Microorganism

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 marine fungi, and 148 filamentous fungi . All microorganisms selected were mesophilic . Yeasts were the most active microbial group in the whole-cell-catalyzed oxidation . Williopsis californica, Williopsis saturnus, and Pachysolen tannophilus were the strains of greatest interest, both as growing cells and as resting cells . The oxidation of the alcohols takes place when cells are in the stationary growth phase (after 48 h of culture) . These three strains are S-stereoselective for the oxidation of racemic secondary alkanols and show stereospecificity in the oxidation of menthol or neo-menthol, whereas iso-menthol is not oxidized . In the case of the 1-tetrahydronaphtol enantiomers, only the S-enantiomer is oxidized . The three strains were immobilized by entrapment using agarose and agar from algae of the Gracilaria genus . The agarose derivatives displayed significant improvement in the stereospecificity of the reactions.

Cytometry, 2004 Sep, 61A(1), 88 - 98
Affinity of single S . cerevisiae cells to 2-NBDglucose under changing substrate concentrations; Achilles J et al.; BACKGROUND: Saccharomyces cerevisiae is a widely employed microorganism in biotechnological processes . Since proliferation and product formation depend on the capacity of the cell to access and metabolize a carbon source, a technique was developed to enable for analyzing the S . cerevisiae H155 cells' affinity to extracellular glucose concentrations . METHODS: The fluorescent glucose analogue 2-NBDglucose was employed as a functional parameter to analyze the cells' affinity to glucose . Structural parameters (proliferation, neutral lipid content, granularity, and cell size) were also investigated . Cells were grown both in batches and in chemostat regimes . RESULTS: The 2-NBDglucose uptake in individual cells proceeds in a time- and concentration-dependent manner and is affected by respiratory and respirofermentative modes of growth . The process is inhibited by D-glucose, D-fructose, D-mannose, and sucrose, but not L-glucose, D-galactose or lactose; maltose is a weak inhibitor . The affinity of the individual cells to 2-NBDglucose was found to be high at low extracellular glucose concentrations, and weak at high concentrations . An additional, underlying pattern in the cells' affinity to glucose was detected, illustrated by the recurrent appearance of two subpopulations showing distinctly differing quantities of this substrate . CONCLUSIONS: A multiparameter flow cytometry approach is presented that enables, for the first time, for analysis of the affinity of individual S . cerevisiae cells to glucose . Besides the adjustment of the yeast cell metabolism to extracellular glucose concentrations by altering their affinity to glucose, at least one further mechanism is clearly involved . Two subpopulations of cells were resolved, with different affinities not correlated with other cellular parameters measured .

Extremophiles . 2004 Sep 4; {Epub ahead of print}
A simple fluorimetric method for the estimation of DNA-DNA relatedness between closely related microorganisms by thermal denaturation temperatures; Gonzalez JM et al.; Determination of whole-genome DNA-DNA similarity is today a standard technique for species delineation in microbial taxonomy . However, these studies demand hard-to-perform and time-consuming experiments . Herein, we present an easy and rapid fluorimetric method to estimate DNA-DNA relatedness between microbial strains from differences of the thermal denaturation temperatures of hybrid and homologous genomic DNA . Double-stranded DNA was specifically stained with SYBR Green I, and its thermal denaturalization was followed by measuring a decrease in fluorescence . A quantitative, real-time PCR thermocycler was used to perform the experiment and obtain fluorescence determinations at increasing temperatures . The proposed method was validated by comparing species of the hyperthermophilic genera Pyrococcus and Thermococcus . The method proves to be an easy, rapid, and inexpensive alternative to estimate DNA-DNA relatedness between closely related species.

Int J Dev Biol, 2004, 48(5-6), 583 - 98
Parallels in invasion and angiogenesis provide pivotal points for therapeutic intervention; Eccles SA; Biological evolution is economical and successful fundamental processes are frequently recapitulated . There are remarkable similarities in the molecular mechanisms which enable tumour cells to invade into surrounding tissues and activated endothelial cells to generate new capillaries, which facilitate the growth and dissemination of cancer . Indeed these pathological processes are themselves based upon key vertebrate developmental processes, and in some cases parallel strategies used by microorganisms to colonise their hosts' tissues . The aim of this review is to explore these parallels in more detail and indicate possible pivotal points for therapeutic intervention . These novel approaches may ultimately optimise the selective targeting of processes involved in tumour invasion and angiogenesis, while sparing normal adult proliferating tissues . Strategies include inhibition of oncogenic pathways in tumour cells which not only stimulate tumour cell growth and invasion, but also initiate neoangiogenesis by upregulation of angiogenic cytokines . Secondly, downstream signalling pathways, transcriptional regulation and effectors common to both processes, and finally points of interaction/cross-talk between tumour cells and endothelial cells which are necessary to enable invasion and angiogenesis to proceed.

Plant Physiol, 2004 Sep, 136(1), 2887 - 94 Epub 2004 Sep 03.
Microbial products trigger amino acid exudation from plant roots; Phillips DA et al.; Plants naturally cycle amino acids across root cell plasma membranes, and any net efflux is termed exudation . The dominant ecological view is that microorganisms and roots passively compete for amino acids in the soil solution, yet the innate capacity of roots to recover amino acids present in ecologically relevant concentrations is unknown . We find that, in the absence of culturable microorganisms, the influx rates of 16 amino acids (each supplied at 2.5 microm) exceed efflux rates by 5% to 545% in roots of alfalfa (Medicago sativa), Medicago truncatula, maize (Zea mays), and wheat (Triticum aestivum) . Several microbial products, which are produced by common soil microorganisms such as Pseudomonas bacteria and Fusarium fungi, significantly enhanced the net efflux (i.e . exudation) of amino acids from roots of these four plant species . In alfalfa, treating roots with 200 microm phenazine, 2,4-diacetylphloroglucinol, or zearalenone increased total net efflux of 16 amino acids 200% to 2,600% in 3 h . Data from (15)N tests suggest that 2,4-diacetylphloroglucinol blocks amino acid uptake, whereas zearalenone enhances efflux . Thus, amino acid exudation under normal conditions is a phenomenon that probably reflects both active manipulation and passive uptake by microorganisms, as well as diffusion and adsorption to soil, all of which help overcome the innate capacity of plant roots to reabsorb amino acids . The importance of identifying potential enhancers of root exudation lies in understanding that such compounds may represent regulatory linkages between the larger soil food web and the internal carbon metabolism of the plant.

Zh Mikrobiol Epidemiol Immunobiol, 2004 May-Jun, (3), 62 - 8
{Detection of bacterial molecular markers in the tissue of cardiac valves in normal and pathological states by gas chromatography and mass spectrometry}; Khabib ON et al.; Samples from cardiac valves of 31 patients were analyzed by gas chromatography and mass spectrometry . The algorithm of mass spectrometric parameters was developed, which permitted the determination of about 200 known microbial fatty acids, aldehydes and sterols, sufficient for the detection and quantitative determination of more that 170 taxons of clinically significant microorganisms on the genus or species levels . The quantitative and qualitative differences in the composition of microbial markers of endocardial valves in normal and pathological states, particularly in cases of infectious endocarditis, were detected . The participation of 37 microbial taxons in the process was confirmed . The level of endocardium colonization in infectious endocarditis reached from 2 to 7 x 10(9) microbial cells/g of valvular tissue (which exceeded twofold the equivalent concentrations of the marker in the normal state) . In terms of quantity, the leading role was played by Cardiobacterium hominis.

Free Radic Res, 2004 Jun, 38(6), 629 - 37
NADPH oxidase-mediated generation of reactive oxygen species is critically required for survival of undifferentiated human promyelocytic leukemia cell line HL-60; Dong JM et al.; Nicotinamide adenine dinucleotide phosphate oxidase (NADPH oxidase) mediated generation of reactive oxygen species (ROS) was originally identified as the powerful host defense machinery against microorganism in phagocytes . But recent reports indicated that some non-phagocytic cells also have the NADPH oxidase activity, and the ROS produced by it may act as cell signal molecule . But as far as today, whether the NADPH oxidase also plays similar role in phagocyte has not been paid much attention . Utilizing the undifferentiated HL-60 promyelocytic leukemia cells as a model, the aim of the present study was to determine whether NADPH oxidase plays a role on ROS generation in undifferentiated HL-60, and the ROS mediated by it was essential for cell's survival . For the first time, we verified that the release of ROS in undifferentiated HL-60 was significantly increased by the stimulation with Calcium ionophore or opsonized zymosan, which are known to trigger respiration burst in phagocytes by NADPH oxidase pathway . Diphenylene iodonium (DPI) or apocynin (APO), two inhibitors of NADPH oxidase, significantly suppressed the increasing of ROS caused by opsonized zymosan . Cell survival assay and fluorescence double dyeing with acridine orange and ethidium bromide showed that DPI and APO, as well as superoxide dismutase (SOD) and catalase (CAT) concentration-dependently decreased the viability of undifferentiated HL-60 cells, whereas exogenous H2O2 can rescue the cells from death obviously . Our results suggested that the ROS, generated by NADPH oxidase play an essential role in the survival of undifferentiated HL-60 cells.

Vnitr Lek, 2004 Jun, 50(6), 453 - 61
{Infection and hemostasis}; Hudecek J et al.; Localised and following systemic inflammatory reaction accompanying progression of infection causes generation of anti-inflammatory cytokines . They activate leucocytes, endothelium, coagulation and fibrinolysis . Sepsis is usually accompanied by already decompensated disseminated intravascular coagulation which significantly affects mortality of patients with this disease . The main cause of hypercoagulation state during sepsis seems to be inhibition of fibrinolysis as a result of overproduction of plasminogen activator inhibitor-1 in later stages of the disease . Some microorganisms have specific properties which affect individual components of hemostasis and thus increase their virulence . Because natural inhibitors of coagulation have not only anticoagulation but also strong anti-inflammatory effect, they seem to be an optimum remedy for fluorid coagulopathy during sepsis . Moreover, their use usually does not increase risk of bleeding.

J Trauma, 2004 Aug, 57(2), 316 - 22
Is bilateral protected specimen brush sampling necessary for the accurate diagnosis of ventilator-associated pneumonia?
Butler KL, Best IM, Oster RA, Katon-Benitez I, Lynn Weaver W, Bumpers HL.
BACKGROUND: Clinical acumen alone is unreliable in establishing a diagnosis of ventilator-associated pneumonia (VAP) and controversy exists over which diagnostic tools should be utilized to confirm a clinical suspicion of VAP . The purpose of this study was to determine the reliability of blind protected specimen brush (PSB) sampling in the diagnosis of VAP and if bilateral PSB sampling is necessary . METHODS: Prospective study comparing blind PSB sampling with bronchoscopic directed PSB sampling in thirty-four consecutive SICU patients with a clinical suspicion of VAP . All patients underwent blind PSB sampling followed by bronchoscopic directed contralateral PSB sampling . RESULTS: Twenty-four of 34 patients (71%) were diagnosed to have VAP . The concordance rate between blind and directed PSB samples was 53% (18/34) . When blind PSB was positive (15/34), the contralateral sample yielded a different microorganism in three patients (9%) . When blind PSB was negative (19/34), infection was present in the contralateral lung in nine patients (26%) . Blind PSB sampling alone was inaccurate in 35% of patients . CONCLUSIONS: The low concordance between blind and directed PSB suggests the need to sample both lung fields . Bilateral PSB sampling can identify unsuspected pathogenic microorganisms in the contralateral lung.

Appl Environ Microbiol, 2004 Sep, 70(9), 5298 - 304
Modified serial analysis of gene expression method for construction of gene expression profiles of microbial eukaryotic species; Coyne KJ et al.; Serial analysis of gene expression (SAGE) is a powerful approach for the identification of differentially expressed genes, providing comprehensive and quantitative gene expression profiles in the form of short tag sequences . Each tag represents a unique transcript, and the relative frequencies of tags in the SAGE library are equal to the relative proportions of the transcripts they represent . One of the major obstacles in the preparation of SAGE libraries from microorganisms is the requirement for large amounts of starting material (i.e., mRNA) . Here, we present a novel approach for the construction of SAGE libraries from small quantities of total RNA by using Y linkers to selectively amplify 3' cDNA fragments . To validate this method, we constructed comprehensive gene expression profiles of the toxic dinoflagellate Pfiesteria shumwayae . SAGE libraries were constructed from an actively toxic fish-fed culture of P . shumwayae and from a recently toxic alga-fed culture . P . shumwayae-specific gene transcripts were identified by comparison of tag sequences in the two libraries . Representative tags with frequencies ranging from 0.026 to 3.3% of the total number of tags in the libraries were chosen for further analysis . Expression of each transcript was confirmed in separate control cultures of toxic P . shumwayae . The modified SAGE method described here produces gene expression profiles that appear to be both comprehensive and quantitative, and it is directly applicable to the study of gene expression in other environmentally relevant microbial species.

Appl Environ Microbiol, 2004 Sep, 70(9), 5177 - 82
Copper ions stimulate polyphosphate degradation and phosphate efflux in Acidithiobacillus ferrooxidans; Alvarez S et al.; For some bacteria and algae, it has been proposed that inorganic polyphosphates and transport of metal-phosphate complexes could participate in heavy metal tolerance . To test for this possibility in Acidithiobacillus ferrooxidans, a microorganism with a high level of resistance to heavy metals, the polyphosphate levels were determined when the bacterium was grown in or shifted to the presence of a high copper concentration (100 mM) . Under these conditions, cells showed a rapid decrease in polyphosphate levels with a concomitant increase in exopolyphosphatase activity and a stimulation of phosphate efflux . Copper in the range of 1 to 2 microM greatly stimulated exopolyphosphatase activity in cell extracts from A . ferrooxidans . The same was seen to a lesser extent with cadmium and zinc . Bioinformatic analysis of the available A . ferrooxidans ATCC 23270 genomic sequence did not show a putative pit gene for phosphate efflux but rather an open reading frame similar in primary and secondary structure to that of the Saccharomyces cerevisiae phosphate transporter that is functional at acidic pH (Pho84) . Our results support a model for metal detoxification in which heavy metals stimulate polyphosphate hydrolysis and the metal-phosphate complexes formed are transported out of the cell as part of a possibly functional heavy metal tolerance mechanism in A . ferrooxidans.

C R Biol, 2004 Jul, 327(7), 639 - 48
Symbiotic microorganisms, a key for ecological success and protection of plants; Selosse MA et al.; Plant-associated microbial diversity encompasses symbionts, protecting their host against various aggressions . Mycorrhizal and rhizospheric microorganisms buffer effects of soil toxic compounds and soil-borne pathogens . Endophytic bacteria and fungi, some of which are vertically inherited through seeds, take part in plant protection by acting directly on aggressive factors (mainly pathogens and herbivores) or by enhancing plant responses . Plant protective microbial symbionts determine the ecological success of plants; they drastically modify plant communities and related trophic webs . This review suggests approaches to improve the inventory of diversity and functions of in situ plant-associated microorganisms.

J Calif Dent Assoc, 2004 Jun, 32(6), 459 - 68
Microbiologic aspects of endodontic infections; Baumgartner JC; Our understanding of endodontic infections and treatment of endodontic disease has increased significantly over the last decade . This article is an update of those findings . Aspects that are reviewed include: portal of entry for microorganisms, virulence and pathogenicity of organisms, descriptions of primary and recurrent endodontic infections, and treatment of endodontic infections.

J Bacteriol, 2004 Sep, 186(18), 6133 - 41
An SOS response induced by high pressure in Escherichia coli; Aertsen A et al.; Although pressure is an important environmental parameter in microbial niches such as the deep sea and is furthermore used in food preservation to inactivate microorganisms, the fundamental understanding of its effects on bacteria remains fragmentary . Our group recently initiated differential fluorescence induction screening to search for pressure-induced Escherichia coli promoters and has already reported induction of the heat shock regulon . Here the screening was continued, and we report for the first time that pressure induces a bona fide SOS response in E . coli, characterized by the RecA and LexA-dependent expression of uvrA, recA, and sulA . Moreover, it was shown that pressure is capable of triggering lambda prophage induction in E . coli lysogens . The remnant lambdoid e14 element, however, could not be induced by pressure, as opposed to UV irradiation, indicating subtle differences between the pressure-induced and the classical SOS response . Furthermore, the pressure-induced SOS response seems not to be initiated by DNA damage, since DeltarecA and lexA1 (Ind-) mutants, which are intrinsically hypersensitive to DNA damage, were not sensitized or were only very slightly sensitized for pressure-mediated killing and since pressure treatment was not found to be mutagenic . In light of these findings, the current knowledge of pressure-mediated effects on bacteria is discussed.

Hautarzt, 2004 Oct, 55(10), 1001 - 3
{Identification of geophilic and zoophilic dermatophytes in siblings with tinea capitis . A pathogenic factor or contamination?}; Lehmann S et al.; Two siblings of African origin presented with multiple scaling patches and alopecia on the scalp four weeks after returning from a vacation in Eritrea . Direct KOH examination revealed fungal elements; Trichophyton mentagrophytes and Trichophyton terrestre were identified in the fungal culture . We discuss the putative pathogenic role of both microorganisms in causing disease . Although infection with Microsporum canis currently accounts for almost fifty percent of all cases of tinea capitis in Germany, other fungi have gained importance due to tourism and increasing migration.

Indian J Exp Biol, 2004 Jul, 42(7), 681 - 5
Effect of trace elements on surface hydrophobicity and adherence of Escherichia coli to uroepithelial cells; Saralaya V et al.; Trace elements have significant effect on the physiology of bacteria . Variation in the concentration of trace elements may affect the expression of virulence by microorganisms . The effect of trace elements on hydrophobicity and adherence of E.coli to uroepithelial cells was studied . Increasing concentrations of Ca2+, Mg2+, Fe3+ and Zn2+ significantly decreased the surface hydrophobicity . Toxic trace elements like Co2+, Cu2+, Mn2+ and Ni2+ did not alter surface hydrophobicity . With regards to adherence of E.coli to uroepithelial cells, only Mg2+ had significant effect . Toxic trace elements decreased the rate of cell adherence . The pathogenic strains of E.coli showed higher surface hydrophobicity and better cell adherence compared to the nonpathogenic strains . There was good correlation between surface hydrophobicity and cell adherence at higher concentrations (0.1 to 0.2mM) of Fe2+ and Zn2+ . The results indicated that trace elements can significantly affect surface hydrophobicity and adherence of E.coli to uroepithelial cells . Such effect may have a significant impact on the initial stages of bacterial infection.

J Am Acad Dermatol, 2004 Sep, 51(3), 327 - 41; quiz 342-4
Rosacea: I . Etiology, pathogenesis, and subtype classification; Crawford GH et al.; Rosacea is one of the most common conditions dermatologists treat . Rosacea is most often characterized by transient or persistent central facial erythema, visible blood vessels, and often papules and pustules . Based on patterns of physical findings, rosacea can be classified into 4 broad subtypes: erythematotelangiectatic, papulopustular, phymatous, and ocular . The cause of rosacea remains somewhat of a mystery . Several hypotheses have been documented in the literature and include potential roles for vascular abnormalities, dermal matrix degeneration, environmental factors, and microorganisms such as Demodex folliculorum and Helicobacter pylori . This article reviews the current literature on rosacea with emphasis placed on the new classification system and the main pathogenic theories.Learning objective At the conclusion of this learning activity, participants should be acquainted with rosacea's defining characteristics, the new subtype classification system, and the main theories on pathogenesis.

FEMS Microbiol Lett, 2004 Sep 1, 238(1), 65 - 70
Construction of bacterial artificial chromosome library from electrochemical microorganisms; Back JH et al.; A microbial fuel cell is a device that directly converts metabolic energy into electricity, using electrochemical technology . The analysis of large genome fragments recovered directly from microbial communities represents one promising approach to characterizing uncultivated electrochemical microorganisms . To further assess the utility of this approach, we constructed large-insert (140 kb) bacterial artificial chromosome (BAC) libraries from the genomic DNA of a microbial fuel cell, which had been operated for three weeks using acetate media . We screened the expression of several ferric reductase activities in the Escherichia coli host, in order to determine the extent of heterologous expression of metal-ion-reducing enzymes in the library . Phylogenetic analysis of 16S rRNA gene sequences recovered from the BAC libraries indicates that they contain DNA from a wide diversity of microbial organisms . The constructed bacterial library proved a powerful tool for exploring metal-ion reductase activities, providing information on the electron transport pathway of electrochemical microbial (ECM) organisms.

Free Radic Biol Med, 2004 Oct 1, 37(7), 977 - 87
Impaired superoxide radical production by bronchoalveolar lavage cells from NO(2)-exposed rats; Olker C et al.; Production of superoxide radicals is a central property of professional phagocytes used to combat invading microorganisms . Even though the number of macrophages and neutrophils is often increased in the lungs of patients with chronic lung diseases, these patients frequently suffer from bacterially induced exacerbations . To understand the underlying mechanisms, we investigated the production of superoxide radicals by bronchoalveolar lavage (BAL) cells in a rat NO(2) exposure model (10 ppm NO(2) for 1, 3, or 20 days) . We showed that cells from NO(2)-exposed animals display a significantly impaired superoxide radical release after zymosan stimulation . The use of specific inhibitors (antimycin or diphenyleneiodonium {DPI}) revealed that the major enzyme systems, NADPH oxidase and complex III of the respiratory chain, are affected . In addition, we investigated gene expression and enzyme activities of antioxidant enzymes . mRNA expression was significantly enhanced for glutathione peroxidase (GPx)-3 and CuZn-superoxide dismutase (SOD) in BAL cells from animals exposed 3 and 20 days, and GPx and SOD enzyme activities were increased in BAL cells from rats exposed 20 days . In conclusion, concomitant occurrence of reduced production and increased scavenging of superoxide radicals resulted in the drastically impaired release of these radicals from BAL cells of NO(2)-exposed rats.

Curr Biol, 1993 Dec 1, 3(12), 842 - 53
A new method for manipulating transgenes: engineering heat tolerance in a complex, multicellular organism; Welte MA et al.; Background:Heat-shock proteins (hsps) are thought to protect cells against stresses, especially due to elevated temperatures . But while genetic manipulation of hsp gene expression can protect microorganisms and cultured metazoan cells against lethal stress, this has so far not been demonstrated in multicellular organisms . Testing whether expression of an hsp transgene contributes to increased stress tolerance is complicated by a general problem of transgene analysis: if the transgene cannot be targeted to a precise site in the genome, newly observed phenotypes may be due to either the action of the transgene or mutations caused by the transgene insertion . Results: To study the relationship between heat tolerance and hsp expression in Drosophila melanogaster, we have developed a novel method for transgene analysis, based upon the site-specific FLP recombinase . The method employs site-specific sister chromatid exchange to create an allelic series of transgene insertions that share the same integration site, but differ in transgene copy number . Phenotypic differences between members of this series can be confidently attributed to the transgenes . Using such an allelic series and a novel thermotolerance assay for Drosophila embryos, we investigated the role of the 70 kD heat-shock protein, Hsp 70, in thermotolerance . At early embryonic stages, Hsp70 accumulation was rate-limiting for thermotolerance, and elevated Hsp70 expression increased survival at extreme temperatures . Conclusion: Our results provide an improved method for analyzing transgenes and demonstrate that, in Drosophila, Hsp70 is a critical thermotolerance factor . They show, moreover, that manipulating the expression of a single hsp can be sufficient to improve the stress tolerance of a complex multicellular organism.

Biotechniques, 2004 Aug, 37(2), 218, 220 - 2
PathoGene: a pathogen coding sequence discovery and analysis resource; Ng KW et al.; PathoGene is a web-based resource that streamlines the process of predicting genes in microorganisms and designs PCR primers for amplification to facilitate sequence analysis and experimentation . PathoGene currently supports primer design for every complete microbial, viral, and fungal genome as cataloged in GenBank by the National Center for Biotechnology Information (NCBI; The resulting primers can then be subjected to a stand-alone Basic Local Alignment Search Tool (BLAST) system called PathoBLAST in which the predicted PCR product and/or primers can be compared against the genome of interest or a similar genome to find related genes or estimate primer quality.

Ying Yong Sheng Tai Xue Bao, 2004 Apr, 15(4), 717 - 22
{Concepts and relative analytical techniques of soil organic matter}; Wu T et al.; The research of soil organic matter (SOM) has been highlighted in soil science . In the past 50 years, new perspectives in the relationship between SOM and sustainability of atmosphere and biomosphere, and strong motivation to find a vivid index for soil quality variation induced the transformation in concepts and analytical techniques of SOM: the curiousness to humic substances faded off since they were dull to anthropogenic activities, and interests were focused on the light fraction of organic matter (LFOM), organic carbon associated with different mineral particles in size, particulate and intra-particulate organic matter (POM and iPOM), water soluble organic matter (WSOM), and microbial biomass carbon (MB-C) . The relative fractionation procedures have been developed, and the main research activities on SOM are transformed from the products of microorganisms (humus) to the organic matter comprised in plant residues at their various decomposition stages and the organic carbon in microorganisms, since they are biologically active and immediately respond to soil cultivation and tillage, crop rotation, and fertilizer application, etc.

