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PubMed2006

Microbial community of biological phosphorus removal process fed with municipal wastewater under different electron acceptor conditions.

The microbial community in a biological phosphorus removal process under different electron acceptor conditions was estimated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) assay and principal-component analysis (PCA). For this purpose, a lab-scale sequencing batch reactor (SBR) fed with municipal wastewater was operated under anaerobic-aerobic, anaerobic-anoxic-aerobic and anaerobic-anoxic conditions. The results of PCR-DGGE targeting the 16S rRNA gene indicated a significant shift in the microbial community with electron acceptor conditions. From the 16S rRNA-based PCA, the microbial shift implies that little oxygen supply caused the deterioration of aerobic bacteria, including aerobic polyphosphate-accumulating organisms (PAOs). Moreover, it also reflects the existence of nitrate-utilizing denitrifiers. On the other hand, although the band patterns of DGGE targeting a functional gene of denitrification (nirS) also showed the microbial shift, the result of PCA differed from that of 16S rRNA-based analysis. There is no conclusive proof that the bacteria represented as the dominant bands detected in the present study are denitrifying-PAOs so far, it should be worthwhile to identify the detected bacteria and to examine their traits as new denitrifying-PAO candidates.

Bacteria↗
PubMed2004

Assessment and management of soil microbial community structure for disease suppression.

Identification of the biological properties contributing to the function of suppressive soils is a necessary first step to the management of such systems for use in the control of soilborne diseases. The development and application of molecular methods for the characterization and monitoring of soil microbial properties will enable a more rapid and detailed assessment of the biological nature of soil suppressiveness. Although suppressive soils have provided a wealth of microbial resources that have subsequently been applied for the biological control of soilborne plant pathogens, the full functional capabilities of the phenomena have not been realized in production agricultural ecosystems. Cultural practices, such as the application of soil amendments, have the capacity to enhance disease suppression, though the biological modes of action may vary from that initially resident to the soil. Plants have a distinct impact on characteristics and activity of resident soil microbial communities, and therefore play an important role in determining the development of the disease-suppressive state. Likewise, plant genotype will modulate these same biological communities, and should be considered when developing strategies to exploit the potential of such a natural disease control system. Implementation of consistently effective practices to manage this resource in an economically and environmentally feasible manner will require more detailed investigation of these biologically complex systems and refinement of currently available methodologies.

Agriculture↗
PubMed2006

Evolutionary product unit based neural networks for regression.

This paper presents a new method for regression based on the evolution of a type of feed-forward neural networks whose basis function units are products of the inputs raised to real number power. These nodes are usually called product units. The main advantage of product units is their capacity for implementing higher order functions. Nevertheless, the training of product unit based networks poses several problems, since local learning algorithms are not suitable for these networks due to the existence of many local minima on the error surface. Moreover, it is unclear how to establish the structure of the network since, hitherto, all learning methods described in the literature deal only with parameter adjustment. In this paper, we propose a model of evolution of product unit based networks to overcome these difficulties. The proposed model evolves both the weights and the structure of these networks by means of an evolutionary programming algorithm. The performance of the model is evaluated in five widely used benchmark functions and a hard real-world problem of microbial growth modeling. Our evolutionary model is compared to a multistart technique combined with a Levenberg-Marquardt algorithm and shows better overall performance in the benchmark functions as well as the real-world problem.

Algorithms↗
PubMed1985

Killed Escherichia coli stimulates macrophage-mediated alterations in hepatocellular function during in vitro coculture: a mechanism of altered liver function in sepsis.

Hepatic dysfunction is a poorly understood and highly lethal component of multiple-system organ failure. Both in vivo and in vitro studies of "liver" function have generally neglected hepatocyte-Kupffer cell interactions. In the following experiments, isolated hepatocytes were cocultivated with unstimulated peritoneal cells, predominately macrophages, which served as a readily available Kupffer cell analog. Coculture of hepatocytes with peritoneal cells resulted in little or no change in [3H]leucine incorporation into hepatocyte protein. When gentamicin-killed Escherichia coli cells (GKEC) were added to coculture, there was a marked decrease in hepatocyte [3H]leucine incorporation. In contrast, GKEC added to hepatocytes alone had no effect. Kinetic data revealed an 8-h delay before any significant decrease in leucine incorporation into hepatocyte protein after the addition of GKEC to the coculture. The maximal decrease in hepatocyte [3H]leucine incorporation occurred 24 h after GKEC were added. The decrease observed 24 h after GKEC were added disappeared almost completely after 48 h of coculture. Similar alterations in cocultured hepatocyte protein synthesis were observed after the addition of phorbol myristate acetate, lipopolysaccharide, or muramyl dipeptide, a component of bacterial peptidoglycan. Hepatocyte viability by trypan blue exclusion was unchanged, and gross morphology by light or electron microscopy was unaffected. We propose that during sepsis, macrophages (Kupffer cells) respond to circulating microbial products and mediate alterations in hepatocyte function. These experiments underscore the important role of Kupffer cell function in attempts to understand hepatic malfunction in multiple-system organ failure.

