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Sample records for conversions locating gene

  1. Sexy gene conversions: locating gene conversions on the X-chromosome.

    PubMed

    Lawson, Mark J; Zhang, Liqing

    2009-08-01

    Gene conversion can have a profound impact on both the short- and long-term evolution of genes and genomes. Here, we examined the gene families that are located on the X-chromosomes of human (Homo sapiens), chimpanzee (Pan troglodytes), mouse (Mus musculus) and rat (Rattus norvegicus) for evidence of gene conversion. We identified seven gene families (WD repeat protein family, Ferritin Heavy Chain family, RAS-related Protein RAB-40 family, Diphosphoinositol polyphosphate phosphohydrolase family, Transcription Elongation Factor A family, LDOC1-related family, Zinc Finger Protein ZIC, and GLI family) that show evidence of gene conversion. Through phylogenetic analyses and synteny evidence, we show that gene conversion has played an important role in the evolution of these gene families and that gene conversion has occurred independently in both primates and rodents. Comparing the results with those of two gene conversion prediction programs (GENECONV and Partimatrix), we found that both GENECONV and Partimatrix have very high false negative rates (i.e. failed to predict gene conversions), which leads to many undetected gene conversions. The combination of phylogenetic analyses with physical synteny evidence exhibits high resolution in the detection of gene conversions.

  2. Sexy gene conversions: locating gene conversions on the X-chromosome.

    PubMed

    Lawson, Mark J; Zhang, Liqing

    2009-08-01

    Gene conversion can have a profound impact on both the short- and long-term evolution of genes and genomes. Here, we examined the gene families that are located on the X-chromosomes of human (Homo sapiens), chimpanzee (Pan troglodytes), mouse (Mus musculus) and rat (Rattus norvegicus) for evidence of gene conversion. We identified seven gene families (WD repeat protein family, Ferritin Heavy Chain family, RAS-related Protein RAB-40 family, Diphosphoinositol polyphosphate phosphohydrolase family, Transcription Elongation Factor A family, LDOC1-related family, Zinc Finger Protein ZIC, and GLI family) that show evidence of gene conversion. Through phylogenetic analyses and synteny evidence, we show that gene conversion has played an important role in the evolution of these gene families and that gene conversion has occurred independently in both primates and rodents. Comparing the results with those of two gene conversion prediction programs (GENECONV and Partimatrix), we found that both GENECONV and Partimatrix have very high false negative rates (i.e. failed to predict gene conversions), which leads to many undetected gene conversions. The combination of phylogenetic analyses with physical synteny evidence exhibits high resolution in the detection of gene conversions. PMID:19487239

  3. A gene conversion located 5' to the A gamma gene in linkage disequilibrium with the Bantu haplotype in sickle cell anemia.

    PubMed

    Bouhassira, E E; Lachman, H; Krishnamoorthy, R; Labie, D; Nagel, R L

    1989-06-01

    Cloning and sequencing of the gamma-globin gene of a sickle cell anemia patient homozygous for the Bantu haplotype has revealed a gene conversion that involves the replacement of an A gamma sequence by a G gamma sequence in the promoter area of the A gamma gene. This event is similar to another gene conversion believed to be responsible for the very high homology between gamma-globin genes, suggesting that the promoter area of these genes is prone to this type of genetic rearrangement. Further analysis demonstrated that the chromosome bearing this gene conversion has a very high frequency among Bantu chromosomes and a very low or nil frequency in other haplotypes linked to the beta s gene. No correlation was found between the G gamma/A gamma ratio and the presence of the gene conversion among Bantu haplotype patients, thus excluding a portion of the gamma gene sequence in the determination of this ratio.

  4. Huntington's disease gene located.

    PubMed

    Kolata, G

    1983-11-25

    Investigators have found a restriction enzyme marker, a piece of DNA that can be located with recombinant DNA techniques, that is so close to the Huntington's disease gene that its presence can be used as an indicator for that gene. If this marker is used as a diagnostic test for Huntington's disease, people at risk for getting the disease will be able to learn whether or not they will in fact develop the disease. The ability to predict the inevitable onset of this progressive, degenerative disease raises ethical questions about counseling, screening, and disclosure of risk status to patients and family members.

  5. The coalescent with gene conversion.

    PubMed Central

    Wiuf, C; Hein, J

    2000-01-01

    In this article we develop a coalescent model with intralocus gene conversion. The distribution of the tract length is geometric in concordance with results published in the literature. We derive a simulation scheme and deduce a number of analytical results for this coalescent with gene conversion. We compare patterns of variability in samples simulated according to the coalescent with recombination with similar patterns simulated according to the coalescent with gene conversion alone. Further, an expression for the expected number of topology shifts in a sample of present-day sequences caused by gene conversion events is derived. PMID:10790416

  6. Gene conversion in human rearranged immunoglobulin genes.

    PubMed

    Darlow, John M; Stott, David I

    2006-07-01

    Over the past 20 years, many DNA sequences have been published suggesting that all or part of the V(H) segment of a rearranged immunoglobulin gene may be replaced in vivo. Two different mechanisms appear to be operating. One of these is very similar to primary V(D)J recombination, involving the RAG proteins acting upon recombination signal sequences, and this has recently been proven to occur. Other sequences, many of which show partial V(H) replacements with no addition of untemplated nucleotides at the V(H)-V(H) joint, have been proposed to occur by an unusual RAG-mediated recombination with the formation of hybrid (coding-to-signal) joints. These appear to occur in cells already undergoing somatic hypermutation in which, some authors are convinced, RAG genes are silenced. We recently proposed that the latter type of V(H) replacement might occur by homologous recombination initiated by the activity of AID (activation-induced cytidine deaminase), which is essential for somatic hypermutation and gene conversion. The latter has been observed in other species, but not in human Ig genes, so far. In this paper, we present a new analysis of sequences published as examples of the second type of rearrangement. This not only shows that AID recognition motifs occur in recombination regions but also that some sequences show replacement of central sections by a sequence from another gene, similar to gene conversion in the immunoglobulin genes of other species. These observations support the proposal that this type of rearrangement is likely to be AID-mediated rather than RAG-mediated and is consistent with gene conversion.

  7. Gene Conversion in Human Genetic Disease

    PubMed Central

    Chen, Jian-Min; Férec, Claude; Cooper, David N.

    2010-01-01

    Gene conversion is a specific type of homologous recombination that involves the unidirectional transfer of genetic material from a ‘donor’ sequence to a highly homologous ‘acceptor’. We have recently reviewed the molecular mechanisms underlying gene conversion, explored the key part that this process has played in fashioning extant human genes, and performed a meta-analysis of gene-conversion events known to have caused human genetic disease. Here we shall briefly summarize some of the latest developments in the study of pathogenic gene conversion events, including (i) the emerging idea of minimal efficient sequence homology (MESH) for homologous recombination, (ii) the local DNA sequence features that appear to predispose to gene conversion, (iii) a mechanistic comparison of gene conversion and transient hypermutability, and (iv) recently reported examples of pathogenic gene conversion events. PMID:24710102

  8. A Pattern Analysis of Gene Conversion Literature

    PubMed Central

    Lawson, Mark J.; Jiao, Jian; Fan, Weiguo; Zhang, Liqing

    2009-01-01

    Gene conversion is an important biological process that involves the transfer of genetic (sequence) information from one gene to another. This can have a variety of effects on an organism, both short-term and long-term and both positive and detrimental. In an effort to better understand this process, we searched through over 3,000 abstracts that contain research on gene conversions, tagging the important data and performing an analysis on what we extract. Through this we established trends that give a better insight into gene conversion research and genetic research in general. Our results show the importance of the process and the importance of continuing gene conversion research. PMID:20148076

  9. Frequent gene conversion between human red and green opsin genes.

    PubMed

    Zhao, Z; Hewett-Emmett, D; Li, W H

    1998-04-01

    To study the evolution of human X-linked red and green opsin genes, genomic sequences in large regions of the two genes were compared. The divergences in introns 3, 4, and 5 and the 3' flanking sequence of the two genes are significantly lower than those in exons 4 and 5. The homogenization mechanism of introns and the 3' flanking sequence of human red and green opsin genes is probably gene conversion, which also occurred in exons 1 and 6. At least one gene conversion event occurred in each of three regions (1, 3, and 5) in the sequences compared. In conclusion, gene conversion has occurred frequently between human red and green opsin genes, but exons 2, 3, 4, and 5 have been maintained distinct between the two genes by natural selection.

  10. Visualizing conserved gene location across microbe genomes

    NASA Astrophysics Data System (ADS)

    Shaw, Chris D.

    2009-01-01

    This paper introduces an analysis-based zoomable visualization technique for displaying the location of genes across many related species of microbes. The purpose of this visualizatiuon is to enable a biologist to examine the layout of genes in the organism of interest with respect to the gene organization of related organisms. During the genomic annotation process, the ability to observe gene organization in common with previously annotated genomes can help a biologist better confirm the structure and function of newly analyzed microbe DNA sequences. We have developed a visualization and analysis tool that enables the biologist to observe and examine gene organization among genomes, in the context of the primary sequence of interest. This paper describes the visualization and analysis steps, and presents a case study using a number of Rickettsia genomes.

  11. Widespread Gene Conversion in Centromere Cores

    PubMed Central

    Shi, Jinghua; Wolf, Sarah E.; Burke, John M.; Presting, Gernot G.; Ross-Ibarra, Jeffrey; Dawe, R. Kelly

    2010-01-01

    Centromeres are the most dynamic regions of the genome, yet they are typified by little or no crossing over, making it difficult to explain the origin of this diversity. To address this question, we developed a novel CENH3 ChIP display method that maps kinetochore footprints over transposon-rich areas of centromere cores. A high level of polymorphism made it possible to map a total of 238 within-centromere markers using maize recombinant inbred lines. Over half of the markers were shown to interact directly with kinetochores (CENH3) by chromatin immunoprecipitation. Although classical crossing over is fully suppressed across CENH3 domains, two gene conversion events (i.e., non-crossover marker exchanges) were identified in a mapping population. A population genetic analysis of 53 diverse inbreds suggests that historical gene conversion is widespread in maize centromeres, occurring at a rate >1×10−5/marker/generation. We conclude that gene conversion accelerates centromere evolution by facilitating sequence exchange among chromosomes. PMID:20231874

  12. Formation of heteroduplex DNA during mammalian intrachromosomal gene conversion.

    PubMed Central

    Bollag, R J; Elwood, D R; Tobin, E D; Godwin, A R; Liskay, R M

    1992-01-01

    We have studied intrachromosomal gene conversion in mouse Ltk- cells with a substrate designed to provide genetic evidence for heteroduplex DNA. Our recombination substrate consists of two defective chicken thymidine kinase genes arranged so as to favor the selection of gene conversion products. The gene intended to serve as the recipient in gene conversion differs from the donor sequence by virtue of a palindromic insertion that creates silent restriction site polymorphisms between the two genes. While selection for gene conversion at a XhoI linker insertion within the recipient gene results in coconversion of the nearby palindromic site in more than half of the convertants, 4% of convertant colonies show both parental and nonparental genotypes at the polymorphic site. We consider these mixed colonies to be the result of genotypic sectoring and interpret this sectoring to be a consequence of unrepaired heteroduplex DNA at the polymorphic palindromic site. DNA replication through the heteroduplex recombination intermediate generates genetically distinct daughter cells that comprise a single colony. We believe that the data provide the first compelling genetic evidence for the presence of heteroduplex DNA during chromosomal gene conversion in mammalian cells. Images PMID:1549110

  13. Bayesian population genomic inference of crossing over and gene conversion.

    PubMed

    Padhukasahasram, Badri; Rannala, Bruce

    2011-10-01

    Meiotic recombination is a fundamental cellular mechanism in sexually reproducing organisms and its different forms, crossing over and gene conversion both play an important role in shaping genetic variation in populations. Here, we describe a coalescent-based full-likelihood Markov chain Monte Carlo (MCMC) method for jointly estimating the crossing-over, gene-conversion, and mean tract length parameters from population genomic data under a Bayesian framework. Although computationally more expensive than methods that use approximate likelihoods, the relative efficiency of our method is expected to be optimal in theory. Furthermore, it is also possible to obtain a posterior sample of genealogies for the data using this method. We first check the performance of the new method on simulated data and verify its correctness. We also extend the method for inference under models with variable gene-conversion and crossing-over rates and demonstrate its ability to identify recombination hotspots. Then, we apply the method to two empirical data sets that were sequenced in the telomeric regions of the X chromosome of Drosophila melanogaster. Our results indicate that gene conversion occurs more frequently than crossing over in the su-w and su-s gene sequences while the local rates of crossing over as inferred by our program are not low. The mean tract lengths for gene-conversion events are estimated to be ∼70 bp and 430 bp, respectively, for these data sets. Finally, we discuss ideas and optimizations for reducing the execution time of our algorithm.

  14. Interchromosomal gene conversion at an endogenous human cell locus.

    PubMed Central

    Quintana, P J; Neuwirth, E A; Grosovsky, A J

    2001-01-01

    To examine the relationship between gene conversion and reciprocal exchange at an endogenous chromosomal locus, we developed a reversion assay in a thymidine kinase deficient mutant, TX545, derived from the human lymphoblastoid cell line TK6. Selectable revertants of TX545 can be generated through interchromosomal gene conversion at the site of inactivating mutations on each tk allele or by reciprocal exchange that alters the linkage relationships of inactivating polymorphisms within the tk locus. Analysis of loss of heterozygosity (LOH) at intragenic polymorphisms and flanking microsatellite markers was used to initially evaluate allelotypes in TK(+) revertants for patterns associated with either gene conversion or crossing over. The linkage pattern in a subset of convertants was then unambiguously established, even in the event of prereplicative recombinational exchanges, by haplotype analysis of flanking microsatellite loci in tk(-/-) LOH mutants collected from the tk(+/-) parental convertant. Some (7/38; 18%) revertants were attributable to easily discriminated nonrecombinational mechanisms, including suppressor mutations within the tk coding sequence. However, all revertants classified as a recombinational event (28/38; 74%) were attributed to localized gene conversion, representing a highly significant preference (P < 0.0001) over gene conversion with associated reciprocal exchange, which was never observed. PMID:11404339

  15. Congenital cataracts: de novo gene conversion event in CRYBB2

    PubMed Central

    Garnai, Sarah J.; Huyghe, Jeroen R.; Reed, David M.; Scott, Kathleen M.; Liebmann, Jeffrey M.; Boehnke, Michael; Ritch, Robert; Pawar, Hemant

    2014-01-01

    Purpose To identify the cause of congenital cataracts in a consanguineous family of Ashkenazi Jewish ancestry. Methods We performed genome-wide linkage analysis and whole-exome sequencing for the initial discovery of variants, and we confirmed the variants using gene-specific primers and Sanger sequencing. Results We found significant evidence of linkage to chromosome 22, under an autosomal dominant inheritance model, with a maximum logarithm of the odds (LOD) score of 3.91 (16.918 to 25.641 Mb). Exome sequencing identified three nonsynonymous changes in the CRYBB2 exon 5 coding sequence that are consistent with the sequence of the corresponding region of the pseudogene CRYBB2P1. The identification of these changes was complicated by possible mismapping of some mutated CRYBB2 sequences to CRYBB2P1. Sequencing with gene-specific primers confirmed that the changes—rs2330991, c.433 C>T (p.R145W); rs2330992, c.440A>G (p.Q147R); and rs4049504, c.449C>T (p.T150M)—present in all ten affected family members are located in CRYBB2 and are not artifacts of cross-reaction with CRYBB2P1. We did not find these changes in six unaffected family members, including the unaffected grandfather who contributed the affected haplotype, nor did we find them in the 100 Ashkenazi Jewish controls. Conclusions Our data are consistent with a de novo gene conversion event, transferring 270 base pairs at most from CRYBB2P1 to exon 5 of CRYBB2. This study highlights how linkage mapping can be complicated by de novo mutation events, as well as how sequence-analysis pipeline mapping of short reads from next-generation sequencing can be complicated by the existence of pseudogenes or other highly homologous sequences. PMID:25489230

  16. Purifying selection against gene conversions between the polyamine transport (TPO) genes of Saccharomyces species.

    PubMed

    Sampathkumar, Gowthami; Drouin, Guy

    2015-02-01

    Saccharomyces species have five TPO genes, TPO1 through TPO5, coding for proteins that are involved in up taking or excreting intracellular spermine, putrescine or spermidine. Here, we investigate the evolutionary fate and functional impacts of gene conversions between these genes. Our results show that gene conversions occurred only between the TPO2 and TPO3 genes of the six Saccharomyces species we studied. They also show that these gene conversions occurred independently in all six species. The facts that they only occur between closely related genes having similar function, and that they are limited to the transmembrane domain of these proteins, suggest that they have little functional impact. These gene conversions therefore likely represent neutral mutations which are not subject to purifying selection. PMID:25135753

  17. Identifying driver genes in cancer by triangulating gene expression, gene location, and survival data.

    PubMed

    Rouam, Sigrid; Miller, Lance D; Karuturi, R Krishna Murthy

    2014-01-01

    Driver genes are directly responsible for oncogenesis and identifying them is essential in order to fully understand the mechanisms of cancer. However, it is difficult to delineate them from the larger pool of genes that are deregulated in cancer (ie, passenger genes). In order to address this problem, we developed an approach called TRIAngulating Gene Expression (TRIAGE through clinico-genomic intersects). Here, we present a refinement of this approach incorporating a new scoring methodology to identify putative driver genes that are deregulated in cancer. TRIAGE triangulates - or integrates - three levels of information: gene expression, gene location, and patient survival. First, TRIAGE identifies regions of deregulated expression (ie, expression footprints) by deriving a newly established measure called the Local Singular Value Decomposition (LSVD) score for each locus. Driver genes are then distinguished from passenger genes using dual survival analyses. Incorporating measurements of gene expression and weighting them according to the LSVD weight of each tumor, these analyses are performed using the genes located in significant expression footprints. Here, we first use simulated data to characterize the newly established LSVD score. We then present the results of our application of this refined version of TRIAGE to gene expression data from five cancer types. This refined version of TRIAGE not only allowed us to identify known prominent driver genes, such as MMP1, IL8, and COL1A2, but it also led us to identify several novel ones. These results illustrate that TRIAGE complements existing tools, allows for the identification of genes that drive cancer and could perhaps elucidate potential future targets of novel anticancer therapeutics.

  18. Fine-resolution mapping of spontaneous and double-strand break-induced gene conversion tracts in Saccharomyces cerevisiae reveals reversible mitotic conversion polarity.

    PubMed Central

    Sweetser, D B; Hough, H; Whelden, J F; Arbuckle, M; Nickoloff, J A

    1994-01-01

    Spontaneous and double-strand break (DSB)-induced gene conversion was examined in alleles of the Saccharomyces cerevisiae ura3 gene containing nine phenotypically silent markers and an HO nuclease recognition site. Conversions of these alleles, carried on ARS1/CEN4 plasmids, involved interactions with heteroalleles on chromosome V and were stimulated by DSBs created at HO sites. Crossovers that integrate plasmids into chromosomes were not detected since the resultant dicentric chromosomes would be lethal. Converted alleles in shuttle plasmids were easily transferred to Escherichia coli and analyzed for marker conversion, facilitating the characterization of more than 400 independent products from five crosses. This analysis revealed several new features of gene conversions. The average length of DSB-induced conversion tracts was 200 to 300 bp, although about 20% were very short (less than 53 bp). About 20% of spontaneous tracts also were also less than 53 bp, but spontaneous tracts were on average about 40% longer than DSB-induced tracts. Most tracts were continuous, but 3% had discontinuous conversion patterns, indicating that extensive heteroduplex DNA is formed during at least this fraction of events. Mismatches in heteroduplex DNA were repaired in both directions, and repair tracts as short as 44 bp were observed. Surprisingly, most DSB-induced gene conversion tracts were unidirectional and exhibited a reversible polarity that depended on the locations of DSBs and frameshift mutations in recipient and donor alleles. Images PMID:8196629

  19. Locational distribution of gene functional classes in Arabidopsis thaliana

    PubMed Central

    Riley, Michael C; Clare, Amanda; King, Ross D

    2007-01-01

    Background We are interested in understanding the locational distribution of genes and their functions in genomes, as this distribution has both functional and evolutionary significance. Gene locational distribution is known to be affected by various evolutionary processes, with tandem duplication thought to be the main process producing clustering of homologous sequences. Recent research has found clustering of protein structural families in the human genome, even when genes identified as tandem duplicates have been removed from the data. However, this previous research was hindered as they were unable to analyse small sample sizes. This is a challenge for bioinformatics as more specific functional classes have fewer examples and conventional statistical analyses of these small data sets often produces unsatisfactory results. Results We have developed a novel bioinformatics method based on Monte Carlo methods and Greenwood's spacing statistic for the computational analysis of the distribution of individual functional classes of genes (from GO). We used this to make the first comprehensive statistical analysis of the relationship between gene functional class and location on a genome. Analysis of the distribution of all genes except tandem duplicates on the five chromosomes of A. thaliana reveals that the distribution on chromosomes I, II, IV and V is clustered at P = 0.001. Many functional classes are clustered, with the degree of clustering within an individual class generally consistent across all five chromosomes. A novel and surprising result was that the locational distribution of some functional classes were significantly more evenly spaced than would be expected by chance. Conclusion Analysis of the A. thaliana genome reveals evidence of unexplained order in the locational distribution of genes. The same general analysis method can be applied to any genome, and indeed any sequential data involving classes. PMID:17397552

  20. Evolution of gene sequence in response to chromosomal location.

    PubMed

    Díaz-Castillo, Carlos; Golic, Kent G

    2007-09-01

    Evolutionary forces acting on the repetitive DNA of heterochromatin are not constrained by the same considerations that apply to protein-coding genes. Consequently, such sequences are subject to rapid evolutionary change. By examining the Troponin C gene family of Drosophila melanogaster, which has euchromatic and heterochromatic members, we find that protein-coding genes also evolve in response to their chromosomal location. The heterochromatic members of the family show a reduced CG content and increased variation in DNA sequence. We show that the CG reduction applies broadly to the protein-coding sequences of genes located at the heterochromatin:euchromatin interface, with a very strong correlation between CG content and the distance from centric heterochromatin. We also observe a similar trend in the transition from telomeric heterochromatin to euchromatin. We propose that the methylation of DNA is one of the forces driving this sequence evolution.

