UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

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

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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

UK PubMed Central (United Kingdom)

The evaluation of biological markers is recognized as necessary to the future of toxicology, epidemiology, and quantitative risk assessment. For biological markers to become widely accepted, their validity...Full Text Available

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

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

Science.gov (United States)

include modeling geometric complexities, coupling between the flow and the .... noted that the AGARD 445.6 wing data set, which has been widely used for .... higher-level computational aeroelastic code validations at transonic flow separation ...

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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 ...

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

Science.gov (United States)

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 ...

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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...

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The aim of this work is the development and experimental validation of a detailed dynamic fuel cell model using the gPROMS modeling environment. The model is oriented towards optimization and control and it relies on material and energy balances as well as electrochemical equations including semi-empirical equations. For the experimental validation of the model a fully automated and integrated hydrogen fuel cell testing unit was used. The predictive power of the model has been compared with the data obtained during load change experiments. A sensitivity analysis has been employed to reveal the most critical empirical model parameters that should be estimated using a systematic estimation procedure. Model predictions are in good agreement with experimental data under a wide range of operati...

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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 ...

UK PubMed Central (United Kingdom)

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

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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 ...

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PMID:16091132

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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.

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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-...

International Nuclear Information System (INIS)

The authors discuss radioimmunoassays (RIAs) for eicosanoids widely used in the field of experimental, clinical and pharmacological research. The main drawback of RIAs is the possibility of low specificity. This was clearly demonstrated during the controversy on plasma levels of 6-keto-PGF_1 #alpha#, the stable hydrolysis product of PGI_2. When extensive purification including reverse phase high pressure liquid chromatography (rp-HPLC) was performed prior to the RIA for 6-keto-PGF_1 #alpha# the levels were at least one order of magnitude less than previously claimed, and did not support the so-called circulating hormone hypothesis.

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The development of detailed chemical kinetic reaction mechanisms for analysis of autoignition and knocking of hydrocarbon fuels is described. In particular, kinetic processes of concern for the oxidation of complex hydrocarbon fuel molecules are emphasized. The wide ranges of temperature and pressure which are encountered by end gases in automobile engine combustion chambers result in extreme demands on reaction mechanisms which are intended to describe knocking conditions and predict rates of combustion and ignition. The reactions and chemical species which are most important in each temperature and pressure regime are discussed, and the validation of these reaction mechanisms through comparison with idealized experimental results is described. 53 refs., 8 figs., 5 tabs.

Science.gov (United States)

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 ...

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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 ...

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

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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 .....

UK PubMed Central (United Kingdom)

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

CERN Document Server

Methods and Procedures for the Verification and Validation of Artificial Neural Networks

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The thermal performance monitoring and optimization system TEMPO is developed at the OECD Halden Reactor Project. The system supports staff of nuclear power plants in identification and correction of problems, which cause small decreases in plant efficiency but which may lead to significant economical losses. The system-wide physical model consists of mathematical description of individual components, such as the reactor, the pumps, the heat exchangers, or the turbines, etc. TEMPO code has recently been extended with new steam generator (SG) models. The present paper summarizes the thermal-hydraulic modelling aspects of the vertical and the horizontal SG. The heat balance equations and their solution are shown with the appropriate initial and boundary conditions. The method of the calculation of the pressure losses are also introduced. The vertical SG model is based on a U-tube structure and treated as a 1D flow channel. The horizontal approach is a superposition ...

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Although incompressible fluid flows can be regarded as a particular case of a general problem, numerical methods and the mathematical formulation aimed to solve compressible and incompressible flows have their own peculiarities, in such a way, that it is generally not possible to attain both regimes with a single approach. In this work, we start from a typically compressible formulation, slightly modified to make use of pressure variables and, through augmenting the stabilising parameters, we end up with a simplified model which is able to deal with a wide range of flow regimes, from supersonic to low speed gas flows. The resulting methodology is flexible enough to allow for the simulation of liquid flows as well. Examples using conservative and pressure variables are shown and the results are compared to those published in the literature, in order to validate the method. (author)

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Terrain attributes derived from digital elevation models have been used widely for mapping soil organic matter (SOM). Among these attributes, the topographic wetness index (TWI), an index for quantitatively indicating the balance between water accumulation and drainage conditions at the local scale, has been shown to correlate with SOM. However, TWIs used in most studies are calculated using a single-flow-direction (SFD) algorithm, which assumes that all water from a grid cell flows into only one neighboring cell. This assumption is not always valid, especially in areas with low relief where movement of water may be divergent. To overcome this SFD limitation, a multiple-flow-direction (MFD) algorithm has been developed, which distributes flow from a grid cell to several downslope neighbors...

