J Clin Microbiol, 2004 Oct, 42(10), 4530 - 5 Nocardia mexicana sp . nov., a new pathogen isolated from human mycetomas; Rodriguez-Nava V et al.; Three isolates collected from human mycetomas and showing an unusual brownish purple pigmentation on Bennett agar plates were analyzed by a polyphasic taxonomic approach, including morphological, biochemical, physiological, and chemotaxonomic properties coupled with genomic and phylogenetic analysis . It clearly appeared that these microorganisms were distinct from their closest phenotypic and genetic match, the most related species according to 16S rRNA gene sequence analysis being Nocardia pseudobrasiliensis . The data obtained indicated that the three clinical strains should be recognized as a new species for which the name Nocardia mexicana sp . nov . is proposed. J Biol Chem, 2004 Dec 17, 279(51), 53078 - 86 Epub 2004 Oct 07. Five histidine kinases perceive osmotic stress and regulate distinct sets of genes in Synechocystis; Paithoonrangsarid K et al.; Microorganisms respond to hyperosmotic stress via changes in the levels of expression of large numbers of genes . Such responses are essential for acclimation to a new osmotic environment . To identify factors involved in the perception and transduction of signals caused by hyperosmotic stress, we examined the response of Synechocystis sp . PCC 6803, which has proven to be a particularly useful microorganism in similar analyses . We screened knockout libraries of histidine kinases (Hiks) and response regulators (Rres) in Synechocystis by DNA microarray and slot-blot hybridization analyses, and we identified several two-component systems, which we designated Hik-Rre systems, namely, Hik33-Rre31, Hik34-Rre1, and Hik10-Rre3, as well as Hik16-Hik41-Rre17, as the transducers of hyperosmotic stress . We also identified Hik2-Rre1 as a putative additional two-component system . Each individual two-component system regulated the transcription of a specific group of genes that were responsive to hyperosmotic stress. Trends Parasitol, 2004 Nov, 20(11), 508 - 11 The surface-mosaic model in host-parasite relationships; Mejia JS et al.; The dynamics of protein adsorption to a microbial surface could be of significance in host-parasite relationships because non-defense proteins might interfere with the binding of defense proteins . A surface mosaic of defense and non-defense proteins formed on the microbial surface could activate one of the tissue reactivity programs via a binary code (help or silence) generated by the adsorbed proteins . Understanding the mechanisms of the mosaic formation and its evolution might help to identify evasion mechanisms used by virulent microorganisms . This also provides a conceptual framework to design new strategies to control the infectious diseases they cause. Int J Hyg Environ Health, 2004 Sep, 207(4), 363 - 8 Well water--one source of Helicobacter pylori colonization; Rolle-Kampczyk UE et al.; Helicobacter pylori (H . pylori) is one of the world's most widespread microorganisms . Its acquisition in humans remains poorly understood, however, epidemiological studies have identified drinking water as reservoir for the bacterium . The aim of this study was to investigate the prevalence of H . pylori infection among individuals using or drinking previously H . pylori tested well water . Applying household cluster sampling, a total of 91 subjects, all using or drinking well water (13 of either H . pylori positive or negative wells), were screened for their H . pylori status . The group was comprised of 73 adults and 19 children under the age of 18 . H . pylori infection was determined using the {13C}urea breath test . A self-administered or parent-completed questionnaire provided information on living conditions and lifestyle habits including the use or drinking of well water . Logistic regression analyses associated the drinking of H . pylori positive well water with a positive colonization status {Odds Ratio (OR) 8.3; 95% confidence interval (95% CI) 2.4-29} . In summary, the use or drinking of H . pylori contaminated well water appears associated with the acquisition of a H . pylori infection . This study is based on a relatively small and inhomogeneous population sample and should be repeated to confirm the results. Rev Argent Microbiol, 2004 Apr-Jun, 36(2), 81 - 4 {Bacteremia by Brucella canis . Isolation with the Bact-Alert system}; Soloaga R et al.; Brucella canis and other species of the genus Brucella can cause human disease . However, this species infrequently cause human disease, including in countries where dogs population is highly infected . A 15 years old male was admitted to the hospital with 15 days history of fever without visible focus . Physical examination revealed pain at liver palpation and axillar, cervical and inguinal lymphoadenomegalies . Abdominal ultrasonography showed spleenomegally, the chest Rx and the trans thoracic echocardiogram were normal . Five blood samples were obtained and cultured in 2 standards bottles (time of positivization 72 - 64.8 hours), and 3 pediatric FAN bottles (time of positivization 74.5; 72 and 67.2 hours) (Bact-Alert system, Biomerieux, Marcy, l'Etolie, France) . The microorganism was presuntive identified as B . canis, and then was confirmed in the National Reference Center Instituto ANLIS "Carlos G . Malbran" . After 14 days of initiating ceftriaxone treatment the patient was afebrile . When the confirmation of Brucella was made, he was discharged and ambulatory was prescribed with doxycycline and rifampin for 21 days . Bones were not compromised and the outcome was good with complete resolution of his illness. Cell Microbiol, 2004 Nov, 6(11), 1011 - 8 Immunity to vacuolar pathogens: what can we learn from Legionella? Neild AL, Roy CR. Intracellular pathogens can manipulate host cellular pathways to create specialized organelles . These pathogen-modified vacuoles permit the survival and replication of bacterial and protozoan microorganisms inside of the host cell . By establishing an atypical organelle, intracellular pathogens present unique challenges to the host immune system . To understand pathogenesis, it is important to not only investigate how these organisms create unique subcellular compartments, but to also determine how mammalian immune systems have evolved to detect and respond to pathogens sequestered in specialized vacuoles . Recent studies have identified genes in the respiratory pathogen Legionella pneumophila that are essential for establishing a unique endoplasmic reticulum-derived organelle inside of mammalian macrophages, making this pathogen an attractive model system for investigations on host immune responses that are specific for bacteria that establish vacuoles disconnected from the endocytic pathway . This review will focus on the host immune response to Legionella and highlight areas of Legionella research that should help elucidate host strategies to combat infections by intracellular pathogens. AIDS Patient Care STDS, 1998 Sep, 12(9), 691 - 6 Reliability of laboratory markers of HIV-1 infection in Argentinian infants at risk of perinatal infection; Mangano A et al.; Early and accurate diagnosis of HIV-1 infection in infants born to HIV-1-seropositive mothers is of great importance . Polymerase chain reaction (PCR), HIV culture, and p24 antigen detection assays were evaluated for their ability to detect the presence of HIV in 195 infants at risk of perinatal infection . Using the Centers for Disease Control and Prevention guidelines for assessing HIV infection status in children younger than 18 months, 70 infants (36%) were diagnosed as HIV-1 infected and 125 (64%) lacked virologic and clinical evidence of infection . PCR and HIV culture were the most sensitive laboratory markers, detecting 100% and 98% of positive samples, respectively, regardless of age at testing . HIV-1 p24 antigen assay was detected in 26 of 38 positive samples but not in negative samples . PCR was performed with three different sets of primers (SK38/SK39-SK19-gag, SK68/SK69-SK70-env, and SK150/SK431-SK102-gag) . The sensitivity/specificity of the individual assays were for SK19, 96.1%/94.25%; SK70, 89.6%/100%; and SK102, 100%/100% . A sample was considered HIV-1 positive when two positive PCR results were obtained with two different pairs of primers, and negative if the sample was negative when three sets of primers were used . False-positive results were occasionally obtained with probe SK19 in six seroreverter infants before serologic status was known . This suggested that the infection was caused by nonreplicative strains or were false-positive results probably by nonspecific amplification due to cross-reaction with other microorganisms; contamination was discarded because there was no specific amplification with the other two primers . All the HIV-1-infected infants were correctly identified with PCR; all except one could be identified with coculture and only 68.4% were confirmed with p24 antigen assay . No seroreverter infant was misdiagnosed using the criteria selected. Macromol Biosci, 2004 Apr 19, 4(4), 399 - 406 The biodeterioration of synthetic resins used in conservation; Cappitelli F et al.; Synthetic resins have been extensively employed by artists in their works of art, e.g . as paint binders, or by conservators for conservation treatments, e.g . as stone consolidants and protectives . It is generally thought that synthetic resins are less prone to chemical, physical and biological deterioration than other organic products but there are many articles in the scientific literature and some reports in the conservation of cultural heritage literature claiming that microorganisms are capable of degrading synthetic resins . This paper reviews the researches on the biodeterioration of synthetic resins used in the conservation of cultural heritage, including stone, painting and textile materials, carried out in the last fifty years. Macromol Biosci, 2004 Mar 15, 4(3), 166 - 74 Microbial polythioesters; Lutke-Eversloh T et al.; This feature article describes the current knowledge on biosynthesis of polythioesters (PTEs), which are exclusively accumulated by microorganisms capable to synthesize the well-known polyhydroxyalkanoates (PHAs) . Two bacterial PTE biosynthesis systems are discussed, both are depending on the cultivation conditions and appropriate feeding regimes . The first system comprises the production of PTE copolymers by Ralstonia eutropha, and the second system has been established in recombinant Escherichia coli to produce PTE homopolymers . Furthermore, synthetic PTEs and other related sulfur containing biopolymers are briefly summarized. Macromol Biosci, 2004 Feb 20, 4(2), 112 - 8 Direct visualization of straw cell walls by AFM; Yan L et al.; The structural relationship of cellulose, hemicellulose, and lignin in plant cell walls is still a mystery needing to be explored . By using atomic force microscopy (AFM) the surface of straw at different layers was directly observed, and the structural characteristics were analyzed by topographic analysis and FT-IR spectra . It was found that a compact layer of wax covered the outside of the straw, which protects the straw from insects and microorganisms . At the boundary of the primary and second wall there appears a network structure of cellulose and hemicellulose, with some lignin localised on the surface of the network . It is consistent with the model of a cell wall suggested by Vincent . Inside the second cell wall, there is a layer mainly composed of a cellulose crystalline region . High-resolution AFM observation reveals that the crystalline structure consists of both triclinic and monoclinic unit cells.An AFM phase image showing the structural relation between cellulose microfibrils, hemicellulose, and lignin in the straw cell wall. Can J Microbiol, 2004 Aug, 50(8), 615 - 21 Molecular and physiological comparisons between Saccharomyces cerevisiae and Saccharomyces boulardii; Fietto JL et al.; In this paper, comparative molecular studies between authentic Saccharomyces cerevisiae strains, related species, and the strain described as Saccharomyces boulardii were performed . The response of a S . boulardii strain and a S . cerevisiae strain (W303) to different stress conditions was also evaluated . The results obtained in this study show that S . boulardii is genetically very close or nearly identical to S . cerevisiae . Metabolically and physiologically, however, it shows a very different behavior, particularly in relation to growth yield and resistance to temperature and acidic stresses, which are important characteristics for a microorganism to be used as a probiotic. Can J Microbiol, 2004 Aug, 50(8), 521 - 77 Azospirillum-plant relationships: physiological, molecular, agricultural, and environmental advances (1997-2003); Bashan Y et al.; This review presents a critical and comprehensive documentation and analysis of the developments in agricultural, environmental, molecular, and physiological studies related to Azospirillum cells, and to Azospirillum