J Lipid Res . 2005 Jan 16; {Epub ahead of print} Paying the price for pathogen protection: toll receptors in atherogenesis; Tobias P et al.; Atherosclerosis is a chronic inflammatory response characterized by the accumulation of cells of innate and acquired immune systems within the intima of the arterial wall . Macrophages are the predominant participant in innate immune responses in atherosclerosis . Protein receptors expressed by macrophages and endothelial cells recognize components and products of microorganisms and play a vital role in innate immunity . In particular the members of the toll-like receptor or TLR family play a critical role in the inflammatory components of atherosclerosis . Both exogenous ligands involved in microbial recognition as well as endogenous ligands involved in sterile inflammation pathways are implicated in the pathology of atherosclerosis . In this review we discuss our current understanding of the role of TLRs and their co-activators in atherosclerosis with particular emphasis on studies in atherosclerosis-prone hypercholesterolemic mice. Vestn Ross Akad Med Nauk, 2004, (11), 29 - 32 {Experimental evaluation of possible transmission of human alpha-2 interferon artificial gene to other microorganism species}; Effects of elevated atmospheric CO2 concentrations on soil microorganisms; School of Biological Sciences, University of Wales, Bangor LL57 2UW, UKEffects of elevated CO(2) on soil microorganisms are known to be mediated by various interactions with plants, for which such effects are relatively poorly documented . In this review, we summarize and synthesize results from studies assessing impacts of elevated CO(2) on soil ecosystems, focusing primarily on plants and a variety the of microbial processes . The processes considered include changes in microbial biomass of C and N, microbial number, respiration rates, organic matter decomposition, soil enzyme activities, microbial community composition, and functional groups of bacteria mediating trace gas emission such as methane and nitrous oxide . Elevated CO(2) in atmosphere may enhance certain microbial processes such as CH(4) emission from wetlands due to enhanced carbon supply from plants . However, responses of extracellular enzyme activities and microbial community structure are still controversy, because interferences with other factors such as the types of plants, nutrient availabilitial in soil, soil types, analysis methods, and types of CO(2) fumigation systems are not fully understood. Proc Natl Acad Sci U S A . 2005 Jan 12; {Epub ahead of print} Nanoscale environments associated with bioweathering of a Mg-Fe-pyroxene; Benzerara K et al.; Microorganisms are believed to create microenvironments leading to reaction products not predictable from equilibrium thermodynamics and to unique biomineral morphologies . Unambiguous evidence for such environments is, however, rare in natural samples . We have used scanning transmission x-ray microscopy and spectromicroscopy at the sub-40-nm scale, coupled with transmission electron microscopy, to examine bioweathering products on a meteoritic Fe-Mg-orthopyroxene colonized by a filamentous microorganism . Our measurements reveal an amorphous Al-rich layer beneath the microorganism, calcium carbonates of unique morphology intimately associated with polysaccharides adjacent to the microorganism, and regions surrounding the microorganism with different iron oxidation states . Our results confirm the presence of different microenvironments at this microorganism-mineral interface and provide unique nanometer-scale views of microbially controlled pyroxene weathering products. Ital J Biochem, 2004 Jul, 53(2), 87 - 91 The effect of hydrocarbon addition on the deamidation rate in immune whey proteins; Bibov MY et al.; The influence of some hydrocarbons that are often used at different stages of immunobiological preparation's production as stabilizers of biological activity on the dynamics of nonenzymatic deamidation in proteins of immune whey against conditionally pathogenic microorganisms obtained by means of membrane ultrafiltration technology is investigated . Preparations of whey were incubated in 10 per cent solutions of glucose, fructose and sorbitol at the conditions similar to physiological ones (0.9% NaCl, pH 5.5) and temperature of about +4 degrees C and +35 degrees C for 7, 14 and 28 days . A sample dissolved in 0.9% NaCl (pH 5.5) without addition of hydrocarbons was used as a "control preparate" . All explored substances brought about the suppressive effect on deamidation rate of asparaginyl residues whereas that of glutaminyl residues, on the contrary, was obviously increased . The possible reasons for these observations are discussed. Crit Care Med, 2005 Jan, 33(1), 115 - 9 Ventilator-associated pneumonia using a closed versus an open tracheal suction system; Lorente L et al.; OBJECTIVE:: The aim of this study was to analyze the prevalence of ventilator-associated pneumonia (VAP) using a closed-tracheal suction system vs . an open system . DESIGN:: Prospective and randomized study, from October 1, 2002, to December 31, 2003 . SETTING:: A 24-bed medical-surgical intensive care unit in a 650-bed tertiary hospital . PATIENTS:: Patients requiring mechanical ventilation for >24 hrs . INTERVENTIONS:: Patients were randomized into two groups; one group was suctioned with the closed-tracheal suctioning system and another group with the open system . MEASUREMENTS:: Throat swabs were taken at admission and twice a week until discharge to classify pneumonia in endogenous and exogenous . MAIN RESULTS:: A total of 443 patients (210 with closed-tracheal suction system and 233 with the open system) were included . There were no significant differences between groups of patients in age, sex, diagnosis groups, mortality, number of aspirations per day, and Acute Physiology and Chronic Health Evaluation II score . No significant differences were found in either the percentage of patients who developed VAP (20.47% vs . 18.02%) or in the number of VAP cases per 1000 mechanical ventilation-days (17.59 vs . 15.84) . There were also no differences in the VAP incidence by mechanical ventilation duration . At the same time, we did not find any differences in the incidence of exogenous VAP . Likewise, there were also no differences in the microorganisms responsible for pneumonia . Patient cost per day for the closed suction was more expensive than the open suction system ($11.11 +/- $2.25 vs . $2.50 +/- $1.12, p < .001) . CONCLUSION:: We conclude that in our study, the closed-tracheal suction system did not reduce VAP incidence, even for exogenous pneumonia. Reprod Biol Endocrinol . 2005 Jan 11;3(1):3 {Epub ahead of print} PGF2alpha induced differential expression of genes involved in turnover of extracellular matrix in rat decidual cells; Callegari EA et al.; In the rat, the decidual tissue is an important component for maternal recognition of pregnancy . Decidualization can be induced by either the implantation of the blastocyst or by artificial stimuli . The process of decidua formation or decidualization, is characterized by growth and differentiation of endometrial stromal cells . Prostaglandin F2alpha (PGF2alpha) has been shown to be involved in inhibition of implantation, alteration of embryo development, induction of luteal regression, and the mediation of pregnancy loss induced by microorganism infections . In order to establish a direct role for PGF2alpha in decidual function, we have evaluated its effects on the expression of an extensive array of genes using primary decidual cell culture . Upon treatment with PGF2alpha sixty genes were significantly down-regulated whereas only six genes were up-regulated (from a total of 1176 genes studied) . Interestingly, the majority of the genes inhibited by PGF2alpha are either directly or indirectly involved in the turnover of the extracellular matrix (ECM) . Genes such as gelatinase A (MMP2), cathepsin L, tissue inhibitor metalloproteinases 2 (TIMP2) and 3 (TIMP3), plasminogen activator inhibitor1 (PAI1), tissue type plasminogen activator (tPA), urokinase plasminogen activator (tPA), endothelin 1, calponin, carboxypeptidase D and calponin acidic were down regulated . The opposite effect was observed for prostromelysin 53 kDa (proMMP3), plasma proteinase I alpha and alpha 1 antiproteinase, all of which were significantly up-regulated by PGF2alpha . The results strongly suggest that the abortificient role of elevated levels of PGF2alpha after implantation is due, in large part, to inhibition of genes involved in the normal turnover of the extracellular matrix necessary for decidual formation. Oral Dis, 2005 Jan, 11(1), 22 - 6 Outcome following treatment for Helicobacter pylori in patients with recurrent aphthous stomatitis; Albanidou-Farmaki E et al.; Objective: The aim of the current study was to investigate any association of Helicobacter Pylori (HP) in recurrent aphthous stomatitis (RAS) and the effect of eradication of the microorganism in the clinical course of the disease . Study design: Forty-eight patients with RAS were included in the study . Twenty-six were women and 22 men, of average age 41.3 +/- 2.44 . Thirty-four out of these 48 patients were HP positive and the rest 14 who were negative were used as a control group . The diagnosis of HP infection was based on the detection of specific immunoglobulin G (IgG), and immunoglubulin A (IgA) antibodies using the enzyme-linked immunoabsorbent assay technique in the serum and the saliva of the patients . In all HP carriers an eradication therapy was administered . After a 2-month period the patients were checked for HP status, using (13) C-UBT . The follow up period was 6-12 months following the eradication therapy . Results: At entry patients with HP infection suffered from more severe symptoms compared with HP negative patients (P < 0.05) . After the administration of HP eradication therapy, patients who had become negative showed a remarkable improvement (62.5%) with reference to recurrence of RAS as well as to symptom intensity . In 29.2% of patients symptoms had disappeared and in 33.3% of patients there was a decrease in both the frequency of recurrence and the intensity of symptoms . After the eradication treatment, the periods between recurrence of RAS in patients who had become negative were statistically significantly longer compared with those before treatment (P < 0.001) . Another important observation was that patients who became negative after eradication therapy were of comparable clinical status with those who were HP negative from the beginning of the study (P > 0.05) . Conclusions: These findings support the concept of a potential association between RAS and HP. J Adv Nurs, 2005 Jan, 49(2), 164 - 72 Evolutionary nursing: the case of infectious diseases; Purssell E; purssell e . (2005) Journal of Advanced Nursing49(2), 164-172 Evolutionary nursing: the case of infectious diseasesAim . The aim of this paper is to examine the effect of evolution on infectious diseases nursing, and propose a model that may help to increase understanding of how hosts and microorganisms co-exist and how humans can alter the delicate balance between them . Background and rationale . Infectious diseases occur as the result of interactions between hosts and microorganisms . There is an increasing acceptance that the evolution of host and parasite is important in the development of infectious diseases . However, such views have made little impact in nursing, and the use of evolutionary interventions remains controversial . Method . The Medline database was searched from 1966 to present using the terms pathogen$, virulen$, evolution, bacteria, and all combinations of these . Additionally reference lists of text books and papers were hand searched for relevant papers . Papers were selected from a variety of disciplines, including infectious diseases, microbiology, evolutionary biology, and ecology . Recurrent themes from these papers were identified and a model of evolutionary nursing constructed . Results . Microorganisms are plentiful, ubiquitous, and rapidly evolving by comparison with humans and other animals . As a result of this, attempts to 'outwit' them have been, and are, doomed to failure . However, through careful management of public and personal health, a balance encouraging co-existence may be possible . A number of specific interventions is proposed . Conclusions . There are a number of key interventions that may reduce the virulence of microorganisms . With an increasing world population, antibiotic resistance and international travel, such an approach may be one way of reducing the morbidity associated with infectious diseases. Vnitr Lek, 1999 Mar, 45(3), 155 - 8 {Chlamydia pneumoniae and the risk of ischaemic heart disease . Prevalence in a group of hospitalized elderly men}; Icso J et al.; Chlamydia pneumoniae (CP) causes frequently nosocomial pneumonia and other inflammations of the upper and lower airways . Initially reports on the association between infection with CP and ischaemic heart disease (IHD) were published in 1988 by Saikku et al . who found a higher antibody titre against CP in acute myocardial infarction and sudden cardiac death as compared with a control group . The mechanism of this phenomenon is explained by the action of Chlamydiae on LDL-cholesterol, cytokines, the tumour necrotizing factor with a subsequent effect on the vascular wall . The authors assessed IgG and IgM antibodies in 39 elderly men using the immunofluorescent method . In addition they assessed the total cholesterol, LDL-cholesterol, triacylglycerol and fibrinogen . They divided the group into a sub-group with manifest IHD (n=22) and a control group without detectable IHD (n=17) . In patients with IHD they found an insignificantly higher prevalence of Ig antibodies against CP as compared with the control group (31.8% and 