism during the uptake and utilization of carbohydrate substrates . Furthermore, the wide ranging collection of such networks in T . maritima suggests that this organism is capable of adapting to a variety of growth environments containing carbohydrate growth substrates. Hematology, 2002 Dec, 7(6), 359 - 69 Thrombus formation with rehydrated, lyophilized platelets; Fischer TH et al.; Stored human platelets are frequently used in hemorrhagic emergencies, but have limited immediate utility for controlling bleeding due to storage lesion and are frequently contaminated with microorganisms . The development of paraformaldehyde-treated, lyophilized and rehydrated (RL) platelets, which are sterile and have a prolonged shelf life (years), ameliorate the efficacy and sterility problems with stored platelets . RL platelets have been shown to have many native functions of fresh platelets in vitro and to mediate hemostasis in vivo in large animal models of hemorrhagic shock and cardiopulmonary bypass induced platelet dysfunction . To further evaluate the functional properties of this transfusion product, we studied the role of RL platelets in three aspects of thrombus formation and lysis . First, the interaction between RL platelets and fibrinogen was investigated . The surface density of unligated GPIIb-IIIa on RL and fresh platelets were, respectively 30000 and 70000 molecules per cell as detected with the monoclonal antibody 10E-5 . Freezing, lyophilization and rehydration steps in the preparation of RL platelets resulted in the surface presentation of 120000 molecules of fibrinogen per cell from alpha granule sources . After ADP activation, RL platelets bound exogenous 125I-labeled fibrinogen in a dose-dependent manner with an affinity that is similar to that of fresh platelets and was inhibited by RGD peptides . 125I-Labeled fibrinogen binding to RL and fresh platelets, respectively, saturated at 14000 and 32000 molecules per cell . Scanning electron microscopic ultrastructural analysis showed that fibrin strands interacted with the surface of RL platelets in a normal manner . The second set of studies investigated the ability of RL platelets to catalyze and amplify the clot formation process in an activation-dependent manner . We showed that RL platelets undergo degranulation in fibrin in clots and functioned as thrombogenic surfaces for the generation of activated coagulation factors and fibrin generation . A final set of studies was performed to investigate fibrin of clots that contained RL platelets . RL platelet clots were lysed in the presence of tissue plasminogen activator with a similar time course as clots without platelets, and lysis occurred faster than when fresh platelets were included in the fibrin mass . The results of these three studies demonstrate that RL platelets are capable of mediating thrombus formation and do not inhibit lysis . Our results help explain how RL platelets restore hemostasis in vivo, and indicate that these cells might be a viable alternative to fresh stored platelets in transfusion medicine. Medicina (Kaunas), 2002, 38(1), 36 - 42 {Dependence of peripheral blood lymphocyte subpopulations on causative microorganisms able to produce superantigens}; Verba V et al.; A retrospective study of 176 immunologically tested patients admitted to Kaunas Medical University Hospital during 1997-2000 was performed . All patients had positive bacteriological culture test result confirming an infectious etiology of the disease . Our results showed that majority of immunological parameters were dependent on such non-specific factors as intensity and localization of the inflammatory process, an overall functional status of the patient, and the number of the disease exacerbation episodes during the last year before admission . In contrast to this, the absolute number of CD4 lymphocytes, the relative amount of HLA-DR positive lymphocytes and the index of neutrophil latex phagocytosis were exceptionally dependent on the species of the causative microorganism, in particular on superantigen producing cocci . In this case, the HLA-DR positive lymphocyte amount and the neutrophil phagocytosis index were significantly higher . In addition, the CD4/CD8 lymphocyte ratio (the immunoregulatory index) was significantly lower in this group . As much as those findings are concordant with the signs of excessive immune activation, we conclude that they reflect a possible superantigenic action of the disease causing bacteria . Therefore, a need for immunomodulating therapy during the infections caused by species able to produce superantigens is confirmed. Pol Merkuriusz Lek, 2002 Sep, 13(75), 238 - 41 {The role of monocytes/macrophages and their cytokines in the development of immunosuppression after severe injury}; Jedynak M et al.; Despite new generations of antibiotics and great improvement in the fields of rescue and modern intensive care medicine, sepsis remains one of the most frequent causes of complications and death in severely injured patients . Shock, bacterial colonization, invasive methods of treatment and immune mechanisms are reported to be responsible for the increased susceptibility of patients to sepsis after trauma . Posttraumatic immune abnormalities consist of two mechanistic entities: inappropriately hyperactive inflammatory processes and profound depression of cell-mediated immune function . Monocytes/macrophages carry out the fundamental protective functions of ingesting and killing invading microorganisms . Macrophages play a central role in the immune response by presenting antigens to lymphocytes, modulating T cell functions and by secreting a large number of inflammatory mediators . Macrophage-derived cytokines play key roles in the amplification of both humoral and cell-mediated immune responses . Depression of macrophage function appears to have serious deleterious effects in critically injured patients and has been associated with increased mortality . Phagocytosis, oxidative burst activity and cytokine secretion are impaired in macrophages early after traumatic injury . However, a widely accepted clinical treatment for post-injury immunosuppression does not currently exist . As our understanding of the pathogenesis of injury-induced immunosuppression progresses, our treatment approaches will likely improve. Clin Cancer Res, 2002 Dec, 8(12), 3877 - 84 Interleukin 15 promotes antigen-independent in vitro expansion and long-term survival of antitumor cytotoxic T lymphocytes; Lu J et al.; The survival and expansion of effector cytotoxic T lymphocytes (CTLs) during an immunological response are critical for the successful elimination of life-threatening attacks by microorganisms, parasites, or malignant cells . Among the numerous factors that regulate the immune response, interleukin (IL)-2, and its close relative, IL-15 are known to function as growth and survival factors for antigen-experienced T cells . However, major differences appear to exist between these lymphokines in their capacity to act on various T-cell types such as CD4+ versus CD8+ or effector versus memory T lymphocytes . Although several studies have been done in the mouse system, less information is available regarding the function of these lymphokines in the human system . Here, we report that IL-15 or high concentrations of IL-2 induced antigen-independent expansion of effector CD8+ CTLs . Neither IL-2 nor IL-15 induced the proliferation of CD4+ T cells . In the absence of antigen, at least one of these lymphokines was required for the long-term survival of the cells in tissue culture . Most significantly, the effector cytolytic activity of CTLs expanded and maintained in IL-15 for up to 60 days remained stable, indicating that these cells do not differentiate into a memory functional phenotype . The expression of IL-15Ralpha, which was detected on CD8+ CTLs but not on CD4+ helper T cells, suggests that this receptor subunit somehow participates in the transduction of the mitogenic signals of IL-15 . The present findings have practical implications for the propagation of antigen-specific T-cell lines in vitro and could be useful for expansion of therapeutic T cells for adoptive transfer. Clin Infect Dis, 2002 Dec 15, 35(12), e141 - 4 Epub 2002 Nov 20. Vertebral osteomyelitis due to Bartonella henselae in adults: a report of 2 cases; Verdon R et al.; We describe 2 adult patients (1 of whom was infected with human immunodeficiency virus) with osteomyelitis due to Bartonella henselae . Diagnosis was established on the basis of direct identification of the microorganism in one case and seroconversion in the other . Both patients recovered completely within 3 months. J Environ Qual, 2002 Nov-Dec, 31(6), 2045 - 50 Volatilization and degradation of soil-applied dimethylselenide; Dungan RS et al.; Dimethylselenide (DMSe) is a highly volatile gas that is produced by indigenous microorganisms in seleniferous soils and sediments; however, little is known about the soil conditions that affect the persistence of DMSe and its transport to the atmosphere . In this study we investigated the effect of moisture content, temperature, and organic amendments on the degradation of soil-applied DMSe . The degradation of DMSe was entirely a result of biological mechanisms, but changes in temperature (20-40 degrees C) and soil moisture content (30-70% of the maximum water holding capacity) had little influence on the degradation rate . In contrast, amending soil with either 1% casein or gluten (by weight) had an inhibitory effect on the degradation of DMSe . After 18 d, 2.1 times more DMSe was present in the casein-amended soil and 2.6 times more DMSe was present in the gluten-amended soil . The transport of DMSe in packed soil columns was also investigated . Increasing the depth to soil surface was found to significantly decrease the amount of DMSe transported to the air . After 6 d, 57% of DMSe injected 10 cm below the soil surface was volatilized . At an injection depth of 20 cm the cumulative emissions were reduced by 38% and at 30 cm the cumulative emissions were reduced by 51% . In columns containing 1% casein or gluten in the top 5 cm of soil the cumulative loss of DMSe was about 9% higher than in unamended soil . Increasing our understanding of the soil conditions that influence the gaseous diffusion of DMSe should help in determining the feasibility of using Se volatilization as a remediation technique. Org Lett, 2002 Dec 12, 4(25), 4483 - 6 A new strategy toward the total synthesis of stachyflin, a potent anti-influenza A