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A novel delta-subdivision proteobacterial lineage from the lower ocean surface layer.

A small-subunit ribosomal RNA (16S rRNA) gene lineage (SAR324) affiliated with the delta-subdivision of the class Proteobacteria (DP) was discovered in a 16S rRNA gene clone library prepared from a water sample collected from 250 m in the western Sargasso Sea. This clone library of nearly full-length amplicons of bacterial 16S rRNA genes has been the subject of previous studies aimed at identifying bacteria that inhibit the lower ocean surface layer. The novel lineage was identified by randomly sequencing clones that did not hybridize to oligonucleotide probes specific for several abundant bacterioplankton groups identified in previous studies. Phylogenetic analysis indicated that SAR324 was most closely affiliated with the DP, although it showed no specific relationship to any DP 16S rRNA genes in databases. Eight of the clones in the library of 148 clones were identified as members of the SAR324 lineage by hybridization to an oligonucleotide probe specific for SAR324. Subsequent hybridizations showed that the SAR324 group is stratified in the lower surface layer of both the Atlantic and Pacific Oceans, with maxima between 160 and 500 m. The repeated discovery of sequences belonging to different gene clusters with similar distributions in this region of the water column suggests that microbial communities in the lower surface layer may be functionally specialized.

Atlantic Ocean↗

Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces.

Planktonic crenarchaeotes are present in high abundance in Antarctic winter surface waters, and they also make up a large proportion of total cell numbers throughout deep ocean waters. To better characterize these uncultivated marine crenarchaeotes, we analyzed large genome fragments from individuals recovered from a single Antarctic picoplankton population and compared them to those from a representative obtained from deeper waters of the temperate North Pacific. Sequencing and analysis of the entire DNA insert from one Antarctic marine archaeon (fosmid 74A4) revealed differences in genome structure and content between Antarctic surface water and temperate deepwater archaea. Analysis of the predicted gene products encoded by the 74A4 sequence and those derived from a temperate, deepwater planktonic crenarchaeote (fosmid 4B7) revealed many typical archaeal proteins but also several proteins that so far have not been detected in archaea. The unique fraction of marine archaeal genes included, among others, those for a predicted RNA-binding protein of the bacterial cold shock family and a eukaryote-type Zn finger protein. Comparison of closely related archaea originating from a single population revealed significant genomic divergence that was not evident from 16S rRNA sequence variation. The data suggest that considerable functional diversity may exist within single populations of coexisting microbial strains, even those with identical 16S rRNA sequences. Our results also demonstrate that genomic approaches can provide high-resolution information relevant to microbial population genetics, ecology, and evolution, even for microbes that have not yet been cultivated.

Amino Acid Sequence↗

Membrane electricity as a convertible energy currency for the cell.

The role of transmembrane electric potential difference (delta psi) in mitochondria, chloroplasts, and bacteria has been considered. Since the electric capacitance of membranes is much lower than the pH buffer capacitance of water phases, delta psi proves to be the primary form of energy produced by generators of electrochemical H+ potential difference (delta mu-H). There are 11 distinct types of delta mu-H-generating systems in coupling membranes, involved in respiratory and light-dependent electron and proton transfer, as well as in ATP and PP1 hydrolysis and synthesis. Bacteriorhodopsin is the simplest delta mu-H generator. However, even in this case, the molecular mechanism of delta psi production remains obscure. Many types of work can be supported by delta mu-H with no ATP involved so that delta mu-H proves to be not only a transient intermediate of oxidative and photosynthetic phosphorylation but also a convertible energy currency for the cell. Among the delta mu-H-supported activities, mechanical work was recently demonstrated. It can be exemplified by the motility systems of (i) flagellar bacteria and (ii) blud--green algae. As was found in multicellular cyanobacteria, delta mu-H can be used for a power transmission over distances as long as 1 mm. It seems to be probable that in large cells of eukaryotes (e.g., in muscle fibers) giant mitochondria may serve as power-transmitting structures. Na+--K+ gradients can be used to stabilize delta mu-H in bacteria. It is suggested that the primary function of unequal distribution of these cations between the microbial cell and the medium is delta mu-H buffering.

