aa genome oryza: Topics by WorldWideScience.org

Genetic Stability of Magnaporthe oryzae during Successive Passages through Rice Plants and on Artificial Medium

The effect of different media and pH on the formation of amylase by Aspergillus oryzae EI 212 is described. Depending upon the composition of the medium and growth...Full Text Available

1970-04-01

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Genetic Diversity Assessment of Rarely Cultivated Traditional Indica Rice (Oryza sativa L.) Varieties

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2010-12-01

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A Proteomic Analysis of Leaf Responses to Enhanced Ultraviolet-B Radiation in Two Rice (Oryza sativa L.) Cultivars Differing in UV Sensitivity

Random amplified polymorphic DNA fingerprinting was performed to assess the genetic diversity among rarely cultivated traditional indica rice (Oryza sativa ...Full Text Available

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Gene expression profiles deciphering rice phenotypic variation between Nipponbare (Japonica) and 93-11 (Indica) during oxidative stress.

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Degradation of the corrosion resistance of anodic oxide films through immersion in the anodising electrolyte

Rice is a very important food staple that feeds more than half the world's population. Two major Asian cultivated rice (Oryza sativa L.) subspecies, japonica and indica, show significant phenotypic variation in their stress responses. However, the molecular mechanisms underlying this phenotypic variation are still largely unknown. A common link among different stresses is that they produce an oxidative burst and result in an increase of reactive oxygen species (ROS). In this study, methyl viologen (MV) as a ROS agent was applied to investigate the rice oxidative stress response. We observed that 93-11 (indica) seedlings exhibited leaf senescence with severe lesions under MV treatment compared to Nipponbare (japonica). Whole-genome microarray experiments were conducted, and 1,062 probe sets were identified with gene expression level polymorphisms between the two rice cultivars in addition to differential expression under MV treatment, which were ...

2010-01-08

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Symbiotic regulation of plant growth, development and reproduction

The deterioration of AA2024, AA6061 and AA7475 anodised in an environmentally-compliant tartaric acid/sulphuric acid electrolyte has been examined as a function of the immersion time in the electrolyte after termination of anodising. By transmission electron microscopy and scanning electron microscopy, degradation of the porous oxide film was qualitatively observed on AA2024. Electrochemical impedance spectroscopy revealed that AA2024 and AA7075 were more sensitive to prolonged immersion in the anodising electrolyte compared with AA6061, due to increased barrier layer thinning rates and increased susceptibility to localized corrosion. Salt spray tests confirmed the previous, indicating decay of anticorrosion performance for AA2024 and AA7075.

2010-07-15

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Comparison of susceptibility to pitting corrosion of AA2024-T4, AA7075-T651 and AA7475-T761 aluminium alloys in neutral chloride solutions using electrochemical noise analysis

The growth and development of rice (Oryzae sativa) seedlings was shown to be regulated epigenetically by a fungal endophyte. In contrast to un-inoculated (nonsymbiotic) plants, endophyte...Full Text Available

2009-03-01

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Structural Characterization and Expression Analysis of the SERK/SERL Gene Family in Rice (Oryza sativa)

The susceptibility to pitting corrosion of AA2024-T4, AA7075-T651 and AA7475-T761 aluminium alloys was investigated in aqueous neutral chloride solution for the purpose of comparison using electrochemical noise measurement. The experimentally measured electrochemical noises were analysed based upon the combined stochastic theory and shot-noise theory using the Weibull distribution function. From the occurrence of two linear regions on one Weibull probability plot, it was suggested that there existed two stochastic processes of uniform corrosion and pitting corrosion; pitting corrosion was distinguished from uniform corrosion in terms of the frequency of events in the stochastic analysis. Accordingly, the present analysis method allowed us to investigate pitting corrosion independently. The susceptibility to pitting corrosion was appropriately evaluated by determining pit embryo formation rate in the stochastic analysis. The ...

2008-01-15

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Levels and Patterns of Nucleotide Variation in Domestication QTL Regions on Rice Chromosome 3 Suggest Lineage-Specific Selection

Somatic embryogenesis (SE) is the developmental restructuring of somatic cells towards the embryogenic pathway and forms the basis of cellular totipotency in angiosperms. With the availability of full-length...Full Text Available

2009-01-01

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Development of a novel data mining tool to find cis-elements in rice gene promoter regions

Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass...Full Text Available

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Chromosome location of Oryza sativa recombination linkage groups.

BackgroundInformation on more than 35 000 full-length Oryza sativa cDNAs, together with associated microarray gene expression data collected under various treatment...Full Text Available

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Anti-albumin antibodies in chronic liver diseases: diagnostic significance of these antibodies in patients with conventional or immunosuppressive therapy.

In situ hybridization, a powerful tool for the molecular cytogeneticist, can be used to physically map repetitive, low-copy, and unique DNA sequences in plant chromosomes. With the availability of a...Full Text Available

1992-09-15

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The two categories of anti-albumin antibodies (AAA), namely precipitins (AA-P) and agglutinins (AA-Aggl), were investigated in 260 patients with morphologically diagnosed chronic liver diseases (CLD)....Full Text Available

1981-02-01

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Texture and Plastic Strain Ratio Changes with the Number of Passes of Asymmetric Rolling in AA1050 Al Alloy Sheet

... c][]_Y\\[YZ\\Wfr[^^^a^^`cgahcdfi jglfhplgecfgh}pjeucjefcd`]_a`a^\\p]m^aa_`b

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RXTE Catches Morphing Magnetar

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2010-12-01

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Glutamate and the aggression neural circuit in adolescent anabolic steroid-treated Syrian hamsters (Mesocricetus auratus).

This exciting new development in neutron star evolution was presented at the Winter 2004 AAS Meeting in Atlantia,Georgia. ...

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Structural and operational complexity of the Geobacter sulfurreducens genome

Adolescent exposure to anabolic androgenic steroids (AAS) alters the development and activity of the glutamate neural system in the latero-anterior hypothalamus (LAH) in hamsters (Mesocricetus auratus); that is, an important neural component of the adolescent AAS-induced aggressive response. In this article, we used retrograde tracing to investigate glutamate-specific alterations in the connections between the LAH and several other nuclei implicated in adolescent AAS-induced aggression. Briefly, hamsters were treated with AAS or sesame-oil control during adolescence and then microinjected with retrograde tracer into the medial amygdala (MeA), lateral septum (LS), or bed nucleus of the stria terminalis (BNST). Brains were then processed for vesicular glutamate transporter 2 (VGLUT2) and examined for AAS-induced changes in the number VGLUT2 cells containing retrograde tracer ...

2011-08-22

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Intrapopulation Genome Size Dynamics in Festuca pallens

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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Whole-genome shotgun assembly and comparison of human genome assemblies

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

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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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Genomics - from Neanderthals to high-throughput sequencing

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2007-06-01

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Preservation of beech and spruce wood by allyl alcohol-based copolymers

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

2006-01-01

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Sudden freeze-out vs continuous emission: duality in hydro-kinetic approach to A+A collisions

Allyl alcohol (AA), acrylonitrile (AN), methyl methacrylate (MMA), monomers and monomer mixtures AA+AN, AA+MMA were used to conserve and consolidate Beech and Spruce. After impregnation, copolymerisation and polymerisation were accomplished by gamma irradiation. The fine structure of wood+polymer(copolymer) composites was investigated by Scanning Electron Microscopy (SEM). It was observed that copolymer obtained from AA+MMA monomer mixture showed the optimum compatibility. The compressional strength and Brinell Hardness Numbers determined for untreated and treated wood samples indicated that the mechanical strength of wood+copolymer composites was increased. It was found that the mechanical strength of the wood samples containing the AA+MMA copolymer was higher than the others. In the presence of P(AA/MMA), at highest conversion, the compressive strength ...

1999-06-01

28

RXTE GOF: News Archive 2004 - HEASARC - NASA

The problem of spectra formation in hydrodynamic approach to A+A collisions is discussed. It is analyzed in terms of the two different objects: distribution and emission functions. We show that though the process of particle liberation, described by the emission function, is, usually, continuous in time, the observable spectra can be also expressed by means of the Landau/Cooper-Frye prescription. We argue that such an approximate duality results from some symmetry properties that systems in A+A collisions reach to the end of hydrodynamic evolution and reduction of the collision rate at post hydrodynamic stage

2004-01-01

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On the ideal gas of tachyons

May 18, 2007 ... This exciting new development in neutron star evolution was presented at the Winter 2004 AAS Meeting in Atlanta, Georgia. ...

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Low frequency fluctuations of diverted plasma flow and their relation to EDGE plasma fluctuations in the Uragan-3M torsatron

The properties of the ideal gas of classical (nonquantum) tachyons are considered. Starting from the definition of thermodynamic functions for this system, it may be found that tachyons and bradyons gases are similar. (AA).

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ALOPECIA AREATA IS NOT ASSOCIATED WITH HELICOBACTER PYLORI

2006 p. 43 Ukraine Beletskii, AA Grigor'eva, LI Sorokovoy, EL Chechkin, VV

2006-09-11

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Tracing Cadmium from Culture to Spikelet: Noninvasive Imaging and Quantitative Characterization of Absorption, Transport, and Accumulation of Cadmium in an Intact Rice Plant¹^[W]^[OA]

Background:Alopecia areata (AA) is an immune-mediated form of hair loss that occurs in all ethnic groups, ages, and both sexes. Helicobacter pylori has...Full Text Available

2009-01-01

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Reducing Rice Seed Storage Protein Accumulation Leads to Changes in Nutrient Quality and Storage Organelle Formation¹^[W]^[OA]

We characterized the absorption and short-term translocation of cadmium (Cd) in rice (Oryza sativa ‘Nipponbare’) quantitatively using serial images observed with a positron-emitting...Full Text Available

2010-04-01

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A new type of scorpion Na⁺-channel-toxin-like polypeptide active on K⁺ channels

Rice (Oryza sativa) seed storage proteins (SSPs) are synthesized and deposited in storage organelles in the endosperm during seed maturation as a nitrogen source for germinating seedlings....Full Text Available

2010-12-01

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Effect of vitamin C on copper retention in young men

We have purified and characterized two peptides, named KAaH1 and KAaH2 (AaH polypeptides 1 and 2 active on K⁺ channels, where AaH stands for Androctonus australis Hector),...Full Text Available

2005-06-01

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The mode and tempo of genome size evolution in eukaryotes

Previous work suggests that supplemental ascorbic acid (AA) may inhibit intestinal copper absorption by stabilizing the less absorbable cuprous state. The authors studied copper absorption in healthy men (age 19-32) fed a constant diet with different amounts of ascorbic acid supplements. The 6 men were confined to a metabolic unit for the entire 14 week study. The basal diet consisted of a 7 day rotating menu which provided an average of 2.1 mg Cu/d and was adequate in all other nutrients except AA (5 mg/d). The basal diet was supplemented with either zero, 60, or 600 mg of AA daily, added to grape juice and consumed at each meal. All feces were collected. Blood was taken weekly for monitoring AA and copper status. Copper absorption was determined by both balance and "6"5Cu stable isotope techniques. As determined by fecal Cu excretion, varying intakes of AA between 0.1 to 10 times ...

1986-04-13

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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

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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

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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

42

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

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

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

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A Computational Framework Discovers New Copy Number Variants with Functional Importance

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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Widespread duplications in the genomes of laboratory stocks of Dictyostelium discoideum

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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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

47

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

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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

49

Genomic view of the evolution of the complement system

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

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Genomic imprinting and the social brain

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

51

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

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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

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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

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Rice RING protein OsBBI1 with E3 ligase activity confers broad-spectrum resistance against Magnaporthe oryzae by modifying the cell wall defence

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

56

British Library Electronic Table of Contents (United Kingdom)

Emerging evidence suggests that E3 ligases play critical roles in diverse biological processes, including innate immune responses in plants. However, the mechanism of the E3 ligase involvement in plant innate immunity is unclear. We report that a rice gene, OsBBI1, encoding a RING finger protein with E3 ligase activity, mediates broad-spectrum disease resistance. The expression of OsBBI1 was induced by rice blast fungus Magnaporthe oryzae, as well as chemical inducers, benzothiadiazole and salicylic acid. Biochemical analysis revealed that OsBBI1 protein possesses E3 ubiquitin ligase activity in vitro. Genetic analysis revealed that the loss of OsBBI1 function in a Tos17-insertion line increased susceptibility, while the overexpression of OsBBI1 in transgenic plants conferred enhanced resi...

2011-01-01

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Genetic studies of fertility and pathogenicity in Magnaporthe grisea (Pyricularia oryzae)

Cellulolytic Enzymes Production via Solid-State Fermentation: Effect of Pretreatment Methods on Physicochemical Characteristics of Substrate.

Crosses between field isolates of Magnaporthe grisea (anamorph, Pyricularia oryzae Cav. and Pyricularia grisea) have led to the development of fertile laboratory strains that infect goosegrass and/or weeping lovegrass. These strains may now be utilized in a rigorous genetic analysis of host species specificity and general pathogenicity. Attempts to improve the fertility of rice pathogens for the goal of undertaking a genetic analysis of host cultivar specificity have so far been unsuccessful. Crosses between M. grisea strains that infect rice, goosegrass or weeping lovegrass demonstrate that host species specificity differences between field isolates of this fungus in some cases have a complete genetic basis, and in other cases have a simple genetic basis. Crosses between a field isolate of the pathogen that infects weeping lovegrass and a field isolate that infects goosegrass have resulted in the identification of a single gene difference that determines ...

1984-01-01

58

SHIPBOARD RADIOLOGICAL - COUNTERMEASURE ...

We investigated the effect of pretreatment on the physicochemical characteristics-crystallinity, bed porosity, and volumetric specific surface of soybean hulls and production of cellulolytic enzymes in solid-state fermentation of Trichoderma reesei and Aspergillus oryzae cultures. Mild acid and alkali and steam pretreatments significantly increased crystallinity and bed porosity without significant change inholocellulosic composition of substrate. Crystalline and porous steam-pretreated soybean hulls inoculated with T. reesei culture had 4 filter paper units (FPU)/g-ds, 0.6?IU/g-ds ?-glucosidase, and 45?IU/g-ds endocellulase, whereas untreated hulls had 0.75?FPU/g-ds, 0.06?IU/g-ds ?-glucosidase, and 7.29?IU/g-ds endocellulase enzyme activities. In A. oryzae steam-pretreated soybean hulls had 47.10?IU/g-ds endocellulase compared to 30.82?IU/g-ds in untreated soybean hulls. Generalized linear statistical model fitted to enzyme activity data ...

2011-06-15

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Percutaneous absorption of aromatic amines in rubber industry workers: impact of impaired skin and skin barrier creams

... H1+80 Remaining H +82 Remaining H+56 IlemaJntng ,H+77 Remaining. Aa pct c/m pct mr/hr pet mr/hr pet ... mr/hr avg. pct c/rnh pt pa pct ...

1959-01-30

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Is alopecia areata an autoimmune-response against melanogenesis-related proteins, exposed by abnormal MHC class I expression in the anagen hair bulb?

