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At least 253 records · Page 14Linked to original sources

PubMed2003

Anti-microbial activities of mannose-binding lectin.

Mannose-binding lectin (MBL; also known as mannan-binding lectin) is involved in first-line defence by binding to bacteria, viruses, protozoa and helminths through a pattern-recognition mode of detection and then initiating a range of host responses. Currently, we have been unable to extrapolate from what we know of the biochemistry of MBL binding to predict accurately the interaction of MBL with individual micro-organisms; even subtle surface alterations have been shown to have an extensive impact on MBL-mediated recognition of pathogens. MBL has a major protective effect through activation of the complement system via MBL-associated serine proteases (MASPs). This can cause the lysis of Gram-negative bacteria and also opsonize a wide spectrum of potential pathogens for phagocytosis. MBL may also influence phagocytosis in the absence of complement activation through an interaction with one or more collectin receptors. This may also be the basis for a direct effect of the protein on inflammatory responses. MBL can alter the function of microbial structures, such as gp120 of HIV, to prevent infection. The protein may also interact with the components of other cascade systems such as the clotting system, which will have a role in microbial pathogenesis. An understanding of these basic mechanisms will be vital if we are to use purified or recombinant MBL in therapeutic applications.

Bacterial Capsules↗

PubMed1997

Protistan communities in aquifers: a review.

Eukaryotic microorganisms (protists) are a very important component of microbial communities inhabiting groundwater aquifers. This is not unexpected when one considers that many protists feed heterotrophically, by means of either phagotrophy (bacterivory) or osmotrophy. Protistan numbers are usually low (< 10(2) per g dw of aquifer material) in pristine, uncontaminated aquifers but may increase by several orders of magnitude in aquifers subject to organic pollution. Small flagellates (typically 2-3(5) microns in size in situ) are by far the dominant protists in aquifers, although amoebae and occasionally ciliates may also be present in much lower numbers. Although a wealth of new taxonomic information is waiting to be brought to light, interest in the identity of aquifer protists is not exclusively academic. If verified, the following hypotheses may prove to be important towards our understanding of the functioning of microbial communities in aquifers: (1) Differences in swimming behavior between species of flagellates lead to feeding heterogeneity and niche differentiation, implying that bacterivorous flagellates graze on different subsets of the bacterial community, and therefore play different roles in controlling bacterial densities. (2) Bacterivorous flagellates grazing on bacteria capable of degrading organic compounds have an indirect effect on the overall rates of biodegradation.

Animals↗

PubMed1999

Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ.

We propose a novel method for studying the function of specific microbial groups in situ. Since natural microbial communities are dynamic both in composition and in activities, we argue that the microbial "black box" should not be regarded as homogeneous. Our technique breaks down this black box with group-specific fluorescent 16S rRNA probes and simultaneously determines 3H-substrate uptake by each of the subgroups present via microautoradiography (MAR). Total direct counting, fluorescent in situ hybridization, and MAR are combined on a single slide to determine (i) the percentages of different subgroups in a community, (ii) the percentage of total cells in a community that take up a radioactively labeled substance, and (iii) the distribution of uptake within each subgroup. The method was verified with pure cultures. In addition, in situ uptake by members of the alpha subdivision of the class Proteobacteria (alpha-Proteobacteria) and of the Cytophaga-Flavobacterium group obtained off the California coast and labeled with fluorescent oligonucleotide probes for these subgroups showed that not only do these organisms account for a large portion of the picoplankton community in the sample examined ( approximately 60% of the universal probe-labeled cells and approximately 50% of the total direct counts), but they also are significant in the uptake of dissolved amino acids in situ. Nearly 90% of the total cells and 80% of the cells belonging to the alpha-Proteobacteria and Cytophaga-Flavobacterium groups were detectable as active organisms in amino acid uptake tests. We suggest a name for our triple-labeling technique, substrate-tracking autoradiographic fluorescent in situ hybridization (STARFISH), which should aid in the "dissection" of microbial communities by type and function.

Animals↗

PubMed2003

Unlocking the molecular structure of fungal melanin using 13C biosynthetic labeling and solid-state NMR.