Adenosine Triphosphate↗

Negative regulation of interleukin-12 production by a rapamycin-sensitive signaling pathway: a brief communication.

Interleukin-12 (IL-12), an important cytokine in host defense against microbial pathogens, regulates natural killer and T-cell function(s) including the induction of gamma-interferon production. The major cellular sources of IL-12 are monocytes/macrophages. Bacteria, bacterial products, and intracellular parasites are the most efficient inducers of IL-12 production. In the present study we show that a signal transduction pathway sensitive to rapamycin may have an important role in the regulation/suppression of Staphylococcus aureus-induced IL-12 production in vitro. Human peripheral blood mononuclear cells, monocytes, or a human monocytic cell line THP-1 were stimulated with S. aureus Cowan strain 1 (SAC) in the presence or absence of rapamycin and investigated for production of IL-12 protein by enzyme-linked immunosorbent assay and IL-12 p40 mRNA accumulation by RNase protection assay or real-time quantitative polymerase chain reaction. The results show that rapamycin significantly enhances SAC-induced IL-12 p70 protein production and IL-12 p40 mRNA accumulation. Further the results demonstrate that wortmannin enhances SAC-induced IL-12 p40 mRNA accumulation, whereas Ly294002 does not. These data indicate that a rapamycin-sensitive signaling pathway may act as a negative feedback cascade in the regulatory mechanisms of IL-12 production.

Androstadienes↗

Periodontal diseases in children and adolescents: 2. Management.

Many of the periodontal diseases affecting children and adolescents can be successfully managed in general dental practice. The decision to treat the young patient in the practice setting or to refer to a periodontal specialist will depend on the complexity of treatment, patient factors and the expertise of the practitioner. Treatment should be provided in three phases: the initial cause-related phase is aimed at controlling microbial plaque; the corrective phase is intended to restore function and aesthetics; supportive periodontal therapy is aimed at preventing recurrence and progression of periodontal disease. Even in cases requiring specialist referral, the dental team in general practice has a key role in the initial and supportive phases of therapy.

Adolescent↗

Rapid removal of nitrate and sulfate in freshwater wetland sediments.

Anaerobic microbial processes play particularly important roles in the biogeochemical functions of wetlands, affecting water quality, nutrient transport, and greenhouse gas fluxes. This study simultaneously examined nitrate and sulfate removal rates in sediments of five southwestern Michigan wetlands varying in their predominant water sources from ground water to precipitation. Rates were estimated using in situ push-pull experiments, in which 500 mL of anoxic local ground water containing ambient nitrate and sulfate and amended with bromide was injected into the near-surface sediments and subsequently withdrawn over time. All wetlands rapidly depleted nitrate added at ambient ground water concentrations within 5 to 20 h, with the rate dependent on concentration. Sulfate, which was variably present in porewaters, was also removed from injected ground water in all wetlands, but only after nitrate was depleted. The sulfate removal rate in ground water-fed wetlands was independent of concentration, in contrast to rates in precipitation-fed wetlands. Sulfate production was observed in some sites during the period of nitrate removal, suggesting that the added nitrate either stimulated sulfur oxidation, possibly by bacteria that can utilize nitrate as an oxidant, or inhibited sulfate reduction by stimulating denitrification. All wetland sediments examined were consistently capable of removing nitrate and sulfate at concentrations found in ground water and precipitation inputs, over short time and space scales. These results demonstrate how a remarkably small area of wetland sediment can strongly influence water quality, such as in the cases of narrow riparian zones or small isolated wetlands, which may be excluded from legal protection.

Bromides↗

Staphylococcal enterotoxin superantigens.