BackgroundSeveral aromatic amines (AA) could cause bladder cancer and are an occupational hygiene problem in the workplace. However, little is known about the percutaneous absorption...Full Text Available

2007-06-01

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Identification and characterization of Aedes aegypti aminopeptidase N as a putative receptor of Bacillus thuringiensis Cry11A toxin

The etiology of alopecia areata (AA), a putative autoimmune disease characterized by sudden hair loss, has remained obscure. It is not understood, how the characteristic inflammatory infiltrate that...Full Text Available

1993-11-01

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GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries

Bacillus thuringiensis subsp. israelensis, which is used worldwide to control Aedes aegypti larvae, produces Cry11Aa and other toxins during...Full Text Available

2009-10-01

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Effect of nutrition conditions and 2M-4Kh herbicide on utilization of N"1"5-labelled fertilizer nitrogen by fiber-flax

There are many methods for introducing random mutations into nucleic acid sequences. Previously, we described a suite of programmes for estimating the completeness and diversity of randomized DNA libraries...Full Text Available

2008-07-01

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Cell volume regulation in hemoglobin CC and AA erythrocytes

Russian (1972). USSR Bagaev, VB Abueva, AA (no.188) p. 137-143.

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AAS 94-164 Demonstration of a Precision Data Reduction Technique ...

Swelling hemoglobin CC erythrocytes stimulates a ouabain-insensitive K flux that restores original cell volume. Studies were performed with the K analog, "8"6Rb. This volume regulatory pathway was characterized for its anion dependence, sensitivity to loop diuretics, and requirement for Na. The swelling-induced K flux was eliminated if intracellular chloride was replaced by nitrate and both swelling-activated K influx and efflux were partially inhibited by 1 mM furosemide or bumetanide. K influx in swollen hemoglobin CC cells was not diminished when Na in the incubation medium was replaced with choline, indicating Na independence of the swelling-induced flux. Identical experiments with hemoglobin AA cells also demonstrated a swelling-induced increase in K flux, but the magnitude and duration of this increase were considerably less than that seen with hemoglobin CC cells. The increased K flux in hemoglobin AA cells was likewise sensitive to ...

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

and a flyby of the asteroid Ida, the enhanced filter is shown to substantially improve the ... twoway range, and ADOR data points acquired at S-band frequencies. .... The result of this fit and its l-sigma uncertainty ellipse is ...

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Why is the null HBT result at RHIC so interesting?

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2006-01-01

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Microstructure Characterization of Magnetic-Pulse-Welded AA 6061-T6 by Electron Backscattered Diffraction

Pion interferometry (HBT of A+A) data have posed a thorn in the theoretical interpretation of AA collisions at RHIC (#sq root#s = 130 AGeV). How can R_o_u_t #approx# R_s_i_d_e #approx# R_l_o_n_g and remain so between AGS and RHIC? Where is the QGP Stall? Can elephants hide along the x_0"+ dimension? We rummage old hydrodynamic scenarios and uncover some previously ignored NULL solutions. (author)

69

Justice and the Human Genome Project

The grain boundary crystallographic misorientations of magnetic-pulse-welded (MPW) aluminum alloy (AA) 6061-T6 in linear and tubular configurations were examined using the electron backscattered diffraction (EBSD) technique. A refined structure of heavily deformed grains with higher grain boundary angles was observed in linear welds. Significant spalling was observed away from the joints, in the interior of tubular welds. The results show the complex interaction of shock waves with the materials during this impact welding process.

2008-08-01

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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

71

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

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

72

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

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

73

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

74

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

75

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

76

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

77

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

78

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

79

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

80

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

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81

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

82

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

83

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

84

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

85

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

86

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

87

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

88

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

89

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

90

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

91

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

92

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

93

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

94

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

95

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

96

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

97

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

98

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

99

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

100

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

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

101

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

102

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

103

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

104

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

105

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

106

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

107

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

108

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

109

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

110

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

111

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

112

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

113

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

114

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

115

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

116

Genomic Careers: Interactive Videos

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

117

Medline Plus

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

118

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

Heat shock factor binds to heat shock elements upstream of heat shock protein 70a and Samui genes to confer transcriptional activity in Bombyx mori diapause eggs exposed to 5^oC

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

119

British Library Electronic Table of Contents (United Kingdom)

To understand the molecular mechanisms of how 5^oC-incubation activates mRNA expression of Hsp70a and Samui genes in Bombyx mori diapause eggs, we first searched the 5'-upstream regions of the Hsp70a and Samui genes for heat shock elements (HSEs) and found two regions [Hsp70aHSE-1 (-95 to -58) and -2 (-145 to -121), and SamuiHSE-1 (-84 to -55) and -2 (-304 to -290)] corresponding to HSEs (repeats of nGAAn and/or nTTCn). We cloned four cDNAs encoding heat shock factor (HSF)-a2 (627 amino acids), -b (685 aa), -c (682 aa) and -d (705 aa), which were produced by alternative splicing. When we exposed diapause eggs to 5^oC beginning at 2 day post-oviposition to break diapause, HSFd mRNA only increased after chilling for 6-8 days, a pattern very similar to those of Hsp70a and Samui mRNAs. To exam...

2011-01-01

120

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

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

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

121

Polyester and multiwalled carbon nanotube composites: characterization, electrical conductivity and antibacterial activity

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

122

British Library Electronic Table of Contents (United Kingdom)

Abstract Poly(butylene terephthalate) (PBT) composites containing multiwalled carbon nanotubes (MWCNTs) were prepared using a melt-blending process and used to examine the effects on the composite structure and properties of replacing PBT with acrylic acid-grafted PBT (PBT-g-AA). PBT-g-AA and multihydroxyl-functionalized MWCNTs (MWCNTs-OH) were used to improve the compatibility and dispersibility of the MWCNTs within the PBT matrix. The composites were characterized morphologically using transmission electron microscopy, and chemically using Fourier transform infrared, solid-state 13C NMR and UV-visible absorption spectroscopy. The antibacterial and electrical conductivity properties of the composites were also evaluated. MWCNTs or MWCNTs-OH enhanced the antibacterial activity and electric...

2011-01-01

123

On the mechanism of the anodic protection of aluminium alloy AA5182 by emeraldine base coatings

Environmental Research Database

Aluminium AA5182 coupons covered by a polyaniline film in the emeraldine base (EB) form showed increasing corrosion potential and decreasing corrosion current as a function of the thickness of the polymer layer. The cathodic reaction was proved not limited by diffusion of species inside the electrolyte solution and oxygen had no effect on the electrochemical behaviour of the coated samples. An EB coating on indium tin oxide conducting layer appeared slightly electroactive in neutral media. The IR spectra of aluminium coated samples, before and after heating in argon atmosphere, confirmed a redox reaction between the polymer film and the metal. This galvanic coupling can explain the good protective behaviour of emeraldine base against corrosion of aluminium.

2007-03-01

124

NEW SLAG-BASED CONCRETES

ObjectivesTo determine the reaction rate of slag during curing and factors affecting reactivity.~%~~%~To measure the rates of chloride ingress into concrete and the extent of chloride binding.~%~~%~To determine conditions for pitting corrosion and the nature of corrosion products.~%~~%~To characterise the reactions in slag-calcium alumina cement hydration and the nature of the products.~%~DescriptionBlast-furnace slag has latent hydraulic properties, giving considerable potential for commercial use in addition to its widespread use as a partial replacement for Portland cement, notably in alkali-activated slag (AAS) and slag-calcium alumina cement (CAC) concretes. Use of AAS concretes is already well-established in China and the former USSR, but their further application is hindered by lack of research into setting, hydration and durability, Slag/CAC blends are new materials whose chemistr ...

1999-01-09

125

Genetic algorithm approach for the determination of the electrical parameters of railway traction lines

British Library Electronic Table of Contents (United Kingdom)

The problem of electrical parameters identification in complex systems, and in particular in electric railway traction systems, is considered. Parameters are determined by an indirect approach: only the terminal variables (voltages and currents and, impedance and admittance, which can be readily calculated) are measured and the per-unit-length electrical parameters are determined using a multiconductor transmission line model of the track section under test. It will be shown that some parameters cannot be measured directly, that they are not constant with frequency and that they may depend on other external conditions. An indirect method for parameters identification is proposed through an adaptive algorithm (AA), so that the calculated terminal variables match the measured ones. The AA is...

2008-01-01

126

Chemistry between crosslinks affects the properties of peptide hydrogels

British Library Electronic Table of Contents (United Kingdom)

Protein hydrogels were prepared by substituting ovalbumin with different concentrations of ethyl vinyl sulfone (EVS) or acrylic acid (AA) and crosslinking with divinyl sulfone (DVS). Fourier transform-infrared (FT-IR) spectroscopic studies confirmed the addition of EVS, AA, and DVS onto the protein. Swelling was assessed as a function of pH in the range of 2.5 to 9.4 and ionic strength. The elastic modulus of the gels was determined in shear and compression. Stress relaxation was assessed in compression. The substituent highly affected swelling and modulus with both hydrogels displaying non-Gaussian behavior in the range of hydrogel environments studied. Acrylic acid substituted ovalbumin exhibited a decreasing modulus with increasing swelling behaving as a polyelectrolyte with low added s...

2011-01-01

127

A prediction of the acoustical properties of induction cookers based on an FVM-LES-acoustic analogy method

British Library Electronic Table of Contents (United Kingdom)

The FVM-LES-acoustic analogy method (FVM-LES-AAM), which is a hybrid prediction technique for the acoustical property computation, is presented and performed in this paper. The FVM-LES-AAM was developed by combining the finite volume method (FVM), the large eddy simulation (LES), and the Ffowcs Williams-Hawkings analogy algorithm (FWH-AA). To predict the acoustical properties of induction cookers, the FVM is used for discretizing the calculation field and building numerical equations, and the LES and FWH-AA are performed for computing the sound sources and predicting the far-field sound, respectively. Using the FVM with the unstructured grids method to discretize the control equation of Navier-Stokes was introduced for illuminating the above numerical simulation procedure. To prove the FVM...

2011-01-01

128

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

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

129

lla3321l.271

Three Homologous Genes Encoding sn-Glycerol-3-Phosphate Acyltransferase 4 Exhibit Different Expression Patterns and Functional Divergence in Brassica napus¹^[C]^[W]^[OA]

... dm}ci yQo^ Q_aaSig[^n uu{mac[jOKf@P\\_rbd_N`T Q]^Y_U[d^UjQe\\[Nc_^xMRV]df\\tH_ ojnpumkmtbcpepmhjpeh mvutleojwd|[inYd_`Zn_`oik }Uh]x_kcb`[Wh`RO_Y`[Zeq\\oX ...

130

Mutations induced in the hypoxanthine phosphoribosyl transferase gene by three urban air pollutants: acetaldehyde, benzo[a]pyrene diolepoxide, and ethylene oxide.

Brassica napus is an allotetraploid (AACC) formed from the fusion of two diploid progenitors, Brassica rapa (AA) and Brassica oleracea...Full Text Available

2011-02-01

131

Mutations at the accommodation gate of the ribosome impair RF2-dependent translation termination

Provisional mutational spectra at the hypoxanthine phosphoribosyl transferase (HPRT) locus in vitro have been worked out for acetaldehyde (AA) and benzo[a]pyrene diolepoxide (BPDE) in human (T)-lymphocytes...Full Text Available

1994-10-01

132

Diabetes-Induced Oxidative Stress Is Mediated by Ca²⁺-Independent Phospholipase A2 in Neutrophils

During protein synthesis, aminoacyl-tRNA (aa-tRNA) and release factors 1 and 2 (RF1 and RF2) have to bind at the catalytic center of the ribosome on the 50S subunit where they take part in peptide bond...Full Text Available

2010-09-01

133

Aarskog-Scott syndrome: Clinical update and report of nine novel mutations of the FGD1 gene

Neutrophils from people with poorly controlled diabetes present a primed phenotype and secrete excessive superoxide. Phospholipase A₂ (PLA₂)-derived arachidonic acid (AA)...Full Text Available

2010-02-01

134

DEFF Research Database (Denmark)

Mutations in the FGD1 gene have been shown to cause Aarskog-Scott syndrome (AAS), or facio-digito-genital dysplasia (OMIM#305400), an X-linked disorder characterized by distinctive genital and skeletal developmental abnormalities with a broad spectrum of clinical phenotypes. To date, 20 distinct mutations have been reported, but little phenotypic data are available on patients with molecularly confirmed AAS. In the present study, we report on our experience of screening for mutations in the FGD1 gene in a cohort of 60 European patients with a clinically suspected diagnosis of AAS. We identified nine novel mutations in 11 patients (detection rate of 18.33%), including three missense mutations (p.R402Q; p.S558W; p.K748E), four truncating mutations (p.Y530X; p.R656X; c.806delC; c.1620delC), one in-frame deletion (c.2020_2022delGAG) and the first reported splice site mutation (c.1935+3A>C). A recurrent mutation (p.R656X) was ...

2010-01-01

135

Clinical application of stable xenon CT-CBF studies without denitrogenation

Engineering Relative Compression of Genomes

Noninvasive and simplified methods for estimating regional cerebral blood flow (CBF) and regional partition coefficient (#lambda#) using the inhalation of stable xenon (Xe"s) and computed tomographic (CT) scanning are described. Thirty percent Xe"s in 70% oxygen was inhaled for 240 seconds and exhaled for 160 seconds during serial CT scanning without denitrogenation in 26 patients with cerebrovascular diseases and four volunteer controls. During the investigation, the end-tidal Xe"s concentration was continuously monitored with a thermoconductivity analyzer to determine the build-up range (A value) and build-up rate constant (K value) of the artery by the curve fitting method. Calculated A and K values were corrected by the following formulae reported previously: for patients aged 0-20 years, A_e = 0.75A_a + 2.15, K_e = 0.67K_a + 0.69; 21-40 years, A_e = 0.56A_a + 3.24, K_e = 0.38K_a + 1.12; 41-60 years, A_e = 0.91A_a + ...

136

Ultraconserved Elements: Analyses of Dosage Sensitivity, Motifs and Boundaries

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

137

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

138

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

139

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

140

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

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

141

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

142

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

143

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

144

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

145

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

146

Manipulating the Xenopus genome with transposable elements

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

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

147

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

148

Human endogenous retroviruses: transposable elements with potential ?

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

149

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

150

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

151

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 ... ...

152

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

153

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

154

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

155

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

156

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

157

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

158

Sucrose phosphate synthase activity in rice grown at elevated CO sub 2 and temperature

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

159

Production of a cellulolytic enzyme system in mixed-culture solid-state fermentation of soybean hulls supplemented with wheat bran

Rice (Oryza sativa L.) was grown at 330 and 660 {mu}L CO{sub 2} L{sup {minus}1} and at 40/33/37, 34/27/31, and 28/21/25{degree}C day/night/paddy water temperatures respectively. Sucrose phosphate synthase (SPS) activity was measured at saturating substrate concentrations at 59 days after planting. SPS activity increased 2 and 3 fold with increasing CO{sub 2} at 28 and 34{degree}C air temperatures respectively. At 40{degree}C SPS activity decreased by 37% at elevated CO{sub 2} and most plants failed to reach maturity. Similar responses were found in leaf samples taken in the dark. These results indicate that SPS, an enzyme involved in the regulation of C partitioning in leaves, increases in activity at elevated CO{sub 2}. This is in contrast to previous results with soybean. The changes in SPS activity will also be discussed in relation to leaf starch/sucrose ratios.