interactions with plants, based solely on information published between 1997 and 2003 . It was designed as an update of previous reviews (Bashan and Levanony 1990; Bashan and Holguin 1997a), with a similar scope of interest . Apart from an update and critical analysis of the current knowledge, this review focuses on the central issues of Azospirillum research today, such as, (i) physiological and molecular studies as a general model for rhizosphere bacteria; (ii) co-inoculation with other microorganisms; (iii) hormonal studies and re-consideration of the nitrogen contribution by the bacteria under specific environmental conditions; (iv) proposed Azospirillum as a non-specific plant-growth-promoting bacterium; (v) re-introduction of the "Additive Hypothesis," which suggests involvement of multiple mechanisms employed by the bacteria to affect plant growth; (vi) comment on the less researched areas, such as inoculant and pesticide research; and (vii) proposes possible avenues for the exploitation of this bacterium in environmental areas other than agriculture. Am J Obstet Gynecol, 2004 Sep, 191(3), 762 - 6 Altered distribution of mannose-binding lectin alleles at exon I codon 54 in women with vulvar vestibulitis syndrome; Babula O et al.; OBJECTIVES: Mannose-binding lectin (MBL) is active in the innate immune defense against microorganisms . In this study, we determined whether vulvar vestibulitis syndrome, a disorder of unknown etiology, was associated with an altered distribution of MBL alleles . STUDY DESIGN: Buccal swabs were obtained from women with vulvar vestibulitis syndrome in New York (62) and from 2 cities in Sweden (60), as well as control women in New York (48) and Sweden (51) . DNA was tested for a single nucleotide polymorphism at codon 54 in exon I by polymerase chain reaction, endonuclease digestion, and gel electrophoresis . Blood samples were also obtained from the New York women and tested by ELISA for plasma MBL concentrations . The relationships between genotype, allele frequencies, blood MBL levels, and diagnosis were analyzed by Fisher exact test and one-way analysis of variance . RESULTS: The variant MBL allele, MBL*B, was detected in 35.5% and 26.7% of vulvar vestibulitis patients from New York and Sweden, respectively . Only 12.5% of New York controls (P=.007) and 9.8% of Swedish controls (P=.01) were MBL*2-positive . All women, with one exception, who were positive for MBL*B were MBL*A/MBL*B heterozygotes . Women who carried MBL*B had almost a 10-fold reduction in median plasma MBL concentrations (278 ng/mL), as opposed to women who were MBL*A homozygotes (1980 ng/mL) (P < .0001) . CONCLUSION: MBL*B carriage and reduced plasma MBL levels are more common in women with vulvar vestibulitis syndrome than in control patients, and may contribute to symptomatology in a subset of patients. J Bone Joint Surg Am, 2004 Oct, 86-A(10), 2305 - 18 Osteomyelitis in long bones; Lazzarini L et al.; Osteomyelitis in long bones remains challenging and expensive to treat, despite advances in antibiotics and new operative techniques . Plain radiographs still provide the best screening for acute and chronic osteomyelitis . Other imaging techniques may be used to determine diagnosis and aid in treatment decisions . The decision to use oral or parenteral antibiotics should be based on results regarding microorganism sensitivity, patient compliance, infectious disease consultation, and the surgeon's experience . A suppressive antibiotic regimen should be directed by the results of cultures . Standard operative treatment is not feasible for all patients because of the functional impairment caused by the disease, the reconstructive operations, and the metabolic consequences of an aggressive therapy regimen . Operative treatment includes debridement, obliteration of dead space, restoration of blood supply, adequate soft-tissue coverage, stabilization, and reconstruction. Appl Environ Microbiol, 2004 Oct, 70(10), 5912 - 5 Evaluation of methods for storage of marine macroorganisms with optimal recovery of bacteria; Siebert K et al.; Marine macroorganisms are a potential source for new bioactive substances . In many cases marine microorganisms--especially bacteria--associated with these macroorganisms are actually producing the bioactive substances . One often is not able to immediately isolate microorganisms from collected macroorganismic materials; we therefore evaluated different methods for storage of such material, e.g., on board research vessels . These methods were the following: storage of macerates in sintered glass beads and 5% trehalose at -20 degrees C (SGT method); storage of sections in 5% dimethyl sulfoxide at -70 degrees C (SD method); storage of macerates at -20 degrees C using the commercial ROTI-STORE system (RS method); storage of macerates at -20 degrees C in 50% glycerol (GC method); and storage of macerates covered by mineral oil at 4 degrees C (MO method) . The SGT and SD methods resulted in numbers of and especially diversity of recoverable bacteria that were higher than for the other methods . Data for the RS method indicated its potential usefulness, too . The MO method resulted in growth during storage, thereby enriching a few selected microorganisms; the GC method resulted in a survival and diversity of recovered bacteria that was too low. Toxicology, 2004 Dec 15, 205(3), 181 - 94 Risk potentials for humans of original and remediated PAH-contaminated soils: application of biomarkers of effect; Roos PH et al.; Contaminated soils represent a potential health risk for the human population . Risk assessment for humans requires specific methods, which must reflect the peculiarities of human behaviour, physiology and biochemistry with respect to contaminant uptake and processing . Biomarkers of effect or exposure have become an appropriate tool . Organic pollutants influence the expression profile of cytochromes P450 (CYP), and CYP1A1 has been shown to be a suitable biomarker for polycyclic aromatic hydrocarbons (PAH) . The latter are widely distributed in soils and constitute an important soil contamination . Upon intake of PAH-contaminated soils, CYP1A1 is induced in various organs of rats and minipigs . Increased CYP1A1-levels in lung, kidney and spleen, after oral soil intake, indicate that contaminants escape the primary duodenal and hepatic metabolism and reach further organs . Dose-response relationships reveal that induction effects are to be expected in children based on known exposure conditions . Generally, CYP1A1-induction does not correlate with results of toxicity tests with lower organisms, performed with the same soils . The organic carbon content is largely responsible for this discrepancy . It severely affects the toxicity of soil bound PAH for microorganisms, but obviously affects the mobilization efficiency for PAH in the gastro-intestinal tract of mammals to a minor extent . Soil remediation by different methods may result in a significant reduction of the PAH content and of toxicity . Ingestion of remediated soils by rats shows, however, that the induction potential for CYP1A1 is only slightly decreased after remediation . This means that the major inducing components resist biological remediation or soil washing and remain in the soil . Because data obtained with experimental animals form the guiding principle for in vitro tests to be developed, the suitability of the animal model used for extrapolations to humans has to be proven . Upon soil ingestion, minipigs show a tissue-specific response pattern, which substantially differs from that of rats, which are widely used as animal models . It is not known which response pattern resembles that of man . In summary, cytochromes P450, in particular CYP1A1, are suitable biomarkers to assess the bioavailability of soil bound contaminants and their effects on mammalian species . There are, however, a number of questions to be answered in order to develop an in vitro test for human risk assessment . This concerns, for example, the identification of the suitable animal model, the identification of biomarkers for other contaminants and concepts to transpose the in vivo data to in vitro technologies or to mathematical modelling. Parasitol Today, 1991, 7(9), 228 - 32 Towards a population genetics of microorganisms: The clonal theory of parasitic protozoa; Tibayrenc M et al.; Over the past 15 years, molecular investigations, including the study of isozymes and DNA markers, have provided much information on the genetic variation, population structure, breeding system and other population characteristics of parasitic protozoa . For some parasitic protozoa, but not for others, the evidence indicates that their reproduction is prevailingly clonal . In this article, Michel Tibayrenc and Francisco Ayala propose that the issue of whether the predominant mode of reproduction of a given micro-organism is clonal or sexual can only be settled by population genetics information, and they summarize evidence favoring a clonal population structure for a number of parasitic protozoa. Microbiol Res, 2004, 159(3), 305 - 14 Purification and biochemical characterization of polygalacturonase II produced in semi-solid medium by a strain of Fusarium moniliforme; Niture SK et al.; A strain of Fusarium moniliforme isolated from a tropical mangrove ecosystem near Mumbai, India and deposited in the National Collection of Industrial Microorganisms (NCIM) as F . moniliforme NCIM 1276 . The organism produced a single extracellular polygalacturonase (PG I) {EC 3.2.1.15} at pH 5 and a single pectate lyase (PL) {EC 4.2.2.2} at pH 8 in liquid medium containing 1% citrus pectin . Growth on semi-solid medium containing wheat bran and orange pulp resulted in a three-fold increase in PG production and a two-fold increase in PL production in comparison with that in liquid medium . The increased production of PG on semi-solid media, as compared to production in liquid media was investigated . The increased production of PG was partly due to the expression of a second polygalacturonase (PG II) isoenzyme by the fungus which was biochemically different from the one produced in liquid medium . The second PG II was a 30.6kDa enzyme, had an alkaline pI of 8.6, the Km was 0.166mg ml(-1), Vmax 13.33 micromol min(-1) mg(-1) and the kcat was 403 min(-1) . It had a specific activity of 18.66U mg(-1) . The differences between the PGs (PG I and PG II) suggest that the two enzymes are the products of different genes . The fungus also produced the same two PGs when it infected Lycopersicon esculentum (tomato) . Only one PL was produced irrespective of growth conditions. New Microbiol, 2004 Jul, 27(3), 235 - 48 Use of simulated blood cultures for antibiotic effect on time to detection of the two blood culture systems BacT/ALERT and BACTEC 9240; Vigano EF et al.; To avoid the influence of pre-analytical steps, this study was performed using sterile blood spiked with defined loads of microorganisms as inoculum . Time-to-Detection (TTD) was evaluated for the most frequently encountered bacteria comparing two commercially available blood culture systems, BD BACTEC 9240 (Becton Dickinson) and BacT/ALERT (Organon Teknika) . The effect of the most widely used antibiotics on TTD was evaluated on both systems . TTD was measured with antibiotics at their trough and at increasing concentrations . The results show that the BACTEC PLUS system recovers more pathogens with shorter time to detection than the BacT/ALERT FAN system when beta-lactam antibiotics (Ampicillin, Cefotaxime) are present at their respective trough concentration corresponding to parenteral therapy . The two systems seem to be equally efficient when Gentamicin, Ciprofloxacin and Trimethoprim/sulfamethoxazole are used; in the case of Vancomycin, BACTEC seems more effective than BacT/ALERT. Prog Lipid Res, 2004 Sep, 43(5), 403 - 48 Arsenolipids; Dembitsky VM et al.; Natural arsenolipids are analogues of neutral lipids, like monoglycerides, glycolipids, phospho- and also phosphonolipids . They have been found in microorganisms, fungi, plants, lichens, in marine mollusks, sponges, other invertebrates, and in fish tissues . This review presented structures of natural arsenolipids (and derivatives), their distribution, biogenesis in algae and invertebrates, synthesis, and also biological activity . Arsenolipids are thought to be end products of arsenate detoxification processes, involving reduction and oxidative methylation and adenosylation . The proposed biogenesis of arsenolipids is based on the natural occurrence of arsenic metabolites, and all the intermediates in the proposed pathway have been identified as natural products of algal origin . Different arseno species are shown to be inhibitors of glycerol kinase, bovine carbonic anhydrase, and also is an effective therapy for acute promyelocytic leukemia, and there has been promising activity noted in other hematologic and solid tumors . Arsonoliposomes demonstrated high anti-trypanosomal activity against Trypanosoma brucei and inhibit growth of some types of cancer cells (HL-60,C6 and GH3). Rev Iberoam Micol, 2004 Mar, 21(1), 10 - 4 Is there a role for antibody testing in the diagnosis of invasive candidiasis? Quindos G, Moragues MD, Ponton J. During the last decades, the use of antibody tests for the diagnosis of invasive mycoses has declined as a consequence of the general belief that they are insensitive and non-specific . However, there is a clear evidence that antibodies can be detected in highly immunodeficient patients (such as bone marrow transplant recipients), and that those antibodies are useful for the diagnosis . Antibody tests are currently in use as diagnostic tools for some primary mycoses, such as the endemic mycoses, aspergilloma, allergic bronchopulmonary aspergilosis and sporothrichosis . For invasive candidiasis, diagnostic methods must differentiate Candida colonization of mucous membranes or superficial infection from tissue invasion by this microorganism . Substantial progress has been made in diagnosis of invasive candidiasis with the development of a variety of methods for the detection of antibodies and antigens . However, no single test has found widespread clinical use and there is a consensus that diagnosis based on a single specimen lacks sensitivity . It is necessary to test sequential samples taken while the patient is at greatest risk for developing invasive candidiasis to optimize the diagnosis . Results obtained from a panel of diagnostic tests in association with clinical aspects will likely be the most useful strategy for early diagnosis and therapy. Analyst, 2004 Oct, 129(10), 963 - 9 Epub 2004 Aug 19. Developing rapid detection of mycobacteria using microwaves; Jing G et al.; In this paper, we describe the development of a culture-based biochip device for rapid detection of mycobacteria in environmental samples . Individual biochips rely upon the unique paraffinophilic nature of mycobacteria to rapidly and selectively adhere to the surface of the device . We used prototype biochips to experimentally demonstrate the concept of rapid and selective detection of mycobacteria by testing pure cultures and using epifluorescence microscopy to visualize microorganisms on the surface . As an alternative, rapid approach for identifying the biomass on the biochip surface, we used microwaves in the 10 to 26 GHz frequency range . The results of this study indicate that different microorganisms are responsible for specific shifts in resonance frequencies of a microwave cavity . By combing the semi-selective paraffin surface of the biochip with the microorganism-specific response to the microwaves, we have developed an improved analytical system with the potential to rapidly identify and enumerate mycobacteria in environmental samples in as little as 2 h. Anal Chem, 2004 Oct 1, 76(19), 5769 - 76 Proteomic profiling of intact mycobacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; Hettick JM et al.; Current methods for the identification of mycobacteria in culture are time-consuming, requiring as long as 12 weeks for positive identification . One potential approach to rapid mycobacterial identification is to utilize proteomic profiling of cultures by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) . In this report, we have applied MALDI-TOF MS to proteomic profiling of cultured microorganisms representing six species of the genus Mycobacterium . We find that analysis of acetonitrile/trifluoroacetic acid cellular extracts produces data similar to that of the analysis of deposited whole cells, while minimizing human contact with the microorganisms and rendering them nonviable . A matrix composition of alpha-cyano-4-hydroxycinnamic acid with fructose yields highly reproducible MALDI-TOF spectra . Statistical analysis of MALDI-TOF MS data allows differentiation of each individual mycobacterial species on the basis of unique mass fingerprints . The methodology allows identification of a number of unique (potentially diagnostic) biomarkers as targets for protein identification by MS/MS experiments . In addition, we observe a number of signals common to all mycobacterial species studied by MALDI-TOF MS, which may be genus-specific biomarkers . The potentially genus-specific biomarkers occur at low mass (<2 kDa) and are likely to be lipids and cell wall components such as mycolic acids . This study demonstrates the potential for mass spectrometry-based identification/classification of mycobacteria. Prikl Biokhim Mikrobiol, 2004 Jul-Aug, 40(4), 455 - 9 {Microorganisms of Lake Baikal and Lake Nyasa as indicators of anthropogenic influence: prospects of use in biotechnology}; Verkhozina VA et al.; Restriction endonucleases (RENs) were detected in 650 microbial strains isolated from water columns and bottom sediments of deep rift lakes, Baikal (Russia) and Nyasa (Southeastern Africa) . They enzymes included unique (Fan I, Aca I, and Sse 91) and very rare (Bsi I, and Cci N I) species not typical of aquatic ecosystems . Water columns, deep cores, and bottom sediments of pure areas of the lakes contained no microorganisms with new RENs . Thus, inshore areas of Lake Baikal exposed to anthropogenic influence may contain mutant bacterial strains expressing RENs that have not been described previously. Free Radic Biol Med, 2004 Nov 1, 37(9), 1412 - 8 Effect of endocrine disruptor para-nonylphenol on the cell growth and oxygen radical generation in Escherichia coli mutant cells deficient in catalase and superoxide dismutase; Okai Y et al.; para-Nonylphenol (NP) had previously been found to have strong suppressive effects of growth of bacterial and yeast cells, and these effects were associated with NP-induced generation of radical oxygen species (ROS) . In the present study, we determined that wild-type strains of Escherichia coli (CSH 7, SY-11, and IFO-3545) were resistant to NP compared with other sensitive microorganisms reported previously . To elucidate the relationship between NP-induced ROS generation and cell growth inhibition in more detail, we analyzed the effect of NP on cell growth and survival of wild-type and mutant E . coli strains deficient in ROS-scavenging enzymes such as catalase and superoxide dismutase (SOD) . The SOD-deficient strain QC 774 (sod A- and sod B-) was much more sensitive to NP than wild-type (CSH 7) and catalase-deficient (UM 1 kat E- and kat G-) strains . As a comparative experiment, when hydrogen peroxide was applied to the same growth and survival assays, UM 1 cells were more sensitive to hydrogen peroxide than QC 774 and CSH 7 . A chemiluminescence (CHL) experiment using MCLA (2-methyl-6-Lf-methylphenyl}-3,7-dihydroimidazc {1,2-alpha} pyrazin-3-one) reflecting predominantly superoxide generation showed that NP caused marked CHL generation in QC 774 cells, but not in CSH 7 and UM 1 cells . However, the CHL experiment using L-012 reflecting predominantly hydroxyl radical and hypochlorite did not exhibit significant CHL generation in QC 774 cells at the same concentrations of NP . Furthermore, supplementation with SOD prevented NP-induced ROS generation and cell survival inhibition of QC 774 cells, but the catalase and metal-chelating agent deferoxamine did not have significant effects . These results suggest that one of the primary actions of NP in cells is the generation of superoxide which may be responsible for NP-induced cell growth inhibition. Bioorg Med Chem Lett, 2004 Nov 1, 14(21), 5423 - 6 Microbial oxidation of terfenadine and ebastine into fexofenadine and carebastine; Mazier C et al.; The oxidation of tert-butyl-phenyl group of title compounds by some microorganisms was studied . We have optimized the conditions of culture to increase the formation of acid metabolites and to avoid the formation of side products . We showed that an oxidative activity is induced by soybean peptones in Streptomyces platensis . The biologically active compounds, fexofenadine and carebastine, are produced in good yield (86-95%) by Absidia corymbifera. J Food Prot, 2004 Sep, 67(9), 1977 - 90 Effect of chemicals on the microbial evolution in foods; Devlieghere F et al.; In contrast with most chemical hazardous compounds, the concentration of food pathogens changes during processing, storage, and meal preparation, making it difficult to estimate the number of microorganisms or the concentration of their toxins at the moment of ingestion by the consumer . These changes are attributed to microbial proliferation, survival, and/or inactivation and must be considered when exposure to a microbial hazard is assessed . The number of microorganisms can also change as a result of physical removal, mixing of food ingredients, partitioning of a food product, or cross-contamination (M . J . Nauta . 2002 . Int . J . Food Microbiol . 73:297-304) . Predictive microbiology, i.e., relating these microbial evolutionary patterns to environmental conditions, can therefore be considered a useful tool for microbial risk assessment, especially in the exposure assessment step . During the early development of the field (late 1980s and early 1990s), almost all research was focused on the modeling of microbial growth over time and the influence of temperature on this growth . Later, modeling of the influence of other intrinsic and extrinsic parameters garnered attention . Recently, more attention has been given to modeling of the effects of chemicals on microbial inactivation and survival . This article is an overview of different applied strategies for modeling the effect of chemical compounds on microbial populations . Various approaches for modeling chemical growth inhibition, the growth-no growth interface, and microbial inactivation by chemicals are reviewed. J Food Prot, 2004 Sep, 67(9), 1967 - 71 ComBase: a common database on microbial responses to food environments; Baranyi J et al.; The advancement of predictive microbiology relies on available data that describe the behavior of microorganisms in different environmental matrices . For such information to be useful to the predictive microbiology research community, data must be organized in a manner that permits efficient access and data retrieval . Here, we describe a database protocol that encompasses observations of bacterial responses to food environments, resulting in a database (ComBase) for predictive microbiology purposes . The data included in ComBase were obtained from cooperating research institutes and from the literature and are publicly available via the Internet. J Dairy Sci, 2004 Jun, 87(6), 1627 - 33 Partial characterization of dextran-degrading enzyme obtained from blue cheese; Wang Y et al.; Degradation of dextran beads was observed when the water-soluble fraction of a blue cheese extract was applied to the top of a Sephadex G-150 or G-200 column . This phenomenon suggests the presence of a specific enzyme that can hydrolyze dextran . After removal of casein components from the blue cheese fraction, ammonium sulfate treatment and gel filtration chromatography were performed to isolate the enzyme fraction . The enzymatic products were analyzed by thin-layer chromatography and gel filtration chromatography and identified as isomaltooligosaccharides . The isoelectric point of this enzyme fraction was approximately 4.9, as determined by isoelectric focusing using Rotofor, and the molecular weight of the fraction was 65 kDa, as estimated by sodium dodecyl sulfate (SDS)-PAGE . Optimum pH for enzymatic activity was 5.0 to 5.3 . A partial N-terminal amino acid sequence of 20 residues was determined to be ATPDEWRSRSIYFMLTDRGA from an enzyme fraction further purified by ion-exchange chromatography and native PAGE . This sequence showed a maximum homology of 80% with alpha-amylase or Taka amylase that originated from various microorganisms. Adv Biochem Eng Biotechnol, 2004, 90, 1 - 33 Recent progress in microbial cultivation techniques; Park EY; Recent advances in the improvement of microbial cultivation are reviewed, with emphasis on biochemical engineering techniques as a means of obtaining high production rate of bioproduct . Possible uses of high cell density culture include their use in food industry as well as in the production of new medicines and in biotechnology . Concentration of microorganisms using a hollow fiber membrane or centrifuge, and increase in cell density by controlling the pH, dissolved oxygen, or carbon source concentrations of the culture broth with control algorithms are discussed . In a culture of filamentous microorganisms the mycelial morphology is hard to define and it is difficult to quantify its amount, and this is one of the bottlenecks hampering the improvement of production rate . Specific features of mycelial cultivation in the presence of highly pulpy mycelia and entangled-pellets are scrutinized by visual inspection through a microscope that is linked to a computer, and using software that can characterize the mycelial morphology . Image analysis technology for analyzing the mycelial image captured by a digital camera is a potential tool for morphological analysis, including analysis of the morphological development of filamentous microorganisms. J