J Sep Sci, 2004 Feb, 27(3), 174 - 80
Microbial diversity in biodeteriorated monuments as studied by denaturing gradient gel electrophoresis; Gonzalez JM et al.; Studies of the microorganisms living on cultural assets and their potential damaging effects begin with an understanding of the microbial diversity present in such samples . Recently, molecular techniques have started to attract considerable interest since they do not require the culture of microorganisms in order to detect their presence . The basic protocol followed during microbial diversity analysis on cultural heritage assets utilizes electrophoretic techniques for separating highly homologous sequences . At present, Denaturing Gradient Gel Electrophoresis (DGGE) is the most frequently reported technique for separating DNA fragments during microbial diversity studies of art objects . In this report, we describe DGGE profiling techniques, show the most common applications, and present some examples of their use in microbial diversity studies on cultural heritage.

J Sep Sci, 2004 Feb, 27(3), 167 - 73
Impact of biological factors on binding media identification in art objects: identification of animal glue in the presence of Aspergillus niger; Tsakalof AK et al.; The materials and especially organic materials used for creation of art objects can be utilized by various microorganisms for their growth and facilitate the microbial colonization of the object . An understanding of the chemical alterations in artefacts caused by the presence of microorganisms can be crucial for correct identification of the materials initially used for the artefact creation--nowadays an important step in restoration and/or art-historical investigation of the art object . The present article describes a model experiment in which we investigated the possible chemical alterations in animal glue films used as substrate for growth of the fungus Aspergillus niger . The sterilized animal glue solution was poured into Petri dishes, inoculated with Aspergillus niger, and subsequently incubated at 15 degrees C for 0, 7, 9, 14, and 28 days . After interruption of incubation, the content of the Petri dish was analyzed for amino acid composition by the GC-MS based method . It was found that the growth of Aspergillus niger on animal glue films did not cause significant changes in the amino acid composition of the film and had no impact on animal glue identification.

Braz J Med Biol Res, 2004 Sep, 37(9), 1353 - 63 Epub 2004 Aug 24.
Normal expression of IFN-gammaR in four patients with uncommon mycobacterial infection phenotypes; Rugeles MT et al.; Several primary immunodeficiency diseases affecting the interleukin 12/interferon gamma (IFN-gamma) pathway have been identified, most of them characterized by recurrent and protracted infections produced by intracellular microorganisms, particularly by several species of mycobacteria . In the present study we analyzed the expression of IFN-gamma receptor (IFN-gammaR) and signal transducer and activator of transcription 1 (STAT-1) in 4 children with Mycobacterium tuberculosis infection of uncommon clinical presentation . These molecules were evaluated by flow cytometry and Western blotting in B cells transformed with Epstein-Barr virus and mutations were scanned by single-strand conformational polymorphisms and DNA sequencing . The expression of IFN-gammaR1 was normal in all 4 patients . The genetic analysis of IFN-gammaR1 and IFN-gammaR2 coding sequences did not reveal any mutation . The expression of the STAT-1 molecule was similar in patients and healthy controls; however, when the phosphorylation of this transcription factor in response to IFN-gamma activation was evaluated by Western blot, a significant lower signal was evident in one patient . These data indicate that there are no alterations in the expression or function of the IFN-gammaR chains in these patients . However, the low level of STAT-1 phosphorylation found in one of these patients might be explained by a defect in one of the molecules involved in the signal transduction pathway after IFN-gamma interacts with its receptor . In the other three patients the inability to eliminate the mycobacteria may be due to a defect in another effector mechanism of the mononuclear phagocytes.

Ophthalmologica, 2004 Sep-Oct, 218(5), 323 - 7
Antifungal activity of intraocularly used liquids against Aspergillus; Economou-Stamatelopoulou C et al.; The antifungal effectiveness of liquids used as intraocular tamponading agents in vitrectomy was tested against a strain of Aspergillus niger . This microorganism is a frequent causative factor of endophthalmitis . The strain belonged to the ATCC collection (A . niger ATCC 16404) . The samples tested were: (a) perfluorocarbons: perfluorodecalin and perfluoroctane, (b) silicone oils: Siloil 1,000 and Siloil 5,000, and (c) balanced salt solutions: BSS and BSS Plus . The experiment consisted in inoculating the samples with the microorganism, in preserving the samples in 25 degrees C in the dark, and in taking small amounts of each product for counting surviving microorganisms at t = 0 and then after 1 day, and 1, 2, 3 and 4 weeks . Among the samples tested, perfluorocarbons and silicone oils conform to the standards . No increase, and in some samples decrease, in the number of microorganisms is observed during the second week, while the number drops to zero at the end of the experiment . Therefore, the use of these liquids is safe .

J Nat Prod, 2004 Aug, 67(8), 1400 - 2
Aureoverticillactam, a novel 22-atom macrocyclic lactam from the marine actinomycete Streptomyces aureoverticillatus; Mitchell SS et al.; During the course of our screening program designed to discover novel anticancer and anti-infective agents from marine microorganisms, a strain of Streptomyces aureoverticillatus (NPS001583) isolated from a marine sediment was found to produce a novel macrocyclic lactam with cytotoxicity against various tumor cell lines . Using extensive MS, UV, and NMR spectral analyses, the structure has been established as compound 1, aureoverticillactam, a 22-atom macrocyclic lactam incorporating both triene and tetraene conjugated olefins.

J Nat Prod, 2004 Aug, 67(8), 1392 - 5
Novel sesquiterpenoid matrix metalloproteinase-3 inhibitors from an acid mine waste extremophile; Stierle AA et al.; Berkeley Pit Lake is a 1500 ft deep abandoned open-pit copper mine filled with 30 billion gallons of acidic, metal-contaminated water . This harsh environment is proving to be a source of unusual, biologically active microorganisms . Bioassay-guided fractionation using signal transduction enzyme assays led to the isolation of three novel bisabolane sesquiterpenes and a novel coumarin . The isolation and characterization of these compounds are reported here.

J Food Prot, 2004 Aug, 67(8), 1574 - 7
Inactivation of Escherichia coli O157:H7 and other naturally occurring microorganisms in apple cider by electron beam irradiation; Wang H et al.; Two Escherichia coli O157:H7 strains, SEA 13 B88 gfp 73ec and B6-914 gfp 90ec, together with two bacteria, three yeasts, and two molds that were randomly selected from a collection of microorganisms found on apples or in apple cider, were inoculated into apple cider and subjected to electron beam irradiation at several doses between 0.0 and 2.3 kGy at the Iowa State University Linear Accelerator Facility . The D-values for the E . coli O157:H7 strains ranged between 0.25 and 0.34 kGy; the D-values for most of the normal flora from apples ranged between 0.24 and 0.59 kGy . By taking into account possible variations in treatment conditions, it was calculated that irradiation at 2.47 kGy should achieve a 5-log reduction of E . coli O157:H7 in apple cider at the 95% confidence level . Naturally occurring yeasts might survive such irradiation treatment.

Int J Hyg Environ Health, 2004 Jul, 207(3), 279 - 95
Development of agroenvironmental indicators to evaluate the hygienic pressure of livestock production on human health; Bigras-Poulin M et al.; Infections by enteropathogenic microorganisms linked to agroenvironmental contamination represent a significant threat to urban and rural communities . To better characterize and manage this risk, it is necessary, not only to accurately describe enteric illnesses occurring over time or across regions, but also to correctly assess exposure attributable to this environmental pollution . New agroenvironmental hygienic pressure indicators (AHPIs) were developed to synthesise relevant data expressing this exposure . They were derived from a conceptual framework for developing sustainable agriculture indicators and specifically adapted for describing the microbial risk of water contamination by livestock operations . The proposed indicators include two components, and five attributes whose values are calculated at the livestock operation level from a set of available data related to the fields of microbiology, animal production, agronomy, hydrology, and meteorology . They are then aggregated at a higher geographical level to better express exposure of human populations to potential of water contamination by zoonotic enteropathogens . The indicators are calculated separately by zoonotic enteropathogens, and by water source (surface or groundwater) . They take into account the various animal species within each livestock operation . When validated, the proposed indicators will allow decision-makers and public health officials to better manage crucial issues in the area of water safety and agriculture.

Vojnosanit Pregl, 2004 May-Jun, 61(3), 315 - 9
{Actinomycosis--a multidisciplinary approach to a clinical problem}; Dokic M et al.; Actinomycosis is caused by microorganisms of the Actinomyces species, found in the oral cavity, gastrointestinal and genital tract . Infection by Actimomyces species mainly causes chronic supurative disease of the oral, cervico-facial, thoracic, and abdominal regions . Clinical manifestations have been described at every level, but the disease is relatively rarely diagnosed . The causative agent is considered to be an opportunistic pathogen associated with infection, trauma, surgical procedures, or associated with a neoplasm or foreign body . Symptoms include intermittent fever, weight loss, abdominal or thoracic pain, pseudotumor and tumor masses, and local symptoms from the infected area . Pseudotumor and tumor masses are diagnosed by ultrasonography and computerized tomography . The diagnosis is confirmed by the presence of a causative agent in biopsy or surgically acquired samples . The treatment includes the administration of high doses of antibiotics (penicillin, amoxicillin, ceftriaxone) for at least 6-12 months, as well as surgical treatment . Penicillin is a drug of choice . This infection is often polymicrobial, so that antibiotic therapy should include agents that act against the associated pathogens . Treatment outcome and prognosis in these three cases were excellent, despite the prolonged course of the extensive disease.

C R Biol, 2004 Jun, 327(6), 571 - 80
Forward genetic dissection of afferent immunity: the role of TIR adapter proteins in innate and adaptive immune responses; Beutler B et al.; The innate immune system senses pathogens largely through signals initiated by proteins known as 'Toll-like receptors' (TLRs), of which ten representatives are known to be encoded in the human genome . The understanding of the biochemical circuitry that maintains the innate capacity for immune recognition and response has loomed as a major hurdle in immunology . A total of five adapter proteins with cytoplasmic domain homology to the TLRs are known to exist in mammals . These proteins show preferential association with individual TLR family members, giving a particular character to the signals that distinct microorganisms initiate, and also initiate the adaptive immune response . The adaptive immune response is dependent upon upregulation of costimulatory molecules (UCM) such as CD80 and CD86 . Forward genetic analysis has revealed that this upregulation depends upon an adapter encoded by a locus known as Lps2, and upon type I interferon receptor signaling.

Obes Surg, 2004 Aug, 14(7), 1012 - 5
Gastric actinomycosis: a rare complication after gastric bypass for morbid obesity; Fernandez-Acenero MJ et al.; A 41-year-old woman in November 2002 underwent a gastric bypass by the Capella technique for morbid obesity . Almost 1 year after the surgery, she developed severe vomiting . Radiological studies confirmed a severe stenosis of the gastrojejunal anastomosis . Two pneumatic dilatations of the stenosis failed . In February 2004, she underwent resection of the stenotic anastomosis . Histology showed an intact mucosa and beneath it an abscess filled with numerous filamentous microorganisms, with typical features of Actinomyces . With the diagnosis of gastric actinomycosis, she received a postoperative course of antibiotherapy with imipenem and was discharged after an uneventful recovery . Gastric actinomycosis is a rare infection, of which only 19 additional cases have been reported in the literature . To our knowledge, this is the first case to affect a patient following batriatric surgery . The reported cases of this entity are reviewed, and the diagnostic criteria that could avoid surgery in these cases are discussed.

Rev Environ Health, 2004 Apr-Jun, 19(2), 83 - 139
Safety evaluation of chemical mixtures and combinations of chemical and non-chemical stressors; Jonker D et al.; Recent developments in hazard identification and risk assessment of chemical mixtures are reviewed . Empirical, descriptive approaches to study and characterize the toxicity of mixtures have dominated during the past two decades, but an increasing number of mechanistic approaches have made their entry into mixture toxicology . A series of empirical studies with simple chemical mixtures in rats is described in some detail because of the important lessons from this work . The development of regulatory guidelines for the toxicological evaluation of chemical mixtures is discussed briefly . Current issues in mixture toxicology include the adverse health effects of ambient air pollution; the application of such modern, sophisticated methodologies as genomics, bioinformatics, and physiologically based pharmacokinetic modeling; and databases for mixture toxicity . Finally, the state of the art of our knowledge on the potential adverse health effects of combined exposures to chemicals and non-chemical stressors (noise, heat/cold, microorganisms, immobilization, restraint, or transportation), research initiatives in these fields, and the development of an indicator for the cumulative health impact of multiple environmental exposures are discussed.

Ecotoxicol Environ Saf, 2004 Oct, 59(2), 249 - 55
Integrated assessment for anaerobic biodegradability of organic compounds using the analytical hierarchy process; Hongwei Y et al.; Anaerobic biodegradability of organic compounds can be assessed from the changes in organic compounds, the end products, and the activity of microorganisms . In this study, all three of these variables were considered to integrate assessment of the anaerobic biodegradability of organic compounds . The analytical hierarchy process (AHP) was introduced to integrate the assessment . Real values between 0 and 10 were determined in the pairwise comparison matrix according to the values of assessment indices of the three variables . A new adjustment method, which can obtain minimum adjustment of the values in matrix, was proposed to reach the acceptable consistency of the matrix . Finally, the anaerobic biodegradability of 14 organic compounds was assessed using AHP.

Environ Pollut, 2005 Jan, 133(1), 17 - 24
Formation and release of non-extractable 14C-Dicamba residues in soil under sterile and non-sterile regimes; Gevao B et al.; The role of native soil microorganisms in the formation and release of non-extractable (14)C-residues, previously treated with (14)C-Dicamba, was investigated to examine their significance to the longer-term environmental effects on non-extractable pesticide residues . A 90 d study compared the fate of Dicamba under sterile and non-sterile regimes . In addition, soils were aged for 30 d and repeatedly extracted with a 0.01 M CaCl(2) solution, to an extraction end point, to produce non-extractable residues . The extracted soil containing non-extractable residues was mixed with clean soil that had been freshly spiked with non-labeled Dicamba at 0.2 mg kg(-1) to increase the bulk volume of the soil and stimulate microbial activity . Sub-samples were then introduced into microcosms to compare the extent of microbially facilitated release and mineralisation with release rates in sterile microcosms . The results show that microorganisms play a significant role in the formation and release of non-extractable Dicamba residues . The release of (14)C-activity in sterile microcosms was linked to physical mixing of the extracted soil with field soil prior to the beginning of the incubations . The released (14)C-activity may be further mineralized, reincorporated into humus, or taken up by plants or other soil inhabiting biota.

Environ Monit Assess, 2004 Aug-Sep, 96(1-3), 273 - 81
The influence of agricultural and urban contamination on leech infestation of freshwater turtles, Phrynops geoffroanus, taken from two areas of the Uberabinha River; De Campos Brites VL et al.; Infestation by leeches on adult freshwater turtles Phrynops geoffroanus in two areas of the Uberabinha River, in Uberlandia, was investigated during the summer (January 2000) . Fifty eight turtles were trapped: 26 (12 males, 14 females) in an agricultural area and 32 (16 males, 16 females) in an area with a more urban environment . The females present larger length and body mass (291.77+/-29.18 mm; 2233.30+/-511.40 g) than males (259.71+/-33.15 mm; 1488.68+/-529.35 g) . Blood samples were drawn from the retrorbital sinus using heparinized micro-hematocrit capillary tubes, for microscopic and direct examination for intracellular parasites . Ectoparasitism by leeches, Placobdella bistriata, on young and adult animals was observed in the limb cavities of 28.1% of the urban area turtles . No leeches were found on the turtles in the agricultural area . Hemogregarine erythrocytic gametocytes were found in 15.4% of the agricultural area turtles, and in 37.5% of the urban area turtles . Concurrent parasitism by leeches and hemogregarines on the same individuals was seen on six turtles . Infections with microorganisms (bacteria and fungus) facilitated by the bites of leeches were not observed in another study on the same sample of infested turtles . However, 19% of the turtles collected in the agricultural area and 15% of the turtles from the urban area presented normocytic acute anemia . The occupation of the soil apparently interfered in the aquatic ecosystem favoring parasitism in the urban area.

Environ Monit Assess, 2004 Aug-Sep, 96(1-3), 35 - 52
A generalized water quality index for Taiwan; Liou SM et al.; By exploring the behavior and limitations of conventional methods for quality evaluation, a better overall index for water quality in Taiwan and its application in Keya River are proposed . The thirteen variables are employed for the quality assessment . Numerical scales relating to the degree of quality are established for each variable to assess variations in quality and to convey findings in a comprehensive manner to others . The employed variables are categorized into three aspects referred to the principal components analysis, which are 'organics', 'particulates' and 'microorganisms' . The overall index consists of the geometric mean for the three defined aspects and multiplying by three coefficients, which reflect quality degrees of temperature, pH and toxicity, respectively . Besides, the arithmetic mean is addressed among the variables associated in the same aspect . Finally, a fresh, mixed aggregation function is developed for ensuring that the index score tells us something useful and does not hide important information . A case study of the Keya River is made to illustrate the application of this new index system . The new proposed index provides comprehensive information for water quality assessment, than the existing index used in Taiwan does.

Vestn Ross Akad Med Nauk, 2004, (6), 31 - 5
{An analysis of the pathogenetic significance of irradiations from mobile phones}; Rumiantsev GI et al.; The biological effects of irradiations from mobile phones produced on different structures of the living matter, e.g . molecular-genetics, cells, organ-and-tissue, body and population, are analyzed in the paper . Possibilities of the genetic and epigenetic mutations, metabolic shifts, different-type cytopathic effects, oncogenesis induction, allergic conditions and of other processes associated with a certain lesion of the main structural-and-functional systems of microorganisms are elucidated . Irradiations from mobile phones are shown to have obvious effects on the molecular-and-genetic as well as on organ-and-tissue levels . However, contradictory enough data are available at the moment, which hamper a true evaluation of the unfavorable effects of the phenomenon both in respect to separate organisms and to a population as a whole . The offered analytic survey demonstrated distinctly a potential threat coming from a widely spread modern factor with the above threat requiring to be verified yet by special methods . It is equally quite obvious that, a need is shaping up to improve, in the future, the methods of detection and verification of "factor with finally non-established risk" as well as to investigate the potential pathological properties of such factors, which can essentially promote the system of the social-and-hygienic monitoring.

Int J Biochem Cell Biol, 2004 Dec, 36(12), 2445 - 62
Regulation and role of autophagy in mammalian cells; Meijer AJ et al.; The recent period has witnessed progress in the understanding of the lysosomal autophagic pathway . The discovery of a family of genes conserved from yeast to humans, and involved in the formation of autophagosomes, has unraveled new protein-conjugation systems and has shed light on the importance of autophagy in physiology and pathophysiology . The elucidation of the molecular control of autophagy will also lead to a better understanding of the role of autophagy during cell death . As a great number of extracellular stimuli (starvation, hormonal or therapeutic treatment) as well as intracellular stimuli (accumulation of misfolded proteins, invasion of microorganisms) is able to modulate the autophagic response, it is not surprising that several signaling pathways are involved in the control of autophagy . The mammalian Target of Rapamycin (mTOR) signaling pathway plays a major role in transmitting autophagic stimuli because of its ability to sense nutrient, metabolic and hormonal signals . In addition, autophagy, which is characterized by a flux of membrane from the formation of the autophagosome to the fusion with the lysosome, is regulated by GTPases, similarly to the vesicular transport along the exocytic/endocytic pathway . The aim of the present review is to give an overview of autophagy and to discuss its regulation by activators and effectors of mTOR and GTPases.

Arch Med Res, 2004 Jul-Aug, 35(4), 348 - 58
Severe combined immunodeficiency syndrome associated with colonic stenosis; Lopez-Herrera G et al.; BACKGROUND: This is the first report in Mexico of a case of severe combined immunodeficiency syndrome (SCID) associated with colonic stenosis . The patient was an 8-month-old Mexican female who died at this age . She suffered infections due to microorganisms such as Mycobacterium tuberculosis, bacille Calmette-Guerin (BCG), Candida sp., and Pneumocystis carinii; and had frequent diarrhea . She was HIV-negative without familial history of immunodeficiency . The aim of the work was to analyze the immunologic status of this patient . METHODS: Peripheral blood from the patient and from a healthy matched control were analyzed by flow cytometry to determine peripheral leukocytes and production of cytokines and their receptors in T-lymphocytes and monocytes . Immunohistochemical analysis was performed in spleen and lymph node sections from the patient and control samples to assess alterations in architectural and cellular distribution within these lymphoid tissues . RESULTS: Peripheral blood analysis demonstrated reduced numbers of both T and B cells and defective expression of cytokines by activated T cells . Postmortem analysis revealed very small T and B cell zones in spleen and lymph nodes, absence of germinal centers and follicular dendritic cell networks, and two zones of stenosis at level of colon sigmoides . CONCLUSIONS: As a whole, these data are consistent with severe combined immunodeficiency (SCID) syndrome; thus, we conclude that this patient may have had a variant of SCID syndrome associated with intestinal stenosis.

Mar Environ Res, 2005 Feb, 59(1), 19 - 45
Impact of sediment organic matter quality on the fate and effects of fluoranthene in the infaunal brittle star Amphiura filiformis; Selck H et al.; Hydrophobic contaminants, such as polycyclic aromatic hydrocarbons (PAHs) readily adsorb to organic matter . The aim of this study was to determine the importance of the quality of sedimentary organic matter for the uptake, biotransformation and toxicity of the PAH, fluoranthene (Flu), in the infaunal brittle star Amphiura filiformis . Brittle stars were exposed to a base sediment covered by a 2 cm Flu-spiked top layer (30 microg Flu/g dry wt . sed.), enriched to the same total organic carbon content with either refractory or labile organic matter . The labile carbon source was concentrated green flagellate: Tetraselmis spp . The refractory carbon source was lignin from a paper mill . Tissue concentrations of Flu both in disk and arm-fractions were determined as total Flu, parent Flu (i.e . untransformed), aqueous Flu-metabolites, polar Flu-metabolites and tissue residue Flu (i.e . unextractable) . Our results showed that sediment particle ingestion is a pathway by which Flu can enter benthic food webs . Flu toxicity (measured as arm-regeneration), but not net accumulation, was dependent on the nutritional quality of the ingested sediment particles . Flu bioaccumulation could not be attributed solely to equilibrium partitioning between organism lipid content and organic content of the sediment . Biotransformation of Flu by brittle stars was very limited and unaffected by organic matter quality . A . filiformis contributed to the downward transport of Flu from the surface sediment to the burrow lining . The limited breakdown of parent Flu by brittle stars and/or microorganisms was relatively higher in burrows compared to surface sediment, and highest in the presence of labile organic matter . Tissue concentrations were higher in disk than in arms, but the proportion of metabolic products relative to parent Flu was higher in arms than in the disk fraction . We estimate that the yearly mobilization of sediment-associated Flu by arm-regeneration in A . filiformis is in the range of 3.8-29.4 microg total Flu eq . m(-2) year(-1) at a sediment concentration of 30 microg Flu/g dry wt . sed.

Trends Parasitol, 2004 Sep, 20(9), 407 - 12
Parasite interaction with host complement: beyond attack regulation; Inal JM; Many orthologous proteins of known mammalian receptors have been discovered in parasites . Besides disguising the parasite as self in terms of the host immune system, evidence is accumulating that these receptors link to signalling pathways in parasites that appear to be involved in their growth or development . Recently, several proteins of the host complement system, which forms part of the innate defence against invading microorganisms, have been shown to possess alternative functions . These complement proteins interact with signalling pathways involved in early development and differentiation, as well as organ and tissue regeneration . By altering cellular interactions and responses, complement is being shown to have novel roles besides the originally described inflammatory role . The possibility exists that, as for other host factors interacting with parasites and affecting their growth or development, host complement proteins could also have such an influence.

Mycol Res, 2004 Jun, 108(Pt 6), 654 - 61
Development of a transformation system for the nematophagous fungus Pochonia chlamydosporia; Atkins SD et al.; The nematophagous fungus Pochonia chlamydosporia is a potential biocontrol agent against root knot and cyst nematodes . Genetic transformation of the fungus to introduce visual marker genes, novel traits, or changes in expression levels of endogenous genes, would greatly enhance understanding of its behaviour on nematode-infested roots and of its interactions with other soil and rhizosphere microorganisms . A transformation system for the introduction of novel genes into P . chlamydosporia has been developed . Methods to generate protoplasts, introduce DNA and regenerate transformed viable fungal mycelium have been optimised, using plasmids carrying the green fluorescent protein marker gene gfp and the hygromycin resistance gene hph . Cultures of P . chlamydosporia were resistant to high levels of a range of fungal inhibitors, including hygromycin, that are commonly used with dominant selectable marker genes in the transformation of other fungi . However, regenerating protoplasts transformed with hph could be selected by their ability to grow through an agar overlay containing 1 mg ml(-1) hygromycin . Green fluorescence was observed in protoplasts and regenerating mycelium after transformation with gfp, but the GFP phenotype was lost on subculture . Maintenance of introduced genes was not stable, and during subculture, PCR assays indicated that the transformants lost both hph and gfp . When these genes were introduced on the same plasmid, segregation of hph and gfp was observed prior to their loss . It was unclear whether the introduced plasmids were able to replicate autonomously in P . chlamydosporia, or if they integrated transiently into the fungal genome . Possible reasons for the instability of the transformants are discussed.

