Chemosphere, 2004 Feb, 54(7), 823 - 9 Effect of Fe0 quantity on the efficiency of integrated microbial-Fe0 treatment processes; Fernandez-Sanchez JM et al.; Batch experiments were conducted with different reaction systems to investigate how the treatment efficiency of integrated microbial-Fe0 processes is affected by the amount of Fe0 added . Abiotic experiments with hexavalent chromium and carbon tetrachloride mixtures corroborated that different pollutants could compete for reactive sites on the iron surface, which would hinder specific degradation rates when the available Fe0 surface area is relatively small (e.g., 11 m(2) l(-1)) . In such cases, reductive precipitation of chromium could occlude reactive sites and significantly inhibit removal efficiency . Microbial participation in the cleanup process was also influenced by the amount of Fe0 added . Increasing the Fe0 dose (and thus the available surface area) had a stimulatory effect possibly due to a higher production of cathodic H2, which can be used as electron donor for reductive biotransformation of many pollutants . However, high Fe0 doses had an inhibitory effect due to a corrosion-induced increase in pH beyond the optimum range of the bacteria . This suggest that there may be a system-specific, optimum quantity of Fe0 that satisfies availability requirements to preclude contaminant competition for reactive sites and biological requirements for H2 production while minimizing inhibitory increases in pH . Results also confirmed extensive RDX mineralization in bioaugmented (but not in abiotic) Fe0 systems, and support the notion that permeable reactive iron barriers performance might be enhanced by the participation of some microorganisms. Scand J Immunol, 2003 Dec, 58(6), 642 - 8 Development of immunoglobulin A in infancy and childhood; Weemaes C et al.; Serum and salivary concentrations of immunoglobulin A1 (IgA1) and IgA2 were studied in 105 Icelandic children aged 0-12 years . Serum concentrations of both IgA1 and IgA2 increased slightly (P < 0.001) during childhood . The salivary IgA1/IgA2 ratio tended to decrease during the same period; this trend is less apparent when omitting the youngest children . The salivary IgA1 and IgA2 output could be high, even in children with low levels of serum IgA . Only polymeric IgA was found in whole saliva . Interestingly, in serum, most IgA1 and IgA2 were polymeric during infancy . The proportion of polymeric IgA decreased, when the concentration of IgA increased . The polymeric form of IgA might provide the infant with better protection against invading microorganisms by activation of the innate immune mechanisms. Br J Dermatol, 2003 Nov, 149(5), 1029 - 34 Effect of Mycobacterium vaccae on atopic dermatitis in children of different ages; Arkwright PD et al.; BACKGROUND: Exposure to environmental microorganisms is associated with variations in the prevalence and severity of atopic diseases . We have previously shown that administration of a Mycobacterium vaccae suspension significantly reduced the severity of atopic dermatitis (AD) in children aged 5-18 years . OBJECTIVES: This study aimed to extend these observations to younger children . METHODS: Fifty-six children aged 2-6 years with moderate to severe AD were enrolled in a randomized, double-blind, placebo-controlled trial and given one intradermal injection of either killed M . vaccae suspension or buffer solution (placebo) . Skin surface area affected and dermatitis severity score were assessed before and 1, 3 and 6 months after treatment . RESULTS: Although a 38-54% reduction in surface area affected by dermatitis was noted at all time points after M . vaccae administration (P = 0.005), this improvement was not significantly different from that observed in the placebo group . Meta-analysis of this and our previous cohort (97 children aged 2-18 years) showed that M . vaccae was associated with a significant improvement in clinical severity at all ages, whereas within the placebo group, younger but not older children showed a similar improvement . CONCLUSIONS: Despite a reduction in clinical severity associated with M . vaccae at all ages, no benefit could be found after administering M . vaccae to children with AD aged 2-6 years when compared with placebo . M . vaccae may offer greater benefit in children over 5 years old, whose AD appears less likely to regress spontaneously. Res Commun Mol Pathol Pharmacol, 2002, 111(1-4), 103 - 13 Inhibitory effect of eight simple coumarins on the lucigenin enhanced chemiluminescence of rabbit neutrophils; Kabeya LM et al.; The generation of superoxide anion (O2*-) and other reactive oxygen species (ROS), such as HO*, HOCl, NO, 1O2 and H2O2, by stimulated polymorphonuclear leukocytes during phagocytosis is a major mechanism of host defense against invading microorganisms . However, large amounts of ROS are suggested to be responsible for many diseases . In this work we studied the inhibitory effect of eight simple coumarins on O2*- generation by rabbit neutrophil upon stimulation with opsonized zymosan, using lucigenin enhanced chemiluminescence assay . We observed that coumarins containing hydroxy or acetoxy substituents at position 7 of the benzopyrone ring were the most active ones (IC50 values ranging from 6.0 +/- 2.8 to 18.6 +/- 2.6 micromol/L) . Substitution of these groups by allyloxy or metoxy groups decreased the activity and unsubstituted coumarin had no effect . Cell damage after exposure to 200 micromol/L of each compound was determined by measurement of the activity of the released cytosolic lactate dehydrogenase and by Trypan Blue dye exclusion test . None of the drugs affected significantly the cellular viability. Eye, 2003 Nov, 17(8), 949 - 56 Immune defense at the ocular surface; Akpek EK et al.; The ocular surface is constantly exposed to a wide array of microorganisms . The ability of the outer ocular system to recognize pathogens as foreign and eliminate them is critical to retain corneal transparency, hence preservation of sight . Therefore, a combination of mechanical, anatomical, and immunological defense mechanisms has evolved to protect the outer eye . These host defense mechanisms are classified as either a native, nonspecific defense or a specifically acquired immunological defense requiring previous exposure to an antigen and the development of specific immunity . Sight-threatening immunopathology with autologous cell damage also can take place after these reactions . This article discusses the innate and acquired corneal elements of the immune defense at the ocular surface . The relative roles of the various factors contributing to prevention of eye infection remain to be fully defined. Plant Physiol, 2003 Dec, 133(4), 1968 - 78 Epub 2003 Nov 20. Identification of AtNDI1, an internal non-phosphorylating NAD(P)H dehydrogenase in Arabidopsis mitochondria; Moore CS et al.; Plant mitochondria contain non-phosphorylating NAD(P)H dehydrogenases (DHs) that are not found in animal mitochondria . The physiological function, substrate specificity, and location of enzymes within this family have yet to be conclusively determined . We have linked genome sequence information to protein and biochemical data to identify that At1g07180 (SwissProt Q8GWA1) from the Arabidopsis Genome Initiative database encodes AtNDI1, an internal NAD(P)H DH in Arabidopsis mitochondria . Three lines of evidence are presented: (a) . The predicted protein sequence of AtNDI1 has high homology with other designated NAD(P)H DHs from microorganisms, (b) . the capacity for matrix NAD(P)H oxidation via the rotenone-insensitive pathway is significantly reduced in the Atndi1 mutant plant line, and (c) . the in vitro translation product of AtNDI1 is imported into isolated mitochondria and located on the inside of the inner membrane. Biochem Biophys Res Commun, 2003 Dec 5, 312(1), 205 - 8 Reappraisal of the 20th-century version of amino acid metabolism; Katagiri M et al.; In this article, we advocate the radical revision of the 20th-century version of amino acid metabolism as follows . (1) Classic studies on the incorporation of {15N}ammonia into glutamate, once considered to be an epoch-making event, are not distinctive proof of the ability of animals to utilize ammonia for the synthesis of alpha-amino nitrogen . (2) Mammalian glutamate dehydrogenase has been implicated to function as a glutamate-synthesizing enzyme albeit lack of convincing proof . This enzyme, in combination with aminotransferases, is now known to play an exclusive role in the metabolic removal of amino nitrogen and energy production from excess amino acids . (3) Dr . William C Rose's "nutritionally nonessential amino acids" are, of course, essential in cellular metabolism; the nutritional nonessentiality is related to their carbon skeletons, many of which are intermediates of glycolysis or the TCA cycle . Obviously, the prime importance of amino acid nutrition should be the means of obtaining amino nitrogen . (4) Because there is no evidence of the presence of any glutamate-synthesizing enzymes in mammalian tissues, animals must depend on plants and microorganisms for preformed alpha-amino nitrogen . This is analogous to the case of carbohydrates . (5) In contrast, individual essential amino acids, similar to vitamins and essential fatty acids, should be considered important nutrients that must be included regularly in sufficient amounts in the diet. Am J Reprod Immunol, 2003 Sep, 50(3), 254 - 62 Placental lesions caused by experimental infection of Sprague-Dawley rats with Mycoplasma pulmonis; Peltier MR et al.; PROBLEM: Sprague-Dawley (SD) rats infected during pregnancy with Mycoplasma pulmonis display adverse pregnancy outcomes that are similar to those observed in women with chorioamnionitis and may provide a good model system for this disease . The placental lesions caused by this microorganism, however, have not been thoroughly characterized . METHOD OF STUDY: Rats were infected with 10(7) colony-forming units (CFU) M . pulmonis or vehicle control on gestation day (gd) 14 and were euthanized on gd 16-18 . Tissues were fixed in 10% neutral buffered formalin, embedded in paraffin, sectioned at 4 microm, and stained with hematoxylin and eosin (H & E) . The slides were coded and examined by a blinded pathologist using light microscopy . RESULTS: Infection with M . pulmonis was associated with necrosis of trophoblast giant cells at gd 18 . Significantly more neutrophils were observed in the decidual region of the apex of the placenta in M . pulmonis infected animals . The vast majority of neutrophils, however, were observed in the decidua in the lateral regions of the placenta and in the adjacent endometrium . CONCLUSIONS: Infection of SD rats with M . pulmonis resulted in histological placentitis similar to that described in deciduitis of humans and represents a good model system for investigations into the pathophysiology of intrauterine infection . The influx of neutrophils seems to migrate from the endometrium towards the lateral regions of the placenta near Reichert's membrane and the divergence of the parietal yolk sac. Biotechniques, 2003 Nov, 35(5), 996 - 1002, 1004-5 Nitrogenase genes in PCR and RT-PCR reagents: implications for studies of diversity of functional genes; Zehr JP et al.; Studies of the diversity of microorganisms in the environment have been facilitated by use of PCR and reverse transcription PCR (RT-PCR) . Inhibition of the PCR by complex sample matrices and low abundance of some target microorganisms require the use of high-sensitivity amplification procedures, involving a large number of cycles or nested PCR methods . Using these methods, we frequently observed contamination of the amplification reagents, including polymerases, by genomic DNA containing nitrogenase (nifH) and rRNA genes . Contaminating genes were sequenced and found to belong to a variety of rRNA clades, but only three major nifH clades . These sequence types included a few nifH sequences reported in previous studies of the environment . Contamination could be reduced by restriction digestion and ultrafiltration of PCR reagents, but efficiency of amplification was also reduced . Our results suggest that studies relying on large numbers of PCR amplification cycles to assess environmental gene diversity should take precautions to assure that clone libraries generated from amplified PCR products are not the result of contaminated PCR reagents. Morfologiia, 2003, 124(4), 66 - 9 {Functional significance of "blind" outgrowths of the lymphatic capillary network}; Aminova GG; The work was aimed at the study of the structural peculiarities of "blind" outgrowths of the lymphatic capillaries and to define their role in the pathogenesis of some diseases . In experiments performed in rabbits by studying the resorption of colloidal solutions, suspensions and hen's blood the subsidiary functional significance of the portion of "blind" outgrowths of the lymphatic capillary network of tendinous center of diaphragm was established . The clavate outgrowths with the narrow mouth may accumulate and store the exogenous material in their lumen . It is concluded that they may accumulate the microorganisms that provoke the relapses of diseases. Bioelectromagnetics, 2003, Suppl 6, S74 - 100 Radio frequency electromagnetic fields: cancer, mutagenesis, and genotoxicity; Heynick LN et al.; We present critiques of epidemiologic studies and experimental investigations, published mostly in peer-reviewed journals, on cancer and related effects from exposure to nonionizing electromagnetic fields in the nominal frequency range of 3 kHz to 300 GHz of interest to Subcommittee 4 (SC4) of the International Committee on Electromagnetic Safety (ICES) . The major topics discussed are presented under the headings Epidemiologic and Other Findings on Human Exposure, Mammals Exposed In Vivo, Mammalian Live