1990-05-01

160

British Library Electronic Table of Contents (United Kingdom)

Solid-state fermentation of soybean hulls supplemented with wheat bran using a co-culture of Trichoderma reesei and Aspergillus oryzae was performed. Three parameters - initial moisture content, incubation temperature, and initial pH - were optimized in culture flasks using response surface methodology. Parameter optimization was carried out with respect to filter paper activity and b-glucosidase activity in the culture. Temperature of 30^oC, pH of 5, and moisture content of 70% were found to be optimum. Optimized parameters were used for laboratory scale-up in static tray fermenters. The maximum filter paper activity of 10.7FPU/g-ds and b-glucosidase of 10.7IU/g-ds were obtained after 96-h incubation period in static tray fermenters in agreement with optimized activities at shake flask le...

2010-01-01

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

161

Energy analysis of biochemical conversion processes of biomass to bioethanol

Transitions between distinct compaction regimes in complexes of multivalent cationic lipids and DNA

Bioethanol is among the most promising of biofuels that can be produced from different biomass such as agricultural products, waste and byproducts. This paper reported on a study that examined the energy conversion of different groups of biomass to bioethanol, including lignocelluloses, starches and sugar. Biochemical conversion generally involves the breakdown of biomass to simple sugars using different pretreatment methods. The energy needed for the conversion steps was calculated in order to obtain mass and energy efficiencies for the conversions. Mass conversion ratios of corn, molasses and rice straw were calculated as 0.3396, 0.2300 and 0.2296 kg of bioethanol per kg of biomass, respectively. The energy efficiency of biochemical conversion of corn, molasses and rice straw was calculated as 28.57, 28.21 and 31.33 per cent, respectively. The results demonstrated that lignocelluloses can be efficiently converted with specific microorganisms such as Mucor indicus, Rhizopus ...

2010-07-01

162

Study of in-medium $\\omega$ meson properties in Ap, pA and AA collisions

We use X-ray scattering and molecular simulations to investigate the structural properties of complexes of multivalent cationic lipids and DNA molecules. At low mole fraction of neutral lipids (NLs), $\\Phi_{\\rm NL}$, the complexes show dramatic DNA compaction down to essentially close packed DNA arrays with a DNA interaxial spacing $d_{\\rm DNA}=25\\AA$. A gradual increase in $\\Phi_{\\rm NL}$ does not lead to a continuous increase in $d_{\\rm DNA}$ as observed for DNA complexes of monovalent cationic lipids (CLs). Instead, distinct spacing regimes exist, with sharp transitions between them. Three packing states have been identified: (i) close packed, (ii) condensed, but not close packed, with $d_{\\rm DNA}=27-28\\AA$, and (iii) an expanded state, where $d_{\\rm DNA}$ increases gradually with $\\Phi_{\\rm NL}$. Based on our experimental and computational results, we conclude that the DNA condensation is mediated by the multivalent cationic ...

2008-01-01

163

Quarkonia and QGP studies

We propose to investigate the in-medium properties of vector $\\omega$ mesons at the normal nuclear density in Ap(pA) collisions and at higher density in AA collisions at the ITEP accelerator facility TWAC. Using of the inverse Ap kinematics will permit us to study the $\\omega$ meson production in a wide momentum interval included the not yet explored range of small meson momenta relative to the projectile nuclei where the mass modification effect in nuclear matter is expected to be the strongest. Momentum dependence of the in-medium $\\omega$ meson width will be studied in the traditional pA kinematics. We intend to use the electromagnetic calorimeter for reconstruction of the $\\omega$ meson invariant mass by detecting photons from the $\\omega \\to \\pi^{0}\\gamma \\to 3\\gamma$ decay. The model calculations and simulations with RQMD generator show feasibility of the proposed experiment. Available now intensity of the ion beams provides a possibility to collect ...

2008-01-01

164

Pitting and stress corrosion cracking resistance of friction stir welded AA 5083

We summarize results of recent studies of heavy quarkonia correlators and spectral functions at finite temperatures from lattice QCD and systematic T-matrix studies using QCD motivated finite-temperature potentials. We argue that heavy quarkonia dissociation shall occur in the temperature range $1.2 \\le T_d/T_c \\le 1.5$ by the interplay of both screening and absorption in the strongly correlated plasma medium. We discuss these effects on the quantum mechanical evolution of quarkonia states within a time-dependent harmonic oscillator model with complex oscillator strength and compare the results with data for $R_{\\rm AA}/R_{\\rm AA}^{\\rm CNM}$ from RHIC and SPS experiments. We speculate whether the suppression pattern of the rather precise NA60 data from In-In collisions may be related to the recently discovered X(3872) state. Theoretical support for this hypothesis comes from the cluster expansion of the plasma Hamiltonian for heavy ...

2011-01-01

165

Pharmacodynamics of a novel designer natriuretic peptide, CD-NP, in a first-in-human clinical trial in healthy subjects.

The corrosion behaviour of friction stir welded (FSW) joints of AA 5083 has been compared to that of MIG welded joints. Pitting and stress corrosion cracking (SCC) resistance in 3.5% NaCl + 0.3 g/l H{sub 2}O{sub 2} and in EXCO (4 M KCl + 0.5 M KNO{sub 3} + 0.1 M HNO{sub 3}) solutions has been determined at 25 C. SCC susceptibility was evaluated by slow strain rate tests (SSRT), at a strain rate of 1 x 10{sup -6}s{sup -1}. Welds obtained by FSW technique showed a higher corrosion resistance in EXCO solution and a lower pitting tendency than the base alloy. Electrochemical measurements (corrosion potential measurements, polarization curves recording) evidenced that FSW weld was cathodic to base alloy. FSW joints were not susceptible to SCC in both test solutions, whereas MIG joints cracked in both solutions. (orig.)

2001-11-01

166

Passivity of 316L stainless steel in borate buffer solution studied by Mott-Schottky analysis, atomic absorption spectrometry and X-ray photoelectron spectroscopy

CD-NP is a novel chimeric natriuretic peptide (NP) consisting of the 22-amino-acid (AA) human C-type natriuretic peptide (CNP), a venodilating peptide with limited renal actions and minimal effects on blood pressure, and the 15-AA C-terminus of Dendroaspis NP (DNP). The rationale for the design of CD-NP was to enhance the renal actions of CNP, the ligand for natriuretic peptide receptor-B, but without inducing excessive hypotension. Here we report the first-in-human studies for CD-NP, which represent the first successful clinical testing of a chimeric NP demonstrating in normal human volunteers that CD-NP possesses cyclic guanosine monophosphate-activating, natriuretic, and aldosterone-suppressing properties without inducing excessive hypotension, laying the foundation for additional studies on this first-in-class new cardiovascular therapeutic in human heart failure, which are now underway worldwide. PMID:19395584

2009-04-24

167

Comparison of digital and analogue data acquisition systems for nuclear spectroscopy

Research highlights: {yields} The polarization curve of 316L SS possesses five turning potentials in passive region. {yields} Films formed at turning potentials perform different electrochemical and semiconductor properties. {yields} Dissolutions and regenerations of passive film at turning potentials are obtained by AAS and XPS. {yields} Turning potentials appearing in passive region are ascribed to the changes of the compositions of the passive films. - Abstract: The passivity of 316L stainless steel in borate buffer solution has been investigated by Mott-Schottky, atomic absorption spectrometry (AAS) and X-ray photoelectron spectroscopy (XPS). The results indicate that the polarization curve in the passive region possesses several turning potentials (0 V{sub SCE}, 0.2 V{sub SCE}, 0.4 V{sub SCE}, 0.6 V{sub SCE} and 0.85 V{sub SCE}). The passive films formed at turning potentials perform different electrochemical and semiconductor properties. ...

2010-11-15

168

A structural and corrosion study of triethoxysilyl and perfluorooctyl functionalized polyhedral silsesquioxane nanocomposite films on AA 2024 alloy

In the present investigation the performance of digital data acquisition (DA) and analogue data acquisition (AA) systems are compared in neutron-induced fission experiments. The DA results are practically identical to the AA results in terms of angular-, energy- and mass-resolution, and both compare very well with literature data. However, major advantages were found with the digital techniques. DA allows for a very efficient #alpha#-particle pile-up correction. This is important when considering the accurate measurement of fission-fragment characteristics of highly #alpha#-active actinide isotopes relevant for the safe operation of Generation IV reactors and the successful reduction of long-lived radioactive nuclear waste. In case of a strong #alpha#-emitter, when applying the #alpha#-particle pile-up correction, the peak-to-valley ratio of the energy distribution was significantly improved. In addition, DA offers a very flexible expanded ...

2010-12-21

169

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

A tri-functional polyhedral oligomeric silsesquioxane (POSS) based silane precursor R_xR_yR_z(SiO_3_/_2)_n (x + y + z = n = 6, 8, 10, ...) bearing 3-(N-(3-triethoxysilylpropyl)ureido)propyl, isooctyl and perfluoropropyl groups was synthesized and investigated as corrosion protective coating for AA 2024 alloy. Infrared reflection-absorption (IR RA) combined with X-ray photoelectron spectroscopy and atomic force microscopy provided information about partial self-assembling of coatings having a fluorine enriched upper layer with a low surface energy (#gamma#"t"o"t = 12.37 mN/m). The structural changes that accompanied corrosion produced under chronocoulometrical conditions were assessed from ex-situ IR RA spectra. A new band at 1690-1700 cm"-"1 appeared above the corrosion potential, and was assigned to the formation of amidonium ions and consequent relaxation of urea-urea associations.

2010-03-01

170

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

171

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

172

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

173

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

174

Probable role of trace elements of some medicinal plants in cardio-vascular diseases

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

175

PDS_VERSION_ID = PDS3 FILE_NAME = "M1102254.IMQ" RECORD_TYPE ...

A number of herbal drugs are used in the Unani (Greco-Arab) System of Medicine for cardiovascular diseases. The herbs were analyzed by flame AAS and ICP-AES to determine if their therapeutic actions can be associated with the elements present in them. Cadmium, cobalt, chromium, copper, iron, potassium, magnesium, manganese, sodium, nickel, phosphorus, lead and zinc were some of the elements which play various roles in cardiovascular affections. An effort was made to correlate the role of these elements in cardiac diseases. (Auth.). 2 tabs., 32 refs.

176

Electron microscopy analysis of grain boundary structure and composition in superplastically deformed Al-Mg alloys

UUv/4sQ d92aa%bvBR 6C7*?+'dI 1Yy! bd*O NdmD $t6b ,2Bw P,. ...... a] ULtd *w rD*M>93y eLeh "l;BdDCd u$g4rA&[` 3zD# a%robOT 9y[1 "$ngz f&6|D&" /(KUH() fG$f ...

177

Connectivity in the Astronomy Digital Library

Evaluation of grain boundary composition and structure in superplastically deformed AA5083-based alloys (Al-4.5Mg-1.6Mn-0.2Zr) was carried out in a field-emission gun transmission electron microscope (FEG-TEM). During superplastic deformation at high homologous temperatures materials undergo extensive grain boundary sliding (GBS) which creates a flow of defects in the near-boundary region. Recent literature has shown that the grain-boundary composition in Al-Mg alloys is not necessarily the same as the matrix, and that these differences can have an effect on GBS.

1996-12-31

178

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

The Astrophysics Data System (ADS) provides an extensive system of links between the literature and other on-line information. Recently, the journals of the American Astronomical Society (AAS) and a group of NASA data centers have collaborated to provide more links between on-line data obtained by space missions and the on-line journals. Authors can now specify which data sets they have used in their article. This information is used by the participants to provide the links between the literature and the data. The ADS is available at: http://ads.harvard.edu

2006-01-01

179

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

180

Prostaglandin (PG) E3 synthesis elicted by adrenergic stimuli in guinea-pig trachea (GPT) is mediated primarily by B2 adrenergic receptors

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

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181

Prostaglandin (PG) E3 synthesis elicted by adrenergic stimuli in guinea-pig trachea (GPT) is mediated primarily by B2 adrenergic receptors

The purpose of this study was to examine arachidonic acid (AA) metabolism and to characterize the type of adrenergic receptor (AR) involved in the production of the major metabolite of this fatty acid. ({sup 14}C)AA was incubated with GPT-rings and the radiolabelled products were extracted and separated by TLC method. The medium was also assayed for radiolabelled immunoreactive PG's (iPG's) and leukotrienes (LT) B4 and C4 by RIA or Enzyme immunoassay (EIA) after exposure to various AR agonists. ({sup 14}C)AA was incorporated into GPT-rings and metabolized mainly into iPGE2 and smaller amounts into PGF2{alpha}. Trace amounts of PGD2 and 6-keto-PGF1{alpha} but not LTB4 or LTC4 were detected by RIA and/or EIA. Incubation of GPT rings for 15 minutes with isoproterenol and salbutamol resulted in a significant increase of PGE2 synthesis (optimum conc: 10{sup {minus}7}, 10{sup {minus}7}M respectively). In ...

1990-02-26

182

Microstructural analysis of as-processed U-10 wt.%Mo monolithic fuel plate in AA6061 matrix with Zr diffusion barrier

The purpose of this study was to examine arachidonic acid (AA) metabolism and to characterize the type of adrenergic receptor (AR) involved in the production of the major metabolite of this fatty acid. ["1"4C]AA was incubated with GPT-rings and the radiolabelled products were extracted and separated by TLC method. The medium was also assayed for radiolabelled immunoreactive PG's (iPG's) and leukotrienes (LT) B4 and C4 by RIA or Enzyme immunoassay (EIA) after exposure to various AR agonists. ["1"4C]AA was incorporated into GPT-rings and metabolized mainly into iPGE2 and smaller amounts into PGF2#alpha#. Trace amounts of PGD2 and 6-keto-PGF1#alpha# but not LTB4 or LTC4 were detected by RIA and/or EIA. Incubation of GPT rings for 15 minutes with isoproterenol and salbutamol resulted in a significant increase of PGE2 synthesis (optimum conc: 10"-"7, 10"-"7M respectively). In contrast, dobutamine, norepinephrine, phenylnephrine ...

1991-04-21

183

GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries.

For higher U-loading in low-enriched U-10 wt.%Mo fuels, monolithic fuel plate clad in AA6061 is being developed as a part of Reduced Enrichment for Research and Test Reactor (RERTR) program. This paper reports the first characterization results from a monolithic U-10 wt.%Mo fuel plate with a Zr diffusion barrier that was fabricated as part of a plate fabrication campaign for irradiation testing in the Advanced Test Reactor (ATR). Both scanning and transmission electron microscopy (SEM and TEM) were employed for analysis. At the interface between the Zr barrier and U-10 wt.%Mo, going from Zr to U(Mo), UZr_2, #gamma#-UZr, Zr solid-solution and Mo_2Zr phases were observed. The interface between AA6061 cladding and Zr barrier plate consisted of four layers, going from Al to Zr, (Al, Si)_2Zr, (Al, Si)Zr_3 (Al, Si)_3Zr, and AlSi_4Zr_5. Irradiation behavior of these intermetallic phases is discussed based on their constituents. Characterization of ...

