yeast genome based: Topics by WorldWideScience.org

Construction of a human MluI YAC library

Prokaryotic genomes can be annotated based on their structural, operational, and functional properties. These annotations provide the pivotal scaffold for understanding cellular functions on a genome-scale,...Full Text Available

2010-09-01

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Morphologie des cellules de levure et la reproduction sexuelle - Apercu general et quelques considerations

The authors describe a cloning strategy for the construction of a human genomic library in yeast artificial chromosomes (YACs) based on complete digestion of high-molecular-weight DNA with the infrequently cutting restriction enzyme MluI. Cloning of MluI fragments in the vector pYAC-RC and one subsequent size fractionation by preparative pulsed-field gel electrophoresis yielded a library with average insert sizes of 600 kb. Ninety-seven percent of the colonies were recombinant. An additional size fractionation of MluI fragments prior to ligation had no significant influence on the size of the YACs. The library currently consists of 5000 clones, which is the equivalent of one human genome. Nineteen percent of the YACs were larger than 1.2 Mb. Since smaller MluI fragments are lost during sizing, they also performed cloning without size fractionation. Only 20% of the colonies were recombinant, probably due ...

1994-05-01

4

British Library Electronic Table of Contents (United Kingdom)

Over the decades, basic research in life sciences has profited greatly from the study of the small unicellular fungal species Saccharomyces cerevisiae. This yeast turned out to be key for the identification and understanding of molecular mechanisms that underlay the basic functions of all eukaryotic cells. These include, but are not limited to, the regulatory mechanisms behind cellular reproduction (cell cycle control), cellular morphogenesis (cell polarity, cytoskeleton and membrane trafficking) and the management of cellular information (chromosome biology, transcription and translation). Rapid access to genomic information of many yeast species, combined with bioinformatics analyses, provide information on the evolutionary history of yeasts and the molecular ancestry of their constituen...

2011-01-01

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Genomic view of the evolution of the complement system

A DNA transposon-based approach to validate oncogenic mutations in the mouse

The recent accumulation of genomic information of many representative animals has made it possible to trace the evolution of the complement system based on the presence or absence of each complement...Full Text Available

2006-09-01

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Genome-wide analysis of N¹-methyl-adenosine modification in human tRNAs

Large-scale cancer genome projects will soon be able to sequence many cancer genomes to comprehensively identify genetic changes in human cancer. Genome-wide association studies have also identified...Full Text Available

2008-12-16

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Yeast artificial chromosome libraries containing large inserts from mouse and human DNA

The N¹-methyl-Adenosine (m¹A58) modification at the conserved nucleotide 58 in the TΨC loop is present in most eukaryotic tRNAs. In yeast, m¹A58 modification...Full Text Available

2010-07-01

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Human type I pituitary adenylate cyclase activating polypeptide receptor (ADCYAP1R): Localization to chromosome band 7p14 and integration into the cytogenetic, physical, and genetic map of chromosome 7

Yeast artificial chromosome (YAC) libraries have been difficult to construct with average insert sizes >400 kilobase pairs when DNA is size-fractionated in low-melting-point agarose. By using yeast chromosomes in mock cloning experiments, the authors found that polyamines should be present whenever agarose containing high molecular weight DNA is melted to protect DNA from degradation. By incorporating polyamines during the cloning procedure, they constructed YAC libraries from mouse and human DNA with average insert sizes of 700 and 620 kilobase pairs, respectively. Several genome equivalents of these YAC libraries were replicated onto the surface of many duplicate agar plates using a 40,000 multipin transfer device. High-density filter replicas were screened by hybridization, and 70 mouse YAC clones from 31 loci and 132 human YAC clones from 49 loci were isolated.

1991-05-15

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Chromosomal localization and structure of the human type II IMP dehydrogenase gene

The gene encoding the human type I pituitary adenylate cyclase activating polypeptide receptor (ADCYAP1R1) was mapped to chromosome 7 by PCR analysis of genomic DNA from a human/rodent somatic cell hybrid mapping panel. This assignment was confirmed and the gene localized to chromosome band 7p14 by fluorescence in situ hybridization. A yeast artificial chromosome containing ADCYAP1R1 was identified in the CEPH {open_quotes}B{close_quotes} Mega-YAC library. This YAC includes two highly polymorphic dinucleotide repeat sequences that will facilitate genetic studies of the contribution of ADCYAP1R1 in disease states of the central nervous and neuroendocrine systems. 13 refs., 1 fig.

1994-10-01

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Effects of dietary glucosylceramide on dermatitis in atopic dermatitis model mice

We determined the chromosomal localization and structure of the gene encoding human type II inosine 5{prime}-monophosphate dehydrogenase (IMPDH, EC 1.1.1.205), an enzyme associated with cellular proliferation, malignant transformation, and differentiation. Using polymerase chain reaction (PCR) primers specific for type II IMPDH, we screened a panel of human-Chinese hamster cell somatic hybrids and a separate deletion panel of chromosome 3 hybrids and localized the gene to 3p21.1{yields}p24.2. Two overlapping yeast artificial chromosome clones containing the full gene for type II IMPDH were isolated and a physical map of 117 kb of human genomic DNA in this region of chromosome 3 was constructed. The gene for type II IMPDH was localized and oriented on this map and found to span no more than 12.5 kb.

1994-05-01

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British Library Electronic Table of Contents (United Kingdom)

The effects of dietary plant and yeast cerebroside (glucosylceramide), a major sphingolipid in plants and yeast, on atopic dermatitis (AD) like symptoms were investigated in a mouse model. After 7 wk of feeding with a diet containing maize glucosylceramide, plasma IgE levels became significantly lower and in contrast, the levels of interleukin (IL)-12, which induces cellular immunity, became significantly higher in the AD mice than in the controls. However, the sphingolipid constituents of the skin fraction in the maize glucosylceramide fed group did not contain sphingoid bases of plant origin, such as 8-unsaturated sphingoid bases. The results of the present study indicated that dietary plant glucosylceramide prevented AD-like symptoms in AD model mice via regulation of Th1/Th2 balance. P...

2010-01-01

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Identification of pork derivatives in food products by species-specific polymerase chain reaction (PCR) for halal verification

British Library Electronic Table of Contents (United Kingdom)

Pork identification in four types of food products, which are sausages and the casings, bread and biscuits, using species-specific polymerase chain reaction (PCR) detection of a conserved region in the mitochondrial (mt) 12S ribosomal RNA (rRNA) gene was developed. Genomic DNA of the food products were successfully extracted except for the casing samples, where no genomic DNA was detected. The extracted genomic DNA was then subjected to PCR amplification targeting the specific regions of the 12S rRNA gene. The genomic DNA from the food products were found to be of good quality and produced clear PCR products on the amplification of 12S rRNA gene of 387 base pairs (bp) from pork species. The species-specific PCR identification yielded excellent results for identification of pork derivatives...

2007-01-01

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Transposon-based screens for cancer gene discovery in mouse models

Studying bacterial transcriptomes using RNA-seq

Significant emphasis has recently been placed on the characterization of the human cancer genome. This effort has been assisted by the development of new DNA sequencing technologies that allow...Full Text Available

2010-08-01

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Multiplexed, rapid detection of H5N1 using a PCR-free nanoparticle-based genomic microarray assay

Genome-wide studies of bacterial gene expression are shifting from microarray technology to second generation sequencing platforms. RNA-seq has a number of advantages over hybridization-based techniques,...Full Text Available

2010-10-01

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Genetic screening: The vista of genomic medicine

BackgroundFor more than a decade there has been increasing interest in the use of nanotechnology and microarray platforms for diagnostic applications. In this report, we describe...Full Text Available

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Generation of a BAC-based physical map of the melon genome

The accelerating development of biochemical and DNA-based diagnostic tests for human genetic conditions in the last decade has engendered a revolution in genetic diagnosis. Both genetic testing and...Full Text Available

2011-01-01

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A piggyBac transposon-based genome-wide library of insertionally mutated Blm-deficient murine ES cells

BackgroundCucumis melo (melon) belongs to the Cucurbitaceae family, whose economic importance among horticulture crops is second only to Solanaceae. Melon has high...Full Text Available

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A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: Basal ecological diversification?

Cultured mouse or human embryonic stem (ES) cells provide access to all of the genes required to elaborate the fundamental components and physiological systems of a mammalian cell. Chemical or insertional...Full Text Available

2009-04-01

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A microarray analysis of the rice transcriptome and its comparison to Arabidopsis

BackgroundThe order Tetraodontiformes consists of approximately 429 species of fishes in nine families. Members of the order exhibit striking morphological diversity and radiated...Full Text Available

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A genomic library-based amplification approach (GL-PCR) for the mapping of multiple IS6110 insertion sites and strain differentiation of Mycobacterium tuberculosis

Arabidopsis and rice are the only two model plants whose finished phase genome sequence has been completed. Here we report the construction of an oligomer microarray based on the presently...Full Text Available

2005-09-01

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British Library Electronic Table of Contents (United Kingdom)

Evidence suggests that insertion of the IS6110 element is not without consequence to the biology of Mycobacterium tuberculosis complex strains. Thus, mapping of multiple IS6110 insertion sites in the genome of biomedically relevant clinical isolates would result in a better understanding of the role of this mobile element, particularly with regard to transmission, adaptability and virulence. In the present paper, we describe a versatile strategy, referred to as GL-PCR, that amplifies IS6110-flanking sequences based on the construction of a genomic library. M. tuberculosis chromosomal DNA is fully digested with HincII and then ligated into a plasmid vector between T7 and T3 promoter sequences. The ligation reaction product is transformed into Escherichia coli and selective PCR amplification...

2006-01-01

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Search for a Methanopyrus-proximal last universal common ancestor based on comparative-genomic analysis

British Library Electronic Table of Contents (United Kingdom)

The origin of life is a long-standing mystery puzzling many people. This mystery possesses not only philosophical but also important biological significance. To unveil this mystery, the searches for the root of life, or the last universal common ancestor (LUCA), based on comparative-genomic analysis have been intensively performed on rRNAs, tRNAs and proteins sequences. The current search pointed to a Methanopyrus-proximal LUCA, which opens up the reconstruction of Lucan biology and helps to delineate the evolutionary pathways.

2011-01-01

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Survival of Genetically Modified and Self-Cloned Strains of Commercial Baker's Yeast in Simulated Natural Environments: Environmental Risk Assessment

Comparison of the Survival and Metabolic Activity of Psychrophilic and Mesophilic Yeasts Subjected to Freeze-Thaw Stress

Although genetic engineering techniques for baker's yeast might improve the yeast's fermentation characteristics, the lack of scientific data on the survival of such strains in natural environments...Full Text Available

2005-11-01

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Cloning and sequencing of cDNA encoding human DNA topoisomerase II and localization of the gene to chromosome region 17q21-22

A mesophilic yeast, Candida utilis, and a psychrophilic yeast, Leucosporidium stokesii, were subjected to freeze-thaw cycling over the range 25 to -60 C. Viability...Full Text Available

1975-06-01

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Exploiting rice-sorghum synteny for targeted development of EST-SSRs to enrich the sorghum genetic linkage map.

Two overlapping cDNA clones encoding human DNA topoisomerase II were identified by two independent methods. In one, a human cDNA library in phage {lambda} was screened by hybridization with a mixed oligonucleotide probe encoding a stretch of seven amino acids found in yeast and Drosophila DNA topoisomerase II; in the other, a different human cDNA library in a {lambda}gt11 expression vector was screened for the expression of antigenic determinants that are recognized by rabbit antibodies specific to human DNA topoisomerase II. The entire coding sequences of the human DNA topoisomerase II gene were determined from these and several additional clones, identified through the use of the cloned human TOP2 gene sequences as probes. Hybridization between the cloned sequences and mRNA and genomic DNA indicates that the human enzyme is encoded by a single-copy gene. The location of the gene was mapped to chromosome 17q21-22 by in situ hybridization of a ...

1988-10-01

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Global Transcriptional Responses of Fission Yeast to Environmental Stress

The sequencing and detailed comparative functional analysis of genomes of a number of select botanical models open new doors into comparative genomics among the angiosperms, with potential benefits for improvement of many orphan crops that feed large populations. In this study, a set of simple sequence repeat (SSR) markers was developed by mining the expressed sequence tag (EST) database of sorghum. Among the SSR-containing sequences, only those sharing considerable homology with rice genomic sequences across the lengths of the 12 rice chromosomes were selected. Thus, 600 SSR-containing sorghum EST sequences (50 homologous sequences on each of the 12 rice chromosomes) were selected, with the intention of providing coverage for corresponding homologous regions of the sorghum genome. Primer pairs were designed and polymorphism detection ability was assessed using parental pairs of two existing sorghum ...

2009-08-08

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Apoptosis at Inflection Point in Liquid Culture of Budding Yeasts

We explored transcriptional responses of the fission yeast Schizosaccharomyces pombe to various environmental stresses. DNA microarrays were used to characterize changes in expression...Full Text Available

2003-01-01

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Promoter Structure Which Affects on the Expression of Yeast MGMT Gene

Budding yeasts are highly suitable for aging studies, because the number of bud scars (stage) proportionally correlates with age. Its maximum stages are known ...Full Text Available

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Effect of Zinc-Enriched Yeast Supplementation on Serum Zinc and Testosterone Concentrations in Ethanol Feeding Rats

Full Text Available

1997-01-01

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Application of Quantitative Real-Time PCR for Enumeration of Total Bacterial, Archaeal, and Yeast Populations in Kimchi

Full Text Available

2008-07-01

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Antifungal activity of the extracts and neolignans from Piper regnellii (Miq.) C. DC. var. pallescens (C. DC.) Yunck

Full Text Available

2009-12-01

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Intrapopulation Genome Size Dynamics in Festuca pallens

Piper regnellii (Miq.) C. DC. var. pallescens (C. DC.) Yunck (Piperaceae) is a medicinal plant traditionally used in Brazil to treat infectious diseases. The extracts obtained from the leaves of P. regnellii were investigated for their antifungal activities against the yeasts Candida albicans, C. krusei, C. parapsilosis, and C. tropicalis. The EtOAc extract presented gnificant activity against Candida albicans with MIC at 125 {mu}g mL{sup -1}, and a moderate activity against both C. krusei and C. parapsilosis with MIC at 500 {mu}g mL{sup -1}. Candida tropicalis was not inhibited by this extract at concentrations as high as 1000 {mu}g mL{sup -1}. Based on these findings, the EtOAc extract was fractionated by silica gel column chromatography into nine fractions. The hexane and CHCl{sub 3} fractions showed varied levels of antifungal activity against all test yeasts. Further column chromatography separation of the hexane ...

2005-11-15

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Structural Chemistry of Human SET Domain Protein Methyltransferases

Background and AimsIt is well known that genome size differs among species. However, information on the variation and dynamics of genome size in wild populations and on the early...Full Text Available

2008-10-01

34

Synthesis and study of the antifungal activity of new mono- and disubstituted derivatives of a genetically engineered polyene antibiotic 28,29-didehydronystatin A1 (S44HP)

There are about fifty SET domain protein methyltransferases (PMTs) in the human genome, that transfer a methyl group from S-adenosyl-L-methionine (SAM) to substrate lysines on histone tails or other peptides. A number of structures in complex with cofactor, substrate, or inhibitors revealed the mechanisms of substrate recognition, methylation state specificity, and chemical inhibition. Based on these structures, we review the structural chemistry of SET domain PMTs, and propose general concepts towards the development of selective inhibitors.

2011-08-22

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British Library Electronic Table of Contents (United Kingdom)

Mono- and disubstituted novel derivatives of the heptaene nystatin analog 28,29-didehydronystatin A1 (S44HP, 1) were obtained by chemical modification of the exocyclic C-16 carboxyl and/or an amino group of mycosamine moiety. The strategy of preparation of mono- and double-modified polyene macrolides was based on the use of intermediate hydrophobic N-Fmoc (9-fluorenylmethoxycarbonyl) derivatives that facilitated the procedures of isolation and purification of new compounds. The antifungal activity of the new derivatives was first tested in vitro against yeasts and filamentous fungi, allowing the selection of the most active compounds that were subsequently tested for acute toxicity in mice. 2-(N,N-dimethylamino)ethylamide of 1 (2) and 2-(N,N-dimethylamino)ethylamide of N-fructopyranosyl-28...

2010-01-01

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Enhancement of bioleaching of a spent Ni/Mo hydroprocessing catalyst by Penicillium simplicissimum

British Library Electronic Table of Contents (United Kingdom)

Statistically based experimental designs were applied to screen and optimize the bioleaching of spent hydrocracking catalyst by Penicillium simplicissimum. Eleven factors were examined for their significance on bioleaching using a Plackett-Burman factorial design. Four significant variables (pulp density, sucrose, NaNO"3, and yeast extract concentrations) were selected for the optimization studies. The combined effect of these variables on metal bioleaching was studied using a central composite design (CCD). Second-order polynomials were established to identify the relationship between the recovery percent of the metals and the four significant variables. The optimal values of the variables for maximum metals bioleaching were as follows: pulp density (4.0%, w/v), sucrose (90g/L), NaNO"3 (2...

2011-01-01

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Modular coherence of protein dynamics in yeast cell polarity system

METABOLIC REGULATION OF ADENOSINE TRIPHOSPHATE SULFURYLASE IN YEAST

In this study, we investigated on a systems level how complex protein interactions underlying cell polarity in yeast determine the dynamic association of proteins with the polar cortical domain (PCD)...Full Text Available

2011-05-03

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In vivo expression and mitochondrial targeting of yeast apoiso-1-cytochrome c fusion proteins.

de Vito, Peter C. (Princeton University, Princeton, N.J.), and Jacques Dreyfuss. Metabolic regulation of adenosine triphosphate sulfurylase in yeast. J. Bacteriol. 88:1341–1348....Full Text Available

1964-11-01

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Heavy metals alter the electrokinetic properties of bacteria, yeasts, and clay minerals.

To define the import pathway for apoiso-1-cytochrome c in vivo, the coding region for bacterial chloramphenicol acetyltransferase (CAT) or yeast copper metallothionein (CuMT) was fused to the carboxy...Full Text Available

1990-11-01

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Evaluation of Acyl Coenzyme A Oxidase (Aox) Isozyme Function in the n-Alkane-Assimilating Yeast Yarrowia lipolytica

The electrokinetic patterns of four bacterial species (Bacillus subtilis, Bacillus megaterium, Pseudomonas aeruginosa, and Agrobacterium radiobacter), two yeasts (Saccharomyces cerevisiae and Candida...Full Text Available

1992-05-01

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Antagonistic Gcn5-Hda1 interactions revealed by mutations to the Anaphase Promoting Complex in yeast

We have identified five acyl coenzyme A (CoA) oxidase isozymes (Aox1 through Aox5) in the n-alkane-assimilating yeast Yarrowia lipolytica, encoded by the POX1...Full Text Available

1999-09-01

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A Novel Function of the DNA Repair Gene rhp6 in Mating-Type Silencing by Chromatin Remodeling in Fission Yeast

BackgroundHistone post-translational modifications are critical for gene expression and cell viability. A broad spectrum of histone lysine residues have been identified in yeast...Full Text Available

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Whole-genome shotgun assembly and comparison of human genome assemblies

Recent studies have indicated that the DNA replication machinery is coupled to silencing of mating-type loci in the budding yeast Saccharomyces cerevisiae, and a similar silencing mechanism...Full Text Available

1998-09-01

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The complete mitochondrial genome of the stomatopod crustacean Squilla mantis.

We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in pairs...Full Text Available

2004-02-17

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The complete mitochondrial genome of the stomatopod crustacean Squilla mantis

PMID:16091132

2005-08-09

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Molecular Imaging in the Age of Genomic Medicine

BackgroundAnimal mitochondrial genomes are physically separate from the much larger nuclear genomes and have proven useful both for phylogenetic studies and for understanding genome...Full Text Available

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DNA double strand breakage after UV irradiation of yeast cells; DNA-Doppelstrangbrueche nach UV-Bestrahlung in Hefezellen

Full Text Available

2007-06-01

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Cholera toxin binding sites in yeast triggers biochemical pathway

No abstract prepared.

2000-07-01

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Characterization of commercially available selenized yeast food supplements

... e Biologia Molecular (SBBq), Sao Paulo, SP (Brazil) 217 p. APPLIED LIFE

1998-05-23

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Genomics - from Neanderthals to high-throughput sequencing

... Rome (Italy) Istituto Superiore di Sanita (Italy) 207 p. ENVIRONMENTAL

2009-04-01

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Effect of UV radiation on the killer phenotype in the wine yeast-saccharomycetes and spontaneous variation of this character

A report on 'The Biology of Genomes' meeting, Cold Spring Harbor, USA, 10-14 May 2006.

2006-01-01

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Molecular evolution and characterization of fungal indoleamine 2,3-dioxygenases.

Spontaneous and ultraviolet-induced changeabilities of wine yeasts from the killer state to sensitive one have been studied. Observed often spontaneous changes of killer and neutral phenotypes under laboratory store conditions as well as high mutation frequency of genetic elements responsible for the killer indication on ultraviolet irradiation testify that often encounterability in nature and in the production of sensitive yeasts is attributed to high frequency of mutation changes of the killer and neutral phenotypes to the sensitive state.

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Personality disorders and biosocial trait theories: The argument for radical legal reform.

Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) are tryptophan-degrading enzymes. Mammalian IDO expression is induced by cytokines and has antimicrobial and immunomodulatory effects. A major role of mammalian TDO is to supply nicotinamide adenine dinucleotide (NAD(+)). In fungi, the IDO homologue is thought to be expressed constitutively and supply NAD(+), as TDO is absent from their genomes. Here, we reveal the distribution of IDO genes among fungal species and characterize their enzymatic activity. The yeast, Saccharomyces cerevisiae has only one IDO gene, whereas the koji-mold, Aspergillus oryzae has two genes, IDO? and IDO?. The A. oryzae IDO? showed more similar enzymatic properties to those of S. cerevisiae IDO than IDO?, suggesting that the A. oryzae IDO? is a functional homologue of the S. cerevisiae IDO. From the IDO? gene, two isoforms, IDO? and IDO?(+) could be generated by alternative splicing. The latter ...

2010-12-18

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Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels

This article reviews antisocial personality disorder, psychopathy, and violence and develops a three factor model of personality traits. Then a discussion of related personality disorders precedes the development of a categorical two factor model of impulsive versus remorseless violence. A paradigm of proactive, medical, and school based early intervention and prevention is advocated as a useful addition to the reactive detention of criminal justice. Integration of psychological tests, neuroimaging, and genomic data in early childhood and school based intervention strategies to prevent the development of conduct disorder and attenuate criminal propensity inform this approach. PMID:20422651

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Local chromatin structure of heterochromatin regulates repeatedDNA stability, nucleolus structure, and genome integrity

BackgroundBiodiesel or ethanol derived from lipids or starch produced by microalgae may overcome many of the sustainability challenges previously ascribed to petroleum-based fuels and first generation plant-based biofuels. The paucity of microalgae genome sequences, however, limits gene-based biofuel feedstock optimization studies. Here we describe the sequencing and de novo transcriptome assembly for the non-model microalgae species, Dunaliella tertiolecta, and identify pathways and genes of importance related to biofuel production.ResultsNext generation DNA pyrosequencing technology applied to D. tertiolecta transcripts produced 1,363,336 high quality reads with an average length of 400 bases. Following quality and size trimming, ~ 45% of the high quality reads were assembled into 33,307 isotigs with a 31-fold coverage and 376,482 singletons. Assembled sequences and singletons ...

2011-03-14

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Automated purification of Borrelia burgdorferi s.l. PCR products with KingFisher"T"M magnetic particle processor prior to genome sequencing

Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project ...

2007-05-05

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Removal of lead from solution using non-living residual brewery yeast

Borrelia burgdorferi sensu lato genospecies were differentiated by PCR-based sequencing of the borrelial flagellin gene. To evaluate the usefulness of KingFisher"T"M magnetic particle processor in PCR product purification, borrelia PCR products were purified with KingFisher"T"M magnetic particle processor prior to cycle sequencing and the quality of the sequence data received was analyzed. KingFisher was found to offer a rapid and reliable alternative for borrelial PCR product purification.

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Genetical approach to oxygen toxicity. [Saccharomyces cerevisiae

A number of preparations of residual non-living brewery yeast were examined for their ability to remove lead from solution. Those preparations included washed and un-washed intact yeast and washed and un-washed homogenates of the yeast cells. Using biosorption isotherm analysis it was found that the washed and un-washed preparations of intact, non-living yeast exhibited maximum biosorption capacities for lead of 127 and 99 mg/g dry weight biomass, respectively. The washed and un-washed cell homogenates exhibited maximum biosorption capacities of 38 and 139 mg lead/g dry weight biomass, respectively. Since it had previously been shown that these preparations of biomass were capable of removing uranium from solution by combined biosorption and precipitation processes, it was decided to examine removal of lead from solution using a form of equilibrium dialysis in which the biomass was retained within a ...

1998-10-01

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The mode and tempo of genome size evolution in eukaryotes

The role of intermediate products of dioxygen reduction in cytotoxic effects ascribed to oxygen molecules was studied in vivo using various yeast mutants with changed response to oxygen stress. It has been documented that superoxide radical exerts its deleterious effects on yeast cells directly and the role of other oxygen species derived from it is hardly detectable. Yeast Saccharomyces cerevisiae, however, cannot be considered as a typical eukaryotic organism due to its inability of synthesizing polyunsaturated fatty acids (pufa). These fatty acids are known as main target molecules during oxidative stress and their peroxidation leads to cytotoxic effects. As fatty acid content could be easily manipulated in yeast, this organism was used to evaluate the contribution of pufa peroxidation process to the cytotoxic effects of oxygen. Results obtained show, that yeast cells containing ...

1986-01-01

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Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples

Eukaryotic genome size varies over five orders of magnitude; however, the distribution is strongly skewed toward small values. Genome size is highly correlated to a number of phenotypic traits, suggesting...Full Text Available

2007-05-01

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Massive turnover of functional sequence in human and other mammalian genomes

BackgroundGenomes store information for building and maintaining organisms. Complete sequencing of many genomes provides the opportunity to study and compare global information properties...Full Text Available

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Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

Despite the availability of dozens of animal genome sequences, two key questions remain unanswered: First, what fraction of any species' genome confers biological function, and second, are apparent...Full Text Available

2010-10-01

63

Genome Sequence and Comparative Analysis of the Solvent-Producing Bacterium Clostridium acetobutylicum

The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble...Full Text Available

2003-10-01

64

Full genome gene expression analysis of the heat stress response in Drosophila melanogaster

The genome sequence of the solvent-producing bacterium Clostridium acetobutylicum ATCC 824 has been determined by the shotgun approach. The genome consists of a 3.94-Mb chromosome and...Full Text Available

2001-08-01

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Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements

The availability of full genome sequences has allowed the construction of microarrays, with which screening of the full genome for changes in gene expression is possible. This method can provide a wealth...Full Text Available

2005-10-01

66

A Computational Framework Discovers New Copy Number Variants with Functional Importance

The recent assembly of the silkworm Bombyx mori genome with 432 Mb on 28 holocentric chromosomes has become a reference in the genomic analysis of the very diverse Order of Lepidoptera....Full Text Available

2010-04-27

67

Sirtuins, Bioageing, and Cancer

Structural variants which cause changes in copy numbers constitute an important component of genomic variability. They account for 0.7% of genomic differences in two individual genomes, of which...Full Text Available

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Iodination of glyceraldehyde 3-phosphate dehydrogenase

The Sirtuins are a family of orthologues of yeast Sir2 found in a wide range of organisms from bacteria to man. They display a high degree of conservation between species, in both sequence and function,...Full Text Available

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Effect of Photosynthetic Bacterial Addition to Chlorella or ${\\omega}-Yeast$ on Growth of Rotifer, Brachionus plicatilis, and its Dietary Value for Flounder, Paralichthys olivaceus, Larvae

1. A high degree of homology in the positions of tyrosine residues in glyceraldehyde 3-phosphate dehydrogenase from lobster and pig muscle, and from yeast, prompted an examination of the reactivity...Full Text Available

1970-09-01

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Widespread duplications in the genomes of laboratory stocks of Dictyostelium discoideum

Full Text Available

2000-03-01

71

Time-dependent ARMA modeling of genomic sequences

BackgroundDuplications of stretches of the genome are an important source of individual genetic variation, but their unrecognized presence in laboratory organisms would be a confounding...Full Text Available

2008-01-01

72

Methods in DNA methylation profiling

BackgroundOver the past decade, many investigators have used sophisticated time series tools for the analysis of genomic sequences. Specifically, the correlation of the nucleotide...Full Text Available

73

Genomics of human longevity

Metastable and somatically heritable patterns of DNA methylation provide an important level of genomic regulation. In this article, we review methods for analyzing these genome-wide epigenetic...Full Text Available

2009-12-01

74

Genomic imprinting and the social brain

In animal models, single-gene mutations in genes involved in insulin/IGF and target of rapamycin signalling pathways extend lifespan to a considerable extent. The genetic, genomic and epigenetic influences...Full Text Available

2011-01-12

75

Genetics, Genomics, and Molecular Biology

Genomic imprinting refers to the parent-of-origin-specific epigenetic marking of a number of genes. This epigenetic mark leads to a bias in expression between maternally and paternally inherited imprinted...Full Text Available

2006-12-29

76

Enzymatic engineering of the porcine genome with transposons and recombinases

Genetics, Genomics, and Molecular Biology USGS scientists develop and integrate new genetic and molecular techniques into systematic analyses to describe individuals and populations of fish .....