Tissues and Cell Preparations Exposed In Vitro, and Mutagenesis and Genotoxicity in Microorganisms and Fruit Flies . Under each major topic, we present minireviews of papers on various specific endpoints investigated . The section on Epidemiologic and Other Findings on Human Exposure is divided into two subsections, the first on possible carcinogenic effects of exposure from emitters not in physical contact with the populations studied, for example, transmitting antennas and other devices . Discussed in the second subsection are studies of postulated carcinogenic effects from use of mobile phones, with prominence given to brain tumors from use of cellular and cordless telephones in direct physical contact with an ear of each subject . In both subsections, some investigations yielded positive findings, others had negative findings, including papers directed toward experimentally verifying positive findings, and both were reported in a few instances . Further research on various important aspects may resolve such differences . Overall, however, the preponderance of published epidemiologic and experimental findings do not support the supposition that in vivo or in vitro exposures to such fields are carcinogenic . Published 2003 Wiley-Liss, Inc. Ann Acad Med Singapore, 2003 Sep, 32(5), 710 - 4 From genesis to genes; Tan SK; Since the beginning of time, our ancestors have been plagued by illnesses and injuries that are not too different from today's diseases . Evidence from prehistoric times and ancient civilisations have shown man's attempts at trying to understand the nature and treatment of these conditions . It was not till the early 19th century that the scientific basis of modern medicine was firmly established when microorganisms were discovered and found to be the cause of many of these illnesses . The 20th century saw quantum leaps made in the understanding of the function of the human body and the therapeutic measures aimed at restoration of any such malfunction . The end of the last millennium was marked by historic achievements made in the Life Sciences, in particular the completion of the sequencing of the Human Genome--the code of life . The beginning of the 21st century has already seen many breakthroughs in medical sciences, especially in the fields of stem cell technology and gene therapy . The number of known illnesses directly related to genetic defects or abnormalities have increased exponentially . Many of today's scourges can be prevented or more effectively treated . Our ability to utilise this new knowledge to combat the ravages of the ageing process and its associated illnesses--degenerative diseases and cancers offer much hope for the future. Appl Microbiol Biotechnol, 2004 May, 64(4), 576 - 87 Epub 2003 Nov 18. Intrinsic bioremediability of an aromatic hydrocarbon-polluted groundwater: diversity of bacterial population and toluene monoxygenase genes; Cavalca L et al.; The functional and phylogenetic biodiversity of bacterial communities in a benzene, toluene, ethylbenzene and xylene (BTEX)-polluted groundwater was analysed . To evaluate the feasibility of using an air sparging treatment to enhance bacterial degradative capabilities, the presence of degrading microorganisms was monitored . The amplification of gene fragments corresponding to toluene monooxygenase (tmo), catechol 1,2-dioxygenase, catechol 2,3-dioxygenase and toluene dioxygenase genes in DNA extracted directly from the groundwater samples was associated with the presence of indigenous degrading bacteria . Five months of air injection reduced species diversity in the cultivable community (as calculated by the Shannon-Weaver index), while little change was noted in the degree of biodiversity in the total bacterial community, as characterised by denaturing gradient gel electrophoresis (DGGE) analysis . BTEX-degrading strains belonged to the genera Pseudomonas, Microbacterium, Azoarcus, Mycobacterium and Bradyrhizobium . The degrading capacities of three strains in batch liquid cultures were also studied . In some of these microorganisms different pathways for toluene degradation seemed to operate simultaneously . Pseudomonas strains of the P24 operational taxonomic unit, able to grow only on catechol and not on BTEX, were the most abundant, and were present in the groundwater community at all stages of treatment, as evidenced both by cultivation approaches and by DGGE profiles . The presence of different tmo-like genes in phylogenetically distant strains of Pseudomonas, Mycobacterium and Bradyrhizobium suggested recent horizontal gene transfer in the groundwater . Chem Phys Lipids, 2003 Dec, 126(2), 225 - 32 Archaeal lipids forming a low energy-surface on air-water interface; Kitano T et al.; Archaea or archaebacteria are the microorganism living in extreme environments such as hot springs and salt lakes . The membrane is featured universally by lipids which possess saturated polyisoprenoid chains in the hydrophobic moiety . This paper concerns the surface properties of Langmuir membranes made of archaeal lipid models (AL) bearing a phytanyl group or (3RS, 7R, 11R)-3,7,11,15-tetramethylhexadecyl group . All of the AL provide a Langmuir membrane on an air-water interface with an abnormally low surface tension (32-37 mN/m at 20-70 degrees C), while the conventional lipids having n-alkyl chains give membranes of 54-56 mN/m . The abnormally low energy surface of AL lipids is considered to arise from the bulky and fluid polyisoprenoid chain. Biochem Biophys Res Commun, 2003 Nov 21, 311(3), 597 - 603 Functionally important amino acids in Saccharomyces cerevisiae aspartate kinase; Bareich DC et al.; Saccharomyces cerevisiae aspartate kinase (AK(Sc)) phosphorylates L-Asp as the first step in the aspartate pathway responsible for the biosynthesis of L-Thr, L-Met, and L-Ile in microorganisms and plants . Using site-directed mutagenesis, we have evaluated the importance of residues in AK(Sc) that are strongly conserved among aspartate kinases or in other small molecule kinases . Steady state kinetic analysis of the purified AK(Sc) variants reveals that several of the targeted amino acids, particularly K18 and H292, have important roles in the enzymatic reaction . These results provide the first identification of amino acid residues crucial to the action of this important metabolic enzyme. Oral Microbiol Immunol, 2003 Dec, 18(6), 339 - 49 Induction of T-cell apoptosis by Actinobacillus actinomycetemcomitans mutants with deletion of ltxA and cdtABC genes: possible activity of GroEL-like molecule; Nalbant A et al.; The pathogenic bacterium Actinobacillus actinomycetemcomitans expresses a leukotoxin (Ltx) and cytolethal distending toxin (CDT) with cytolytic properties . CDT also has cytostatic properties, inducing a G2 cell cycle block . The extent of the contribution of these, as well as other toxins, to the cytolytic and cytostatic activities of this microorganism have not been defined and the aim of this study was to determine their contribution . To that end, a naturally transformable A . actinomycetemcomitans clinical strain (D7S-smooth) was used to construct a series of deletion mutants (DeltacdtA, DeltacdtB, DeltacdtC, DeltacdtABC, DeltaltxA, DeltaltxA/DeltacdtABC) . Human peripheral blood mononuclear cells were incubated with cell-associated and extracellular bacterial preparations . The ability of wild type and isogenic mutants to induce T-cell apoptosis and cell cycle arrest was compared . The expression of ltxA and each of the cdt gene loci partially contributed to A . actinomycetemcomitans apoptosis, since each of the isogenic mutants exhibited reduced ability to induce T-cell apoptosis . Conversely, the ability to induce cell cycle block was abolished in each of the cdt isogenic mutants . A mutant with simultaneous deletion of ltxA and cdtABC genes retained potent ability to induce apoptosis in its cell-associated, but not extracellular, preparation . Neutralization with Escherichia coli anti-GroEL monoclonal antibody, lead to significant diminution of apoptosis-inducing activity of the DeltaltxA/DeltacdtABC cell-associated preparation . These data provide evidence for the expression of other A . actinomycetemcomitans cytolytic molecule(s) distinct from CDT and leukotoxin, with a possible role for GroEL-like molecule in T-cell apoptosis. Eur J Biochem, 2003 Nov, 270(21), 4243 - 53 Reconstruction of the central carbon metabolism of Aspergillus niger; David H et al.; The topology of central carbon metabolism of Aspergillus niger was identified and the metabolic network reconstructed, by integrating genomic, biochemical and physiological information available for this microorganism and other related fungi . The reconstructed network may serve as a valuable database for annotation of genes identified in future genome sequencing projects on aspergilli . Based on the metabolic reconstruction, a stoichiometric model was set up that includes 284 metabolites and 335 reactions, of which 268 represent biochemical conversions and 67 represent transport processes between the different intracellular compartments and between the cell and the extracellular medium . The stoichiometry of the metabolic reactions was used in combination with biosynthetic requirements for growth and pseudo-steady state mass balances over intracellular metabolites for the quantification of metabolic fluxes using metabolite balancing . This framework was employed to perform an in silico characterisation of the phenotypic behaviour of A . niger grown on different carbon sources . The effects on growth of single reaction deletions were assessed and essential biochemical reactions were identified for different carbon sources . Furthermore, application of the stoichiometric model for assessing the metabolic capabilities of A . niger to produce metabolites was evaluated by using succinate production as a case study. Eur J Biochem, 2003 Nov, 270(22), 4555 - 63 Construction of hybrid peptide synthetases for the production of alpha-l-aspartyl-l-phenylalanine, a precursor for the high-intensity sweetener aspartame; Duerfahrt T et al.; Microorganisms produce a large number of pharmacologically and biotechnologically important peptides by using nonribosomal peptide synthetases (NRPSs) . Due to their modular arrangement and their domain organization NRPSs are particularly suitable for engineering recombinant proteins for the production of novel peptides with interesting properties . In order to compare different strategies of domain assembling and module fusions we focused on the selective construction of a set of peptide synthetases that catalyze the formation of the dipeptide alpha-l-aspartyl-l-phenylalanine (Asp-Phe), the precursor of the high-intensity sweetener alpha-l-aspartyl-l-phenylalanine methyl ester (aspartame) . The de novo design of six different Asp-Phe synthetases was achieved by fusion of Asp and Phe activating modules comprising adenylation, peptidyl carrier protein and condensation domains . Product release was ensured by a C-terminally fused thioesterase domains and quantified by HPLC/MS analysis . Significant differences of enzyme activity caused by the fusion strategies were observed . Two forms of the Asp-Phe dipeptide were detected, the expected alpha-Asp-Phe and the by-product beta-Asp-Phe . Dependent on the turnover rates ranging from 0.01-0.7 min-1, the amount of alpha-Asp-Phe was between 75 and 100% of overall product, indicating a direct correlation between the turnover numbers and the ratios of alpha-Asp-Phe to beta-Asp-Phe . Taken together these results provide useful guidelines for the rational construction of hybrid peptide synthetases. Dev Biol (Basel), 2003, 113, 61 - 4 Current issues in validation of chromatography; Sofer G; Chromatography has now been used successfully for more than 20 years to provide the requisite purity for biologicals, but there remain some issues of concern . These issues include carryover and cleaning validation, potential for contamination by microorganisms, potential leachables, and resin lifespan . Compounding these issues is the fact that chromatography media have a very large surface area, and it is not always clear what is occurring at the surface . Furthermore, there are multiple, interactive operating parameters that have the potential to influence chromatographic performance. Am J Vet Res, 2003 Nov, 64(11), 1421 - 8 Detection of novel chlamydiae in cats with ocular disease; von Bomhard W et al.; OBJECTIVE: To detect and characterize the full range of chlamydial infections in cats with ocular disease by use of polymerase chain reaction (PCR) assays, cytologic examination, immunohistochemical analysis, and evaluation of clinical information including status for feline herpesvirus-1 (FeHV-1) . SAMPLE POPULATION: DNA extracted from 226 conjunctival samples obtained from cats with clinically diagnosed keratitis or conjunctivitis and 30 conjunctival samples from healthy cats . PROCEDURE: PCR assays for the 16S rRNA gene specific for the order Chlamydiales and a new Chlamydophila felis (formerly Chlamydia psittaci) species-specific 23S rRNA gene were performed . Seventy-four conjunctival samples were prepared with Romanowsky-type stain, grouped on the basis of inflammatory pattern, and screened for chlamydial inclusions by use of immunohistochemical analysis . Clinical information and FeHV-1 status were recorded . RESULTS: 26 (12%) specimens had positive results for the only known feline chlamydial pathogen, C felis . Surprisingly, an additional 88 (39%) were positive for non-C felis chlamydial DNA . Identification of non-C felis chlamydial DNA by direct sequencing revealed 16S rRNA gene sequences that were 99% homologous to the sequence for Neochlamydia hartmannellae, an amebic endosymbiont . Chlamydial prevalence was significantly higher in cats with ocular disease . CONCLUSIONS AND CLINICAL RELEVANCE: Application