virus agent: concise route to the tetracyclic core structure; Nakatani M et al.; {reaction: see text} A new strategy directed toward the total synthesis of stachyflin, a potent and novel anti-influenza A virus agent isolated from a microorganism, has been presented through the enantioselective synthesis of the tetracyclic core structure . The synthetic method features a BF(3) x Et(2)O-induced domino epoxide-opening/rearrangement/cyclization reaction as the key step. Nucl Med Commun, 2002 Dec, 23(12), 1177 - 82 Detection of inflammatory lymph nodes in rabbits by 99mTc-HIG lymphoscintigraphy; Ergun EL et al.; Tc-Human immunoglobulin G ( Tc-HIG) is a well-known radiopharmaceutical for the evaluation of inflammatory lesions . Recently, it has been demonstrated as a new agent for the visualization of the lymphatic system by our group . Our aim was to investigate the feasibility of detection of inflammatory lymph nodes by Tc-HIG lymphoscintigraphy . Ten adult New Zealand rabbits were used as group A . In a baseline study, 37 MBq Tc-HIG (0.1 ml) was injected into both hind legs of the rabbits, and sequential posterior gamma imaging with the rabbits lying prone was performed at 5, 15, 30, 60, 90 and 120 min using a single-headed gamma camera (Toshiba GCA G01 E) . One week later, microorganisms ( ) were injected in a volume of 0.1 ml intradermally into the web space between the second and third toes in the bilateral hind legs of each rabbit in order to obtain inflammation in the popliteal lymph nodes . After 4 days, 37 MBq Tc-HIG (0.1 ml) was injected into the hind legs of the rabbits bilaterally, and sequential posterior gamma imaging was performed as described above (second study) . Another group of 10 adult New Zealand rabbits (group B) was injected with the same microorganisms in the right hind legs only . After 4 days, scintigraphic imaging was carried out in the same way as described above (third study) . Regions of interest were drawn over the injection sites and popliteal lymph nodes on each image for semiquantitative analysis . Count rates for each were calculated and a decay correction was applied . Time-activity curves were generated to show the percentage retention of radioactivity in each region . After the scintigraphic study, some of the group B rabbits were killed by intravenous injection of pentobarbitone (100-150 mg.kg, and both left and right lymph nodes were removed for microscopic examination . On the scintigrams, lymphatic channels and popliteal lymph nodes were visualized within 15 min . In the second study, bilateral popliteal lymph nodes were visualized more clearly than in the baseline study . The right popliteal lymph nodes of the rabbits were more clearly visualized in the third study . Semiquantitative analysis showed a higher percentage uptake of radioactivity in the right compared to the left popliteal lymph nodes in group B rabbits . Microscopic examination of the tissue sections demonstrated inflammation in the right lymph nodes of group B rabbits . In this preliminary study, it was found that Tc-HIG is a new promising agent for the demonstration and evaluation of inflammatory lymph nodes. J Chromatogr A, 2002 Nov 8, 976(1-2), 103 - 11 Investigating the effects of protein patterns on microorganism identification by high-performance liquid chromatography-mass spectrometry and protein database searches; Ho YP et al.; High-performance liquid chromatography-electrospray ionization mass spectrometry (HPLC-ESI-MS) has been employed for separation and detection of protein biomarkers from E . coli samples . LC-MS is suitable for microbial identification because it can couple on-line with sample clean-up devices and is readily amenable to automation . In this work, we have investigated the effects of sample preparation methods on the detection of bacterial proteins by LC-MS . Many factors effect the degree of variations in the protein patterns (i.e . number and masses of proteins) . For example, changing the polarity as well as pH of the extraction solvent may control the number of detected proteins . It is also noted that the protein patterns can vary even when the total ion chromatography plots seem to be the same under the same sample preparation conditions . Further, we have tested experimentally the influence of LC-MS-analyzed protein patterns (molecular masses between 2000 and 60,000) on microbial identification by protein database searches . This is in contrast to the current database search approach, where only the masses of smaller proteins (< or = 20,000) from direct matrix-assisted laser/desorption ionization MS are used . In spite of the variations in protein patterns, all the database search results show that the best matches come from the correct microorganism. Int J Occup Med Environ Health, 2002, 15(3), 303 - 8 Firefighting efforts may lead to massive fungal growth and exposure within one week . A case report; Rautiala SH et al.; A case study on extensive fungal growth that occurred in an apartment building after firefighting efforts is described in this paper . Exposure to airborne microorganisms (both viable and total) was investigated by filter sampling in three periods before and during remedial actions after the fire . Material samples were also analyzed . Extensive mold growth was observed on the building materials as soon as eight days after the fire . High concentrations of fungal spores, 10(7) cfu/g, were found when material samples were analyzed . Concentrations of airborne fungal spores (10(4) spores/m3) were also high and increased by two orders of magnitude during the demolition of moldy building materials and during the clean-up after the demolition . The proportions of airborne viable fungi in comparison with the total spore concentrations were 28-83% immediately after the fire, but they had decreased to <1% two months after the fire during the reconstruction phase . Paecilomyces was the main fungal genus in the indoor air before and during the demolition, while Penicillium dominated during the reconstruction . Paecilomyces was not detected in the outdoor air . Paecilomyces and Penicillium were also found in the material samples . The results show that fast and extensive mold growth in a building may take place also in subarctic climates, at least during summer . High concentrations of fungal spores are released to the air during the demolition of moldy building materials and the following clean-up . Therefore, personal protection is necessary during such work. Ocul Immunol Inflamm, 2002 Mar, 10(1), 27 - 39 Distribution, markers, and functions of retinal microglia; Chen L et al.; Retinal microglia originate from hemopoietic cells and invade the retina from the retinal margin and the optic disc, most likely via the blood vessels of the ciliary body and iris, and the retinal vasculature, respectively . The microglial precursors that appear in the retina prior to vascularization are major histocompatibility complex (MHC) class I- and II-positive and express the CD45 marker, but lack specific macrophage markers . They differentiate into ramified parenchymal microglia in the adult retina . A second category of microglial precursors, which do express specific macrophage markers, migrate into the retina along with vascular precursors . They appear around blood vessels in the adult retina and are similar to macrophages or cells of the mononuclear phagocyte series (MPS) . Microglia are distributed in the outer plexiform layer (OPL), outer nuclear layer (ONL), inner plexiform layer (IPL), ganglion cell layer (GCL), and nerve fiber layer (NFL) of the primate retina . The pattern of microglial distribution in the avascular retina of the quail indicates that blood vessels are not responsible for the final location of microglia in the retina . In the human retina, microglia express MHC class I, MHC class II, CD45, CD68, and S22 markers . In the rat and mouse retina, OX41, OX42, OX3, OX6, OX18, ED1, Mac-1, F4/80, 5D4 anti-keratan sulfate, and lectins are used to recognize microglia . Microglial cells play an important role in host defense against invading microorganisms, immunoregulation, and tissue repair . During neurodegeneration, activated microglial cells participate in the phagocytosis of debris and facilitate regenerative processes . In autoimmune disease, microglia have dual functions: initiating uveoretinitis, but also limiting subsequent inflammation . Retinal microglia may be associated with vitreoretinopathy, diabetic retinopathy, glaucoma, and age-related macular degeneration . The goal of this article was to review the present knowledge about retinal microglia and the function of retinal microglia in pathological conditions. Am J Infect Control, 2002 Dec, 30(8), S1 - 46 Guideline for Hand Hygiene in Health-Care Settings . Recommendations of the Healthcare Infection Control Practices Advisory Committee and the HIPAC/SHEA/APIC/IDSA Hand Hygiene Task Force; Boyce JM et al.; The Guideline for Hand Hygiene in Health-Care Settings provides health-care workers (HCWs) with a review of data regarding handwashing and hand antisepsis in health-care settings . In addition, it provides specific recommendations to promote improved hand-hygiene practices and reduce transmission of pathogenic microorganisms to patients and personnel in health-care settings . This report reviews studies published since the 1985 CDC guideline (Garner JS, Favero MS . CDC guideline for handwashing and hospital environmental control, 1985 . Infect Control 1986;7:231-43) and the 1995 APIC guideline (Larson EL, APIC Guidelines Committee . APIC guideline for handwashing and hand antisepsis in health care settings . Am J Infect Control 1995;23:251-69) were issued and provides an in-depth review of hand-hygiene practices of HCWs, levels of adherence of personnel to recommended handwashing practices, and factors adversely affecting adherence . New studies of the in vivo efficacy of alcohol-based hand rubs and the low incidence of dermatitis associated with their use are reviewed . Recent studies demonstrating the value of multidisciplinary hand-hygiene promotion programs and the potential role of alcohol-based hand rubs in improving hand-hygiene practices are summarized . Recommendations concerning related issues (e.g., the use of surgical hand antiseptics, hand lotions or creams, and wearing of artificial fingernails) are also included. Environ Microbiol, 2002 Nov, 4(11), 770 - 3 A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature; Gonzalez JM et al.; G+C mol% content in microorganisms