Melanins are enigmatic pigments found in all biological kingdoms that are associated with a variety of functions, including microbial virulence. Despite being ubiquitous in nature, melanin pigments have long resisted atomic-level structural examination because of their insolubility and amorphous organization. Cryptococcus neoformans is a human pathogenic fungus that melanizes only when provided with exogenous substrate, thus offering a unique system for exploring questions related to melanin structure at the molecular level. We have exploited the requirement for exogenous substrate in melanin synthesis as well as the capabilities of high-resolution solid-state nuclear magnetic resonance (NMR) to establish the predominantly aliphatic composition of l-dopa melanin and to introduce (13)C labels that permit the identification of proximal carbons in the developing biopolymer. By swelling solid melanin samples in organic solvents and using two-dimensional heteronuclear NMR in conjunction with magic-angle spinning, we have identified chemical bonding patterns typical of alkane, alkene, alcohol, ketone, ester, and indole functional groups. These findings demonstrate the feasibility of a novel approach to determining the structure of melanin using metabolic labeling and NMR spectroscopy.

Carbon Radioisotopes↗

PubMed2001

Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes.

Recent work in computational genomics has shown that a functional association between two genes can be derived from the existence of a fusion of the two as one continuous sequence in another genome. For each of 30 completely sequenced microbial genomes, we established all such fusion links among its genes and determined the distribution of links within and among 15 broad functional categories. We found that 72% of all fusion links related genes of the same functional category. A comparison of the distribution of links to simulations on the basis of a random model further confirmed the significance of intracategory fusion links. Where a gene of annotated function is linked to an unclassified gene, the fusion link suggests that the two genes belong to the same functional category. The predictions based on fusion links are shown here for Methanobacterium thermoautotrophicum, and another 661 predictions are available at http://fusion.bu.edu.

Gene Expression Regulation, Bacterial↗

PubMed2003

Cross-talk in the innate immune system: neutrophils instruct recruitment and activation of dendritic cells during microbial infection.

Type I inflammatory cytokines are essential for immunity to many microbial pathogens, including Toxoplasma gondii. Dendritic cells (DC) are key to initiating type 1 immunity, but neutrophils are also a source of chemokines and cytokines involved in Th1 response ignition. We found that T. gondii triggered neutrophil synthesis of CC chemokine ligand (CCL)3, CCL4, CCL5, and CCL20, chemokines that were strongly chemotactic for immature DC. Moreover, supernatants obtained from parasite-stimulated polymorphonuclear leukocytes induced DC IL-12(p40) and TNF-alpha production. Parasite-triggered neutrophils also released factors that induced DC CD40 and CD86 up-regulation, and this response was dependent upon parasite-triggered neutrophil TNF-alpha production. In vivo evidence that polymorphonuclear leukocytes exert an important influence on DC activation was obtained by examining splenic DC cytokine production following infection of neutrophil-depleted mice. These animals displayed severely curtailed splenic DC IL-12 and TNF-alpha production, as revealed by ex vivo flow cytometric analysis and in vitro culture assay. Our results reveal a previously unrecognized regulatory role for neutrophils in DC function during microbial infection, and suggest that cross-talk between these cell populations is an important component of the innate immune response to infection.

Animals↗

PubMed2003

Comparative oxidation and net emissions of methane and selected non-methane organic compounds in landfill cover soils.