29.4% resp.).IgM antibodes were found more frequently in the control group as compared with patients with IHD . Total cholesterol and triacylglycerol were insignificantly higher, HDL cholesterol was lower in patients with IHD as compared with controls . Fibrinogen was paradoxically insignificantly higher in controls as compared with patients with IHD . The authors explain these findings by the fact that the group was formed by elderly men (mean age 73 and 68 years resp.) who had an equal chance of CP infection.At this age arteriosclerosis is already developed and the differences are only in severity and site of the process . In the conclusiuon the authors state that the role of CP, as well as of other microorganisms in the pathogenesis of atherosclerosis is probable, although their investigation did not confirm it unequivocally . It is important to consider also possible interactions of many known and newly detected risk factors. Appl Environ Microbiol, 2005 Jan, 71(1), 392 - 9 Use of Gradient Plates To Study Combined Effects of Temperature, pH, and NaCl Concentration on Growth of Monascus ruber van Tieghem, an Ascomycetes Fungus Isolated from Green Table Olives; Panagou EZ et al.; The effect of temperature, pH, and sodium chloride concentration on the growth of the Ascomycetes fungus Monascus ruber van Tieghem, the main spoilage microorganism during storage of table olives, was studied by using the gradient plate technique . Gradients of NaCl (3 to 9%, wt/vol) at right angles to gradients of pH (2 to 6.8) were prepared for the plates, which were incubated at 25, 30, and 35 degrees C . Visible fungal growth, expressed in optical density units, was recorded by image analysis and graphically presented in the form of three-dimensional grids . Results obtained from the plates indicated that the fungus was salt and acid tolerant, being able to grow at NaCl concentrations of up to 9% (wt/vol) and pH values of as low as 2.2, depending on the incubation temperature . The inhibitory effect of NaCl increased as the pH decreased progressively at 25 and 30 degrees C but not at 35 degrees C . Growth was better at 30 and 25 degrees C as judged by the larger extent of the plates covered by mycelium compared with that at 35 degrees C, where no growth was observed at pHs below 3.7 . Differentiation between vegetative (imperfect-stage) and reproductive (perfect-stage) growth was evident on all plates, providing useful information about the effect of environmental conditions on the form of fungal growth . When the growth/no-growth surface model was obtained by applying linear logistic regression, it was found that all factors (pH, NaCl, and temperature) and their interactions were significant . Plots of growth/no-growth interfaces for P values of 0.1, 0.5, and 0.9 described the results satisfactorily at 25 and 35 degrees C, whereas at 35 degrees C the model predicted lower minimum pH values for growth in the range of 7 to 10% NaCl than those observed on the plates . Overall, it is suggested that the fungus cannot be inhibited by any combination of pH and NaCl within the limits of the brine environment, so further processing is required to ensure product stability in the market. Appl Environ Microbiol, 2005 Jan, 71(1), 270 - 5 Different Inactivation Behaviors of MS-2 Phage and Escherichia coli in TiO2 Photocatalytic Disinfection; Cho M et al.; Despite a wealth of experimental evidence concerning the efficacy of the biocidal action associated with the TiO(2) photocatalytic reaction, our understanding of the photochemical mechanism of this particular biocidal action remains largely unclear . It is generally accepted that the hydroxyl radical (.OH), which is generated on the surface of UV-illuminated TiO(2), plays the main role . However, our understanding of the exact mode of action of the hydroxyl radical in killing microorganisms is far from complete, and some studies report that other reactive oxygen species (ROS) (H(2)O(2) and O(2).(-), etc.) also play significant roles . In particular, whether hydroxyl radicals remain bound to the surface or diffuse into the solution bulk is under active debate . In order to examine the exact mode of action of ROS in inactivating the microorganism, we tested and compared the levels of photocatalytic inactivation of MS-2 phage and Escherichia coli as representative species of viruses and bacteria, respectively . To compare photocatalytic microbial inactivation with the photocatalytic chemical degradation reaction, para-chlorobenzoic acid, which rapidly reacts with a hydroxyl radical with a diffusion-limited rate, was used as a probe compound . Two different hydroxyl radical scavengers, tert-butanol and methanol, and an activator of the bulk phase hydroxyl radical generation, Fe(2+), were used to investigate their effects on the photocatalytic mode of action of the hydroxyl radical in inactivating the microorganism . The results show that the biocidal modes of action of ROS are very different depending on the specific microorganism involved, although the reason for this is not clear . It seems that MS-2 phage is inactivated mainly by the free hydroxyl radical in the solution bulk but that E . coli is inactivated by both the free and the surface-bound hydroxyl radicals . E . coli might also be inactivated by other ROS, such as O(2).(-) and H(2)O(2), according to the present results. Appl Environ Microbiol, 2005 Jan, 71(1), 149 - 58 Activity and diversity of methanogens in a petroleum hydrocarbon-contaminated aquifer; Kleikemper J et al.; Methanogenic activity was investigated in a petroleum hydrocarbon-contaminated aquifer by using a series of four push-pull tests with acetate, formate, H(2) plus CO(2), or methanol to target different groups of methanogenic Archaea . Furthermore, the community composition of methanogens in water and aquifer material was explored by molecular analyses, i.e., fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes amplified with the Archaea-specific primer set ARCH915 and UNI-b-rev, and sequencing of DNA from dominant DGGE bands . Molecular analyses were subsequently compared with push-pull test data . Methane was produced in all tests except for a separate test where 2-bromoethanesulfonate, a specific inhibitor of methanogens, was added . Substrate consumption rates were 0.11 mM day(-1) for methanol, 0.38 mM day(-1) for acetate, 0.90 mM day(-1) for H(2), and 1.85 mM day(-1) for formate . Substrate consumption and CH(4) production during all tests suggested that at least three different physiologic types of methanogens were present: H(2) plus CO(2) or formate, acetate, and methanol utilizers . The presence of 15 to 20 bands in DGGE profiles indicated a diverse archaeal population . High H(2) and formate consumption rates agreed with a high diversity of methanogenic Archaea consuming these substrates (16S rRNA gene sequences related to several members of the Methanomicrobiaceae) and the detection of Methanomicrobiaceae by using FISH (1.4% of total DAPI {4',6-diamidino-2-phenylindole}-stained microorganisms in one water sample; probe MG1200) . Considerable acetate consumption agreed with the presence of sequences related to the obligate acetate degrader Methanosaeata concilii and the detection of this species by FISH (5 to 22% of total microorganisms; probe Rotcl1) . The results suggest that both aceticlastic and CO(2)-type substrate-consuming methanogens are likely involved in the terminal step of hydrocarbon degradation, while methanogenesis from methanol plays a minor role . DGGE profiles further indicate similar archaeal community compositions in water and aquifer material . The combination of hydrogeological and molecular methods employed in this study provide improved information on the community and the potential activity of methanogens in a petroleum hydrocarbon-contaminated aquifer. Yi Chuan, 2003 Nov, 25(6), 757 - 61 {Advances of salt-tolerant mechanism in yeast.}; Fu C et al.; Yeast is a model eukoryotic organism and salt-tolerant microorganism.The regulative mechanism of gene expression and signal transduction and ion transport of yeast is similar to that of higher eukoryotic organism.The research on salt-tolerant mechanism of yeast will be helpful to the illustrate the salt-tolerant mechanism of higher eukoryotic organism.This review summarized the signal transduction pathway and molercular responses of yeast under salt stress and the major research methods in the research on the salt-tolerant mechenism in yeast. Yi Chuan, 2003 Sep, 25(5), 623 - 7 {Horizontal gene transfer.}; Ou JH et al.; In this paper the conception of horizontal gene transfer (HGT) was introduced,and main mode of HGT was also enumerated as follows:HGT by medium such as plasmid and virus etc.and the HGT without any medium.The transfer of genes from one species to another especially between remote species was emphasized by the information from genome sequencing.The problems about evolution phylogenies and safety of GEMs (gene engineered microorganisms) for HGT were discussed. Lancet, 2005 Jan 1, 365(9453), 63 - 78 Septic shock; Annane D et al.; Septic shock, the most severe complication of sepsis, is a deadly disease . In recent years, exciting advances have been made in the understanding of its pathophysiology and treatment . Pathogens, via their microbial-associated molecular patterns, trigger sequential intracellular events in immune cells, epithelium, endothelium, and the neuroendocrine system . Proinflammatory mediators that contribute to eradication of invading microorganisms are produced, and anti-inflammatory mediators control this response . The inflammatory response leads to damage to host tissue, and the anti-inflammatory response causes leucocyte reprogramming and changes in immune status . The time-window for interventions is short, and treatment must promptly control the source of infection and restore haemodynamic homoeostasis . Further research is needed to establish which fluids and vasopressors are best . Some patients with septic shock might benefit from drugs such as corticosteroids or activated protein C . Other therapeutic strategies are under investigation, including those that target late proinflammatory mediators, endothelium, or the neuroendocrine system. APMIS, 2004 Dec, 112(11-12), 930 - 6 Impact of pathogenicity islands in bacterial diagnostics; Oelschlaeger TA et al.; Oelschlaeger TA, Hacker J . Impact of pathogenicity islands in bacterial diagnostics . APMIS 2004;112:930-6.Pathogenicity islands (PAIs) are a distinct class of genomic islands (GEIs), which are acquired by horizontal gene transfer . PAIs harbour virulence genes and some, in addition, antibiotic resistance genes . More often genes conferring antibiotic resistance are encoded by GEIs not containing virulence genes . Both types of genetic elements are found in genomes of various human, animal and plant pathogens . There are PAIs and GEIs which are specific for a certain serotype(s), strain, or pathotype of a species . Furthermore, there are also PAIs which are more widespread and found in bacterial pathogens causing a certain pathogenic effect in the host . Even the lack of a certain PAI might be characteristic for a defined subspecies . Obviously, PAIs can be used as markers for diagnostic purposes to help identify a certain bacterial pathogen, subtype it, estimate the pathogenic potential, and in some cases predict its antibiotic resistance . This all might be achieved for known PAIs/GEIs without cultivating the microorganism of interest by employing PCR and/or DNA-chip technology . Even yet unknown PAIs can be identified in silico if the genome sequence of the bacterial pathogen under investigation is known . The more PAIs and antibiotic harbouring GEIs are identified and characterized the greater will be the benefits also for diagnostics. Curr Pharm Des, 2005, 11(1), 11 - 6 The importance of guidelines in the development and application of probiotics; Reid G; Probiotics, defined as "Live microorganisms which when administered in adequate amounts confer a health benefit on the host" have many attributes including the lack of adverse side effects associated with their use . While probiotics have proven benefits, the optimism associated with their use is counterbalanced by the fact that many so-called "probiotic" products are unreliable in content and unproven clinically . Therefore much remains to be done to gain the acceptance of the broader medical community . Recognition of the obvious product inequality and the lack of any regulatory guidelines lead to the development of Operating Standards in 2002 (FAO/WHO), that would ensure product safety, reliability and a level playing field for all companies producing probiotic products . The guidelines constitute a set of parameters required for a product/strain to be termed "probiotic" and also the clinically relevant steps to be followed to move probiotics closer to being embraced by the medical community . These include i) implementation of Guidelines for use of probiotics; ii) phase I, II and III clinical trials to prove health benefits that are as good as or better than standard prevention or treatments for a particular condition or disease; iii) Good Manufacturing Practice and production of high quality products; iv) studies to identify mechanism of action in vivo; v) informative/ precise labelling; vi) development of probiotic organisms that can carry vaccines to hosts and/or anti- viral probiotics; vii) expansion of proven strains to benefit the oral cavity, nasopharynx, respiratory tract, stomach, vagina, bladder and skin as well as for cancer, allergies and recovery from surgery/ injury. Infect Control Hosp Epidemiol, 2004 Dec, 25(12), 1077 - 82 Periodically changing ventilator circuits is not necessary to prevent ventilator-associated pneumonia when a heat and moisture exchanger is used; Lorente L et al.; OBJECTIVE: To analyze the efficacy of