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Comparative and phylogenomic studies on the mitochondrial genomes of Pentatomomorpha (Insecta: Hemiptera: Heteroptera)

BackgroundSwine is an important agricultural commodity and biomedical model. Manipulation of the pig genome provides opportunity to improve production efficiency, enhance disease...Full Text Available

78

Cancer gene discovery in mouse and man

BackgroundNucleotide sequences and the gene arrangements of mitochondrial genomes are effective tools for resolving phylogenetic problems. Hemipteroid insects are known to possess...Full Text Available

79

Supercritical fluid extraction from dried banana peel (Musa spp., genomic group AAB): Extraction yield, mathematical modeling, economical analysis and phase equilibria

AbstractThe elucidation of the human and mouse genome sequence and developments in high-throughput genome analysis, and in computational tools, have made it possible to profile entire...Full Text Available

2009-12-01

80

British Library Electronic Table of Contents (United Kingdom)

Supercritical fluid extraction from dried banana peel (Musa spp., subgroup Prata, genomic group AAB, popularly known in Brazil as Enxerto) was studied. The aspects investigated were: overall extraction curve (OEC), mass transfer modeling of the yield curves, economical analysis of the process and phase equilibrium data for the pseudo-ternary system of banana peel extract, carbon dioxide and ethanol. The extraction operating conditions evaluated were: pressure ranging from 100bar to 300bar, temperature from 40 to 50^oC and constant solvent flow rate of 5.0gCO2/min. Experimental extraction data were correlated using three kinetic models based on mass transfer equations (logistic, diffusion and Esquivel models). Phase equilibrium measurements were performed using pressure from 64.9bar to 239....

2010-01-01

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81

Identification of three related human GRO genes encoding cytokine functions

A multi-marker model for detecting chromosomal segments displaying QTL activity

The product of the human GRO gene is a cytokine with inflammatory and growth-regulatory properties; GRO is also called MGSA for melanoma growth-stimulatory activity. The authors have identified two additional genes, GRO#beta# and GRO#gamma#, that share 90% and 86% identity at the deduced amino acid level with the original GRO#alpha# isolate. One amino acid substitution of proline in GRO#alpha# by leucine in GRO#beta# and GRO#gamma# leads to a large predicted change in protein conformation. Significant differences also exist in the 3' untranslated region, including different numbers of ATTTA repeats associated with mRNA instability. A 122-base-pair region in the 3' region is conserved among the three GRO genes, and a part of it is also conserved in the Chinese hamster genome, suggesting a role in regulation. DNA hybridization with oligonucleotide probes and partial sequence analysis of the genomic clones confirm that the ...

82

An ELISA-based high throughput protein truncation test for inherited breast cancer

A statistical method is presented for detecting quantitative trait loci (QTLs), based on the linear model. Unlike methods able to detect a few well separated QTLs and to estimate their effects and positions, this method considers the genome as a whole and enables the detection of chromosomal segments involved in the differences between two homozygous lines, and their backcross, doubled haploid, or F[sub 2] progenies, for a quantitative trait. Genetic markers must be codominant, but missing markers are accepted, provided they are missing independently from the experiment. Asymptotic properties, which are of practical use, are developed. This method does not rely on strong genetic hypotheses, and thus does not permit any precise genetic analysis of the trait under study, but it does assess which regions of the genome are involved, whatever the complexity of the genetic determinism (number, effects and interactions among ...

1993-08-01

83

The Functionally Conserved Nucleoporins Nup124p from Fission Yeast and the Human Nup153 Mediate Nuclear Import and Activity of the Tf1 Retrotransposon and HIV-1 VprV?

IntroductionBreast cancer is the most diagnosed and second leading cause of cancer deaths in the U.S. female population. An estimated 5 to 10 percent of all breast cancers are inherited, caused by mutations in the breast cancer susceptibility genes (BRCA1/2). As many as 90% of all mutations are nonsense mutations, causing a truncated polypeptide product. A popular and low cost method of mutation detection has been the protein truncation test (PTT), where target regions of BRCA1/2 are PCR amplified, transcribed/translated in a cell-free protein synthesis system and analyzed for truncated polypeptides by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and autoradiography. We previously reported a novel High Throughput Solid-Phase PTT (HTS-PTT) based on an enzyme-linked immunosorbent assay (ELISA) format that eliminates the need for radioactivity, SDS-PAGE and subjective interpretation of the results. Here, we report the next generation HTS-PTT ...

2010-10-04

84

Morphological Instabilities in a growing Yeast Colony Experiment and Theory

We report that the fission yeast nucleoporin Nup124p is required for the nuclear import of both, retrotransposon Tf1-Gag as well as the retroviral HIV-1 Vpr. Failure to import Tf1-Gag into the nucleus...Full Text Available

2005-04-01

85

Kes1p shares homology with human oxysterol binding protein and participates in a novel regulatory pathway for yeast Golgi-derived transport vesicle biogenesis.

We study the growth of colonies of the yeast Pichia membranaefaciens on agarose film. The growth conditions are controlled in a setup where nutrients are supplied through an agarose film suspended over a solution of nutrients. As the thickness of the agarose film is varied, the morphology of the front of the colony changes. The growth of the front is modeled by coupling it to a diffusive field of inhibitory metabolites. Qualitative agreement with experiments suggests that such a coupling is responsible for the observed instability of the front.

1997-01-01

86

Dissecting toxin immunity in virus-infected killer yeast uncovers an intrinsic strategy of self-protection

The yeast phosphatidylinositol transfer protein (Sec14p) is required for biogenesis of Golgi-derived transport vesicles and cell viability, and this essential Sec14p requirement is abrogated by inactivation...Full Text Available

1996-12-02

87

Toxin-secreting “killer” yeasts were initially identified >40 years ago in Saccharomyces cerevisiae strains infected with a double-stranded RNA “killer”...Full Text Available

2006-03-07

88

DNA repair genes

Arginine aminoacylation identity is context-dependent and ensured by alternate recognition sets in the anticodon loop of accepting tRNA transcripts.

Fission yeast S. pombe is assumed to be a good model for cloning of human DNA repair genes, because human gene is normally expressed in S. pombe and has a very similar protein sequence to yeast protein. We have tried to elucidate the DNA repair mechanisms of S. pombe as a model system for those of mammals. (J.P.N.)

1995-12-01

89

Amino acid sequences that determine the nuclear localization of yeast histone 2B.

Yeast arginyl-tRNA synthetase recognizes the non-modified wild-type transcripts derived from both yeast tRNA(Arg) and tRNA(Asp) with equal efficiency. It discriminates its cognate natural substrate,...Full Text Available

1996-09-16

90

A heteromeric complex containing the centromere binding factor 1 and two basic leucine zipper factors, Met4 and Met28, mediates the transcription activation of yeast sulfur metabolism.

Histone-beta-galactosidase protein fusions were used to identify the domain of yeast histone 2B, which targets this protein to the nucleus. Amino acids 28 to 33 in H2B were required for nuclear localization...Full Text Available

1987-11-01

91

A New Metal-Binding Site for Yeast Phosphoglycerate Kinase as Determined by the Use of a Metal-ATP Analog

Transcription activation of sulfur metabolism in yeast is dependent on two DNA binding factors, the centromere binding factor 1 (Cbf1) and Met4. While the role of Met4 was clearly established by showing...Full Text Available

1996-05-15

92

Expression and Characterization of a New Esterase Cloned Directly from Agrobacterium tumefaciens Genome

Suicide substrate β, γ-bidentate Rh(III)ATP (RhATP) was used to map the metal ion-binding site in yeast phosphoglycerate kinase (PGK). Cleavage of the RhATP-inactivated enzyme with...Full Text Available

1997-02-01

93

Molecular characterization of the Spirometra mansonoides genome: renaturation kinetics, methylation, and hybridization to human cDNA probes.

Full Text Available

2006-01-01

94

Justice and the Human Genome Project

High molecular weight DNA from pleroceroid larvae of the tapeworm Spirometra mansonoides was purified from isolated nuclei by conventional techniques. The DNA so isolated has a melting temperature (Tm) of 87 degrees C and a guanine plus cytosine (G/C) content of 44%. 5-Methyl cytosine could not be detected in plerocercoid DNA by HPLC analysis of DNA hydrolysates, by radiolabeling 5'-termini of MspI digests with polynucleotide kinase, or by comparing restriction patterns generated by MspI and HpaII. Renaturation kinetics demonstrated that the genome of S. mansonoides contains repetitive as well as single copy sequences and has a genome size estimated at approx. 1.6 X 10(9) bp. Hybridization was carried out between plerocercoid DNA and cDNAs for human beta-actin, alpha-tubulin and growth hormone (hGH). Rationale for this analysis was based on known homologies among actin and tubulin genes in numerous species and on apparent ...

1990-06-21

95

Interpreting Mammalian Evolution using Fugu Genome Comparisons

Most of the essays gathered in this volume were first presented at a conference, Justice and the Human Genome, in Chicago in early November, 1991. The goal of the, conference was to consider questions of justice as they are and will be raised by the Human Genome Project. To achieve its goal of identifying and elucidating the challenges of justice inherent in genomic research and its social applications the conference drew together in one forum members from academia, medicine, and industry with interests divergent as rate-setting for insurance, the care of newborns, and the history of ethics. The essays in this volume address a number of theoretical and practical concerns relative to the meaning of genomic research.

1992-01-01

96

Probiotic-Induced Priming of Innate Immunity to Protect Against Rotaviral Infection

Comparative sequence analysis of the human and the pufferfish Fugu rubripes (fugu) genomes has revealed several novel functional coding and noncoding regions in the human genome. In particular, the fugu genome has been extremely valuable for identifying transcriptional regulatory elements in human loci harboring unusually high levels of evolutionary conservation to rodent genomes. In such regions, the large evolutionary distance between human and fishes provides an additional filter through which functional noncoding elements can be detected with high efficiency.

2004-04-02

97

British Library Electronic Table of Contents (United Kingdom)

Understanding of probiotic-induced regulatory gene expression and networking is critical to further explore their roles in controlling infection. Transcriptional profile of selected innate immune genes in primary bovine intestinal epithelial cells was assessed over a time course of incubation with the probiotic Lactobacillus plantarum 299v. Based on gene expression results, a time point was chosen to prime epithelial cells with the probiotic prior to infection with rotavirus. Plaque assays and genomic analysis provided the basis for establishing the efficacy of probiotics in preventing a rotaviral infection. Plaque assays revealed that the probiotic is capable of decreasing (at least by 100-fold) the levels of live virus when the cells were primed with the probiotic. Results from gene expr...

2010-01-01

98

Mitochondrial NADH:ubiquinone oxidoreductase (complex I) in eukaryotes: A highly conserved subunit composition highlighted by mining of protein databases

British Library Electronic Table of Contents (United Kingdom)

Complex I (NADH:ubiquinone oxidoreductase) is the largest enzyme of the mitochondrial respiratory chain. Compared to its bacterial counterpart which encompasses 14-17 subunits, mitochondrial complex I has almost tripled its subunit composition during evolution of eukaryotes, by recruitment of so-called accessory subunits, part of them being specific to distinct evolutionary lineages. The increasing availability of numerous broadly sampled eukaryotic genomes now enables the reconstruction of the evolutionary history of this large protein complex. Here, a combination of profile-based sequence comparisons and basic structural properties analyses at the protein level enabled to pinpoint homology relationships between complex I subunits from fungi, mammals or green plants, previously identified...

2011-01-01

99

Hsp90 gene, an additional target for discrimination between the potato cyst nematodes, Globodera rostochiensis and G. pallida, and the related species, G. tabacum tabacum

British Library Electronic Table of Contents (United Kingdom)

The heat-shock gene, Hsp90, was targeted as a new variable genomic region to supplement other DNA-based tests for identification and discrimination of Globodera pallida, G. rostochiensis and G. tabacum tabacum. Populations of the potato cyst nematodes, G. pallida and G. rostochiensis (PCN), originating from Canada, France, Belgium and USA, together with two populations of G. tabacum tabacum from the USA and France were used for the amplification of a fragment of the Hsp90 gene. General and specific primers and probes for each species were derived from the consensus and non-consensus regions of the aligned sequences, respectively. A triplex conventional PCR assay, using a general forward and reverse or three specific reverse primers, as well as a real-time PCR using general primers and spec...

2011-01-01

100

Algorithms for Internal Validation Clustering Measures in the Post Genomic Era

A non-uniformly sampled 4D HCC(CO)NH-TOCSY experiment processed using maximum entropy for rapid protein sidechain assignment

Inferring cluster structure in microarray datasets is a fundamental task for the -omic sciences. A fundamental question in Statistics, Data Analysis and Classification, is the prediction of the number of clusters in a dataset, usually established via internal validation measures. Despite the wealth of internal measures available in the literature, new ones have been recently proposed, some of them specifically for microarray data. In this dissertation, a study of internal validation measures is given, paying particular attention to the stability based ones. Indeed, this class of measures is particularly prominent and promising in order to have a reliable estimate the number of clusters in a dataset. For those measures, a new general algorithmic paradigm is proposed here that highlights the richness of measures in this class and accounts for the ones already available in the literature. Moreover, some of the most representative validation measures are also ...

2011-01-01

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101

Alcohol fermentation in olive oil extraction effluents

One of the stiffest challenges in structural studies of proteins using NMR is the assignment of sidechain resonances. Typically, a panel of lengthy 3D experiments are acquired in order to establish connectivities and resolve ambiguities due to overlap. We demonstrate that these experiments can be replaced by a single 4D experiment that is time-efficient, yields excellent resolution, and captures unique carbon-proton connectivity information. The approach is made practical by the use of non-uniform sampling in the three indirect time dimensions and maximum entropy reconstruction of the corresponding 3D frequency spectrum. This 4D method will facilitate automated resonance assignment procedures and it should be particularly beneficial for increasing throughput in NMR-based structural genomics initiatives.

2010-05-01

102

ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes

Eight culture-collection yeast strains of various species and five newly isolated stains were tested for both growth in olive oil extraction effluents and fermentation of the sugars in the same media. The culture-collection yeast strains did not grow in an effluent containing 2.86% sugar (w/v), 8 g/litre phenolic substances, 4.58 g/litre titratable acidity and pH 4.96, whereas the newly isolated strains of Torulopsis sp. MK-1, Saccharomyces norbensis MC-1, S. oleaceus MC-2 and S. oleaginosus grew well and fermented the sugars. In the medium mentioned above, they produced alcohol in amounts of 1.63 to 1.38%, respectively. None of the yeasts grew in an olive oil extraction effluent vacuum-concentrated to over 13-14% of dry matter. The strain of T. sp. MK-1 showed a higher stability.

1989-01-01

103

Multicolor FISH mapping with Alu-PCR-amplified YAC clone DNA determines the order of markers in the BRCA1 region on chromosome 17q12-q21

Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions (ECRs) in vertebrate genomes entitled ECRbase that is constructed from a collection of pairwise vertebrate genome alignments produced by the ECR Browser database. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a collection of promoters in all vertebrate genomes presented in the database. The database also contains a collection of annotated transcription factor binding sites (TFBS) in all ECRs and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and two pufferfish genomes. It is freely accessible at http://ECRbase.dcode.org.

2006-08-08

104

Biological assessments of a mixture of endocrine disruptors at environmentally relevant concentrations in water following UV/H{sub 2}O{sub 2} oxidation

A gene designated BRCA1, implicated in the susceptibility to early-onset familial breast cancer, has recently been localized to chromosome 17q12-q21. To date, the order of DNA markers mapped within this region has been based on genetic linkage analysis. The authors report the use of multicolor fluorescence in situ hybridization to establish a physically based map of five polymorphic DNA markers and 10 cloned genes spanning this region. Three cosmid clones and Alu-PCR-Generated products derived from 12 yeast artificial chromosome clones representing each of these markers were used in two-color mapping experiments to determine an initial proximity of markers relative to each other on metaphase chromosomes. Interphase mapping was then employed to determine the order and orientation of closely spaced loci by direct visualization of fluorescent signals following hybridization of three probes, each detected in a different color. ...

1993-09-01

105

Variants within the yeast Ty sequence family encode a class of structurally conserved proteins.

Numerous studies have investigated degradation of individual endocrine disrupting compounds (EDCs) in lab or natural waters. However, natural variations in water matrices and mixtures of EDCs in the environment may confound analysis of the treatment efficiency. Because chemical based analytical methods cannot represent the combined or synergistic activities between water quality parameters and/or the EDC mixtures at environmentally relevant concentrations ({mu}g L{sup -1}-ng L{sup -1}), bioanalytical assessments of residual estrogenic activity in treated water were used to evaluate the performance of the UV based advanced oxidation process for estrogenic contaminants in water. Four EDCs including estradiol (E{sub 2}), ethinyl estradiol (EE{sub 2}), bisphenol-A (BPA) and nonylphenol (NP) were spiked individually or as a mixture at {mu}g L{sup -1}-ng L{sup -1} in laboratory or natural river water. The removal rates of estrogenic activity were ...

2007-04-15

106

The requirement of yeast replication origins for pre-replication complex proteins is modulated by transcription

The Ty transposable elements of Saccharomyces cerevisiae form a heterogeneous family within which two broad structural classes (I and II) exist. The two classes differ by two large substitutions and...Full Text Available

1985-06-11

107

The recruitment of acetylated and unacetylated tropomyosin to distinct actin polymers permits the discrete regulation of specific myosins in fission yeast

The mini-chromosome maintenance proteins Mcm2–7 are essential for DNA replication. They are loaded onto replication origins during G1 phase of the cell cycle to form a pre-replication complex...Full Text Available

2005-01-01

108

The fission yeast gene pmt1+ encodes a DNA methyltransferase homologue.

Tropomyosin (Tm) is a conserved dimeric coiled-coil protein, which forms polymers that curl around actin filaments in order to regulate actomyosin function. Acetylation of the Tm N-terminal...Full Text Available

2010-10-01

109

Structure-Function Study of the N-terminal Domain of Exocyst Subunit Sec3*

DNA methylation of cytosine residues is a widespread phenomenon and has been implicated in a number of biological processes in both prokaryotes and eukaryotes. This methylation occurs at the 5-position...Full Text Available

1995-01-25

110

Some highlights of research on aging with invertebrates, 2010

The exocyst is an evolutionarily conserved octameric complex involved in polarized exocytosis from yeast to humans. The Sec3 subunit of the exocyst acts as a spatial landmark for exocytosis through...Full Text Available

2010-04-02

111

SIRT1 contributes to telomere maintenance and augments global homologous recombination

This annual review focuses on invertebrate model organisms, which continue to yield fundamental new insights into mechanisms of aging. This year, the budding yeast has been used to understand how asymmetrical...Full Text Available

2011-02-01

112

PtdIns 3-Kinase Orchestrates Autophagosome Formation in Yeast

Yeast Sir2 deacetylase is a component of the silent information regulator (SIR) complex encompassing Sir2/Sir3/Sir4. Sir2 is recruited to telomeres through Rap1, and this complex spreads into subtelomeric...Full Text Available

2010-12-27

113

Overexpression of human virus surface glycoprotein precursors induces cytosolic unfolded protein response in Saccharomyces cerevisiae

Eukaryotic cells can massively transport their own cytoplasmic contents into a lytic compartment, the vacuole/lysosome, for recycling through a conserved system called autophagy. The key process in...Full Text Available

2011-01-01

114

O2-dependent methionine auxotrophy in Cu,Zn superoxide dismutase-deficient mutants of Saccharomyces cerevisiae.

BackgroundThe expression of human virus surface proteins, as well as other mammalian glycoproteins, is much more efficient in cells of higher eukaryotes rather than yeasts. The limitations...Full Text Available

115

Nuclear Pore Complex Number and Distribution throughout the Saccharomyces cerevisiae Cell Cycle by Three-Dimensional Reconstruction from Electron Micrographs of Nuclear Envelopes

Mutant strains of the yeast Saccharomyces cerevisiae which lack functional Cu,Zn superoxide dismutase (SOD-1) do not grow aerobically unless supplemented with methionine. The molecular basis of this...Full Text Available

1990-04-01

116

Mitochondrial transmission during mating in Saccharomyces cerevisiae is determined by mitochondrial fusion and fission and the intramitochondrial segregation of mitochondrial DNA.

The number of nuclear pore complexes (NPCs) in individual nuclei of the yeast Saccharomyces cerevisiae was determined by computer-aided reconstruction of entire nuclei from electron...Full Text Available

1997-11-01

117

Mammalian Sirtuins and Energy Metabolism

To gain insight into the process of mitochondrial transmission in yeast, we directly labeled mitochondrial proteins and mitochondrial DNA (mtDNA) and observed their fate after the fusion of two cells....Full Text Available

1997-07-01

118

MAPPING THE INITIATOR BINDING TAF2 SUBUNIT IN THE STRUCTURE OF HYDRATED YEAST TFIID

Sirtuins are highly conserved NAD⁺-dependent protein deacetylases and/or ADP-ribosyltransferases that can extend the lifespan of several lower model organisms including yeast, worms and flies....Full Text Available

119

Legionella fairfieldensis sp. nov. isolated from cooling tower waters in Australia.

SummaryThe general transcription factor TFIID is a large multi-subunit complex required for the transcription of most protein-encoding genes by RNA polymerase II. Taking advantage...Full Text Available

2009-03-11

120

Insights into Cdc13 dependent telomere length regulation

Three Legionella-like organisms were isolated from water from the cooling towers of two Australian institutions. The strains grew on buffered charcoal-yeast extract (BCYE) agar but not on BCYE agar...Full Text Available

1991-03-01

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121

Increased Ethanol Productivity in Xylose-Utilizing Saccharomyces cerevisiae via a Randomly Mutagenized Xylose Reductase?

Cdc13 is a single stranded telomere binding protein that specifically localizes to the telomere ends of budding yeasts and is essential for cell viability. It caps the ends of chromosomes thus preventing...Full Text Available

122

Improving yield of industrial biomass propagation by increasing the Trx2p dosage

Baker's yeast (Saccharomyces cerevisiae) has been genetically engineered to ferment the pentose sugar xylose present in lignocellulose biomass. One of the reactions controlling the...Full Text Available

2010-12-01

123

Identification of Potential Calorie Restriction-Mimicking Yeast Mutants with Increased Mitochondrial Respiratory Chain and Nitric Oxide Levels

The beneficial effect of improving yeast redox response by increasing thioredoxin levels has been shown. Decreased lipid and protein oxidation is reflected in an increased biomass yield. In addition,...Full Text Available

2010-09-01

124

Identification and Characterization of CPS1 as a Hyaluronic Acid Synthase Contributing to the Pathogenesis of Cryptococcus neoformans Infection?

Calorie restriction (CR) induces a metabolic shift towards mitochondrial respiration; however, molecular mechanisms underlying CR remain unclear. Recent studies suggest that CR-induced mitochondrial...Full Text Available

125

Fuzzy-decision-making problems of fuel ethanol production using a genetically engineered yeast

Cryptococcus neoformans is a pathogenic yeast that often causes devastating meningoencephalitis in immunocompromised individuals. We have previously identified the C. neoformans...Full Text Available

2007-08-01

126

Fermentability of Corn Syrups with Different Dextrose Equivalents Added to Various Grape Juices¹

A fuzzy-decision-making procedure is applied to find the optimal feed policy of a fed-batch fermentation process for fuel ethanol production using a genetically engineered Saccharomyces yeast 1400 (pLNH33). The policy consisted of feed flow rate, feed concentration, and fermentation time. The recombinant yeast 1400 (pLNH33) can utilize glucose and xylose simultaneously to produce ethanol. However, the parent yeast utilizes glucose only. A partially selective model is used to describe the kinetic behavior of the process. In this study, this partially selective fermentation process is formulated as a general multiple-objective optimal control problem. By using an assigned membership function for each of the objectives, the general multiple-objective optimization problem can be converted into a maximizing decision problem. In order to obtain a global solution, a hybrid method of differential evolution is introduced to solve ...

1998-08-01

127

Expansions, contractions, and fragility of the spinocerebellar ataxia type 10 pentanucleotide repeat in yeast

It was found that neither the enzymes of the grapes nor those of wine yeast Saccharomyces ellipsoideus strain 223 attacked the higher polysaccharides present in corn syrups. The alcohol...Full Text Available

1967-03-01

128

Exit from the Golgi Is Required for the Expansion of the Autophagosomal Phagophore in Yeast Saccharomyces cerevisiae

Spinocerebellar ataxia 10 (SCA10) is an autosomal dominant disease caused by large-scale expansions of the (ATTCT)_n repeat within an intron of the human ATXN10 gene. In contrast...Full Text Available

2011-02-15

129

Engineering ligand-responsive RNA controllers in yeast through the assembly of RNase III tuning modules

The delivery of proteins and organelles to the vacuole by autophagy involves membrane rearrangements that result in the formation of large vesicles called autophagosomes. The mechanism underlying autophagosome...Full Text Available

2010-07-01

130

Cloning and Analysis of a Candida albicans Gene That Affects Cell Surface Hydrophobicity

The programming of cellular networks to achieve new biological functions depends on the development of genetic tools that link the presence of a molecular signal to gene-regulatory activity. Recently,...Full Text Available

2011-07-01

131

Chemical complementation: A reaction-independent genetic assay for enzyme catalysis

The opportunistic pathogenic yeast Candida albicans exhibits growth phase-dependent changes in cell surface hydrophobicity, which has been correlated with adhesion to host tissues....Full Text Available

2001-06-01

132

Biotransformation of Explosives by the Old Yellow Enzyme Family of Flavoproteins

A high-throughput assay for enzyme activity has been developed that is reaction independent. In this assay, a small-molecule yeast three-hybrid system is used to link enzyme catalysis to transcription...Full Text Available

2002-12-24

133

Arabidopsis thaliana Chromosome 4 Replicates in Two Phases That Correlate with Chromatin State

Several independent studies of bacterial degradation of nitrate ester explosives have demonstrated the involvement of flavin-dependent oxidoreductases related to the old yellow enzyme (OYE) of yeast....Full Text Available

2004-06-01

134

Affinity maturation of human botulinum neurotoxin antibodies by light chain shuffling via yeast mating

DNA replication programs have been studied extensively in yeast and animal systems, where they have been shown to correlate with gene expression and certain epigenetic modifications. Despite the conservation...Full Text Available

2010-06-01

135

A Novel Form of Transcriptional Silencing by Sum1-1 Requires Hst1 and the Origin Recognition Complex

Botulism is caused by the botulinum neurotoxins (BoNTs), the most poisonous substance known. Because of the high potency of BoNT, development of diagnostic and therapeutic antibodies for botulism requires...Full Text Available

2010-04-01

136

Whole-genome cancer analysis as an approach to deeper understanding of tumour biology

In the yeast Saccharomyces cerevisiae, a and α mating-type information is stored in transcriptionally silenced cassettes called HML and HMR....Full Text Available

2001-05-01

137

Using Regulatory and Epistatic Networks to Extend the Findings of a Genome Scan: Identifying the Gene Drivers of Pigmentation in Merino Sheep

Recent advances in DNA sequencing technology are providing unprecedented opportunities for comprehensive analysis of cancer genomes, exomes, transcriptomes, as well as epigenomic components. The integration...Full Text Available

2010-01-19

138

Transcriptional mapping of the 3' end of the bovine syncytial virus genome.

