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At least 145 records · Page 8Linked to original sources

PubMed2005

Immunostimulatory functions of membrane-bound and exported heat shock protein 70.

In the search for tumor-specific antigens, microbial and eukaryotic heat shock proteins (HSP) have been identified. Intracellularly, HSPs function as molecular chaperones supporting folding and transport of a great variety of polypeptides and proteins under normal physiological conditions and following stress stimuli. Furthermore, interferon-gamma and elevated body temperature induced by exercise have been found to increase serum levels of HSPs in humans. Extracellularly localized or plasma membrane-bound HSPs elicit a potent anti-cancer immune response mediated either by the adaptive or innate immune system. Following uptake of HSP (HSP70 and gp96)-peptide complexes by antigen presenting cells (APCs) and "cross-presentation" of HSP-chaperoned peptides on MHC class I molecules, a CD8-specific T cell response is induced. Apart from chaperoning tumor-specific peptides, HSPs per se provide activatory signals for the innate immune system. Binding of peptide-free HSP70 to APCs via Toll-like receptors (TLRs) initiates the secretion of pro-inflammatory cytokines and thus results in a broad non-specific immunostimulation. An unusual membrane localization of Hsp70, the major heat-inducible member of the HSP70 family, on tumor cells but not on corresponding normal tissues was found to act as a tumor-specific recognition structure for natural killer (NK) cells. Soluble as well as cell membrane-bound HSP70 can directly activate the cytolytic and migratory capacity of NK cells. APCs and tumor cells actively release HSP70s in lipid vesicles with biophysical properties of exosomes. These HSP70-presenting exosomes are thought to stimulate the adaptive and innate immune system in vivo. Taken together, depending on their intra/extracellular localization, peptide loading status, origin and route of application, HSPs either exert immune activation as danger signals in cancer immunity or protect cells from lethal damage induced by exogenous stress stimuli.

CD8-Positive T-Lymphocytes↗

PubMed1993

From genotype to phenotype: computer-based modeling of gene expression with STELLA II.

STELLA II is a microcomputer program that is designed to simulate and animate the dynamics generated by biological systems in a quantitative fashion. The program employs the Macintosh user interface and includes a tool kit for assembling models, plus menus for setting parameters and selecting input or output. Quantitative relationships among components may be expressed with user-defined equations, graphical functions or data from spreadsheets. System dynamics are simulated by running the program after defining initial conditions, and results may be viewed immediately using windows for graphical or tabular plots. The present article describes how STELLA II may be used to simulate gene expression as an adjunct to experimentation or student-directed learning.

Bacteria↗

PubMed1997

Bacteria, molds, and toxins in water-damaged building materials.

Microbial toxins and eukaryotic cell toxicity from indoor building materials heavily colonized by fungi and bacteria were analyzed. The dominant colonizers at water-damaged sites of the building were Stachybotrys chartarum (10(3) to 10(5) visible conidia cm-2), Penicillium and Aspergillus species (10(4) CFU mg-1), gram-negative bacteria (10(4) CFU mg-1), and mycobacteria (10(3) CFU mg-1). The mycobacterial isolates were most similar to M. komossense, with 98% similarity of the complete 16S rDNA sequence. Limulus assay of water extracts prepared from a water-damaged gypsum liner revealed high contents of gram-negative endotoxin (17 ng mg-1 of E. coli lipopolysaccharide equivalents) and beta-D-glucan (210 ng mg-1 of curdlan equivalents). High-performance liquid chromatography analysis of the methanol extracts showed that the water-damaged gypsum liner also contained satratoxin (17 ng mg-1). This methanol-extracted substance was 200 times more toxic to rabbit skin and fetus feline lung cells than extract of gypsum liner sampled from a non-water-damaged site. The same extract contained toxin(s) that paralyzed the motility of boar spermatozoa at extremely low concentrations; the 50% effective concentration was 0.3 microgram of dry solids per ml. This toxicity was not explainable by the amount of bacterial endotoxin, beta-D-glucan, or satratoxin present in the same extract. The novel in vitro toxicity test that utilized boar spermatozoa as described in this article is convenient to perform and reproducible and was a useful tool for detecting toxins of microbial origin toward eukaryotic cells not detectable in building materials by the other methods.

Animals↗

PubMed2001

Escherichia coli ykfE ORFan gene encodes a potent inhibitor of C-type lysozyme.