is one of the recommended characteristics for the standard description of bacterial species . In this study we present a novel fluorimetric method to estimate the G+C mol% content in microorganisms . Double-stranded DNA was specifically stained with SYBR Green I, and its thermal denaturalization was followed by measuring a decrease in fluorescence using a real-time PCR thermocycler . Unlike most previous determinations of G+C mol%, in this study only DNA from microorganisms with an available completely sequenced genome were used to prepare the calibration curves . Calibration curves showed a linear relationship between G+C mol% content and melting temperature and they were performed both in the absence and presence of 30% formamide . This protocol proves to be a rapid and inexpensive method to estimate DNA base ratios of novel microorganisms. Environ Microbiol, 2002 Nov, 4(11), 654 - 66 Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys; Sait M et al.; The culturability of microorganisms in a 10 cm core of an Australian pasture soil was investigated using a minimal agar medium with xylan as the growth substrate . Culturability decreased with increasing depth, from a maximum of 19% of the total microscopically countable cells in the 0-2 cm section to 2.4% in the 8-10 cm section . Seventy-one isolates from the core were identified by comparative 16S rRNA gene sequence analysis . Many of these isolates belong to groups of globally distributed soil bacteria, including well-characterized families of the classes Alphaproteobacteria and Betaproteobacteria, and of the subclass Actinobacteridae . Other isolates belong to groups with few or no cultivated representatives: 10 isolates in two subdivisions of the phylum Acidobacteria, five isolates in a new order and nine isolates in a new family of the class Alphaproteobacteria, two isolates in a new order of the class Gammaproteobacteria, three isolates in two new families of the subclass Actinobacteridae, and two isolates in the subclass Rubrobacteridae . These new isolates represent the first laboratory cultures able to be assigned to some of these groups and greatly increase the number of cultivated strains known for others . This demonstrates that a minimal change in cultivation strategy (using a polymeric growth substrate and longer incubation times) can result in the isolation of globally distributed but previously uncultured phylogenetically novel soil bacteria. J Microbiol Methods, 2003 Feb, 52(2), 267 - 71 Development of a fluorescence in situ hybridization method for cheese using a 16S rRNA probe; Ercolini D et al.; A 16S rRNA fluorescence in situ hybridization (FISH) method for cheese was developed to allow detection in situ of microorganisms within the dairy matrix . An embedding procedure using a plastic resin was applied to Stilton cheese, providing intact embedded cheese sections withstanding the hybridization reaction . The use of a fluorescein-labelled 16S rRNA Domain Bacteria probe allowed observation of large colonies of microbial cells homogeneously distributed in the cheese matrix . FISH experiments performed on cheese suspensions provided images of the different microbial morphotypes occurring . The technique has great potential to study the spatial distribution of microbial populations in situ in foods, especially where the matrix is too fragile to allow manipulation of cryosections . Turk J Pediatr, 2002 Oct-Dec, 44(4), 283 - 8 Frequency of Mycoplasma pneumoniae among atypical pneumonia of childhood; Oguz F et al.; We aimed to investigate the frequency of Mycoplasma pneumoniae among atypical pneumonia of childhood that is acquired from the community and to determine a practical approach to the diagnosis of these patients . In this prospective study, 55 patients (31 male and 24 female) with atypical pneumonia were investigated with conventional laboratory and radiological methods as well as culture and polymerase chain reaction (PCR) on throat swab . In addition, serum of the patients was tested for M . pneumoniae specific IgM . The patients were reevaluated clinically at 3-5 days and 3-4 weeks and serologically at 3-4 weeks . The data on patients with M . pneumoniae pneumonia were compared with the other patients with atypical pneumonia and controls . All patients were treated with macrolide antibiotics . The mean age of the patients was 7.8+/-2.9 years . The frequency of M . pneumoniae by this method was 34.5% . Neither clinical, laboratory, or epidemiological data nor response to macrolide antibiotics was useful in detecting the etiology of atypical pneumonia . Diagnostic sensitivity and specificity of IgM+IgG antibodies plus PCR on throat swab were estimated as 100% . M . pneumoniae was an important microorganism in the etiology of atypical pneumonia of childhood in our community . In order to prevent loss of time with beta-lactamase antibiotics, which are usually started in severe pneumonia, serologic tests and PCR must be done during the initial evaluation of the patient for the reliable diagnosis of M . pneumoniae, which will increase the chance of early and appropriate therapy. Anal Bioanal Chem, 2002 Nov, 374(6), 1101 - 4 Epub 2002 Oct 19. Empirical method for prediction of the coordination environment of Eu(III) by time-resolved laser-induced fluorescence spectroscopy; Ozaki T et al.; The number of water molecules in the inner-sphere (N(H2O)) was determined for Eu(III) and the strength of ligand field (R(E/M)) was evaluated for a variety of coordination environments from the luminescence lifetime and the relative intensity at 615 nm and at 592 nm, by time-resolved laser-induced fluorescence spectroscopy . When R(E/M) and deltaN(H2O) for Eu(III) with a known coordination environment were plotted clear regularity was apparent between the location of the R(E/M)-deltaN(H2O) plot and the coordination environment of Eu(III) . Here, deltaN(H2O) was calculated by use of the equation, deltaN(H2O)=9-N(H2O) . Unknown coordination environments of Eu(III) can, in turn, be characterized, including both the inner- and the outer-sphere, simply by plotting R(E/M) and deltaN(H2O) for Eu(III) on the diagram . This empirical method is effective for prediction of the coordination environment of hydrated and complexed Eu(III) in solutions and that of the adsorbed Eu(III) on ion-exchange resins and by microorganisms. J Biol Chem, 2003 Feb 7, 278(6), 3552 - 61 Epub 2002 Nov 26. Prophenoloxidase-activating proteinase-2 from hemolymph of Manduca sexta . A bacteria-inducible serine proteinase containing two clip domains; Jiang H et al.; Proteolytic activation of prophenoloxidase in insects is a component of the host defense system against invading pathogens and parasites . We have purified from hemolymph of the tobacco hornworm, Manduca sexta, a new serine proteinase that cleaves prophenoloxidase . This enzyme, designated prophenoloxidase-activating proteinase-2 (PAP-2), differs from another PAP, previously isolated from integuments of the same insect (PAP-1) . PAP-2 contains two clip domains at its amino terminus and a catalytic domain at its carboxyl terminus, whereas PAP-1 has only one clip domain . Purified PAP-2 cleaved prophenoloxidase at Arg(51) but yielded a product that has little phenoloxidase activity . However, in the presence of two serine proteinase homologs, active phenoloxidase was generated at a much higher level, and it formed covalently linked, high molecular weight oligomers . The serine proteinase homologs associate with a bacteria-binding lectin in M . sexta hemolymph, indicating that they may be important for ensuring that the activation of prophenoloxidase occurs only in the vicinity of invading microorganisms . PAP-2 mRNA was not detected in naive larval fat body or hemocytes, but it became abundant in these tissues after the insects were injected with bacteria. Front Biosci, 2003 Jan 01, 8, e23 - 35 Coxsackievirus experimental heart diseases; Gauntt C et al.; Many microorganisms, particularly viruses, can cause myocarditis, an inflammatory disease of the heart . The frequency of and major factors that contribute to this disease, including a pronounced gender (male) bias, age and genetic background parameters are discussed, along with signs and symptoms of disease in infants to adults . Individuals with acute disease generally recover without sequelae; the chronic form can develop into idiopathic dilated cardiomyopathy and death can follow . Among viruses most frequently associated with cases in the U.S., the coxsackieviruses group B (CVB) are major etiologic agents . The association between the CVB and disease is based on detection of viral RNA in heart biopsy specimens by polymerase chain reaction assays . Excellent CVB-, particularly coxsackievirus B3 (CVB3)-, mouse models of the disease have identified mechanisms of induction and establishment of chronic myocarditis . CVB3-murine models share many biologic parameters of the acute and chronic diseases in humans, and show that cardiopathologic alterations result from virus-induced and immunologic reactions in heart tissues . Several immune responses to a CVB3 infection that become cardiopathogenic, instead of protective, are discussed in an attempt to explain why immunosuppressive treatments are not effective . Bed rest and supportive therapy are the current treatment for patients with myocarditis. Contemp Top Lab Anim Sci, 1998 Mar, 37(2), 50 - 51 Effectiveness of Rack Sanitation Procedures for Elimination of Bacteria from Automatic Watering Manifolds; Costello T et al.; An important responsibility of animal care programs is to protect research animals from exposure to potentially pathogenic microorganisms . To validate the need for steam sterilization of rodent automatic watering racks, we evaluate the post-sanitation microbial contamination of experimentally inoculated racks and of racks that had been used to house conventional mice . We tested three sanitation protocols: rack-washer sanitation without manifold flush, sanitation that included manifold flush, and sanitation that included manifold flush followed by autoclaving . Rack sanitation, with or without manifold flush, did not reliably eliminate microbial flora from the lixits or manifold drainage water . A total of 43% of all non-autoclaved racks were positive for bacterial contamination after sanitation, and racks that had been used for conventional animal housing were more frequently positive than were experimentally inoculated racks (79% vs 18%) . These data indicate that steam sterilization is necessary for