of a broad-range detection method resulted in identification of a new agent associated with ocular disease in cats . Finding chlamydia-like agents such as N hartmannellae in coinfections with their obligate amebic host, Hartmannella vermiformis, raises questions about the potential role of these microorganisms in causation or exacerbation of ocular disease in cats. Quintessence Int, 2003 Nov-Dec, 34(10), 733 - 8 Reestablishing biologic width with forced eruption; Felippe LA et al.; Maintenance of gingival health is one of the keys for the longevity of teeth, as well as for the longevity of restorations . In this context, the biologic width functions as a barrier against the entrance of microorganisms into the internal medium of the periodontal ligament and into the gingival and osseous connective tissue . This clinical case describes a technique to reestablish the biologic width of a central incisor using forced extrusion and done without post-treatment corrective surgery. Biofouling, 2003 Apr, 19 Suppl, 249 - 54 Wood digestion in Pselactus spadix Herbst--a weevil attacking marine timber structures; Oevering P et al.; Pselactus spadix tunnels timber structures in the marine environment . Recent studies reported a cosmopolitan distribution for this weevil, which is frequently found in harbour and port areas . P . spadix feeds on timber (hardwood and softwood) in immature and adult life stages, but its digestion of wood components had not been investigated . Using dry weight analyses of tunnel walls and frass produced, P . spadix adults consumed Scots pine with soft rot decay at a rate of 1.59 +/- 0.37 mg d-1 and the digestibility of this substrate was 57.96 +/- 5.89 (i.e . for 100 mg consumed SR-pine, 58 mg was digested) . Using gravimetric analysis to quantify structural wood components in tunnel walls and frass, P . spadix adults were found to digest cellulose, lignin and hemicellulose with digestibility coefficients of 82.2, 41.2 and 14.5 respectively . Fourier Transform Infrared (FTIR) spectroscopy analyses of tunnel walls and frass of adults and larvae from soft rotted pine also indicated digestion of all structural components, with larvae digesting cellulose and lignin more efficiently than adults . When FTIR was employed to analyse adult tunnel walls and frass from undecayed pine, cellulose and hemicellulose were digested, but no evidence of lignin digestion was found . This study shows that adults digest lignin when soft rot is present and suggests a symbiotic function of wood degrading microorganisms. Medicina (Kaunas), 2003, 39 Suppl 2, 55 - 9 {Octanhydroxamate of iron: synthesis, analysis and investigation of stability}; Palma P et al.; Hydroxamic acids are found as chelates in plants, as metabolites of bacteria and funges . Some aerobic microorganisms synthesize hydroxamic acids, which transmit iron from environment to the cells of the plants . Fourteen hydroxamic acids were synthesized and their interaction with iron (II and III) was investigated . The purpose of this investigation was synthesis of hydroxamic acids, creation of stable iron chelate with one of these acids, preparation of the methods of analysis, investigation of the stability of chelate and application for prophylaxis and treatment of iron deficiency anemia . We used octanhydroxamic acid for creation of chelate with iron . The synthesis of this acid was the cheapest and compound with iron appeared stable . Iron chelates after acid hydrolysis were analyzed by quantity of iron (9.8-12.3%) . We used complexometric titration method with dinatrium salt of ethylendiamintetraacetic acid without indication for quantitative analysis . Iron (II) chelate is less stable, therefore, we used Fe (III) octanhydroxamate for further investigations . Preliminary trials with rabbits confirm rapid assimilation of iron (III) chelate from gastrointestinal tract and activation of erythropoiesis. Mol Microbiol, 2003 Nov, 50(3), 857 - 70 Cell cycle- and age-dependent activation of Sod1p drives the formation of stress resistant cell subpopulations within clonal yeast cultures; Sumner ER et al.; Phenotypic heterogeneity describes non-genetic variation that exists between individual cells within isogenic populations . The basis for such heterogeneity is not well understood, but it is evident in a wide range of cellular functions and phenotypes and may be fundamental to the fitness of microorganisms . Here we use a suite of novel assays applied to yeast, to provide an explanation for the classic example of heterogeneous resistance to stress (copper) . Cell cycle stage and replicative cell age, but not mitochondrial content, were found to be principal parameters underpinning differential Cu resistance: cell cycle-synchronized cells had relatively uniform Cu resistances, and replicative cell-age profiles differed markedly in sorted Cu-resistant and Cu-sensitive subpopulations . From a range of potential Cu-sensitive mutants, cup1Delta cells lacking Cu-metallothionein, and particularly sod1Delta cells lacking Cu, Zn-superoxide dismutase, exhibited diminished heterogeneity . Furthermore, age-dependent Cu resistance was largely abolished in cup1Delta and sod1Delta cells, whereas cell cycle-dependent Cu resistance was suppressed in sod1Delta cells . Sod1p activity oscillated approximately fivefold during the cell cycle, with peak activity coinciding with peak Cu-resistance . Thus, phenotypic heterogeneity in copper resistance is not stochastic but is driven by the progression of individual cells through the cell cycle and ageing, and is primarily dependent on only Sod1p, out of several gene products that can influence the averaged phenotype . We propose that such heterogeneity provides an important insurance mechanism for organisms; creating subpopulations that are pre-equipped for varied activities as needs may arise (e.g . when faced with stress), but without the permanent metabolic costs of constitutive expression. Clin Microbiol Infect, 2003 Aug, 9(8), 766 - 79 The multiple roles of Fas ligand in the pathogenesis of infectious diseases; Dockrell DH; Fas ligand (FasL) is a type II transmembrane protein that plays a critical role in immune homeostasis by binding to its receptor Fas (CD95) and inducing apoptosis . Fas/FasL dysregulation contributes to infectious disease pathogenesis . Microorganisms may inhibit Fas signal transduction to prolong intracellular survival and prevent killing by immune effector cells . FasL may be upregulated in directly infected cells to enhance killing of responding immune cells and facilitate immune evasion . The host response to infection may aim to induce apoptosis in directly infected cells, but immune cells that target directly infected cells can induce Fas-mediated apoptosis of uninfected bystander cells . FasL also contributes to the generation and regulation of the inflammatory response in infection . The multiple roles of FasL in infectious disease pathogenesis are discussed in the context of viral, bacterial and parasitic infections. Biochemistry (Mosc), 2003 Oct, 68(10), 1132 - 5 Halogenating enzymes in the biosynthesis of antibiotics; Burd VN et al.; Using blot hybridization, it has been shown that microorganisms producing halogen-containing antibiotics--Pseudomonas pyrrocinia, P . aureofaciens ACN, P . aureofaciens Pa1, P . fluorescens CHA0, Actinoplanes sp., Kitasatasporia sp., Sacharothrix aerocolonigenes, Actinomadura melliaura, and Streptomyces albogriseolus--contain the genes of the halogenating enzymes related to tryptophan-7-halogenase and monodechloroaminopyrrolnitrin halogenase from P . fluorescens BL 915. Anal Chem, 2003 Nov 15, 75(22), 6056 - 62 Compound-specific stable isotope analysis of soil mesofauna using thermally assisted hydrolysis and methylation for ecological investigations; Evans CJ et al.; Stable isotope mass spectrometric approaches are proving to be valuable tools in unravelling biotic interactions in complex ecosystems, yielding information on trophic preferences and functional roles of individual species . Gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS) provides considerable opportunities to assist in studies concerned with ecosystem processes mediated by soil invertebrates and microorganisms by determination of delta(13)C values of individual compounds, for example, lipids, amino acids etc . However, techniques conventionally adopted for "wet" chemical extractions and derivatizations necessary for compound-specific stable isotope determinations restrict the size of soil organism that can be studied and can limit investigations of individuals or even parts of individuals . We demonstrate here that individual soil mesofauna can be probed directly for their fatty acid stable isotope signatures by pyrolysis-GC/C/IRMS . A thermally assisted hydrolysis and methylation (THM) reaction is described for the determination of delta(13)C fatty acid values using trimethylsulfonium hydroxide (TMSH) . Authentic fatty acids, acyl lipids, and individual Collembola (Folsomia candida) raised on C(3) and C(4) isotopically labeled yeast were analyzed initially by py-GC/MS with TMSH and then by py-GC/C/IRMS . A kinetic isotope effect (KIE) observed with the THM reaction prevents direct calculation of the fatty acid delta(13)C values by simple mass balance equations . However, the KIE is shown to be both reproducible and robust and can therefore be accounted for by the use of correction factors . The fatty acid methyl ester compositions of individual F . candida and their respective delta(13)C values were determined and shown to agree with those obtained by conventional "wet" chemical procedures applied to much larger numbers of Collembola, thus enhancing the scope to which stable isotopes can be applied to the study of invertebrates in complex food webs in any environment. Turk J Gastroenterol, 2003 Jun, 14(2), 145 - 7 Spontaneous bacterial peritonitis due to Brucella infection; Gursoy S et al.; Brucella infection is a systemic disease, but the microorganism rarely causes infections in the gastrointestinal system such as hepatitis, cholecystitis, colitis and pancreatitis . Spontaneous bacterial peritonitis due to Brucella is extremely rare . Herein, we report a case of cirrhosis complicated with nongranulomatous hepatitis and peritonitis, both due to Brucella . A 63 year-old man with diabetes mellitus was admitted to hospital with complaints of weakness, backache, abdominal pain and abdominal swelling . On the basis of physical examination and laboratory findings, cryptogenic cirrhosis and spontaneous bacterial peritonitis were diagnosed . Due to persistent fever and backache, serum Brucella agglutination test was performed and found to be positive . Brucella melitensis was isolated from ascitic fluid culture . Liver biopsy findings revealed cirrhosis and a nongranulomatous hepatitis which was thought might be due to Brucella infection . Doxycycline and rifampicin, in addition to diuretics were administered for spontaneous ascites infection due to Brucella . A week later, the patient's condition improved and he became afebrile . After two months of therapy, the ascites had almost disappeared. J Vet Sci, 2000 Dec, 1(2), 105 - 11 Using pig biliary system, in vivo propagation of Enterocytozoon bieneusi, an AIDS-related zoonotic pathogen; Lee JH; A microsporidian parasite Enterocytozoon bieneusi is the most common microorganism recognized in AIDS patients, and slow scientific progress is attributed to our inability to propagate the parasite . We report upon the development of a system of propagation using the pig biliary system . The parasite spores were continuously detected in the bile samples post onset of spore shedding in the gall bladder, which suggests that this organism maintain persistent infection in the biliary system and that the hepatobiliary tree may represent a reservoir of infection . In conclusion the biliary tree is an adequate niche for the propagation of E . bieneusi . This work has also resulted in the development of a procedure of ultrasound-guided cholecystocentesis for aspirating biles . This is a simple and non-surgical procedure, and creates no signs of clinical complications in the livers and the gall bladders after dozens of separate attempts . Thus, this is a very useful and safe technique for the aspiration of bile from live animals. Microbes Infect, 2003 Nov, 5(14), 1337 - 44 Regulation of the neutrophil-mediated inflammatory response to infection; Kobayashi SD et al.; Human polymorphonuclear leukocytes (PMNs) are the first line of defense against invading microorganisms and contribute significantly to inflammation . Recent evidence suggests that resolution of neutrophil-mediated inflammation is facilitated by an apoptosis differentiation program, a final stage of transcriptionally regulated PMN maturation that is accelerated significantly by phagocytosis. Bioorg Chem, 2003 Dec, 31(6), 494 - 502 Reconstitution of UDP-galactopyranose mutase with 1-deaza-FAD and 5-deaza-FAD: analysis and mechanistic implications; Huang Z et al.; The galactofuranose moiety found in many surface constituents of microorganisms is derived from UDP-D-galactopyranose (UDP-Galp) via a unique ring contraction reaction catalyzed by a FAD-dependent UDP-Galp mutase . When the enzyme is reduced by sodium dithionite, its catalytic efficiency increases significantly . Since the overall transformation exhibits no net change in the redox state of the parties involved, how the enzyme-bound FAD plays an active role in the reaction mechanism is puzzling . In this paper, we report our study of the catalytic properties of UDP-Galp mutase reconstituted with deaza-FADs . It was found that the mutase reconstituted with FAD or 1-deazaFAD has comparable activity, while that reconstituted with 5-deazaFAD is catalytically inactive . Because 5-deazaFAD is restricted to net two-electron process, yet FAD and 1-deazaFAD can