Immunogenetics, 2004 Aug, 56(5), 311 - 20 Epub 2004 Jul 30.
Discriminating self from nonself with short peptides from large proteomes; Burroughs NJ et al.; We studied whether the peptides of nine amino acids (9-mers) that are typically used in MHC class I presentation are sufficiently unique for self:nonself discrimination . The human proteome contains 28,783 proteins, comprising 10(7) distinct 9-mers . Enumerating distinct 9-mers for a variety of microorganisms we found that the average overlap, i.e., the probability that a foreign peptide also occurs in the human self, is about 0.2% . This self:nonself overlap increased when shorter peptides were used, e.g., was 30% for 6-mers and 3% for 7-mers . Predicting all 9-mers that are expected to be cleaved by the immunoproteasome and to be translocated by TAP, we find that about 25% of the self and the nonself 9-mers are processed successfully . For the HLA-A*0201 and HLA-A*0204 alleles, we predicted which of the processed 9-mers from each proteome are expected to be presented on the MHC . Both alleles prefer to present processed 9-mers to nonprocessed 9-mers, and both have small preference to present foreign peptides . Because a number of amino acids from each 9-mer bind the MHC, and are therefore not exposed to the TCR, antigen presentation seems to involve a significant loss of information . Our results show that this is not the case because the HLA molecules are fairly specific . Removing the two anchor residues from each presented peptide, we find that the self:nonself overlap of these exposed 7-mers resembles that of 9-mers . Summarizing, the 9-mers used in MHC class I presentation tend to carry sufficient information to detect nonself peptides amongst self peptides.

Biosci Biotechnol Biochem, 2004 Aug, 68(8), 1649 - 56
An appropriate increase in the transcription of Aspergillus nidulans uvsC improved gene targeting efficiency; Natsume T et al.; Gene targeting to knock out the activity of specific genes has become important due to recent progress in genomics research . But this technique is still unavailable for many organisms, including economically important microorganisms, due to the high background of ectopic integration during genetic transformation . Strategies to improve targeting efficiency have included manipulating the expression of genes that are involved in homologous recombination . In this study, transcription of Aspergillus nidulans uvsC was elevated using the promoter sequences of the glyceraldehyde-3-phosphate dehydrogenase and Taka-amylase A genes from A . nidulans and A . oryzea respectively . Although a several-fold increase in the efficiency of targeting was observed at 3 loci, mycelial growth was suppressed in strains that had higher levels of uvsC transcription . These results suggest that uvsC is a rate-limiting factor in gene targeting, and that the increased efficiency of this targeting is hindered by a negative effect of increased transcription on cell proliferation.

Biosci Biotechnol Biochem, 2004 Aug, 68(8), 1627 - 33
Isolation of a cadmium-releasing bacterium and characterization of its novel protease; Ren S et al.; Microorganisms were screened for their ability to release cadmium from scallop hepatopancreas, which is the main residue after removing of the edible parts of scallop . The isolated strain, 23-0-11, identified as Arthrobacter nicotinovorans, secreted a protease which released cadmium from scallop hepatopancreas into the liquid medium . The molecular mass of the enzyme was estimated to be 27 kDa . The sequence of the 15 N-terminal amino acids of the protease showed no close similarity with any other protein . Compared with a commercial enzyme, the purified protease had greater ability to release cadmium . The enzyme activity was greatest at 50 degrees C and pH 7.0, and was enhanced in the presence of Ca(2+), Mg(2+) and Mn(2+), while being strongly inhibited by Co(2+) . The inhibition profile by the serine protease inhibitor, phenylmethylsulphonyl fluoride (PMSF), confirmed that the protease belonged to the serine protease family.

Am J Clin Nutr, 2004 Sep, 80(3), 539 - 49
Betaine in human nutrition; Craig SA; Betaine is distributed widely in animals, plants, and microorganisms, and rich dietary sources include seafood, especially marine invertebrates ( approximately 1%); wheat germ or bran ( approximately 1%); and spinach ( approximately 0.7%) . The principal physiologic role of betaine is as an osmolyte and methyl donor (transmethylation) . As an osmolyte, betaine protects cells, proteins, and enzymes from environmental stress (eg, low water, high salinity, or extreme temperature) . As a methyl donor, betaine participates in the methionine cycle-primarily in the human liver and kidneys . Inadequate dietary intake of methyl groups leads to hypomethylation in many important pathways, including 1) disturbed hepatic protein (methionine) metabolism as determined by elevated plasma homocysteine concentrations and decreased S-adenosylmethionine concentrations, and 2) inadequate hepatic fat metabolism, which leads to steatosis (fatty accumulation) and subsequent plasma dyslipidemia . This alteration in liver metabolism may contribute to various diseases, including coronary, cerebral, hepatic, and vascular diseases . Betaine has been shown to protect internal organs, improve vascular risk factors, and enhance performance . Databases of betaine content in food are being developed for correlation with population health studies . The growing body of evidence shows that betaine is an important nutrient for the prevention of chronic disease.

Water Sci Technol, 2004, 50(1), 309 - 14
Assessment of virulence-factor activity relationships (VFARs) for waterborne diseases; Jenkins TM et al.; Virulence-factor activity relationship (VFAR) is a concept that was developed as a way to relate the architectural and biochemical components of a microorganism to its potential to cause human disease . Development of these relationships requires specialised bioinformatics databases that do not exist at present . A pilot-scale VFAR database was designed for three different waterborne organisms: Escherichia coli, Norovirus and Cryptosporidium, to evaluate VFAR relationships . For the web-based database, each organism has separate pages containing virulence genes, occurrence genes, primer sets and probes, taxonomy, outbreaks, and serotype/species/genogroup/genotype . As the database continues to grow, it will be possible to relate the occurrence and prevalence of certain genes in various microorganisms to outbreak data and, subsequently, to establish the utility of using a combination of specific genes as markers of virulence and in establishing virulence-factor activity relationships (VFARs) . The database and the VFARs established will be of use to the regulatory community as a way to assist with prioritising those organisms, which need to be regulated.

Water Sci Technol, 2004, 50(1), 277 - 80
Comparison of agar-based methods for the isolation and enumeration of heterotrophic bacteria with the new multidose IDEXX SimPlate method; Vulindlu M et al.; Pour and spread plates are the conventional methods of choice for the isolation and enumeration of heterotrophic microorganisms in treated water supplies . The tests are performed at 22 degrees C and 37 degrees C for 72 h and 48 h respectively . Counts at 22 degrees C are associated with pollution of water systems from external sources, while counts at 37 degrees C are used as an indication of treatment plant performance and the deterioration of the general quality of water . Conventional methods using Yeast Extract Agar for a pour plate and R2A agar for a spread plate were compared with the multidose IDEXX SimPlate method for the isolation and enumeration of heterotrophic bacteria in water . SimPlate gave a significantly higher count on average than the conventional methods . The R2A method showed the next highest count, being significantly higher than Yeast Extract Agar . In addition, unlike the pour and spread plate methods, SimPlate was easier to use, reduced labour, and the test results were far easier to read.

Water Sci Technol, 2004, 50(1), 173 - 8
Using ultraviolet light for disinfection of finished water; Bukhari Z et al.; Ultraviolet light is now recognised to be very effective for inactivation of Cryptosporidium parvum oocysts; however, its application for disinfection of finished water necessitates validation of UV reactors prior to their installation . Although reactor performance will likely be assessed using non-pathogenic microorganisms as biodosimetry surrogates, it would be prudent for the water industry to simultaneously measure Cryptosporidium oocysts inactivation in controlled bench-scale studies using the water matrix intended for disinfection . The likelihood of that occurring is dependent upon the availability of infectivity measurement procedures that are more user-friendly than the mouse infectivity assays currently used . This study describes a modified cell culture procedure that would enable reliable measurement of changes in oocysts' infectivity following their UV treatment . Also, a number of different biodosimetry surrogates were examined and one selected for comparing the UV doses delivered between bench-scale and full-scale biodosimetry studies . Impacts of UV disinfection on production of disinfection byproducts, effects of lamp ageing on effectiveness of disinfection and the costs associated with employing this technology were also examined.

Diabet Med, 2004 Sep, 21(9), 1035 - 40
Type 1 diabetes mellitus in childhood: a matched case control study in Lancashire and Cumbria, UK; Marshall AL et al.; AIMS: The aim of the study was to identify environmental risk factors for insulin-dependent diabetes mellitus (Type 1 DM) in childhood . METHODS: A matched case-control study of Type 1 DM conducted in Lancashire and Cumbria, UK, using a structured interview . Cases (n=196, participation rate 83%) were children under 16 years of age diagnosed prior to October 1998 and attending diabetic clinics . Controls (n=381) were healthy children from the community matched by gender and by age (within a few days of birth) . The data were analysed by logistic regression using the technique of Breslow and Day for matched case control studies . RESULTS: The multivariate regression model showed that the following factors were significantly associated with the risk of developing Type 1 DM (odds ratio, 95% confidence intervals): sharing a room with a sibling (0.458, 0.290-0.721), social contact with other children when aged 6-11 months (0.439, 0.256-0.752), consumption of sugary food (0.080, 0.024-0.261), parental insulin dependent diabetes mellitus (10.651, 3.086-36.761), maternal thyroid disease (4.861, 1.681-14.058), consuming more than one pint of milk per day prior to school entry (0.498, 0.310-0.802), maternal smoking during pregnancy (0.373, 0.218-0.636), a father with no academic qualifications (0.504, 0.278-0.913), maternal age at time of birth (0.900, 0.854-0.948), maternal infections in pregnancy (2.453, 1.011-5.948), other maternal illnesses or conditions in pregnancy (2.007, 1.139-3.535), belonging to an Asian family (0.104, 0.028-0.394), and regular contact with pets and other animals (0.552, 0.309-0.987) . CONCLUSION: Many of the results are consistent with the hygiene hypothesis which links improved living standards with decreased exposure to microorganisms and increased risk of immune mediated disease in childhood . These findings challenge the idea that improved hygiene acts exclusively through a Th2 mechanism leading to atopic disease as Type 1 DM is mediated by a Th1 reaction . The association with maternal smoking could be due to recall bias but a causal link cannot be excluded with confidence.

Environ Pollut, 2004 Nov, 132(2), 333 - 9
Chelator induced phytoextraction and in situ soil washing of Cu; Kos B et al.; In a soil column experiment, we investigated the effect of 5 mmol kg(-1) soil addition of citric acid, ethylenediamine tetraacetate (EDTA), diethylenetriamine-pentaacetate (DTPA) and {S,S}-stereoisomer of ethylenediamine-disuccinate (EDDS) on phytoextraction of Cu from a vineyard soil with 162.6 mg kg(-1) Cu, into the test plant Brassica rapa var . pekinensis . We also examined the use of a horizontal permeable barrier, composed of layers of nutrient enriched sawdust and apatite, for reduction of chelator induced Cu leaching . The addition of all chelators, except citric acid, enhanced Cu mobility and caused leaching of 19.5-23% of initial total Cu from the soil column . However, Cu plant uptake did not increase accordingly; the most effective was the EDDS treatment, in which plant Cu concentration reached {Formula: see text} Cu and increased by 3.3-times over the control treatment . The addition of none of the chelators in the concentration range from 5 to 15 mmol kg(-1) exerted any toxic effect on respiratory soil microorganisms . When EDDS was applied into the columns with horizontal permeable barriers, only 0.53 +/- 0.32% of the initial total Cu was leached . Cu (36.7%) was washed from the 18 cm soil layer above the barrier and accumulated in the barrier . Our results indicate that rather than for a reduction of Cu leaching during rather ineffective chelate induced Cu phytoextraction, horizontal permeable barriers could be more effective in a new remediation technique of controlled in situ soil washing of Cu with biodegradable chelates .

Zhonghua Fu Chan Ke Za Zhi, 2004 Jun, 39(6), 382 - 4
{Microorganism contamination in in vitro fertilization-embryo transfer system and their sources}; Zhu GJ et al.; OBJECTIVE: To investigate the incidence of microorganism contamination in in vitro fertilization-embryo transfer (IVF-ET) and to determine the sources of microorganism . METHODS: Two thousand one hundred and seventy-four cycles of in vitro fertilization from January 1999 to June 2003 were evaluated retrospectively and bacterial cultures were performed in 61 semen samples from asymptomatic men with normal semen parameters and in 34 follicle fluid samples from infertility women through oocyte picking up procedures . RESULTS: Microorganisms were found in 11 cases . The incidence of their contamination in IVF culture system was 0.51% and the most common microorganisms were Escherichia coli and fungi . Microorganisms were detected in 97% of unprocessed semen, 10% in processed semen, 6% in semen mixed with media and 9% in follicle fluid . CONCLUSIONS: The incidence of microorganism contamination was 0.51% and the most common microorganisms were Escherichia coli and fungi . Semen may have the potential to contaminate IVF culture system.

Vet Clin Pathol, 1983, 12(3), 7 - 14
Superoxide, superoxide dismutase and the respiratory burst; Bender HS et al.; Phagocytes undergo a sharp burst of oxygen consumption when engulfing bacteria . This oxygen is enzymatically reduced to toxic metabolites which are essential to the bactericidal action of the cell . Oxygen metabolites formed in this burst as well as other intermediates formed in biological reduction reactions do not selectively reserve their toxicity for microorganisms . Cells help to guard their organelles against the toxic effects of oxygen by producing intracellular enzymes such as superoxide dismutase . Though superoxide dismutase is found in relatively high concentrations inside cells, there are only small amounts in extracellular fluids . This may account for some of the local tissue damage surrounding aggregates of neutrophils in inflammatory reactions . A pharmacological preparation of superoxide dismutase has shown efficacy in preventing some of the pathological changes seen in degenerative arthritis.

Eur J Nutr . 2004 May 6;:1-7 {Epub ahead of print}
In vivo and in vitro evidences that carotenoids could modulate the neutrophil respiratory burst during dietary manipulation; Walrand S et al.; BACKGROUND . The primary role of polymorphonuclear neutrophils (PMNs) is to destroy pathogenic microorganisms after phagocytosis by producing reactive oxygen species (ROS) and toxic molecules . However, PMNs produce sufficient amounts of ROS during an oxidative burst to be autotoxic and detrimental to their own functions and to possibly cause DNA damage, protein and lipid oxidation and cell membrane destructuration . OBJECTIVE . The aim of this study was to investigate in vivo the role of the antioxidant capacities of carotenoids in modulating ROS content in PMNs during oxidative burst . Moreover to investigate the direct or indirect effect of carotenoids, the modification of PMN ROS content was explored after in vitro supplementation with beta-carotene or lycopene, chosen taking account of their vitamin A and no vitamin A precursor effect, respectively . DESIGN . In vivo study: Venous blood was collected from 10 healthy male volunteers and ROS production from phorbol myristate acetate (PMA)-stimulated PMNs was determined, by flow cytometry using the fluorescent dye dihydrorhodamine 123, at baseline, after 3 weeks of carotenoid depletion (carotenoid intake limited to 25% of usual intake) and after 5 weeks of carotenoid repletion (30 mg beta-carotene, 15 mg lycopene and 9mg lutein per day) . In vitro study: ROS content in PMA-stimulated PMNs isolated from carotenoid depleted subjects and controls was quantified after an in vitro enrichment with beta-carotene (1 micro mol/L) or lycopene (0.3 micro mol/L) . RESULTS . In vivo carotenoid depletion increased PMN H(2)O(2) content after PMA activation by 38% (p < 0.05 vs baseline),while supplementation for 5 weeks restored basal H(2)O(2) generation (p < 0.05 vs depletion) . Although H(2)O(2) measurement in PMNs from non-depleted subjects was not affected by an in vitro supply with beta-carotene or lycopene, a significant decrease in H(2)O(2) content by 78.9 % and 81.2%, respectively, was observed in PMNs from carotenoid depleted subjects (p < 0.01 vs depleted control subjects) . CONCLUSIONS . The carotenoid ROS quenching capacities control both in vivo and in vitro the PMNs ROS generation and probably protect these cells against DNA, membrane lipid and protein damages during oxidative burst . Moreover, these effects appear independent from the metabolic conversion of carotenoids to vitamin A.

Scand J Infect Dis, 2004, 36(6-7), 428 - 30
Evidence of chronic Chlamydia pneumoniae infection in patients with Behçet's disease; Ayaslioglu E et al.; Behcet's disease is a chronic vasculitis of unknown aetiology . Particular viral and bacterial pathogens have long been suspected of playing a role in the pathogenesis of the disease . Chlamydia pneumoniae is an intracellular bacterium capable of causing chronic infections . Some reports have suggested that the microorganism might be involved in the pathogenesis of vasculitis . The purpose of the present study was to investigate a possible correlation between C . pneumoniae infection and Behcet's disease . For this purpose, 90 consecutive patients with Behcet's disease and 50 healthy controls were enrolled . Immunoglobulin A (IgA) and IgG antibodies to C . pneumoniae were determined by 2 different techniques, namely indirect fluorescent antibody assay (IFA) and enzyme linked immunosorbent assay (ELISA) . IgA antibodies to C . pneumoniae were detected in 17 (18.9%) patients with Behcet's disease and in 1 (2%) healthy control by IFA . By ELISA 27 patients (30.0%) and 6 controls (12.0%) had C . pneumoniae IgA . A significant difference was observed for IgA seropositivity between the 2 groups . Although IgG seropositivity between the 2 groups did not differ significantly, the number of individuals with IgG titres of > or = 1:1000 was significantly higher in the patient group (43.1%) compared with the control group (13.9%) . These finding provide serological evidence of chronic C . pneumoniae infection in association with Behcet's disease.

Mol Microbiol, 2004 Aug, 53(4), 1003 - 9
Small molecules that regulate lifespan: evidence for xenohormesis; Lamming DW et al.; Barring genetic manipulation, the diet known as calorie restriction (CR) is currently the only way to slow down ageing in mammals . The fact that CR works on most species, even microorganisms, implies a conserved underlying mechanism . Recent findings in the yeast Saccharomyces cerevisiae indicate that CR extends lifespan because it is a mild biological stressor that activates Sir2, a key component of yeast longevity and the founding member of the sirtuin family of deacetylases . The sirtuin family appears to have first arisen in primordial eukaryotes, possibly to help them cope with adverse conditions . Today they are found in plants, yeast, and animals and may underlie the remarkable health benefits of CR . Interestingly, a class of polyphenolic molecules produced by plants in response to stress can activate the sirtuins from yeast and metazoans . At least in the case of yeast, these molecules greatly extend lifespan by mimicking CR . One explanation for this surprising observation is the 'xenohormesis hypothesis', the idea that organisms have evolved to respond to stress signalling molecules produced by other species in their environment . In this way, organisms can prepare in advance for a deteriorating environment and/or loss of food supply.

Environ Microbiol, 2004 Sep, 6(9), 970 - 80
Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea; Treusch AH et al.; Complex genomic libraries are increasingly being used to retrieve complete genes, operons or large genomic fragments directly from environmental samples, without the need to cultivate the respective microorganisms . We report on the construction of three large-insert fosmid libraries in total covering 3 Gbp of community DNA from two different soil samples, a sandy ecosystem and a mixed forest soil . In a fosmid end sequencing approach including 5376 sequence tags of approximately 700 bp length, we show that mostly bacterial and, to a much lesser extent, archaeal and eukaryotic genome fragments (approximately 1% each) have been captured in our libraries . The diversity of putative protein-encoding genes, as reflected by their distribution into different COG clusters, was comparable to that encoded in complete genomes of cultivated microorganisms . A huge variety of genomic fragments has been captured in our libraries, as seen by comparison with sequences in the public databases and by the large variation in G+C contents . We dissect differences between the libraries, which relate to the different ecosystems analysed and to biases introduced by different DNA preparations . Furthermore, a range of taxonomic marker genes (other than 16S rRNA) has been identified that allows the assignment of genome fragments to specific lineages . The complete sequences of two genome fragments identified as being affiliated with Archaea, based on a gene encoding a CDC48 homologue and a thermosome subunit, respectively, are presented and discussed . We thereby extend the genomic information of uncultivated crenarchaeota from soil and offer hints to specific metabolic traits present in this group.

Environ Microbiol, 2004 Sep, 6(9), 948 - 58
Construction, characterization, and use of small-insert gene banks of DNA isolated from soil and enrichment cultures for the recovery of novel amidases; Gabor EM et al.; To obtain new amidases of biocatalytic relevance, we used microorganisms indigenous to different types of soil and sediment as a source of DNA for the construction of environmental gene banks, following two different strategies . In one case, DNA was isolated from soil without preceding cultivation to preserve a high degree of (phylo)genetic diversity . Alternatively, DNA samples were obtained from enrichment cultures, which is thought to reduce the number of clones required to find a target enzyme . To selectively sustain the growth of organisms exhibiting amidase activity, cultures were supplied with a single amide or a mixture of different aromatic and non-aromatic acetamide and glycine amide derivatives as the only nitrogen source . Metagenomic DNA was cloned into a high-copy plasmid vector and transferred to E . coli, and the resulting gene banks were searched for positives by growth selection . In this way, we isolated a number of recombinant E . coli strains with a stable phenotype, each expressing an amidase with a distinct substrate profile . One of these clones was found to produce a new and highly active penicillin amidase, a promising biocatalyst that may allow higher yields in the enzymatic synthesis of beta-lactam antibiotics.

Environ Microbiol, 2004 Sep, 6(9), 928 - 37
Suppressive subtractive hybridization as a tool for identifying genetic diversity in an environmental metagenome: the rumen as a model; Galbraith EA et al.; Molecular techniques previously used for genome comparisons of closely related bacterial species could prove extremely valuable for comparisons of complex microbial communities, or metagenomes . Our study aimed to determine the breadth and value of suppressive subtractive hybridization (SSH) in a pilot-scale analysis of metagenomic DNA from communities of microorganisms in the rumen . Suppressive subtractive hybridization was performed using total genomic DNA isolated from rumen fluid samples of two hay-fed steers, arbitrarily designated as tester or driver . Ninety-six subtraction DNA fragments from the tester metagenome were amplified, cloned and the DNA sequences were determined . Verification of the isolation of DNA fragments unique to the tester metagenome was accomplished through dot blot and Southern blot hybridizations . Tester-specific SSH fragments were found in 95 of 96 randomly selected clones . DNA sequences of subtraction fragments were analysed by computer assisted DNA and amino acid comparisons . Putative translations of 26 (32.1%) subtractive hybridization fragments exhibited significant similarity to Bacterial proteins, whereas 15 (18.5%) distinctive subtracted fragments had significant similarity to proteins from Archaea . The remainder of the subtractive hybridization fragments displayed no similarity to GenBank sequences . This metagenomic approach has exposed an unexpectedly large difference in Archaeal community structure between the rumen microbial populations of two steers fed identical diets and housed together . 16S rRNA dot blot hybridizations revealed similar proportions of Bacteria and Archaea in both rumen samples and suggest that the differences uncovered by SSH are the result of varying community structural composition . Our study demonstrates a novel approach to comparative analyses of environmental microbial communities through the use of SSH.

J Vet Diagn Invest, 2004 Jul, 16(4), 333 - 6
Equine abortion and premature birth associated with Cellulosimicrobium cellulans infection; Bolin DC et al.; During the 2002 and 2003 foaling seasons, Cellulosimicrobium (Cellumonas) cellulans (formerly Oerskovia xanthineolytica) was the principal microorganism isolated from fetal tissues or placentas from cases of equine abortion, premature birth, and term pregnancies . Significant pathologic findings included chronic placentitis and pyogranulomatous pneumonia . In addition, microscopic and macroscopic alterations in the allantochorion from 4 of 7 cases of placentitis were similar to those caused by Crossiella equi and other nocardioform bacteria . This report confirms a causative role of C . cellulans infection in equine abortion.

J Zoo Wildl Med, 2004 Jun, 35(2), 185 - 96
Trauma-induced aneurysmal bone cysts in two psittacine species (Cacatua alba and Nymphicus hollandicus); Heatley JJ et al.; An umbrella cockatoo (Cacatua alba) and two cockatiels (Nymphicus hollandicus) were presented with rapidly enlarging masses of the head or wing joints . Historic trauma to these areas was confirmed in two cases . All birds were >2 yr of age, and two were female . Cytologic examination of fluid aspirated from masses in two cases was described as serosanguineous cytologically but failed to reveal inflammation, neoplasia, or microorganisms . Radiographic evaluation of these masses included proliferation and lysis of bone, suggestive of a neoplastic process . Histopathologic examination of surgically excised tissues revealed proliferative new bone and an absence of neoplastic tissue in all cases, consistent with aneurysmal bone cyst formation . Despite the guarded prognosis reported for other companion animals, these case results suggest a good prognosis for aneurysmal bone cyst in psittaciformes . Complete surgical excision and histopathologic examination is recommended for definitive diagnoses of aneurysmal bone cyst . Postoperative bandaging and rational antibiotic use are indicated to prevent excessive motion and secondary infection of affected sites, respectively.