periodically changing ventilator circuits for decreasing the rate of ventilator-associated pneumonia when a heat and moisture exchanger (HME) is used for humidification . The Centers for Disease Control and Prevention recommended not changing the circuits periodically . DESIGN: Randomized, controlled trial conducted between April 2001 and August 2002 . SETTING: A 24-bed, medical-surgical intensive care unit in a 650-bed, tertiary-care hospital . PATIENTS: All patients requiring mechanical ventilation during more than 72 hours from April 2001 to August 2002 . INTERVENTIONS: Patients were randomized into two groups: (1) ventilation with change of ventilator circuits every 48 hours and (2) ventilation with no change of circuits . Throat swabs were taken on admission and twice weekly until discharge to classify pneumonia as endogenous or exogenous . RESULTS: Three hundred four patients (143 from group 1 and 161 from group 2) with similar characteristics (age, gender, Acute Physiology and Chronic Health Evaluation II score, diagnostic group, and mortality) were analyzed . There was no significant difference in the rate of pneumonia between the groups (23.1% vs 23.0% and 15.5 vs 14.8 per 1,000 ventilator-days) . There was no significant difference in the incidence of exogenous pneumonia per 1,000 days of mechanical ventilation (1.71 vs 1.25) . There was no difference in the distribution of microorganisms causing pneumonia . CONCLUSIONS: Circuit change using an HME for humidification does not decrease pneumonia and represents an unnecessary cost. Zh Mikrobiol Epidemiol Immunobiol, 2004 Nov-Dec, (6), 113 - 21 {Bartonella and bartonellosis--emerging and re-emerging infections . Taxonomy, bacteriology, pathogenesis and genetics}; Identification of Helicobacter pylori DNA in Iranian patients with gallstones; Professor Alborzi Clinical Microbiology Research Centre, Shiraz University of Medical Sciences, Shiraz, Iran . s_farshad@yahoo.com In order to identify Helicobacter in gallstones of Iranian patients with biliary disease, gallstone and bile samples from 33 patients were subjected to rapid urease test, culture and Multiplex PCR using primers based on 16s rRNA and isocitrate dehydrogenase genes for the identification of Helicobacter genus and H . pylori respectively . This PCR was also done on bile samples from 40 autopsied gallbladders with normal pathology (control group) . In 18.1% of stone and 12.1% of bile samples, H . pylori DNA was detected using PCR . Rapid urease and culture tests were negative for all samples . The PCR was negative in the control group . In conclusion, H . pylori DNA was detected in stone samples of Iranian patients with gallstones but we are not sure of their viability . To clarify the clinical role of Helicobacter in gallbladder diseases, studies using accurate tests on larger patient and control groups are needed to ascertain whether this microorganism is an innocent bystander or active participant in gallstone formation. Am J Otolaryngol, 2005 January-February, 26(1), 51 - 53 Cold dissection versus bipolar cauterizing tonsillectomy for bacteriemia; Kocaturk S et al.; Abstract Objective The purpose of this study is to compare transient bacteriemia ratios between cold dissection tonsillectomy and bipolar cauterizing tonsillectomy, and also to analyze the bacteria detected with superficial/central tonsillar cultures . Methods A total of 86 patients that were grouped as 46 patients of cold dissection tonsillectomy and 40 patients of bipolar cauterizing tonsillectomy were included in this study . Preoperative surface swab cultures, intraoperative central swab cultures of tonsils, and preoperative and postoperative blood culture samples were obtained . Antibiotic sensitivity tests were determined . Fischer exact chi 2 test was performed to compare the results of postoperative bacteriemia of both techniques statistically . Results Postoperative bacteriemia was detected in 6 (13%) patients of cold dissection tonsillectomy group . In 5 (83.3%) of the 6 postoperative bacteriemia patients of cold dissection tonsillectomy group, isolated microorganism was confirmed both in the blood cultures and in the central swab cultures of tonsils, and resistance to penicillin was established . No patient of bipolar cauterizing tonsillectomy group appeared with postoperative bacteriemia . There was a statistically significant difference ( P = .028) for postoperative bacteriemia between cold dissection tonsillectomy group and bipolar cauterizing tonsillectomy group . Conclusion We recommend bipolar cauterizing tonsillectomy for high-risk patients. J Clin Microbiol, 2005 Jan, 43(1), 445 - 7 Controlled clinical comparison of plastic versus glass bottles of BacT/ALERT PF medium for culturing blood from children; Petti CA et al.; The plastic pediatric BacT/ALERT (bioMerieux, Durham, N.C.) PF (PPF) is a new nonvented aerobic culture medium in a clear plastic bottle designed to prevent breakage . We compared the performance of the new PPF bottle to that of the present glass BacT/ALERT PF bottle for the recovery of microorganisms as well as for the time to detection of growth in samples of blood obtained for culture from children . We found that the PPF and PF bottles were comparable for recovery of microorganisms and that the safety advantage of plastic bottles can be achieved without compromising performance. J Immunol, 2005 Jan 15, 174(2), 1046 - 54 Restricted IgA repertoire in both B-1 and B-2 cell-derived gut plasmablasts; Stoel M et al.; Mucosal IgA is the most abundantly produced Ig upon colonization of the intestinal tract with commensal organisms in the majority of mammals . The repertoire of these IgA molecules is still largely unknown; a large amount of the mucosal IgA cannot be shown to react with the inducing microorganisms . Analysis of the repertoire of used H chain Ig (V(H)) genes by H-CDR3 spectrotyping, cloning, and sequencing of V(H) genes from murine intestinal IgA-producing plasma cells reveals a very restricted usage of V(H) genes and multiple clonally related sequences . The restricted usage of V(H) genes is a very consistent observation, and is observed for IgA plasma cells derived from B-1 or conventional B-2 cells from different mouse strains . Clonal patterns from all analyzed V(H) gene sequences show mainly independently acquired somatic mutations in contrast to the clonal evolution patterns often observed as a consequence of affinity maturation in germinal center reactions in peripheral lymphoid organs and Peyer's patches . Our data suggest a model of clonal expansion in which many mucosal IgA-producing B cells develop in the absence of affinity maturation . The affinity of most produced IgA might not be the most critical factor for its possible function to control the commensal organisms, but simply the abundance of large amounts of IgA that can bind with relatively unselected affinity to redundant epitopes on such organisms. J Immunol, 2005 Jan 15, 174(2), 671 - 9 Phagocytosis-induced apoptosis in macrophages is mediated by up-regulation and activation of the bcl-2 homology domain 3-only protein bim; Kirschnek S et al.; Cell death by apoptosis is important in immune cell homeostasis and in the defense against infectious microorganisms . The physiological event of uptake and intracellular destruction of bacteria is a powerful apoptotic stimulus to macrophages and neutrophil granulocytes . In this study, we provide a molecular analysis of phagocytosis-induced apoptosis . Apoptosis was blocked by Bcl-2 in a mouse macrophage cell line and in primary mouse macrophages . Analysis of the upstream mechanisms revealed that apoptosis was triggered by the Bcl-2 homology domain 3-only protein Bim/Bod . Contact with bacteria or bacterial components induced a strong increase in Bim-expression through TLR and MyD88 . Inhibition of the MAPK p38 and JNK reduced both up-regulation of Bim and apoptosis . Phosphorylation of Bim was further observed in mouse macrophages, which appeared to be the result of TLR-dependent phosphatase inhibition . Although TLR-induced Bim was, unlike Bim in resting cells, not bound to the microtubuli cytoskeleton, the up-regulation of Bim was not sufficient to cause apoptosis . A second signal was required that was generated in the process of phagocytosis . Phagocytosis-induced apoptosis was strongly reduced in Bim(-/-) macrophages . These data provide the molecular context of a form of apoptosis that may serve to dispose of terminally differentiated phagocytes. J Food Prot, 2004 Dec, 67(12), 2719 - 26 Efficacy of pasteurization conditions for the inactivation of Mycobacterium avium subsp . paratuberculosis in milk; Stabel JR et al.; Mycobacterium avium subsp . paratuberculosis, the causative agent of a chronic enteritis in ruminants (Johne's disease), has been linked to Crohn's disease in humans . This microorganism is shed by infected animals primarily in the feces but is also shed in the milk at much lower levels . Therefore, dairy products from infected animals may be one mode of transmission of this animal pathogen . This study was designed to evaluate the effectiveness of the holder and high-temperature short-time pasteurization standards on the destruction of M . paratuberculosis . One hundred eighty experiments were conducted in this study using a slug-flow pasteurizer unit and a laboratory scale pasteurizer unit . Ultrahigh-temperature milk was inoculated at two concentrations, 10(8) and 10(5) CFU/ml, with three different field strains of M . paratuberculosis . Five different time-temperature combinations were evaluated: 62.7 degrees C for 30 min, 65.5 degrees C for 16 s, 71.7 degrees C for 15 s, 71.7 degrees C for 20 s, and 74.4 degrees C for 15 s . Three replicates of each experiment were run for the pasteurizer unit, time-temperature combination, and strain of M . paratuberculosis . Treatment of milk regardless of bacterial strain or pasteurizer unit resulted in an average 5.0- and 7.7-log kill for the low and high concentrations of inoculum, respectively . Milk treated for cheese production (65.5 degrees C for 16 s) resulted in a much lower and more variable kill . Results from this study indicate that the current U.S . minimum standards for batch and high-temperature short-time pasteurization of grade A milk significantly reduced the survivability of M . paratuberculosis, but some bacteria survived subpasteurization heat treatment of milk used for cheese manufacture. J Zhejiang Univ Sci, 2005 Feb, 6(2), 147 - 54 Studies on nutrient uptake of rice and characteristics of soil microorganisms in a long-term fertilization experiments for irrigated rice; Zhang QC et al.; The ecosystem characteristics of soil microorganism and the nutrient uptake of irrigated rice were investigated in a split-block experiment with different fertilization treatments, including control (no fertilizer application), PK, NK, NP, NPK fertilization, in the main block, and conventional rice and hybrid rice comparison, in the sub block . Average data of five treatments in five years indicated that the indigenous N supply (INS) capacity ranged from 32.72 to 93.21 kg/ha; that indigenous P supply (IPS) capacity ranged from 7.42 to 32.25 kg/ha; and that indigenous K supply (IKS) capacity ranged from 16.24 to 140.51 kg/ha, which showed that soil available nutrient pool depletion might occur very fast and that P, K deficiency has become a constraint to increasing yields of consecutive crops grown without fertilizer application . It was found that soil nutrient deficiency and unbalanced fertilization to rice crop had negative effect on the diversity of the microbial community and total microbial biomass in the soil . The long-term fertilizer experiment (LTFE) also showed that balanced application of N, P and K promoted microbial biomass growth and improvement of community composition . Unbalanced fertilization reduced microbial N and increased C/N ratio of the microbial biomass . Compared with inbred rice, hybrid rice behavior is characterized by physiological advantage in nutrient uptake and lower internal K use efficiency. J Agric Food Chem, 2005 Jan 12, 53(1), 70 - 5 Factors affecting triadimefon degradation in soils; Singh N; The degradation of triadimefon {1-(4-chlorophenoxy)-3,3-dimethyl-1-(1H-1,2,4-triazol-1-yl)butan-2-one} was studied in two soils, mollisol and inseptisol, under varying conditions of moisture and temperature, and the role of cow manure amendment and soil sterilization on fungicide degradation was ascertained . The soil moisture content affected the pathway followed for triadimefon degradation . In nonflooded soils (60% water-holding capacity), triadimefon was reduced to triadimenol, and in flooded soils, it was metabolized to the diol derivative {1-(1H-1,2,4-triazol-1-yl)-3,3-dimethylbutan-2-one-1,4-diol} . In nonflooded soils, triadimefon was more persistent in soil having more organic carbon content (mollisol), and the amendment of cow manure (5%) further enhanced its persistence . On the contrary, in flooded soil systems, the higher the soil organic carbon content was, the less persistent was the fungicide, and amendment of cow manure further enhanced its degradation . Triadimefon degradation was faster at 35 degrees C than at 27 degrees C . Triadimefon degradation in soils was mediated by the microorganisms, and no triadimefon degradation was observed in sterile soils . Triadimefon (1 mg/kg) did not affect soil phosphatase activity in either of the soils; however, soil dehydrogenase activity was significantly reduced, especially in mollisol soil. Int Dent J, 2004 Dec, 54(6 Suppl 1), 344 - 51 Nutrition and oral health in Africa; Enwonwu CO et al.; Poverty, low birth weight, low life expectation at birth, widespread malnutrition, numerous endemic infections, little or no access to safe water, poor oral hygiene, deplorable environmental sanitation and political instability among other problems, characterise