  1. Location, location, location: the evolutionary history of CD1 genes and the NKR-P1/ligand systems.

    PubMed

    Rogers, Sally L; Kaufman, Jim

    2016-08-01

    CD1 genes encode cell surface molecules that present lipid antigens to various kinds of T lymphocytes of the immune system. The structures of CD1 genes and molecules are like the major histocompatibility complex (MHC) class I system, the loading of antigen and the tissue distribution for CD1 molecules are like those in the class II system, and phylogenetic analyses place CD1 between class I and class II sequences, altogether leading to the notion that CD1 is a third ancient system of antigen presentation molecules. However, thus far, CD1 genes have only been described in mammals, birds and reptiles, leaving major questions as to their origin and evolution. In this review, we recount a little history of the field so far and then consider what has been learned about the structure and functional attributes of CD1 genes and molecules in marsupials, birds and reptiles. We describe the central conundrum of CD1 evolution, the genomic location of CD1 genes in the MHC and/or MHC paralogous regions in different animals, considering the three models of evolutionary history that have been proposed. We describe the natural killer (NK) receptors NKR-P1 and ligands, also found in different genomic locations for different animals. We discuss the consequence of these three models, one of which includes the repudiation of a guiding principle for the last 20 years, that two rounds of genome-wide duplication at the base of the vertebrates provided the extra MHC genes necessary for the emergence of adaptive immune system of jawed vertebrates. PMID:27457887

  2. Genes Downregulated in Endometriosis Are Located Near the Known Imprinting Genes

    PubMed Central

    Higashiura, Yumi; Koike, Natsuki; Akasaka, Juria; Uekuri, Chiharu; Iwai, Kana; Niiro, Emiko; Morioka, Sachiko; Yamada, Yuki

    2014-01-01

    There is now accumulating evidence that endometriosis is a disease associated with an epigenetic disorder. Genomic imprinting is an epigenetic phenomenon known to regulate DNA methylation of either maternal or paternal alleles. We hypothesize that hypermethylated endometriosis-associated genes may be enriched at imprinted gene loci. We sought to determine whether downregulated genes associated with endometriosis susceptibility are associated with chromosomal location of the known paternally and maternally expressed imprinting genes. Gene information has been gathered from National Center for Biotechnology Information database geneimprint.com. Several researchers have identified specific loci with strong DNA methylation in eutopic endometrium and ectopic lesion with endometriosis. Of the 29 hypermethylated genes in endometriosis, 19 genes were located near 45 known imprinted foci. There may be an association of the genomic location between genes specifically downregulated in endometriosis and epigenetically imprinted genes. PMID:24615936

  3. Evidence of extensive non-allelic gene conversion among LTR elements in the human genome

    PubMed Central

    Trombetta, Beniamino; Fantini, Gloria; D’Atanasio, Eugenia; Sellitto, Daniele; Cruciani, Fulvio

    2016-01-01

    Long Terminal Repeats (LTRs) are nearly identical DNA sequences found at either end of Human Endogenous Retroviruses (HERVs). The high sequence similarity that exists among different LTRs suggests they could be substrate of ectopic gene conversion events. To understand the extent to which gene conversion occurs and to gain new insights into the evolutionary history of these elements in humans, we performed an intra-species phylogenetic study of 52 LTRs on different unrelated Y chromosomes. From this analysis, we obtained direct evidence that demonstrates the occurrence of ectopic gene conversion in several LTRs, with donor sequences located on both sex chromosomes and autosomes. We also found that some of these elements are characterized by an extremely high density of polymorphisms, showing one of the highest nucleotide diversities in the human genome, as well as a complex patchwork of sequences derived from different LTRs. Finally, we highlighted the limits of current short-read NGS studies in the analysis of genetic diversity of the LTRs in the human genome. In conclusion, our comparative re-sequencing analysis revealed that ectopic gene conversion is a common event in the evolution of LTR elements, suggesting complex genetic links among LTRs from different chromosomes. PMID:27346230

  4. Evidence of extensive non-allelic gene conversion among LTR elements in the human genome.

    PubMed

    Trombetta, Beniamino; Fantini, Gloria; D'Atanasio, Eugenia; Sellitto, Daniele; Cruciani, Fulvio

    2016-01-01

    Long Terminal Repeats (LTRs) are nearly identical DNA sequences found at either end of Human Endogenous Retroviruses (HERVs). The high sequence similarity that exists among different LTRs suggests they could be substrate of ectopic gene conversion events. To understand the extent to which gene conversion occurs and to gain new insights into the evolutionary history of these elements in humans, we performed an intra-species phylogenetic study of 52 LTRs on different unrelated Y chromosomes. From this analysis, we obtained direct evidence that demonstrates the occurrence of ectopic gene conversion in several LTRs, with donor sequences located on both sex chromosomes and autosomes. We also found that some of these elements are characterized by an extremely high density of polymorphisms, showing one of the highest nucleotide diversities in the human genome, as well as a complex patchwork of sequences derived from different LTRs. Finally, we highlighted the limits of current short-read NGS studies in the analysis of genetic diversity of the LTRs in the human genome. In conclusion, our comparative re-sequencing analysis revealed that ectopic gene conversion is a common event in the evolution of LTR elements, suggesting complex genetic links among LTRs from different chromosomes. PMID:27346230

  5. Evidence of extensive non-allelic gene conversion among LTR elements in the human genome.

    PubMed

    Trombetta, Beniamino; Fantini, Gloria; D'Atanasio, Eugenia; Sellitto, Daniele; Cruciani, Fulvio

    2016-01-01

    Long Terminal Repeats (LTRs) are nearly identical DNA sequences found at either end of Human Endogenous Retroviruses (HERVs). The high sequence similarity that exists among different LTRs suggests they could be substrate of ectopic gene conversion events. To understand the extent to which gene conversion occurs and to gain new insights into the evolutionary history of these elements in humans, we performed an intra-species phylogenetic study of 52 LTRs on different unrelated Y chromosomes. From this analysis, we obtained direct evidence that demonstrates the occurrence of ectopic gene conversion in several LTRs, with donor sequences located on both sex chromosomes and autosomes. We also found that some of these elements are characterized by an extremely high density of polymorphisms, showing one of the highest nucleotide diversities in the human genome, as well as a complex patchwork of sequences derived from different LTRs. Finally, we highlighted the limits of current short-read NGS studies in the analysis of genetic diversity of the LTRs in the human genome. In conclusion, our comparative re-sequencing analysis revealed that ectopic gene conversion is a common event in the evolution of LTR elements, suggesting complex genetic links among LTRs from different chromosomes.

  6. Structure and location of the murine adrenoleukodystrophy gene

    SciTech Connect

    Kennedy, M.A.; Rowland, S.A.; Dodd, A.

    1996-03-05

    X-linked adrenoleukodystrophy (ALD) is a degenerative neurological disease characterized by the accumulation of very long chain fatty acids in various tissues and demyelination of the central nervous system. The human gene responsible for the disease encodes a membrane-bound ATP-binding transporter protein that is located in peroxisomes. We isolated the mouse adrenoleukodystrophy gene, determined its structure, and mapped it both cytogentically and genetically. The mouse gene is very similar in structure to the human gene, consisting of 10 exons arranged over a 22-kb genomic region. We localized it in band B of the mouse X chromosome by fluorescence in situ hybridization analysis and, using a new microsatellite repeat polymorphism, determined the map location as 47 cM from the X centromere. We found evidence for other sequences in the mouse genome related to the 3{prime} end of Aldgh. This study paves the way for the construction of gene-targeting plasmids that may be used to develop an animal model of ALD. 35 refs., 5 figs.

  7. Enhancer of terminal gene conversion, a new mutation in Drosophila melanogaster that induces telomere elongation by gene conversion.

    PubMed Central

    Melnikova, Larisa; Georgiev, Pavel

    2002-01-01

    Telomeres of Drosophila melanogaster contain arrays of the retrotransposon-like elements HeT-A and TART. Terminally deleted chromosomes can be maintained for many generations. Thus, broken chromosome ends behave as real telomeres. It was previously shown that gene conversion may extend the broken ends. Here we found that the frequency of terminal DNA elongation by gene conversion strongly depends on the genotype. A dominant E(tc) (Enhancer of terminal gene conversion) mutation markedly increases the frequency of this event but does not significantly influence the frequency of HeT-A and TART attachment to the broken chromosome end and recombination between directly repeated sequences at the end of the truncated chromosome. The E(tc) mutation was mapped to the 91-93 region on chromosome 3. Drosophila lines that bear the E(tc) mutation for many generations have telomeres, consisting of HeT-A and TART elements, that are longer than those found in wild-type lines. Thus, the E(tc) mutation plays a significant role in the control of telomere elongation in D. melanogaster. PMID:12454074

  8. The Location of Genes Governing Long First Internode of Corn

    PubMed Central

    Troyer, A. F.

    1997-01-01

    Knowing breeding behavior and cytological location of traits helps breeders. My objective was to locate dominant genes for long first internode of corn (Zea mays L.). I determined that Hopi Indian corn PI213733 (variety Komona) displayed the trait and grew well in the U.S. Corn Belt. I crossed PI213733 to 26 translocation tester stocks in Minnesota inbred A188 background, backcrossed semi-sterile plants carrying the translocation to A188 the next generation, and grew the segregating generation planted in trenches 15 cm deep with ridges of dirt 10 cm high one year, in trenches 25 cm deep the other year and also at normal (6 cm) depth. Emerged plants were classified for semi-sterility or for normal pollen. I concluded from multiple testers for each chromosome arm that dominant genes for long first internode are located (chromosome and region) on 3S, on 6 near the centromere, and on 9S; spurious associations occurred for two testers. Measurement of cell lengths indicated that PI213733 had more cells than A188 both in upper and in lower mesocotyl sections and that lower, older cells elongated sooner. I found a normal-sized kernel with twin embryos that developed two long first internode seedlings indicating that the amount of endosperm did not limit mesocotyl growth. PMID:9093865

  9. Diversification of the Primary Antibody Repertoire by AID-Mediated Gene Conversion.

    PubMed

    Lanning, Dennis K; Knight, Katherine L

    2015-01-01

    Gene conversion, mediated by activation-induced cytidine deaminase (AID), has been found to contribute to generation of the primary antibody repertoire in several vertebrate species. Generation of the primary antibody repertoire by gene conversion of immunoglobulin (Ig) genes occurs primarily in gut-associated lymphoid tissues (GALT) and is best described in chicken and rabbit. Here, we discuss current knowledge of the mechanism of gene conversion as well as the contribution of the microbiota in promoting gene conversion of Ig genes. Finally, we propose that the antibody diversification strategy used in GALT species, such as chicken and rabbit, is conserved in a subset of human and mouse B cells.

  10. The gene for type A streptococcal exotoxin (erythrogenic toxin) is located in bacteriophage T12.

    PubMed Central

    Weeks, C R; Ferretti, J J

    1984-01-01

    The infection of Streptococcus pyogenes T25(3) with the temperate bacteriophage T12 results in the conversion of the nontoxigenic strain to type A streptococcal exotoxin (erythrogenic toxin) production. Although previous research has established that integration of the bacteriophage genome into the host chromosome is not essential for exotoxin production, the location of the gene on the bacteriophage or bacterial chromosome had not been determined. In the present investigation, recombinant DNA techniques were used to determine whether the gene specifying type A streptococcal exotoxin (speA) production is located on the bacteriophage chromosome. Bacteriophage T12 was obtained from S. pyogenes T25(3)(T12) by induction with mitomycin C, and after isolation of bacteriophage DNA by phenol-chloroform extraction, the DNA was digested with restriction enzymes and ligated with Escherichia coli plasmid pHP34 or the Streptococcus-E. coli shuttle vector pSA3. Transformation of E. coli HB101 with the recombinant molecules allowed selection of E. coli clones containing bacteriophage T12 genes. Immunological assays with specific antibody revealed the presence of type A streptococcal exotoxin in sonicates of E. coli transformants. Subcloning experiments localized the speA gene to a 1.7-kilobase segment of the bacteriophage T12 genome flanked by SalI and HindIII sites. Introduction of the pSA3 vector containing the speA gene into Streptococcus sanguis (Challis) resulted in transformants that secreted the type A exotoxin. Immunological analysis showed that the type A streptococcal exotoxin produced by E. coli and S. sanguis transformants was identical to the type A exotoxin produced by S. pyogenes T25(3)(T12). Southern blot hybridizations with the cloned fragment confirmed its presence in the bacteriophage T12 genome and its absence in the T25(3) nonlysogen. Therefore, the gene for type A streptococcal exotoxin is located in the bacteriophage genome, and conversion of S. pyogenes T

  11. Patterns of Gene Conversion in Duplicated Yeast Histones Suggest Strong Selection on a Coadapted Macromolecular Complex

    PubMed Central

    Scienski, Kathy; Fay, Justin C.; Conant, Gavin C.

    2015-01-01

    We find evidence for interlocus gene conversion in five duplicated histone genes from six yeast species. The sequences of these duplicated genes, surviving from the ancient genome duplication, show phylogenetic patterns inconsistent with the well-resolved orthology relationships inferred from a likelihood model of gene loss after the genome duplication. Instead, these paralogous genes are more closely related to each other than any is to its nearest ortholog. In addition to simulations supporting gene conversion, we also present evidence for elevated rates of radical amino acid substitutions along the branches implicated in the conversion events. As these patterns are similar to those seen in ribosomal proteins that have undergone gene conversion, we speculate that in cases where duplicated genes code for proteins that are a part of tightly interacting complexes, selection may favor the fixation of gene conversion events in order to maintain high protein identities between duplicated copies. PMID:26560339

  12. Location of gene expression in CNS using hybridization histochemistry.

    PubMed

    Penschow, J D; Haralambidis, J; Aldred, P; Tregear, G W; Coghlan, J P

    1986-01-01

    In this chapter we have placed heavy emphasis on our own recent work to lay out a workable recipe for hybridization histochemistry. Only a trickle of papers followed the initial benchmark excursions into in situ labeling of tissue sections. Our own entry into this field was as late starters in 1978, but since then a confluence of important questions and technical advances has served to make hybridization histochemistry much more attractive and universally applicable as a research tool. Hybridization histochemistry allows the location of anatomical sites of gene expression and viral replication with unique specificity and is able to solve some problems for which there is no other suitable technique available in the central nervous system. For example, allowing that peptides may enter neurons by a variety of mechanisms and then be christened neuroendocrine peptides, it has become a compelling issue to know which cells are manufacturing the peptide. Thus, much can be learned by the approach elegantly demonstrated by Gee et al., of locating mRNA and its peptide product within the same neuron. The intracellular location of specific mRNA for a neuropeptide in a cell body indicates a very high probability that the peptide is secreted as a neurotransmitter or a neuromodulator from sites associated with the cell body. Our introduction of the use of whole mouse sections and large sections of brain of large animals in hybridization histochemistry has great potential in locating hormonal, enzymatic, and growth factor gene expression. The technique has been applied most elegantly by others to developmental studies and for the examination of viral infection. Resolution down to a single cell in heterogeneous tissue was beyond the original expectation of the capability of 32P-labeled probes and single cells in sections shown in Fig. 2 is probably the limit of resolution with this isotope. There is no reason why other isotopes, fluorescent labels, or labels suitable for EM should

  13. Methods for locating ground faults and insulation degradation condition in energy conversion systems

    DOEpatents

    Agamy, Mohamed; Elasser, Ahmed; Galbraith, Anthony William; Harfman Todorovic, Maja

    2015-08-11

    Methods for determining a ground fault or insulation degradation condition within energy conversion systems are described. A method for determining a ground fault within an energy conversion system may include, in part, a comparison of baseline waveform of differential current to a waveform of differential current during operation for a plurality of DC current carrying conductors in an energy conversion system. A method for determining insulation degradation within an energy conversion system may include, in part, a comparison of baseline frequency spectra of differential current to a frequency spectra of differential current transient at start-up for a plurality of DC current carrying conductors in an energy conversion system. In one embodiment, the energy conversion system may be a photovoltaic system.

  14. Gene conversion and DNA sequence polymorphism in the sex-determination gene fog-2 and its paralog ftr-1 in Caenorhabditis elegans.

    PubMed

    Rane, Hallie S; Smith, Jessica M; Bergthorsson, Ulfar; Katju, Vaishali

    2010-07-01

    Gene conversion, a form of concerted evolution, bears enormous potential to shape the trajectory of sequence and functional divergence of gene paralogs subsequent to duplication events. fog-2, a sex-determination gene unique to Caenorhabditis elegans and implicated in the origin of hermaphroditism in this species, resulted from the duplication of ftr-1, an upstream gene of unknown function. Synonymous sequence divergence in regions of fog-2 and ftr-1 (excluding recent gene conversion tracts) suggests that the duplication occurred 46 million generations ago. Gene conversion between fog-2 and ftr-1 was previously discovered in experimental fog-2 knockout lines of C. elegans, whereby hermaphroditism was restored in mutant obligately outcrossing male-female populations. We analyzed DNA-sequence variation in fog-2 and ftr-1 within 40 isolates of C. elegans from diverse geographic locations in order to evaluate the contribution of gene conversion to genetic variation in the two gene paralogs. The analysis shows that gene conversion contributes significantly to DNA-sequence diversity in fog-2 and ftr-1 (22% and 34%, respectively) and may have the potential to alter sexual phenotypes in natural populations. A radical amino acid change in a conserved region of the F-box domain of fog-2 was found in natural isolates of C. elegans with significantly lower fecundity. We hypothesize that the lowered fecundity is due to reduced masculinization and less sperm production and that amino acid replacement substitutions and gene conversion in fog-2 may contribute significantly to variation in the degree of inbreeding and outcrossing in natural populations.

  15. Recombination and Gene Flux Caused by Gene Conversion and Crossing over in Inversion Heterokaryotypes

    PubMed Central

    Navarro, A.; Betran, E.; Barbadilla, A.; Ruiz, A.

    1997-01-01

    A theoretical analysis of the effects of inversions on recombination and gene flux between arrangements caused by gene conversion and crossing over was carried out. Two different mathematical models of recombination were used: the Poisson model (without interference) and the Counting model (with interference). The main results are as follows. (1) Recombination and gene flux are highly site-dependent both inside and outside the inverted regions. (2) Crossing over overwhelms gene conversion as a cause of gene flux in large inversions, while conversion becomes relatively significant in short inversions and in regions around the breakpoints. (3) Under the Counting model the recombination rate between two markers depends strongly on the position of the markers along the inverted segment. Two equally spaced markers in the central part of the inverted segment have less recombination than if they are in a more extreme position. (4) Inversions affect recombination rates in the uninverted regions of the chromosome. Recombination increases in the distal segment and decreases in the proximal segment. These results provide an explanation for a number of observations reported in the literature. Because inversions are ubiquitous in the evolutionary history of many Drosophila species, the effects of inversions on recombination are expected to influence DNA variation patterns. PMID:9178017

  16. Identifying concerted evolution and gene conversion in mammalian gene pairs lasting over 100 million years

    PubMed Central

    Carson, Andrew R; Scherer, Stephen W

    2009-01-01

    Background Concerted evolution occurs in multigene families and is characterized by stretches of homogeneity and higher sequence similarity between paralogues than between orthologues. Here we identify human gene pairs that have undergone concerted evolution, caused by ongoing gene conversion, since at least the human-mouse divergence. Our strategy involved the identification of duplicated genes with greater similarity within a species than between species. These genes were required to be present in multiple mammalian genomes, suggesting duplication early in mammalian divergence. To eliminate genes that have been conserved due to strong purifying selection, our analysis also required at least one intron to have retained high sequence similarity between paralogues. Results We identified three human gene pairs undergoing concerted evolution (BMP8A/B, DDX19A/B, and TUBG1/2). Phylogenetic investigations reveal that in each case the duplication appears to have occurred prior to eutherian mammalian radiation, with exactly two paralogues present in all examined species. This indicates that all three gene duplication events were established over 100 million years ago. Conclusion The extended duration of concerted evolution in multiple distant lineages suggests that there has been prolonged homogenization of specific segments within these gene pairs. Although we speculate that selection for homogenization could have been utilized in order to maintain crucial homo- or hetero- binding domains, it remains unclear why gene conversion has persisted for such extended periods of time. Through these analyses, our results demonstrate additional examples of a process that plays a definite, although unspecified, role in molecular evolution. PMID:19583854

  17. Long-Lasting Gene Conversion Shapes the Convergent Evolution of the Critical Methanogenesis Genes

    PubMed Central

    Wang, Sishuo; Chen, Youhua; Cao, Qinhong; Lou, Huiqiang

    2015-01-01

    Methanogenesis and its key small-molecule methyltransferase Mtr complex are poorly understood despite their pivotal role in Earth’s global carbon cycle. Mtr complex is encoded by a conserved mtrEDCBAFGH operon in most methanogens. Here we report that two discrete lineages, Methanococcales and Methanomicrobiales, have a noncanonical mtr operon carrying two copies of mtrA resulting from an ancient duplication. Compared to mtrA-1, mtrA-2 acquires a distinct transmembrane domain through domain shuffling and gene fusion. However, the nontransmembrane domains (MtrA domain) of mtrA-1 and mtrA-2 are homogenized by gene conversion events lasting throughout the long history of these extant methanogens (over 2410 million years). Furthermore, we identified a possible recruitment of ancient nonmethanogenic methyltransferase genes to establish the methanogenesis pathway. These results not only provide novel evolutionary insight into the methanogenesis pathway and methyltransferase superfamily but also suggest an unanticipated long-lasting effect of gene conversion on gene evolution in a convergent pattern. PMID:26384370

  18. Quantitative trait locus gene mapping: a new method for locating alcohol response genes.

    PubMed

    Crabbe, J C

    1996-01-01

    Alcoholism is a multigenic trait with important non-genetic determinants. Studies with genetic animal models of susceptibility to several of alcohol's effects suggest that several genes contributing modest effects on susceptibility (Quantitative Trait Loci, or QTLs) are important. A new technique of QTL gene mapping has allowed the identification of the location in mouse genome of several such QTLs. The method is described, and the locations of QTLs affecting the acute alcohol withdrawal reaction are described as an example of the method. Verification of these QTLs in ancillary studies is described and the strengths, limitations, and future directions to be pursued are discussed. QTL mapping is a promising method for identifying genes in rodents with the hope of directly extrapolating the results to the human genome. This review is based on a paper presented at the First International Congress of the Latin American Society for Biomedical Research on Alcoholism, Santiago, Chile, November 1994. PMID:12893462

  19. Intronic gene conversion in the evolution of human X-linked color vision genes.

    PubMed

    Shyue, S K; Li, L; Chang, B H; Li, W H

    1994-05-01

    Human red and green visual pigment genes are X-linked duplicate genes. To study their evolutionary history, introns 2 and 4 (1,987 and 1,552 bp, respectively) of human red and green pigment genes were sequenced. Surprisingly, we found that intron 4 sequences of these two genes are identical and that the intron 2 sequences differ by only 0.3%. The low divergences are unexpected because the duplication event producing the two genes is believed to have occurred before the separation of the human and Old World monkey (OWM) lineages. Indeed, the divergences in the two introns are significantly lower than both the synonymous divergence (3.2% +/- 1.1%) and the nonsynonymous divergence (2.0% +/- 0.5%) in the coding sequences (exons 1-6). A comparison of partial sequences of exons 4 and 5 of human and OWM red and green pigment genes supports the hypothesis that the gene duplication occurred before the human-OWM split. In conclusion, the high similarities in the two intron sequences might be due to very recent gene conversion, probably during evolution of the human lineage.

  20. Molecular genetics of Psoriasis (Principles, technology, gene location, genetic polymorphism and gene expression)

    PubMed Central

    Al Robaee, Ahmad A.

    2010-01-01

    Summary: Psoriasis is a common inflammatory skin disease with an etiology bases on both environmental and genetic factors. As is the case of many autoimmune diseases its real cause remains poorly defined. However, it is known that genetic factors contribute to disease susceptibility. The linkage analysis has been used to identify multiple loci and alleles that confer risk of the disease. Some other studies have focused upon single nucleotide polymorphisms (SNPs) for mapping of probable causal variants. Other studies, using genome-wide analytical techniques, tried to link the disease to copy number variants (CNVs) that are segments of DNA ranging in size from kilobases to megabases that vary in copy number. CNVs represent an important element of genomic polymorphism in humans and harboring dosage-sensitive genes may cause or predispose to a variety of human genetic diseases. The mechanisms giving rise to SNPs and CNVs can be considered as fundamental processes underlying gene duplications, deletions, insertions, inversions and complex combinations of rearrangements. The duplicated genes being the results of ‘successful’ copies are fixed and maintained in the population. Conversely, many ‘unsuccessful’ duplicates remain in the genome as pseudogenes. There is another form of genetic variations termed copy-neutral loss of heterozygosity (LOH) with less information about their potential impact on complex diseases. Additional studies would include associated gene expression variations with either SNPs or CNVs. Now many genetic techniques such as PCR, real time PCR, microarray and restriction fragment length analysis are available for detecting genetic polymorphisms, gene mapping and estimation of gene expression. Recently, the scientists have used these tools to define genetic signatures of disease, to understand genetic causes of disease and to characterize the effects of certain drugs on gene expression. This review highlights the principles, technology and

  1. Hydrothermal conversion of big bluestem for bio-oil production: the effect of ecotype and planting location.

    PubMed

    Gan, Jing; Yuan, Wenqiao; Johnson, Loretta; Wang, Donghai; Nelson, Richard; Zhang, Ke

    2012-07-01

    Three ecotypes (CKS, EKS, IL) and one cultivar (KAW) of big bluestem (Andropogon gerardii) that were planted in three locations (Hays, KS; Manhattan, KS; and Carbondale, IL) were converted to bio-oil via hydrothermal conversion. Significant differences were found in the yield and elemental composition of bio-oils produced from big bluestem of different ecotypes and/or planting locations. Generally, the IL ecotype and the Carbondale, IL and Manhattan, KS planting locations gave higher bio-oil yield, which can be attributed to the higher total cellulose and hemicellulose content and/or the higher carbon but lower oxygen contents in these feedstocks. Bio-oil from the IL ecotype also had the highest carbon and lowest oxygen contents, which were not affected by the planting location. Bio-oils from big bluestem had yield, elemental composition, and chemical compounds similar to bio-oils from switchgrass and corncobs, although mass percentages of some of the compounds were slightly different.

  2. Conversion of Hanford site well locations to Washington coordinate system of 1983, South Zone 1991 (WCS83S)

    SciTech Connect

    Burnett, R.A.; Tzemos, S.; Dietz, L.A.

    1993-12-01

    Past construction and survey practices have resulted in the use of multiple local coordinate systems for measuring and reporting the horizontal position of wells and other facilities and locations on the Hanford Site. This report describes the development of a coordinate transformation process and algorithm and its application to the conversion of the horizontal coordinates of Hanford site wells from the various local coordinate systems and datums to a single standard coordinate system, the Washington Coordinate system of 1983, South Zone 1991 (WCS83S). The coordinate transformation algorithm, implemented as a computer program called CTRANS, uses standard two-dimensional translation, rotation, and scaling transformation equations and can be applied to any set of horizontal point locations. For each point to be transformed, the coefficients of the transformation equations are calculated locally, using the coordinates of the three nearest registration points (points with known locations in both coordinate systems). The report contains a discussion of efforts to verify and validate both the software and the well location data, a description of the methods used to estimate transformation and registration point accuracy, instructions for using the computer program, and a summary of the Hanford well conversion results for each local coordinate system and datum. Also included are the results of using recent U.S. Army Corps of Engineers survey data to obtain estimated measures of location errors in wells for which the local coordinate data source is undocumented, unverified, and therefore of unknown accuracy.