The surface emissions of methane (CH4) and non-methane organic compounds (NMOCs) were determined at two different areas at a French landfill: a permanently covered and fully vegetated area (40 cm coarse sand + 80 cm of loam) and a temporarily covered area (40 cm of coarse sand). The 37 NMOCs quantified in the landfill gas samples included alkanes (C1-C10), alkenes (C1-C4), halogenated hydrocarbons (including (H)CFCs), and aromatic hydrocarbons. Both positive and negative CH4 fluxes ranging from -0.01 to 0.008 g m(-2) d(-1) were measured from the permanently covered cell. However, high spatial variation was observed, and a hot spot with a high flux (10 g m(-2) d(-1)) was identified. A higher CH4 emission occurred from the temporarily covered cell (CH4 flux of 49.9 g m(-2) d(-1)) as compared to the permanently covered cell. The NMOC fluxes from the permanently covered zone were all very small with both positive and negative fluxes in the order of 10(-7) to 10(-5) g m(-2) d(-1). Higher and mainly positive NMOC fluxes in the order of 10(-5) to 10(-4) g m(-2) d(-1) were obtained from the temporarily covered zone. The lower emission from the permanently covered and fully vegetated cell was attributable to the thicker soil layer, which functions as microbial habitat for methanotrophic bacteria. The NMOC oxidation capacity was investigated in soil microcosms incubated with CH4. Maximal oxidation rates for the halogenated aliphatic compounds varied between 0.06 and 8.56 microg (g of soil)(-1) d(-1). Fully substituted hydrocarbons (tetrachloromethane, perchloroethylene, CFC-11, CFC-12, and CFC-113) were not degraded in the presence of CH4 and O2. Benzene and toluene were rapidly degraded, giving very high maximal oxidation rates (28 and 39 microg (g of soil)(-1) d(-1)). On the basis of the emission measurements and the batch experiments conducted, a general pattern was observed between emissions and biodegradability of various NMOCs. The emissions mainly consisted of compounds that were not degradable or slowly degradable, while an uptake of easily degradable compounds was registered. As an example, perchloroethylene, trichloromethane, CFC-11, and CFC-12 were emitted, while atmospheric consumption of aromatic hydrocarbons and lower chlorinated hydrocarbons such as vinyl chloride, dichloromethane, and chloromethane was observed. This study demonstrates that landfill soil covers show a significant potential for CH4 oxidation and co-oxidation of NMOCs. Under certain conditions, landfills may even function as sinks for CH4 and selected NMOCs, like aromatic hydrocarbons and lower chlorinated compounds.

Air Pollution↗

PubMed2001

Comparative effects of a genetically engineered insect virus and a growth-regulating insecticide on microbial communities in aquatic microcosms.

The effects of a genetically engineered insect baculovirus on indigenous aquatic microbial communities were determined in closed, recirculating aquatic microcosms, and compared with the effects of a natural strain of the virus and of a growth-regulating insecticide, Dimilin. The recombinant virus was a nuclear polyhedrosis virus (NPV) of the spruce budworm (Choristoneura fumiferana (Cf)) with a lacZ marker gene inserted into the egt region of the CfNPV. The natural virus was Ireland strain CfNPV. Microbial measurement endpoints included decomposition activity (mass loss of organic material), respiration on two different substrates (O2 consumption), heterotrophic bacterial abundance (plate counts), and microbial community metabolic profiles (carbon source utilization patterns in Biolog GN microplates). Viral DNA of both the natural strain and the recombinant viruses, detected by polymerase chain reaction techniques, settled out of the microcosm water and accumulated on bottom substrates within 3 days of the microcosm inoculations. The viral DNA persisted in bottom substrates for the duration of the 21-day experimental period, although there was some evidence that the recombinant virus was less stable than the natural strain in particulate organic matter. No significant changes in microbial decomposition or respiration activity, bacterial abundance, or average metabolic responses were detected by a time trend analysis in microcosms inoculated with either the lacZ recombinant virus or the natural Ireland strain CfNPV. Significant effects on microbial decomposition and respiration activity were detected in microcosms treated with the growth-regulating insecticide at, and above, the expected environmental concentrations. Despite significant effects on microbial community functional attributes in Dimilin-treated microcosms, there were no detectable changes in community structure in terms of metabolic profiles or bacterial abundance.

DNA, Viral↗

PubMed1998

Role of early cytokines, including alpha and beta interferons (IFN-alpha/beta), in innate and adaptive immune responses to viral infections.