Biol Chem, 2004 Dec 10, 279(50), 51749 - 59 Epub 2004 Dec 10. The methylerythritol phosphate pathway is functionally active in all intraerythrocytic stages of Plasmodium falciparum; Cassera MB et al.; Two genes encoding the enzymes 1-deoxy-D-xylulose-5-phosphate synthase and 1-deoxy-D-xylulose-5-phosphate reductoisomerase have been recently identified, suggesting that isoprenoid biosynthesis in Plasmodium falciparum depends on the methylerythritol phosphate (MEP) pathway, and that fosmidomycin could inhibit the activity of 1-deoxy-D-xylulose-5-phosphate reductoisomerase . The metabolite 1-deoxy-D-xylulose-5-phosphate is not only an intermediate of the MEP pathway for the biosynthesis of isopentenyl diphosphate but is also involved in the biosynthesis of thiamin (vitamin B1) and pyridoxal (vitamin B6) in plants and many microorganisms . Herein we report the first isolation and characterization of most downstream intermediates of the MEP pathway in the three intraerythrocytic stages of P . falciparum . These include, 1-deoxy-D-xylulose-5-phosphate, 2-C-methyl-D-erythritol-4-phosphate, 4-(cytidine-5-diphospho)-2-C-methyl-D-erythritol, 4-(cytidine-5-diphospho)-2-C-methyl-D-erythritol-2-phosphate, and 2-C-methyl-D-erythritol-2,4-cyclodiphosphate . These intermediates were purified by HPLC and structurally characterized via biochemical and electrospray mass spectrometric analyses . We have also investigated the effect of fosmidomycin on the biosynthesis of each intermediate of this pathway and isoprenoid biosynthesis (dolichols and ubiquinones) . For the first time, therefore, it is demonstrated that the MEP pathway is functionally active in all intraerythrocytic forms of P . falciparum, and de novo biosynthesis of pyridoxal in a protozoan is reported . Its absence in the human host makes both pathways very attractive as potential new targets for antimalarial drug development. Curr Opin Microbiol, 2004 Oct, 7(5), 513 - 8 Mathematical models in microbial systems biology; Stelling J; Systems biology aims at an understanding of the genotype-phenotype relations brought about by cellular networks . Mathematical models as formal representations are central for handling the associated complexity . Recently, model-based analysis of microorganisms has begun, for instance, to reveal functional modules in metabolic and transcriptional networks, to predict cellular behavior from genome-scale physicochemical constraints, and to suggest novel design principles for well-studied bacterial subsystems such as chemotaxis . Guided by common themes such as modularity, optimality and robustness, iterative model development promises further progress towards a system-level understanding. Antiviral Res, 2004 Oct, 64(1), 63 - 8 Lactoferrin inhibits human papillomavirus binding and uptake in vitro; Drobni P et al.; Lactoferrin (LF), a member of the transferrin family, is a bi-globular protein secreted in milk, saliva, tears, seminal fluid, endocervix and vaginal secretions . LF is an important player in the defence against pathogenic microorganisms and has also been shown to have activity against several viruses including herpesvirus, adenovirus, rotavirus and poliovirus . The antiviral activity of LF is directed against the early steps of viral infection and the LF antiviral effect against herpesvirus is mediated through LF binding to the herpesvirus receptor heparan sulfate . Human papillomavirus (HPV) causes genital warts and is a prerequisite for cervical cancer . HPV can also use heparan sulfate on the cell surface as a receptor . We studied the inhibition by LF on HPV entry by incubating HaCaT cells and HPV-16 virus-like particles (VLPs) with either human (HLF) or bovine lactoferrin (BLF) . LF inhibited internalization of HPV-16 particles using CFDA-SE-labelled VLPs that only fluoresce after internalisation . By using a western blot assay we also found dose-dependent LF inhibition of HPV-16 VLP binding to the HaCaT cell surface . BLF was a more potent inhibitor of HPV entry than human LF . It was also clear that LF acted early in the HPV uptake process. Anal Biochem, 2004 Oct 15, 333(2), 303 - 8 Chemiluminescent assay for detection of viable microorganisms; Yamashoji S et al.; The redox reaction between quinone and viable microorganisms produces active oxygen species . In this study, the production rates of active oxygen species were determined by a luminol chemiluminescent assay, and the luminescence intensity was found to be proportional to the viable cell number . The high sensitivity of the luminol chemiluminescent assay was achieved with Mo-ethylenediaminetetraacetate complex and menadione or coenzyme Q1 . The detectable cell densities of bacteria and yeasts were found to be approximately several thousand colony-forming units (CFU/ml) when assays were performed with a 96-well microplate luminometer . The chemiluminescent assay requires 10 min for incubation of quinone and microorganisms and 2s for photon counting . Single Escherichia coli was detected after 4h of cultivation and centrifugation (5 min x 2) . This simple chemiluminescent assay is expected to be useful for the rapid detection of viable bacteria and yeast. Curr Opin Chem Biol, 2004 Oct, 8(5), 534 - 9 Raman spectroscopy in chemical bioanalysis; Baena JR et al.; Advances in instrumentation are making Raman spectroscopy the tool of choice for an increasing number of (bio)chemical applications . Raman is an interesting option for several reasons, including the sensitivity to small structural changes, non-invasive sampling capability, minimal sample preparation, and high spatial resolution in the case of Raman micro-spectroscopy . Herein we discuss the most recent technical approaches employed, from the well-known surface enhanced resonance Raman spectroscopy to non-linear Raman techniques such as coherent anti-stokes Raman spectroscopy (CARS) and related techniques . Relevant applications of Raman spectroscopy in the fields of clinical pathology, in vivo and ex vivo imaging, classification and detection of microorganisms and chemical analysis in the past three years are also included. Infect Genet Evol, 2004 Sep, 4(3), 199 - 203 The development of a typing method for an uncultivable microorganism: the example of Pneumocystis jirovecii; Hauser PM; The development of a molecular typing method for the uncultivable fungus Pneumocystis jirovecii is described . The method consists of the amplification by PCR of four variable regions of P . jirovecii genome, followed by the detection of the polymorphisms by the single-strand conformation polymorphism technique . About 70% of the patients harbored two or rarely three alleles of at least one of the four genomic regions . This was shown to most probably be due to co-infections with several P . jirovecii types . Each combination of four alleles of the four genomic regions defines a type . Analysis of the alleles and their abundance allows identification of the co-infecting types in about 65% of the specimens co-infected with two types . The method has been validated by the evaluation of several criteria . The main advantage of the method is that it is relatively cheap and that up to 50 specimens can be analysed at the same time . Its main disadvantage is that about 30% of the specimens cannot be typed because of the complexity of the alleles configuration . This multitarget typing method has been used for several epidemiological purposes. Nepal Med Coll J, 2004 Jun, 6(1), 56 - 9 A comparative study of cost analysis of antibiotic use in clinics and hospitals of Kathmandu Valley, Nepal; Jauhari AC et al.; Excessive use of antibiotics (AB) has resulted in resistant strains of microorganisms, adverse drug reactions (ADR's) and cross-resistance . This study showed that AB are being used indiscriminately . We carried out a retrospective comparative cost analysis study on the use of AB in clinics and hospitals on a larger population by analyzing 1200 prescriptions of various diseases containing AB and cost effectiveness was compared . It was found that surgeons prescribed costliest AB whereas physicians used cheapest AB . Overall the costliest treatment was prescribed by gynecologists of hospitals, and the most economical treatment was prescribed by pediatricians in the clinics. Biotechnol Bioeng, 2004 Oct 20, 88(2), 135 - 47 Modeling aerobic carbon oxidation and storage by integrating respirometric, titrimetric, and off-gas CO2 measurements; Pratt S et al.; A method for detailed investigation of aerobic carbon degradation processes by microorganisms is presented . The method relies on an integrated use of the respirometric, titrimetric, and off-gas CO(2) measurements . The oxygen uptake rate (OUR), hydrogen ion production rate (HPR), and the carbon dioxide transfer rate (CTR) resulting from the biological as well as physicochemical processes, coupled with a metabolic model characterizing both the growth and carbon storage processes, enables the comprehensive study of the carbon degradation processes . The method allows the formation of carbon storage products and the biomass growth rates to be estimated without requiring any off-line biomass or liquid-phase measurements, although the practical identifiability of the system could be improved with additional measurements . Furthermore, the combined yield for biomass growth and carbon storage is identifiable, along with the affinity constant with respect to the carbon substrate . However, the individual yields for growth and carbon storage are not identifiable without further knowledge about the metabolic pathways employed by the microorganisms in the carbon conversion . This is true even when more process variables are measured . The method is applied to the aerobic carbon substrate degradation by a full-scale sludge using acetate as an example carbon source . The sludge was able to quickly take up the substrate and store it as poly-beta-hydroxybutyrate (PHB) . The PHB formation rate was a few times faster than the biomass growth rate, which was confirmed by off-line liquid- and solid-phase analysis . The estimated combined yield for biomass growth and carbon storage compared closely to that determined from the theoretical yields reported in literature based on thermodynamics . This suggests that the theoretical yields may be used as default parameters for modeling purposes. Ig Sanita Pubbl, 2004 May-Jun, 60(3), 141 - 50 Practical aspects of decontamination of the unconventional transmissible agents that cause sporadic and variant Creutzfeldt-Jakob disease and other similar human diseases; Taylor D; Although the unconventional agents that cause transmissible degenerative encephalopathies have not yet been completely characterised, they are known to be relatively resistant to decontamination procedures that are effective with conventional microorganisms . The implications for the safe decontamination and sterilisation of devices and instruments used in human medicine are discussed. J Nat Prod, 2004 Sep, 67(9), 1595 - 7 Hydroxylation of 10-deoxoartemisinin by Cunninghamella elegans; Parshikov IA et al.; The microbial metabolism of 10-deoxoartemisinin (1), a derivative of the antimalarial drug artemisinin, was investigated . Various strains of fungi were investigated for their ability to transform 1 . Of these microorganisms, only Cunninghamella elegans was capable of transforming 1 to 5beta-hydroxy-10-deoxoartemisinin (2), 4alpha-hydroxy-1,10-deoxoartemisinin (3), and 7beta-hydroxy-10-deoxoartemisinin (4) . The metabolites 2 and 4 retained an intact peroxide group and are therefore useful scaffolds for synthetic modification in the search for new antimalarial agents. Ocul Immunol Inflamm, 2004 Sep, 12(3), 215 - 25 The contribution of aqueous humor cytology in the differential diagnosis of anterior uvea inflammations; Kalogeropoulos CD et al.; BACKGROUND: Cytology of the aqueous humor can confirm the diagnosis of many intraocular conditions by revealing inflammatory cells, ghost red cells, lens material, and microorganisms . PURPOSE: The purpose of this study was to emphasize the contribution of aqueous humor fine needle aspiration cytology in cases where there is a clinical diagnostic dilemma whether an infectious or a noninfectious inflammatory process of the uvea is present . METHODS: Collection of 0.15-0.2 ml aqueous humor was carried out with an insulin needle . The aspirated aqueous was then prepared for examination using either the Cytospin or the Thin-Prep technique and smears were stained with modified Papanikolaou and May-Grunwald-Giemsa stains . RESULTS: Cytology of the aqueous humor essentially facilitated the differential diagnosis in 16 cases with an anterior uveal inflammation clinical picture . The cases included phacoanaphylactic endophthalmitis (n = 6), chronic postoperative bacterial endophthalmitis (n = 3), phacolytic glaucoma (n = 2), ghost cell glaucoma (n = 2), metastatic endophthalmitis (n = 1), post-traumatic lenticular abscess (n = 1), and iridocyclitis (n = 1) . Treatment of the cases was successful . CONCLUSIONS: In selected cases, cytology of the aqueous