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We have developed an energy-extension method of a Bragg curve counter (BCC) at the high-energy end for the measurements of double-differential cross-sections (DDXs) of fragment productions induced by tens of MeV protons. In this method, we estimate the incident energies of the fragments penetrating a BCC on the basis of the energy loss and atomic number (Z). We applied this method to the DDX measurements of the {sup nat}C(p, Li) and {sup nat}C(p, Be) reactions induced by 70 MeV protons. The validity of this method has been confirmed by comparing the DDXs of beryllium with theoretical predictions of the PHITS code and the two-body kinematics. This method improves the energy acceptance of the BCC for light fragments twice as wide as that of a conventional method without remodeling of the BCC and any loss of the original advantages.

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Phenytoin (PHT), phenobarbital (PHB), lamotrigine (LTG), and topiramate (TPM) are some of the most widely used antiepileptic drugs (AEDs). Monitoring of their concentrations in serum is important for the treatment of epilepsy. A reference measurement procedure (RMP) for certification of PHT, PHB, LTG, and TPM in serum has been developed and critically evaluated. Isotopically labeled compounds of PHT, PHB, LTG, and TPM are used as internal standards for the four AEDs. The four drugs and their respective labeled internal standards are simultaneously extracted from serum using solid-phase extraction prior to reversed-phase liquid chromatography?tandem mass spectrometry (LC-MS/MS). Chromatographic separation was performed using a C18 column. Electrospray ionization (ESI) in the positive ion mo...

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In the absence of empirical outdoor thermal comfort studies it has been widely assumed that indoor thermal comfort theory generalises to outdoor settings without modification. Many indoor models were developed to describe thermal discomfort, not stress, therefore their relevance to conditions that vary greatly from neutrality, as many outdoor climatic conditions do, has not been critically validated in the field to date. The thermal comfort of 1018 subjects in outdoor and semi-outdoor locations in subtropical Sydney was investigated by a questionnaire and a comprehensive package of micro-meteorological instruments. The thermal neutrality in terms of the thermal comfort index OUT{sub S}ET* of 26.2 {sup o}C was significantly higher than the indoor SET* counterpart of 24{sup o}C (ASHRAE Trans. 92 (1986) 709). (author)

Science.gov (United States)

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) ...

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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 ...

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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 ...

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The EUROTRAC sub-project ''Tropospheric Ozone Research'' (TOR) follows a dual strategy: - Observation of the chemical processes contributing to the oxygen balance directly in the atmosphere; - Establishment of a validated data base for model calculations. Both tasks require simultaneous measurements of a wide range of chemical and meteorological components. In the case of the investigation of the chemical processes, it is also desirable to measure the free radicals directly involved in ozone production. In the project described, a measuring station was set up. For a period of two years and a half, continuous measurements were made of ozone and its chemical precursors (NO, NO_2, NO_y, VOC, CO), as well as other photooxidants (H_2O_2 and organic hydroperoxides, organic nitrates), the photolysis frequency of NO_2, and meteorological parameters (wind, temperature, moisture, aerosols). The station was located on the Schauinsland mountain in the ...

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As a three-year joint university-industry effort, development of a generalized boiling transition analysis method has been started in 2002 aiming at enhanced capabilities of subchannel analysis for a wide variety of BWR-type fuel bundle geometry from ordinary BWR to tight lattice fuel bundles. For this purpose, five dominant factors affecting boiling transition phenomena have been identified on which our efforts of experimentation and numerical analyses are focused. In this report, as the first-year achievement, we will describe a master plan of the development and contents for experimental approaches to construct thermal-hydraulic databases. The databases will be utilized for the developments of constitutive equations to describe the basic characteristics of the elementary processes. The planned experiments are divided into two groups. One is air-water experiments at atmospheric pressure, and the other is steam-water experiments up to 1 MPa. The former group of ...