2010-07-01

184

Effect of applied tensile stress on intergranular corrosion of AA2024-T3

There are many methods for introducing random mutations into nucleic acid sequences. Previously, we described a suite of programmes for estimating the completeness and diversity of randomized DNA libraries generated by a number of these protocols. Our programmes suggested some empirical guidelines for library design; however, no information was provided regarding library diversity at the protein (rather than DNA) level. We have now updated our web server, enabling analysis of translated libraries constructed by site-saturation mutagenesis and error-prone PCR (epPCR). We introduce GLUE-Including Translation (GLUE-IT), which finds the expected amino acid completeness of libraries in which up to six codons have been independently varied (according to any user-specified randomization scheme). We provide two tools for assisting with experimental design: CodonCalculator, for assessing amino acids corresponding to given randomized codons; and AA-Calculator, for finding ...

2008-04-28

185

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

The effect of uniaxial tensile stress on intergranular corrosion (IGC) of AA2024-T3 was studied using the foil penetration technique. Standard ASTM G49 fixed-displacement jigs were modified to allow the use of sheet samples, which were then attached to an electrochemical cell as in the foil penetration setup. The time for IGC to penetrate samples of varying thickness was monitored. This method provides a new approach to bridge the gap between IGC and intergranular stress corrosion cracking (IGSCC). Samples with various orientations relative to the rolling direction were studied in 1.0 M NaCl at controlled anodic potentials. Potentiodynamic polarization measurements indicated that the two breakdown potentials typically observed for AA2024-T3 were lower for stressed samples than for unstressed samples, and the current at a given potential was higher. The penetration rate depended on potential and was higher for stressed samples than for ...

2004-02-01

186

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

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

187

SEPT9_i1 and genomic instability: Mechanistic insights and relevance to tumorigenesis

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

188

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

189

Federal technology transfer and the human genome project. Background paper

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

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

190

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

191

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

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

192

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

193

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

194

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

195

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

196

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

197

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

198

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

199

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

200

Transposon-based screens for cancer gene discovery in mouse models

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

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201

Transposable elements in fish functional genomics: technical challenges and perspectives

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

202

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

203

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

204

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

205

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

206

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

207

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

208

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

209

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

210

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

211

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

212

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

213

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

214

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

215

Studying bacterial transcriptomes using RNA-seq

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

216

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

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

217

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

218

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

219

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

220

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

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221

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

222

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

223

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

224

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

225

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

226

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

227

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

228

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

229

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

230

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

231

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

232

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

233

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

234

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

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

235

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

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

236

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

237

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

238

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

239

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

240

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

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241

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

242

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

243

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

244

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

245

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

246

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

247

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

248

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

249

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

250

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

251

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

252

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

253

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

254

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

255

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

256

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

257

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

258

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

259

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

260

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

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261

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

262

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

263

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

264

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

265

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

266

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

267

Genetic screening: The vista of genomic medicine

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

268

Genetic aspects of birth defects: new understandings of old problems

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

269

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

270

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

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

271

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

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

272

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

273

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

274

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

275

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

276

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

277

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

278

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

279

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

280

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

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281

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

282

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...

283

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

284

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

285

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

286

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

287

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

288

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

289

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

290

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

291

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

292

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

293

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

294

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

295

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

296

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

297

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

298

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

299

Altering the ribosomal subunit ratio in yeast maximizes recombinant protein yield

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

300

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

BackgroundThe production of high yields of recombinant proteins is an enduring bottleneck in the post-genomic sciences that has yet to be addressed in a truly rational manner. Typically...Full Text Available

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301

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

302

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

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

303

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

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

304

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

305

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

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

306

A new evolutionary scenario for the Mycobacterium tuberculosis complex

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

307

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

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

308

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

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

309

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

310

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

311

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

312

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

313

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

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

314

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

315

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

The LCG PI project using interfaces for physics data analysis

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

316

Synthesis and characterization of conducting polymer composite (PAn/TiO{sup 2}) for cathode material in rechargeable battery

In the context of the LHC Computing Grid (LCG) project, the Applications Area develops and maintains that part of the physics applications software and associated infrastructure that is shared among the LHC experiments. The "Physicist Interface" (PI) project of the LCG Application Area encompasses the interfaces and tools by which physicists will directly use the software, providing implementations based on agreed standards like the AIDA interfaces for data analysis. In collaboration with users from the experiments, work has started with implementing the AIDA interfaces for (binned and unbinned) histogramming, fitting and minimization as well as manipulation of tuples. These implementations have been developed by re-using existing packages either directly or by using a (thin) layer of wrappers. In addition, bindings of these interfaces to the Python interpreted language have been done using the dictionary subsystem of the LCG-AA/SEAL project. The actual status and ...

2004-01-01

317

Study of some Ayurvedic Indian medicinal plants for the essential trace elemental contents by instrumental neutron activation analysis and atomic absorption spectroscopy techniques

This paper deals with the preparation and characterization of polyaniline/TiO{sub 2} composite by XRD, UV-VIS spectra, TGA/DTA and FTIR. The composite is used as a cathode material for rechargeable battery comprising of zinc container as the anode, cellulose acetate as the separator and polyvinyl sulfate and carboxy methyl cellulose as the solid polymer electrolytes (SPE). By using the PAn/TiO{sub 2} composite as the cathode material, the cylindrical AA type rechargeable battery was fabricated and the following output was observed. The open circuit voltage (OCV) is 1.4 V and current is 250 mA to 1.0 A, 50 recharge cycles, power density is 350 A h/kg and power efficiency is 70%.

2003-02-01

318

One-step synthesis of reduced graphite oxide-silver nanocomposite

Elemental analysis of some medicinal plants used in the Indian Ayurvedic system was performed by employing instrumental neutron activation analysis (INAA) and atomic absorption spectroscopy (AAS) techniques. The samples were irradiated with thermal neutrons in a nuclear reactor and the induced activity was counted by gamma ray spectrometry using an efficiency calibrated high resolution high purity germanium (HPGe) detector. Most of the medicinal plants were found to be rich in one or more of the elements under study. The variation in elemental concentration in same medicinal plants samples collected in summer, winter and rainy seasons was studied and the biological effects of these elements on human beings are discussed. (orig.)

2009-07-01

319

British Library Electronic Table of Contents (United Kingdom)

Here, a general approach for the preparation of reduced graphite oxide (rGO)-silver nanocomposite has been investigated. Graphite oxide (GO) sheets are used as the nanoscale substrates for the formation of rGO-silver composite. GO sheets and Ag ions can be reduced at the same time, under a mild condition using l-ascorbic acid (l-AA) as reducing agent. This simple approach should find practical applications in the production of rGO-silver nanocomposite. The SEM analysis indicates that the silver particles are dispersed on graphene sheets. Raman signals of rGO in the composite are increased by the attached silver nanoparticles, displaying surface-enhanced Raman scattering activity. The degree of enhancement can be adjusted by varying the quantity of silver nanoparticles in the composite. In ...

2011-01-01

320

On the curvature in logarithmic plots of rate coefficients for chemical reactions

Microanalytical method development for Fe, Cu and Zn determination in colorectal cancer cells

In terms of the reduced potential energy barrier ? = ?uTS/kT, the rate coefficients for chemical reactions are usually expressed as proportional to e-?. The coupling between vibrational modes of the medium to the reaction coordinate leads to a proportionality of the regularized gamma function of Euler Q(a,?) = ?(a,?)/?(a), with a being the number of modes coupled to the reaction coordinate. In this work, the experimental rate coefficients at various temperatures for several chemical reactions were fitted to the theoretical expression in terms of Q(a,?) to determine the extent of its validity and generality. The new expression affords lower deviations from the experimental points in 29 cases out of 38 and it accounts for the curvature in the logarithmic plots of rate coefficients versus inverse temperature. In the absence of tunneling, conventional theories predict the curvature of these plots to be identically zero.

2011-05-06

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321

British Library Electronic Table of Contents (United Kingdom)

Microanalytical methods suitable for the determination of Fe, Cu in HT-29 (human colon adenocarcinoma) cells treated with different iron compounds (Fe(II) sulfate, Fe(III) chloride, Fe(III) citrate and Fe(III) transferrin) and cultured in medium supplemented or not with 10% (v/v) fetal calf serum (FCS) by total reflection X-ray fluorescence spectrometry (TXRF) and simultaneous graphite furnace atomic absorption spectrometry (GF-AAS) were developed. The developed TXRF method was also suitable for Zn determination in the samples. The main advantage of the proposed methods is the execution of all sample preparation steps following incubation and prior to the elemental analysis in the same Eppendorf tubes. Sample preparation was performed at microscale (115mL sample volume) with 65% nitric aci...

2011-01-01

322

Interactions of -lactoglobulin with serotonin and arachidonyl serotonin

British Library Electronic Table of Contents (United Kingdom)

Abstract -Lactoglobulin (-LG) is a lipocalin, which is the major whey protein of cow's milk and the milk of other mammals. However, it is absent from human milk. The biological function of -LG is not clear, but its potential role in carrying fatty acids through the digestive tract has been suggested. -LG has been found in complexes with lipids such as butyric and oleic acids and has a high affinity for a wide variety of compounds. Serotonin (5-hydroxytryptamine, 5-HT), an important compound found in animals and plants, has various functions, including the regulation of mood, appetite, sleep, muscle contraction, and some cognitive functions such as memory and learning. In this study, the interaction of serotonin and one of its derivatives, arachidonyl serotonin (AA-5HT), with -LG was invest...

2011-01-01

323

Biosorption of lead by citrobacter freundii immobilized on hazelnut shells

Application of a new water-soluble polyethylenimine polymer sorbent for simultaneous separation and preconcentration of trace amounts of copper and manganese and their determination by atomic absorption spectrophotometry

Biosorption of lead from aqueous solutions by living and immobilized cell of C. freundii was examined as a function of metal concentration in a batch laboratory bioreactor. Lead concentrations were analyzed using Atomic Absorption Spectrophotometer (AAS). X-ray Energy Dispersion (EDX) analyses were made in order to determine the accumulation of lead on the cells and shell surfaces. Before and after the experiments the biomaterials and adsorbents were examined by Scanning Electron Microscopy (SEM). Biosorption was detected over a range of initial lead concentrations from 25{times}10{sup -3} to 200{times}10{sup -3} kg/m{sup 3}. 15 refs., 4 figs.

1996-12-31

324

Primary study on lesion mimic mutants of rice (oryza sativa L.)

In this work, a water-soluble polymer, polyethylenimine (PEI) was used for the simultaneous separation and preconcentration of trace Cu and Mn prior to their determination by flame atomic absorption spectrometry. For this purpose, the sample and the PEI solution were mixed and the metal-bound polymer was precipitated by adding acetone. The precipitate was separated and dissolved in a minimum amounts of water and aspirated into a flame AAS. By increasing the ratio of the volumes of sample to water used in dissolving the precipitate, the analyte elements were concentrated as needed. The sorption is quantitative in the pH ?6. Detection limits were 5.2 ?g/L for Cu and 5.4 ?g/L for Mn. This method is simple, fast and precise.

2006-04-21

325

Influence of various forms of dialyzable leukocyte extracts on rat adjuvant arthritis

Nineteen lesion mimic mutants (xsl1-19) of japonica rice Xiushui11 were obtained by ?-rays irradiation treatment. All mutants belonged to whole life lesion mimic. Lesion mimic of mutants didn't largen after tillering stage, leaves didn't wither, and no effect on the plants exsert spikes and seed. When the highest temperature in day exceeded 32 degree C in seedling stage, lesion mimic of all mutant expect xsl19 disappeared. Under 32 degree C, lesion mimic would appear gradually, and symptoms weren't inhibited by high temperature after 5 leaf stage. The plant heights of all lesion mimic mutants were 47.56-63.54 cm in the tillering stage, and that of CK was 83.75 cm; but the dwarf phenomenon of mutants only appeared before tillering stage, and didn't affect plant heights finally; the heading dates of mutants were the same to the CK, the ear length of all mutants were 9.43-15.19 cm, and that of CK was 16.41 cm; the total grain quantity per spike of all mutants were 88.17-165.33, and those ...

2007-08-01

326

Electron-beam induced RAFT-graft polymerization of poly(acrylic acid) onto PVDF

Adjuvant-induced arthritis in rats is a chronic inflammatory disease, widely as an animal model for rheumatoid arthritis. In our study the effect of various fractions of dialyzable leukocyte extract (DLE): DLE I-molecular weight below 10 kDa (commercial preparation), DLE II-molecular weight below 5 kDa (suppressor fraction), DLE III-molecular weight 5-10 kDa on rat adjuvant-induced arthritis was studied. The adjuvant arthritic (AA) rats were treated with DLE fractions i.p. in solutions containing an active substance isolated from 12.5 x 10{sup 6} and 6.25 x 10{sup 6} leukocytes from day 1 (adjuvant injected) through day 18, every second day (total 9 times). Various markers in inflammation, immune function and joint destruction were evaluated: hind paw volume, serum hyaluronic acid, serum albumin and biopterin in urine. All these markers showed a significant improvement after using fraction DLE II in comparison with AA controls. Fractions DLE I ...

1994-12-31

327

Aliphatic acids: influence on sulfate mobility in a forested Cecil soil

This paper explores for the first time the post-radiation-induced-graft polymerization on solid substrate using reversible addition-fragmentation transfer (RAFT) mechanism. Radiation-induced graft polymerization onto polymers is a potentially interesting technique to create easily new materials from highly resistant polymers, e.g. surface graft polymerization of acrylic acid (AA) onto poly(vinylidene difluoride) (PVDF) improves its surface properties without losing its excellent mechanical properties. As a consequence of the radical nature of the polymerization processes it is difficult to control molecular weight of grafted chains, and therefore design and standardize the properties of the final product. RAFT polymerization is a suitable method to obtain monodisperse polymers. The ability of the RAFT agents to control the polymer chain length could be an interesting approach to improve the grafted polymers obtained by post-radiation-induced-graft polymerization ...

2005-07-01

328

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

Dissolved organic substances derived from forest litter are believed to influence the retention and movement of SO{sub 4}{sup 2{minus}} in forest soils. A column study was conducted in which {sup 35}SO{sub 4} was surface applied to a soil and leached with either low-molecular-weight aliphatic acids (AA) or a forest-litter extract. Oxalic, malonic, and succinic acids were used in the concentration range 8.0 {times} 10{sup {minus}3} to 1.0 {times} 10{sup {minus}5} mol L{sup {minus}1}. Movement of {sup 35}SO{sub 4} was determined with column depth, as was the {sup 35}SO{sub 4} activity in the collected leachates. Labeled SO{sub 4} soil movement was found to increase with increasing AA concentration. Leachate {sup 35}SO{sub 4} activity was observed to increase in the order malonic > succinic > oxalic for acid treatments > 1.0 {times} 10{sup {minus}4} mol L{sup {minus}1}. The 1.0 {times} 10{sup {minus}5} mol L{sup {minus}1} acid treatments ...