Innate cytokine responses are important mediators of early defense against infections. Certain of their effects can be delivered directly to activate protective mechanisms in infected cells. Others activate innate immune cells, including natural killer (NK) cells and macrophages, to mediate defense. Still others shape adaptive immune responses. The compositions and magnitudes of innate cytokine responses are modulated, by the nature of the infectious agent, to facilitate accessing of the anti-microbial defense functions most beneficial in defense against the particular infection. In the context of viral infections, interferons alpha and beta (IFN-alpha/beta) are induced to high levels, and help to mediate and regulate immune responses most effective against this class of agents. The cytokines induce anti-viral mechanisms in infected cells, negatively regulate interleukin 12 expression, and activate NK cell-mediated lysis. Protective development of adaptive immunity to viral infections includes prominent CD8 T cell expansion and activation, and IFN-alpha/beta can mediate functions with the potential to promote these T cell responses. Together, the characteristics define regulation of unique or unique prominent defense mechanisms in place to fight off viral infections.

Animals↗

PubMed1990

Perfluorochemicals for gas transport and improvement of cell cultures.

This paper has considered the effects and potential application of PFCs, their emulsions and emulsion components for regulating growth and metabolic functions of microbial, animal and plant cells in culture. PFCs will help to overcome problems encountered in conventional culture systems (e.g. limited gas supply, mechanical damage), especially where cells are grown to high density. While the commercial potential of PFCs for in vitro systems has not yet been fully exploited, the most exciting areas for future developments are in the culture of animal and plant cell lines of importance in biotechnology and medicine.

Animals↗

PubMed1992

Heat shock proteins in health and disease.

Heat shock proteins are among the most abundant proteins of the biosphere. They not only play a major role under stress conditions but also perform important physiological functions. The present review summarizes the potential contribution of heat shock proteins to health and disease related to immunity: their contribution to antibody assembly and antigen presentation; their role in host cell protection against "immune stress"; their participation in tumor surveillance; their relation to gamma/delta T-cell recognition; their function as microbial virulence factors; their dominant antigenicity for the immune response against microbial pathogens; and their possible role as autoantigens. The findings summarized here illustrate the marked liaison between heat shock proteins and the immune response, which may be both beneficial and detrimental to the host.

Animals↗

PubMed2001

Toward the bioremediation of dioxin-polluted soil: structural and functional analyses of in situ microbial populations by quinone profiling and culture-dependent methods.

In order to obtain basic information toward the bioremediation of dioxin-polluted soil, microbial communities in farmland soils polluted with high concentrations of polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) were studied by quinone profiling as well as conventional microbiological methods. The concentration of PCDD/Fs in the polluted soils ranged from 36 to 4,980 pg toxicity equivalent quality (TEQ) g(-1) dry weight of soil. There was an inverse relationship between the levels of PCDD/Fs and microbial biomass as measured by direct cell counting and quinone profiling. The most abundant quinone type detected was either MK-6 or Q-10. In addition, MK-8, MK-8(H2), and MK-9(H8) were detected in significant amounts. Numerical analysis of quinone profiles showed that the heavily polluted soils (> or = 1,430 pg TEQ g(-1)) contained different community structures from lightly polluted soils (< or = 56 pg TEQ g(-1)). Cultivation of the microbial populations in the heavily polluted soils with dibenzofuran or 2-chlorodibenzofuran resulted in enrichment of Q-10-containing bacteria. When the heavily polluted soil was incubated in static bottles with autoclaved compost as an organic nutrient additive, the concentrations of PCDD/Fs in the soil were decreased by 22% after 3 months of incubation. These results indicate that dioxin pollution exerted a significant effect on microbial populations in soil in terms of quantity, quality, and activity. The in situ microbial populations in the dioxin-polluted soil were suggested to have a potential for the transformation of PCDD/Fs and oxidative degradation of the lower chlorinated ones thus produced.

Biodegradation, Environmental↗

PubMed2004

Metagenomics--the key to the uncultured microbes.

It is widely accepted that up to 99.8% of the microbes present in many environments are not readily culturable. 'Metagenome technology' tries to overcome this bottleneck by developing and using culture-independent approaches. From the outset, metagenome-based approaches have led to the accumulation of an increasing number of DNA sequences, but until this time the sequences retrieved have been those of uncultured microbes. These genomic sequences are currently exploited for novel biotechnological and pharmaceutical applications and to increase our knowledge on microbial ecology and physiology of these microbes. Using the metagenome sequences to fully understand how complex microbial communities function and how microbes interact within these niches represents a major challenge for microbiologists today.