The complete nucleotide sequences of over 37 microbial and three eukaryote genomes are already publicly available, and more sequencing is in progress. Despite this accumulation of data, newly sequenced microbial genomes continue to reveal up to 50% of functionally uncharacterized "anonymous" genes. A majority of these anonymous proteins have homologues in other organisms, whereas the rest exhibit no clear similarity to any other sequence in the data bases. This set of unique, apparently species-specific, sequences are referred to as ORFans. The biochemical and structural analysis of ORFan gene products is of both evolutionary and functional interest. Here we report the cloning and expression of Escherichia coli ORFan ykfE gene and the functional characterization of the encoded protein. Under physiological conditions, the protein is a homodimer with a strong affinity for C-type lysozyme, as revealed by co-purification and co-crystallization. Activity measurements and fluorescence studies demonstrated that the YkfE gene product is a potent C-type lysozyme inhibitor (K(i) approximately 1 nm). To denote this newly assigned function, ykfE has now been registered under the new gene name Ivy (inhibitor of vertebrate lysozyme) at the E. coli genetic stock center.

Amino Acid Sequence↗

PubMed2004

Bacterial inhibition of eukaryotic pro-inflammatory pathways.

Eukaryotic cells perceive and respond to microbes, both pathogenic and commensal, by activation of signaling cascades such as the NF-kappaB pathway. Induction of such pathways leads to the upregulation of a program of gene expression that mediates pro-inflammatory and anti-apoptotic effector proteins. This host response is usually effective in clearing or controlling an infection. For pathogens (and potentially, symbionts) to continue their lifecycle, it is necessary to evade or repress these cellular responses. There has been recent interest in bacteria that can inhibit pro-inflammatory pathways, in some cases by the actions of soluble effector proteins secreted via a Type III secretion system. Certain effector proteins with this function possess enzymatic activity toward ubiquitin and related molecules. Ubiquitination is an increasingly recognized regulatory modification in eukaryotic cells, and microbial effectors that modulate this key host system may have diverse effects on infected cells and mediate many aspects of eukaryotic-prokaryotic interactions.

Animals↗

PubMed1993

Attachment factors of Bordetella pertussis: mimicry of eukaryotic cell recognition molecules.

Bacteria localize to specific target organs during infection by recognizing eukaryotic cell surface addresses. This address system exists to facilitate normal trafficking of host cells such as leukocytes. The mechanisms by which bacteria subvert host targeting codes provide a unique link between microbial pathogenesis and eukaryotic cell trafficking, and can point to a new array of antibodies and peptides of potential therapeutic value.

Amino Acid Sequence↗

PubMed2006

Evaluating support for the current classification of eukaryotic diversity.

Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification--plants, animals, fungi, and protists--have been transformed through numerous permutations into the current system of six "supergroups." The intent of the supergroup classification system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is increasing in popularity in the literature and is appearing in introductory biology textbooks. We evaluate the stability and support for the current six-supergroup classification of eukaryotes based on molecular genealogies. We assess three aspects of each supergroup: (1) the stability of its taxonomy, (2) the support for monophyly (single evolutionary origin) in molecular analyses targeting a supergroup, and (3) the support for monophyly when a supergroup is included as an out-group in phylogenetic studies targeting other taxa. Our analysis demonstrates that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature. We highlight several trends contributing to the instability and discuss the requirements for establishing robust clades within the eukaryotic tree of life.

Animals↗

PubMed2006

[Diversity and function of symbiotic microbes in the gut of lower termites].

The gut of lower termites harbor a complex microbial community, including eukaryotic flagellates and prokaryotic bacteria and archaea, which play important roles in the wood-cellulose digestion of these termites. The hindguts of lower termites are characterized with an enlarged paunch with steep oxygen and hydrogen gradient and not randomly distributed abundant microorganisms. The symbiotic flagellates in the gut of lower termites, which are normally associated with epibionts or endobionts, are phylogenetically affiliated with Trichomonadida, Hypermastigida and Oxymonadida. They endocytose wood particles and ferment the polysaccharide components to acetate, CO2 and H2, which are further metabolized by symbiotic prokaryotes as energy and nutrition sources in the termites. Cellulose genes such as glycosyl hydrolase family 45 have been identified in gut protists with molecular approach. Phylogenetic analysis have revealed that in the gut of lower termites, such as several Reticulitermites species, most of the dominant bacteria belong to phyla like "Termite group 1", Spirochaetes, Firmicutes, Bacteroidetes, and Proteobacteria. These bacteria clones normally form distinct termite clusters in phylogenetic trees, which show the existence of specific microbial diversity in the termite guts. Most of the symbiotic archaea in the gut of lower termites are methanogens and affiliated with the genus Methanobrevibacter by phylogenetic analysis and pure culture. The symbiotic bacteria and archaea may involve in the reduction of CO2 and the metabolism of N2 in these termite guts. However, the functions and metabolic mechanisms of the symbiotic flagellates and prokaryotes in the gut of lower termites are still remaining to be further elucidated.