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The application of neural networks, alone or in conjunction with other advanced technologies (expert systems, fuzzy logic, and/or genetic algorithms), to some of the problems of complex engineering systems has the potential to enhance the safety, reliability, and operability of these systems. Typically, the measured variables from the systems are analog variables that must be sampled and normalized to expected peak values before they are introduced into neural networks. Often data must be processed to put it into a form more acceptable to the neural network (e.g., a fast Fourier transformation of the time-series data to produce a spectral plot of the data). Specific applications described include: (1) Diagnostics: State of the Plant (2) Hybrid System for Transient Identification, (3) Sensor Validation, (4) Plant-Wide Monitoring, (5) Monitoring of Performance and Efficiency, and (6) Analysis of Vibrations. Although specific examples described ...

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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.

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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.

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

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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.

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Accurately predicting wind turbine blade loads and response is important for the proper design of wind turbines. The need to accurately predict both deterministic and stochastic blade loads is now widely recognized. Previous rotor code development and validation efforts at NREL have concentrated on prediction of deterministic and stochastic blade loads for rigid hub rotors. During the past year this effort was expanded for predicting blade and shaft loads for two-bladed teetering hub rotors. The NREL (formerly SERI) Teetering Rotor Analysis Program (STRAP), a derivative of the Force and Loads Analysis Program (FLAP), can include the effects of rotor undersling, delta-3 and the effects of a concentrated hub mass. The degrees of freedom include rotor teeter and symmetric and asymmetric rotor flap modes. A time-dependent, prescribed yaw motion can also be input to the code. Loads due to turbulent wind inputs are also calculated. In this paper, ...

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A dipole magnet based on the common coil design, using prereacted Nb{sub 3}Sn superconductor, is under development at Fermilab, for a future Very Large Hadron Collider. This magnet has some innovative design and technological features such as single layer coils, a 22 mm wide 60-strand Rutherford type cable and stainless steel collars reinforced by horizontal bridges inserted between coil blocks. Both left and right coils are wound simultaneously into the collar structure and then impregnated with epoxy. In order to optimize the design and fabrication techniques an R&D program is underway. The production of cables with the required characteristics was shown possible. Collar laminations were produced, assembled and tested in order to check the effectiveness of the bridges and the validity of the mechanical design. A mechanical model consisting of a 165 mm long section of the magnet straight section was assembled and tested. This paper ...

International Nuclear Information System (INIS)

Whether exposure to electromagnetic fields (EMFs) cause cancer has been vigorously debated for many years and has been the most vexing issue with which ICNIRP has had to deal during its short existence. There have been three parts of the electromagnetic spectrum that the issue of cancer has raised: static (0 Hz) magnetic fields, extremely low frequency (ELF) fields (defined as > 0-300 Hz, but concerns have been raised almost exclusively at the power frequencies of 50/60 Hz), and radiofrequency (RF) fields (300 Hz -300 GHz). By far the major problems have arisen during the construction of new high voltage transmission lines and mobile telephone systems. Actions by protest groups concerned with possible health effects, especially with cancer in children, has now reached such a scale that it is costing electrical utilities and communications companies billions of dollars annually world-wide. With such high stakes, ICNIRP has had to be extremely careful in its ...

International Nuclear Information System (INIS)

RELAP5 (Reactor Excursion and Leak Analysis Program) is a system code developed at the Idaho National Environmental and Engineering Laboratory for thermal hydraulic analysis of nuclear reactors. The code RELAP5 is widely used for safety analysis studies of commercial nuclear power plants. However, recent released version of RELAP5/3.2 and over present significant capabilities for analysis of nuclear reactor research systems. As a contribution to the assessment of RELAP5/3.3 for research reactor safety analysis, experimental data from the University of Massachusetts Lowell Research Reactor UMLRR are used. The UMLRR is a 1 MW, light water moderated and cooled, graphite-reflected, open-pool type research reactor. This paper presents the development and the validation of a UMLRR-RELAP model using experimental data. For this purpose, a series of experiments were performed for benchmarking RELAP5 calculations for research reactor systems. As a result ...