Blood, 2004 Dec 15, 104(13), 4038 - 45 Epub 2004 Dec 15.
Dectin-1 uses novel mechanisms for yeast phagocytosis in macrophages; Herre J et al.; The phagocytosis of pathogens is a critical event in host defense, not only for clearance of the invading microorganism, but also for the subsequent immune response . We have examined Dectin-1, a proinflammatory nonopsonic receptor for beta-glucans, and show that it mediates the internalization of beta-glucan-bearing ligands, including yeast particles . Although requiring tyrosine phosphorylation and the cytoplasmic immunoreceptor tyrosine-based activation motif (ITAM)-like motif, uptake mediated by Dectin-1 was different from any previously reported phagocytic receptor and was not dependent on Syk-kinase in macrophages . Furthermore, intracellular trafficking of this receptor was influenced by the nature of the beta-glucan ligand, which has significance for the biologic activity of these immunomodulatory carbohydrates.

J Biol Chem, 2004 Oct 29, 279(44), 46143 - 52 Epub 2004 Aug 09.
Self-protection mechanism in D-cycloserine-producing Streptomyces lavendulae . Gene cloning, characterization, and kinetics of its alanine racemase and D-alanyl-D-alanine ligase, which are target enzymes of D-cycloserine; Noda M et al.; An antibiotic, D-cycloserine (DCS), inhibits the catalytic activities of alanine racemase (ALR) and d-alanyl-d-alanine ligase (DDL), which are necessary for the biosynthesis of the bacterial cell wall . In this study, we cloned both genes encoding ALR and DDL, designated alrS and ddlS, respectively, from DCS-producing Streptomyces lavendulae ATCC25233 . Each gene product was purified to homogeneity and characterized . Escherichia coli, transformed with a pET vector carrying alrS or ddlS, displays higher resistance to DCS than the same host carrying the E . coli ALR- or DDL-encoded gene inserted into the pET vector . Although the S . lavendulae DDL was competitively inhibited by DCS, the K(i) value (920 microM) was obviously higher (40 approximately 100-fold) than those for E . coli DdlA (9 microM) or DdlB (27 microM) . The high K(i) value of the S . lavendulae DDL suggests that the enzyme may be a self-resistance determinant in the DCS-producing microorganism . Kinetic studies for the S . lavendulae ALR suggest that the time-dependent inactivation rate of the enzyme by DCS is absolutely slower than that of the E . coli ALR . We conclude that ALR from DCS-producing S . lavendulae is also one of the self-resistance determinants.

J Theor Biol, 2004 Oct 7, 230(3), 343 - 9
A Malthusian curb on spatial structure in microorganism populations; Martin AP; That all organisms are born in the company of a parent but die alone is a fundamental biological asymmetry . It has been suggested that this provides a deep-rooted source of spatial pattern formation for microorganisms even at the scale of the population . Such a theory, however, neglects the strong influence in nature of the limited and spatially variable availability of food . The tendency, first recognized by Thomas Malthus in the 18th century, of a population to out-strip its food resources will eventually lead, through local starvation, to the suppression of a heterogeneity growing within a population . Using a generic model it is demonstrated that including local food limitation of breeding strongly dampens spatial structure otherwise resulting from birth and death . The extent of this damping is shown to be a function of the strength of the coupling between organisms and their food and of the total abundance of organic material . Moreover, this work provides an example of a density-dependent process acting to diminish spatial structure rather than to create it and highlights the rich variety of behaviour that is missed by continuum models which fail to represent such local dynamics.

Pediatr Neurol, 2004 Aug, 31(2), 133 - 8
Three cases of central nervous system complications associated with Mycoplasma pneumoniae; Candler PM et al.; We report three new cases of acute central nervous system disease occurring shortly after Mycoplasma pneumoniae infection . The clinical phenotypes were characterized by encephalopathy (n = 2), optic neuritis (n = 1), transverse myelitis (n = 1), and seizures (n = 1) . Although there was strong supportive evidence of preceding M . pneumoniae infection, cerebrospinal fluid polymerase chain reaction for M . pneumoniae was negative in all three patients . We propose that these cases resulted from a para-infectious immune-mediated process rather than parenchymal invasion by the microorganism . The two patients treated with steroids improved rapidly, and all three patients have made a full recovery . We review the literature regarding M . pneumoniae central nervous system complications and discuss the proposed pathologic mechanisms; para-infectious immune-mediated disease and parenchymal invasion of the central nervous system . Systematic investigation to discriminate between these two processes will be essential to select appropriate antibiotic and immunomodulatory therapies.

Br J Anaesth, 2004 Oct, 93(4), 532 - 9 Epub 2004 Aug 06.
Comparison of manufacturers' specifications for 44 types of heat and moisture exchanging filters; Dellamonica J et al.; BACKGROUND: Although heat and moisture exchanging filters (HMEF) are recommended for use during anaesthesia, the criteria for choosing a filter are not clearly defined . Manufacturers offer many different types of HMEF with various technical characteristics . We compared the technical specifications provided by the manufacturers for different types of HMEF . METHODS: Filter manufacturers were asked to provide technical information . Additional information was obtained from websites . Information about 44 filters (16 mechanical and 28 electrostatic) was collated . RESULTS: Filter performances were estimated with different sizes of microorganism and durations of challenge . Twenty-eight filters had not been tested by independent laboratories . For 12 of the filters, information obtained from websites and from the manufacturers differed . Most filter specifications claimed high efficiency, particularly for filtration, microbial challenge number and test duration . Electrostatic filters used in anaesthesia were claimed to have high filtration efficiency, similar to the efficiency provided by mechanical filters . Excluding moisture output values did not alter the general conclusions . CONCLUSIONS: Technical aspects of the tests, international standards, and independent validation should be considered when a filter is chosen.

J Biol Chem, 2004 Oct 22, 279(43), 44362 - 9 Epub 2004 Aug 05.
A two-component flavin-dependent monooxygenase involved in actinorhodin biosynthesis in Streptomyces coelicolor; Valton J et al.; The two-component flavin-dependent monooxygenases belong to an emerging class of enzymes involved in oxidation reactions in a number of metabolic and biosynthetic pathways in microorganisms . One component is a NAD(P)H:flavin oxidoreductase, which provides a reduced flavin to the second component, the proper monooxygenase . There, the reduced flavin activates molecular oxygen for substrate oxidation . Here, we study the flavin reductase ActVB and ActVA-ORF5 gene product, both reported to be involved in the last step of biosynthesis of the natural antibiotic actinorhodin in Streptomyces coelicolor . For the first time we show that ActVA-ORF5 is a FMN-dependent monooxygenase that together with the help of the flavin reductase ActVB catalyzes the oxidation reaction . The mechanism of the transfer of reduced FMN between ActVB and ActVA-ORF5 has been investigated . Dissociation constant values for oxidized and reduced flavin (FMNox and FMNred) with regard to ActVB and ActVA-ORF5 have been determined . The data clearly demonstrate a thermodynamic transfer of FMNred from ActVB to ActVA-ORF5 without involving a particular interaction between the two protein components . In full agreement with these data, we propose a reaction mechanism in which FMNox binds to ActVB, where it is reduced, and the resulting FMNred moves to ActVA-ORF5, where it reacts with O2 to generate a flavinperoxide intermediate . A direct spectroscopic evidence for the formation of such species within ActVA-ORF5 is reported.

Curr Opin Biotechnol, 2004 Aug, 15(4), 298 - 304
Dealing with complexity: evolutionary engineering and genome shuffling; Petri R et al.; Comparative analysis of the growing number of microbial genome sequences has shown a high plasticity of genomes and several mechanisms for the adaptation of microbial cells to changing environmental conditions have been discovered . By contrast, the underlying metabolic networks of microorganisms are under strict control and relatively rigid, which poses a significant challenge for rational metabolic engineering approaches . Recursive shuffling of whole genomes has recently been demonstrated as an effective new evolutionary whole-cell engineering approach for the rapid improvement of industrially important microbial phenotypes.

Commun Agric Appl Biol Sci, 2003, 68(2 Pt A), 85 - 92
Nutrient removal in a sequencing batch reactor operated with short anaerobic/aerobic cycles; Freitas F et al.; A single sequencing batch reactor operated with short intermittent aeration cycles was used to simultaneously remove carbon, nitrogen and phosphorus . The complete cycle, comprising feeding, anaerobiosis, aerobiosis, settling and decanting, was only 36 minutes long . The system has shown high and stable nutrient removal at 30 degrees C with acetate as carbon source and it has proved to be rather robust and dynamic, efficiently adapting to most of the changes in operating parameters tested: presence of nitrate in the feeding medium, different substrates (propionate and butyrate), temperature and nutrient shock loads . For the optimum conditions used, a removal efficiency of over 90% was obtained for each nutrient . Description of the population kinetics was obtained for each operating condition, by performing batch tests . Kinetic and stoichiometric parameters were used to infer the relative contribution of each group of microorganisms on SBR performance . Compared to the traditional SBR operated with cycles of 6 hours, the use of short intermittent aeration cycles of 36 minutes corresponds to a 40% reduction on aeration time.

Pharmazie, 2004 Jul, 59(7), 502 - 5
Antimycobacterial arylidenecyclohexanones and related Mannich bases; Dimmock JR et al.; Several series of 2-arylidenecyclohexanones and related Mannich bases as well as various 2,6-bis(arylidene)cyclohexanones were evaluated against Mycobacterium tuberculosis H37Rv . Using a concentration of 12.5 microg/ml, nearly half of the unsaturated ketones inhibited the growth of the microorganism by 21-66% while all of the Mannich bases achieved 99% or greater inhibition . The relative hydrophobicities and widths of the molecules may have been contributing factors as to whether bioactivity was present or absent . Two of the Mannich bases demonstrated noteworthy potencies towards Mycobacterium avium . The conclusion was drawn that Mannich bases of 2-arylidenecyclohexanones represent a novel class of antimycobacterials.

Infection, 2004 Aug, 32(4), 242 - 5
Mixed lung infection by Legionella pneumophila and Legionella gormanii detected by fluorescent in situ hybridization; Buchbinder S et al.; A mixed infection by Legionella pneumophila and a nonpneumophila Legionella species was detected in a lung biopsy specimen obtained from a patient with atypical pneumonia by fluorescent in situ hybridization (FISH) . This result was confirmed by polymerase chain reaction (PCR) . Sequencing of PCR products confirmed mixed infection by L . pneumophila and L . gormanii . Culture for Legionella spp . was negative and serology showed a rise only in IgG anti- Legionella pneumophila titer . To our knowledge, this is the first report of a mixed infection by L . pneumophila and a non-pneumophila Legionella species detected by FISH . Because FISH is a rapid and culture independent method that detects specific microorganisms in biopsy specimens it is recommended, in particular, for the detection of fastidious bacteria.

Sichuan Da Xue Xue Bao Yi Xue Ban, 2004 Jul, 35(4), 563 - 7
{Application of M-RAPD technique to obtain the genomic fingerprints of various pathogenic microbials}; Liu G et al.; OBJECTIVE: To obtain genomic fingerprints of different pathogenic microbials and make certain whether their patterns can be used in the identification of microbials by means of multiplex random amplified polymorphic DNA analysis (M-RAPD) . METHODS: Arbitrary primers of 10 oligonucleotides were randomly grouped, and various microbials chromosomal DNA were amplified with three combinatorial primers at a special higher annealing temperature . The products were detected by 15 g/L agarose electrophoresis and the patterns were analyzed by the software of Gelworks 1d Intermediate . RESULTS: Specific and resistant DNA fingerprints for different pathogenic microbials with combinatorial primers were gained . The profiles were clear, well-distributed and the number was great . The products of the three primers included most products of every two primers and would appear with no relation to their length, but small products had more opportunity; three primers could provide information contents half as many again as that two primers could provide for the same pathogenic microbials . There were obvious differences among different drug-resistant strains and between the drug-resistant strains and the corresponding reference strains, but different strains of the same microorganism had more similarity than discrepancy . The analytic data of the software of Gelworks 1d Intermediate also support our results . CONCLUSION: M-RAPD is a simple and rapid technique for the identification of different kinds of pathogenic microbials, and it can provide rich genetic information.

Immunogenetics . 2004 Jul 30; {Epub ahead of print}
Discriminating self from nonself with short peptides from large proteomes; Burroughs NJ et al.; We studied whether the peptides of nine amino acids (9-mers) that are typically used in MHC class I presentation are sufficiently unique for self:nonself discrimination . The human proteome contains 28,783 proteins, comprising 10(7) distinct 9-mers . Enumerating distinct 9-mers for a variety of microorganisms we found that the average overlap, i.show $132#e., the probability that a foreign peptide also occurs in the human self, is about 0.2% . This self:nonself overlap increased when shorter peptides were used, e.show $132#g., was 30% for 6-mers and 3% for 7-mers . Predicting all 9-mers that are expected to be cleaved by the immunoproteasome and to be translocated by TAP, we find that about 25% of the self and the nonself 9-mers are processed successfully . For the HLA-A*0201 and HLA-A*0204 alleles, we predicted which of the processed 9-mers from each proteome are expected to be presented on the MHC . Both alleles prefer to present processed 9-mers to nonprocessed 9-mers, and both have small preference to present foreign peptides . Because a number of amino acids from each 9-mer bind the MHC, and are therefore not exposed to the TCR, antigen presentation seems to involve a significant loss of information . Our results show that this is not the case because the HLA molecules are fairly specific . Removing the two anchor residues from each presented peptide, we find that the self:nonself overlap of these exposed 7-mers resembles that of 9-mers . Summarizing, the 9-mers used in MHC class I presentation tend to carry sufficient information to detect nonself peptides amongst self peptides.

Appl Microbiol Biotechnol . 2004 Jul 28; {Epub ahead of print}
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.

Arch Pediatr, 2004 Aug, 11(8), 898 - 902
{Management of acute infantile diarrhoea: a study on community pharmacy counseling in the Midi-Pyrenees region}; Lapeyre-Mestre M et al.; Counselling by community pharmacists is becoming an accepted standard for pharmacy practice . However, drugs available in children without prescription form are scarce, and most of the over-the-counter drugs have not been tested and approved in children . OBJECTIVES: The aim of this study was to investigate attitude and knowledge of community pharmacists about advice and treatment in children with acute diarrhoea . MATERIAL AND METHODS: We sent a postal questionnaire to a sample of 176 community pharmacies in the Midi-Pyrenees area (South western France), asking what they would give as advice and/or drugs in a simulated case of acute diarrhoea in an eight-month-old baby . For each question (interview of the mother, counselling about hygiene and dietetics, monitoring and drugs), we compared pharmacists answers to available evidence-based data and/or guidelines in the literature and to Summary Products Characteristics (SPC) for each reported drug . Forty one percent of pharmacies answered, giving 101 exploitable questionnaires . RESULTS: Only 48.5% of subjects have recommended a rehydration solution . 71.3% recommended an inadequate beverage (soda) and 40% recommended stopping food intake despite WHO guidelines . Most of pharmacists (77%) noticed a drug with an appropriate indication and a paediatric mention in the SPC . However, in 12.9% of cases, drugs were contra-indicated or inadequate (loperamide, nifuroxazide, microorganisms available in capsules) . CONCLUSION: Even if an appropriate advice was given by most of the responders, improvements in advice are needed: too many pharmacists recommended anti-diarrhoeal drugs and withholding milk despite evidence about their lack of effectiveness on dehydration prevention . Conversely, rehydration solutions, which have been proved their effectiveness since many years, are not sufficiently proposed.

Fungal Genet Biol, 2004 Sep, 41(9), 872 - 6
Biomechanical evidence for convergent evolution of the invasive growth process among fungi and oomycete water molds; Money NP et al.; Diverse microorganisms traditionally called fungi are recognized as members of two kingdoms: mushroom-forming species and their relatives in the Fungi, and oomycete water molds in the Stramenopila . Phylogenetic analysis suggests that these kingdoms diverged early in the evolution of eukaryotes . The phylogenetic detachment of the fungi and oomycetes is reflected in radical differences in their biochemistry, cell structure, and development . In terms of their biological activities, however, they show great similarity, because both groups form colonies of filamentous hyphae that invade and decompose solid food sources . Here we present biomechanical evidence of the convergent evolution of the invasive growth process in these microorganisms . Using miniature strain gauges to measure the forces exerted by single hyphae, we show that the hyphae of species in both kingdoms exert up to 2 atmospheres of hydrostatic pressure as they extend at their tips . No other eukaryotes have adopted this process for meeting their nutritional needs.

Nat Med, 2004 Aug, 10(8), 801 - 5
Regulatory T cells and mechanisms of immune system control; O'Garra A et al.; The immune system evolved to protect the host against the attack of foreign, potentially pathogenic, microorganisms . It does so by recognizing antigens expressed by those microorganisms and mounting an immune response against all cells expressing them, with the ultimate aim of their elimination . Various mechanisms have been reported to control and regulate the immune system to prevent or minimize reactivity to self-antigens or an overexuberant response to a pathogen, both of which can result in damage to the host . Deletion of autoreactive cells during T- and B-cell development allows the immune system to be tolerant of most self-antigens . Peripheral tolerance to self was suggested several years ago to result from the induction of anergy in peripheral self-reactive lymphocytes . More recently, however, it has become clear that avoidance of damage to the host is also achieved by active suppression mediated by regulatory T (T(reg)) cell populations . We discuss here the varied mechanisms used by T(reg) cells to suppress the immune system.

J Dent Educ, 2004 Aug, 68(8), 819 - 22
Need for genetics education in U.S . dental and dental hygiene programs; Behnke AR et al.; The two major afflictions of the oral cavity are dental caries and gingival/periodontal disease . While microorganisms have long been acknowledged as important etiologic factors, the most recent research data demonstrate that both of these pathologic conditions have a strong hereditary base, i.e., even in the presence of putative pathogenic microorganisms, if the host individual is not genetically susceptible, ensuing disease will be mild or even nonexistent . In the face of this evidence for heritability of the two major oral diseases, we evaluated what educational experiences in genetics were provided to students in U.S . dental schools and dental hygiene programs in 2003-04 . Our survey of fifty-four dental schools revealed that only one requires a formal genetics course before admission, and only six incorporate a required genetics course within the dental curriculum . Of the 264 dental hygiene programs surveyed, none require a formal genetics course as a prerequisite for admission, and none require a formal genetics course within their curricula . The enormous successes, and future promise, of the Human Genome Project suggest that genetics will soon dominate the future of medicine and dentistry, in prediction of diseases, disease diagnosis, and, eventually, therapy for genetically based disorders . It is therefore incumbent upon dental and dental hygiene education programs to provide genetics education for tomorrow's practitioners.

Can J Microbiol, 2004 Jun, 50(6), 415 - 21
The fate of a genetically modified Pseudomonas strain and its transgene during the composting of poultry manure; Guan J et al.; The fate of the genetically modified (GM) Pseudomonas chlororaphis strain 3732 RN-L11 and its transgene (lacZ insert) during composting of chicken manure was studied using plate count and nested polymerase chain reaction (PCR) methods . The detection sensitivity of the nested PCR method was 165 copies of the modified gene per gram of moist compost or soil . Compost microcosms consisted of a 100-g mixture of chicken manure and peat, whereas soil microcosms were 100-g samples of sandy clay loam . Each microcosm was inoculated with 4 x 1010 CFU of P . chlororaphis RN-L11 . In controlled temperature studies, neither P . chlororaphis RN-L11 nor its transgene could be detected in compost microcosms after incubation temperature was elevated to 45 degrees C or above for one or more days . In contrast, in the compost microcosms incubated at 23 degrees C, the target organism was not detected by the plate count method after 6 days, but its transgene was detectable for at least 45 days . In compost bins, the target organism was not recovered from compost microcosms or soil microcosms at different levels in the bins for 29 days . However, the transgene was detected in 8 of the 9 soil microcosms and in only 1 of the 9 compost microcosms . The compost microcosm in which transgene was detected was at the lower level of the bin where temperatures remained below 45 degrees C . The findings indicated that composting of organic wastes could be used to reduce or degrade heat sensitive GM microorganisms and their transgenes.

J Physiol, 2004 Sep 15, 559(Pt 3), 751 - 9 Epub 2004 Jul 29.
Electroneutral ammonium transport by basolateral rhesus B glycoprotein; Ludewig U; The liver and kidney are important tissues for ammonium (NH4+/NH3) metabolism and excretion . The rhesus B glycoprotein (RhBG) is a membrane protein expressed in liver and kidney with similarity to NH4+ transporters found in microorganisms, plants and animals . In the kidney, RhBG is predominantly localized to basolateral membranes of distal tubule epithelia, including connecting tubules and collecting ducts . These epithelia display mainly electroneutral ammonium transport, in contrast to other tubular sites, where net NH4+ transport occurs . In accordance with its localization, human RhBG mediates saturable, electroneutral transport of the ammonium analogue methylammonium when heterologously expressed in Xenopus oocytes . Uptake of methylammonium saturates with a Km = 2.6 mm . Methylammonium uptake is inhibited by ammonium and this inhibition saturates with a Ki approximately 3 mm . Electric current measurements and intracellular pHi determinations suggest that RhBG acts as an electroneutral NH4+ -H+ exchanger.

Annu Rev Phytopathol, 2004, 42, 243 - 70
Microbial diversity in soil: selection microbial populations by plant and soil type and implications for disease suppressiveness; Garbeva P et al.; An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats . The extent of the diversity of microorganisms in soil is seen to be critical to the maintenance of soil health and quality, as a wide range of microorganisms is involved in important soil functions . This review focuses on recent data relating how plant type, soil type, and soil management regime affect the microbial diversity of soil and the implication for the soil's disease suppressiveness . The two main drivers of soil microbial community structure, i.e., plant type and soil type, are thought to exert their function in a complex manner . We propose that the fact that in some situations the soil and in others the plant type is the key factor determining soil microbial diversity is related to the complexity of the microbial interactions in soil, including interactions between microorganisms and soil and microorganisms and plants . A conceptual framework, based on the relative strengths of the shaping forces exerted by plant and soil versus the ecological behavior of microorganisms, is proposed.

Annu Rev Phytopathol, 2004, 42, 185 - 209
Systemic acquired resistance; Durrant WE et al.; Systemic acquired resistance (SAR) is a mechanism of induced defense that confers long-lasting protection against a broad spectrum of microorganisms . SAR requires the signal molecule salicylic acid (SA) and is associated with accumulation of pathogenesis-related proteins, which are thought to contribute to resistance . Much progress has been made recently in elucidating the mechanism of SAR . Using the model plant Arabidopsis, it was discovered that the isochorismate pathway is the major source of SA during SAR . In response to SA, the positive regulator protein NPR1 moves to the nucleus where it interacts with TGA transcription factors to induce defense gene expression, thus activating SAR . Exciting new data suggest that the mobile signal for SAR might be a lipid molecule . We discuss the molecular and genetic data that have contributed to our understanding of SAR and present a model describing the sequence of events leading from initial infection to the induction of defense genes.

Nature, 2004 Jul 29, 430(6999), 551 - 4
Fine-scale phylogenetic architecture of a complex bacterial community; Acinas SG et al.; Although molecular data have revealed the vast scope of microbial diversity, two fundamental questions remain unanswered even for well-defined natural microbial communities: how many bacterial types co-exist, and are such types naturally organized into phylogenetically discrete units of potential ecological significance? It has been argued that without such information, the environmental function, population biology and biogeography of microorganisms cannot be rigorously explored . Here we address these questions by comprehensive sampling of two large 16S ribosomal RNA clone libraries from a coastal bacterioplankton community . We show that compensation for artefacts generated by common library construction techniques reveals fine-scale patterns of community composition . At least 516 ribotypes (unique rRNA sequences) were detected in the sample and, by statistical extrapolation, at least 1,633 co-existing ribotypes in the sampled population . More than 50% of the ribotypes fall into discrete clusters containing less than 1% sequence divergence . This pattern cannot be accounted for by interoperon variation, indicating a large predominance of closely related taxa in this community . We propose that such microdiverse clusters arise by selective sweeps and persist because competitive mechanisms are too weak to purge diversity from within them.