  3. Mitotic and Meiotic Gene Conversion of Ty Elements and Other Insertions in Saccharomyces Cerevisiae

    PubMed Central

    Vincent, A.; Petes, T. D.

    1989-01-01

    We examined meiotic and mitotic gene conversion events involved in deletion of Ty elements and other insertions from the genome of the yeast Saccharomyces cerevisiae. We found that Ty elements and one other insertion were deleted by mitotic gene conversion less frequently than point mutations at the same loci. One non-Ty insertion similar in size to Ty, however, did not show this bias. Mitotic conversion events deleting insertions were more frequently associated with crossing over than those deleting point mutations. In meiosis, conversion events duplicating the element were more common than those that deleted the element for one of the loci (HIS4) examined. PMID:2547693

  4. The Natural History of Class I Primate Alcohol Dehydrogenases Includes Gene Duplication, Gene Loss, and Gene Conversion

    PubMed Central

    Carrigan, Matthew A.; Uryasev, Oleg; Davis, Ross P.; Zhai, LanMin; Hurley, Thomas D.; Benner, Steven A.

    2012-01-01

    Background Gene duplication is a source of molecular innovation throughout evolution. However, even with massive amounts of genome sequence data, correlating gene duplication with speciation and other events in natural history can be difficult. This is especially true in its most interesting cases, where rapid and multiple duplications are likely to reflect adaptation to rapidly changing environments and life styles. This may be so for Class I of alcohol dehydrogenases (ADH1s), where multiple duplications occurred in primate lineages in Old and New World monkeys (OWMs and NWMs) and hominoids. Methodology/Principal Findings To build a preferred model for the natural history of ADH1s, we determined the sequences of nine new ADH1 genes, finding for the first time multiple paralogs in various prosimians (lemurs, strepsirhines). Database mining then identified novel ADH1 paralogs in both macaque (an OWM) and marmoset (a NWM). These were used with the previously identified human paralogs to resolve controversies relating to dates of duplication and gene conversion in the ADH1 family. Central to these controversies are differences in the topologies of trees generated from exonic (coding) sequences and intronic sequences. Conclusions/Significance We provide evidence that gene conversions are the primary source of difference, using molecular clock dating of duplications and analyses of microinsertions and deletions (micro-indels). The tree topology inferred from intron sequences appear to more correctly represent the natural history of ADH1s, with the ADH1 paralogs in platyrrhines (NWMs) and catarrhines (OWMs and hominoids) having arisen by duplications shortly predating the divergence of OWMs and NWMs. We also conclude that paralogs in lemurs arose independently. Finally, we identify errors in database interpretation as the source of controversies concerning gene conversion. These analyses provide a model for the natural history of ADH1s that posits four ADH1 paralogs in

  5. Mouse histone H2A and H2B genes: four functional genes and a pseudogene undergoing gene conversion with a closely linked functional gene.

    PubMed Central

    Liu, T J; Liu, L; Marzluff, W F

    1987-01-01

    The sequence of five mouse histone genes, two H2a and three H2b genes on chromosome 13 has been determined. The three H2b genes all code for different proteins, each differing in two amino acids from the others. The H2b specific elements present 5' to H2b genes from other species are present in all three mouse H2b genes. All three H2b genes are expressed in the same relative amounts in three different mouse cell lines and fetal mice. The H2b gene with the H2b specific sequence closest to the TATAA sequence is expressed in the highest amount. One of the H2a genes lacks the first 9 amino acids, the promoter region, the last 3 amino acids and contains an altered 3' end sequence. Despite these multiple defects, there is only one nucleotide change between the two H2a genes from codon 9 to 126. This indicates that a recent gene conversion has occurred between these two genes. The similarity of the nucleotide sequences in the coding regions of mouse histone genes is probably due to gene conversion events targeted precisely at the coding region. Images PMID:3562244

  6. Maximum-likelihood estimation of gene location by linkage disequilibrium

    SciTech Connect

    Hill, W.G. ); Weir, B.S. )

    1994-04-01

    Linkage disequilibrium, D, between a polymorphic disease and mapped markers can, in principle, be used to help find the map position of the disease gene. Likelihoods are therefore derived for the value of D conditional on the observed number of haplotypes in the sample and on the population parameter Nc, where N is the effective population size and c the recombination fraction between the disease and marker loci. The likelihood is computed explicitly for the case of two loci with heterozygote superiority and, more generally, by computer simulations assuming a steady state of constant population size and selective pressures or neutrality. It is found that the likelihood is, in general, not very dependent on the degree of selection at the loci and is very flat. This suggests that precise information on map position will not be obtained from estimates of linkage disequilibrium. 15 refs., 5 figs., 21 tabs.

  7. The genomic organization of a human creatine transporter (CRTR) gene located in Xq28

    SciTech Connect

    Sandoval, N.; Bauer, D.; Brenner, V.

    1996-07-15

    During the course of a large-scale sequencing project in Xq28, a human creatine transporter (CRTR) gene was discovered. The gene is located approximately 36 kb centromeric to ALD. The gene contains 13 exons and spans about 8.5 kb of genomic DNA. Since the creatine transporter has a prominent function in muscular physiology, it is a candidate gene for Barth syndrome and infantile cardiomyopathy mapped to Xq28. 19 refs., 1 fig., 1 tab.

  8. Preaching about the converted: how meiotic gene conversion influences genomic diversity.

    PubMed

    Cole, Francesca; Keeney, Scott; Jasin, Maria

    2012-09-01

    Meiotic crossover (CO) recombination involves a reciprocal exchange between homologous chromosomes. COs are often associated with gene conversion at the exchange site where genetic information is unidirectionally transferred from one chromosome to the other. COs and independent assortment of homologous chromosomes contribute significantly to the promotion of genomic diversity. What has not been appreciated is the contribution of another product of meiotic recombination, noncrossovers (NCOs), which result in gene conversion without exchange of flanking markers. Here, we review our comprehensive analysis of recombination at a highly polymorphic mouse hotspot. We found that NCOs make up ∼90% of recombination events. Preferential recombination initiation on one chromosome allowed us to estimate the contribution of CO and NCO gene conversion to transmission distortion, a deviation from Mendelian inheritance in the population. While NCO gene conversion tracts are shorter, and thus have a more punctate effect, their higher frequency translates into an approximately two-fold greater contribution than COs to gene conversion-based allelic shuffling and transmission distortion. We discuss the potential impact of mammalian NCO characteristics on evolution and genomic diversity. PMID:22954222

  9. Gene conversions and unequal crossovers between CYP21 (steroid 21-hydroxylase gene) and CYP21P involve different mechanisms.

    PubMed Central

    Tusié-Luna, M T; White, P C

    1995-01-01

    Most cases of congenital adrenal hyperplasia, the inherited inability to synthesize cortisol, are caused by mutations in the steroid 21-hydroxylase gene (CYP21). Steroid 21-hydroxylase deficiency is unusual among genetic diseases in that approximately 95% of the mutant alleles have apparently been generated by recombination between a normally active gene (CYP21) and a linked pseudogene (CYP21P). Approximately 20% of mutant alleles carry DNA deletions of 30 kb that have presumably been generated by unequal meiotic crossing-over, whereas 75% carry one or more mutations in CYP21 that are normally found in the CYP21P pseudogene. These latter mutations are termed "gene conversions," although the mechanism by which they are generated is not well understood. To assess the frequency at which these different recombination events occur, we have used PCR to detect de novo deletions and gene conversions in matched sperm and peripheral blood leukocyte DNA samples from normal individuals. Deletions with breakpoints in a 100-bp region in intron 2 and exon 3 were detected in sperm DNA samples with frequencies of approximately 1 in 10(5)-10(6) genomes but were never detected in the matching leukocyte DNA. Gene conversions in the same region occur in approximately 1 in 10(3)-10(5) genomes in both sperm and leukocyte DNA. These data suggest that whereas deletions occur exclusively in meiosis, gene conversions occur during both meiosis and mitosis, or perhaps only during mitosis. Thus, gene conversions must occur by a mechanism distinct from unequal crossing-over. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 PMID:7479886

  10. The Response of Dopa Decarboxylase Activity to Variations in Gene Dosage in Drosophila: A Possible Location of the Structural Gene

    PubMed Central

    Hodgetts, Ross B.

    1975-01-01

    A location of the structural gene(s) for dopa decarboxylase (EC 4.1.1.26) is proposed on the basis of enzyme determinations in a set of duplication-bearing aneuploids, which revealed only one dosage-sensitive region in the Drosophila genome. This region lies between 36EF and 37D on the left arm of chromosome 2. PMID:1126620

  11. The extent of migration of the Holliday junction is a crucial factor for gene conversion in Rhizobium etli.

    PubMed

    Castellanos, Mildred; Romero, David

    2009-08-01

    Gene conversion, defined as the nonreciprocal transfer of DNA, is one result of homologous recombination. Three steps in recombination could give rise to gene conversion: (i) DNA synthesis for repair of the degraded segment, (ii) Holliday junction migration, leading to heteroduplex formation, and (iii) repair of mismatches in the heteroduplex. There are at least three proteins (RuvAB, RecG, and RadA) that participate in the second step. Their roles have been studied for homologous recombination, but evidence of their relative role in gene conversion is lacking. In this work, we showed the effect on gene conversion of mutations in ruvB, recG, and radA in Rhizobium etli, either alone or in combination, using a cointegration strategy previously developed in our laboratory. The results indicate that the RuvAB system is highly efficient for gene conversion, since its absence provokes smaller gene conversion segments than those in the wild type as well as a shift in the preferred position of conversion tracts. The RecG system possesses a dual role for gene conversion. Inactivation of recG leads to longer gene conversion tracts than those in the wild type, indicating that its activity may hinder heteroduplex extension. However, under circumstances where it is the only migration activity present (as in the ruvB radA double mutant), conversion segments can still be seen, indicating that RecG can also promote gene conversion. RadA is the least efficient system in R. etli but is still needed for the production of detectable gene conversion tracts.

  12. Effects of Aging and Anatomic Location on Gene Expression in Human Retina

    PubMed Central

    Cai, Hui; Fields, Mark A.; Hoshino, Risa; Priore, Lucian V. Del

    2012-01-01

    Objective: To determine the effects of age and topographic location on gene expression in human neural retina. Methods: Macular and peripheral neural retina RNA was isolated from human donor eyes for DNA microarray and quantitative RT-PCR analyses. Results: Total RNA integrity from human donors was preserved. Hierarchical clustering analysis demonstrates that the gene expression profiles of young, old, macula, and peripheral retina cluster into four distinct groups. Genes which are highly expressed in macular, peripheral, young, or old retina were identified, including inhibitors of Wnt Signaling Pathway (DKK1, FZD10, and SFRP2) which are preferably expressed in the periphery. Conclusion: The transcriptome of the human retina is affected by age and topographic location. Wnt pathway inhibitors in the periphery may maintain peripheral retinal cells in an undifferentiated state. Understanding the effects of age and topographic location on gene expression may lead to the development of new therapeutic interventions for age-related eye diseases. PMID:22666212

  13. Apparent gene conversions involving the SMN gene in the region of the spinal muscular atrophy locus on chromosome 5

    SciTech Connect

    Steege, G. van der; Grootscholten, P.M.; Cobben, J.M.; Scheffer, H.; Buys, C.H.C.M.

    1996-10-01

    The survival motor neuron (SMN) gene has been described as a determining gene for spinal muscular atrophy (SMA). SMN has a closely flanking, nearly identical copy ({sup C}BCD541). Gene and copy gene can be discriminated by sequence differences in exons 7 and 8. The large majority of SMA patients show homozygous deletions of at least exons 7 and 8 of the SMN gene. A minority of patients show absence of SMN exon 7 but retention of exon 8. This is explained by results of our present analysis of 13 such patients providing evidence for apparent gene-conversion events between SMN and the centromeric copy gene. Instead of applying a separate analysis for absence or presence of SMN exons 7 and 8, we used a contiguous PCR from intron 6 to exon 8. In every case we found a chimeric gene with a fusion of exon 7 of the copy gene and exon 8 of SMN and absence of a normal SMN gene. Similar events, including the fusion counterpart, were observed in a group of controls, although in the presence of a normal SMN gene. Chimeric genes as the result of fusions of parts of SMN and {sup C}BCD541 apparently are far from rare and may partly explain the frequently observed SMN deletions in SMA patients. 23 refs., 4 figs.

  14. Gene Conversion Violates the Stepwise Mutation Model for Microsatellites in Y-Chromosomal Palindromic Repeats

    PubMed Central

    Balaresque, Patricia; King, Turi E; Parkin, Emma J; Heyer, Evelyne; Carvalho-Silva, Denise; Kraaijenbrink, Thirsa; de Knijff, Peter; Tyler-Smith, Chris; Jobling, Mark A

    2014-01-01

    The male-specific region of the human Y chromosome (MSY) contains eight large inverted repeats (palindromes), in which high-sequence similarity between repeat arms is maintained by gene conversion. These palindromes also harbor microsatellites, considered to evolve via a stepwise mutation model (SMM). Here, we ask whether gene conversion between palindrome microsatellites contributes to their mutational dynamics. First, we study the duplicated tetranucleotide microsatellite DYS385a,b lying in palindrome P4. We show, by comparing observed data with simulated data under a SMM within haplogroups, that observed heteroallelic combinations in which the modal repeat number difference between copies was large, can give rise to homoallelic combinations with zero-repeats difference, equivalent to many single-step mutations. These are unlikely to be generated under a strict SMM, suggesting the action of gene conversion. Second, we show that the intercopy repeat number difference for a large set of duplicated microsatellites in all palindromes in the MSY reference sequence is significantly reduced compared with that for nonpalindrome-duplicated microsatellites, suggesting that the former are characterized by unusual evolutionary dynamics. These observations indicate that gene conversion violates the SMM for microsatellites in palindromes, homogenizing copies within individual Y chromosomes, but increasing overall haplotype diversity among chromosomes within related groups. PMID:24610746

  15. Loss of two introns from the Magnolia tripetala mitochondrial cox2 gene implicates horizontal gene transfer and gene conversion as a novel mechanism of intron loss.

    PubMed

    Hepburn, Nancy J; Schmidt, Derek W; Mower, Jeffrey P

    2012-10-01

    Intron loss is often thought to occur through retroprocessing, which is the reverse transcription and genomic integration of a spliced transcript. In plant mitochondria, several unambiguous examples of retroprocessing are supported by the parallel loss of an intron and numerous adjacent RNA edit sites, but in most cases, the evidence for intron loss via retroprocessing is weak or lacking entirely. To evaluate mechanisms of intron loss, we designed a polymerase chain reaction (PCR)-based assay to detect recent intron losses from the mitochondrial cox2 gene within genus Magnolia, which was previously suggested to have variability in cox2 intron content. Our assay showed that all 22 examined species have a cox2 gene with two introns. However, one species, Magnolia tripetala, contains an additional cox2 gene that lacks both introns. Quantitative PCR showed that both M. tripetala cox2 genes are present in the mitochondrial genome. Although the intronless gene has lost several ancestral RNA edit sites, their distribution is inconsistent with retroprocessing models. Instead, phylogenetic and gene conversion analyses indicate that the intronless gene was horizontally acquired from a eudicot and then underwent gene conversion with the native intron-containing gene. The models are presented to summarize the roles of horizontal gene transfer and gene conversion as a novel mechanism of intron loss.

  16. Biased gene conversion skews allele frequencies in human populations, increasing the disease burden of recessive alleles.

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2014-10-01

    Gene conversion results in the nonreciprocal transfer of genetic information between two recombining sequences, and there is evidence that this process is biased toward G and C alleles. However, the strength of GC-biased gene conversion (gBGC) in human populations and its effects on hereditary disease have yet to be assessed on a genomic scale. Using high-coverage whole-genome sequences of African hunter-gatherers, agricultural populations, and primate outgroups, we quantified the effects of GC-biased gene conversion on population genomic data sets. We find that genetic distances (FST and population branch statistics) are modified by gBGC. In addition, the site frequency spectrum is left-shifted when ancestral alleles are favored by gBGC and right-shifted when derived alleles are favored by gBGC. Allele frequency shifts due to gBGC mimic the effects of natural selection. As expected, these effects are strongest in high-recombination regions of the human genome. By comparing the relative rates of fixation of unbiased and biased sites, the strength of gene conversion was estimated to be on the order of Nb ≈ 0.05 to 0.09. We also find that derived alleles favored by gBGC are much more likely to be homozygous than derived alleles at unbiased SNPs (+42.2% to 62.8%). This results in a curse of the converted, whereby gBGC causes substantial increases in hereditary disease risks. Taken together, our findings reveal that GC-biased gene conversion has important population genetic and public health implications.

  17. Evolutionary Stasis in Cycad Plastomes and the First Case of Plastome GC-Biased Gene Conversion.

    PubMed

    Wu, Chung-Shien; Chaw, Shu-Miaw

    2015-07-01

    In angiosperms, gene conversion has been known to reduce the mutational load of plastid genomes (the plastomes). Particularly, more frequent gene conversions in inverted repeat (IR) than in single copy (SC) regions result in contrasting substitution rates between these two regions. However, little has been known about the effect of gene conversion in the evolution of gymnosperm plastomes. Cycads (Cycadophyta) are the second largest gymnosperm group. Evolutionary study of their plastomes is limited to the basal cycad genus, Cycas. In this study, we addressed three questions. 1) Do the plastomes of other cycad genera evolve slowly as previously observed in the plastome of Cycas taitungensis? 2) Do substitution rates differ between their SC and IR regions? And 3) Does gene conversion occur in the cycad plastomes? If yes, is it AT-biased or GC-biased? Plastomes of eight species from other eight genera of cycads were sequenced. These plastomes are highly conserved in genome organization. Excluding ginkgo, cycad plastomes have significantly lower synonymous and nonsynonymous substitution rates than other gymnosperms, reflecting their evolutionary stasis in nucleotide mutations. In the IRs of cycad plastomes, the reduced substitution rates and GC-biased mutations are associated with a GC-biased gene conversion (gBGC) mechanism. Further investigations suggest that in cycads, gBGC is able to rectify plastome-wide mutations. Therefore, this study is the first to uncover the plastomic gBGC in seed plants. We also propose a gBGC model to interpret the dissimilar evolutionary patterns as well as the compositionally biased mutations in the SC and IR regions of cycad plastomes. PMID:26116919

  18. Evolutionary Stasis in Cycad Plastomes and the First Case of Plastome GC-Biased Gene Conversion

    PubMed Central

    Wu, Chung-Shien; Chaw, Shu-Miaw

    2015-01-01

    In angiosperms, gene conversion has been known to reduce the mutational load of plastid genomes (the plastomes). Particularly, more frequent gene conversions in inverted repeat (IR) than in single copy (SC) regions result in contrasting substitution rates between these two regions. However, little has been known about the effect of gene conversion in the evolution of gymnosperm plastomes. Cycads (Cycadophyta) are the second largest gymnosperm group. Evolutionary study of their plastomes is limited to the basal cycad genus, Cycas. In this study, we addressed three questions. 1) Do the plastomes of other cycad genera evolve slowly as previously observed in the plastome of Cycas taitungensis? 2) Do substitution rates differ between their SC and IR regions? And 3) Does gene conversion occur in the cycad plastomes? If yes, is it AT-biased or GC-biased? Plastomes of eight species from other eight genera of cycads were sequenced. These plastomes are highly conserved in genome organization. Excluding ginkgo, cycad plastomes have significantly lower synonymous and nonsynonymous substitution rates than other gymnosperms, reflecting their evolutionary stasis in nucleotide mutations. In the IRs of cycad plastomes, the reduced substitution rates and GC-biased mutations are associated with a GC-biased gene conversion (gBGC) mechanism. Further investigations suggest that in cycads, gBGC is able to rectify plastome-wide mutations. Therefore, this study is the first to uncover the plastomic gBGC in seed plants. We also propose a gBGC model to interpret the dissimilar evolutionary patterns as well as the compositionally biased mutations in the SC and IR regions of cycad plastomes. PMID:26116919

  19. Evolutionary Stasis in Cycad Plastomes and the First Case of Plastome GC-Biased Gene Conversion.

    PubMed

    Wu, Chung-Shien; Chaw, Shu-Miaw

    2015-06-27

    In angiosperms, gene conversion has been known to reduce the mutational load of plastid genomes (the plastomes). Particularly, more frequent gene conversions in inverted repeat (IR) than in single copy (SC) regions result in contrasting substitution rates between these two regions. However, little has been known about the effect of gene conversion in the evolution of gymnosperm plastomes. Cycads (Cycadophyta) are the second largest gymnosperm group. Evolutionary study of their plastomes is limited to the basal cycad genus, Cycas. In this study, we addressed three questions. 1) Do the plastomes of other cycad genera evolve slowly as previously observed in the plastome of Cycas taitungensis? 2) Do substitution rates differ between their SC and IR regions? And 3) Does gene conversion occur in the cycad plastomes? If yes, is it AT-biased or GC-biased? Plastomes of eight species from other eight genera of cycads were sequenced. These plastomes are highly conserved in genome organization. Excluding ginkgo, cycad plastomes have significantly lower synonymous and nonsynonymous substitution rates than other gymnosperms, reflecting their evolutionary stasis in nucleotide mutations. In the IRs of cycad plastomes, the reduced substitution rates and GC-biased mutations are associated with a GC-biased gene conversion (gBGC) mechanism. Further investigations suggest that in cycads, gBGC is able to rectify plastome-wide mutations. Therefore, this study is the first to uncover the plastomic gBGC in seed plants. We also propose a gBGC model to interpret the dissimilar evolutionary patterns as well as the compositionally biased mutations in the SC and IR regions of cycad plastomes.

  20. Nucleotide sequence and revised map location of the arn gene from bacteriophage T4.

    PubMed

    Kim, B C; Kim, K; Park, E H; Lim, C J

    1997-10-31

    Non-glucosylated (Glu-) T-even phage DNAs are restricted by Escherichia coli RgIA and RgIB endonucleases with different specificities. RgIB endonuclease activity is strongly inhibited by anti-restriction endonuclease (Arn) encoded by the bacteriophage T4 genome. The nucleotide sequence of the arn gene encoding Arn was determined. The product of the cloned arn gene was overexpressed by the T7 RNA polymerase/promoter system, and its molecular size is consistent with that predicted from the open reading frame of the arn gene. The arn gene is located between the asiA gene and motA gene in the region of 161,300-161,578 nucleotides.

  1. Caffeine inhibits gene conversion by displacing Rad51 from ssDNA.

    PubMed

    Tsabar, Michael; Mason, Jennifer M; Chan, Yuen-Ling; Bishop, Douglas K; Haber, James E

    2015-08-18

    Efficient repair of chromosomal double-strand breaks (DSBs) by homologous recombination relies on the formation of a Rad51 recombinase filament that forms on single-stranded DNA (ssDNA) created at DSB ends. This filament facilitates the search for a homologous donor sequence and promotes strand invasion. Recently caffeine treatment has been shown to prevent gene targeting in mammalian cells by increasing non-productive Rad51 interactions between the DSB and random regions of the genome. Here we show that caffeine treatment prevents gene conversion in yeast, independently of its inhibition of the Mec1(ATR)/Tel1(ATM)-dependent DNA damage response or caffeine's inhibition of 5' to 3' resection of DSB ends. Caffeine treatment results in a dosage-dependent eviction of Rad51 from ssDNA. Gene conversion is impaired even at low concentrations of caffeine, where there is no discernible dismantling of the Rad51 filament. Loss of the Rad51 filament integrity is independent of Srs2's Rad51 filament dismantling activity or Rad51's ATPase activity and does not depend on non-specific Rad51 binding to undamaged double-stranded DNA. Caffeine treatment had similar effects on irradiated HeLa cells, promoting loss of previously assembled Rad51 foci. We conclude that caffeine treatment can disrupt gene conversion by disrupting Rad51 filaments.

  2. Caffeine inhibits gene conversion by displacing Rad51 from ssDNA

    PubMed Central

    Tsabar, Michael; Mason, Jennifer M.; Chan, Yuen-Ling; Bishop, Douglas K.; Haber, James E.