329

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

330

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

331

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

332

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

333

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

334

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

335

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

336

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

337

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

338

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

339

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

340

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

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341

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

342

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

343

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

344

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

345

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

346

Production of bone cement composites: effect of fillers, co-monomer and particles properties

Preconcentration and determination of trace amounts of lead (II) as thenoyltrifluoroacetone complex with dibenzo-18-crown-6 by synergistic extraction and atomic absorption spectrometry

Artificial bone cements (BCs) based on poly(methyl methacrylate) (PMMA) powders and methyl methacrylate (MMA) liquid monomer also present in their formulation small amounts of other substances, including a chemical initiator compound and radiopaque agents. Because inadequate mixing of the recipe components during the manufacture of the bone cement may compromise the mechanical properties of the final pieces, new techniques to incorporate the fillers into the BC and their effect upon the mechanical properties of BC pieces were investigated in the present study. PMMA powder composites were produced in situ in the reaction vessel by addition of X-ray contrasts to the reacting MMA mixture. It is shown that this can lead to much better mechanical properties of test pieces, when compared to standard bone cement formulations, because enhanced dispersion of the radiopaque agents can be achieved. Moreover, it is shown that the addition of hydroxyapatite (HA) and acrylic acid ...

347

Post-column reaction detector for platinum(II) antieoplastic agents

A new method for the preconcentration and determination of trace amounts of lead at the {mu}g/L level in natural waters has been established based on the formation of the thenoyltrifluoroacetone (TTA) complex with dibenzo-18-crown-6 (DB18C6) by means of synergistic extraction and back-extraction combined with atomic absorption spectrometry (AAS). The effect of various factors (synergism with TTA and DB18C6, shaking time, preconcentration factor, composition of the extracted species, and foreign ions etc.) on the extraction and back-extraction of lead has been investigated in detail. The lead-TTA chelate in o-dichlorobenzene forms a stable adduct with DB18C6 as Pb(TTA){sub 2} DB18C6. The stability constant ({beta}) of the adduct determined by curve fitting method was log {beta} = 4.2. The amount of lead in natural waters such as tap water (Kanazawa University) and Kakehashi river (Komatsu City) determined by the present method was found to be 0.64 {+-} 0.02 {mu}g/L ...

1998-07-01

348

Oxide growth on aluminium alloys in the presence of ammonium fluoborate

The development and evaluation of a post-column reaction detector sensitive to platinum(II) complexes is presented in which sodium bisulfite is used as the derivatizing agent with potassium dichromate as an activating agent. The influences of mobile phase changes (i.e., pH, organic modifiers, electrolytes), oxygen, metal ions, and order of reagent addition on reaction kinetics and product yield are defined and used in optimization of detector response. Detection at lambda/sub max/ 290 nm results in an on-line post-column sensitivity of 40-60 ng/mL for selected cis-dichloroplatinum complexes and a sensitivity of 300-1200 ng/mL for four (substituted)-malonato-platinum complexes. The reaction detector is used to monitor the kinetics of aquation of cisplatin (CDDP) and to quantitate CDDP degradation in plasma. As the sensitivity for CDDP in plasma is comparable to that achieved from high pressure liquid chromatography (HPLC) effluent fractionation/off-line flameless atomic absorption ...

1984-03-01

349

On Sums of Generating Sets in (Z_2)^n

The aim of this study as to determine the mechanisms involved in using ammonium fluoborate as a reducing atmosphere when preheating a high magnesium content aluminium alloy. Rutherford Backscattering (RBS) has been the major technique used in the analysis of samples, it revealed significant reduction in both the diffusion of magnesium to the surface and the calculated oxide thickness in the presence of NH{sub 4}BF{sub 4}. At temperatures above 500 deg C in air, SEM images revealed depressions and voids due to incipient melting at various stages, around the grain boundaries. Grain boundaries effectively acted as pipes aiding the diffusion of magnesium to the surface. These results have been verified through compositional analysis with both RBS and auger electron spectroscopy (AES). Results from NH{sub 4}BF{sub 4} atmosphere preheat conditions showed significant improvements. It was verified experimentally that above 500 deg C , AA5182 alloys undergo incipient ...

1996-12-31

350

Keck Diffraction-Limited Imaging of the Young Quadruple Star System HD 98800

Let A and B be two affinely generating sets of (Z_2)^n. As usual, we denote their Minkowski sum by A+B. How small can A+B be, given the cardinalities of A and B? We give a fairly tight answer to this question. Our bound is attained when both A and B are unions of cosets of a certain subgroup of (Z_2)^n. These cosets are arranged as Hamming balls, the smaller of which has radius 1. By similar methods, we reprove the Freiman-Ruzsa theorem in (Z_2)^n, with an optimal upper bound. Denote by F(K) the maximal spanning constant || / |A|, over all subsets A of (Z_2)^n with doubling constant |A+A| / |A| < K. We explicitly calculate F(K), and in particular show that 4^K / 4K < F(K) (1+o(1)) < 4^K / 2K. This improves the estimate F(K) = poly(K) 4^K, found recently by Green and Tao and by Konyagin.

2011-01-01

351

Host derived inflammatory phospholipids regulate rahU (PA0122) Gene, Protein, and Biofilm Formation in Pseudomonas aeruginosa

This paper presents diffraction-limited 1-18 micron images of the young quadruple star system HD 98800 obtained with the W. M. Keck 10-m telescopes using speckle and adaptive optics imaging at near-IR wavelengths and direct imaging at mid-IR wavelengths. The two components of the visual binary, A and B, both themselves spectroscopic binaries, were separable at all wavelengths, allowing us to determine their stellar and circumstellar properties. Combining these observations with spectroscopic data from the literature, we derive an age of 10 Myr, masses of 0.93 and 0.64 M_sun and an inclination angle of 58 deg for the spectroscopic components of HD 98800 B, and an age of 10 Myr and a mass of 1.1 M_sun for HD 98800 Aa. Our data confirm that the large mid-IR excess is entirely associated with HD 98800 B. This excess exhibits a black body temperature of 150 K and a strong 10 micron silicate emission feature. The theoretical equilibrium radius of large, perfectly ...

2001-01-01

352

British Library Electronic Table of Contents (United Kingdom)

This study describes the role of "inflammatory" oxidized (Ox) phospholipids in regulation of rahU (PA0122) expression and biofilm formation in Pseudomonas aeruginosa (383) wild type (rahU+) and rahU mutant (rahU-) strains. Functional analysis of RahU protein from P. aeruginosa in presence of Ox-phospholipids show: (a) LysoPC modulates RahU gene/and protein expression in rahU+ cells; (b) rahU promoter activity is increased by lysoPC and inhibited by PAPC, Ox-PAPC and arachidonic acid; the latter inhibitory effect can be reversed by lysoPC, which was enzymatically derived from PAPC; (c) biofilm formation increased in rahU- cells as compared to rahU+; and (d) inhibition of rahU promoter activity by PAPC and AA (but not lysoPC) showed significantly augmented biofilm formation in rahU+ but not ...

2011-01-01

353

Functionalizing titania nanoparticle surfaces in a fluidized bed plasma reactor

Determination of impurities in sialon by ICP-AES

Functionalizing nanoparticle surfaces is essential for achieving homogeneous dispersions of monodisperse particles in polymer nanocomposites for successful utilization in engineering applications. Functionalization reduces the surface energy of the nanoparticles, thereby limiting the tendency to agglomerate. Moreover, reactive groups on the surface can also participate in the polymerization, creating covalent bonds between the inorganic and organic phases. In this paper, a fluidized bed inductively coupled plasma (FB-ICP) reactor is used to break apart the agglomerates and functionalize commercial TiO2 nanoparticle powders in a batch of several grams. The fluidized bed could be implemented into a continuous flow reactor, potentially making this a viable method to treat larger quantities of commercial powders. The particles are treated with acrylic acid (AA) and tetraethylorthosilicate (TEOS) plasma and the functionalized particles were collected separately from ...

2009-11-18

354

Cd speciation in biomass fly ash particles after size separation by centrifugal SPLITT

Impurities (Ca, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, Ti, Y, Zn and Zr) in sialon powder were determined by the following procedure: A sample (0.5 g) was heated with a mixture of hydrofluoric acid (3 ml) and nitric acid (1 ml) in a Teflon pressure vessel at 170degC for 16 h. The contents of the vessel were transferred into a platinum crucible containing phosphoric acid (4 ml) and heated on a hot plate until the opaque appearance of the content changed to a clear-syrupy fluid. The fluid was diluted to 100 ml with water and used for ICP-AES analysis of all impurity elements except K, which was determined by AAS. It was necessary to match closely the matrix concentrations (H_3PO_4, Al and/or Y) of the standard solutions with those of sialon sample solutions for the determination of impurities because of interferences of the matrix components. This method was successfully applied to the determination of impurities in commercial sialon samples. (author).

355

Acidity of H-Y zeolites: Role of extralattice aluminum

The finest particle size fractions ({le} 25 {mu}m) in four fly ash samples from fluidised bed combustion of three biomass based fuels and a municipal solid waste fuel were size separated using a centrifugal SPLITT fractionation cell. The ashes were separated into different size fractions and the cadmium concentration, partition and speciation in each separated fraction were then investigated in relation to their possible leaching. The fractionation was evaluated by environmental scanning electron microscopy, which also provided indications of the associations between Cd and other main elements on the particles through the use of X-ray fluorescence mapping. The total concentration of Cd in each fraction was determined by AAS analysis which showed different dependence on the ash particle size in the case of biomass or waste fuels. In addition, the speciation of Cd in each fraction, investigated by sequential chemical extractions and X-ray powder diffraction analysis, ...

2002-08-01

356

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

The nature of extralattice aluminum and its effect on acidity in zeolites was studied. A series of zeolites (some commercial), dealuminated by various methods, were obtained having Si/Al ratios between 1.5 and 20. These were characterized using volumetric sorption, XRD, AA, NMR, and reaction studies. Samples dealuminated using ammonium hexafluorosilicate were found to contain little or no extralattice aluminum. In contrast, steam-dealuminated zeolites had large amounts of extralattice aluminum. In some cases a significant portion of the extralattice aluminum was unobservable by [sup 27]Al NMR, suggesting the existence of an aluminum species of low symmetry. Proton NMR indicated that all the protons were associated with the lattice aluminum atoms. Depending on the preparation history, different groups of H-Y zeolites exhibited different maxima in catalytic activity as a function of aluminum content. The maxima in catalytic activity for n-pentane cracking was found ...

1993-02-01

357

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

358

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

359

Structural Chemistry of Human SET Domain Protein Methyltransferases

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

360

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

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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361

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

362

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

363

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

364

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

365

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

366

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

367

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

368

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

369

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

370

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

371

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

372

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

373

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

374

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

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

375

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

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

376

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

377

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

378

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, ...

379

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

380

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

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381

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

382

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

383

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

384

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

385

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

386

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

387

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

388

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

389

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

390

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

391

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

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

392

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

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

393

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

394

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

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

395

Identification of three related human GRO genes encoding cytokine functions

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

396

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

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 three forms are derived ...

397

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

398

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

399

Construction of a human MluI YAC library

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

400

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

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 to unligated vector fragments that were ...

1994-05-01

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401

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

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 QTLs). Simultaneous use of ...

1993-08-01

402

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

403

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

404

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

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

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

405

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

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

406

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

407

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

408

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

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

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.

409

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

410

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

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

411

Transcriptional regulation in Drosophila: the post-genome challenge.

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 were subjected to BLAST similarity searches and annotated with Gene Ontology (GO) and ...

2011-03-14

412

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

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

413

Zinc/air battery R and D research and development of bifunctional oxygen electrode: Tasks I and II, Final report

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 similarities between ...

1990-06-21

414

The mechanism of metal nanoparticle formation in plants: limits on accumulation

Studies were conducted of the bifunctional oxygen electrode. The development of a rechargeable metal-oxygen (air) cell has been hampered to a great extent by the lack of a stable and cost effective oxygen electrode capable of use during both charge and discharge. The first type of bifunctional electrode consists of two distinct catalytifc layers. The oxygen reduction catalyst layer containing a supported gold catalyst is in contact with a hydrophilic nickel layer in which evolution of oxygen takes place. Loadings of gold from 0.5 to 1.0 mg/cm/sup 2/ were investigated; carbon, graphite, metal, and spinel oxides were evaluated as substrates. The second part of the research effort was centered on developing a reversible oxygen electrode containing only one catalytic layer for both reduction and evolution of oxygen. The work was directed specifically to the study of perovskite type of oxides with the composition AA/sup 1/BO/sub 3/ where A is an element of the ...

1986-12-01

415

Spectral absorption properties of colored dissolved organic matter (CDOM) and total suspended matter (TSM) of inland waters

Metal nanoparticles have many potential technological applications. Biological routes to the synthesis of these particles have been proposed including production by vascular plants, known as phytoextraction. While many studies have looked at metal uptake by plants, particularly with regard to phytoremediation and hyperaccumulation, few have distinguished between metal deposition and metal salt accumulation. This work describes the uptake of AgNO{sub 3}, Na{sub 3}Ag(S{sub 2}O{sub 3}){sub 2}, and Ag(NH{sub 3}){sub 2}NO{sub 3} solutions by hydroponically grown Brassica juncea and the quantitative measurement of the conversion of these salts to silver metal nanoparticles. Using X-ray absorption near edge spectroscopy (XANES) to determine the metal speciation within the plants, combined with atomic absorption spectroscopy (AAS) for total Ag, the quantity of reduction of Ag{sup I} to Ag{sup 0} is reported. Transmission electron microscopy (TEM) showed Ag particles of ...

2009-08-15

416

Partitioning of trace metals in the chemical fractions of bed-load sediments of Nahr-Ibrahim river, Lebanon

Spectral absorption properties of total suspended matter (TSM) and colored dissolved organic matter (CDOM) are important for the use of the bio-optical model to estimate water quality parameters. This study aims to investigate the variation in the absorption coefficients of TSM and CDOM of inland waters. A total of 92 water samples were collected from Shitoukoumen Reservoir and Songhua Lake in Northeast China, analyzed for TSM and Chl-a, and measured for the absorption coefficient of TSM, CDOM and total pigments using a laboratory spectrophotometer. The absorption coefficient of TSM has been decomposed for phytoplankton and inorganic sediments. The results show that for Shitoukoumen Reservoir, CDOM has strong absorptions with shallow absorption slopes (i.e., the coefficient S in a(?)=a(?0)exp[-S(?- ?0)]) and large absorption at 355 nm; and for Songhua Lake, CDOM follows similar spectral absorption curves but less variation in the S value. The results also show TSM ...