Bacteria↗

PubMed2005

Bacteriophages--potential for application in wastewater treatment processes.

Bacteriophages are viruses that infect and lyse bacteria. Interest in the ability of phages to control bacterial populations has extended from medical applications into the fields of agriculture, aquaculture and the food industry. Here, the potential application of phage techniques in wastewater treatment systems to improve effluent and sludge emissions into the environment is discussed. Phage-mediated bacterial mortality has the potential to influence treatment performance by controlling the abundance of key functional groups. Phage treatments have the potential to control environmental wastewater process problems such as: foaming in activated sludge plants; sludge dewaterability and digestibility; pathogenic bacteria; and to reduce competition between nuisance bacteria and functionally important microbial populations. Successful application of phage therapy to wastewater treatment does though require a fuller understanding of wastewater microbial community dynamics and interactions. Strategies to counter host specificity and host cell resistance must also be developed, as should safety considerations regarding pathogen emergence through transduction.

Bacteria↗

PubMed2000

Comparative analysis shows that bacterivory, not viral lysis, controls the abundance of heterotrophic prokaryotic plankton.

Empirical models derived from literature data were used to compare the factors controlling prokaryotic abundance (PN) and prokaryotic heterotrophic production (PHP) in solar salterns. These empirical relationships were generated as multiple linear regressions with PN or PHP as dependent variables, while the independent variables were chosen to reflect the likely sources of organic matter, inorganic nutrients and temperature. These variables were then measured in solar salterns and the predictions made by the general relationships were compared to actual saltern values of PN and PHP. Saltern ponds of salinity higher than 100 per thousand departed significantly from the general relationships, while the ponds of salinity lower than 100 per thousand fitted well within the range of values predicted by the general models. The most likely explanation for the discrepancy of the former was the absence of bacterivory. This hypothesis was tested with data from other very different aquatic systems: karstic lakes with anaerobic hypolimnia and two marine areas in the Mediterranean and the Southern Ocean. The anoxic regions of karstic lakes departed significantly from the predictions of the general model, while the oxic layers conformed to the predictions. As in the case of salterns, this difference could be explained by the presence of significant predation in the oxic, but not in the anoxic, layers of these lakes. Finally, two marine areas with similar predation pressure on prokaryotes but very different impacts of viral lysis were tested. In all cases, PN values conformed to the predictions, suggesting that lysis due to viruses is not the main factor controlling PN in aquatic systems, which is more likely to be determined by the balance between bacterivory and resource supply. The present work also demonstrates the usefulness of empirical comparative analyses to generate predictions and to draw inferences on the functioning of microbial communities.

Journal Article↗

PubMed2000

Microbial superantigens: from structure to function.

Superantigens are highly potent immune stimulators with a unique ability to interact simultaneously with MHC class II molecules and T cell receptors, forming a trimolecular complex that induces profound T-cell proliferation and massive cytokine production. Recent structural studies have provided a wealth of information regarding these complex interactions, and it is now emerging that, despite their common 3-D architecture, superantigens are able to crosslink MHC class II molecules and T cell receptors in a variety of ways.

Amino Acid Motifs↗

PubMed1998

In situ methods for assessment of microorganisms and their activities.

Recent technical developments in the field of molecular biology and microsensors are beginning to enable microbiologists to study the abundance, localization and activity of microorganisms in situ. The various new methods on their own bear high potential but it is the combination of studies on structure and function of microbial communities that will yield the most detailed insights in the way microorganisms operate in nature.

Bacteria↗

PubMed1999

Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products.

Terminal restriction fragment length polymorphism is a recent molecular approach that can assess subtle genetic differences between strains as well as provide insight into the structure and function of microbial communities. The technique has both high sensitivity and throughput making it ideal for comparative analyses.

Ecosystem↗