J Morphol, 2004 Sep, 261(3), 286 - 311
Life stages and reproductive components of the Marmorkrebs (marbled crayfish), the first parthenogenetic decapod crustacean; Vogt G et al.; Recently, we briefly reported on the first case of parthenogenesis in the decapod Crustacea which was found in the Marmorkrebs or marbled crayfish, a cambarid species of unknown geographic origin and species identity . Curiously, this animal is known only from aquarium populations, where it explosively propagates . By means of light and electron microscopic techniques we have now investigated the reproductive components of this crayfish, using more than 100 specimens ranging from hatchling to repeatedly spawned adult . Additionally, we documented its principal life stages . Our results revealed that the external sexual characters and also the gonads of the marbled crayfish are purely female, making this fast-reproducing species a good model for investigating female reproductive features in crayfish . Testicular tissues, ovotestes, or male gonoducts, gonopores, or gonopods were never found, either in small juveniles or large adult specimens, confirming the parthenogenetic nature of this crayfish . Parthenogenesis may have arisen spontaneously or by interspecific hybridization since Wolbachia-like feminizing microorganisms were not found in the ovaries . The external sexual characters of the marbled crayfish are first recognized in Stage 4 juveniles and are structurally complete approximately 2 months after hatching in specimens of approximately 2 cm total length . In the same life stage the ovary is fully differentiated as well, although the oocytes are in previtellogenic and primary vitellogenic stages only . The architecture of the mature ovary and also the synchronous maturation of cohorts of primary vitellogenic oocytes by secondary vitellogenesis are in general agreement with data published on ovaries of bisexual crayfish . New results were obtained with respect to the muscular nature of the ovarian envelope and its extensive proliferation after the first spawning, the distribution of hemal sinuses in the ovarian envelope and in the interstitium around the oogenetic pouches, the high transport activity of the follicle cells, and the colonization of oogenetic pouches by previtellogenic oocytes that originate in the germaria . Investigation of the nuclei of oocytes in the germaria and oogenetic pouches revealed no signs of meiosis, as usually found in females of bisexual decapods, suggesting that parthenogenesis in the marbled crayfish might be an apomictic thelytoky . The detection of new rickettsial and coccidian infections in the ovary and further organs raises fears that the marbled crayfish might endanger native European species by transmission of pathogens once escaped into the wild .

Reproduction, 2004 Aug, 128(2), 207 - 18
Phagocytosis as a potential mechanism for microbial defense of mouse placental trophoblast cells; Amarante-Paffaro A et al.; Trophoblast giant cells are active phagocytes during implantation and post-implantation . Phagocytosis decreases during placental maturation as the phagocytic function of nutrition is gradually replaced by the direct uptake of nutrients by the labyrinth zone trophoblast . We hypothesize that, after placental maturation, trophoblast cells maintain phagocytic functions for purposes other than nutrition . This study employs histological techniques to examine the ability of trophoblast cells to phagocytose microorganisms (yeast or bacteria)--in vivo in females receiving thioglycolate to activate macrophages and in vitro in the presence of phagocytic promoters such as interferon-gamma and complement component C3 . Placental trophoblast cells from the second half of gestation show basal phagocytosis that can be dramatically up-regulated by these promoters when microorganisms are inoculated into pregnant animals or introduced into culture systems . Stimulated trophoblast cells phagocytosed organisms more rapidly and in greater numbers than non-stimulated trophoblast exposed to the same numbers of organisms . Taken together, our results indicate that trophoblast cells do not lose their ability to phagocytose during the placentation process, which may imply that trophoblast cells participate in embryonic and fetal innate immune defense through elimination of microorganisms present at the maternal-fetal interface .

Ann Occup Hyg, 2004 Aug, 48(6), 541 - 6 Epub 2004 Jul 27.
Six month tracking of microbial growth in a metalworking fluid after system cleaning and recharging; Veillette M et al.; Large volumes of metalworking fluids (MWFs) are used in manufacturing industries for cooling and lubrication of metal pieces and tools during machining . MWFs accumulate microbial growth through continuous recirculation and reuse . We studied the progression of microbial contamination for 6 months after dumping, cleaning and recharging (DCR) of a large semi-synthetic MWF system managed with several biocides . Fresh, uncontaminated fluid was added to the system after extensive cleaning . The following samples were collected and analyzed: pre-DCR fluid (before system cleaning); neat fluid diluted to 6% with water; in use MWF 12 h and 1, 3 and 6 months post-DCR . Samples were analyzed for total microorganism concentrations by direct counting using fluorescence microscopy and by plate counting on various media (R2A, BHI, Middlebrooks and rose bengal under aerobic conditions) . In addition, PCR was performed for the detection of mycobacteria . There was a rapid progression in the total bacterial counts as determined by fluorescence microscopy: 5.7 x 10(7) cells/ml in the pre-DCR used fluid, no measurable bacteria in the neat fluid, 6.9 x 10(6) cells/ml after 12 h and 2.2 x 10(6), 3.6 x 10(8) and 6.1 x 10(8) cells/ml after 1, 3 and 6 months, respectively . On average, only 0.2% of the direct count organisms were quantified on R2A cultures . PCR showed the presence of mycobacteria in the used MWF at 3 and 6 months . Mycobacteria were also identified from cultures on Middlebrooks and R2A . This study demonstrates that standard methods for cleaning MWF systems are inadequate since residual bacteria in the system can rapidly repopulate the newly charged MWF.

BMC Bioinformatics . 2004 Jul 27;5(1):102.
A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in estimating genetic relationships: an application to papillomavirus DNA sequences; Qiao B et al.; BACKGROUND: Determination of genetic relatedness among microorganisms provides information necessary for making inferences regarding phylogeny . However, there is little information available on how well the genetic relationships inferred from different genotyping methods agree with true genetic relationships . In this report, two genotyping methods - restriction fragment analysis (RFA) and partial genome DNA sequencing - were each compared to complete DNA sequencing as the definitive standard for classification . RESULTS: Using the Genbank database, 16 different types or subtypes of papillomavirus were selected as study samples, because numerous complete genome sequences were available . RFA was achieved by computer-simulated digestion . The genetic similarity of samples, based on RFA, was determined from the proportion of fragments that matched in size . DNA sequences of four specific genes (E1, E6, E7, and L1), representing partial genome sequencing, were also selected for comparison to complete genome sequencing . Laboratory error was not taken into account . Evaluation of the correlation between genetic similarity matrices (Mantel's r) and comparisons of the structure of the derived dendrograms (partition metric) indicated that partial genome sequencing (for single genes) had higher agreement with complete genome sequencing, achieving a maximum Mantel's r = 0.97 and a minimum partition metric = 10 . RFA had lower agreement, with a maximum Mantel's r = 0.60 and a minimum partition metric = 18 . CONCLUSIONS: This simulation indicated that for smaller genomes, such as papillomavirus, partial genome sequencing is superior to restriction fragment analysis in representing genetic relatedness among isolates . The generalizability of these results to larger genomes, as well as the impact of laboratory error, remains to be demonstrated.

Curr Pharm Des, 2004, 10(19), 2335 - 43
Cancer-specific ligands identified from screening of peptide-display libraries; Mori T; Although monoclonal antibodies have demonstrated clinical potentials as tumor targeting agents, poor tumor penetration of the antibodies due to the size of molecules and liver/bone marrow toxicity by non-specific uptake of the antibodies are the two major limitations of antibody therapy . Peptidic targeting agents may ease the problems associated with antibody cancer therapy . Combinatorial libraries displayed on microorganisms have successfully been utilized to discover cell surface-binding peptides, which can be tumor-targeting agents . Among many molecular display techniques, phage display has been the most popular approach . Peptides can be used as targeting molecules of receptor-targeted toxins and gene therapy, imaging and/or therapeutic agents, and nano-medical technologies . Recent results from preclinical studies with various peptides support their targeting potential and suggest that the role of peptides as targeting molecules in drug development should be further exploited.

Orig Life Evol Biosph, 2004 Aug, 34(4), 421 - 38
Microbial life and temperature: a semi empirical approach; Garzon L; Many groups have examined the effect of temperature on the survival of microorganisms, resulting in the development of several models . Some of these models are based on the Arrhenius equation and the others are based on multidimensional response surface equations . We argue that the former are inadequate and the latter lack biological meaning . We show that an equation (the GLE equation) deduced from the Theory of Rate Processes is more accurate than the Arrhenius equation . The excellent standard deviation values of the apparent free energy of activation obtained with the GLE equation for microbial growth, embryogenic and other processes show that this equation is more suitable than the Arrhenius equation . The GLE equation shows how temperature affects survival . Thus, organisms survive longer at low temperatures than at normal temperatures . The recent discovery of microorganisms in Siberian permafrost samples that are several million years old, in deep oil fields, mines and other extreme habitats appears to be consistent with the GLE equation . Another example, the enhanced resistance of spores at extreme temperatures can be easily explained by their high apparent free energy of activation We also examined the implications of the GLE equation on food sterilization practices and on exobiology.

Oecologia, 2004 Sep, 141(1), 84 - 93 Epub 2004 Jul 20.
Aphid effects on rhizosphere microorganisms and microfauna depend more on barley growth phase than on soil fertilization; Vestergard M et al.; This paper gives the first reports on aphid effects on rhizosphere organisms as influenced by soil nutrient status and plant development . Barley plants grown in pots fertilized with N but without P (N), with N and P (NP), or not fertilized (0) were sampled in the early growth phase (day 25), 1 week before and 1 week after spike emergence . Aphids were added 16 days before sampling was carried out . In a separate experiment belowground respiration was measured on N and NP fertilized plant-soil systems with aphid treatments comparable to the first experiment . Aphids reduced numbers of rhizosphere bacteria and fungal feeding nematodes 1 week before spike emergence . Before spike emergence, aphids reduced belowground respiration in NP treatments . These findings strongly indicate that aphids reduced allocation of photoassimilates to roots and deposition of root exudates in the growth phase of the plant . Contrary to this, 1 week after spike emergence numbers of bacteria, fungal feeding nematodes and Protozoa were higher in rhizospheres of plants subjected to aphids probably because aphids enhanced root mortality and root decomposition . Protozoa and bacterial feeding nematodes were stimulated at different experimental conditions with nematodes being the dominant bacterial grazers at N fertilization and Protozoa in the NP treatment before spike emergence.

J Theor Biol, 2004 Sep 7, 230(1), 133 - 44
Computational prediction of conserved operons and phylogenetic footprinting of transcription regulatory elements in the metal-reducing bacterial family Geobacteraceae; Yan B et al.; Members of the family Geobacteraceae are an important group of microorganisms from the delta subdivision of Proteobacteria that couple the oxidation of organic compounds to metal reduction . In order to uncover transcription regulatory interactions in these organisms, we used computational methods to identify conserved operons and putative cis-regulatory transcription elements . We identified 26 putative operons with gene order and function conserved among two species of Geobacteraceae, Geobacter sulfurreducens and Geobacter metallireducens . Most of these operons were also conserved in Desulfovibrio vulgaris, an additional metal reducing organism from family Desulfovibrionaceae of the delta subdivision of Proteobacteria . The predicted conserved operons were investigated for the presence of transcription factor binding sites by two different methods, (i) comparison of non-coding regions in conserved operons, and (ii) neural network promoter prediction . Predicted motifs were screened to identify most likely transcription factor binding sites and ribosome-binding sites . We provide information on motifs in Geobacteraceae similar to known transcription factor binding sites in Escherichia coli, conserved motifs in other bacterial species, putative palindromic sites, and predicted ribosome-binding sites . These predictions will aid in further elucidation of regulatory networks of gene interactions in Geobacteraceae.

Parasitol Today . 1996 Jul;12(7):257.
Leishmania and the pathogenesis of HIV infection; Tremblay M et al.; Acquired immunodeficiency syndrome (AIDS) and leishmaniasis overlap in several parts of the world, and microorganisms responsible for these human diseases infect and replicate within the macrophage . Therefore, the opportunity that the pathogenesis of the human immunodeficiency virus (HIV) and Leishmania infections could be modulated within dually infected individual is optimized . The most prominent clinical feature of AIDS is the development of debilitating secondary infections induced by several opportunistic microorganisms, including protozoa . Michel Tremblay, Martin Olivier and Richard Bernier here focus on the recently reported information on the putative cofactor role that the intracellular pathogen of the genus Leishmania may play in the pathogenesis of HIV infection.

Langmuir, 2004 Aug 3, 20(16), 6827 - 33
Biological synthesis of strontium carbonate crystals using the fungus Fusarium oxysporum; Rautaray D et al.; The total biological synthesis of SrCO(3) crystals of needlelike morphology arranged into higher order quasi-linear superstructures by challenging microorganisms such as fungi with aqueous Sr(2+) ions is described . We term this procedure "total biological synthesis" since the source of carbonate ions that react with aqueous Sr(2+) ions is the fungus itself . We believe that secretion of proteins during growth of the fungus Fusarium oxysporum is responsible for modulating the morphology of strontianite crystals and directing their hierarchical assembly into higher order superstructures.

J Clin Apheresis, 2004, 19(2), 66 - 70
Immunotherapy using autologous monocyte-derived dendritic cells pulsed with leukemic cell lysates for acute myeloid leukemia relapse after autologous peripheral blood stem cell transplantation; Lee JJ et al.; Although a second stem cell transplantation (SCT) can be used as salvage therapy in patients with relapsing leukemia after SCT, most of these patients have a poor outcome . We tried clinical vaccination using monocyte-derived dendritic cells (DCs) pulsed with leukemic lysates to treat relapsing acute myeloid leukemia (AML) after autologous SCT . To generate DCs, CD14+ cells isolated from peripheral blood stem cell products were cultured in AIM-V in the presence of GM-CSF and IL-4 . Adding TNF-alpha on day 6 induced maturation of the DCs, which were harvested on day 8 or 9 . The DCs were incubated with tumor lysate and KLH for 2 hr at 37 degrees C . After certifying the absence of microorganisms and endotoxins, the patients received four DC vaccinations at two- to three-week intervals . Two patients received four DC vaccinations with means of 7.8 x 10(6) and 9 x 10(6) DCs at two- to three-week intervals . The DC vaccinations were well tolerated with no apparent side effects . After the vaccinations, the patients showed immunological responses with positive delayed-type hypersensitivity skin reaction and increasing autologous T cells stimulatory capacity to the DCs; however, the BM blast percentage of the patients did not improve . The results suggest that DCs are a feasible cellular therapy for relapsing AML after autologous SCT.

Exp Mol Med, 2004 Jun 30, 36(3), 259 - 67
Paradoxical effects of elastase inhibitor guamerin on the tissue repair of two different wound models: sealed cutaneous and exposed tongue wounds; Lee SK et al.; Innate elastase inhibitors are known to be putatively involved in the regulation of tissue inflammation by inhibiting polymorphonuclear leukocyte (PMN) derived proteinases . The aim of this study was to evaluate affects of leukocyte elastase suppression and PMN infiltration on wound healing in mouse by administering the recombinant elastase inhibitor guamerin (rEIG) in two different wound models; 1) impaired pin-punctured dorsal mucosa of anterior tongue wound, 60 mice, treated with saline containing rEIG that were fed ad libitum and 2) stable linear excisional cutaneous wound, 40 mice, covered with fibrin sealant containing rEIG . The progress of healing was analyzed by histological methods . The tongue wounds treated with rEIG became edematous around the pin-punctured tongue wound, and influx of inflammatory cells and PMN into the underlying stromal tissue were seen rapidly after wounding and peaked between 2-4 days . Whereas the control mice showed almost no wheal formation in the pin-punctured wound, a far lesser levels of PMN infiltration, and almost complete wound closure in 4 days . In the other model, the liner excisional cutaneous wound treated with fibrin sealant containing rEIG showed early wound constriction, lesser degree of inflammatory cells influx, and complete reepithelialization in 4-5 days, whereas the wound of control mice with the fibrin sealant alone showed contrary delayed reepithelialization, greater degree of inflammatory cell infiltration, and consequencial formation of greater granulation tissue at wound site . Taken together, these data suggest paradoxical effects of rEIG on the wound healing where in the wound exposed to infiltrating milieu of microorganisms in the oral cavity, the rEIG aggravates the wound healing by interfering with other innate defensive factors and extended greater flux of PMNs to inflamed wound site, while in the wound enclosed by fibrin, the rEIG accelerated wound healing by inhibiting the inflammation-generated proteases and the acute inflammatory reaction.

Microbiol Immunol, 2004, 48(7), 535 - 9
Ultrastructure of a Japanese Rickettsial strain genetically identified as Rickettsia helvetica which was originally found in Europe; Yano Y et al.; A rickettsial strain IO-1 has been isolated from a tick, Ixodes ovatus, in Japan and genetically identified as Rickettsia helvetica, a member of the spotted fever group rickettsiae . Ultrastructural observations were made on the microorganism . The ultrastructure of R . helvetica IO-1 appeared to be generally the same as that previously shown for other rickettsiae of the spotted fever and typhus groups . The rickettsiae were primarily found free in the cytoplasm of L929 cultured cells . Occasionally, the rickettsiae may also invade the host cell nucleus; however, the frequency of the nuclear localization was very low.

Infect Immun, 2004 Aug, 72(8), 4772 - 83
Anaplasma phagocytophilum utilizes multiple host evasion mechanisms to thwart NADPH oxidase-mediated killing during neutrophil infection; Carlyon JA et al.; Anaplasma phagocytophilum, the etiologic agent of human anaplasmosis, is a bacterial pathogen that specifically colonizes neutrophils . Neutrophils utilize the NADPH oxidase complex to generate superoxide (O(2)(-)) and initiate oxidative killing of microorganisms . A . phagocytophilum's unique tropism for neutrophils, however, indicates that it subverts and/or avoids oxidative killing . We therefore examined the effects of A . phagocytophilum infection on neutrophil NADPH oxidase assembly and reactive oxygen species (ROS) production . Following neutrophil binding, Anaplasma invasion requires at least 240 min . During its prolonged association with the neutrophil plasma membrane, A . phagocytophilum stimulates NADPH oxidase assembly, as indicated by increased cytochrome b(558) mobilization to the membrane, as well as colocalization of Rac and p22(phox) . This initial stimulation taxes the host neutrophil's finite oxidase reserves, as demonstrated by time- and bacterial-dose-dependent decreases in secondary activation by N-formyl-methionyl-leucyl-phenylalanine (FMLP) or phorbol myristate acetate (PMA) . This stimulation is modest, however, and does not diminish oxidase stores to nearly the extent that Escherichia coli, serum-opsonized zymosan, FMLP, or PMA do . Despite the apparent activation of NADPH oxidase, no change in ROS-dependent chemiluminescence is observed upon the addition of A . phagocytophilum to neutrophils, indicating that the bacterium may scavenge exogenous O(2)(-) . Indeed, A . phagocytophilum rapidly detoxifies O(2)(-) in a cell-free system . Once internalized, the bacterium resides within a protective vacuole that excludes p22(phox) and gp91(phox) . Thus, A . phagocytophilum employs at least two strategies to protect itself from neutrophil NADPH oxidase-mediated killing.

Arch Pathol Lab Med, 2004 Aug, 128(8), 911 - 4
Xanthogranulomatous funiculitis and orchiepididymitis: report of 2 cases with immunohistochemical study and literature review; Nistal M et al.; Two patients with xanthogranulomatous inflammation are described, one with involvement of the spermatic cord and the other with 1 testicle and epididymis affected . To our knowledge, only 12 cases of xanthogranulomatous orchiepididymitis have been reported previously, one of which also presented a xanthogranulomatous funiculitis . Clinically, our patients presented with spermatic cord enlargement (case 1) and chronic orchitis that did not respond to treatment with antibiotics (case 2) . Histopathologically, both cases showed extensive xanthogranulomatous inflammation with numerous foamy macrophages that were associated with colonies of microorganisms suggestive of actinomyces in case 1 . Additionally, Escherichia coli was cultured from the surgical specimen of case 2 . The possible underlying pathology may be diabetes in case 1 and phlebitis associated with chronic orchitis in case 2 . Differential diagnoses with other lesions that are rich in macrophages, such as malakoplakia, and those testicular neoplasms without serologic tumor markers are discussed.

Environ Toxicol, 2004 Aug, 19(4), 318 - 28
Physical and chemical aspects of long-term biodeterioration of some polymers and composites; Lugauskas A et al.; A biodeterioration study was performed on synthetic polymeric materials including homogenous film made from poly(tetrafluorine ethylene), copolymer film made from tetrafluorine ethylene and perfluoromethyl vinyl ether, vulcanized rubber containing natural caoutchouc, and vulcanized rubber, the main component of which was synthetic butadiene nitrile caoutchouc . The materials were exposed for 12 years to the open air, in mycological containers, and in a cellar in maritime climate conditions: air humidity 72%-90% and seasonal average temperature of 17 degrees C in summer and -2.5 degrees C in winter . The studies of optical and electron microscopy revealed that microorganisms were able to develop not only on the surface of the materials but also to penetrate inside into deeper layers . The fungi that produced the most intensive deterioration in the fluorine polymers and vulcanized rubbers belonged to the Alternaria, Aspergillus, Aureobasidium, Cladosporium, Penicillium, Oidiodendron and Trichoderma genera . The fungi Aspergillus fumigatus, A . niger, Aureobasidium pullulans, and Trichoderma viride produced the most intensive deterioration in the fluorine films, whereas Alternaria tenuissima, Cladosporium herbarum, C . sphaerospermum, and fungi of the Oidiodendron genus were widespread on vulcanized rubbers . Fungi of the Aspergillus and Penicillium genera prevailed on both fluorine films and rubbers exposed in a cellar . Infrared spectroscopy indicated that the structures of poly(tetrafluorine ethylene) and the copolymer of tetrafluorine ethylene and perfluoromethyl vinyl ether did not change after the 12-year exposure; only insignificant changes in surface morphology were observed by optical microscopy . Vulcanized rubber made both from natural and from synthetic caoutchouc exposed for the same length of time showed rather evident changes in appearance and structure . X-ray graphical analysis revealed that new crystallization of the caoutchouc and a possible change in chemical composition of the fillers had occurred .

FEMS Microbiol Lett, 2004 Aug 1, 237(1), 133 - 8
Monitoring of the bacterial composition of dairy starter cultures by RAPD-PCR; Giraffa G et al.; Randomly amplified polymorphic DNA (RAPD)-PCR was used to verify the species composition of commercial dairy starters and to detect possible shifts in strain composition of these cultures . After RAPD-PCR analysis, not all the strains isolated in the years 2001 and 2002 fell within the same dendrogram cluster of the strains isolated in the year 2000 and used as reference strains . Changes in composition of the microbial population and/or voluntary immission of new biotypes with respect to the original strain formulation had occurred in the starters . The microbial composition of modern dairy starters represents a key point because the complex relationships among microorganisms can easily be altered . Little variations in the microbial composition could have unexpected effects on cheese quality.

Biochem J . 2004 Jul 22; Pt {Epub ahead of print}
Effects of deletions at the carboxyl terminus of tobacco acetohydroxyacid synthase on the enzyme activity and cofactor binding; Kim J et al.; Acetohydroxyacid synthase (AHAS) catalyzes the first committed step in the biosynthesis of branched-chain amino acids, such as valine, leucine, and isoleucine . Due to the unique presence of these biosynthetic pathways in plants and microorganisms, AHAS has been widely investigated as an attractive target of several classes of herbicides . Recently, the crystal structure of the catalytic subunit of yeast AHAS has been resolved at 2.8A, showing that the active site is located at the dimer interface and is near the herbicide-binding site . In this structure, the existence of two disordered regions, a "mobile loop" and a C-terminal "lid", is worth notice . Although these regions contain the residues that are known to be important in substrate specificity and in herbicide resistance, they are poorly folded into any distinct secondary structure and are not within contact distance of the cofactors . In this study, we have tried to demonstrate the role of these regions of tobacco AHAS by constructing variants with serial deletion, based on the structure of yeast AHAS . In contrast to the wild-type AHAS, the truncated mutant which removes the C-terminal "lid", Delta630, and the internal deletion mutant without "mobile loop", Delta567-582, impaired the binding affinity for ThDP, and showed different elution profiles representing a monomeric form in gel filtration chromatography . Our results suggest that these regions are involved in the binding/stabilization of the active dimer and ThDP binding.

Zhonghua Nan Ke Xue, 2004 Jun, 10(6), 461 - 4
{Progress in studies of male infertility resulting from chronic prostatitis}; Fan Z et al.; Chronic prostatitis (CP) is a very common disease in the male genitourinary system . It can result in male infertility mainly by affecting the motility or the function of spermatozoa and the physical and chemical nature of semen . At present, researches on the mechanism of male infertility resulting from CP mainly focus on ROS, immunological mechanism, lack of zinc and pathogenetic microorganism . This article briefly reviews the progress in these aspects.

Parassitologia, 2003 Jun, 45(2), 89 - 96
Ultrastructural evidence of the degenerative events occurring during embryogenesis of the filarial nematode Brugia pahangi after tetracycline treatment; Sacchi L et al.; Intracellular bacteria belonging to the genus Wolbachia have been described in filarial nematodes and these microorganisms appear to have evolved an obligatory mutualistic association with their filarial hosts . In fact, antibiotic treatment leads to the clearance of bacteria from worms resulting in a block in embryogenesis and, eventually, death of adult filariae . Currently, the antifilarial action of antibiotic treatment is interpreted as a secondary consequence of the bacteriostatic activity against Wolbachia endosymbionts . Here, we demonstrate by transmission electron microscopy the degenerative events occurring during embryogenesis of Brugia pahangi after tetracycline treatment . After 56 days of treatment the cytoplasm of hypodermal cords was totally void of Wolbachia and numerous vacuoles, residual of cytolitic activity, were observed . In the ovary, the morphology of the oocytes was well conserved 33 days after treatment, but the texture of symbiotic bacteria appeared altered . After 56 days of treatment embryogenesis was dramatically affected and the terminal portion of the ovary appeared totally empty . The authors suggest that the symbiotic bacteria play a direct role in worm metabolism and a long-term bacteriostatic effect may block bacterial activity involved in the active control of cytolysis . As a consequence, the bacteriophorous vacuole is transformed into a digestive vacuole and the whole symbiotic population is disrupted.