2010-08-01

417

New Forming Limits For Light Alloys By Means Of Electromagnetic Forming And Numerical Simulation Of The Process

Full text.Sediments are the ultimate sink of trace elements. The total metal analysis may only give information concerning possible enrichment of metals. The analysis of metal partitioning in the different chemical components of sediments (exchangeable, carbonate, easily reducible, moderately reducible, organic and residual); give a detailed information on the way in which these metals are bound to sediments, their mobilization capacity and their ability to affect water quality under different environmental conditions. The studied river basin is dominated by limestone formation, the enrichment of metals in the carbonate sediment fraction is a high probability. The objective of the study was to determine the percentage of the total metal content (Fe, Mn, Zn, Cu and Pb) in the six chemical fractions of the bed load sediments of Nahr-Ibrahim river during the dry season and verify the role of carbonate for metal sediment deposition. Bed load sediments were sampled at five locations 13Km ...

1999-11-02

418

New Forming Limits For Light Alloys By Means Of Electromagnetic Forming And Numerical Simulation Of The Process

It is well known that one of the main advantages of the high speed forming (HSF) processes is the improvement in the forming limits of the used materials.Using the Electromagnetic Forming (EMF) technology two materials have been tested with different mechanical and physical properties: the AA5754 aluminium and the AZ31B magnesium alloys.The EMF process principle can be described as follows: A significant amount of electrical energy is stored in a bank of capacitors which are suddenly discharged releasing all the stored energy. This electric discharge runs through a coil which generates an intense transient magnetic field. At the same time transient Eddy currents are induced in the electrically conductive part placed some millimetres far from the coil. Another intense magnetic field is generated due to those Eddy currents but on the opposite direction as the one generated by the coil. A big magnetic repulsion force is created between the part and the coil. This ...

2007-04-07

419

Investigation of amine amino acid salts for carbon dioxide absorption

It is well known that one of the main advantages of the high speed forming (HSF) processes is the improvement in the forming limits of the used materials.Using the Electromagnetic Forming (EMF) technology two materials have been tested with different mechanical and physical properties: the AA5754 aluminium and the AZ31B magnesium alloys.The EMF process principle can be described as follows: A significant amount of electrical energy is stored in a bank of capacitors which are suddenly discharged releasing all the stored energy. This electric discharge runs through a coil which generates an intense transient magnetic field. At the same time transient Eddy currents are induced in the electrically conductive part placed some millimetres far from the coil. Another intense magnetic field is generated due to those Eddy currents but on the opposite direction as the one generated by the coil. A big magnetic repulsion force is created between the part and the coil. This ...

2007-04-07

420

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

The carbon dioxide capture potential of amine amino acid salts (AAAS), formed by mixing equinormal amounts of amino acids; e.g. glycine. B-alanine and sarcosine, with an organic base; 3-(methylamino)propylamine (MAPA), was assessed by comparison with monoethanolamine (MEA), and with amino acid salt (AAS) from amino acid neutralized with an inorganic base; potassium hydroxide (KOH). Carbon dioxide absorption and desorption experiments were carried out on the solvent systems at 40{sup o}C and 80{sup o}C respectively. Experimental results showed that amine amino acid salts have similar CO{sub 2} absorption properties to MEA of the same concentration. They also showed good signs of stability during the experiments. Amino acid salt from an inorganic base, KOH, showed lower performance in CO{sub 2} absorption than the amine amino acid salts (AAAS) mainly due to a lower equilibrium temperature sensitivity. AAAS showed better performance than MEA of same concentration. ...

2010-09-15

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421

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

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

422

Translational bioinformatics and healthcare informatics: computational and ethical challenges.

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 using ...

2010-10-04

423

Transient suppression of MLH1 allows effective single-nucleotide substitution by single-stranded DNA oligonucleotides

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

424

British Library Electronic Table of Contents (United Kingdom)

Short synthetic single-stranded oligodeoxyribonucleotides (ssODNs) can be used to introduce subtle modifications into the genome of mouse embryonic stem cells (ESCs). We have previously shown that effective application of ssODN-mediated gene targeting in ESC requires (transient) suppression of DNA mismatch repair (MMR). However, whereas transient down-regulation of the mismatch recognition protein MSH2 allowed substitution of 3 or 4 nucleotides, 1 or 2 nucleotide substitutions were still suppressed. We now demonstrate that single- or dinucleotide substitution can effectively be achieved by transient down-regulation of the downstream MMR protein MLH1. By exploiting highly specific real-time PCR, we demonstrate the feasibility of substituting a single basepair in a non-selectable gene. Howev...

2011-01-01

425

Thyroid Cathepsin K: Roles in Physiology and Thyroid Disease

British Library Electronic Table of Contents (United Kingdom)

The human genome encodes 11 cysteine cathepsins belonging to the papain-like family of cysteine peptidases that are known predominantly as endo-lysosomal enzymes. However, it is now understood that the functions and activities of cysteine cathepsins are not limited to endo-lysosomal compartments, as they are also active in the peri- and extracellular space. The thyroid gland is an endocrine organ where such intra- and extracellular proteolytic activities are required to solubilize the prohormone thyroglobulin from its luminal, covalently cross-linked storage forms for subsequent processing into smaller protein fragments and thyroid hormone liberation. Cathepsin K has been identified as one of the cysteine cathepsins with a crucial role in thyroglobulin processing. However, cathepsin K has ...

2011-01-01

426

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

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

427

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

428

Report on NCI symposium: comparison of mechanisms of carcinogenesis by radiation and chemical agents. II. Cellular and animal models

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

429

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

The point at which the common final pathway for induction of cancer by chemical carcinogens and ionizing radiation has not been identified. Although common molecular targets are suggested by recent findings about the role of oncogenes, the mechanism by which the deposition of radiation energy and the formation of adducts or other DNA lesions induced by chemicals affects the changes in the relevant targets may be quite different. The damage to DNA that plays no part in the transformation events, but that influences the stability of the genome, and therefore, the probability of subsequent changes that influence tumorigenesis may be more readily induced by some agents than others. Similarly, the degree of cytotoxic effects that disrupt tissue integrity and increase the probability of expression of initiated cells may be dependent on the type of carcinogen. Also, evidence was presented that repair of the initial lesions could be demonstrated after exposure to low-LET ...

1984-05-20

430

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

431

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

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

432

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

433

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

434

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

435

Ionizing radiation is a potent inducer of mitotic recombination in mouse embryonic stem cells

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

436

British Library Electronic Table of Contents (United Kingdom)

Maintenance of genomic integrity in embryonic cells is pivotal to proper embryogenesis, organogenesis and to the continuity of species. Cultured mouse embryonic stem cells (mESCs), a model for early embryonic cells, differ from cultured somatic cells in their capacity to remodel chromatin, in their repertoire of DNA repair enzymes, and in the regulation of cell cycle checkpoints. Using 129XC3HF1 mESCs heterozygous for Aprt, we characterized loss of Aprt heterozygosity after exposure to ionizing radiation. We report here that the frequency of loss of heterozygosity mutants in mESCs can be induced several hundred-fold by exposure to 5-10Gy of X-rays. This induction is 50-100-fold higher than the induction reported for mouse adult or embryonic fibroblasts. The primary mechanism underlying the...

2011-01-01

437

Involvement of the Tpl-2/cot oncogene in MMTV tumorigenesis.

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

438

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

439

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

440

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

Human cDNA mapping using fluorescence in situ hybridization

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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441

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

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

442

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

443

High-throughput proteomics of breast carcinoma cells: a focus on FTICR-MS

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

444

Genotyping of Candida albicans on the basis of polymorphisms of ALT repeats in the repetitive sequence (RPS)

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

445

British Library Electronic Table of Contents (United Kingdom)

SummaryBackgroundCandida albicans is one of the most important etiologic agents causing superficial and deep fungal infections. For prevention of candidiasis, it is important to develop a rapid system that discriminates C. albicans at the strain level.ObjectiveTo develop a system that can identify C. albicans at the strain level.MethodsGenomic DNAs were purified from 179 clinical isolates of C. albicans, and were used as templates for PCR amplification of 25S rDNA and ALT repeats in repetitive sequences (RPSs). PCR products generated from ALT repeats were digested with EcoRI and/or ClaI in order to study the relationships between restriction profiles and amplification profiles.ResultsOne hundred and seventy nine clinical isolates were grouped into genotypes A (92 isolates), B (38 isolates)...

2006-01-01

446

Genomic survey of prepulse inhibition in mouse chromosome substitution strains

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

447

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

448

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

449

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

450

DNA repair: As influenced by age, nutrition, and exposure to toxic substances

Comparative profiling of the transcriptional response to soybean cyst nematode infection of soybean roots by deep sequencing

In evaluating the risk associated with low levels of exposure to toxicants, it is clear that DNA repair, one of the main defenses against agent damage, is not a constant. It can be modified by age, time of day, and physiological state. Nutrition, especially caloric restriction (CR), can modify almost every step in the process of protecting genomic integrity. And history of exposure can modify DNA repair. Thus, the conditions of exposure are almost as important to toxicity as the exposure itself, even at the level of DNA repair. Extrapolation from high to low dose, to be consistent with what is known, should be less a mathematical exercise than an exercise in toxicological judgement, which puts the exposure in proper perspective. This appears to be true at almost every level in the process including a response with a toxic stimulus, even those thought to be very basic, such as DNA repair.

451

British Library Electronic Table of Contents (United Kingdom)

To gain insight into the changes in the transcriptome of soybean roots during soybean cyst nematode (SCN) infection, we conducted genome-wide gene expression profiling using serial analysis of gene expression (SAGE) combined with Solexa sequencing. More than 3 million tags were generated from the SCN-infected and uninfected roots, and 366941 and 314591 clean UniTags were obtained from SCN-infected and uninfected samples, respectively. In the SCN-infected sample, 48249 UniTags represented 18114 reference genes. In the uninfected control, 46290 UniTags represented 19323 reference genes. Comparison of tag frequencies identified 1405 genes that were expressed at greater levels in SCN-infected roots than in uninfected roots, and 1191 genes that were expressed at lower levels. Quantitative real-...

2011-01-01

452

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

Association of the polymorphism of the CAG repeat in the mitochondrial DNA polymerase gamma gene (POLG) with testicular germ-cell cancer

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

453

British Library Electronic Table of Contents (United Kingdom)

Background: A possible association between the polymorphic CAG repeat in the DNA polymerase gamma (POLG) gene and the risk of testicular germ-cell tumours (TGCT) was investigated in this study. The hypothesis was prompted by an earlier preliminary study proposing an association of the absence of the common 10-CAG-long POLG allele with testicular cancer as well as previously reported in some European populations' association with male subfertility, which is a condition carrying an increased risk of TGCT. Patients and methods: The number of CAG repeats in both POLG alleles was established in 243 patients with TGCT and in 869 controls by the analysis of the genomic DNA fragment. Results: A significantly higher proportion of men homozygous allele of other than the common 10 CAG repeats was fou...

2008-01-01

454

Algorithms for Internal Validation Clustering Measures in the Post Genomic Era

Agrobacterium-mediated transformation of cotton (Gossypium hirsutum L.) with a fungal phytase gene improves phosphorus acquisition

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 considered. Experiments on 12 ...

2011-01-01

455

British Library Electronic Table of Contents (United Kingdom)

A phytase gene (phyA), isolated from Aspergillus ficuum (AF537344), was introduced into cotton (Gossypium hirsutum L.) by Agrobacterium-mediated transformation to increase the phosphorus (P) acquisition efficiency of cotton. Southern and Northern blot analyses showed that the phyA was successfully incorporated into the cotton genome and expressed in transgenic lines. After growing for 45?days with phytate (Po) as the only P source, the shoot and root dry weights of the transgenic plants all increased by nearly 2.0-fold relative to those of wild-type plants, but were similar to those of transgenic plants supplied with inorganic phosphorus. The phytase activities of root extracts prepared from transgenic plants were 2.4- to 3.6-fold higher than those from wild-type plants, and the extracellu...

2011-01-01

456

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

[Cloning of the gene for thermostable Thermus aquaticus YT1 DNA polymerase and its expression in Escherichia coli].

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

457

Radiation accidents in the Southern Urals (1949-1967) and human genome damage.

Using the phasmid vector pSL5, the genomic DNA fragment of T. aquaticus YT1 which contained the thermostable DNA polymerase (Taq-polymerase) gene was cloned. The BglII fragment of this genome locus was subcloned in the BamHI site of the pUC19 plasmid. To optimize the Taq-polymerase gene expression in E. coli cells, the gene was cloned in the correct reading frame regarding the initiation ATG codon of the pPR-TGATG-1 expression vector. The gene expression in this vector was controlled by the phage lambda PR promoter and the temperature-sensitive phage lambda repressor. We used PCR to amplify the short 5'-end fragment of the Taq-polymerase gene coding for the part into which an artificial SacI site was introduced. This site has been used for cloning the PCR product into the pPR-TGATG-1 vector, and the missing gene part was cloned into the KpnI site of the PCR product from the natural cloned gene. The cells of the E. coli PVG-A1 strain, which was ...

458

Evolution of Hox Post-Transcriptional Regulation by Alternative Polyadenylation and MicroRNA Modulation Within 12 Drosophila Genomes.

A series of radioactive catastrophes (from 1948 to 1967) in the Southern Urals in the USSR led to intensive environmental contamination. Radioactive wastes were dispersed over the 20000 km(2) territory of four provinces-Chelyabinsk, Sverdlovsk, Tyumen' and Kurgan-due to the activity of the military facility that was built in 1948 for the production of nuclear bomb plutonium. The results of 50 years of investigations into the consequences of these disasters allow a general picture of the events that occurred to be reconstructed and allow the medical consequences of the irradiation of about half a million residents to be depicted. However, due to the atmosphere of secrecy and inadequate medical procedures, the results of medical studies of radiation victims are scant. The current protocols present a unique opportunity to study the DNA damage at the nucleotide resolution level in the genome of inhabitants of the given region, who presumably received chronic doses of ...

2002-11-01

459

Construction of a genome-wide human BAC-Unigene resource. Final progress report, 1989--1996

Hox genes encode a family of transcriptional regulators that operate differential developmental programs along the anteroposterior axis of bilateral animals. Regulatory changes affecting Hox gene expression are believed to have been crucial for the evolution of animal body plans. In Drosophila melanogaster, Hox expression is post-transcriptionally regulated by microRNAs (miRNAs) acting on target sites located in the 3' untranslated regions (3'UTRs) of Hox mRNAs. Notably, recent work has shown that during D. melanogaster development Hox genes produce mRNAs with variable 3'UTRs (short and long forms) in different sets of tissues as a result of alternative polyadenylation; importantly, Hox short and long 3'UTRs contain very different target sites for miRNAs. Here, we use a computational approach to explore the evolution of Hox 3'UTRs treated with especial regard to miRNA regulation. Our work is focused on the 12 Drosophila species for which genomic sequences are ...

