Microorganisms

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 human behaviour . Input from behavioural and social sciences is essential when designing studies to investigate compliance . Interventions to increase compliance with hand hygiene practices must be appropriate for different cultural and social needs . New strategies to promote hand hygiene worldwide include the formation of public-private partnerships.

J Infect, 2005 Jan, 50(1), 46 - 52
Demonstration of intracellular microorganisms (Rickettsia spp., Chlamydia pneumoniae, Bartonella spp.) in pathological human aortic valves by PCR; Nilsson K et al.; Objectives . Rickettsiae, which causes vasculitis, has not been linked to atherosclerotic cardiovascular disease in contrast to Chlamydia pneumoniae whose association with coronary artery disease and with sclerotic heart valves in patients undergoing aortic valve replacement is well established, even if causality is yet to unproven . In the search for any of these infectious agents, 84 pathological and 15 normal aortic heart valves of patients undergoing forensic autopsy were analysed by PCR and DNA-sequencing . Methods . Two to four pieces of all valves were examined by semi-nested PCR, with primers specific for 16S rDNA, citrate synthase (gltA) and 17 kDa outer membrane protein (OMP) genes . Results . Genetic material from Rickettsia spp . and C . pneumoniae was found in 17 (20.2%) and 22 (26.2%), respectively, of the 84 pathological aortic valves . In 35 (41.7%) of these 84 valves either C . pneumoniae or Rickettsia spp . were detected by PCR and in six cases (7.1%) these two organisms co-existed . In one case with Lambl's excrescences, previously considered as aseptic, presence of rickettsia-like organisms also was demonstrated by light microscopy, immunohistochemistry and sequencing of the amplified PCR product showing 100% homology with the published sequence for R . helvetica . In three of the 15 control valves, genetic material from only C . pneumoniae was detected compared to Rickettsia spp . that was significantly detected only in the pathological valves (Fisher's Exact test, 1-sided {Formula: see text} ) . Conclusions . The findings suggest that Rickettsia spp . also have a role in the pathogenesis of aortic valve disease.

Proteomics . 2004 Dec 15; {Epub ahead of print}
Mass spectrometry and database search in the analysis of proteins from the fungus Pleurotus ostreatus; Matis M et al.; Tandem mass spectrometry is a method of choice for rapid analysis in proteomics . Identification and characterization of proteins from organisms with sequenced genomes is today a routine procedure as will be identification of proteins from organisms with unsequenced genomes with new developing tools . Here, we report the use of isotopic labeling with electrospray ionisation (ESI)-tandem mass spectrometry for de novo sequencing in combination with database search taking advantage of different programs for identification of fungal proteins . Using this approach we could identify the proteins of interest . Nevertheless, the identification of a novel protein responsible for the conversion of testosterone into androstenedione was still a difficult task, mostly due to the low homology of steroid transforming enzymes, especially those from microorganisms . Protein p27 was identified as the vanillate O-demethylase oxidoreductase, p33 and p36 as two isoenzymes of malate dehydrogenase, and p45 as citrate synthase . By rechecking the sequences using additional programs it could be shown that the protein p36 has a higher local homology to the steroid-transforming enzyme than to the malate dehydrogenase . Therefore, we assume that p36 is a pluripotent enzyme most probably responsible for the 17beta-hydroxysteroid dehydrogenase activity.

Mol Cell Biol, 2005 Jan, 25(1), 88 - 99
Disruption of the langerin/CD207 gene abolishes Birbeck granules without a marked loss of Langerhans cell function; Kissenpfennig A et al.; Langerin is a C-type lectin expressed by a subset of dendritic leukocytes, the Langerhans cells (LC) . Langerin is a cell surface receptor that induces the formation of an LC-specific organelle, the Birbeck granule (BG) . We generated a langerin(-/-) mouse on a C57BL/6 background which did not display any macroscopic aberrant development . In the absence of langerin, LC were detected in normal numbers in the epidermis but the cells lacked BG . LC of langerin(-/-) mice did not present other phenotypic alterations compared to wild-type littermates . Functionally, the langerin(-/-) LC were able to capture antigen, to migrate towards skin draining lymph nodes, and to undergo phenotypic maturation . In addition, langerin(-/-) mice were not impaired in their capacity to process native OVA protein for I-A(b)-restricted presentation to CD4(+) T lymphocytes or for H-2K(b)-restricted cross-presentation to CD8(+) T lymphocytes . langerin(-/-) mice inoculated with mannosylated or skin-tropic microorganisms did not display an altered pathogen susceptibility . Finally, chemical mutagenesis resulted in a similar rate of skin tumor development in langerin(-/-) and wild-type mice . Overall, our data indicate that langerin and BG are dispensable for a number of LC functions . The langerin(-/-) C57BL/6 mouse should be a valuable model for further functional exploration of langerin and the role of BG.

Ren Fail, 2004 Nov, 26(6), 633 - 9
Genetic determination of TNF and myeloperoxidase production in dialyzed patients with diabetic nephropathy; Buraczynska K et al.; INTRODUCTION: Diabetic nephropathy accounts for more than 20% of the cases of chronic renal failure . For many patients, the method of renal replacement therapy is chronic ambulatory peritoneal dialysis (CAPD) . Diabetes, through glucose autooxidation and production of free radicals, causes protein glycation . Products of protein glycation increase the concentrations of proinflammatory cytokines . The tumor necrosis factor (TNF) is one of the most important cytokines of cellular response and inflammation . Its level is increased in chronic renal failure . Numerous polymorphisms have been identified within and around the TNF gene, which is located on chromosome 6 . Single nucleotide polymorphisms, such as a polymorphism at a position -308, probably have a direct influence on the TNF production . Myeloperoxidase (MPD) is a heme enzyme, participating in oxygen mechanisms of microorganism killing by phagocytes . Chronic renal failure patients show a significant reduction in the intracellular myeloperoxidase level . In the promoter region of myeloperoxidase gene, at position -463, G to A transition has been found, which causes a decreased gene expression . The aim of the present study was an analysis of genetic basis of TNF and myeloperoxidase production in dialyzed patients with diabetic nephropathy . SUBJECTS AND METHODS: The study group consisted of 37 diabetic nephropathy patients treated with peritoneal dialysis . The control subjects were 58 dialyzed patients with other primary renal diseases and 115 healthy individuals . TNF and myeloperoxidase gene polymorphisms were detected by polymerase chain reaction (PCR) and amplification products were digested with the NcoI and AciI restriction enzymes respectively . ELISA determined the TNF and MPO levels in plasma . RESULTS: We haven't found significant differences in TNF genotype and allele frequencies between the groups; however, diabetic nephropathy patients seemed to have a lower frequency of TNF1/TNF1 genotype . In diabetic nephropathy patients, the median TNF plasma level was 43.8 pg/mL, and in other renal diseases it was 36.8 pg/ mL . The difference was significant (p<0.05) . The differences in TNF levels between both groups and the control group (1.7 pg/mL) were highly significant (p<0.001) . There was a statistically significant difference in MPO genotype frequencies between patients with diabetic nephropathy and patients with other renal diseases (p<0.05) . GG and AA genotypes were significantly more common in patients with diabetic nephropathy . The genotype distribution in patients with other renal diseases was similar to the distribution in the control group . Median plasma MPO level in diabetic nephropathy patients was similar to patients with other renal diseases . A significantly lower level (p<0.05) was observed in the control group . In diabetic nephropathy, we have also observed a correlation between the MPO genotype and an earlier onset of the disease . For the TNF genotype, we haven't found such a relationship . There was also no relationship between the TNF and MPO genotypes and time to end-stage renal disease (ESRD) . There were no differences in the frequency of peritonitis between patients with diabetic nephropathy and dialyzed patients with other renal diseases . DISCUSSION: In conclusion, we found that in diabetic nephropathy patients molecular variants of TNF are more frequent than in nondiabetic patients with chronic renal failure and these changes might be associated with altered ability to TNF synthesis . Analysis of the myeloperoxidase genotypes showed significant difference in genotype distribution in dialyzed patients with diabetic nephropathy . This, however, requires further studies to confirm the relationship with the disease.

Eur Arch Otorhinolaryngol . 2004 Dec 15; {Epub ahead of print}
Lemierre's syndrome: three cases and a review; Dool H et al.; Postanginal sepsis, also called Lemierre's syndrome, is a rare but acute medical condition complicating oropharyngeal infection . The pathogenesis consists of the development of internal jugular vein septic thrombophlebitis leading to metastatic infections in the lung and other sites . The causative microorganism is most often Fusobacterium necrophorum . We present three patients with Lemierre's syndrome who presented to the Leiden University Medical Center and give a review of the literature.

Eur J Clin Microbiol Infect Dis . 2004 Dec 14; {Epub ahead of print}
Value of anaerobic blood cultures in pediatrics; Gene A et al.; The aim of the study presented here was to evaluate the utility of anaerobically incubated blood cultures for detecting infections in pediatric patients . During a 2-year period 9,165 pediatric blood samples were processed, and significant microorganisms were recovered from 497 (5.4%) of them . Only two of the microorganisms isolated were strictly anaerobic . Of the total isolates, 13% were detected in anaerobic bottles solely . Considering that the quantity of blood available from pediatric patients for blood cultures is usually small, it may be reasonable to limit the use of anaerobic blood cultures to patients with the highest risk.

FEMS Microbiol Lett, 2004 Dec 15, 241(2), 233 - 42
The modular xylanase Xyn10A from Rhodothermus marinus is cell-attached, and its C-terminal domain has several putative homologues among cell-attached proteins within the phylum Bacteroidetes; Karlsson EN et al.; Until recently, the function of the fifth domain of the thermostable modular xylanase Xyn10A from Rhodothermus marinus was unresolved . A putative homologue to this domain was however identified in a mannanase (Man26A) from the same microorganism which raised questions regarding a common function . An extensive search of all accessible data-bases as well as the partially sequenced genomes of R . marinus and Cytophaga hutchinsonii showed that homologues of this domain were encoded by multiple genes in microorganisms in the phylum Bacteroidetes . Moreover, the domain occurred invariably at the C-termini of proteins that were predominantly extra-cellular/cell attached . A primary structure motif of three conserved regions including structurally important glycines and a proline was also identified suggesting a conserved 3D fold . This bioinformatic evidence suggested a possible role of this domain in mediating cell attachment . To confirm this theory, R . marinus was grown, and activity assays showed that the major part of the xylanase activity was connected to whole cells . Moreover, immunocytochemical detection using a Xyn10A-specific antibody proved presence of Xyn10A on the R . marinus cell surface . In the light of this, a revision of experimental data present on both Xyn10A and Man26A was performed, and the results all indicate a cell-anchoring role of the domain, suggesting that this domain represents a novel type of module that mediates cell attachment in proteins originating from members of the phylum Bacteroidetes.

Arch Oral Biol, 2005 Jan, 50(1), 89 - 96
Ultrastructural study of calculus-enamel and calculus-root interfaces; Rohanizadeh R et al.; The attachment of dental calculus to the tooth (enamel or cementum) surface affects the ease or difficulty of its removal . Understanding the ultrastructural features of the calculus-tooth interface will help in the development of efficient strategies for efficient removal of dental calculus . Objective: The aim of this study was to determine the ultrastructural characteristics of the calculus-tooth interface in relation to the occurrence of calculus fracture . Design: Investigation of the ultrastructural characteristics of the calculus-tooth interface was made on eight human molars with mature supragingival and subgingival calculus using scanning electron microscopy (SEM), transmission electron microscopy (TEM) and fourier transform infra-red (FT-IR) spectroscopy . Results: Fractures were shown by SEM to consistently occur within the calculus itself, but not at the calculus-tooth interface . Higher magnification revealed that the enamel apatite crystals (in the case of supragingival calculus) or the cementum apatite crystals (in the case of subgingival calculus) appeared intimately connected with the calculus crystals at the calculus-enamel or calculus-cementum interface . TEM micrographs confirmed this intimate direct connection or fusion (epitaxial growth) of calculus crystals with enamel and cementum apatite crystals . FT-IR showed lower concentrations of organic phase attributed to microorganisms and higher concentrations of collagen at the calculus-cementum interface compared to that in the calculus away from the interface . Conclusion: Difficulty in complete calculus removal from tooth surfaces (especially from cementum or dentin) may be due in part to the intimate contact between the calculus and the tooth, due to the chemical bonding between the calculus crystals and the tooth apatite crystals and occasional fusion (i.e., epitaxial growth) of the calculus calcium phosphate crystals with the enamel, dentin or apatite crystals . This cohesive bonding results in fracture planes occurring within the calculus instead of at the calculus-tooth interface.

Acta Clin Belg, 2004 Jul-Aug, 59(4), 189 - 93
Hand hygiene, the crusade of the infection control specialist . Alcohol-based handrub: the solution!
Simon AC.
Hands of healthcare workers are the main route of transmission of microorganisms responsible for nosocomial infections . Compliance with hand hygiene procedures however is still grossly insufficient . Rubbing hands with alcohol-based solutions in order to decontaminate hands instead of handwashing, as proposed in new recommendations is one way of solving the problem . Alcohol is more efficient and faster acting than antiseptic soaps and takes care of the real or perceived constraints of healthcare workers against hand hygiene . The pocketsize bottle version of the alcohol-based solution significantly improves doctors' compliance with hand hygiene.

Dev Biol (Basel), 2004, 117, 9 - 13
Regulation of autogenous biologicals in the United States; Schmellik-Sandage CS et al.; The U.S . Department of Agriculture's Center for Veterinary Biologics (CVB) is charged with protecting American agriculture . As part of this effort, CVB licenses manufacturers to produce special biologics for use in individual flocks or livestock herds afflicted by a particular microorganism . These special products, autogenous biologicals, are inactivated vaccines used by or under the direction of a veterinarian or USDA-approved specialist and are produced under a variety of special licensing requirements.

Microbes Infect, 2004 Dec, 6(15), 1388 - 94
Pleiotropic function of Toll-like receptors; Kaisho T et al.; A group of type I transmembrane proteins, Toll-like receptors (TLRs) discriminate various microorganism-associated molecular structures that can function as immune adjuvants . Each TLR signaling has an overlapping but distinct function, which largely depends on intracellular adaptor molecules . Clarifying the functions and signaling of TLRs should provide us with critical information for manipulating the host defense mechanism.

Alcohol, 2004 Jul, 33(3), 191 - 7
Chronic ethanol ingestion and the risk of acute lung injury: a role for glutathione availability?
Brown LA, Harris FL, Ping XD, Gauthier TW.
Although pulmonary function is not altered, a history of alcohol abuse is an independent outcome variable in the development of acute respiratory distress syndrome . In the absence of cirrhosis, alcohol abuse decreased glutathione, the key antioxidant lining the alveolar space, by 80% and is associated with alveolar barrier leak . Neither the glutathione pool nor barrier leak was corrected by abstinence for 1 week . This aberrant glutathione homeostasis may contribute to enhanced alveolar permeability, thereby increasing susceptibility to the development of acute respiratory distress syndrome . In a rat model, chronic ingestion of ethanol decreased pulmonary glutathione concentration, increased alveolar barrier permeability, and increased the risk of acute lung injury . In alveolar type II cells, chronic ingestion of ethanol altered cellular functions such as decreased surfactant processing, decreased barrier integrity, and increased sensitivity to cytotoxin-induced apoptosis in vitro and in vivo . In alveolar macrophages, chronic ingestion of ethanol decreased phagocytosis of microorganisms and decreased cell viability, events that would increase the risk of pneumonia . A central role for glutathione availability was demonstrated by the normalization of cellular function and viability of type II cells and macrophages as well as decreased sensitivity to endotoxemia-induced acute lung injury when glutathione precursors were added to the ethanol diet . These results support the suggestion that chronic ingestion of ethanol increased the risk of acute lung injury not through ethanol per se but through the chronic oxidative stress that resulted from ethanol-induced glutathione depletion . Because chronic oxidative stress alters cellular functions and viability, the lung becomes more susceptible when a second hit such as sepsis occurs.

Mikrobiologiia, 2004 Sep-Oct, 73(5), 698 - 707
{On the problem of anaerobic methane oxidation}; Endodontics: Part 8 . Filling the root canal system; Department of Adult Dental Care, Glasgow Dental Hospital and School, 378 Sauchiehall Street, Glasgow G2 3JZ, Scotland, UK . p.carrotte@dental.gla.ac.uk

The purpose of the obturation phase of a root filling is two-fold; to prevent microorganisms from re-entering the root canal system, and to isolate any microorganisms that may remain within the tooth from nutrients in tissue fluids . The seal at the apical end of the root canal is achieved by a well-fitting gutta-percha master point, and accessory points, although heated techniques may result in a better seal . The seal at the coronal end is achieved by the application of a layer of resin-modified glass ionomer cement as accessory canals may lead from the floor of the pulp chamber to the furcation area . It must always be remembered that success will only be achieved if the root canal system has been as thoroughly debrided as possible of infected material.

Nature, 2004 Dec 9, 432(7018), 747 - 50
Spatial scaling of microbial eukaryote diversity; Green JL et al.; Patterns in the spatial distribution of organisms provide important information about mechanisms that regulate the diversity of life and the complexity of ecosystems . Although microorganisms may comprise much of the Earth's biodiversity and have critical roles in biogeochemistry and ecosystem functioning, little is known about their spatial diversification . Here we present quantitative estimates of microbial community turnover at local and regional scales using the largest spatially explicit microbial diversity data set available (> 10(6) sample pairs) . Turnover rates were small across large geographical distances, of similar magnitude when measured within distinct habitats, and did not increase going from one vegetation type to another . The taxa-area relationship of these terrestrial microbial eukaryotes was relatively flat (slope z = 0.074) and consistent with those reported in aquatic habitats . This suggests that despite high local diversity, microorganisms may have only moderate regional diversity . We show how turnover patterns can be used to project taxa-area relationships up to whole continents . Taxa dissimilarities across continents and between them would strengthen these projections . Such data do not yet exist, but would be feasible to collect.

J Biomed Sci, 2004 Nov-Dec, 11(6), 847 - 54
Hypoxia modulates expression of the 70-kD heat shock protein and reduces Leishmania infection in macrophages; Degrossoli A et al.; Hypoxia, a microenvironmental factor present in diseased tissues, has been recognized as a specific metabolic stimulus or a signal of cellular response . Experimental hypoxia has been reported to induce adaptation in macrophages such as differential migration, elevation of proinflammatory cytokines and glycolytic enzyme activities, and decreased phagocytosis of inert particles . In this study we demonstrate that although exposure to hypoxia (5% O2, 5% CO2, and balanced N2) did not change macrophage viability, or 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) cleavage and proliferation, it significantly reduced expression of the 70-kD heat shock protein (HSP70), which was restored to prehypoxia levels after reoxygenation . The influence of low oxygen tension on macrophage functional activity was also studied, i.e . the ability of these cells to maintain or resist infection by a microorganism . We demonstrate that macrophages from two different sources (a murine cell line and primary cells) exposed to hypoxia were efficiently infected with Leishmania amazonensis, but after 24 h showed a reduction in the percentage of infected cells and of the number of intracellular parasites per macrophage, indicating that hypoxia induced macrophages to kill the intracellular parasites . These results support the notion that hypoxia, a microenvironmental factor, can modulate macrophage protein expression and functional activity . 2004 National Science Council, ROC and S . Karger AG, Basel

Caries Res, 2005 Jan-Feb, 39(1), 52 - 9
Effect of fluoridated toothpicks and dental flosses on enamel and dentine and on plaque composition in situ; Sarner B et al.; The aim was to evaluate the effect of two toothpicks and two dental flosses on demineralized enamel and dentine and on plaque composition, using an in situ model with simulated approximal spaces within dentures . Fifteen subjects with full dentures were recruited and 14 completed the study . It consisted of two crossover periods, the first comparing a birch toothpick with AmF and a birch toothpick with NaF, and the second comparing a dental floss with AmF + NaF and a dental floss without F . Between these four periods, there was a control period without any approximal cleaning . In small, rectangular sample holders, one enamel and one dentine specimen were embedded, forming a triangular, approximal-like space . Two sample holders were mounted in the premolar-molar region of the upper or lower dentures . The subjects used the toothpicks or dental flosses 3 times/day for 4 weeks . The results showed that all toothpicks and dental flosses inhibited further demineralization compared to the control period (p < 0.001) . The dental flosses were somewhat more effective in this respect than the toothpicks, especially in dentine . There were relatively small numerical differences between AmF and NaF toothpicks, but in favour of NaF regarding mineral gain (p < 0.05) . The fluoridated floss gave somewhat less lesion depth in dentine than the non-fluoridated floss (p < 0.01) . Toothpicks and flosses resulted in lower counts of microorganisms in plaque compared to the control period (p < 0.001); the AmF toothpick gave a more pronounced reduction than the NaF toothpick (p < 0.001) .

J Dairy Sci, 2005 Jan, 88(1), 49 - 54
Exfoliation of Helicobacter pylori from Gastric Mucin by Glycopolypeptides from Buttermilk; Matsumoto M et al.; In the human stomach, Helicobacter pylori, an ulcer pathogenic bacterium, colonizes the gastric mucosal layer primarily . The ability of glycopolypeptides (GPP) prepared from buttermilk to exfoliate H . pylori bound to gastric mucin was investigated . The GPP were prepared from buttermilk by digestion with trypsin, papain, pancreatin, bromelain, or pepsin . Helicobacter pylori ATCC 43504(T) and 43579 adhered more strongly to all of the GPP tested than to whole buttermilk, the soluble fraction of buttermilk, gastric mucin prepared from mouse stomach, or commercial pig gastric mucin . The GPP digested with trypsin, papain, or pancreatin were significantly more adherent . When the GPP concentration was 10 mg/mL, bound H . pylori ATCC 43504(T), 43579, and 5 clinical isolates were exfoliated markedly from immobilized porcine gastric mucin following treatment with GPP digested with trypsin or pancreatin . This ability of GPP did not correlate with sialic acid content, indicating that sialic acid content is not important in the exfoliation of this microorganism . Such an ability may depend on the structure or number of sugar chains, or the position of sialic acid . We conclude that GPP promote the exfoliation of H . pylori bound to gastric mucin and prevent the de novo adherence of this microorganism . As such, GPP are a promising food material for preventing H . pylori infection.

Ann N Y Acad Sci, 2004 Nov, 1033, 30 - 41
Kinetics, pharmacokinetics, and regulation of L-carnitine and acetyl-L-carnitine metabolism; Rebouche CJ; In mammals, the carnitine pool consists of nonesterified L-carnitine and many acylcarnitine esters . Of these esters, acetyl-L-carnitine is quantitatively and functionally the most significant . Carnitine homeostasis is maintained by absorption from diet, a modest rate of synthesis, and efficient renal reabsorption . Dietary L-carnitine is absorbed by active and passive transfer across enterocyte membranes . Bioavailability of dietary L-carnitine is 54-87% and is dependent on the amount of L-carnitine in the meal . Absorption of L-carnitine dietary supplements (0.5-6 g) is primarily passive; bioavailability is 14-18% of dose . Unabsorbed L-carnitine is mostly degraded by microorganisms in the large intestine . Circulating L-carnitine is distributed to two kinetically defined compartments: one large and slow-turnover (presumably muscle), and another relatively small and rapid-turnover (presumably liver, kidney, and other tissues) . At normal dietary L-carnitine intake, whole-body turnover time in humans is 38-119 h . In vitro experiments suggest that acetyl-L-carnitine is partially hydrolyzed in enterocytes during absorption . In vivo, circulating acetyl-L-carnitine concentration was increased 43% after oral acetyl-L-carnitine supplements of 2 g/day, indicating that acetyl-L-carnitine is absorbed at least partially without hydrolysis . After single-dose intravenous administration (0.5 g), acetyl-L-carnitine is rapidly, but not completely hydrolyzed, and acetyl-L-carnitine and L-carnitine concentrations return to baseline within 12 h . At normal circulating l-carnitine concentrations, renal l-carnitine reabsorption is highly efficient (90-99% of filtered load; clearance, 1-3 mL/min), but displays saturation kinetics . Thus, as circulating L-carnitine concentration increases (as after high-dose intravenous or oral administration of L-carnitine), efficiency of reabsorption decreases and clearance increases, resulting in rapid decline of circulating L-carnitine concentration to baseline . Elimination kinetics for acetyl-L-carnitine are similar to those for L-carnitine . There is evidence for renal tubular secretion of both L-carnitine and acetyl-L-carnitine . Future research should address the correlation of supplement dosage, changes and maintenance of tissue L-carnitine and acetyl-L-carnitine concentrations, and metabolic and functional changes and outcomes.

Microbiol Mol Biol Rev, 2004 Dec, 68(4), 745 - 70
Metabolic interdependence of obligate intracellular bacteria and their insect hosts; Zientz E et al.; Mutualistic associations of obligate intracellular bacteria and insects have attracted much interest in the past few years due to the evolutionary consequences for their genome structure . However, much less attention has been paid to the metabolic ramifications for these endosymbiotic microorganisms, which have to compete with but also to adapt to another metabolism--that of the host cell . This review attempts to provide insights into the complex physiological interactions and the evolution of metabolic pathways of several mutualistic bacteria of aphids, ants, and tsetse flies and their insect hosts.

Microbiol Mol Biol Rev, 2004 Dec, 68(4), 630 - 8
Streamlined regulation and gene loss as adaptive mechanisms in Prochlorococcus for optimized nitrogen utilization in oligotrophic environments; Garcia-Fernandez JM et al.; Prochlorococcus is one of the dominant cyanobacteria and a key primary producer in oligotrophic intertropical oceans . Here we present an overview of the pathways of nitrogen assimilation in Prochlorococcus, which have been significantly modified in these microorganisms for adaptation to the natural limitations of their habitats, leading to the appearance of different ecotypes lacking key enzymes, such as nitrate reductase, nitrite reductase, or urease, and to the simplification of the metabolic regulation systems . The only nitrogen source utilizable by all studied isolates is ammonia, which is incorporated into glutamate by glutamine synthetase . However, this enzyme shows unusual regulatory features, although its structural and kinetic features are unchanged . Similarly, urease activities remain fairly constant under different conditions . The signal transduction protein P(II) is apparently not phosphorylated in Prochlorococcus, despite its conserved amino acid sequence . The genes amt1 and ntcA (coding for an ammonium transporter and a global nitrogen regulator, respectively) show noncorrelated expression in Prochlorococcus under nitrogen stress; furthermore, high rates of organic nitrogen uptake have been observed . All of these unusual features could provide a physiological basis for the predominance of Prochlorococcus over Synechococcus in oligotrophic oceans.