Energy Technology Data Exchange (ETDEWEB)

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 ...

Energy Technology Data Exchange (ETDEWEB)

Non-first order (FO) kinetics models are of three types; second order (SO), general order (GO) and mixed order (MO). It is shown that all three of these have constraints in their energy level schemes and their applicable parameter values. In nature such restrictions are not expected to exist. The thermoluminescence (TL) glow peaks produced by these models shift their position and change their shape as the trap occupancies change. Such characteristics are very unlike those found in samples of real materials. In these models, in general, retrapping predominates over recombination. It is shown that the quasi-equilibrium (QE) assumption implied in the derivation of the TL equation of these models is quite valid, thus disproving earlier workers' conclusion that QE cannot be held under retrapping dominant conditions. However notwithstanding their validity, they suffer from the shortcomings as stated above and have certain lacunae. For ...

Science.gov (United States)

In neurodegenerative conditions such as Alzheimer's and prion disease it has been shown that host genetic background can have a significant effect on susceptibility. Indeed, human genome-wide association studies (GWAS) have implicated several candidate genes. Understanding such genetic susceptibility is relevant to risks of developing variant CJD (vCJD) in populations exposed to bovine spongiform encephalopathy (BSE) and understanding mechanisms of neurodegeneration. In mice, aspects of prion disease susceptibility can be modelled by examining the incubation period following experimental inoculation. Quantitative trait linkage studies have already identified multiple candidate genes; however, it is also possible to take an individual candidate gene approach. Rarb and Stmn2 were selected as candidates based on the known association with vCJD. Because of the increasing overlap described between prion and Alzheimer's diseases we also chose Clu, Picalm and Cr1, which ...

Science.gov (United States)

... Standards Validation Group National Computer Systems Laboratory National Institute of Standards and Technology ... STANDARD. ... (See test Ci )i3A. ...

CERN Document Server

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.

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

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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

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

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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

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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

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

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Energy Technology Data Exchange (ETDEWEB)

The quality of molecular dynamics (MD) simulations of proteins depends critically on the biomolecular force field that is used. Such force fields are defined by force-field parameter sets, which are generally determined and improved through calibration of properties of small molecules against experimental or theoretical data. By application to large molecules such as proteins, a new force-field parameter set can be validated. We report two 3.5 ns molecular dynamics simulations of hen egg white lysozyme in water applying the widely used GROMOS force-field parameter set 43A1 and a new set 45A3. The two MD ensembles are evaluated against NMR spectroscopic data NOE atom-atom distance bounds, {sup 3}J{sub NH{alpha}} and {sup 3}J{sub {alpha}}{sub {beta}} coupling constants, and {sup 1}5N relaxation data. It is shown that the two sets reproduce structural properties about equally well. The 45A3 ensemble fulfills the atom-atom distance bounds derived ...

Science.gov (United States)

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

Energy Technology Data Exchange (ETDEWEB)

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 ...

Energy Technology Data Exchange (ETDEWEB)

Planning is an important part of computational model verification and validation (V&V) and the requisite planning document is vital for effectively executing the plan. The document provides a means of communicating intent to the typically large group of people, from program management to analysts to test engineers, who must work together to complete the validation activities. This report provides guidelines for writing a validation plan. It describes the components of such a plan and includes important references and resources. While the initial target audience is the DART Full System Model teams in the nuclear weapons program, the guidelines are generally applicable to other modeling efforts. Our goal in writing this document is to provide a framework for consistency in validation plans across weapon systems, different types of models, and different scenarios. Specific details contained in any ...