Staphylococcal enterotoxins (SE) are a family of structurally related proteins that are produced by Staphylococcus aureus. They play a role in the pathogenesis of food poisoning and are the most potent activators of T lymphocytes known. The receptors for SE on antigen-presenting cells are major histocompatibility complex class II molecules. Recent studies have shown that a complex of SE and major histocompatibility complex class II molecules is required for binding to the variable region of the T cell antigen receptor beta-chain. SE mitogenic activity is dependent on induction of interleukin 2, which may be intimately involved in the mechanism of SE toxicity. The minor lymphocyte-stimulating "endogenous" self-superantigen has recently been shown to be a retroviral gene product, so that this too is apparently a microbial superantigen. An understanding of the mechanism of action of these microbial superantigens has implications for normal and pathological immune functions.

Animals↗

Early response cytokines and innate immunity: essential roles for TNF receptor 1 and type I IL-1 receptor during Escherichia coli pneumonia in mice.

The early response cytokines, TNF and IL-1, have overlapping biologic effects that may function to propagate, amplify, and coordinate host responses to microbial challenges. To determine whether signaling from these early response cytokines is essential to orchestrating innate immune responses to intrapulmonary bacteria, the early inflammatory events induced by instillation of Escherichia coli into the lungs were compared in wild-type (WT) mice and mice deficient in both TNF receptor 1 (TNFR1) and the type I IL-1 receptor (IL1R1). Neutrophil emigration and edema accumulation induced by E. coli were significantly compromised by TNFR1/IL1R1 deficiency. Neutrophil numbers in the circulation and within alveolar septae did not differ between WT and TNFR1/IL1R1 mice, suggesting that decreased neutrophil emigration did not result from decreased sequestration or delivery of intravascular neutrophils. The nuclear translocation of NF-kappa B and the expression of the chemokine macrophage inflammatory protein-2 did not differ between WT and TNFR1/IL1R1 lungs. However, the concentration of the chemokine KC was significantly decreased in the bronchoalveolar lavage fluids of TNFR1/IL1R1 mice compared with that in WT mice. Thus, while many of the molecular and cellular responses to E. coli in the lungs did not require signaling by either TNFR1 or IL1R1, early response cytokine signaling was critical to KC expression in the pulmonary air spaces and neutrophil emigration from the alveolar septae.

Active Transport, Cell Nucleus↗

CpG-A oligonucleotides induce a monocyte-derived dendritic cell-like phenotype that preferentially activates CD8 T cells.

Human B cells and plasmacytoid dendritic cells recognize CpG motifs within microbial DNA via Toll-like receptor 9. Two functionally distinct types of CpG motif containing oligonucleotides (CpG ODN) have been described, CpG-A and CpG-B. In contrast to CpG-B, CpG-A induces high amounts of type I IFN (IFN-alpha and IFN-beta) in plasmacytoid dendritic cells. In the present study, we examined the effects of CpG-A on human primary monocytes. In PBMC stimulated with CpG-A and GM-CSF, monocytes showed excellent survival, increased in size and granularity, and within 3 days developed a dendritic cell-like phenotype that was characterized by down-regulation of CD14, partial up-regulation of CCR7, and an increased surface expression of costimulatory and Ag-presenting molecules. This effect could be inhibited by a combination of blocking Abs to type I IFN, and no such CpG-A-induced changes were observed in purified monocytes. Although IL-12 production by this dendritic cell-like phenotype required additional stimulation with CD40 ligand, this cell type spontaneously up-regulated IL-15 expression. Consistent with the known effect of IL-15 on effector and memory CD8 T cells, the frequency of CCR7(-)/CD45RA(-) CD8 T cells was selectively increased in allogeneic T cell assays. Furthermore, this dendritic cell type was more potent to support both the generation and the IFN-gamma production of autologous influenza matrix peptide-specific memory CD8 T cells as compared with dendritic cells generated in the presence of GM-CSF and IL-4. In conclusion, monocytes exposed to the cytokine milieu provided by CpG-A rapidly develop a dendritic cell-like phenotype that is well equipped to support CD8 T cell responses.

Adjuvants, Immunologic↗

Evaluation of antioxidative and mutagenic properties of 50% ethanolic extract from red beans fermented by Aspergillus oryzae.