Extending genome wide association analysis by the inclusion of gene expression data may assist in the dissection of complex traits. We examined piebald, a pigmentation phenotype in both human and Merino...Full Text Available

139

The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

The bovine syncytial virus, a member of the retroviral subfamily Spumavirinae, causes a persistent, asymptomatic infection in cattle. Nucleotide sequence analysis of the viral genome revealed two overlapping...Full Text Available

1994-02-01

140

Targeted plasmid integration into the human genome by an engineered zinc-finger recombinase

BackgroundFood supply from the ocean is constrained by the shortage of domesticated and selected fish. Development of genomic models of economically important fishes should assist...Full Text Available

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141

Synthesis and degradation of dinoflagellate plastid-encoded psbA proteins are light-regulated, not circadian-regulated

The development of new methods for gene addition to mammalian genomes is necessary to overcome the limitations of conventional genetic engineering strategies. Although a variety of DNA-modifying enzymes...Full Text Available

2011-09-01

142

Replication Stress Induces Genome-wide Copy Number Changes in Human Cells that Resemble Polymorphic and Pathogenic Variants

In many dinoflagellate species, the plastid genome has been proposed to exist as a limited number of single-gene minicircles, and many genes normally found in the plastid genome are nuclear-encoded....Full Text Available

2005-02-22

143

Reciprocal Silencing, Transcriptional Bias and Functional Divergence of Homeologs in Polyploid Cotton (Gossypium)

Copy number variants (CNVs) are an important component of genomic variation in humans and other mammals. Similar de novo deletions and duplications, or copy number changes (CNCs), are now known to be...Full Text Available

2009-03-13

144

Rai1 duplication causes physical and behavioral phenotypes in a mouse model of dup(17)(p11.2p11.2)

Polyploidy is an important force in the evolution of flowering plants. Genomic merger and doubling induce an extensive array of genomic effects, including immediate and long-term alterations in the...Full Text Available

2009-06-01

145

Rab protein evolution and the history of the eukaryotic endomembrane system

Genomic disorders are conditions that result from DNA rearrangements, such as deletions or duplications. The identification of the dosage-sensitive gene(s) within the rearranged genomic interval is...Full Text Available

2006-11-01

146

Presence of two independent chromosomes in the Brucella melitensis 16M genome.

Spectacular increases in the quantity of sequence data genome have facilitated major advances in eukaryotic comparative genomics. By exploiting homology with classical model organisms, this makes possible...Full Text Available

2010-10-01

147

Parallel Loss of Plastid Introns and Their Maturase in the Genus Cuscuta

Mapping the restriction fragments of the Brucella melitensis 16M genome with a new restriction endonuclease, PacI, which cut the DNA into only eight fragments, indicated that this species contains two...Full Text Available

1993-02-01

148

Nucleocapsid and Matrix Protein Contributions to Selective Human Immunodeficiency Virus Type 1 Genomic RNA Packaging

Plastid genome content and arrangement are highly conserved across most land plants and their closest relatives, streptophyte algae, with nearly all plastid introns having invaded the genome in their...Full Text Available

149

Natural mutagenesis of human genomes by endogenous retrotransposons

The nucleocapsid protein (NC) of retroviruses plays a major role in genomic RNA packaging, and some evidence has implicated the matrix protein (MA) of certain retroviruses in viral RNA binding. To further...Full Text Available

1998-03-01

150

Molecular characterization of a Chinese variant of the Flury-LEP strain

SUMMARYTwo abundant classes of mobile elements, namely Alu and L1 elements, continue to generate new retrotransposon insertions in human genomes. Estimates suggest that these...Full Text Available

2010-06-25

151

Mobilizing diversity: transposable element insertions in genetic variation and disease

The entire genome of rabies virus vaccine strain Flury-LEP-C, a Chinese variant of the rabies virus vaccine strain Flury-LEP, was sequenced. The overall length of the genome of Flury-LEP-C strain was...Full Text Available

152

Large-scale cross-species oncogenomics identifies candidate oncogenes and tumor suppressor genes

Transposable elements (TEs) comprise a large fraction of mammalian genomes. A number of these elements are actively jumping in our genomes today. As a consequence, these insertions provide a source...Full Text Available

153

Isolation of BAC Clones Containing Conserved Genes from Libraries of Three Distantly Related Moths: A Useful Resource for Comparative Genomics of Lepidoptera

While genomic alterations identified in human tumors using techniques such as comparative genomic hybridisation (CGH) may be recurrent, they frequently encompass large regions, in some cases...Full Text Available

2010-02-01

154

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

Lepidoptera, butterflies and moths, is the second largest animal order and includes numerous agricultural pests. To facilitate comparative genomics in Lepidoptera, we isolated BAC clones containing...Full Text Available

2011-01-01

155

Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria Revealed by the Complete Genome Sequence

BackgroundGenome-scale metabolic reconstructions have been recognised as a valuable tool for a variety of applications ranging from metabolic engineering to evolutionary studies....Full Text Available

156

Impact of genetic changes to the CRPV genome and their application to the study of pathogenesis in vivo

The gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically...Full Text Available

2005-11-01

157

The cottontail rabbit papillomavirus (CRPV)/rabbit model has been used to study oncogenicity and immunogenicity of different antigens from the papillomavirus genome and has therefore served...Full Text Available

2007-02-20

158

Genomic cloning and characterization of a ricin gene from Ricinus communis.

BackgroundA large fraction of the human genome is attributable to L1 retrotransposon sequences. Not only do L1s themselves make up a significant portion of the genome, but L1-encoded...Full Text Available

2003-01-01

159

Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns"

A genomic clone that specifies a single polypeptide precursor for ricin, a toxic lectin of Ricinus communis (castor bean), was isolated, sequenced and Sl mapped. The gene encodes a 64 kDa precursor...Full Text Available

1985-11-25

160

Genome-wide detection and characterization of positive selection in human populations

BackgroundThe genomes of prokaryotes and lower eukaryotes display a very strong 11 bp periodic bias in the distribution of their nucleotides. This bias is present throughout a given...Full Text Available

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

161

Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms...Full Text Available

2007-10-18

162

Genome-Wide Identification and Evolutionary Analysis of the Animal Specific ETS Transcription Factor Family

BackgroundCucumber, Cucumis sativus L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular...Full Text Available

163

Genome size and wing parameters in passerine birds

The ETS proteins are a family of transcription factors (TFs) that regulate a variety of biological processes. We made genome-wide analyses to explore the classification of the ETS gene family. We identified...Full Text Available

164

Genetic susceptibility to systemic lupus erythematosus in the genomic era

Despite their status as the most speciose group of terrestrial vertebrates, birds exhibit the smallest and least variable genome sizes among tetrapods. It has been suggested that this is because powered...Full Text Available

2009-01-07

165

Estimating Missing Heritability for Disease from Genome-wide Association Studies

Our understanding of the genetic basis of systemic lupus erythematosus (SLE) has been rapidly advanced using large-scale, case–control, candidate gene studies as well as genome-wide...Full Text Available

2010-12-01

166

Epitope tagging of endogenous proteins for genome wide Chromatin immunoprecipitation analysis

Genome-wide association studies are designed to discover SNPs that are associated with a complex trait. Employing strict significance thresholds when testing individual SNPs avoids false positives at...Full Text Available

2011-03-11

167

Dynamic Rearrangements Determine Genome Organization and Useful Traits in Soybean1[C][W

The development of chromatin immunoprecipitation methods coupled with DNA microarray (ChIP-chip) technology has enabled genome-wide identification of cis-DNA regulatory elements to which transcription...Full Text Available

2009-01-01

168

Completely phased genome sequencing through chromosome sorting

Soybean (Glycine max) is a paleopolyploid whose genome has gone through at least two rounds of polyploidy and subsequent diploidization events. Several studies have investigated the...Full Text Available

2009-11-01

169

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta

The two haploid genome sequences that a person inherits from the two parents represent the most fundamentally useful type of genetic information for the study of heritable diseases and the development...Full Text Available

2011-01-04

170

Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss

BackgroundPlastid genome content and protein sequence are highly conserved across land plants and their closest algal relatives. Parasitic plants, which obtain some or all of their...Full Text Available

171

Bunyamwera virus can repair both insertions and deletions during RNA replication

BackgroundThe bacterial genus Listeria contains pathogenic and non-pathogenic species, including the pathogens L. monocytogenes and L. ivanovii,...Full Text Available

172

Biophysical characterization of recombinant proteins: A key to higher structural genomics success

The genomic termini of RNA viruses contain essential cis-acting signals for such diverse functions as packaging, genome translation, mRNA transcription, and RNA replication, and thus...Full Text Available

2010-06-01

173

Behavioral genomics of honeybee foraging and nest defense

Hundreds of genomes have been successfully sequenced to date, and the data are publicly available. At the same time, the advances in large-scale expression and purification of recombinant proteins have...Full Text Available

2010-10-01

174

Avian Nephritis Virus (ANV) as a New Member of the Family Astroviridae and Construction of Infectious ANV cDNA

The honeybee has been the most important insect species for study of social behavior. The recently released draft genomic sequence for the bee will accelerate honeybee behavioral genetics. Although...Full Text Available

2007-04-01

175

Analysis of illegitimate genomic integration mediated by zinc-finger nucleases: implications for specificity of targeted gene correction

The complete RNA genome of the avian nephritis virus (ANV) associated with acute nephritis in chickens has been molecularly cloned and sequenced. Excluding the poly(A) tail, the genome comprises 6,927...Full Text Available

2000-09-01

176

A proposal to sequence the genome of a garter snake (Thamnophis sirtalis)

BackgroundFormation of site specific genomic double strand breaks (DSBs), induced by the expression of a pair of engineered zinc-finger nucleases (ZFNs), dramatically increases the...Full Text Available

177

A haplotype map of the human genome

Here we develop an argument in support of sequencing a garter snake (Thamnophis sirtalis) genome, and outline a plan to accomplish this. This snake is a common, widespread, nonvenomous...Full Text Available

178

A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish

Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million...Full Text Available

2005-10-27

179

A Marker-Dense Physical Map of the Bradyrhizobium japonicum Genome

BackgroundThe genomic organisation of the Major Histocompatibility Complex (MHC) varies greatly between different vertebrates. In mammals, the classical MHC consists of a large number...Full Text Available

180

Yeast as a Model System to Study Tau Biology

Bacterial artificial chromosome (BAC) clones are effective mapping and sequencing reagents for use with a wide variety of small and large genomes. This report describes the development of a physical...Full Text Available

2001-08-01

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181

Cell cultures are more sensitive than Saccharamoyces cervisiae tests for assessing the toxicity of aquatic pollutants

Hyperphosphorylated and aggregated human protein tau constitutes a hallmark of a multitude of neurodegenerative diseases called tauopathies, exemplified by Alzheimer's disease. In spite of an enormous amount of research performed on tau biology, several crucial questions concerning the mechanisms of tau toxicity remain unanswered. In this paper we will highlight some of the processes involved in tau biology and pathology, focusing on tau phosphorylation and the interplay with oxidative stress. In addition, we will introduce the development of a human tau-expressing yeast model, and discuss some crucial results obtained in this model, highlighting its potential in the elucidation of cellular processes leading to tau toxicity.

2011-04-06

182

Genomic Careers: Interactive Videos

Cultured fish and human cells have been used as bioassay systems for the evaluation of the toxicity of aquatic pollutants. Numerous assays using bacteria and yeast have also been used for such purposes. The authors report the toxicity of aquatic pollutants (Cd, Hg, and Ni), using cell culture systems and the yeast Saccharomyces cervisiae test. Cd, Hg, and Ni were chosen as model compounds of pollutants because the related toxicity is now fairly well established.

1988-07-01

183

Medline Plus

... the nature of DNA testing. 07:56 - President / CEO of a Biotechnology / Pharmaceutical Company - Sherri Bale President ...

184

Exons, Introns and Talking Genes: The Sience Behind the Human Genome Project

The effect of substrate modification on microbial growth on surfaces

This book presents in simple terms the basis of molecular genetics and how it is used to obtain an understanding of the human genome. The author's central focus is the transistion of genetics from statistics to experimental manipulations, and he offers analogies that help readers visualize the genome, thereby avoiding conventional scientific presentations. He illustrates how genetics is used in scientific laboratories, in courtrooms, and in hospitals. Little is presented about the complex social and ethical issues raised by the Human Genome project.

1993-01-01

185

Genome-Wide Association Study SNPs in the Human Genome Diversity Project Populations: Does Selection Affect Unlinked SNPs with Shared Trait Associations?

The principle aim of the program was to produce a novel, non-leaching antimicrobial surface for commercial development and future use in the liquid food packaging industry. Antimicrobial surfaces which exist presently have been produced to combat the growth of prokaryotic organisms and usually function as slow release systems. A system which could inhibit eukaryotic growth without contaminating the surrounding 'environment' with the inhibitor was considered of great commercial importance. The remit of this study was concerned with creating a surface which could control the growth of eukaryotic organisms found in fruit juice with particular interest in the yeast, Saccharomyces cerevisiae. Putative antimicrobial surfaces were created by the chemical modification of the test substrate polymers; nylon and ethylvinyl alcohol (EVOH). Surfaces were chemically modified by the covalent coupling of antimicrobial agents known to be active against the ...

1998-07-01

186

Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC₁population between gossypium hirsutum and G. barbadense

Genome-wide association studies (GWAS) have identified more than 2,000 trait-SNP associations, and the number continues to increase. GWAS have focused on traits with potential consequences for human...Full Text Available

2011-01-01

187

Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park

BackgroundCotton, with a large genome, is an important crop throughout the world. A high-density genetic linkage map is the prerequisite for cotton genetics and breeding. A genetic...Full Text Available

188

Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

A novel, obligately anaerobic, extremely thermophilic, cellulolytic bacterium, designated OB47T, was isolated from Obsidian Pool, Yellowstone National Park, WY, USA. The isolate was a non-motile, non-spore forming, Gram-positive rod approximately 2 m long by 0.2 m wide and grew at temperatures between 55-85oC with the optimum at 78oC. The pH range for growth was 6.0-8.0 with values of near 7.0 being optimal. Growth on cellobiose produced the fastest specific growth rates at 0.75 hr-1. The organism also displayed fermentative growth on glucose, maltose, arabinose, fructose, starch, lactose, mannose, sucrose, galactose, xylose, arabinogalactan, Avicel, xylan, filter paper, processed cardboard, pectin, dilute acid-pretreated switchgrass and Populus. OB47T was unable to grow on mannitol, fucose, lignin, Gelrite, acetate, glycerol, ribose, sorbital, carboxymethylcellulose and casein. Yeast extract stimulated growth and thiosulfate, sulfate, nitrate, and sulfur were not ...

2010-02-01

189

Proteomic analysis of the shistosome tegument and its surface membranes

It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in the L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation ...

2011-01-01

190

Scientific Electronic Library Online (English)

Abstract in english The tegument surface of the adult schistosome, bounded by a normal plasma membrane overlain by a secreted membranocalyx, holds the key to understanding how schistosomes evade host immune responses. Recent advances in mass spectrometry (MS), and the sequencing of the Schistosoma mansoni transcriptome/genome, have facilitated schistosome proteomics. We detached the tegument from the worm body and enriched its surface membranes by differential extraction, before subjecting t (more) he preparation to liquid chromatography-based proteomics to identify its constituents. The most exposed proteins on live worms were labelled with impearmeant biotinylation reagents, and we also developed methods to isolate the membranocalyx for analysis. We identified transporters for sugars, amino acids, inorganic ions and water, which confirm the importance of the tegument plasma membrane in nutrient acquisition and solute balance. Enzymes, ...

2006-10-01

191

Mapping quantitative trait loci controlling milk production in dairy cattle by exploiting progeny testing

High genetic diversity of HIV-1 was found in men who have sex with men in Shijiazhuang, China

We have exploited {open_quotes}progeny testing{close_quotes} to map quantitative trait loci (QTL) underlying the genetic variation of milk production in a selected dairy cattle population. A total of 1,518 sires, with progeny tests based on the milking performances of >150,000 daughters jointly, was genotyped for 159 autosomal microsatellites bracketing 1645 centimorgan or approximately two thirds of the bovine genome. Using a maximum likelihood multilocus linkage analysis accounting for variance heterogeneity of the phenotypes, we identified five chromosomes giving very strong evidence (LOD score {ge} 3) for the presence of a QTL controlling milk production: chromosomes 1, 6, 9, 10 and 20. These findings demonstrate that loci with considerable effects on milk production are still segregating in highly selected populations and pave the way toward marker-assisted selection in dairy cattle breeding. 44 refs., 4 figs., 3 tabs.

1995-02-01

192

British Library Electronic Table of Contents (United Kingdom)

Men who have sex with men (MSM) have become one of the populations with severely HIV prevalence in China. However, very few genetic studies have been done on HIV-1 spreading in this population. In this study, the genetic characterization of HIV-1 strains prevalent in the MSM in Shijiazhuang, China, was analyzed basing on the HIV-1 full-length gag, pol, and partial env gene. 21 drug-naive HIV-1 sero-positive patients were enrolled into the study. Full length gag, pol, partial env genes and some near full length genomes were amplified with nest RT-PCR followed by sequencing. Multiple subtypes, including CRF01_AE (52.9%), subtype B (35.3%) and CRF07_BC (11.8%), were found in the population. Phylogenetic analysis showed close relationship between our strains with those from Beijing MSM but not...

2011-01-01

193

Evaluation of Toll-like receptors 3 (c.1377C/T) and 9 (G2848A) gene polymorphisms in cervical cancer susceptibility

British Library Electronic Table of Contents (United Kingdom)

Cervical cancer is emerging as a leading cause of morbidity and mortality in women worldwide. Toll-like Receptor (TLR) gene polymorphisms may contribute to subsequent inter-individual variability in cancer susceptibility. The present study aimed to identify the role of TLR 3 (c.1377C/T) [rs3775290] and TLR 9 (G2848A) [rs352140] gene polymorphisms in the risk of developing cervical cancer in North India. Peripheral blood samples were collected from 200 histopathologically confirmed cervical cancer patients from North India and 200 unrelated, cancer-free, age-matched healthy female controls of similar ethnicity. Genomic DNA was extracted using the salting-out method, and genotyped for TLR 3 and TLR 9 using polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP). O...

2011-01-01

194

Common colorectal cancer risk variants in SMAD7 are associated with survival among prediagnostic nonsteroidal anti-inflammatory drug users: A population-based study of postmenopausal women

British Library Electronic Table of Contents (United Kingdom)

Abstract Common single nucleotide polymorphisms (SNPs) in SMAD7 (18q21) have been linked to colorectal cancer (CRC) risk in genome-wide association studies, but little is known about their effects on survival. SMAD7 regulates gastrointestinal inflammation by inhibiting transforming growth factor- (TGFB), which can act as both a tumor suppressor and a promoter of metastasis. Regular use of cyclooxygenase-2 (COX2) inhibitors, such as nonsteroidal anti-inflammatory drugs (NSAIDs), reduces the risk of developing CRC. Because COX2 overexpression reduces the growth suppressing effects of TGFB, we hypothesized that survival may depend on both SMAD7 genotype and prediagnostic NSAID use. Postmenopausal women, ages 50-74, diagnosed with incident invasive CRC from 1997 to 2002 were identified using t...

2011-01-01

195

Global Molecular Characterization of the Chromate Stress Response in Shewanella oneidensis MR-1: Identification of a Putative DNA-Binding Response Regulator and Azoreductase Involved in Cr(VI) Detoxification

Homology analyses of the protein sequences of fatty acid synthases from chicken liver, rat mammary gland, and yeast

Shewanella oneidensis MR-1 is a model environmental organism that possesses diverse respiratory capacities, including the ability to reduce soluble Cr(VI) to sparingly soluble, less toxic Cr(III). Effective bioremediation of Cr-contaminated sites requires knowledge of the molecular mechanisms and regulation of heavy metal resistance and biotransformation by dissimilatory metal-reducing bacteria. Towards this goal, our ERSP-funded work is focused on the identification and functional analysis of genes/proteins comprising the response pathways for chromate detoxification and/or reduction. Previous transcriptomic profiling and whole-cell proteomic analyses implicated the involvement of a functionally undefined DNA-binding response regulator (SO2426) and a putative azoreductase (SO3585) in the chromate stress response of MR-1. Here we describe a detailed functional analysis of SO2426 and SO3585 in order to begin to understand the role of these proteins in the cellular response to chromate. ...

2006-04-05

196

Assessment of the role of oxygen and mitochondria in heat shock induction of radiation and thermal resistance in Saccharomyces cerevisiae

Homology analyses of the protein sequences of chicken liver and rat mammary gland fatty acid synthases were carried out. The amino acid sequences of the chicken and rat enzymes are 67% identical. If conservative substitutions are allowed, 78% of the amino acids are matched. A region of low homologies exists between the functional domains, in particular around amino acid residues 1059-1264 of the chicken enzyme. Homologies between the active sites of chicken and rat and of chicken and yeast enzymes have been analyzed by an alignment method. A high degree of homology exists between the active sites of the chicken and rat enzymes. However, the chicken and yeast enzymes show a lower degree of homology. The DADPH-binding dinucleotide folds of the {beta}-ketoacyl reductase and the enoyl reductase sites were identified by comparison with a known consensus sequence for the DADP- and FAD-binding dinucleotide folds. The active sites of all of the enzymes ...

1989-11-01

197

Engineering Relative Compression of Genomes

In response to a heat shock, the yeast Saccharomyces cerevisiae undergoes a large increase in its resistance to heat and, by the induction of its recombinational DNA repair capacity, a corresponding increase in resistance to radiation. Yeast which lack mitochondrial DNA, mitochondria-controlled protein synthetic apparatus, aerobic respiration, and electron transport (rho/sup 0/ strain) were used to assess the role of O/sub 2/, mitochondria, and oxidative processes controlled by mitochondria in the induction of these resistances. We have found that rho/sup 0/ yeast grown and heat shocked in either the presence or absence of O/sub 2/ are capable of developing both radiation and heat resistance. We conclude that neither the stress signal nor its cellular consequences of induced heat and radiation resistance are directly dependent on O/sub 2/, mitochondrial DNA, or mitochondria-controlled protein synthetic or oxidative ...

1983-10-01

198

Removal of uranium from solution using residual brewery yeast: combined biosorption and precipitation

Technology progress in DNA sequencing boosts the genomic database growth at faster and faster rate. Compression, accompanied with random access capabilities, is the key to maintain those huge amounts of data. In this paper we present an LZ77-style compression scheme for relative compression of multiple genomes of the same species. While the solution bears similarity to known algorithms, it offers significantly higher compression ratios at compression speed over a order of magnitude greater. One of the new successful ideas is augmenting the reference sequence with phrases from the other sequences, making more LZ-matches available.

2011-01-01

199

Pectinolytic yeast isolates for cold-active polygalacturonase production

Whilst unwashed preparations of biomass from a local brewery had an apparent maximum biosorption capacity for uranium of 360 mg/g (dry weight biomass) washing reduced this maximum to 150 mg/g. Homogenization of both biomass preparations and recovery of cellular debris had no significant effect on the maximum biosorption capacities although at lower equilibrium concentrations of uranium differences in the biosorption capacities were detected. When unwashed biomass was retained by a semi-permeable membrane 40% of uranium used in the experiments precipitated outside that membrane. Therefore a significant proportion of the uranium removed from solution, and previously attributed to biosorption by the yeast biomass, resulted from precipitation brought about by interaction with low molecular weight components loosely associated with the biomass. (Author).

1997-04-01

200

British Library Electronic Table of Contents (United Kingdom)

Pectin rich cold stored spoiled fruits, vegetables and cold soils were screened and different pectinolytic isolates were obtained by enrichment culturing and ruthenium red plate assay. Among the primary isolates 10-15% were yeast isolates. Six isolates with higher zones of pectin hydrolysis were selected and tested for polygalacturonase (PGU) production at room temperature (25 degrees C) and at 5 degrees C. One isolate identified as Saccharomyces sp. with highest polygalacturonase activity at 5 degrees C was used for enzyme production using raw fruit pectins as substrates. The isolate was identified by preliminary cultural, morphological and sugar fermentation tests. PGU production was high in raw pectin substrates like orange peel (21 U/ml), apple peel (20 U/ml ), mango peel (19 U/ml), ...

2011-01-01

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201

Microbiological quality and biophenol content of hot air-dried Thassos cv. table olives upon storage

British Library Electronic Table of Contents (United Kingdom)

Abstract Microbiological quality and biophenol content evolution was studied in minimally processed Thassos cv table olives by hot air dehydration under mild conditions (40C, 24-h, aw-=-0.893) and storage under characteristic packaging conditions (vacuum, 100% N2 and air) at 4 and 20C over a period of 180 days. No salt was used in the production line or packaging. The undesirable microorganisms (Enterobacteriaceae, Staphylococcus aureus, Bacillus, Clostridium) were undetectable until the end of the storage period. Also, modified atmospheres prevented fungal growth at both temperatures apart from the samples stored in air, in which Penicillium and Aspergillus spp. were identified. At 20C, a coexistence of mesophilic bacteria and yeasts occurred. At 4C, yeasts were the predominant microflora...

2011-01-01

202

Extrinsic allergic alveolitis induced by the yeast Debaryomyces hansenii.

Ultraconserved Elements: Analyses of Dosage Sensitivity, Motifs and Boundaries

A 65-yr-old female developed cough, fever and dyspnoea following repeated exposure to a home ultrasonic humidifier. High-resolution computed tomography showed ground-glass opacity in both lung fields. Arterial blood gas analysis gave an oxygen tension of 8.38 kPa (63 Torr). Pulmonary function testing revealed restrictive ventilatory impairment with a reduction in the diffusing capacity. The diagnosis of extrinsic allergic alveolitis (EAA) was confirmed by radiographic findings, pathological evidence of alveolitis and reproductive development by a provocation test to the humidifier water. The yeast Debaryomyces Hansenii was the only microorganism cultured from the water of the humidifier. The double diffusion precipitating test and lymphocyte proliferative response was positive for an extract of D. Hansenii, providing evidence to incriminate this fungus. This is the first described case of EAA caused by D. Hansenii. PMID:12449192

2002-11-01

203

The Importance of Mitochondrial DNA in Aging and Cancer

Ultraconserved elements (UCEs) are sequences that are identical between reference genomes of distantly related species. As they are under negative selection and enriched near or in specific classes...Full Text Available

2008-12-01

204

The COG database: an updated version includes eukaryotes

Mitochondrial dysfunction has been implicated in premature aging, age-related diseases, and tumor initiation and progression. Alterations of the mitochondrial genome accumulate both in aging tissue...Full Text Available

205

Systems medicine: the future of medical genomics and healthcare

BackgroundThe availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an...Full Text Available

206

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

High-throughput technologies for DNA sequencing and for analyses of transcriptomes, proteomes and metabolomes have provided the foundations for deciphering the structure, variation and function of the...Full Text Available

207

Polymer Genomics: An Insight into Pharmacology and Toxicology of Nanomedicines 1

BackgroundOrthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood...Full Text Available

208

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

Synthetic polymers and nanomaterials display selective phenotypic effects in cells and in the body that affect signal transduction mechanisms involved in inflammation, differentiation, proliferation,...Full Text Available

2006-12-30

209

Open-source software accelerates bioinformatics

Eukaryotic genomes are packaged in two basic forms, euchromatin and heterochromatin. We have examined the composition and organization of Drosophila melanogaster heterochromatin in...Full Text Available

2011-02-01

210

Nucleomorph Ribosomal DNA and Telomere Dynamics in Chlorarachniophyte Algae

A report on the Wellcome Trust/Cold Spring Harbor Genome Informatics meeting, Cold Spring Harbor, USA, 7-11 May 2003.