Animals↗
PubMed2000

CD14-dependent clearance of apoptotic cells: relevance to the immune system.

Until very recently, the function of CD14 was thought to be limited to innate immune responses to bacterial and other microbial structures. It is now known that macrophage CD14 serves an additional unexpected function, namely as a receptor involved in the recognition and phagocytosis of cells undergoing apoptosis. In stark contrast to its role in eliciting pro-inflammatory responses following binding of microbial ligands, macrophage CD14 mediates clearance of apoptotic cells without inciting inflammation. Increasing interest in the profoundly important final stage of apoptosis - the engulfment process - together with significant advances in knowledge of the immunological consequences of apoptotic-cell clearance and of the means by which signal transduction may be achieved following CD14-ligand binding have begun to produce a clearer picture of the role of CD14 in the immune system.

Apoptosis↗
PubMed1999

Introducing optimal experimental design in predictive modeling: a motivating example.

Predictive microbiology emerges more and more as a rational quantitative framework for predicting and understanding microbial evolution in food products. During the mathematical modeling of microbial growth and/or inactivation, great, but not always efficient, effort is spent on the determination of the model parameters from experimental data. In order to optimize experimental conditions with respect to parameter estimation, experimental design has been extensively studied since the 1980s in the field of bioreactor engineering. The so-called methodology of optimal experimental design established in this research area enabled the reliable estimation of model parameters from data collected in well-designed fed-batch reactor experiments. In this paper, we introduce the optimal experimental design methodology for parameter estimation in the field of predictive microbiology. This study points out that optimal design of dynamic input signals is necessary to maximize the information content contained within the resulting experimental data. It is shown that from few dynamic experiments, more pertinent information can be extracted than from the classical static experiments. By introducing optimal experimental design into the field of predictive microbiology, a new promising frame for maximization of the information content of experimental data with respect to parameter estimation is provided. As a case study, the design of an optimal temperature profile for estimation of the parameters D(ref) and z of an Arrhenius-type model for the maximum inactivation rate kmax as a function of the temperature, T, was considered. Microbial inactivation by heating is described using the model of Geeraerd et al. (1999). The need for dynamic temperature profiles in experiments aimed at the simultaneous estimation of the model parameters from measurements of the microbial population density is clearly illustrated by analytical elaboration of the mathematical expressions involved on the one hand, and by numerical simulations on the other.

Bacteria↗
PubMed1996

Phenotype variability of identical genotypes: the need for a combined approach in cyanobacterial taxonomy demonstrated on Merismopedia-like isolates

Five Merismopedia-like cyanobacterial strains were collected from microbial mats at Norderney Island, subcultured in the laboratory, and finally grown as unicyanobacterial cultures. As a sixth strain, Merismopedia glauca from the rising dbl quote, left (low)Sammlung von Algenkulturen" at Gottingen (SAG) was used for comparisons. According to morphological and physiological characteristics initially observed in the field and during initial subculturing, the five strains were assigned to the species Merismopedia glauca, Merismopedia punctata, or Merismopedia elegans. However, after prolonged maintenance under laboratory conditions, the formation of platelet-like colonies stopped, whereas cell sizes, production of extracellular polymeric substances, and division patterns were stably maintained. These physiological and morphological parameters allowed us to divide the six strains into two clusters. This division was further supported by the profiling of total cell protein and phycobilisomes using SDS-PAGE. The nearly complete 16S rDNA sequence of three of the six isolates was determined. The comparative sequencing analysis revealed an almost 100% identity of these three Merismopedia-like strains. The evolutionary distance dendrogram constructed placed this Merismopedia cluster into a common line of descent with Synechocystis sp. strain PCC6906. Based on the analysis of common stretches of 1,050 nucleotides, the overall similarity between the sequence types of rising dbl quote, left (low)Merismopedia" and rising dbl quote, left (low)Synechocystis" is 96-97%. The values of the different methods for taxonomic classification of unicyanobacterial strains, the relationship of the cyanobacterial genera Merismopedia, Synechococcus, Synechocystis, and Eucapsis sp., and the functional role of different Merismopedia morphologies within microbial mats are discussed. It is suggested that all analyzed Merismopedia strains be combined into one species, namely Merismopedia punctata Meyen (1839).