Biochimie, 2004 Nov, 86(11), 807 - 15
Fatty acid biosynthesis in microorganisms being used for Single Cell Oil production; Ratledge C; Single cell oils (SCOs) are now produced by various microorganisms as commercial sources of arachidonic acid (ARA) and docosahexaenoic acid (DHA) . These oils are now used extensively as dietary supplements in infant formulas . An understanding of the underlying biochemistry and genetics of oil accumulation in such microorganisms is therefore essential if lipid yields are to be improved . Also an understanding of the biosynthetic pathways involved in the production of these polyunsaturated fatty acids (PUFAs) is also highly desirable as a prerequisite to increasing their content in the oils . An account is provided of the biosynthetic machinery that is necessary to achieve oil accumulation in an oleaginous species where it can account for lipid build up in excess of 70% of the cell biomass . Whilst PUFA production in most microorganisms uses a conventional fatty acid synthase (FAS) system followed by a series of desaturases and elongases, in Schizochytrium sp., and probably related thraustochytrid marine protists, PUFA synthesis now appears to be via a polyketide synthase (PKS) route . This route is discussed . It clearly represents a major departure from conventional fatty acid biosynthesis, possibly as a means of decreasing the amount of NADPH that is needed in the overall process.

Mol Immunol, 2005 Feb, 42(3), 279 - 87
The lung collectins, SP-A and SP-D, modulate pulmonary innate immunity; Sano H et al.; Pulmonary surfactant, which covers the peripheral airway, is a mixture of lipids and proteins . The hydrophilic surfactant proteins A (SP-A) and D (SP-D) play important roles in host defense mechanisms of the lung . These proteins belong to a collectin subgroup in which lectin domains are associated with collagenous structures . Collectins involve mannose-binding lectin, and are considered to function in innate immune systems . SP-A and SP-D interact with various microorganisms and pathogen-derived components . They act as opsonins by binding and agglutinating pathogens . The lung collectins also possess direct inhibitory effects on bacterial growth . SP-A and SP-D associate with immune cells, and activate various cellular functions . The direct interactions of SP-A and SP-D with macrophages result in modulation of phagocytosis or the production of reactive oxygen species . Moreover, by associating with cell surface pattern-recognition receptors, SP-A and SP-D regulate inflammatory cellular responses such as the release of lipopolysaccharides-induced proinflammatory cytokines . Animal models of SP-A- or SP-D-deficiency reveal significant defect in host defense . Significant susceptibility to bacterial and viral infections, delayed microbial clearance, and overexpression of proinflammatory cytokines are observed in SP-A or SP-D knockout mice . A more complete understanding of the mechanisms is required, but the biological relevance of SP-A and SP-D against various respiratory infections has been increasingly recognized.

Biomed Pharmacother, 2004 Dec, 58(10), 610 - 3
Screening of bioactive metabolites for pancreatic regeneration chemotherapy; Takatsuna H et al.; Plants and microorganisms are the treasury of bioactive metabolites including useful chemical ligands . Chemical ligands that induce beta-cell differentiation may be useful as new therapeutic agents for both type-1 and type-2 diabetes mellitus . We isolated conophylline from the leaves of Ervatamia microphylla as an agent that induce insulin production in rat pancreatic acinar carcinoma cells.

J Theor Biol, 2005 Feb 21, 232(4), 587 - 604
A generalized model of social and biological contagion; Dodds PS et al.; We present a model of contagion that unifies and generalizes existing models of the spread of social influences and microorganismal infections . Our model incorporates individual memory of exposure to a contagious entity (e.g . a rumor or disease), variable magnitudes of exposure (dose sizes), and heterogeneity in the susceptibility of individuals . Through analysis and simulation, we examine in detail the case where individuals may recover from an infection and then immediately become susceptible again (analogous to the so-called SIS model) . We identify three basic classes of contagion models which we call epidemic threshold, vanishing critical mass, and critical mass classes, where each class of models corresponds to different strategies for prevention or facilitation . We find that the conditions for a particular contagion model to belong to one of the these three classes depend only on memory length and the probabilities of being infected by one and two exposures, respectively . These parameters are in principle measurable for real contagious influences or entities, thus yielding empirical implications for our model . We also study the case where individuals attain permanent immunity once recovered, finding that epidemics inevitably die out but may be surprisingly persistent when individuals possess memory.

Tissue Eng, 2004 Sep-Oct, 10(9-10), 1446 - 55
In vivo and in vitro degradation of urea and uric acid by encapsulated genetically modified microorganisms; O'Loughlin JA et al.; This study was undertaken to characterize the capacity of a combination of genetically modified bacteria to lower elevated levels of urea and uric acid and thus to serve as a potential adjunct to maintenance dialysis in patients with chronic renal failure . Two strains of genetically modified bacteria expressing enzymes, urease to degrade urea and uricase to degrade uric acid, were identified, combined, and dispersed in 600-microm alginate microcapsules suitable for oral administration . In 24 h in vitro experiments, 5 mL of these capsules completely cleared 95% of the urea and >99% of the uric acid from 100 mL of a challenge solution formulated to the concentration of these solutes in a presenting hemodialysis patient . The process of urea degradation was found to be intracellular and each bacterial strain was specific for its substrate . Solute degradation in vivo was evaluated with a chemically induced model of acute renal failure, using Sprague-Dawley rats . Orally administered capsules were found to remain in the gastrointestinal tract for at least 6 h . The severity of azotemia and hyperuricaemia after chemical induction of acute renal failure was reduced by 64 and 31%, respectively, on administration of the capsules . Reduction of urea concentration (but not uric acid concentration) in vivo required coadministration of an ion-exchange resin to adsorb ammonia . Oral delivery of a combination of genetically modified microorganisms should be further explored in chronic renal failure models as a useful adjunct to dialysis or to immunosorption for the treatment of uremia.

Respir Res . 2004 Dec 10;5(1):28.
Coccidioides posadasii infection alters the expression of pulmonary surfactant proteins (SP)-A and SP-D; Awasthi S et al.; BACKGROUND: Coccidioidomycosis or Valley Fever is caused by Coccidioides in Southwest US and Central America . Primary pulmonary infection is initiated by inhalation of air-borne arthroconidia . Since, lung is the first organ that encounters arthroconidia, different components of the pulmonary innate immune system may be involved in the regulation of host defense . Pulmonary surfactant proteins (SP)-A and SP-D have been recognized to play an important role in binding and phagocytosis of various microorganisms, but their roles in Coccidioides infection are not known . METHODS: In this study, we studied the changes in amounts of pulmonary SP-A, SP-D and phospholipid in murine model of Coccidioides posadasii infection, and binding of SP-A and SP-D to Coccidioidal antigens . Mice were challenged intranasally with a lethal dose of C . posadasii (n = 30 arthroconidia) and bronchoalveolar lavage fluid (BALF) samples were collected on day 10, post infection . In another group of animals, mice were immunized with protective formalin killed spherule (FKS) vaccine prior to infection . The concentrations of BALF SP-A, SP-D, total phospholipid were measured using enzyme linked immunosorbent assay and biochemical assays . RESULTS: We found that in lavage fluid samples of C . posadasii infected mice, the concentrations of total phospholipid, SP-A and SP-D were 17 % (SEM 3.5, p < 0.001), 38 % (SEM 5.8, p < 0.001) and 4 % (SEM 1.3, p < 0.001) of those in lavage fluid samples of non-infected control mice, respectively . However, the concentrations of SP-A and SP-D remained unchanged in BALF samples of C . posadasii protected mice after immunization with FKS vaccine . Also, we found that both SP-A and SP-D bind to Coccidiodal antigens . CONCLUSION: Our results suggest that the C . posadasii infection perturbs the pulmonary SP-A, SP-D, and phospholipids, potentially enabling the disease progression and promoting fungal dissemination.

Phytochemistry, 2004 Aug, 65(15), 2205 - 9
Biotransformation of hydrocortisone by a natural isolate of Nostoc muscorum; Yazdi MT et al.; Hydrocortisone was converted in the culture of an isolated strain of the cyanobacterium Nostoc muscorum PTCC 1636 into some androstane and pregnane derivatives . The microorganism was, isolated during a screening program from soil samples collected from paddy fields of north of Iran . The bioproducts obtained were purified using chromatographic methods and identified as 11beta-hydroxytestosterone, 11beta-hydroxyandrost-4-en-3,17-dione and 11beta,17alpha,20beta,21-tetrahydroxypregn-4-en-3-one on the basis of their spectroscopic features.

Schweiz Monatsschr Zahnmed, 2004, 114(11), 1151 - 65
{Halitosis--Part 2: Diagnosis and therapy}; Lang B et al.; Halitosis may be diagnosed organoleptically or instrumentally . The latter method employs gas chromatography, sulphide monitors or electronic noses . Therapy is strictly cause-related . Non-oral causes must be examined by a specialist in accordance with the diagnosed syndrome . Where oral causes prevail, the therapy focuses on a reduction of microorganisms and the bacterial nutrient supply as well as the conversion of VSC into non-volatile sulphur compounds and, if required, the additional application of oral cosmetics.

Biol Res, 2004, 37(4 Suppl A), 783 - 93
Isolation and expression of the genes coding for the membrane bound transglycosylase B (MltB) and the transferrin binding protein B (TbpB) of the salmon pathogen Piscirickettsia salmonis; Wilhelm V et al.; We have isolated and sequenced the genes encoding the membrane bound transglycosylase B (MltB) and the transferring binding protein B (TbpB) of the salmon pathogen Piscirickettsia salmonis . The results of the sequence revealed two open reading frames that encode proteins with calculated molecular weights of 38,830 and 85,140 . The deduced aminoacid sequences of both proteins show a significant homology to the respective protein from phylogenetically related microorganisms . Partial sequences coding the amino and carboxyl regions of MltB and a sequence of 761 base pairs encoding the amino region of TbpB have been expressed in E . coli . The strong humoral response elicited by these proteins in mouse confirmed the immunogenic properties of the recombinant proteins . A similar response was elicited by both proteins when injected intraperitoneally in Atlantic salmon . The present data indicates that these proteins are good candidates to be used in formulations to study the protective immunity of salmon to infection by P . salnonis.

Curr Drug Targets Inflamm Allergy, 2004 Dec, 3(4), 455 - 8
Pulmonary complications in diabetes mellitus: the role of glycemic control; Ardigo D et al.; Insulin deficiency induces an increase in blood glucose levels that, in long run, becomes toxic for many organs and systems . Microangiopathy and derangements in the immune function are known consequences of hyperglycemia, but the way in which these systemic alterations may affect pulmonary function has been scarcely investigated . Although confirmation from large clinical trials is still to come, the diabetic disease seems to hit the pulmonary microcirculation as any other organ by increasing vessel wall thickness and impairing gas exchange, which leads to a measurable loss of function and respiratory efficiency . In addition, a diabetic lung is more susceptible to low respiratory tract infections by atypical microorganisms and more likely to host severe episodes of pneumonia than a normal, non-diabetic lung . This is a review of current knowledge on the impact of diabetes mellitus in lung health . We have paid special attention to the role of metabolic control in preventing damage to the lung by sustained hyperglycemia.

G Ital Med Lav Ergon, 2004 Oct-Dec, 26(4), 370 - 4
{Biological pollution and allergic diseases}; Carrer P et al.; House dust mites, pets, microorganisms such as fungi and bacteria are the main causes of indoor allergens . The diseases correlated to the presence of these allergens are of increasing importance in public health as well as in occupational medicine . Indoor allergens are widespread in residential buildings as well as in public and in office buildings . Surveys conducted in Italian office buildings demonstrated detectable allergen concentrations in most of these buildings . In some cases, the concentrations were higher than the proposed risk threshold for allergenic sensitisation or for the elicitation of symptoms in allergic individuals . The health effects of exposure to indoor allergens mainly include allergic asthma and rhinoconjunctivitis caused by IgE reactions in predisposed subjects . Moreover, exposure to indoor biological agents can cause extrinsic allergic alveolitis or other effects such as the so-called "humidifier fever" due to contaminated humidifiers . Standardized methods for the measurement of indoor allergen levels are available, and may be useful for the diagnosis and treatment of individual allergic patients or for group studies in order to evaluate the relationship between allergen indoor levels and health effects or to assess indoor allergen levels in private or public buildings for preventative purposes.

Oral Surg Oral Med Oral Pathol Oral Radiol Endod, 2004 Dec, 98(6), 665 - 72
The role of oral microbial colonization in ventilator-associated pneumonia; Brennan MT et al.; The present article reviews the association between microbial colonization of the oral cavity and the lungs in critically ill patients that develop ventilator-associated pneumonia (VAP) in the intensive care unit (ICU) setting . The risk factors and microorganisms associated with VAP are presented . The role of oral colonization of VAP-associated pathogens (VAP-AP) in the development of VAP is examined . We explore the potential factors involved in oral colonization of VAP-AP, which are atypical bacteria for the oral cavity . Strategies for the prevention or moderation of oral colonization of VAP-AP have had limited success . We need a deeper understanding of the pathophysiology of VAP in order to reduce the morbidity, mortality, and cost from this common complication in ICU medicine and surgery.

J Clin Microbiol, 2004 Dec, 42(12), 5467 - 71
Analysis of Trichosporon isolates obtained from the houses of patients with summer-type hypersensitivity pneumonitis; Sugita T et al.; Summer-type hypersensitivity pneumonitis (SHP) is type III or IV allergies developed by repeated inhalation of arthroconidia of Trichosporon species . We identified 105 strains obtained from the homes of 36 SHP patients by analysis of the intergenic spacer (IGS) 1 region, which is located between the 26S and 5S rRNA genes; in addition, we analyzed the IGS genotypes of the strains . Serologically, Trichosporon species are classified as serotype I, II, III, or I-III . Of the 105 strains, 43 (41.1%), 53 (50.5%), and 9 (8.6%) strains were isolated as serotypes I, II, and III, respectively . Serotype I, II, and III strains were recovered from 19 (52.8%), 29 (80.6%), and 4 (11.1%) of the 36 houses of SHP patients, respectively . No serotype I-III strains were isolated from the houses . Of 43 serotype I strains, 42 (97.7%) were identified as Trichosporon dermatis, and the remaining one was T . terricola . Of 53 serotype II strains, 37 (69.8%) were identified as T . asahii, and the remaining serotype II isolates were T . aquatile (1.9%), T . coremiiforme (7.5%), T . faecale (1.9%), T . japonicum (15.1%), and T . ovoides (3.8%) . There were nine serotype III strains comprised of T . montevideense (77.8%) and T . domesticum (22.2%) . Intraspecies diversity was found only in T . asahii . This microorganism also causes opportunistic infections (trichosporonosis); seven genotypes of its IGS 1 region have been identified . While the strains of T . asahii obtained from Japanese patients with trichosporonosis were genotype I, the strains from the houses of SHP patients were genotype III . Based on our analysis, we conclude that the strains that play the most significant roles in the development of SHP are T . dermatis, T . asahii genotype 3, and T . montevideense, representing serotypes I, II, and III, respectively.

Arch Biochem Biophys, 2005 Jan 1, 433(1), 193 - 211
Structure--function studies on the iron-sulfur flavoenzyme glutamate synthase: an unexpectedly complex self-regulated enzyme; Vanoni MA et al.; Glutamate synthase (GltS) is, with glutamine synthetase, the key enzyme of ammonia assimilation in bacteria, microorganisms and plants . GltS isoforms result from the assembly and co-evolution of conserved functional domains . They share a common mechanism of reductive glutamine-dependent glutamate synthesis from 2-oxoglutarate, which takes place within the alpha subunit ( approximately 150 kDa) of the NADPH-dependent bacterial enzyme and the corresponding polypeptides of other GltS forms, and involves: (i) an Ntn-type amidotransferase domain and (ii) a flavin mononucleotide-containing (beta/alpha)(8) barrel synthase domain connected by (iii) a approximately 30 A-long intramolecular ammonia tunnel . The synthase domain harbors the {3Fe/4S}(0,+1) cluster of the enzyme, which participates in the electron transfer process from the physiological reductant: reduced ferredoxin in the plant-type enzyme or NAD(P)H in the bacterial and the non-photosynthetic eukaryotic form . The NAD(P)H-dependent GltS requires a tightly bound flavin adenine dinucleotide-dependent reductase (beta subunit, approximately 50 kDa), also determining the presence of two low-potential {4Fe-4S}(+1,+2) clusters . Structural, functional and computational data available on GltS and related enzymes show how the enzyme may control and coordinate the reactions taking place at the glutaminase and synthase sites by sensing substrate binding and cofactor redox state.

Water Sci Technol, 2004, 50(9), 83 - 9
Enhanced heavy metal bioleaching efficiencies from anaerobically digested sewage sludge with coinoculation of Acidithiobacillus ferrooxidans ANYL-1 and Blastoschizomyces capitatus Y5; Wong JW et al.; Prolonged bioleaching period was required to remove heavy metals from anaerobically digested sewage sludge in the presence of low molecular weight organic acids . The purpose of the present study was therefore to enhance metal solubilization efficiencies through introducing organic acid-degrading microorganisms into this artificial bioleaching system . An acetic and propionic acid-degrading yeast Blastoschizomyces capitatus Y5 was successfully isolated from a local Yuen Long sewage sludge and it could achieve optimum growth in synthetic liquid media containing 2000 mg l(-1) acetic acid or 1000 mg l(-1) propionic acid . When it was inoculated simultaneously with Acidithiobacillus ferrooxidans ANYL-1 into anaerobically digested sewage sludge, which contained 648 mg l(-1) acetic acid and 731 mg l(-1) propionic acid, both acids were completely decomposed within 24 hours . As a result, ferrous iron oxidation was greatly improved, resulting in enhanced metal solubilization . Compared with the 8, 10 and 12 days required for maximum solubilization of Zn, Cu and Cr for the control sludge, the bioleaching period was significantly shortened to 4, 5 and 8 days respectively for sludge receiving co-inoculation.

Med Oral Patol Oral Cir Bucal, 2004, 9 Suppl, 101 - 7; 92-100
Periodontal diseases as bacterial infection; Bascones-Martinez A et al.; The periodontal disease is conformed by a group of illnesses affecting the gums and dental support structures . They are caused by certain bacteria found in the bacterial plaque . These bacteria are essential to the onset of illness; however, there are predisposing factors in both the host and the microorganisms that will have an effect on the pathogenesis of the illness . Periodontopathogenic bacterial microbiota is needed, but by itself, it is not enough to cause the illness, requiring the presence of a susceptible host . These diseases have been classified as gingivitis, when limited to the gums, and periodontitis, when they spread to deeper tissues . Classification of periodontal disease has varied over the years . The one used in this work was approved at the International Workshop for a Classification of Periodontal Diseases and Conditions, held in 1999 . This study is an overview of the different periodontal disease syndromes . Later, the systematic use of antibiotic treatment consisting of amoxicillin, amoxicillin-clavulanic acid, and metronidazole as first line coadjuvant treatment of these illnesses will be reviewed.

EMBO Rep, 2004 Dec, 5(12), 1142 - 7
Survival of protozoan intracellular parasites in host cells; Leiriao P et al.; The most common human diseases are caused by pathogens . Several of these microorganisms have developed efficient ways in which to exploit host molecules, along with molecular pathways to ensure their survival, differentiation and replication in host cells . Although the contribution of the host cell to the development of many intracellular pathogens (particularly viruses and bacteria) has been unequivocally established, the study of host-cell requirements during the life cycle of protozoan parasites is still in its infancy . In this review, we aim to provide some insight into the manipulation of the host cell by parasites through discussing the hurdles that are faced by the latter during infection.

Vaccine, 2004 Dec 6, 22 Suppl 1, S21 - 4
Host cell-pathogen interface: molecular mechanisms and genetics; Schumann RR; Host factors determining the host-pathogen interaction are crucial for the reaction pattern leading to the threat of nosocomial infections . A soluble protein with the ability to recognize a variety of microorganisms is LPS binding protein (LBP) . The recently identified family of Toll-like receptors (TLRs) represents the major group of cellular signaling receptors for pathogens . The discovery of genetic variations of these proteins caused by single nucleotide polymorphisms (SNPs) has led to first studies aimed at elucidating a potential link between genomic variation of the host and susceptibility to infections . The current state of these analyses is summarized here.

Biomaterials, 2005 May, 26(14), 2033 - 42
Effective use of optimized, high-dose (50kGy) gamma irradiation for pathogen inactivation of human bone allografts; Grieb TA et al.; The safety of tissue allografts has come under increased scrutiny due to recent reports of allograft-associated bacterial and viral infections in tissue recipients . We report that 50kGy of gamma irradiation, nearly three times the dose currently used, is an effective pathogen inactivation method when used under optimized conditions that minimize damage to the tissue . Cancellous bone dowels treated with a radioprotectant solution and 50kGy of optimized irradiation had an ultimate compressive strength and modulus of elasticity equal to conventionally irradiated (18kGy) and non-irradiated control bone grafts . We subjected bone dowels treated with this pathogen inactivation method to an in vitro cytotoxicity test using three different mammalian cell lines and concluded that the treated grafts were not cytotoxic . The log reduction of nine pathogens spiked into radioprotectant-treated bone irradiated to 50kGy was also tested . We achieved 4.9logs of inactivation of a model virus for HIV and hepatitis C and 5logs inactivation of a model virus for human parvovirus B-19 . Complete inactivation (6.0-9.2logs) of seven clinically relevant microorganisms was demonstrated . The results show that a combination of radioprotectants and optimized, high-dose gamma irradiation is a viable method for producing safer cancellous bone grafts that have the mechanical strength of existing grafts.

Appl Environ Microbiol, 2004 Dec, 70(12), 7229 - 35
Characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library; Yun J et al.; It has been estimated that less than 1% of the microorganisms in nature can be cultivated by conventional techniques . Thus, the classical approach of isolating enzymes from pure cultures allows the analysis of only a subset of the total naturally occurring microbiota in environmental samples enriched in microorganisms . To isolate useful microbial enzymes from uncultured soil microorganisms, a metagenome was isolated from soil samples, and a metagenomic library was constructed by using the pUC19 vector . The library was screened for amylase activity, and one clone from among approximately 30,000 recombinant Escherichia coli clones showed amylase activity . Sequencing of the clone revealed a novel amylolytic enzyme expressed from a novel gene . The putative amylase gene (amyM) was overexpressed and purified for characterization . Optimal conditions for the enzyme activity of the AmyM protein were 42 degrees C and pH 9.0; Ca2+ stabilized the activity . The amylase hydrolyzed soluble starch and cyclodextrins to produce high levels of maltose and hydrolyzed pullulan to panose . The enzyme showed a high transglycosylation activity, making alpha-(1, 4) linkages exclusively . The hydrolysis and transglycosylation properties of AmyM suggest that it has novel characteristics and can be regarded as an intermediate type of maltogenic amylase, alpha-amylase, and 4-alpha-glucanotransferase.

Biophys J, 2005 Jan, 88(1), L07 - 9 Epub 2004 Dec 01.
Properties of Metabolic Networks: Structure versus Function; Mahadevan R et al.; Biological data from high-throughput technologies describing the network components (genes, proteins, metabolites) and their associated interactions have driven the reconstruction and study of structural (topological) properties of large-scale biological networks . In this article, we address the relation of the functional and structural properties by using extensively experimentally validated genome-scale metabolic network models to compute observable functional states of a microorganism and compare the "structure versus function" attributes of metabolic networks . It is observed that, functionally speaking, the essentiality of reactions in a node is not correlated with node connectivity as structural analyses of other biological networks have suggested . These findings are illustrated with the analysis of the genome-scale biochemical networks of three species with distinct modes of metabolism . These results also suggest fundamental differences among different biological networks arising out of their representation and functional constraints.

Ambio, 2004 Nov, 33(7), 418 - 35
Responses to projected changes in climate and UV-B at the species level; Callaghan TV et al.; Environmental manipulation experiments showed that species respond individualistically to each environmental-change variable . The greatest responses of plants were generally to nutrient, particularly nitrogen, addition . Summer warming experiments showed that woody plant responses were dominant and that mosses and lichens became less abundant . Responses to warming were controlled by moisture availability and snow cover . Many invertebrates increased population growth in response to summer warming, as long as desiccation was not induced . CO2 and UV-B enrichment experiments showed that plant and animal responses were small . However, some microorganisms and species of fungi were sensitive to increased UV-B and some intensive mutagenic actions could, perhaps, lead to unexpected epidemic outbreaks . Tundra soil heating, CO2 enrichment and amendment with mineral nutrients generally accelerated microbial activity . Algae are likely to dominate cyanobacteria in milder climates . Expected increases in winter freeze-thaw cycles leading to ice-crust formation are likely to severely reduce winter survival rate and disrupt the population dynamics of many terrestrial animals . A deeper snow cover is likely to restrict access to winter pastures by reindeer/caribou and their ability to flee from predators while any earlier onset of the snow-free period is likely to stimulate increased plant growth . Initial species responses to climate change might occur at the sub-species level: an Arctic plant or animal species with high genetic/racial diversity has proved an ability to adapt to different environmental conditions in the past and is likely to do so also in the future . Indigenous knowledge, air photographs, satellite images and monitoring show that changes in the distributions of some species are already occurring: Arctic vegetation is becoming more shrubby and more productive, there have been recent changes in the ranges of caribou, and "new" species of insects and birds previously associated with areas south of the treeline have been recorded . In contrast, almost all Arctic breeding bird species are declining and models predict further quite dramatic reductions of the populations of tundra birds due to warming . Species-climate response surface models predict potential future ranges of current Arctic species that are often markedly reduced and displaced northwards in response to warming . In contrast, invertebrates and microorganisms are very likely to quickly expand their ranges northwards into the Arctic.

