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At least 955 records · Page 53Linked to original sources
PubMed2006

Transcriptional control of activation-induced cytidine deaminase and error-prone DNA polymerases is functionally mature in the B cells of infants at birth.

Somatic hypermutation (SHM) of immunoglobulin genes requires activation-induced cytidine deaminase (AID). The error-prone DNA polymerases, such as Pol eta, Pol zeta, and Pol iota, also have been implicated in the process. Human adult antibodies directed to microbial pathogens are increased in affinity and function compared with those of infants. Adult antibodies achieve this increased affinity through somatic mutations, which are lacking in the B cells of infants. It is unknown if infant B cells are capable of upregulating the cell machinery needed to introduce mutations after stimulation through the antigen receptor. We show here that infant B cells exhibit similar kinetics and magnitude of transcription of AID and pol eta genes and only marginally lower levels of pol iota and pol zeta genes after stimulation through the B cell receptor. These data suggest that the ability to upregulate gene transcription of enzymes mediating SHM is not a limiting determinant of the functional quality of infant antibody responses.

Adult↗
PubMed2001

Recent advances in computational genomics.

In the post-genomic era, the new discipline of functional genomics is now facing the challenge of associating a function (as well as estimating its relevance to industrial applications) to about 100,000 microbial, plant or animal genes of known sequence but unknown function. Besides the design of databases, computational methods are increasingly becoming intimately linked with the various experimental approaches. Consequently, bioinformatics is rapidly evolving into independent fields addressing the specific problems of interpreting i) genomic sequences, ii) protein sequences and 3D-structures, as well as iii) transcriptome and macromolecular interaction data. It is thus increasingly difficult for the biologist to choose the computational approaches that perform best in these various areas. This paper attempts to review the most useful developments of the last 2 years.

Computational Biology↗
PubMed2004

Enzyme production-based approach for determining the functions of microorganisms within a community.

The functions of specific microorganisms in a microbial community were investigated during the composting process. Cerasibacillus quisquiliarum strain BLx(T) and Bacillus thermoamylovorans strain BTa were isolated and characterized in our previous studies based on their dominance in the composting system. Strain BLx(T) degrades gelatin, while strain BTa degrades starch. We hypothesized that these strains play roles in gelatinase and amylase production, respectively. The relationship between changes in the abundance ratios of each strain and those of each enzyme activity during the composting process was examined to address this hypothesis. The increase in gelatinase activity in the compost followed a dramatic increase in the abundance ratio of strain BLx(T). Zymograph analysis demonstrated that the pattern of active gelatinase bands from strain BLx(T) was similar to that from the compost. Gelatinases from both BLx(T) and compost were partially purified and compared. Homologous N-terminal amino acid sequences were found in one of the gelatinases from strain BLx(T) and that of compost. These results indicate strain BLx(T) produces gelatinases during the composting process. Meanwhile, the increase in the abundance ratio of strain BTa was not concurrent with that of amylase activity in the compost. Moreover, the amylase activity pattern of strain BTa on the zymogram was different from that of the compost sample. These results imply that strain BTa may not produce amylases during the composting process. To our knowledge, this is the first report demonstrating that the function of a specific microorganism is directly linked to a function in the community, as determined by culture-independent and enzyme-level approaches.

Amino Acid Sequence↗
PubMed1987

Estimating downwind concentrations of viable airborne microorganisms in dynamic atmospheric conditions.

A Gaussian plume model has been modified to include an airborne microbial survival term that is a best-fit function of laboratory experimental data of weather variables. The model has been included in an algorithm using microbial source strength and local hourly mean weather data to drive the model through a summer- and winter-day cycle. For illustrative purposes, a composite airborne "virus" (developed using actual characteristics from two viruses) was used to show how wind speed could have a major modulating effect on near-source viable concentrations. For example, at high wind speeds such as those occurring during the day, or with short travel times, near-source locations experience high viable concentrations because the microorganisms have not had time to become inactivated. As the travel time increases, because of slow wind speed or longer distances, die-off modulation by sunshine, relative humidity, temperature, etc., potentially becomes increasingly predominant.

Air Microbiology↗
PubMed1983

Ceftazidime as a single agent in the treatment of severe Pseudomonas aeruginosa infections.