undergo concerted two-electron as well as stepwise one-electron redox reactions, the above results support a radical mechanism for the mutase catalyzed reaction . In addition, the activity of the mutase reconstituted with FAD was found to increase considerably at high pHs . These observations have allowed us to propose a new mechanism involving one-electron transfer from the reduced FAD to an oxocarbenium intermediate generated by C-1 elimination of UDP to give a hexose radical and a flavin semiquinone . Subsequent radical recombination leads to a coenzyme-substrate adduct which may play a central role to facilitate the opening and recyclization of the galactose ring . A deprotonation step, accompanied or followed the electron transfer step, to increase the nucleophilicity of the flavin radical anion may account for the activity enhancement at pH > 8. J Leukoc Biol, 2004 Jan, 75(1), 3 - 4 Epub 2003 Nov 11. Series introduction: Innate host defense of the respiratory epithelium; Hiemstra PS et al.; This series overviews the current knowledge of the innate-immune system of the lung . Special emphasis is put on mechanisms used by epithelial cells of the respiratory tract to contribute to host defense . This defense function is important, as the lung is especially prone to microbial exposure . The exchange of oxygen and carbon dioxide requires the ventilation of a large volume of environmental air that may contain respiratory pathogens . Furthermore, the digestive pathway shares with the airways the pharynx, opening another possibility for the uptake of microorganisms into the respiratory tract . Host defense is provided by a multilayered and complex system that aims to avoid colonization and infection of the lung . A classic view separates the inborn, innate-immune system from adaptive mechanisms that involve antigen-specific lymphocytes. Arch Dis Child, 2003 Nov, 88(11), 981 - 4 The potential of recombinant surfactant protein D therapy to reduce inflammation in neonatal chronic lung disease, cystic fibrosis, and emphysema; Clark H et al.; By lowering surface tension at the air-water interface in the surfactant deficient premature lung, exogenous surfactant replacement therapy for neonatal respiratory distress syndrome has been highly successful in decreasing mortality after preterm birth . It has emerged in recent years that surfactant components not present in current surfactant formulations--particularly surfactant associated proteins A and D (SP-A and SP-D)-have additional roles in host defence distinct from the surface tension lowering effects of surfactant . SP-A and SP-D are calcium dependent carbohydrate binding proteins of the innate immune system important in the first line defence of the lung against microorganisms and in the control of lung inflammation . This review addresses the possibility that recently developed recombinant forms of SP-D could be useful therapeutically in attenuating inflammatory processes in neonatal chronic lung disease, cystic fibrosis, and emphysema. J Ind Microbiol Biotechnol, 2003 Nov, 30(11), 627 - 35 Epub 2003 Nov 11. Detection and characterization of chitinases and other chitin-modifying enzymes; Howard MB et al.; Multiple industrial and medical uses of chitin and its derivatives have been developed in recent years . The demand for enzymes with new or desirable properties continues to grow as additional uses of chitin, chitooligosaccharides, and chitosan become apparent . Microorganisms, the primary degraders of chitin in the environment, are a rich source of valuable chitin-modifying enzymes . This review summarizes many methods that can be used to isolate and characterize chitin-modifying enzymes including chitin depolymerases, chitodextrinases, chitin deacetylases, N-acetylglucosaminidases, chitin-binding proteins, and chitosanases . Chitin analogs, zymography, detection of reducing sugars, genomic library screening, chitooligosaccharide electrophoresis, degenerate PCR primer design, thin layer chromatography, and chitin-binding assays are discussed. J Virol, 2003 Dec, 77(23), 12639 - 45 Blocking immune evasion as a novel approach for prevention and treatment of herpes simplex virus infection; Judson KA et al.; Many microorganisms encode immune evasion molecules to escape host defenses . Herpes simplex virus type 1 glycoprotein gC is an immunoevasin that inhibits complement activation by binding complement C3b . gC is expressed on the virus envelope and infected cell surface, which makes gC potentially accessible to blocking antibodies . Mice passively immunized with gC monoclonal antibodies prior to infection were protected against herpes simplex virus challenge only if the gC antibodies blocked C3b binding . Mice treated 1 or 2 days postinfection with gC monoclonal antibodies that block C3b binding had less severe disease than control mice treated with nonimmune immunoglobulin G (IgG) . Mice immunized with gC protein produced antibodies that blocked C3b binding to gC . Immunized mice were significantly protected against challenge by wild-type virus, but not against a gC mutant virus lacking the C3b binding domain, suggesting that protection was mediated by antibodies that target the gC immune evasion domain . IgG and complement from subjects immunized with an experimental herpes simplex virus glycoprotein gD vaccine neutralized far more mutant virus defective in immune evasion than wild-type virus, supporting the importance of immune evasion molecules in reducing vaccine potency . These results suggest that it is possible to block immune evasion domains on herpes simplex virus and that this approach has therapeutic potential and may enhance vaccine efficacy. Environ Monit Assess, 2003 Nov, 89(1), 35 - 41 Effect of common pesticides used in the Niger Delta basin of southern Nigeria on soil microbial populations; Ekundayo EO; The effects of eleven pesticides on the populations of bacteria, actinomycetes, fungi and protozoa was investigated by treating a garden soil with their recommended rates . The microbial populations were estimated using the standard plate-count technique . Of the 11 pesticides investigated, phenylmercuric acetate (agrosan) at 50 microg g(-1) inhibited bacterial density the most, i.e . from 4,600,000 to 220 cells g(-1) . The pesticides were Pentachloronitrobenzene (PCNB), tetramethylmethylthiuram disulphide (thiram), 1-naphthylmethylcarbamate (Vetox 85), 1,2,3,4,5,6-hexachlorocyclohexane (Gammalin 20), phenylmercuric acetate (Agrosan), tetrachloroterephthalic acid (Dacthal), 4-nitrophenyl-2-nitro-4-trifluoromethylphenyl ether (Preforan), 2-ethyl-6-methyl-N-2-methoxy-1-methyl ethyl-chloroacetanide (Dual), Benlate, Brestan and Gramoxone . Pentachloronitrobenzene (PCNB) at 240,000 microg g(-1) reduced bacterial population from 4,600,000 to 2,100 cells g(-1), whereas tetramethylthiuram disulphide (thiram) at 100 microg g(-1) suppressed it by 2 log orders of magnitude . Soil application of 1-naphthylmethylcarbamate (Vetox 85) at 100 microg g(-1) and 1,2,3,4,5,6,-hexachlorocyclohexane (Gamalin 20) at 1,300 microg g(-1) repressed the bacterial numbers by 2 log orders of magnitude each . Pentachloronitrobenzene reduced the actinomycetes density from 340,000 to 320 cells g(-1) and completely eliminated all fungal and protozoan propagules from the soil . The Gammalin 20 completely wiped out all the fungi, whereas phenylmercuric acetate totally eliminated all the protozoa and reduced the fungal population from 34,000 to 60 cells g(-1) . In general, protozoa and fungi were more susceptible to fungicides than bacteria and actinomycetes . Pentachloronitrobenzene, 1,2,3,4,5,6,-hexachlorocyclohexane and phenylmercuric acetate were toxic particularly to soil microorganisms, whereas the herbicides dacthal, Preforan and Dual were quite harmless in soil at application rates of 0.1, 0.06 and 0.02 microg g(-1) respectively. Arch Pharm Res, 2003 Oct, 26(10), 868 - 73 Differential effect of bovine serum albumin on ginsenoside metabolite-induced inhibition of alpha3beta4 nicotinic acetylcholine receptor expressed in Xenopus oocytes; Lee JH et al.; Ginsenosides, major active ingredients of Panax ginseng, that exhibit various pharmacological and physiological actions are transformed into compound K (CK) or M4 by intestinal microorganisms . CK is a metabolite derived from protopanaxadiol (PD) ginsenosides, whereas M4 is a metabolite derived from protopanaxatriol (PT) ginsenosides . Recent reports shows that ginsenosides might play a role as pro-drugs for these metabolites . In present study, we investigated the effect of bovine serum albumin (BSA), which is one of major binding proteins on various neurotransmitters, hormones, and other pharmacological agents, on ginsenoside Rg2-, CK-, or M4-induced regulation of alpha3beta4 nicotinic acetylcholine (ACh) receptor channel activity expressed in Xenopus oocytes . In the absence of BSA, treatment of ACh elicited inward peak current (I(ACh)) in oocytes expressing alpha3beta4 nicotinic ACh receptor . Co-treatment of ginsenoside Rg2, CK, or M4 with ACh inhibited I(ACh) in oocytes expressing (alpha3beta4 nicotinic ACh receptor with reversible and dose-dependent manner . In the presence of 1% BSA, treatment of ACh still elicited I(ACh) in oocytes expressing alpha3beta4 nicotinic ACh receptor and co-treatment of ginsenoside Rg2 or M4 but not CK with ACh inhibited I(ACh) in oocytes expressing alpha3beta4 nicotinic ACh receptor with reversible and dose-dependent manner . These results show that BSA interferes the action of CK rather than M4 on the inhibitory effect of I(ACh) in oocytes expressing alpha3beta4 nicotinic ACh receptor and further suggest that BSA exhibits a differential interaction on ginsenoside metabolites. C R Biol, 2003 Aug, 326(8), 739 - 50 {Viability of heterotrophic bacteria in the Bay of Marseilles}; Gregori G et al.; Marine microorganism activities are commonly assessed by bulk methods and assigned to the total cell count . The presence in significant amounts of ghost, dead, and damaged cells makes such as assignment a non-correct one . A Nucleic Acid Double Staining protocol (NADS) of fresh water bacteria (Barbesti et al., Cytometry 40 (2000) 214-218) has been adapted to resolve viable, damaged and dead cells in marine environments (Gregori et al., Appl . Environ . Microbiol . 67 (2001) 4662-4670) . The present reports the first in situ application of this approach, conducted in the Bay of Marseilles in winter and spring periods at two sites with contrasted features. Trends Microbiol, 2003 Nov, 11(11), 536 - 41 Genes and proteins involved in bacterial magnetic particle formation; Matsunaga T et al.; Magnetic bacteria synthesize intracellular magnetosomes that impart a cellular swimming behaviour referred to as magnetotaxis . The magnetic structures aligned in chains are postulated to function as biological compass needles allowing the bacterium to migrate along redox gradients through the Earth's geomagnetic field lines . Despite the discovery of this unique group of microorganisms 28 years ago, the mechanisms of magnetic crystal biomineralization have yet to be fully elucidated . This review describes the current knowledge of the genes and proteins involved in magnetite formation in magnetic bacteria and the biotechnological applications of biomagnetites in the interdisciplinary fields of nanobiotechnology, medicine and environmental management. J Clin Microbiol, 2003 Nov, 41(11), 5238 - 9 Evaluation of acridine orange staining as a replacement of subcultures for BacT/ALERT-positive, gram stain-negative blood cultures; Adler H et al.; Among 18,424 blood culture sets processed during a study period of 18 months, 85 bottles that were positive by the BacT/ALERT system were Gram stain negative . Both acridine orange staining and subcultures detected microorganisms in a total of 12 bottles . Acridine orange staining can replace subcultures of false-positive blood cultures. J Clin Microbiol, 2003 Nov, 41(11), 5153 - 8 Microarrays for genotyping human group a rotavirus by multiplex capture and type-specific primer extension; Lovmar L et al.; Human group A rotavirus (HRV) is the major cause of severe gastroenteritis in infants worldwide . HRV shares the feature of a high degree of genetic diversity with many other RNA viruses, and therefore, genotyping of this organism is more complicated than genotyping of more stable DNA viruses . We describe a novel microarray-based method that allows high-throughput genotyping of RNA viruses with a high degree of polymorphism by multiplex capture and type-specific extension on microarrays . Denatured reverse transcription (RT)-PCR products derived from two outer capsid genes of clinical isolates of HRV were hybridized to immobilized capture oligonucleotides representing the most commonly occurring P and G genotypes on a microarray . Specific primer extension of the type-specific capture oligonucleotides was applied to incorporate the fluorescent nucleotide analogue cyanine 5-labeled dUTP as a detectable label . Laser scanning and fluorescence detection of the microarrays was followed by visual or computer-assisted interpretation of the fluorescence patterns generated on the microarrays . Initially, the method detected HRV in all 40 samples and correctly determined both the G and the P genotypes of 35 of the 40 strains analyzed . After modification by inclusion of additional capture oligonucleotides specific for the initially unassigned genotypes, all genotypes could be correctly defined . The results of genotyping with the microarray fully agreed with the results obtained by nucleotide sequence analysis and sequence-specific multiplex RT-PCR . Owing to its robustness, simplicity, and general utility, the microarray-based method may gain wide applicability for the genotyping of microorganisms, including highly variable RNA and DNA viruses. Nucleic Acids Res . 