eliminating bacteria from automatic watering systems . These observations are particularly important in light of increasing numbers of immune-impaired rodents that may be inadvertently and unnecessarily exposed to microbial pathogens via the automatic watering system. J Clin Microbiol, 2002 Dec, 40(12), 4771 - 5 Are there naturally occurring pleomorphic bacteria in the blood of healthy humans? McLaughlin RW, Vali H, Lau PC, Palfree RG, De Ciccio A, Sirois M, Ahmad D, Villemur R, Desrosiers M, Chan EC. Dark-field microscopy of blood from healthy individuals revealed the existence of pleomorphic microorganisms . These bacteria exhibited limited growth and susceptibility to antibiotics and could be detected by fluorescent in situ hybridization and flow cytometry . They were further characterized by analysis of their 16S rRNA and gyrB genes. Emerg Infect Dis, 2002 Nov, 8(11), 1342 - 6 Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis; Hughes AL et al.; Comparison of the pattern of synonymous nucleotide substitution between two complete genomes of Mycobacterium tuberculosis at 3298 putatively orthologous loci showed a mean percent difference per synonymous site of 0.000328 0.000022 . Although 80.5% of loci showed no synonymous or nonsynonymous nucleotide differences, the level of polymorphism observed at other loci was greater than suggested by previous studies of a small number of loci . This level of nucleotide difference leads to the conservative estimate that the common ancestor of these two genotypes occurred approximately 35000 ago, which is twice as high as some recent estimates of the time of origin of this species . Our results suggest that a large number of loci should be examined for an accurate assessment of the level of nucleotide diversity in natural populations of pathogenic microorganisms. Clin Exp Immunol, 2002 Dec, 130(3), 449 - 58 The scavenger receptor, cysteine-rich domain-containing molecule gp-340 is differentially regulated in epithelial cell lines by phorbol ester; Kang W et al.; Gp-340 is a glycoprotein belonging to the scavenger receptor cysteine rich (SRCR) group B family . It binds to host immune components such as lung surfactant protein D (SP-D) . Recent studies found that gp-340 interacts directly with pathogenic microorganisms and induces their aggregation, suggesting its involvement in innate immunity . In order to investigate further its potential immune functions in the appropriate cell lines, the expression of gp-340 in four conventional immune cell lines (U937, HL60, Jurkat, Raji), and two innate immune-related epithelial cell lines (A549 derived from lung and AGS from stomach), was examined by RT-PCR and immunohistochemistry . The resting immune cell lines showed weak or no gp-340 mRNA expression; while the two epithelial cell lines expressed gp-340 at much higher level, which was differentially regulated by phorbol myristate acetate (PMA) treatment . In the A549 cells, gp-340 was up-regulated along with the PMA-induced proinflammatory expression of both IL-6 and IL-8 . In AGS cells, PMA down-regulation of gp-340 was seen in parallel with an up-regulation of the two mature gastric epithelial specific proteins TFF1 (trefoil factor 1) and TFF2, which are implicated as markers of terminal differentiation . Analysis of the distribution of gp-340, together with the TFFs and SP-D in normal lung and gastric mucosa, supported further our in vitro data . We conclude that the differential regulation of gp-340 in the two epithelial cell lines by PMA indicates that gp-340 s involvement in mucosal defence and growth of epithelial cells may vary at different body locations and during different stages of epithelial differentiation. Jpn Heart J, 2002 Sep, 43(5), 475 - 85 Pacemaker related endocarditis: analysis of seven cases; Erdinler I et al.; Vegetative electrode infection following permanent pacemaker implantation is a rare and serious complication . Among 1920 patients who underwent permanent pacemaker implantation in our institute between 1980 and 2000, 7 patients aged 65 to 78 years were diagnosed to have pacemaker related endocarditis . In this study, the clinical course and management strategies for these patients are reviewed . The most frequently encountered factors contributing to development of pacemaker infection were local complications such as postoperative hematoma and inflammation, and recurrent surgical interventions on the pacemaker system . In blood cultures S . aureus was the most common causative microorganism . Echocardiography could be performed in 5 patients . Three patients were referred to open-heart surgery for total removal of the pacemaker system, and one patient had his pacemaker system removed percutaneously . The remaining 3 patients did not agree to either surgical or percutaneous removal . These patients have been under antibiotic therapy for approximately 3 years and they still do not have any signs of a serious infection . Consequently, in patients with permanent pacemakers, infective endocarditis should be considered in the presence of fever and local symptoms . Blood cultures should be obtained and echocardiography should be performed . Complete removal of the pacemaker system with intensive antibiotic treatment is necessary for complete eradication of the infection . However, if percutaneous or surgical removal of the electrodes cannot be done because of high perioperative risk or the patient does not agree to undergo either method, medical treatment with long term antibiotic use may be considered as an alternative. Appl Environ Microbiol, 2002 Dec, 68(12), 6403 - 4 The environmental pathogen Mycobacterium ulcerans grows in amphibian cells at low temperatures; Drancourt M et al.; Mycobacterium ulcerans, the etiological agent of Buruli ulcers, is an environmental pathogen . We cultivated it in an amphibian (XTC-2) cell line that grows at 28 degrees C . By counting of Ziehl-Neelsen-stained mycobacteria and by quantitative PCR analysis, we found that M . ulcerans multiplies rapidly in association with XTC-2 cells . Transmission electron microscopy demonstrated the presence of intracellular M . ulcerans microorganisms . These data suggest an intracellular environmental niche, and we propose use of XTC-2 cells for isolation of M . ulcerans from environmental sources. Appl Environ Microbiol, 2002 Dec, 68(12), 6392 - 8 Bacterial group II introns in a deep-sea hydrothermal vent environment; Podar M et al.; Group II introns are catalytic RNAs and mobile retrotransposable elements known to be present in the genomes of some nonmarine bacteria and eukaryotic organelles . Here we report the discovery of group II introns in a bacterial mat sample collected from a deep-sea hydrothermal vent near 9 degrees N on the East Pacific Rise . One of the introns was shown to self-splice in vitro . This is the first example of marine bacterial introns from molecular population structure studies of microorganisms that live in the proximity of hydrothermal vents . These types of mobile genetic elements may prove useful in improving our understanding of bacterial genome evolution and may serve as valuable markers in comparative studies of bacterial communities. Appl Environ Microbiol, 2002 Dec, 68(12), 6121 - 8 Molecular analysis of the nitrate-reducing community from unplanted and maize-planted soils; Philippot L et al.; Microorganisms that use nitrate as an alternative terminal electron acceptor play an important role in the global nitrogen cycle . The diversity of the nitrate-reducing community in soil and the influence of the maize roots on the structure of this community were studied . The narG gene encoding the membrane bound nitrate reductase was selected as a functional marker for the nitrate-reducing community . The use of narG is of special interest because the phylogeny of the narG gene closely reflects the 16S ribosomal DNA phylogeny . Therefore, targeting the narG gene provided for the first time a unique insight into the taxonomic composition of the nitrate-reducing community in planted and unplanted soils . The PCR-amplified narG fragments were cloned and analyzed by restriction fragment length polymorphism (RFLP) . In all, 60 RFLP types represented by two or more clones were identified in addition to the 58 RFLP types represented by only one clone . At least one clone belonging to each RFLP type was then sequenced . Several of the obtained sequences were not related to the narG genes from cultivated bacteria, suggesting the existence of unidentified nitrate-reducing bacteria in the studied soil . However, environmental sequences were also related to NarG from many bacterial divisions, i.e., Actinobacteria and alpha, beta, and gamma proteobacteria . The presence of the plant roots resulted in a shift in the structure of the nitrate-reducing community between the unplanted and planted soils . Sequencing of RFLP types dominant in the rhizosphere or present only in the rhizosphere revealed that they are related to NarG from the Actinobacteria in an astonishingly high proportion. Appl Environ Microbiol, 2002 Dec, 68(12), 6106 - 13 Linking of microorganisms to phenanthrene metabolism in soil by analysis of (13)C-labeled cell lipids; Johnsen AR et al.; Phenanthrene-metabolizing soil microbial communities were characterized by examining mineralization of {(14)C}phenanthrene, by most-probable-number (MPN) counting, by 16S-23S spacer DNA analysis of the numerically dominant, culturable phenanthrene-degrading isolates, and by examining incorporation of {(13)C}phenanthrene-derived carbon into sterols and polar lipid fatty acids (PLFAs) . An unpolluted agricultural soil, a roadside soil diffusely polluted with polycyclic aromatic hydrocarbons (PAHs), and two highly PAH-polluted soils from industrial sites were analyzed . Microbial phenanthrene degraders were not detected by MPN counting in the agricultural soil and the roadside soil . In the industrial soils, phenanthrene degraders constituted 0.04 and 3.6% of the total number of CFU . 