the lives of many Africans, particularly in sub-Saharan Africa . In African countries undergoing rapid urbanisation, health problems associated with undernutrition and overnutrition coexist, and these result from lifestyle changes which promote physical inactivity, increased consumption of fats and refined carbohydrates, as well as abuse of tobacco and alcohol . Thus, in several African countries, inflammatory oral diseases (e.g . periodontal diseases, acute necrotising gingivitis, noma) resulting from inappropriate interactions between microorganisms and the malnourished, immunocompromised host, have continued to pose serious health problems . There are suggestions of increasing incidence of squamous cell carcinoma, probably related to increased use of alcohol and tobacco, which elicit nutrient deficiencies and oxidative stress . Additionally, there is an increase in caries prevalence particularly in the poor urban areas . The latter is related not only to increased availability of refined sugars, but also to limited access to the caries preventive effects of fluorides . Good dietary practices through judicious combination of available foods should therefore feature prominently in the promotion of optimal oral health in Africa. Mycopathologia, 2004 Nov, 158(4), 427 - 30 First large-scale isolation of Prototheca zopfii from milk produced by dairy herds in Italy; Buzzini P et al.; A total of 1045 milk samples collected from infected and non infected quarters of 269 cows were investigated . This study showed that 4.7% of samples possessed cells of Prototheca spp . (10(6)cells/ml) . The presence of other pathogenic microorganisms was also monitored . Prototheca spp . isolates were classified on the basis of current taxonomic guidelines and identified as P . zopfii . Susceptibility tests carried out in vitro by using 25 antibiotic compounds revealed that the strains of P . zopfii . were susceptible only to nystatin and amphotericin B (58 and 33% of total strains, respectively) . The present study represents the first large-scale investigation carried out in Italy on the isolation of this achlorophyllous yeast-like microalga in milk samples produced by dairy herds. Bosn J Basic Med Sci, 2004 Feb, 4(1), 57 - 61 Etiological findings in endodontic-periodontal infections; Lacevic A et al.; The endodontium and periodontium are closely related and disease of one may lead to secondary disease in the other . The differential diagnosis of endodontic and periodontal disease is of vital importance, so that the appropriate treatment can be done . Microorganisms play a primary role in endodontic and periodontal infections . The magnitude of the host response will be directly proportional to the virulence and the number of microbial cells present . Tissue damage caused by bacteria is mediated by either direct or indirect mechanisms . Direct harmful effects caused by bacteria involve their products, such as enzymes (collagenase, hyaluronidase, condroitinase, acid phosphatase), exotoxins and metabolites (bytrate, propionate, ammonium polyamines, sulphured compounds) . In addition, bacterial components such as peptidoglycan, teichoic acid, fimbriae, outer membrane proteins, capsule, and lypopolysaccharide, stimulate the development of host immune reaction capable of causing severe tissue destruction. J Dermatol, 2004 Sep, 31(9), 741 - 7 Erythema nodosum and granulomatous lesions preceding acute myelomonocytic leukemia; Anan T et al.; A 65-year-old female with a one-month history of painful eruptions on her lower extremities was admitted to our hospital . Histological examination revealed erythema nodosum (EN), and the patient was treated with oral prednisolone (PSL; 20 mg daily) . The eruptions subsided in two weeks . One month later, painful reddish eruptions recurred on her upper limbs and abdomen in addition to her lower extremities . A skin biopsy from an abdominal erythematous plaque revealed a non-caseating granuloma without microorganisms or foreign-body materials . These eruptions also disappeared with treatment with oral PSL (20 mg daily) . No underlying disease, including sarcoidosis, diabetes mellitus, or rheumatoid arthritis, was found . However, five months later, the patient developed conspicuous leukocytosis . She was diagnosed with acute myelomonocytic leukemia (M4) and treated with chemotherapy . After complete remission had been achieved, the EN reappeared, in association with an increase in blastic cells in the bone marrow . Serum levels of tumor necrosis factor-alpha and interleukin-1 beta, which are thought to be essential for granuloma formation and induction of EN, were markedly elevated . Physicians must remember that recurrent EN and granulomatous lesions can be a prodromal sign of leukemia. Med Arh, 2004, 58(5), 271 - 4 {Prevention strategy of virus-hepatitis B and hepatitis C}; Zvizdic S et al.; Infections by Hepatitis B and Hepatitis C viruses, as well as infections caused by microorganisms transmitted through blood, blood products or in any other way, are now reality for all medical workers . This danger is stilll becoming increased for those medial workers who are more exposed in their everyday work to contaminated human blood or other biological materials . Therefore, the health institutions must introduce prevention measures against possible infection, but also the protection procedures to be applied immediately before and after incidental exposition to infectious material . They are especially essential at the occasion of incidental injuries of the persons by medical instruments which had been in the contact with blood . That is why it is obligatory for the employees of the health care institutions to be vaccinated against possible infection by Hepatitis B. Med Oral Patol Oral Cir Bucal, 2005 Jan-Feb, 10(1), 77 - 85 Update on dry socket: A review of the literature; Torres-Lagares D et al.; Dry socket is a postoperative complication that occurs after a dental extraction and has been defined as an inflammation of the alveolus . If this inflammation should surpass the alveolar walls, it would result in a located osteitis . The frequency of appearance of dry socket has been reported in a very wide margin, from 1% until 70% . It is generally accepted that most dry sockets appear after extraction of third retained molars, in which the occurrence of this complication is about 20-30% of dental extractions, ten times more than in the rest of dental extractions . In this work we review the forms of clinical appearance, the risk factors related to this affection and the etiopathogenic theories that try to explain its appearance . The treatment management is also examined . Fibrinolitic agents, laundries, antiseptic, and antibiotics have been studied for its prevention, according to the pathogenic theories of dry socket . We analyze and critize the different drugs and their results . In conclusion from the revised data, we think it is possible to defend a pathogenic model in which the bacterial fibrinolytic mechanisms and the microorganism of the own patient may contribute to produce the dry socket. Math Biosci, 2004 Dec, 192(2), 85 - 109 Epub 2004 Dec 08. Predicting stability of mixed microbial cultures from single species experiments: 1 . Phenomenological model; Pilyugin SS et al.; The growth of mixed microbial cultures on mixtures of substrates is a fundamental problem of both theoretical and practical interest . On the one hand, the literature is abundant with experimental studies of mixed-substrate phenomena {T . Egli, The ecological and physiological significance of the growth of heterotrophic microorganisms with mixtures of substrates, Adv . Microbiol . Ecol . 14 (1995) 305-386} . On the other hand, a number of mathematical models of mixed-substrate growth have been analyzed in the last three decades . These models typically assume specific kinetic expressions for substrate uptake and biomass growth rates and their predictions are formulated in terms of parameters of the model . In this work, we formulate and analyze a general mathematical model of mixed microbial growth on mixtures of substitutable substrates . Using this model, we study the effect of mutual inhibition of substrate uptake rates on the stability of the equilibria of the model . Specifically, we address the following question: How much of the dynamics exhibited by two competing species can be inferred from single species data? We provide geometric criteria for stability of various types of equilibria corresponding to non-competitive exclusion, competitive exclusion, and coexistence of two competing species in terms of growth isoclines and consumption curves . A growth isocline is a curve in the plane of substrate concentrations corresponding to the zero net growth of a given species . In {G.T . Reeves, A . Narang, S.S . Pilyugin, Growth of mixed cultures on mixtures of substitutable substrates: The operating diagram for a structured model, J . Theor . Biol . 226 (2004) 143-157}, we introduced consumption curves as sets of all possible combinations of substrate concentrations corresponding to balanced growth of a single microbial species . Both types of curves can be obtained in single species experiments. J Environ Manage, 2005 Jan, 74(2), 187 - 94 Epub 2004 Nov 11. Influence of the carbon source on the anaerobic biomass adhesion on polyurethane foam matrices; Ribeiro R et al.; This work focuses on the influence of the source of organic matter on the process of biomass adhesion on polyurethane foam matrices in fixed-bed anaerobic immobilized-sludge reactors . Five experiments were performed in differential 'gradientless' reactors fed with meat extract (protein), glucose, starch, lipids and complex substrate . The polyurethane foam colonization process was monitored temporally in each experiment to identify the amount of biomass buildup, extracellular polymer production and the morphological characteristics of the cells adhering to the support . Different immobilization patterns were observed for the different substrates used . The morphological variety was found to be dependent on the substrate constituents . Polymer excretion was apparently crucial in the colonization process of the polyurethane matrices and was likely related to cell fixation on the support . The production of extracellular polymeric substances speeded up the initial fixation of microorganisms on the polyurethane surface. Biochemistry (Mosc), 2004 Nov, 69(11), 1305 - 9 Role of Inhibitors of Proteolytic Enzymes in Plant Defense against Phytopathogenic Microorganisms; Valueva TA et al.; This review analyzes the literature on various mechanisms of proteolytic enzyme inhibitors involved in plant defense against attack by phytopathogenic microorganisms . The action of proteinase inhibitors from plants upon the enzymes from pathogenic microorganisms and viruses is reviewed . Considerable attention is given to the induction of proteinase inhibitors in plants in response to the invasion of pathogens . Some aspects of application of proteinase inhibitors in biotechnology for production of transgenic plants with enhanced resistance to diseases are discussed. Biochemistry (Mosc), 2004 Nov, 69(11), 1252 - 67 Catalytic mechanism and application of formate dehydrogenase; Tishkov VI et al.; NAD+-dependent formate dehydrogenase (FDH) is an abundant enzyme that plays an important role in energy supply of methylotrophic microorganisms and in response to stress in plants . FDH belongs to the superfamily of D-specific 2-hydroxy acid dehydrogenases . FDH is widely accepted as a model enzyme to study the mechanism of hydride ion transfer in the active center of dehydrogenases because the reaction catalyzed by the enzyme is devoid of proton transfer steps and implies a substrate with relatively simple structure . FDH is also widely used in enzymatic syntheses of optically active compounds as a versatile biocatalyst for NAD(P)H regeneration consumed in the main reaction . This review covers the late developments in cloning genes of FDH from various sources, studies of its catalytic mechanism and physiological role, and its application for new chiral syntheses. Ann Agric Environ Med, 2004, 11(2), 215 - 20 Inactivation of fungi in vitro by photosensitization: preliminary results; Luksiene Z et al.; Photosensitization is based on the interaction of 2 completely non-toxic agents--a photosensitizer, accumulated in microorganisms, and visible light . This interaction induces radical-based cytotoxic reactions in the presence of oxygen . The photosensitization phenomenon is widely involved in the treatment of tumors in oncology, in curing arthritis and atherosclerosis . In this work, the possibility to inactivate pathogenic and harmful fungi by photosensitization is shown . A new treatment methodology is proposed on the basis of effective inactivation of the several micromycetes, such as Aspergillus flavus, Trichothecium roseum, Fusarium avenaceum, Rhizopus oryzae, by photosensitization. Ann Agric Environ Med, 2004, 11(2), 185 - 97 Filamentous microorganisms and their fragments in indoor air--a review; Gorny RL; The paper summarizes the current state of knowledge regarding the role of filamentous microorganisms (i.e., fungi and actinomycetes) and their submicrometer propagules (fragments) in formation of indoor bioaerosol . It discusses the importance of water damages in buildings and the role of humidity as a cause of fungal and actinomycetal contamination and subsequent deterioration of indoor spaces . The importance of the size of airborne microbial propagules for adverse health effects is broadly commented as well . Regarding the microbial fragments, the method of their release from the contaminated surfaces (including factors influencing their aerosolization, i.e., air velocity, colony structure, moisture conditions, vibration of the surface, time factor), modern measurement techniques and newly obtained