Ophthal Plast Reconstr Surg, 2004 Jul, 20(4), 285 - 90
Clinicopathologic analysis of 15 explanted hydroxyapatite implants; Jordan DR et al.; PURPOSE: To report the clinical findings, treatment, outcomes, and histopathologic findings in patients with suspected orbital implant infection requiring implant removal . METHODS: Retrospective, observational case series of 14 patients (15 hydroxyapatite orbital implants) undergoing implant removal from September 1994 through December 2002 . Patient age, type of surgery, implant type, symptoms, treatment, histopathology of implant, and follow-up course were analyzed . RESULTS: Of the 14 patients, 7 were female and 7 were male . The mean age at explantation was 42 years . The most common symptoms were discharge and socket tenderness . The most common signs were conjunctival inflammation (edema, hyperemia), discharge, and recurrent pyogenic granuloma . Clinical evidence of infection was documented in 13 patients . Histopathologic assessment of the 15 explanted implants showed acute inflammation and necrosis (abscess) with identification of microorganisms (5 patients), acute inflammation and necrosis without identification of microorganisms (4 patients), chronic inflammation with identification of microorganisms (1 patient), chronic inflammation without identification of microorganisms (3 patients), and a predominant foreign body granulomatous response without identification of microorganisms (2 patients) . Osseous metaplasia was seen in 10 implants . Prompt resolution of symptoms and signs occurred in all but one case . CONCLUSIONS: The clinical course of porous orbital implant infection may be prolonged, and the early symptom of recurrent discharge, a common problem for implant recipients, may delay diagnosis . Implant infection should be suspected when there is persistent conjunctival inflammation and discharge after implant placement despite antibiotic therapy, discomfort on implant palpation, and recurrent pyogenic granuloma (indicative of implant exposure) . Implant removal is usually required in these cases . If orbital pain (not necessarily related to implant palpation) is the main complaint, without signs of conjunctival inflammation and with or without discharge, one should consider other reasons for the symptoms.

Biotechnol Lett, 2004 Jul, 26(14), 1173 - 8
Co-expression of bacterial hemoglobin overrides high glucose-induced repression of foreign protein expression in Escherichia coli W3110; Kim YK et al.; Co-expression of Vitreoscilla hemoglobin (VHb) can enhance production of foreign proteins in several microorganisms, including Escherichia coli . Production of foreign proteins {green fluorescent protein (GFP) and organophosphorous hydrolase (OPH)} has been examined in two typical industrial E . coli strains, W3110 (a K12 derivative) and BL21 (a B derivative) . In particular, we investigated the effects of VHb co-expression and media glucose concentration on target protein production . We employed the nar O(2)-dependent promoter for self-tuning of VHb expression based on the natural changes in dissolved O(2) levels over the duration of culture . Foreign protein production in strain BL21 was decreased by a high glucose concentration but co-expression of VHb had no effect on this . In contrast, co-expression of VHb in strain W3110 overrode the glucose-induced repression and resulted in steady expression of foreign proteins.

Chin Med J (Engl), 2004 Jul, 117(7), 1066 - 71
Characterization of DNA antigens from immune complexes deposited in the skin of patients with systemic lupus erythematosus; Zeng FQ et al.; BACKGROUND: Skin lesions are common manifestations in systemic lupus erythematosus (SLE) . It is still unknown what the definite pathogenesis of skin involvement was and whether DNA participated in it . Our study was designed to explore the pathogenetic role and nature of nuclear antigen (DNA) deposited in the skin lesions of patients with SLE . METHODS: Thirty skin samples from patients with SLE and 2 normal skin samples were studied . Extracellular DNA was evaluated by indirect immunofluorescence methods . The deposited immune complexes were extracted by cryoprecipitation, and DNA was then isolated with phenol and chloroform . DNA fragment sizes were detected by agarose gel electrophoresis . Finally, 8 different probes were used to analyze the origin of these DNA molecules using Dot hybridization . RESULTS: Extracellular DNA staining was found only in skin lesions, mainly those located in the basement membrane zone, vascular wall, and hair follicle wall . Normal skin and non-lesion SLE skin showed no fluorescence at locations outside the nuclei . There were no differences in the rate and intensity of extracellular DNA staining when comparing active phase to remission phase patients . No relationship was found between extracellular DNA and circulating anti-dsDNA antibodies . Deposited DNA fragments clustered into four bands of somewhat discrete sizes: 20 000 bp, 1300 bp, 800-900 bp, 100-200 bp . Small sized fragments (100-200 bp) were positively correlated with disease activity (P < 0.05, r = 0.407) . Dot hybridization showed significant homology of the various extracellular DNA fragments examined with human genomic DNA, but not with DNA from the microorganisms and viruses we examined . There were also homologies between DNA samples from different individuals . CONCLUSIONS: DNA and its immune complexes may contribute to the pathogenesis of skin lesions in SLE . These DNA molecules range in size from 100 bp to 20 kb and may be endogenous in origin.

J Invertebr Pathol, 2004 Jul, 86(3), 111 - 6
Multiple displacement amplification in combination with high-fidelity PCR improves detection of bacteria from single females or eggs of Metaseiulus occidentalis (Nesbitt) (Acari: Phytoseiidae); Jeyaprakash A et al.; Amplifying microbial DNA by the polymerase chain reaction (PCR) from single phytoseiid mites has been difficult, perhaps due to the low titer of bacteria and to interference by the relatively larger amounts of mite genomic DNA . In this paper we evaluate the efficiency of standard and high-fidelity PCR protocols subsequent to amplification of the whole genome by a multiple displacement amplification (MDA) procedure developed by Dean et al . DNA from the phytoseiid Phytoseiulus persimilis (Athias-Henriot) was tested because it lacks a Cytophaga-like organism (CLO) and we could add known amounts of a plasmid containing a cloned 16S rRNA gene fragment from a CLO from Metaseiulus occidentalis (Nesbitt) . P . persimilis genomic DNA was mixed with the serially diluted plasmid and amplified using MDA followed by either standard or high-fidelity PCR . MDA followed by high-fidelity PCR was most efficient and successfully amplified an expected 1.5-kb band from as little as 0.01fg of the plasmid, which is equivalent to about 1 copy . MDA followed by high-fidelity PCR also consistently amplified Wolbachia- or CLO-specific products from naturally infected single females or eggs of M . occidentalis, which will allow detailed studies of infection frequency and transmission of several microorganisms associated with this predatory mite.

Water Sci Technol, 2004, 49(10), 115 - 22
Anaerobic bioprocessing of sewage sludge, focusing on degradation of linear alkylbenzene sulfonates (LAS); Angelidaki I et al.; Anaerobic degradation of sludge amended with linear alkylbenzene sulfonates (LAS) was tested in a one stage continuous stirred tank reactor (CSTR) and a two stage reactor system consisting of a CSTR as first step and upflow anaerobic sludge bed (UASB) reactor as the second step . Anaerobic removal of LAS was only observed at the second step but not at the first step . Removal of LAS in the UASB reactors was approx . 80% where half was due to absorption and the other half was apparently due to biological removal as shown from the LAS mass balance . At the end of the experiment the reactors were spiked with 14C-LAS which resulted in 5.6% 14CO2 in the produced gas . Total mass balance of the radioactivity was however not achieved . In batch experiments it was found that LAS at concentrations higher than 50 mg/l is inhibitory for most microbial groups of the anaerobic process . Therefore, low initial LAS concentration is a prerequisite for successful LAS degradation . The results from the present study suggest that anaerobic degradation of LAS is possible in UASB reactors when the concentration of LAS is low enough to avoid inhibition of microorganisms active in the anaerobic process.

Acta Med Austriaca, 2004 Feb, 31(1), 13 - 7
{Natural therapy instead of chemistry? Probiotics in gastroenterology}; Kirchgatterer A et al.; Probiotics are living microorganisms that upon ingestion exert health benefits . The impact of probiotics on gut flora represents a new and interesting therapeutic approach in a number of diseases of the gastrointestinal tract . According to actual publications and guidelines of medical societies, the clinical relevance of probiotics can be described as follows: (a) In the case of ulcerative colitis, available data demonstrate benefits of probiotic therapy . (b) The available data regarding pouchitis are limited, but the therapeutic effect seems to be excellent . (c) In the case of Crohn's disease, the role of probiotics is not clearly defined, thus the results of new trials have to be awaited before probiotic therapy is recommended . (d) Further indications such as antibiotic-associated diarrhea, acute pancreatitis or irritable bowel syndrome have been reported recently . The results of these clinical trials have been encouraging, but they often included only a small number of patients and therefore a clear-cut assessment seems difficult at the moment.

Chir Organi Mov, 2003 Oct-Dec, 88(4), 345 - 50
Bacterial contamination of musculoskeletal allografts; Maso A et al.; Based on the indications in the literature of the transmission of highly pathogenic bacteria in musculoskeletal allograft implants, the cultural results for allografts removed and implanted in conditions of asepsis between 1997 and 2000 in BTM were analyzed: 4014 allografts (3117 from a living donor, 897 from a cadaver) and 3479 implants (2191 with allografts from living donors and 1288 with allografts from cadavers) . Explanted tissues: these were positive to culture in 292 out of 3117 (9.4%) allografts from living donors; the bacteria isolated showed low pathogenicity . Out of 897 allografts 117 cadaver donors bacteria with low pathogenicity were isolated in 68 (7.6%) and high pathogenicity in 12 (1.3%) . Implants: cultures were positive in 116/2191 (5.3%) implants with allografts from living donors and in 55/1288 (4.3%) implants with allografts from cadavers . The bacteria isolated are the same as those shown in the explants . In living donors contamination is similar as regards incidence and type of microorganism to that observed in surgical theatres during routine surgery . Contamination seems to be greater in allografts removed from cadavers who died as a result of trauma, in the presence of positive hemocultures, prolonged catheterization and intubation, explantation of the pelvis and removal of several organs and tissues prior to musculoskeletal allograft.

J Dairy Sci, 2004 Apr, 87(4), 1047 - 50
Short communication: docosahexaenoic acid promotes vaccenic acid accumulation in mixed ruminal cultures when incubated with linoleic acid; AbuGhazaleh AA et al.; Previous studies found that feeding dairy cows a blend of fish and soybean oils enhanced milk vaccenic acid (VA) and conjugated linoleic acid (CLA) concentrations more than when the oils were fed separately . In these studies, the authors concluded that a component in fish oil was stimulating ruminal VA production from other sources of unsaturated fatty acids; however, that component was not identified . The objective of this study was to determine whether docosahexaenoic acid (DHA), an omega-3 fatty acid (FA) in fish oil, is the active component that promotes trans-C18:1 FA, VA in particular, accumulation using cultures of mixed ruminal microorganisms . Treatments consisted of control, control plus 5 mg of DHA (DH), control plus 30 mg of soybean oil (SBO), and control plus 5 mg of DHA and 30 mg of SBO (DHSBO) . Treatments were incubated in triplicate in 125-mL flasks, and 5 mL of culture contents was taken at 0 and 24 h for fatty acid analysis by gas-liquid chromatography . After 24 h of incubation, the level of trans-C18:1 FA (14.1 and 11.7 mg/culture) and VA (13.0 and 10.2 mg/culture) increased more with added DHA than with added SBO, respectively . Combining DHA and SBO yielded higher quantities of trans-C18:1 FA (21.3 mg/culture) and VA (19.8 mg/culture) in the cultures than either fat source alone . These data suggest that DHA is the component in fish oil that promotes VA accumulation when incubated with linoleic acid.

J Dairy Sci, 2004 Apr, 87(4), 1038 - 46
Ruminal biohydrogenation in Holstein cows fed soybean fatty acids as amides or calcium salts; Lundy FP et al.; Fatty amides of high oleate fats and calcium salts of palm oil were reported to resist biohydrogenation by ruminal microorganisms . This study was conducted to determine whether converting polyunsaturated fat sources to amides and calcium salts had equal ability to resist biohydrogenation . A total mixed ration consisting of forage and concentrate contained (dry basis): 1) 2.45% soybean oil (SBO), 2) 2.75% calcium salt of SBO, 3) 2.75% amide of SBO, or 4) 2.75% of a mixture of the calcium salt and amide (80:20, wt/wt) of SBO . The 4 diets were fed ad libitum to 4 multiparous lactating Holstein cows fitted with ruminal cannulas in a 4 x 4 Latin square with 21-d periods . Omasal samples were taken to measure postruminal fatty acid content and determine the extent of ruminal biohydrogenation . Adding SBO to the diets as either calcium salts or amides increased omasal flow of C18:2 (n-6) from 25 to 39 g/d . Omasal flow of C18:1 increased from 36 to 49 g/d when SBO was fed to cows as calcium salts, but increased to 86 g/d when SBO was fed as amides . Adding the soybean amide to the diet more than doubled the delivery of C18:1 (n-9) to the omasum of lactating cows, but it also increased trans fatty acid production in the rumen accompanied by milk fat depression . In this study, calcium salts and amide derivatives of fatty acids were both effective in enhancing omasal flow of unsaturataed fatty acids in lactating dairy cows . Amides were more effective than calcium salts for increasing the postruminal flow of oleic acid.

Immunol Res, 2004, 30(1), 15 - 28
Manipulation of iron to determine survival: competition between host and pathogen; Laham N et al.; Iron is an essential nutrient that can determine cellular survival . Many organisms have evolved sophisticated mechanisms for iron uptake and transport to support their growth . The dual dependence on iron of both the host and invading pathogen initiates a competition for this nutrient following infection . Microorganisms have developed various strategies to acquire iron from the host . These are counter-balanced by an iron-withholding strategy that the host deploys as part of its defense system . This strategy, involving many iron-regulatory proteins, mediates iron depletion at the mucosal surfaces, in the extracellular environment, and within the cells . Iron is sequestered into storage by the host in order to deprive the pathogens of this factor and to prevent their proliferation . This system can be compromised . In particular, new evidence is emerging that suggests that viruses are able to specifically target and regulate proteins involved in iron homeostasis . This review focuses on the procedures employed by the host and viruses to regulate iron as a means of defense and survival, respectively.

Evid Based Complement Alternat Med, 2004 Jun 1, 1(1), 71 - 82
Traditional and Modern Biomedical Prospecting: Part I-the History: Sustainable Exploitation of Biodiversity (Sponges and Invertebrates) in the Adriatic Sea in Rovinj (Croatia); Muller WE et al.; Nature, especially the marine environment, provides the most effective drugs used in human therapy . Among the metazoans, the marine sponges (phylum Porifera), which are sessile filter feeders, produce the most potent and highly selective bioactive secondary metabolites . These animals (or their associated symbiotic microorganisms) synthesize secondary metabolites whose activity and selectivity has developed during their long evolutionary history (evochemistry) . The exploitation of these resources has become possible due to the progress in molecular and cell biology . BIOTECmarin, the German Center of Excellence follows this rationale . In the past, these animals have been successfully and extensively utilized to isolate bioactive compounds and biomaterials for human benefit . Pharmaceuticals prepared from marine animals, primarily sponges, have been applied since ancient times (Hippocrates, Aristotle and later Plinius) . It has been reported that extracts and/or components from sponges can be used for the treatment of specific diseases . For a systematic and applied-oriented exploitation, the successful development of effective compounds largely depends on quality of the institutional infrastructure of marine stations and more so on the biodiversity . The Center for Marine Research in Rovinj (Croatia) fulfils these prerequisites . Founded in 1891, this institute has to its credit major discoveries related to exploitation of secondary metabolites/biomaterials from sponges for therapeutical application and to obtain biomaterials for general wellbeing . This is the first part of a review focusing on biomedical prospecting . Here, we have mainly described the historic background . The details of techniques, substances, approaches and outlooks will be discussed in the second part.

Cell Tissue Bank, 2000, 1(4), 313 - 316
The Analysis of Bacterial Results in the Kidney Perfusion Fluid and Bone Allografts in Human Multiorgan Donors; Bettin D et al.; In 19 young human multiorgan donors, we simultaneously analyzed the bacterial contamination of the kidney perfusion fluid and all retrieved bone allografts . Donor exclusion criteria were done according to the American and European Association of Tissue Banks excluding all patients with perforating wounds . The kidney perfusate revealed a contamination in 17 of 19 (89.5%) donors . Allograft testing demonstrated positive bacterial growth in 34 of 76 allografts (44.7%) . Microorganisms originated from the normal skin flora and could be related to contamination during the harvesting procedure . In 5 cases we cultured identical bacterial subspecies in both cultures as a possible sign for systemic bacterial spreading during the multiorgan harvesting procedure.

Mol Microbiol, 2004 Aug, 53(3), 745 - 54
Light matters: phototaxis and signal transduction in unicellular cyanobacteria; Bhaya D; Many photosynthetic microorganisms have evolved the ability to sense light quality and/or quantity and can steer themselves into optimal conditions within the environment . Phototaxis and gliding motility in unicellular cyanobacteria require type IV pili, which are multifunctional cell surface appendages . Screens for cells exhibiting aberrant motility uncovered several non-motile mutants as well as some that had lost positive phototaxis (consequently, they were negatively phototactic) . Several negatively phototactic mutants mapped to the tax1 locus, which contains five chemotaxis-like genes . This locus includes a gene that encodes a putative photoreceptor (TaxD1) for positive phototaxis . A second chemotaxis-like cluster (tax3 locus) appears to be involved in pilus biogenesis . The biosynthesis and regulation of type IV pilus-based motility as well as the communication between the pilus motor and photosensory molecules appear to be complex and tightly regulated . Furthermore, the discovery that cyclic AMP and novel gene products are necessary for phototaxis/motility suggests that there might be additional levels of communication and signal processing .

J Biomater Sci Polym Ed, 2004, 15(6), 753 - 66
Effect of polyethylene glycol grafted onto islet capsules on prevention of splenocyte and cytokine attacks; Lee DY et al.; In the graft rejection of transplanted islets, the host's immune cells recognize the islets as antigens, which then stimulate the immune cells to begin the cytokine secretion and also the proliferation of immune cells . To prevent the recognition of islets by the immune cells, we grafted biocompatible polyethylene glycol (PEG) onto the collagen capsule of islets without incurring any changes in the morphology and function of islets . To evaluate the efficiency of PEG grafting, PEG-grafted islets were cultured with splenocytes consisting mainly of lymphocytes and macrophages . A splenocyte proliferation assessment using a BrdU incorporation assay showed that the PEG-grafted islets did not stimulate the splenocytes . In addition, the viability and microorganisms in islet cells of co-cultured PEG-grafted islets were not altered . However, in the co-culture of free islets (control) splenocytes were stimulated; they mainly secreted TNF-alpha and strongly affected the viability and structure of free islets . Furthermore, when islets were treated with the rat recombinant TNF-alpha for 7 days, the viabilities of PEG-grafted and free islets were significantly damaged, although the viability of PEG-grafted islets was higher than that of free islets by nearly three times . These results demonstrate that PEG grafted on the surface of islets could prevent the recognition of islets by splenocytes, but could not completely protect islets from cytokines.

Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz, 2004 Jul, 47(7), 611 - 21
{The emergence of old and new epidemics as a consequence of human actions}; Kurth R; In the era of antibiotics and vaccines and prior to the appearance of AIDS, well-known infectious diseases received decreasing clinical attention . Occasionally, the opinion was also expressed that new types of infectious diseases could no longer be expected . However, a more detailed analysis of the state of infectious diseases yields quite a different picture . A variety of new infectious diseases has clinically been defined over the last few decades . New viruses, bacteria, and parasites with pathogenic potential for humans have been detected and well-known microorganisms have spread beyond their original geographic areas . Infectious agents, in particular viruses, permanently alter their genomes and may thus gain new clinical relevance . This article demonstrates that primarily the behavior of man influenced the nature and distribution of infectious diseases in the past and will affect the spread of infectious diseases in the future.

Prostaglandins Leukot Essent Fatty Acids, 2004 Sep, 71(3), 185 - 90
Role of leukotrienes in killing of Mycobacterium bovis by neutrophils; Coffey MJ et al.; The neutrophil (PMN) plays an important role in the phagocytosis and killing of microorganisms . Pro-inflammatory leukotrienes (LT) play an important role in various disease states . However LT elaborated by PMN have also been shown to be important in host defense, specifically phagocytosis and killing of microorganisms . Defective LT synthesis by phagocytes correlates with their reduced anti-microbial activity . Therefore, we determined if LT played an important role in the killing of Mycobacteria bovis (M . bovis) by PMN . Endogenous LT play a role in the killing of mycobacteria since the LT synthesis inhibitor MK-886 reversed the killing of M . bovis by PMN . Increased synthesis of LT occurred following incubation of PMN with M . bovis . Treatment with granulocyte-colony stimulating factor, which augments PMN LT synthesis, also boosted anti-microbial activity . Furthermore, exogenous LTB4 augmented dose-dependent killing of M . bovis by PMN . In conclusion, LT play a vital role in promoting mycobactericidal actions of PMN.

Comp Biochem Physiol B Biochem Mol Biol, 2004 Jul, 138(3), 265 - 76
Methyl-branched hydrocarbons, major components of the waxy material coating the embryos of the viviparous cockroach Diploptera punctata; Nelson DR et al.; The viviparous cockroach Diploptera punctata carries a wax-coated batch of embryos in a brood sac . When the embryos are expelled into saline, flakes of wax from the surface of the embryos float to the surface . In contrast, embryos of the ovoviviparous species such as Rhyparobia maderae are not nourished by the mother during embryogenesis and do not have a copious waxy coating . As a first step in determining the function of this copious wax layer on the batch of embryos of D . punctata, its composition was compared to that of the waxy material on the outer cuticular surface of the mother (female cuticle) by thin-layer chromatography (TLC) and gas chromatography-mass spectrometry . The major lipid class on the embryos was hydrocarbons with lesser amounts of wax esters and long-chain alcohols . Hydrocarbons from both sources had similar elution times and chemical composition, but were markedly different in the amounts of the major methyl-branched hydrocarbon components . A mixture of 3,X-dimethyl alkanes were 44% of the hydrocarbons on the embryos and were only 29% on the female cuticle . However, trimethylalkanes were only 22% of the hydrocarbons on the embryos and were 34% of the hydrocarbons on the female cuticle . The major hydrocarbons from both sources were mixtures of methyl-branched alkanes with backbones of 33 and 35 carbon atoms . Methyl-branched tritriacontanes were 59% of embryo and 35% of female cuticular hydrocarbons; methyl-branched pentatriacontanes were 19% of embryo and 42% of female hydrocarbons . The difference in proportions of the similar hydrocarbons on the outer cuticular surface of the female and those covering the embryos may suggest that the evolution of copious nutrient secretion for the embryos was accompanied by selection for a mixture of hydrocarbons that prevents water loss by the embryos and protects them against invasion by microorganisms without preventing the movement of nutrient fluid into the embryos.

Anal Chem, 2004 Jul 15, 76(14), 4017 - 22
Identification of biomarkers of whole Coxiella burnetii phase I by MALDI-TOF mass spectrometry; Shaw EI et al.; Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) specific biomarkers have been shown to be an effective tool for identifying microorganisms . In this study, we demonstrate the feasibility of using this technique to detect the obligate intracellular bacterium Coxiella burnetii, a category B bioterrorism agent . Specific biomarkers were detected in C . burnetii Nine Mile phase I (NMI) strain purified from embryonated egg yolk sac preparations . Whole organisms were applied directly to the MALDI target . MALDI-TOF MS analysis of C . burnetii NMI grown and purified at different times and places revealed a group of unique, characteristic, and reproducible spectral markers in the mass range of 1000-25000 Da . Statistical analysis of the averaged centroided masses uncovered at least 24 peptides or biomarkers . Three biomarkers observed in the MALDI-TOF MS spectrum consistently matched proteins that had been previously described in C . burnetii, one of them being the small cell variant protein A . MALDI-TOF MS analysis of whole organisms represents a sensitive and specific option for characterizing C . burnetii isolates, especially when coupled with antigen capture techniques . The method also has potential for several applications in basic microbial research, including regulation of gene expression.