Journal Article↗
PubMedDate not supplied

Microbial inclusions with special reference to PHA inclusions and intracellular boundary envelopes.

Polyhydroxyalkanoates (PHAs), in the form of metabolic storage reserves, are assembled in intracellular cytoplasmic inclusions, often called granules. This review discusses both the structure and function of this assembly. In addition an overview of other microbial cellular inclusions is presented. This is not a compilation of all such structures but a description of those that are similar in many ways to either the structure or function of the PHA inclusions and are made up of monolayer envelopes and their storage compounds. Not unique, such inclusions provide many similar examples which, in turn, provide useful analogies to the PHA inclusions. A study of the PHA inclusions has been carried out in a comparative electron microscope examination and by protein analysis of a number of organisms and E. coli transformants.

Bacteria↗
PubMed2005

Trophic interactions in the methanogenic microbial community of low-temperature terrestrial ecosystems.

The formation of methane in various ecosystems is due to the functioning of an anaerobic community, which combines trophically different groups of microorganisms. The methanogenic microbial community is a complex biological system, which responds to low temperatures by changes in its trophic structure resulting in redistributing matter flows. The enhanced activity of homoacetogenic bacteria at low temperature plays a significant role in this redistribution. Due to their relatively high growth rates and metabolic versatility, homoacetogens can successfully compete with fermenting bacteria and hydrogenotrophic methanogenic archaea for common substrates. The concentration of hydrogen is an important regulatory factor in the psychroactive methanogenic community. At low temperature methanogenic archaea possessing a higher affinity for hydrogen than homoacetogens provide for interspecies H2 transport in syntrophic reactions of fatty acid decomposition. The formation of a balanced community at low temperature is a longtime process. Cold terrestrial ecosystems are dominated by psychroactive (psychrotolerant) microorganisms, which can grow over a wide range of ambient temperatures.

Archaea↗
PubMed2000

Substrate specificities of microbial transglutaminase for primary amines.

Transglutaminase (epsilon-glutaminyl-peptide:amine gamma-glutaminyl-transferase, EC 2.3.2.13) (TGase) is an enzyme that catalyzes acyl transfer reactions between primary amines and Gln residues in proteins and peptides. The substrate specificity of TGase for primary amines was investigated to incorporate various functional groups into proteins and peptides. In this study, microbial transglutaminase and guinea pig liver transglutaminase were used. For the primary amines to be incorporated into benzyloxycarbonyl-L-Gln-Gly (Z-Gln-Gly), they were required to have more than four carbon chains without side chains between the functional groups. These results suggest that with appropriate primary amines as spacers, various functional groups, carboxyl groups, phosphate groups, saccharides, and so on, can be incorporated into proteins by using TGase.

Amines↗
PubMedDate not supplied

Zinc and infection.

Zinc is necessary for the normal functioning of all living systems. In microbes and mammals vital biological roles of zinc include the presence of this metal in metalloenzymes and membrane stabilization. In addition, zinc may bind nonspecifically to sulfhydryl, histidine, or other moieties on membranes, enzymes, or other proteins and alter their activity. Serum levels of zinc decrease sharply in many infections. Levels slightly below normal seem to be associated with optimal phagocytic function, and low concentrations of zinc may decrease microbial virulence. Brief decreases in serum levels appear to have no detrimental effect on host immunity and may act as a protective measure by decreasing the ability of indigenous or infecting microbes to thrive. However, prolonged zinc deficiency in mammals is associated with depressed T-cell function but near normal B-cell function. More work is needed for better understanding of zinc-related biochemistry and for determining the relationship between zinc status and susceptibility to infection in mammals.

Animals↗
PubMed1988

Single cell protein as food and feed.

This review pertains the current knowledge concerned with the application of SCP in human and animal nutrition. General factors limiting the utilization of microbial proteins in human nutrition, such as toxicological barriers, nutritive value and functional properties, are discussed. Special attention is paid to several modern procedures of protein extraction from microbial cells, reduction of nucleic acids level as well as preparation of protein isolates. According to the data presented the latter can be considered as valuable protein substitutes. Significantly less nutritive problems are being concerned with the application of SCP in animal nutrition. Successful feeding experiments with chicken and pigs are discussed. Under these experimental conditions 10-20% of the protein in the feedstuff can be replaced by SCP. Moreover, several in Poland obtained protein-vitamin preparations are described. These originated from selected yeast and propionic acid bacteria grown in whey and its ultrafiltrates and can be considered as valuable food and feed supplements.