    2015-01-01

    Efficient repair of chromosomal double-strand breaks (DSBs) by homologous recombination relies on the formation of a Rad51 recombinase filament that forms on single-stranded DNA (ssDNA) created at DSB ends. This filament facilitates the search for a homologous donor sequence and promotes strand invasion. Recently caffeine treatment has been shown to prevent gene targeting in mammalian cells by increasing non-productive Rad51 interactions between the DSB and random regions of the genome. Here we show that caffeine treatment prevents gene conversion in yeast, independently of its inhibition of the Mec1ATR/Tel1ATM-dependent DNA damage response or caffeine's inhibition of 5′ to 3′ resection of DSB ends. Caffeine treatment results in a dosage-dependent eviction of Rad51 from ssDNA. Gene conversion is impaired even at low concentrations of caffeine, where there is no discernible dismantling of the Rad51 filament. Loss of the Rad51 filament integrity is independent of Srs2's Rad51 filament dismantling activity or Rad51's ATPase activity and does not depend on non-specific Rad51 binding to undamaged double-stranded DNA. Caffeine treatment had similar effects on irradiated HeLa cells, promoting loss of previously assembled Rad51 foci. We conclude that caffeine treatment can disrupt gene conversion by disrupting Rad51 filaments. PMID:26019181

  3. Quantification of GC-biased gene conversion in the human genome.

    PubMed

    Glémin, Sylvain; Arndt, Peter F; Messer, Philipp W; Petrov, Dmitri; Galtier, Nicolas; Duret, Laurent

    2015-08-01

    Much evidence indicates that GC-biased gene conversion (gBGC) has a major impact on the evolution of mammalian genomes. However, a detailed quantification of the process is still lacking. The strength of gBGC can be measured from the analysis of derived allele frequency spectra (DAF), but this approach is sensitive to a number of confounding factors. In particular, we show by simulations that the inference is pervasively affected by polymorphism polarization errors and by spatial heterogeneity in gBGC strength. We propose a new general method to quantify gBGC from DAF spectra, incorporating polarization errors, taking spatial heterogeneity into account, and jointly estimating mutation bias. Applying it to human polymorphism data from the 1000 Genomes Project, we show that the strength of gBGC does not differ between hypermutable CpG sites and non-CpG sites, suggesting that in humans gBGC is not caused by the base-excision repair machinery. Genome-wide, the intensity of gBGC is in the nearly neutral area. However, given that recombination occurs primarily within recombination hotspots, 1%-2% of the human genome is subject to strong gBGC. On average, gBGC is stronger in African than in non-African populations, reflecting differences in effective population sizes. However, due to more heterogeneous recombination landscapes, the fraction of the genome affected by strong gBGC is larger in non-African than in African populations. Given that the location of recombination hotspots evolves very rapidly, our analysis predicts that, in the long term, a large fraction of the genome is affected by short episodes of strong gBGC.

  4. Role of Double-Strand Break End-Tethering during Gene Conversion in Saccharomyces cerevisiae

    PubMed Central

    Haber, James E.

    2016-01-01

    Correct repair of DNA double-strand breaks (DSBs) is critical for maintaining genome stability. Whereas gene conversion (GC)-mediated repair is mostly error-free, repair by break-induced replication (BIR) is associated with non-reciprocal translocations and loss of heterozygosity. We have previously shown that a Recombination Execution Checkpoint (REC) mediates this competition by preventing the BIR pathway from acting on DSBs that can be repaired by GC. Here, we asked if the REC can also determine whether the ends that are engaged in a GC-compatible configuration belong to the same break, since repair involving ends from different breaks will produce potentially deleterious translocations. We report that the kinetics of repair are markedly delayed when the two DSB ends that participate in GC belong to different DSBs (termed Trans) compared to the case when both DSB ends come from the same break (Cis). However, repair in Trans still occurs by GC rather than BIR, and the overall efficiency of repair is comparable. Hence, the REC is not sensitive to the “origin” of the DSB ends. When the homologous ends for GC are in Trans, the delay in repair appears to reflect their tethering to sequences on the other side of the DSB that themselves recombine with other genomic locations with which they share sequence homology. These data support previous observations that the two ends of a DSB are usually tethered to each other and that this tethering facilitates both ends encountering the same donor sequence. We also found that the presence of homeologous/repetitive sequences in the vicinity of a DSB can distract the DSB end from finding its bona fide homologous donor, and that inhibition of GC by such homeologous sequences is markedly increased upon deleting Sgs1 but not Msh6. PMID:27074148

  5. Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates

    PubMed Central

    Palamara, Pier Francesco; Francioli, Laurent C.; Wilton, Peter R.; Genovese, Giulio; Gusev, Alexander; Finucane, Hilary K.; Sankararaman, Sriram; Sunyaev, Shamil R.; de Bakker, Paul I.W.; Wakeley, John; Pe’er, Itsik; Price, Alkes L.

    2015-01-01

    The rate at which human genomes mutate is a central biological parameter that has many implications for our ability to understand demographic and evolutionary phenomena. We present a method for inferring mutation and gene-conversion rates by using the number of sequence differences observed in identical-by-descent (IBD) segments together with a reconstructed model of recent population-size history. This approach is robust to, and can quantify, the presence of substantial genotyping error, as validated in coalescent simulations. We applied the method to 498 trio-phased sequenced Dutch individuals and inferred a point mutation rate of 1.66 × 10−8 per base per generation and a rate of 1.26 × 10−9 for <20 bp indels. By quantifying how estimates varied as a function of allele frequency, we inferred the probability that a site is involved in non-crossover gene conversion as 5.99 × 10−6. We found that recombination does not have observable mutagenic effects after gene conversion is accounted for and that local gene-conversion rates reflect recombination rates. We detected a strong enrichment of recent deleterious variation among mismatching variants found within IBD regions and observed summary statistics of local sharing of IBD segments to closely match previously proposed metrics of background selection; however, we found no significant effects of selection on our mutation-rate estimates. We detected no evidence of strong variation of mutation rates in a number of genomic annotations obtained from several recent studies. Our analysis suggests that a mutation-rate estimate higher than that reported by recent pedigree-based studies should be adopted in the context of DNA-based demographic reconstruction. PMID:26581902

  6. Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates.

    PubMed

    Palamara, Pier Francesco; Francioli, Laurent C; Wilton, Peter R; Genovese, Giulio; Gusev, Alexander; Finucane, Hilary K; Sankararaman, Sriram; Sunyaev, Shamil R; de Bakker, Paul I W; Wakeley, John; Pe'er, Itsik; Price, Alkes L

    2015-12-01

    The rate at which human genomes mutate is a central biological parameter that has many implications for our ability to understand demographic and evolutionary phenomena. We present a method for inferring mutation and gene-conversion rates by using the number of sequence differences observed in identical-by-descent (IBD) segments together with a reconstructed model of recent population-size history. This approach is robust to, and can quantify, the presence of substantial genotyping error, as validated in coalescent simulations. We applied the method to 498 trio-phased sequenced Dutch individuals and inferred a point mutation rate of 1.66 × 10(-8) per base per generation and a rate of 1.26 × 10(-9) for <20 bp indels. By quantifying how estimates varied as a function of allele frequency, we inferred the probability that a site is involved in non-crossover gene conversion as 5.99 × 10(-6). We found that recombination does not have observable mutagenic effects after gene conversion is accounted for and that local gene-conversion rates reflect recombination rates. We detected a strong enrichment of recent deleterious variation among mismatching variants found within IBD regions and observed summary statistics of local sharing of IBD segments to closely match previously proposed metrics of background selection; however, we found no significant effects of selection on our mutation-rate estimates. We detected no evidence of strong variation of mutation rates in a number of genomic annotations obtained from several recent studies. Our analysis suggests that a mutation-rate estimate higher than that reported by recent pedigree-based studies should be adopted in the context of DNA-based demographic reconstruction.

  7. Oscillatory kinetics of gene expression: Protein conversion and slow mRNA transport

    SciTech Connect

    Zhdanov, V. P.

    2009-06-15

    The negative feedback between mRNA and regulatory-protein production may result in oscillations in the kinetics of gene expression if the mRNA-protein interplay includes protein conversion. Using a mean-field kinetic model, we show that such oscillations can be amplified due to limitations of the mRNA transport between the nucleus and cytoplasm. This effect may be dramatic for the mRNA population in the nucleus.

  8. Target gene mutational pattern in Lynch syndrome colorectal carcinomas according to tumour location and germline mutation

    PubMed Central

    Pinheiro, Manuela; Pinto, Carla; Peixoto, Ana; Veiga, Isabel; Lopes, Paula; Henrique, Rui; Baldaia, Helena; Carneiro, Fátima; Seruca, Raquel; Tomlinson, Ian; Kovac, Michal; Heinimann, Karl; Teixeira, Manuel R

    2015-01-01

    Background: We previously reported that the target genes in sporadic mismatch repair (MMR)-deficient colorectal carcinomas (CRCs) in the distal colon differ from those occurring elsewhere in the colon. This study aimed to compare the target gene mutational pattern in microsatellite instability (MSI) CRC from Lynch syndrome patients stratified by tumour location and germline mutation, as well as with that of sporadic disease. Methods: A series of CRC from Lynch syndrome patients was analysed for MSI in genes predicted to be selective MSI targets and known to be involved in several pathways of colorectal carcinogenesis. Results: The most frequently mutated genes belong to the TGF-β superfamily pathway, namely ACVR2A and TGFBR2. A significantly higher frequency of target gene mutations was observed in CRC from patients with germline mutations in MLH1 or MSH2 when compared with MSH6. Mutations in microsatellite sequences (A)7 of BMPR2 and (A)8 of MSH3 were significantly more frequent in the distal CRC. Additionally, we observed differences in MSH3 and TGFBR2 mutational frequency between Lynch syndrome and sporadic MSI CRC regarding tumour location. Conclusions: Our results indicate that the pattern of genetic changes differs in CRC depending on tumour location and between Lynch syndrome and sporadic MSI CRC, suggesting that carcinogenesis can occur by different pathways even if driven by generalised MSI. PMID:26247575

  9. A New Map Location of Gene Stb3 for Resistance to Septoria Tritici Blotch in Wheat

    PubMed Central

    Goodwin, Stephen B.; Cavaletto, Jessica R.; Hale, Iago L.; Thompson, Ian; Xu, Steven X.; Adhikari, Tika B.; Dubcovsky, Jorge

    2016-01-01

    Septoria tritici blotch (STB), caused by Mycosphaerella graminicola (synonym: Zymoseptoria tritici; asexual stage: Septoria tritici), is an important disease of wheat worldwide. Management of the disease usually is by host resistance or fungicides. However, M. graminicola has developed insensitivity to most commonly applied fungicides so there is a continuing need for well-characterized sources of host resistance to accelerate the development of improved wheat cultivars. Gene Stb3 has been a useful source of major resistance, but its mapping location has not been well characterized. Based on linkage to a single marker, a previous study assigned Stb3 to a location on the short arm of chromosome 6D. However, the results from the present study show that this reported location is incorrect. Instead, linkage analysis revealed that Stb3 is located on the short arm of wheat chromosome 7A, completely linked to microsatellite (SSR) locus Xwmc83 and flanked by loci Xcfa2028 (12.4 cM distal) and Xbarc222 (2.1 cM proximal). Linkage between Stb3 and Xwmc83 was validated in BC1F3 progeny of other crosses, and analyses of the flanking markers with deletion stocks showed that the gene is located on 7AS between fraction lengths 0.73 and 0.83. This revised location of Stb3 is different from those for other STB resistance genes previously mapped in hexaploid wheat but is approximately 20 cM proximal to an STB resistance gene mapped on the short arm of chromosome 7Am in Triticum monococcum. The markers described in this study are useful for accelerating the deployment of Stb3 in wheat breeding programs.

  10. Global differential expression of genes located in the Down Syndrome Critical Region in normal human brain

    PubMed Central

    Montoya, Julio Cesar; Fajardo, Dianora; Peña, Angela; Sánchez, Adalberto; Domínguez, Martha C; Satizábal, José María

    2014-01-01

    Background: The information of gene expression obtained from databases, have made possible the extraction and analysis of data related with several molecular processes involving not only in brain homeostasis but its disruption in some neuropathologies; principally in Down syndrome and the Alzheimer disease. Objective: To correlate the levels of transcription of 19 genes located in the Down Syndrome Critical Region (DSCR) with their expression in several substructures of normal human brain. Methods: There were obtained expression profiles of 19 DSCR genes in 42 brain substructures, from gene expression values available at the database of the human brain of the Brain Atlas of the Allen Institute for Brain Sciences", (http://human.brain-map.org/). The co-expression patterns of DSCR genes in brain were calculated by using multivariate statistical methods. Results: Highest levels of gene expression were registered at caudate nucleus, nucleus accumbens and putamen among central areas of cerebral cortex. Increased expression levels of RCAN1 that encode by a protein involved in signal transduction process of the CNS were recorded for PCP4 that participates in the binding to calmodulin and TTC3; a protein that is associated with differentiation of neurons. That previously identified brain structures play a crucial role in the learning process, in different class of memory and in motor skills. Conclusion: The precise regulation of DSCR gene expression is crucial to maintain the brain homeostasis, especially in those areas with high levels of gene expression associated with a remarkable process of learning and cognition. PMID:25767303

  11. The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family.

    PubMed

    Lin, Choun-Sea; Chen, Jeremy J W; Huang, Yao-Ting; Chan, Ming-Tsair; Daniell, Henry; Chang, Wan-Jung; Hsu, Chen-Tran; Liao, De-Chih; Wu, Fu-Huei; Lin, Sheng-Yi; Liao, Chen-Fu; Deyholos, Michael K; Wong, Gane Ka-Shu; Albert, Victor A; Chou, Ming-Lun; Chen, Chun-Yi; Shih, Ming-Che

    2015-01-01

    The NAD(P)H dehydrogenase complex is encoded by 11 ndh genes in plant chloroplast (cp) genomes. However, ndh genes are truncated or deleted in some autotrophic Epidendroideae orchid cp genomes. To determine the evolutionary timing of the gene deletions and the genomic locations of the various ndh genes in orchids, the cp genomes of Vanilla planifolia, Paphiopedilum armeniacum, Paphiopedilum niveum, Cypripedium formosanum, Habenaria longidenticulata, Goodyera fumata and Masdevallia picturata were sequenced; these genomes represent Vanilloideae, Cypripedioideae, Orchidoideae and Epidendroideae subfamilies. Four orchid cp genome sequences were found to contain a complete set of ndh genes. In other genomes, ndh deletions did not correlate to known taxonomic or evolutionary relationships and deletions occurred independently after the orchid family split into different subfamilies. In orchids lacking cp encoded ndh genes, non cp localized ndh sequences were identified. In Erycina pusilla, at least 10 truncated ndh gene fragments were found transferred to the mitochondrial (mt) genome. The phenomenon of orchid ndh transfer to the mt genome existed in ndh-deleted orchids and also in ndh containing species. PMID:25761566

  12. The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family

    PubMed Central

    Lin, Choun-Sea; Chen, Jeremy J. W.; Huang, Yao-Ting; Chan, Ming-Tsair; Daniell, Henry; Chang, Wan-Jung; Hsu, Chen-Tran; Liao, De-Chih; Wu, Fu-Huei; Lin, Sheng-Yi; Liao, Chen-Fu; Deyholos, Michael K.; Wong, Gane Ka-Shu; Albert, Victor A.; Chou, Ming-Lun; Chen, Chun-Yi; Shih, Ming-Che

    2015-01-01

    The NAD(P)H dehydrogenase complex is encoded by 11 ndh genes in plant chloroplast (cp) genomes. However, ndh genes are truncated or deleted in some autotrophic Epidendroideae orchid cp genomes. To determine the evolutionary timing of the gene deletions and the genomic locations of the various ndh genes in orchids, the cp genomes of Vanilla planifolia, Paphiopedilum armeniacum, Paphiopedilum niveum, Cypripedium formosanum, Habenaria longidenticulata, Goodyera fumata and Masdevallia picturata were sequenced; these genomes represent Vanilloideae, Cypripedioideae, Orchidoideae and Epidendroideae subfamilies. Four orchid cp genome sequences were found to contain a complete set of ndh genes. In other genomes, ndh deletions did not correlate to known taxonomic or evolutionary relationships and deletions occurred independently after the orchid family split into different subfamilies. In orchids lacking cp encoded ndh genes, non cp localized ndh sequences were identified. In Erycina pusilla, at least 10 truncated ndh gene fragments were found transferred to the mitochondrial (mt) genome. The phenomenon of orchid ndh transfer to the mt genome existed in ndh-deleted orchids and also in ndh containing species. PMID:25761566

  13. Location and cloning of the ketal pyruvate transferase gene of Xanthomonas campestris.

    PubMed Central

    Marzocca, M P; Harding, N E; Petroni, E A; Cleary, J M; Ielpi, L

    1991-01-01

    Genes required for xanthan polysaccharide synthesis (xps) are clustered in a DNA region of 13.5 kb in the chromosome of Xanthomonas campestris. Plasmid pCHC3 containing a 12.4-kb insert of xps genes has been suggested to include a gene involved in the pyruvylation of xanthan gum (N.E. Harding, J.M. Cleary, D.K. Cabañas, I. G. Rosen, and K. S. Kang, J. Bacteriol. 169:2854-2861, 1987). An essential step toward understanding the biosynthesis of xanthan gum and to enable genetic manipulation of xanthan structure is the determination of the biochemical function encoded by the xps genes. On the basis of biochemical characterization of an X. campestris mutant which produces pyruvate-free xanthan gum, complementation studies, and heterologous expression, we have identified the gene coding for the ketal pyruvate transferase (kpt) enzyme. This gene was located on a 1.4-kb BamHI fragment of pCHC3 and cloned in the broad-host-range cloning vector pRK404. An X. campestris kpt mutant was constructed by mini-Mu(Tetr) mutagenesis of the cloned gene and then by recombination of the mutation into the chromosome of the wild-type strain. PMID:1657892

  14. Location and cloning of the ketal pyruvate transferase gene of Xanthomonas campestris.

    PubMed

    Marzocca, M P; Harding, N E; Petroni, E A; Cleary, J M; Ielpi, L

    1991-12-01

    Genes required for xanthan polysaccharide synthesis (xps) are clustered in a DNA region of 13.5 kb in the chromosome of Xanthomonas campestris. Plasmid pCHC3 containing a 12.4-kb insert of xps genes has been suggested to include a gene involved in the pyruvylation of xanthan gum (N.E. Harding, J.M. Cleary, D.K. Cabañas, I. G. Rosen, and K. S. Kang, J. Bacteriol. 169:2854-2861, 1987). An essential step toward understanding the biosynthesis of xanthan gum and to enable genetic manipulation of xanthan structure is the determination of the biochemical function encoded by the xps genes. On the basis of biochemical characterization of an X. campestris mutant which produces pyruvate-free xanthan gum, complementation studies, and heterologous expression, we have identified the gene coding for the ketal pyruvate transferase (kpt) enzyme. This gene was located on a 1.4-kb BamHI fragment of pCHC3 and cloned in the broad-host-range cloning vector pRK404. An X. campestris kpt mutant was constructed by mini-Mu(Tetr) mutagenesis of the cloned gene and then by recombination of the mutation into the chromosome of the wild-type strain. PMID:1657892

  15. Accelerated Evolution of Schistosome Genes Coding for Proteins Located at the Host–Parasite Interface

    PubMed Central

    Philippsen, Gisele S.; Wilson, R. Alan; DeMarco, Ricardo

    2015-01-01

    Study of proteins located at the host–parasite interface in schistosomes might provide clues about the mechanisms utilized by the parasite to escape the host immune system attack. Micro-exon gene (MEG) protein products and venom allergen-like (VAL) proteins have been shown to be present in schistosome secretions or associated with glands, which led to the hypothesis that they are important components in the molecular interaction of the parasite with the host. Phylogenetic and structural analysis of genes and their transcripts in these two classes shows that recent species-specific expansion of gene number for these families occurred separately in three different species of schistosomes. Enrichment of transposable elements in MEG and VAL genes in Schistosoma mansoni provides a credible mechanism for preferential expansion of gene numbers for these families. Analysis of the ratio between synonymous and nonsynonymous substitution rates (dN/dS) in the comparison between schistosome orthologs for the two classes of genes reveals significantly higher values when compared with a set of a control genes coding for secreted proteins, and for proteins previously localized in the tegument. Additional analyses of paralog genes indicate that exposure of the protein to the definitive host immune system is a determining factor leading to the higher than usual dN/dS values in those genes. The observation that two genes encoding S. mansoni vaccine candidate proteins, known to be exposed at the parasite surface, also display similar evolutionary dynamics suggests a broad response of the parasite to evolutionary pressure imposed by the definitive host immune system. PMID:25567667

  16. Contrasting evolutionary histories of MHC class I and class II loci in grouse—Effects of selection and gene conversion

    USGS Publications Warehouse

    Minias, Piotr; Bateson, Zachary W; Whittingham, Linda A; Johnson, Jeff A.; Oyler-McCance, Sara J.; Dunn, Peter O

    2016-01-01

    Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens.

  17. Suppression of Tla1 gene expression for improved solar conversion efficiency and photosynthetic productivity in plants and algae

    DOEpatents

    Melis, Anastasios; Mitra, Mautusi

    2010-06-29

    The invention provides method and compositions to minimize the chlorophyll antenna size of photosynthesis by decreasing TLA1 gene expression, thereby improving solar conversion efficiencies and photosynthetic productivity in plants, e.g., green microalgae, under bright sunlight conditions.

  18. Transcriptional regulation and locations of Agrobacterium tumefaciens genes required for complete catabolism of octopine.

    PubMed

    Cho, K; Fuqua, C; Winans, S C

    1997-01-01

    By screening for octopine-inducible gene expression, we previously identified all the genes required for utilization of octopine as a source of carbon, nitrogen, and energy. They are (i) octopine oxidase, which converts octopine to arginine and pyruvate and is encoded by the ooxAB operon, (ii) arginase, which converts arginine to ornithine and urea and is encoded by arcA, (iii) ornithine cyclodeaminase, which converts ornithine to proline and ammonia and is encoded by the homologous arcB and ocd genes, and (iv) proline dehydrogenase, which converts proline to glutamate and is encoded by putA. Here we describe the regulation and localization of each of these genes. The ooxA-ooxB-ocd operon was previously shown to reside on the Ti plasmid and to be directly inducible by octopine. The arcAB operon is directly inducible by arginine, while it is induced by octopine only in strains that can convert octopine to arginine. Ornithine may also be a direct inducer of arcAB. putA is directly inducible by proline, while induction by octopine and by arginine (and probably by ornithine) requires their conversion to proline. Genetic studies indicate that arcAB and putA are localized on a conjugal genetic element. This element can be transferred to other Agrobacterium tumefaciens strains by a mechanism that does not require recA-dependent homologous recombination. Transfer of this genetic element from A. tumefaciens R10 requires at least one tra gene found on its Ti plasmid, indicating that this element is not self-transmissible but is mobilizable by the Ti plasmid. The DNA containing the arcAB and putA genes comigrates with a 243-kb linear molecular weight standard on field inversion electrophoretic gels. PMID:8981973

  19. Gene structure, chromosomal location, and basis for alternative mRNA splicing of the human VCAM1 gene

    SciTech Connect

    Cybulsky, M.I.; Fries, J.W.U.; Williams, A.J.; Sultan, P.; Gimbrone, M.A. Jr.; Collins, T. ); Eddy, R.; Byers, M.; Shows, T. )

    1991-09-01

    Vascular cell adhesion molecule 1 (VCAM-1) is a cell surface glycoprotein adhesive for certain blood leukocytes and tumor cells, which is expressed by activated endothelium in a variety of pathologic conditions including atherosclerosis. Genomic clones encoding the VCAM1 gene were isolated and the organization of the gene was determined. The gene, which is present in a single copy in the human genome, contains 9 exons spanning {approx}25 kilobases of DNA. Exons 2-8 contain C2 or H-type immunoglobulin domains. At least two different VCAM-1 precursors can be generated from the human gene as a result of alternative mRNA splicing events, which include or exclude exon 5. A consensus TATAA element is located upstream of the transcriptional start site. The VCAM1 promoter contains consensus binding sites for NF-{kappa}B, the GATA family of transcription factors, as well as an AP1 site. The VCAM1 gene was assigned to the 1p31-32 region of chromosome 1 based on the analysis of human-mouse hybrid cell lines and in situ hybridization. Structural analysis of the human VCAM1 gene provides the basis for alternative mRNA splicing and an initial approach to elucidating the regulation of VCAM-1 expression.

  20. Group I intron located in PR protein homologue gene in Youngia japonica.

    PubMed

    Nishida, H; Ogura, A; Yokota, A; Yamaguchi, I; Sugiyama, J

    2000-03-01

    A Youngia japonica strain had a group I intron that was suggested to have been transferred from Protomyces inouyei, a pathogenic fungus of Y. japonica. It was located in the miraculin homologue coding gene by reverse complementation. The deduced amino acid sequence of this miraculin homologue of Y. japonica was similar to the amino acid sequences of tobacco and tomato pathogenesis-related proteins. PMID:10803963

  1. Dragon Gene Start Finder: An Advanced System for Finding Approximate Locations of the Start of Gene Transcriptional Units

    PubMed Central

    Bajic, Vladimir B.; Seah, Seng Hong

    2003-01-01

    We present an advanced system for recognition of gene starts in mammalian genomes. The system makes predictions of gene start location by combining information about CpG islands, transcription start sites (TSSs), and signals downstream of the predicted TSSs. The system aims at predicting a region that contains the gene start or is in its proximity. Evaluation on human chromosomes 4, 21, and 22 resulted in Se of over 65% and in a ppv of ∼78%. The system makes on average one prediction per 177,000 nucleotides on the human genome, as judged by the results on chromosome 21. Comparison of abilities to predict TSS with the two other systems on human chromosomes 4, 21, and 22 reveals that our system has superior accuracy and overall provides the most confident predictions. PMID:12869582

  2. A physical model study of the travel times and conversion point locations of P-SV converted waves in vertical transversely isotropic media

    NASA Astrophysics Data System (ADS)

    Tseng, C.