Ceftazidime was administered intravenously in doses of 1 to 6 g/day to 21 patients with serious Pseudomonas aeruginosa infections (12 pulmonary, 6 septicaemias, 3 urinary tract infections). Mean MIC was 1.0 mg/l. Eighteen (86%) of the 21 patients responded satisfactorily (cured or improved). The selection or emergence of resistant organisms during treatment (mostly Candida, Staphylococcus aureus, and enterococci) was noted in 6 patients. Toxicity was minimal (eosinophilia and reversible mild liver function abnormalities).

Adolescent↗
PubMedDate not supplied

[Adaptive functions of extracellular autoregulators of microorganisms].

Information about the functions of extracellular autoregulators, which adapt microorganisms to the stresses "scheduled" in the development cycle of microbial cultures (stresses of new medium, starvation, or space exhaustion (high cell density)) is summarized in the review. In a number of bacteria and yeasts, derivatives of alkylhydroxybenzenes (AHB), particularly of the class of alkyl resorcinols, act as autoregulators with adaptogenic functions. The chemical structure of AHB determines their amphiphility; capacity for physical and chemical interaction with membrane lipids, proteins, and DNA; properties as natural modifiers of biological membranes and enzymes; and the expression of antioxidant activity. Increase of AHB concentration up to the critical level (10(-5)-10(-4) M) results in cessation of cell division and in transition of the microbial culture to the stationary phase; further increase to 10(-4)-10(-3) M induces a transition of some of the cells of a post-stationary culture to the anabiotic state with the formation of cystlike resting cells (CRC), even in non-spore-forming bacteria. AHB participate in the regulation of the phenotypic variability of bacteria. The dynamics of extra- and intracellular concentrations of AHB in growing microbial cultures and the polymodality of their effect determine the adaptogenic functions of AHB as autoinhibitors of culture growth, autoinducers of anabiosis, and autoinhibitors of germination of resting forms. Manifestation of any given function depends on the concentration of AHB, the physiological state of the recipient cells, and on environmental factors. The species nonspecificity of AHB effects points to their significant role in the regulation of the development and functioning of microbial communities.

Adaptation, Physiological↗
PubMedDate not supplied

Dental plaque as a microbial biofilm.

New technologies have provided novel insights into how dental plaque functions as a biofilm. Confocal microscopy has confirmed that plaque has an open architecture similar to other biofilms, with channels and voids. Gradients develop in areas of dense biomass over short distances in key parameters that influence microbial growth and distribution. Bacteria exhibit an altered pattern of gene expression either as a direct result of being on a surface or indirectly as a response to the local environmental heterogeneity within the biofilm. Bacteria communicate via small diffusible signalling molecules (e.g. competence-stimulating peptide, CSP; autoinducer 2); CSP induces both genetic competence and acid tolerance in recipient sessile cells. Thus, rates of gene transfer increase in biofilm communities, and this is one of several mechanisms (others include: diffusion-reaction, neutralization/inactivation, slow growth rates, novel phenotype) that contribute to the increased antimicrobial resistance exhibited by bacteria in biofilms. Oral bacteria in plaque do not exist as independent entities but function as a co-ordinated, spatially organized and fully metabolically integrated microbial community, the properties of which are greater than the sum of the component species. A greater understanding of the significance of dental plaque as a mixed culture biofilm will lead to novel control strategies.

Bacterial Adhesion↗
PubMed2000

The University of Minnesota Biocatalysis/Biodegradation database: microorganisms, genomics and prediction.

The University of Minnesota Biocatalysis/Biodegradation Database (http://www.labmed.umn.edu/umbbd/ ) begins its fifth year having met its initial goals. It contains approximately 100 pathways for microbial catabolic metabolism of primarily xenobiotic organic compounds, including information on approximately 650 reactions, 600 compounds and 400 enzymes, and containing approximately 250 microorganism entries. It includes information on most known microbial catabolic reaction types and the organic functional groups they transform. Having reached its first goals, it is ready to move beyond them. It is poised to grow in many different ways, including mirror sites; fold prediction for its sequenced enzymes; closer ties to genome and microbial strain databases; and the prediction of biodegradation pathways for compounds it does not contain.

Biodegradation, Environmental↗
PubMed2005

Modeling the survival of Salmonella spp. in chorizos.