Various bean products fermented by microorganisms are commonly consumed in Asian diets; however, the safety or functional properties of fermented beans can vary with different microbial species and with different processes being applied to different beans. The objectives of this study were to evaluate the antioxidative and mutagenic properties of 50% ethanolic extracts from red beans fermented by Aspergillus oryzae. The extracts' antioxidative activities, including alpha,alpha;-diphenyl-beta-picryl-hydrazyl (DPPH) radical-scavenging effects, Fe(2+)-chelating ability, and reducing power, were studied in vitro. The antioxidative effects provided by the extracts depended strongly on their concentrations. In general, antioxidative activity increased with extract concentration to a certain point and then leveled off as the concentration further increased. The fermented red bean extracts showed less of a scavenging effect on the DPPH radical and less reducing power than the commercial antioxidants alpha-tocopherol and butylated hydroxytoluene, but better Fe(2+)-chelating ability. No mutagenicity or toxicity effect on any of the tested strains (Salmonella Typhimurium TA97, TA98, TA100, TA102, and TA1535) was found for the 50% ethanolic extracts of fermented red beans with the Ames mutagenicity assay. These results suggest that the 50% ethanolic extracts were not mutagenic.

Antioxidants↗

Role of interleukin-13 in innate and adaptive immunity.

Initially thought to be functionally redundant with IL-4 as a predominant anti-inflammatory factor secreted during type-2 T-cell responses, IL-13 possesses a number of additional properties that distinguish it from IL-4 in addition to having both anti-inflammatory and immune activating properties. This review centers primarily on the role of IL-13 in the regulation of cellular functions of innate immunity and acquired immunity against certain microbial pathogens. First, we discuss IL-13's regulation of innate cell targets and its impact on inflammation, antigen uptake and antigen presentation. Second, we focus on IL-13's involvement in acquired immunity to infectious helminths and protozoa. The role of this cytokine in immune responses is still being determined but evidence to date suggests this molecule has been conserved as an important regulatory factor involved in both early innate and late adaptive responses.

Adaptation, Physiological↗

[Interactions in the parasite-host system in chronic obstructive lung diseases].

The interactions in "parasite-host" system were studied in 120 patients with chronic obstructive pulmonary diseases (COPD) living in Samara. The significant interrelation between the composition of intestinal and pneumotropic microflora was revealed. It is conditioned both by the mechanisms of cooperation between some types of bacteria and by their translocation from one organs to another. The data obtained demonstrate the complex influence of abnormal microbial ecology in lungs and intestine on formation of "parasite-host" system and the significance of its function in COPD pathogenesis. The results of investigation show the necessity to include the measures for correction of microbial ecology disorders into the general complex of COPD therapy.

Asthma↗

A model for the role of the proline-linked pentose-phosphate pathway in phenolic phytochemical bio-synthesis and mechanism of action for human health and environmental applications.