Animals↗

PubMed2005

Global metabolite analysis of yeast: evaluation of sample preparation methods.

Sample preparation is considered one of the limiting steps in microbial metabolome analysis. Eukaryotes and prokaryotes behave very differently during the several steps of classical sample preparation methods for analysis of metabolites. Even within the eukaryote kingdom there is a vast diversity of cell structures that make it imprudent to blindly adopt protocols that were designed for a specific group of microorganisms. We have therefore reviewed and evaluated the whole sample preparation procedures for analysis of yeast metabolites. Our focus has been on the current needs in metabolome analysis, which is the analysis of a large number of metabolites with very diverse chemical and physical properties. This work reports the leakage of intracellular metabolites observed during quenching yeast cells with cold methanol solution, the efficacy of six different methods for the extraction of intracellular metabolites, and the losses noticed during sample concentration by lyophilization and solvent evaporation. A more reliable procedure is suggested for quenching yeast cells with cold methanol solution, followed by extraction of intracellular metabolites by pure methanol. The method can be combined with reduced pressure solvent evaporation and therefore represents an attractive sample preparation procedure for high-throughput metabolome analysis of yeasts.

Freeze Drying↗

PubMed2000

Nitric oxide involvement in Drosophila immunity.

The augmented production of nitric oxide (NO) was observed during the hemocyte-mediated melanotic encapsulation responses of Drosophila melanogaster and D. teissieri. When introduced into the hemocoel of D. melanogaster larvae, NO activated the gene encoding the antimicrobial peptide Diptericin. These observations, together with previous studies documenting the production of superoxide anion (O(*-)(2)) and H(2)O(2) in immune-challenged Drosophila, provide evidence that reactive intermediates of both oxygen (ROI) and nitrogen (RNI) constitute a part of the cytotoxic arsenal employed by Drosophila in defense against both microbial pathogens and eukaryotic parasites. These ROI and RNI appear to represent an evolutionarily conserved innate immune response that is mediated by regulatory proteins that are homologous to those of mammalian species.

Animals↗

PubMed2005

Translational effects of differential codon usage among intragenic domains of new genes in Drosophila.

Evolved codon usages often pose a technical challenge over the expressing of eukaryotic genes in microbial systems because of changed translational machinery. In the present study, we investigated the translational effects of intragenic differential codon usage on the expression of the new Drosophila gene, jingwei (jgw), a chimera derived from two unrelated parental genes: Ymp and Adh. We found that jgw possesses a strong intragenic differential usage of synonymous codons, i.e. the Adh-derived C-domain has a significantly higher codon bias than that of the Ymp-derived N-domain (P=0.0023 by t-test). Additional evolutionary analysis revealed the heterogeneous distribution of rare codons, implicating its role in gene regulation and protein translation. The in vitro expression of jgw further demonstrated that the heterogeneous distribution of rare codons has played a role in regulating gene expression, particularly, affecting the quality of protein translation.

Alcohol Dehydrogenase↗

PubMed1997

Structure and function of the low Mr phosphotyrosine protein phosphatases.

Phosphotyrosine protein phosphatases (PTPases) catalyse the hydrolysis of phosphotyrosine residues in proteins and are hence implicated in the complex mechanism of the control of cell proliferation and differentiation. The low Mr PTPases are a group of soluble PTPases displaying a reduced molecular mass; in addition, a group of low molecular mass dual specificity (ds)PTPases which hydrolyse phosphotyrosine and phosphoserine/threonine residues in proteins are known. The enzymes belonging to the two groups are unrelated to each other and to other PTPase classes except for the presence of a CXXXXXRS/T sequence motif containing some of the catalytic residues (active site signature) and for the common catalytic mechanism, clearly indicating convergent evolution. The low Mr PTPases have a long evolutionary history since microbial (prokaryotic and eukaryotic) counterparts of both tyrosine-specific and dsPTPases have been described. Despite the relevant number of data reported on the structural and catalytic features of a number of low Mr PTPases, only limited information is presently available on the substrate specificity and the true biological roles of these enzymes, in prokaryotic, yeast and eukaryotic cells.

Amino Acid Sequence↗

PubMed2006

Sexual acquisition of beneficial symbionts in aphids.