16S-23S spacer DNA analysis followed by partial 16S DNA sequencing of representative isolates from one of the industrial soils showed that one-half of the isolates belonged to the genus Sphingomonas and the other half were closely related to an unclassified beta-proteobacterium . The (13)C-PLFA profiles of the two industrial soils were relatively similar and resembled the profiles of phenanthrene-degrading Sphingomonas reference strains and unclassified beta-proteobacterium isolates but did not match the profiles of Pseudomonas, Mycobacterium, or Nocardia reference strains . The (13)C-PLFA profiles of phenanthrene degraders in the agricultural soil and the roadside soil were different from each other and different from the profiles of the highly polluted industrial soils . Only in the roadside soil were 10me/12me18:0 PLFAs enriched in (13)C, suggesting that actinomycetes metabolized phenanthrene in this soil . The (13)C-PLFA profiles of the unpolluted agricultural soil did not resemble the profiles of any of the reference strains . In all of the soils investigated, no excess (13)C was recovered in the 18:2omega6,9 PLFA, suggesting that fungi did not contribute significantly to assimilation of {(13)C}phenanthrene. Med Hypotheses, 2003 Jan, 60(1), 69 - 83 Are lipid peroxidation processes induced by changes in the cell wall structure and how are these processes connected with diseases? Spiteller G. Apparently nature uses the unique sensitivity of polyunsaturated fatty acids (PUFAs) versus oxygen to generate chemical signals if the surface of a cell is influenced by an outside or inside event; for instance the attack of microorganisms, proliferation, aging or by treatment of isolated cells with surfactants . It seems that mammalian and plant cells respond equally to such changes in their structures by transformation of polyunsaturated fatty acids localized in the phospholipid layer of the cell wall to lipidhydroperoxides (LOOHs) . These lipid peroxidation (LPO) processes involve all PUFAs, not only arachidonic acid.Slight physiological changes of the cell wall for instance by proliferation seem to activate enzymes, e.g., phospholipases and lipoxygenases (LOX) . When an outside impact (for instance by attack of microorganisms) exceeds a certain level LOX commit suicide and liberate iron ions . These start a nonenzymatic LPO . Enzymatic and nonenzymatic LPO distinguish fundamentally which has not been recognized in the past . In the enzymatic LPO processes peroxyl radicals generated as intermediates cannot leave the enzyme complex . In contrast in a nonenzymatic LPO process peroxyl radicals are not trapped . They attack nearly any kind of biological molecules, for instance proteins . Thus only the amount of an outside impact decides if proliferation, apoptosis, or necrosis is started.Some evidence indicates that cancer might be the consequence of a low response of cells to induce apoptotic LPO processes . In contrast to high level of LPO processes induces diseases combined with inflammation, for instance rheumatic arthritis . After consumption of food rich in linoleic acid its LPO products become increased in low density lipoprotein (LDL) . This LDL is able to enter endothelial cells and damage cells from inside, long before an inflammatory response is detectable. Gene Expr, 2002, 10(5-6), 213 - 30 A DNA microarray-based approach to elucidate the effects of the immunosuppressant SR31747A on gene expression in Saccharomyces cerevisiae; Cinato E et al.; SR31747A is an immunosuppressive agent that arrests cell proliferation in the yeast Saccharomyces cerevisiae . In this microorganism, SR31747A was shown to inhibit the ERG2 gene product, namely the delta8-delta7 sterol isomerase, involved in the ergosterol biosynthesis pathway . Although previous genetic experiments pointed to this enzyme as the target for SR31747A in yeast, the existence of other potential targets could not be ruled out . To enlighten this issue, we undertook a DNA microarray-based approach in which the expression profile of SR31747A-treated wild-type cells defining the "drug signature" was compared with the "mutant signature," the expression profile of the corresponding ERG2-deleted strain . We observed that treatment of ERG2-positive cells with SR31747A resulted in the modulation of mRNA levels of numerous genes . Among them, 121 werealso affected in untreated ERG2-disrupted cells compared with wild-type cells . By contrast, drug exposure did not induce any significant transcriptional change in the ERG2 null mutant . These results were consistent with SR31747A being an inhibitor of the sterol isomerase and demonstrated the absence of any additional SR31747A target . The detailed analysis of the observed 121 modulated genes provides new insights into the cellular response to ergosterol deprivation induced by SR31747A through inhibition of the ERG2 gene product. Astrobiology, 2002 Spring, 2(1), 77 - 82 Aspartic acid racemization and age-depth relationships for organic carbon in Siberian permafrost; Brinton KL et al.; We have analyzed the degree of racemization of aspartic acid in permafrost samples from Northern Siberia, an area from which microorganisms of apparent ages up to a few million years have previously been isolated and cultured . We find that the extent of aspartic acid racemization in permafrost cores increases very slowly up to an age of approximately 25,000 years (around 5 m in depth) . The apparent temperature of racemization over the age range of 0-25,000 years, determined using measured aspartic acid racemization rate constants, is -19 degrees C . This apparent racemization temperature is significantly lower than the measured environmental temperature (-11 to -13 degrees C) and suggests active recycling of D-aspartic acid in Siberian permafrost up to an age of around 25,000 years . This indicates that permafrost organisms are capable of repairing some molecular damage incurred while in a "dormant" state over geologic time. Astrobiology, 2002 Spring, 2(1), 59 - 76 Planetary resources and astroecology . Planetary microcosm models of asteroid and meteorite interiors: electrolyte solutions and microbial growth--implications for space populations and panspermia; Mautner MN; Planetary microcosms were constructed using extracts from meteorites that simulate solutions in the pores of carbonaceous chondrites . The microcosms were found to support the growth of complex algal and microbial populations . Such astroecology experiments demonstrate how a diverse ecosystem could exist in fluids within asteroids, and in meteorites that land on aqueous planets . The microcosm solutions were obtained by extracting nutrient electrolytes under natural conditions from powders of the Allende (CV3) and Murchison (CM2) meteorites at low (0.02 g/ml) and high (10.0 g/ml) solid/solution ratios . The latter solutions contain > 3 mol/L electrolytes and about 10 g/L organics, that simulate natural fluids in asteroids during aqueous alteration and in the pores of meteorites, which can help prebiotic synthesis and the survival of early microorganisms . These solutions and wet solids were in fact found to support complex self-sustaining microbial communities with populations of 4 x 10(5) algae and 6 x 10(6) bacteria and fungi for long periods (> 8 months) . The results show that planetary microcosms based on meteorites can: assay the fertilities of planetary materials; identify space bioresources; target astrobiology exploration; and model past and future space-based ecosystems . The results show that bioresources in the carbonaceous asteroids can sustain a biomass of 10(18) kg, comprising 10(32) microorganisms and a human population of 10(14) . The results also suggest that protoplanetary nebulae can support and disperse microorganisms and can be therefore effective environments for natural and directed panspermia. Astrobiology, 2002 Spring, 2(1), 43 - 57 Fluid inclusion studies of chemosynthetic carbonates: strategy for seeking life on Mars; Parnell J et al.; Fluid inclusions in minerals hold the potential to provide important data on the chemistry of the ambient fluids during mineral precipitation . Especially interesting to astrobiologists are inclusions in low-temperature minerals that may have been precipitated in the presence of microorganisms . We demonstrate that it is possible to obtain data from inclusions in chemosynthetic carbonates that precipitated by the oxidation of organic carbon around methane-bearing seepages . Chemosynthetic carbonates have been identified as a target rock for astrobiological exploration . Other surficial rock types identified as targets for astrobiological exploration include hydrothermal deposits, speleothems, stromatolites, tufas, and evaporites, each of which can contain fluid inclusions . Fracture systems below impact craters would also contain precipitates of minerals with fluid inclusions . As fluid inclusions are sealed microchambers, they preserve fluids in regions where water is now absent, such as regions of the martian surface . Although most inclusions are < 5 microns, the possibility to obtain data from the fluids, including biosignatures and physical remains of life, underscores the advantages of technological advances in the study of fluid inclusions . The crushing of bulk samples could release inclusion waters for analysis, which could be undertaken in situ on Mars. Zh Mikrobiol Epidemiol Immunobiol, 2002 Jul-Aug, (4), 63 - 72 {Integrative processes in modern epidemiology}; Litvin VIu et al.; The integration of achievements in population ecology and the molecular genetics of pathogenic microorganisms into nowadays epidemiology of infectious diseases and the formation of its corresponding trends are discussed . The decisive role of highly complicated key problems of general epidemiology, such as the regularities of the autochthonous existence of pathogenic bacteria in the environment, the mechanisms of the pathogenicity regulation of infective agents and the formation of their epidemic variants, the mechanisms of the prolonged reservation of pathogenic bacteria at interepidemic (interepizootic) periods, the mechanisms of transformation of active (vegetative) and dormant forms in bacterial populations at different stages of epidemic and epizootic cycles, is demonstrated . The detection and analysis of such processes, and especially their latent mechanisms, become possible with the use of new concepts and methodological approaches, highly productive for the progress of epidemiology. Mikrobiologiia, 2002 Sep-Oct, 71(5), 690 - 6 {The classification and the monitoring of the state of mouth riverine and lacustrine ecosystems in lake Baikal based on the composition of local microbiocenoses and their activity}; Maksimov VV et al.; The paper presents the results of the long-term investigation of microbial communities in the technogenically vulnerable mouth riverine and lacustrine ecosystems of Lake Baikal . The structural and functional parameters of the microbial communities were analyzed from the standpoint of developing destructive