Endocr Pract, 1995, 1(2), 103 - 15
The pathogenesis of graves' disease; Volpe MD R; We have hypothesized over many years that Graves' disease (GD) and the other autoimmune thyroid diseases (AITD) are each due to antigen-specific defects in suppressor (regulatory) T lymphocyte function . There have been several reports dealing with the role of regulatory T lymphocyte subsets, ie., that will prevent autoimmune disease in these and other organ-specific autoimmune diseases . In AITD, suppressor T cells have been shown to be less well activated by relevant antigen, but are normally activated by irrelevant antigen; suppressor T cells from normal persons react equally well to both . In GD, these cells have been shown to be inadequately activated by TSH receptor antigen, but are normally activated by irrelevant autoantigen . This reduction is partial only, and insufficient itself to precipitate the autoimmune disease; further insults from the environment are necessary to further reduce generalized regulatory cell activity, adding to the genetically induced specific regulatory cell dysfunction, which appears in turn to be due to a specific defect in the presentation of a specific antigen . This, in turn, may relate to abnormalities of the genes responsible for antigen presentation . The end result is activation of appropriate helper and effector T cells, the stimulation by these of appropriate B lymphocytes, and the concurrent production of cytokines . These events lead to functional changes within the target cell which itself will express Class II antigens, heat shock proteins, and intercellular adhesion molecules, all of which amplify the immune response . Moreover, the activation of helper T lymphocytes by specific antigen depends on the availability of normal amounts of antigen being presented to them by antigen-presenting cells . Thus, there is no need to invoke any primary abnormality or infection of the thyroid cell, or any cross-reacting antigen of microorganismic origin to initiate this process . What is required is an abnormality of antigen-presentation such that regulatory cells are not properly activated, plus some additive environmental disturbance acting on the immune system . GD specifically results from the production by B lymphocytes of an antibody directed against the TSH receptor which stimulates the thyrocyte in a manner similar to TSH, but for a much longer interval . There are also antibodies to the thyrotrophin (TSH) receptor which block the action of TSH . Thyroid stimulating antibody is typical of GD and is detectable in about 95% of cases, but is also seen in destructive thyroiditis transiently . It tends to decline with antithyoid drug therapy, and rises further (for several months) after 131 I treatment . It may slowly decline after subtotal thyroidectomy . It also declines in the third trimester of pregnancy but sometimes is sufficiently high to cause foetal and neonatal passive transfer GD . It tends to rebound in the mother after delivery and may result in postpartum GD . The blocking antibody may cause atrophic thyroiditis and hypothyroidism . Antimicrosomal antibody has now been shown to be antithyroperoxidase . It correlates moderately well with thyroid dysfunction in Hashimoto's thyroiditis (HT) and GD, while antithyroglobulin is of much less value . Graves' ophthalmopathy is still not well understood, and its precise relationship to Graves' hyperthyroidism has yet to be worked out . However the retroorbital fibroblast is now emerging as the most likely target cell, with retroorbital muscle involvement possibly secondary . A recent observation of a genomic point mutation on the TSH receptor on fibroblasts from patients with Graves' ophthalmopathy but not normal persons raises interesting possibilities . (Endocr Pract . 1995;1:102-114)

Mem Inst Oswaldo Cruz, 2004 Mar, 99(2), 159 - 65 Epub 2004 Jun 24.
Abnormal expression of CD54 in mixed reactions of mononuclear cells from hyper-IgE syndrome patients; Martinez AM et al.; Hyper-IgE syndrome (HIES) is a rare multisystem disorder characterized by increased susceptibility to infections associated with heterogeneous immunologic and non-immunologic abnormalities . Most patients consistently exhibit defective antigen-induced-T cell activation, that could be partly due to altered costimulation involving accessory molecules; however, the expression of these molecules has never been documented in HIES . Therefore, we investigated the expression of CD11a, CD28, CD40, CD54, CD80, CD86, and CD154 in peripheral blood mononuclear cells from six patients and six healthy controls by flow cytometry after autologous and mixed allogeneic reactions . Only the allogeneic stimuli induced significant proliferative responses and interleukin 2 and interferon gamma production in both groups . Most accessory, molecules showed similar expression between patients and controls with the exception of CD54, being expressed at lower levels in HIES patients regardless of the type of stimulus used . Decreased expression of CD54 could partly explain the deficient T cell activation to specific recall antigens in HIES patients, and might be responsible for their higher susceptibility to infections with defined types of microorganisms.

J Chromatogr A, 2004 Jun 11, 1039(1-2), 105 - 11
Detection of hypophosphite, phosphite, and orthophosphate in natural geothermal water by ion chromatography; McDowell MM et al.; Current doctrine states that phosphorus is incorporated into cells in the pentavalent(V) oxidation state as orthophosphate . However, recent studies show that microorganisms contain enzymes used to metabolize reduced forms of phosphorous, including phosphite(III) and hypophosphite(I), which suggests that there is a natural source for these chemical species . This paper will discuss suppressed conductivity ion chromatography methods developed to detect hypophosphite, phosphite, and orthophosphate in a geothermal water matrix containing fluoride, chloride, bromide, nitrate, hydrogen carbonate and sulfate . All peaks were clearly resolved, and calibrations were linear with estimated 3sigma detection limits of 0.83, 0.39, and 0.35 microM for hypophosphite, phosphite, and orthophosphate, respectively.

Langmuir, 2004 Jul 20, 20(15), 6401 - 6
Adsorption of an endoglucanase from the hyperthermophilic Pyrococcus furiosus on hydrophobic (polystyrene) and hydrophilic (silica) surfaces increases protein heat stability; Koutsopoulos S et al.; The interaction of an endoglucanase from the hyperthermophilic microorganism Pyrococcus furiosus with two types of surfaces, that is, hydrophobic polystyrene and hydrophilic silica, was investigated, and the adsorption isotherms were determined . The adsorbed hyperthermostable enzyme did not undergo loss of biological activity . A model was proposed for the mechanism of interaction of the enzyme with the surface based on the shape of the adsorption isotherm, the morphological characteristics of the enzyme, and the thermodynamic parameters of the system . The enzyme was irreversibly immobilized at the solid/liquid interface even at high temperatures, and most interestingly, it acquired further heat stabilization upon adsorption . The denaturation temperature increased from 108 degrees C in solution to 116 degrees C upon adsorption on hydrophilic silica particles . Adsorption on the hydrophobic polystyrene surface even shifted the denaturation temperature to 135 degrees C, the most extreme experimentally determined protein denaturation temperature ever reported . Maintenance of the biological function particularly at high temperatures is important for the development of solid substrate immobilized enzymes for applications in biocatalysis and biotechnology . This also presents an additional stabilization mechanism employed by nature where the extracellular hyperthermostable enzyme remains folded and active at the extreme temperatures of its natural environment by adsorption on the surface of rocks and other materials appearing in the surroundings of the microorganism .

Diagn Microbiol Infect Dis, 2004 Jul, 49(3), 189 - 96
Morphotypic and genotypic characterization of sequential Candida parapsilosis isolates from an outbreak in a pediatric intensive care unit; Garcia San Miguel L et al.; Candidemia outbreaks that due to cross-infection are an emerging problem in hospitals . Typing of microorganisms is an essential tool for understanding the epidemiologic aspects of the infection . Techniques based on phenotypic characteristics are inexpensive and easy to perform but are limited by their lack of reproducibility . This study assessed the value of several phenotypic and genotypic techniques that are used in epidemiologic investigations of Candida parapsilosis in clinical practice and used a combination of these methods to analyze outbreak of C . parapsilosis candidemia . Random amplification of polymorphic DNA polymerase chain reaction with several primers was unsatisfactory because it lacked discriminatory power . By simplifying the reading of the morphotypes, we increased their reproducibility for each malt agar and 2,3,5-triphenyltetrazolium media (97% and 90%) and thus their suitability for its use . The combination of electrophoretic karyotype and the simplified morphotypes was rapid and practical to characterize the different clusters involved in the intensive care unit outbreak.

J Clin Microbiol, 2004 Jul, 42(7), 2913 - 8
High-throughput method for detecting genomic-deletion polymorphisms; Goguet de la Salmoniere YO et al.; DNA microarrays have been successfully used with different microorganisms, including Mycobacterium tuberculosis, to detect genomic deletions relative to a reference strain . However, the cost and complexity of the microarray system are obstacles to its widespread use in large-scale studies . In order to evaluate the extent and role of large sequence polymorphisms (LSPs) or insertion-deletion events in bacterial populations, we developed a technique, termed deligotyping, which hybridizes multiplex-PCR products to membrane-bound, highly specific oligonucleotide probes . The approach has the benefits of being low cost and capable of simultaneously interrogating more than 40 bacterial strains for the presence of 43 genomic regions . The deletions represented on the membrane were selected from previous comparative genomic studies and ongoing microarray experiments . Highly specific probes for these deletions were designed and attached to a membrane for hybridization with strain-derived targets . The targets were generated by multiplex PCR, allowing simultaneous amplifications of 43 different genomic loci in a single reaction . To validate our approach, 100 strains that had been analyzed with a high-density microarray were analyzed . The membrane accurately detected the deletions identified by the microarray approach, with a sensitivity of 99.9% and a specificity of 98.0% . The deligotyping technique allows the rapid and reliable screening of large numbers of M . tuberculosis isolates for LSPs . This technique can be used to provide insights into the epidemiology, genomic evolution, and population structure of M . tuberculosis and can be adapted for the study of other organisms.

AIDS Res Hum Retroviruses, 2004 Jun, 20(6), 600 - 7
gp340 (SAG) binds to the V3 sequence of gp120 important for chemokine receptor interaction; Wu Z et al.; Human saliva contains multiple components that inhibit HIV-1 infection in vitro, which may contribute to low oral HIV-1 transmission . Salivary agglutinin (SAG) is a high-molecular-weight glycoprotein encoded by DMBT-1 and identical to gp340, a member of the lung scavange receptor, cysteine-rich receptor family . gp340 binds to surfactants A and D, which is believed to function in the clearance of microorganisms from the lung, as part of the innate immune response . Previously we reported that SAG (gp340) specifically inhibits HIV-1 infection with broad activity against diverse HIV-1 isolates . This gp340 inhibitory activity is mediated by binding to viral gp120 and involves a region different from the CD4-binding site on gp120 . Here, we report that the gp340-binding region is localized to a linear, highly conserved sequence near the stem of the V3 loop that is critical for chemokine receptor interaction during viral binding and infection . The interaction of gp340 with gp120 is enhanced by prebinding of sCD4 to gp120, suggesting that gp340 inhibitory activity is mediated by blocking access of the gp120 to the chemokine receptor.

J Nutr Sci Vitaminol (Tokyo), 2004 Apr, 50(2), 69 - 77
Recent progress of vitamin B6 biosynthesis; Sakai A et al.; This review is the current summary of vitamin B6 (B6) biosynthesis in Escherichia coli and other microorganisms . The de novo biosynthesis of B6 has been studied extensively for last three decades . However, the de novo biosynthesis of B6 still remains unclear in spite of its simple structure . For the first two decades, B6 biosynthesis had been mainly studied with E . coli using genetic, nutritional, and isotopic labeling experiments . According to these studies, some compounds including glycolaldehyde were identified as the precursor . During the last decade, gene manipulate techniques were rapidly developed, and complete genome sequences of some microorganisms became available . Using these new tools, valuable information has been provided . The complete DNA sequence of pdx genes and other genes, which are possibly involved in B6 biosynthesis, were shown . The roles of some genes and precursors were proposed . Besides E . coli, B6 biosynthesis in other microorganisms has been also studied . In some microorganisms, snz/sno was reported to be involved in B6 biosynthesis . Intriguingly these genes show no similarity to any of the E . coli pdx genes, and are not found in E . coli . Microorganisms having snz/sno gene homologues lack homologues to pdxA/pdxJ genes, whereas those with homologues to pdxA/pdxJ lack snz/sno gene homologues . Therefore, it is most likely that there are at least two kinds of B6 biosynthetic pathways in microorganisms . These studies provided important clues of B6 biosynthesis, but the entire picture of the B6 biosynthetic pathway remains unclear.

Nature, 2004 Jul 8, 430(6996), 242 - 9
The challenge of emerging and re-emerging infectious diseases; Morens DM et al.; Infectious diseases have for centuries ranked with wars and famine as major challenges to human progress and survival . They remain among the leading causes of death and disability worldwide . Against a constant background of established infections, epidemics of new and old infectious diseases periodically emerge, greatly magnifying the global burden of infections . Studies of these emerging infections reveal the evolutionary properties of pathogenic microorganisms and the dynamic relationships between microorganisms, their hosts and the environment.

Curr Opin Infect Dis, 2004 Aug, 17(4), 329 - 33
Nursing resources: a major determinant of nosocomial infection?
Hugonnet S, Harbarth S, Sax H, Duncan RA, Pittet D.
PURPOSE OF REVIEW: There is growing concern that changes in nurse workforce and hospital-restructuring interventions negatively impact on patient outcomes . This review focuses on the association between understaffing and health-care-associated infections . RECENT FINDINGS: There is a large number of studies showing that overcrowding, understaffing or a misbalance between workload and resources are important determinants of nosocomial infections and cross-transmission of microorganisms . Importantly, not only the number of staff but also the level of their training affects outcomes . The nurse workforce is ageing, mainly due to fewer individuals' engaging in a nursing career . This phenomenon, combined with cost-driven downsizing, contributes to a nursing shortage, and this tendency is not expected to revert unless important system changes are implemented . The causal pathway between understaffing and infection is complex, and factors might include lack of time to comply with infection control recommendations, job dissatisfaction, job-related burnout, absenteeism and a high staff turnover . SUMMARY: The evidence that cost-driven downsizing and changes in staffing patterns causes harm to patients cannot be ignored, and should not be considered as an inevitable outcome . More research is needed to better define the optimal patient-to-nurse ratio in various hospital settings and to estimate the economical impact of the nursing shortage . All quality-improvement interventions should carefully take into account systems and processes to be successful, as the issue of staffing is essentially a structural problem.

Curr Opin Infect Dis, 2004 Aug, 17(4), 309 - 16
Epidemiology and control of antibiotic resistance in the intensive care unit; Carlet J et al.; PURPOSE OF REVIEW: Resistance to antibiotics is very high in the intensive care units of many countries, although there are several exceptions . Some infections are becoming extremely difficult to treat . The risk of cross-transmission of those strains is very high . This review focuses on recent data (2003 to the present) that may help understanding and dealing with this serious public health problem . RECENT FINDINGS: Intensive care units can be considered as 'factories' for creating, disseminating and amplifying resistance to antibiotics, for many reasons: importation of resistant microorganisms at admission, selection of resistant strains with an extensive use of broad-spectrum antibiotics, cross-transmission of resistant strains via the hands or the environment . Some national programs can be considered as failures, as in the UK and the USA . Other countries have been able to maintain a low level of resistance (Scandinavian countries, Netherlands, Switzerland, Germany, Canada) . There is clearly an 'inoculum effect' above which preventive measures become poorly efficient . Several preventive measures have been proposed including preventive isolation, systematic screening at admission, local, national or international antibiotic guidelines, antibiotic prescriptions advice by infectious-disease teams, antibiotic prevention with selective digestive decontamination, antibiotic strategies such as 'cycling', or rather, for some authors, the use of an 'a la carte' antibiotic strategy which could be considered as a 'patient-to-patient antibiotic rotation' . SUMMARY: There is obviously an international concern regarding the level of resistance to antibiotics in the intensive-care-unit setting . A strong program including prevention of cross-transmission and better usage of antibiotics seems to be needed in order to be successful . We do not know if this kind of program will enable countries with a very high endemic level of resistance to decrease the level in future years.

Appl Environ Microbiol, 2004 Jul, 70(7), 4371 - 4
Combined immunomagnetic separation-molecular beacon-reverse transcription-PCR assay for detection of hepatitis A virus from environmental samples; Abd El Galil KH et al.; In this study, a molecular-beacon-based real-time reverse transcription (RT)-PCR assay was developed to detect the presence of hepatitis A virus (HAV) in environmental samples . A 125-bp, highly conserved 5' noncoding region of HAV was targeted . The sensitivity of the real-time RT-PCR assay was tested with 10-fold dilutions of viral RNA, and a detection limit of 1 PFU was obtained . The specificity of the assay was demonstrated by testing with other environmental pathogens and indicator microorganisms, and only HAV was positively identified . When combined with immunomagnetic separation, the real-time RT-PCR assay successfully detected as few as 20 PFU in seeded groundwater samples . Because of its simplicity and specificity, this assay has broad applications for the rapid detection of HAV in contaminated foods or water.

Appl Environ Microbiol, 2004 Jul, 70(7), 4367 - 70
Genotyping of Cryptosporidium isolates from Chamelea gallina clams in Italy; Traversa D et al.; Chamelea gallina clams collected from the mouths of rivers along the Adriatic Sea (central Italy) were found to harbor Cryptosporidium parvum (genotype 2), which is the lineage involved in zoonotic transmission . The clams were collected from the mouths of rivers near whose banks ruminants are brought to graze . This paper reports the environmental spread of C . parvum in Italy and highlights the fact that genotyping of seaborne Cryptosporidium isolates is a powerful tool with which to investigate the transmission patterns and epidemiology of this microorganism.

Brief Funct Genomic Proteomic, 2003 Jan, 1(4), 356 - 71
Genome analysis technologies: towards species identification by genotype; Naimuddin M et al.; Traditional identification of species has been based on phenotypic traits, although it is clear that, theoretically, genotype-based classification is more accurate . This is especially the case for microorganisms which possess less identifiable traits and are more easily influenced by environment . Therefore, technology that allows identification of species based on genotype is highly desirable . Whole genome sequencing can provide a sufficient amount of information and can be determinative for this purpose but is very impractical for routine use . Thus, a competent technology is needed that allows a reproducible reduction in the amount of information required about a whole genome, while still providing sufficiently accurate identification . It is almost imperative for such a technology to be of a high cost-performance and of easy handling . Universality and portability are also strongly desired . Based on these criteria, the current state of genome analysis technologies are reviewed . Among various methodologies discussed here, amplified fragment length polymorphism (AFLP), genome profiling (GP) and microarrays are the subject of particular attention . As species identification is a base for most fields of biology including microbiology, ecology, epidemiology and for various biotechnologies, it is of paramount importance to establish a more efficient, easily handled and more objective methodology, in parallel with conventional phenotype-based methodologies . GP is currently considered to have the most optimal nature for identification of species since it can reproducibly reduce a huge amount of genome information to a manageable size by way of random polymerase chain reaction and can extract a sufficient amount of information for species identification from the DNA fragments thus profiled by temperature gradient gel electrophoresis . The potential ability of DNA microarrays for this purpose is also discussed and promises much for the future.

J Appl Microbiol, 2004, 97(2), 285 - 92
Detection of free and plankton-associated Helicobacter pylori in seawater; Cellini L et al.; AIMS: To detect both free and plankton-associated Helicobacter pylori in seawater samples collected on the Italian coast of the Adriatic Sea using a nested-PCR . METHODS AND RESULTS: Dissolved oxygen, pH, salinity and chlorophyll 'a' were the parameters recorded together with the characterization of zooplanktonic organisms . Plankton-associated H . pylori DNA was searched for in water samples filtered through 200 and 64 microm nylon nets whereas free bacteria were retained with the subsequent filtration through 0.22 microm pore-size membranes . Nested-PCR using primers for the glmM (ureC) gene was performed to reveal the presence of H . pylori . The DNA sequencing of amplified products confirmed the specificity of the assay . The sensitivity of the nested-PCR assay for H . pylori detection was 62 CFU per 100 ml in spiked water samples . Helicobacter pylori either free or bound to planktonic organisms was found in seven of 12 monthly samples . In particular, free bacteria were detected during the summer sampling and in November, December and March associated to planktonic cells . CONCLUSIONS: The presence of free and plankton-associated H . pylori in seawater suggests that it can be a significant reservoir and a potential route of transmission for the microorganism . SIGNIFICANCE AND IMPACT OF THE STUDY: Our study seems to provide a promising background to define new and effective strategies for surveillance of this human pathogen.

J Occup Environ Hyg, 2004 Aug, 1(8), 505 - 14
Personal exposures to inorganic and organic dust in manual harvest of California citrus and table grapes; Lee K et al.; The aim of this study was to determine characteristics of personal exposure to inorganic and organic dust during manual harvest operations of California citrus and table grapes . Personal exposures to inhalable dust and respirable dust were measured five times over a 4-month period of harvesting season . We analyzed components of the dust samples for mineralogy, respirable quartz, endotoxin, and total and culturable microorganisms . Workers manually harvesting were exposed to a complex mixture of inorganic and organic dust . Exposures for citrus harvest had geometric means of 39.7 mg/m(3) for inhalable dust and 1.14 mg/m(3) for respirable dust . These exposures were significantly higher than those for table grape operations and exceeded the threshold limit value for inhalable dust and respirable quartz . Exposures for table grape operations were lower than the threshold limit value, except inhalable dust exposure during leaf pulling . Considered independently, exposures to inhalable dust and respirable quartz in citrus harvest may be high enough to cause respiratory health effects . The degree of vigorous contact with foliage appeared to be a significant determining factor of exposures in manual harvesting.

Scand J Immunol, 2004 Jul-Aug, 60(1-2), 23 - 9
The potential role of mannan-binding lectin in the clearance of self-components including immune complexes; Saevarsdottir S et al.; Mannan-binding lectin (MBL) is a pattern recognition receptor in the innate immune system . It recognizes certain sugar residues arranged in a pattern that enables MBL to bind with sufficient strength . Such sugar patterns are common on the surface of many microorganisms, and MBL has therefore been considered to be an agent that can discriminate between self and nonself . There is, however, increasing evidence supporting that MBL, like many membrane-bound C-type lectin-like receptors, also helps to dispose of various outworn or abnormal body components . Most self-components are protected with sialic acid or galactose that disrupt the pattern of the sugars that MBL can bind, but MBL may be significantly involved in the elimination of self-components that have lost these protective terminal residues . The role of MBL in the clearance of invading pathogens has previously been thoroughly reviewed . Here, we review some findings that support the notion that MBL may contribute to noninflammatory removal of immune complexes and abnormal cells by the reticuloendothelial system . Defects in this clearance mechanism may cause an accumulation of potentially dangerous self-components, thereby increasing the likelihood of chronic inflammation and autoimmunity.

Scand J Immunol, 2004 Jul-Aug, 60(1-2), 3 - 5; discussion 6-8
Response to Cohn: The immune system rejects the harmful, protects the useful and neglects the rest of microorganisms; Dembic Z; The immune system is seen as a guardian of tissue integrity . It would analyse the extent and quality of damage and respond adequately . If no ill effects were found, the system would ignore disturbance, but if beneficial effects were found, it could protect certain microorganisms (establishing commensalism), perhaps via regulatory cells . The Integrity hypothesis proposes three basic groups of intercellular signals for cells of all tissues and assumes that they govern communication between dendritic cells, T cells and B cells . Signal-1 would be the main information source resulting with generation of intracellular mediators that are bound to travel into the nucleus to achieve reaction . Signal-2 represents the generation of additional signal transducers representing a modifier at the level of cytosol . And, signal-3 would be a modifier at nuclear level, perhaps guarding accessibility to chromosome or genetic locus.

J Agric Food Chem, 2004 Jul 14, 52(14), 4487 - 92
Removal of monomeric phenols in dry mill olive residue by saprobic fungi; Sampedro I et al.; The dry olive residue (DOR) obtained from the olive oil extraction process has toxic components against plants and microorganism growth, particularly monomeric phenols . In this investigation nine saprobic fungi were found to be capable of completely removing these phenols from the solid after 20 weeks of growth, although the rate depended on the type of fungi and phenol . Results showed that most of the fungi tested first eliminated o-diphenols and then non-o-diphenols . However, some fungi did not follow this trend . Phanerochaete chrysosporium first removed hydroxytyrosol and tyrosol and later their glucosides and, in contrast, Paecylomyces farinosus hydrolyzed hydroxytyrosol and tyrosol glucosides at the first stage, 2 weeks of growth, and then eliminated all monomeric phenols . The behavior of this fungus seems of great interest for recovering phenolic antioxidants from the DOR . Similarly, differences in DOR decolorization capacity among the fungi tested were also observed . Coriolopsis rigida showed the highest capacity, followed by Phebia radiata, Pycnoporus cinnabarinus, and Pha . chrysosporium . Therefore, both decolorization and monomeric phenol elimination pointed out that saprobic fungi could be used to detoxify the DOR obtained from the two-phase system of the olive oil extraction process.

Ann Agric Environ Med, 2004, 11(1), 109 - 14
Ixodes ricinus as a vector of Borrelia burgdorferi sensu lato, Anaplasma phagocytophilum and Babesia microti in urban and suburban forests; Stanczak J et al.; In the suburban and urban forests in the cities of Gdansk, Sopot and Gdynia (northern Poland), Ixodes ricinus ticks should be considered as the vector of pathogenic microorganisms that may cause significant diseases in wild and domestic animals and humans . These microorganisms include etiologic agents of Lyme disease, human anaplasmosis (HA) and babesiosis: Borrelia burgdorferi sensu lato, Anaplasma phagocytophilum and Babesia microti, respectively . DNA extracts from 701 ticks collected in 15 localities were examined by PCR for the simultaneous detection of these 3 pathogens . Overall, 14 % were infected with A . phagocytophilum followed by 12.4 % with B . burgdorferi s.l . and 2.3 % with B . microti . In total, the percentage of infected females (32.9 %) was 2.4 times higher than in males (13.7 %) and 3.2 times higher than in nymphs (10.3 %) . Among adult ticks (n = 303), 8.3 % were dually infected with A . phagocytophilum and B . burgdorferi s.l., 2.0 % with the agent of human anaplasmosis and B . microti and 0.3 % with borreliae and B . microti.