Ambio, 2004 Nov, 33(7), 404 - 17
Biodiversity, distributions and adaptations of Arctic species in the context of environmental change; Callaghan TV et al.; The individual of a species is the basic unit which responds to climate and UV-B changes, and it responds over a wide range of time scales . The diversity of animal, plant and microbial species appears to be low in the Arctic, and decreases from the boreal forests to the polar deserts of the extreme North but primitive species are particularly abundant . This latitudinal decline is associated with an increase in super-dominant species that occupy a wide range of habitats . Climate warming is expected to reduce the abundance and restrict the ranges of such species and to affect species at their northern range boundaries more than in the South: some Arctic animal and plant specialists could face extinction . Species most likely to expand into tundra are boreal species that currently exist as outlier populations in the Arctic . Many plant species have characteristics that allow them to survive short snow-free growing seasons, low solar angles, permafrost and low soil temperatures, low nutrient availability and physical disturbance . Many of these characteristics are likely to limit species' responses to climate warming, but mainly because of poor competitive ability compared with potential immigrant species . Terrestrial Arctic animals possess many adaptations that enable them to persist under a wide range of temperatures in the Arctic . Many escape unfavorable weather and resource shortage by winter dormancy or by migration . The biotic environment of Arctic animal species is relatively simple with few enemies, competitors, diseases, parasites and available food resources . Terrestrial Arctic animals are likely to be most vulnerable to warmer and drier summers, climatic changes that interfere with migration routes and staging areas, altered snow conditions and freeze-thaw cycles in winter, climate-induced disruption of the seasonal timing of reproduction and development, and influx of new competitors, predators, parasites and diseases . Arctic microorganisms are also well adapted to the Arctic's climate: some can metabolize at temperatures down to -39 degrees C . Cyanobacteria and algae have a wide range of adaptive strategies that allow them to avoid, or at least minimize UV injury . Microorganisms can tolerate most environmental conditions and they have short generation times which can facilitate rapid adaptation to new environments . In contrast, Arctic plant and animal species are very likely to change their distributions rather than evolve significantly in response to warming.

Adv Colloid Interface Sci, 2004 Nov 29, 111(1-2), 117 - 29
Flocculation of cellular suspensions by polyelectrolytes; Barany S et al.; The regularities, kinetics and mechanisms of flocculation of Escherichia coli and B . thuringiensis var . israelensis (Bti) cellular suspensions by water-soluble polymers-and first of all cationic polyelectrolytes of different charge density and stiffness of the macromolecule chain have been investigated . The effect of the focculant dose and nature, its charge density, the hydrophobic-hydrophilic balance in macromolecule, the suspension concentration, the mode of adding the reagent, the pH and the medium composition on the degree of aggregation of cells both in perikinetic regime and in a flowing system is considered . It has been shown that the main laws of microorganism's suspension flocculation are the same as the laws of flocculation of inorganic dispersions but at the same time the first process is much more complicated because the cell-flocculant interactions are strongly affected by products of cell metabolism, components of the culture liquor, pH value, electrolyte content as well as by the changing structure of the cell surface . On the basis of complex measurements of polymer adsorption and its effect on the electrokinetic potential and degree of aggregation of cells, a conclusion is made that the aggregation of E . coli cells by flexible polyelectrolytes like polydiethylaminoethylmetacrylate and its copolymers with acrylic acid, acrylamide and vinylpyrrolidone is due to charge neutralization, while the flocculation in the presence of rigid-chain chitosan and its derivatives is caused mainly by "bridging" between cells via adsorbed macromolecules . Extraction of cells from suspension can be enhanced by combination of electroflotation and flocculation by cationic polyelectrolytes . It has been shown that dilute suspensions of Bti bacteria can be effectively flocculated and concentrated using different cationic and anionic polyelectrolytes that is necessary for its formulation and use as anti-mosquito agent.

Orig Life Evol Biosph, 2004 Dec, 34(6), 615 - 26
Growth of methanogens on a Mars soil simulant; Kral TA et al.; Currently, the surface of Mars is probably too cold, too dry, and too oxidizing for life, as we know it, to exist . But the subsurface is another matter . Life forms that might exist below the surface could not obtain their energy from photosynthesis, but rather they would have to utilize chemical energy . Methanogens are one type of microorganism that might be able to survive below the surface of Mars . A potential habitat for existence of methanogens on Mars might be a geothermal source of hydrogen, possibly due to volcanic or hydrothermal activity, or the reaction of basalt and anaerobic water, carbon dioxide, which is abundant in the martian atmosphere, and of course, subsurface liquid water . We report here that certain methanogens can grow on a Mars soil simulant when supplied with carbon dioxide, molecular hydrogen, and varying amounts of water.

Annu Rev Genet, 2004, 38, 525 - 52
Metagenomics: genomic analysis of microbial communities; Riesenfeld CS et al.; Uncultured microorganisms comprise the majority of the planet's biological diversity . Microorganisms represent two of the three domains of life and contain vast diversity that is the product of an estimated 3.8 billion years of evolution . In many environments, as many as 99% of the microorganisms cannot be cultured by standard techniques, and the uncultured fraction includes diverse organisms that are only distantly related to the cultured ones . Therefore, culture-independent methods are essential to understand the genetic diversity, population structure, and ecological roles of the majority of microorganisms . Metagenomics, or the culture-independent genomic analysis of an assemblage of microorganisms, has potential to answer fundamental questions in microbial ecology . This review describes progress toward understanding the biology of uncultured Bacteria, Archaea, and viruses through metagenomic analyses.

Annu Rev Genet, 2004, 38, 175 - 202
The genetics of geochemistry; Croal LR et al.; Bacteria are remarkable in their metabolic diversity due to their ability to harvest energy from myriad oxidation and reduction reactions . In some cases, their metabolisms involve redox transformations of metal(loid)s, which lead to the precipitation, transformation, or dissolution of minerals . Microorganism/mineral interactions not only affect the geochemistry of modern environments, but may also have contributed to shaping the near-surface environment of the early Earth . For example, bacterial anaerobic respiration of ferric iron or the toxic metalloid arsenic is well known to affect water quality in many parts of the world today, whereas the utilization of ferrous iron as an electron donor in anoxygenic photosynthesis may help explain the origin of Banded Iron Formations, a class of ancient sedimentary deposits . Bacterial genetics holds the key to understanding how these metabolisms work . Once the genes and gene products that catalyze geochemically relevant reactions are understood, as well as the conditions that trigger their expression, we may begin to predict when and to what extent these metabolisms influence modern geochemical cycles, as well as develop a basis for deciphering their origins and how organisms that utilized them may have altered the chemical and physical features of our planet.

Langmuir, 2004 Dec 7, 20(25), 10818 - 28
Deviation from the classical colloid filtration theory in the presence of repulsive DLVO interactions; Tufenkji N et al.; A growing body of experimental evidence suggests that the deposition behavior of microbial particles (e.g., bacteria and viruses) is inconsistent with the classical colloid filtration theory (CFT) . Well-controlled laboratory-scale column deposition experiments were conducted with uniform model particles and collectors to obtain insight into the mechanisms that give rise to the diverging deposition behavior of microorganisms . Both the fluid-phase effluent particle concentration and the profile of retained particles were systematically measured over a broad range of physicochemical conditions . The results indicate that, in the presence of repulsive Derjaguin-Landau-Verwey-Overbeek (DLVO) interactions, the concurrent existence of both favorable and unfavorable colloidal interactions causes significant deviation from the CFT . A dual deposition mode model is presented which considers the combined influence of "fast" and "slow" particle deposition . This model is shown to adequately describe both the spatial distribution of particles in the packed bed and the suspended particle concentration at the column effluent.

Clin Diagn Virol, 1994 Oct, 2(6), 313 - 21
Multiple viral infections in the immunocompromised host: recognition and interpretation; Landry ML; Background: During the past decade, diagnostic virology has become an integral part of patient management . Concurrent infection with multiple viruses occurs in both the healthy and immunocompromised host . Many common viruses result in latent infection with the potential for reactivation throughout the life of the host . Superimposed on this are transient infections with yet other viruses . Objectives: To review multiple viral infections in immunocompromised hosts, focusing on laboratory recognition and interpretation of results . Study design: A review of the literature, with case examples from the author's laboratory . Results: Viral infections are more likely to cause morbidity and mortality in immunodeficient hosts, and early recognition and treatment may be lifesaving . To detect two or more viruses shed concurrently from the same body site requires the use of multiple test modalities, which are now available in many clinical laboratories . Establishing the significance of a virus isolate is a complex process . Knowledge of the specimen source, virus quantitation and characteristics of the patient are helpful . Careful evaluation of the patient's clinical findings together with other laboratory test results, including histopathology, X-rays and the detection of other microorganisms, is also essential . Conclusions: The recognition and interpretation of multiple virus infections requires heightened awareness as well as close cooperation and communication between the professionals in the laboratory and physicians at the bedside.

J Agric Food Chem, 2004 Dec 1, 52(24), 7382 - 8
Degradation and binding of atrazine in surface and subsurface soils; Blume E et al.; Understanding the dissipation rates of chemicals in unsaturated and saturated zones of subsurface soils will help determine if reductions of concentrations to acceptable levels will occur . Chemical properties and microbial biomass and activity were determined for the surface (0-15 cm), lower root (50-105 cm), and vadose (175-220 cm) zones in a Huntington silty clay loam (Fluventic Hapludoll) collected from an agricultural field near Piketon, OH . The rates of sorption, mineralization, and transformation (formation of bound residues and metabolites) of atrazine were determined . Microbial activity was estimated from the mineralization of (14)C-benzoate . We observed decreased levels of nutrients (total organic carbon, N, and P) and microbial biomass with depth, while activity as measured with benzoate metabolism was higher in the vadose zone than in either the surface or the root zones . Sorption coefficients (K(f)) declined from 8.17 in the surface to 3.31 in the vadose zone . Sorption was positively correlated with organic C content . Rates of atrazine mineralization and bound residues formation were, respectively, 12-2.3-fold lower in the vadose than in the surface soil . Estimated half-lives of atrazine ranged from 77 to 101 days in the surface soil, but increased to over 900 days in the subsurface soils . The decreased dissipation of atrazine with increasing depth in the profile is the result of decreased microbial activity toward atrazine, measured either as total biomass or as populations of atrazine-degrading microorganisms . The combination of reduced dissipation and low sorption indicates that there is potential for atrazine movement in the subsurface soils.

Curr Opin Biotechnol, 2004 Dec, 15(6), 576 - 83
Small-molecule natural products: new structures, new activities; Baker DD et al.; A wide variety of novel small-molecule natural products has recently been reported . These compounds were isolated from marine and terrestrial sources, and from a variety of animals, plants and microorganisms . With the breadth of diversity represented in these bioactive small molecules, the future of natural product drug discovery looks bright.

Klin Khir, 2004 Aug, (8), 19 - 21
{The role of enteropathogenic infection, local immunity, and autosensibilisation in pathogenesis of acute surgical diseases of peritoneal cavity by the example of acute appendicitis}; Zhuchenko OP; The complex of interrelated pathogenic factors in development of postoperative suppurative inflammatory complication with abdominal cavity organs lesion was studied on the example of an acute appendicitis . It includes enteropathogenic microorganisms, insufficiency of local immunity, deficiency of immunoglobulins, lysozym . Findings show the possibility in seeking the measures of prevention of emergent state, in particular, an acute appendicitis.

Cell Mol Biol (Noisy-le-grand), 2004 Jul, 50(5), 591 - 604
Biogeochemical features of lipids in endolithic microbial communities in the Ross Desert (McMurdo Dry Valleys), Antarctica; Matsumoto GI et al.; Endolithic microbial communities inhabiting porous rocks in the cold, dry mountainous regions of Antarctica have been studied extensively as examples of life's adaptations to extreme environments . Here, we examine hydrocarbons and fatty acids occurring in these communities in order to clarify their biogeochemical features with respect to source organisms, microbial activity, fossilization processes and the influence of Gondwanaland sediments . Unusually, long-chain (>C19) n-alkanes and anteiso-alkanes were often the major hydrocarbons in the samples . A suite of n-alkanoic acids (n-C9-n-C32) and long-chain anteiso-alkanoic acids (a-C20-a-C30) were found, along with short-chain iso- and anteiso-alkanoic acids, and n-alkenoic acids . The relationship between long-chain n-alkanoic acids (n-C20-n-C32) and long-chain anteiso-alkanoic acids suggests that these compounds probably originated from the same group of microorganisms, such as bacteria or endolithic lichens, under moderate pH conditions (pH 3-5) . Relatively high trans/cis-C16:1 alkenoic acid ratios suggest the presence of unfavorable environmental conditions in the endolithic microbial habitat . Normal-alkenoic/alkanoic acid ratios may be a useful marker for the fossilization of endolithic microbial communities . Thermally matured triterpanes and steranes from fossilized associations on Mount Fleming strongly suggest the presence of Gondwanaland sediments formed during Devonian and Jurassic (400-180 million years ago).

Cell Mol Biol (Noisy-le-grand), 2004 Jul, 50(5), 563 - 73
Ecophysiology of psychrophilic and psychrotolerant microorganisms; Bolter M; This review describes psychrophilic and psychrotolerant microorganisms, which are abundant in different kinds of environments . Their ecophysiological properties and strategies for survival are reviewed in relation to their occurrences in marine and terrestrial environments, with special reference to the deep-sea, the sea ice and the permafrost soils.

Cell Mol Biol (Noisy-le-grand), 2004 Jul, 50(5), 543 - 51
Abundance and function of bacteria in the Southern Ocean; Delille D; The very low water temperatures existing in polar oceans that experience seasonal advance and retreat of pack ice do not inhibit the presence of large bacterial populations . Bacteria may contribute significantly to the energy transfers within the Southern Ocean . In the last decades, notable progress has been made in the knowledge of the role of marine bacteria in the Southern Ocean . A short overview of the abundance and function ofAntarctic marine bacteria is given, with respect to metabolic activity . The importance of spatial and temporal variability is described . The ecological function of Antarctic marine bacterioplankton is discussed . Depending on food web structure, bacteria may be either a link in food webs supporting metazoan production, or a sink where bacterial production is metabolised by microorganisms . In the more oligotrophic areas and during certain periods of the year bacterial biomass dominates phytoplankton . The microbial food web is therefore the dominant pathway for carbon and energy flow in Antarctic seawater.

Cell Mol Biol (Noisy-le-grand), 2004 Jul, 50(5), 537 - 42
A preliminary study of airborne microbial biodiversity over Peninsular Antarctica; Hughes KA et al.; This study used PCR-based molecular biological identification techniques to examine the biodiversity of air sampled over Rothera Point (Antarctic Peninsula) . 16S rDNA fragments of 132 clones were sequenced and identified to reveal a range of microorganisms, including cyanobacteria, actinomycetes, diatom plastids and other uncultivated bacterial groups . Matches for microorganisms that would be considered evidence of human contamination were not found . The closest matches for many of the sequences were from Antarctic clones already in the databases or from other cold environments . Whilst the majority of the sequences are likely to be of local origin, back trajectory calculations showed that the sampled air may have travelled over the Antarctic Peninsula immediately prior to reaching the sample site . As a result, a proportion of the detected biota may be of non-local origin . Conventional identification methods based on propagule morphology or culture are often inadequate due to poor preservation of characteristic features or loss of viability during airbome transfer . The application of molecular biological techniques in describing airbome microbial biodiversity represents a major step forward in the study of airborne biota over Antarctica and in the distribution of microorganisms and propagules in the natural environment.

Clin Dev Immunol, 2004 Sep-Dec, 11(3-4), 205 - 13
A review of the physiological and immunological functions of biliary epithelial cells: targets for primary biliary cirrhosis, primary sclerosing cholangitis and drug-induced ductopenias; Wu CT et al.; Our understanding of biliary epithelial cells (BEC) in physiobiology and immunology has steadily expanded . BEC transports IgA as well as IgM into bile, synthesizes and secretes various chemokines, cytokines, and expresses adhesion molecules involved in cell interaction and signal transduction . These then suggest a myriad of potential roles for BEC in defense from invading microorganisms as well as the pathogenesis of diverse immunologically driven diseases such as primary biliary cirrhosis (PBC), graft-versus-host disease, and primary sclerosing cholangitis (PSC) . Despite the progress, there still remain many areas of BEC biology that require further investigation . Most importantly, it remains to be clarified that the extent to which the immunologic activities observed in BEC represent a BEC response to tissue injury or whether BEC themselves are the active participants in the pathogenesis of various cholestatic immunological diseases, including PBC and PSC.

Environ Toxicol Chem, 2004 Nov, 23(11), 2769 - 79
Location-specific ecotoxicological risk assessment of metal-polluted soils; Van Beelen P et al.; When chemical analysis indicates metal pollution, a second-tier method is needed to evaluate whether toxic effects occur at the polluted sites . A method based on pollution-induced community tolerance (PICT) was developed using samples taken from locations polluted with sewage more than 20 years ago . Microorganisms extracted from soil samples were exposed to a concentration range of zinc, nickel, copper, chromium (III), or chromium (VI) salts in a buffer suspension . The remaining activity of the intoxicated microorganisms was determined by color formation with 31 different organic substrates in microtiter plates . Microorganisms from moderately Zn-polluted sites (>45 mg/kg) showed an increased tolerance for zinc . Nickel tolerance was observed at 51 mg Ni/kg soil, chromium (VI) tolerance at 923 mg Cr/kg . In most cases, tolerance also was observed at higher concentrations . High concentrations of 1,494 mg Cu/kg or 3,935 mg Cr/kg did not show PICT, indicating a limited bioavailability of Cu and Cr at these sites . The benefits of our method are its greater sensitivity compared to other tests used at these sites, and its specificity for those metals that exceed allowable levels.

J Biol Chem . 2004 Nov 22; {Epub ahead of print}
Isolation and characterization of bifunctional escherichia coli TatA mutant proteins that allow efficient Tat-dependent protein translocation in the absence of TatB; Blaudeck N et al.; In Escherichia coli, the Tat system promotes the membrane translocation of a subset of exported proteins across the cytoplasmic membrane . Four genes (tatA, tatB, tatC, and tatE) have been identified that encode the components of the E . coli Tat translocation apparatus . Whereas TatA and TatE can functionally substitute for each other, the TatB and the TatC proteins have been shown to perform distinct functions . In contrast to Tat systems of the ABC(E) type found in E . coli and many other bacteria, some microorganisms possess a TatAC-type translocase that consists of TatA and TatC only, suggesting that, in these systems, TatB is not required or that one of the remaining components (TatA or TatC) additionally takes over the TatB function . We have addressed the molecular basis for the difference in subunit composition between TatABC(E) and TatAC-type systems by using a genetic approach . A plasmid-encoded E . coli minimal Tat translocase consisting solely of TatA and TatC was shown to mediate a low level translocation of a sensitive Tat-dependent reporter protein . Suppressor mutations in the minimal Tat translocase were isolated which compensate for the absence of TatB and which showed substantial increases in translocation activities . All mutations mapped to the extreme aminoterminal domain of TatA . No mutations affecting TatC were identified . These results suggest that in TatAC-type systems, the TatA protein represents a bifunctional component fulfilling both the TatA and TatB functions . Furthermore, our results indicate that the structure of the aminoterminal domain of TatA is decisive for whether or not TatB is required.

Anim Reprod Sci, 2005 Jan, 85(1-2), 81 - 93
The effect of Mycoplasma mycoides ssp . mycoides LC of bovine origin on in vitro fertilizing ability of bull spermatozoa and embryo development; Sylla L et al.; Several Mycoplasma species may adversely affect bovine spermatozoa viability and embryo development . Mycoplasma mycoides ssp . mycoides large-colony (LC) has been isolated from naturally aborted bovine fetuses and from bull semen . The objective of this study was to evaluate whether M . mycoides ssp . mycoides LC contaminated bovine ejaculates could (i) impair in vitro fertilizing ability of bull spermatozoa, (ii) impair embryo development, and (iii) evaluate potential spread by reproductive technologies . In the present study, spermatozoa of 10 fertile bulls were contaminated with M . mycoides ssp . mycoides LC, at a final concentration of 1.5 million CFU/ml and incubated for 60 min before evaluating spermatozoa motility and acrosome reaction inducibility with calcium ionophore . In addition, in vitro contaminated semen of a bull previously shown to have a good in vitro fertilizing ability, was used in an IVF procedure . Embryo development stage on Day-7 of culture was evaluated . Spermatozoa and embryos at morula and blastocyst stages were routinely processed for transmission electron microscopy observation . Both mean total and progressive motility decreased (P < 0.01 ) upon spermatozoa incubation with Mycoplasma . One-hour incubation with calcium ionophore increased the percentage of acrosome-reacted spermatozoa, although Mycoplasma contamination reduced calcium ionophore treatment efficacy (P < 0.05) . Ultrastructurally, Mycoplasma microorganisms appeared as moderately electron-dense sphere-shaped particles, adhering to cell membranes . Sperm mid-piece sections showed numeric aberrations of the central singlets such as nine + zero or nine + one of the axonemal complex . Further morphological abnormalities included partial or total absence of dinein arms and radial fibers, with lack of the bridge and the central ring in 35.00 +/- 4.20% of contaminated cells, whereas these abnormalities were not observed in uninfected ones . The IVF trials showed that two-four cell blocks were higher (P < 0.05) in the infected group . Ultrastructure of Day-7 contaminated embryos showed Mycoplasma particles adhering and infiltrating the outer layer of the zona pellucida . Our investigations suggest that M . mycoides ssp . mycoides LC contaminating the bovine ejaculate induced adverse effects on in vitro spermatozoa-fertilizing ability and embryonic development . Some satisfactory quality transferable embryos could be produced in contaminated IVF systems . This could imply a potential transmission of this microorganism through reproductive technologies.

Curr Opin Microbiol, 2004 Dec, 7(6), 594 - 601
Building filaments in the air: aerial morphogenesis in bacteria and fungi; Elliot MA et al.; To disperse their spores to new sites, filamentous fungi and bacteria need to erect aerial filaments, which develop into fruiting bodies and spore-bearing structures . The first challenge to aerial development is breaking surface tension at an aqueous-air interface, and in both groups of microorganisms, surface-active proteins take part in the initiation of aerial morphogenesis . Comparative analysis of fungi and bacteria is providing new insights into the means by which aerial filamentation is accomplished.

Int J Phytoremediation, 2004, 6(3), 253 - 68
Plant-assisted degradation of phenanthrene as assessed by solid-phase microextraction (SPME); Hynes RK et al.; The soil bacterium Sphingomonas yanoikuyae was isolated from a petroleum-contaminated soil and grown on mineral salts agar overlaid with the polycyclic aromatic hydrocarbon phenanthrene . The effect of white mustard, Sinapis alba, on phenanthrene degradation by S . yanoikuyae in artificially contaminated Redi-earth-sand was examined . Solid-phase-microextraction (SPME) gas chromatography-flame ionization detection (GC-FID) was used to quantify the concentration of phenanthrene in the gas phase of Magenta jars containing S . alba and S . yanoikuyae, each alone and with no additions . Gas chromatography-mass spectrometry (GC-MS) of Soxhlet extracts was used to determine the concentration of phenanthrene remaining in Redi-earth-sand . The gas phase concentration of phenanthrene in nonsterile Redi-earth-sand decreased by 99.7% in treatments with S . alba plus S . yanoikuyae, by 98.6% with S . alba, by 96.7% with S . yanoikuyae, and by 95.8% with no additions . Under gnotobiotic conditions, the gas phase concentration of phenanthrene in Redi-earth-sand decreased by 94% in treatments with S . alba plus S . yanoikuyae, by 77% with S . yanoikuyae, by 26% with S . alba, and 0% with no additions . The concentration of phenanthrene in Redi-earth-sand under gnotobiotic conditions decreased in treatments with S . alba plus S . yanoikuyae by 88%, by 67% with S . yanoikuyae, by 13% with S . alba, and 0% with no additions as measured in Soxhlet extracts . These results suggest that SPME-GC can be used to rapidly assess the potential of plants and microorganisms to reduce the level of unaged polyaromatic hydrocarbons such as phenanthrene in soil . This method provided results that were consistent with the more costly Soxhlet extraction method and was less time consuming.

Sheng Wu Yi Xue Gong Cheng Xue Za Zhi, 2004 Oct, 21(5), 864 - 6
{Microbial corrosion of dental alloy}; Li L et al.; There is a very complicated electrolytical environment in oral cavity with plenty of microorganisms existing there . Various forms of corrosion would develop when metallic prosthesis functions in mouth . One important corrosive form is microbial corrosion . The metabolic products, including organic acid and inorganic acid, will affect the pH of the surface or interface of metallic prosthesis and make a change in composition of the medium, thus influencing the electron-chemical reaction and promoting the development of corrosion . The problem of develpoment of microbial corrosion on dental alloy in the oral environment lies in the primary condition that the bacteria adhere to the surface of alloy and form a relatively independent environment that promotes corrosion.

Spec Care Dentist, 2004 Sep-Oct, 24(5), 250 - 3
Intrauterine infections: a literature review; Franca CM et al.; During gestation, many microorganisms can infect the fetus, causing severe birth defects . Such organisms and the resulting clinical syndromes have been categorized as TORCH infections, a useful acronym referring to Toxoplasma gondii, other microorganisms (like syphilis), rubella virus, cytomegalovirus, and herpesviruses . Since dental patients typically report pregnancy or previous infections as part of their health history, and TORCH infections can manifest oral symptoms, the dentist is in a position to act as an educator and screener for these infections . This article reviews TORCH agents for dentists to help the clinician in educating pregnant patients about the risks these infections pose to the fetus . The authors also note oral symptoms related to these infections.

Yi Chuan Xue Bao, 2004 Oct, 31(10), 1082 - 8
{Three Bombyx mori genes, chi, gluE and fruA, encode proteins homologous to microorganism and primary analysis of horizontal gene transfer}; Cheng TC et al.; According to the analysis of large scale EST sequencing of silkworm, Bombyx mori, we found that chi, glue and fruA of silkworm have very high homology at amino acid level and closely phylogenetic relative with that of microorganism, but lower similarity with genes of eelworm (Caenorhabditis elegans), fruitfly (Drosophila melanogaster), mosquito (Anopheles gambiae) and other relative insects, respectively . It indicates that each of them is likely to have common ancestor with that of microorganism . Namely, microbial genes were likely transferred to silkworm by horizontal gene transfer, instead of the vertical inheritance in evolutionary manner.

Biomedica, 2004 Sep, 24(3), 302 - 17
{Role of Langerhans cells in the immunity of leishmaniasis}; Zuluaga M et al.; Immune response induced against Leishmania parasites is influenced by several factors, one of the most important being the type of Antigen Presenting Cell (APC) . Langerhans cells, a subpopulation of APC, are sentinel cells for detecting invader microorganisms; they reside in skin tissues at levels where the phlebotomine fly vector inoculates Leishmania parasites . Presence of microorganisms can induce activation of Langerhans cells, leading to their maturation and migration towards lymph nodes . There, Langerhans cells present antigens to T cells for their subsequent activation and specific differentiation into effector cells . Early after a Leishmania infection, few T cells have been observed at sites of infection, suggesting that infected macrophages have little opportunity to locate T cells specific for elimination of Leishmania parasites . However, Langerhans cells may be the cells available to provide signals for the stimulation of parasite-specific T-cell responses in the lymph node and for inducing T-cell migration to the infected skin . Herein, the main characteristics of Langerhans cells are reviewed, with special emphasis on their participation in cutaneous inflammatory response . The role of these cells in infections caused by protozoan parasites of the Leishmania genus is discussed.