2003-01-01

211

British Library Electronic Table of Contents (United Kingdom)

ABSTRACT. Chlorarachniophytes are enigmatic marine unicellular algae that acquired photosynthesis by secondary endosymbiosis. Chlorarachniophytes are unusual in that the nucleus of the engulfed algal cell (a green alga) persists in a miniaturized form, termed a nucleomorph. The nucleomorph genome of the model chlorarachniophyte, Bigelowiella natans CCMP621, is 373 kilobase pairs (kbp) in size, the smallest nuclear genome characterized to date. The B. natans nucleomorph genome is composed of three chromosomes, each with canonical eukaryotic telomeres and sub telomeric ribosomal DNA (rDNA) operons transcribed away from the chromosome end. Here we present the complete rDNA operon and telomeric region from the nucleomorph genome of Lotharella oceanica CCMP622, a newly characterized chlorarachn...

2010-01-01

212

Manipulating the Xenopus genome with transposable elements

Human endogenous retroviruses: transposable elements with potential ?

The study of amphibian embryogenesis has provided important insight into the mechanisms of vertebrate development. The frog Xenopus laevis has been an important model of vertebrate...Full Text Available

2007-01-01

213

Human cDNA mapping using fluorescence in situ hybridization. Final progress report, April 1, 1994--July 31, 1997

Human endogenous retroviruses (HERVs) are a significant component of a wider family of retroelements that constitute part of the human genome. These viruses, perhaps representative of previous exogenous...Full Text Available

2004-10-01

214

Genome analysis with inter-nucleotide distances

The ultimate goal of this research is to generate and apply novel technologies to speed completion and integration of the human genome map and sequence with biomedical problems. To do this, techniques were developed and genome-wide resources generated. This includes a genome-wide Mapped and Integrated BAC/PAC Resource that has been used for gene finding, map completion and anchoring, breakpoint definition and sequencing. In the last period of the grant, the Human Mapped BAC/PAC Resource was also applied to determine regions of human variation and to develop a novel paradigm of primate evolution through to humans. Further, in order to more rapidly evaluate animal models of human disease, a BAC Map of the mouse was generated in collaboration with the MTI Genome Center, Dr. Bruce Birren.

1997-12-31

215

Extracellular Signaling through the Microenvironment: A Hypothesis Relating Carcinogenesis, Bystander Effects, and ...

Motivation: DNA sequences can be represented by sequences of four symbols, but it is often useful to convert the symbols into real or complex numbers for further analysis. Several mapping...Full Text Available

2009-12-01

216

Evaluating Phylogenetic Congruence in the Post-Genomic Era

... Extracellular Signaling through the Microenvironment: A Hypothesis Relating Carcinogenesis, Bystander Effects, and Genomic InstabilityMary Helen Barcellos-Hoff1a ... ...

217

Developmentally programmed endoreduplication in animals

Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for...Full Text Available

2011-01-01

218

Computational biology for ageing

Development of a fertilized egg into an adult human requires trillions of cell divisions, the vast majority of which duplicate their genome once and only once. Nevertheless, trophoblast giant...Full Text Available

2009-05-15

219

Comparing Genomes within the Species Mycobacterium tuberculosis

High-throughput genomic and proteomic technologies have generated a wealth of publicly available data on ageing. Easy access to these data, and their computational analysis, is of great importance in...Full Text Available

2011-01-12

220

Comparative genomics of insect juvenile hormone biosynthesis?

The study of genetic variability within natural populations of pathogens may provide insight into their evolution and pathogenesis. We used a Mycobacterium tuberculosis high-density...Full Text Available

2001-04-01

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221

Ancestral Genomes, Sex, and the Population Structure of Trypanosoma cruzi

The biosynthesis of insect juvenile hormone (JH) and its neuroendocrine control are attractive targets for chemical control of insect pests and vectors of disease. To facilitate the molecular...Full Text Available

2006-04-01

222

A framework for evolutionary systems biology

Acquisition of detailed knowledge of the structure and evolution of Trypanosoma cruzi populations is essential for control of Chagas disease....Full Text Available

2006-03-01

223

Distributed Data Integration Infrastructure

BackgroundMany difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often...Full Text Available

224

Yeast ribosomal protein L1 is required for the stability of newly synthesized 5S rRNA and the assembly of 60S ribosomal subunits.

The Internet is becoming the preferred method for disseminating scientific data from a variety of disciplines. This can result in information overload on the part of the scientists, who are unable to query all of the relevant sources, even if they knew where to find them, what they contained, how to interact with them, and how to interpret the results. A related issue is keeping up with current trends in information technology often taxes the end-user's expertise and time. Thus instead of benefiting from this information rich environment, scientists become experts on a small number of sources and technologies, use them almost exclusively, and develop a resistance to innovations that can enhance their productivity. Enabling information based scientific advances, in domains such as functional genomics, requires fully utilizing all available information and the latest technologies. In order to address this problem we are developing a ...

2003-02-24

225

Wide cross-species aminoacyl-tRNA synthetase replacement in vivo: yeast cytoplasmic alanine enzyme replaced by human polymyositis serum antigen.

Ribosomal protein L1 from Saccharomyces cerevisiae binds 5S rRNA and can be released from intact 60S ribosomal subunits as an L1-5S ribonucleoprotein (RNP) particle. To understand the nature of the...Full Text Available

1993-05-01

226

The k43 gene, required for chorion gene amplification and diploid cell chromosome replication, encodes the Drosophila homolog of yeast origin recognition complex subunit 2

Because of variations in tRNA sequences in evolution, tRNA synthetases either do not acylate their cognate tRNAs from other organisms or execute misacylations which can be deleterious in vivo. We report...Full Text Available

1995-05-23

227

The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors

Lethal alleles of the Drosophila k43 gene result in small or missing imaginal discs, greatly reduced mitotic index, and fragmented and abnormally condensed chromosomes. A female-sterile...Full Text Available

1997-04-15

228

Specific requirement of the chromatin modifier mSin3B in cell cycle exit and cellular differentiation

In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3′- and 5′-ends of 261 yeast genes by...Full Text Available

2010-08-01

229

SWI/SNF and Asf1 Independently Promote Derepression of the DNA Damage Response Genes under Conditions of Replication Stress

The Sin3-histone deacetylase (HDAC) corepressor complex is conserved from yeast to humans. Mammals possess two highly related Sin3 proteins, mSin3A and mSin3B, which serve as scaffolds tethering HDAC...Full Text Available

2008-03-18

230

Primary organization of nucleosomal core particles is invariable in repressed and active nuclei from animal, plant and yeast cells.

The histone chaperone Asf1 and the chromatin remodeler SWI/SNF have been separately implicated in derepression of the DNA damage response (DDR) genes in yeast cells treated with genotoxins that cause...Full Text Available

231

Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli

A refined map for the linear arrangement of histones along DNA in nucleosomal core particles has been determined by DNA-protein crosslinking. On one strand of 145-bp core DNA, histones are aligned in...Full Text Available

1985-05-24

232

BackgroundThe large sensitivity, high reproducibility and essentially unlimited dynamic range of real-time PCR to measure gene expression in complex samples provides the opportunity...Full Text Available

233

Molecular methods

Metabolomic analysis of the plant pathogenic fungi Fusarium graminearum and Fusarium culmorum

Chapter 5, describes some of the most important molecular methods used in the study of chromosome structure and function. The methods discussed include fragmentation of DNA, cloning, flow cytometry and chromosome sorting, is situ hybridization, polymerase chain reaction (PCR), and yeast artificial chromosomes (YACs). 18 refs., 3 figs., 1 tab.

1993-12-31

234

Environmental Research Database

DescriptionThis project is part of the BBSRCs special initiative on plant and microbial metabolomics. The project will primarily focus on the trichothecene mycotoxin producing Ascomycete fungus Fusarium graminearum (Fg) which causes ear blight disease of small grain cereals. The project aims to explore the metabolome of various wild-type and single gene deletion Fg strains and to compare some of these with the identical gene mutation in the budding yeast, S. cerevisiae (Sc) and the saprophytic filamentous [continued...

2008-01-31

235

Hybridization with synthetic oligonucleotides

Functional and Topological Analysis of Yeast Acyl-CoA:Diacylglycerol Acyltransferase 2, an Endoplasmic Reticulum Enzyme Essential for Triacylglycerol Biosynthesis*

Procedures are described for the use of synthetic oligonucleotides for Southern blot experiments and gene bank screening, and the effect of various mismatches on the efficiency of hybridization is demonstrated. The following topics are discussed: sensitivity vs. specificity, hybridization of a 12-mer to the lambda endolysin gene; hybridization of oligonucleotide probes to the E. coli lac operator; hybridization of synthetic probes to the CYC1 gene of yeast; and cloning eucaryotic genes. (HLW)

1978-01-01

236

Enhanced Degradation of an Endocrine-Disrupting Chemical, Butyl Benzyl Phthalate, by Fusarium oxysporum f. sp. pisi Cutinase

Acyl-CoA:diacylglycerol acyltransferase (EC 2.3.1.20) is a membrane protein present mainly in the endoplasmic reticulum. It catalyzes the final and committed step in the biosynthesis of triacylglycerol,...Full Text Available

2011-04-15

237

Biological solubilization of coal in aqueous and nonaqueous media

Compared to yeast esterase, fungal cutinase degraded butyl benzyl phthalate (BBP) far more efficiently; i.e., almost 60% of the BBP disappeared within 7.5 h. Also, the final chemical composition significantly...Full Text Available

2002-09-01

238

Assembly of 60S ribosomal subunits is perturbed in temperature-sensitive yeast mutants defective in ribosomal protein L16.

Current investigations into the biological solubilization of coal with microorganisms focus on the production of solubilizing activity in fungi. Test organisms for this work include a species of the yeast Candida previously isolated from a lignite outcrop, and P. chrysosporium, a filamentous higher fungus which has played a major role in lignin biodegradation research. The studies described are primarily exploratory in nature, and are fundamental to the design of more sophisticated inquiries into the physiology of fungal coal solubilization.

1987-01-01

239

Targeted Capture and Next-Generation Sequencing Identifies C9orf75, Encoding Taperin, as the Mutated Gene in Nonsyndromic Deafness DFNB79

Temperature-sensitive mutants defective in 60S ribosomal subunit protein L16 of Saccharomyces cerevisiae were isolated through hydroxylamine mutagenesis of the RPL16B gene and plasmid shuffling. Two...Full Text Available

1991-11-01

240

Genome-wide association studies of gastric adenocarcinoma and esophageal squamous cell carcinoma identify a shared susceptibility locus in PLCE1 at 10q23

Targeted genome capture combined with next-generation sequencing was used to analyze 2.9 Mb of the DFNB79 interval on chromosome 9q34.3, which includes 108 candidate genes. Genomic...Full Text Available

2010-03-12

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241

Draft Genome Sequence of Shewanella sp. Strain HN-41, Which Produces Arsenic-Sulfide Nanotubes.

We conducted a genome-wide association study of gastric cancer (GC) and esophageal squamous cell carcinoma (ESCC) in ethnic Chinese subjects in which we genotyped 551,152 single nucleotide polymorphisms...Full Text Available

2010-09-01

242

A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function

The dissimilatory metal reducing bacterium Shewanella sp. strain HN-41 was first reported to produce novel photoactive As-S nanotubes via reduction of As(V) and S(2)O(3)(2-) under anaerobic conditions. Here we report the draft genome sequence and annotation of strain HN-41. PMID:21868804

2011-09-01

243

A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4

BackgroundThe mitochondrial genome of the Octocorallia has several characteristics atypical for metazoans, including a novel gene suggested to function in DNA repair. This mtMutS...Full Text Available

244

Complete genome sequence of Actinosynnema mirum type strain (101T)

Case-parent trios were used in a genome wide association study of cleft lip with/without cleft palate (CL/P). SNPs near two genes not previously associated with CL/P [MAFB:...Full Text Available

2010-06-01

245

Bisulfite genomic sequencing of DNA from dried blood spot microvolume samples.

Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO2 atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome ...

2009-05-20

246

[Development of efficient DNA isolation procedures for Cryptosporidium and Trichinella PCR detection in fecal samples].

DNA methylation is an important event in epigenetic changes in cells, and a fundamental regulator of gene transcription. Bisulfite genomic sequencing is a powerful technique used in studies of DNA methylation. However, the established procedures often require relatively large amounts of DNA. In everyday practice, samples submitted for analysis might contain very small amounts of poor quality material, as is often the case with forensic stain samples. In this study, we assess a modified, more efficient method of bisulfite genomic sequencing. Genomic DNA extracted from 3-mm dried blood spots using QIAamp micro kit was treated with sodium bisulfite (using EpiTect kit). Subsequent methylation-specific PCR (MSP) followed by DNA sequencing displayed the differentially methylated region of imprinted gene SNRPN. Our results show that this new combination of efficient DNA extraction and bisulfite treatment provides high quality ...

2011-07-01

247

Comparing compressed sequences for faster nucleotide BLAST searches.

PCR detection of genetic material of the parasites present in faeces may be an alternative for microscopic and serological tests routinely used for diagnosing parasitic enteral infections. However, small amount of target DNA combined with low efficiency of total DNA extraction, and presence of PCR inhibitors in the samples to be amplified, may cause false negative detection results. The aim of this work was to evaluate the impact of DNA isolation procedure used on the amplification of DNA fragments from the genomes of protozoan Cryptosporidium parvum and the nematode Trichinella spiralis. Two methods based on different principles of biological material lysis were evaluated; NucliSENS miniMAG employing simultaneously applied chemical lysis and mechanical disruption or mechanical disruption followed by enzymatic lysis in case of QIAamp DNA Stool Mini Kit. Both of the analyzed systems for nucleic acids purification allowed isolation of DNA from ...

2009-01-01

248

Trans-generational radiation-induced chromosomal instability in the female enhances the action of chemical mutagens

Molecular biologists, geneticists, and other life scientists use the BLAST homology search package as their first step for discovery of information about unknown or poorly annotated genomic sequences. There are two main variants of BLAST: BLASTP for searching protein collections and BLASTN for nucleotide collections. Surprisingly, BLASTN has had very little attention; for example, the algorithms it uses do not follow those described in the 1997 BLAST paper and no exact description has been published. It is important that BLASTN is state-of-the-art: Nucleotide collections such as GenBank dwarf the protein collections in size, they double in size almost yearly, and they take many minutes to search on modern general purpose workstations. This paper proposes significant improvements to the BLASTN algorithms. Each of our schemes is based on compressed bytepacked formats that allow queries and collection sequences to be compared four ...

249

SEPT9_i1 and genomic instability: Mechanistic insights and relevance to tumorigenesis

Genomic instability can be produced by ionising radiation, so-called radiation-induced genomic instability, and chemical mutagens. Radiation-induced genomic instability occurs in both germinal and somatic cells and also in the offspring of irradiated individuals, and it is characterised by genetic changes including chromosomal rearrangements. The majority of studies of trans-generational, radiation-induced genomic instability have been described in the male germ line, whereas the authors who have chosen the female as a model are scarce. The aim of this work is to find out the radiation-induced effects in the foetal offspring of X-ray-treated female rats and, at the same time, the possible impact of this radiation-induced genomic instability on the action of a chemical mutagen. In order to achieve both goals, the quantity and quality of chromosomal damage were analysed. In order to ...

2008-04-02

250

British Library Electronic Table of Contents (United Kingdom)

Abstract Septins are highly conserved cytoskeletal GTP-binding proteins implicated in numerous cellular processes from apoptosis to vesicle trafficking. Septins have been associated with leukemia and solid tumor malignancies, including breast, ovarian, and prostate. We previously reported that high SEPT9_i1 expression in human mammary epithelial cell lines (HMECs) led to malignant cellular phenotypes such as increased cell proliferation, invasiveness, motility, and genomic instability. Our goal here was to better understand how SEPT9_i1 expression might contribute to genomic instability and malignant progression. First, we confirmed that even transient expression of SEPT9_i1 was sufficient to increase aneuploidy in HMECs. We then analyzed SEPT9_i1 by immunoprecipitation and immunofluoresce...

2011-01-01

251

Federal technology transfer and the human genome project. Background paper

What, why, and when we image: considerations for diagnostic imaging and clinical research in the Children's Oncology Group

As with other areas of biomedical research, the expectation is that the results of genome research will yield commercially valuable products of benefits to human health. The report, analyzes universities`, companies`, and researchers` experiences and perspectives since enactment of federal laws to enhance technology transfer--especially as it pertains to research funded by the National Institutes of Health and the Department of Energy, the agencies funding U.S. efforts in the Human Genome Project. OTA prepared this background paper with the assistance of a panel of advisors and reviewers selected for their expertise and diverse points of view. Additionally, hundreds of individuals cooperated with OTA staff through interviews or by providing written material. These authorities were drawn from government, academia, industry, and professional societies worldwide.

1995-09-01

252

The retinoic acid receptor beta (Rarb) region of Mmu14 is associated with prion disease incubation time in mouse.

Success in improving treatment outcomes in childhood cancer has been achieved almost exclusively through multicenter and multidisciplinary clinical and applied research over several decades. While biologically rational as well as empirical approaches have led to combination chemotherapy and multimodality approaches to therapy, which have given rise to evidence-based practice standards, similar scientific rigor has not always been as evidently applied to modalities utilized to assess initial disease burden and, more important, response to investigational approaches to therapy. As the empirical approach to therapeutic advances has likely maximized its benefit, future progress will require translation of biologic discovery most notably from the areas of genomics and proteomics. Hence, attempts to improve efficacy of therapy will require a parallel effort to minimize collateral damage of future therapeutic approaches, and such a parallel approach ...

2009-02-15

253

The Sorcerer II Global Ocean Sampling Expedition: Expanding theUniverse of Protein Families

In neurodegenerative conditions such as Alzheimer's and prion disease it has been shown that host genetic background can have a significant effect on susceptibility. Indeed, human genome-wide association studies (GWAS) have implicated several candidate genes. Understanding such genetic susceptibility is relevant to risks of developing variant CJD (vCJD) in populations exposed to bovine spongiform encephalopathy (BSE) and understanding mechanisms of neurodegeneration. In mice, aspects of prion disease susceptibility can be modelled by examining the incubation period following experimental inoculation. Quantitative trait linkage studies have already identified multiple candidate genes; however, it is also possible to take an individual candidate gene approach. Rarb and Stmn2 were selected as candidates based on the known association with vCJD. Because of the increasing overlap described between prion and Alzheimer's diseases we also chose Clu, ...

2010-12-06

254

Structural Insights into the Interaction of the Evolutionarily Conserved ZPR1 Domain Tandem with Eukaryotic EF1A, Receptors, and SMN Complexes

Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling (GOS) sequences. The GOS dataset covers nearly all known prokaryotic protein families. A total of 3,995 medium- and large-sized clusters consisting of only GOS sequences are identified, out of which 1,700 have no detectable homology to known families. The GOS-only clusters contain a higher than expected proportion of sequences of viral origin, thus reflecting a poor sampling of viral diversity until now. Protein domain distributions in the GOS dataset and current protein databases show distinct biases. Several protein domains that were previously categorized as kingdom specific are shown to have GOS examples in ...

2006-03-23

255

Hybrid incompatibilities in the parasitic wasp genus Nasonia: negative effects of hemizygosity and the identification of transmission ratio distortion loci.

Eukaryotic genomes encode a zinc finger protein (ZPR1) with tandem ZPR1 domains. In response to growth stimuli, ZPR1 assembles into complexes with eukaryotic translation elongation factor 1A (eEF1A) and the survival motor neurons protein. To gain insight into the structural mechanisms underlying the essential function of ZPR1 in diverse organisms, we determined the crystal structure of a ZPR1 domain tandem and characterized the interaction with eEF1A. The ZPR1 domain consists of an elongation initiation factor 2-like zinc finger and a double-stranded {beta} helix with a helical hairpin insertion. ZPR1 binds preferentially to GDP-bound eEF1A but does not directly influence the kinetics of nucleotide exchange or GTP hydrolysis. However, ZPR1 efficiently displaces the exchange factor eEF1B from preformed nucleotide-free complexes, suggesting that it may function as a negative regulator of eEF1A activation. Structure-based mutational and ...

2007-01-01

256

Genetic heterogeneity in type 1 Gaucher disease: Multiple genotypes in Ashkenazic and non-Ashkenazic individuals

The occurrence of hybrid incompatibilities forms an important stage during the evolution of reproductive isolation. In early stages of speciation, males and females often respond differently to hybridization. Haldane's rule states that the heterogametic sex suffers more from hybridization than the homogametic sex. Although haplodiploid reproduction (haploid males, diploid females) does not involve sex chromosomes, sex-specific incompatibilities are predicted to be prevalent in haplodiploid species. Here, we evaluate the effect of sex/ploidy level on hybrid incompatibilities and locate genomic regions that cause increased mortality rates in hybrid males of the haplodiploid wasps Nasonia vitripennis and Nasonia longicornis. Our data show that diploid F(1) hybrid females suffer less from hybridization than haploid F(2) hybrid males. The latter not only suffer from an increased mortality rate, but also from behavioural and spermatogenic sterility. Genetic mapping in ...

2011-08-31

257

Empirical Evaluation of a New Method for Calculating Signal to Noise Ratio (SNR) for Microarray Data Analysis

Nucleotide sequence analysis of a genomic clone from an Ashkenazic Jewish patient with type 1 Gaucher disease revealed a single-base mutation (adenosine to guanosine transition) in exon 9 of the glucocerebrosidase gene. This change results in the amino acid substitution of serine for asparagine. Transient expression studies following oligonucleotide-directed mutagenesis of the normal cDNA confirmed that the mutation results in loss of glucocerebrosidase activity. Allele-specific hybridization with oligonucleotide probes demonstrated that this mutation was found exclusively in type 1 phenotype. None of the 6 type 2 patients, 11 type 3 patients, or 12 normal controls had this allele. In contrast, 15 of 24 type 1 patients had one allele with this mutation, and 3 others were homozygous for the mutation. Furthermore, some of the Ashkenazic Jewish type 1 patients had only one allele with this mutation, suggesting that even in this population there is ...

258

Detecting and Genotyping Escherichia coli O157:H7 using multiplexed PCR and nucleic acid microarrays

Signal-to-noise-ratio (SNR) thresholds for microarray data analysis were experimentally determined with an oligonucleotide array that contained perfect match (PM) and mismatch (MM) probes based upon four genes from Shewanella oneidensis MR-1. A new SNR calculation, called signal to both standard deviations ratio (SSDR) was developed, and evaluated along with other two methods, signal to standard deviation ratio (SSR), and signal to background ratio (SBR). At a low stringency, the thresholds of SSR, SBR, and SSDR were 2.5, 1.60 and 0.80 with oligonucleotide and PCR amplicon as target templates, and 2.0, 1.60 and 0.70 with genomic DNA as target templates. Slightly higher thresholds were obtained at the high stringency condition. The thresholds of SSR and SSDR decreased with an increase in the complexity of targets (e.g., target types), and the presence of background DNA, and a decrease in the composition of targets, while SBR remained unchanged ...

2008-03-06

259

An Arabidopsis thaliana methyltransferase Capable of Methylating Farnesoic Acid

Rapid detection and characterization of food borne pathogens such as Escherichia coli O157:H7 is crucial for epidemiological investigations and food safety surveillance. As an alternative to conventional technologies, we examined the sensitivity and specificity of nucleic acid microarrays for detecting and genotyping E. coli O157:H7. The array was composed of oligonucleotide probes (25-30 mer) complementary to four virulence loci (intimin, Shiga-like toxins I and II, and hemolysin A). Target DNA was amplified from whole cells or from purified DNA via single or multiplexed polymerase chain reaction (PCR), and PCR products were hybridized to the array without further modification or purification. The array was 32-fold more sensitive than gel electrophoresis and capable of detecting amplification products from < 1 cell equivalent of genomic DNA (1 fg). Immunomagnetic capture, PCR and a microarray were subsequently used to detect 55 CFU ml-1 (E. coli O157:H7) ...

2000-12-01

260

A human breast cell model of pre-invasive to invasive transition

We previously reported the identification of a new family of plant methyltransferases (MTs), named the SABATH family, that use S-adenosyl-l-methionine (SAM) to methylate a carboxyl moiety or a nitrogen-containing functional group on a diverse array of plant compounds. The Arabidopsis genome alone contains 24 distinct SABATH genes. To identify the catalytic specificities of members of this protein family in Arabidopsis, we screened recombinantly expressed and purified enzymes with a large number of potential substrates. Here, we report that the Arabidopsis thaliana gene At3g44860 encodes a protein with high catalytic specificity towards farnesoic acid (FA). Under steady-state conditions, this farnesoic acid carboxyl methyltransferase (FAMT) exhibits K{sub M} values of 41 and 71 {mu}M for FA and SAM, respectively. A three-dimensional model of FAMT constructed based upon similarity to the experimentally determined structure of Clarkia breweri ...

2006-01-01

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261

Mutations in cyr1 and pat1 reveal pheromone-induced G1 arrest in the fission yeast Schizosaccharomyces pombe

A crucial step in human breast cancer progression is the acquisition of invasiveness. There is a distinct lack of human cell culture models to study the transition from pre-invasive to invasive phenotype as it may occur 'spontaneously' in vivo. To delineate molecular alterations important for this transition, we isolated human breast epithelial cell lines that showed partial loss of tissue polarity in three-dimensional reconstituted-basement membrane cultures. These cells remained non-invasive; however, unlike their non-malignant counterparts, they exhibited a high propensity to acquire invasiveness through basement membrane in culture. The genomic aberrations and gene expression profiles of the cells in this model showed a high degree of similarity to primary breast tumor profiles. The xenograft tumors formed by the cell lines in three different microenvironments in nude mice displayed metaplastic phenotypes, including squamous and basal ...

2008-03-10

262

DEFF Research Database (Denmark)

Investigations into sexual differentiation and pheromone response in the fission yeast Schizosaccharomyces pombe are complicated by the need to first starve the cells of nitrogen. Most mating-related experiments are therefore performed on non-dividing cells. Here we overcome this problem by using two mutants that bypass the nutritional requirements and respond to the M-factor mating pheromone in rich medium. The first mutant lacks the cyr1 gene which encodes adenylate cyclase and these cells contain no measurable amounts of cAMP. When M-factor is added to a growing h+ cyr1- strain it causes a transient G1 arrest of cell division, transcription of mat1-Pm, and elongation of the cells to form shmoos. The second mutant contains the temperature-sensitive pat1-114 allele. At 30 degrees C this mutant was previously shown not only to bypass the nutritional signal but also to stop growing in a state derepressed for pheromone-controlled functions. We now report that an h+ ...

1994-01-01

263

Mitochondrial genetic damage induced in yeast by a photoactivated furocoumarin in combination with ethidium bromide or ultraviolet light

Management of industrial solid wastes in Alexandria, Egypt

Ethidium bromide (EB) and ultraviolet light (UV) in combination are known to produce a synergistic induction of 'petite' mutants in yeast. Two other agents were combined with EB, 3-Carbethoxypsoralene (3 CPs) activated by 365 nm light or #gamma# rays. EB in combination with 3 CPs also resulted in an enhanced production of 'petite' mutants. After the photoaddition of 3 CPs in exponential phase cells, recovery of the 'petite' mutation during dark liquid holding was inhibited by the presence of EB producing an enhanced number of 'petite' mutants. The behavior of mitochondrial antibiotic resistance markers after individual and combined treatments with EB and 3 CPs indicates a random loss of markers after EB and a preferential loss of a certain region for the 3 CPs photoaddition. The combination of the two agents leads to an additivity of total drug marker losses rather than a synergistic loss. The combination of EB with #gamma# rays produced no enhancement in 'petite' ...