A noted cost of mating is the risk of acquiring sexually transmitted infections that are detrimental to the recipient. But many microbial associates of eukaryotes are mutualistic, raising the possibility that sexual contact provides the opportunity to acquire symbionts that are beneficial. In aphids, facultative bacterial symbionts, which benefit hosts by conferring resistance to natural enemies or to heat, are transmitted maternally with high fidelity and are maintained stably throughout hundreds of parthenogenetic generations in the laboratory. Data from field populations indicate that horizontal transfer of these facultative symbionts is frequent, and transfections are readily achieved by microinjection or ingestion in artificial diet. However, no natural mechanism for the horizontal transfer of these symbionts has been identified. Here we demonstrate that during sexual reproduction, male-borne symbionts can be acquired by females and subsequently transferred to sexually and parthenogenetically produced progeny, establishing stable, maternally transmitted associations. In our experiments, sexually transmitted symbionts resulted in (i) infection of previously uninfected matrilines, (ii) a double infection in a matriline already bearing a different symbiont, and (iii) replacement of the maternal symbiont. We also observed some cases in which maternal symbionts failed to become established in sexually produced progeny. Microscopy indicated that symbionts were abundant in the male reproductive system, which demonstrates a natural route of nonmaternal transfer of insect symbionts. Because such transfer can generate coinfections, thereby creating opportunities for symbiont competition and recombination, paternal inheritance has major consequences for expectations regarding symbiont evolution.

Animals↗

PubMed1986

Gastrointestinal microflora in mammalian nutrition.

A mammal is a complex organism consisting of eukaryotic animal cells and eukaryotic and prokaryotic microbial cells. Most of the microorganisms reside in communities in the gastrointestinal tract. These gastrointestinal microfloras are known to serve nutritional functions in ruminants, pseudoruminants, and monogastric mammals with only modest or no foregut fermentations but with extensive hindgut fermentations in blind cecal pouches. In adult animals, the microflora hydrolyzes exogenous (dietary) and endogenous polymers, and provides the adult with all or at least a significant proportion of its carbon, energy, vitamins, and macromolecular building blocks. The flora also functions as a conservator of nitrogen that would otherwise be excreted as urea. In exchange, the flora competes directly with the host tissues for nutrients ingested in the diet, and also competes indirectly by somewhat repressing the absorptive capacities of the animal tissues. When the synergism is in balance, the animal tissues and the microflora operate in harmony for the health and nutritional welfare of the host as a whole. The system may be unbalanced by antibacterial drugs that destroy the microflora and by diseases of the animal tissues that destroy the controls regulating where indigenous communities localize in the tract, their microbial composition, and their biochemical activities. At such times, the nutrition of the animal tissues can be adversely affected to the extreme. Humans living in developed and developing countries have extensive microfloras in their hindguts. Humans living in developing countries may also have extensive microfloras in their small bowels. Those floras may function in nutrition of the animal tissues of man much the same as do floras in similar locations in the gastrointestinal tracts of mammals other than man. However, animals of some species other than human gain much of the nutritional benefit from their microflora through the practice of coprophagy. Since adult humans do not normally practice coprophagy, any nutritional benefit from the microflora depends upon the capacity of the bowel mucosa, principally that of the large bowel, to absorb bacterial products, e.g. short-chain volatile fatty acids. Such absorption undoubtedly occurs, but is surely not a major source of carbon and energy for the animal tissues of man.

Anaerobiosis↗

PubMed2006

Soluble adamantyl glycosphingolipid analogs as probes of glycosphingolipid function.

Despite the extensive structural characterization of glycosphingolipids (GSLs), their functions in cell physiology and pathobiology remain elusive. This is largely owing to the fact that they are difficult to handle, being insoluble in aqueous media, and that no one gene alone determines their synthesis. The heterogeneity of the lipid moiety provides a further confounding factor. GSLs are central components within lipid rafts, which are major foci for transmembrane signaling and interactions between eukaryotic cells and microbial pathogens. GSL receptor function often requires the lipid moiety, and lipid-free sugar analogs are ineffective inhibitors. In order to overcome some of these problems, we have synthesized adamantyl GSL analogs which, in part, mimic GSL membrane receptor function in solution. These compounds are made by replacing the endogenous fatty acid with an adamantan frame. This rigid hydrophobic structure surprisingly increases the water solubility of the conjugate and retains receptor function. These GSL mimics provide probes to study GSL receptor function within cells. They compete with native GSLs for ligand binding and are taken up by cells to potentially alter GSL-mediated interaction. We are focused on two derivatives, adamantyl globotriaosyl ceramide and adamantyl sulfogalactosyl ceramide, and have used these analogs to probe GSL function in microbial pathology and hsp70 function. This chapter describes the syntheses and uses of these mimics.

Adamantane↗

PubMed2003

Endothelial responses to bacterial toxins in sepsis.