Nat Rev Microbiol, 2004 Dec, 2(12), 946 - 53
Iron and microbial infection; Schaible UE et al.; The use of iron as a cofactor in basic metabolic pathways is essential to both pathogenic microorganisms and their hosts . It is also a pivotal component of the innate immune response through its role in the generation of toxic oxygen and nitrogen intermediates . During evolution, the shared requirement of micro- and macroorganisms for this important nutrient has shaped the pathogen-host relationship . Here, we discuss how pathogens compete with the host for iron, and also how the host uses iron to counteract this threat.

Eur Spine J, 2004 Nov, 13(7), 645 - 51 Epub 2004 Nov.
Implant removal for late-developing infection after instrumented posterior spinal fusion for scoliosis: reinstrumentation reduces loss of correction . A retrospective analysis of 45 cases; Muschik M et al.; A retrospective follow-up study of patients who, having undergone instrumented posterior spinal fusion for scoliosis, experienced late infection and then underwent either implant removal alone or implant removal and instrumented refusion . We conducted this study to determine whether it is possible to avoid loss of correction by a single-stage implant removal and reinstrumentation procedure . There have been a few reports of late-appearing infections after spinal instrumentation . Implant bulk, metallurgic reactions, and contamination with low-virulence microorganisms have been suggested as possible etiologic factors . The clinical symptoms include pain, swelling, redness, and spontaneous drainage of fluid . Complete instrumentation removal and systemic antibiotics is usually curative . We retrospectively reviewed 45 patients who underwent instrumented posterior spinal fusion for scoliosis and experienced development of late infections and, after a mean of 3 years after the initial procedure, either underwent implant removal alone { n=35, instrumentation removal (HR) group} or additionally underwent reinstrumentation and fusion { n=10, reinstrumentation and fusion (RI&F) group} . Three patients were reinstrumented 1.5 years after instrumentation removal, and seven underwent a one-stage rod removal and reinstrumentation/refusion procedure . Allergic predisposition, protracted postoperative fever, and pseudarthrosis appear to increase the risk of late-developing infection after posterior spinal fusion . All wounds in both groups healed uneventfully . Preoperative radiographic Cobb measurements showed no statistically significant between-group differences . At follow-up, however, outcome was clearly better in the RI&F group: Loss of correction was significantly smaller in reinstrumented patients . Thus, the thoracic Cobb angle was 28+/-16 degrees (range 0-55 degrees ) in the RI&F group versus 42+/-15 degrees (21-80 degrees ) in the HR group, and the lumbar Cobb angle was 22+/-11 degrees (10-36 degrees ) in the RI&F group versus 29+/-12 degrees (13-54 degrees ) in the HR group . The results of our study demonstrate that wound healing is usually uneventful after instrumentation removal for late infection, also when patients undergo instrumented refusion in a one-stage procedure . Reinstrumentation appears to achieve permanent correction of scoliosis.

Appl Microbiol Biotechnol . 2004 Nov 12; {Epub ahead of print}
Transgenic tobacco expressing fungal laccase promotes the detoxification of environmental pollutants; Sonoki T et al.; The phytoremediation of soils contaminated with organic pollutants offers a low-cost method for removal of such pollutants . We have attempted to enhance the environmental decontamination functions of plants by introducing appropriate enzymatic activities from microorganisms . In the present study, we introduced an extracellular fungal enzyme, the laccase of Coriolus versicolor, into tobacco plants . One transgenic plant, designated FL4, produced laccase that was secreted into the rhizosphere . FL4 was able to remove 20 mumol bisphenol A or pentachlorophenol per gram dry weight . The efficiency of this removal was apparently greater than that of control lines . Our results should stimulate efforts to develop plant-based technologies for the removal of environmental pollutants from contaminated environments.

Microb Ecol, 2004 Aug, 48(2), 254 - 62 Epub 2004 Jun 10.
Degradation of 2,4-dichlorophenoxyacetic acid (2,4-d) by a hypersaline microbial mat and related functional changes in the mat community; Grotzschel S et al.; Microbial mats possibly possess degradation capacities for haloorganic pollutants because of their wide range of different functional groups of microorganisms combined with extreme diurnal changes in pH, oxygen, and sulfide gradients . In this study, 20 mg/l of the chlorinated herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) was applied to a pristine hypersaline cyanobacterial mat from Guerrero Negro, Mexico, under a light regime of 12 h dark/12 h light (600 mumol photons/m(2)s) . The loss of 2,4-D was followed by chemical GC analysis; functional changes within the mat were determined with microelectrodes for oxygen, photosynthesis, pH, and sulfide . The depletion of 2,4-D due to photooxidation or sorption processes was checked in control experiments . Within 13 days, the light/dark incubated mats degraded 97% of the herbicide, while in permanent darkness only 35% were degraded . Adsorption of 2,4-D to the mat material, agar, or glass walls was negligible (4.6%), whereas 21% of the herbicide was degraded photochemically . The 2,4-D removal rate in the light/dark incubations was comparable to values reported for soils . The phototrophic community of the mat was permanently inhibited by the 2,4-D addition by 17% on average . The sulfate reduction in the entire mat and the respiration in the photic zone were inhibited more strongly but returned to original levels . Since at the end of the experiment the photosynthetic and respiratory activity of the mats were almost as high as in the beginning and 2,4-D almost completely disappeared, we conclude that the examined mats represent a robust and effective system for the degradation of the herbicide where probably the aerobic heterotrophic population is a major player in the degradation process.

Microb Ecol, 2004 Aug, 48(2), 246 - 53 Epub 2004 Jun 24.
Degradation of 4-chlorophenol at low temperature and during extreme temperature fluctuations by Arthrobacter chlorophenolicus A6; Backman A et al.; Low average temperatures and temperature fluctuations in temperate soils challenge the efficacy of microbial strains used for clean up of pollutants . In this study, we investigated the cold tolerance of Arthrobacter chlorophenolicus A6, a microorganism previously shown to degrade high concentrations of 4-chlorophenol at 28 degrees C . Luciferase activity from a luc-tagged derivative of the strain (A6L) was used to monitor the metabolic status of the population during 4-chlorophenol degradation . The A6L strain could degrade 200-300 mug mL(-1) 4-chlorophenol in pure cultures incubated at 5 degrees C, although rates of degradation, growth and the metabolic status of the cells were lower at 5 degrees C compared to 28 degrees C . When subjected to temperature fluctuations between 5 and 28 degrees C, A6L continued to degrade 4-chlorophenol and remained active . In soil microcosm experiments, the degradation rates were significantly faster the first week at 28 degrees C, compared to 5 degrees C . However, this difference was no longer seen after 7 days, and equally low 4-chlorophenol concentrations were reached after 17 days at both temperatures . During 4-chlorophenol degradation in soil, CFU and luciferase activity values remained constant at both 5 and 28 degrees C . However, once most of the 4-chlorophenol was degraded, both values decreased by 1-1.5 logarithmic values at 28 degrees C, whereas they remained constant at 5 degrees C, indicating a high survival of the cells at low temperatures . Because of the ability of A . chlorophenolicus A6 to degrade high concentrations of 4-chlorophenol at 5 degrees C, together with its tolerance to temperature fluctuations and stress conditions found in soil, this strain is a promising candidate for bioaugmentation of chlorophenol-contaminated soil in temperate climates.

Insect Biochem Mol Biol, 2004 Dec, 34(12), 1257 - 68
Phenoloxidase activity in Apis mellifera honey bee pupae, and ecdysteroid-dependent expression of the prophenoloxidase mRNA; Zufelato MS et al.; Phenoloxidase (monophenol, l-dopa: oxygen oxidoreductase, EC 1.14.18.1) is a multicopper oxidase, which plays an important role in melanin synthesis, necessary for defense against intruding microorganisms and parasites, wound healing and cuticle pigmentation . A phenoloxidase from the hemolymph of honey bee pupae exhibited an apparent molecular mass of 70 kDa, as estimated by gel filtration and SDS-PAGE . Optimal pH and temperature were 6.5 and 20 degrees C, respectively . Activity was fully stable for 30 min at 50 degrees C . Like phenoloxidases from the hemolymph of other insects, the honey bee enzyme was activated by trypsin and inhibited by protease inhibitors and phenylthiourea . Only high concentrations of sodium azide effectively inhibited the detected activity . A low concentration (5 microM) of Ca2+, Mg2+, and Mn2+ had a stimulatory effect on the activity . Single Michaelis-Menten curves were observed for l-dopa and dopamine oxidation, but the affinity of the enzyme for dopamine was greater than for L-dopa . Semiquantitative RT-PCR and Southern blot analysis using a 359 bp labeled probe, and quantification of the prophenoloxidase mRNA levels by real-time PCR showed increased amounts of transcripts in hemocytes and integument from young pupae injected with 20-hydroxyecdysone.

Clin Exp Immunol, 2004 Dec, 138(3), 521 - 5
Significantly increased levels of mannose-binding lectin (MBL) in rheumatic heart disease: a beneficial role for MBL deficiency; Schafranski MD et al.; Although mannose-binding lectin (MBL) is known to be involved in the primary defense against microorganisms, there are emerging lines of evidence for an active proinflammatory role for MBL in different chronic diseases . In this study we determined the circulating levels of MBL in patients with rheumatic heart disease (RHD) . A total of 100 patients (77 women, 23 men; mean age 45.8 +/- 11 years, range 19-76 years) with chronic RHD, and a previous diagnosis of rheumatic fever, were studied . Transthoracic echocardiography was performed in all patients to evaluate valvular heart disease . Ninety-nine healthy individuals matched for age, sex and ethnic origin were included as controls . MBL concentration was measured by enzyme-linked immunosorbent assay and C3 and C4 levels by turbidimetry . MBL levels were significantly higher in patients with RHD than in healthy subjects (mean +/- SEM: 3036.2 +/- 298.9 ng/ml versus 1942.6 +/- 185.5 ng/ml, P <0.003) . In addition, MBL deficiency was more prevalent in controls (17.1%) than in patients (9% P <0.09) . Concentrations of C4 were within the normal range (22.7 +/- 0.8 mg/dl, normal: 10.0-40.0 mg/dl), while C3 concentrations were found to be elevated (109.2 +/- 3.6 mg/dl, normal: 50.0-90.0 mg/dl) . No correlation was observed between serum MBL levels and valve area or the type of surgical procedure . The significantly elevated circulating MBL levels in patients with RHD together with the greater prevalence of MBL deficiency in controls suggest that MBL may cause undesirable complement activation contributing to the pathogenesis of RHD.

Clin Exp Immunol, 2004 Dec, 138(3), 517 - 20
L-ficolin in children with recurrent respiratory infections; Atkinson AP et al.; The lectin pathway of complement activation is used by a collectin, mannan-binding lectin (MBL), and two ficolins, L-ficolin and H-ficolin, to opsonize microorganisms for phagocytosis . We published evidence recently that MBL insufficiency is associated with recurrent respiratory infections in childhood . We have now measured serum L-ficolin in 313 respiratory infection patients and 74 healthy control children . L-ficolin concentrations below the lower limit of the control group were found in 6% of the patients (P <0.02) and were associated most strongly with children having co-existing atopic disorders (11%; P=0.002) . We suggest that L-ficolin may have a role in protection from microorganisms complicating allergic disease.

Langmuir, 2004 Nov 23, 20(24), 10361 - 6
In situ characterization of aluminum-containing mineral-microorganism aqueous suspensions using scanning transmission X-ray microscopy; Yoon TH et al.; In situ characterization of colloidal particles under hydrous conditions is one of the key requirements for understanding their state of aggregation and impact on the transport of pollutants in aqueous environments . Scanning transmission X-ray microscopy (STXM) is one of the few techniques that can satisfy this need by providing element- and chemical-state-specific 2-D maps at a spatial resolution better than 50 nm using soft X-rays from synchrotron radiation wiggler or undulator sources tuned to the absorption edges of different elements . X-ray absorption near-edge structure (XANES) spectra can also be collected simultaneously at a similar spatial resolution and can provide phase identification in many cases . In this study, we report STXM images and XANES spectroscopy measurements at or above the Al K-edge (E = 1559.6 eV) of various Al-containing minerals and synthetic oxides {alpha-Al2O3 (corundum), gamma-Al2O3, gamma-AlOOH (boehmite), alpha-Al(OH)3 (bayerite), KAl2(AlSi3O10)(OH)2 (muscovite), (Al,Mg)8(Si4O10)4(OH)8.nH2O (montmorillonite), and Mg6Al2(OH)16CO3.4H2O (hydrotalcite)} and demonstrate the capability of this spectromicroscopic tool to identify different Al-containing mineral colloids in multiphase mixtures in aqueous solution . We also demonstrate that STXM imaging at or above the C K-edge (E = 284.2 eV) and Al K-edge can provide unique information on the interactions between bacteria and Al-containing nanoparticles in aqueous suspensions . STXM images of a mixture of Caulobacter crescentus and montmorillonite and corundum particles just above the C and Al K-edges show that the mineral particles and bacteria are closely associated in aggregates, which is likely due to the binding of bacteria to clay and corundum particles by extracellular polysaccharides.

Methods, 2004 Dec, 34(4), 488 - 95
Textmining in support of knowledge discovery for vaccine development; Schonbach C et al.; Complete genome data of infectious microorganisms permit systematic computational sequence-based predictions and experimental testing of candidate vaccine epitopes . Both, predictions and the interpretation of experiments rely on existing information in the literature which is mostly manually extracted and curated . The growing amount of data and literature information has created a major bottleneck for the interpretation of results and maintenance of curated databases . The lack of suitable free-text information extraction, processing, and reporting tools prompted us to develop a knowledge discovery support system that enhances the understanding of immune response and vaccine development . The current prototype system, Gene expression/epitpopes/protein interaction (GEpi), focuses on molecular functions of HIV-infected T-cells and HIV epitope information, using textmining, and interrelation of biomolecular data from domain-specific databases with MEDLINE abstract-inferred information . Results showed that extraction and processing of molecular interaction, disease associations, and gene ontology-derived functional information generate intuitive knowledge reports that aid the interpretation of host-pathogen interaction . In contrast, epitope (word and sequence) information in MEDLINE abstracts is surprisingly sparse and often lacks necessary context information, such as HLA-restriction . Since the majority of epitope information is found in tables, figures, and legends of full-text articles, its extraction may not require sophisticated natural language processing techniques . Support of vaccine development through textmining requires therefore the timely development of domain-specific extraction rules for full-text articles, and a knowledge model for epitope-related information.

Mech Ageing Dev, 2004 Oct-Nov, 125(10-11), 799 - 810
Nuclear factor kappa B activation by NADPH oxidases; Clark RA et al.; Reactive oxygen species (ROS) initiate activation of the transcription factor NF-kappaB in a variety of cell systems . Perhaps the most potent biological source of ROS is the NADPH oxidase of phagocytic cells, a multi-component system that catalyzes the formation of superoxide anion . Although phagocytes use this oxidase to kill ingested microorganisms, the products also mediate a broad range of biological oxidation reactions and some evidence exists for activation of NF-kappaB through this mechanism . Moreover, the components of the phagocyte NADPH oxidase are present in certain non-phagocytic cells and recently discovered homologues of the catalytic component gp91(phox) are expressed in a number of tissues . We explored the hypothesis that the products of NADPH oxidases cause the activation of NF-kappaB . K562 human erythrokeukemia cells transfected with constructs for expression of gp91(phox), plus other essential NADPH oxidase components generated substantial amounts of superoxide when activated with phorbol ester, lesser amounts with arachidonic acid exposure, and none with TNFalpha . Gel shift assays demonstrated induction of NF-kappaB in K562 cells exposed to TNFalpha and specificity was shown by oligonucleotide competition . Supershift assays demonstrated the presence in nuclear complexes of the NF-kappaB components p65/RelA and p50 . Nuclear complexes of identical electrophoretic mobility were induced in phorbol ester-stimulated K562 cells that expressed the complete NADPH oxidase system, but not in cells lacking one of the essential oxidase components . K562 cells were relatively resistant to NF-kappaB induction by exogenous peroxide, but certain other cell types (HEK293 and HeLaS3) demonstrated such induction upon exposure to reagent hydrogen peroxide or glucose oxidase plus glucose and this was blocked by catalase . Finally, we found a biphasic pattern of gp91(phox) expression in rat liver during aging . High levels observed in young animals decreased in middle age, but increased again in old age . Collectively, these studies demonstrate the potential for NADPH-dependent induction of NF-kappaB and raise the possibility of a role for this pathway in the biology of aging.

Diagn Microbiol Infect Dis, 2004 Nov, 50(3), 159 - 66
Bartonella quintana-induced apoptosis inhibition of human endothelial cells is associated with p38 and SAPK/JNK modulation and with stimulation of mitosis; Liberto MC et al.; Previous studies demonstrated that live Bartonella quintana often induces angioproliferative lesions in humans . It modulates endothelial cell apoptotic and inflammatory patterns, thus inducing a very early overexpression of caspase 8 and Apaf-1 and increasing mRNA production of TNF-alpha, interleukin-8, and E-selectin . However, starting at 10 hours postinfection, the bacteria provoke antiapoptotic effects that induce an increase of bcl-2 gene transcription . To gain further insight into the cellular mechanisms that regulate apoptosis, survival and proliferation, we studied the modulation of mitogen-activated protein kinase (MAPK) and the activation state of cdc2 kinase, which regulates progression into mitosis . Confocal microscopy findings indicated a maximum rate of Bartonella entry into host cells between postinfection hours 6 and 10 . Live bacteria caused substantially higher apoptosis of human umbilical vein endothelial cells-cryopreserved (HUVEC-C) than heat- and trypsin-inactivated microorganisms . During the first 6 hours postinfection, B . quintana triggered a peak of apoptosis, induced activation of p38 MAPK and stress-activated protein kinase/c-Jun N-terminal kinase (SAPK/JNK), with bacterial clusters appearing at the cellular surface of the HUVEC-C . However, at 8 to 24 hours postinfection, B . quintana was internalized and inhibited proapoptotic signals such as p38 MAPK and SAPK/JNK while inducing antiapoptotic signals . Indeed, expression of the bcl-2 gene and the increase of the bcl-2 kinase active form was concomitant to activation of mitosis, as shown by cdc2 protein activation . These data thus suggest that mechanisms that induce mitotic activity and inhibit apoptotic signals may contribute to the ability of B . quintana to cause vascular proliferation.

J Immunol Methods, 2004 Oct, 293(1-2), 97 - 106
Enzyme-linked immunomagnetic chemiluminescent detection of Escherichia coli O157:H7; Gehring AG et al.; E . coli O157:H7 is a pathogenic microorganism that has been implicated in numerous cases of foodborne illnesses . A variety of rapid methods exist that show promise for the presumptive detection of this pathogen without the immediate need for incubating test samples for hours to days in microbial enrichment and culture media . In recent years, highly sensitive chemiluminescence has become a more affordable and portable detection method . Chemiluminescent detection has been coupled with the selectivity of antibodies, magnetic microparticle separation/isolation, and enzymatic signal amplification in order to develop a rapid method, termed enzyme-linked immunomagnetic chemiluminescence (ELIMCL) . This work presents the application of ELIMCL to the detection of E . coli O157:H7 in pristine buffered saline with a detection limit of 7.6 x 10(3) for live cells in approx . 75 min assay time . The blocking agent casein and the surfactant Tween 20 were used to lower background luminescence and thus maximize signal-to-noise ratios . After 5.5 h of enrichment culture, ELIMCL was demonstrated to detect E . coli O157:H7 inoculated in ground beef at 10 CFU/g in a total assay time of about 7 h.

Biotechnol Bioeng, 2005 Jan 5, 89(1), 113 - 22
Anaerobic degradation of solid material: importance of initiation centers for methanogenesis, mixing intensity, and 2D distributed model; Vavilin VA et al.; Batch anaerobic codigestion of municipal household solid waste (MHSW) and digested manure in mesophilic conditions was carried out . The different waste-to-biomass ratios and intensity of mixing were studied theoretically and experimentally . The experiments showed that when organic loading was high, intensive mixing resulted in acidification and failure of the process, while low mixing intensity was crucial for successful digestion . However, when loading was low, mixing intensity had no significant effect on the process . We hypothesized that mixing was preventing establishment of methanogenic zones in the reactor space . The methanogenic zones are important to withstand inhibition due to development of acids formed during acidogenesis . The 2D distributed models of symmetrical cylinder reactor are presented based on the hypothesis of the necessity of a minimum size of methanogenic zones that can propagate and establish a good methanogenic environment . The model showed that at high organic loading rate spatial separation of the initial methanogenic centers from active acidogenic areas is the key factor for efficient conversion of solids to methane . The initial level of methanogenic biomass in the initiation centers is a critical factor for the survival of these centers . At low mixing, most of the initiation methanogenic centers survive and expand over the reactor volume . However, at vigorous mixing the initial methanogenic centers are reduced in size, averaged over the reactor volume, and finally dissipate . Using fluorescence in situ hybridization, large irregular cocci of microorganisms were observed in the case with minimal mixing, while in the case with high stirring mainly dead cells were found . (c) 2004 Wiley Periodicals, Inc.

Bioinformatics . 2004 Nov 11; {Epub ahead of print}
An improved algorithm for stoichiometric network analysis: theory and applications; Urbanczik R et al.; MOTIVATION: Genome scale analysis of the metabolic network of a microorganism is a major challenge in bioinformatics . The combinatorial explosion, which occurs during the construction of elementary fluxes (non-redundant pathways) requires sophisticated and efficient algorithms to tackle the problem . RESULTS: Mathematically, the calculation of elementary fluxes amounts to characterizing the space of solutions to a mixed system of linear equalities, given by the stoichiometry matrix, and linear inequalities, arising from the irreversibility of some or all of the reactions in the network . Previous approaches to this problem, have iteratively solved for the equalities while satisfying the inequalities throughout the process . In an extension of previous work (Wagner, J . Phys Chem . B, 108, 2004), here we consider the complementary approach and derive an algorithm which satisfies the inequalities one by one while staying in the space of solution of the equality constraints . Benchmarks on different subnetworks of the central carbon metabolism of E . Coli show that this new approach yields a significant reduction in the execution time of the calculation . This reduction arises since the odds that an intermediate elementary flux already fulfills an additional inequality are larger than when having to satisfy an additional equality constraint . AVAILABILITY: The code is available upon request . SUPPLEMENTARY INFORMATION: Pseudo code and a Mathematica implementation of the algorithm is on the OUP server.

J Biol Chem . 2004 Nov 10; {Epub ahead of print}
Crystal structure of Jun a 1, the major cedar pollen allergen from Juniperus ashei, reveals a parallel beta-helical core; Czerwinski EW et al.; Pollen from cedar and cypress trees is a major cause of seasonal hypersensitivity in humans in several regions of the Northern Hemisphere . We report the first crystal structure of a cedar allergen, Jun a 1 from the pollen of the mountain cedar Juniperus ashei, Cupressaceae . The core of the structure consists primarily of a parallel ss-helix, which is nearly identical to that found in the pectin/pectate lyases from several plant pathogenic microorganisms . Four IgE epitopes mapped to the surface of the protein are accessible to the solvent . The conserved vWiDH sequence is covered by the first 30 residues of the N-terminus . The potential reactive arginine, analogous to the pectin/pectate lyase reaction site, is accessible to the solvent, but the substrate binding groove is blocked by a histidine-aspartate salt-bridge, a glutamine and an a-helix, all of which are unique to Jun a 1 . These observations suggest that steric hindrance in Jun a 1 precludes enzyme activity . The overall results suggest that it is the structure of Jun a 1 that makes it a potent allergen.

Curr Infect Dis Rep, 2004 Dec, 6(6), 462 - 468
Innate Immune System Gene Polymorphisms in Women with Vulvovaginal Infections; Genc MR et al.; The innate immune responses at mucosal surfaces of the lower female genital tract play a central role in preventing the establishment of infection . Variability in the genes regulating innate immune recognition or response to infectious microorganisms could explain interindividual differences in susceptibility to infection and severity of infectious disorders . Of the numerous genetic variations identified within immunoregulatory genes, only a few have so far been studied in relation to infectious disorders of the lower female genital tract . Although these studies broaden our understanding of the genetic influence on mucosal innate immunity and microbiologic outcome, they also highlight the complexity of links between genotypical and phenotypical features, ie, the influence of a single genetic marker on the phenotype is at best moderate and is not constant in every ethnic/racial group . Such inconsistency is primarily attributed to gene-to-gene interactions and demographic genetic variability . Large case-control studies evaluating multiple genetic markers simultaneously in well-defined subgroups will characterize patients more accurately and pave the way to personalized medicine.

Curr Infect Dis Rep, 2004 Dec, 6(6), 426 - 434
Current Strategies for Prevention of Surgical Site Infections; Nichols RL; Surgical site infections (SSIs) are a common complication that follows all types of operative procedures . These infections are usually caused by the exogenous and endogenous microorganisms that enter the operative wound during the course of surgery . The general and procedure-specific risk factors for the development of SSI have been identified and are discussed in this article . Factors that influence the SSI rate and the current strategies for prevention of SSIs are also presented . Emphasis is placed on the efficacious use of antibiotic prophylaxis in surgery . A discussion of the principles of antibiotic prophylaxis, including choice of agents, route of administration, and timing, is offered . It appears that the use of less invasive laparoscopic surgical approaches, as practiced widely today, will be associated with an overall decreased incidence of SSI.

Am J Primatol, 2004 Nov, 64(3), 337 - 43
Isolation and identification of fungi from vaginal flora in three species of captive Leontopithecus; Moraes IA et al.; The ability to reproduce in captivity is an essential component of lion tamarin (Leontopithecus) conservation programs . However, infections such as vaginitis, cervicitis, and endometritis are important diseases that may influence the reproduction of these animals . Therefore, it is important to detect continuous or occasional vaginal microbial populations, and to understand their potential role as an endogenous source of infection {Collins, 1964; Blue, 1983; Pugh et al., 1986} . Vaginal swabs were collected from 25 female tamarins of the three currently available species (L . rosalia, L . chrysopygus, and L . chrysomelas) at the Center of Primatology in Rio de Janeiro, Brazil . The swabs were processed according to standard mycological protocols, and isolates were biochemically characterized . Fungal isolates were recovered from 16 animals (64.0%) . The results showed that 70.6% of the isolated microorganisms consisted of yeast, including three species of Candida (mainly C . glabrata) . We suggest that this species is a resident member of the normal vaginal flora in Leontopithecus . Filamentous fungi (mainly from Trichosporon, Aspergillus, and Penicilliumgenera) constituted 29.4% of the isolates, and were considered to be transitory contaminants of the genital area . We suggest that colonization of the vaginal environment is related to the endocrine pattern associated with the reproductive status of these animals, but not to parity.