The combination of immunodeficiency, inflammatory process and nutritional status that is characteristic of infective and food-borne illness is more evident in chronic diet- and environment-influenced chronic diseases such as diabetes, obesity, cardiovascular disease, cancer, arthritis and neuro-degeneration diseases. These chronic diseases tend to be oxidation-linked and may manifest in communities around the world, irrespective of income. In addressing the challenges of the above diseases, a significant role for dietary phytochemicals is emerging. Phytochemicals are required from a spectrum of food for at least their antioxidant role, if not for other properties, to protect tissues from activities that manifest themselves into what we call chronic disease. Among the diverse groups of phytochemicals, phenolic antioxidants and antimicrobials from food plants are being targeted for designed dietary intervention to manage major oxidation-linked diseases such as diabetes, cardiovascular diseases, arthritis, cognition diseases and cancer. Foods containing phenolic phytochemicals are also being targeted to manage bacterial infections associated with chronic diseases such as peptic ulcer, urinary tract infections, dental caries and food-borne bacterial infections. Plants produce phenolic metabolites as a part of growth, developmental and stress adaptation response. These stress and developmental responses are being harnessed to design consistent phytochemical profiles for safety and clinical relevancy using novel tissue culture and bioprocessing technologies. The biochemical strategy for harnessing phenolic phytochemicals for human health and wellness is based on the hypothesis that phenolic metabolites in plants are efficiently produced through an alternative mode of metabolism linking proline synthesis with pentose-phosphate pathway. In this model, stress-induced proline biosynthesis is coupled to pentose-phosphate pathway, driving the synthesis of NADPH(2) and sugar phosphates for anabolic pathways, including phenolic and antioxidant response pathways, while simultaneously providing reducing equivalents needed for mitochondrial oxidative phosphorylation in the form of proline as an alternative to NADH from Krebs/TCA cycle. Based on this model, tissue culture techniques and elicitation concepts have been used to stimulate phenolic metabolites with an antioxidant response in germinating seeds, sprouts and clonal lines of dietary plants. From our initial investigations, a model has been proposed in which the proline-linked pentose-phosphate pathway is suggested to be critical for modulating protective antioxidant response pathways in diverse biological systems, including biochemical and cellular pathways important for human health. The proposed proline-linked pentose-phosphate pathway model provides a mechanism for understanding the mode of action of phenolic phytochemicals in modulating antioxidant pathways and provides avenues by which dietary approaches may manage oxidation-linked chronic and infectious diseases. The model also has implications for the development of antimicrobial phenolic phytochemicals against bacterial pathogens in an era of increasing antibiotic resistance. Further, this model also has relevance for improving fungal and yeast-based food bioprocessing for designing functional foods and for environmental bioremediation using plant and microbial systems, as well as for improving agricultural and food systems in harsh environments.

Antioxidants↗

Male accessory gland proteins in Drosophila: a multifaceted field [corrected].

Male accessory gland in Drosophila is a secretory tissue of the reproductive system. The proteins synthesized in the accessory gland are tissue specific, stage specific-seen only during the adult stage and sex specific in the sense of male limited expression. These secretions that form a component of the seminal fluid are transferred to the female at the time of copulation and play an important role in reproduction. In conjunction with sperm, these secretory proteins assure reproductive success by reducing the female's receptivity to mating and escalating the rate of egg laying. Some of these proteins are antibacterial in nature with a likely function of protecting the female's genital tract against microbial infection during/after mating. Most of the genes involved in the synthesis of accessory gland proteins are autosomal but a few are still X-linked. Their male specific expression is achieved at the time of sex determination. The level of expression of these genes is dose dependent and they follow Mendelian pattern of segregation. Further, majority of these proteins are rapidly evolving with high rates of non-synonymous substitutions. In this review, by considering the work carried out in different fields, we have tried to generate a comprehensive picture about the male accessory gland and the role of its proteins in the reproduction of Drosophila.

Animals↗

Removal of micro-particles by microbial granules used for aerobic wastewater treatment.

Microbial granules with a diameter from 0.4 mm to 3.0 mm have been produced by fast sedimentation and retention of microbial aggregates in sequencing batch airlift reactors used for model wastewater treatment. The wastewater was with or without addition of calcium salt. The granules were able not only to degrade organic matter but to remove nano- and micro-particles from wastewater due to microchannels and pores in the matrix of the granules. To detect the removal of 0.1 microm, 0.6 pm, 4.2 microm fluorescent microspheres, and cells of Escherichia coli, stained by permeable nucleic acid stain SYTO9, the granules were incubated with these particles. The rate of particle removal and their accumulation in the granules was measured by a Fluoview300 confocal laser scanning microscope (CLSM) (Olympus, Japan); a FACSCalibur flow cytometer (Becton Dickinson, CA, USA), and a fluorescence spectrometer LS-50B (Perkin-Elmer, UK). The release or removal of biological and non-biological particles was analyzed by a flow cytometer after DNA staining. Total number of the particles bigger than 0.1 microm in the reactors was approximately 4 x 10(7) per ml, and 23% of these particles were bacterial cells. The 0.1 microm and 4.2. microm microbeads were accumulated within 250 microm in the upper layer of the microbial granule but externally added cells of Escherichia coli penetrated to the depth of approximately 800 microm in the granules without calcium addition. Microbial granules contained also attached ciliates but accumulation of the particles in protozoan cells was smaller than in the granule matrix. Kinetics of particle sorption was revealed by flow cytometry and fluorescence spectrometry. Almost half of the stained cells of E. coli can be removed by the granules for one hour. The ability of the microbial granules to remove the particles can enhance their function in aerobic treatment of wastewater.