processes . The analysis showed that the total number of microorganisms (TNM), the number of saprophytic bacteria (NSB), and bacterial production (BP) were greater in the river-mouth water than in the near-mouth lake water . In the offshore direction, TNM and NSB decreased by a factor of 1.5 to 2, and BP decreased by a factor of 4 to 7 . Based on TNM, NSB, and BP data, we classified the Lake Baikal rivers with respect to the degree of the impact of human activities on them . The degrading capability of the riverine microbial communities was found to be such that they degrade daily from tenths of a percent to 3.5% of the total amount of organic compounds polluted the river waters. Eur Respir J, 2002 Nov, 20(5), 1351 - 3 Extrinsic allergic alveolitis induced by the yeast Debaryomyces hansenii; Yamamoto Y et al.; A 65-yr-old female developed cough, fever and dyspnoea following repeated exposure to a home ultrasonic humidifier . High-resolution computed tomography showed ground-glass opacity in both lung fields . Arterial blood gas analysis gave an oxygen tension of 8.38 kPa (63 Torr) . Pulmonary function testing revealed restrictive ventilatory impairment with a reduction in the diffusing capacity . The diagnosis of extrinsic allergic alveolitis (EAA) was confirmed by radiographic findings, pathological evidence of alveolitis and reproductive development by a provocation test to the humidifier water . The yeast Debaryomyces Hansenii was the only microorganism cultured from the water of the humidifier . The double diffusion precipitating test and lymphocyte proliferative response was positive for an extract of D . Hansenii, providing evidence to incriminate this fungus . This is the first described case of EAA caused by D . Hansenii. Astrobiology, 2001 Spring, 1(1), 89 - 109 The physics, biology, and environmental ethics of making mars habitable; McKay CP et al.; The considerable evidence that Mars once had a wetter, more clement, environment motivates the search for past or present life on that planet . This evidence also suggests the possibility of restoring habitable conditions on Mars . While the total amounts of the key molecules--carbon dioxide, water, and nitrogen--needed for creating a biosphere on Mars are unknown, estimates suggest that there may be enough in the subsurface . Super greenhouse gases, in particular, perfluorocarbons, are currently the most effective and practical way to warm Mars and thicken its atmosphere so that liquid water is stable on the surface . This process could take approximately 100 years . If enough carbon dioxide is frozen in the South Polar Cap and absorbed in the regolith, the resulting thick and warm carbon dioxide atmosphere could support many types of microorganisms, plants, and invertebrates . If a planet-wide martian biosphere converted carbon dioxide into oxygen with an average efficiency equal to that for Earth's biosphere, it would take > 100,000 years to create Earth-like oxygen levels . Ethical issues associated with bringing life to Mars center on the possibility of indigenous martian life and the relative value of a planet with or without a global biosphere. Astrobiology, 2001 Winter, 1(4), 447 - 65 Mineralogical biosignatures and the search for life on Mars; Banfield JF et al.; If life ever existed, or still exists, on Mars, its record is likely to be found in minerals formed by, or in association with, microorganisms . An important concept regarding interpretation of the mineralogical record for evidence of life is that, broadly defined, life perturbs disequilibria that arise due to kinetic barriers and can impart unexpected structure to an abiotic system . Many features of minerals and mineral assemblages may serve as biosignatures even if life does not have a familiar terrestrial chemical basis . Biological impacts on minerals and mineral assemblages may be direct or indirect . Crystalline or amorphous biominerals, an important category of mineralogical biosignatures, precipitate under direct cellular control as part of the life cycle of the organism (shells, tests, phytoliths) or indirectly when cell surface layers provide sites for heterogeneous nucleation . Biominerals also form indirectly as by-products of metabolism due to changing mineral solubility . Mineralogical biosignatures include distinctive mineral surface structures or chemistry that arise when dissolution and/or crystal growth kinetics are influenced by metabolic by-products . Mineral assemblages themselves may be diagnostic of the prior activity of organisms where barriers to precipitation or dissolution of specific phases have been overcome . Critical to resolving the question of whether life exists, or existed, on Mars is knowing how to distinguish biologically induced structure and organization patterns from inorganic phenomena and inorganic self-organization . This task assumes special significance when it is acknowledged that the majority of, and perhaps the only, material to be returned from Mars will be mineralogical. Antonie Van Leeuwenhoek, 2002 Aug, 81(1-4), 557 - 64 Mechanisms of natural soil suppressiveness to soilborne diseases; Mazzola M; Suppressive soils are characterized by a very low level of disease development even though a virulent pathogen and susceptible host are present . Biotic and abiotic elements of the soil environment contribute to suppressiveness, however most defined systems have identified biological elements as primary factors in disease suppression . Many soils possess similarities with regard to microorganisms involved in disease suppression, while other attributes are unique to specific pathogen-suppressive soil systems . The organisms operative in pathogen suppression do so via diverse mechanisms including competition for nutrients, antibiosis and induction of host resistance . Non-pathogenic Fusarium spp . and fluorescent Pseudomonas spp . play a critical role in naturally occurring soils that are suppressive to Fusarium wilt . Suppression of take-all of wheat, caused by Gaeumannomyces graminis var . tritici, is induced in soil after continuous wheat monoculture and is attributed, in part, to selection of fluorescent pseudomonads with capacity to produce the antibiotic 2,4-diacetylphloroglucinol . Cultivation of orchard soils with specific wheat varieties induces suppressiveness to Rhizoctonia root rot of apple caused by Rhizoctonia solani AG 5 . Wheat cultivars that stimulate disease suppression enhance populations of specific fluorescent pseudomonad genotypes with antagonistic activity toward this pathogen . Methods that transform resident microbial communities in a manner which induces natural soil suppressiveness have potential as components of environmentally sustainable systems for management of soilborne plant pathogens. Antonie Van Leeuwenhoek, 2002 Aug, 81(1-4), 549 - 56 Significance of lytic enzymes from Trichoderma spp . in the biocontrol of fungal plant pathogens; Viterbo A et al.; The use of specific mycolytic soil microorganisms to control plant pathogens is an ecological approach to overcome the problems caused by standard chemical methods of plant protection . The ability to produce lytic enzymes is a widely distributed property of rhizosphere-competent fungi and bacteria . Due to the higher activity of Trichoderma spp . lytic enzymes as compared to the same class of enzymes from other microorganisms and plants, effort is being aimed at improving biocontrol agents and plants by introducing Trichoderma genes via genetic manipulations . An overview is presented of the data currently available on lytic enzymes from the mycoparasitic fungus Trichoderma. Antonie Van Leeuwenhoek, 2002 Aug, 81(1-4), 509 - 20 Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms; Kowalchuk GA et al.; A coupling of above-ground plant diversity and below-ground microbial diversity has been implied in studies dedicated to assessing the role of macrophyte diversity on the stability, resilience, and functioning of ecosystems . Indeed, above-ground plant communities have long been assumed to drive below-ground microbial diversity, but to date very little is known as to how plant species composition and diversity influence the community composition of micro-organisms in the soil . We examined this relationship in fields subjected to different above-ground biodiversity treatments and in field experiments designed to examine the influence of plant species on soil-borne microbial communities . Culture-independent strategies were applied to examine the role of wild or native plant species composition on bacterial diversity and community structure in bulk soil and in the rhizosphere . In comparing the influence of Cynoglossum officinale (hound's tongue) and Cirsium vulgare (spear thistle) on soil-borne bacterial communities, detectable differences in microbial community structure were confined to the rhizosphere . The colonisation of the rhizosphere of both plants was highly reproducible, and maintained throughout the growing season . In a separate experiment, effects of plant diversity on bacterial community profiles were also only observed for the rhizosphere . Rhizosphere soil from experimental plots with lower macrophyte diversity showed lower diversity, and bacterial diversity was generally lower in the rhizosphere than in bulk soil . These results demonstrate that the level of coupling between above-ground macrophyte communities and below-ground microbial communities is related to the tightness of the interactions involved . Although plant species composition and community structure appear to have little discernible effect on microbial communities inhabiting bulk soil, clear and reproducible changes in microbial community structure and diversity are observed in the rhizosphere. Antonie Van Leeuwenhoek, 2002 Aug, 81(1-4), 357 - 64 The consequences of volatile organic compound mediated bacterial and fungal interactions; Wheatley RE; Microbial interactions via infochemicals are fundamental to the development of spatial distribution and activity variations in ecosystems . Microorganisms produce a wide range of infochemicals, frequently secondary metabolites, most of which are soluble and many volatile . Volatile organic compounds (VOCs) have been identified in soil atmospheres and related to community structure and function . VOC profiles produced by microorganisms are consistent, relating to cultural conditions, environment and inputs, and so to population and function dynamics . VOC-mediated interactions can result in functional responses by the organisms