Glycobiology . 2004 Nov 10; {Epub ahead of print}
Isolation, characterization and extra-embryonic secretion of the Xenopus laevis embryonic epidermal lectin, XEEL; Nagata S; The Xenopus laevis embryonic epidermal lectin (XEEL) is a novel member of a group of lectins including mammalian intelectins, frog oocyte cortical granule lectins and plasma lectins in lower vertebrates and ascidians . We isolated the XEEL protein from the extract of tailbud embryos by affinity chromatography on a galactose-Sepharose column . The XEEL protein is a homohexamer of 43-kDa N-glycosylated peptide subunits linked by disulfide bonds . It requires Ca(2+) for saccharide binding and shows a higher affinity to pentoses than hexoses and disaccharides . HEK-293T cells transfected with an expression vector containing the XEEL cDNA secrete into the culture medium the recombinant XEEL (rXEEL) that is similar to the purified XEEL in its molecular nature and saccharide-binding properties . Substitution of Asn-192 to Gln removed the N-linked carbohydrate and inhibited secretion of rXEEL, but did not abolish the activity to bind to galactose-Sepharose . The embryo's XEEL content, as estimated by Western blot analyses, increases during neurula/tailbud stages and declines after one week post-fertilization . Immunofluorescence and immuno-electron microscopic analyses showed localization of the XEEL protein in a typical secretory granule pathway of non-ciliated epidermal cells . When tailbud embryos were cultured in the standard medium, XEEL was accumulated in the medium, indicating secretion of XEEL into the environmental water . The rate of XEEL secretion greatly increased at around the hatching stage and stayed at a high level during the first week after hatching . XEEL may have a role in innate immunity to protect embryos and larvae against pathogenic microorganisms in the environmental water.

J Eukaryot Microbiol, 2004 Sep-Oct, 51(5), 497 - 501
Introductory remarks: bacterial endosymbionts or pathogens of free-living amebae1; Marciano-Cabral F; Free-living amebae are ubiquitous in the environment and can be isolated from a variety of habitats including water, soil, air, hospital water systems, dental units, contact lens cases, and cooling towers . The interaction of amebae with other microorganisms in their environment is varied . Bacteria are a major food source for free-living amebae . However, some bacteria have established a stable symbiotic relationship with amebae . Recent reports indicate an association of amebae with intracellular bacterial pathogens . Such amebae may serve as reservoirs for maintaining and dispersing pathogenic bacteria in the environment or as vectors of bacterial disease in humans.

Vet Res, 2004 Nov-Dec, 35(6), 709 - 13
Determination of an efficient and reliable method for DNA extraction from ticks; Halos L et al.; Molecular detection of pathogenic microorganisms in ticks is based on DNA amplification of the target pathogen; therefore, extraction of DNA from the tick is a major step . In this study, we compared three different tick DNA extraction protocols based on an enzymatic digestion by proteinase K followed by DNA extraction by a commercial kit (method 1), or on mortar crushing, proteinase K digestion and phenol/chloroform DNA extraction (method 2) and fine crushing with a beads beater, proteinase K digestion and DNA extraction using a commercial kit (method 3) . The absence of PCR inhibitors and the DNA quality were evaluated by PCR amplification of the tick mitochondrial 16S rRNA gene using tick-specific primers . With method 1, 23/30 (77%) of the samples were extracted; with method 2, 30/31 (97%) of the samples were extracted and with method 3, 30/30 (100%) of the samples were extracted . DNA extraction efficiency using method 3 is significantly higher than DNA extraction efficiency using method 1 (100% versus 77%, P < 0.05) . There was no significant difference between methods 2 and 3 . Method 3 was however more adapted to cohort studies than method 2 . This technique was validated for cohort tick DNA extraction and applicable to the treatment of small samples such as nymphs and soft ticks with 100% efficiency.

J Med Entomol, 2004 Sep, 41(5), 853 - 60
Diel feeding periodicity of larval anopheline mosquitoes on microorganisms and microinvertebrates: a spatial and temporal comparison of Anopheles quadrimaculatus (Diptera: Culicidae) diets in a Michigan pond; Wallace JR et al.; Diel feeding activity of third and fourth instars of Anopheles quadrimaculatus Say were studied in a Michigan permanent pond . This field study examined the consumption of microbial and microinvertebrate food resources over a diel (24-h) period between two habitats (open water and vegetated areas) . A fluorochromatic stain (4,6-diamidino-2-phenylindole) was used to quantify microbial dietary components within larval guts and habitats . Microbial analyses show that bacteria were the most abundant food type, followed by detritus, algae, and invertebrate parts/protozoans (IPP) . Larval consumption of cladocerans was significantly greater at midnight than noon . Larval gut analyses examined every hour over a 24-h period provided significant evidence as to the approximate time larvae switch microinvertebrate dietary resources . Habitat had a significant effect on microinvertebrate consumption by An . quadrimaculatus larvae . Larvae consumed more water mites and rotifers in the open water areas than vegetated zones . We found that An . quadrimaculatus larvae do not preferentially feed on microinvertebrates over a diel period, however, larvae may feed selectively on rotifers in open water habitats . Knowledge of the "feeding area" or microhabitats, with respect to where and when larvae optimally forage as well as particle sizes and food types consumed in the natural habitats will enhance the success of bacteria and other particulate larvicides.

J Biol Rhythms, 2004 Oct, 19(5), 445 - 58
Clock gene evolution and functional divergence; Tauber E et al.; In considering the impact of the earth's changing geophysical conditions during the history of life, it is surprising to learn that the earth's rotational period may have been as short as 4 h, as recently as 1900 million years ago (or 1.9 billion years ago) . The implications of such figures for the origin and evolution of clocks are considerable, and the authors speculate on how this short rotational period might have influenced the development of the "protoclock" in early microorganisms, such as the Cyanobacteria, during the geological periodsin which they arose and flourished . They then discuss the subsequent duplication of clock genes that took place around and after the Cambrian period, 543 million years ago, and its consequences . They compare the relative divergences of the canonical clock genes, which reveal the Per family to be the most rapidly evolving . In addition, the authors use a statistical test to predict which residues within the PER and CRY families may have undergone functional specialization.

J Pharm Biomed Anal, 2004 Nov 19, 36(4), 815 - 21
An API LC/MS/MS quantitation method for ansamitocin P-3 (AP3) and its preclinical pharmacokinetics; Liu Z et al.; Ansamitocin P-3 (AP3) is a potent maytansinoid antitumor agent isolated from microorganisms and mosses . In this study, a highly sensitive and specific electrospray ionization (ESI) liquid chromatography-tandem mass spectrometry (LC/MS/MS) method for quantitation of AP3 was developed and validated . AP3 was extracted from rat plasma along with the internal standard, depsipeptide FK228 (NSC-630176, FR) with ethyl acetate . Components in the extract were separated on a 50mm x 2.1mm Betabasic C 85 microm stainless steel column by isocratic elution with 70% acetonitrile/0.9% formic acid . The liquid flow was passed through a pre-source splitter and 5% of the eluent was introduced into the API source . The components were analyzed in the multiple-reaction-monitoring (MRM) mode as the precursor/product ion pair of m/z 635.2/547.2 for AP3 and of m/z 541.5/424.0 for the internal standard FR . Linear calibration curves were obtained in the range 1-500 ng/mL using 0.2 mL rat plasma . The within-day coefficients of variation (CVs) were 12.9, 6.7, and 5.5% and the between-day CVs were 10.4, 6.5, and 6.4% (all n = 5) at 1, 10, and 200 ng/mL, respectively . A formulation based on normal saline and PEG300 was then developed and Sprague-Dawley male rats were given this formulated drug by i.v . bolus . Plasma drug concentrations were measured by this method and the pharmacokinetics were analyzed by standard techniques . Plasma concentration-time profiles were found to follow a triexponential decline and the terminal phase was nearly flat, suggesting that the drug distributed in deep tissue compartments or organs and then equilibrates slowly with the blood stream.

Int J Med Microbiol, 2004 Oct, 294(5), 337 - 44
Antigen delivery by dendritic cells; Moll H; Dendritic cells (DC) link the innate and adaptive arms of the immune system and thus orchestrate the immune response to pathogens . A novel immune intervention strategy to control infectious diseases is based on the use of the potent immunostimulatory properties of DC for vaccination and immunotherapy . Recent advances in our understanding of DC biology and the molecular mechanisms by which DC instruct the development of an appropriate immune response to microorganisms provide means for DC-based approaches to manipulate the immune system . In experimental systems, DC vaccination has been documented to mediate protection against a wide spectrum of infectious diseases caused by viral, bacterial, parasitic and fungal pathogens . The protocols for the generation, stimulation and antigen loading of DC are being optimized, and methods for DC targeting in situ are likely to become available soon, thus paving the way for clinical applications of DC-based vaccines.

Biosens Bioelectron, 2004 Nov 15, 20(5), 945 - 55
The application of ultrasound as a rapid method to provide DNA fragments suitable for detection by DNA biosensors; Mann TL et al.; Contamination of food and water supplies by microorganisms such as Escherichia coli, the need for point-of-care bedside analysis of biological samples, and concerns about terrorist attacks using biological organisms, have made the development of fast, reliable, and sensitive analytical methodologies for use in monitoring of pathogens very important . With a variety of biosensors being developed for extremely sensitive and rapid nucleic acid diagnostics, it has become even more important to shift focus towards creation of methods to decrease the amount of time and effort necessary for sample preparation . The application of ultrasound has the potential to create DNA fragments from genomic material with lengths that are suitable for determination using biosensors and microarrays . For example, application of 85 W power at a frequency of 20 kHz can produce a preponderance of fragments of 100-400 base pairs (bp) within several seconds, and sample processing can lead to over 75% conversion from genomic material to fragments in times of 20-30 s . A proportion of these fragments are in a single-stranded state and are suitable for hydridization with immobilized single-stranded DNA probe oligonucleotides using a fiber optic biosensor . Control of factors such as salt concentration, exposure time, ultrasound power, and the initial temperature of the solution, can affect the length and form (single- or double-stranded) of DNA fragments that are generated by ultrasound, and average fragment length can be adjusted by selection of these operating parameters.

J Coll Physicians Surg Pak, 2004 Nov, 14(11), 694 - 7
Microbiology services in public sector hospitals of Pakistan; Memon BA; The purpose of clinical microbiology laboratory is to identify the actual etiologic agent(s) of infectious disease(s) based on morphological, biochemical, immunological and molecular procedures . Proficiency in isolating and identifying microorganisms, determining drug resistance of isolates; and in reporting the results is essential for the early detection and treatment of nosocomial pathogens . A Microbiologist is essentially interlinked with committees regarding hospital policy-making, infection-control, surveillance, investigation of infections in patients and personnel and maintaining a continuing education program . In the final analysis, the patients' well-being and health benefit most from clinical microbiology laboratory . This overview emphasizes the role of microbiology laboratory in government hospitals of Pakistan and general health care, without which the problem of multiple antibiotic resistance can only become worse.

Cell Mol Biol (Noisy-le-grand), 2004 Jun, 50(4), 469 - 77
High hydrostatic pressure inactivated human tumour cells preserve their immunogenicity; Korn A et al.; High hydrostatic pressure (HHP) is an established method to inactivate biomolecules and microoganisms . It is routinely used for the sterilization of foodstuff . Recently, new applications as inactivation of microorganisms and tumour cells for bone transplants or for cancer vaccines have emerged . Characterization of the HHP-induced cellular responses are a prerequisite for its clinical use . To this end, we investigated the fate of human cells after HHP by cytofluorometry . We observed that the induction by HHP of cell death is time- and pressure-dependent . Surprisingly, an HHP-treatment of 100 MPa did not reduce viability at any time point . Pressures from 150 to 250 MPa-induced programmed cell death in most cells . However, survivors were observed in long term culture experiments under these conditions . Pressures above 300 MPa immediately induced cell death by necrosis and completely inactivated the cells . In contrast to inactivation by other necrosis inducing treatments like heat, freeze/thaw, or chemical agents, HHP avoids generation of Maillard products and disintegration and lysis of the cells . Instead HHP generates a gelatinised mixture of antigens captured in a distinct and robust particle and maintains their humoral immunogenicity . The high viscosity of the internal matrix of a pressurised cell is reflected by the slow penetration of the low molecular compound propidium iodide and limits the bleeding of antigen before uptake by antigen presenting cells . Taken together, HHP is an alternative method for the inactivation of mammalian cells in clinical settings.

Cell Mol Biol (Noisy-le-grand), 2004 Jun, 50(4), 429 - 36
Psychropiezophilic microorganisms; Margesin R et al.; Bacteria living in the deep-sea have several unusual features that allow them to thrive in their extreme environment . Most isolated strains are not only piezophilic but also psychrophilic . In this short review, we summarize the current knowledge about psychrophiezophilic microorganisms with regard to their taxonomy and cellular fatty acids composition . Their biotechnological potential is also described.

Mod Pathol . 2004 Nov 05; {Epub ahead of print}
Pulmonary lymphohistiocytic reactions temporally related to etanercept therapy; Yousem SA et al.; This report details the pulmonary pathologic findings in four patients with rheumatoid arthritis, who developed new onset of pulmonary signs and symptoms with alveolar infiltrates temporally related to the institution of etanercept therapy . Biopsy findings showed an interstitial and air space lymphohistiocytic infiltrate with non-necrotizing granulomas, in the setting of negative cultures and special stains for microorganisms . The association with etanercept therapy and granulomatous reactions is discussed along with the differential diagnosis.Modern Pathology advance online publication, 5 November 2004; doi:10.1038/modpathol.3800333.

J Clin Microbiol, 2004 Nov, 42(11), 4919 - 24
Molecular detection of Coxiella burnetii in the sera of patients with Q fever endocarditis or vascular infection; Fenollar F et al.; In the absence of a specific diagnosis based on serology, chronic Q fever is inevitably fatal . However, diagnosis is often delayed because the test is not widely available . To shorten the diagnostic delay, we adapted a nested-PCR assay with serum as a template and the LightCycler as a thermal cycler, termed LCN-PCR . We retrospectively and prospectively applied this method to samples from 48 patients diagnosed with Q fever endocarditis or vascular infection and to samples from 100 controls with endocarditis caused by other microorganisms . We also prospectively applied this technique to samples from 30 patients treated for a Q fever endocarditis and to samples from 13 patients with a convalescent acute Q fever with ambiguous immunoglobulin G (IgG) phase I titer . LCN-PCR had a specificity of 100% . It was positive only in samples from patients with evolutive Q fever, as none of the samples from patients with a treated chronic Q fever or with a convalescent acute Q fever presented positive results . When performed prospectively on recently stored sera, the sensitivity of LCN-PCR is 64% (7 of 11 samples; P = 0.004), but the efficiency of LCN-PCR was dramatically altered by the storage of specimens at -20 degrees C . High IgG phase I titers decreased the sensitivity of LCN-PCR . A significant difference was observed among LCN-PCR results for sera with IgG phase I titers of > or =1:25,600 compared to sera with IgG phase I titers of <1:25,600 (0 of 15 samples versus 13 of 33 samples; P = 0.004) . In patient samples with titers below 1:25,600 tested prospectively, sensitivity was 100% (7 of 7) . The LCN-PCR assay may be helpful in establishing an early diagnosis of chronic Q fever.

Appl Environ Microbiol, 2004 Nov, 70(11), 6884 - 6
Evaluation of the LIVE/DEAD BacLight kit for detection of extremophilic archaea and visualization of microorganisms in environmental hypersaline samples; Leuko S et al.; Extremophilic archaea were stained with the LIVE/DEAD BacLight kit under conditions of high ionic strength and over a pH range of 2.0 to 9.3 . The reliability of the kit was tested with haloarchaea following permeabilization of the cells . Microorganisms in hypersaline environmental samples were detectable with the kit, which suggests its potential application to future extraterrestrial halites.

Appl Environ Microbiol, 2004 Nov, 70(11), 6643 - 9
Heavy-metal stress and developmental patterns of arbuscular mycorrhizal fungi; Pawlowska TE et al.; The rate of global deposition of Cd, Pb, and Zn has decreased over the past few decades, but heavy metals already in the soil may be mobilized by local and global changes in soil conditions and exert toxic effects on soil microorganisms . We examined in vitro effects of Cd, Pb, and Zn on critical life stages in metal-sensitive ecotypes of arbuscular mycorrhizal (AM) fungi, including spore germination, presymbiotic hyphal extension, presymbiotic sporulation, symbiotic extraradical mycelium expansion, and symbiotic sporulation . Despite long-term culturing under the same low-metal conditions, two species, Glomus etunicatum and Glomus intraradices, had different levels of sensitivity to metal stress . G . etunicatum was more sensitive to all three metals than was G . intraradices . A unique response of increased presymbiotic hyphal extension occurred in G . intraradices exposed to Cd and Pb . Presymbiotic hyphae of G . intraradices formed presymbiotic spores, whose initiation was more affected by heavy metals than was presymbiotic hyphal extension . In G . intraradices grown in compartmentalized habitats with only a portion of the extraradical mycelium exposed to metal stress, inhibitory effects of elevated metal concentrations on symbiotic mycelial expansion and symbiotic sporulation were limited to the metal-enriched compartment . Symbiotic sporulation was more sensitive to metal exposure than symbiotic mycelium expansion . Patterns exhibited by G . intraradices spore germination, presymbiotic hyphal extension, symbiotic extraradical mycelium expansion, and sporulation under elevated metal concentrations suggest that AM fungi may be able to survive in heavy metal-contaminated environments by using a metal avoidance strategy.

Appl Environ Microbiol, 2004 Nov, 70(11), 6542 - 50
Representative freshwater bacterioplankton isolated from Crater Lake, Oregon; Page KA et al.; High-throughput culturing (HTC) methods that rely on dilution to extinction in very-low-nutrient media were used to obtain bacterial isolates from Crater Lake, Oregon . 16S rRNA sequence determination and phylogenetic reconstruction were used to determine the potential ecological significance of isolated bacteria, both in Crater Lake and globally . Fifty-five Crater Lake isolates yielded 16 different 16S rRNA gene sequences . Thirty of 55 (55%) Crater Lake isolates had 16S rRNA gene sequences with 97% or greater similarity to sequences recovered previously from Crater Lake 16S rRNA gene clone libraries . Furthermore, 36 of 55 (65%) Crater Lake isolates were found to be members of widely distributed freshwater groups . These results confirm that HTC is a significant improvement over traditional isolation techniques that tend to enrich for microorganisms that do not predominate in their environment and rarely correlate with 16S rRNA gene clone library sequences . Although all isolates were obtained under dark, heterotrophic growth conditions, 2 of the 16 different groups showed evidence of photosynthetic capability as assessed by the presence of puf operon sequences, suggesting that photoheterotrophy may be a significant process in this oligotrophic, freshwater habitat.

Appl Environ Microbiol, 2004 Nov, 70(11), 6525 - 34
Coupling of functional gene diversity and geochemical data from environmental samples; Palumbo AV et al.; Genomic techniques commonly used for assessing distributions of microorganisms in the environment often produce small sample sizes . We investigated artificial neural networks for analyzing the distributions of nitrite reductase genes (nirS and nirK) and two sets of dissimilatory sulfite reductase genes (dsrAB1 and dsrAB2) in small sample sets . Data reduction (to reduce the number of input parameters), cross-validation (to measure the generalization error), weight decay (to adjust model parameters to reduce generalization error), and importance analysis (to determine which variables had the most influence) were useful in developing and interpreting neural network models that could be used to infer relationships between geochemistry and gene distributions . A robust relationship was observed between geochemistry and the frequencies of genes that were not closely related to known dissimilatory sulfite reductase genes (dsrAB2) . Uranium and sulfate appeared to be the most related to distribution of two groups of these unusual dsrAB-related genes . For the other three groups, the distributions appeared to be related to pH, nickel, nonpurgeable organic carbon, and total organic carbon . The models relating the geochemical parameters to the distributions of the nirS, nirK, and dsrAB1 genes did not generalize as well as the models for dsrAB2 . The data also illustrate the danger (generating a model that has a high generalization error) of not using a validation approach in evaluating the meaningfulness of the fit of linear or nonlinear models to such small sample sizes.

Hum Reprod . 2004 Nov 4; {Epub ahead of print}
Aseptic technology of vitrification of human pronuclear oocytes using open-pulled straws; Isachenko V et al.; BACKGROUND: The aim of this study was to compare the viability of human pronuclear oocytes subjected to vitrification using cooling by direct submerging of open-pulled straws in liquid nitrogen versus vitrification by cooling of open-pulled straws located inside a closed 0.5 ml straw (aseptic system) . METHODS: Two- and three-pronuclei stage oocytes (n=114) were cryopreserved in super-open-pulled straws by vitrification in 20% ethylene glycol +20% dimethylsulphoxide (DMSO) + osmotic active and neutral non-permeable cryoprotectants with a four-step exposure in 20, 33, 50 and 100% vitrification solution for 2, 1 and 1 min, and 30-50 s, respectively at room temperature, and plunging into liquid nitrogen . Oocytes of group 1 (n=42) were rapidly cooled at a speed of 20 000 degrees C/min by direct plunging of open-pulled straws into liquid nitrogen . Oocytes of group 2 (n=44) were first located in 0.5 ml straws, which were closed at both sides by metal balls, and then plunged into liquid nitrogen . This method resulted in a cooling speed of 200 degrees C/min . For both groups, oocytes were thawed rapidly at a speed of 20 000 degrees C/min using an identical protocol . Oocytes subsequently were expelled into a graded series of sucrose solutions (1.0, 0.75, 0.5, 0.25 and 0.12 mol/l) at 2.5 min intervals . RESULTS: Oocyte development up to expanded blastocyst stage after in vitro culture was 15% in group 1, 14% in group 2 and 29% in an untreated control group . CONCLUSION: The deposition of human pronuclear oocytes in open-pulled straws which are placed inside a hermetically closed container guarantees a complete isolation of oocytes from liquid nitrogen and avoids potential contamination by pathogenic microorganisms . The combination of direct plunging of this container into liquid nitrogen and rapid warming makes this process as efficient as conventional vitrification.

Biofizika, 2004 Sep-Oct, 49(5), 912 - 9
{On the regulation of the ecological community structure by a variation of the concentration ratios of resources in environment}; Protease-activated receptors: protease signaling in the gastrointestinal tract; University of California San Francisco, 521 Parnassus Avenue, Room C317, San Francisco, California 94143-0660, USASerine proteases from the circulation, inflammatory cells, digestive glands and microorganisms can signal to cells by cleaving protease-activated receptors (PARs), a family of four G-protein-coupled receptors . Proteases cleave PARs at specific sites to expose tethered ligand domains that bind to and activate the cleaved receptors . Despite this irreversible mechanism of activation, PAR signaling is tightly regulated to prevent the uncontrolled stimulation of cells . Although PARs are found in all organ systems, protease signaling is of particular interest in the gastrointestinal tract, where proteases regulate neurotransmission, secretion, motility, epithelial permeability and intestinal inflammation, and can thus contribute to disease.

Prog Lipid Res, 2004 Nov, 43(6), 534 - 52
GDSL family of serine esterases/lipases; Akoh CC et al.; GDSL esterases and lipases are hydrolytic enzymes with multifunctional properties such as broad substrate specificity and regiospecificity . They have potential for use in the hydrolysis and synthesis of important ester compounds of pharmaceutical, food, biochemical, and biological interests . This new subclass of lipolytic enzymes possesses a distinct GDSL sequence motif different from the GxSxG motif found in many lipases . Unlike the common lipases, GDSL enzymes do not have the so called nucleophile elbow . Studies show that GDSL hydrolases have a flexible active site that appears to change conformation with the presence and binding of the different substrates, much like the induced fit mechanism proposed by Koshland . Some of the GDSL enzymes have thioesterase, protease, arylesterase, and lysophospholipase activity, yet they appear to be the same protein with similar molecular weight ( approximately 22-60 kDa for most esterases), although some have multiple glycosylation sites with higher apparent molecular weight . GDSL enzymes have five consensus sequence (I-V) and four invariant important catalytic residues Ser, Gly, Asn, and His in blocks I, II, III, and V, respectively . The oxyanion structure led to a new designation of these enzymes as SGNH-hydrolase superfamily or subfamily . Phylogenetic analysis revealed that block IIA which belonged to the SGNH-hydrolases was found only in clade I . Therefore, this family of hydrolases represents a new example of convergent evolution of lipolytic enzymes . These enzymes have little sequence homology to true lipases . Another important differentiating feature of GDSL subfamily of lipolytic enzymes is that the serine-containing motif is closer to the N-terminus unlike other lipases where the GxSxG motif is near the center . Since the first classification of these subclass or subfamily of lipases as GDSL(S) hydrolase, progress has been made in determining the consensus sequence, crystal structure, active site and oxyanion residues, secondary structure, mechanism of catalysis, and understanding the conformational changes . Nevertheless, much still needs to be done to gain better understanding of in vivo biological function, 3-D structure, how this group of enzymes evolved to utilize many different substrates, and the mechanism of reactions . Protein engineering is needed to improve the substrate specificity, enantioselectivity, specific activity, thermostability, and heterologous expression in other hosts (especially food grade microorganisms) leading to eventual large scale production and applications . We hope that this review will rekindle interest among researchers and the industry to study and find uses for these unique enzymes.

Biosens Bioelectron, 2004 Nov 1, 20(4), 668 - 83
Potential of DNA microarrays for developing parallel detection tools (PDTs) for microorganisms relevant to biodefense and related research needs; Hashsham SA et al.; Development of parallel detection tools using microarrays is critically reviewed in view of the need for screening multiple microorganisms in a single test . Potential research needs with respect to probe design and specificity, validation, sample concentration, selective target enrichment and amplification, and data analysis are discussed . Data illustrating selected probe design issues for detecting multiple targets in mixed microbial systems is presented . Challenges with respect to cost, time, and ease of use compared to other methods are also summarized.