264

solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database

This paper presents a summary of the first phase of the EPA project, which encompasses surveys of residues from industrial sources in Alexandria. Studies to date indicate that wastes from various industries can be recovered economically. Wastes such as tin cans, glass, wastepaper, and food residues from processing of fruits, starch, and beer are examples of reusable industrial wastes in Egypt. The results of experimental studies for reuse of residues from oil refining, starch and yeast processing, and steel pickling are presented. Spent clay from edible oil refining is currently discarded, causing both handling and disposal problems. This clay contains as much as 40% oil; 90% can be recovered by extraction. The recovered oil can be successfully used in soap production, and the spent clay can be reused in oil bleaching. Other examples include starch and yeast wastes, which can be used for animal feed, and spent pickling liquor, which can be used ...

1983-03-01

265

piggyBac is a flexible and highly active transposon as compared to Sleeping Beauty, Tol2, and Mos1 in mammalian cells

BackgroundA common approach to understanding the genetic basis of complex traits is through identification of associated quantitative trait loci (QTL). Fine mapping QTLs requires...Full Text Available

266

chipD: a web tool to design oligonucleotide probes for high-density tiling arrays

A nonviral vector for highly efficient site-specific integration would be desirable for many applications in transgenesis, including gene therapy. In this study we directly compared the genomic integration...Full Text Available

2006-10-10

267

Visual Genome-Wide RNAi Screening to Identify Human Host Factors Required for Trypanosoma cruzi Infection

chipD is a web server that facilitates design of DNA oligonucleotide probes for high-density tiling arrays, which can be used in a number of genomic applications such as ChIP-chip or gene-expression...Full Text Available

2010-07-01

268

Viruses with More Than 1,000 Genes: Mamavirus, a New Acanthamoeba polyphaga mimivirus Strain, and Reannotation of Mimivirus Genes

The protozoan parasite Trypanosoma cruzi is the etiologic agent of Chagas disease, a neglected tropical infection that affects millions of people in the Americas. Current chemotherapy...Full Text Available

269

Ubiquitin over-expression phenotypes and ubiquitin gene molecular misreading during aging in Drosophila melanogaster

The genome sequence of the Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, is reported. With 1,191,693 nt in length and 1,023 predicted protein-coding genes, the Mamavirus...Full Text Available

2011-01-01

270

Two separate domains within vesicular stomatitis virus phosphoprotein support transcription when added in trans.

Molecular Misreading (MM) is the inaccurate conversion of genomic information into aberrant proteins. For example, when RNA polymerase II transcribes a GAGAG motif it synthesizes at low frequency RNA...Full Text Available

271

Tumour suppressor ING1b maintains genomic stability upon replication stress

The structural phosphoprotein NS of vesicular stomatitis virus, in association with the virion-associated RNA polymerase L protein, transcribes the genome ribonucleoprotein template in vitro. It contains...Full Text Available

1987-12-01

272

Tumor-Endothelial Interaction Links the CD44⁺/CD24^- Phenotype with Poor Prognosis in Early-Stage Breast Cancer1

The lesion bypass pathway, which is regulated by monoubiquitination of proliferating cell nuclear antigen (PCNA), is essential for resolving replication stalling due to DNA lesions. This process is...Full Text Available

2011-05-01

273

Transposons as tools for enhancer trap screens in vertebrates

Materials and MethodsThe genomic effects of tumor-endothelial interactions in cancer are not yet well characterized. To study this interaction in breast...Full Text Available

2009-10-01

274

Transposable elements in fish functional genomics: technical challenges and perspectives

DNA transposons are efficient tools in transgenesis and have therefore become popular in the analysis of the regulatory genome in vertebrates via enhancer trap screens. Here, I discuss recent progress...Full Text Available

2007-01-01

275

Transposable elements are enriched within or in close proximity to xenobiotic-metabolizing cytochrome P450 genes

The recent introduction of several transposable elements in zebrafish opens new frontiers for genetic manipulation in this important vertebrate model. This review discusses transposable elements as...Full Text Available

2007-01-01

276

Transcriptional Organization of the Avian Adenovirus CELO

BackgroundTransposons, i.e. transposable elements (TEs), are the major internal spontaneous mutation agents for the variability of eukaryotic genomes. To address the general issue...Full Text Available

277

Tissue Effect on Genetic Control of Transcript Isoform Variation

A detailed map of the transcriptional organization of the CELO virus genome was produced. Recent computer analysis of CELO virus has indicated the presence of 38 putative open reading frames (ORFs)....Full Text Available

1998-11-01

278

The struggle for life of the genome's selfish architects

Current genome-wide association studies (GWAS) are moving towards the use of large cohorts of primary cell lines to study a disease of interest and to assign biological relevance to the genetic signals...Full Text Available

2009-08-01

279

The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for QTL discovery and systems genetics

Transposable elements (TEs) were first discovered more than 50 years ago, but were totally ignored for a long time. Over the last few decades they have gradually attracted increasing interest from research...Full Text Available

280

The missing graphical user interface for genomics

Mouse genetic resources include inbred strains, recombinant inbred lines, chromosome substitution strains, heterogeneous stocks, and the Collaborative Cross (CC). These resources were generated through...Full Text Available

2007-07-01

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281

The complete mitochondrial genome of Atelura formicaria (Hexapoda: Zygentoma) and the phylogenetic relationships of basal insects.

AbstractThe Galaxy package empowers regular users to perform rich DNA sequence analysis through a much-needed and user-friendly graphical web interface.See research article...Full Text Available

2010-01-01

282

The chromosomal association/dissociation of the chromatin insulator protein Cp190 of Drosophila melanogaster is mediated by the BTB/POZ domain and two acidic regions

In this study, the complete sequence of the mitochondrial DNA (mtDNA) of Atelura formicaria (Hexapoda: Zygentoma) is described. The molecule is 15.205 bp in length and it is the third complete mt genome sequenced from the Zygentoma. The genome organization conforms with the putative ancestral insect gene arrangement. All protein coding genes use standard initiation codons (methionine and isoleucine). The exception is nad4 that starts with GTG, a codon used for this purpose in other insect species. A peculiar strand skew bias is observed, given that the PCGs encoded on the J-strand contain more thymines than adenines and more cytosines than guanines. This trend in nucleotide composition has been observed also in the "firebrat" Thermobia domestica (Zygentoma, Lepismatidae), but differs from that of the majority of hexapod species, including Tricholepidion gertschi (Zygentoma, Lepidotrichidae), where adenines and cytosines outnumber thymines and ...

2009-03-11

283

The Pseudomonas aeruginosa PA01 Gene Collection

BackgroundChromatin insulators or boundary elements are a class of functional elements in the eukaryotic genome. They regulate gene transcription by interfering with promoter-enhancer...Full Text Available

284

The Human Ageing Genomic Resources: online databases and tools for biogerontologists

Pseudomonas aeruginosa, a common inhabitant of soil and water, is an opportunistic pathogen of growing clinical relevance. Its genome, one of the largest among bacteria [5570 open reading...Full Text Available

2004-10-01

285

The Exceptionally Large Genome of Hendra Virus: Support for Creation of a New Genus within the Family Paramyxoviridae

SummaryAgeing is a complex, challenging phenomenon that will require multiple, interdisciplinary approaches to unravel its puzzles. To assist basic research on ageing, we developed...Full Text Available

2009-02-01

286

The Anopheles gambiae glutathione transferase supergene family: annotation, phylogeny and expression profiles

An outbreak of acute respiratory disease in Hendra, a suburb of Brisbane, Australia, in September 1994 resulted in the deaths of 14 racing horses and a horse trainer. The causative agent was a new member...Full Text Available

2000-11-01

287

Ternary Complex Formation on the Adenovirus Packaging Sequence by the IVa2 and L4 22-Kilodalton Proteins?

BackgroundTwenty-eight genes putatively encoding cytosolic glutathione transferases have been identified in the Anopheles gambiae genome. We manually annotated these...Full Text Available

288

Structural analysis of a hepatitis B virus genome integrated into chromosome 17p of a human hepatocellular carcinoma.

Assembly of infectious adenovirus particles requires seven functionally redundant elements at the left end of the genome, termed A repeats, that direct packaging of the DNA. Previous studies revealed...Full Text Available

2007-11-01

289

Structural Basis for Acetylated Histone H4 Recognition by the Human BRD2 Bromodomain*

Hepatitis B virus (HBV) is clearly a factor in the development of hepatocellular carcinoma, but its mechanism of action remains obscure. One possibility is that the HBV integration event alters the...Full Text Available

1988-11-01

290

Statistical properties of nucleotide clusters in DNA sequences*

Recognition of acetylated chromatin by the bromodomains and extra-terminal domain (BET) family proteins is a hallmark for transcriptional activation and anchoring viral genomes to mitotic chromosomes...Full Text Available

2010-03-05

291

Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus

Using the complete genome of Plasmodium falciparum 3D7 which has 14 chromosomes as an example, we have examined the distribution functions for the amount of C or G and A or T consecutively...Full Text Available

2005-05-01

292

Severe teratozoospermia and its influence on pronuclear morphology, embryonic cleavage and compaction

BackgroundRNA turnover plays an important role in the gene regulation of microorganisms and influences their speed of acclimation to environmental changes. We investigated whole-genome...Full Text Available

2010-01-01

293

Restriction endonuclease analysis of porcine Pasteurella multocida isolates from Quebec.

BackgroundFertilization, cell division and embryo development depend on genomic contributions from male and female gametes. We hypothesize that teratozoospermic sperm influences...Full Text Available

294

Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays

We have used restriction endonuclease analysis (REA) of genomic DNA to classify porcine Pasteurella multocida isolates with similar capsular and somatic serotypes, and to monitor the distribution of...Full Text Available

1990-10-01

295

ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data

We use high-density single nucleotide polymorphism (SNP) genotyping microarrays to demonstrate the ability to accurately and robustly determine whether individuals are in a complex genomic DNA mixture....Full Text Available

2008-08-01

296

Remobilization of Tol2 transposons in Xenopus tropicalis

BackgroundEukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals) within which replicons are activated relatively synchronously....Full Text Available

297

Reduced-Median-Network Analysis of Complete Mitochondrial DNA Coding-Region Sequences for the Major African, Asian, and European Haplogroups

BackgroundThe Class II DNA transposons are mobile genetic elements that move DNA sequence from one position in the genome to another. We have previously demonstrated that the naturally...Full Text Available

298

Reconstruction of the complete human cytomegalovirus genome in a BAC reveals RL13 to be a potent inhibitor of replication

The evolution of the human mitochondrial genome is characterized by the emergence of ethnically distinct lineages or haplogroups. Nine European, seven Asian (including Native American), and three African...Full Text Available

2002-05-01

299

Polymorphic Regions Affecting Human Height Also Control Stature in Cattle

Human cytomegalovirus (HCMV) in clinical material cannot replicate efficiently in vitro until it has adapted by mutation. Consequently, wild-type HCMV differ fundamentally from the passaged strains...Full Text Available

2010-09-01

300

Palindromic Sequence Plays a Critical Role in Human Foamy Virus Dimerization

Orthologous positions of 55 genes associated with height in four human populations were located on the bovine genome. Single nucleotide polymorphisms close to eight of these genes were significantly...Full Text Available

2011-03-01

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301

Onset of Quiescence Following p53 Mediated Down-Regulation of H2AX in Normal Cells

The retroviral RNA genome is dimeric, consisting of two identical strands of RNA linked near their 5′ ends by a dimer linkage structure. Previously it was shown that human foamy virus (HFV)...Full Text Available

2001-04-01

302

New common variants affecting susceptibility to basal cell carcinoma

Normal cells, both in vivo and in vitro, become quiescent after serial cell proliferation. During this process, cells can develop immortality with genomic instability,...Full Text Available

303

New Pathogenicity Marker Found in the Plasticity Region of the Helicobacter pylori Genome

In a follow-up to our previously reported genome-wide association study of cutaneous basal cell carcinoma (BCC)1, we describe here several new susceptibility...Full Text Available

2009-08-01

304

Mutations in TPRN Cause a Progressive Form of Autosomal-Recessive Nonsyndromic Hearing Loss

Comparison of gastric carcinoma and gastritis isolates showed the presence of genes, probably carcinoma associated (JHP947 and JHP940), that are situated in a Helicobacter...Full Text Available

2003-04-01

305

Mutational Analysis of cis-Acting RNA Signals in Segment 7 of Influenza A Virus?

We performed genome-wide homozygosity mapping in a large consanguineous family from Morocco and mapped the autosomal-recessive nonsyndromic hearing loss (ARNSHL) in this family to the DFNB79...Full Text Available

2010-03-12

306

Mapping cis-Regulatory Domains in the Human Genome UsingMulti-Species Conservation of Synteny

The genomic viral RNA (vRNA) segments of influenza A virus contain specific packaging signals at their termini that overlap the coding regions. To further characterize cis-acting signals...Full Text Available

2008-12-01

307

Longitudinal assessment of lung cancer progression in the mouse using in vivo micro-CT imaging

Our inability to associate distant regulatory elements with the genes that they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major obstacle is the large genomic space surrounding targeted genes in which such elements could potentially reside. In order to delineate gene regulatory boundaries we used whole-genome human-mouse-chicken (HMC) and human-mouse-frog (HMF) multiple alignments to compile conserved blocks of synteny (CBS), under the hypothesis that these blocks have been kept intact throughout evolution at least in part by the requirement of regulatory elements to stay linked to the genes that they regulate. A total of 2,116 and 1,942 CBS>200 kb were assembled for HMC and HMF respectively, encompassing 1.53 and 0.86 Gb of human sequence. To support the existence of complex long-range regulatory domains within these CBS we analyzed the prevalence and distribution of ...

2005-06-13

308

Lin28a transgenic mice manifest size and puberty phenotypes identified in human genetic association studies

Purpose: Small animal micro-CT imaging is being used increasingly in preclinical biomedical research to provide phenotypic descriptions of genomic models. Most of this imaging is coincident...Full Text Available

2010-09-01

309

Kinetic Complexity of the Global Response to Glucocorticoid Receptor Action

Recently, genome-wide association studies (GWAS) have linked the human LIN28B locus to height and timing of menarche [1-Full Text Available

2010-07-01

310

Involvement of the Matrix and Nucleocapsid Domains of the Bovine Leukemia Virus Gag Polyprotein Precursor in Viral RNA Packaging

We have characterized the kinetic response of gene targets throughout the murine genome to transcriptional modulation by the glucocorticoid receptor (GR). In contrast to a model in which multiple genes...Full Text Available

2009-04-01

311

Interpopulation hybridization results in widespread viability selection across the genome in Tigriopus californicus

The RNA packaging process for retroviruses involves a recognition event of the genome-length viral RNA by the viral Gag polyprotein precursor (PrGag), an important step in particle morphogenesis. The...Full Text Available

2003-09-01

312

Integrase-directed recovery of functional genes from genomic libraries

BackgroundGenetic interactions within hybrids influence their overall fitness. Understanding the details of these interactions can improve our understanding of speciation. One experimental...Full Text Available

313

Insights into the Genome of Large Sulfur Bacteria Revealed by Analysis of Single Filaments

Large population sizes, rapid growth and 3.8 billion years of evolution firmly establish microorganisms as a major source of the planet's biological and genetic diversity. However, up to 99% of the...Full Text Available

2009-09-01

314

Inferring transcription factor complexes from ChIP-seq data

Marine sediments are frequently covered by mats of the filamentous Beggiatoa and other large nitrate-storing bacteria that oxidize hydrogen sulfide using either oxygen or nitrate, which...Full Text Available

2007-09-01

315

In vitro dimerization of human immunodeficiency virus type 1 (HIV-1) spliced RNAs

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) allows researchers to determine the genome-wide binding locations of individual transcription factors (TFs) at high resolution....Full Text Available

2011-08-01

316

Impaired replication dynamics at the FRA3B common fragile site

The human immunodeficiency virus type 1 (HIV-1) packages its genomic RNA as a dimer of homologous RNA molecules that has to be selected among a multitude of cellular and viral RNAs. Interestingly, spliced...Full Text Available

2007-12-01

317

Identification of plasmid and Bacillus subtilis chromosomal recombination sites used for pE194 integration.

Chromosomal common fragile sites (CFSs) are genetically unstable regions of the genome that are induced by conditions that impair DNA replication. In this report, we show that treatment with the DNA...Full Text Available

2010-01-01

318

Identification of genomic differences between Campylobacter jejuni subsp. jejuni and C. jejuni subsp. doylei at the nap locus leads to the development of a C. jejuni subspeciation multiplex PCR method

The plasmid pE194 (3.7 kilobases) is capable of integrating into the genome of the bacterial host Bacillus subtilis in the absence of the major homology-dependent RecE recombination system. Multiple...Full Text Available

1989-05-01

319

Identification of copy number variations and common deletion polymorphisms in cattle

BackgroundThe human bacterial pathogen Campylobacter jejuni contains two subspecies: C. jejuni subsp. jejuni (Cjj)...Full Text Available

320

Identification of a Central DNA Flap in Feline Immunodeficiency Virus

BackgroundRecently, the discovery of copy number variation (CNV) led researchers to think that there are more variations of genomic DNA than initially believed. Moreover, a certain...Full Text Available

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321

Identification of Genes Affecting the Toxicity of Anti-Cancer Drug Bortezomib by Genome-Wide Screening in S. pombe

A duplication of the polypurine tract (PPT) at the center of the human immunodeficiency virus type 1 (HIV-1) genome (the cPPT) has been shown to prime a separate plus-strand initiation and to result...Full Text Available

2001-10-01

322

Identification and In Vivo Characterization of NvFP-7R, a Developmentally Regulated Red Fluorescent Protein of Nematostella vectensis

Bortezomib/PS-341/Velcade, a proteasome inhibitor, is widely used to treat multiple myeloma. While several mechanisms of the cytotoxicity of the drug were proposed, the actual mechanism remains elusive....Full Text Available

323

Human Immunodeficiency Virus type-1 reverse transcriptase exists as post-translationally modified forms in virions and cells

BackgroundIn recent years, the sea anemone Nematostella vectensis has emerged as a critical model organism for comparative genomics and developmental biology. Although...Full Text Available

324

Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis

BackgroundHIV-1 reverse transcriptase (RT) is a heterodimer composed of p66 and p51 subunits and is responsible for reverse transcription of the viral RNA genome into DNA. RT can...Full Text Available

325

Genomic but Not Antigenomic Hepatitis Delta Virus RNA Is Preferentially Exported from the Nucleus Immediately after Synthesis and Processing

BackgroundThe Gram-negative bacterium Burkholderia pseudomallei (Bp) is the causative agent of the human disease melioidosis. To understand the evolutionary mechanisms...Full Text Available

326

Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent

Hepatitis delta virus (HDV) contains a viroid-like circular RNA that replicates via a double rolling circle replication mechanism. It is generally assumed that HDV RNA is synthesized and remains exclusively...Full Text Available

2002-04-01

327

Genomic Expression Libraries for the Identification of Cross-Reactive Orthopoxvirus Antigens

Harmful algal blooms, caused by rapid growth and accumulation of certain microalgae in the ocean, pose considerable impacts on marine environments, aquatic industries and even public health. Here, we...Full Text Available

2005-01-01

328

Genomic Evidence for the Evolution of Streptococcus equi: Host Restriction, Increased Virulence, and Genetic Exchange with Human Pathogens

Increasing numbers of human cowpox virus infections that are being observed and that particularly affect young non-vaccinated persons have renewed interest in this zoonotic disease. Usually causing...Full Text Available

329

Genomic Diversity and Evolution of Mycobacterium ulcerans Revealed by Next-Generation Sequencing

The continued evolution of bacterial pathogens has major implications for both human and animal disease, but the exchange of genetic material between host-restricted pathogens is rarely considered....Full Text Available

2009-03-01

330

Genomic Content of Bordetella pertussis Clinical Isolates Circulating in Areas of Intensive Children Vaccination

Mycobacterium ulcerans is the causative agent of Buruli ulcer, the third most common mycobacterial disease after tuberculosis and leprosy. It is an emerging infectious disease that...Full Text Available

2009-09-01

331

Genome-wide profiling of forum domains in Drosophila melanogaster

BackgroundThe objective of the study was to analyse the evolution of Bordetella pertussis population and the influence of herd immunity in different areas of the...Full Text Available

332

Genome-wide linkage scan for contraction velocity characteristics of knee musculature in the Leuven Genes for Muscular Strength Study

Forum domains are stretches of chromosomal DNA that are excised from eukaryotic chromosomes during their spontaneous non-random fragmentation. Most forum domains are 50–200 kb in length....Full Text Available

2011-05-01

333

Genome-wide expression profiling reveals distinct clusters of transcriptional regulation during bovine preimplantation development in vivo

The torque-velocity relationship is known to be affected by ageing, decreasing its protective role in the prevention of falls. Interindividual variability in this torque-velocity relationship is partly...Full Text Available

2008-09-01

334

Genome-Wide Transcriptome Profiling of Region-Specific Vulnerability to Oxidative Stress in the Hippocampus

Bovine embryos can be generated by in vitro fertilization or somatic nuclear transfer; however, these differ from their in vivo counterparts in many aspects and exhibit a higher proportion of developmental...Full Text Available

2008-12-16

335

Genome-Wide Transcriptional Response of Chemostat-Cultured Escherichia coli to Zinc

Neurons in the hippocampal CA1 region are particularly sensitive to oxidative stress (OS), whereas those in CA3 are resistant. To uncover mechanisms for selective CA1 vulnerability to OS, we...Full Text Available

2007-08-01

336

Genome-Wide Analysis Reveals a Major Role in Cell Fate Maintenance and an Unexpected Role in Endoreduplication for the Drosophila FoxA Gene Fork Head

Zinc is an essential trace metal ion for growth, but an excess of Zn is toxic and microorganisms express diverse resistance mechanisms. To understand global bacterial responses to excess Zn, we conducted...Full Text Available

2005-02-01

337

Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse

Transcription factors drive organogenesis, from the initiation of cell fate decisions to the maintenance and implementation of these decisions. The Drosophila embryonic salivary gland...Full Text Available

338

Genetic aspects of birth defects: new understandings of old problems

Campylobacter is one of the leading causes of food-borne gastroenteritis and has a high prevalence in poultry. Campylobacter jejuni subsp. jejuni 327 is a subspecies...Full Text Available

339

Generation of microsatellite repeat families by RTE retrotransposons in lepidopteran genomes

Over the past two decades, combined advances in genetics, developmental biology and biochemistry have transformed the study of human birth defects. This review describes the importance of genome architecture,...Full Text Available

2007-07-01

340

Gene-gene and gene-environment interactions: new insights into the prevention, detection and management of coronary artery disease

BackgroundDeveloping lepidopteran microsatellite DNA markers can be problematical, as markers often exhibit multiple banding patterns and high frequencies of non-amplifying "null"...Full Text Available

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341

Gene expression patterns in four brain areas associate with quantitative measure of estrous behavior in dairy cows

Despite the recent success of genome-wide association studies (GWASs) in identifying loci consistently associated with coronary artery disease (CAD), a large proportion of the genetic components of...Full Text Available

342

Functional interaction between the Werner Syndrome protein and DNA polymerase ?

BackgroundThe decline noticed in several fertility traits of dairy cattle over the past few decades is of major concern. Understanding of the genomic factors underlying fertility,...Full Text Available

343

Exploring nervous system transcriptomes during embryogenesis and metamorphosis in Xenopus tropicalis using EST analysis

Werner Syndrome (WS) is an inherited disease characterized by premature onset of aging, increased cancer incidence, and genomic instability. The WS gene encodes a 1,432-amino acid polypeptide (WRN)...Full Text Available

2000-04-25

344

Evidence That Two Major Replicons Comprise the Genome of Staphylococcus Aureus.

BackgroundThe western African clawed frog Xenopus tropicalis is an anuran amphibian species now used as model in vertebrate comparative genomics. It provides the...Full Text Available

345

Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations

In Staphylococcus aureus, a pronounced shift in position of the acriflavin resistance locus was observed when gene order was determined by marker frequency analysis of cells of various ages. In young cells (2-hour culture), acriflavin resistance was mappe...

1967-01-01

346

Differentiation of trophoblast stem cells into giant cells is triggered by p57/Kip2 inhibition of CDK1 activity

Many pathogens colonize different anatomical sites, but the selective pressures contributing to survival in the diverse niches are poorly understood. Group A Streptococcus (GAS) is...Full Text Available

2011-03-22

347

Dietary factors related to body weight in adult Vietnamese in the rural area of Haiphong, Vietnam: the Korean Genome and Epidemiology Study (KoGES)

Genome endoreduplication during mammalian development is a rare event for which the mechanism is unknown. It first appears when fibroblast growth factor 4 (FGF4) deprivation induces differentiation...Full Text Available

2008-11-01

348

Detection of Streptococcus mutans Genomic DNA in Human DNA Samples Extracted from Saliva and Blood

The objectives of this study were to examine the association between dietary factors and underweight and overweight adult Vietnamese living in the rural areas of Vietnam. A cross-sectional study of...Full Text Available

2010-06-01

349

DNA Damage during G2 Phase Does Not Affect Cell Cycle Progression of the Green Alga Scenedesmus quadricauda

Caries is a multifactorial disease, and studies aiming to unravel the factors modulating its etiology must consider all known predisposing factors. One major factor is bacterial colonization,...Full Text Available

2011-01-01

350

Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, ...

DNA damage is a threat to genomic integrity in all living organisms. Plants and green algae are particularly susceptible to DNA damage especially that caused by UV light, due to their light dependency...Full Text Available

351

Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae

Cyteogenetic maps of sorghum chromosomes 3-7, 9, and 10 were constructed on the basis of the fluorescence in situ hybridization (FISH) of ~ ... regions of heterchromatin were delimited for all 10 sorghum chrom...

352

Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA

BackgroundOncidium spp. produce commercially important orchid cut flowers. However, they are amenable to intergeneric and inter-specific crossing making phylogenetic...Full Text Available

353

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

RNAs transcribed from the mitochondrial genome of Physarum polycephalum are heavily edited. The most prevalent editing event is the insertion of single Cs, with Us and dinucleotides...Full Text Available

2011-08-01

354

Comparative Transcriptional and Genomic Analysis of Plasmodium falciparum Field Isolates

BackgroundStructured noncoding RNAs perform many functions that are essential for protein synthesis, RNA processing, and gene regulation. Structured RNAs can be detected by comparative...Full Text Available

2010-01-01

355

Common genetic variation and susceptibility to partial epilepsies: a genome-wide association study

Mechanisms for differential regulation of gene expression may underlie much of the phenotypic variation and adaptability of malaria parasites. Here we describe transcriptional variation among culture-adapted...Full Text Available

2009-10-01

356

Common Familial Colorectal Cancer Linked to Chromosome 7q31: a genome-wide analysis

Partial epilepsies have a substantial heritability. However, the actual genetic causes are largely unknown. In contrast to many other common diseases for which genetic association-studies have successfully...Full Text Available

2010-07-01

357

Chiropteran types I and II interferon genes inferred from genome sequencing traces by a statistical gene-family assembler

Present investigations suggest that approximately 30% of colorectal cancer (CRC) cases arise on the basis of inherited factors. We hypothesize that the majority of inherited factors are moderately...Full Text Available

2008-11-01

358

Capture of genomic DNA on glass microscope slides

BackgroundThe rate of emergence of human pathogens is steadily increasing; most of these novel agents originate in wildlife. Bats, remarkably, are the natural reservoirs of many...Full Text Available

359

Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing

It is well known that DNA strands bind to silica surfaces in the presence of high concentrations of chaotropic salts. We developed simple methods to evaluate binding and recovery of DNA on flat...Full Text Available

2007-06-15

360

Blood leukocyte DNA hypomethylation and gastric cancer risk in a high-risk Polish population

BackgroundMimivirus, a giant dsDNA virus infecting Acanthamoeba, is the prototype of the mimiviridae family, the latest addition to the family of the nucleocytoplasmic...Full Text Available

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361

Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa

Global hypomethylation has been shown to increase genome instability potentially leading to increased cancer risk. We determined whether global methylation in blood leukocyte DNA was associated...Full Text Available

2010-10-15

362

Analysis of genomic differences among Clostridium botulinum type A1 strains

BackgroundThe Gram-negative, xylem-limited phytopathogenic bacterium Xylella fastidiosa is responsible for causing economically important diseases in grapevine,...Full Text Available

363

Analysis of European mtDNAs for Recombination

BackgroundType A1 Clostridium botulinum strains are a group of Gram-positive, spore-forming anaerobic bacteria that produce a genetically, biochemically, and biophysically...Full Text Available

364

An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer

The standard paradigm postulates that the human mitochondrial genome (mtDNA) is strictly maternally inherited and that, consequently, mtDNA lineages are clonal. As a result of mtDNA clonality, phylogenetic...Full Text Available

2001-01-01

365

An initial comparative map of copy number variations in the goat (Capra hircus) genome

BackgroundGenomics has substantially changed our approach to cancer research. Gene expression profiling, for example, has been utilized to delineate subtypes of cancer, and facilitated...Full Text Available

366

An excess of rare genetic variation in ABCE1 among Yorubans and African-American individuals with HIV-1

BackgroundThe goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of...Full Text Available

367

An Integrated Genomics Approach to Define Niche Establishment by Rhodococcus fascians1[C][W][OA

Signatures of natural selection occur throughout the human genome and can be detected at the sequence level. We have re-sequenced ABCE1, a host candidate gene essential for...Full Text Available

2009-12-01

368

Actin-like sequences are present on human X and Y chromosomes.