International Nuclear Information System (INIS)

In the framework of spallation neutron sources and accelerator-driven systems, the international PISA (Proton-induced Spallation) collaboration has initiated measurements of total- and double-differential cross-sections for products of spallation reactions in a wide range of target nuclei (GU) at the COSY proton accelerator in Julich (Germany). The purpose is to study secondary particle production created in structural, window and target materials via proton beams up to 2.5 GeV of incident kinetic energy. Residual nuclei [H, He up to intermediate mass fragment (IMF)] production cross-sections are of great importance for estimating the damage to target and structure materials involving the planned spallation neutron sources, given that the lifetime of window and target materials is directly associated to those cross-sections. The demand for reliable theoretical predictions on production cross-sections is by no means satisfied by the models and codes that are ...

International Nuclear Information System (INIS)

The Ranque-Hilsch tube is a particular type of vortex tube device. The flow enters the device tangentially near one end and exits from the open ends of the tube. The inlet air is of a uniform temperature throughout while the outputs are of different temperatures. One outlet is hotter and the other is colder than the inlet air. This device has no moving parts and does not require any additional power for its operation other than that supplied to the device to compress the inlet air. It has, however, not been widely used, mainly because of its low efficiency. In this paper, a simplified 2-dimensional computational fluid dynamics model for the flow in the vortex tube is developed using FLUENT. This model makes use of the assumption of axial symmetry throughout the entire flow domain. Compared to a three-dimensional computational solution, the simplified model requires significantly less computational time. This is important because the model is to be used for an ...

International Nuclear Information System (INIS)

Research highlights: ? Mathematical model represents a power system which consists of synchronous machine connected to infinite bus through transmission line. ? Power system stabilizer was designed based on optimal pole shifting controller. ? The system performances was tested through load disturbances at different operating conditions. ? The system performance with the proposed optimal pole shifting controller is compared with the conventional pole placement controller. ? The digital simulation results indicated that the proposed controller has a superior performance. -- Abstract: Power system stabilizer based on optimal pole shifting is proposed. An approach for shifting the real parts of the open-loop poles to any desired positions while preserving the imaginary parts is presented. In each step of this approach, it is required to solve a first-order or a second-order linear matrix Lyapunov equation for shifting one real pole or two complex conjugate poles, respectively. This ...

Science.gov (United States)

The Nuclear Regulatory Commission stipulates in 10 CFR 61 that disposed low-level radioactive waste (LLW) be stabilized. To provide guidance to disposal vendors and nuclear station waste generators for implementing those requirements, the NRC developed the Technical Position on Waste Form, Revision 1. That document details a specified set of recommended testing procedures and criteria, including several tests for determining the biodegradation properties of waste forms. Cement has been widely used to solidify LLW; however, the resulting waste forms are sometimes susceptible to failure due to the actions of waste constituents, stress, and environment. The purpose of this research program is to develop modified microbial degradation test procedures that will be more appropriate than the existing procedures for evaluating the effects of microbiologically influenced chemical attack on cement-solidified LLW. Groups of microorganisms indigenous to LLW disposal sites are ...

Energy Technology Data Exchange (ETDEWEB)

We have developed a kinetic Monte Carlo (kMC) simulator that links atomic migration and binding energies determined primarily from first principles calculations to macroscopic phenomena and laboratory time scales. Input for the kMC simulation is obtained from a combination of ab initio planewave pseudopotential calculations, molecular dynamics simulations, and experimental data. The simulator is validated against an extensive series of experimental studies of the diffusion of B spikes in self-implanted Si. The implant energy, dose, and dose rate, as well as the detailed thermal history of the sample, are included. Good agreement is obtained with the experimental data for temperatures between 750 and 950 C and times from 15 to 255 s. At 1050o C we predict too little diffusion after 105 s compared to experiment: apparently, some mechanism which is not adequately represented by our model becomes important at this temperature. Below 1050o C, the kMC simulation produces ...

Energy Technology Data Exchange (ETDEWEB)

A phenomenological model of turbulent combustion has been developed and validated against data from wide ranging tests on a Ricardo E6 engine. Most tests used iso-octane, with a range of air fuel ratios and ignition timings, for tests at full throttle (with and without knock) and at part throttle. Some full throttle tests were also conducted with methanol and toluene. The engine performance was characterized by mean and coefficient of variation (CoV) of: the peak pressure, the maximum rate of pressure rise, the IMEP, the burn rate and flame speed measurements. The results have been used to argue that the cycle-by-cycle variations in combustion should be characterized by the CoV of IMEP in preference to the CoV of the maximum cylinder pressure. Evidence is also presented to support the observation that the cycle-by-cycle variations in combustion are lower when the early combustion is more rapid. It has also been shown that the CoV of IMEP is a ...