Clin Microbiol Infect, 2004 Nov, 10(11), 951 - 3
Vertebral osteomyelitis caused by non-tuberculous mycobacteria; Petitjean G et al.; Vertebral osteomyelitis caused by non-tuberculous mycobacteria is a rare disease, with only 31 cases and one nosocomial outbreak reported in the literature (MedLine review between 1965 and December 2003) . The clinical features are often indistinguishable from those of pyogenic osteomyelitis . Early diagnosis of such infections is a major challenge because of the slow growth of these microorganisms . No consensus guidelines for the treatment of these infections exist . Prolonged anti-mycobacterial therapy in combination with surgical debridement is recommended.

Mikrobiologiia, 2004 Jul-Aug, 73(4), 553 - 7
{High-temperature microbial sulfate reduction can be accompanied by magnetite formation}; An integrated view of suppressor T cell subsets in immunoregulation; Department of Medicine and Pathology, Columbia University College of Physicians and Surgeons, New York, New York 10032, USAThe immune system evolved to protect organisms from a virtually infinite variety of disease-causing agents but to avoid harmful responses to self . Because immune protective mechanisms include the elaboration of potent inflammatory molecules, antibodies, and killer cell activation--which together can not only destroy invading microorganisms, pathogenic autoreactive cells, and tumors, but also mortally injure normal cells--the immune system is inherently a "double-edged sword" and must be tightly regulated . Immune response regulation includes homeostatic mechanisms intrinsic to the activation and differentiation of antigen-triggered immunocompetent cells and extrinsic mechanisms mediated by suppressor cells . This review series will focus on recent advances indicating that distinct subsets of regulatory CD4+ and CD8+ T cells as well as NK T cells control the outgrowth of potentially pathogenic antigen-reactive T cells and will highlight the evidence that these suppressor T cells may play potentially important clinical roles in preventing and treating immune-mediated disease . Here we provide a historical overview of suppressor cells and the experimental basis for the existence of functionally and phenotypically distinct suppressor subsets . Finally, we will speculate on how the distinct suppressor cell subsets may function in concert to regulate immune responses.

Biochim Biophys Acta, 2004 Nov 3, 1666(1-2), 19 - 39
Diversity and versatility of lipid-protein interactions revealed by molecular genetic approaches; Dowhan W et al.; The diversity in structures and physical properties of lipids provides a wide variety of possible interactions with proteins that affect their assembly, organization, and function either at the surface of or within membranes . Because lipids have no catalytic activity, it has been challenging to define many of their precise functions in vivo in molecular terms . Those processes responsive to lipids are attuned to the native lipid environment for optimal function, but evidence that lipids with similar properties or even detergents can sometimes partially replace the natural lipid environment has led to uncertainty as to the requirement for specific lipids . The development of strains of microorganisms in which membrane lipid composition can be genetically manipulated in viable cells has provided a set of reagents to probe lipid functions . These mutants have uncovered previously unrecognized roles for lipids and provided in vivo verification for putative functions described in vitro . In this review, we summarize how these reagent strains have provided new insight into the function of lipids . The role of specific lipids in membrane protein folding and topological organization is reviewed . The evidence is summarized for the involvement of anionic lipid-enriched domains in the organization of amphitropic proteins on the membrane surface into molecular machines involved in DNA replication and cell division.

Planta . 2004 Oct 23; {Epub ahead of print}
Two genes encoding different truncated hemoglobins are regulated during root nodule and arbuscular mycorrhiza symbioses of Medicago truncatula; Vieweg MF et al.; The MtTrHb1 and MtTrHb2 genes of the model legume Medicago truncatula Gaertn . encode proteins homologous to truncated hemoglobins (TrHb) from plants and a range of different microorganisms . Induction of MtTrHb1 in root nodules and expression of MtTrHb2 in root nodules, as well as in mycorrhizal roots, were shown by quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) . The promoters of both genes were PCR-amplified and fused to the gusAint coding region . By analysing these gusAint-fusions in transgenic root tissues, we were able to localize their activity in root nodules and in roots colonized by arbuscular mycorrhizal (AM) fungi . Whereas the promoter of MtTrHb1 was activated in the infected cells of the nitrogen-fixing zone of root nodules, the MtTrHb2 promoter was predominantly active in the nodule vascular tissue . This expression pattern correlates with the presence of an 'organ-specific element' (OSE)-like sequence in the MtTrHb1 promoter, which is not present in the MtTrHb2 regulatory unit . Concerning the AM symbiosis, only the MtTrHb2 promoter mediated an expression in arbuscule-containing cells and in the root vascular tissue of mycorrhizal root segments colonized by the fungus Glomus intraradices.

Nat Rev Immunol, 2004 Nov, 4(11), 912 - 21
Complementary and alternative medicine: assessing the evidence for immunological benefits; Goldrosen MH et al.; With words such as AIDS, allergy and autoimmunity embedded in the popular lexicon, we often equate health with the precision and the tenor of responses to allergens and microorganisms . This leads many people to seek their own solutions to sustain, restore or even boost their immune competence, hoping to live more comfortably and longer . Here, we consider the social and clinical contexts in which these promises of enhanced immunity are pursued through popular practices known as complementary and alternative medicine and the evidence that supports these.

Eur Respir J, 2004 Nov, 24(5), 805 - 10
Effects of acute hypovolaemia by furosemide on tracheal transepithelial potential difference and mucus in dogs; Nakagawa NK et al.; Furosemide is a potent diuretic that affects water transfer across the respiratory epithelium, which is closely related to the transepithelial potential difference (PD) . Water is a critical factor that determines mucus transport; an important lung defence mechanism that removes particles and microorganisms from the respiratory system . The aim of the present study was to investigate the acute effects of furosemide and hypovolaemia on tracheal PD and mucus properties . A total of 36 male mixed-breed dogs were submitted to anaesthesia, mechanical ventilation and haemodynamic monitoring . They were randomly assigned to three groups consisting of: a control group, a furosemide (40 mg i.v.) + hypovolaemia group, and a furosemide (40 mg i.v.) + volume replacement group . Tracheal PD and mucus samples were collected at time 0, 1 and 2 h after intervention . Mucus properties were analysed by means of a magnetic microrheometer and in vitro mucociliary transportability on the frog palate . Compared to controls, furosemide decreased PD to intermediate values, and only significantly when associated with hypovolaemia (-13+/-5 and -8+/-2 mV, time 0 and 2 h, respectively) . In addition to the direct effect of furosemide, these results indicate that hypovolaemia also affects ion transport in the tracheal membrane . Furosemide and hypovolemia have no acute effects on respiratory mucus properties.

Biophys J, 2005 Jan, 88(1), 467 - 474 Epub 2004 Oct 29.
Structural Features of a Hyperthermostable Endo-{beta}-1,3-glucanase in Solution and Adsorbed on "Invisible" Particles; Koutsopoulos S et al.; Conformational characteristics and the adsorption behavior of endo-beta-1,3-glucanase from the hyperthermophilic microorganism Pyrococcus furiosus were studied by circular dichroism, steady-state and time-resolved fluorescence spectroscopy, and calorimetry in solution and in the adsorbed state . The adsorption isotherms were determined on two types of surfaces: hydrophobic Teflon and hydrophilic silica particles were specially designed so that they do not interact with light and therefore do not interfere with spectroscopic measurements . We present the most straightforward method to study structural features of adsorbed macromolecules in situ using common spectroscopic techniques . The enzyme was irreversibly adsorbed and immobilized in the adsorbed state even at high temperatures . Adsorption offered further stabilization to the heat-stable enzyme and in the case of adsorption on Teflon its denaturation temperature was measured at 133 degrees C, i.e., the highest experimentally determined for a protein . The maintenance of the active conformation and biological function particularly at high temperatures is important for applications in biocatalysis and biotechnology . With this study we also suggest that nature may employ adsorption as a complementary mode to maintain structural integrity of essential biomolecules at extreme conditions of temperature.

Huan Jing Ke Xue, 2004 Jul, 25(4), 74 - 7
{Cultivation of aerobic granular sludge in SBR by seeding anaerobic granular sludge}; Hu LL et al.; Anaerobic granular sludge was inoculated to an aerobic SBR, where CH3COONa was used as the carbon source . Observations on the change of granules' shape and structure revealed that the granules experienced a shape-keeping and component-replacing process . The sludge concentration increased at first 4 weeks and then decreased to reach a constant of 5g/L at 35d with its SVI of 30 - 40mL/g . Granular sludge dominated in the reactor and suspended sludge concentration was less than 0.5g/L during the end of the process . Anaerobic granular sludge, in which spheral bacteria was the main microorganism, was successfully developed to aerobic granular sludge in which filamentous and bacillius bacteria were the dominant microorganism.

Mikrobiol Z, 2004 Jul-Aug, 66(4), 92 - 109
{Classification of mollicutes}; Detection of methane in the atmosphere of Mars; Istituto di Fisica dello Spazio Interplanetario INAF-IFSI, Via del Fosso del Cavaliere 100, 00133 Rome, Italy . formisan@nike.ifsi.rm.cnr.it

We report a detection of methane in the martian atmosphere by the Planetary Fourier Spectrometer onboard the Mars Express spacecraft . The global average methane mixing ratio is found to be 10 +/- 5 parts per billion by volume (ppbv) . However, the mixing ratio varies between 0 and 30 ppbv over the planet . The source of methane could be either biogenic or nonbiogenic, including past or present subsurface microorganisms, hydrothermal activity, or cometary impacts.

Scand J Infect Dis, 2004, 36(10), 761 - 4
Granulicatella (Abiotrophia) adiacens infection associated with a total knee arthroplasty; Riede U et al.; We describe the first case of prosthetic joint associated infection due to Granulicatella adiacens (formerly Abiotrophia adiacens) . Diagnosis was made by broad spectrum PCR, and later by culture . Diagnosis and treatment of this microorganism is difficult . Two y after revision and antibiotic treatment, infection was under control but not cured.

J Environ Radioact, 2005, 78(2), 151 - 77
The removal of uranium from mining waste water using algal/microbial biomass; Kalin M et al.; We describe a three step process for the removal of uranium (U) from dilute waste waters . Step one involves the sequestration of U on, in, and around aquatic plants such as algae . Cell wall ligands efficiently remove U(VI) from waste water . Growing algae continuously renew the cellular surface area . Step 2 is the removal of U-algal particulates from the water column to the sediments . Step 3 involves reducing U(VI) to U(IV) and transforming the ions into stable precipitates in the sediments . The algal cells provide organic carbon and other nutrients to heterotrophic microbial consortia to maintain the low E(H), within which the U is transformed . Among the microorganisms, algae are of predominant interest for the ecological engineer because of their ability to sequester U and because some algae can live under many extreme environments, often in abundance . Algae grow in a wide spectrum of water qualities, from alkaline environments (Chara, Nitella) to acidic mine drainage waste waters (Mougeotia, Ulothrix) . If they could be induced to grow in waste waters, they would provide a simple, long-term means to remove U and other radionuclides from U mining effluents . This paper reviews the literature on algal and microbial adsorption, reduction, and transformation of U in waste streams, wetlands, lakes and oceans.

Ann Thorac Surg, 2005 Nov, 78(5), 1623 - 9
Latent infective endocarditis: epidemiology and clinical characteristics of patients with unsuspected endocarditis detected after elective valve replacement; Shapira N et al.; BACKGROUND: The diagnosis of infective endocarditis is usually made on the basis of clinical and laboratory criteria and may be confirmed by histologic examination or culture of excised valves . We tried to determine the incidence and significance of inflammatory changes in valves excised during operations for reasons other than infective endocarditis . METHODS: The charts and histopathology of all patients undergoing valve replacement during a 10-year period (1993-2002) were reviewed . A total of 868 patients underwent a total of 970 valve replacements during this period, of whom 11 patients (1.3%) were for endocarditis, with the remaining 857 (98.7%) for other indications . All excised valves were cultured and examined histologically for the presence of inflammatory infiltrates, vegetations, and microorganisms . RESULTS: In 8 of 857 patients (0.9%), the histologic examination unexpectedly demonstrated an infiltrate suggestive of endocarditis . Blood and valve cultures, and serologic tests for Mycoplasma, Chlamydia, Legionella, Q fever, Brucella, Rickettsiae, VDRL, and Bartonella were negative in all but 1 patient, who was found to have Q fever . All received a prolonged course of antibiotics . Six patients had an uneventful recovery; 1 had intramyocardial abscesses and expired during cardiac reoperation; and 1 had recurrent fever and dehiscence of the aortic and mitral valve prostheses and after two cardiac reoperations remains in severe heart failure . CONCLUSIONS: The presence of an unexpected inflammatory infiltrate in heart valves excised for reasons other than endocarditis may occur in 0.9% of such operations; these infiltrates could indicate presence of endocarditis . A microbial origin should be sought, and patients should receive empiric antibiotic treatment for endocarditis.

Rev Clin Esp, 2004 Nov, 204(11), 583 - 7
{Prognostic value of antibodies anti-Chlamydia pneumoniae in ischemic heart disease}; Gonzalez Castaneda C et al.; INTRODUCTION AND OBJECTIVES: Coronary artery disease has been related to infection by Chlamydia pneumoniae even only in a few studies the association between presence of antibodies to this microorganism and the prognosis of patients with ischemic heart disease has been assessed . The objective of our study was to assess the impact of positivity of anti-Chlamydia pneumoniae antibodies in the morbidity and mortality associated to ischemic heart disease . METHODS: 249 patients with ischemic cardiopathy were evaluated (97 with myocardial infarction, 83 with unstable angina and 69 with stable angina), recluted along 1 year and with 3-year follow-up . IgG anti-Chlamydia pneumoniae antibodies were measured with microimmunofluorescence . The cut off point considered for positive serology was set in 1/64 . RESULTS: In the group of 97 patients with acute myocardial infarction, 43% showed positive titers of IgG antibody to C . pneumoniae . We observed a statistically significant association (p = 0.007) between positive serology and higher survival of acute myocardial infarction patients . A logistic regression was carried out with mortality, age, and serology as variables; age was the only variable that explained mortality (p = 0.0012), and the serology lost its statistical meaning . In the groups of 83 patients with unstable angina and of 69 patients with stable angina, 42% and 58%, respectively, showed positive serology for C . pneumoniae . We did not find a statistically significant association in both groups between positive serology to C . pneumoniae and the prognostic factors related to morbidity and mortality (rehospitalization and mortality) . CONCLUSIONS: The presence of IgG antibodies to C . pneumoniae is not a marker of morbidity and mortality in our population of patients with ischemic heart disease.

Biochem J . 2004 Oct 28; {Epub ahead of print}
Identification and characterization of Sulfolobus solfataricus D-gluconate dehydratase: A key enzyme in the nonphosphorylated Entner-Doudoroff pathway; Kim S et al.; The extremely thermoacidophilic archaeon Sulfolobus solfataricus utilizes D-glucose as a sole carbon and energy source via the nonphosphorylated Entner-Doudoroff pathway . It has been suggested that this microorganism metabolizes D-gluconate, the oxidized form of D-glucose, to pyruvate and D-glyceraldehyde by using two unique enzymes, D-gluconate dehydratase and 2-keto-3-deoxy-D-gluconate aldolase . In this study, we report the purification and characterization of D-gluconate dehydratase from S . solfataricus, which catalyzes the conversion of D-gluconate to 2-keto-3-deoxy-D-gluconate . D-Gluconate dehydratase was purified 400-fold from extracts of S . solfataricus by ammonium sulfate fractionation and chromatography on DEAE-Sepharose, Q-Sepharose, Phenyl Sepharose, and Mono Q . The native protein showed a molecular weight of 350 kDa by gel filtration, whereas sodium dodecyl sulfate-polyacrylamide gels indicated a molecular weight of 44 kDa indicating that D-gluconate dehydratase is an octameric protein . The enzyme showed maximal activity at temperatures between 80 and 90 degrees C and pH's between 6.5 and 7.5, and a half-life of 40 min at 100 degrees C . Divalent metal ions such as Co 2+, Mg 2+, Mn 2+, and Ni 2+ activated whereas EDTA inhibited the enzyme . A metal analysis of the purified protein revealed the presence of one Co 2+ ion per enzyme monomer . Of 22 aldonic acids tested, only D-gluconate served as a substrate, with a K m of 0.45 mM and a V max of 0.15 units/mg enzyme . From N-terminal sequences of the purified enzyme, it was found that the gene product of SSO3198 in the S . solfataricus genome database corresponded to D-gluconate dehydratase (gnaD) . We also found that the D-gluconate dehydratase of S . solfataricus is a phosphoprotein and that its catalytic activity is regulated by a phosphorylation-dephosphorylation mechanism . This is the first report on biochemical and genetic characterization of D-gluconate dehydratase involved in the nonphosphorylated Entner-Doudoroff pathway.

Jpn J Infect Dis, 2004 Oct, 57(5), S13 - 4
Biosynthesis and sorting of myeloperoxidase in hematopoietic cells; Olsson I et al.; The neutrophil granulocytes have a critical role in innate immunity through killing of phagocytized microorganisms, in which myeloperoxidase (MPO) participates . MPO is stored in cytoplasmic azurophil lysosome-like granules together with other antibiotic proteins and digestive enzymes . During passage in the secretory pathway pro-MPO is folded, subjected to oligosaccharide modification, and retrieval from constitutive secretion to become targeted to azurophil granules for final processing and storage . Propeptide-deleted MPO precursor was found not to be processed to mature MPO and not to be targeted for storage but instead degraded or secreted . This indicated that the propeptide of the MPO precursor was a prerequisite for the final processing and granule targeting of proMPO . When the MPO propeptide was expressed as a chimera with a normally secretory protein, the ER retention of the chimera was prolonged compared with that of the native protein . Thus, the propeptide of MPO precursor may also mediate the normally long ER-residence of proMPO . Both mature MPO and secreted proMPO contained complex oligosaccharide side chains indicating that proMPO and, thus, mature MPO has passed the medial Golgi stack where complex oligosaccharides are formed, and exited at TGN like other proteins targeted for azurophil granules.

Ying Yong Sheng Tai Xue Bao, 2004 Jul, 15(7), 1231 - 5
{Effect of straw return to field and fertilization in autumn on dryland corn growth and on water and fertilizer efficiency}; Zhou H et al.; A ten years location experiment of various kinds straw return to field and deep fertilization in autumn was conducted in Shouyang dryland experimental area of Shanxi Province to study their effect on the growth and yield of dryland corn, the use efficency of soil water and fertilizer, and the changes of soil fertility . The results showed that this kind of experimental method could better solve the contradiction of deep fertilization with maintaining soil moisture and keeping a full stand of seedlings in spring, and the competition of water and fertilizer between the degradation of crop remains and the seedlings . What is more, the abundant resources of crop remains were used more sufficiently, the activity of soil microorganisms was more active, and soil fertility was obviously improved, which was proved by the complete and strong seedlings and developed roots, the photosynthesis and transpiration rates were enhanced, the water use efficiency (WUE) was increased by 3.26 - 3.51 kg x hm(-2) x mm(-1), and the accumulated water consumption was decreased by 8.1 - 264.5 mm . During plant growth period, the utilization rate of fertilizer N and P could increase 3.9% - 13.9% and 3.0% - 9.1%, respectively, and the use efficiency of water and fertilizer was higher . The ten years accumulated yield increased 12.10 - 17.27 t x hm(-2), a rise of 25.6% - 36.5%, and in the meantime, higher soil fertility and productivity were maintained.

Ying Yong Sheng Tai Xue Bao, 2004 Jul, 15(7), 1177 - 81
{Effect of tillage system on soil animal, microorganism and enzyme activity in paddy field}; Gao M et al.; A long-term experiment showed that under ridge-no-tillage, the amount of soil animal in 0 - 20 cm layer was 14700 ind . x m(-2), while under no-tillage and fallow in winter, paddy-upland rotation, and conventional tillage, it was 10450, 7950 and 6275 ind . x m(-2), respectively . Soil microbial biomass and microbial biomass N were more in spring and autumn, and less in summer . Soil enzyme activity was higher in surface soil layer and lower in bottom soil layer . The amount of soil animal, microbial biomass and microbial biomass N and soil enzyme activity was in order of ridge-no-tillage > paddy-upland rotation > no-tillage and fallow in winter > conventional tillage . The results also indicated that ridge-no-tillage was advantageous to improve soil ecological environment and soil fertility in paddy field.

Ying Yong Sheng Tai Xue Bao, 2004 Jul, 15(7), 1174 - 6
{Interaction between chlopyrifos and microorganisms in soils}; Liu X et al.; The experimental results showed that in sterilized soils, the degradation rate of 50 mg x kg(-1), 500 mg x kg(-1) and 5,000 g x kg(-1) chlopyrifos was very slow (only 20% after 60 d), and in soils which previously treated with chlopyrifos, the degradation rate of 50 mg x kg(-1), 500 mg x kg(-1) and 5,000 mg x kg(-1) chlopyrifos was 100%, 90% and 80%, respectively . However, in un-sterilized and untreated soils, the degradation rate was at the medium of the rates mentioned-above, indicating that soil microorganisms played an important role in chlopyrifos degradation, and using chlopyrifos could induce the chlopyrifos degrading ability of soil microorganisms . Compared to the soils untreated with chlopyrifos, the soils treated with 50 mg x kg(-1) and 500 mg x kg(-1) chlopyrifos had somewhat increased bacteria and fungi during a short period of treatment, which recovered to normal level after 60 days . But, when treated with 5,000 mg x kg(-1) chlopyrifos, the bacteria and fungi were inhibited, and couldn't recover after 60 days . Under the same treatment condition, the number of bacteria and fungi was not different between soils previously treated and untreated with chlopyrifos, which indicated that enhanced degradation of chlopyrifos was not decided by the numbers of bacteria and fungi, but by their ability of enhanced degradation.

Emerg Infect Dis, 2004 Oct, 10(10), 1721 - 8
Dihydropteroate synthase gene mutations in Pneumocystis and sulfa resistance; Huang L et al.; Pneumocystis pneumonia (PCP) remains a major cause of illness and death in HIV-infected persons . Sulfa drugs, trimethoprim-sulfamethoxazole (TMP-SMX) and dapsone are mainstays of PCP treatment and prophylaxis . While prophylaxis has reduced the incidence of PCP, its use has raised concerns about development of resistant organisms . The inability to culture human Pneumocystis, Pneumocystis jirovecii, in a standardized culture system prevents routine susceptibility testing and detection of drug resistance . In other microorganisms, sulfa drug resistance has resulted from specific point mutations in the dihydropteroate synthase (DHPS) gene . Similar mutations have been observed in P . jirovecii . Studies have consistently demonstrated a significant association between the use of sulfa drugs for PCP prophylaxis and DHPS gene mutations . Whether these mutations confer resistance to TMP-SMX or dapsone plus trimethoprim for PCP treatment remains unclear . We review studies of DHPS mutations in P . jirovecii and summarize the evidence for resistance to sulfamethoxazole and dapsone.

Amino Acids, 2004 Dec, 27(3-4), 231 - 47 Epub 2004 Oct 22.
Marfey's reagent for chiral amino acid analysis: A review; Bhushan R et al.; The present paper describes characteristics and application of Marfey's reagent (MR) including general protocols for synthesis of the reagent and diastereomers along with advantages, disadvantages and the required precautions . Applications, and comparison with other derivatizing agents, for the resolution of complex mixtures of DL-amino acids, amines and non-proteinogenic amino acids, peptides/amino acids from microorganisms, cysteine residues in peptides, and evaluation of racemizing characteristics have been discussed . Separation mechanisms of resolution of amino acid diastereomers and replacement of Ala-NH(2) by suitable chiral moieties providing structural analogs and different chiral variants and their application as a derivatizing agent to examine the efficiency, and reactivity of the reagent have been focussed . Use of MR for preparing CSPs for direct enantiomeric resolution has also been included.

Microbiol Immunol, 2004, 48(10), 761 - 6
Fluconazole-resistant pathogens Candida inconspicua and C . norvegensis: DNA sequence diversity of the rRNA intergenic spacer region, antifungal drug susceptibility, and extracellular enzyme production; Sugita T et al.; The opportunistic fungal pathogens Candida inconspicua and C . norvegensis are very rarely isolated from patients and are resistant to fluconazole . We collected 38 strains of the two microorganisms isolated from Europe and Japan, and compared the polymorphism of the rRNA intergenic spacer (IGS) and internal transcribed spacer (ITS) regions, antifungal drug susceptibility, and extracellular enzyme production as a potential virulence factor . While the IGS sequences of C . norvegensis were not very divergent (more than 96.7% sequence similarity among the strains), those of C . inconspicua showed remarkable diversity, and were divided into four genotypes with three subtypes . In the ITS region, no variation was found in either species . Since the sequence similarity of the two species is approximately 70% at the ITS region, they are closely related phylogenetically . Fluconazole resistance was reconfirmed for the two microorganisms but they were susceptible to micafungin and amphotericin B . No strain of either species secreted aspartyl proteinase or phospholipase B . These results provide basal information for accurate identification, which is of benefit to global molecular epidemiological studies and facilitates our understanding of the medical mycological characteristics of C . inconspicua and C . norvegensis.

Biosci Biotechnol Biochem, 2004 Oct, 68(10), 2171 - 7
Biotransformation of various alkanes using the Escherichia coli expressing an alkane hydroxylase system from Gordonia sp . TF6; Fujii T et al.; Biotransformation using alkane-oxidizing bacteria or their alkane hydroxylase (AH) systems have been little studied at the molecular level . We have cloned and sequenced genes from Gordonia sp . TF6 encoding an AH system, alkB2 (alkane 1-monooxygenase), rubA3 (rubredoxin), rubA4 (rubredoxin), and rubB (rubredoxin reductase) . When expressed in Escherichia coli, these genes allowed the construction of biotransformation systems for various alkanes . Normal alkanes with 5 to 13 carbons were good substrates for this biotransformation, and oxidized to their corresponding 1-alkanols . Surprisingly, cycloalkanes with 5 to 8 carbons were oxidized to their corresponding cycloalkanols as well . This is the first study to achieve biotransformation of alkanes using the E . coli expressing the minimum component genes of the AH system . Our biotransformation system has facilitated assays and analysis leading to improvement of AH systems, and has indicated a cycloalkane oxidation pathway in microorganisms for the first time.