Rhodococcus fascians is a Gram-positive phytopathogen that induces shooty hyperplasia on its hosts through the secretion of cytokinins. Global transcriptomics using microarrays combined...Full Text Available

2009-03-01

369

A supervised approach for predicting patient survival with gene expression data

The human genome contains greater than 20 actin-related sequences, six of which at least are expressed as protein. We have shown by blot hybridization the presence of actin-like sequences on both the...Full Text Available

1984-08-01

370

A novel role of the aryl hydrocarbon receptor (AhR) in centrosome amplification - implications for chemoprevention

Rapid development in genomics in recent years has allowed the simultaneous measurement of the expression levels of thousands of genes using DNA microarrays. This has offered tremendous potential...Full Text Available

2010-01-01

371

A novel custom high density-comparative genomic hybridization array detects common rearrangements as well as deep intronic mutations in dystrophinopathies

BackgroundCentrosome aberrations can cause genomic instability and correlate with malignant progression in common human malignancies such as breast and prostate cancer. Deregulation...Full Text Available

372

A new evolutionary scenario for the Mycobacterium tuberculosis complex

BackgroundThe commonest pathogenic DMD changes are intragenic deletions/duplications which make up to 78% of all cases and point mutations (roughly 20%) detectable...Full Text Available

373

A genomic and proteomic investigation of the impact of preimplantation factor on human decidual cells

The distribution of 20 variable regions resulting from insertion-deletion events in the genomes of the tubercle bacilli has been evaluated in a total of 100 strains of Mycobacterium tuberculosis,...Full Text Available

2002-03-19

374

A genome-wide study of PDZ-domain interactions in C. elegans reveals a high frequency of non-canonical binding

OBJECTIVEPreimplantation factor (PIF) is a novel, 15 amino acid peptide, secreted by viable embryos. This study aims to elucidate PIF’s effects in human endometrial...Full Text Available

2010-05-01

375

A Response Regulator That Represses Transcription of Several Virulence Operons in the Group A Streptococcus

BackgroundProteins may evolve through the recruitment and modification of discrete domains, and in many cases, protein action can be dissected at the domain level. PDZ domains are...Full Text Available

376

A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale

A search for homologs of the Bacillus subtilis PhoP response regulator in the group A streptococcus (GAS) genome revealed three good candidates. Inactivation of one of these, recently...Full Text Available

1999-06-01

377

A Coxiella burnetti repeated DNA element resembling a bacterial insertion sequence.

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is critical, however, for both basic and clinical research into brain function....Full Text Available

2009-03-01

378

Mineral biotechnology. Microbial aspects of mineral beneficiation, metal extraction, and environmental control

A DNA fragment located on the 3' side of the Coxiella burnetii htpAB operon was determined by Southern blotting to exist in approximately 19 copies in the Nine Mile I genome. The DNA sequences of this...Full Text Available

1992-09-01

379

Mechanism of biodegradation of paraquat by Lipomyces starkeyi

Papers in this book illustrate the utility of mineral biotechnology with respect to biobeneficiation, bioleaching, bioremediation and biomineralization. Papers of particular interest to the coal industry include: depression of pyrite flotation by yeast and bacteris (S.K. Kawatra and T.C. Eisele); desulfurization of coal by microbial flotation in a semicontinuous system (T. Nagaoka and others); biochemical removal of HAP precursors from coal - INEEL slurry column testing (K.S. Noah and G.J. Olson); microorganisms, biotechnology and acid rock drainage - emphasis on passive-biological control and treatment methods (N. Kuyucak); and utility of bioreagents in mineral processing (P. Somasundaran and others).

2001-07-01

380

Mechanism of biodegradation of paraquat by Lipomyces starkeyi

The biodegradation of ring-/sup 14/C- and methyl-/sup 14/C-labeled paraquat by the soil yeast Lipomyces starkeyi was studied in vitro. It was found that the degradation of paraquat (acting as a sole source of culture nitrogen) resulted in the accumulation in the extracellular medium of radiolabeled acetic acid. The culture also evolved radiolabeled CO/sub 2/. The results suggest that the degradation of paraquat by L. starkeyi is associated with the integrity of the cell wall and that disruption or removal of the wall results in a complete loss of degradative capability. A mechanism for the degradation of paraquat by this organism is postulated.

1985-05-01

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381

Latvian scientists research into chemical uses of timber

The biodegradation of ring-"1"4C- and methyl-"1"4C-labeled paraquat by the soil yeast Lipomyces starkeyi was studied in vitro. It was found that the degradation of paraquat (acting as a sole source of culture nitrogen) resulted in the accumulation in the extracellular medium of radiolabeled acetic acid. The culture also evolved radiolabeled CO_2. The results suggest that the degradation of paraquat by L. starkeyi is associated with the integrity of the cell wall and that disruption or removal of the wall results in a complete loss of degradative capability. A mechanism for the degradation of paraquat by this organism is postulated.

382

Antifungal activity of Glycyrrhiza glabra extracts and its active constituent glabridin

Scientists of the Institute of Wood Chemistry of the Latvian Academy of Sciences have developed two highly efficient processes for producing furfural, a feedstock for varnishes, synthetic resins and plastics. It is made of production wastes, including branches and small-dimension timber. By one process, the raw material is chipped, treated first with diluted sulphuric acid and then with steam heated to 250 degrees C. The other uses concentrated sulphuric acid as a catalyst. Besides furfural, this process also yields sugar solutions used in alcohol and nutrient yeast production.

1982-03-20

383

British Library Electronic Table of Contents (United Kingdom)

Glabridin, an active constituent of Glycyrrhiza glabra roots, was found to be active against both yeast and filamentous fungi. Glabridin also showed resistance modifying activity against drug resistant mutants of Candida albicans at a minimum inhibitory concentration of 31.25-250 g/mL. Although the compound was reported earlier to be active against Candida albicans, but this is the first report of its activity against drug resistant mutants. Copyright Copyright 2009 John Wiley & Sons, Ltd.

2009-01-01

384

Genome Sequence of a Lancefield Group C Streptococcus zooepidemicus Strain Causing Epidemic Nephritis: New Information about an Old Disease

The enhanced genomic instability was induced by alpha particle and low-energy ion irradiation in somatic cells of Arabidopsis thaliana

Outbreaks of disease attributable to human error or natural causes can provide unique opportunities to gain new information about host-pathogen interactions and new leads for pathogenesis research. Poststreptococcal glomerulonephritis (PSGN), a sequela of infection with pathogenic streptococci, is a common cause of preventable kidney disease worldwide. Although PSGN usually occurs after infection with group A streptococci, organisms of Lancefield group C and G also can be responsible. Despite decades of study, the molecular pathogenesis of PSGN is poorly understood. As a first step toward gaining new information about PSGN pathogenesis, we sequenced the genome of Streptococcus equi subsp. zooepidemicus strain MGCS10565, a group C organism that caused a very large and unusually severe epidemic of nephritis in Brazil. The genome is a circular chromosome of 2,024,171 bp. The genome shares extensive gene content, including many ...

2008-08-21

385

Genomic analysis of the symbiotic marine crenarchaeon, Cenarchaeumsymbiosum

Although low-energy ion radiation has been proven to have a wide range of biological effects and led to fruitful achievements as a new mutagenic source for genetic modification, there still exist some disputes about its mutagenic mechanisms because of its short-penetrating property. In present research, Arabidopsis thaliana transgenic for GUS recombination substrate was used to evaluate the genomic instability induced by irradiations of alpha particle (3.3MeV) and Low-energy-Argon ion (30 KeV). A pronounced effects of alpha particle irradiation to Arabidopsis thaliana seedlings and Argon ion irradiation to seeds on the somatic homologous recombination frequency (sHRF) were reported. The sHRFs increased 1.88-fold and 2.42-fold, respectively, which indicated that the short-penetrating radiation could effectively induce the plant genomic instability in either dry seeds or seedlings with active metabolism. The local alpha particle irradiation of ...

2008-08-12

386

The mouse formin (Fmn) gene: Genomic structure, novel exons, and genetic mapping

Crenarchaea are ubiquitous and abundant microbial constituents of soils, sediments, lakes and ocean waters, yet relatively little is known about their fundamental evolutionary, ecological, and physiological properties. To better describe the ubiquitous nonthermophilic Crenarchaea, we analyzed the genome sequence of one representative, the uncultivated sponge symbiont, Cenarchaeum symbiosum. C. symbiosum genotypes coinhabiting the same host partitioned into two dominant populations, corresponding to previously described a- and b-type ribosomal RNA variants. Although synthetic, overlapping a- and b-type ribotypes harbored significant genetic variability. A single tiling path comprising the dominant a-type genotype was assembled, and used to explore the biological properties of C. symbiosum and its planktonic relatives. Out of a total of 2,066 predicted open reading frames, 36% were more highly conserved with other Archaea. The remainder partitioned between bacteria ...

2006-06-24

387

Genetic effects of introgression genomic components from Sea Island cotton (Gossypium barbadense L.) on fiber related traits in upland cotton (G. hirsutum L.)

Mutations in the mouse formin (Fmn) gene, formerly known as the limb deformity (ld) gene, give rise to recessively inherited limb deformities and renal malformations or aplasia. The Fmn gene encodes many differentially processed transcripts that are expressed in both adult and embryonic tissues. To study the genomic organization of the Fmn locus, we have used Fmn probes to isolate and characterize genomic clones spanning 500 kb. Our analysis of these clones shows that the Fmn gene is composed of at least 24 exons and spans 400 kb. We have identified two novel exons that are expressed in the developing embryonic limb bud as well as adult tissues such as brain and kidney. We have also used a microsatellite polymorphism from within the Fmn gene to map it genetically to a 2.2-cM interval between D2Mit58 and D2Mit103. 36 refs., 6 figs., 1 tab.

1997-02-01

388

British Library Electronic Table of Contents (United Kingdom)

The germplasm with exotic genomic components especially from Sea Island cotton (Gossypium barbadense L. Gb) is the dominant genetic resources to enhance fiber quality of upland cotton (G. hirsutum L., Gh). Due to low efficiency of phenotypic evaluation and selection on fiber quality, genetic dissection of favorable alleles using molecular markers is essential. Genetic dissection on putative Gb introgressions related to fiber traits were conducted by SSR markers with mapping populations derived from a cross between Luyuan343 (LY343), a superior fiber quality introgression line (IL) with genomic components from Gb, and an elite Upland cotton cv. Lumianyan#22 (LMY22). Among 82 polymorphic loci screened out from 4050 SSRs, 42 were identified as putative introgression alleles. A total of 29 fib...

2011-01-01

389

Gene discovery in the Acanthamoeba castellanii genome

Fiscal 1998 industrial science and technology R and D project. Research report on R and D of genome informatics technology (Development of stable oil supply measures using complex biosystem); 1998 nendo genome informatics gijutsu kenkyu kaihtsu seika hokokusho. Fukugo seibutsukei riyo sekiyu antei kyokyu taisaku kaihatsu

Acanthamoeba castellanii is a free-living amoeba found in soil, freshwater, and marine environments and an important predator of bacteria. Acanthamoeba castellanii is also an opportunistic pathogen of clinical interest, responsible for several distinct diseases in humans. In order to provide a genomic platform for the study of this ubiquitous and important protist, we generated a sequence survey of approximately 0.5 x coverage of the genome. The data predict that A. castellanii exhibits a greater biosynthetic capacity than the free-living Dictyostelium discoideum and the parasite Entamoeba histolytica, providing an explanation for the ability of A. castellanii to inhabit adversity of environments. Alginate lyase may provide access to bacteria within biofilms by breaking down the biofilm matrix, and polyhydroxybutyrate depolymerase may facilitate utilization of the bacterial storage compound polyhydroxybutyrate as a food source. Enzymes for the ...

2005-08-01

390

Evolutionary dynamics of Newcastle disease virus

This report describes the fiscal 1998 result on development of genome informatics technology. As comparative analysis technique of genes, the combination of electrophoresis and PCR was used. For improvement of the throughput and reproducibility of the technique, module- shuffling primers were used, and the multi(96)-arrayed capillary fragment analyzer was devised. The system detecting SNPs rapidly was also developed successfully. As analysis technology of DNA sequence by use of triple- stranded DNA formation, study was made on construction of long cDNA libraries, selective subtraction of specific sequences from libraries, and the basic technology of homologous cloning. Study was also made on each reaction step of IGCR technique for fast analysis, and specifications of a fluorescence transfer monitor. As modeling technique of genetic sequence information, the simulation model was developed for gene expression regulatory networks during muscle differentiation, and ...

1999-03-01

391

Complete genome sequence of Conexibacter woesei type strain (ID131577T)

A comprehensive dataset of NDV genome sequences was evaluated using bioinformatics to characterize the evolutionary forces affecting NDV genomes. Despite evidence of recombination in most genes, only one event in the fusion gene of genotype V viruses produced evolutionarily viable progenies. The codon-associated rate of change for the six NDV proteins revealed that the highest rate of change occurred at the fusion protein. All proteins were under strong purifying (negative) selection; the fusion protein displayed the highest number of amino acids under positive selection. Regardless of the phylogenetic grouping or the level of virulence, the cleavage site motif was highly conserved implying that mutations at this site that result in changes of virulence may not be favored. The coding sequence of the fusion gene and the genomes of viruses from wild birds displayed higher yearly rates of change in virulent viruses than in ...

2009-08-15

392

The genetic basis of salinity tolerance in Arctic charr (Salvelinus alpinus).

The genus Conexibacter (Monciardini et al. 2003) represents the type genus of the family Conexibacteraceae (Stackebrandt 2005, emend. Zhi et al. 2009) with Conexibacter woesei as the type species of the genus. C. woesei is a representative of a deep evolutionary line of des-cent within the class Actinobacteria. Strain ID131577T was originally isolated from temperate forest soil in Gerenzano (Italy). Cells are small, short rods that are motile by peritrichous fla-gella. They may form aggregates after a longer period of growth and, then as a typical charac-teristic, an undulate structure is formed by self-aggregation of flagella with entangled bacteri-al cells. Here we describe the features of the organism, together with the complete sequence and annotation. The 6,359,369 bp long genome of C. woesei contains 5,950 protein-coding and 48 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.

2010-01-01

393

Wiley::The Wiley Encyclopedia of Packaging Technology, 3rd Edition

ABSTRACT: BACKGROUND: The capacity to maintain internal ion homeostasis amidst changing conditions is particularly important for teleost fishes whose reproductive cycle is dependent upon movement from freshwater to seawater. Although the physiology of seawater osmoregulation in mitochondria-rich cells of fish gill epithelium is well understood, less is known about the underlying causes of inter- and intraspecific variation in salinity tolerance. We used a genome-scan approach in Arctic charr (Salvelinus alpinus) to map quantitative trait loci (QTL) correlated with variation in four salinity tolerance performance traits and six body size traits. Comparative genomics approaches allowed us to infer whether allelic variation at candidate gene loci (e.g., ATP1alpha1b, NKCC1, CFTR, and cldn10e) could have underlain observed variation. RESULTS: Combined parental analyses yielded genome-wide significant QTL on linkage groups 8, 14 ...

2011-09-21

394

Wastenet

...The+Wiley+Encyclopedia+of+Packaging+Technology%2C+3rd+Edition FO21+Food+Packaging Wiley::The Wiley Encyclopedia of Packaging Technology, 3rd Edition WILEY ...US | HELP Home / Chemistry / Food Science & Technology / Food Processing, Production & Manufacture / Food Packaging / The Wiley Encyclopedia of Packaging Technology, 3rd Edition ...Manufacture Sensory Science Food Biotechnology Food Chemistry Food Engineering Related Titles Food Packaging Brewing Yeast and Fermentation by Chris Boulton, David Quain Food ...Editor) Journal of Food Process Engineering Journal of Food Processing and Preservation Packaging Research in Food Product Design and Development by Howard R. ...

395

The antimicrobial efficacy of a silver alginate dressing against a broad spectrum of clinically relevant wound isolates

British Library Electronic Table of Contents (United Kingdom)

Wound dressings impregnated with silver have a role to play in aiding to reduce both the dressing and wound microbial bioburden. It is therefore imperative that antimicrobial wound dressings have efficacy on a broad range of clinical significant microorganisms. Accordingly, this study aimed to determine the antimicrobial efficacy of a silver alginate dressing against 115 wound isolates that had been isolated routinely from patients at West Virginia University Hospital. Standardised corrected zones of inhibition (CZOIs) were performed on all clinical isolates. It was found that the silver alginate dressing was able to inhibit the growth of all microorganisms tested. In particular, the silver alginate dressing inhibited the growth of Candida albicans and yeasts with CZOI of 3-115 mm. All met...

2011-01-01

396

The DFNA5 gene, responsible for hearing loss and involved in cancer, encodes a novel apoptosis-inducing protein

British Library Electronic Table of Contents (United Kingdom)

DFNA5 was first identified as a gene causing autosomal dominant hearing loss (HL). Different mutations have been found, all exerting a highly specific gain-of-function effect, in which skipping of exon 8 causes the HL. Later reports revealed the involvement of the gene in different types of cancer. Epigenetic silencing of DFNA5 in a large percentage of gastric, colorectal and breast tumors and p53-dependent transcriptional activity have been reported, concluding that DFNA5 acts as a tumor suppressor gene in different frequent types of cancer. Despite these data, the molecular function of DFNA5 has not been investigated properly. Previous transfection studies with mutant DFNA5 in yeast and in mammalian cells showed a toxic effect of the mutant protein, which was not seen after transfection ...

2011-01-01

397

Loss of cell components during rehydration of dried Rhodotorula glutinis and its implications for lead uptake

British Library Electronic Table of Contents (United Kingdom)

Abstract Microbial cells are routinely dried and ground before they are used in metal biosorption studies. In this work, a metal biosorbent was prepared by drying biomass of the yeast Rhodotorula glutinis in an oven at 70C for 24-h followed by grinding. Two forms of the prepared biosorbent particles, washed and unwashed, were examined for their ability to remove lead from solution. It was found that the unwashed biosorbent exhibited higher lead uptake than the washed biosorbent. Analysis of the supernatant of washed cells incubated in water and that of unwashed cells incubated in lead solution revealed the presence of protein, carbohydrates, organic acids and inorganic phosphate. Overall, the washed and unwashed cells leached, respectively, 14.5 and 13.4% of their initial dry weight (100-m...

2011-01-01

398

In vitro effects of medium tonicity, nutrient concentration, and free chlorine content on Acanthamoeba

British Library Electronic Table of Contents (United Kingdom)

Background: The environment preferred by Acanthamoeba trophozoites and the mechanism by which the amebae enters the cornea are not yet fully understood. A better understanding of the pathogenesis of this disease may help with prevention and treatment. Purpose: To define the preferred environments for Acanthamoeba survival and proliferation in vitro by examining the effect of tonicity, nutrient concentration, and free chlorine content on Acanthamoeba. Materials and methods: Human corneal isolates of Acanthamoeba castellanii and Acanthamoeba polyphaga trophozoites were cultured at 22^oC (room temperature) in PYG (peptone-yeast extract-glucose) medium. The effect of tonicity on amebae was determined by incubating trophozoites in sodium chloride solutions in concentrations ranging from 0% to 1...

2011-01-01

399

Curcumin Binding to DNA and RNA

British Library Electronic Table of Contents (United Kingdom)

Curcumin, the yellow pigment from the rhizoma of Curcuma longa, is a widely studied phytochemical with a variety of biological activities. The ongoing research and clinical trials have proved that this natural phenolic compound has great and diverse pharmacological potencies. Beside its effective antioxidant, antiinflammatory, and antimicrobial/antiviral properties, curcumin is also considered as a cancer chemopreventive agent. While the antioxidant activity of curcumin is well documented, its interaction with DNA and RNA is not fully investigated. This study was designed to examine the interactions of curcumin with calf thymus DNA and yeast RNA in aqueous solution at physiological conditions, using constant DNA and RNA concentration (6.25?mM) and various curcumin/polynucleotide (phosphate...

2009-01-01

400

Comparison of media and methods for detecting and enumerating Listeria monocytogenes in refrigerated cabbage.

Biological treatment of wine of distilleries

Direct plating, selective enrichment, and cold enrichment followed by secondary selective enrichment procedures were compared for detecting and enumerating Listeria monocytogenes in chopped cabbage stored at 5 degrees C for up to 64 days. Addition of Fe3+ to solid media enhanced detection of the organism. Cold enrichment (5 degrees C) in nutrient broth and brain heart infusion broth followed by secondary enrichment (48 h, 30 degrees C) in Trypticase soy-yeast extract-antibiotic broth and thiocyanate-nalidixic acid broth and plating on selective agar media (Doyle and Schoeni selective enrichment agar [minus acriflavin hydrochloride, supplemented with 5 micrograms of Fe3+/ml] and McBride Listeria agar) resulted in the detection of highest populations. PMID:3111369

1987-05-01

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

401

Bioconvertion of spent cellulose sausage casings

The potential of the yeast Candida tropicalis and Candida guillermondii was evaluated and an isolated partnership of microorganisms of waters of the Medellin River, conformed by two bacteria and one leavening, to degrade the content of organic matter present in wine produced by the factory of Licores and Alcoholes de Antioquia (FLA) in aerobic process with biomass production. For each one of the microorganisms in study this capacity of removal in units of chemical demand of oxygen was quantified (CDO); in addition, parameters were analyzed such as yield of the biomass in relation to the removed CDO and to total reducing sugars (TRS) consumed, time of fermentation and speed of growth different dilutions from wine. Also the possible inhibition was analyzed that the present phenolic compounds in this wine can cause in the biological process of degradation.

402

British Library Electronic Table of Contents (United Kingdom)

Cellulose sausage cellulose casings are used extensively in the manufacture of sausages in meat packaging. After stripping the meat, spent casings mainly contain cellulose and residual meat juice with salt, nitrate and nitrite. Disposal of spent sausage casings has serious economic and environmental concerns for the sausage industry. This work describes bioconversion of spent cellulose casings (SCC) into enzymes, lactic acid and ethanol by using cellulolytic fungi, lactobacillus and yeasts. The solid substrate cultivation (SSC) of Trichoderma reesei RUT C-30 on SCC and blends gave a maximum of 152 filter paper cellulase (FPase) activity and about 100 carboxymethylcellulase activity (CMCase)/g dry weight substrate. The SSC produced enzyme-rich casing with 50 FPase when directly mixed as suc...

2008-01-01

403

Antimicrobial silver-montmorillonite nanoparticles to prolong the shelf life of fresh fruit salad

British Library Electronic Table of Contents (United Kingdom)

In this work, silver-montmorillonite (Ag-MMT) antimicrobial nanoparticles have been obtained by allowing silver ions from nitrate solutions to replace the Na^+ of natural montmorillonite and then to be reduced by a thermal treatment. Ag-MMT were used as active antimicrobial compounds to improve the shelf life of fresh fruit salad. In order to assess their influence on product shelf life, sensorial and microbiological quality has been monitored during the storage. The microbiological quality was determined by monitoring the principal spoilage microorganisms (mesophilic and psychrotrophic bacteria, coliforms, lactic acid bacteria, yeasts and molds). Additionally, the evolution of sensorial quality was assessed by monitoring color, odor, firmness and product overall quality. The Ag-MMT nanopa...

2011-01-01

404

Amphiphysin (Amph) maps to the proximal region of mouse chromosome 13

Aerobic Decolorization and Detoxification of a Disperse Dye in Textile Effluent by a New Isolate of Bacillus sp.

Amphiphysin is a protein concentrated in neuronal synapses and peripherally associated with neurotransmitter vesicles. It is expressed in many neurons of the central and peripheral nervous systems, in the adrenal medulla, in the anterior and posterior pituitary, in cell lines of the endocrine pancreas, and in spermatocytes. Its subcellular localization and tissue distribution indicate a potential involvement in mechanisms of regulated exocytosis. A role in the dynamic organization of the membrane-associated cytoskeleton is suggested by structural homology to the products of two yeast genes, RVS161 and RVS167, whose mutation results in an abnormal actin distribution, disturbs budding morphology, and impairs cell entry into stationary phase. Limited stretches of sequence similarity, including an SH3 domain, are also shared with other actin-binding proteins. Amphiphysin is the dominant autoantigen in paraneoplastic Stiff-Man syndrome, a neurological autoimmune ...

1995-07-20

405

British Library Electronic Table of Contents (United Kingdom)

A number of aerobic species capable of decolorizing some of the dyes in a textile mill effluent were isolated. One of the isolates was able to decolorize Terasil black dye under aerobic conditions in the presence of an exogenous carbon source after 5 days. Glucose or starch (%1 ea) are essential for decolorization but the process proceeds faster in the presence of 0.5% yeast extract. Results of the BOD5 show that the untreated effluent samples have a low BOD value, whereas treated samples show an initial increase in BOD up to 15 days followed by a decrease after 20 days. FT-IR and GC-MS data also reveal that the initial components in the untreated effluent disappear after 20 days of treatment, confirming biodegradation of the dye. Phytotoxicity tests on the untreated effluent samples using...

2006-01-01

406

A lytic enzyme cocktail from Streptomyces sp. B578 for the control of lactic and acetic acid bacteria in wine

British Library Electronic Table of Contents (United Kingdom)

Beside yeasts, lactic acid bacteria (LAB) are the most abundant microbes in must during vinification. Whereas Oenococcos oeni is commercially used as a starter culture for the biological acid reduction in wines, other species are responsible for different types of wine spoilage. Members of the genera Pediococcus, Weissella, Leuconostoc, and Lactobacillus are producers of exopolysaccharide slimes, biogenic amines, acetic acid, and other off-flavors. In order to control microbial growth, different procedures such as heating of must and addition of sulfite or lysozyme from egg white are generally applied. Yet, because of health risks, the application of sulfite should be reduced and lysozyme is not effective against all LAB. In this study, we describe exoenzymes from a Streptomyces sp. strain...

2009-01-01

407

Universal Similarity

Summary of the OA biomarkers workshop 2010 - genetics and genomics: new targets in OA

We survey a new area of parameter-free similarity distance measures useful in data-mining, pattern recognition, learning and automatic semantics extraction. Given a family of distances on a set of objects, a distance is universal up to a certain precision for that family if it minorizes every distance in the family between every two objects in the set, up to the stated precision (we do not require the universal distance to be an element of the family). We consider similarity distances for two types of objects: literal objects that as such contain all of their meaning, like genomes or books, and names for objects. meaning, like genomes or books, and names for objects. The latter may have literal embodyments like the first type, but may also be abstract like ``red'' or ``christianity.'' For the first type we consider a family of computable distance measures corresponding to parameters expressing similarity according to particular features between ...