Animal Feed↗
PubMed2002

Identifying functional links between genes using conserved chromosomal proximity.

Conservation of proximity of a pair of genes across multiple genomes generally indicates that their functions could be linked. Here, we present a systematic evaluation using 42 complete microbial genomes from 25 phylogenetic groups to test the reliability of this observation in predicting function for genes. We find a relationship between the number of phylogenetic groups in which a gene pair is proximate and the probability that the pair belongs to a common pathway. Our method produces 1586 links between ortholog families substantiated by observed proximity in genomes representing at least three phylogenetic groups. Of the pairs annotated in the KEGG database, 80% are in the same biological pathway in KEGG.

Chromosome Mapping↗
PubMed2005

IL-2 production by dendritic cells is not critical for the activation of cognate and innate effectors in draining lymph nodes.

Dendritic cells (DC) are unique antigen-presenting cells capable of triggering NK cell effector functions and priming naive T cells in vivo. Microbial stimulation induces early IL-2 production by mouse DC. Previous reports demonstrated that IL-2 is enriched at the site of DC/T cell interaction and promotes allogeneic T cell proliferation. However, the direct role of DC-derived IL-2 in the differentiation of cytotoxic T lymphocytes and in NK cell triggering in vivo has not been investigated. Lipopolysaccharide (LPS) stimulation of mouse bone marrow-derived DC results in early IL-2 production unless IL-4 is introduced in DC cultures. Here we show that IL-2 produced by LPS-activated DC is dispensable for cognate T cell responses since IL-2 loss of function DC elicit OVA-specific Tc1 effector and memory lymphocytes in draining lymph nodes in a setting where ex vivo cultured DC do not transfer antigens to host DC. Moreover, adoptively transferred IL-2 loss of function DC maintain their capacity to trigger NK cell proliferation/recruitment in lymph nodes. Therefore, immediate inducible IL-2 production by DC following microbial infection might play a regulatory role at ports of entry rather than in secondary lymphoid organs.

Adoptive Transfer↗
PubMed1994

Proliferative and cytolytic responses of human gamma delta T cells display a distinct specificity pattern.

The function and physiological role of gamma delta T cells are still unknown. Concerning the specificity of these cells, a proliferative response towards microbial ligands has been noted, whereas in terms of effector functions in humans a cytolytic activity against a variety of tumour targets is most prominent. Here we show data demonstrating that the cytolytic activity of activated human gamma delta T cells does not reflect the specificity of these cells in primary in vitro stimulation; moreover, we provide evidence that the recognition of target cells by gamma delta T cells can have different qualities. gamma delta T cells proliferate vigorously in primary in vitro reaction upon stimulation with various B-cell tumour lines but not with the T-cell lines Jurkat or Molt-4. However, gamma delta T cells stimulated primarily with phytohaemagglutinin or with cells from B-cell lines gain unrestricted cytolytic activity against a broad set of tumour targets, including Jurkat and Molt-4; the same set of targets is capable of inducing release of serine esterases (SE) from gamma delta T-effector cells. Whereas the cytolytic activity in the 51Cr-assay against the B-cell lines and against Molt-4 depends on the presence of Ca2+ ions in the assay, the lysis of Jurkat cells is only slightly reduced upon removal of Ca2+ from the medium; the SE release, however, is Ca2+ dependent in all cases. Taken together, these data suggest several different ways of target cell recognition by gamma delta T cells leading to either proliferation or triggering of cytolytic activity, and argue against an involvement of the gamma delta T-cell receptor in the cytotoxic activity of gamma delta T cells.

Calcium↗
PubMed2005

Mapping of orthologous genes in the context of biological pathways: An application of integer programming.

Mapping biological pathways across microbial genomes is a highly important technique in functional studies of biological systems. Existing methods mainly rely on sequence-based orthologous gene mapping, which often leads to suboptimal mapping results because sequence-similarity information alone does not contain sufficient information for accurate identification of orthology relationship. Here we present an algorithm for pathway mapping across microbial genomes. The algorithm takes into account both sequence similarity and genomic structure information such as operons and regulons. One basic premise of our approach is that a microbial pathway could generally be decomposed into a few operons or regulons. We formulated the pathway-mapping problem to map genes across genomes to maximize their sequence similarity under the constraint that the mapped genes be grouped into a few operons, preferably coregulated in the target genome. We have developed an integer-programming algorithm for solving this constrained optimization problem and implemented the algorithm as a computer software program, p-map. We have tested p-map on a number of known homologous pathways. We conclude that using genomic structure information as constraints could greatly improve the pathway-mapping accuracy over methods that use sequence-similarity information alone.

Algorithms↗