2003 Nov 15;31(22):e139. Direct measurement of lymphocyte receptor diversity; Ogle BM et al.; The ability to mount an immune defense against infectious microorganisms and their products, and against tumors is believed to be a direct function of lymphocyte diversity . Because the diversity of lymphocyte receptor genes is >1000-fold more diverse than the entire genome and varies between genetically identical individuals, measuring lymphocyte diversity has been a daunting challenge . We developed a novel technique for measuring lymphocyte diversity directly using gene chips . We reasoned and here demonstrate that the frequency of hybridization of nucleic acids coding for lymphocyte receptors to the oligonucleotides on a gene chip varies in direct proportion to diversity . We applied the technique to detect changes in lymphocyte diversity in mice with known B cell alterations and in persons with known T cell repertoire defects . This approach is the first to provide direct analysis of lymphocyte receptor diversity and should facilitate fundamental study of the adaptive immune system and clinical efforts to assess immunological diseases . In addition, this approach could be more broadly applied, for example to measure diversity of viral quasi-species. Mol Cell Probes, 2003 Dec, 17(6), 289 - 94 A specific PCR for the detection of Mycoplasma putrefaciens, one of the agents of the contagious agalactia syndrome of goats; Peyraud A et al.; Mycoplasma putrefaciens is listed as one of the etiologic agents of the contagious agalactia syndrome by the world organisation for animal health . This species has been characterized only recently, 1974, and the number of outbreaks caused by this microorganism so far is very scarce . It induces mastitis in infected goats although other symptoms such as arthritis in adults and septicaemia in kids are also frequently described . Up to now, the identification of M . putrefaciens relied on classical isolation and identification techniques which present a number of limitations . Specific primers for PCR have been designed based on sequence comparisons of the ArcB gene among the 'Mycoplasma mycoides cluster' and related species such as Mycoplasma cottewii and Mycoplasma yeatsii . Sequence alignments confirmed the taxonomic position of M . putrefaciens, which is related to the 'M . mycoides cluster' but also very close to M . yeatsii . The polymorphism observed amongst the different ArcB sequences allowed the determination of a primer pair yielding a specific amplification of a 316 bp-long DNA fragment by PCR . This PCR was validated in two different laboratories with a variety of mycoplasma strains isolated from goats . This new PCR technique will be very useful for a quicker determination of M . putrefaciens strains as well as a better understanding of the prevalence of M . putrefaciens infections. Biometrics, 2003 Sep, 59(3), 505 - 11 Estimating the accuracy of polymerase chain reaction-based tests using endpoint dilution; Hughes JP et al.; Polymerase chain reaction (PCR)-based tests for various microorganisms or target DNA sequences are generally acknowledged to be highly "sensitive," yet the concept of sensitivity is ill-defined in the literature on these tests . We propose that sensitivity should be expressed as a function of the number of target DNA molecules in the sample (or specificity, when the target number is 0) . However, estimating this "sensitivity curve" is problematic, since it is difficult to construct samples with a fixed number of targets . Nonetheless, using serially diluted replicate aliquots of a known concentration of the target DNA sequence, we show that it is possible to disentangle random variations in the number of target DNA molecules from the underlying test sensitivity . We develop parametric, nonparametric, and semiparametric (spline-based) models for the sensitivity curve . The methods are compared on a new test for M . genitalium. Environ Technol, 2003 Sep, 24(9), 1097 - 102 Toxicity of heavy metals for microorganisms isolated from slow sand filter schmutzdecke; Muhammad N et al.; This paper describes the susceptibility of three species of environmental bacteria isolated from the schmutzdecke of biologically active slow sand filters to cadmium, chromium and lead . The microorganisms, all identified as members of the genus Pseudomonas, were grown in tryptic soy broth with various concentrations of the selected heavy metals . The mean generation times (MGT) of the bacteria were compared to evaluate the toxic effects of the heavy metals . All three species tolerated high doses of heavy metals and the MGTs increased exponentially as the heavy metal concentrations increased; 12 mg l(-1) was the highest dose tested and the bacteria continued to grow albeit at very slow rates . In dilute media, the toxic effects of heavy metals were enhanced, illustrating the protection effect of organic matter and heavy metal complex formation . Growth studies of the isolated microorganisms on half-strength tryptic soy agar containing 6 mg l(-1) heavy metals also proved useful in determining toxicity. Org Biomol Chem, 2003 Oct 21, 1(20), 3500 - 6 The first fluorogenic assay for detecting a Baeyer-Villigerase activity in microbial cells; Gutierrez MC et al.; The first fluorogenic assay allowing for detection of microbial enzymes able to perform Baeyer-Villiger oxidation is described . This is based on the use of 4-oxopentyl umbelliferyl ether 1 as a fluorogenic substrate . When Baeyer-Villigerases active against this test ketone are present in the selected whole cells, 1 is transformed into 3-hydroxypropyl umbelliferyl ether 3, which, in a subsequent step, releases the fluorescent product umbelliferone . Different microorganisms, known to be endowed with Baeyer-Villigerase activity, were assayed. Vestn Ross Akad Med Nauk, 2003, (9), 37 - 9 {Polymerase chain reaction in the diagnosis of viral infections in the newborn}; Asadi Mobarkhan SM et al.; Two hundred and ten newborns from among a high risk group were examined for intrauterine infections by polymerase chain reaction (PCR) with the aim of assessing the clinical information density of the method in the diagnostic sphere . The patients were examined for the presence of DNA/RNA viruses and bacteria . Genetic samples of various causative agents were detected in 49% of the newborns . No correlation was established between the clinical pattern and the presence of DNA of certain microorganisms . The most severe condition of newborns was noted in cases when a DNA causative agent was found in several different biological samples . The highest mortality (in per cent) was registered in the group of newborns with detected DNA of Herpesviridae viruses . The PCR clinical value was affirmed for establishing a disease etiology in newborns. J Biomed Mater Res B Appl Biomater, 2003 Nov 15, 67(2), 675 - 9 Electrospun nanofibrous polyurethane membrane as wound dressing; Khil MS et al.; Produced via electrospinning, polyurethane membrane, which has a unique property, has been of interest in medical fields . Electrospinning is a process by which nanofibers can be produced by an electrostatically driven jet of polymer solution . Electrospun fibers are collected in the form of membranes . The porous structured electrospun membrane is particularly important for its favorable properties: it exudates fluid from the wound, does not build up under the covering, and does not cause wound desiccation . The electrospun nanofibrous membrane shows controlled evaporative water loss, excellent oxygen permeability, and promoted fluid drainage ability, but still it can inhibit exogenous microorganism invasion because its pores are ultra-fine . Histological examination indicates that the rate of epithelialization is increased and the dermis becomes well organized if wounds are covered with electrospun nanofibrous membrane . This electrospun membrane has potential applications for wound dressing based upon its unique properties . J Leukoc Biol, 2004 Mar, 75(3), 428 - 33 Epub 2003 Nov 03. Shielding the double-edged sword: negative regulation of the innate immune system; Kobayashi KS et al.; The innate immune system is evolutionarily conserved among all multicellular organisms and is the first line of defense against microorganisms . It enables the host not only to combat pathogenic organisms but also to cohabit with nonpathogenic microorganisms by balancing the host-microorganism interaction . The innate immune response is activated rapidly (within hours) compared with adaptive immunity . Activation of the innate immune system allows the activation of the adaptive immune response by production of proinflammatory cytokines and by providing stimulatory signals via major histocompatibility complex molecules and costimulatory molecules such as CD40, CD80, or CD86; together, these lead to the full activation of both immune systems to fight against pathogenic microorganisms . Activation of the innate immune system, however, can be a double-edged sword for the host . Proinflammatory cytokines mediate a positive feedback loop on the innate immune system, and overproduction of cytokines, if unchecked, is hazardous to the host and may cause severe outcomes such as hyperthermia, organ failure, and even death in extreme cases . Moreover, if the overproduction of proinflammatory cytokines persists, it may cause chronic inflammatory diseases . During evolution, the innate immune system has acquired complicated regulatory systems to control itself so that this "sword" will not kill the host . Various mechanisms including inhibition of Toll-like receptor signaling by interleukin-1 receptor-associated kinase-M have evolved for this purpose and are important not only to fight against pathogenic microorganisms efficiently but also are critical for the peaceful coexistence with commensal bacterial flora. Riv Biol, 2003 May-Aug, 96(2), 317 - 26 The microbial DNA cycle in soil; England LS et al.; Upon microbial cell death and lysis in soil, the free or naked DNA is exposed to the dynamic environment of the soil . The DNA can be enzymatically degraded by nucleases (DNases), bind to soil components, genetically transform competent bacterial cells and be a nutrient for other microorganisms . In this article we discuss the dual role of DNA as genetic material and as a nutrient source in the soil environment. Riv Biol, 2003 May-Aug, 96(2), 271 - 91 Measure of species variability for a microbial taxonomy based on the relative resemblance; Cardinali G; The concept of species currently in use in microbial taxonomy is based on sex because derives from that developed in zoology and botany . The absence of sex as the only system to reproduce does not allow to use the hybridization as the test to assess the conspecificity of microbial strains, forcing microbial taxonomists to use relative resemblance among strains as the only tool to define microbial species and to classify new microorganisms . Relative resemblance can be intuitively defined as the situation in which two strains of the same species must be more similar than each of them with a strain of any other species . Unfortunately, there are several algorithms to define the similarity between two strains, but none can be used to estimate the average distance between several members of the same species . This paper describes the problems inherent with the definition of species without hybridization tests and proposes two algorithms for a standard estimation of the overall variability of a species with the data obtained from a sample of strains . These measures will allow the non-subjective determination of the overall similarity among members of the same species using results from both phenotypic and molecular analyses . Both algorithms are based on a bootsrapping procedure implemented by RHO and SMA, two software applications freely available from the internet . These applications allow an easy evaluation of parameters such as the overall variability and levels of confidence associated with the sample of strains and the panel of characters under study. Riv Biol, 2003 May-Aug, 96(2), 241 - 60 The contribution of plant biology to the concept of virus (1886-1917); Pennazio S; Between 1860 and 1880 the so-called "theory of the infective germ", which stated in final way that every infectious disease was produced by a living pathogen agent, achieved great consent . The criteria of determining the presence of infectious pathogens (fungi, bacteria, protozoa) were established by "Koch's postulate", a set of experimental procedures conceived for isolating and determining single pathogens . In the last quarter of the 19th century became however evident that the agents of severe infectious diseases could not be identified through the "postulates" . These agents could not be seen in light microscopy nor cultured in vitro but could pass through the thin pores of filters which hold back cellular micro-organisms . This last characteristic became a selective method to recognise these peculiar agents, from then named "filterable viruses" . Most microbiologists considered the filterable viruses as living micro-organisms because of their extraordinary capacity of in vivo proliferation, and the impossibility of pointing out their structures was due to limits of the experimental techniques . Between the end of the 19th century and 1917, four plant biologists suggested that the filterable viruses were complex chemical substances rather than cellular microorganisms . Their contribution, not appreciated by the contemporary colleagues, laid the foundation of the modern concept of virus. Biotechnol Bioeng, 2003 Dec 20, 84(6), 700 - 9 Data reconciliation and parameter estimation in flux-balance analysis; Raghunathan AU et al.; Flux blance analysis (FBA) has been shown to be a very effective tool to interpret and predict the metabolism of various microorganisms when the set of available