results of the immunological reactivity of fragments are discussed . The novel ideas concerning the dynamic description of the release process of microbial propagules from their sources are also presented. Environ Health Perspect, 2005 Jan, 113(1), 55 - 61 Impacts of co-solvent flushing on microbial populations capable of degrading trichloroethylene; Ramakrishnan V et al.; With increased application of co-solvent flushing technologies for removal of nonaqueous phase liquids from groundwater aquifers, concern over the effects of the solvent on native microorganisms and their ability to degrade residual contaminant has also arisen . This study assessed the impact of ethanol flushing on the numbers and activity potentials of trichloroethylene (TCE)-degrading microbial populations present in aquifer soils taken immediately after and 2 years after ethanol flushing of a former dry cleaners site . Polymerase chain reaction analysis revealed soluble methane monooxygenase genes in methanotrophic enrichments, and 16S rRNA analysis identified Methylocystis parvus with 98% similarity, further indicating the presence of a type II methanotroph . Dissimilatory sulfite reductase genes in sulfate-reducing enrichments prepared were also observed . Ethanol flushing was simulated in columns packed with uncontaminated soils from the dry cleaners site that were dosed with TCE at concentrations observed in the field; after flushing, the columns were subjected to a continuous flow of 500 pore volumes of groundwater per week . Total acridine orange direct cell counts of the flushed and nonflushed soils decreased over the 15-week testing period, but after 5 weeks, the flushed soils maintained higher cell counts than the nonflushed soils . Inhibition of methanogenesis by sulfate reduction was observed in all column soils, as was increasing removal of total methane by soils incubated under methanotrophic conditions . These results showed that impacts of ethanol were not as severe as anticipated and imply that ethanol may mitigate the toxicity of TCE to the microorganisms. Rev Esp Cardiol, 2003 Jul, 56(Supl.1), 2 - 6 Rapamycin: from the Laboratory to the Treatment of Patients' Arteries; Fuster V; The history of rapamycin dates from 1965, when it was isolated from a microorganism in soil and its antibiotic properties were confirmed . Since its discovery, many scientific papers have demonstrated its antifungal and immunosuppressive properties . Our team pioneered in the study of the mechanism of action of rapamycin, motivated by its enormous promise as a therapeutic agent in atherosclerotic disease . We reported how it can inhibit the proliferation and migration of smooth muscle cells after a mechanical aggression, and demonstrated that this effect is mediated by p27 activation by rapamycin . The participation of p27, a key cyclin in the modulation of cell replication, in rapamycin's molecular signaling also spurred expectations in the field of oncological research because it involves a non-redundant system of regulation of the cell cycle susceptible to mutatio . The interesting characteristics of this active principle suggested that it would be worthwhile to investigate its protective effect in an experimental porcine model of angioplasty . Rapamycin showed that it can notably reduce vascular wall thickening, thus helping to preserve patency after angioplasty . Shortly after this study, the use of rapamycin-coated stents designed to release the active principle into the area of the atherosclerotic lesion was accompanied by an effective preservation of the arterial lumen in experimental models . It also produced a highly significant reduction in the rate of post-stent restenosis in various clinical studies in humans . However, the potential of this type of stent in diabetic patients is still unknown and we are on the point of beginning a large clinical trial (the FREEDOM study) to investigate its impact on the management of diabetic patients . Experimental and clinical evidence indicates that the development of oral agents capable of modifying the progression of atherosclerotic disease by acting on molecular targets involved in the control of the cell cycle will be a challenge in the coming years. Vestn Khir Im I I Grek, 2004, 163(4), 13 - 6 {Treatment of acute pyoinflammatory diseases of the lungs and pleura under control of microorganism persistence factors}; Physiological and pathological roles of alpha3beta1 integrin; Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Shinagawa-ku, Tokyo 142-8501, Japan . tsuji@hoshi.ac.jp alpha3beta1 integrin has been considered to be a mysterious adhesion molecule due to the pleiotropy in its ligand-binding specificity . However, recent studies have identified laminin isoforms as high-affinity ligands for this integrin, and demonstrated that alpha3beta1 integrin plays a number of essential roles in development and differentiation, mainly by mediating the establishment and maintenance of epithelial tissues . Furthermore, alpha3beta1 integrin is also implicated in many other biological phenomena, including cell growth and apoptosis, angiogenesis and neural functions . This integrin receptor forms complexes with various other membrane proteins, such as the transmembrane-4 superfamily proteins (tetraspanins), cytoskeletal proteins and signaling molecules . Recently, lines of evidence have been reported showing that complex formation regulates integrin functions in cell adhesion and migration, signal transduction across cell membranes, and cytoskeletal organization . In addition to these roles in physiological processes, alpha3beta1 integrin performs crucial functions in various pathological processes, especially in wound healing, tumor invasion and metastasis, and infection by pathogenic microorganisms. Ying Yong Sheng Tai Xue Bao, 2004 Oct, 15(10), 1958 - 62 {Research advances in soil fungal diversity and molecular ecology}; Zhang J et al.; Fungi are a kind of important soil microorganisms that participate in the decomposition of organic materials and supply nutrients to the plant through symbiosis . But, they can also reduce the output of food due to the existence of pathogenic fungi . Soil fungal diversity plays a fundamentally unique role in maintaining the balance of ecosystem and in supplying large amount of undeveloped resources for the people . In this paper, soil fungal diversity was expatiated from the viewpoints of species diversity, habitant diversity and functional diversity, and furthermore, the research advances in the molecular ecology of soil fungal diversity were reviewed from the aspects of the fungal diversity of farmland, woodland, pasture, extreme environment, and other complex environments . The affecting factors of soil fungal diversity were discussed, and the development trend of the study on soil fungal diversity was also approached. Ying Yong Sheng Tai Xue Bao, 2004 Oct, 15(10), 1943 - 6 {Function and application of soil microorganisms in forest ecosystem}; Li Y et al.; Soil microorganism is an important part of forest ecosystem, and plays an important role in sustainable development of forestry . In this paper, we summarized the main functions of soil microorganisms in forest sustainable development from the aspects of 1) the role of soil microorganism and microbiomass; 2) the function of mycorrhizal fungi; 3) the impact of pathogen; and 4) the effect of PGPR . Finally, we also discussed the research trends of forest soil microorganism and its application . Some study areas which should be further studied were also proposed. Ying Yong Sheng Tai Xue Bao, 2004 Oct, 15(10), 1907 - 10 {Effects of long-term fertilization on soil microorganism and its role in adjusting and controlling soil fertility}; Sun R et al.; To clarify the relationships between soil microorganisms and soil fertility under the condition of long-term fertilization, a 12-year fertilization experiment was installed on a fluvo-aquic soil, and the amount of soil microorganisms and the content of soil nutrients were determined and analyzed . The results showed that chemical fertilizers combined with organic manure could significantly improve soil fertility and increase the amount of soil microorganisms . Organic manure was obviously superior to corn straw in improving soil fertility . The correlation between soil microorganisms and soil fertility was significant . A positive correlation was found between the amount of bacteria and azotobacteria and the contents of organic matter, total N, alkalified N, total P and available P . The relationship between the amount of fungi and actinomycetes and the content of soil nutrients was not obvious. J Prosthet Dent, 2005 Jan, 93(1), 76 - 85 Effects of polishing techniques on the surface roughness of acrylic denture base resins; Kuhar M et al.; Statement of problem Rough surfaces of denture bases promote adhesion of microorganisms and plaque formation . It is therefore important to know how different polishing systems affect surface roughness of denture base acrylic resins . Purpose The objective of this study was to compare the effects of 4 chairside polishing kits and 2 conventional laboratory techniques used for polishing 3 different acrylic denture base resins . Material and methods Using contact profilometric measurement, the surface texture of 54 specimens (15 x 30 x 3 mm) per acrylic material (autopolymerized ProBase Cold, heat-polymerized ProBase Hot, and injection heat-polymerized SR Ivocap plus) was studied before and after cutting with a tungsten carbide bur, and during and after chairside polishing with 4 polishing kits (Exa Technique, Acrylic Polisher HP blue, AcryPoint, Becht Polishing Cream), and after conventional polishing with 2 polishing systems (Universal Polishing Paste for Resins and Metals, Lesk Polishing Liquid) . There were 9 specimens for each acrylic resin material and polishing method combination . Conventional lathe polishing with polishing paste served as the control . Mean average surface roughness (R a ) values of each specimen group were analyzed using a 2-way analysis of variance, the Scheffe post-hoc test, and paired t test (alpha=.05) with the Bonferroni adjustment . After testing the polished acrylic resin surfaces were evaluated under a scanning electron microscope . Results The highest mean average surface roughness (R a = 2.86 +/- 0.8 mum to 3.99 +/- 1.31 mum) was measured for surfaces finished with a tungsten carbide bur . The lowest surface roughness values (R a = 0.02 +/- 0.01 mum) were determined for acrylic resin specimens polished with a lathe and polishing paste . The R a values of resin specimens after polishing with chairside silicone polishing kits ranged from 0.05 +/- 0.0 mum to 0.35 +/- 0.05 mum . Mean average R a values of specimens polished with a polishing cream alone (R a = 1.01 +/- 0.17 mum to 1.68 +/- 0.47 mum) were significantly higher ( P <.05) than those obtained with other polishing systems tested, which was confirmed by scanning electron microscope images of acrylic resin surfaces . Significant differences in mean average surface roughness were found between autopolymerizing and injected heat-polymerizing resin specimens . In addition, scanning electron microscopy revealed increased porosity of autopolymerizing resin specimens . Conclusions Conventional laboratory polishing was found to produce the smoothest surface of denture base acrylic resin . Chairside silicone polishing kits produced a significantly smoother surface of acrylic resin than specimens polished with a tungsten carbide bur . The presence of large pores was characteristic for the autopolymerizing resin material. Anal Chem, 2005 Jan 1, 77(1), 319 - 26 Array-based binary analysis for bacterial typing; Shepard JR et al.; An allele-specific oligonucleotide microarray was developed for rapid typing of pathogens based on analysis of genomic variations . Using a panel of Escherichia coli strains as a model system, selected loci were sequenced to uncover differences, such as single- or multiple-nucleotide polymorphisms as well as insertion/deletions (indels) . While typical genomic profiling experiments employ specific sequences targeted to genomic DNA unique to a single strain or virulent gene, the present array is designed to type bacteria based on a patterned signature response across multiple loci . In the signature concept, all strains are interrogated by hybridizing their amplified DNA to an array containing multiple probe sequences . Allele-specific oligonucleotide probe sequences targeting each of these variable regions were synthesized and included in a custom fiber-optic array . For each locus, a set of specific probe sequences is selected, such that hybridization gives a binary signal/no signal response to each of the probes . Using this strategy for multiple loci, many pathogens or microorganisms could be classified using a limited number of probes . Because of the advantages of the fiber-optic array platform over other array formats, including sensitivity and speed, the platform described in this paper is capable of supporting a high-throughput diagnostic strategy. Huan Jing Ke Xue, 2004 Sep, 25(5), 143 - 7 {Stratification of bulk density and its dynamics in the process of co-composting}; Chen TB et al.; Co-composting of sewage sludge and pig manure was studied . At the stages of temperature starting and high temperature, the bulk density were 0.82 g x cm(-3) and 0.66 g x cm(-3), respectively, but oxygen in the pile at each stage was enough for the microorganism to live on . At the stage of cooling, the bulk density was 0.58 g x cm(-3), which made aeration better . The bulk density was 0.54 g x cm(-3) at the stage of maturing when aeration is best . The stratified effect of bulk density occurred, near the door of the pile at the stages of starting and high temperature, almost all parts of the pile at the stage of cooling, however, it weakened at the stage of the