2011-03-24

460

Cloning, Expression, Crystallization and Preliminary Crystallographic Analysis of a Pentapeptide-repeat Protein (Rfr23) from the Bacterium Cyanothece 51142l

Currently, over 30,000 mapped STSs and 27,000 mapped Unigenes (non-redundant, unigene sets of cDNA representing EST clusters) are available for human alone. A total of 44,000 Unigene cDNA clones have been supplied by Research Genetics. Unigenes, or cDNAs are excellent resource for map building for two reasons. Firstly, they exist in two alternative forms -- as both sequence information for PCR primer pairs, and cDNA clones -- thus making library screening by colony hybridization as well as pooled library PCR possible. The authors have developed an efficient and robust procedure to screen genomic libraries with large number of DNA probes. Secondly, the linkage and order of expressed sequences, or genes are highly conserved among human, mouse and other mammalian species. Therefore, mapping with cDNA markers rather than random anonymous STSs will greatly facilitate comparative, evolutionary studies as well as physical map building. They have currently deconvoluted ...

1996-12-31

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461

Biological and Chemical Security

A unique feature of cyanobacteria genomes is the abundance of genes that code for hypothetical proteins containing tandem pentapeptide repeats approximately described by the consensus motif A(N/D)LXX. To date, the structures of two pentapeptide-repeat proteins (PRPs) have been determined, with the tandem pentapeptide-repeat sequences observed to adopt a novel type of right-handed quadrilateral ?-helix, or Rfr-fold, in both structures. One structure, Mycobacterium tuberculosis MfpA, is a 183-residue protein that contains 30 consecutive pentapeptide repeats and appears to offer antibiotic resistance by acting as a DNA mimic. The other structure, Cyanothece 51142 Rfr32, is a 167-residue protein that contains 21 consecutive pentapeptide repeats. The function of Rfr32, like the other 35 hypothetical PRPs identified in the genome of Cyanothece, is unknown. In an effort to understand the role of PRPs in cyanobacteria and to better characterize the ...

2006-01-01

462

Scaling of the distribution function and the critical exponents near the point of a marginal stability under the Vlasov-Poisson equations

The LLNL Chemical & Biological National Security Program (CBNP) provides science, technology and integrated systems for chemical and biological security. Our approach is to develop and field advanced strategies that dramatically improve the nation's capabilities to prevent, prepare for, detect, and respond to terrorist use of chemical or biological weapons. Recent events show the importance of civilian defense against terrorism. The 1995 nerve gas attack in Tokyo's subway served to catalyze and focus the early LLNL program on civilian counter terrorism. In the same year, LLNL began CBNP using Laboratory-Directed R&D investments and a focus on biodetection. The Nunn-Lugar-Domenici Defense Against Weapons of Mass Destruction Act, passed in 1996, initiated a number of U.S. nonproliferation and counter-terrorism programs including the DOE (now NNSA) Chemical and Biological Nonproliferation Program (also known as CBNP). In 2002, the Department of Homeland Security ...

2002-12-19

463

Neutron activation analysis for determination of selected trace elements responsible for immunity in foodstuffs and water in egypt

A model system, described by the consistent Vlasov-Poisson equations under periodical boundary conditions, has been studied numerically near the point of a marginal stability. The power laws, typical for a system, undergoing a second-order phase transition, hold in a vicinity of the critical point: (i) A {proportional_to} -{theta}{sup {beta}}, {beta}=1.907{+-}0.006 for {theta} {<=} 0, where A is the saturated amplitude of the marginally-stable mode; (ii) {chi} {proportional_to} {theta}{sup -{gamma}} as {theta} {yields} 0, {gamma}={gamma}{sub -}=1.020{+-}0.008 for {theta} < 0, and {gamma}={gamma}{sub +}=0.995{+-}0.020 for {theta} > 0, where {chi}={partial_derivative}A/{partial_derivative}F{sub 1} at F{sub 1} {yields} 0 is the susceptibility to external drive of the strain F{sub 1}; (iii) at {theta}=0 the system responds to external drive as A {proportional_to} F{sub 1}{sup 1/{delta}}, and {delta}=1.544{+-}0.002. {theta}=(<v{sup 2}>-<v{sub ...

2000-08-01

464

Hydrogen activities in the European Union work-programme. Paper

Selenium (Se), zinc (Zn), magnesium (Mg), molybdenum (Mo) and vanadium (V) in 28 types of Egyptian common foodstuffs as well as drinking and irrigation water samples were determined using neutron activation analysis (NAA) and atomic absorption spectrometry (AAS). The samples were collected from 74 sites over 13 governorates as well as the Nile river, wells and tap water in the regions of the Nile Delta, Sinai, the east and west desert, and north and south Egypt. These trace elements were chosen according to international references, which show the close relationship of their deficiencies to immunity-related diseases. Calculation values of daily uptake per capita were made with the results of analysis. The results, as calculated per 100 g dry weight, showed that some Egyptian foods are rich in Se including such fish (0.94 #mu#g), sesame (0.88 #mu#g), beef meat (0.48 #mu#g), instant tea (0.42 #mu#g), mushroom (0.34 #mu#g) and eggs (0.3 #mu#g), whereas the vegetables ...

465

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

Looking at some of the national and international developments in hydrogen technology it becomes clear which important contributions the hydrogen technology oriented activities of the EU have helped to prepare and trigger: (a) Transport Energy Strategy (TES): This initiative of 7 major German automobile and mineral oilcompanies is aimed at an industrial consensus on one or two gasoline alternative fuels, which are to be presented to the German Ministry of Transport. An intermediate trend is that hydrogen may become the fuel of choice. (b) BMW: The Bayerischen Motorenwerke have already very early exposed themselves to the vehicle and component development of hydrogen as a vehicle fuel, focussing on a strategy from CNG to LNG and LH{sub 2}. (c) Opel and GM: Opel has recently announced they have chosen hydrogen as the primary long term fuel for their fuel cell vehicles to be commercialized starting in 2004. (d) CFCP: The California Fuel Cell Partnership with partners from industry and ...

2000-07-01

466

Tree and fruit traits of progenies from the cross between (Annona cherimola Mill.??A. squamosa L.)??A. reticulata L. and approaches for the introgression of valuable genes from A. reticulata L.

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

467

British Library Electronic Table of Contents (United Kingdom)

Annona reticulata L. possesses many traits desirable in other edible annonas, and hybridization is the simplest means to combine desirable features of related species. In this study, A. reticulata was hybridized with atemoya (A. cherimola Mill.??A. squamosa L.), and 250 trispecies hybrids were studied for 28 traits (12 tree traits and 16 fruit traits) with the objective of salvaging useful genes from the three edible annonas and determining the extent of variation in the progeny. The heterozygous nature of Annona spp. and simultaneous segregation of three distant genomes resulted in a tremendous heterogeneity in the progenies. The fitness of the progenies ranged from very vigorous to very weak, with a wide range of values for tree height (1.75?5.9?m), canopy spread (1.15?5.07?m) and trunk...

2010-01-01

468

Trans-activation of the JC virus late promoter by the tat protein of type 1 human immunodeficiency virus in glial cells

The mitochondrial genome of the entomophagous endoparasite Xenosvesparum (Insecta: Strepsiptera)

Progressive multifocal leukoencephalopathy (PML) is a demyelinating disease of the central nervous system caused by the JC virus (JCV), a human papovavirus. PML is a relatively rare disease seen predominantly in immunocompromised individuals and is a frequent complication observed in AIDS patients. The significantly higher incidence of PML in AIDS patients than in other immunosuppressive disorders has suggested that the presence of human immunodeficiency virus type 1 (HIV-1) in the brain may directly or indirectly contribute to the pathogenesis of this disease. In the present study the authors have examined the expression of the JCV genome in both glial and non-glial cells in the presence of HIV-1 regulatory proteins. They find that the HIV-1-encoded trans-regulatory protein tat increases the basal activity of the JCV late promoter, JCV{sub L}, in glial cells. They conclude that the presence of the HIV-1-encoded tat protein may positively affect the JCV lytic cycle ...

1990-05-01

469

TMPRSS6 rs855791 modulates hepcidin transcription in vitro and serum hepcidin levels in normal individuals.

In this study, the nearly complete sequence (14,519 bp) of the mitochondrial DNA (mtDNA) of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera) is described. All protein coding genes (PCGs) are in the arrangement known to be ancestral for insects, but three tRNA genes (trnA, trnS(gcu), and trnL(uag)) have transposed to derived positions and there are three tandem copies of trnH, each of which is potentially functional. All of these rearrangements except for that of trnL(uag) is within the short span between nad3 and nad4 and there are numerous blocks of unassignable sequence in this region, perhaps as remnants of larger scale predisposing rearrangements. X. vesparum mtDNA nucleotide composition is strongly biased toward As and Ts, as is typical for insect mtDNAs. There is also significant strand skew in the distribution of these nucleotides, with the J-strand being richer in A than T and in C than G, and the N-strand showing an opposite skew for complementary pairs of ...

2005-12-01

470

Systems Biology Approach in Chlamydomonas Reveals Connections between Copper Nutrition and Multiple Metabolic Steps[C][W][OA

The iron hormone hepcidin is inhibited by matriptase-2, a liver serine-protease encoded by TMPRSS6 gene. Cleaving the BMP-coreceptor hemojuvelin, matriptase-2 impairs the BMP/SMAD signaling pathway, downregulates hepcidin and facilitates iron absorption. TMPRSS6 inactivation causes iron-deficiency-anemia refractory to iron administration both in humans and mice. Genome wide association studies have shown that the SNP rs855791, which causes the matriptase-2 V736A amino acid substitution, is associated with variations of serum iron, transferrin saturation, hemoglobin and erythrocyte traits. Here we show that in vitro matriptase-2 736(A) inhibits hepcidin more efficiently than 736(V). Moreover, in a genotyped population, after exclusion of samples with iron deficiency and inflammation, hepcidin, hepcidin/transferrin saturation and hepcidin/ferritin ratios were significantly lower and iron parameters were consistently higher in homozygotes 736(A) than in 736(V). Our ...

2011-08-26

471

Sympatric Distribution of Three Human Taenia Tapeworms Collected between 1935 and 2005 in Korea

In this work, we query the Chlamydomonas reinhardtii copper regulon at a whole-genome level. Our RNA-Seq data simulation and analysis pipeline validated a 2-fold cutoff and 10 RPKM (reads per kilobase of mappable length per million mapped reads) (~1 mRNA per cell) to reveal 63 CRR1 targets plus another 86 copper-responsive genes. Proteomic and immunoblot analyses captured 25% of the corresponding proteins, whose abundance was also dependent on copper nutrition, validating transcriptional regulation as a major control mechanism for copper signaling in Chlamydomonas. The impact of copper deficiency on the expression of several O2-dependent enzymes included steps in lipid modification pathways. Quantitative lipid profiles indicated increased polyunsaturation of fatty acids on thylakoid membrane digalactosyldiglycerides, indicating a global impact of copper deficiency on the photosynthetic apparatus. Discovery of a putative plastid copper chaperone and a membrane ...

2011-04-01

472

Smooth muscle myosin heavy chain locus (MYH11) maps to 16p13. 13-p13. 12 and establishes a new region of conserved synteny between human 16p and mouse 16

Taeniasis has been known as one of the prevalent parasitic infections in Korea. Until recently, Taenia saginata had long been considered a dominant, and widely distributed species but epidemiological profiles of human Taenia species in Korea still remain unclear. In order to better understand distribution patterns of human Taenia tapeworms in Korea, partial nucleotide sequences of mitochondrial cox1 and ITS2 (internal transcribed spacer 2) were determined, along with morphological examinations, on 68 Taenia specimens obtained from university museum collections deposited since 1935. Genomic DNA was extracted from formalin-preserved specimens. Phylogenetic relationships among the genotypes (cox1 haplotype) detected in this study were inferred using the neighbor-joining method as a tree building method. Morphological and genetic analyses identified 3 specimens as T. solium, 51 specimens as T. asiatica, and 14 specimens as T. saginata. Our results indicate that all 3 ...

2008-12-20

473

Regulatory role of neuron-restrictive silencing factor in expression of TRPC1

The human smooth muscle myosin heavy chain locus (MYH11) was mapped by fluorescence in situ hybridization to the middle of the p arm of chromosome 16 using a genomic cosmid clone containing coding sequences of the gene as probe. Probe from coding sequence, when applied to Southern blots of a panel of hybrids containing different portions of human chromosome 16, localized the gene to 16p13.13-13.12. Coding sequence PCR primers, when used on the DNA from a CHO-mouse hybrid clone mapping panel informative for mouse chromosomes, showed that the gene was located on mouse chromosome 16. These results correct a recent assignment of MYH11 from 16q12.2 to the region of the 16p-arm inversion breakpoint seen in acute myelomonocytic leukemia (AMML) M4Eo and demonstrate that the conflicting data do not result from the presence of additional MYH genes on the q arm of the chromosome. Also, a new region of conserved synteny between human 16p and mouse 16 is established. 10 refs., ...

1993-10-01

474

Proteomic analysis of the shistosome tegument and its surface membranes

Neuron-restrictive silencer factor (NRSF) binds its consensus element to repress the transcription of various genes. The dominant-negative form (dnNRSF) has a hypertrophic effect on cardiogenesis through an unidentified mechanism. We examined the involvement of transient receptor potential (TRP) channel proteins, using transgenic mice overexpressing dnNRSF (dnNRSF mice). Electrophoretic mobility-shift assays revealed an interaction between NRSF and a neuron-restrictive silencer element-like sequence in intron 4 of TRPC1 genomic DNA. According to RT-PCR and Western analyses, TRPC1 was up-regulated in dnNRSF mouse heart. Transient overexpression of TRPC1 in HEK 293T cells increased the activity of the nuclear factor in activated T cells (NFAT) promoter and stimulated store-operated Ca"2"+ channel (SOCC)-mediated Ca"2"+ entry. Transfection of TRPC1 into primary cardiomyocytes increased NFAT activity, indicating a major role for TRPC1 in NFAT activation. Our findings ...

2006-12-22

475

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, including phosphohydrolases, ...

2006-10-01

476

Overexpression of a maize dehydrin gene, ZmDHN2b, in tobacco enhances tolerance to low temperature

British Library Electronic Table of Contents (United Kingdom)

Dehydrins, a subfamily of group 2 LEA proteins, are intrinsically unstructured plant proteins that accumulate in the late stages of seed development and in vegetative tissues subjected to water deficit, salinity, low temperature, or abscisic acid treatment. In this study, we isolated and characterized ZmDHN2b, a maize dehydrin gene. The genomic organization of the ZmDHN2b gene and its expression in maize seedlings were analyzed. To investigate the function of ZmDHN2b, we generated transgenic tobacco plants constitutively overexpressing ZmDHN2b. Ectopic expression of ZmDHN2b in tobacco accelerated seed germination and seedling growth at 15?C. Furthermore, ZmDHN2b-overexpressing lines had lower levels of cold-induced malondialdehyde and less electrolyte leakage than wild-type tobacco at 4?C....