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Aim: To investigate interpretative accuracy and reporting time for radiologists performing computed tomography (CT) colonography in day-to-day non-academic clinical practice. Materials and methods: Thirteen radiologists from seven centres, who were reporting CT colonography in non-academic daily clinical practice, interpreted a dataset of 15 colonoscopically validated cases in a controlled environment. Ten cases had either a cancer or polyp >10 mm; one case had a medium polyp and four were normal. Correct case categorization and interpretation times were compared using analysis of variance to aggregated results obtained from both experienced observers and observers recently trained using 50 cases, working in an academic environment. The effect of experience was determined using Spearman's rank correlation. Results: Individual accuracy was highly variable, range 53% (95% CI 27-79%) to 93% (95% CI 68-100%). Mean accuracy overall was significantly ...

International Nuclear Information System (INIS)

In the present paper we estimate the effect of sodium in the in-service inspection of non-magnetic steam generators tubes using eddy current technique and eddy current probes based on a differential double bobbin coil configuration. Experimental measurements of defects signals in steam generator tubes of fast breeder reactor are compared with simulations results of a two-dimensional axisymmetric finite element code to validate a reliable electromagnetic model of the system (eddy current coils, steam generator tube, defect) when there is no sodium on the outer steam generator tube surface. The electromagnetic code is used to evaluate the sodium band and sodium layer signals when a defect is located under steam generator support plate. Using a multi-frequency algorithm, its parameters are determined in the 'no sodium condition' (there is no sodium on the outer steam generator tube surface), defects signal is enhanced during eddy currents inspection, even when the ...

Energy Technology Data Exchange (ETDEWEB)

Detailed chemical kinetic reaction mechanisms have been developed to describe the pyrolysis and oxidation of nine n-alkanes larger than n-heptane, including n-octane (n-C{sub 8}H{sub 18}), n-nonane (n-C{sub 9}H{sub 20}), n-decane (n-C{sub 10}H{sub 22}), n-undecane (n-C{sub 11}H{sub 24}), n-dodecane (n-C{sub 12}H{sub 26}), n-tridecane (n-C{sub 13}H{sub 28}), n-tetradecane (n-C{sub 14}H{sub 30}), n-pentadecane (n-C{sub 15}H{sub 32}), and n-hexadecane (n-C{sub 16}H{sub 34}). These mechanisms include both high temperature and low temperature reaction pathways. The mechanisms are based on our previous mechanisms for the primary reference fuels n-heptane and iso-octane, using the reaction class mechanism construction first developed for n-heptane. Individual reaction class rules are as simple as possible in order to focus on the parallelism between all of the n-alkane fuels included in the mechanisms, and these mechanisms will be refined further in the future to incorporate greater levels of ...

Science.gov (United States)

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 ...

UK PubMed Central (United Kingdom)

The identification and validation of biomarkers for diagnosing Alzheimer's disease (AD) and other forms of dementia are increasingly important. To date, ELISA measurement of β-amyloid(1–42),...Full Text Available

Energy Technology Data Exchange (ETDEWEB)

The thesis gives an overview of the validation process for thermal-hydraulic system codes and it presents in more detail the assessment and validation of the French code CATHARE for VVER calculations. Three assessment cases are presented: loop seal clearing, core reflooding and flow in a horizontal steam generator. The experience gained during these assessment and validation calculations has been used to analyze the behavior of the horizontal steam generator and the natural circulation in the geometry of the Loviisa nuclear power plant. Large part of the work has been performed in cooperation with the CATHARE-team in Grenoble, France. (41 refs., 11 figs., 8 tabs.).

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This viewgraph presentation provides an overview of research designed to provide a numerical

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...

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...

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

Science.gov (United States)

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 ...