The survival of Salmonella spp. in chorizos has been studied under the effect of storage conditions; namely temperature (T=6, 25, 30 degrees C), air inflow velocity (F=0, 28.4 m/min), and initial water activity (a(w0)=0.85, 0.90, 0.93, 0.95, 0.97). The pH was held at 5.0. A total of 20 survival curves were experimentally obtained at various combinations of operating conditions. The chorizos were stored under four conditions: in the refrigerator (Ref: T=6 degrees C, F=0 m/min), at room temperature (RT: T=25 degrees C, F=0 m/min), in the hood (Hd: T=25 degrees C, F=28.4 m/min), and in the incubator (Inc: T=30 degrees C, F=0 m/min). Semi-logarithmic plots of counts vs. time revealed nonlinear trends for all the survival curves, indicating that the first-order kinetics model (exponential distribution function) was not suitable. The Weibull cumulative distribution function, for which the exponential function is only a special case, was selected and used to model the survival curves. The Weibull model was fitted to the 20 curves and the model parameters (alpha and beta) were determined. The fitted survival curves agreed with the experimental data with R(2)=0.951, 0.969, 0.908, and 0.871 for the Ref, RT, Hd, and Inc curves, respectively. Regression models relating alpha and beta to T, F, and a(w0) resulted in R(2) values of 0.975 for alpha and 0.988 for beta. The alpha and beta models can be used to generate a survival curve for Salmonella in chorizos for a given set of operating conditions. Additionally, alpha and beta can be used to determine the times needed to reduce the count by 1 or 2 logs t(1D) and t(2D). It is concluded that the Weibull cumulative distribution function offers a powerful model for describing microbial survival data. A comparison with the pathogen modeling program (PMP) revealed that the survival kinetics of Salmonella spp. in chorizos could not be adequately predicted using PMP which underestimated the t(1D) and t(2D). The mean of the Weibull probability density function correlated strongly with t(1D) and t(2D), and can serve as an alternative to the D-values normally used with first-order kinetic models. Parametric studies were conducted and sensitivity of survival to operating conditions was evaluated and discussed in the paper. The models derived herein provide a means for the development of a reliable risk assessment system for controlling Salmonella spp. in chorizos.

Animals↗
PubMed2004

Breaking into the epithelial apical-junctional complex--news from pathogen hackers.

The epithelial apical-junctional complex is a key regulator of cellular functions. In addition, it is an important target for microbial pathogens that manipulate the cell to survive, proliferate and sometimes persist within a host. Out of a myriad of potential molecular targets, some bacterial and viral pathogens have selected a subset of protein targets at the apical-junctional complex of epithelial cells. Studying how microbes use these targets also teaches us about the inherent physiological properties of host molecules in the context of normal junctional structure and function. Thus, we have learned that three recently uncovered components of the apical-junctional complex of the Ig superfamily--junctional adhesion molecule, Nectin and the coxsackievirus and adenovirus receptor--are important regulators of junction structure and function and represent critical targets of microbial virulence gene products.

Animals↗
PubMed2001

Finding drug targets in microbial genomes.

In this era of genomic science, knowledge about biological function is integrated increasingly with DNA sequence data. One area that has been significantly impacted by this accumulation of information is the discovery of drugs to treat microbial infections. Genome sequencing and bioinformatics is driving the discovery and development of novel classes of broad-spectrum antimicrobial compounds, and could enable medical science to keep pace with the increasing resistance of bacteria, fungi and parasites to current antimicrobials. This review discusses the use of genomic information in the rapid identification of target genes for antimicrobial drug discovery.

Journal Article↗
PubMed2002

Adsorbed poly(ethyleneoxide)-poly(propyleneoxide) copolymers on synthetic surfaces: spectroscopy and microscopy of polymer structures and effects on adhesion of skin-borne bacteria.

Poly(ethyleneoxide)-copoly(propyleneoxide) (PEO-PPO) polymer coatings were evaluated for their resistance to the attachment of the marker organism Serratia marcescens and the skin-borne bacteria Staphylococcus epidermidis. The copolymers were adsorbed onto poly(styrene) films-chosen as simplified physicochemical models of skin surfaces-and their surface characteristics probed by contact angle goniometry, attenuated total reflectance-Fourier transform infrared (ATR-FTIR), atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). These functional surfaces were then presented to microbial cultures, bacterial attachment was assessed by fluorescence microscopy and AFM, and the structures of the polymer films examined again spectroscopically. Surface characterization data suggest that the adsorbed copolymer was partially retained at the surface and resisted bacterial attachment for 24 h. Quantitative evaluation of cell attachment was carried out by scintillation counting of (14)C-labeled microorganisms in conjunction with plate counts. The results show that a densely packed layer of PEO-PPO copolymer can reduce attachment of skin commensals by an order of magnitude, even when the coating is applied by a simple adsorptive process. The work supports the hypothesis that adhesion of microorganisms to biological substrates can be reduced if a pretreatment with an appropriate copolymer can be effected in vivo.