measurements is not sufficient to determine the fluxes within the cell . In this methodology, an underdetermined stoichiometric model is solved using a linear programming (LP) approach . The predictions of FBA models can be improved if noisy measurements are checked for consistency, and these in turn are used to estimate model parameters . In this work, a formal methodology for data reconciliation and parameter estimation with underdetermined stoichiometric models is developed and assessed . The procedure is formulated as a nonlinear optimization problem, where the LP is transformed into a set of nonlinear constraints . However, some of these constraints violate standard regularity conditions, making the direct numerical solution very difficult . Hence, a barrier formulation is used to represent these constraints, and an iterative procedure is defined that allows solving the problem to the desired degree of convergence . This methodology is assessed using a stoichiometric yeast model . The procedure is used for data reconciliation where more reliable estimations of noisy measurements are computed . On the other hand, assuming unknown biomass composition, the procedure is applied for simultaneous data reconciliation and biomass composition estimation . In both cases it is verified that the f measurements required to get unbiased and reliable estimations is reduced if the LP approach is included as additional constraints in the optimization . Biotechnol Bioeng, 2003 Dec 20, 84(6), 627 - 38 Non-thermal bacterial inactivation with dense CO(2); Spilimbergo S et al.; The use of CO(2) under pressure (dense CO(2)) is one of the most promising techniques to achieve cold pasteurization and/or sterilization of liquid and solid materials, and is likely to replace or partially substitute currently and widely applied thermal processes . Although the ability of CO(2) to inactivate microorganisms has been known since the 1950's, only within the last 15 years it has received special attention, and the scientific and economic interest towards practical applications is presently growing more and more . Here we collect and discuss the relevant current knowledge about the potentials of dense CO(2) as a non-thermal technology in the field of microbial inactivation . We summarize the state of the art, including definitions, description of the equipment, relevant applications, in both simple suspensions and complex media, for the treatment of a wide range of microorganisms in both liquid and solid substrates . Finally, we also summarize and discuss the different hypotheses about the mechanisms of inactivation . Appl Microbiol Biotechnol, 2004 Apr, 64(3), 410 - 5 Epub 2003 Nov 01. A thermodynamic interpretation of cell hydrophobicity in aerobic granulation; Liu Y et al.; Aerobic granulation can be regarded as a microorganism-to-microorganism self-immobilization process, in which cell hydrophobicity could be a decisive parameter in determining the microorganism-to-microorganism interaction and structural compactness of aerobic granules . This study looked into the thermodynamic interpretation of cell hydrophobicity in aerobic granulation; and a model that correlates microbial interaction and relative cell hydrophobicity defined as the ratio of cell hydrophobicity over cell hydrophilicity was derived . This model describes how cell hydrophobic and hydrophilic interactions affect aerobic granulation and offers deep insights into the thermodynamic mechanisms of microbial aggregation . The model prediction was in good agreement with experimental data . Results showed that aerobic granulation was a function of cell hydrophobicity over cell hydrophilicity, i.e . a high cell hydrophobicity strongly favors microbial aggregation and results in a more compact structure. Curr Top Microbiol Immunol, 2004, 282, 1 - 30 Phosphoinositide involvement in phagocytosis and phagosome maturation; Botelho RJ et al.; Cells of the innate immune system engulf invading microorganisms into plasma membrane-derived vacuoles called phagosomes . Newly formed phagosomes gradually acquire microbicidal properties by a maturation process which involves sequential and coordinated rounds of fusion with endomembranes and concomitant fission . Some pathogens interfere with this maturation sequence and thereby evade killing by the immune cells, managing to survive intracellularly as parasites . Phosphoinositides seem to be intimately involved in the processes of phagosome formation and maturation, and initial observations suggest that the ability of some microorganisms to survive intracellularly is associated with alterations in phosphoinositide metabolism . This chapter presents a brief overview of phosphoinositides in cells of the immune system, their metabolism in the context of phagocytosis and phagosome maturation and their possible derangements during infectious pathogenosis. Mikrobiyol Bul, 2003 Apr-Jun, 37(2-3), 215 - 21 {Medical importance of yeast killer toxin}; Cerikcioglu N; Yeast killer toxins (YKT) are exotoxins produced by several yeasts including certain Candida species . They can kill fungi, bacteria and even protozoa by binding to the specific receptors on their cell surfaces . On the basis of their killer effect, studies have been carried out on the differentiation of fungi and some bacteria by using YKT as epidemiological tools . Following biotyping procedures, idiotypic and anti-idiotypic antibodies produced against YKT have been shown to exhibit great potential in protection and immunotherapy against several microorganisms, promising as novel approaches to fight against microbial diseases . In this review article, the structural properties, ecologic and epidemiologic importance, therapeutic, prophylactic and immunotherapy studies of yeast killer toxins, have been discussed. Crit Rev Microbiol, 2003, 29(3), 215 - 21 Cell wall-deficient (CWD) bacterial pathogens: could amylotrophic lateral sclerosis (ALS) be due to one? Koch AL. Recently, a number of diseases that had been thought previously to be caused by something other than an infectious agent are now known to be caused by bacteria . It now appears that it is not uncommon that bacteria, viruses, or fungi can cause diseases even when these organisms have not been detected or cultured . The most recent, well-publicized case is that of stomach ulcers; these are largely due to Helicobacter pylori infections . Here, the possibility is explored that amylotrophic lateral sclerosis (ALS) is caused by a cell wall-deficient microorganism. Biofizika, 2003 Sep-Oct, 48(5), 940 - 9 {Spectral studies of a single cell of marine microplankton . History and perspectives}; Karnaukhov VN et al.; Methods and instruments for the spectral analysis of single cells of sea microplankton under the conditions of expeditions to the Mediterranean Sea and tropical zone of the Atlantic Ocean were proposed . Special emphasis was given to the ways of adaptation of sea microplankton communities to unfavorable environment with the formation of autotrophic and heterotrophic symbiont organisms (Radiolarian, Foraminifera, etc.) having closed cycles of phosphate metabolism and variotrophic microorganisms (Cyanophyceae and Dinoflagellata class). Genetika, 2003 Sep, 39(9), 1180 - 4 {Induction of SOS-response of cells exposed to autoregulatory factors of microorganisms}; Margulis AB et al.; Among examined microbial growth regulators of alkyl hydroxybenzene group (hexylresorcinol, methylresorcinol, and hydroxyethylphenol), only hexylresorcinol induces cellular SOS response, demonstrating a dose-dependent increase of the induction factor in the SOS chromotest with the Escherichia coli PQ37 strain . At the highest of used concentrations (100 micrograms/ml), hydroxyethylphenol and nonalkylated resorcinol were shown to exert a weak toxic effect, reducing the activity of constitutive alkaline phosphatase, but did not induce SOS response . Nontoxic methylresorcinol did not induce genome damage, which can trigger SOS functions . It is concluded that substitutions in phenolic ring affect genotoxic activity of alkylresorcinols. Chemosphere, 2004 Jan, 54(4), 569 - 74 Plant uptake of aldicarb from contaminated soil and its enhanced degradation in the rhizosphere; Sun H et al.; Experiments were conducted to investigate the degradation of aldicarb, an oxime carbamate insecticide, in sterile, non-sterile and plant-grown soils, and the capability of different plant species to accumulate the pesticide . The degradation of aldicarb in soil followed first-order kinetics . Half lives (t1/2) of aldicarb in sterile and non-sterile soil were 12.0 and 2.7 days, respectively, which indicated that microorganisms played an important part in the degradation of aldicarb in soil . Aldicarb disappeared more quickly (p< or =0.05) in the soil with the presence of plants, and t1/2 of the pesticide were 1.6, 1.4 and 1.7 days in the soil grown with corn, mung bean and cowpea, respectively . Comparison of plant-promoted degradation and plant uptake showed that the enhanced removal of aldicarb in plant-grown soil was mainly due to plant-promoted degradation in the rhizosphere. Bioessays, 2003 Nov, 25(11), 1119 - 28 Pathogenic archaea: do they exist? Cavicchioli R, Curmi PM, Saunders N, Thomas T. Archaea are microorganisms that are distinct from bacteria and eukaryotes . They are prevalent in extreme environments, and yet found in most ecosystems . They are a natural component of the microbiota of most, if not all, humans and other animals . Despite their ubiquity and close association with humans, animals and plants, no pathogenic archaea have been identified . Because no archaeal pathogens have yet been identified, there is a general assumption that archaeal pathogens do not exist . This review examines whether this is a good assumption by investigating the potential for archaea to be or become pathogens . This is achieved by addressing: the diversity of archaea versus known pathogens, opportunities for archaea to demonstrate pathogenicity and be detected as pathogens, reports linking archaea with disease, and immune responses to archaea . In addition, molecular and genomic data are examined for the presence of systems utilised in pathogenesis . The view of this report is that, although archaea can presently be described as non-pathogenic, they have the potential to be (discovered as) pathogens . The present optimistic view that there are no archaeal pathogens is tainted by a severe lack of relevant knowledge, which may have important consequences in the future . Astrobiology, 2003 Summer, 3(2), 393 - 406 Temperature and moisture conditions for life in the extreme arid region of the Atacama desert: four years of observations including the El Niño of 1997-1998; McKay CP et al.; The Atacama along the Pacific Coast of Chile and Peru is one of the driest and possibly oldest deserts in the world . It represents an extreme habitat for life on Earth and is an analog for life in dry conditions on Mars . We report on four years (September 1994-October 1998) of climate and moisture data from the extreme arid region of the Atacama . Our data are focused on understanding moisture sources and their role in creating suitable environments for photosynthetic microorganisms in the desert surface . The average air temperature was 16.5 degrees C and 16.6 degrees C in 1995 and 1996, respectively . The maximum air temperature recorded was 37.9 degrees C, and the minimum was -5.7 degrees C . Annual average sunlight was 336 and 335 W m(-2) in 1995 and 1996, respectively . Winds averaged a few meters per second, with strong fohn winds coming from the west exceeding 12 m s(-1) . During our 4 years of observation there was only one significant rain event of 2.3 mm, which occurred near midnight local time . We suggest that this event was a rainout of a heavy fog . It is of interest that the strong El Nino of 1997-1998 brought heavy rainfall to the deserts of Peru, but did not bring significant rain to the central Atacama in Chile . Dew occurred at our station frequently following high nighttime relative humidity, but is not a significant source of moisture in the soil or under stones . Groundwater also does not contribute to surface moisture . Only the one rain event of 2.3 mm resulted in liquid water in the soil and beneath stones for a total of only 65-85 h over 4 years . The paucity of liquid water under stones is consistent with the apparent absence of hypolithic (under-stone) cyanobacteria, the only known primary producers in such extreme deserts. Astrobiology, 2003 Summer, 3(2), 343 - 50 Subfreezing activity of microorganisms and the potential habitability of Mars' polar regions; Jakosky BM et al.; The availability of water-ice at the surface in the Mars polar cap and within the top meter of the high-latitude regolith raises the question of whether liquid water can exist there under some circumstances and possibly support the existence of biota . We examine the minimum temperatures at which liquid water can exist at ice grain-dust grain and ice grain-ice grain contacts, the minimum subfreezing temperatures at which terrestrial organisms can grow or multiply, and the maximum temperatures that can occur in martian high-latitude and polar regions, to see if there is overlap . Liquid water can exist at grain contacts above about -20 degrees C . Measurements of growth in organisms isolated from Siberian permafrost indicate growth at -10 degrees C and metabolism at -20 degrees C . Mars polar and high-latitude temperatures rise above -20 degrees C at obliquities greater than ~40 degrees, and under some conditions rise above 0 degrees C . Thus, the environment in the Mars polar regions has overlapped habitable conditions within relatively recent epochs, and Mars appears to be on the edge of being habitable at present . The easy accessibility of the polar surface layer relative to the deep subsurface