    2013-12-01

    In exploration seismology, subsurface medium commonly exhibits anisotropy, characterized by a vertical transversely isotropic (VTI) model. Due to the need of exploring small reservoirs in complex structures, the seismic exploration is extended to deal with anisotropic media. The P-S converted wave seismic exploration is a relatively inexpensive, broadly applicable, and effective way to obtain the S-wave information of the medium. In anisotropic traveltime analysis, the moveout curve of horizontal P-SV event can help to determine the ratio of the P- and SV-wave vertical velocities, the normal moveout (NMO) velocity of SV-waves, and the anisotropy parameters. The P-SV conversion point (CP) location is of great importance to P-SV data binning, NMO corrections and common conversion point (CCP) stacking, and the anisotropy has a more significant effect on the conversion point location than on the moveout. In this study, we attempt to inspect the theoretical non-hyperbolic moveout and CP equations for the P-SV waves reflected from a VTI layer by numerical calculations and physical modeling. We are also interested in visualizing the variations of the conversion point locations from a designed VTI medium. In traveltime analysis, the theoretical moveout curve is accurate up to offsets about one and a half times the reflector depth (x/z=1.5). However, the moveout curve computed by Fermat's principle fits well to the physical data. The CP locations of P-SV waves are similar to those calculated by Fermat's principle and theoretical CP equation, which are verified by the physical modeling.

  3. Gene conversion as a secondary mechanism of short interspersed element (SINE) evolution

    SciTech Connect

    Kass, D.H.; Batzer, M.A.; Deininger, P.L. |

    1995-01-01

    The Alu repetitive family of short interspersed elements (SINEs) in primates can be subdivided into distinct subfamilies by specific diagnostic nucleotide changes. The older subfamilies are generally very abundant, while the younger subfamilies have fewer copies. Some of the youngest Alu elements are absent in the orthologous loci of nonhuman primates, indicative of recent retroposition events, the primary mode of SINE evolutions. PCR analysis of one young Alu subfamily (Sb2) member found in the low-density lipoprotein receptor gene apparently revealed the presence of this element in the green monkey, orangutan, gorilla, and chimpanzee genomes, as well as the human genome. However, sequence analysis of these genomes revealed a highly mutated, older, primate-specific Alu element was present at this position in the nonhuman primates. Comparison of the flanking DNA sequences upstream of this Alu insertion corresponded to evolution expected for standard primate phylogeny, but comparison of the Alu repeat sequences revealed that the human element departed from this phylogeny. The change in the human sequence apparently occurred by a gene conversion event only within the Alu element itself, converting it from one of the oldest to one of the youngest Alu subfamilies. Although gene conversions of Alu elements are clearly very rare, this finding shows that such events can occur and contribute to specific cases of SINE subfamily evolution.

  4. Genomic distribution of AFLP markers relative to gene locations for different eukaryotic species

    PubMed Central

    2013-01-01

    Background Amplified fragment length polymorphism (AFLP) markers are frequently used for a wide range of studies, such as genome-wide mapping, population genetic diversity estimation, hybridization and introgression studies, phylogenetic analyses, and detection of signatures of selection. An important issue to be addressed for some of these fields is the distribution of the markers across the genome, particularly in relation to gene sequences. Results Using in-silico restriction fragment analysis of the genomes of nine eukaryotic species we characterise the distribution of AFLP fragments across the genome and, particularly, in relation to gene locations. First, we identify the physical position of markers across the chromosomes of all species. An observed accumulation of fragments around (peri) centromeric regions in some species is produced by repeated sequences, and this accumulation disappears when AFLP bands rather than fragments are considered. Second, we calculate the percentage of AFLP markers positioned within gene sequences. For the typical EcoRI/MseI enzyme pair, this ranges between 28 and 87% and is usually larger than that expected by chance because of the higher GC content of gene sequences relative to intergenic ones. In agreement with this, the use of enzyme pairs with GC-rich restriction sites substantially increases the above percentages. For example, using the enzyme system SacI/HpaII, 86% of AFLP markers are located within gene sequences in A. thaliana, and 100% of markers in Plasmodium falciparun. We further find that for a typical trait controlled by 50 genes of average size, if 1000 AFLPs are used in a study, the number of those within 1 kb distance from any of the genes would be only about 1–2, and only about 50% of the genes would have markers within that distance. Conclusions The high coverage of AFLP markers across the genomes and the high proportion of markers within or close to gene sequences make them suitable for genome scans and

  5. A candidate gene conversion event associated with natural and induced hypermutation of a human V[sub H]5 gene

    SciTech Connect

    Fairhurst, G.R.; Valles-Ayoub, Y.; Neshat, M.; Braun, J. )

    1994-03-15

    Follicular lymphomas undergo somatic hypermutation which results in substantial intraclonal heterogeneity and may contribute to tumor growth. To directly assay the mechanism of somatic hypermutation, the authors established a PCR-based assay to characterize rearranged V[sub H]5 genes of UV-irradiated germinal center (GC) B cells. This approach is based on the rationale that single-stranded intermediates of UV-induced DNA repair would mimic the physiological substrate for hypermutation. The authors predicted that UV-irradiated GC, but not mantle zone (MZ), B cells would introduce mutations selectively at rearranged, but not unrearranged V genes. This prediction was validated by two independent experiments in which tonsil cells were fractionated into GC or MZ B cells, UV-irradiated or left untreated, and cultured to allow time for DNA repair. Unrearranged and rearranged V[sub H][sub 5] genes were selectively PCR-amplified and analyzed by restriction digest or SSCP. In both experiments, a unique and predominant mutation was identified soley in rearranged V[sub H]5 genes of UV-irradiated GC B cells. Data suggest that these mutations are templated in the genome. One mutation was PCR-amplified from HeLa DNA and is widely distributed, whereas the other appears at low frequency in the population and has been isolated from two familial CLL and a T cell lymphoma. Identification of putative V[sub H]5 pseudogenes, now in progress, would strongly implicate gene conversion in diversification of the immunoglobulin repertoire.

  6. Gene Conversion in the Evolution of Both the H-2 and Qa Class I Genes of the Murine Major Histocompatibility Complex

    PubMed Central

    Kuhner, M.; Watts, S.; Klitz, W.; Thomson, G.; Goodenow, R. S.

    1990-01-01

    In order to better understand the role of gene conversion in the evolution of the class I gene family of the major histocompatibility complex (MHC), we have used a computer algorithm to detect clustered sequence similarities among 24 class I DNA sequences from the H-2, Qa, and Tla regions of the murine MHC. Thirty-four statistically significant clusters were detected; individual analysis of the clusters suggested at least 25 past gene conversion or recombination events. These clusters are comparable in size to the conversions observed in the spontaneously occurring H-2K(bm) and H-2K(km2) mutations, and are distributed throughout all exons of the class I gene. Thus, gene conversion does not appear to be restricted to the regions of the class I gene encoding their antigen-presentation function. Moreover, both the highly polymorphic H-2 loci and the relatively monomorphic Qa and Tla loci appear to have participated as donors and recipients in conversion events. If gene conversion is not limited to the highly polymorphic loci of the MHC, then another factor, presumably natural selection, must be responsible for maintaining the observed differences in level of variation. PMID:2076814

  7. Refining the genetic location of the gene for X linked hydrocephalus within Xq28.

    PubMed Central

    Jouet, M; Feldman, E; Yates, J; Donnai, D; Paterson, J; Siggers, D; Kenwrick, S

    1993-01-01

    The most common inherited form of hydrocephalus, X linked hydrocephalus (HSAS), is characterised by mental retardation, adducted thumbs, and spastic paraplegia. Genetic analysis has mapped the locus for HSAS to subchromosomal band Xq28 within a region of approximately 2 megabases of DNA. In order to refine the location of the disease gene we have conducted genetic linkage analysis with Xq28 marker loci in four additional HSAS families. A lod score of 4.26 with polymorphic marker DXS52 (St14) confirms the linkage of HSAS to Xq28. Identification of a recombination event between the HSAS gene and Xq28 loci F8C and DXS605 (2-19) reduces the size of the interval likely to contain the disease locus to about 1.5 megabases, the distance between DXS605 and DXS52. The locus for neural cell adhesion molecule, L1CAM, maps within this interval and therefore represents a candidate gene for HSAS. PMID:8474107

  8. Epithelial expression and chromosomal location of human TLE genes: Implications for notch signaling and neoplasia

    SciTech Connect

    Liu, Yanling; Dehni, Ghassan; Stifani, S.

    1996-01-01

    The TLE genes are the human homologues of Drosophila groucho, a member of the Notch signaling pathway. This pathway controls a number of different cell-fate choices in invertebrates and vertebrates. We are interested in investigating the functions of the TLE gene family during epithelial determination and carcinogenesis. We show that expression of individual TLE genes correlates with immature epithelial cells that are progressing toward their terminally differentiated state, suggesting a role during epithelial differentiation. In both normal tissues and conditions resulting from incorrect or incomplete maturation events, such as metaplastic and neoplastic transformations, TLE expression is elevated and coincides with Notch expression, implicating these molecules in the maintenance of the undifferentiated state in epithelial cells. We also show that TLE1 and TLE2 are organized in a tandem array at chromosomal location 19p13.3, while TLE3 maps to 15q22. 26 refs., 4 figs.

  9. Expansions and contractions in 36-bp minisatellites by gene conversion in yeast.

    PubMed Central

    Pâques, F; Richard, G F; Haber, J E

    2001-01-01

    The instability of simple tandem repeats, such as human minisatellite loci, has been suggested to arise by gene conversions. In Saccharomyces cerevisiae, a double-strand break (DSB) was created by the HO endonuclease so that DNA polymerases associated with gap repair must traverse an artificial minisatellite of perfect 36-bp repeats or a yeast Y' minisatellite containing diverged 36-bp repeats. Gene conversions are frequently accompanied by changes in repeat number when the template contains perfect repeats. When the ends of the DSB have nonhomologous tails of 47 and 70 nucleotides that must be removed before repair DNA synthesis can begin, 16% of gene conversions had rearrangements, most of which were contractions, almost always in the recipient locus. When efficient removal of nonhomologous tails was prevented in rad1 and msh2 strains, repair was reduced 10-fold, but among survivors there was a 10-fold reduction in contractions. Half the remaining events were expansions. A similar decrease in the contraction rate was observed when the template was modified so that DSB ends were homologous to the template; and here, too, half of the remaining rearrangements were expansions. In this case, efficient repair does not require RAD1 and MSH2, consistent with our previous observations. In addition, without nonhomologous DSB ends, msh2 and rad1 mutations did not affect the frequency or the distribution of rearrangements. We conclude that the presence of nonhomologous ends alters the mechanism of DSB repair, likely through early recruitment of repair proteins including Msh2p and Rad1p, resulting in more frequent contractions of repeated sequences. PMID:11333226

  10. Bcl6 Is Required for Somatic Hypermutation and Gene Conversion in Chicken DT40 Cells.

    PubMed

    Williams, Alan M; Maman, Yaakov; Alinikula, Jukka; Schatz, David G

    2016-01-01

    The activation induced cytosine deaminase (AID) mediates diversification of B cell immunoglobulin genes by the three distinct yet related processes of somatic hypermutation (SHM), class switch recombination (CSR), and gene conversion (GCV). SHM occurs in germinal center B cells, and the transcription factor Bcl6 is a key regulator of the germinal center B cell gene expression program, including expression of AID. To test the hypothesis that Bcl6 function is important for the process of SHM, we compared WT chicken DT40 B cells, which constitutively perform SHM/GCV, to their Bcl6-deficient counterparts. We found that Bcl6-deficient DT40 cells were unable to perform SHM and GCV despite enforced high level expression of AID and substantial levels of AID in the nucleus of the cells. To gain mechanistic insight into the GCV/SHM dependency on Bcl6, transcriptional features of a highly expressed SHM target gene were analyzed in Bcl6-sufficient and -deficient DT40 cells. No defect was observed in the accumulation of single stranded DNA in the target gene as a result of Bcl6 deficiency. In contrast, association of Spt5, an RNA polymerase II (Pol II) and AID binding factor, was strongly reduced at the target gene body relative to the transcription start site in Bcl6-deficient cells as compared to WT cells. However, partial reconstitution of Bcl6 function substantially reconstituted Spt5 association with the target gene body but did not restore detectable SHM. Our observations suggest that in the absence of Bcl6, Spt5 fails to associate efficiently with Pol II at SHM targets, perhaps precluding robust AID action on the SHM target DNA. Our data also suggest, however, that Spt5 binding is not sufficient for SHM of a target gene even in DT40 cells with strong expression of AID.

  11. Bcl6 Is Required for Somatic Hypermutation and Gene Conversion in Chicken DT40 Cells

    PubMed Central

    Williams, Alan M.; Maman, Yaakov; Alinikula, Jukka; Schatz, David G.

    2016-01-01

    The activation induced cytosine deaminase (AID) mediates diversification of B cell immunoglobulin genes by the three distinct yet related processes of somatic hypermutation (SHM), class switch recombination (CSR), and gene conversion (GCV). SHM occurs in germinal center B cells, and the transcription factor Bcl6 is a key regulator of the germinal center B cell gene expression program, including expression of AID. To test the hypothesis that Bcl6 function is important for the process of SHM, we compared WT chicken DT40 B cells, which constitutively perform SHM/GCV, to their Bcl6-deficient counterparts. We found that Bcl6-deficient DT40 cells were unable to perform SHM and GCV despite enforced high level expression of AID and substantial levels of AID in the nucleus of the cells. To gain mechanistic insight into the GCV/SHM dependency on Bcl6, transcriptional features of a highly expressed SHM target gene were analyzed in Bcl6-sufficient and -deficient DT40 cells. No defect was observed in the accumulation of single stranded DNA in the target gene as a result of Bcl6 deficiency. In contrast, association of Spt5, an RNA polymerase II (Pol II) and AID binding factor, was strongly reduced at the target gene body relative to the transcription start site in Bcl6-deficient cells as compared to WT cells. However, partial reconstitution of Bcl6 function substantially reconstituted Spt5 association with the target gene body but did not restore detectable SHM. Our observations suggest that in the absence of Bcl6, Spt5 fails to associate efficiently with Pol II at SHM targets, perhaps precluding robust AID action on the SHM target DNA. Our data also suggest, however, that Spt5 binding is not sufficient for SHM of a target gene even in DT40 cells with strong expression of AID. PMID:26900682

  12. Multiple heterologies increase mitotic double-strand break-induced allelic gene conversion tract lengths in yeast.

    PubMed Central

    Nickoloff, J A; Sweetser, D B; Clikeman, J A; Khalsa, G J; Wheeler, S L

    1999-01-01

    Spontaneous and double-strand break (DSB)-induced allelic recombination in yeast was investigated in crosses between ura3 heteroalleles inactivated by an HO site and a +1 frameshift mutation, with flanking markers defining a 3.4-kbp interval. In some crosses, nine additional phenotypically silent RFLP mutations were present at approximately 100-bp intervals. Increasing heterology from 0.2 to 1% in this interval reduced spontaneous, but not DSB-induced, recombination. For DSB-induced events, 75% were continuous tract gene conversions without a crossover in this interval; discontinuous tracts and conversions associated with a crossover each comprised approximately 7% of events, and 10% also converted markers in unbroken alleles. Loss of heterozygosity was seen for all markers centromere distal to the HO site in 50% of products; such loss could reflect gene conversion, break-induced replication, chromosome loss, or G2 crossovers. Using telomere-marked strains we determined that nearly all allelic DSB repair occurs by gene conversion. We further show that most allelic conversion results from mismatch repair of heteroduplex DNA. Interestingly, markers shared between the sparsely and densely marked interval converted at higher rates in the densely marked interval. Thus, the extra markers increased gene conversion tract lengths, which may reflect mismatch repair-induced recombination, or a shift from restoration- to conversion-type repair. PMID:10511547

  13. Location, Location, Location!

    ERIC Educational Resources Information Center

    Ramsdell, Kristin

    2004-01-01

    Of prime importance in real estate, location is also a key element in the appeal of romances. Popular geographic settings and historical periods sell, unpopular ones do not--not always with a logical explanation, as the author discovered when she conducted a survey on this topic last year. (Why, for example, are the French Revolution and the…

  14. Gene conversion from SLG to SRK resulting in self-compatibility in Brassica rapa.

    PubMed

    Fujimoto, Ryo; Sugimura, Tetsu; Nishio, Takeshi

    2006-01-23

    Self-compatible S-54 homozygotic plants were found in progenies of an F(1) hybrid cultivar in Chinese cabbage. Pollination tests revealed that this self-compatibility is controlled by the S locus and caused by the loss of the recognition function of the stigma. SRK, the gene for the recognition molecule in the stigma, was normally transcribed and translated in the self-compatible plants. The 1034-bp region in the receptor domain of SRK in the self-compatible plants was 100% identical to SLG in S-54, while that in self-incompatible S-54 homozygotic plants was 95.1% identical. These results suggest that the self-compatibility of the S-54 homozygotes is due to amino-acid changes caused by gene conversion from SLG to SRK.

  15. Structural characterization and chromosomal location of the mouse macrophage migration inhibitory factor gene and pseudogenes

    SciTech Connect

    Bozza, M.; Gerard, C.; Kolakowski, L.F. Jr.

    1995-06-10

    Macrophage migration inhibitory factor, MIF, is a cytokine released by T-lymphocytes, macrophages, and the pituitary gland that serves to integrate peripheral and central inflammatory responses. Ubiquitous expression and developmental regulation suggest that MIF may have additional roles outside of the immune system. Here we report the structure and chromosomal location of the mouse Mif gene and the partial characterization of five Mif pseudogenes. The mouse Mif gene spans less than 0.7 kb of chromosomal DNA and is composed of three exons. A comparison between the mouse and the human genes shows a similar gene structure and common regulatory elements in both promoter regions. The mouse Mif gene maps to the middle region of chromosome 10, between Bcr and S100b, which have been mapped to human chromosomes 22q11 and 21q22.3, respectively. The entire sequence of two pseudogenes demonstrates the absence of introns, the presence of the 5{prime} untranslated region of the cDNA, a 3{prime} poly(A) tail, and the lack of sequence similarity with untranscribed regions of the gene. The five pseudogenes are highly homologous to the cDNA, but contain a variable number of mutations that would produce mutated or truncated MIF-like proteins. Phylogenetic analyses of MIF genes and pseudogenes indicate several independent genetic events that can account for multiple genomic integrations. Three of the Mif pseudogenes were also mapped by interspecific backcross to chromosomes 1, 9, and 17. These results suggest that Mif pseudogenes originated by retrotransposition. 46 refs., 5 figs., 1 tab.

  16. A W-linked palindrome and gene conversion in New World sparrows and blackbirds.

    PubMed

    Davis, Jamie K; Thomas, Pamela J; Thomas, James W

    2010-07-01

    A hallmark feature of the male-specific region of the human Y chromosome is the presence of large and near-identical palindromes. These palindromes are maintained in a state of near identity via gene conversion between the arms of the palindrome, and both neutral and selection-based theories have been proposed to explain their enrichment on the human Y and X chromosomes. While those proposed theories would be applicable to sex chromosomes in other species, it has not been established whether near-identical palindromes are a common feature of sex chromosomes in a broader range of taxa, including other tetrapods. Here, we report the genomic sequencing and features of a 279-kb region of the non-recombining portion of the W chromosome spanning the CHD1W locus in a New World sparrow, the white-throated sparrow (Zonotrichia albicollis), and the corresponding region on the Z chromosome. As has been observed for other Y and W chromosomes, we detected a high repetitive element content (51%) and low gene content on the white-throated sparrow W chromosome. In addition, we identified a 22-kb near-identical (>99%) palindrome on the W chromosome that flanks the 5' end of the CHD1W gene. Signatures of gene conversion were readily detected between the arms of this palindrome, as was the presence of this palindrome in other New World sparrows and blackbirds. Near-identical palindromes are therefore present on the avian W chromosome and may persist due to the same forces proposed for the enrichment of these elements on the human sex chromosomes.

  17. A W-linked palindrome and gene conversion in New World sparrows and blackbirds.

    PubMed

    Davis, Jamie K; Thomas, Pamela J; Thomas, James W

    2010-07-01

    A hallmark feature of the male-specific region of the human Y chromosome is the presence of large and near-identical palindromes. These palindromes are maintained in a state of near identity via gene conversion between the arms of the palindrome, and both neutral and selection-based theories have been proposed to explain their enrichment on the human Y and X chromosomes. While those proposed theories would be applicable to sex chromosomes in other species, it has not been established whether near-identical palindromes are a common feature of sex chromosomes in a broader range of taxa, including other tetrapods. Here, we report the genomic sequencing and features of a 279-kb region of the non-recombining portion of the W chromosome spanning the CHD1W locus in a New World sparrow, the white-throated sparrow (Zonotrichia albicollis), and the corresponding region on the Z chromosome. As has been observed for other Y and W chromosomes, we detected a high repetitive element content (51%) and low gene content on the white-throated sparrow W chromosome. In addition, we identified a 22-kb near-identical (>99%) palindrome on the W chromosome that flanks the 5' end of the CHD1W gene. Signatures of gene conversion were readily detected between the arms of this palindrome, as was the presence of this palindrome in other New World sparrows and blackbirds. Near-identical palindromes are therefore present on the avian W chromosome and may persist due to the same forces proposed for the enrichment of these elements on the human sex chromosomes. PMID:20535633

  18. Conversion of the Salmonella phase 1 flagellin gene fliC to the phase 2 gene fljB on the Escherichia coli K-12 chromosome.

    PubMed Central

    Okazaki, N; Matsuo, S; Saito, K; Tominaga, A; Enomoto, M

    1993-01-01

    The Escherichia coli-Salmonella typhimurium-Salmonella abortus-equi hybrid strain EJ1420 has the two Salmonella flagellin genes fliC (antigenic determinant i) and fljB (determinant e,n,x) at the same loci as in the Salmonella strains and constitutively expresses the fliC gene because of mutations in the genes mediating phase variation. Selection for motility in semisolid medium containing anti-i flagellum serum yielded 11 motile mutants, which had the active fliC(e,n,x) and silent fljB(e,n,x) genes. Genetic analysis and Southern hybridization indicated that they had mutations only in the fliC gene, not in the fljB gene or the control elements for phase variation. Nucleotide sequence analysis of the fliC(e,n,x) genes from four representative mutants showed that the minimum 38% (565 bp) and maximum 68% (1,013 bp) sequences of the fliC(i) gene are replaced with the corresponding sequences of the fljB(e,n,x) gene. One of the conversion endpoints between the two genes lies somewhere in the 204-bp homologous sequence in the 5' constant region, and the other lies in the short homologous sequence of 6, 8, or 38 bp in the 3' constant region. The conversions include the whole central variable region of the fljB gene, resulting in fliC(e,n,x) genes with the same number of nucleotides (1,503 bp) as the fljB gene. We discuss the mechanisms for gene conversion between the two genes and also some intriguing aspects of flagellar antigenic specificities in various Salmonella serovars from the viewpoint of gene conversion. Images PMID:8423149

  19. Radiation hybrid mapping of a cytokine gene cluster located in the proximal region of 5q

    SciTech Connect

    Segal, A.L.; McPherson, J.D.; Wasmuth, J.J.

    1994-09-01

    The long (q) arm of chromosome 5 has been shown to contain a large number of genes encoding growth factors, growth factor receptors, hormone receptors and neurotransmitter receptors. IL-3, IL-4, IL-5, IL-9, IL-13, GM-CSF and IRF-1 are located in the 5q22-31.1 interval, while three GABA receptors map to 5q33-34. A number of receptors, including the prolactin and growth hormone receptors, the IL-7 receptor and the leukemia inhibitory factor receptor, map to proximal 5p. Genes encoding three of the complement components, C6, C7 and C9, are also located in the same region. YAC data indicates that C6 and C7 lie within 170 kb of each other. We have used a panel of 180 Chinese hamster-human radiation hybrids possessing fragments of human chromosome 5 to construct a physical map of this region of 5q. Two-point and multi-point analyses were done on the data and significant LOD scores (from 3 to 30) were observed. LIFR, PRLR, GHR, IL-7R, C6, C7, C9, TARS, and a number of CEPH-Genethon dinucleotide repeat markers were ordered and mapped. Yeast artificial chromosomes and cosmids have been isolated and inter-Alu PCR products from them are being used to construct a contig and to improve the physical map. The long term goal of this work is to identify and characterize new genes in the region.