Adsorption↗
PubMed1995

Aerosol administration of antibiotics.

Antibiotics can be aerosolized to the lower respiratory tract of patients with pulmonary infections. With attention to stability of the antibiotic, its ability to be aerosolized, and particle size of the aerosol, rational design of an antibiotic aerosol treatment regimen is possible. The choice of nebulizer for aerosol antibiotic administration depends not only on drug stability under the nebulization conditions, but practical considerations such as ease of use in the home and expense. In general, a greater volume of respirable aerosol is generated by an ultrasonic device in comparison to the jet nebulizers. Of the factors affecting antibiotic delivery to the lower respiratory tract, the patients and their disease are the most important. This patient effect is not directly amenable to medical intervention, but can be controlled through measurement of antibiotic concentrations in respiratory secretions, seeking a target estimated from the best available in vitro data.

Administration, Inhalation↗
PubMedDate not supplied

Composite linear models for incomplete multinomial data.

A composite linear model (CLM) is a matrix model for incomplete multinomial data. A CLM provides a unified approach for maximum likelihood inference which is applicable to a wide variety of problems involving incomplete multinomial data. By formulating a model as a CLM, one can simplify computation of maximum likelihood estimates and asymptotic standard errors. As an example, we use CLM to test marginal homogeneity for ordered categories, subject to both ignorable and non-ignorable missing-data mechanisms.

Algorithms↗
PubMed1993

An unexpected correlation between cardinal temperatures of microbial growth highlighted by a new model.

A new model for the prediction of microbial-specific growth rate as a function of temperature is presented. The four parameters of this model are the three cardinal temperatures (Tmax, Tmin and Topt) and the specific growth rate at the optimum temperature (mu opt). A comparison with three other models was made on the basis of several criteria (simplicity and biological significance of parameters, applicability, quality of fit, minimum structural correlations and ease of determination of parameters). A detailed comparison of a 217-point data set, and an extensive comparison of 47 different data sets show that the new model is better than its competitors. The three cardinal temperatures were found to be independent of mu opt. A very strong and unexpected linear correlation between the cardinal temperatures was observed. The consequences of this biological result are discussed, even though causes remain unknown.

Bacteria↗
PubMed1982

Regulation of macrophage accessory functions by interactions involving lymphokines and endotoxin.

It is important to reemphasize the observation that two distinct regulatory molecules, colony-stimulating factor (CSF) and interferon, can directly influence macrophage accessory functions. CSF stimulates macrophages to secrete interleukin 1 (IL 1) whereas interferon induces a conversion to Ia antigen expression. Either directly or indirectly these functions can also be influenced by a combination of lymphokines and bacterial lipopolysaccharides (LPS). As is the case with effector functions, it is apparent that specific regulatory molecules exist which function to amplify the influence of microbial products on macrophage accessory activities.

Animals↗
PubMed1976

Preparation of isolated single cardiac cells from adult frog atrial tissue.

Isolated cardiac cells from bullfrog atrial tissue can be readily prepared by digestion of intact fragments of atrial tissue with trypsin and collagenase. These isolated cells have dimensions of about 5 mum in width and range in length from 300 mum to over 500 mum. Such isolated cells may prove useful for the investigation of contractile activity of cardiac muscle at the single cell level and at the sarcomere level within the single cell.

Animals↗
PubMed1998

Galectins: versatile modulators of cell adhesion, cell proliferation, and cell death.

Lectins, or carbohydrate binding proteins, recognize specific oligosaccharide structures on glycoproteins and glycolipids. Several families of animal lectins have been identified; for some of these lectins, functions such as leukocyte adhesion and microbial opsonization have been described. The galectins are a family of lectins found in species ranging from sponges and nematodes to humans. Members of the galectin family have been proposed to mediate cell adhesion, to regulate cell growth, and to trigger or inhibit apoptosis. The expression pattern of different galectins changes during development, and this pattern is also altered at sites of inflammation and in breast, colon, prostate, and thyroid carcinomas. In addition, the level of expression of some galectins by tumor cells has been shown to be correlated with metastatic potential. The mechanisms by which galectins exert these diverse effects remain largely unknown. Some glycoprotein counterreceptors recognized by certain galectins have been identified; this is an important first step in understanding the cell-type specific effects of different galectins. This review discusses the way in which the modulation of galectin activity may affect strategies for treatment of a variety of human diseases, including autoimmunity and cancer.

Animals↗