make these viable locations to search for evidence of life. Life Sci, 2003 Nov 21, 74(1), 87 - 97 A novel and potent biological antioxidant, Kinobeon A, from cell culture of safflower; Kanehira T et al.; Kinobeon A was originally isolated from cultured cells of safflower (Carthamus tinctorius L., Compositae) . It had never previously been directly isolated from safflower or other plants, animals or microorganisms . In this report, we demonstrate the anti-oxidative effects of kinobeon A and compare the results with those two known natural antioxidants, lignan (nordihydroguaiaretic acid) and quercetin . The NADPH-induced microsomal lipid peroxidation system was employed to assess anti-oxidative effects of kinobeon A . Addition of kinobeon A to the system significantly decreased the formation of thiobarbituric acid reactive substances (TBARS) in a dose-dependent manner with effects similar to those of lignan and quercetin . Formation of TBARS was completely inhibited at 10 microM of kinobeon A . Employing the xanthine/xanthine oxidase/nitroblue tetrazolium system and the KO2/XTT system, the superoxide anion scavenging activity of kinobeon A was greater than that of lignan or quercetin . IC50 values calculated for kinobeon A in these two systems were 1 microM and 0.8 microM, respectively . Kinobeon A exerted cytoprotective effects following oxidative treatments with hydrogen peroxide, cumene hydroperoxide, menadione and xanthine oxidase (XOD) . Addition of kinobeon A to the systems markedly enhanced survival ratios of Madin-Darby bovine kidney cells, while their survival significantly decreased with the oxidative treatment alone . Kinobeon A exhibited stronger effect on the cell viability than lignan or quercetin when menadion or XOD were used as inducing reagents of oxidative stress . The present study demonstrates for the first time that kinobeon A prevents oxidative stresses and could be a useful cytoprotective reagent. Chemosphere, 2004 Jan, 54(3), 225 - 33 The degradability of biodegradable plastics in aerobic and anaerobic waste landfill model reactors; Ishigaki T et al.; Degradabilities of four kinds of commercial biodegradable plastics (BPs), polyhydroxybutyrate and hydroxyvalerate (PHBV) plastic, polycaprolactone plastic (PCL), blend of starch and polyvinyl alcohol (SPVA) plastic and cellulose acetate (CA) plastic were investigated in waste landfill model reactors that were operated as anaerobically and aerobically . The application of forced aeration to the landfill reactor for supplying aerobic condition could potentially stimulate polymer-degrading microorganisms . However, the individual degradation behavior of BPs under the aerobic condition was completely different . PCL, a chemically synthesized BP, showed film breakage under the both conditions, which may have contributed to a reduction in the waste volume regardless of aerobic or anaerobic conditions . Effective degradation of PHBV plastic was observed in the aerobic condition, though insufficient degradation was observed in the anaerobic condition . But the aeration did not contribute much to accelerate the volume reduction of SPVA plastic and CA plastic . It could be said that the recalcitrant portions of the plastics such as polyvinyl alcohol in SPVA plastic and the highly substituted CA in CA plastic prevented the BP from degradation . These results indicated existence of the great variations in the degradability of BPs in aerobic and anaerobic waste landfills, and suggest that suitable technologies for managing the waste landfill must be combined with utilization of BPs in order to enhance the reduction of waste volume in landfill sites. Biotechnol Bioeng, 2003 Dec 5, 84(5), 544 - 51 Swirling flow implementation in a photobioreactor for batch and continuous cultures of Porphyridium cruentum; Muller-Feuga A et al.; Light is the main limiting factor in photoautotrophic-intensive production of microorganisms, and improvement of its use is an important concern for photobioreactor design and operation . Swirling flows, which are known to improve mass and photon transfers, were applied to annular light chambers of a photobioreactor and studied by simulation and microalgal culture . Two hydrodynamic conditions were compared: axial flow generating poor radial mixing, and tangential flow generating three-dimensional swirling motion . Batch and continuous cultures of the Rhodophyte Porphyridium cruentum were performed in a 100-L, 1.5-m(2), fully controlled photobioreactor with eight light chambers . The inlet design of these chambers was modified to create the hydrodynamic conditions for comparison . Various intensities of swirling motion were used, characterized by the velocity factor (VF), defined as the ratio between annular chamber flow and inlet aperture sections . Experiments were performed within the range of photon flux densities (PFD) optimizing the yield of light energy transformation into living substance for the species and the temperature used . Culture kinetics with swirling flows generated by apertures of VF = 2, 4, and 9 were compared with pseudoaxial VF = 2 chosen as reference . Batch cultures with VF = 4 swirling flow showed no significant difference, whereas continuous cultures proved more discriminating . Although no significant difference was obtained for VF = 2, a 7% increase of steady-state productivity and a 26% decrease in time required to reach this steady state were obtained with VF = 4 swirling flow . This beneficial effect of swirling flow could have accounted for increased mixing . Conversely, VF = 9 swirling flow resulted in a 9% decrease of steady-state productivity and a 9% increase in the time required to reach this steady state, a negative effect that could have accounted for increased shear stress . CO(2) bioconversion yield at steady state showed a 34% increase for VF = 4 . These results suggest that swirling motion makes microalgal cultures more efficient, provided that the resulting adverse effects remain acceptable . Experimental investigation was completed by a theoretical approach in which simulation of continuous cultures of P . cruentum was based on the hydrodynamic conditions achieved in the photobioreactor . Although the results obtained with pseudoaxial flow were correctly predicted, simulations with swirling flow showed a marked enhancement of productivity not observed experimentally . The influence of side effects induced by increased mixing (particularly hydrodynamic shear stress) was considered with respect to modeling assumptions . Comparison of experimental results with theoretical simulation provided a better understanding of the mixing effect, a key factor in improving the efficiency of such bioprocesses . Curr Opin Microbiol, 2003 Oct, 6(5), 446 - 51 Multidrug efflux pumps and resistance: regulation and evolution; Paulsen IT; Multidrug transporters have long puzzled researchers because of their ability to extrude multiple structurally dissimilar toxic chemotherapeutic agents . They appear to be essentially ubiquitous with many microorganisms possessing large arsenals of predicted multidrug efflux transporters . Recent reports on the structures of multidrug efflux transporters and their cognate regulators have suggested that the basis of multidrug recognition is the presence of large flexible hydrophobic cavities capable of accommodating different compounds that are bound via hydrogen bonding and/or electrostatic interactions . This structural data provides the context for understanding other questions about the evolution of multidrug transporters and their natural physiological roles. Enferm Infecc Microbiol Clin, 2003 Nov, 21(9), 484 - 7 {In vitro activity of voriconazole and three other antifungal agents against dermatophytes}; Serrano-Martino Mdel C et al.; INTRODUCTION: The increase in infections due to dermatophytes in recent years led us to study the effectiveness of new antifungal formulations against these microorganisms . METHODS: The in vitro activity of a new antifungal agent, voriconazole, was compared with three other antifungal agents, itraconazole, fluconazole and terbinafine, against 120 dermatophytes belonging to four species (61 Trichophyton mentagrophytes, 34 Microsporum canis, 13 M . gypseum and 12 T . rubrum) . A broth microdilution method was used following the recommendations of the NCCLS document M38-P with some modifications . RESULTS: Terbinafine was the most active agent against the dermatophytes studied (MIC90 < or = 0.03 mg/ml), followed by voriconazole (MIC90, 0.25 micro g/ml) and itraconazole (MIC90, 0.5 micro g/ml) . Fluconazole was the least active antifungal agent . The most susceptible species was M . canis . CONCLUSIONS: Voriconazole was found to have effective activity against dermatophytes. Anal Chem, 2003 Aug 1, 75(15), 3817 - 22 Microorganism identification by matrix-assisted laser/desorption ionization mass spectrometry and model-derived ribosomal protein biomarkers; Pineda FJ et al.; An improved data analysis method is described for rapid identification of intact microorganisms from MALDI-TOF-MS data . The method makes no use of mass spectral fingerprints . Instead, a microorganism database is automatically generated that contains biomarker masses derived from ribosomal protein sequences and a model of N-terminal Met loss . We quantitatively validate the method via a blind study that seeks to identify microorganisms with known ribosomal protein sequences . We also include in the database microorganisms with incompletely known sets of ribosomal proteins to test the specificity of the method . With an optimal MALDI protocol, and at the 95% confidence level, microorganisms represented in the database with 20 or more biomarkers (i.e., those with complete or nearly completely sequenced genomes) are correctly identified from their spectra 100% of the time, with no incorrect identifications . Microorganisms with seven or less biomarkers (i.e., incompletely sequenced genomes) are either not identified or misidentified . Robustness with respect to variations in sample preparation protocol and mass analysis protocol is demonstrated by collecting data with two different matrixes and under two different ion-mode configurations . Statistical analysis suggests that, even without further improvement, the method described here would successfully scale up to microorganism databases with roughly 1000 microorganisms . The results demonstrate that microorganism identification based on proteome data and modeling can perform as well as methods based on mass spectral fingerprinting. FEMS Microbiol Lett, 2003 Oct 10, 227(1), 87 - 92 A generalized transducing thiophage (TPC-1) of a facultative sulfur chemolithotrophic bacterium, Bosea thiooxidans CT5, of alpha-Proteobacteria, isolated from Indian soil; Deb C et al.; We have isolated and characterized a double-stranded DNA bacteriophage (TPC-1) of Bosea thiooxidans, a facultative sulfur chemolithotrophic bacterium . The name 'thiophage' is introduced for phage(s) infecting sulfur chemolithotrophic bacteria . Electron micrographs showed the phage particle with an icosahedral head and a very short wedge-like tail . TPC-1 is classified as the C1 morphotype of the Podoviridae family . Restriction map and terminal ends detection by end fill labeling of the TPC-1 genomic DNA showed that the genome is linear with 5' protruding cohesive termini . Contour length mapping of the DNA genome also revealed it to be a linear fragment with size ( approximately 44 kb) corresponding with the size estimated from restriction fragment analyses and proved the non-redundant nature of the linear genome topology . In colorless sulfur chemolithotrophic microorganisms, TPC-1 is the first report of a generalized transducing thiophage. J Biomol Screen, 2003 Oct, 8(5), 559 - 65 A high-throughput amenable colorimetric assay for enantioselective screening of nitrilase-producing microorganisms using pH sensitive indicators; Banerjee A et al.; Based on the color change of an indicator due to the release of hydrogen ion from a nitrilase-catalyzed reaction, a rapid colorimetric method was established for the enantioselective screening of nitrilase-producing microorganisms . The formation of acids due to the nitrilase-mediated hydrolysis of nitriles causes a drop in the pH, which in turn results in a change of color of the solution (containing indicator) that can be observed visually . The buffer (0.01 M phosphate, pH 7.2) and indicator (Bromothymol blue, 0.01%) were selected in such a way that both have the same affinity for the released protons . The enantioselectivity of nitrilases was estimated by comparing the hydrolysis of (R)-mandelonitrile with that of racemate under the same conditions . The method was used to screen a library of nitrilase-producing microorganisms, isolated in the authors' laboratory for their ability to enantioselectively hydrolyze mandelonitrile to mandelic acid, an important chiral building block. Internist (Berl), 2003 Sep, 44(9), 1180 - 5 {A 41 year-old male patient with fever of unknown origin and bacteremia with actinobacillus actinomycetemcomitans}; Rosenkranz S et al.; A 41-year-old male patient presented with fever of unknown origin which had been present for 5 months . The primary diagnostic procedures did not identify an infectious focus . After a lag phase of 13 days, blood cultures became positive for Actinobacillus actinomycetemcomitans, which belongs to the HACEK group of microorganisms . According to the DUKE criteria, infective endocarditis was diagnosed despite negative transesophageal echocardiography (TEE) . The sensitivity of TEE is estimated between 86 and 94% . An infected tooth was extracted as a possible focus, and the patient was treated with i.v . antibiotics for 5 weeks according to the guidelines of the AHA and ACC . The fever was permanently terminated, and the further course of the patient was uneventful . Despite negative TEE, the diagnosis "infective endocarditis" should not be rejected, and blood cultures should be grown for up to 30 days. Appl Microbiol Biotechnol, 2003 Dec, 63(3), 249 - 57 Epub 2003 Oct 18. Bioleaching review part B: progress in bioleaching: applications of microbial processes by the minerals industries; Olson GJ et al.; This review describes the historical development and current state of metals leaching and sulfide mineral biooxidation by the minerals industries . During the past 20 years commercial processes employing microorganisms for mineral recovery have progressed from rather uncontrolled copper dump leaching to mineral oxidation and leaching in designed bioheaps for oxidation of refractory gold ores and for copper recovery . Also during this period of time, stirred tank bioleaching has been commercialized for cobalt recovery and for biooxidation of refractory gold ores . Chalcopyrite bioleaching in stirred tanks is on the verge of commercialization . Commercial applications of biohydrometallurgy have advanced due to favorable process economics and, in some cases, reduced environmental problems compared to conventional metal recovery processes such as smelting . Process development has included recognition of the importance of aeration of bioheaps, and improvements in stirred tank reactor design and operation . Concurrently, knowledge of the key microorganisms involved in these processes has advanced, aided by advances in molecular biology to characterize microbial populations. ORL J Otorhinolaryngol Relat Spec, 2003 Jul-Aug, 65(4), 202 - 5 Local pathogenic bacteria in allergic rhinitis: a novel concept of its pathogenesis; Gluck U et al.; BACKGROUND: It is still unclear to what extent microorganisms are involved in the pathogenesis of allergic rhinitis . OBJECTIVE: Therefore, we examined the mucosal colonization with potential pathogenic bacteria (PPB) of the nasal cavity in allergic and nonallergic subjects . METHODS: In an open prospective study of 389 office workers (297 men, mean age 42.5 years, and 92 women, mean age 36.7 years), bacterial swabs were taken selectively from both nasal cavities . Standard skin tests for various aeroallergens and negative control tests were conducted in parallel in these subjects . RESULTS: In the 389 subjects, we found positive skin tests in 58 (15%); 37 of these revealed a high level of sensitivity, whilst the other 21 persons had low to moderate levels . Ninety percent of the 58 sensitive persons had PPB in their nasal cavity while only 36% (119) of the remaining 331 subjects with negative skin tests were shown to have PPB in nasal cultures (p < 0.001) . Sixty-four percent of the sensitized subjects with PPB were found to have more than 2 PPB species and a positive correlation with the intensity of the skin reaction . In contrast, only 18% (22) of the 119 nonallergic test persons with PPB had more than 1 PPB species . CONCLUSIONS: This finding of an unusually high frequency of nasal PPB in subjects with positive skin tests to aeroallergens may indicate an involvement of PPB in the pathogenesis of allergic rhinitis . Yet, further data are still lacking to support this novel concept . J Bacteriol, 2003 Nov, 185(21), 6385 - 91 Investigation of the role of electrostatic charge in activation of the Escherichia coli response regulator CheY; Smith JG et al.; In a two-component regulatory system, an important means of signal transduction in microorganisms, a sensor kinase phosphorylates a response regulator protein on an aspartyl residue, resulting in activation . The active site of the response regulator is highly charged (containing a lysine, the phosphorylatable aspartate, two additional aspartates involved in metal binding, and an Mg(2+) ion), and introduction of the dianionic phosphoryl group results in the repositioning of charged moieties . Furthermore, substitution of one of the Mg(2+)-coordinating aspartates with lysine or arginine in the Escherichia coli chemotaxis response regulator CheY results in phosphorylation-independent activation . In order to examine the consequences of altered charge distribution for response regulator activity and to identify possible additional amino acid substitutions that result in phosphorylation-independent activation, we made 61 CheY mutants in which residues close to the site of phosphorylation (Asp57) were replaced by various charged amino acids . Most substitutions (47 of 61) resulted in the complete loss of CheY activity, as measured by the inability to support clockwise flagellar rotation . However, 10 substitutions, all introducing a new positive charge, resulted in the loss of chemotaxis but in the retention of some clockwise flagellar rotation . Of the mutants in this set, only the previously identified CheY13DK and CheY13DR mutants displayed clockwise activity in the absence of the CheA sensor kinase . The absence of negatively charged substitution mutants with residual activity suggests that the introduction of additional negative charges into the active site is particularly deleterious for CheY function . Finally, the spatial distribution of positions at which amino acid substitutions are functionally tolerated or not tolerated is consistent with the presently accepted mechanism of response regulator activation and further suggests a possible role for Met17 in signal transduction by CheY. Immunity, 2003 Oct, 19(4), 561 - 9 Natural killer cells activated by MHC class I(low) targets prime dendritic cells to induce protective CD8 T cell responses; Mocikat R et al.; Conserved molecular patterns derived from pathogenic microorganisms prime antigen-presenting dendritic cells (DC) to induce adaptive T cell responses . In contrast, virus-infected or tumor cells that express low levels of major histocompatibility complex (MHC) class I activate natural killer (NK) cells for direct killing . It is unknown whether NK cell recognition of MHC class I(low) targets can also induce adaptive T cell responses . Here, we show that MHC class I(low) targets initiate a cascade of immune responses, starting with the immediate activation of NK cells . The activated NK cells then prime DC to produce IL-12 and to induce highly protective CD8 T cell memory responses . Therefore, sensing of MHC class I(low) targets by NK cells can link innate and adaptive immunity to induce protective T cell responses and may alarm the immune system during early infection with noncytopathic viruses. J Environ Sci (China), 2003 Sep, 15(5), 590 - 4 Analysis of parental strain DNA fragments existing in GEMs-Fhhh; Hao CB et al.; There were 6 target DNA fragments of the three parental strains existing in the cell of GEMs (genetically engineered microorganism strain) Fhhh measured in this research by PCR(polymerase chain reaction) . The determination showed that GEMs Fhhh contained all the 6 target DNA fragments, mnp1, mnp2, lip1, lip2, FLO1 and 16S rDNA, and had the molecular genetic stability . Meanwhile the PCR production of each parental strain could only had its target DNA fragments and was different from each other . It may illustrate that the technique of the inter-kingdom protoplast fusion for the construction of GEMs Fhhh through the process of intercellular gene recombination could be used as a reliable bioengineering technique to create the specific functional stain for the pollution control. Eur J Med Chem, 2003 Sep, 38(9), 837 - 40 Synthesis of some novel imidazolinones as potent anticonvulsant agents; Joshi H et al.; Imidazolinone derivatives of IIa-IIc, IIIa-IIIf and IVa-IVf have been synthesised by the condensation of some known sulpha drugs with 5-oxazolone derivatives, which were prepared by Erlenmeyer condensation of benzoyl glycine with different aldehydes in the presence of sodium acetate and acetic anhydride . The constitution of the products has been supported by elemental analysis and IR, 1H-NMR spectral data . The products have been screened for their (a) in vitro growth inhibitory activity against several microorganisms and (b) in vivo anticonvulsant activity. Arch Pharm Res, 2003 Sep, 26(9), 686 - 96 Synthesis and biological investigations of new thiazolidinone and oxadiazoline coumarin derivatives; Abd Elhafez OM et al.; Ethyl (coumarin-4-oxy)acetate 1 was prepared through the reaction of 4-hydroxycoumarin with ethyl bromoacetate . Compound 1 was allowed to react with hydrazine hydrate to produce coumarin-4-oxyacetic hydrazide 2 . The synthesis of N-(arylidene and alkylidene)-coumarin-4-oxyacetic hydrazones 3-20 was performed . The preparation of 2-substituted-3-{(coumarin-4-oxy) acetamido}thiazolidinones 21-26 and 2-{(coumarin-4-oxy)methyl}-4-acetyl-5-substituted-delta2-1,3,4-oxadiazolines 27-33 was performed by the reaction of the hydrazones 3, 4, 7, 9, 12, 14 with mercaptoacetic acid and the hydrazones 3, 4, 5, 7, 12, 15, 16 with acetic anhydride, respectively . The antiviral activities, cytotoxicities and structure-activity relationship (SAR) towards different microorganisms of the prepared compounds were studied. Adv Microb Physiol, 2003, 47, 255 - 310 Microbial globins; Wu G et al.; Globins are an ancient and diverse superfamily of proteins . The globins of microorganisms were relatively ignored for many decades after their discovery by Warburg in the 1930s and rediscovery by Keilin in the 1950s . The relatively recent focus on them has been fuelled by recognition of their structural diversity and fine-tuning to fulfill (probably) discrete functions but particularly by the finding that a major role of certain globins is in protection from the stresses caused by exposure to nitric oxide (NO)--itself a molecule that has attracted intense curiosity recently . At least three classes of microbial globin are recognised, all having features of the classical globin protein fold . The first class is typified by the myoglobin-like haemprotein Vgb from the bacterium Vitreoscilla, which has attracted considerable attention because of its ability to improve growth and metabolism for biotechnological gain in a variety of host cells, even though its physiological function is not fully understood . The truncated globins are widely distributed in bacteria, microbial eukaryotes as well as plants and are characterised by being 20-40 residues shorter than Vgb . The polypeptide is folded into a two-over-two helical structure while retaining the essential features of the globin superfamily . Roles in oxygen and NO metabolism have been proposed . The third and best understood class comprises the flavohaemoglobins, which were first discovered and partly characterised in yeast . These are distinguished by the presence of an additional domain with binding sites for FAD and NAD(P)H . Widely distributed in bacteria, these proteins undoubtedly confer protection from NO and nitrosative stresses, probably by direct consumption of NO . However, a bewildering array of enzymatic capabilities and the presence of an active site in the haem pocket reminiscent of peroxidases hint at other functions . A full understanding of microbial globins promises advances in controlling the interactions of pathogenic bacteria with their animal and plant hosts, and manipulations of microbial oxygen transfer with biotechnological applications. Am J Clin Pathol, 2003 Oct, 120(4), 567 - 74 Immunostaining of visceral leishmaniasis caused by Leishmania infantum using monoclonal antibody (19-11) to the Leishmania homologue of receptors for activated C-kinase; Hofman V et al.; It sometimes is difficult to diagnose leishmaniasis in tissue sections or in smears, particularly in unusual sites or if few parasites are present in the lesion . Leishmania species must be differentiated morphologically from a variety of other microorganisms, including Toxoplasma gondii, Histoplasma capsulatum, Trypanosoma cruzi, and Penicillium marneffei . We tested the value of monoclonal antibody p19-11 raised against the Leishmania homologue of receptors for activated C-kinase (LACK) as an immunohistochemical marker for amastigotes of Leishmania infantum . We evaluated a total of 117 paraffin-embedded lesions due to L infantum (92 cases), T gondii (15 cases), H capsulatum (5 cases), T cruzi (3 cases), and P marneffei (2 cases) . Amastigotes of Leishmania species were detected in 92 (100%) of the leishmaniasis lesions . There were no false-positive LACK immunoreactions in any of the toxoplasmosis, histoplasmosis, trypanosomiasis, or penicilliosis specimens (0/25) . We found the anti-LACK antibody p19-11 to be a highly specific and sensitive paraffin-reactive immunohistochemical marker for the confirmation or identification of Leishmania species in tissue sections. J Pediatr (Rio J), 2003 Sep-Oct, 79(5), 467 - 70 {Chronic recurrent multifocal osteomyelitis of the mandible: report of three cases}; Paim LB et al.; OBJECTIVE: To report three cases of chronic recurrent multifocal osteomyelitis of the mandible, an inflammatory disease affecting one or more bones with absence of isolated microorganisms in affected areas . DESCRIPTION: The first case is a 13 year-old female presenting with pain and fever after dental treatment . The patient received antibiotic treatment for osteomyelitis, but developed progressive enlargement of the mandible and palmoplantar pustulosis . Bone scintigraphy showed intense and diffuse uptake in the mandible . The swelling decreased after indomethacin and hyperbaric oxygen therapy . Case 2 is a 9 year-old female patient with recurrent pain and edema of the right mandible for three years . The diagnosis of osteomyelitis was established and amoxicillin introduced . After three months, tomography showed diffuse mandible osteolysis . Indomethacin and hyperbaric oxygen therapy were introduced, however the patient presented a relapse and was treated with prednisone, rofecoxib and methotrexate . Patient 3, a 10 year-old male, had palmoplantar pustulosis and recurrent en