involved that result in selective advantage to some community members . Positive, negative or neutral interactions can occur between a very wide range of soil bacteria and fungi . These effects include both stimulation and inhibition of growth, by 40 and 60%, respectively, and enzyme production . These effects are usually transient, e.g . removal of an antagonist is followed by complete recovery . Up- and down-regulation of gene expression, by mRNA and protein profiling has been demonstrated . VOCs have played an important role during the evolution of microorganisms in the context of their communities. Antonie Van Leeuwenhoek, 2002 Aug, 81(1-4), 343 - 51 Mycorrhizosphere interactions to improve plant fitness and soil quality; Barea JM et al.; Arbuscular mycoruhizal fungi are key components of soil microbiota and obviously interact with other microorganisms in the rhizosphere, i.e . the zone of influence of plant roots on microbial populations and other soil constituents . Mycorrhiza formation changes several aspects of plant physiology and some nutritional and physical properties of the rhizospheric soil . These effects modify the colonization patterns of the root or mycovrhizas (mycorrhizosphere) by soil microorganisms . The rhizosphere of mycorrhizal plants, in practice a mycorrhizosphere, harbors a great array of microbial activities responsible for several key ecosystem processes . This paper summarizes the main conceptual principles and accepted statements on the microbial interactions between mycorrhizal fungi and other members of rhizosphere microbiota and discusses current developments and future trends concerning the following topics: (i) effect of soil microorganisms on mycorrhiza formation; (ii) mycorrhizosphere establishment; (iii) interactions involved in nutrient cycling and plant growth; (iv) interactions involved in the biological control of plant pathogens; and (v) interactions to improve soil quality . The main conclusion is that microbial interactions in the rhizosphere of mycorrhizal plants improve plant fitness and soil quality, critical issues for a sustainable agricultural development and ecosystem functioning. Antonie Van Leeuwenhoek, 2002 Aug, 81(1-4), 293 - 308 Significance of predation by protists in aquatic microbial food webs; Sherr EB et al.; Predation in aquatic microbial food webs is dominated by phagotrophic protists, yet these microorganisms are still understudied compared to bacteria and phytoplankton . In pelagic ecosystems, predaceous protists are ubiquitous, range in size from 2 gm flagellates to > 100 microm ciliates and dinoflagellates, and exhibit a wide array of feeding strategies . Their trophic states run the gamut from strictly phagotrophic, to mixotrophic: partly autotrophic and partly phagotrophic, to primarily autotrophic but capable of phagotrophy . Protists are a major source of mortality for both heterotrophic and autotrophic bacteria . They compete with herbivorous meso- and macro-zooplankton for all size classes of phytoplankton . Protist grazing may affect the rate of organic sinking flux from the euphotic zone . Protist excretions are an important source of remineralized nutrients, and of colloidal and dissolved trace metals such as iron, in aquatic systems . Work on predation by protists is being facilitated by methodological advances, e.g., molecular genetic analysis of protistan diversity and application of flow cytometry to study population growth and feeding rates . Examples of new research areas are studies of impact of protistan predation on the community structure of prey assemblages and of chemical communication between predator and prey in microbial food webs. Antonie Van Leeuwenhoek, 2002 Aug, 81(1-4), 189 - 95 Origins and diversification of sulfate-respiring microorganisms; Stahl DA et al.; If the diversification of microbial life can be depicted as a single tree, as inferred by comparative sequencing of ribosomal RNAs, this could provide a framework for defining the order of emergence of new metabolic pathways . However, recent recognition that lateral gene transfer has been a significant force in microbial evolution has created uncertainty about the interpretation of taxonomies based on gene sequences . In this context, the origins and evolution of sulfate respiration will be evaluated considering the evolutionary history of a central enzyme in this process, the dissimilatory sulfite reductase . These studies suggest at least two major lateral transfer events during the early diversification of sulfate respiring microorganisms . The high sequence conservation of this enzyme has also provided a mechanism to directly explore the natural diversity of sulfate-respiring organisms using molecular techniques, avoiding the bias of culture-based identification . These studies suggest that the habitat range and evolutionary diversity of this key functional group of organisms is greater than now appreciated. Antonie Van Leeuwenhoek, 2002 Aug, 81(1-4), 117 - 33 Principles of the light-limited chemostat: theory and ecological applications; Huisman J et al.; Light is the energy source that drives nearly all ecosystems on planet Earth . Yet, light limitation is still poorly understood . In this paper, we present an overview of the principles of the light-limited chemostat . The theory for light-limited chemostats differs considerably from the standard theory for substrate-limited chemostats . In particular, photons cannot be mixed by vigorous stirring, so that phototrophic organisms experience the light-limited chemostat as a heterogeneous environment . Similar to substrate-limited chemostats, however, light-limited chemostats do reach a steady state . This allows the study of phototrophic microorganisms under well-controlled light conditions, at a constant specific growth rate, for a prolonged time . The theory of the light-limited chemostat is illustrated with several examples from laboratory experiments, and a variety of ecological applications are discussed. Antonie Van Leeuwenhoek, 2002 Aug, 81(1-4), 107 - 15 Trade-offs and coexistence in microbial microcosms; Bohannan BJ et al.; Trade-offs among the abilities of organisms to respond to different environmental factors are often assumed to play a major role in the coexistence of species . There has been extensive theoretical study of the role of such trade-offs in ecological communities but it has proven difficult to study such trade-offs experimentally . Microorganisms are ideal model systems with which to experimentally study the causes and consequences of ecological trade-offs . In model communities of E . coli B and T-type bacteriophage, a trade-off in E . coli between resistance to bacteriophage and competitive ability is often observed . This trade-off can allow the coexistence of different ecological types of E . coli . The magnitude of this trade-off affects, in predictable ways, the structure, dynamics and response to environmental change of these communities . Genetic factors, environmental factors, and gene-by-environment interactions determine the magnitude of this trade-off . Environmental control of the magnitude of trade-offs represents one avenue by which environmental change can alter community properties such as invasability, stability and coexistence. Antonie Van Leeuwenhoek, 2002 Aug, 81(1-4), 85 - 97 Molecular biology of extremophiles: recent progress on the hyperthermophilic archaeon Sulfolobus; Ciaramella M et al.; Extremophiles are microorganisms that flourish in habitats of extreme temperature, pH, salinity, or pressure . All extreme environments are dominated by microorganisms belonging to Archaea, the third domain of life, evolutionary distinct from Bacteria and Eucarya . Over the past few years the biology of extremophilic Archaea has stimulated a lot of interest, aimed at understanding at molecular level the adaptation to their life conditions, as well as their evolutionary relationships to other organisms . Here, we review recent insights in the molecular biology of thermoacidophilic Archaea of the genus Sulfolobus, which has been used as a model system for biochemical, structural, and genetic studies in Archaea and extremophiles in general . With the recent completion of the genome sequence of Sulfolobus solfataricus it is expected that these organisms will contribute new discoveries in the near future. Antonie Van Leeuwenhoek, 2002 Aug, 81(1-4), 73 - 83 Novel thermoactive glucoamylases from the thermoacidophilic Archaea Thermoplasma acidophilum, Picrophilus torridus and Picrophilus oshimae; Serour E et al.; The thermoacidophilic Archaea Thermoplasma acidophilum (optimal growth at 60 degrees C and pH 1-2), Picrophilus torridus and Picrophilus oshimae (optimal growth at 60 degrees C and pH 0.7) were able to utilize starch as sole carbon source . During growth these microorganisms secreted heat and acid-stable glucoamylases into the culture fluid . Applying SDS gel electrophoresis activity bands were detected with appearent molecular mass (Mw) of 141.0, 95.0 kDa for T . acidophilum, 133.0, 90.0 kDa for P . torridus and 140.0, 85.0 kDa for P . oshimae . The purified enzymes were incubated with various polymeric substrates such as starch, pullulan, panose and isomaltose . The product pattern, analyzed by HPLC, showed that in all cases glucose was formed as the sole product of hydrolysis . The purified glucoamylases were optimally active at pH 2.0 and 90 degrees C and have an isoelectric points (pI) between 4.5 and 4.8 . Enzymatic activity was detected even at pH 1.0 and 100 degrees C . The glucoamylases were thermostable at elevated temperature with a half-life of 24 h at 90 degrees C for both P . torridus and T acidophilum, and 20 h at 90 degrees C for P oshimae . The enzyme system of T acidophilum has a lower Km value for soluble starch (1.06 mg/ml) than the enzymes from P . oshimae and P . torridus (4.35 mg/ml and 2.5 mg/ml), respectively . Enzyme activity was not affected by Na+, Mg++, Ca++, Ni++, Zn++, Fe++, EDTA and DTT. Mol Biol Evol, 2002 Dec, 19(12), 2265 - 76 Evolution of microbial genomes: sequence acquisition and loss; Berg OG et al.; We present models describing the acquisition and deletion of novel sequences in populations of microorganisms . We infer that most novel sequences are neutral . Thus, sequence duplications and gene transfer between organisms sharing the same environment are rarely expected to generate adaptive functions . Two classes of models are considered: (1) a homogeneous population with constant size, and (2) an island model in which