  20. Altitudinal Variation at Duplicated β-Globin Genes in Deer Mice: Effects of Selection, Recombination, and Gene Conversion

    PubMed Central

    Storz, Jay F.; Natarajan, Chandrasekhar; Cheviron, Zachary A.; Hoffmann, Federico G.; Kelly, John K.

    2012-01-01

    Spatially varying selection on a given polymorphism is expected to produce a localized peak in the between-population component of nucleotide diversity, and theory suggests that the chromosomal extent of elevated differentiation may be enhanced in cases where tandemly linked genes contribute to fitness variation. An intriguing example is provided by the tandemly duplicated β-globin genes of deer mice (Peromyscus maniculatus), which contribute to adaptive differentiation in blood–oxygen affinity between high- and low-altitude populations. Remarkably, the two β-globin genes segregate the same pair of functionally distinct alleles due to a history of interparalog gene conversion and alleles of the same functional type are in perfect coupling-phase linkage disequilibrium (LD). Here we report a multilocus analysis of nucleotide polymorphism and LD in highland and lowland mice with different genetic backgrounds at the β-globin genes. The analysis of haplotype structure revealed a paradoxical pattern whereby perfect LD between the two β-globin paralogs (which are separated by 16.2 kb) is maintained in spite of the fact that LD within both paralogs decays to background levels over physical distances of less than 1 kb. The survey of nucleotide polymorphism revealed that elevated levels of altitudinal differentiation at each of the β-globin genes drop away quite rapidly in the external flanking regions (upstream of the 5′ paralog and downstream of the 3′ paralog), but the level of differentiation remains unexpectedly high across the intergenic region. Observed patterns of diversity and haplotype structure are difficult to reconcile with expectations of a two-locus selection model with multiplicative fitness. PMID:22042573

  1. Minisatellite variants generated in yeast meiosis involve DNA removal during gene conversion.

    PubMed Central

    Bishop, A J; Louis, E J; Borts, R H

    2000-01-01

    Two yeast minisatellite alleles were cloned and inserted into a genetically defined interval in Saccharomyces cerevisiae. Analysis of flanking markers in combination with sequencing allowed the determination of the meiotic events that produced minisatellites with altered lengths. Tetrad analysis revealed that gene conversions, deletions, or complex combinations of both were involved in producing minisatellite variants. Similar changes were obtained following selection for nearby gene conversions or crossovers among random spores. The largest class of events involving the minisatellite was a 3:1 segregation of parental-size alleles, a class that would have been missed in all previous studies of minisatellites. Comparison of the sequences of the parental and novel alleles revealed that DNA must have been removed from the recipient array while a newly synthesized copy of donor array sequences was inserted. The length of inserted sequences did not appear to be constrained by the length of DNA that was removed. In cases where one or both sides of the insertion could be determined, the insertion endpoints were consistent with the suggestion that the event was mediated by alignment of homologous stretches of donor/recipient DNA. PMID:10978271

  2. A role for DNA polymerase delta in gene conversion and crossing over during meiosis in Saccharomyces cerevisiae.

    PubMed Central

    Maloisel, Laurent; Bhargava, Jaya; Roeder, G Shirleen

    2004-01-01

    A screen for mutants of budding yeast defective in meiotic gene conversion identified a novel allele of the POL3 gene. POL3 encodes the catalytic subunit of DNA polymerase delta, an essential DNA polymerase involved in genomic DNA replication. The new allele, pol3-ct, specifies a protein missing the last four amino acids. pol3-ct shows little or no defect in DNA replication, but displays a reduction in the length of meiotic gene conversion tracts and a decrease in crossing over. We propose a model in which DNA synthesis determines the length of strand exchange intermediates and influences their resolution toward crossing over. PMID:15280229

  3. Characterization of a rabbit germ-line VH gene that is a candidate donor for VH gene conversion in mutant Alicia rabbits.

    PubMed

    Chen, H T; Alexander, C B; Mage, R G

    1995-06-15

    Normal rabbits preferentially rearrange the 3'-most VH gene, VH1, to encode Igs with VHa allotypes, which constitute the majority of rabbit serum Igs. A gene conversion-like mechanism is employed to diversify the primary Ab repertoire. In mutant Alicia rabbits that derived from a rabbit with VHa2 allotype, the VH1 gene was deleted. Our previous studies showed that the first functional gene (VH4) or VH4-like genes were rearranged in 2- to 8-wk-old homozygous Alicia. The VH1a2-like sequences that were found in splenic mRNA from 6-wk and older Alicia rabbits still had some residues that were typical of VH4. The appearances of sequences resembling that of VH1a2 may have been caused by gene conversions that altered the sequences of the rearranged VH or there may have been rearrangement of upstream VH1a2-like genes later in development. To investigate this further, we constructed a cosmid library and isolated a VH1a2-like gene, VH12-1-6, with a sequence almost identical to VH1a2. This gene had a deleted base in the heptamer of its recombination signal sequence. However, even if this defect diminished or eliminated its ability to rearrange, the a2-like gene could have acted as a donor for gene-conversion-like alteration of rearranged VH genes. Sequence comparisons suggested that this gene or a gene like it could have acted as a donor for gene conversion in mutant Alicia and in normal rabbits.

  4. Duplication, selection and gene conversion in a Drosophila mojavensis female reproductive protein family.

    PubMed

    Kelleher, Erin S; Markow, Therese A

    2009-04-01

    Protein components of the Drosophila male ejaculate, several of which evolve rapidly, are critical modulators of reproductive success. Recent studies of female reproductive tract proteins indicate they also are extremely divergent between species, suggesting that reproductive molecules may coevolve between the sexes. Our current understanding of intersexual coevolution, however, is severely limited by the paucity of genetic and evolutionary studies on the female molecules involved. Physiological evidence of ejaculate-female coadaptation, paired with a promiscuous mating system, makes Drosophila mojavensis an exciting model system in which to study the evolution of reproductive proteins. Here we explore the evolutionary dynamics of a five-paralog gene family of female reproductive proteases within populations of D. mojavensis and throughout the repleta species group. We show that the proteins have experienced ongoing gene duplication and adaptive evolution and further exhibit dynamic patterns of pseudogenation, copy number variation, gene conversion, and selection within geographically isolated populations of D. mojavensis. The integration of these patterns in a single gene family has never before been documented in a reproductive protein.

  5. Duplication, Selection and Gene Conversion in a Drosophila mojavensis Female Reproductive Protein Family

    PubMed Central

    Kelleher, Erin S.; Markow, Therese A.

    2009-01-01

    Protein components of the Drosophila male ejaculate, several of which evolve rapidly, are critical modulators of reproductive success. Recent studies of female reproductive tract proteins indicate they also are extremely divergent between species, suggesting that reproductive molecules may coevolve between the sexes. Our current understanding of intersexual coevolution, however, is severely limited by the paucity of genetic and evolutionary studies on the female molecules involved. Physiological evidence of ejaculate–female coadaptation, paired with a promiscuous mating system, makes Drosophila mojavensis an exciting model system in which to study the evolution of reproductive proteins. Here we explore the evolutionary dynamics of a five-paralog gene family of female reproductive proteases within populations of D. mojavensis and throughout the repleta species group. We show that the proteins have experienced ongoing gene duplication and adaptive evolution and further exhibit dynamic patterns of pseudogenation, copy number variation, gene conversion, and selection within geographically isolated populations of D. mojavensis. The integration of these patterns in a single gene family has never before been documented in a reproductive protein. PMID:19204376

  6. Signatures of selection and gene conversion associated with human color vision variation.

    PubMed

    Verrelli, Brian C; Tishkoff, Sarah A

    2004-09-01

    Trichromatic color vision in humans results from the combination of red, green, and blue photopigment opsins. Although color vision genes have been the targets of active molecular and psychophysical research on color vision abnormalities, little is known about patterns of normal genetic variation in these genes among global human populations. The current study presents nucleotide sequence analyses and tests of neutrality for a 5.5-kb region of the X-linked long-wave "red" opsin gene (OPN1LW) in 236 individuals from ethnically diverse human populations. Our analysis of the recombination landscape across OPN1LW reveals an unusual haplotype structure associated with amino acid replacement variation in exon 3 that is consistent with gene conversion. Compared with the absence of OPN1LW amino acid replacement fixation since divergence from chimpanzee, the human population exhibits a significant excess of high-frequency OPN1LW replacements. Our results suggest that subtle changes in L-cone opsin wavelength absorption may have been adaptive during human evolution. PMID:15252758

  7. Signatures of selection and gene conversion associated with human color vision variation.

    PubMed

    Verrelli, Brian C; Tishkoff, Sarah A

    2004-09-01

    Trichromatic color vision in humans results from the combination of red, green, and blue photopigment opsins. Although color vision genes have been the targets of active molecular and psychophysical research on color vision abnormalities, little is known about patterns of normal genetic variation in these genes among global human populations. The current study presents nucleotide sequence analyses and tests of neutrality for a 5.5-kb region of the X-linked long-wave "red" opsin gene (OPN1LW) in 236 individuals from ethnically diverse human populations. Our analysis of the recombination landscape across OPN1LW reveals an unusual haplotype structure associated with amino acid replacement variation in exon 3 that is consistent with gene conversion. Compared with the absence of OPN1LW amino acid replacement fixation since divergence from chimpanzee, the human population exhibits a significant excess of high-frequency OPN1LW replacements. Our results suggest that subtle changes in L-cone opsin wavelength absorption may have been adaptive during human evolution.

  8. Signatures of Selection and Gene Conversion Associated with Human Color Vision Variation

    PubMed Central

    Verrelli, Brian C.; Tishkoff, Sarah A.

    2004-01-01

    Trichromatic color vision in humans results from the combination of red, green, and blue photopigment opsins. Although color vision genes have been the targets of active molecular and psychophysical research on color vision abnormalities, little is known about patterns of normal genetic variation in these genes among global human populations. The current study presents nucleotide sequence analyses and tests of neutrality for a 5.5-kb region of the X-linked long-wave “red” opsin gene (OPN1LW) in 236 individuals from ethnically diverse human populations. Our analysis of the recombination landscape across OPN1LW reveals an unusual haplotype structure associated with amino acid replacement variation in exon 3 that is consistent with gene conversion. Compared with the absence of OPN1LW amino acid replacement fixation since divergence from chimpanzee, the human population exhibits a significant excess of high-frequency OPN1LW replacements. Our results suggest that subtle changes in L-cone opsin wavelength absorption may have been adaptive during human evolution. PMID:15252758

  9. GC-biased gene conversion impacts ribosomal DNA evolution in vertebrates, angiosperms, and other eukaryotes.

    PubMed

    Escobar, Juan S; Glémin, Sylvain; Galtier, Nicolas

    2011-09-01

    Ribosomal DNA (rDNA) is one of the most conserved genes in eukaryotes. The multiples copies of rDNA in the genome evolve in a concerted manner, through unequal crossing over and/or gene conversion, two mechanisms related to homologous recombination. Recombination increases local GC content in several organisms through a process known as GC-biased gene conversion (gBGC). gBGC has been well characterized in mammals, birds, and grasses, but its phylogenetic distribution across the tree of life is poorly understood. Here, we test the hypothesis that recombination affects the evolution of base composition in 18S rDNA and examine the reliability of this thoroughly studied molecule as a marker of gBGC in eukaryotes. Phylogenetic analyses of 18S rDNA in vertebrates and angiosperms reveal significant heterogeneity in the evolution of base composition across both groups. Mammals, birds, and grasses experience increases in the GC content of the 18S rDNA, consistent with previous genome-wide analyses. In addition, we observe increased GC contents in Ostariophysi ray-finned fishes and commelinid monocots (i.e., the clade including grasses), suggesting that the genomes of these two groups have been affected by gBGC. Polymorphism analyses in rDNA confirm that gBGC, not mutation bias, is the most plausible explanation for these patterns. We also find that helix and loop sites of the secondary structure of ribosomal RNA do not evolve at the same pace: loops evolve faster than helices, whereas helices are GC richer than loops. We extend analyses to major lineages of eukaryotes and suggest that gBGC might have also affected base composition in Giardia (Diplomonadina), nudibranch gastropods (Mollusca), and Asterozoa (Echinodermata). PMID:21444650

  10. A Metagenomic Perspective on Changes to Nutrient-cycling Genes Following Forest-to-agriculture Conversion in the Amazon Basin

    NASA Astrophysics Data System (ADS)

    Meyer, K. M.; Womack, A. M.; Rodrigues, J.; Nüsslein, K.; Bohannan, B. J. M.

    2014-12-01

    Forest-to-agriculture conversion has been shown to alter nutrient cycling and the community composition of soil microorganisms. However, few studies have looked simultaneously at how the abundance, composition, and diversity of microbial genes involved in nutrient cycling change with conversion. We used shotgun metagenomic sequencing to analyze soil from primary rainforest and converted cattle pasture sampled at the Fazenda Nova Vida in Rondônia, Brazil. The diversity, richness, and evenness of nutrient cycling genes were significantly higher in the pasture, and the composition of nutrient cycling communities differed significantly between land use types. These results largely mirror taxonomic shifts following Amazon rainforest conversion, which tends to increase diversity, richness, and evenness of soil microbial communities. The abundance of genes related to N cycling and methane flux differed between land use types. Methanotrophy genes decreased in abundance in the pasture, whereas methanogenesis genes were not significantly different between land use types. These changes could underlie the commonly observed shift from methane sink to source following forest-to-agriculture conversion. Multiple genes in the nitrogen cycle also differed with land use, including genes related to N-fixation and ammonification. Metagenomics provides a unique perspective on the consequences of land use change on microbial community structure and function.

  11. Gene Location and DNA Density Determine Transcription Factor Distributions in E. coli

    NASA Astrophysics Data System (ADS)

    Kuhlman, Thomas; Cox, Edward

    2013-03-01

    The diffusion coefficient of the prototypical transcription factor LacI within living Escherichia coli has been measured directly by in vivo tracking to be D = 0.4 μm2/s. At this rate, simple models of diffusion lead to the expectation that LacI and other proteins will rapidly homogenize throughout the cell. We have tested this expectation of spatial homogeneity by single molecule visualization of LacI molecules non-specifically bound to DNA in fixed cells. Contrary to expectation, we find that the distribution depends on the spatial location of its encoding gene. We demonstrate that the spatial distribution of LacI is also determined by the local state of DNA compaction, and that E. coli can dynamically redistribute proteins by modifying the state of its nucleoid. Finally, we show that LacI inhomogeneity increases the strength with which targets located proximally to the LacI gene are regulated. We propose a model for intranucleoid diffusion which can reconcile these results with previous measurements of LacI diffusion. This work was supported by the National Institutes of Health [GM078591, GM071508] and the Howard Hughes Medical Institute [52005884]. TEK is supported by an NIH Ruth Kirschstein NRSA Fellowship [F32GM090568-01A1].

  12. Intellectual ability in the duchenne muscular dystrophy and dystrophin gene mutation location.

    PubMed

    Milic Rasic, V; Vojinovic, D; Pesovic, J; Mijalkovic, G; Lukic, V; Mladenovic, J; Kosac, A; Novakovic, I; Maksimovic, N; Romac, S; Todorovic, S; Savic Pavicevic, D

    2014-12-01

    Duchenne muscular dystrophy (DMD) is the most common form of muscular dystrophy during childhood. Mutations in dystrophin (DMD) gene are also recognized as a cause of cognitive impairment. We aimed to determine the association between intelligence level and mutation location in DMD genes in Serbian patients with DMD. Forty-one male patients with DMD, aged 3 to 16 years, were recruited at the Clinic for Neurology and Psychiatry for Children and Youth in Belgrade, Serbia. All patients had defined DMD gene deletions or duplications [multiplex ligation-dependent probe amplification (MLPA), polymerase chain reaction (PCR)] and cognitive status assessment (Wechsler Intelligence Scale for Children, Brunet-Lezine scale, Vineland-Doll scale). In 37 patients with an estimated full scale intelligence quotient (FSIQ), six (16.22%) had borderline intelligence (70location when we assumed their functional consequence on dystrophin isoforms and when mutations in the 5'-untranslated region (5'UTR) of Dp140 (exons 45-50) were assigned to affect only Dp427 and Dp260. Mutations affecting Dp140 and Dp71/Dp40 have been associated with more frequent and more severe cognitive impairment. Finally, the same classification of mutations explained the greater proportion of FSIQ variability associated with cumulative loss of dystrophin isoforms. In conclusion, cumulative loss of dystrophin isoforms increases the risk of intellectual impairment in DMD and characterizing the genotype can define necessity of early cognitive interventions in DMD patients. PMID:25937795

  13. A cII-dependent promoter is located within the Q gene of bacteriophage lambda.

    PubMed

    Hoopes, B C; McClure, W R

    1985-05-01

    We have found a cII-dependent promoter, PaQ, within the Q gene of bacteriophage lambda. Transcription experiments and abortive initiation assays performed in vitro showed that the promoter strength and the cII affinity of PaQ were comparable to the other cII-dependent lambda promoters, PE and PI. The location and leftward direction of PaQ suggests a possible role in the delay of lambda late-gene expression by cII protein, a phenomenon that has been called cII-dependent inhibition. We have constructed a promoter down mutation, paq-1, by changing a single base pair in the putative cII binding site of the promoter by oligonucleotide site-directed mutagenesis. The paq-1 mutant promoter required about 4-fold higher cII concentrations for maximal activation compared to the wild-type PaQ. We tested the hypothesis that PaQ is responsible in part for the delay of lambda late-gene expression by recombining the paq-1 mutation into a phage showing severe cII-dependent inhibition. We found that the paq-1 mutation relieved the cII-dependent growth defect of this phage. The paq-1 mutation (in combination with lambda cI857) resulted in a clear-plaque phenotype at the permissive temperature of 32 degrees C. The role of the PaQ-initiated antisense transcript in the control of lambda development is discussed.

  14. Sequence divergence in two tandemly located pilin genes of Eikenella corrodens.

    PubMed Central

    Tønjum, T; Weir, S; Bøvre, K; Progulske-Fox, A; Marrs, C F

    1993-01-01

    Eikenella corrodens normally inhabits the human respiratory and gastrointestinal tracts but is frequently the cause of abscesses at various sites. Using the N-terminal portion of the Moraxella nonliquefaciens pilin gene as a hybridization probe, we cloned two tandemly located pilin genes of E. corrodens 31745, ecpC and ecpD, and expressed the two pilin genes separately in Escherichia coli. A comparison of the predicted amino acid sequences of E. corrodens 31745 EcpC and EcpD revealed considerable divergence between the sequences of these two pilins and even less similarity to EcpA and EcpB of E. corrodens type strain ATCC 23834. EcpC from E. corrodens 31745 displayed high degrees of homology to the pilins of Neisseria gonorrhoeae and Pseudomonas aeruginosa. EcpD from E. corrodens 31745 showed the highest homologies with the pilin of one of the three P. aeruginosa classes, whereas EcpA and EcpB of strain ATCC 23834 most closely resemble Moraxella bovis pilins. These findings raise interesting questions about potential genetic transfer between different bacterial species, as opposed to convergent evolution. Images PMID:8478080

  15. Walking tree heuristics for biological string alignment, gene location, and phylogenies

    NASA Astrophysics Data System (ADS)

    Cull, P.; Holloway, J. L.; Cavener, J. D.

    1999-03-01

    Basic biological information is stored in strings of nucleic acids (DNA, RNA) or amino acids (proteins). Teasing out the meaning of these strings is a central problem of modern biology. Matching and aligning strings brings out their shared characteristics. Although string matching is well-understood in the edit-distance model, biological strings with transpositions and inversions violate this model's assumptions. We propose a family of heuristics called walking trees to align biologically reasonable strings. Both edit-distance and walking tree methods can locate specific genes within a large string when the genes' sequences are given. When we attempt to match whole strings, the walking tree matches most genes, while the edit-distance method fails. We also give examples in which the walking tree matches substrings even if they have been moved or inverted. The edit-distance method was not designed to handle these problems. We include an example in which the walking tree "discovered" a gene. Calculating scores for whole genome matches gives a method for approximating evolutionary distance. We show two evolutionary trees for the picornaviruses which were computed by the walking tree heuristic. Both of these trees show great similarity to previously constructed trees. The point of this demonstration is that WHOLE genomes can be matched and distances calculated. The first tree was created on a Sequent parallel computer and demonstrates that the walking tree heuristic can be efficiently parallelized. The second tree was created using a network of work stations and demonstrates that there is suffient parallelism in the phylogenetic tree calculation that the sequential walking tree can be used effectively on a network.

  16. Gene Flow between Sympatric Life History Forms of Oncorhynchus mykiss Located above and below Migratory Barriers

    PubMed Central

    Van Doornik, Donald M.; Berejikian, Barry A.; Campbell, Lance A.

    2013-01-01

    Oncorhynchus mykiss have a diverse array of life history types, and understanding the relationship among types is important for management of the species. Patterns of gene flow between sympatric freshwater resident O. mykiss, commonly known as rainbow trout, and anadromous O. mykiss, commonly known as steelhead, populations are complex and poorly understood. In this study, we attempt to determine the occurrence and pathways of gene flow and the degree of genetic similarity between sympatric resident and anadromous O. mykiss in three river systems, and investigate whether resident O. mykiss are producing anadromous offspring in these rivers, two of which have complete barriers to upstream migration. We found that the population structure of the O. mykiss in these rivers appears to be influenced more by the presence of a barrier to upstream migration than by life history type. The sex ratio of resident O. mykiss located above a barrier, and smolts captured in screw traps was significantly skewed in favor of females, whereas the reverse was true below the barriers, suggesting that male resident O. mykiss readily migrate downstream over the barrier, and that precocious male maturation may be occurring in the anadromous populations. Through paternity analyses, we also provide direct confirmation that resident O. mykiss can produce offspring that become anadromous. Most (89%) of the resident O. mykiss that produced anadromous offspring were males. Our results add to the growing body of evidence that shows that gene flow does readily occur between sympatric resident and anadromous O. mykiss life history types, and indicates that resident O. mykiss populations may be a potential repository of genes for the anadromous life history type. PMID:24224023

  17. Conversion and Distribution of Cobalamin in Euglena gracilis z, with Special Reference to Its Location and Probable Function within Chloroplasts

    PubMed Central

    Isegawa, Yuji; Nakano, Yoshihisa; Kitaoka, Shozaburo

    1984-01-01

    Cobalamin is essentially required for growth by Euglena gracilis and shown to be converted to coenzyme forms promptly after feeding cyanocobalamin. Concentrations of coenzymes, methylcobalamin, and 5′-deoxyadenosylcobalamin, reached about 1 femtomole/106 cells 2 hours after feeding cyanocobalamin to cobalamin-limited cells. Cobalamins all were bound to proteins in Euglena cells and located in subcellular fractions of chloroplasts, mitochondria, microsomes, and cytosol. Incorporated cobalamin into chloroplasts was localized in thylakoids. Methylcobalamin existed in chloroplasts, mitochondria, and cytosol, while 5′-deoxyadenosylcobalamin was in mitochondria and the cytosol, 2 h after feeding cyanocobalamin to Euglena cells. Quantitative alterations of methylcobalamin and 5′-deoxyadenosylcobalamin in chloroplasts suggest their important functions as coenzymes in this organelle. The occurrence of functional cobalamins in chloroplasts has not been reported in other photosynthetic eukaryotes. PMID:16663929

  18. Fission yeast Mus81.Eme1 Holliday junction resolvase is required for meiotic crossing over but not for gene conversion.

    PubMed Central

    Smith, Gerald R; Boddy, Michael N; Shanahan, Paul; Russell, Paul

    2003-01-01

    Most models of homologous recombination invoke cleavage of Holliday junctions to explain crossing over. The Mus81.Eme1 endonuclease from fission yeast and humans cleaves Holliday junctions and other branched DNA structures, leaving its physiological substrate uncertain. We report here that Schizosaccharomyces pombe mus81 mutants have normal or elevated frequencies of gene conversion but 20- to 100-fold reduced frequencies of crossing over. Thus, gene conversion and crossing over can be genetically separated, and Mus81 is required for crossing over, supporting the hypothesis that the fission yeast Mus81.Eme1 protein complex resolves Holliday junctions in meiotic cells. PMID:14704204

  19. Yeast genes required for conversion of grape precursors to varietal thiols in wine.

    PubMed

    Santiago, Margarita; Gardner, Richard C

    2015-08-01

    Three varietal thiols are important for the tropical fruit aromas of Sauvignon blanc: 4-mercapto-4-methylpentan-2-one (4MMP), 3-mercaptohexanol (3MH) and its acetylated derivative 3-mercaptohexyl acetate (3MHA). These thiols are produced by yeast during fermentation from precursors in grape juice. Here we identify genes in Saccharomyces cerevisiae that are required for the transport and cleavage of two thiol precursors: cysteine-4MMP and glutathione-3MH. A full-length copy of IRC7 is absolutely required for the cleavage of both precursors in the tested strains; the deleted form of the enzyme found in most yeast strains is incapable of converting these compounds into detectable thiols. By using strains that overexpress full-length IRC7, we further show that the glutathione transporter OPT1 and the transpeptidase CIS2 are also required for conversion of glut-3MH to its varietal thiol. No transporter for cys-4MMP was identified: a strain deleted for all nine known cysteine transport genes was still capable of converting cys-4MMP to its varietal thiol, and was also able to take up cysteine at high concentrations. Based on these results, we conclude that cysteine and glutathione precursors make a relatively minor contribution to 3MH production from most grape juices.