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

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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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

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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

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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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

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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

UK PubMed Central (United Kingdom)

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

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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

UK PubMed Central (United Kingdom)

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

Science.gov (United States)

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...

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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

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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

Science.gov (United States)

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...

UK PubMed Central (United Kingdom)

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

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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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

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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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

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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

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.

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... widely distributed from the Red Sea to the Arabian Gulf region and there are no known major threats. It ... ...

International Nuclear Information System (INIS)

For models with several time-dependent components, generalized entropies can be defined. This is shown for the Bianchi type IX model. We first derive the Cardy-Verlinde formula under the assumption that the first law of thermodynamics is valid. This leads to an explicit expression of the total entropy associated with this type of universe. Assuming the validity of the Cardy entropy formula, we obtain expressions for the corresponding Bekenstein, Bekenstein-Hawking and Hubble entropies. We discuss the validity of the Cardy-Verlinde formula and possible extensions of the outlined procedure to other time-dependent models.

Science.gov (United States)

Typing Workshop": [Introductions] [Intro, DNA Basics, and Historical Perspective] [DNA Extraction] [Validation and QA/QC] [DNA Quantitation] [PCR Amplification] [STR Loci and Kits]...

British Library Electronic Table of Contents (United Kingdom)

PURPOSE.- The study aims to clinically validate the defining characteristics (DCs) of the nursing diagnosis (ND) of Activity Intolerance for patients with ischemic heart disease and refractory angina. METHODS.- Cross-sectional study was used, involving 22 patients with ND of Activity Intolerance. The Fehring method was used to validate the ND. FINDINGS.- Most DCs presented reliability indexes between 0.5 and 0.79. Three DCs presented reliability indexes - 0.8. CONCLUSION.- All DCs were validated, and electrocardiographic changes indicating ischemia, verbal report of fatigue, and abnormal rate response to activity were considered as DC major. IMPLICATIONS FOR NURSING PRACTICE.- This study is relevant in daily nursing practice for guidance in establishing the care plan and describing the ass...

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measure meteorological variables and bulk water temper- ature. The locations of the buoys are given in Table 1. TB2 and TB3 were moved slightly farther south ...

UK PubMed Central (United Kingdom)

BackgroundAdequate pain assessment is critical for evaluating the efficacy of analgesic treatment in clinical practice and during the development of new therapies. Yet the currently...Full Text Available

Energy Technology Data Exchange (ETDEWEB)

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.

Energy Technology Data Exchange (ETDEWEB)

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 ...

International Nuclear Information System (INIS)

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 ...

CERN Document Server

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 ...

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...

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,...

Energy Technology Data Exchange (ETDEWEB)

2D simulation modeling of a river basin is based on notion of a River Basin as an opened non equilibrium nature system. All components of the system (elevation, water, soil properties and others) are linked to single multi - functional model. The objective of flood simulation is one the model functions. The objectives of the paper are as follows: a mean scale basin floods computing and the model validation; a large scale basin simulation and demands for its validation; results and demands for flood hazard assessment. (orig.)

Energy Technology Data Exchange (ETDEWEB)

Piping in nuclear power plants is vital to the proper operation and safety of these facilities. To assure safety in the unlikely event of a pipe break, it is necessary to evaluate the consequences from the resulting whipping pipe on neighboring components and structures. Numerical simulations allow for rapid evaluation of these consequences. Before simulations can be accepted, however, the methodology and computer codes must be validated against experimental results. This paper uses a probabilistic approach to validate pipe whip simulations against limited experimental results. Probabilistic analysis software was developed and coupled to existing deterministic finite element software. An example of a whipping pipe impacting against a reinforced concrete slab was simulated. The described probabilistic approach was used to validate the numerical simulations. The conclusions obtained were that the numerical simulations of ...

Science.gov (United States)

... more than expected in developing a unique bond strength measurement protocol that is important for a wide range of bond strength measurements. ...

UK PubMed Central (United Kingdom)

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

Science.gov (United States)

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.

UK PubMed Central (United Kingdom)

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

Environmental Research Database

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...

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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

UK PubMed Central (United Kingdom)

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