humor reveals specific, with regard to the clinical entity, cell populations and other elements and thus contributes effectively to the differential diagnosis and therapeutic approach to some anterior uvea inflammations. J Environ Radioact, 2004, 77(3), 369 - 80 Influence of microorganisms on the behavior of technetium and other elements in paddy soil surface water; Ishii N et al.; Insolubilization patterns of technetium (Tc) and other trace elements (Sc, Co, Zn, Se, Rb, Sr, Y, Nb, Ce, Pm, Gd, Lu, Hf, and Re) in surface water covering paddy fields were compared to gain insight into the behavior of Tc in an agricultural environment . The insolubilization of Tc, which did not pass through a 0.2-microm-pore-size filter, was mainly caused by bacteria . Among the 14 other elements investigated, Nb was insolubilized by bacteria and the amounts of insoluble Nb were positively correlated with those of Tc . Although Re is a chemical analog of Tc, no similarity was observed . These results suggest that Tc behaves similarly to Nb in the insolubilization in surface water covering paddy fields. J Biotechnol, 2004 Sep 30, 113(1-3), 281 - 94 Toward large-scale modeling of the microbial cell for computer simulation; Ishii N et al.; In the post-genomic era, the large-scale, systematic, and functional analysis of all cellular components using transcriptomics, proteomics, and metabolomics, together with bioinformatics for the analysis of the massive amount of data generated by these "omics" methods are the focus of intensive research activities . As a consequence of these developments, systems biology, whose goal is to comprehend the organism as a complex system arising from interactions between its multiple elements, becomes a more tangible objective . Mathematical modeling of microorganisms and subsequent computer simulations are effective tools for systems biology, which will lead to a better understanding of the microbial cell and will have immense ramifications for biological, medical, environmental sciences, and the pharmaceutical industry . In this review, we describe various types of mathematical models (structured, unstructured, static, dynamic, etc.), of microorganisms that have been in use for a while, and others that are emerging . Several biochemical/cellular simulation platforms to manipulate such models are summarized and the E-Cell system developed in our laboratory is introduced . Finally, our strategy for building a "whole cell metabolism model", including the experimental approach, is presented. J Biotechnol, 2004 Sep 30, 113(1-3), 263 - 79 Dual nutrient limited growth: models, experimental observations, and applications; Zinn M et al.; Dual nutrient limited growth, the control of the cell growth rate (kinetic aspect) or the restriction of the amount of biomass (stoichiometric aspect) by two nutrients at the same time, is a relatively unknown ability of the microorganisms and consequently, still not mentioned in textbooks to date . Nevertheless, multiple nutrient limited or controlled growth has been reported for different systems; e.g . ecosystems, batch, fed-batch, and chemostat cultures . Generally, dual nutrient limited growth has been observed when the microorganism of interest: (a) showed a variation of the cellular composition, (b) was able to accumulate a storage compound, (c) changed the cell metabolism, or (d) excreted metabolic intermediates . Consequently, stoichiometric models have been developed to estimate the growth conditions leading to dual nutrient limited growth . A general problem of the kinetic aspect is the accurate measurement of the growth controlling nutrients in the culture broth (microg l(-1) range), as the cells may consume residual nutrients during sampling . Nevertheless, most models of dual limited growth deal with the kinetic aspect although the control experiments are difficult to carry out . The aim of this survey is to introduce this special growth feature with respect to basic models, experimental data, and potential applications in bioprocesses. Res Microbiol, 2004 Oct, 155(8), 688 - 91 Broad diversity of viable bacteria in 'sterile' (0.2 microm) filtered water; Hahn MW; Filtration of liquids through 0.2-microm filters is a common and often-used method for the removal of microorganisms from heat-sensitive solutions . Such 0.2 microm filtrations are frequently referred to as 'sterile filtration', reflecting the general belief that all living organisms are excluded from the filtrate . However, it has been demonstrated that a few bacterial species can pass through 0.2-microm filters . Despite these observations, it is generally assumed that most bacteria are unable to pass through these filters . In contrast to this assumption, a wide diversity of 19 bacterial taxa was isolated by the acclimatization method from 0.2 microm-filtrated freshwater samples . All isolates were able to grow on substrate-rich agar plates . The size of the isolated strains ranged from <1 to >10 microm in cell length . The obtained isolates belong to the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Spirochaetes . Previous studies which did not use the acclimatization method reported that only two out of the 19 taxa passed through 0.2- or 0.45-microm filters . The majority of the obtained isolates were more closely related to uncultured than to previously cultured bacteria . It is assumed that the obtained taxa represent only a small fraction of the bacteria able to pass through 0.2-microm filters, and it is concluded that microbiologists may have dramatically underestimated the diversity of 0.2 microm-filterable bacteria. Res Microbiol, 2004 Oct, 155(8), 636 - 46 A Sphingomonas bacterium interacting with epithelial cells; Ammendolia MG et al.; Bacteria of the genus Sphingomonas are environmental organisms that have recently been implicated in a variety of community-acquired and nosocomial infections . During studies on bacteria-cell interactions, we incurred a microorganism contaminating our HeLa cell culture, possibly from water utilized for reagent preparation; this bacterium appeared to tightly adhere to cell monolayers and to survive, with only limited growth rate, which did not seem to alter cells as far as shape, growth rate or survival were concerned . The contaminating organism was isolated and partially characterized by morphological, genetic, and biochemical assays . Mechanisms of cell interaction and entry into epithelial cells were investigated by electron microscopy, immunofluorescence, and biochemical inhibitors . Morphological and biochemical features indicated that the microorganism belonged to the genus Sphingomonas . Electron microscopy showed that contact between the Sphingomonas bacterium and epithelial cells leads to a dramatic alteration of the cell surface, with formation of numerous microvillar extensions plus membrane ruffling . Confocal microscopy and the use of inhibitors showed that actin microfilaments were involved during attachment and entry into HeLa cells . Macropinosome formation and an inhibitory effect by amiloride indicate that internalization occurs in part via a macropinocytosis mechanism . Moreover, cholesterol distribution at the site of bacterial binding suggests that Sphingomonas bacteria could use the lipid rafts as initial binding sites. Proteomics, 2004 Oct, 4(10), 2987 - 90 Presentation of differentially regulated proteins within a web-accessible proteome database system of microorganisms; Pleissner KP et al.; Web-accessible proteome databases represent indispensable tools for quantitative and comparative proteomics research . The majority of two-dimensional gel electrophoresis (2-DE) databases contains clickable 2-DE gel images and descriptive textual information such as protein name, Mr/pI values, methods of identification, cellular localization and other information on proteins . Although a great part of the work in comparative proteomics consists of the analysis of 2-DE gels using image analysis approaches, most proteome databases lack the ability to present protein abundance data and their alterations within experiments via the web . Now, differentially regulated proteins detected in microbial experiments by quantitative gel image analysis are presented in a web-accessible relational database DIFF (Differentially Regulated Proteins) . The DIFF database is a part of the proteome database system for microbial research available at http://www.mpiib-berlin.mpg.de/2D-PAGE. Appl Microbiol Biotechnol, 2004 Oct, 65(5), 497 - 503 Epub 2004 Jul 28. Gibberellin production by bacteria and its involvement in plant growth promotion and yield increase; Bottini R et al.; This review focuses on studies with bacteria for which biosynthesis/production of the plant hormones gibberellins have been demonstrated . Actual data on gibberellin metabolism by bacteria are analyzed in comparison with the biosynthetic pathways known for vascular plants and fungi . The potential involvement of gibberellins produced by symbiotic and soil-endophytic microorganisms in plant growth promotion and yield increase is also discussed. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz, 2004 Sep, 47(9), 841 - 7 {Chemical food contaminants}; Schrenk D; Chemical food contaminants are substances which are neither present naturally in the usual raw material used for food production nor are added during the regular production process . Examples are environmental pollutants or contaminants derived from agricultural production of crops or livestock or from inadequate manufacturing of the food product itself . More difficult is the classification of those compounds formed during regular manufacturing such as products of thermal processes including flavoring substances . In these cases, it is common practice to call those compounds contaminants which are known for their adverse effects such as acrylamide, whereas constituents which add to the food-specific flavor such as Maillard products formed during roasting, baking etc . are not termed contaminants . From a toxicological viewpoint this distinction is not always clear-cut . Important groups of chemical contaminants are metals such as mercury or lead, persistent organic pollutants such as polychlorinated biphenyls and related pollutants, which are regularly found in certain types of food originating from background levels of these compounds in our environment . Furthermore, natural toxins form microorganisms or plants, and compounds formed during thermal treatment of food are of major interest . In general, a scientific risk assessment has to be carried out for any known contaminant . This comprises an exposure analysis and a toxicological and epidemiological assessment . On these grounds, regulatory and/or technological measures can often improve the situation . Major conditions for a scientific risk assessment and a successful implementation of regulations are highly developed food quality control, food toxicology and nutritional epidemiology. Shock, 2004 Oct, 22(4), 297 - 308 Immunomodulation and sepsis: impact of the pathogen; Moine P et al.; Infection begins when microorganisms overcome host barriers and multiply within host tissues . To contain the infection, the host mounts an inflammatory response that mobilizes defense systems and kills the invading microorganisms . A focal inflammatory response is usually sufficient to eradicate the organisms . However, when it fails to contain the infection, the organisms, their toxins, and numerous host mediators are released into the bloodstream, producing a systemic inflammatory response and organ failure . Microorganisms have coevolved with their hosts, thereby acquiring means of overcoming host defense mechanisms or even taking advantage of innate host responses . Many pathogens avoid recognition by the host or dampen host immune responses via sophisticated pathogen-host interactions . Some pathogens benefit from the inflammatory response . According to current hypotheses regarding the pathogenesis of sepsis, the host generates both an innate immune response identical for all pathogens and an adaptive pathogen-specific response . Determining whether the innate response benefits the pathogen or the host is essential for understanding host-pathogen interactions . In this review, we discuss how pathogens interfere with innate and adaptive immune responses to escape eradication by the host. Environ Toxicol Chem, 2004 Jun, 23(6), 1425 - 30 Effects of a rhamnolipid biosurfactant on the reductive dechlorination of polychlorinated biphenyls by St . Lawrence River (North America) microorganisms; Cho YC et al.; The effect of a rhamnolipid biosurfactant on the reductive dechlorination of polychlorinated biphenyls was investigated with the use of clean sediments spiked with Aroclor 1248 . The surfactant was added to the contaminated sediments at four different concentrations (5, 10, 25, and 50 microg/g sediment {ppm} on a sediment dry wt basis), and dechlorination was followed over a 40-week period . The rate of overall dechlorination was enhanced at the three highest concentrations . Dechlorination at the lowest concentration (5 ppm) was not different from that in surfactant-free sediments . On a congener basis, enhanced dechlorination was mostly found in the congeners that have high threshold concentrations for dechlorination . These congeners are characterized by an initial increase in concentration before dechlorination starts . At the three highest biosurfactant concentrations, this initial concentration increase was absent or dramatically reduced . Therefore, the enhancement in dechlorination appears to be caused by an increase in bioavailability at high surfactant concentrations . The biosurfactant also reduced the lag time before dechlorination began in these congeners . Among those congeners that have low threshold concentrations, dechlorination enhancement was found only in two peaks . For these two, there was no lag period, either with or without the rhamnolipids . The maximum level of dechlorination and the congener pattern of final dechlorination products were identical, regardless of biosurfactant concentration. Am J Ind Med, 2004 Oct, 46(4), 327 - 32 Endotoxins isolated from the air of a Danish paper mill and the relation to change in lung function: an 11-year follow-up; Sigsgaard T et al.; BACKGROUND: A decline in lung function has been associated with farming, cotton spinning, and work in the animal feed industry . The aim of the study was to reveal if loss of lung function was associated to work at a paper mill . METHODS: Ninety-seven male paper workers (PW), and 55 control workers were examined . Hygiene samples included total dust, endotoxins, and microorganisms . Interview, pulmonary function testing, and skin prick test (SPT) were performed and yearly decline in lung function was calculated . RESULTS: The exposure for endotoxin (LPS) ranged from Median (Max-Min) 69 (370-6) EU/m3, in the wet-end of the paper machines to 6 (19-16) in the pulping area . The lung function decline among the controls was comparable to the decrements among the maintenance and repair workers at the paper factory, around 51-54 and 37-38 ml/year among smokers' and non-smokers, respectively . After adjustment for baseline FEV1, the variables associated to an increased loss of FEV1 were age smoking and cough . For FVC we found an inverse relation between exposure and yearly decline . CONCLUSION: No increase in loss of lung function is seen among workers exposed to up to 200 EU/m3 of LPS. J Dairy Sci, 2004 Sep, 87(9), 2761 - 8 Flow characteristics of a pilot-scale high temperature, short time pasteurizer; Tomasula PM et al.; In this study, we present a method for determining the fastest moving particle (FMP) and residence time distribution (RTD) in a pilot-scale high temperature, short time (HTST) pasteurizer to ensure that laboratory or pilot-scale HTST apparatus meets the Pasteurized Milk Ordinance standards for pasteurization of milk and can be used for obtaining thermal inactivation data . The overall dimensions of the plate in the pasteurizer were 75 x 115 mm, with a thickness of 0.5 mm and effective diameter of 3.0 mm . The pasteurizer was equipped with nominal 21.5- and 52.2-s hold tubes, and flow capacity was variable from 0 to 20 L/h.Tracer studies were used to determine FMP times and RTD data to establish flow characteristics . Using brine milk as tracer, the FMP time for the short holding section was 18.6 s and for the long holding section was 36 s at 72 degrees C, compared with the nominal times of 21.5 and 52.2 s, respectively . The RTD study indicates that the short hold section was 45% back mixed and 55% plug flow for whole milk at 72 degrees C . The long hold section was 91% plug and 9% back mixed for whole milk at 72 degrees C . This study demonstrates that continuous laboratory and pilot-scale pasteurizers may be used to study inactivation of microorganisms only if the flow conditions in the holding tube are established for comparison with commercial HTST systems. J Microbiol Methods, 2004 Nov, 59(2), 243 - 52 Comparison of a membrane surface adhesion recovery method with an IMS method for use in a polymerase chain reaction method to detect Escherichia coli O157:H7 in minced beef; Fitzmaurice J et al.; In this study, enrichment procedures and two recovery methods, a membrane surface adhesion technique and an immunomagnetic separation (IMS), were compared for use in conjunction with a multiplex polymerase chain reaction (PCR) method with a view to describing a fast (24 h) and economical test for detection of Escherichia coli O157:H7 in meat samples . The study showed no significant difference between three different enrichment media (BHI, E . coli (E.C.) broth+novobiocin, modified tryptone soya broth (mTSB)+novobiocin) or two incubation temperatures (37 or 41.5 degrees C) for growth of E . coli O157:H7 in minced beef . Minced beef samples inoculated with E . coli O157:H7 at 40 cfu g(-1) were incubated at 37 degrees C for 16 h in E.C . broth+novobiocin reaching numbers of (log(10)7.82-8.70) . E . coli O157:H7 were recovered by attachment to polycarbonate membranes immersed in the enriched cultures for 15 min or by immunomagnetic separation . Subsequent treatment of recovered membranes or IMS beads with lysis buffer and phenol/chloroform/isoamyl alcohol was used to extract the DNA from the extracted E . coli O157:H7 cells . The results show when E . coli O157:H7 was present at high levels in the enriched meat sample (log(10)9.6-7.5 cfu ml(-1); >16-h enrichment), the membrane and IMS techniques recovered similar levels of the pathogen and the microorganism was detectable by PCR using both methods . At lower levels of E . coli O157:H7 (log(10)6.4), only the IMS method could recover the pathogen but at levels below this neither method could recover sufficient numbers of the pathogens to allow detection . The conclusion of the study is that with sufficient enrichment time (16 h) the membrane surface adhesion membrane extraction method used in combination with multiplex PCR has the potential for a rapid and economical detection method. Syst Appl Microbiol, 2004 Aug, 27(4), 492 - 500 Validation of the official control method based on Polymerase Chain Reaction (PCR) for identification of authorised probiotic yeast in animal feed; Leuschner RG et al.; Council Directive 70/524/EEC regulates the application of probiotic (microorganisms) additives in feeding stuffs . In the present study a method for the differentiation and strain identification of authorised probiotic Saccharomyces cereviseae strains in feeding stuffs by Polymerase Chain Reaction (PCR) was validated . Four different samples of animal feeding stuffs containing yeast at levels between 10(5) to 10(7) CFU/g were examined . Samples were enumerated on chloramphenicol glucose yeast extract agar and colonies were selected from these plates for DNA extraction and subsequent analysis . The PCR method using delta sequence primers produced an 'amplified sequence polymorphism' characteristic for the test strain . Feeds supplemented with one of four probiotic yeast strains each were analysed by seven of nine invited laboratories . All laboratories returned valid results with the exception of one laboratory that had insufficiently separated bands on the gel . The method had a good reproducibility for probiotic yeast isolates from feed of all four authorised probiotic yeast strains (APYS) CBS 493.94, APYS CNCM 1-1079, APYS CNCM 1-1077, APYS NCYC SC47 and of a commercially available yeast reference strain, NCYC 81 . The PCR method is to be considered by CEN and ISO as official control method for identification of authorised probiotic Saccharomyces cerevisiae strains from feeding stuffs. Chem Commun (Camb), 2004 Sep 21, (18), 2120 - 1 Epub 2004 Aug 06. Rapid identification of new bacterial alcohol dehydrogenases for (R)- and (S)-enantioselective reduction of ss-ketoesters; Zhang J et al.; New bacterial alcohol dehydrogenases with high and complementary enantioselectivity for the reduction of ethyl 3-keto-4,4,4-trifluorobutyrate 1 and methyl 3-keto-3-(3'-pyridyl)-propionate 3 have been rapidly identified by use of a new methodology consisting of preselection of microorganisms based on degradation ability and high-throughput screening with a miniaturized system coupled with fast analysis of enantioselectivities . Plant Cell, 2004 Oct, 16(10), 2785 - 94 Epub 2004 Sep 14. Arabidopsis nonsymbiotic hemoglobin AHb1 modulates nitric oxide bioactivity; Perazzolli M et al.; Nitric oxide (NO) is a widespread signaling molecule, and numerous targets of its action exist in plants . Whereas the activity of NO in erythrocytes, microorganisms, and invertebrates has been shown to be regulated by several hemoglobins, the function of plant hemoglobins in NO detoxification has not yet been elucidated . Here, we show that Arabidopsis thaliana nonsymbiotic hemoglobin AHb1 scavenges NO through production of S-nitrosohemoglobin and reduces NO emission under hypoxic stress, indicating its role in NO detoxification . However, AHb1 does not affect NO-mediated hypersensitive cell death in response to avirulent Pseudomonas syringae, suggesting that it is not involved in the removal of NO bursts originated from acute responses when NO mediates crucial defense signaling functions. J Infect Chemother, 2004 Aug, 10(4), 239 - 41 Blood culture examinations at a community hospital without a microbiology laboratory: using an automated blood culture system and performing a Gram stain on positive culture bottles in the institution; Saito T et al.; To elucidate the existence of microorganisms from blood culture bottles in hospitals without a microbiology laboratory, we changed the system of blood culture examinations . The Oxoid signal blood culture system and submission of all blood cultures to the clinical testing industry was used from July 2002 to December 2002 (first period) . Use of the BacT/Alert system and performing of Gram stain for positive culture bottles in our institutions was conducted from January 2003 to June 2003 (latter period) . A total of 210 and 193 blood cultures were processed during the first and latter periods, respectively . There were 40 (19.0%) positive cultures in the first period and 32 (16.6%) positive cultures in the latter period . The times from the specimen collection to the Gram stain result that were required were 3.8 and 1.0 days in the first period and the latter period, respectively . The times required for the final report of the blood cultures in the first period and in the latter period were 5.8 and 4.9 days, respectively . We conclude that using a continuous monitoring, automated blood culture system and performing Gram stain for positive culture bottles in institutions without microbiology laboratories may be useful for medical doctors to rapidly determine the existence of microorganisms and to begin adequate antiinfective therapy. Appl Microbiol Biotechnol, 2004 Nov, 65(6), 720 - 6 Epub 2004 Sep 10. Screening for novel lipolytic enzymes from uncultured soil microorganisms; Lee SW et al.; The construction and screening of metagenomic libraries constitute a valuable resource for obtaining novel biocatalysts . In this work, we present the construction of a metagenomic library in Escherichia coli using fosmid and microbial DNA directly isolated from forest topsoil and screened for lipolytic enzymes . The library consisted of 33,700 clones with an average DNA insert size of 35 kb . Eight unique lipolytic active clones were obtained from the metagenomic library on the basis of tributyrin hydrolysis . Subsequently, secondary libraries in a high-copy-number plasmid were generated to select lipolytic subclones and to characterize the individual genes responsible for the lipolytic activity . DNA sequence analysis of six genes revealed that the enzymes encoded by the metagenomic genes for lipolytic activity were novel with 34-48% similarity to known enzymes . They had conserved sequences similar to those in the hormone-sensitive lipase family . Based on their deduced amino acid similarity, the six genes encoding lipolytic enzymes were further divided into three subgroups, the identities among which ranged from 33% to 45% . The six predicted gene products were successfully expressed in E . coli and secreted into the culture broth . Most of the secreted enzymes showed a catalytic activity for hydrolysis of p-nitrophenyl butyrate (C(4)) but not p-nitrophenyl palmitate (C(16)). J Biol Chem, 2004 Nov 26, 279(48), 50257 - 66 Epub 2004 Nov 26. Antigen stability controls antigen presentation; Thai R et al.; We investigated whether protein stability controls antigen presentation using a four disulfide-containing snake toxin and three derivatives carrying one or two mutations (L1A, L1A/H4Y, and H4Y) . These mutations were anticipated to increase (H4Y) or decrease (L1A) the antigen non-covalent stabilizing interactions, H4Y being naturally and frequently observed in neurotoxins . The chemically synthesized derivatives shared similar three-dimensional structure, biological activity, and T epitope pattern . However, they displayed differential