maturing . The depth had remarkable influence upon the bulk density of compost, by the axis of the pile at the stage of the starting, near the inner wall at the stage of high temperature, for the whole pile at the stage of cooling, and near the door and axis at the stage of maturing . The door had significant effect on the bulk density for both stages of starting and maturing . The bulk density increased with the depth of the pile at every stage of composting . Dynamics of bulk density met with two-order kinetic equation. FEMS Microbiol Lett, 2005 Jan 1, 242(1), 185 - 193 Development of a nested PCR detection procedure for Nectria fuckeliana direct from Norway spruce bark extracts; Langrell SR; A pair of primers specific for Nectria fuckeliana, a bark infecting pathogen predominantly of Norway spruce (Picea abies), were designed from comparisons of nucleotide sequences of the nuclear ribosomal internal transcribed spacer (ITS) regions of nine isolates from Norway, Lithuania, Switzerland, Austria, Slovakia, Scotland (Larix sp.) and New Zealand (Pinus radiata), and other closely related nectriaceous species, including Neo . Neomacrospora, and 'N' . mammoidea, to which it exhibits taxonomic similarities . Complete ITS sequence homology was observed between each of the nine N . fuckeliana isolates, regardless of geographic provenance, including a previously published Danish strain . Primers Cct1 and Cct2 consistently amplified a single product of 360 bp from DNA prepared from 20 isolates covering the principle range of the disease from Central and Northern Europe, but not from other Neonectria, 'Nectria' or a range of species commonly encountered in forest ecosystems, as well as P . abies or P . radiata DNA . A quick, simple and efficient mechanical lysis procedure for the extraction of high quality total DNA from bark, coupled with post-extraction polyvinylpolypyrrolidone (PVPP) chromatography purification, is described to facilitate successful PCR detection of N . fuckeliana direct from bark extracts . Detection of N . fuckeliana from bark preparations was only possible following nested PCR of PVPP purified extracts using universal primers ITS5 and 4 in first round amplification . The identity of products from bark tissues was confirmed by Southern hybridisation and sequencing . Using the above procedure, positive diagnosis of N . fuckeliana was achievable within 5 h and has the potential for full exploitation as both a forest management and ecological research tool . As the DNA extraction procedure described here has been successful in application against other tree species, it has potential for incorporation into other molecular diagnostic systems for other microorganisms responsible for other wood or tree bark diseases. FEMS Microbiol Lett, 2005 Jan 1, 242(1), 147 - 54 The involvement of cAMP in the growth inhibition of filamentous fungus Rhizopus nigricans by steroids; Jeraj N et al.; Several steroids, in particular progesterone, are toxic for the filamentous fungus Rhizopus nigricans and, at high concentrations, inhibit its growth . Previous studies on this microorganism revealed progesterone specific receptors coupled to G proteins at the plasma membrane . In this study, the next step of steroid signalling in R . nigricans following G protein activation is investigated, together with the possible impact of this pathway on fungal growth inhibition . The intracellular level of cAMP decreased in the presence of steroids, demonstrating the probable involvement of cAMP signalling in the response of R . nigricans to steroids . Results of the growth analysis in the presence of cAMP increasing agents suggest that the role of cAMP in fungal growth inhibition by steroids cannot be ruled out, but it would appear to be minor and not make a major contribution to growth inhibition. Chemosphere, 2005 Feb, 58(5), 579 - 84 A comparative study on the dissipation and microbial metabolism of organophosphate and carbamate insecticides in orchaqualf and fluvaquent soils of West Bengal; Das AC et al.; An experiment has been conducted under laboratory conditions to investigate the effect of phorate (an organophosphate insecticide) and carbofuran (a carbamate insecticide) at their recommended field rates (1.5 and 1.0 kga.i.ha(-1), respectively) on the growth and multiplication of microorganisms as well as rate of dissipation and persistence of the insecticidal residues including their metabolites in laterite (typic orchaqualf) and alluvial (typic fluvaquent) soils of West Bengal . Application of phorate and carbofuran in general, induced growth and development of bacteria, actinomycetes, fungi, N(2)-fixing bacteria and phosphate solubilizing microorganisms in both the soils and the stimulation was more pronounced with phorate as compared to carbofuran . Application of phorate recorded highest stimulation of fungi in laterite and actinomycetes in alluvial soil . Carbofuran on the other hand, augmented fungi and N(2)-fixing bacteria in laterite and actinomycetes in alluvial soil . Bacterial population was inhibited due to the application of carbofuran in alluvial soil . Phorate sulfoxide and phorate sulfone, the two metabolites of phorate and 3-hydroxycarbofuran and 3-ketocarbofuran, the two metabolites of carbofuran isolated were less persistent in both the soils . Phorate persisted in laterite and alluvial soils up to 45 and 60 days, respectively depicting the half-life (T(1/2)) 9.7 and 11.5 days, respectively while the T(1/2) of carbofuran for the said soils were 16.9 and 8.8 days, respectively . No metabolite of carbofuran was detected in soils after 30 days of incubation while phorate sulfone persisted in alluvial soil even after 60 days of application of the insecticide. Med Mal Infect, 2004 Nov, 34(11), 522 - 9 {Impact of genetic modifications on infectious diseases}; Houdebine LM; Genetic engineering offers the theoretical possibility to transfer any natural or modified gene into any living organism . This generates new and diverse situations which may contribute to the spreading of infectious diseases or on the contrary to control them . Problems may theoretically come from uncontrolled genes providing resistance to antibiotics, from the activation of genomic retroviral sequences, from enhanced sensitivity of the organism to pathogens, as well as from the generation of mutated microorganisms with a higher pathogenecity . On the contrary, various genetic modifications may create organisms resistant to infectious diseases, generate safe and efficient recombinant vaccines, or provide patients with proteins which stimulate their defense mechanisms . The major impacts of genetic modifications in the development of infectious diseases or on the contrary in their eradication are analyzed in this article. Environ Technol, 2004 Nov, 25(11), 1305 - 12 Compost stability assessment using a secondary metabolite: geosmin; Li HF et al.; Composting is a process involved not only in transformation of organic matter (OM), but also for transition of the microbial community . Microorganisms can directly provide important information on the stages and characteristics of composting . This paper was aimed at characterizing compost stability by a microbial secondary metabolite, geosmin, which is a volatile compound presenting an earthy smell . Since secondary metabolite production is dependent on the nutrient state of microorganisms, its production in association with physical and chemical parameters was monitored in the laboratory-scale and plant-scale composting processes . The results showed that the peaked geosmin liberation was consistent with stable state of composting indicated by the ambient temperature achieved, a slightly alkaline product and steady states of dissolved organic carbon (DOC), N and P contents and OM degradation in the laboratory-scale experiment . It was also in accordance with the stability identified by the facilities and CO2 respiration rate in the plant-scale composting . In addition, the production of geosmin was correlated with the C/N ratio for the solid sample . These results demonstrated that geosmin levels could be used as an index for the compost stability assessment in different composting processes with various organic solid wastes. Mol Nutr Food Res . 2004 Dec 22; {Epub ahead of print} Production, properties, and applications of hydrocolloid cellular solids; Nussinovitch A; Many common synthetic and edible materials are, in fact, cellular solids . When classifying the structure of cellular solids, a few variables, such as open vs . closed cells, flexible vs . brittle cell walls, cell-size distribution, cell-wall thickness, cell shape, the uniformity of the structure of the cellular solid and the different scales of length are taken into account . Compressive stress-strain relationships of most cellular solids can be easily identified according to their characteristic sigmoid shape, reflecting three deformation mechanisms: (i) elastic distortion under small strains, (ii) collapse and/or fracture of the cell walls, and (iii) densification . Various techniques are used to produce hydrocolloid (gum) cellular solids . The products of these include (i) sponges, obtained when the drying gel contains the occasionally produced gas bubbles; (ii) sponges produced by the immobilization of microorganisms; (iii) solid foams produced by drying foamed solutions or gels containing oils, and (iv) hydrocolloid sponges produced by enzymatic reactions . The porosity of the manufactured cellular solid is subject to change and depends on its composition and the processing technique . The porosity is controlled by a range of methods and the resulting surface structures can be investigated by microscopy and analyzed using fractal methods . Models used to describe stress-strain behaviors of hydrocolloid cellular solids as well as multilayered products and composites are discussed in detail in this manuscript . Hydrocolloid cellular solids have numerous purposes, simple and complex, ranging from dried texturized fruits to carriers of vitamins and other essential micronutrients . They can also be used to control the acoustic response of specific dry food products, and have a great potential for future use in countless different fields, from novel foods and packaging to medicine and medical care, daily commodities, farming and agriculture, and the environmental, chemical, and even electronic industries. Izv Akad Nauk Ser Biol, 2004 Nov-Dec, (6), 740 - 8 {Ecological strategies of soil microbial communities under plants of meadow ecosystems}; Aerobic degradation of polychlorinated biphenyls; Department of Environmental Microbiology, German Research Center for Biotechnology, Mascheroder Weg 1, 38124, Braunschweig, Germany, dpi@gbf.deThe microbial degradation of polychlorinated biphenyls (PCBs) has been extensively studied in recent years . The genetic organization of biphenyl catabolic genes has been elucidated in various groups of microorganisms, their structures have been analyzed with respect to their evolutionary relationships, and new information on mobile elements has become available . Key enzymes, specifically biphenyl 2,3-dioxygenases, have been intensively characterized, structure/sequence relationships have been determined and enzymes optimized for PCB transformation . However, due to the complex metabolic network responsible for PCB degradation, optimizing degradation by single bacterial species is necessarily limited . As PCBs are usually not mineralized by biphenyl-degrading organisms, and cometabolism can result in the formation of toxic metabolites, the degradation of chlorobenzoates has received special attention . A broad set of bacterial strategies to degrade chlorobenzoates has recently been elucidated, including new pathways for the degradation of chlorocatechols as central intermediates of various chloroaromatic catabolic pathways . To optimize PCB degradation in the environment beyond these metabolic limitations, enhancing degradation in the rhizosphere has been suggested, in addition to the application of surfactants to overcome bioavailability barriers . However, further research is necessary to understand the complex interactions between soil/sediment, pollutant, surfactant and microorganisms in different environments. Microb Ecol . 