  20. Study on performance of magnetic fluorescent nanoparticles as gene carrier and location in pig kidney cells

    NASA Astrophysics Data System (ADS)

    Wang, Yan; Cui, Haixin; Sun, Changjiao; Du, Wei; Cui, Jinhui; Zhao, Xiang

    2013-03-01

    We evaluated the performance of green fluorescent magnetic Fe3O4 nanoparticles (NPs) as gene carrier and location in pig kidney cells. When the mass ratio of NPs to green fluorescent protein plasmid DNA reached 1:16 or above, DNA molecules can be combined completely with NPs, which indicates that the NPs have good ability to bind negative DNA. Atomic force microscopy (AFM) experiments were carried out to investigate the binding mechanism between NPs and DNA. AFM images show that individual DNA strands come off of larger pieces of netlike agglomerations and several spherical nanoparticles are attached to each individual DNA strand and interact with each other. The pig kidney cells were labelled with membrane-specific red fluorescent dye 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate and nucleus-specific blue fluorescent dye 4',6-diamidino-2-phenylindole dihydrochloride. We found that green fluorescent nanoparticles can past the cell membrane and spread throughout the interior of the cell. The NPs seem to locate more frequently in the cytoplasm than in the nucleus.

  1. Sequence analysis, chromosomal location, and developmental expression of the mouse preproendothelin-1 gene

    SciTech Connect

    Maemura, Koji; Kurihara, Hiroki; Kurihara, Yukiko

    1996-01-15

    Recent studies have designated endothelins (ETs) as morphogenetic factors in embryonic development. In the present study, we cloned and characterized the mouse preproendothelin-1 (preproET-1) gene (Edn1) and examined its expression in reference to development. Edn1 comprises five exons, and the open reading frame encodes the 202-amino-acid preproET-1. The sequences and structural organization of Edn1 are highly homologous to those of other species, especially in the terminal 200-bp sequence of the 3{prime}-noncoding region. Interspecific backcross mapping located Edn1 in the central region of chromosomal 13, where a mouse mutation, congenital hydrocephalus (ch), is also mapped. The highest expression of Edn1 mRNA is detected in the lung in adult mice, whereas Edn1 is predominantly expressed in the epithelium and mesenchyme of the pharyngeal arches and in the endothelium of the large arteries. Edn1 expression and ET-1 peptide levels in the lung progressively increase during the perinatal stage, whereas the expression of Edn3, a gene encoding ET-3, reciprocally decreases. These results suggest that Edn1 expression is developmentally regulated in different tissues and organs in mice in a spatial- and temporal-specific manner. 36 refs., 7 figs.

  2. The gene for Nijmegen breakage syndrome (V2) is not located on chromosome 11

    SciTech Connect

    Kenshi Komatsu; Shinya Matsuura; Hiroshi Tauchi; Satoru Endo

    1996-04-01

    Ataxia telanglectasia (AT) is an autosomal recessive disorder characterized by oculocutaneous telangiectasia and cerebellar ataxia. Individuals with this disorder display immunological impairments, hypersensitivity to ionizing radiation, and a predisposition to cancer. There has been reported genetic heterogeneity in AT, which appeared to include four genetic complementation groups in classical AT - i.e., A, B/C, D, E - and two variants, so-called Nijmegen breakage syndrome (NBS), V1 and V2. Among the four groups of classical AT, no significant differences in clinical appearance have been seen. Familial linkage analyses have produced evidence that genes for all four complementation groups in classical AT reside in a narrow region on chromosome 11q22-23. On the other hand, NBS patients have neither cerebellar ataxia nor telanglectasia but do display microcephaly and a developmental delay. However, patients share features with AT, such as high radiosensitivity, radioresistant DNA synthesis (RDS), and chromosome instability, suggesting that the same pathway (or part thereof) is impaired in both syndromes. The underlying gene for NBS has not yet been identified, and its location in the human genome is still unknown. 15 refs., 3 figs.

  3. The human liver glycogen synthase isozyme gene is located on the short arm of chromosome 12

    SciTech Connect

    Nuttall, F.Q.; Gannon, M.C. ); Kubic, V.L.; Hoyt, K.J. )

    1994-01-15

    Glycogen synthase catalyzes the rate-limiting step in glycogen synthesis. Its activity is regulated by a complex phosphorylation-dephosphorylation mechanism and by allosteric stimulators and inhibitors. Two isozymes of synthase, a skeletal muscle type and liver type, have been identified in rabbit and rat tissues using specific polyclonal antibodies. The skeletal muscle type isozyme is present in several organs in addition to skeletal muscle; the liver isozyme has been identified only in liver. Recently, we have purified and characterized the human liver synthase isozyme. We also have cloned and sequenced the gene from a human liver cDNA library. Using the entire cDNA coding sequence as a probe, we report here the localization of the liver synthase isozyme gene to the short arm of chromosome 12. These studies revealed a centromeric signal on chromosome 12 together with signal to glycogen synthase on the short arm of this chromosome in the p11.2-p12.2 region. Measurements of the relative distance from the midpoint of the centromere to the signal corresponding to glycogen synthase suggests that the locus is in the p12.2 band rather than in the more centromeric location.

  4. Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases

    PubMed Central

    Moehle, Erica A.; Rock, Jeremy M.; Lee, Ya-Li; Jouvenot, Yann; DeKelver, Russell C.; Gregory, Philip D.; Urnov, Fyodor D.; Holmes, Michael C.

    2007-01-01

    Efficient incorporation of novel DNA sequences into a specific site in the genome of living human cells remains a challenge despite its potential utility to genetic medicine, biotechnology, and basic research. We find that a precisely placed double-strand break induced by engineered zinc finger nucleases (ZFNs) can stimulate integration of long DNA stretches into a predetermined genomic location, resulting in high-efficiency site-specific gene addition. Using an extrachromosomal DNA donor carrying a 12-bp tag, a 900-bp ORF, or a 1.5-kb promoter-transcription unit flanked by locus-specific homology arms, we find targeted integration frequencies of 15%, 6%, and 5%, respectively, within 72 h of treatment, and with no selection for the desired event. Importantly, we find that the integration event occurs in a homology-directed manner and leads to the accurate reconstruction of the donor-specified genotype at the endogenous chromosomal locus, and hence presumably results from synthesis-dependent strand annealing repair of the break using the donor DNA as a template. This site-specific gene addition occurs with no measurable increase in the rate of random integration. Remarkably, we also find that ZFNs can drive the addition of an 8-kb sequence carrying three distinct promoter-transcription units into an endogenous locus at a frequency of 6%, also in the absence of any selection. These data reveal the surprising versatility of the specialized polymerase machinery involved in double-strand break repair, illuminate a powerful approach to mammalian cell engineering, and open the possibility of ZFN-driven gene addition therapy for human genetic disease. PMID:17360608

  5. Complete nucleotide sequences of two adjacent early vaccinia virus genes located within the inverted terminal repetition.

    PubMed

    Venkatesan, S; Gershowitz, A; Moss, B

    1982-11-01

    The proximal part of the 10,000-base pair (bp) inverted terminal repetition of vaccinia virus DNA encodes at least three early mRNAs. A 2,236-bp segment of the repetition was sequenced to characterize two of the genes. This task was facilitated by constructing a series of recombinants containing overlapping deletions; oligonucleotide linkers with synthetic restriction sites provided points for radioactive labeling before sequencing by the chemical degradation method of Maxam and Gilbert (Methods Enzymol. 65:499-560, 1980). The ends of the transcripts were mapped by hybridizing labeled DNA fragments to early viral RNA and resolving nuclease S1-protected fragments in sequencing gels, by sequencing cDNA clones, and from the lengths of the RNAs. The nucleotide sequences for at least 60 bp upstream of both transcriptional initiation sites are more than 80% adenine . thymine rich and contain long runs of adenines and thymines with some homology to procaryotic and eucaryotic consensus sequences. The gene transcribed in the rightward direction encodes an RNA of approximately 530 nucleotides with a single open reading frame of 420 nucleotides. Preceding the first AUG, there is a heptanucleotide that can hybridize to the 3' end of 18S rRNA with only one mismatch. The derived amino acid sequence of the protein indicated a molecular weight of 15,500. The gene transcribed in the leftward direction encodes an RNA 1,000 to 1,100 nucleotides long with an open reading frame of 996 nucleotides and a leader sequence of only 5 to 6 nucleotides. The derived amino acid sequence of this protein indicated a molecular weight of 38,500. The 3' ends of the two transcripts were located within 100 bp of each other. Although there are adenine . thymine-rich clusters near the putative transcriptional termination sites, specific AATAAA polyadenylic acid signal sequences are absent.

  6. GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands

    PubMed Central

    Lassalle, Florent; Périan, Séverine; Bataillon, Thomas; Nesme, Xavier; Duret, Laurent; Daubin, Vincent

    2015-01-01

    The characterization of functional elements in genomes relies on the identification of the footprints of natural selection. In this quest, taking into account neutral evolutionary processes such as mutation and genetic drift is crucial because these forces can generate patterns that may obscure or mimic signatures of selection. In mammals, and probably in many eukaryotes, another such confounding factor called GC-Biased Gene Conversion (gBGC) has been documented. This mechanism generates patterns identical to what is expected under selection for higher GC-content, specifically in highly recombining genomic regions. Recent results have suggested that a mysterious selective force favouring higher GC-content exists in Bacteria but the possibility that it could be gBGC has been excluded. Here, we show that gBGC is probably at work in most if not all bacterial species. First we find a consistent positive relationship between the GC-content of a gene and evidence of intra-genic recombination throughout a broad spectrum of bacterial clades. Second, we show that the evolutionary force responsible for this pattern is acting independently from selection on codon usage, and could potentially interfere with selection in favor of optimal AU-ending codons. A comparison with data from human populations shows that the intensity of gBGC in Bacteria is comparable to what has been reported in mammals. We propose that gBGC is not restricted to sexual Eukaryotes but also widespread among Bacteria and could therefore be an ancestral feature of cellular organisms. We argue that if gBGC occurs in bacteria, it can account for previously unexplained observations, such as the apparent non-equilibrium of base substitution patterns and the heterogeneity of gene composition within bacterial genomes. Because gBGC produces patterns similar to positive selection, it is essential to take this process into account when studying the evolutionary forces at work in bacterial genomes. PMID:25659072

  7. Polycyclic aromatic hydrocarbon degrading gene islands in five pyrene-degrading Mycobacterium isolates from different geographic locations.

    PubMed

    Zhang, Chun; Anderson, Anne J

    2012-01-01

    Mycobacterium sp. strain KMS utilizes pyrene, a high-molecular weight polycyclic aromatic hydrocarbon (PAH), as a sole carbon source. Bioinformatic analysis of the genome of isolate KMS predicted 25 genes with the potential to encode 17 pyrene-induced proteins identified by proteomics; these genes were clustered on both the chromosome and a circular plasmid. RT-PCR analysis of total RNA isolated from KMS cells grown with or without pyrene showed that the presence of pyrene increased the transcript accumulation of 20 of the predicted chromosome- and plasmid-located genes encoding pyrene-induced proteins. The transcribed genes from both the chromosome and a circular plasmid were within larger regions containing genes required for PAH degradation constituting PAH-degrading gene islands. Genes encoding integrases and transposases were found within and outside the PAH-degrading gene islands. The lower GC content of the genes within the gene island (61%-64%) compared with the average genome content (68%) suggested that these mycobacteria initially acquired these genes by horizontal gene transfer. Synteny was detected for the PAH-degrading islands in the genomes of two additional Mycobacterium isolates from the same PAH-polluted site and of two other pyrene-degrading Mycobacterium from different sites in the United States of America. Consequently, the gene islands have been conserved from a common ancestral strain.

  8. Horizontal transfer and gene conversion as an important driving force in shaping the landscape of mitochondrial introns.

    PubMed

    Wu, Baojun; Hao, Weilong

    2014-04-16

    Group I introns are highly dynamic and mobile, featuring extensive presence-absence variation and widespread horizontal transfer. Group I introns can invade intron-lacking alleles via intron homing powered by their own encoded homing endonuclease gene (HEG) after horizontal transfer or via reverse splicing through an RNA intermediate. After successful invasion, the intron and HEG are subject to degeneration and sequential loss. It remains unclear whether these mechanisms can fully address the high dynamics and mobility of group I introns. Here, we found that HEGs undergo a fast gain-and-loss turnover comparable with introns in the yeast mitochondrial 21S-rRNA gene, which is unexpected, as the intron and HEG are generally believed to move together as a unit. We further observed extensively mosaic sequences in both the introns and HEGs, and evidence of gene conversion between HEG-containing and HEG-lacking introns. Our findings suggest horizontal transfer and gene conversion can accelerate HEG/intron degeneration and loss, or rescue and propagate HEG/introns, and ultimately result in high HEG/intron turnover rate. Given that up to 25% of the yeast mitochondrial genome is composed of introns and most mitochondrial introns are group I introns, horizontal transfer and gene conversion could have served as an important mechanism in introducing mitochondrial intron diversity, promoting intron mobility and consequently shaping mitochondrial genome architecture.

  9. Inherited differences in crossing over and gene conversion frequencies between wild strains of Sordaria fimicola from "Evolution Canyon".

    PubMed Central

    Saleem, M; Lamb, B C; Nevo, E

    2001-01-01

    Recombination generates new combinations of existing genetic variation and therefore may be important in adaptation and evolution. We investigated whether there was natural genetic variation for recombination frequencies and whether any such variation was environment related and possibly adaptive. Crossing over and gene conversion frequencies often differed significantly in a consistent direction between wild strains of the fungus Sordaria fimicola isolated from a harsher or a milder microscale environment in "Evolution Canyon," Israel. First- and second-generation descendants from selfing the original strains from the harsher, more variable, south-facing slope had higher frequencies of crossing over in locus-centromere intervals and of gene conversion than those from the lusher north-facing slopes. There were some significant differences between strains within slopes, but these were less marked than between slopes. Such inherited variation could provide a basis for natural selection for optimum recombination frequencies in each environment. There were no significant differences in meiotic hybrid DNA correction frequencies between strains from the different slopes. The conversion analysis was made using only conversions to wild type, because estimations of conversion to mutant were affected by a high frequency of spontaneous mutation. There was no polarized segregation of chromosomes at meiosis I or of chromatids at meiosis II. PMID:11779798

  10. BRCA1 and CtIP suppress long tract gene conversion between sister chromatids

    PubMed Central

    Chandramouly, Gurushankar; Kwok, Amy; Huang, Bin; Willis, Nicholas A.; Xie, Anyong; Scully, Ralph

    2013-01-01

    BRCA1 controls early steps of the synthesis-dependent strand annealing (SDSA) pathway of homologous recombination, but has no known role following Rad51-mediated synapsis. Here we show that BRCA1 influences post-synaptic homologous recombination events, controlling the balance between short- (STGC) and long-tract gene conversion (LTGC) between sister chromatids. Brca1 mutant cells reveal a bias towards LTGC that is corrected by expression of wild type but not cancer-predisposing BRCA1 alleles. The LTGC bias is enhanced by depletion of CtIP but reversed by inhibition of 53BP1, implicating DNA end resection as a contributor to the STGC/LTGC balance. The impact of BRCA1/CtIP loss on the STGC/LTGC balance is abolished when the second (non-invading) end of the break is unable to support termination of STGC by homologous pairing (“annealing”). This suggests that BRCA1/CtIP-mediated processing of the second end of the break controls the annealing step that normally terminates SDSA, thereby suppressing the error-prone LTGC outcome. PMID:23994874

  11. Diazepam binding inhibitor gene expression: Location in brain and peripheral tissues of rate

    SciTech Connect

    Alho, H.; Fremeau, R.T. Jr.; Tiedge, H.; Wilcox, J.; Bovolin, P.; Brosius, J.; Roberts, J.L.; Costa, E.

    1988-09-01

    Diazepam binding inhibitor (DBI), an endogenous 10-kDa polypeptide was isolated from rat and human brain by monitoring displacement of radioactive diazepam bound to specific recognition sites in brain synaptic and mitochondrial membranes. The cellular location of DBI mRNA was studied in rat brain and selected peripheral tissues by in situ hybridization histochemistry with a /sup 35/S-labeled single-stranded complementary RNA probe. DBI mRNA was heterogeneously distributed in rat brain, with particularly high levels in the area postrema, the cerebellar cortex, and ependyma of the third ventricle. Intermediate levels were found in the olfactory bulb, pontine nuclei, inferior colliculi, arcuate nucleus, and pineal gland. Relatively low but significant levels of silver grains were observed overlying many mesencephalic and telencephalic areas that have previously been shown to contain numerous DBI-immunoreactive neurons and a high density of central benzodiazepine receptors. In situ hybridizations also revealed high levels of DBI mRNA in the posterior lobe of the pituitary gland, liver, and germinal center of the white pulp of spleen, all tissues that are rich in peripheral benzodiazepine binding sites. The tissue-specific pattern of DBI gene expression described here could be exploited to further understand the physiological function of DBI in the brain and periphery.

  12. Rearrangement by inversion of a T-cell receptor delta variable region gene located 3' of the delta constant region gene.

    PubMed Central

    Korman, A J; Maruyama, J; Raulet, D H

    1989-01-01

    We have located a T-cell receptor variable (V) delta gene segment immediately 3' of the delta constant (C) region gene and 5' to the known joining (J) alpha gene segments. This V delta gene is in the opposite transcriptional polarity to C delta and has rearranged to C delta by inversion in a gamma/delta-expressing hybridoma, DN7.3. This V delta gene is commonly rearranged in adult but not fetal gamma/delta-expressing thymocytes and has not been observed among alpha gene rearrangements reported to date. The reciprocal joining sequence isolated from this cell line contains N region nucleotides between the recombination signal sequences, in contrast to previously analyzed reciprocal joints. The results are discussed in the context of models accounting for ordered V gene usage during lymphocyte development. Images PMID:2789518

  13. vls Antigenic Variation Systems of Lyme Disease Borrelia: Eluding Host Immunity through both Random, Segmental Gene Conversion and Framework Heterogeneity.

    PubMed

    Norris, Steven J

    2014-12-01

    Spirochetes that cause Lyme borreliosis (also called Lyme disease) possess the vls locus, encoding an elaborate antigenic variation system. This locus contains the expression site vlsE as well as a contiguous array of vls silent cassettes, which contain variations of the central cassette region of vlsE. The locus is present on one of the many linear plasmids in the organism, e.g. plasmid lp28-1 in the strain Borrelia burgdorferi B31. Changes in the sequence of vlsE occur continuously during mammalian infection and consist of random, segmental, unidirectional recombination events between the silent cassettes and the cassette region of vlsE. These gene conversion events do not occur during in vitro culture or the tick portion of the infection cycle of B. burgdorferi or the other related Borrelia species that cause Lyme disease. The mechanism of recombination is largely unknown, but requires the RuvAB Holliday junction branch migrase. Other features of the vls locus also appear to be required, including cis locations of vlsE and the silent cassettes and high G+C content and GC skew. The vls system is required for long-term survival of Lyme Borrelia in infected mammals and represents an important mechanism of immune evasion. In addition to sequence variation, immune selection also results in significant heterogeneity in the sequence of the surface lipoprotein VlsE. Despite antigenic variation, VlsE generates a robust antibody response, and both full-length VlsE and the C6 peptide (corresponding to invariant region 6) are widely used in immunodiagnostic tests for Lyme disease.

  14. Transcriptional Profiling Identifies Location-Specific and Breed-Specific Differentially Expressed Genes in Embryonic Myogenesis in Anas Platyrhynchos

    PubMed Central

    Zhang, Rong-Ping; Liu, He-He; Liu, Jun-Ying; Hu, Ji-Wei; Yan, Xi-Ping; Wang, Ding-Min-Cheng; Li, Liang; Wang, Ji-Wen

    2015-01-01

    Skeletal muscle growth and development are highly orchestrated processes involving significant changes in gene expressions. Differences in the location-specific and breed-specific genes and pathways involved have important implications for meat productions and meat quality. Here, RNA-Seq was performed to identify differences in the muscle deposition between two muscle locations and two duck breeds for functional genomics studies. To achieve those goals, skeletal muscle samples were collected from the leg muscle (LM) and the pectoral muscle (PM) of two genetically different duck breeds, Heiwu duck (H) and Peking duck (P), at embryonic 15 days. Functional genomics studies were performed in two experiments: Experiment 1 directly compared the location-specific genes between PM and LM, and Experiment 2 compared the two breeds (H and P) at the same developmental stage (embryonic 15 days). Almost 13 million clean reads were generated using Illumina technology (Novogene, Beijing, China) on each library, and more than 70% of the reads mapped to the Peking duck (Anas platyrhynchos) genome. A total of 168 genes were differentially expressed between the two locations analyzed in Experiment 1, whereas only 8 genes were differentially expressed when comparing the same location between two breeds in Experiment 2. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) were used to functionally annotate DEGs (differentially expression genes). The DEGs identified in Experiment 1 were mainly involved in focal adhesion, the PI3K-Akt signaling pathway and ECM-receptor interaction pathways (corrected P-value<0.05). In Experiment 2, the DEGs were associated with only the ribosome signaling pathway (corrected P-value<0.05). In addition, quantitative real-time PCR was used to confirm 15 of the differentially expressed genes originally detected by RNA-Seq. A comparative transcript analysis of the leg and pectoral muscles of two duck breeds not only improves our

  15. The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography.

    PubMed

    Lapierre, Marguerite; Blin, Camille; Lambert, Amaury; Achaz, Guillaume; Rocha, Eduardo P C

    2016-07-01

    Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present.

  16. The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography

    PubMed Central

    Lapierre, Marguerite; Blin, Camille; Lambert, Amaury; Achaz, Guillaume; Rocha, Eduardo P. C.

    2016-01-01

    Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present. PMID:26931140

  17. Biased Gene Conversion and GC-Content Evolution in the Coding Sequences of Reptiles and Vertebrates

    PubMed Central

    Figuet, Emeric; Ballenghien, Marion; Romiguier, Jonathan; Galtier, Nicolas

    2015-01-01

    Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins. PMID:25527834

  18. Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates.

    PubMed

    Figuet, Emeric; Ballenghien, Marion; Romiguier, Jonathan; Galtier, Nicolas

    2014-12-19

    Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins.

  19. The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography.

    PubMed

    Lapierre, Marguerite; Blin, Camille; Lambert, Amaury; Achaz, Guillaume; Rocha, Eduardo P C

    2016-07-01

    Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present. PMID:26931140

  20. Evolutionary dynamics of 5S rDNA location in acridid grasshoppers and its relationship with H3 histone gene and 45S rDNA location.

    PubMed

    Cabral-de-Mello, Diogo C; Cabrero, Josefa; López-León, María Dolores; Camacho, Juan Pedro M

    2011-07-01

    We analyze the chromosomal location of 5S rDNA clusters in 29 species of grasshoppers belonging to the family Acrididae. There was extensive variation among species for the number and location of 5S rDNA sites. Out of 148 sites detected, 75% were proximally located, 21.6% were interstitial, and only 3.4% were distal. The number of 5S rDNA sites per species varied from a single chromosome pair (in six species) to all chromosome pairs (in five species), with a range of intermediate situations. Thirteen chromosomes from eight species carried two 5S rDNA clusters. At intraspecific level, differences among populations were detected in Eyprepocnemis plorans, and some heteromorphisms have also been observed in some species. Double FISH for 5S rDNA and H3 histone gene DNA, performed on 17 of these 29 species, revealed that both markers are sometimes placed in a same chromosome but at different location, whereas they appeared to co-localize in five species (Calliptamus barbarus, Heteracris adpersa, Aiolopus strepens, Oedipoda charpentieri and O. coerulescens). Double fiber-FISH in A. strepens and O. coerulescens showed that the two DNAs are closely interspersed with variable relative amounts of both classes of DNA. Finally, no correlation was observed between the number of 5S and 45S rDNA clusters in 23 species where this information was available. These results are discussed in the light of possible mechanisms of spread that led to the extensive variation in the number of clusters observed for both rDNA types in acridid grasshoppers.

  1. Isolation and characterization of a gene from Aspergillus parasiticus associated with the conversion of versicolorin A to sterigmatocystin in aflatoxin biosynthesis.