2005-01-01

408

British Library Electronic Table of Contents (United Kingdom)

On November fourth and fifth 2010 a group of more than 100 international investigators gathered in Atlanta for the second Osteoarthritis (OA) Biomarkers Global Initiative workshop titled ''Genetics and Genomics: New Targets in OA''. The first workshop took place in April 2009 and focused on in vitro (soluble) biomarkers whilst the third and final workshop will take place in 2012 and will focus on imaging biomarkers. The OA Research Society International (OARSI) has organized the workshops. In addition to OARSI, the National Institute of Arthritis, Musculoskeletal and Skin Diseases, the Arthritis Foundation, Amgen, Genzyme, the American Orthopaedic Society for Sports Medicine and Pfizer sponsored the second meeting. It was clear from this meeting that experiments in the genetics, epigenetic...

2011-01-01

409

Selective changes of retroelement expression in human prostate cancer

British Library Electronic Table of Contents (United Kingdom)

Retroelements constitute a large part of the human genome. These sequences are mostly silenced in normal cells, but genome-wide DNA hypomethylation in cancers might lead to their re-expression. Whether this re-expression really occurs in human cancers is largely unkown. We therefore investigated expression and DNA methylation of several classes of retroelements in human prostate cancer tissues and cell lines by quantitative reverse transcription-polymerase chain reaction and pyrosequencing, respectively. The most striking finding was strong and generalized increased expression of the HERV-K_22q11.23 provirus in cancers, including de novo expression of a spliced accessory Np9 transcript in some tumors. In parallel, DNA methylation in the long terminal repeat (LTR) decreased. Conversely, HER...

2011-01-01

410

Introduction to the Special Issue: Human Linkage Studies for Behavioral Traits

British Library Electronic Table of Contents (United Kingdom)

In the post Genome era, the aim of behavior genetics has shifted from estimating the relative contributions of genes and environmental factors to (co-)variation in human complex traits, to localization of genes and identification of functional genetic variants. This special issue reflects this transition and presents fifteen papers that report on genome-wide linkage scans for complex traits in humans and on methodological tools and innovations. Six papers focus on cognition and report overlapping linkage peaks on chromosomes 6p and 14p. Papers on addictive behavior, i.e. smoking and alcohol dependence and its endophenotypes, find moderate LOD scores on chromosomes 6p, 5q, 4p and 7q, respectively. Three papers concentrate on emotionality, depression and loneliness and examine chromosomes 2q...

2006-01-01

411

Genomic architecture of aggression: Rare copy number variants in intermittent explosive disorder

British Library Electronic Table of Contents (United Kingdom)

Abstract Copy number variants (CNVs) are known to be associated with complex neuropsychiatric disorders (e.g., schizophrenia and autism) but have not been explored in the isolated features of aggressive behaviors such as intermittent explosive disorder (IED). IED is characterized by recurrent episodes of aggression in which individuals act impulsively and grossly out of proportion from the involved stressors. Previous studies have identified genetic variants in the serotonergic pathway that play a role in susceptibility to this behavior, but additional contributors have not been identified. Therefore, to further delineate possible genetic influences, we investigated CNVs in individuals diagnosed with IED and/or personality disorder (PD). We carried out array comparative genomic hybridizati...

2011-01-01

412

Genome-wide association study identifies variants in the CFH region associated with host susceptibility to meningococcal disease

British Library Electronic Table of Contents (United Kingdom)

Meningococcal disease is an infection caused by Neisseria meningitidis. Genetic factors contribute to host susceptibility and progression to disease, but the genes responsible for disease development are largely unknown. We report here a genome-wide association study for host susceptibility to meningococcal disease using 475 individuals with meningococcal disease (cases) and 4,703 population controls from the UK. We performed, in Western European and South European cohorts (consisting of 968 cases and 1,376 controls), two replication studies for the most significant SNPs. A cluster of complement factor SNPs replicated independently in both cohorts, including SNPs within complement factor H (CFH) (rs1065489 (p.936D

2010-01-01

413

Complete genome sequences of Brucella melitensis strains M28 and M5-90, with different virulence backgrounds.

An integrated genome research network for studying the genetics of alcohol addiction

Brucella melitensis is a Gram-negative coccobacillus bacteria belonging to the Alphaproteobacteria subclass. It is an important zoonotic pathogen that causes brucellosis, a disease affecting sheep, cattle, and sometimes humans. The B. melitensis strain M5-90, a live attenuated vaccine cultured from the B. melitensis virulent strain M28, has been an effective tool to control brucellosis in goats and sheep in China. Here we report the complete genome sequences of B. melitensis M28 and M5-90, strains with different virulence backgrounds, which will serve as a valuable reference for future studies. PMID:21478357

2011-04-08

414

British Library Electronic Table of Contents (United Kingdom)

Abstract Alcohol drinking is highly prevalent in many cultures and contributes to the global burden of disease. In fact, it was shown that alcohol constitutes 3.2% of all worldwide deaths in the year 2006 and is linked to more than 60 diseases, including cancers, cardiovascular diseases, liver cirrhosis, neuropsychiatric disorders, injuries and foetal alcohol syndrome. Alcoholism, which has been proven to have a high genetic load, is one potentially fatal consequence of chronic heavy alcohol consumption, and may be regarded as one of the most prevalent neuropsychiatric diseases afflicting our society today. The aim of the integrated genome research network -Genetics of Alcohol Addiction--which is a German inter-/trans-disciplinary life science consortium consisting of molecular biologists,...

2010-01-01

415

Reactive biomolecular divergence in genetically altered yeast cells and isolated mitochondria as measured by biocavity laser spectroscopy : a rapid diagnostic method for studying cellular responses to stress and disease.

Ethanol production and a case study of ethanol produced from sweet sorghum stalks via solid state fermentation

We report an analysis of four strains of baker's yeast (Saccharomyces cerevisiae) using biocavity laser spectroscopy. The four strains are grouped in two pairs (wild type and altered), in which one strain differs genetically at a single locus, affecting mitochondrial function. In one pair, the wild-type rho+ and a rho0 strain differ by complete removal of mitochondrial DNA (mtDNA). In the second pair, the wild-type rho+ and a rho- strain differ by knock-out of the nuclear gene encoding Cox4, an essential subunit of cytochrome c oxidase. The biocavity laser is used to measure the biophysical optic parameter Deltalambda, a laser wavelength shift relating to the optical density of cell or mitochondria that uniquely reflects its size and biomolecular composition. As such, Deltalambda is a powerful parameter that rapidly interrogates the biomolecular state of single cells and mitochondria. Wild-type cells and mitochondria produce Gaussian-like distributions ...

2006-12-01

416

3-Methyl-3-deazaadenine, a stable isostere of N3-methyl-adenine, is efficiently bypassed by replication in vivo and by transcription in vitro.

Ethanol has excellent fuel properties, such as high octane, high heat of vaporization and low photochemical reactivity in the atmosphere. It is less volatile than gasoline and there is lower smog formation from evaporative emissions of pure ethanol compared to gasoline. As such, ethanol has emerged as an important alternative energy source that is sustainable, efficient, cost effective, convenient and safe. In 2006, global production of ethanol reached 13.5 billion gallons, up from 12.1 billion gallons in 2005. However, in light of the current debate of food versus fuel, the industry must shift to non-food feedstocks. This paper described an emerging technology to cost-effectively produce ethanol from sweet sorghum stalks, the most promising alternative feedstock to corn, via solid state fermentation (SSF). Experiments of advanced solid state fermentation (ASSF) for ethanol production from sweet sorghum by Saccharomyces cerevisiae were conducted in laboratory and pilot scales studies. ...

2008-07-01

417

The normal developmental regulation of a cloned sgs3 'glue' gene chromosomally integrated in Drosophila melanogaster by P element transformation.

The goal of the present work was to determine the impact of N3-methyladenine (3-mA), an important lesion generated by many environmental agents and anticancer drugs, on in vivo DNA replication and in vitro RNA transcription. Due to 3-mA chemical instability, the stable isostere 3-methyl-3-deazaadenine (3-m-c(3)A) was site specifically positioned into an oligodeoxynucleotide. The oligomer was, then incorporated into a vector system that is rapidly converted to ssDNA inside yeast cells and requires DNA replication opposite the lesion for plasmid clonal selection. For control purposes, an adenine or a stable apurinic/apyrimidinic (AP)-lesion was placed at the same site. The presence of each lesion in the oligonucleotide was confirmed by MALDI-TOF analysis. Plasmids were then transfected into yeast cells. While the AP-site dramatically reduced plasmid replication in all strains, the 3-m-c(3)A had a slight effect in the rad30 background which ...

2011-06-14

418

The Complete Genome Sequence of Yersinia pseudotuberculosis IP31758, the Causative Agent of Far East Scarlet-Like Fever

A 7-kb genomic segment containing the coding sequence for the Drosophila melanogaster Formosa variant of salivary gland secretion protein 3 (sgs3) has been inserted into the snw y, bw, st strain of...Full Text Available

1983-01-01

419

The Acidic Domain of Hepatitis C Virus NS4A Contributes to RNA Replication and Virus Particle Assembly?

The first reported Far East scarlet-like fever (FESLF) epidemic swept the Pacific coastal region of Russia in the late 1950s. Symptoms of the severe infection included erythematous skin rash and desquamation,...Full Text Available

2007-08-01

420

Sequencing and Comparative Genomic Analysis of pK29, a 269-Kilobase Conjugative Plasmid Encoding CMY-8 and CTX-M-3 ?-Lactamases in Klebsiella pneumoniae?

Hepatitis C virus NS3-4A is a membrane-bound enzyme complex that exhibits serine protease, RNA helicase, and RNA-stimulated ATPase activities. This enzyme complex is essential for viral genome replication...Full Text Available

2011-02-01

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421

Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo)

A 269-kilobase conjugative plasmid, pK29, from a Klebsiella pneumoniae strain was sequenced. The plasmid harbors multiple antimicrobial resistance genes, including those encoding CMY-8...Full Text Available

2007-08-01

422

Production of Infectious Genotype 1b Virus Particles in Cell Culture and Impairment by Replication Enhancing Mutations

BackgroundLand plant genomes contain multiple members of a eukaryote-specific gene family encoding proteins with pentatricopeptide repeat (PPR) motifs. Some PPR proteins were shown...Full Text Available

423

Environmental Research Database

With the advent of subgenomic hepatitis C virus (HCV) replicons, studies of the intracellular steps of the viral replication cycle became possible. These RNAs are capable of self-amplification in cultured human hepatoma cells, but save for the genotype 2a isolate JFH-1, efficient replication of these HCV RNAs requires replication enhancing mutations (REMs), previously also called cell culture adaptive mutations. These mutations cluster primarily in the central region of non-structural protein 5A (NS5A), but may also reside in the NS3 helicase domain or at a distinct position in NS4B. Most efficient replication has been achieved by combining REMs residing in NS3 with distinct REMs located in NS4B or NS5A. However, in spite of efficient replication of HCV genomes containing such mutations, they do not support production of infectious virus particles. By using the genotype 1b isolate Con1, in this study we show that REMs interfere with HCV assembly. Strongest ...

2009-06-12

424

Plant Sulphur Nutrition

DescriptionThe recent sequencing of the complete genomes of several streptomycete species revealed the presence of a large number of cryptic' secondary metabolic gene clusters, and led to the realisation that these organisms have the ability to produce many more natural products than had previously been recognised. One of the aims of our work is to identify the physiological signals and regulatory mechanisms responsible for the activation of these 'cryptic' pathways, thus unleashing the full biosynthetic p [continued...

2010-01-31

425

Ordered Cloned DNA Map of the Genome of Vibrio cholerae 569B and Localization of Genetic Markers

Meta-Analysis for Genome-Wide Association Study Identifies Multiple Variants at the BIN1 Locus Associated with Late-Onset Alzheimer's Disease

By using a low-resolution macrorestriction map as the foundation (R. Majumder et al., J. Bacteriol. 176:1105–1112, 1996), an ordered cloned DNA map of the 3.2-Mb chromosome of the hypertoxinogenic...Full Text Available

1998-02-01

426

Isolation, sequence, and expression in Escherichia coli of an unusual thioredoxin gene from the cyanobacterium Anabaena sp. strain PCC 7120.

Recent GWAS studies focused on uncovering novel genetic loci related to AD have revealed associations with variants near CLU, CR1, PICALM and BIN1....Full Text Available

427

Investigation of genomic instability by assay of DNA fingerprint from the offspring of male mice exposed to chronic low-level #gamma#-radiation

Two sequences with homology to a thioredoxin oligonucleotide probe were detected by Southern blot analysis of Anabaena sp. strain PCC 7120 genomic DNA. One of the sequences was shown to code for a protein...Full Text Available

1989-01-01

428

Intragenic rearrangements of a mycoreovirus induced by the multifunctional protein p29 encoded by the prototypic hypovirus CHV1-EP713

By polymerase chain reaction with arbitrary primer (AP-PCR), the possibility of transmission of genome instability to somatic cells of the offspring (F_1 generation) from male parents of mice exposed to chronic low-dose #gamma#-radiation was studied. Male mice 15 days after exposure to 10-50 cGy were mated with unirradiated females. Biopsies were taken from tale tips of two month-old mice progeny for DNA separation. Primer in the AP-PCR was 20-mer oligonucleotide flanking the micro-satellite locus Atplb2 on chromosome 11 of the mouse. Comparative analysis of individual fingerprints of AP-PCR products on DNA-templates from the offspring of irradiated and unirradiated male mice revealed an increased variability of micro-satellite-associated sequences in the genome of the offspring of males exposed to 25 and 50 cGy. DNA-fingerprints of the offspring of male mice exposed to chronic irradiation doses 10 and 25 cGy. 15 days before fertilization (at ...

2000-11-20

429

Human thrombomodulin gene is intron depleted: nucleic acid sequences of the cDNA and gene predict protein structure and suggest sites of regulatory control.

Mycoreovirus 1 (MyRV1), a member of the Reoviridae family possessing a genome consisting of 11 dsRNA segments (S1–S11), and the prototype hypovirus (CHV1-EP713)...Full Text Available

2008-12-01

430

Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing

We have isolated a human thrombomodulin cDNA, and a human genomic clone containing the putative promoter domain, as well as the translated and untranslated regions of the endothelial cell receptor....Full Text Available

1987-09-01

431

Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation

BackgroundThe beta-defensin gene cluster (DEFB) at chromosome 8p23.1 is one of the most copy number (CN) variable regions of the human genome. Whereas individual DEFB CNs have been...Full Text Available

432

Genomic sequence for human prointerleukin 1 beta: possible evolution from a reverse transcribed prointerleukin 1 alpha gene.

BackgroundEstrogen receptors alpha (ERα) and beta (ERβ) are transcription factors (TFs) that mediate estrogen signaling and define the hormone-responsive phenotype...Full Text Available

433

Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.)

We have isolated the human prointerleukin 1 (proIL-1) beta gene from leukocyte and fetal liver libraries. The nucleotide sequence and its gene organization reveals that the proIL-1 beta gene is composed...Full Text Available

1986-10-24

434

Genome analysis of F. nucleatum sub spp vincentii and its comparison with the genome of F. nucleatum ATCC 25586.

BackgroundCotton fiber development undergoes rapid and dynamic changes in a single cell type, from fiber initiation, elongation, primary and secondary wall biosynthesis, to fiber...Full Text Available

2009-01-01

435

Genome Sequence of a Lancefield Group C Streptococcus zooepidemicus Strain Causing Epidemic Nephritis: New Information about an Old Disease

We present the draft genome sequence and its analysis for Fusobacterium nucleatum sub spp. vincentii (FNV), and compare that genome with F. nucleatum ATCC 25586 (FN). A total of 441 FNV open reading frames (ORFs) with no orthologs in FN have been identified. Of these, 118 ORFs have no known function and are unique to FNV, whereas 323 ORFs have functional orthologs in other organisms. In addition to the excretion of butyrate, H2S and ammonia-like FN, FNV has the additional capability to excrete lactate and aminobutyrate. Unlike FN, FNV is likely to incorporate galactopyranose, galacturonate, and sialic acid into its O-antigen. It appears to transport ferrous iron by an anaerobic ferrous transporter. Genes for eukaryotic type serine/threonine kinase and phosphatase, transpeptidase E-transglycosylase Pbp1A are found in FNV but not in FN. Unique ABC transporters, cryptic phages, and three types of restriction-modification systems have been ...

2003-06-01

436

Explore - The Lab - Australian Broadcasting Corporation's Gateway to Science

Outbreaks of disease attributable to human error or natural causes can provide unique opportunities to gain new information about host-pathogen interactions and new leads for pathogenesis research....Full Text Available

437

Wastenet

...Explore - The Lab - Australian Broadcasting Corporation's Gateway to Science Radio TV Shop News Sport Local Children Science Environment more Topics help Science Home News in Science Features Explore TV & Radio Dr Karl Play Podcasts DNA - The discovery of the double helix structure of DNA completely changed biology and opened up the new field of genetics. The 'backbone of life' has given us the human genome, stem cell research, ...

438

Evolution of a cluster of innate immune genes (?-defensins) along the ancestral lines of chicken and zebra finch

Environmentally-Induced Malignancies: An In Vivo Model to Evaluate the Health Impact of Chemicals in Mixed Waste

BackgroundAvian β-defensins (AvBDs) represent a group of innate immune genes with broad antimicrobial activity. Within the chicken genome, previous work identified 14 AvBDs...Full Text Available

439

Dramatic Effects of 2-Bromo-5,6-Dichloro-1-?-d-Ribofuranosyl Benzimidazole Riboside on the Genome Structure, Packaging, and Egress of Guinea Pig Cytomegalovirus

Occupational and environmental exposure to organic ligands, solvents, fuel hydrocarbons, and polychlorinated biphenyls are linked with increased risk of hematologic malignancies. DOE facilities and waste sites in the U.S. are contaminated with mixtures of potentially hazardous chemicals such as metals, organic ligands, solvents, fuel hydrocarbons, polychlorinated biphenyls and radioactive isotopes. A major goal of this project was to establish linkage between chemical/radiation exposure and induction of genomic damage in target populations with the capability to undergo transformation.

2001-05-04

440

Differential decay of parent-of-origin-specific genomic sharing in cystic fibrosis-affected sib pairs maps a paternally imprinted locus to 7q34

The halogenated benzimidazoles BDCRB (2-bromo-5,6-dichloro-1-β-d-riborfuranosyl benzimidazole riboside) and TCRB (2,5,6-trichloro-1-β-d-riborfuranosyl benzimidazole...Full Text Available

2004-02-01

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

441

Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels

Cystic fibrosis (CF) is a monogenic disease characterized by a high variability of disease severity and outcome that points to the role of environmental factors and modulating genes that shape the course...Full Text Available

2010-05-01

442

DNA rearrangements from #gamma#-irradiated normal human fibroblasts preferentially occur in transcribed regions of the genome

Genome sequences are essential tools for comparative and mutational analyses. Here we present the short read sequence of mouse chromosome 17 from the Mus musculus domesticus derived...Full Text Available

2009-01-01

443

Computational identification of developmental enhancers:conservation and function of transcription factor binding-site clustersin drosophila melanogaster and drosophila psedoobscura

Full text: DNA rearrangement events leading to chromosomal aberrations are central to ionizing radiation-induced cell death. Although DNA double-strand breaks are probably the lesion that initiates formation of chromosomal aberrations, little is understood about the molecular mechanisms that generate and modulate DNA rearrangement. Examination of the sequences that flank sites of DNA rearrangement may provide information regarding the processes and enzymes involved in rearrangement events. Accordingly, we developed a method using inverse PCR that allows the detection and sequencing of putative radiation-induced DNA rearrangements in defined regions of the human genome. The method can detect single copies of a rearrangement event that has occurred in a particular region of the genome and, therefore, DNA rearrangement detection does not require survival and continued multiplication of the affected cell. Ionizing radiation-induced DNA ...

2003-08-17

444

Comparative transcriptional pathway bioinformatic analysis of dietary restriction, Sir2, p53 and resveratrol life span extension in Drosophila

Background The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. Results We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene, and assayed embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the ...

2004-08-06

445

A multiple comparison approach using whole genome transcriptional arrays was used to identify genes and pathways involved in calorie restriction/dietary restriction (DR) life span extension in Drosophila....Full Text Available

2011-03-15

446

Biochemical and Structural Characterization of the Secreted Chorismate Mutase (Rv1885c) from Mycobacterium tuberculosis H₃₇R_v: an *AroQ Enzyme Not Regulated by the Aromatic Amino Acids

The state of chromatin during the cell cycle was examined using synchronized cultures of CHO hamster cells. Results support Mazia's dynamic chromosome cycle model and indicate that DNA-interactive chemotherapeutic agents elicit different types of kinetic responses in treated cells, suggesting a degree of specificity of interaction between various alkylating and intercalating agents and the genome. Effects of sarkosyl crystals, heparin, and chemotherapeutic agents, neocarzinostatin and adriamycin, on chromation are discussed. (HLW)

1976-01-01

447

Analysis of the transcript encoding the latent Epstein-Barr virus nuclear antigen I: a potentially polycistronic message generated by long-range splicing of several exons.

The gene Rv1885c from the genome of Mycobacterium tuberculosis H₃₇R_v encodes a monofunctional and secreted chorismate mutase (*MtCM) with a 33-amino-acid...Full Text Available

2006-12-01

448

Analysis of the 10q11 Cancer Risk Locus Implicates MSMB and NCOA4 in Human Prostate Tumorigenesis

The Epstein-Barr virus nuclear antigen (EBNA I) present in latently infected cells is encoded in a 2-kilobase exon contained in the BamHI K viral genomic fragment. This exon is, however, found within...Full Text Available

1985-12-01

449

A Nonparametric Mean-Variance Smoothing Method to Assess Arabidopsis Cold Stress Transcriptional Regulator CBF2 Overexpression Microarray Data

Genome-wide association studies (GWAS) have established a variant, rs10993994, on chromosome 10q11 as being associated with prostate cancer risk. Since the variant is located outside of a protein-coding...Full Text Available

2010-11-01

450

Role-based access control

Microarray is a powerful tool for genome-wide gene expression analysis. In microarray expression data, often mean and variance have certain relationships. We present a non-parametric mean-variance smoothing...Full Text Available

451

Studies on the biosorption of uranium by a thermotolerant, ethanol-producing strain of Kluyveromyces marxianus

Role-based access control

2007-01-01

452

Potential anti fungal agents. Synthesis and activity of 2-alkylthiopyridine-4-carbothioamides

The ability of residual biomass from the thermotolerant ethanol-producing yeast strain Kluyveromyces marxianus IMB3 to function as a biosorbent for uranium has been examined. It was found that the biomass had an observed maximum biosorption capacity of 120 mg U/g dry weight of biomass. The calculated value for the biosorption maximum, obtained by fitting the data to the Langmuir model was found to be 130 mg U/g dry weight biomass. Maximum biosorption capacities were examined at a number of temperatures and both the observed and calculated values obtained for those capacities increased with increasing temperature. Decreasing the pH of the biosorbate solution resulted in a decrease in uptake capacity. When biosorption reactions were carried out using sea-water as the diluent it was found that the maximum biosorption capacity of the biomass increased significantly. Using transmission electron microscopy, uranium crystals were shown to be concentrated on the outer ...

1997-06-01

453

NADP Regulates the Yeast GAL Induction System

A series of 2-alkylthiopyrine-4-carbothioamides were synthesized, and their anti-fungal potency was tested. The chemical structures were proved by infrared spectroscopy (IR) and {sup 1}H nuclear magnetic resonance ({sup 1}H-NMR) data and by elemental analysis. The minimal inhibitory concentration (MIC) and minimal fungicidal concentration (MFC) assessment were used for the estimation of potential activity in vitro. The study comprising 21 clinical isolates of fungi showed that two compounds exhibited fair inhibitory activity against some yeasts and dermatophytes. Selective fungistatic activity against non-dermatophytes (MIC = 3.12-25.0 {mu}g/mL) was found also in another compound. None of the above compounds showed inhibitory activity against non-dermatophyte filamentous fungi. Microbiological activity of 2-alkylthiopyridine-4-carbothioamides appears to be mainly related to hydrophobicity of alkyl in position 2. (authors). 10 refs., 8 tabs.

1996-05-01

454

Molecular studies of the uncoupling protein

Transcriptional regulation of the galactose-metabolizing genes in Saccharomyces cerevisiae depends on three core proteins: Gal4p, the transcriptional activator that binds to upstream activating DNA sequences (UASGAL); Gal80p, a repressor that binds to the carboxyl terminus of Gal4p and inhibits transcription; and Gal3p, a cytoplasmic transducer that, upon binding galactose and adenosine 5'-triphosphate, relieves Gal80p repression. The current model of induction relies on Gal3p sequestering Gal80p in the cytoplasm. However, the rapid induction of this system implies that there is a missing factor. Our structure of Gal80p in complex with a peptide from the carboxyl-terminal activation domain of Gal4p reveals the existence of a dinucleotide that mediates the interaction between the two. Biochemical and in vivo experiments suggests that nicotinamide adenine dinucleotide phosphate (NADP) plays a key role in the initial induction event.

2008-01-01

455

Evaluation of heavy-metal ion toxicity in fish cells using a combined stress protein and cytotoxicity assay

The uncoupling protein (UCP) is a proton/anion transporter found in the inner mitochondrial membrane of brown adipocyte. Although UCP has nor been detected in mitochondria from any other tissue, it shares structural and catalytic properties with several other mitochondrial carrier proteins. Although UCP was discovered only recently it is one of the most extensively studied mitochondrial carrier proteins.More recently, the mouse, rat, and human genes encoding for UCP have been isolated and sequenced. The availability of these various tools has led to several significant observations. UCP gene expression is strongly controlled at the level of transcription by signals that are activated after the stimulation of brown adipocytes by norepinephrine. The comparison of UCP gene with the genes encoding the adenine nucleotide translocator revealed the existence of structural and evolutionary homologies. Moreover, in humans the UCP gene and one form of adenine nucleotide translocator gene are ...

1991-06-01

456

Effects of paraquat on Escherichia coli: Differences between B and K-12 strains

All organisms, from bacteria and yeast to humans, respond to physical and chemical stressors by increasing the synthesis of a small group of cellular stress proteins.'' The authors have developed a simple in vitro system for quickly screening environmentally relevant stressors to detect stress-induced proteins that are good candidates for biomarkers. Polyacrylamide gel electrophoresis was used to detect stressor-induced, concentration-dependent changes in cellular stress protein levels in two fish cell culture systems, whereas simultaneous in vitro neutral red uptake cytotoxicity assays measured the stressors effect on cellular physiology. There was a direct concentration-dependent relationship between sublethal cytotoxic effects and the increases in stress protein levels. Increases of 50 to 200% were detected in stress proteins from desert topminnow, Poeciliopsis lucida, hepatoma-derived cell cultures exposed to cadmium or copper. Three proteins ...

1994-08-01

457

Biosorption of Ni (II) by Schizosaccharomyces pombe: kinetic and thermodynamic studies

Escherichia coli B and K-12 are equally susceptible to the bacteriostatic effects of aerobic paraquat, but they differed strikingly when the lethality of paraquat was evaluated. E. coli B suffered an apparent loss of viability when briefly exposed to paraquat, whereas E. coli K-12 did not. This difference depended on the ability of the B-strain, but not the K-12 strain, to retain internalized paraquat; the B strain was killed on aerobic tryptic soy-yeast extract plates during the incubation which preceded the counting of colonies. This difference in retention of paraquat between strains was demonstrated by delayed loss of viability, by growth inhibition, and by cyanide-resistant respiration after brief exposure to paraquat, washing, and testing in fresh medium. This difference was also shown by using ({sup 14}C)paraquat. This previously unrecognized difference between E. coli B and K-12 has been the cause of apparently contradictory reports and should lead to some ...

1990-02-01

458

British Library Electronic Table of Contents (United Kingdom)

The potential of the dried yeast, wild-type Schizosaccharomyces pombe, to remove Ni(II) ion was investigated in batch mode under varying experimental conditions including pH, temperature, initial metal ion concentration and biosorbent dose. Optimum pH for biosorption was determined as 5.0. The highest equilibrium uptake of Ni(II) on S. pombe, q e, was obtained at 25??C as 33.8?mg?g?1. It decreased with increasing temperature within a range of 25?50??C denoting an exothermic behaviour. Increasing initial Ni(II) concentration up to 400?mg?L?1 also elevated equilibrium uptake. No more adsorption took place beyond 400?mg?L?1. Equilibrium data fitted better to Langmuir model rather than Freundlich model. Sips, Redlich?Peterson, and Kahn isotherm equations modelled the investigated system with a...