the population is subdivided into patches that are in contact through slow migration . Distributions of gene frequencies are derived in a Moran model with overlapping generations . We find that novel, neutral or near-neutral coding sequences in microorganisms will not be fixed globally because they offer large target sizes for mutations and because the populations are so large . At most, such genes may have a transient presence in only a small fraction of the population . Consequently, a microbial population is expected to have a very large diversity of transient neutral gene content . Only sequences that are under strong selection, globally or in individual patches, can be expected to persist . We suggest that genome size is maintained in microorganisms by a quasi-steady state mechanism in which random fluctuations in the effective acquisition and deletion rates result in genome sizes that vary from patch to patch . We assign the genomic identity of a global population to those genes that are required for the participation of patches in the genetic sweeps that maintain the genomic coherence of the population . In contrast, we stress the influence of sequence loss on the isolation and the divergence (speciation) of novel patches from a global population. Med Hypotheses, 2002 Dec, 59(6), 626 - 9 The psychological puzzle presented by physiological acts; Seely S; Physiological acts present the puzzle that we are unable to explain how we performed them, how we solved the technical difficulties involved in their execution . For instance, when we sing, we produce various musical notes by changing the shape of the larynx . The normal person does not even know what the larynx looks like, let alone its configurations corresponding to various notes and the combination of the 19 muscles acting on the larynx that has to be activated to bring about the required configuration . Some psychologists offer the explanation that the technical details are worked out by a computer-like mechanism . But how could a computer start controlled cell proliferation in the repair of an injury? Another idea (originally put forward by Leibniz around 1700) is the complex character of the mind . The mind may incorporate a multitude of personalities . Subordinate personalities, some, perhaps, specialising on various tasks, may carry out the orders of the commanding personality . Objection: most physiological tasks, for instance digestion or the fight against invading microorganisms, are completely unconscious . The 'myself' personality could not even issue commands regarding the repair of injuries or the fight against microorganisms . PROPOSED SOLUTION: At an early stage of evolution the body of a higher animal divides itself into three compartments, each specialising on a different task of life . The three parts correspond to the entoderm, mesoderm and ectoderm appearing at an early part of ontogenetic development . The task of the entoderm is metabolism, that of the mesoderm mainly the mechanical aspects of life, that of the ectoderm gathering information from and reacting to the outside world . Each of these is probably of a composite character . The myself personality is the equivalent of the ectoderm, not of the whole body . The technical details of its commands are worked out by subordinate personalities . So are the commands of the mesodermal and entodermal divisions . Dreams could be attempts of communication between the germ layers . Clin Microbiol Infect, 2002 Nov, 8(11), 749 - 52 Detection of Brucella melitensis by the BacT/Alert automated system and Brucella broth culture; Ozkurt Z et al.; This study was conducted to evaluate the ability of the BacT/Alert automated blood culture system to detect Brucella spp . in comparison with traditional Brucella broth culture . Overall, 100 (50 bone marrow and 50 blood samples) paired cultures were obtained, and 59 were positive by at least one method . The Brucella broth culture method detected all 59 positive cultures (100%), and the BacT/Alert system detected 30 (50.8%) (P < 0.05) . The mean detection times for B . melitensis were 4.5 days in the BacT/Alert system and 5 days in Brucella broth culture (P > 0.05) . There is no significant difference between the two methods with respect to growth time of the microorganism, but Brucella broth culture is more sensitive than the BacT/Alert system. J Nat Prod, 2002 Nov, 65(11), 1683 - 4 A new carotenoid glycosyl ester isolated from a marine microorganism, Fusarium strain T-1; Sakaki H et al.; A new carotenoid glycosyl ester, neurosporaxanthin beta-D-glucopyranoside (2), together with neurosporaxanthin (1), beta-carotene, gamma-carotene, and torulene were isolated from cultured cells of a marine microorganism, strain T-1, which was identified as Fusarium sp . Their structures were determined by chemical and spectral data. Med Sci Monit, 2002 Nov, 8(11), BR454 - 9 Uric acid is a main electron donor to peroxidases in human blood plasma; Padiglia A et al.; BACKGROUND: Peroxidases are widely distributed and have been isolated from many higher-order plants, animal tissues, yeast and microorganisms . During measurements of peroxidase activities in samples of human plasma, we noticed the presence of a compound in the plasma which was interfering with the peroxidase assay . In this paper we describe the purification and characterization of this factor, which was identified as uric acid . MATERIAL/METHODS: The procedure used to purify uric acid from plasma involved ultra-filtration of the plasma, heat denaturation, DEAE-cellulose chromatography, and high performance liquid chromatography . The lyophilized powder was tested for homogeneity using an HPLC apparatus and capillary electrophoresis . Genuine uric acid samples were used for comparison . RESULTS: The compound obtained by the above-reported purification procedure was identified as uric acid by spectrophotometric analysis through comparison with genuine uric acid samples . Spectrophotometric measurements indicated that uric acid was degraded by HRP in the presence of H2O2 . CONCLUSIONS: The experimental procedures described above allowed us to isolate and identify uric acid as the component in human plasma that acts as a true substrate for peroxidases. Microbes Infect, 2002 Nov, 4(13), 1327 - 33 Human herpesvirus 6 and Chlamydia pneumoniae as etiologic agents in multiple sclerosis - a critical review; Swanborg RH et al.; Multiple sclerosis (MS) is thought by many investigators to have an infectious component, and several microorganisms have been associated with the disease during the last three decades . Recent studies have implicated both human herpesvirus 6 (HHV-6) and the obligate intracellular bacterium Chlamydia pneumoniae in the etiology of MS . As with earlier studies of other potential agents, however, evidence linking either of these organisms to the disease is equivocal . In this article, we review data for and against involvement of HHV-6 and C . pneumoniae in MS, as well as evidence concerning auxiliary factors, such as possession of the APOE epsilon4 allele, which may influence the role of these organisms in pathogenesis . Further, we suggest several lines of investigation that should clarify whether either or both pathogens are associated meaningfully with this disease. J Basic Microbiol, 2002, 42(6), 396 - 407 Diversity of microfungi in the phylloplane of plants growing in a Mediterranean ecosystem; Pereira PT et al.; Mediterranean ecosystems have not been investigated as natural habitats for microorganisms in general, and microfungi in particular . Plants harvested in "Serra da Arrabida" (38 degrees 27' N, 9 degrees 02' W), a Mediterranean ecosystem in Portugal, were analyzed for the filamentous microfungi inhabiting their surface . Two field locations with distinct climatic characteristics were studied: 'Fonte do Veado' (38 degrees 28'50" N, 9 degrees 0'17" W; 300 m elevation) located on the northern slope, and 'Mata do Solitario' (38 degrees 27'55" N, 8 degrees 59'35" W; 50 m elevation), on the southern slope . From Veado zone, leaf samples yielded a total of 3,049 isolates, ranging from 317 to 1,328/sample (mean = 762) . The number of species/sample ranged from 12 to 24 . From Solitario zone, leaf samples yielded a total of 1,337 isolates, ranging from 189 to 528/sample (mean = 334) . The number of species/sample, in this case, ranged from 10 to 17 . Veado zone showed a wider range of species . The fungal species more frequently isolated from both zones (Aureobasidium pullulans (De Bary) Arnaud, Cladosporium cladosporioides (Fresen.) De Vries, C . sphaerospermum Penzig and Alternaria alternata (Fr.) Keissler) were found in all plant samples and represents 80% (Veado) and 85% (Solitario) of the total isolates. Curr Opin Ophthalmol, 2002 Dec, 13(6), 393 - 6 Sarcoidosis; Jones NP; Sarcoidosis commonly involves the eye, causing uveitis, the lacrimal gland, and the cranial nerves, including the optic nerve itself . Several microorganism types have recently been located in sarcoid granulomas, suggesting an infective cause in predisposed individuals . The approach to diagnosis has been refined, including the use of high-resolution computed tomography of the chest . New ophthalmic manifestations have been described, suggesting a wider role for sarcoidosis in intraocular inflammation, and indocyanine green angiography has clarified choroidal involvement . Immunosuppressive and anticytokine treatments can be effective in severe systemic sarcoidosis and should be considered in sight-threatening disease. Protein Sci, 2002 Dec, 11(12), 2958 - 68 Cloning, overexpression, and characterization of a bacterial Ca2+-dependent phospholipase D; Yang H et al.; Phospholipase D (PLD), an important enzyme involved in signal transduction in mammals, is also secreted by many microorganisms . A highly conserved HKD motif has been identified in most PLD homologs in the PLD superfamily . However, the Ca(2+)-dependent PLD from Streptomyces chromofuscus exhibits little homology to other PLDs . We have cloned (using DNA isolated from the ATCC type strain), overexpressed in Escherichia coli (two expression systems, pET-23a(+) and pTYB11), and purified the S . chromofuscus PLD . Based on attempts at sequence alignment with other known Ca(2+)-independent PLD enzymes from Streptomyces species, we mutated five histidine residues (His72, His171, His187, His200, His226) that could be part of variants of an HKD motif . Only H187A and H200A showed dramatically reduced activity . However, mutation of these histidi