thermal unfolding capacities, ranging from 65 to 98 degrees C . Using these differentially stable derivatives, we demonstrated that antigen stability controls antigen proteolysis, antigen processing in antigen-presenting cells, T cell stimulation, and kinetics of expression of T cell determinants . Therefore, non-covalent interactions that control the unfolding capacity of an antigen are key parameters in the efficacy of antigen presentation . By affecting the stabilizing interaction network of proteins, some natural mutations may modulate the subsequent T-cell stimulation and might help microorganisms to escape the immune response. Exp Parasitol, 2004 Jul-Aug, 107(3-4), 189 - 99 The modelling of mononuclear phagocyte-connective tissue adhesion in vitro: application to disclose a specific inhibitory effect of Leishmania infection; Carvalhal DG et al.; In this work, we have developed an adhesion assay to study interactions between mononuclear phagocytes and connective tissue in vitro and show its potential use to study diseases caused by intracellular microorganisms . The assay reproduces most of the characteristics of macrophage adhesion to connective tissue in vivo, such as: preferential adhesion to inflamed connective tissue, divalent cation and integrin dependence, and up-regulation upon cell activation . The phagocyte adhesion to connective tissue was inhibited by infection with Leishmania (58+/-22%, p < 0.05) and was not affected by infection with Mycobacterium or by endocytosis of latex beads . Manganese partially reverted the loss in adherence produced by Leishmania infection, indicating that the mechanisms regulating the function of integrins are affected by cell infection with Leishmania . This assay might be a useful tool for the study of the mechanisms by which mononuclear phagocytes play a role in the immune-inflammatory response and in the development of lesions. Rev Med Interne, 2004 Sep, 25(9), 629 - 35 {Cationic anti-microbial peptides: from innate immunity study to drug development}; Andres E et al.; OBJECTIVE: Host defense, cationic anti-microbial peptides are recognized as an important component of innate immune response in most multicellular organisms . NEW FEATURES: They are cationic amphipathic peptides, comprising 20-50 amino acids . Several hundreds of peptides have been characterized . They have broad spectrum of activity against bacterial, fungal and viral pathogens . The mode of action is best known for cecropins and magainins, which act upon the cytoplasmic membrane of microorganisms, causing its disruption by a detergent like activity and pore formation . Several of these peptides or analogs (from magainin, protegrin, indolicidin and histatin) are in advanced clinical development, especially for localized infections . PROJECTS AND PERSPECTIVES: Several other molecules (rBPI, heliomicin and thanatine) are currently under development for various systemic infections . They may represent important drugs of the further anti-infectious therapeutic arsenal. Hepatogastroenterology, 2004 Sep-Oct, 51(59), 1551 - 3 Helicobacter pylori infection in patients with ulcer recurrence after partial gastrectomy; Huang WH et al.; BACKGROUND/AIMS: Recurrent ulceration of the stomach occurs in some patients after surgery for peptic ulcer disease . The aim of this study is to evaluate the association of Helicobacter pylori infection with ulcer recurrence in patients after partial gastrectomy due to peptic ulcer disease . METHODOLOGY: A total of 186 patients after partial gastrectomy with Billroth I or Billroth II anastomosis presenting with dyspepsia or bleeding were included . An ulcer recurrence was documented by endoscopic examination . Biopsy specimens were taken from the remnant gastric bodies in all patients . H . pylori infection was diagnosed by either a positive biopsy urease test or the presence of the microorganism on histology . RESULTS: Eighty-three (44.6%) patients among the 186 patients had recurrent ulcers . H . pylori infection was found in 29 (36%) patients in the ulcer group and 42 (41%) patients in the non-ulcer group . The incidence of H . pylori infection did not differ significantly between the two groups (P>0.05) . CONCLUSIONS: H . pylori infection may not play an important role in the pathogenesis of recurrent ulcer after partial gastrectomy . Other factors should be studied further. Kansenshogaku Zasshi, 2004 Jul, 78(7), 588 - 96 {The effects of fluorescent lamp coated with a photocatalyst film on the number of floating microorganisms or smell molecules in a room installed with the lamp}; Fujimaki W et al.; Fluorescent lamp that is coated with a photocatalyst film, titanium dioxide (TiO2), can catalyze the microorganisms and smell producing molecules that touch the membrane . In this report, we examined the effect of this coated lamp by the number of floating microorganisms or smell molecules in a room installed with this lamp . The number of floating microorganisms was examined independently in different laboratories before and after installing the lamps in an animal facility and a vegetable processing room of a food company . We found that the number of floating microorganisms was significantly reduced after the installation of this coated lamp . To test for smell molecules, acetaldehyde was injected into a closed chamber installed with the coated lamp and the result was compared to a control where a regular fluorescent lamp was used . The acetaldehyde concentration did not change with the regular lamp but was halved after 1h with the photocatalyst coated lamp . To test the effect in real settings, questionnaires were filled out by restroom users in several different places . About 90% of those surveyed answered that there was a reduction of smell after the installation of the photocatalyst coated lamp . We concluded that the installation of this coated fluorescent lamp reduced not only the floating microorganisms but the smell in various practical situations. Blood Purif, 2004, 22(5), 435 - 9 Epub 2004. Direct dialysis quantification: investigation of the impact of dialysate preservation techniques on solute assays; Kanagasundaram NS et al.; AIMS: Urease-producing microorganisms may lower urea nitrogen (UN) during dialysate-side dosing . We investigated the impact of 3 proven preservatives (acetic acid, ceftazidime, thimerosal) on UN concentration, and the concentrations of creatinine (CR) and beta2-microglobulin (beta2M) . METHODS: The UN, CR and beta2M concentrations were assayed in 3 separate aliquots from 20 spent dialysate samples (ceftazidime, 125 mg/l, or 1% thimerosal, 1 ml/l, vs . control) . The beta2M concentration was assayed in 10 further spent dialysate collections (concentrated glacial acetic acid, 5 ml/l, vs . control) . Solute concentrations were compared with the concordance correlation coefficient (rc) . RESULTS: Ceftazidime and thimerosal had little effect on the concentrations of UN and CR (rc >0.97) . For the beta2M concentration, agreement remained good (rc >0.96) for ceftazidime and thimerosal (although the former tended to lower concentrations) but acetic acid was less optimal (rc = 0.893) . CONCLUSIONS: Ceftazidime and thimerosal may be used as dialysate preservatives without affecting the UN or CR concentrations . Thimerosal is to be preferred when studying beta2M . Acetic acid produces unacceptable inaccuracy when measuring beta2M. Proc Natl Acad Sci U S A, 2004 Sep 21, 101(38), 13726 - 31 Epub 2004 Sep 09. Amine-synthesizing enzyme N-substituted formamide deformylase: screening, purification, characterization, and gene cloning; Fukatsu H et al.; N-substituted formamide was produced through the hydration of an isonitrile by isonitrile hydratase in the isonitrile metabolism . The former compound was further degraded by a microorganism, strain F164, which was isolated from soil through an acclimatization culture . The N-substituted formamide-degrading microorganism was identified as Arthrobacter pascens . The microbial degradation was found to proceed through an enzymatic reaction, the N-substituted formamide being hydrolyzed to yield the corresponding amine and formate . The enzyme, designated as N-substituted formamide deformylase (NfdA), was purified and characterized . The native enzyme had a molecular mass of approximately 61 kDa and consisted of two identical subunits . It stoichiometrically catalyzed the hydrolysis of N-benzylformamide (an N-substituted formamide) to benzylamine and formate . Of all of the N-substituted formamides tested, N-benzylformamide was the most suitable substrate for the enzyme . However, no amides were accepted as substrates . The gene (nfdA) encoding this enzyme was also cloned . The deduced amino acid sequence of nfdA exhibited the highest overall sequence identity (28%) with those of regulatory proteins among known proteins . Only the N-terminal region (residues 58-72) of NfdA also showed significant sequence identity (27-73%) to that of each member of the amidohydrolase superfamily, although there was no similarity in the overall sequence except in the above limited region. J Contam Hydrol, 2004 Oct, 74(1-4), 19 - 38 The influence of system complexity on bacterial transport in saturated porous media; Jordan FL et al.; A series of miscible-displacement column experiments were conducted under saturated flow conditions to systematically investigate the influence of physical and biological complexity on bacterial activity and fate in the presence and absence of a non-sorbing growth substrate, salicylate . Bacterial elution was monitored for three different systems; System I--a sterilized, inoculated, well-sorted sand, System II--a sterilized, inoculated, heterogeneous loamy sand (Hayhook), and System III--two different unsterilized loamy sands (Hayhook and Vinton) each with their associated indigenous microbial community . Results show that System I behaved ideally with respect to both cell and substrate transport, wherein: (1) growth occurred in response to substrate addition, (2) cell elution increased in response to the substrate pulse, and (3) breakthrough curves were reproducible for both substrate and cell elution . In contrast, System II showed ideal behavior with respect to substrate transport but showed variable behavior for cell transport . Further, there was no measurable growth in response to substrate addition and no increase in cell elution during the salicylate pulse . System III exhibited non-ideal behavior for both substrate and cell transport . Of particular interest is the fact that the indigenous communities of the two soils behaved differently . Specifically, for the Hayhook soil, an increased elution response was observed for the heterotrophic population while the salicylate-degrading community was preferentially retained in the column . In contrast for the Vinton soil, the substrate pulse did not elicit an elution response from either the heterotrophic or salicylate-degrading community from the culturable, indigenous Vinton microorganisms . For Systems II and III, the observed variability appears to be associated with the biological component of the system, since sterile controls were reproducible . This type of systematic study is critical for understanding cell and substrate transport behavior in complex, heterogeneous systems, and illustrates the potential uncertainty associated with measurements in such systems. FEMS Microbiol Lett, 2004 Sep 15, 238(2), 429 - 37 Mycobacterium leprae infection of human Schwann cells depends on selective host kinases and pathogen-modulated endocytic pathways; Alves L et al.; Mycobacterium leprae, an obligate intracellular pathogen, shows a unique tropism for Schwann cells (SC) . This leads to the peripheral neuropathy disorder observed in leprosy . In this study, we investigated signal transduction events and the intracellular fate of M . leprae during the interaction of the microorganism with SC . First, we demonstrated that the human schwannoma cell line ST88-14 readily phagocytized the bacteria as observed by time-lapse microscopy, actin staining and electron microscopy . The effect of specific kinase inhibitors on M . leprae internalization was then investigated showing that functional protein tyrosine kinase, calcium-dependent protein kinase and phosphatidylinositol 3-kinase, but not cAMP-dependent protein kinase are essential for phagocytosis of the bacteria . Similar results were obtained when irradiated and live bacteria were compared and when M . leprae was pre-coated with recombinant histone-like-protein/laminin binding protein, a bacterial adhesin . In addition, experiments were performed to analyze the bacterial trafficking within the endosomal network by labeling the acidified intracellular compartments of M . leprae-infected SC with the Lysotracker acidotrophic probe . Acidification of vesicles containing live M . leprae was minimal in both RAW murine macrophages and SC, although phagosomes containing heat-killed bacteria seem to follow normal endocytic maturation . These data indicate that the invading bacteria interfere with normal