Biosci Biotechnol Biochem, 2004 Oct, 68(10), 2120 - 7
A novel zinc-containing alpha-keto ester reductase from actinomycete: an approach based on protein chemistry and bioinformatics; Ishihara K et al.; We have achieved the purification of an alpha-keto ester reductase (SCKER) from S . coelicolor A3(2) whole cells . SCKER proved to be a homotetramer of 132 kDa containing one equivalent of zinc ion per subunit . The enzyme differed from other alpha-keto ester reductases from microorganisms with regard to subunit structure and metal ion dependency . From a computer search using the protein data banks, the N-terminal amino acid sequence of SCKER was consistent with that of a possible zinc containing alcohol dehydrogenase in S . coelicolor A3(2) . None of three hypothetical proteins of S . coelocor A3(2) having a high homology sequence with those of already purified alpha-keto ester reductases from S . thermocyaneoviolaceus {Yamaguchi, H., et al., Biosci . Biotechnol . Biochem., 66, 588-597 (2002)} was identical with that of SCKER.

Infect Immun, 2004 Nov, 72(11), 6433 - 45
RpoS is not central to the general stress response in Borrelia burgdorferi but does control expression of one or more essential virulence determinants; Caimano MJ et al.; Borrelia burgdorferi, the Lyme disease spirochete, undergoes dramatic changes in antigenic composition as it cycles between its arthropod and mammalian hosts . A growing body of evidence suggests that these changes reflect, at least in part, the need for spirochetes to adapt to the physiological stresses imposed by abrupt changes in environmental conditions and nutrient availability . In many microorganisms, global responses are mediated by master regulators such as alternative sigma factors, with Escherichia coli RpoS (sigmaS) serving as a prototype . The importance of this transcriptional activator in other bacteria, coupled with the report by Hubner et al . (A . Hubner, X . Yang, D . M . Nolen, T . G . Popova, F . C . Cabello, and M . V . Norgard, Proc . Natl . Acad . Sci . USA 98:12724-12729, 2001) demonstrating that the borrelial RpoS ortholog controls expression of OspC and decorin-binding protein A (DbpA), prompted us to examine more closely the roles of RpoS-dependent and -independent differential gene expression in physiological adaptation by the Lyme disease spirochete . We observed that B . burgdorferi rpoS (rpoSBb) was induced following temperature shift and transcript levels were further enhanced by reduced pH (pH 6.8) . Using quantitative real-time reverse transcription-PCR (RT-PCR), we demonstrated that, in contrast to its ortholog (rpoSEc) in Escherichia coli, rpoSBb was expressed at significant levels in B . burgdorferi throughout all phases of growth following temperature shift . By comparing a B . burgdorferi strain 297 rpoSBb mutant to its wild-type counterpart, we determined that RpoSBb was not required for survival following exposure to a wide range of environmental stresses (i.e., temperature shift, serum starvation, increased osmolality, reactive oxygen intermediates, and increased or reduced oxygen tension), although the mutant was more sensitive to extremes of pH . While B . burgdorferi strains lacking RpoS were able to survive within intraperitoneal dialysis membrane chambers at a level equivalent to that of the wild type, they were avirulent in mice . Lastly, RT-PCR analysis of the ospE-ospF-elp paralogous lipoprotein families complements earlier findings that many temperature-inducible borrelial loci are controlled in an RpoSBb-independent manner . Together, these data point to fundamental differences between the role(s) of RpoS in B . burgdorferi and that in E . coli . Rather than functioning as a master regulator, RpoSBb appears to serve as a stress-responsive activator of a subset of virulence determinants that, together with the RpoS-independent, differentially expressed regulon, encompass the spirochete's genetic programs required for mammalian host adaptation.

Arq Gastroenterol, 2004 Jan-Mar, 41(1), 71 - 6 Epub 2004 Oct 15.
{Efficacy of the dosing regimen of pantoprazole 40 mg, amoxicillin 1000 mg and clarithromycin 500 mg, twice daily for 7 days, in the eradication of Helicobacter pylori in patients with peptic ulcer}; Coelho LG et al.; AIM: This is an open label, multicenter trial to determine the efficacy of the association of pantoprazole, clarithromycin and amoxicillin to eradicate Helicobacter pylori in patients with peptic ulcer . MATERIAL AND METHODS: Seventy-one patients (36 females, 35 males, average age 41.9 years) from three Brazilian university centers (located in the cities of Belo Horizonte and Porto Alegre), with peptic ulcers confirmed by endoscopy, and infections by H . pylori proven by at least two diagnostic testings were admitted in the trial . An association of pantoprazole 40 mg, clarithromycin 500 mg and amoxicillin 1.0 g was administered to patients twice daily for 7 days . RESULTS: By the end of treatment all patients were examined for digestive symptoms, presence of adverse events, and treatment adherence . Sixty days after the end of the treatment a new endoscopy with biopsies and respiratory function testing with 13C-urea breath test was performed in order to determine the eradication rates of that microorganism . Patients showing negative results at least in the 13C-urea breath test and in one other test (urease or histology) were considered H . pylori-negative . By the end of the trial, 60/69 (87%, CI 95% = 78.9-94.8) patients had the H . pylori eradicated in the per protocol analysis and 60/71 (84.5%, CI 95% = 76-92.9) in the intention-to-treat analysis . One patient was withdrawn from the trial due to a diarrhea . Twelve (16.9%) patients showed adverse symptoms that were deemed as mild symptoms . CONCLUSION: Our conclusion is that the association of pantoprazole, amoxicillin and clarithromycin administered during 7 days is an effective and well-tolerated alternative as regards the eradication of H . pylori in patients with peptic ulcer in Brazil.

Semin Thromb Hemost, 2004 Oct, 30(5), 549 - 57
Molecular mechanisms in thrombotic thrombocytopenic purpura; Tsai HM; Thrombotic thrombocytopenic purpura (TTP) is characterized by thrombocytopenia and microangiopathic hemolysis . Unlike the typical hemolytic uremic syndrome (HUS), which follows infection with shiga toxin-producing microorganisms, most cases of TTP do not have an obvious etiology . Recent studies revealed that a plasma zinc metalloprotease ADAMTS (a disintegrin and metalloprotease with thrombospondin type 1 motif) 13 cleaves von Willebrand factor in a shear-dependent manner . Deficiency of ADAMTS13, due to autoimmune inhibitors of the protease or genetic mutation in the ADAMTS13 gene, results in a propensity to the development of von Willebrand factor-platelet aggregation and intravascular thrombosis characteristic of TTP . The identification of the molecular defect in TTP raises the prospect that this hitherto mysterious disorder will be managed with a more rationally designed strategy in the near future.

Curr Treat Options Cardiovasc Med, 2004 Dec, 6(6), 441 - 449
Current Treatment Options for Patients with Endocarditis: The Evolving Indications for Cardiac Surgery; Cabell CH et al.; Infective endocarditis (IE) is a serious and deadly disease . Despite medical advances over the past half century, more than one half of patients with IE suffer a serious complication, and the mortality rate remains approximately 20% during the initial hospitalization and approaches 40% at 1 year . In patients with documented IE, the treatment centers on two main aspects: effective antibiotic therapy and consideration of surgical therapy . Effective antibiotic therapy is the mainstay of treatment and focuses on sustained bactericidal concentrations tailored specifically to the causative microorganism . Surgical therapy is also an important option for many patients with IE . The goals of surgical therapy are to eradicate the focus of infection, to repair endocardial destruction, and to prevent the development of complications and relapse of infection . Ideally, surgical therapy should offer a survival advantage over medical therapy alone . Recent evidence supports the survival benefit of surgery in patients with IE, specifically in those with heart failure and complicated, left-sided IE . Future therapeutic strategies may include broader indications for surgery, as well as new treatments such as immune-modulating agents.

Nat Rev Microbiol, 2004 Nov, 2(11), 898 - 907
Escherichia coli acid resistance: tales of an amateur acidophile; Foster JW; Gastrointestinal pathogens are faced with an extremely acidic environment . Within moments, a pathogen such as Escherichia coli O157:H7 can move from the nurturing pH 7 environment of a hamburger to the harsh pH 2 milieu of the stomach . Surprisingly, certain microorganisms that grow at neutral pH have elegantly regulated systems that enable survival during excursions into acidic environments . The best-characterized acid-resistance system is found in E . coli.

Nat Rev Microbiol, 2004 Nov, 2(11), 886 - 97
Genome-scale models of microbial cells: evaluating the consequences of constraints; Price ND et al.; Microbial cells operate under governing constraints that limit their range of possible functions . With the availability of annotated genome sequences, it has become possible to reconstruct genome-scale biochemical reaction networks for microorganisms . The imposition of governing constraints on a reconstructed biochemical network leads to the definition of achievable cellular functions . In recent years, a substantial and growing toolbox of computational analysis methods has been developed to study the characteristics and capabilities of microorganisms using a constraint-based reconstruction and analysis (COBRA) approach . This approach provides a biochemically and genetically consistent framework for the generation of hypotheses and the testing of functions of microbial cells.

Biochem Soc Trans, 2004 Nov, 32(Pt 5), 785 - 8
The role of SHIP1 in macrophage programming and activation; Rauh MJ et al.; The SHIP1 (SH2-containing inositol-5'-phosphatase 1) acts as a negative regulator of proliferation, survival and end cell activation in haemopoietic cells . It does so, at least in part, by translocating to membranes after extracellular stimulation and hydrolysing the phosphoinositide 3-kinase-generated second messenger, PtdIns(3,4,5)P(3) to PtdIns(3,4)P(2) . SHIP1(-/-) mice have, as a result, an increased number of neutrophils and monocyte/macrophages because their progenitors display enhanced survival and proliferation . These mice also suffer from osteoporosis because of an increased number of hyperactive osteoclasts and a significant neutrophil infiltration of the lungs . Interestingly, SHIP1(-/-) mice do not display endotoxin tolerance and we have found that lipopolysaccharide-induced endotoxin tolerance is contingent on up-regulating SHIP1, through the production of autocrine-acting transforming growth factor-beta, in bone-marrow-derived macrophages and mast cells . Intriguingly, unlike bone-marrow-derived macrophages, SHIP1(-/-) peritoneal and alveolar macrophages produce 10-fold less NO than wild-type macrophages because these in vivo-generated macrophages have very high arginase I levels and this enzyme competes with inducible nitric oxide synthase for the substrate L-arginine . It is probable that, in the face of chronically increased PtdIns(3,4,5)P(3) levels in their myeloid progenitors, SHIP1(-/-) mice display a skewed development away from M1 (killer) macrophages (which have high inducible nitric oxide synthase levels and produce NO to kill microorganisms and tumour cells), towards M2 (healing) macrophages (which have high arginase levels and produce ornithine to promote host-cell growth and collagen formation) . This skewing probably occurs to avoid septic shock and suggests that the phosphoinositide 3-kinase pathway plays a critical role in programming macrophages.

Crit Rev Biotechnol, 2004, 24(2-3), 59 - 83
Ferulic acid: an antioxidant found naturally in plant cell walls and feruloyl esterases involved in its release and their applications; Mathew S et al.; Ferulic acid is the most abundant hydroxycinnamic acid in the plant world and maize bran with 3.1% (w/w) ferulic acid is one of the most promising sources of this antioxidant . The dehydrodimers of ferulic acid are important structural components in the plant cell wall and serve to enhance its rigidity and strength . Feruloyl esterases are a subclass of the carboxylic acid esterases that hydrolyze the ester bond between hydroxycinnamic acids and sugars present in plant cell walls and they have been isolated from a wide range of microorganisms, when grown on complex substrates such as cereal brans, sugar beet pulp, pectin and xylan . These enzymes perform a function similar to alkali in the deesterification of plant cell wall and differ in their specificities towards the methyl esters of cinnamic acids and ferulolylated oligosaccharides . They act synergistically with xylanases and pectinases and facilitate the access of hydrolases to the backbone of cell wall polymers . The applications of ferulic acid and feruloyl esterase enzymes are many and varied . Ferulic acid obtained from agricultural byproducts is a potential precursor for the production of natural vanillin, due to the lower production cost.

Cancer Invest, 2004, 22(3), 445 - 65
Beyond hematoxylin and eosin--the role of immunohistochemistry in surgical pathology; Jaffer S et al.; Immunohistochemistry, a technique that microscopically detects cellular constituents via specific antibodies, has revolutionized the field of surgical pathology by tremendously empowering the hematoxylin and eosin (H&E) slide . In the investigation of the unknown primary, it enables detecting the origin of the tumor by use of tissue- or organ-specific antibodies as well as antibodies associated with minimal histogenetic differentiation . It has almost perfected the pathologist's ability to make specific diagnoses such as those of mesothelioma, melanoma, and neuroendocrine tumors . These diagnoses should be reached by interpreting the immunohistochemical results in the context of a detailed morphological analysis and differential diagnosis based on the H&E . Other important uses include detection of microinvasive and micrometastatic disease . Through the use of prognostic markers, immunohistochemistry can provide valuable information regarding tumor behavior and therapy . Lastly, immunohistochemistry serves a small but valuable role in highlighting microorganisms, particularly viruses.

Int Microbiol, 2004 Sep, 7(3), 193 - 8
Fe-Si biominerals in the Vilyuchinskie hot springs, Kamchatka Peninsula, Russia; Belkova NL et al.; The micromorphological structure of microbial mats (biomats) from the hot springs of the Vilyuchinskaya hydrothermal system, Kamchatka Peninsula, Russia, were investigated . The Vilyuchinskie hot springs had a discharge temperature of 55-56 degrees C and Na-Ca-HCO3-type waters rich in silicic and boric acids . Water and biomats had high concentrations of Fe, Mn, Sr, and As . Enumeration of total bacterial abundance (TBA) demonstrated a low density of bacterial populations . However, the fractions of metabolically active bacteria and respiring iron-oxidizing bacteria in the hot-spring water were high, comprising 68 and 21% of TBA, respectively . Scanning electron microscopy equipped with an energy dispersive X-ray spectrometer (SEM-EDX) showed that unicellular rod-shaped bacteria about 5-microm long predominated in the brown biomats . The mineral capsules of these bacteria contained large amounts of Fe and Si . Extracellular and intracellular particles were observed by transmission electron microscopy . Fe-oxidizing bacteria were isolated from the biomats on agar plates with selective medium . Therefore, it can be concluded that microorganisms inhabiting the biomats of the Vilyuchinskie hot springs are essential for the deposition of Fe-minerals at neutral pH.

Int Microbiol, 2004 Sep, 7(3), 181 - 91
Hijacking of eukaryotic functions by intracellular bacterial pathogens; Alonso A et al.; Intracellular bacterial pathogens have evolved as a group of microorganisms endowed with weapons to hijack many biological processes of eukaryotic cells . This review discusses how these pathogens perturb diverse host cell functions, such as cytoskeleton dynamics and organelle vesicular trafficking . Alteration of the cytoskeleton is discussed in the context of the bacterial entry process (invasion), which occurs either by activation of membrane-located host receptors ("zipper" mechanism) or by injection of bacterial proteins into the host cell cytosol ("trigger" mechanism) . In addition, the two major types of intracellular lifestyles, cytosolic versus intravacuolar (phagosomal), which are the consequence of alterations in the phagosome-lysosome maturation route, are compared . Specific examples illustrating known mechanisms of mimicry or hijacking of the host target are provided . Finally, recent advances in phagosome proteomics and genome expression in intracellular bacteria are described . These new technologies are yielding valuable clues as to how these specialized bacterial pathogens manipulate the mammalian host cell.

Metab Eng, 2004 Oct, 6(4), 340 - 51
Metabolic network analysis on Phaffia rhodozyma yeast using 13C-labeled glucose and gas chromatography-mass spectrometry; Cannizzaro C et al.; Carotenoid production by microorganisms, as opposed to chemical synthesis, could fulfill an ever-increasing demand for 'all natural' products . The yeast Phaffia rhodozyma has received considerable attention because it produces the red pigment astaxanthin, commonly used as an animal feed supplement . In order to have a better understanding of its metabolism, labeling experiments with {1-(13)C}glucose were conducted with the wildtype strain (CBS5905T) and a hyper-producing carotenoid strain (J4-3) in order to determine their metabolic network structure and estimate intracellular fluxes . Amino acid labeling patterns, as determined by GC-MS, were in accordance with a metabolic network consisting of the Embden-Meyerhof-Parnas pathway, the pentose phosphate pathway, and the TCA cycle . Glucose was mainly consumed along the pentose phosphate pathway ( approximately 65% for wildtype strain), which reflected high NADPH requirements for lipid biosynthesis . Although common to other oleaginous yeast, there was no, or very little, malic enzyme activity for carbon-limited growth . In addition, there was no evidence of phosphoketolase activity . The central carbon metabolism of the mutant strain was similar to that of the wildtype strain, though the relative pentose phosphate flux was lower and the TCA cycle flux in accordance with the biomass yield being lower.

Metab Eng, 2004 Oct, 6(4), 300 - 12
Engineering precursor flow for increased erythromycin production in Aeromicrobium erythreum; Reeves AR et al.; Metabolic engineering technology for industrial microorganisms is under development to create rational, more reliable, and more cost-effective approaches to strain improvement . Strain improvement is a critical component of the drug development process, yet the genetic basis for high production by industrial microorganisms is still a mystery . In this study, a search was begun for genetic modifications critical for high-level antibiotic production . The model system used was erythromycin production studied in the unicellular actinomycete, Aeromicrobium erythreum . A tagged-mutagenesis approach allowed reverse engineering of improved strains, revealing two genes, mutB and cobA, in the primary metabolic branch for methylmalonyl-CoA utilization . Knockouts in these genes created a permanent metabolic switch in the flow of methylmalonyl-CoA, from the primary branch into a secondary metabolic branch, driving erythromycin overproduction . The model provides insights into the regulation and evolution of secondary metabolism.

Trends Biotechnol, 2004 Nov, 22(11), 600 - 5
Proteomics of the Drosophila immune response; Engstrom Y et al.; Completion of the Drosophila genome has enabled the use of proteomic approaches for studying complex processes such as the innate immune defense against microorganisms . Microbial infection leads to the activation of responses involving changes at translational and post-translational levels . Proteomics is a tool for assessing such changes in protein expression, localization and post-translational modification . Recently, several studies have reported whole-genome analyses of the Drosophila immune response, both at the transcriptome and proteome levels, leading to a more comprehensive view of fly immunity . In this review, we describe and compare the proteomic techniques used in these analyses and discuss the results obtained by differential protein profiling of the Drosophila immune response.

Mikrobiyol Bul, 2004 Jul, 38(3), 261 - 4
{Meningitis due to Pseudomonas stutzeri: a case report}; Tasdelen Fisgin N et al.; Pseudomonas stutzeri is a saprophytic microorganism that rarely causes severe infections . In this report, a 28 days old male patient with meningomyelocele at birth was presented . The patient was admitted to the hospital with fever, and diagnosed as meningitis on the basis of physical examination and leukocytosis (blood: 16.380/mm3, cerebrospinal fluid (CSF): 130/mm3; 90% PMNL) . Following diagnosis ceftriaxone therapy was started led to improvement in clinical and laboratory findings . However on the 20th day, the clinical signs and symptoms became worse, and the patient was diagnosed to develop a second meningitis attack by laboratory examination of CSF . P . stutzeri was isolated from the CSF culture, and the isolate was found to be resistant to ceftriaxone . Upon this result the therapy has changed to meropenem . On the 5th day of the therapy, the patient has slightly improved and he was discharged due to the wishes of his parents, however he died two days after discharge . This first case of P . stutzeri meningitis in neonates was presented to withdraw attention to this clinical entity.

Med Hypotheses, 2004, 63(5), 847 - 54
Hypotheses on a germline origin of antibody diversity . Possible applications: improvement of the efficiency of immune response and autoimmune disease treatment; Berger G; In this paper, the antibody reaction is supposed to be due to the combination of a limited number of different antibodies against the epitopes of the antigen . In addition, the efficient part of the epitopes of proteins is assumed to be the size of dipeptides . The 400 different dipeptides would be distributed in two sets, those which are foreign to the host, against which would be directed antibodies, and those which are present in the proteins of the self, which would elicit no reaction . Each chain of the antibodies would recognise one aminoacid and 40 genes would be sufficient (20 for the light chains and 20 for the heavy chains) to code for the variable parts of the immunoglobulins against proteic antigens . With these hypotheses, the combination of antibodies against at least four different epitopes of the size of dipeptides can account for the main characteristics of the antibody reaction: response against any foreign proteic antigen and specificity . In fact, the epitopes have been found to be larger than dipeptides, several additional aminoacids are involved in the antibody-binding sites . Somatic mutations and VDJ recombinations are selected to give the maximal affinity for the antigens . However, these mechanisms have not been shown to create different specificities from the same V genes . Moreover, the phenomenon of heteroclisis and the decrease, due to mutations, of antigen-binding capacity of antibodies, sometimes observed, are better explained by the model proposed here than by the classical theory . The modification of the epitope subset of the self, by intrathymic injection of antibodies against particular pathogens, is proposed to improve the immune response when microorganisms develop immune escape mechanisms . On the other hand, in the case of autoimmune diseases, the displacement of autoantibodies against self-epitopes could be carried out by the injection into the thymus of specific anti-idiotypic antibodies.

Mol Immunol, 2005 Feb, 42(2), 161 - 82
Role of cytokines and chemokines in the regulation of innate immunity and HIV infection; Alfano M et al.; The earliest defense against microbial infection is represented by the responses of the innate (or natural) immune system, that also profoundly regulates the adaptive (or acquired) T- and B-cell immune responses . Activation of the innate immune system is primed by microbial invasion in response to conserved structures present in large groups of microorganisms (LPS, peptidoglycan, double-stranded RNA), and is finely tuned by different cell types (including dendritic cells, macrophages, natural killer cells, natural killer T cells, and gammadelta T cells) . In addition, several soluble factors (complement components, defensins, mannose-binding lectins, interferons, cytokines and chemokines) can play a major role in the regulation of both the innate and adaptive immunity . In this review, we will briefly overview the regulation of some cellular subsets of the innate immune system particularly involved in human immunodeficiency virus (HIV) infection and then focus our attention on those cytokines and chemokines whose levels of expression are more profoundly affected by HIV infection and that, conversely, can modulate virus infection and replication.

Chemosphere, 2004 Nov, 57(8), 953 - 9
Physicochemical forms of technetium in surface water covering paddy and upland fields; Ishii N et al.; The behavior of an element in the environment depends on its physicochemical form . Basic data for the behavior of technetium in an agricultural environment were obtained by determining the physicochemical forms of Tc in 28 surface water samples from paddy and upland fields . Most of the (95m)Tc was present as TcO(4)(-) in the samples . The relative amount of this chemical form was 72% on average . A significant amount of insoluble Tc (particles more than 0.2 microm in size), however, was found in some samples . The maximum amount of the insoluble Tc was 91% . Other forms were found in insignificant amounts . The amount of insoluble Tc was relatively high in paddy soil samples . Paddy soils, gley soils and gray lowland soils were particularly effective in the insolubilization of Tc . Among the soil characteristics studied, cation exchange capacity, anion exchange capacity, and active aluminum showed significant correlations with the relative amount of insoluble Tc . When microorganisms were eliminated from the surface water samples before the addition of (95m)TcO(4)(-), little insoluble Tc was found, suggesting that microorganisms cause the physicochemical transformation . These results showed that the physicochemical form of Tc changes from TcO(4)(-) to insoluble forms in surface water covering paddy fields . The insoluble forms would restrict the mobility of Tc in paddy fields.

Trends Microbiol, 2004 Nov, 12(11), 484 - 8
Toll-like receptors as an escape mechanism from the host defense; Netea MG et al.; Toll-like receptors (TLRs) are probably the most important class of pattern-recognition receptors . Recognition of pathogen-associated molecular patterns (PAMPs) by TLRs, either alone or in heterodimerization with other TLR or non-TLR receptors, induces the production of signals that are responsible for the activation of genes important for an effective host defense, especially those of proinflammatory cytokines . Recent studies also suggest that pathogenic microorganisms can modulate or interfere with TLR-mediated pattern recognition and can use TLRs as an escape mechanism from the host defense . Three major TLR-mediated escape mechanisms have been identified: TLR2-induced immunosuppression, especially through induction of interleukin (IL)-10 release; blockade of TLR recognition; and TLR-mediated induction of viral replication . Thus, TLR signals are not only beneficial to the host, but in certain situations the activation of particular TLR responses by microorganisms might serve as an escape mechanism from the host defense.

Mol Cell Probes, 2004 Dec, 18(6), 383 - 8
An isothermal amplification system based on the tandem-repeated DNA probe; Peng XM et al.; The hybridization methods and polymerase-based amplification methods are usually employed to detect pathogens and gene expressions quantitatively in clinical practices nowadays . However, the sensitiveness of the former and the specificity of the latter are not yet satisfied . To solve this problem, some promising comprehensive methods have been developed recently . Here we reported a new comprehensive method, a tandem repeated DNA probe-based amplification (TRPBA) system . To establish the TRPBA, TR48, an artificial tandem repeated DNA probe with 48 repeats of a 50 base pair unit was constructed . It could be efficiently amplified by Bst DNA polymerase at 61 degrees C for only 1 h . The products were analyzed either by direct gel electrophoresis or by gel electrophoresis after the digestion with restriction endonuclease HincII . The sensitiveness was as few as 100 copies per test, which was comparable with PCR-based techniques . The TR48 splicing with the DNA fragment of hepatitis B virus used as probe could successfully develop TRPBA to detect hepatitis B virus DNA . The TRPBA can be used in the future to detect many other genes or microorganisms simply by splicing TR48 with their DNA fragments . Thus, TRPBA might be useful because of its sensitiveness and simpleness.

Annu Rev Microbiol, 2004, 58, 649 - 90
Endangered antarctic environments; Cowan DA et al.; The Antarctic continent harbors a range of specialized and sometimes highly localized microbial biotopes . These include biotopes associated with desiccated mineral soils, rich ornithogenic soils, glacial and sea ice, ice-covered lakes, translucent rocks, and geothermally heated soils . All are characterized by the imposition of one or more environmental extremes (including low temperature, wide temperature fluctuations, desiccation, hypersalinity, high periodic radiation fluxes, and low nutrient status) . As our understanding of the true microbial diversity in these biotopes expands from the application of molecular phylogenetic methods, we come closer to the point where we can make an accurate assessment of the impacts of environmental change, human intervention, and other natural and unnatural impositions . At present, it is possible to make reasonable predictions about the physical effects of local climate change, but only general predictions on possible changes in microbial community structure . The consequences of some direct human impacts, such as physical disruption of microbial soil communities, are obvious if not yet quantitated . Others, such as the dissemination of nonindigenous microorganisms into indigenous microbial communities, are not yet understood.