2011-01-01

459

A procedure for batch separation of sup 14 C-hexose from sup 14 C-sucrose

Molecular cloning, genomic organization, and chromosomal localization of the human pancreatitis-associated protein (PAP) gene

This presentation describes a method for separating {sup 14}C-hexose from {sup 14}C-sucrose in extracts of plant tissue. Portions of ethanol extracts are treated with activated charcoal in microcentrifuge tubes. Aliquots are removed, ethanol evaporated and replaced with reaction mixture that phosphorylates hexose (HEPPS, K{sub 2}HPO{sub 4}, Mg(C{sub 2}H{sub 3}O{sub 2}){sub 2}, ovalbumen, Na{sub 2}ATP, yeast hexokinase). After a time course, the hexokinase reaction is stopped (slowed considerably) to minimize effects of contamination enzyme activities. The stopping agent used is lyxose, a nonphosphorylable analogue of glucose. The strong anionic charge of phosphate introduced through the hexokinase action results in binding (> 95%) of hexose-phosphate to anion-exchange resin. Sucrose remains unbound (> 95%) in solution. This batch ion-exchange is performed in microcentrifuge tubes to allow many samples to be processed simultaneously. Recovery of radiolabel in ...

1991-05-01

460

Molecular cloning of the human homeobox gene goosecoid (GSC) and mapping of the gene to human chromosome 14q32. 1

Pancreatitis-associated protein (PAP) is a secretory pancreatic protein present in small amounts in normal pancreas and overexpressed during the acute phase of pancreatitis. In this paper, the authors describe the cloning, characterization, and chromosomal mapping of the human PAP gene. The gene spans 2748 bp and contains six exons interrupted by five introns. The gene has a typical promoter containing the sequences TATAAA and CCAAT 28 and 52 bp upstream of the cap site, respectively. They found striking similarities in genomic organization as well as in the promoter sequences between the human and rat PAP genes. The human PAP gene was mapped to chromosome 2p12 using rodent-human hybrid cells and in situ chromosomal hybridization. This localization coincides with that of the reg/lithostathine gene, which encodes a pancreatic secretory protein structurally related to PAP, suggesting that both genes derived from the same ancestral gene by duplication. 35 refs., 4 ...

1994-01-01

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

461

Human tissue factor pathway inhibitor (TFPI) gene: Complete genomic structure and localization on the genetic map of chromosome 2q

Goosecoid is a homeobox gene first isolated from a Xenopus dorsal lip cDNA library. Homologous genes have been isolated from mouse, zebrafish, and chick. In all species examined, the gene is expressed and plays an important role during the process of gastrulation in early embryonic development. The authors report here the cloning of the human goosecoid (GSC) from a genomic library and the sequence of its encoded protein. The genomic organization and protein sequence of the human gene are highly conserved with respect to those of its Xenopus and mouse counterparts: all three genes consist of three exons, with conserved exon-intron boundaries. The sequence of the homeo-domain is 100% conserved in most vertebrates. Using somatic cell hybrid and chromosomal in situ hybridization, the gene was mapped to chromosome 14q32.1. 30 refs., 3 figs., 2 tabs.

1994-05-15

462

Genomic cloning and chromosomal localization of HRY, the human homolog to the Drosophila segmentation gene, hairy

Tissue factor pathway inhibitor (TFPI), a protease inhibitor that circulates in association with plasma lipoproteins (VLDL, LDL and HDL), helps to regulate the extrinsic blood coagulation cascade. The authors have cloned a 125-kb genomic region containing the entire human TFPI gene on six overlapping cosmids and prepared a restriction map of this contig to clarify gene structure. More than half (45 kb) of the 85-kb gene is occupied with 5[prime] noncoding elements: coding begins at exon 3. A HindIII RFLP identified with one cosmid was genotyped in the CEPH panel of 559 reference families. Linkage analysis using markers on human chromosome 2 located the TFPI gene on 2q, 36 cM proximal to D2S43(pYNZ15) and 13 cM distal to the crystalline [gamma]-polypeptide locus CRYGP1(p5G1). 31 refs., 3 figs., 3 tabs.

1993-08-01

463

Genome lability in radiation-induced transformants of C3H 10T1/2 mouse fibroblasts

The Drosophila hairy gene encodes a basic helix- loop-helix protein that functions in at least two steps during Drosophila development: (1) during embryogenesis, when it partakes in the establishment of segments, and (2) during the larval stage, when it functions negatively in determining the pattern of sensory bristles on the adult fly. In the rat, a structurally homologous gene (RHL) behaves as an immediate-early gene in its response to growth factors and can, like that in Drosophila, suppress neuronal differentiation events. Here, the authors report the genomic cloning of the human hairy gene homolog (HRY). The coding region of the gene is contained within four exons. The predicted amino acid sequence reveals only four amino acid differences between the human and rat genes. Analysis of the DNA sequence 5[prime] to the coding region reveals a putatitve untranslated exon. To increase the value of the HRY gene as a genetic marker and to assess its potential ...

1994-03-01

464

The nucleotide sequence and organization of nuclear 5S rRNA genes in yellow lupine

We have been investigating radiation-induced neoplastic transformants of C3H 10T1/2 mouse fibroblasts for evidence of heritable changes. C3H 10T1/2 cells were treated with 8 Gy X rays. After approximately 8 weeks of culture, type II/III foci were isolated from the monolayer using cloning rings. Cell lines developed from these foci, and clones established from these cell lines, were examined for DNA content. The isolated focus-derived populations and derived clones often display aneuploidy and/or polyploidization. In one instance a clone (derived from a single cell) displayed multiple polyploidies. During passage the ploidy of many of the anomalous populations gradually reverted to the ploidy of the non-neoplastically transformed state. The morphological features associated with the neoplastic transformation event were nevertheless retained. The results demonstrate that exposure to radiation can induce, in association with morphological neoplastic transformation, a heritable, ...

1994-04-01

465

The effect of mitochondrial dysfunction on cytosolic nucleotide metabolism

We have isolated a genomic clone containing 'Lupinus luteus' 5S ribosomal RNA genes by screening with 5S rDNA probe clones that were hybridized previously with the initiator methionine tRNA preparation (contaminated) with traces of rRNA or its degradation products). The clone isolated contains ten repeat units of 342 bp with 119 bp fragment showing 100% homology to the 5S rRNA from yellow lupine. Sequence analysis indicates only point heterogeneities among the flanking regions of the genes. (author). 6 refs, 3 figs.

1993-01-01

466

DEFF Research Database (Denmark)

Several enzymes of the metabolic pathways responsible for metabolism of cytosolic ribonucleotides and deoxyribonucleotides are located in mitochondria. Studies described in this paper suggest dysfunction of the mitochondria to affect these metabolic pathways and limit the available levels of cytosolic ribonucleotides and deoxyribonucleotides, which in turn can result in aberrant RNA and DNA synthesis. Mitochondrial dysfunction has been linked to genomic instability, and it is possible that the limiting effect of mitochondrial dysfunction on the levels of nucleotides and resulting aberrant RNA and DNA synthesis in part can be responsible for this link. This paper summarizes the parts of the metabolic pathways responsible for nucleotide metabolism that can be affected by mitochondrial dysfunction.

2010-01-01

467

RFLP for a DNA clone which maps to 19q13. 2-19qter (D19S63)

Mitochondrial DNA variants in Drosophila melanogaster are expressed at the level of the organismal phenotype.

pD10 is a 0.85 kb fragment with BamHI ends cloned in pSP64. It was sub-cloned from {lambda}D10 which was isolated from a genomic library constructed in {lambda}EMBL3 from a rodent human somatic cell hybrid. The probe was localized to 19q13.2-19qter on a panel of rodent human somatic cell hybrids. Co-dominant segregation was shown in 32 families of 280 individuals.

1990-02-25

468

Characterization of eight microsatellite markers in the white sea bream, Diplodus sargus (Teleostei, Sparidae)

A plethora of experimental studies use mtDNA as a marker of demographic processes without questioning the possibility that selection may bias their interpretations. We studied four lines of Drosophila melanogaster that have a standardized nuclear DNA but variable mtDNA. We completed the sequencing of the mitochondrial genomes (excluding the A+T rich region) and compiled the differences. We then assayed male influence on oviposition, starvation resistance, lipid proportion and physical activity. We discuss these results in terms of the known differences between the lines and conclude that naturally occurring mtDNA variants in D. melanogaster are expressed at the level of the organismal phenotype. PMID:21757031

2011-07-05

469

British Library Electronic Table of Contents (United Kingdom)

Abstract The white sea bream, Diplodus sargus (Teleostei, Sparidae), is a species with a high commercial importance in Mediterranean aquaculture. There is currently little information available about the genetic characteristics of cultured populations. In this survey, we have developed eight polymorphic microsatellites for the white sea bream using an enriched genome library protocol. All of them were polymorphic in the 67 individuals tested, 32 of which were wild specimens, and 35 were individuals from a captive F1 broodstock. These markers can potentially be useful tools for use in population genetic studies.

2008-01-01

470

An improved colony PCR procedure for genetic screening of Chlorella and related microalgae.

Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments.

A colony PCR technique was applied for both genomic and chloroplast DNA in the green microalgae Chlorella. Of five different lysis buffers, Chelex-100 was superior for DNA extraction, PCR and DNA storage. It also was insensitive to variations in cell density. The conditions established for an improved PCR formulation are applicable for screening of genetically-engineered transformants as well as bioprospecting of natural microalgal isolates. Besides multiple Chlorella species, we also demonstrate the efficacy of Chelex-100 for colony PCR with a number of other microalgal strains, including Chlamydomonas reinhardtii, Dunaliella salina, Nannochloropsis sp., Coccomyxa sp., and Thalassiosira pseudonana. PMID:21431847

2011-03-24

471

Transcriptional regulation in Drosophila: the post-genome challenge.

The emergence of bacterial antibiotic resistance is a growing problem, yet the variables that influence the rate of emergence of resistance are not well understood. In a microfluidic device designed to mimic naturally occurring bacterial niches, resistance of Escherichia coli to the antibiotic ciprofloxacin developed within 10 hours. Resistance emerged with as few as 100 bacteria in the initial inoculation. Whole-genome sequencing of the resistant organisms revealed that four functional single-nucleotide polymorphisms attained fixation. Knowledge about the rapid emergence of antibiotic resistance in the heterogeneous conditions within the mammalian body may be helpful in understanding the emergence of drug resistance during cancer chemotherapy. PMID:21940899

2011-09-23

472

Soybean Based Diets and CVD Risk Factors

Drosophila melanogaster has long been at the forefront of studies of transcriptional regulation in animals. Many fundamental ideas--such as cis control elements that act over long distances, the regulation of development by hierarchical cascades of transcription factors, dosage compensation, and position effect variegation--originated from studies of the fruit fly. The recent completion of the euchromatic DNA sequence of Drosophila is another breakthrough. The sequence data highlight important unanswered questions. For example, only one-fifth of the 124 Mb of Drosophila euchromatic DNA codes for protein. The function of the remaining 100 Mb of mostly unique DNA is largely unknown. Some proportion of this non-reading frame DNA must encode the functional recognition sites targeted by the approximately 700 sequence-specific DNA binding proteins that regulate transcription in Drosophila, but what proportion? Most or very little? Promoter sequences by definition contain all of the cis ...

2001-03-01

473

Network Security Prevention Model Based-Immune

Hypercholesterolemia

2005-09-15

474

A Control System for Traffic Light Based on GPRS

Not Available

2009-10-01

475

Coupling of Realistic Rate Estimates with Genomics for Assessing Contaminant Attenuation and Long-Term Plume Containment - Task 4: Modeling - Final Report

Not Available

2011-08-01

476

Tissue structure, nuclear organization and gene expression in normal and malignant breast

Trichloroethene (TCE), a common groundwater contaminant, can be degraded under certain conditions by microorganisms that occur naturally in the subsurface. TCE can be degraded under anaerobic conditions to less chlorinated compounds and ultimately into the non-chlorinated, non-hazardous end product, ethene, via anaerobic reductive dechlorination (ARD). ARD is widely recognized as a TCE degradation mechanism, and occurs in active groundwater remediation and can occur during monitored natural attenuation (MNA). MNA relies on natural processes, such as dispersion and degradation, to reduce contaminant concentrations to acceptable levels without active human intervention other than monitoring. TCE can also be biodegraded under aerobic conditions via cometabolism, in which microbial enzymes produced for other purposes fortuitously also react with TCE. In cometabolism, TCE is oxidized directly to non-hazardous products. Cometabolism as a TCE-degrading process under aerobic conditions is less ...

2005-10-31

477

Computer based training cost-benefit model

Because every cell within the body has the same genetic information, a significant problem in biology is to understand how cells within a tissue express genes selectively. A sophisticated network of physical and biochemical signals converge in a highly orchestrated manner to bring about the exquisite regulation that governs gene expression in diverse tissues. Thus, the ultimate decision of a cell to proliferate, express tissue-specific genes, or apoptose must be a coordinated response to its adhesive, growth factor, and hormonal milieu. The unifying hypothesis examined in this overview is that the unit of function in higher organisms is neither the genome nor the cell alone but the complex, three-dimensional tissue. This is because there are bidirectional connections between the components of the cellular microenvironment (growth factors, hormones, and extracellular matrix) and the nucl2048 These connections are made via membrane-bound receptors and transmitted to ...

2000-01-27

478

Translational bioinformatics and healthcare informatics: computational and ethical challenges.

The costs of establishing a computer-based training program for FFTF reactor operators are analyzed.

1984-01-01

479

The SOS-LUX-TOXICITY-Test on the International Space Station

Exponentially growing biological and bioinformatics data sets present a challenge and an opportunity for researchers to contribute to the understanding of the genetic basis of phenotypes. Due to breakthroughs in microarray technology, it is possible to simultaneously monitor the expressions of thousands of genes, and it is imperative that researchers have access to the clinical data to understand the genetics and proteomics of the diseased tissue. This technology could be a landmark in personalized medicine, which will provide storage for clinical and genetic data in electronic health records (EHRs). In this paper, we explore the computational and ethical challenges that emanate from the intersection of bioinformatics and healthcare informatics research. We describe the current situation of the EHR and its capabilities to store clinical and genetic data and then discuss the Genetic Information Nondiscrimination Act. Finally, we posit that the synergy obtained from the collaborative ...

2009-09-16

480

British Library Electronic Table of Contents (United Kingdom)

For the safety of astronauts and to ensure the stability and integrity of the genome of microorganisms and plants used in bioregenerative life support systems, it is important to improve our knowledge of the combined action of (space) radiation and microgravity. The SOS-LUX-TOXICITY test, as part of the TRIPLE-LUX project (accepted for flight at Biolab in Columbus on the International Space Station, (ISS)), will provide an estimation of the health risk resulting from exposure of astronauts to the radiation environment of space in microgravity. The project will: (i) increase our knowledge of biological/health threatening action of space radiation and enzymatic DNA repair; (ii) uncover cellular mechanisms of synergistic interaction of microgravity and space radiation; (iii) provide specified...

2006-01-01

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

481

The Computation Directorate at Lawrence Livermore National Laboratory

Sequences of versatile, broad-host-range vectors of the RK2 family.

The Computation Directorate at Lawrence Livermore National Laboratory has four major areas of work: (1) Programmatic Support -- Programs are areas which receive funding to develop solutions to problems or advance basic science in their areas (Stockpile Stewardship, Homeland Security, the Human Genome project). Computer scientists are 'matrixed' to these programs to provide computer science support. (2) Livermore Computer Center (LCC) -- Development, support and advanced planning for the large, massively parallel computers, networks and storage facilities used throughout the laboratory. (3) Research -- Computer scientists research advanced solutions for programmatic work and for external contracts and research new HPC hardware solutions. (4) Infrastructure -- Support for thousands of desktop computers and numerous LANs, labwide unclassified networks, computer security, computer-use policy.

2006-09-07

482

Response of the panicles exserted from the caulis and from various effective tillers at four stages of panicle development to neck blast in rice

Plasmid pRK404-a smaller derivative of RK2-is a tetracycline-resistant broad-host-range vector that carries a multiple cloning site and the lacZ(alpha) peptide that enables blue/white selection for cloned inserts in Escherichia coli. We present herein the complete and annotated sequence of pRK404 and three related vectors-pRK437, pRK442, and pRK442(H). These derivatives have proven to be valuable tools for genetic manipulation in Gram-negative bacteria. The knowledge of their complete sequences will facilitate efficient future engineering of them and will enhance their general applicability to the design of genetic systems for use in organisms for which new genomic sequence data are becoming available.

2003-07-01

483

British Library Electronic Table of Contents (United Kingdom)

The rice japonica variety Nipponbare and the indica variety 93-11, the genomic DNA sequences of which are known, were used to analyze the response of the panicles exserted from the caulis and from various effective tillers at four stages of panicle development to neck blast. Disease incidence in the necks (DIN), disease incidence in the rachis nodes (DIRN), lesion length in the necks (LLN), and number of conidia in the necks (NCN) were measured after inoculating the panicles in vitro of two rice varieties with Magnaporthe oryzae. Both Nipponbare and 93-11 were susceptible, DIN and DIRN of all panicles being 100% in both the varieties except DIRN in several panicles at stage 1 (the panicle fully exserted) in Nipponbare. Both LLN and NCN of panicles decreased as the panicles continued to dev...

2011-01-01

484

Metabolomic Study on the Halophyte Suaeda salsa in the Yellow River Delta

British Library Electronic Table of Contents (United Kingdom)

Abstract Plant metabolomics has been well established and applied across multiple fields including medicine, biotechnology, and environmental sciences in the post-genomic era. The Chenopodiaceae C3 halophyte Suaeda salsa is the most important plant species in the vegetation of saline soil and even intertidal zone in the Yellow River Delta, which is economically consumed as food, widely used as a bioindicator of environmental stresses (salinity, drought, and pollution) and typically applied for the phyto-remediation of degraded wetland. However, no global studies have been focused on the metabolic profile of this halophyte which is widely applied in environment related research areas. In metabolomics, the first crucial step is the preparation of plant samples. In this work, several strategi...

2011-01-01

485

Mapping Equivalence for Symbolic Sequences: Theory and Applications

Isolation and characterization of microsatellite markers in Acca sellowiana (Berg) Burret.

Processing of symbolic sequences represented by mapping of symbolic data into numerical signals is commonly used in various applications. It is a particularly popular approach in genomic and proteomic sequence analysis. Numerous mappings of symbolic sequences have been proposed for various applications. It is unclear however whether the processing of symbolic data provides an artifact of the numerical mapping or is an inherent property of the symbolic data. This issue has been long ignored in the engineering and scientific literature. It is possible that many of the results obtained in symbolic signal processing could be a byproduct of the mapping and might not shed any light on the underlying properties embedded in the data. Moreover, in many applications, conflicting conclusions may arise due to the choice of the mapping used for numerical representation of symbolic data. In this paper, we present a novel framework for the analysis of the equivalence of the ...

2009-01-01

486

Involvement of the Tpl-2/cot oncogene in MMTV tumorigenesis.

Acca sellowiana has commercial potential because of the quality and the unique flavor of its fruit. Conservation of natural populations and management of breeding programmes would benefit from the availability of molecular markers that could be used to characterize levels and distribution of genetic variability. Thus, 13 microsatellite markers were developed from an enriched genomic library of A. sellowiana. They were characterized using 40 samples. The expected and observed heterozygosities ranged from 0.513 to 0.913 and from 0.200 to 0.889, respectively. These are the first microsatellite loci characterized from A. sellowiana that will contribute to improve researches on the genetic conservation, characterization and breeding. PMID:21586063

2008-07-08

487

Immortalization of human foreskin keratinocytes by various human papillomavirus DNAs corresponds to their association with cervical carcinoma

We report for the first time a relationship between the Tpl-2/cot oncogene and Mouse Mammary Tumor Virus (MMTV) associated transformation of mammary gland cells. A sub-genomic library generated from a primary mammary gland tumor yielded a novel MMTV integration site which disrupted the Tpl-2/cot proto-oncogene between exons 7 and 8. Comparison of a cell line derived from normal mammary gland (comma-D) and a cell line established from an MMTV induced mammary tumor (GR) demonstrated similar rearrangements within Tpl-2/cot for the GR cells but not in the comma-D cells. These rearrangements in the cell line were accompanied by an increase in the level of Tpl-2/cot specific mRNA. This data suggests that Tpl-2/cot expression may be important in epithelial cell transformation or tumor progression. PMID:8934549

1996-11-01

488

Identification and characterization of retinoid-active short-chain dehydrogenases/reductases in Drosophila melanogaster

Normal human foreskin keratinocytes cotransfected with the neomycin resistance gene and recombinant human papillomavirus (HPV) DNAs (types 16, 18, 31, and 33) that have a high or moderate association with cervical malignancy acquired immortality and contained integrated and transcriptionally active viral genomes. Only transcripts from the intact E6 and E7 genes were detected in at least one cell line, suggesting that one or both of these genes are responsible for immortalization. Recombinant HPV DNAs with low or no oncogenic potential for cervical cancer (HPV1a, -5, -6b, and -11) induced small G418-resistant colonies that senesced as did the nontransfected cells. These colonies contained only episomal virus DNA; therefore, integration of HPV sequences is important for immortalization of keratinocytes. This study suggests that the virus-encoded immortalization function contributes to the pathogenesis of cervical carcinoma.

1989-01-01

489

British Library Electronic Table of Contents (United Kingdom)

Background In chordates, retinoid metabolism is an important target of short-chain dehydrogenases/reductases (SDRs). It is not known whether SDRs play a role in retinoid metabolism of protostomes, such as Drosophila melanogaster. Methods Drosophila genome was searched for genes encoding proteins with ?50% identity to human retinol dehydrogenase 12 (RDH12). The corresponding proteins were expressed in Sf9 cells and biochemically characterized. Their phylogenetic relationships were analyzed using PHYLIP software. Results A total of six Drosophila SDR genes were identified. Five of these genes are clustered on chromosome 2 and one is located on chromosome X. The deduced proteins are 300 to 406 amino acids long and are associated with microsomal membranes. They recognize all-trans-retinaldehyd...

2009-01-01

490

Human cDNA mapping using fluorescence in situ hybridization

High-throughput proteomics of breast carcinoma cells: a focus on FTICR-MS

Genetic mapping is approached using the techniques of high resolution fluorescence in situ hybridization (FISH). This technology and the results of its application are designed to rapidly generate whole genome as tool box of expressed sequence to speed the identification of human disease genes. The results of this study are intended to dovetail with and to link the results of existing technologies for creating backbone YAC and genetic maps. In the first eight months, this approach generated 60--80% of the expressed sequence map, the remainder expected to be derived through more long-term, labor-intensive, regional chromosomal gene searches or sequencing. The laboratory has made significant progress in the set-up phase, in mapping fetal and adult brain and other cDNAs, in testing a model system for directly linking genetic and physical maps using FISH with small fragments, in setting up a database, and in establishing the validity and throughput of the system.

1993-03-04

491

Growth regulation of Legionella Pneumophila in biofilms and amoebae; Wachstumsregulation von Legionella Pneumophila in Biofilmen und Amoeben

Discovery of better biomarkers for diagnosis, prognosis, and therapy-response prediction is the most critical task of a scientific quest aimed at developing newly designed, tailor-made therapies for patients with cancer. Consequently, a proteome wide analysis, in addition to genomic studies, is an absolute requirement for a complete functional understanding of tumor biology. Ultra-sensitive, high-performance Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) currently holds an important role in fulfilling the demands of biomarker discovery. In this review, we describe the applicability of FTICR MS for breast cancer proteomics, particularly for the analysis of complex protein mixtures obtained from a limited number of cells typically available from clinical specimens.

2008-06-05

492

Genomic survey of prepulse inhibition in mouse chromosome substitution strains

This final report for the Swiss Federal Office of Energy (SFOE) presents the results of studies made on the regulation of the growth of Legionella Pneumophila bacteria in biofilms and amoebae. In a first project, the formation of biofilms by Legionella Pneumophila bacteria was analysed in static and dynamic systems using a complex growth medium. Under static and dynamic clinical and environmental conditions, the adherence of the biofilms on polystyrene tissue was studied. This was also examined under dynamic flow conditions. In a second part of the project, the regulation of growth of Legionella Pneumophila in amoebae was examined in that changes were made to the genome of the bacteria. The importance of the work for the de-activation of Legionella Pneumophila bacteria in biofilms is noted in the conclusions of the report.

2006-07-01

493

British Library Electronic Table of Contents (United Kingdom)

Prepulse inhibition (PPI) is a measure of sensorimotor gating, a pre-attentional inhibitory brain mechanism that filters extraneous stimuli. Prepulse inhibition is correlated with measures of cognition and executive functioning, and is considered an endophenotype of schizophrenia and other psychiatric illnesses in which patients show PPI impairments. As a first step toward identifying genes that regulate PPI, we performed a quantitative trait locus (QTL) screen of PPI phenotypes in a panel of mouse chromosome substitution strains (CSSs). We identified five CSSs with altered PPI compared with the host C57BL/6J strain: CSS-4 exhibited decreased PPI, whereas CSS-10, -11, -16 and -Y exhibited higher PPI compared with C57BL/6J. These data indicate that A/J chromosomes 4, 10, 11, 16 and Y harbor...

2009-01-01

494

Fusion of protoplasts with irradiated micro protoplasts as a tool for radiation hybrid panel in citrus;Fusao de protoplastos com microprotoplastos irradiados como ferramenta para painel hibrido de radiacao em citros

Epigenetic regulation of autosomal gene expression by sex chromosomes

The objective of this work was to combine asymmetric somatic hybridization (donor-recipient fusion or gamma fusion) to microprotoplast-mediated chromosome transfer, as a tool to be used for chromosome mapping in Citrus. Swinglea glutinosa micro protoplasts were irradiated either with 50, 70, 100 or 200 gamma rays and fused to cv. Ruby Red grapefruit or Murcott tangor protoplasts. Cell colonies were successfully formed and AFLP analyses confirmed presence of S. glutinosa in both 'Murcott' tangor and 'Ruby Red' grapefruit genomes. (author)

2009-12-15

495

British Library Electronic Table of Contents (United Kingdom)

Males and females display differences in physiology, behaviour and susceptibility to many diseases. Genome-wide transcription profiling studies have uncovered large-scale sex differences in autosomal gene expression in somatic tissues that are thought to underlie such 'sexual dimorphisms'. Because males and females differ genetically mainly in their sex chromosome complement, most sex differences can be traced back to the X and Y chromosomes. Although sex hormones are usually considered the main architects of sexual dimorphisms, recent studies have demonstrated that sex chromosomes can also induce sex differences in somatic gene expression in the absence of hormonal differences. The recent discovery of epigenetic sex differences that are not hormone-induced brings us closer to understandin...

2011-01-01

496

Effect of Diaporthe RNA virus 1 (DRV1) on growth and pathogenicity of different Diaporthe species

British Library Electronic Table of Contents (United Kingdom)

A 4.1?kbp positive-strand RNA virus known as Diaporthe RNA virus 1 (DRV1) occurs in hypovirulent, non-sporulating isolates of the fungal pathogen Diaporthe perjuncta. A full-length cDNA clone of DRV1 was developed and RNA transcribed from the cDNA clone used to transfect different Diaporthe spp. The transfected species included three D. ambigua isolates and an unidentified Phomopsis asexual state of a Diaporthe sp. Successful transfections were confirmed using RT-PCR. Although the in vitro-transcribed positive sense single-stranded RNA used for transfection included vector sequences at both ends, the genomes of progeny virus from DRV1-transfected isolates were free of the vector sequences. Transfection resulted in morphological changes in these fungal pathogens. However, the presence of DR...

2011-01-01

497

DNA repair: As influenced by age, nutrition, and exposure to toxic substances