The virulence of pathogenic bacteria is critically dependent on their ability to produce toxins that attack eukaryotic target cells. Microbial toxins are either structural components of the bacterial cell wall (endotoxins) or actively secreted proteins (exotoxins). Sepsis and septic shock, which represent major causes of mortality in modern intensive care medicine, are caused by an inadequate inflammatory and immunological host response to bacterial infection. Emerging evidence suggests that the systemic spread of microbial toxins, rather than bacteremia itself, is the crucial event in the pathogenesis of this dramatic dysregulation. The endothelium, with its diversity of physiological functions is a main target of bacterial toxins. The resulting endothelial dysfunction is believed to contribute to the underlying pathomechanisms and the collapse of homeostasis of organ function. In vitro, bacterial toxins induce subtle alterations of endothelial cell function rather than massive cell damage. Furthermore, bacterial toxins targeting endothelial cells severely alter the behavior of extravascular cells and circulating leukocytes via excessive formation of vasoactive mediators and overexpression of adhesion molecules. Research on the effects of microbial toxins on vascular endothelium has broadened our general understanding of microbial strategies to induce organ damage, even in the absence of viable bacteria. Combining antitoxin strategies with antibiotic therapy may prove to be of benefit to patients suffering from bacterial sepsis in the future.

Animals↗

PubMed2005

Eukaryotic UDP-galactopyranose mutase (GLF gene) in microbial and metazoal pathogens.

Galactofuranose (Gal(f)) is a novel sugar absent in mammals but present in a variety of pathogenic microbes, often within glycoconjugates that play critical roles in cell surface formation and the infectious cycle. In prokaryotes, Gal(f) is synthesized as the nucleotide sugar UDP-Gal(f) by UDP-galactopyranose mutase (UGM) (gene GLF). Here we used a combinatorial bioinformatics screen to identify a family of candidate eukaryotic GLFs that had previously escaped detection. GLFs from three pathogens, two protozoa (Leishmania major and Trypanosoma cruzi) and one fungus (Cryptococcus neoformans), had UGM activity when expressed in Escherichia coli and assayed in vivo and/or in vitro. Eukaryotic GLFs are closely related to each other but distantly related to prokaryotic GLFs, showing limited conservation of core residues around the substrate-binding site and flavin adenine dinucleotide binding domain. Several eukaryotes not previously investigated for Gal(f) synthesis also showed strong GLF homologs with conservation of key residues. These included other fungi, the alga Chlamydomonas and the algal phleovirus Feldmannia irregularis, parasitic nematodes (Brugia, Onchocerca, and Strongyloides) and Caenorhabditis elegans, and the urochordates Halocynthia and Cionia. The C. elegans open reading frame was shown to encode UGM activity. The GLF phylogenetic distribution suggests that Gal(f) synthesis may occur more broadly in eukaryotes than previously supposed. Overall, GLF/Gal(f) synthesis in eukaryotes appears to occur with a disjunct distribution and often in pathogenic species, similar to what is seen in prokaryotes. Thus, UGM inhibition may provide an attractive drug target in those eukaryotes where Gal(f) plays critical roles in cellular viability and virulence.

Amino Acid Sequence↗

PubMed2004

Host specificity in marine sponge-associated bacteria, and potential implications for marine microbial diversity.

Biodiversity is fundamental to both eukaryote and prokaryote ecology, yet investigations of diversity often differ markedly between the two disciplines. Host specificity - the association of organisms with only a few (specialism) or many (generalism) host species - is recognized within eukaryote ecology as a key determinant of diversity. In contrast, its implications for microbial diversity have received relatively little attention. Here we explore the relationship between microbial diversity and host specificity using marine sponge-bacteria associations. We used a replicated, hierarchical sampling design and both 16S rDNA- and rpoB-based denaturing gradient gel electrophoresis (DGGE) to examine whether three co-occurring sponges from temperate Australia -Cymbastela concentrica, Callyspongia sp. and Stylinos sp. - contained unique, specialized communities of microbes. Microbial communities varied little within each species of sponge, but variability among species was substantial. Over five seasons, the microbial community in C. concentrica differed significantly from other sponges, which were more similar to seawater. Overall, three types of sponge-associated bacteria were identified via 16S rDNA sequencing of excised DGGE bands: 'specialists'- found on only one host species, 'sponge associates'- found on multiple hosts but not in seawater, and 'generalists' from multiple hosts and seawater. Analogous to other high diversity systems, the degree of specificity of prokaryotes to host eukaryotes could have a potentially significant effect on estimates of marine microbial diversity.

Animals↗