Annu Rev Microbiol, 2004, 58, 489 - 519
Circadian rhythms in microorganisms: new complexities; Lakin-Thomas PL et al.; Recent advances in understanding circadian (daily) rhythms in the genera Neurospora, Gonyaulax, and Synechococcus are reviewed and new complexities in their circadian systems are described . The previous model, consisting of a unidirectional flow of information from input to oscillator to output, has now expanded to include multiple input pathways, multiple oscillators, multiple outputs; and feedback from oscillator to input and output to oscillator . New posttranscriptional features of the frq/white-collar oscillator (FWC) of Neurospora are described, including protein phosphorylation and degradation, dimerization, and complex formation . Experimental evidence is presented for frq-less oscillator(s) (FLO) downstream of the FWC . Mathematical models of the Neurospora system are also discussed.

Annu Rev Microbiol, 2004, 58, 425 - 51
Recent advances in the characterization of ambient pH regulation of gene expression in filamentous fungi and yeasts; Penalva MA et al.; All microorganisms must adapt to the pH of their environment . One aspect of this adaptation, particularly important for organisms that grow over a wide pH range, is the ability to express appropriately genes whose roles ultimately involve functions at the cell surface or in the environment . Genes encoding permeases, secreted enzymes, enzymes involved in synthesis of exported metabolites such as toxins and antibiotics, and probably enzymes modifying secreted proteins posttranslationally all fall into this category . Here we discuss the most recent findings on the transcriptional regulatory system in fungi that enables such genes to be expressed only when the ambient pH is conducive to their ultimate functions . The intriguing issue of how pH is sensed and how the resulting signal is transmitted to the transcription factor involves at least one late endosome component . Proper functioning of the regulatory system responding to ambient pH is essential for fungal pathogenicity of both animals and plants.

Annu Rev Microbiol, 2004, 58, 99 - 117
Anaerobic oxidation of methane and ammonium; Strous M et al.; Anaerobic oxidation of methane and ammonium are two different processes catalyzed by completely unrelated microorganisms . Still, the two processes do have many interesting aspects in common . First, both of them were once deemed biochemically impossible and nonexistent in nature, but have now been identified as major factors in global carbon and nitrogen cycling . Second, the microorganisms responsible for both processes cannot be grown in pure culture yet; their detection and identification were based on molecular ecology, tracer studies, use of lipid biomarkers, and enrichment cultures . Third, these microorganisms grow extremely slowly (doubling time from weeks to months) . Fourth, both processes have a good potential for application in biotechnology . Because both anaerobic methane and ammonium oxidation have been separately and excellently reviewed elsewhere, we focus on aspects of interest in the context of current developments in microbiology and explore the added value of reviewing these two processes in one place.

Environ Sci Technol, 2004 Sep 15, 38(18), 4768 - 74
Comparative evaluation of chloroethene dechlorination to ethene by Dehalococcoides-like microorganisms; Cupples AM et al.; Reductive dehalogenation of tetrachloroethene (PCE), trichloroethene (TCE), cis-1,2-dichloroethene (DCE), and vinyl chloride (VC) was examined in four cultures containing Dehalococcoides-like microorganisms . Dechlorination and growth kinetics were compared using a Monod growth-rate model for multiple electron acceptor usage with competition . Included were the Victoria mixed culture containing Dehalococcoides species strain VS (from Victoria, TX), the mixed culture KB-1/VC (from southern Ontario), the Pinellas mixed culture (from Pinellas, FL), and D . ethenogenes strain 195 . All cultures, with the exception of D . ethenogenes strain 195, grew with VC as catabolic electron acceptor . A dilution method was developed that allows a valid comparison to be made of dehalogenating kinetics between different mixed cultures . Using this procedure, maximum growth rates on VC were found to be similar for strain VS and KB-1/VC (0.42-0.49 +/- 0.02 d(-1)) but slower for the Pinellas culture (0.28 +/- 0.01 d(-1)) . The 16S rRNA gene sequences were determined to ensure that no cross contamination between cultures had occurred . Following enrichment of the VC dechlorinating microorganisms on VC, the cultures were amended with DCE, TCE, or PCE . The three mixed cultures failed to dechlorinate PCE or did so very slowly . However, the dilution technique indicated that all experienced growth on TCE and DCE as well as on VC . Maximum growth rates on DCE alone were quite similar (0.43-0.46 d(-1)), while the Pinellas culture grew faster on TCE alone (0.49 d(-1)) than did the other two mixed cultures (0.33-0.35 d(-1)) . Half-velocity and inhibition constants for growth on TCE were also determined for the three mixed cultures; both constants were found to be essentially equal and the same for the different cultures, varying between only 8.6 and 10.5 microM . The ability of the strain VS, KB-1/VC, and Pinellas cultures to utilize TCE rapidly with conversion to ethene is quite different from that of any other reported microorganism . It was separately confirmed with more traditional cell-counting techniques that strain VS coupled TCE, as well as DCE and VC, utilization with growth . This is the first report of an organism obtaining energy for growth through every step in the reduction of TCE to ethene . Also, as suggested by the dilution technique, the dehalogenating organisms in the KB-1/VC and Pinellas cultures appear to obtain growth from TCE utilization as well . Such ability to grow while dehalogenating TCE to ethene will be an important advantage for their use in bioaugmentation.

Dis Colon Rectum, 2004 Sep, 47(9), 1544 - 6 Epub 2004 Aug 19.
Regression of rectal mucosa-associated lymphoid tissue lymphoma but persistence of Helicobacter pylori infection of gastric mucosa after administration of levofloxacin: report of a case; Dohden K et al.; PURPOSE: Several articles have reported regression of rectal lymphoma of mucosa-associated lymphoid tissue after anti- Helicobacter pylori therapy . It remains unclear, however, whether lymphoma of rectal mucosa-associated lymphoid tissue is related to Helicobacter pylori infection . METHODS: A 60-year-old woman visited our hospital with a complaint of hematochezia . On colonoscopy a pale, ulcerated protrusion approximately 3.5 cm in diameter was found in the rectum . Pathologic diagnosis of a biopsy specimen was low-grade mucosa-associated lymphoid tissue lymphoma . The patient received a ten-day course of levofloxacin, and the cycle was repeated three times over seven months . RESULTS: Although persistence of Helicobacter pylori infection was confirmed, the tumor regressed completely . CONCLUSION: Our findings in this case suggest that rectal lymphoma of mucosa-associated lymphoid tissue may be related to unknown microorganisms other than Helicobacter pylori . Levofloxacin may be effective for treatment of rectal lymphoma of mucosa-associated lymphoid tissue regardless of Helicobacter pylori infection.

Curr Microbiol, 2004 Nov, 49(5), 361 - 5
Effect of dipeptides on the growth of Oenococcus oeni in synthetic medium deprived of amino acids; Aredes Fernandez PA et al.; Oenococcus oeni has numerous amino acid requirements for growth and dipeptides could be important for its nutrition . In this paper the individual or combined effect of dipeptides on growth of O . oeni X2L in synthetic media deficient in one or more amino acids with L-malic acid was investigated . Utilization of dipeptides, glucose, and L-malic acid was also analyzed . Dipeptides were constituted by at least one essential amino acid for growth . Dipeptides containing two essential amino acids, except leucine, had a more favorable effect than free amino acids on the growth rate . Gly-Gly was consumed to a greater extent than Leu-Leu and a rapid exodus of glycine to the extracellular medium accompanied it . The microorganism could use glycine in exchange for other essential amino acids outside the cell, favoring growth . In the presence of Leu-Leu, the increase in glucose consumption rate could be related to the additional energy required for dipeptide uptake.

Fertil Steril, 2004 Oct, 82(4), 799 - 804
Can endometrial infection/inflammation explain implantation failure, spontaneous abortion, and preterm birth after in vitro fertilization?
Romero R, Espinoza J, Mazor M.
The endometrial cavity is frequently invaded by microorganisms, and subclinical endometrial infection or inflammation may play a role in implantation failure after IVF, spontaneous abortion, and preterm birth . Microbial products and host-inflammatory mediators such as cytokines and chemokines can cause trophoblast apoptosis and the cascade of events leading to expulsion of the embryo or fetus.

BMC Biotechnol . 2004 Oct 13;4(1):22.
Reduction of arsenic content in a complex galena concentrate by Acidithiobacillus ferrooxidans; Makita M et al.; BACKGROUND: Bioleaching is a process that has been used in the past in mineral pretreatment of refractory sulfides, mainly in the gold, copper and uranium benefit . This technology has been proved to be cheaper, more efficient and environmentally friendly than roasting and high pressure moisture heating processes . So far the most studied microorganism in bioleaching is Acidithiobacillus ferrooxidans . There are a few studies about the benefit of metals of low value through bioleaching . From all of these, there are almost no studies dealing with complex minerals containing arsenopyrite (FeAsS) . Reduction and/or elimination of arsenic in these ores increase their value and allows the exploitation of a vast variety of minerals that today are being underexploited . RESULTS: Arsenopyrite was totally oxidized . The sum of arsenic remaining in solution and removed by sampling represents from 22 to 33% in weight (yield) of the original content in the mineral . The rest of the biooxidized arsenic form amorphous compounds that precipitate . Galena (PbS) was totally oxidized too, anglesite (PbSO4) formed is virtually insoluble and remains in the solids . The influence of seven factors in a batch process was studied . The maximum rate of arsenic dissolution in the concentrate was found using the following levels of factors: small surface area of particle exposure, low pulp density, injecting air and adding 9 K medium to the system . It was also found that ferric chloride and carbon dioxide decreased the arsenic dissolution rate . Bioleaching kinetic data of arsenic solubilization were used to estimate the dilution rate for a continuous culture . Calculated dilution rates were relatively small (0.088-0.103 day(-1)) . CONCLUSION: Proper conditions of solubilization of arsenic during bioleaching are key features to improve the percentage (22 to 33% in weight) of arsenic removal . Further studies are needed to determine other factors that influence specifically the solubilization of arsenic in the bioleaching system such as: pH, dissolved oxygen concentration, redox potentials, nature of concentrate and temperature among others . At . ferrooxidans was able to completely oxidize the minerals present during the arsenic bioleaching . Other elements present originally in the concentrate such as Zn, Sb, and Cu were also solubilized . The process of bioleaching is expected to be influenced by mechanisms that still need to be established due to the diversity of the minerals involved and by the presence of traces of metals in the concentrate . The increase in pulp density generates a decrease in the dissolved arsenic concentration . This decrease is greater in runs where air was not injected to the system . The maximum rate of arsenic dissolution in the concentrate was found using; small surface area of particle exposure, low pulp density, injecting air and adding 9 K medium to the system . The effect of addition of ferric chloride during the arsenic bioleaching resulted in a decrease of the solubilized arsenic in the system . The presence of CO2 is associated to the decrease in arsenic dissolution.

Gut, 2004 Nov, 53(11), 1617 - 23
Maintaining remission of ulcerative colitis with the probiotic Escherichia coli Nissle 1917 is as effective as with standard mesalazine; Kruis W et al.; BACKGROUND AND AIMS: Evidence exists for the pathogenic role of the enteric flora in inflammatory bowel disease . Probiotics contain living microorganisms which exert health effects on the host . We compared the efficacy in maintaining remission of the probiotic preparation Escherichia coli Nissle 1917 and established therapy with mesalazine in patients with ulcerative colitis . PATIENTS AND METHODS: In total, 327 patients were recruited and assigned to a double blind, double dummy trial to receive either the probiotic drug 200 mg once daily (n = 162) or mesalazine 500 mg three times daily (n = 165) . The study lasted for 12 months and patients were assessed by clinical and endoscopic activity indices (Rachmilewitz) as well as by histology . The primary aim of the study was to confirm equivalent efficacy of the two drugs in the prevention of relapses . RESULTS: The per protocol analysis revealed relapses in 40/110 (36.4%) patients in the E coli Nissle 1917 group and 38/112 (33.9%) in the mesalazine group (significant equivalence p = 0.003) . Subgroup analyses showed no differences between the treatment groups in terms of duration and localisation of disease or pretrial treatment . Safety profile and tolerability were very good for both groups and were not different . CONCLUSIONS: The probiotic drug E coli Nissle 1917 shows efficacy and safety in maintaining remission equivalent to the gold standard mesalazine in patients with ulcerative colitis . The effectiveness of probiotic treatment further underlines the pathogenetic significance of the enteric flora.

J Neuroinflammation . 2004 Oct 12;1(1):18.
Using animal models to determine the significance of complement activation in Alzheimer's disease; Loeffler DA; Complement inflammation is a major inflammatory mechanism whose function is to promote the removal of microorganisms and the processing of immune complexes . Numerous studies have provided evidence for an increase in this process in areas of pathology in the Alzheimer's disease (AD) brain . Because complement activation proteins have been demonstrated in vitro to exert both neuroprotective and neurotoxic effects, the significance of this process in the development and progression of AD is unclear . Studies in animal models of AD, in which brain complement activation can be experimentally altered, should be of value for clarifying this issue . However, surprisingly little is known about complement activation in the transgenic animal models that are popular for studying this disorder . An optimal animal model for studying the significance of complement activation on Alzheimer's - related neuropathology should have complete complement activation associated with senile plaques, neurofibrillary tangles (if present), and dystrophic neurites . Other desirable features include both classical and alternative pathway activation, increased neuronal synthesis of native complement proteins, and evidence for an increase in complement activation prior to the development of extensive pathology . In order to determine the suitability of different animal models for studying the role of complement activation in AD, the extent of complement activation and its association with neuropathology in these models must be understood.

Int Endod J, 2004 Nov, 37(11), 776 - 81
A scanning electron microscope study of plaque accumulation on silk and PVDF suture materials in oral mucosa; Parirokh M et al.; AIM: To examine plaque accumulation on silk and polyvinylidene fluoride (PVDF) sutures at different time intervals . METHODOLOGY: Twenty-one male albino rabbits received sutures under general and local anaesthesia . After 3, 5 and 7 days sutures were removed and processed for scanning electron microscope (SEM) observation . The Friedman and the Wilcoxon tests were used to compare contamination on PVDF and silk suture materials at different time intervals . RESULTS: At all time intervals, the whole surface of silk sutures was covered with a thick layer of bacterial plaque and debris . Microorganisms and blood cells on the surface and between the filaments of the silk suture material were observed . Light debris appeared around the knot area of PVDF sutures after 3 days . At 5 and 7 days, contamination could be seen in scattered areas along the suture material . The average contaminated area was smaller on PVDF suture materials, which were removed at 5 than at 7 days after insertion . At 3 days, PVDF sutures showed significantly less contamination than at 5 and 7 days (P = 0.002) . There were statistically significant differences between silk and PVDF sutures at 3, 5 and 7 days . CONCLUSION: SEM observation showed that PVDF sutures were contaminated less than silk sutures at 3, 5 and 7 days.

Mol Immunol, 2004 Nov, 41(11), 1089 - 98
Complement: a unique innate immune sensor for danger signals; Gasque P; The complement (C) inflammatory cascade is part of the phylogenetically ancient innate immune response and is crucial to our natural ability to ward off infection . It has three critical physiologic activities: (i) defending against microbial infections by triggering the generation of a membranolytic complex (C5b9 complex) at the surface of the pathogen and C fragments (named opsonins, i.e., C1q, C3b and iC3b) which interact with C cell surface receptors (CR1, CR3 and CR4) to promote phagocytosis . Soluble C anaphylatoxins (C4a, C3a and C5a) greatly control the local pro-inflammatory response through the chemotaxis and activation of leukocytes; (ii) bridging innate and adaptive immunity (essentially through C receptor type 2, CR2, expressed by B cells) and (iii) disposing of immune complexes and the products of the inflammatory injury (i.e., other danger signals, e.g., toxic cell debris and apoptotic corpses) to ensure the protection and healing of the host . The regulatory mechanisms of C are finely balanced so that, on the one hand, the deposition of C is focused on the surface of invading microorganisms and, on the other hand, the deposition of C on normal cells is limited by several key C inhibitors (e.g., CD46, CD55 and CD59) . Knowledge of the unique molecular and cellular innate immunological interactions that occur in the development and resolution of pathology should facilitate the design of effective therapeutic strategies to fight selectively against intruders.

Mol Immunol, 2004 Nov, 41(11), 1063 - 75
Infectious non-self recognition in invertebrates: lessons from Drosophila and other insect models; Royet J; The vertebrate innate immune system recognizes infectious non-self by employing a set of germline-encoded receptors such as nucleotide-binding oligomerisation domain proteins (NODs) or Toll-like receptors (TLRs) . These proteins are involved in the recognition of various microbial-derived molecules, including lipopolysaccharide (LPS), peptidoglycan (PGN) and beta1,3-glucan . Drosophila Toll receptors are not directly dedicated to non-self recognition and insect NOD orthologues have not yet been identified . Studies started more than 20 years ago and conducted on different insect models have identified other receptors on which invertebrate innate systems rely to sense invading microorganisms.

Mol Immunol, 2004 Nov, 41(11), 1055 - 62
Plant perception systems for pathogen recognition and defence; Gomez-Gomez L; Recognition of and defence against microbial infections are universal adaptations of multicellular organisms . Plants express a sophisticated molecular system for recognition of and response to potentially pathogenic microorganism . Although the environments of plant and animal cells are vastly different and present unique challenges to invading pathogens, the molecular basis of the innate immune response shows remarkable evolutionary conservation in both kingdoms . Even if more cellular components are continually being identified in plants, the mechanism, interactions and responses are only partly understood . Furthermore, most of this research has been performed in the model plant Arabidopsis thaliana and a significant effort will be needed to understand the above processes in crop species and in natural populations . In this review I will describe examples of the best characterized recognition systems in plants, that mediate pathogen perception either through the perception of highly variable and non-essential pathogen molecules or via conserved microbial structures called pathogen associated molecular patterns (PAMPs).

Nature, 2004 Nov 4, 432(7013), 104 - 7 Epub 2004 Oct 10.
Adaptive divergence in pigment composition promotes phytoplankton biodiversity; Stomp M et al.; The dazzling diversity of the phytoplankton has puzzled biologists for decades . The puzzle has been enlarged rather than solved by the progressive discovery of new phototrophic microorganisms in the oceans, including picocyanobacteria, pico-eukaryotes, and bacteriochlorophyll-based and rhodopsin-based phototrophic bacteria . Physiological and genomic studies suggest that natural selection promotes niche differentiation among these phototrophic microorganisms, particularly with respect to their photosynthetic characteristics . We have analysed competition for light between two closely related picocyanobacteria of the Synechococcus group that we isolated from the Baltic Sea . One of these two has a red colour because it contains the pigment phycoerythrin, whereas the other is blue-green because it contains high contents of the pigment phycocyanin . Here we report theory and competition experiments that reveal stable coexistence of the two picocyanobacteria, owing to partitioning of the light spectrum . Further competition experiments with a third marine cyanobacterium, capable of adapting its pigment composition, show that this species persists by investing in the pigment that absorbs the colour not used by its competitors . These results demonstrate the adaptive significance of divergence in pigment composition of phototrophic microorganisms, which allows an efficient utilization of light energy and favours species coexistence.

Phytochemistry, 2004 Oct, 65(20), 2803 - 7
Isolation of an alpha-methylene-gamma-butyrolactone derivative, a toxin from the plant pathogen Lasiodiplodia theobromae; He G et al.; Lasiodiplodia theobromae is known as a multi-infectious microorganism that causes considerable crop damage, particularly to tropical fruits . When the fruits are infected by L . theobromae, the typical symptom is the appearance of black spots on the surface of the infected fruit . When injected in to the peel of banana, the culture filtrate of L . theobromae induced formation of black spots . The structure of the isolated compound responsible for this effect was determined to be (3S,4R)-3-carboxy-2-methylene-heptan-4-olide on the basis of analysis of MS, IR, and 1H and 13C NMR spectroscopic data, including HMQC, HMBC, and 1H-1H COSY experiments . The active compound was not only isolated from the culture filtrate derived from potato dextrose medium, but also from the extract of infected peels of bananas.

Biochem Biophys Res Commun, 2004 Nov 12, 324(2), 840 - 8
Genetic and pharmacological inhibition of poly(ADP-ribose) polymerase-1 interferes in the chlamydial life cycle; Yelamos J et al.; Chlamydiaceae are intracellular bacteria responsible for a variety of infections, ranging from asymptomatic to very severe, in humans and animals . We have investigated the role of poly(ADP-ribose) polymerase-1 (PARP-1) in Chlamydophila abortus infection using PARP-1-/- and their littermates PARP-1+/+ mice . Infection was resolved more efficiently by PARP-1-/- than PARP-1+/+ mice . However, the inflammatory response was similar in both strains, suggesting a potential role for PARP-1 in the cross-talk between this microorganism and the host cells . PARP-1-/- fibroblasts showed a 10-fold lower rate of chlamydiae production than PARP-1+/+ . Moreover, a strong inhibition of bacterial production was also observed after pharmacological inhibition of PARP-1 activity in McCoy cells . Likewise, PARP-1 inhibition induced a higher level of cell death of infected cells, interfering in this way with the normal bacterial cell cycle . Overall, we identify PARP-1 as a new molecule involved in chlamydial developmental cycle, although the intrinsic mechanisms deserve further studies.

Annu Rev Cell Dev Biol, 2004, 20, 367 - 94
Cell biology of mycobacterium tuberculosis phagosome; Vergne I et al.; Phagocytosis and phagolysosome biogenesis represent fundamental biological processes essential for proper tissue homeostasis, development, elimination of invading microorganisms, and antigen processing and presentation . Phagosome formation triggers a preprogrammed pathway of maturation into the phagolysosome, a process controlled by Ca2+ and the regulators of organellar trafficking centered around the small GTP-binding proteins Rabs and their downstream effectors, including lipid kinases, organellar tethering molecules, and membrane fusion apparatus . Mycobacterium tuberculosis is a potent human pathogen parasitizing macrophages . It interferes with the Rab-controlled membrane trafficking and arrests the maturing phagosome at a stage where no harm can be done to the pathogen while the delivery of nutrients and membrane to the vacuole harboring the microorganism continues . This process, referred to as the M . tuberculosis phagosome maturation arrest or inhibition of phagosome-lysosome fusion, is critical for M . tuberculosis persistence in human populations . It also provides a general model system for dissecting the phagolysosome biogenesis pathways . Here we review the fundamental trafficking processes targeted by M . tuberculosis and the mycobacterial products that interfere with phagosomal maturation.

Biotechnol Bioeng, 2004 Dec 5, 88(5), 671 - 4
Unexpected distribution of immobilized microorganisms within alginate beads; Zohar-Perez C et al.; Immobilization refers to the prevention of free cell movement by natural or artificial means . It has always been assumed that immediately after an immobilization procedure is performed, cells are distributed homogeneously in the beads that entrap them . However, in this study, Escherichia coli and Trichoderma asperellum distribution in alginate-gel beads was found to be nonhomogeneous . In fact, there was a greater presence of cells on the surface of the alginate beads than in their cores.

J Biomed Mater Res, 2004 Dec 1, 71A(3), 419 - 29
Cytokine secretion from mononuclear cells cultured in vitro with starch-based polymers and poly-L-lactide; Marques AP et al.; The cytokine network is one of the major controlling systems of the inflammatory process, driving the magnitude and duration of the host response against invading microorganisms, foreign materials, or altered internal stimuli . Pro- and antiinflammatory cytokines were quantified after in vitro culture of a mixed population of monocytes/macrophages and lymphocytes with biodegradable polymers . Different blends of starch-based polymers and their composites filled with hydroxyapatite were studied and compared with poly-L-lactide . Interleukin (IL)-1beta, IL-6, and tumour necrosis factor-alpha were investigated as the markers of immunological reactivity because they are known to act at the early stages of injury/invasion . Interferon-gamma, recognized as a proinflammatory cytokine, although not present during early responses was also investigated . Contrarily, IL-4 derived from T lymphocytes, was investigated because it is an immunoregulator that counteracts some aspects of inflammation . T lymphocyte activation was also determined by quantifying IL-2 . The results support the hypothesis that different biodegradable polymers can affect mononuclear cell activation and the production of several cytokines associated with the inflammatory process . No IL-2 or interferon-gamma was found in the culture supernatants after 3, 7, and 14 days in the presence of any of the materials . IL-6 was detected in the highest amounts, for all the conditions, followed by tumour necrosis factor-alpha . IL-1beta was produced in very low amounts, being undetectable with some of the starch-based materials . IL-4 was the only cytokine that did not demonstrate any significant difference within this group of materials . Starch-based polymers and composites induced lower production of proinflammatory cytokines in comparison to poly-L-lactide.

Clin Infect Dis, 2004 Oct 1, 39(7), 980 - 6 Epub 2004 Sep 10.
Clinical predictors of bacterial involvement in exacerbations of chronic obstructive pulmonary disease; van der Valk P et al.; BACKGROUND: The wide use of antibiotics for treatment of exacerbations of chronic obstructive pulmonary disease (COPD) lacks evidence . The efficacy is debatable, and bacterial involvement in exacerbation is difficult to verify . The aim of this prospective study was to identify factors that can help to estimate the probability that a microorganism is involved in exacerbation of COPD and, therefore, predict the success of antibiotic treatment . METHODS: Clinical data and sputum samples were obtained from 116 patients during exacerbation of COPD . Bacterial infection was defined by the abundant presence of >or=1 potential pathological microorganism in relation to the normal flora in sputum . RESULTS: Of 116 exacerbations, 22 (19%) had bacterial involvement . The combination of a negative result of a sputum Gram stain, a relevant nonclinical decrease in lung function (compared with baseline measurements), and occurrence of <2 exacerbations in the previous year were 100% predictive of a nonbacterial origin of the exacerbation . The presence of all 3 of these clinical characteristics yielded a positive predictive value of 67% for a bacterial exacerbation . CONCLUSIONS: Patients presenting with an exacerbation who have a negative result of a sputum Gram stain, do not have a clinically relevant decrease in lung function, and who have not experienced <2 exacerbations of COPD in the previous year do not require antibiotic treatment . A treatment protocol taking into account these variables might lead to a 5%-24% reduction in unnecessary treatment with antibiotics, depending on actual prescription rates.

J Clin Microbiol, 2004 Oct, 42(10), 4893 - 6
Mitral bioprosthetic valve endocarditis caused by an unusual microorganism, Gemella morbillorum, in an intravenous drug user; Zakir RM et al.; We report a case of Gemella morbillorum mitral bioprosthetic valve endocarditis with perivalvular extension in a 44-year-old human immunodeficiency virus-positive man who is an active intravenous drug user together with review of all published cases . This is only the second reported case of Gemella morbillorum endocarditis in a patient with a prosthetic valve.

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