2011-01-01

477

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

Identification of the binding domain for NADP"+ of human glucose-6-phosphate dehydrogenase by sequence analysis of mutants

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

478

Human cDNA mapping using fluorescence in situ hybridization. Progress report, April 1, 1992--December 31, 1992

Human erythrocyte glucose-6-phosphate is normally quite stable in the presence of 10 #mu#M NADP"+. Certain glucose-6-phosphate dehydrogenase variants lose virtually all their activity at this concentration of NADP"+ but are reactivated by 200 #mu#M NADP"+. Such variants presumably have a defect in their NADP"+-binding site. The authors analyzed the sequence of cDNA or genomic DNA from seven unrelated patients with hemolytic anemia due to the inheritance of variants that are reactivated by NADP"+. Six patients had substitutions of one of three adjacent amino acids, and the seventh patient had another amino acid substitution 23 residues downstream. These amino acids are highly conserved, all being present in rat and all but one being found also in Drosophila. The anomalous electrophoretic behavior of some of the variants can be explained by their loss of ability to bind NADP"+. The conclude that the region in which these mutations occur defines the binding domain for ...

479

Homo-d-lactic acid production from mixed sugars using xylose-assimilating operon-integrated Lactobacillus plantarum

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

480

British Library Electronic Table of Contents (United Kingdom)

In order to achieve efficient d-lactic acid fermentation from a mixture of xylose and glucose, the xylose-assimilating xylAB operon from Lactobacillus pentosus (PXylAB) was introduced into an l-lactate dehydrogenase gene (ldhL1)-deficient Lactobacillus plantarum (?ldhL1-xpk1::tkt-?xpk2) strain in which the phosphoketolase 1 gene (xpk1) was replaced with the transketolase gene (tkt) from Lactococcus lactis, and the phosphoketolase 2 (xpk2) gene was deleted. Two copies of xylAB introduced into the genome significantly improved the xylose fermentation ability, raising it to the same level as that of ?ldhL1-xpk1::tkt-?xpk2 harboring a xylAB operon-expressing plasmid. Using the two-copy xylAB integrated strain, successful homo-d-lactic acid production was achieved from a mixture of 25?g/l xylos...

2011-01-01

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481

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

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

482

Genetic diversity associated with in vitro and conventional bud propagation of Saccharum varieties using RAPD analysis

British Library Electronic Table of Contents (United Kingdom)

Abstract Polymorphisms in the genomic DNA of eight varieties maintained by conventional bud propagation (via rhizomes) and by in vitro shoot tip cultures were detected by RAPD analysis of sugarcane varieties. The study estimated the genetic diversity induced after in vitro multiplication of these varieties. Higher (28.9%) and lower (12%) numbers of polymorphic bands were detected in plants propagated via rhizomes; the genetic similarity estimate varying from 0.63 to 0.80. Plants of SP90-3723 and SP91-1049, or RB85-5113 and SP90-3723, varieties involving greater genetic distances may be indicated as progenitors in breeding programmes. In vitro multiplication of RB86-7515, RB85-5113, RB83-5054 and SP86-42 varieties increases genetic variability, while in vitro multiplication of SP91-1049, SP...

2008-01-01

483

First report of the complete sequence of Sida golden yellow vein virus from Jamaica.

Evolution of a molecular switch: universal bacterial GTPases regulate ribosome function.

Begomoviruses are phytopathogens that threaten food security [18]. Sida spp. are ubiquitous weed species found in Jamaica. Sida samples were collected island-wide, DNA was extracted via a modified Dellaporta method, and the viral genome was amplified using degenerate and sequence-specific primers [2, 11]. The amplicons were cloned and sequenced. Sequence analysis revealed that a DNA-A molecule isolated from a plant in Liguanea, St. Andrew, was 90.9% similar to Sida golden yellow vein virus-[United States of America:Homestead:A11], making it a strain of SiGYVV. It was named Sida golden yellow vein virus-[Jamaica:Liguanea 2:2008] (SiGYVV-[JM:Lig2:08]). The cognate DNA-B, previously unreported, was successfully cloned and was most similar to that of Malvastrum yellow mosaic Jamaica virus (MaYMJV). Phylogenetic analysis suggested that this virus was most closely related to begomoviruses that infect malvaceous hosts in Jamaica, Cuba and Florida in the United States. ...

2011-05-29

484

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

The GTPases comprise a protein superfamily of highly conserved molecular switches adapted to many diverse functions. These proteins are found in all domains of life and often perform essential roles in fundamental cellular processes. Analysis of data from genome sequencing projects demonstrates that bacteria possess a core of 11 universally conserved GTPases (elongation factor G and Tu, initiation factor 2, LepA, Era, Obg, ThdF/TrmE, Ffh, FtsY, EngA and YchF). Investigations aimed at understanding the function of GTPases indicate that a second conserved feature of these proteins is that they elicit their function through interaction with RNA and/or ribosomes. An emerging concept suggests that the 11 universal GTPases are either necessary for ribosome function or transmitting information from the ribosome to downstream targets for the purpose of generating specific cellular responses. Furthermore, it is suggested that progenitor GTPases were early regulators of RNA ...

2001-07-01

485

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

486

Differentially expressed genes in hypothalamus in relation to genomic regions under selection in two chicken lines resulting from divergent selection for high or low body weight

British Library Electronic Table of Contents (United Kingdom)

Long-term divergent selection for low or high body weight from the same founder population has generated two extremely divergent lines of chickens, the high- (HWS) and low-weight (LWS) selected lines. At selection age (56?days), the lines differ by more than nine times in body weight. The HWS line chickens are compulsive feeders, whereas in the LWS line, some individuals are anorexic and others have very low appetite. Previous studies have implicated the central nervous system and particularly the hypothalamus in these behavioural differences. Here, we compared the mRNA expression in hypothalamus tissue from chickens on day?4 post-hatch using oligonucleotide arrays and found that the divergent selection had resulted in minor but multiple expression differences. Differentially expressed gen...

2011-01-01

487

Data Merging for Integrated Microarray and Proteomic Analysis

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

The functioning of even a simple system is much more complicated than the sum of its genes, proteins and metabolites. A premise of systems biology is that molecular profiling will lead to the discovery and characterization of important disease pathways. However, as multiple levels of effector pathway regulation appear to be the norm rather than the exception, a significant challenge presented by high-throughput genomics and proteomics technologies is to extract the biological implications of complex data. Thus, integration of heterogeneous types of data generated from diverse global technology platforms represents the first challenge in developing the necessary foundational databases needed for predictive modeling of cell and tissue responses. Given the apparent difficulty in defining the correspondence between gene expression and protein abundance measured in several systems to date, how do we make sense of these data and design the next experiment? In this ...

2006-05-10

488

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

489

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

Chromosome mapping of human CDC25A and CDC25B phosphatases

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 cloned fragment to ...

1988-10-01

490

Chromosomal study in lymphocytes from subjects living or working in buildings constructed with radioactively contaminated rebar

The human CDC25 tyrosine phosphatases trigger activation of CDC2 by removing inhibitory phosphates; thus the genes encoding these phosphatases may be suspected as potential oncogenes due to their role in promoting cell division. To date, three human CDC25 genes have been identified: CDC25A, B, and C. This communication describes the mapping of CDC25A to chromosome 3p21 and CDC25B to chromosome 20p13 by fluorescence in situ hybridization with confirmation by the polymerase chain reaction of hamster-human somatic cell hybrid DNA. 3p21 is near an area frequently involved in karyotypic abnormalities in renal carcinomas, small cell carcinomas of the lung, and benign tumors of the salivary gland. 20p13 does not seem to be a common area for karyotypic alteration in tumors. Mapping of these genes to their chromosomal loci may help identify tumors with abnormal regulation of CDC25 genes due to genomic alterations. 15 refs., 3 figs.

1993-10-01

491

Chromosomal study in lymphocytes from subjects living or working in buildings constructed with radioactively contaminated rebar

It has recently been found that many buildings in Taiwan were constructed with radioactively contaminated rebar, which raised great concern among the residents as well as governmental officials. In order to investigate the possible cytogenetic damage to the residents of contaminated buildings, a G-banding method was carried out on the lymphocytes of 30 radiation-exposed individuals from four families and one office building, as well as 15 control individuals from laboratory personnel. The estimated cumulative radiation doses for the exposed people range from 19.63 to 280.50 mSv. Altogether, 13 females and 17 males belonging to the radiation-exposed group, and 7 females and 8 males in the control group, were included in this study. With the exception of one sample, at least 500 metaphase spreads were scored and analyzed for each individual. All the recognizable structural aberrations of chromosomes or chromatids were recorded and statistically analyzed. Comparison of either percentage ...

1997-07-03

492

Characterization of a novel missense mutation on murine Pax3 through ENU mutagenesis.

It has recently been found that many buildings in Taiwan were constructed with radioactively contaminated rebar, which raised great concern among the residents as well as governmental officials. In order to investigate the possible cytogenetic damage to the residents of contaminated buildings, a G-banding method was carried out on the lymphocytes of 30 radiation-exposed individuals from four families and one office building, as well as 15 control individuals from laboratory personnel. The estimated cumulative radiation doses for the exposed people range from 19.63 to 280.50 mSv. Altogether, 13 females and 17 males belonging to the radiation-exposed group, and 7 females and 8 males in the control group, were included in this study. With the exception of one sample, at least 500 metaphase spreads were scored and analyzed for each individual. All the recognizable structural aberrations of chromosomes or chromatids were recorded and statistically analyzed. Comparison of either percentage ...

493

CHRNA5 as negative regulator of nicotine signaling in normal and cancer bronchial cells: effects on motility, migration and p63 expression

N-ethyl-N-nitrosourea (ENU) mutagenesis has led to the elucidation of several regulator genes for melanocyte and skin development. Here we characterized a mutant from ENU mutagenesis with similar phenotype as that of Splotch mutant, including exencephaly, spina bifida and abnormal limbs in homozygotes as well as white belly spotting and occasionally loop-tail in heterozygotes. This novel mutant was named as Sp(xG). Through genome-wide linkage analysis in backcross progenies with microsatellite markers, the Sp(xG) was confined to a region between D1MIT415 and D1MIT7 on chromosome 1, where notable Pax3 gene was located. Direct sequencing revealed that Sp(xG) carried a nucleotide A894G missense transition in exon 6 of Pax3 gene that resulted in Asn to Asp substitution at amino acid 269 within the highly-conserved homeodomain (HD) DNA recognition module, which was the first point mutation found in this domain in mice. This N269D mutation impaired the transactivation ...

2011-07-19

494

British Library Electronic Table of Contents (United Kingdom)

Genome-wide association studies have linked lung cancer risk with a region of chromosome 15q25.1 containing CHRNA3, CHRNA5 and CHRNB4 encoding a3, a5 and b4 subunits of nicotinic acetylcholine receptors (nAChR), respectively. One of the strongest associations was observed for a non-silent single-nucleotide polymorphism at codon 398 in CHRNA5. Here, we have used pharmacological (antagonists) or genetic (RNA interference) interventions to modulate the activity of CHRNA5 in non-transformed bronchial cells and in lung cancer cell lines. In both cell types, silencing CHRNA5 or inhibiting receptors containing nAChR a5 with a-conotoxin MII exerted a nicotine-like effect, with increased motility and invasiveness in vitro and increasing calcium influx. The effects on motility were enhanced by addit...

2011-01-01

495

Brookhaven highlights. [Fiscal year 1992, October 1, 1991--September 30, 1992

This publication provides a broad overview of the research programs and efforts being conducted, built, designed, and planned at Brookhaven National Laboratory. This work covers a broad range of scientific disciplines. Major facilities include the Alternating Gradient Synchrotron (AGS), with its newly completed booster, the National Synchrotron Light Source (NSLS), the High Flux Beam Reactor (HFBR), and the RHIC, which is under construction. Departments within the laboratory include the AGS department, accelerator development, physics, chemistry, biology, NSLS, medical, nuclear energy, and interdepartmental research efforts. Research ranges from the pure sciences, in nuclear physics and high energy physics as one example, to environmental work in applied science to study climatic effects, from efforts in biology which are a component of the human genome project to the study, production, and characterization of new materials. The paper provides an overview of the ...

1992-12-31

496

Brookhaven highlights

Analysis of the roles of E6 binding to E6TP1 and nuclear localization in the human papillomavirus type 31 life cycle

This publication provides a broad overview of the research programs and efforts being conducted, built, designed, and planned at Brookhaven National Laboratory. This work covers a broad range of scientific disciplines. Major facilities include the Alternating Gradient Synchrotron (AGS), with its newly completed booster, the National Synchrotron Light Source (NSLS), the High Flux Beam Reactor (HFBR), and the RHIC, which is under construction. Departments within the laboratory include the AGS department, accelerator development, physics, chemistry, biology, NSLS, medical, nuclear energy, and interdepartmental research efforts. Research ranges from the pure sciences, in nuclear physics and high energy physics as one example, to environmental work in applied science to study climatic effects, from efforts in biology which are a component of the human genome project to the study, production, and characterization of new materials. The paper provides an overview of the ...

1992-01-01

497

British Library Electronic Table of Contents (United Kingdom)

The E6 oncoproteins of high-risk human papillomaviruses provide important functions not only for malignant transformation but also in the productive viral life cycle. E6 proteins have been shown to bind to a number of cellular factors, but only a limited number of analyses have investigated the effects of these interactions on the viral life cycle. In this study, we investigated the consequences of HPV 31 E6 binding to E6TP1, a putative Rap1 GAP protein. HPV 16 E6 has been shown to bind as well as induce the rapid turnover of E6TP1, and similar effects were observed with HPV 31 E6. Mutation of amino acid 128 in HPV 31 E6 was found to abrogate the ability to bind and degrade E6TP1 but did not alter binding to another ?-helical domain protein, E6AP. When HPV 31 genomes containing mutations a...

2007-01-01

498

Analysis of the 5{prime} region of PMS2 reveals heterogeneous transcripts and a novel overlapping gene

Aging, tumor suppression and cancer: High-wire act!

The PMS2 gene encodes a protein that is involved in DNA mismatch repair and is mutated in a subset of patients with hereditary nonpolyposis colon cancer (HNPCC). The previously published PMS2 cDNA sequence lack an upstream in-frame stop codon preceding the presumptive initiating methionine. To evaluate the 5` terminus of the PMS2 coding region further, we isolated additional cDNA clones, RT-PCR products, and the corresponding 5` genomic segment of the PMS2 locus. The PMS2 gene transcripts were found to have heterogeneous but colinear 5` termini, one of which contained an in-frame termination codon preceding the initiating methionine. In addition, a novel gene encoding a 34.5-kDa polypeptide was found to initiate transcriptionally within PMS2 from the opposite strand. 23 refs., 5 figs., 2 tabs.

1995-09-20

499

A microscale protein NMR sample screening pipeline

Evolutionary theory holds that aging is a consequence of the declining force of natural selection with age. We discuss here the evidence that among the causes of aging in complex multicellular organisms, such as mammals, is the antagonistically pleiotropic effects of the cellular responses that protect the organism from cancer. Cancer is relatively rare in young mammals, owing in large measure to the activity of tumor suppressor mechanisms. These mechanisms either protect the genome from damage and/or mutations, or they elicit cellular responses--apoptosis or senescence--that eliminate or prevent the proliferation of somatic cells at risk for neoplastic transformation.We focus here on the senescence response, reviewing its causes, regulation and effects. In addition, we describe recent data that support the idea that both senescence and apoptosis may indeed be the double-edged swords predicted by the evolutionary hypothesis of antagonistic pleiotropy--protecting ...

2004-08-15

500