2004 Dec 21; {Epub ahead of print} New PCR Primers for the Screening of NRPS and PKS-I Systems in Actinomycetes: Detection and Distribution of These Biosynthetic Gene Sequences in Major Taxonomic Groups; Ayuso-Sacido A et al.; Nonribosomal peptide synthetases (NRPS) and type I polyketide synthases (PKS-I) are biosynthetic systems involved in the synthesis of a large number of important biologically active compounds produced by microorganisms, among others by actinomycetes . In order to assess the occurrence of these biosynthetic systems in this metabolically active bacterial group, we designed new PCR primers targeted to specifically amplify NRPS and PKS-I gene sequences from actinomycetes . The sequence analysis of amplified products cloned from two model systems and used to validate these molecular tools has shown the extreme richness of NRPS or PKS-I-like sequences in the actinomycete genome . When these PCR primers were tested on a large collection of 210 reference strains encompassing all major families and genera in actinomycetes, we observed that the wide distribution of these genes in the well-known productive Streptomyces species is also extended to other minor lineages where in some cases very few bioactive compounds have been identified to date. Environ Biosafety Res, 2002 Oct, 1(1), 9 - 18 Towards safer vectors for the field release of recombinant bacteria; Davison J; The prospect of the deliberate environmental release of genetically manipulated microorganisms has given rise to a great deal of polemic . Amongst the rational scientific concerns are those concerned with the fate of the released bacteria, the fate of the recombinant genes that they carry, the selective pressures acting upon them in different environmental situations and the long term effects on the environment and human health . All recombinant DNA is carried by vectors (plasmids, transposons or bacteriophage or remnants of these) . Thus the way in which recombinant constructions are made may itself lead to potential biosafety concerns, irrespective of the host bacterium and the recombinant DNA fragment of primary interest . The purpose of the present review is to assess progress in improved vector design aimed at eliminating risks due to the way recombinant vectors are constructed . Improved vector constructions include the avoidance of the use, or removal, of antibiotic resistance genes, the use of defective transposons rather than plasmids in order to reduce horizontal transfer and the development of conditionally lethal suicide systems . More recently, new site-specific recombination systems have permitted transposon vectors to be manipulated following strain construction, but before environmental release, so that virtually all recombinant DNA not directly involved in the release experiment is eliminated . Such bacteria are thus pseudo-wild type in that they contain no heterologous DNA other than the genes of interest. Arch Surg, 2004 Dec, 139(12), 1371 - 5 Emergence of antibiotic resistance in infected pancreatic necrosis; De Waele JJ et al.; BACKGROUND: Overall, the use of antibiotics in the treatment of patients with severe acute pancreatitis has increased owing to the use of antibiotic prophylaxis . HYPOTHESIS: The incidence of antibiotic-resistant (AB-R) bacteria in infected pancreatitis is related to prolonged antibiotic treatment and may affect outcome . DESIGN: Case series . SETTING: Fifty-six-bed intensive care unit of a tertiary care center . PATIENTS: Forty-six consecutive patients with infected pancreatic necrosis . MAIN OUTCOME MEASURES: Occurrence rate of AB-R organisms in pancreatic infection, overall duration of antibiotic treatment prior to infection, and mortality, defined as inhospital mortality . RESULTS: Infection with AB-R microorganisms was found in 24 (52%) of 46 patients . Primary infection was present in 7 patients; in 21 patients, nosocomial surinfection with AB-R organisms occurred . Patients with AB-R infections were treated with antibiotics for a longer period (24 vs 15 days, P<.05), while disease severity and the incidence of organ failure were not statistically significantly different . The intensive care unit stay was significantly longer in patients with AB-R infections (23 vs 31 days, P = .02) . Mortality was not statistically significantly different in patients with AB-R infections (37% vs 28%, P = .23) . CONCLUSIONS: The occurrence rate of infections with AB-R organisms in our patients with severe acute pancreatitis was high and was associated with a longer intensive care unit stay, but no increased mortality could be demonstrated . The duration of antibiotic treatment was increased in patients in whom AB-R infections developed. J Biol Chem . 2004 Dec 16; {Epub ahead of print} Gln-tRNAGln formation from Glu-tRNAGln requires cooperation of an asparaginase and a Glu-tRNAGln kinase; Feng L et al.; Gln-tRNAGln is synthesized from Glu-tRNAGln in most microorganisms by a tRNA-dependent amidotransferase (AdT) in a reaction requiring ATP and an amide donor such as glutamine . GatDE is a heterodimeric AdT that is ubiquitous in archaea . GatD resembles bacterial asparaginases, and is expected to function in amide donor hydrolysis . We show here that Methanothermobacter thermautotrophicus GatD acts as a glutaminase, but only in the presence of both Glu-tRNAGln and the other subunit GatE . The fact that only Glu-tRNAGln but not tRNAGln could activate the glutaminase activity of GatD suggests that glutamine hydrolysis is tightly coupled to transamidation . M . thermautotrophicus GatDE enzymes mutated in GatD at each of the four critical asparaginase active site residues lost the ability to hydrolyze glutamine, and were unable to convert Glu-tRNAGln to Gln-tRNAGln when glutamine was the amide donor . However, ammonium chloride rescued the activities of these mutants, suggesting the integrity of the ATPase and the transferase activities in the mutant GatDE enzymes was maintained . In addition, pyroglutamyl-tRNAGln accumulated during the reaction catalyzed by the glutaminase-deficient mutants or by GatE alone . The pyroglutamyl-tRNA is most likely a cyclized by-product derived from phosphoryl-Glu-tRNAGln, the proposed high-energy intermediate in Glu-tRNAGln transamidation . That GatE alone could form the intermediate indicates that GatE is a Glu tRNAGln kinase . The activation of Glu-tRNAGln via -phosphorylation bears similarity to the mechanism used by glutamine synthetase, which may point to an ancient link between glutamine synthesized for metabolism and translation. J Contam Hydrol, 2004 Dec, 75(3-4), 281 - 96 Quantifying the effects of fumarate on in situ reductive dechlorination rates; Hageman KJ et al.; In situ methods are needed to evaluate the effectiveness of chemical amendments at enhancing reductive dechlorination rates in groundwater that is contaminated with the priority pollutant, trichloroethene (TCE) . In this communication, a method that utilizes single-well, "push-pull" tests to quantify the effects of chemical amendments on in situ reductive dechlorination rates is presented and demonstrated . Five push-pull tests were conducted in each of five monitoring wells located in a TCE-contaminated aquifer at the site of a former chemical manufacturing facility . Rates for the reductive dechlorination of the fluorinated TCE-surrogate, trichlorofluoroethene (TCFE), were measured before (test 1) and after (test 5) three successive additions (tests 2-4) of fumarate . Fumarate was selected to stimulate the growth and activity of indigenous microorganisms with the metabolic capability to reduce TCFE and TCE . In three wells, first-order rate constants for the reductive dechlorination of TCFE increased by 8.2-92 times following fumarate additions . In two wells, reductive dechlorination of TCFE was observed after fumarate additions but not before . The transformation behavior of fumarate was also monitored following each fumarate addition . Correlations between the reductive dechlorination of TCFE and the reduction of fumarate to succinate were observed, indicating that these reactions were supported by similar biogeochemical conditions at this site. Vet Res, 2005 Jan-Feb, 36(1), 79 - 87 Evidence of Bartonella sp . in questing adult and nymphal Ixodes ricinus ticks from France and co-infection with Borrelia burgdorferi sensu lato and Babesia sp; Halos L et al.; Ticks are known vectors for a wide range of pathogenic microorganisms . Their role in the transmission of some others is so far only suspected . Ticks can transmit multiple pathogens, however, little is known about the co-existence of these pathogens within questing ticks . We looked for the presence of DNA from three micro-organisms, Bartonella sp., Borrelia burgdorferi sensu lato and Babesia sp . which are known or suspected tick-borne pathogens, using a cohort of 92 questing Ixodes ricinus ticks collected from pastures in northern France . DNA was extracted from each individual tick and the presence of the three pathogens was investigated using Polymerase Chain Reaction (PCR) amplification . Nine among 92 samples (9.8%) demonstrated PCR products using Bartonella specific primers, 3 among 92 (3.3%) using Borrelia burgdorferi sensu lato specific primers and 19 among 92 (20.6%) using Babesia specific primers . Seven among 92 samples (7.6%) were PCR positive for at least two of the pathogens and one sample was positive for all three . Adult ticks (12/18; 67%) showed significantly higher infection rates compared to nymphs (11/74; 15%) for all three pathogens (P < 0.001) . This study is the demonstration of the simultaneous presence of Bartonella sp., Borrelia burgdorferi sensu lato and Babesia sp . in questing Ixodes ricinus ticks. Prikl Biokhim Mikrobiol, 2004 Nov-Dec, 40(6), 639 - 44 {Microbacterium oxydans, a symbiont of Djungarian hamster, displaying probiotic properties}; 15th Chapter of Surgeons Lecture: Surgeon of the new millennium--surgeon et al.; Prof Tan Ser Kiat, Singapore Health Services Pte Ltd, SingaporeThe surgeon of the new millennium has come a long way from his humble beginnings in the Middle Ages as the lowly barber-surgeon . The skills and techniques developed by outstanding surgeons like Astley Cooper of the 19th century have withstood the test of time and have been refined by subsequent generations of surgical masters . The scientific basis of modern surgery was put on a firm footing in the early 19th century through the discovery of anaesthesia and microorganisms as a cause of many diseases and surgical complications . The 20th century brought about rapid progress in medicine, information technology (IT) and the life sciences, and closed with a big bang with the completion of the sequencing of the human genome . For the surgeon of the 21st century to remain relevant, he must embrace the concept of the Total Surgeon . Not doing so will render him irrelevant in the course of time, for having good surgical technique alone is insufficient . He must also lead in scientific endeavours to push the frontiers of the life sciences in attempts to solve the insoluble, and be scholarly in thought, attitude and behaviour . In other words, he must be a Surgeon-Scientist-Scholar. Nat Rev Microbiol, 2005 Jan, 3(1), 70 - 80 Tuberculosis - metabolism and respiration in the absence of growth; Boshoff HI et al.; Human tuberculosis is a complex disease caused by bacterial populations that are located in discrete lesions (microenvironments) in a single host . Some of these microenvironments are conducive to replication, whereas others restrict bacterial growth without necessarily sterilizing the infecting microorganisms . The physical and biochemical milieu in these lesions is poorly defined . None of the existing animal models for tuberculosis (except perhaps non-human primates) reproduce the diversity of disease progression that is seen in humans . Nonetheless, transcriptomics and studies using bacterial mutants have led to testable hypotheses about metabolic functions that are essential for viability in the absence of replication . A complete picture of bacterial metabolism must balance reducing equivalents while maintaining an energized membrane and basic cellular processes. Nat Rev Microbiol, 2005 Jan, 3(1), 36 - 46 LPS, TLR4 and infectious disease diversity; Miller SI et al.; Innate immune receptors recognize microorganism-specific motifs . One such receptor-ligand complex is formed between the mammalian Toll-like receptor 4 (TLR4)-MD2-CD14 complex and bacterial lipopolysaccharide (LPS) . Recent research indicates that there is significant phylogenetic and individual diversity in TLR4-mediated responses . In addition, the diversity of LPS structures and the differential recognition of these structures by TLR4 have been associated with several bacterial diseases . This review will examine the hypothesis that the variability of bacterial ligands such as LPS and their innate immune receptors is an important factor in determining the outcome of infectious disease. Nat Rev Microbiol, 2005 Jan, 3(1), 23 - 35 Palaeomicrobiology: current issues and perspectives; Drancourt M et al.; Palaeomicrobiology is an emerging field that is devoted to the detection, identification and characterization of microorganisms in ancient remains . Data indicate that host-associated microbial DNA can survive for almost 20,000 years, and environmental bacterial DNA preserved in permafrost samples has been dated to 400,000-600,000 years . In addition to frozen and mummified soft tissues, bone and dental pulp can also be used to search for microbial pathogens . Various techniques, including microscopy and immunodetection, can be used in palaeomicrobiology, but most data have been obtained using PCR-based molecular techniques . Infections caused by bacteria, viruses and parasites have all been diagnosed using palaeomicrobiological techniques . Additionally, molecular typing of ancient pathogens could help to reconstruct the epidemiology of past epidemics and could feed into current models of emerging infections, therefore contributing to the development of appropriate preventative measures. Nat Biotechnol, 2005 Jan, 23(1), 88 - 93 Epub 2004 Dec 19. Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes; Uchiyama T et al.; Recent awareness that most microorganisms in the environment are resistant to cultivation has prompted scientists to directly clone useful genes from environmental metagenomes . Two screening methods are currently available for the metagenome approach, namely, nucleotide sequence-based screening and enzyme activity-based screening . Here we have introduced and optimized a third option for the isolation of novel catabolic operons, that is, substrate-induced gene expression screening (SIGEX) . This method is based on the knowledge that catabolic-gene expression is generally induced by relevant substrates and, in many cases, controlled by regulatory elements situated proximate to catabolic genes . For SIGEX to be high throughput, we constructed an operon-trap gfp-expression vector available for shotgun cloning that allows for the selection of positive clones in liquid cultures by fluorescence-activated cell sorting . The utility of SIGEX was demonstrated by the cloning of aromatic hydrocarbon-induced genes from a groundwater metagenome library and subsequent genome-informatics analysis. Environ Int, 2005 Jan, 31(1), 25 - 31 Identification of metal toxicity in sewage sludge leachate; Fjallborg B et al.; Sewage sludge is a source of organic matter and nutrients with the potential for being used as a fertilizer . However, metals in sewage sludge might accumulate in soil after repeated sludge applications, and metal concentrations might reach concentrations that are toxic to microorganisms, soil organisms and/or plants . This toxicity might change with time due to kinetic factors or abiotic factors such as freezing, drying or rainfall . The objective of this study was to determine toxicity of sewage sludge leachate from a lysimeter with 50 cm of sludge applied . Attempts were also made to identify the cause of toxicity of the sludge leachate by toxicity identification and evaluation (TIE) techniques . Sludge leachate was collected monthly during 1 experimental year (August 2001 to August 2002) . Metal concentrations were analysed, and the toxicity was determined with Daphnia magna (48-h immobility) . The effect of EDTA or sodium thiosulphate addition, filtration through a CM-resin or a Millex-resin on toxicity was also tested . The results showed that toxicity of the sludge leachate apparently varied during the year, and that filtration through the CM-resin reduced most of the toxicity followed by the addition of EDTA . None of the other treatments reduced the toxicity of the sludge leachate . This indicated that one or more metals were responsible for the observed toxicity . Further calculations of toxic units (TU) suggested that Zn contributed most to the toxicity . Results also indicated that Ca concentrations in the sludge leachate reduced the toxicity of Zn. FEMS Immunol Med Microbiol, 2005 Jan 1, 43(1), 21 - 7 Prevalence of antibodies against Simkania negevensis in a healthy Japanese population determined by the microimmunofluorescence test; Yamaguchi T et al.; Simkania negevensis has been associated with bronchiolitis in infants and community-acquired pneumonia in adults . Reports of exposure to this microorganism are only available from Israel, North America and Western Europe . Currently, no standard method for diagnosis of S . negevensis infection has been established nor have prevalence rates been shown in Japan . For the first time we demonstrated the ability of the microimmunofluorescence (MIF) test to detect S . negevensis-specific immunoglobulin G and exposure to S . negevensis in Japan . The positive rate in healthy volunteers was 4.3% (25/588), with rates increasing with age . Results indicate the usefulness of the MIF test as a serological method for detecting S . negevensis-specific antibodies . A standard serological test for infection with S . negevensis is needed. J Biotechnol, 2005 Jan 26, 115(2), 211 - 20 A novel and efficient enzymatic method for the production of peptides from unprotected starting materials; Yokozeki K et al.; We report herein the development of a novel and efficient enzymatic method for the production of oligopeptides . This newly discovered method is a simple, cost-effective process, using unprotected amino acids as substrates in an aqueous solution and producing peptides in high yield . The target of our initial screen was l-alanyl-l-glutamine, a dipeptide of significant industrial interest by virtue of its widespread use in infusion therapy . By means of the screening of microorganisms that can catalyze the peptide-forming reaction producing l-alanyl-l-glutamine from l-alanine methylester (acyl donor) and l-glutamine (nucleophile), we discovered that Empedobacter brevis ATCC 14234 produced l-alanyl-l-glutamine most efficiently . The newly found enzyme purified from E . brevis ATCC 14234 facilitates significantly high production yields of l-alanyl-l-glutamine from l-alanine methylester and l-glutamine in an aqueous solution-more than 80% yield based on l-alanine methylester . In addition, this enzyme has wide substrate specificity-both for acyl donors and nucleophiles-and can catalyze peptide-forming reactions not only to produce various dipeptides from the corresponding amino acid esters and amino acids but also to produce various oligopeptides from the corresponding amino acid esters and peptides. Bioresour Technol, 2005 May, 96(7), 805 - 12 Biological activity in the composting reactor of the bio-toilet system; Zavala MA et al.; The bio-toilet is becoming commercially available and it is actually used in Japan in public parks, sightseeing areas, and households; however, the biological activity in the system during degradation of toilet wastes, particularly faeces, is unknown . Thus, in this study activity of microorganisms in the bio-toilet system during degradation of faeces was assessed through the quantification of reductions in total solids (TS), volatile solids (VS), and chemical oxygen demand (COD) during batch tests in laboratory-scale composting reactors . Additionally, the fate of nitrogen and its transformation processes in such reactors were evaluated . TS, VS, and COD reductions were on the order of 56%, 70%, and 75%, respectively, irrespective of the organic loading regarded . Total nitrogen (T-N) reductions quantified 94%, regardless of the organic loading . Furthermore, all T-N reductions observed during composting were equivalent to the NH(3)-N released from the reactor, i.e., 94% of ammonia was lost. Bioresour Technol, 2005 May, 96(7), 797 - 803 Laboratory study of inocula production for composting processes; Vargas-Garcia MC et al.; Six ligno-cellulolytic fungi were tested regarding to examine their capability to grow on agricultural wastes and produce inocula for composting . Two residues were used: pepper plant wastes and almond shell residues . Results showed the latter as the most adequate substrate for growth of fungi tested . On the contrary, Trichoderma koningii, as well as HLC1 and HLC3, both fungi isolated from almond shell wastes, were able to persist in pepper plant wastes . Modifications of aeration and pH significantly influenced growth of Coriolus versicolor, HLC1 and Phanerochaete . flavido alba and P . flavido alba and Phlebia radiata, respectively, while P . flavido alba was the only microorganism whose growth was not significantly altered by temperature . In competitive assays, where fungi were growth together with other species, growth of both microorganisms isolated from almond shell residues, HLC1 and HLC3, were stimulated while T . koningii showed the better results in sterile conditions. Water Res, 2005 Jan, 39(1), 199 - 209 Anaerobic microbial mobilization and biotransformation of arsenate adsorbed onto activated alumina; Sierra-Alvarez R et al.; Due to the enactment of a stricter drinking water standard for arsenic in the United States, larger quantities of arsenic will be treated resulting in larger volumes of treatment residuals . The current United States Environmental Protection Agency recommendation is to dispose spent adsorbent residuals from arsenic treatment into non-hazardous municipal solid waste (MSW) landfills . The potential of microorganisms to alter the speciation affecting the mobility of arsenic in the disposal environment is therefore a concern . The purpose of this paper was to evaluate the potential of an anaerobic microbial consortium to biologically mobilize arsenate (As(V)) adsorbed onto activated alumina (AA), a common adsorbent used for treating arsenic in drinking water . Three anaerobic columns (0.27l) packed with 100g dry weight of AA containing 0.657mg adsorbed As(V) (expressed as arsenic) per gram dry weight were continuously flushed with synthetic landfill leachate for 257 days . The fully biologically active column was inoculated with methanogenic anaerobic sludge (10g volatile suspended solids l(-1) column) and was operated with a mixture of volatile fatty acids (VFA) in the feed (2.5g chemical oxygen demand l(-1) feed) . At the end of the experiment, 37% of the arsenic was removed from the column, of which 48% was accounted for by arsenical species identified in the column effluent . The most important form of arsenic eluted was arsenite (As(III)), accounting for nearly all of the identified arsenic in periods of high mobilization . Additionally, two methylated metabolites, methylarsonic acid and dimethylarsinic acid were observed . Mobilization of arsenic is attributed to the biological reduction of As(V) to As(III) since literature data indicates that As(III) is more weakly adsorbed to AA compared to As(V) . Batch and continuous assays confirmed that VFA, present in landfill leachates, served as an electron donating substrate supporting enhanced rates of As(V) reduction to As(III) . Two control columns, lacking inoculum and/or VFA in the feed displayed low mobilization of arsenic compared to the fully biologically active column . Therefore, leachates generated in MSW landfills could potentially result in the biologically catalyzed mobilization of arsenic from As(V)-laden drinking water residuals. J Med Entomol, 2004 Nov, 41(6), 1064 - 7 A prospective cross-over field trial shows protection of lemon eucalyptus extract against tick bites; Gardulf A et al.; Ixodes ricinus can transmit several microorganisms, out of which Borrelia burgdorferi and tick-borne encephalitis (TBE) virus are the most important pathogens in humans . A lemon eucalyptus extract (Citriodiol) has been shown to be a natural repellent against mosquitoes, stable flies, and midges . We have investigated whether the use of the extract would reduce the number of attached I . ricinus ticks in humans . A volunteer sample of 111 individuals was recruited among healthy, outdoor active adults living in two highly I . ricinus-infested areas . They were randomly divided into two groups: one group applied the Citriodiol spray daily for 2 wk to the lower extremities, whereas the other group was instructed not to use any type of repellent on any part of the body . After 2 wk, the scheme was reversed . All volunteers filled in a daily diary, giving information about outdoor activities and the number of observed, attached, or not yet attached ticks, including the anatomical location of the ticks found . Forty-two attached ticks were reported during the weeks when the Citriodiol spray was used, and 112 were reported when it was not . The median number of reported attached ticks per person decreased from 1.5 (range, 0-9) to 0.5 (range, 0-2; P < 0.05) during the weeks when the repellent was used . The number of reported attached ticks noted below the waist was 13/42 (31%) during the period when the spray was used and 73/112 (65%) when no spray was used (P < 0.001) . No evident redistribution of attached ticks from protected areas to unprotected areas was seen . Citriodiol may become a useful means in reducing the number of tick bites and thereby tick-borne infections, although additional studies are warranted. Ann Ital Chir, 2004 May-Jun, 75(3), 293 - 7 {Coagulation disorders following severe trauma: surgeon's role in prevention}; Miniello S et al.; INTRODUCTION: Severe trauma must be considered a "systemic disease" that could lead to severe systemic complications . PHYSIOPATHOLOGIC IMPLICATIONS: Coagulation disorders are present in most trauma patients as hemorrhagic disorder, thrombosis, or like in DIC, with both coexistent phenomenon . Trauma determine the activations of intrinsic and extrinsic coagulation pathways, and of platelets . Intrinsic pathway activation induce a pro-coagulant function and the activation of fibrinolytic system . Both system activation explain low incidence of deep venous thrombosis . Post-traumatic activation of extrinsic coagulation lead to thrombin and fibrin production . In trauma patients platelets activation is related to endothelial damage, exposition of collagen, interaction with PAF and presence of microorganisms . Post-traumatic DIC is characterized by procoagulant factors activation, with intravascular deposit of fibrin and thrombosis, and by hemorrhagic disorders due to consumption of platelet and procoagulant factors . Lower levels of antithrombin III, in trauma patients, are strictly related to severity of damage and shock . Coagulation disorders related to sepsis, that often complicate trauma, are added to those determined by trauma, with a negative synergic effect . Medical treatment with massive infusion of colloid and crystalloid solution, and fluid, and massive transfusion of plasma and red blood cells can determine dilutional thrombocytopenia, reduced activity of coagulation factors and reduced haemostatic activity of RBC due to excessive haemodilution--Hct <20% . PREVENTION STRATEGY: To avoid post-traumatic coagulation disorders is important to prevent sepsis, thrombocytopenia and reduced activity of coagulation factors and of RBC, as well as prevent and immediately treat shock . The early use of high dose antithrombin concentrate, is important to prevent DIC and MOFS, and administer subcutaneous or intravenous heparin, in absence of hemorrhagic disorders that contraindicate its use. Int J Infect Dis, 2005 Jan, 9(1), 3 - 14 Hand hygiene: simple and complex; Jumaa PA; This review gives an overview of hand hygiene in healthcare and in the community, including some aspects which have attracted little attention, such as hand drying and cultural issues determining hand hygiene behaviour . Hand hygiene is the most effective measure for interrupting the transmission of microorganisms which cause infection both in the community and in the healthcare setting . Using hand hygiene as a sole measure to reduce infection is unlikely to be successful when other factors in infection control, such as environmental hygiene, crowding, staffing levels and education are inadequate . Hand hygiene must be part of an integrated approach to infection control . Compliance with hand hygiene recommendations is poor worldwide . While the techniques involved in hand hygiene are simple, the complex interdependence of factors which determine hand hygiene behaviour makes the study of hand hygiene complex . It is now recognised that improving compliance with hand hygiene recommendations depends on altering hum