Aerobiosis↗

[Congenital components of immunity: Toll-like receptors in the normal state and in immunopathology].

This review deals with rapidly accumulating information on a highly important components of the congenital immune system: Toll-like receptors playing a leading role in the recognition of microbial patterns. The data on the main structural and functional features of Toll-like receptors and their distribution in the body are summarized. The main signal paths are characterized and the key molecules which take part in the transduction are pointed out. Special attention is paid to the activating action of lipopolysaccharides through TLR4. Pathological processes developing as the result of damages in the structure and function of Toll-like receptors in humans and experimental animals are determined.

Animals↗

[Thermophilic microbial metal reduction].

Thermophilic microorganisms can reduce Fe(III), Mn(IV), Cr(VI), U(VI), Tc(VII), Co(III), Mo(VI), Au(I, III), and Hg(II). Ferric iron and Mn(IV) can be used as electron acceptors during growth; the physiological role of the reduction of the other metals is unclear. The process of microbial dissimilatory reduction of Fe(III) is the most thoroughly studied. Iron-reducing prokaryotes have been found in virtually all of the recognized types of terrestrial ecosystems, from hot continental springs to goethermally heated subsurface sediments. Thermophilic iron reducers do not belong to a phylogenetically homogenous group and include representatives of many bacterial and archaeal taxa. Iron reducing thermophiles can couple Fe(III) reduction with oxidation of a wide spectrum of organic and inorganic compounds. In the thermophilic microbial community, they can fulfil both degradative and productive functions. Thermophilic prokaryotes probably carried out global reduction of metals on Earth in ancient times, and, at the same time, they are promising candidates for use in modern biotechnological processes.

Archaea↗

Endoscopically guided aerobic cultures in postsurgical patients with chronic rhinosinusitis.

BACKGROUND: There is considerable amount of debate in the literature regarding the microbial flora of normal, acutely infected, and chronically infected paranasal sinuses. Few studies have specifically looked at the microbial flora of healthy and infected sinus cavities after functional endoscopic sinus surgery. METHODS: One hundred thirty-four cultures were studied. All cultures were obtained using a standard technique. The nasal cavities were decongested and anesthetized, and nasal endoscopy was performed. When purulent secretions were identified, specimens of purulent secretions were obtained for incubation. Sensitivities were tested according to microorganisms identified. Empiric therapy generally consisted of afluoroquinolone, amoxicillin/clavulanate, or a later-generation cephalosporin, and adjustment in individual instances when appropriate. RESULTS: Twelve cultures showed no growth, 86 grew a single microorganism, and 35 grew two or more microorganisms for a total of 151 microorganisms identified. The most common microorganisms were Staphylococcus aureus, coagulase-negative staphylococci, and Pseudomonas aeruginosa. Other organisms that were cultured <5% of the time included Streptococcus pneumoniae, Haemophilus influenza, Moraxella catarrhalis, Serratia liquefaciens, Stenotrophomonas (Xanthomonas) maltophilia, alcaligenes, Fusobacterium, Escherichia coli, diphtheroids, Acinetobacter species, Klebsiella species, skin flora, and mixed Gram-negative and Gram-positives. CONCLUSION: Endoscopically guided aerobic cultures in postsurgical patients with acute exacerbations of chronic rhinosinusitis most commonly grew S. aureus, coagulase-negative staphylococci, and pseudomonal species. These cultures altered antibiotic treatment management decisions in a significant number of cases regardless of patients' clinical characteristics or history of previous culture.

Bacteria, Aerobic↗