Biotechnol Bioeng, 2004 Jul 20, 87(2), 213 - 8
Kinetic studies on the aggregation of Aspergillus niger conidia; Grimm LH et al.; Morphology has a crucial effect on productivity and the supply of substrate for cultures of filamentous fungi . However, cultivation parameters leading to the desired morphology are often chosen empirically as the mechanisms governing the processes involved are usually unknown . For coagulating microorganisms like Aspergillus niger the morphological development is considered to start with the aggregation of conidia right after inoculation . To elucidate the mechanism of this process, kinetic studies were carried out using an in-line particle size analyzer . Based on the data obtained from these experiments a model for conidial aggregation is proposed in this article . It consists of two separate aggregation steps . The first one takes place immediately after inoculation, but only leads to a small decrease of total particle concentration . Most suspended conidia aggregate after a second aggregation step triggered by germination and hyphal growth . Aggregation velocity of this second phase is linearly dependent on the particle growth rate .

J Anesth, 1988 Mar 1, 2(1), 41 - 5
The effect of human SOD on the survival rate in rats with temporary splanchnic ischemia; Ogawa R et al.; The accumulation of oxygen free radicals is reported to occur in the organs subjected to temporary ischemia followed by reperfusion, resulting in the fatal outcome of the animals . The effects of human SOD, a representative scavenger of oxygen free radicals, on the survival rates were investigated in the rats with temporary splanchnic ischemia . The temporary ischemia was induced by the occlusion of anterior mesenteric and celiac arteries for 30 min under anesthesia . Prior and after treatment with 2 mg/100 g of human SOD, iv or sc, produced significant improvements in survival rates . Human SOD, cloned from human placenta DNA and expressed in microorganisms, has extreme homogeneity . The results suggest the possible introduction of human SOD into clinical field as an effective scavenger of oxygen free radicals.(Ogawa R, Bitoh H, Ohi Y: The effect of human SOD on the survival rate in rats with temporary splanchnic ischemia . J Anesth 2: 41-45, 1988)

Int J Legal Med, 2004 Aug, 118(4), 224 - 34 Epub 2004 May 15.
Development of the AmpFISTR SEfiler PCR amplification kit: a new multiplex containing the highly discriminating ACTBP2 (SE33) locus; Coticone SR et al.; The AmpFISTR SEfiler kit co-amplifies 11 short tandem repeat loci including SE33 in a single multiplex . After establishing the optimum in primer titration studies, the primer concentrations of all loci in the multiplex were chosen such that the heterozygote peak height ratios of each of the loci were balanced . The combined primer set was then tested to determine the robustness of the multiplex under various conditions . Different MgCl(2) concentrations were evaluated to establish the optimum concentration for the multiplex . The amplification of the various loci in the multiplex was tested at several annealing temperatures (55-63 degrees C) . Additionally, DNA from primates, non-primates and microorganisms were amplified to investigate the specificity of the kit . The stability of the AmpFISTR SEfiler kit was determined by addition of hematin, to simulate inhibition, and the use of degraded DNA . Population studies revealed a probability of identity of 6.47x10(-15) for African Americans and 7.46x10(-14) for US Caucasians . To assess the ability of the multiplex to analyze forensic samples, testing on blood, oral swabs and mixtures was performed . Based on the various studies, it was determined that the AmpFISTR SEfiler PCR amplification kit can be used to successfully analyze a variety of forensic, databasing and paternity samples.

J Ethnopharmacol, 2004 Aug, 93(2-3), 319 - 23
In vitro study of the antioxidant and immunomodulatory activity of aqueous infusion of Bidens pilosa; Abajo C et al.; Bidens pilosa is an annual plant from tropical America with anti-inflammatory properties in hepatitis, laryngitis, headache and digestive disorders, among others . Its wide pharmacological applications can be attributed to its chemical composition, with inhibitory effects on pathogenic microorganisms and flavonoids, which show strong antioxidant capacities . We investigated the antioxidant activity of an aqueous infusion of Bidens pilosa by studying its protective effect on the hemolysis induced by an initiator of radicals such as 2,2'-azobis(2-amidinopropane) dihydrochloride (AAPH) . The immunomodulatory activity of the infusion was tested using whole blood cells . Cytokine production increased in whole blood stimulated or not by lipopolysaccharides (LPSs) . The infusion is also characterized by its capacity to protect erythrocytes from the phototoxic effect of chlorpromazine, which allows its use as a potential photoprotector . Finally, it did not show ocular irritation, as demonstrated by the effect on hemoglobin denaturation . This study supports the health benefits of the ingestion of the infusion.

Immunol Lett, 2004 Jun 15, 94(1-2), 43 - 6
Hyperresponsiveness of neutrophils from gp 91phox deficient patients to lipopolysaccharide and serum amyloid A; Hatanaka E et al.; We demonstrate here that neutrophils from chronic granulomatous disease (CGD) patients release larger amounts of interleukin-8 (IL-8) and tumor necrosis factor alpha (TNF-alpha) than neutrophils from control subjects . Incremental cytokine production was observed under both basal and stimulated conditions in neutrophils from two CGD (gp 91phox) patients . The basal production of IL-8 was over seven-fold greater in CGD patients . The two samples assayed showed 3- and 10-fold increases in TNF-alpha . Basically, the same magnitude of increment was observed in lypopolysaccharide (LPS) and serum amyloid A protein (SAA)-stimulated cells . We also found that the levels of SAA and IL-8 were higher in the serum of CGD patients than the levels found in the serum of healthy donors . The increased responsiveness of neutrophils from CGD patients may be closely related with a deficiency in the assembly of the nicotinamide adenine dinucleotide phosphate (NADPH)-oxidase enzyme system, or it may be due to a frequent inflammatory condition in these patients . In the latter case, the increased serum levels of systemic inflammatory factors, among them SAA, would contribute to the sustained accumulation and activation of phagocytes . Whatever the origin, the excessive production of cytokines may lead to inappropriate activation and tissue injury and even to increased susceptibility to invasive microorganisms, impairing the quality life of CGD patients.

J Microbiol Methods, 2004 Aug, 58(2), 169 - 88
Methods of studying soil microbial diversity; Kirk JL et al.; Soil microorganisms, such as bacteria and fungi, play central roles in soil fertility and promoting plant health . This review examines and compares the various methods used to study microbial diversity in soil.

Pediatr Emerg Care, 2004 Jul, 20(7), 433 - 6
Utility of anaerobic blood cultures in a pediatric emergency department; Freedman SB et al.; OBJECTIVES: To determine the frequency with which clinically significant bacterial pathogens are isolated only from the anaerobic blood culture medium in children evaluated for bacteremia and to describe the clinical features associated with these positive cultures . METHODS: Retrospective review of all blood cultures received from the emergency department in the microbiology laboratory . Clinically significant pathogens were defined as microorganisms that rarely are considered to be contaminants or microorganisms that are recovered from multiple blood cultures or sites from the same individual . Charts of all patients with positive anaerobic cultures for clinically significant pathogens in the presence of negative aerobic cultures were reviewed . The setting was an urban tertiary care pediatric emergency department . RESULTS: 2675 paired blood cultures were performed between January 1, 1998 and December 31, 2000 . Growth of a bacterial organism occurred in 595 of the paired samples . Two hundred seventy-eight were clinically significant pathogens . One hundred sixty-two (58.3%) were present in both the aerobic and anaerobic mediums, 85 (30.6%) were only in the aerobic medium, and 31 (11.2%) were only in the anaerobic medium . Most patients with growth only in the anaerobic medium had underlying conditions (ie, central venous line, immunocompromised, congenital heart disease, liver disease, age < 3 months) . No obligate anaerobic organisms were detected . CONCLUSIONS: In a pediatric emergency department setting, almost all pathogenic bacteria were isolated from aerobic culture mediums in otherwise healthy children . The yield of routinely performed anaerobic blood cultures is low . In previously healthy children, it may be optimal to inoculate the entire blood volume obtained into the aerobic medium.

J Biol Chem, 2004 Sep 24, 279(39), 40729 - 36 Epub 2004 Jul 01.
The structure and mechanism of serine acetyltransferase from Escherichia coli; Pye VE et al.; Serine acetyltransferase (SAT) catalyzes the first step of cysteine synthesis in microorganisms and higher plants . Here we present the 2.2 A crystal structure of SAT from Escherichia coli, which is a dimer of trimers, in complex with cysteine . The SAT monomer consists of an amino-terminal alpha-helical domain and a carboxyl-terminal left-handed beta-helix . We identify His(158) and Asp(143) as essential residues that form a catalytic triad with the substrate for acetyl transfer . This structure shows the mechanism by which cysteine inhibits SAT activity and thus controls its own synthesis . Cysteine is found to bind at the serine substrate site and not the acetyl-CoA site that had been reported previously . On the basis of the geometry around the cysteine binding site, we are able to suggest a mechanism for the O-acetylation of serine by SAT . We also compare the structure of SAT with other left-handed beta-helical structures .

Virology, 2004 Jul 20, 325(1), 18 - 23
Inhibition of porcine endogenous retroviruses by RNA interference: increasing the safety of xenotransplantation; Karlas A et al.; Transplantation of porcine xenografts into human recipients is a realistic option to overcome the growing worldwide shortage of suitable allogeneic organs . However, there remains the risk of infection by porcine endogenous retroviruses (PERVs) that cannot be eliminated like that by other microorganisms by breeding pigs under specified pathogen-free conditions . To reduce the release of PERVs by porcine transplants, a new approach, RNA interference (RNAi), was applied . Here, we show significant reduction of PERV expression by synthetic short interfering RNAs (siRNAs) corresponding to different parts of the viral genes gag, pol, and env . The most inhibitory sequences were selected and expressed as short hairpin RNAs (shRNAs) by a polymerase III vector system leading to persistent suppression of PERV replication . Cells or organs from transgenic pigs producing such shRNAs should increase the safety of xenotransplantation.

Curr Opin Plant Biol, 2004 Aug, 7(4), 377 - 83
Knocking on the heaven's wall: pathogenesis of and resistance to biotrophic fungi at the cell wall; Schulze-Lefert P; New findings challenge the traditional view of the plant cell wall as passive structural barrier to invasion by fungal microorganisms . A surveillance system for cell wall integrity appears to sense perturbation of the cell wall structure upon fungal attack and is interconnected with known plant defence signalling pathways . Biotrophic fungi might manipulate this surveillance system for the establishment of biotrophy . The attempts of fungi to invade also induce a sub-cellular polarisation in attacked cells, which activates an ancient vesicle-associated resistance response that possibly enables the focal transport of regulatory cargo and the secretion of toxic cargo . The underlying resistance machinery might have been subverted by biotrophic fungi for pathogenesis.

Pol J Vet Sci, 2004, 7(2), 113 - 6
Optimisation of the time of milk sample decontamination with 0.75% cethylpirydinium chloride upon identification of Mycobacterium avium subsp . paratuberculosis; Wiszniewska A et al.; Isolation of MAP from biological material, including milk, is very difficult . No matter how the fresh milk is obtained, it contains a certain number of rapidly growing microorganisms . Therefore, the decontamination process is applied in the methods of MAP isolation . Investigations were therefore undertaken to determine the optimal time of milk sample decontamination with 0.75% CPC . The experiment was divided into two parts: determination of the survival time of M.smegmatis and E . coli in 0.75% CPC and determination of the time of raw milk decontamination . The results suggest that the optimal time of milk sample decontamination is 15 min.

Adv Exp Med Biol, 2004, 547, 5 - 17
High-throughput techniques for analyzing complex bacterial communities; Stahl DA; A more complete understanding of microbial diversity and the environmental processes they control will require much more than a biotic inventory . It will require a deeper understanding of the basic features of systems organization and inter-population interactions . Communities, not total biomass, control net process rates driving the biogeochemical cycles sustaining the biosphere . Although the general patterns of macroorganismal diversity are relatively well known, spatial and temporal patterns of microorganismal diversity are essentially unknown . Having tools capable of resolving these patterns is a prerequisite to developing an understanding of the relationship between community structure and function . This talk discusses conceptual and technical developments that now provide the framework for systematically resolving temporal and spatial patterns of microorganisms and relating those patterns to processes at local and system levels . Of particular emphasis will be ongoing studies using highly parallel analyses with DNA microarrays for intensive monitoring of microbial populations in environmental systems . Although microarray technology is reasonably well established for studies of model organisms in well-defined laboratory settings, the application of this technology to environmental systems of uncharacterized diversity imposes additional demands on implementation; in particular, the requirement for optimized discrimination between target and non-target nucleic acids in complex, and undefined, mixtures . To increase the resolving power (information content) of our DNA microarray format, we are investigating the use of thermal dissociation of hybrids immobilized on individual array elements to resolve target and non-target sequences that differ by a single nucleotide . These studies, combined with specialized algorithms for optimizing the readout of the microarray should serve for informed environmental application . Initial studies have validated the general approach for analyses of sediment systems.

Glycobiology, 2004 Nov, 14(11), 53R - 62R Epub 2004 Jun 30.
History of lectins: from hemagglutinins to biological recognition molecules; Sharon N et al.; The occurrence in nature of erythrocyte-agglutinating proteins has been known since the turn of the 19th century . By the 1960s it became apparent that such proteins also agglutinate other types of cells, and that many of them are sugar-specific . These cell-agglutinating and sugar-specific proteins have been named lectins . Although shown to occur widely in plants and to some extent also in invertebrates, very few lectins had been isolated until the early 1970s, and they had attracted little attention . This attitude changed with the demonstration that lectins are extremely useful tools for the investigation of carbohydrates on cell surfaces, in particular of the changes that the latter undergo in malignancy, as well as for the isolation and characterization of glycoproteins . In subsequent years numerous lectins have been isolated from plants as well as from microorganisms and animals, and during the past two decades the structures of hundreds of them have been established . Concurrently, it was shown that lectins function as recognition molecules in cell-molecule and cell-cell interactions in a variety of biological systems . Here we present a brief account of 100-plus years of lectin research and show how these proteins have become the focus of intense interest for biologists and in particular for the glycobiologists among them.

Biodegradation, 2004 Jun, 15(3), 153 - 60
Chlorophenol removal from soil suspensions: effects of a specialised microbial inoculum and a degradable analogue; Baggi G et al.; Two soils of different contamination history were tested in slurry for their self-remediability towards mono-, di- and trisubstituted chlorophenols . The landfill soil showed poor ability in removing the compounds . Instead, the soil from the golf course, treated for many years with a 2,4,6-trichlorophenol derivative (Prochloraz), remediated different concentrations of the same 2,4,6TCP, 2,4-dichlorophenol and monochlorophenol isomers, singly and in mixtures, at varying degradation rates . Ralstonia eutropha TCP, a specialised microorganism capable of degrading 2,4,6TCP, proved highly efficient in removing the compound from both tested soils . The same microbial inoculum allowed total removal of the ternary mixture of monochlorophenol isomers from the golf course soil, but it did not accelerate the removal of the same compounds when singly supplied . The addition of phenol as a degradable analogue was more effective in co-metabolically removing not only the single monochlorophenols, but also their mixtures, the removal occurring faster and independently of the presence of the microbial inoculum . From the golf course soil, a microorganism, phenotypically and genetically identical to R . eutropha TCP, was isolated and classified as R . eutropha TCP II.

Biochem J, 2004 Oct 15, 383(Pt 2), 277 - 83
Stabilization of model membranes during drying by compatible solutes involved in the stress tolerance of plants and microorganisms; Hincha DK et al.; Many organisms accumulate compatible solutes under environmental stress conditions . Cyanobacteria accumulate compatible solutes in response to increased external salinity, with tolerance increasing from Suc (sucrose) or trehalose to 2-O-(alpha-D-glucopyranosyl)-glycerol and glycinebetaine accumulating species . It is not clear how these different solutes influence salt tolerance . One possible explanation may be a differential ability of these solutes to stabilize membranes under stress conditions . We therefore performed drying experiments with liposomes in the presence of compatible solutes . Suc, trehalose and sorbitol protected liposomes from leakage of a soluble marker and from membrane fusion during drying and rehydration . 2-O-(alpha-D-glucopyranosyl)-glycerol was less effective and glycinebetaine showed hardly any effect . In combination with Suc, the latter two solutes showed improved protection . Lipid-phase transitions are known to contribute to solute leakage from liposomes . We determined phase transitions in dry membranes in the absence or presence of the solutes, using Fourier-transform infrared spectroscopy . The ability of the solutes to decrease the phase transition temperature corresponded closely to their ability to protect the liposomes against solute leakage . All solutes interacted with the phosphate in the lipid headgroups . The magnitude of the shift in the asymmetric P=O stretching vibration correlated closely with the lipid-phase transition temperature . This indicates that the degree of membrane protection afforded by the solutes is mainly determined by their ability to interact with the membrane lipids . However, this is not a determinant of cellular protection against salt stress, as the solutes show a reverse order when ranked with regard to protection against these stresses.

Expert Rev Mol Diagn, 2004 Jul, 4(4), 559 - 69
Molecular diagnosis of human granulocytic anaplasmosis; Dumler JS et al.; Human granulocytic anaplasmosis, formerly known as human granulocytic ehrlichiosis, is caused by the microorganism Anaplasma phagocytophilum that is transmitted by Ixodes tick bites . The disease state ranges from subclinical to fatal but may be difficult to differentiate from other febrile conditions without specific tests . Rapid and early diagnosis is important since the infection may be fatal and specific antibiotic therapy is required . The bacterium is an obligate intracellular pathogen of neutrophils . Thus, early diagnosis is best achieved by amplification of nucleic acids from the blood . An increasing number of potential gene targets for diagnostic assays have been described and the incipient release of an Anaplasma phagocytophilum genome sequence will not only help to better understand the disease but may facilitate improvements in diagnostic strategies . Copyright Future Drugs Ltd.

J Environ Qual, 2004 May-Jun, 33(3), 806 - 15
Impact of genetically modified crops on soil- and plant-associated microbial communities; Dunfield KE et al.; Transgenic or genetically modified plants possess novel genes that impart beneficial characteristics such as herbicide resistance . One of the least understood areas in the environmental risk assessment of genetically modified crops is their impact on soil- and plant-associated microbial communities . The potential for interaction between transgenic plants and plant residues and the soil microbial community is not well understood . The recognition that these interactions could change microbial biodiversity and affect ecosystem functioning has initiated a limited number of studies in the area . At this time, studies have shown the possibility that transgenes can be transferred to native soil microorganisms through horizontal gene transfer, although there is not evidence of this occurring in the soil . Furthermore, novel proteins have been shown to be released from transgenic plants into the soil ecosystem, and their presence can influence the biodiversity of the microbial community by selectively stimulating the growth of organisms that can use them . Microbial diversity can be altered when associated with transgenic plants; however, these effects are both variable and transient . Soil- and plant-associated microbial communities are influenced not only by plant species and transgene insertion but also by environmental factors such as field site and sampling date . Minor alterations in the diversity of the microbial community could affect soil health and ecosystem functioning, and therefore, the impact that plant variety may have on the dynamics of the rhizosphere microbial populations and in turn plant growth and health and ecosystem sustainability, requires further study.

Environ Sci Technol, 2004 Jun 1, 38(11), 3040 - 6
Effects of the biologically produced polymer alginic acid on macroscopic and microscopic calcite dissolution rates; Perry TD 4th et al.; Dissolution of carbonate minerals has significant environmental effects . Microorganisms affect carbonate dissolution rates by producing extracellular metabolites, including complex polysaccharides such as alginic acid . Using a combined atomic force microscopy (AFM)/flowthrough reactor apparatus, we investigated the effects of alginic acid on calcite dissolution . Macroscopic dissolution rates, derived from the aqueous metal ion concentrations, are 10(-5.5) mol m(-2) s(-1) for 5 < pH < 12 in the absence of alginic acid compared to 10(-4.8) mol m(-2) s(-1) in its presence . The AFM images demonstrate that alginic acid preferentially attacks the obtuse steps of dissolution pits on the calcite surface . In pure water, the obtuse and acute steps retreat at similar rates, and the pits are nearly isotropic except under highly acidic conditions . In alginic acid, the acute step retreat rate is nearly unchanged in comparison to water, whereas the obtuse step retreat rate increases with decreasing pH values . As a result, the pits remain rhombohedral but propagate faster in the obtuse direction . To explain these observations, we propose that alginic acid preferentially forms dissolution active surface complexes with calcium atoms on the obtuse step, which results in anisotropic ligand-promoted dissolution.

J Food Prot, 2004 Jun, 67(6), 1247 - 51
Efficacy of acidic electrolyzed water for microbial decontamination of cucumbers and strawberries; Koseki S et al.; An examination was made of the efficacy of acidic electrolyzed water (AcEW, 30 ppm free available chlorine), ozonated water (5 ppm ozone), and a sodium hypochlorite solution (NaOCl, 150 ppm free available chlorine) for use as potential sanitizers of cucumbers and strawberries . AcEW and NaOCl reduced the aerobic mesophiles naturally present on cucumbers within 10 min by 1.4 and 1.2 log CFU per cucumber, respectively . The reduction by ozonated water (0.7 log CFU per cucumber) was significantly less than that of AcEW or NaOCl (P < or = 0.05) . Cucumbers washed in alkaline electrolyzed water for 5 min and then treated with AcEW for 5 min showed a reduction in aerobic mesophiles that was at least 2 log CFU per cucumber greater than that of other treatments (P < or = 0.05) . This treatment was also effective in reducing levels of coliform bacteria and fungi associated with cucumbers . All treatments offered greater microbial reduction on the cucumber surface than in the cucumber homogenate . Aerobic mesophiles associated with strawberries were reduced by less than 1 log CFU per strawberry after each treatment . Coliform bacteria and fungi associated with strawberries were reduced by 1.0 to 1.5 log CFU per strawberry after each treatment . Microbial reduction was approximately 0.5 log CFU per strawberry greater on the strawberry surface than in the strawberry homogenate . However, neither treatment was able to completely inactivate or remove the microorganisms from the surface of the cucumber or strawberry.

Lin Chuang Er Bi Yan Hou Ke Za Zhi, 2004 Mar, 18(3), 129 - 31
{Expression of human beta-defensin in palatine tonsil}; Wang C et al.; OBJECTIVE: To examine the expression of human beta-defensin-1 (hBD-1) and human beta-defensin-2 (hBD-2) in palatine tonsil of normal subjects and patients with chronic tonsillitis, and to investigate the role of palatine tonsil in the innate immunity system . METHOD: Eighteen specimens of hyperplastic tonsils (n = 8) and chronic tonsillitis(n = 10) were examined using reverse transcriptase-polymerase chain reaction (RT-PCR) . RESULT: beta-defensin 1 mRNA was expressed in all tissue specimens, at levels that did not differ significantly (P > 0.05) . beta-defensin 2 mRNA was detected in the specimens of chronic tonsillitis, but almost not in the normal subjects . Its expression level was significantly higher in chronic inflamed tonsils than in normal controls(P < 0.05) . CONCLUSION: These results suggest that beta-defensin of the palatine tonsil may play an important role in innate defense against microorganisms.

Anesthesiology, 2004 Jul, 101(1), 104 - 9
An in vivo evaluation of the mycobacterial filtration efficacy of three breathing filters used in anesthesia; Vezina DP et al.; BACKGROUND: The use of breathing filters (BFs) has been recommended to protect the anesthesia apparatus in proven or suspected cases of tuberculosis . Some investigators have also suggested the use of BF to alleviate the need to change anesthesia breathing circuits after each case . This study evaluated the filtration efficacy of three different BFs to prevent mycobacterial contamination of breathing circuits in a model that uses a test animal . METHODS: Ten Pall BB25A (pleated hydrophobic) (Pall Canada Ltd., Mississauga, Ontario, Canada), six DAR Barrierbac S (felted electrostatic; Mallinckrodt DAR, Mirandola, Italy), and six Baxter Airlife (felted electrostatic; Baxter Canada, Mississauga, Ontario, Canada) BFs were studied . For each BF tested, 20 ml of a high concentration suspension of Mycobacterium chelonae (range, 2.0 x 10 to 9.0 x 10 colony-forming units/ml) was nebulized during 2 h at the proximal end of the endotracheal tube of anesthetized pigs . At the end of the nebulization period, the BFs were sampled for culture . The titer reduction value (number of microorganisms challenging the BF divided by the number of microorganisms recovered downstream of the BF) and the removal efficiency (difference between the number of microorganisms challenging the BF and the number of microorganisms recovered downstream of the BF, divided by the number of microorganisms challenging the BF) were calculated . RESULTS: The median titer reduction values were 5.6 x 10, 6.0 x 10, and 8.0 x 10 (P < 0.0005), and the median removal efficiencies were greater than 99.999%, greater than 99.999%, and 100% (P = not significant) for the DAR Barrierbac S, the Baxter Airlife, and the Pall BB25A, respectively . CONCLUSIONS: Among the three BFs studied, only the Pall BB25A completely prevented the passage of M . chelonae, thus protecting the anesthesia breathing circuit from mycobacterial contaminationPublication Types:

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