endocytic pathway maturation of bacteria-containing phagosomes within SC. Biochem Biophys Res Commun, 2004 Aug 13, 321(1), 124 - 31 Differential induction of gene promoter constructs by constitutively active human TLRs; Hasan UA et al.; Antigen presenting cells can sense microorganisms through activation of members of the Toll like receptor family (TLRs), which initiate signals leading to transcription of many inflammation-associated genes . TLRs and IL-1R, through their TIR domains, activate NFkappaB and mitogen-activated protein kinase pathways and upregulate a set of specific target genes . Recent evidence points to several differences in signaling pathways activated by individual TLRs . To evaluate the basic signaling potential of individual TIR signaling domains, we generated constitutively active versions of all known human TLRs by fusing mouse CD4 extracellular portion with the TLR transmembrane and TIR domains . A panel of promoters from genes known to be activated by TLRs as well as artificial promoter constructs with transcription factor binding sites were selected to measure their response in the presence of constitutively active CD4TLR fusion molecules . These studies show for the first time that a unique panel of promoters appears to be highly induced by CD4TLR1, 6 (TLRs that usually function through heterodimerisation with TLR2), and CD4TLR10 . We also observed that CD4TLR4 is the most potent gene activator compared to all other ten human TLRs . Preliminary analyses of several promoter deletions showed that TLRs use different sequence elements to activate these reporters . In addition, since different ligands for a single TLR (e.g., TLR9) can induce different pathways, the CD4TLR fusions seem to activate all the pathways and therefore can be used to assess the overall signaling capacity of a given TLR . Finally, analysis of promoter constructs induced by the only orphan TLR, TLR10, allowed the identification of the ENA78 promoter as a tool for screening its ligands. Clin Nephrol, 2004 Aug, 62(2), 158 - 61 A rare cause of anemia due to intestinal tuberculosis in a renal transplant recipient; Kandutsch S et al.; A renal transplant recipient with stable allograft function presented with massive hemorrhagic diarrhea and severe anemia . No microbial infection could be found in stool cultures . Early colonoscopy showed severe colitis with ulceration . Histological samples confirmed granulomatous inflammation with acid-resistant Ziehl-Neelson-positive microorganisms of mycobacterial type . Polymerase chain reaction (PCR) analysis of native mucosal biopsies specified the infectious organism as Mycobacterium tuberculosis complex . The patient responded well to antimycobacterial therapy and was still asymptomatic after 6 months with a stable graft function . Our case shows that tuberculosis can be a severe clinical problem in transplant recipients . Most of the patients with intestinal tuberculosis, reported to literature, were diagnosed post mortem or after explorative laparotomy and bowel resection . Thus, intestinal tuberculosis should be considered when a transplant recipient shows abdominal symptoms with no clear evidence of another infection . Proper diagnosis and treatment resulted in a beneficial outcome in our patient. J Clin Endocrinol Metab, 2004 Sep, 89(9), 4734 - 45 Affinity-enrichment of thyrotropin receptor autoantibodies from Graves' patients and normal individuals provides insight into their properties and possible origin from natural antibodies; Latrofa F et al.; We used purified recombinant TSH receptor (TSHR) antigen prepared in mammalian cells to affinity-enrich TSHR autoantibodies from Graves' patients' IgG . Autoantibody enrichment, assayed by TSH binding inhibitory activity, was 20- to 1000-fold . Thyroid-stimulating antibody activity enrichment, although more difficult to quantitate, was comparable . TSHR-autoantibody approximate affinities for the holoreceptor assessed indirectly by TSH binding inhibition were 4-27 x 10(-9) m, an underestimate because 100% TSHR autoantibody purity was not attained . Consistent with previous data for serum, highly enriched TSHR autoantibodies in three of four patients showed lambda light chain bias . However, in contrast to expectations, antigen-enriched IgG was skewed primarily toward IgG2 and IgG3, subclasses associated with polysaccharides and microorganisms, respectively . Subclass depletion studies on antigen-enriched IgG indicated that TSHR autoantibodies were predominantly IgG1 and, surprisingly, IgG4 . As controls, we affinity-enriched pooled IgG from normal individuals on TSHR antigen . This enriched IgG had detectable TSH binding inhibitory activity, although with lower specific activity than, and lacking the thyroid stimulatory activity of, Graves' IgG . Moreover, these natural IgG class autoantibodies largely recognized the same conformational variation in the TSHR N-terminal region as disease-associated TSHR autoantibodies . These studies suggest that TSHR autoantibodies may arise from natural autoantibodies, possibly by class switching from cross-reacting antibodies to microorganisms. Annu Rev Cell Dev Biol . 2004 Jun 15; {Epub ahead of print} 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 pre-programmed 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 continues harboring the microorganism . 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 . Expected online publication date for the Annual Review of Cell and Developmental Biology Volume 20 is October 6, 2004 . Please see for revised estimates. Annu Rev Entomol . 2004 Sep 7; {Epub ahead of print} Pheromone-Mediated Aggregation in Nonsocial Insects and Arthropods: An Evolutionary Ecological Perspective; Wertheim B et al.; Although the use of aggregation pheromones has been reported for hundreds of nonsocial arthropod species, the evolutionary ecological aspects of this behavior have received little attention . Despite the elaborate literature on mechanisms, robust data on costs and benefits of aggregation pheromones are scant . Existing literature indicates that, in contrast to the diversity of mechanisms, the ecological conditions in which aggregation pheromones are used are more alike . This points to a few general categories for costs and benefits of aggregation pheromones, and these are discussed . We subsequently review interspecific interactions that may be affected by the use of aggregation pheromones . We encounter a strikingly frequent association of aggregation pheromones with fungi and microorganisms and address cross-attraction by competitor species and exploitation by natural enemies . We show that aggregative behavior by individuals through the use of pheromones can profoundly affect ecological interactions and advocate further evolutionary and ecological investigations of pheromone-mediated aggregation . Expected online publication date for the Annual Review of Entomology Volume 50 is December 3, 2004 . Please see for revised estimates. Annu Rev Genet . 2004 Jul 14; {Epub ahead of print} 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 . Expected online publication date for the Annual Review of Genetics Volume 38 is November 10, 2004 . Please see for revised estimates. Annu Rev Genet . 2004 Jun 11; {Epub ahead of print} 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 . Expected online publication date for the Annual Review of Genetics Volume 38 is November 10, 2004 . Please see for revised estimates. Annu Rev Microbiol . 2004 Jul 14; {Epub ahead of print} Endangered Antarctic Environments; Cowan DA et al.; The Antarctic continent harbours a range of specialized and sometimes highly localised 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 characterised 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 will be able to 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 . Expected online publication date for the Annual Review of Microbiology Volume 58 is September 8, 2004 . Please see for revised estimates. Annu Rev Microbiol . 2004 Jun 11; {Epub ahead of print} 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 . Expected online publication date for the Annual Review of Microbiology Volume 58 is September 8, 2004 . Please see for revised estimates. Annu Rev Microbiol . 2004 Mar 26; {Epub ahead of print} Anaerobic Oxidation of Methane and Ammonium; Strous M et al.; Anaerobic oxidation of methane (AMO) and ammonium (anammox) 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 was 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 . Expected online publication date for the Annual Review of Microbiology Volume 58 is September 8, 2004 . Please see for revised estimates. J Sep Sci, 2004 Jul, 27(10-11), 767 - 78 Monoliths for fast bioseparation and bioconversion and their applications in biotechnology; Jungbauer A et al.; Monoliths have consolidated their position in bioseparation . More than 200 different applications have been reported in the past two decades and their advantages compared to conventional chromatography demonstrated . These include the high mass transfer efficiency due to the convective flow enabled by the macroporous character of the matrix . Recently plasmid DNA and viruses were separated with high efficiency and cryogels and monolithic superporous agarose were developed for capture of proteins from crude homogenates and separation of microorganisms or lymphocytes . Currently four companies manufacture monoliths mainly for analytical applications although monoliths with a volume of 0.8 liter are commercially available and 8 L are available as prototypes . A book entitled "Monolithic materials: preparation, properties and applications" was published in 2003 and became standard reference of the status of this area . This review focuses on the progress in monoliths that goes beyond the scope of this reference book . Less progress has been made in the field of bioconversions in spite of the fact that monolithic supports exhibit better performance than beads in enzymatic processing of macromolecules . It appears that the scientific community has not yet realized that supports for these applications are readily available . In addition, monoliths will further substantially advance bioseparations of both small and large molecules in the future. Front Biosci, 2004 Sep 01, 9, 3156 - 62 Mechanisms of inflammation: the good, the bad and the ugly; Laroux FS; To the general public, the term, inflammation, is associated with pain, swelling, fever and a general sense of unease ranging from mere nuisance to debilitating illness . Under normal circumstances, the process of inflammation is actually a protective response designed to ward off invasion of the person by pathogens such as bacteria, viruses and/or parasites . The immune system of higher mammals (e.g . humans) is comprised of two distinct, arms, termed the innate and the adaptive systems . While these two components play unique roles in controlling pathogens, each relies, in some part, upon the effective function of the other in order to efficiently eliminate invading microorganisms . There are however situations in which this complex system is unable to properly function leading to unresolved infections and/or chronic states of inflammation . This review will summarize the basic mechanisms involved in the inflammatory process as well as discuss some of the key mediators and modulators of this process. J Small Anim Pract, 2004 Aug, 45(8), 401 - 4 Bacteriological study of the liver in dogs; Niza MM et al.; This study aimed to confirm the possible presence of bacteria in the liver of healthy dogs . Laparotomy was performed in 20 animals admitted for routine abdominal surgery . To be selected for the study, dogs had to be healthy adults without clinical liver disease, signs of infection or macroscopic liver abnormalities . Biopsy samples were histologically and bacteriologically examined . Bacteriological analysis was negative for the livers of eight of the dogs . The remaining animals harboured a diverse bacterial flora in their liver . Twelve bacterial species were identified . Histology showed that the livers of 19 dogs had minor or no abnormalities, and only one animal had interstitial fibrosis and trabecular disarrangement . Histological changes were not related to the presence of bacteria . Thus the results showed that the liver of healthy dogs may harbour different bacterial species . These microorganisms did not cause any detectable manifestation of disease, despite being potential pathogens. Biotechnol Bioeng, 2004 Sep 5, 87(5), 632 - 40 Williopsis californica, Williopsis saturnus, and Pachysolen tannophilus: novel microorganisms for stereoselective oxidation of secondary alcohols; Carballeira Rodriguez JD et al.; A screening of 416 microorganisms from different taxonomical groups (bacteria, actinomycetes, yeasts, and filamentous fungi) has been performed looking for active strains in the stereoselective oxidation of secondary alcohols . The working collection was composed of 71 bacterial strains, 45 actinomycetes, 59 yeasts, 60 basidiomycetes, 33 marin