    PubMed Central

    Skory, C D; Chang, P K; Cary, J; Linz, J E

    1992-01-01

    DNA isolated from the wild-type aflatoxin-producing (Afl+) fungus Aspergillus parasiticus NRRL 5862 was used to construct a cosmid genomic DNA library employing the homologous gene (pyrG) encoding orotidine monophosphate decarboxylase for selection of fungal transformants. The cosmid library was transformed into an Afl- mutant, A. parasiticus CS10 (ver-1 wh-1 pyrG), deficient in the conversion of the aflatoxin biosynthetic intermediate versicolorin A to sterigmatocystin. One pyrG+ Afl+ transformant was identified. DNA fragments from this transformant, recovered by marker rescue, contained part of the cosmid vector including the pyrG gene, the ampr gene, and a piece of the original genomic insert DNA. Transformation of these rescued DNA fragments into A. parasiticus CS10 resulted in production of wild-type levels of aflatoxin and abundant formation of sclerotia. The gene responsible for this complementation (ver-1) was identified by Northern RNA analysis and transformation with subcloned DNA fragments. The approximate locations of transcription initiation and polyadenylation sites of ver-1 were determined by an RNase protection assay and cDNA sequence analysis. The predicted amino acid sequence, deduced from the ver-1 genomic and cDNA nucleotide sequences, was compared with the EMBL and GenBank data bases. The search revealed striking similarity with Streptomyces ketoreductases involved in polyketide biosynthesis. Images PMID:1339261

  2. Conserved structure and adjacent location of the thrombin receptor and protease-activated receptor 2 genes define a protease-activated receptor gene cluster.

    PubMed Central

    Kahn, M.; Ishii, K.; Kuo, W. L.; Piper, M.; Connolly, A.; Shi, Y. P.; Wu, R.; Lin, C. C.; Coughlin, S. R.

    1996-01-01

    BACKGROUND: Thrombin is a serine protease that elicits a variety of cellular responses. Molecular cloning of a thrombin receptor revealed a G protein-coupled receptor that is activated by a novel proteolytic mechanism. Recently, a second protease-activated receptor was discovered and dubbed PAR2. PAR2 is highly related to the thrombin receptor by sequence and, like the thrombin receptor, is activated by cleavage of its amino terminal exodomain. Also like the thrombin receptor, PAR2 can be activated by the hexapeptide corresponding to its tethered ligand sequence independent of receptor cleavage. Thus, functionally, the thrombin receptor and PAR2 constitute a fledgling receptor family that shares a novel proteolytic activation mechanism. To further explore the relatedness of the two known protease-activated receptors and to examine the possibility that a protease-activated gene cluster might exist, we have compared the structure and chromosomal locations of the thrombin receptor and PAR2 genes. MATERIALS AND METHODS: The genomic structures of the two protease-activated receptor genes were determined by analysis of lambda phage, P1 bacteriophage, and bacterial artificial chromosome (BAC) genomic clones. Chromosomal location was determined with fluorescent in situ hybridization (FISH) on metaphase chromosomes, and the relative distance separating the two genes was evaluated both by means of two-color FISH and analysis of YACs and BACs containing both genes. RESULTS: Analysis of genomic clones revealed that the two protease-activated receptor genes share a two-exon genomic structure in which the first exon encodes 5'-untranslated sequence and signal peptide, and the second exon encodes the mature receptor protein and 3'-untranslated sequence. The two receptor genes also share a common locus with the two human genes located at 5q13 and the two mouse genes at 13D2, a syntenic region of the mouse genome. These techniques also suggest that the physical distance separating

  3. Differences in transcript abundance of genes on BTA15 located within a region associated with gain in beef steers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Six markers on the Illumina Bovine 50k BeadChip within a 229 Kb region on bovine chromosome 15 were associated (P=0.002) with average daily gain (ADG) in beef cattle. We chose to evaluate seven genes located within this region for variation in RNA transcript abundance in a library of tissue samples ...

  4. Major gene for field stem rust resistance co-locates with resistance gene Sr12 in "Thatcher" wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Stem rust, caused by Puccinia graminis (Pgt), is a damaging disease of wheat that can be controlled by utilizing effecting stem rust resistance genes. "Thatcher" wheat carries complex resistance to stem rust that is enhanced in the presence of the resistance gene Lr34. The purpose of this study was ...

  5. Cytochrome P450 and actin genes expressed in Helicoverpa zea and Helicoverpa armigera: paralogy/orthology identification, gene conversion and evolution.

    PubMed

    Li, Xianchun; Berenbaum, May R; Schuler, Mary A

    2002-03-01

    Molecular phylogenetic analysis was conducted using conserved cytoplasmic actin and diversified cytochrome P450 (P450) sequences isolated from Helicoverpa zea and Helicoverpa armigera, two species thought to be closely related based on allozyme analyses. These sequences were compared in turn with published sequences from other insects to gain insight into how different gene families evolve. In Bombyx mori and these Helicoverpa species, cytoplasmic actin genes are present as a pair of tandemly duplicated paralogs with coding sequence identities as high as 95.5% (B. mori), 98.9% (H. zea) and 98.5% (H. armigera) due to recent 5'-polar gene conversions. Phylogeny and interspecies comparisons assign the six actin genes into two orthologous groups: HaA3a/HzA3a/BmA3 and HaA3b/HzA3b/BmA4, which exhibit more similarities between H. zea and H. armigera than between Helicoverpa species and B. mori. Like the actin genes in H. zea, four CYP6B genes exist as two pairs of duplicated paralogs with recent 5'-polar gene conversions. Interspecific comparisons and phylogeny analysis identified three groups of orthologous CYP6B genes: H. zea CYP6B8 or CYP6B28/H. armigera CYP6B7, H. zea CYP6B27/H. armigera CYP6B6, and H. zea CYP6B9/H. armigera CYP6B2/Heliothis virescens CYP6B10. The low degree of divergence in the first two of these groups is comparable to allelic variation within a single species. These orthologous relationships and the high degrees of similarity in both actin and P450 genes strongly indicate that these Helicoverpa species are extremely closely related.

  6. A new human gene (DXS1357E) with ubiquitous expression, located in Xq28 adjacent to the adrenoleukodystrophy gene

    SciTech Connect

    Mosser, J.; Sarde, C.O.; Vicaire, S.

    1994-07-15

    The authors have isolated a new human gene (DXS1357E; laboratory name: CDM) localized in Xq28. This gene is transcribed from the same CpG island as the adrenoleukodystrophy gene (ALD) and is oriented in the opposite direction. It encodes a 1.5-kb transcript that exhibits ubiquitous expression and contains a single open reading frame. The 246 deduced amino acid sequence suggests the presence of membrane-associated segments and a weak similarity with the rod-like tail portion of heavy chain myosins from different species. The DXS1357E gene may be a candidate for one of the many diseases mapping to this region. A preliminary analysis did not show rearrangements of the gene in 19 independent patients with Emery-Dreifuss muscular dystrophy. 21 refs., 2 figs.

  7. Identifier (ID) elements are not preferentially located to brain-specific genes: high ID element representation in other tissue-specific- and housekeeping genes of the rat.

    PubMed

    Goldman, Andrés; Capoano, Carlos A; González-López, Evangelina; Geisinger, Adriana

    2014-01-01

    BC1 is a short non-coding RNA from rodents, which is transcribed by RNA pol III. Its RNA is highly abundant in the brain, where it exerts a post-transcriptional regulatory role in dendrites. Upon transcription, retroposition and insertion, BC1 gives rise to a subclass of short interspersed repetitive sequences (SINEs) named identifier (ID) elements. IDs can become integrated inside non-coding regions of RNA pol II transcription units, and - although challenged by a couple of reports - their preferential location to brain-specific genes has been long proposed. Furthermore, an additional, cis-regulatory role in the control of brain-specific pol II-directed transcripts has been suggested for these sequences. In this work we used Northern blot and in silico analyses to examine IDs' location among pol II transcription units in different tissues, and in housekeeping genes. ID sequences appeared distributed in a similar fashion within tissue-specific hnRNA populations of the brain, testis and liver, and within housekeeping primary transcripts as well. Moreover, when the lengths of the unprocessed transcripts were considered, ID representation was higher in housekeeping ones. On the other hand, ID elements appeared similarly distributed among the different gene regions, with the obvious exclusion of those sequences where strict constraints for proper gene expression exist. Altogether, the widespread distribution of ID elements in all the analyzed genes - including housekeeping - and in all gene regions, suggests a random location, raising questions about the specific cis-regulatory role of those sequences.

  8. De novo transcriptome assembly and identification of genes associated with feed conversion ratio and breast muscle yield in domestic ducks.

    PubMed

    Zhu, Feng; Yuan, Jian-Ming; Zhang, Zhen-He; Hao, Jin-Ping; Yang, Yu-Ze; Hu, Shen-Qiang; Yang, Fang-Xi; Qu, Lu-Jiang; Hou, Zhuo-Cheng

    2015-12-01

    Breast muscle yield and feed conversion efficiency are the major breeding aims in duck breeding. Understanding the role of specific transcripts in the muscle and small intestine might lead to the elucidation of interrelated biological processes. In this study, we obtained jejunum and breast muscle samples from two strains of Peking ducks that were sorted by feed conversion ratio (FCR) and breast muscle percentage into two-tailed populations. Ten RNA-Seq libraries were developed from the pooled samples and sequenced using the Hiseq2000 platform. We created a reference duck transcript database using de novo assembly methods, which included 16 663 irredundant contigs with an N50 length of 1530 bp. This new duck reference cDNA dataset significantly improved the mapping rate for RNA-Seq data, from 50% to 70%. Mapping and annotation were followed by Gene Ontology analysis, which showed that numerous genes were differentially expressed between the low and high FCR groups. The differentially expressed genes in the jejunum were enriched in biological processes related to immune response and immune response activation, whereas those in the breast muscle were significantly enriched in biological processes related to muscle cell differentiation and organ development. We identified new candidate genes, that is, PCK1, for improving the FCR and breast muscle yield of ducks and obtained much better reference duck transcripts. This study suggested that de novo assembly is essential when applying transcriptome analysis to a species with an incomplete genome. PMID:26545935

  9. De novo transcriptome assembly and identification of genes associated with feed conversion ratio and breast muscle yield in domestic ducks.

    PubMed

    Zhu, Feng; Yuan, Jian-Ming; Zhang, Zhen-He; Hao, Jin-Ping; Yang, Yu-Ze; Hu, Shen-Qiang; Yang, Fang-Xi; Qu, Lu-Jiang; Hou, Zhuo-Cheng

    2015-12-01

    Breast muscle yield and feed conversion efficiency are the major breeding aims in duck breeding. Understanding the role of specific transcripts in the muscle and small intestine might lead to the elucidation of interrelated biological processes. In this study, we obtained jejunum and breast muscle samples from two strains of Peking ducks that were sorted by feed conversion ratio (FCR) and breast muscle percentage into two-tailed populations. Ten RNA-Seq libraries were developed from the pooled samples and sequenced using the Hiseq2000 platform. We created a reference duck transcript database using de novo assembly methods, which included 16 663 irredundant contigs with an N50 length of 1530 bp. This new duck reference cDNA dataset significantly improved the mapping rate for RNA-Seq data, from 50% to 70%. Mapping and annotation were followed by Gene Ontology analysis, which showed that numerous genes were differentially expressed between the low and high FCR groups. The differentially expressed genes in the jejunum were enriched in biological processes related to immune response and immune response activation, whereas those in the breast muscle were significantly enriched in biological processes related to muscle cell differentiation and organ development. We identified new candidate genes, that is, PCK1, for improving the FCR and breast muscle yield of ducks and obtained much better reference duck transcripts. This study suggested that de novo assembly is essential when applying transcriptome analysis to a species with an incomplete genome.

  10. The pronatriodilatin gene is located on the distal short arm of human chromosome 1 and on mouse chromosome 4.

    PubMed

    Yang-Feng, T L; Floyd-Smith, G; Nemer, M; Drouin, J; Francke, U

    1985-11-01

    Atrial natriuretic factors (ANF) are polypeptides having natriuretic, diuretic, and smooth muscle-relaxing activities that are synthesized from a single larger precursor: pronatriodilatin. Chromosomal assignment of the gene coding for human pronatriodilatin was accomplished by in situ hybridization of a [3H]-labeled pronatriodilatin probe to human chromosome preparations and by Southern blot analysis of somatic cell hybrid DNAs with normal and rearranged chromosomes 1. The human pronatriodilatin gene was mapped to the distal short arm of chromosome 1, in band 1p36. Southern blot analysis of mouse X Chinese hamster somatic cell hybrids was used to assign the mouse pronatriodilatin gene to chromosome 4. This assignment adds another locus to the conserved syntenic group of homologous genes located on the distal half of the short arm of human chromosome 1 and on mouse chromosome 4.

  11. A novel human gene encoding a G-protein-coupled receptor (GPR15) is located on chromosome 3

    SciTech Connect

    Heiber, M.; Marchese, A.; O`Dowd, B.F.

    1996-03-05

    We used sequence similarities among G-protein-coupled receptor genes to discover a novel receptor gene. Using primers based on conserved regions of the opioid-related receptors, we isolated a PCR product that was used to locate the full-length coding region of a novel human receptor gene, which we have named GPR15. A comparison of the amino acid sequence of the receptor gene, which we have named GPR15. A comparison of the amino acid sequence of the receptor encoded by GPR15 with other receptors revealed that it shared sequence identity with the angiotensin II AT1 and AT2 receptors, the interleukin 8b receptor, and the orphan receptors GPR1 and AGTL1. GPR15 was mapped to human chromosome 3q11.2-q13.1. 12 refs., 2 figs.

  12. The human gene for neurotrophic tyrosine kinase receptor type 2 (NTRK2) is located on chromosome 9 but is not the familial dysautonomia gene

    SciTech Connect

    Slaugenhaupt, S.A. |; Liebert, C.B.; Lucente, D.E.

    1995-02-10

    The neurotrophic tyrosine kinase receptor type 2 (NTRK2) gene is a member of the trk family of tyrosine protein kinases, which encode receptors for the nerve growth factor-related proteins known as neurotrophins. The neurotrophins and their receptors have long been considered candidate genes for familial dysautonomia (FD), a hereditary sensory neuropathy resulting from the congenital loss of both sensory and autonomic neurons. The DYS gene has recently been mapped to human chromosome 9q31-q33, and therefore we set out to determine the chromosomal localization of the candidate gene NTRK2. A mouse trkB probe was hybridized to both somatic cell hybrids containing human chromosome 9 and a human chromosome 9 flow-sorted cosmid library. The human homologue of trkB, NTRK2, was assigned to chromosome 9. To localize the NTRK2 gene further, a dinucleotide repeat polymorphism was identified within a cosmid that contains NTRK2 exon sequences. This marker was genotyped in the CEPH reference pedigrees and places the NTRK2 gene near D9S1 on the proximal long arm of human chromosome 9. The NTRK2 gene is located approximately 22 cm proximal to DYS and shows several recombinants in disease families. Therefore, the NTRK2 gene can now be excluded as a candidate gene for familial dysautonomia. 18 refs., 1 fig.

  13. Use of the Twin Design to Examine Evocative Gene-Environment Effects within a Conversational Context

    PubMed Central

    DeThorne, Laura Segebart; Hart, Sara Ann

    2010-01-01

    The purpose of this study was to highlight the role of twin designs in understanding children’s conversational interactions. Specifically, we (a) attempted to replicate the findings of genetic effects on children’s conversational language use reported in DeThorne et al. (2008), and (b) examined whether the language used by examiners in their conversation with twins reflected differences in the children’s genetic similarity. Behavioral genetic analyses included intraclass correlations and model fitting procedures applied to 514 same-sex twins (202 MZ, 294 DZ, 10 unknown zygosity) from the Western Reserve Reading Project (Petrill, Deater-Deckard, Thompson, DeThorne, & Schatschneider, 2006). Analyses focused on child and examiner measures of talkativeness, average utterance length, vocabulary diversity, and grammatical complexity from a fifteen-minute conversational exchange. Substantial genetic effects on children’s conversational language measures replicated results from DeThorne et al. (2008) using an expanded sample. However, no familiality was reflected in the examiner language measures. Modest phenotypic correlations between child and examiner language measures suggested that differences in examiner language use may elicit differences in child language use, but evidence of evocative rGE in which genetic differences across children evoke differences in examiner language use, was not found. The discussion focuses on a comparison of findings to previous studies and implications for future research. PMID:22102850

  14. Breakpoint analysis of Turner patients with partial Xp deletions: implications for the lymphoedema gene location

    PubMed Central

    Boucher, C.; Sargent, C.; Ogata, T.; Affara, N.

    2001-01-01

    BACKGROUND—Turner syndrome is characterised by a 45,X karyotype and a variety of skeletal, lymphoedemic, and gonadal anomalies. Genes involved in the Turner phenotype are thought to be X/Y homologous with the X genes escaping X inactivation. Haploinsufficiency of the SHOX gene has been reported to cause the short stature seen in Turner syndrome patients. More recently, mutations of this gene have been shown to be associated with other skeletal abnormalities, suggesting that haploinsufficiency of SHOX causes all the Turner skeletal anomalies. No such gene has yet been identified for the lymphoedemic features.
METHODS—Fluorescence in situ hybridisation (FISH) analysis with PAC clones on nine patients with partially deleted X chromosomes was performed.
RESULTS/DISCUSSION—The Turner syndrome stigmata for each patient are described and correlation between the breakpoint and the phenotype discussed. A lymphoedema critical region in Xp11.4 is proposed and its gene content discussed with respect to that in the previously reported Yp11.2 lymphoedema critical region.


Keywords: Turner syndrome; lymphoedema; Xp11.4 PMID:11546827

  15. Fungal and cyanobacterial gene expression in a lichen symbiosis: Effect of temperature and location.

    PubMed

    Steinhäuser, Sophie S; Andrésson, Ólafur S; Pálsson, Arnar; Werth, Silke

    2016-10-01

    Organisms have evolved different cellular mechanisms to deal with environmental stress, primarily through complex molecular mechanisms including protein refolding and DNA repair. As mutualistic symbioses, lichens offer the possibility of analyzing molecular stress responses in a particularly tight interspecific relationship. We study the widespread cyanolichen Peltigera membranacea, a key player in carbon and nitrogen cycling in terrestrial ecosystems at northern latitudes. We ask whether increased temperature is reflected in mRNA levels of selected damage control genes, and do the response patterns show geographical associations? Using real-time PCR quantification of 38 transcripts, differential expression was demonstrated for nine cyanobacterial and nine fungal stress response genes (plus the fungal symbiosis-related lec2 gene) when the temperature was increased from 5 °C to 15 °C and 25 °C. Principle component analysis (PCA) revealed two gene groups with different response patterns. Whereas a set of cyanobacterial DNA repair genes and the fungal lec2 (PC1 group) showed an expression drop at 15 °C vs. 5 °C, most fungal candidates (PC2 group) showed increased expression at 25 °C vs. 5 °C. PC1 responses also correlated with elevation. The correlated downregulation of lec2 and cyanobacterial DNA repair genes suggests a possible interplay between the symbionts warranting further studies. PMID:27647237

  16. A linear discrete dynamic system model for temporal gene interaction and regulatory network influence in response to bioethanol conversion inhibitor HMF for ethanologenic yeast

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A linear discrete dynamic system model is constructed to represent the temporal interactions among significantly expressed genes in response to bioethanol conversion inhibitor 5-hydroxymethylfurfural for ethanologenic yeast Saccharomyces cerevisiae. This study identifies the most significant linear...

  17. Low-temperature affected LC-PUFA conversion and associated gene transcript level in Nannochloropsis oculata CS-179

    NASA Astrophysics Data System (ADS)

    Ma, Xiaolei; Zhang, Lin; Zhu, Baohua; Pan, Kehou; Li, Si; Yang, Guanpin

    2011-09-01

    Nannochloropsis oculata CS-179, a marine eukaryotic unicellular microalga, is rich in long-chain polyunsaturated fatty acids (LC-PUFAs). Culture temperature affected cell growth and the composition of LC-PUFAs. At an initial cell density of 1.5 × 106 cell mL-1, the highest growth was observed at 25°C and the cell density reached 3 × 107 cell mL-1 at the beginning of logarithmic phase. The content of LC-PUFAs varied with culture temperature. The highest content of LC-PUFAs (43.96%) and EPA (36.6%) was gained at 20°C. Real-time PCR showed that the abundance of Δ6-desaturase gene transcripts was significantly different among 5 culture temperatures and the highest transcript level (15°C) of Nanoc-D6D took off at cycle 21.45. The gene transcript of C20-elongase gene was higher at lower temperatures (10, 15, and 20°C), and the highest transcript level (20°C) of Nanoc-E took off at cycle 21.18. The highest conversion rate (39.3%) of Δ6-desaturase was also gained at 20°C. But the conversion rate of Nanoc-E was not detected. The higher content of LC-PUFAs was a result of higher gene transcript level and higher enzyme activity. Compared with C20-elongase gene, Δ6-desaturase gene transcript and enzyme activity varied significantly with temperature. It will be useful to study the mechanism of how the content of LC-PUFAs is affected by temperature.

  18. The fibulin-1 gene (FBLN1) is located on human chromosome 22 and on mouse chromosome 15

    SciTech Connect

    Mattei, M.G.; Pan, T.C.; Zhang, R.Z.

    1994-07-15

    Fibulin-1 is a calcium-binding glycoprotein present in the extracellular matrix and in the serum. The gene coding for fibulin-1 (FBLN1) was located by in situ hybridization of {sup 3}H-labeled cDNA probes to human and mouse metaphase chromosomes. The gene was assigned to the q13.2-q13.3 region of human chromosome 22 and to the E-F band of mouse chromosome 15. The finding extends the evolutionary conservation between human chromosome 22 and mouse chromosome 15. 11 refs., 2 figs.

  19. Genomic location of the major ribosomal protein gene locus determines Vibrio cholerae global growth and infectivity.

    PubMed

    Soler-Bistué, Alfonso; Mondotte, Juan A; Bland, Michael Jason; Val, Marie-Eve; Saleh, María-Carla; Mazel, Didier

    2015-04-01

    The effects on cell physiology of gene order within the bacterial chromosome are poorly understood. In silico approaches have shown that genes involved in transcription and translation processes, in particular ribosomal protein (RP) genes, localize near the replication origin (oriC) in fast-growing bacteria suggesting that such a positional bias is an evolutionarily conserved growth-optimization strategy. Such genomic localization could either provide a higher dosage of these genes during fast growth or facilitate the assembly of ribosomes and transcription foci by keeping physically close the many components of these macromolecular machines. To explore this, we used novel recombineering tools to create a set of Vibrio cholerae strains in which S10-spec-α (S10), a locus bearing half of the ribosomal protein genes, was systematically relocated to alternative genomic positions. We show that the relative distance of S10 to the origin of replication tightly correlated with a reduction of S10 dosage, mRNA abundance and growth rate within these otherwise isogenic strains. Furthermore, this was accompanied by a significant reduction in the host-invasion capacity in Drosophila melanogaster. Both phenotypes were rescued in strains bearing two S10 copies highly distal to oriC, demonstrating that replication-dependent gene dosage reduction is the main mechanism behind these alterations. Hence, S10 positioning connects genome structure to cell physiology in Vibrio cholerae. Our results show experimentally for the first time that genomic positioning of genes involved in the flux of genetic information conditions global growth control and hence bacterial physiology and potentially its evolution.

  20. Zebrafish U6 small nuclear RNA gene promoters contain a SPH element in an unusual location.

    PubMed

    Halbig, Kari M; Lekven, Arne C; Kunkel, Gary R

    2008-09-15

    Promoters for vertebrate small nuclear RNA (snRNA) genes contain a relatively simple array of transcriptional control elements, divided into proximal and distal regions. Most of these genes are transcribed by RNA polymerase II (e.g., U1, U2), whereas the U6 gene is transcribed by RNA polymerase III. Previously identified vertebrate U6 snRNA gene promoters consist of a proximal sequence element (PSE) and TATA element in the proximal region, plus a distal region with octamer (OCT) and SphI postoctamer homology (SPH) elements. We have found that zebrafish U6 snRNA promoters contain the SPH element in a novel proximal position immediately upstream of the TATA element. The zebrafish SPH element is recognized by SPH-binding factor/selenocysteine tRNA gene transcription activating factor/zinc finger protein 143 (SBF/Staf/ZNF143) in vitro. Furthermore, a zebrafish U6 promoter with a defective SPH element is inefficiently transcribed when injected into embryos.

  1. The gene for the Ellis-van Creveld syndrome is located on chromosome 4p16

    SciTech Connect

    Polymeropoulos, M.H.; Ide, S.E.; Wright, M.

    1996-07-01

    Ellis-van Creveld syndrome (EVC) is an autosomal recessive disorder characterized by disproportionate dwarfism, polydactyly, and congenital heart disease. This rare disorder is found with increased frequency among the Old Order Amish community in Lancaster County, Pennsylvania. We have used linkage analysis to localize the gene responsible for the EVC phenotype in nine interrelated Amish pedigrees and three unrelated families from Mexico, Ecuador, and Brazil. We now report the linkage for the Ellisvan Creveld syndrome gene to markers on the distal short arm of human chromosome 4, with Z{sub max} = 6.91 at {theta} = 0.02 for marker HOX7, in a region proximal to the FGFR3 gene responsible for the achondroplasia phenotype. 17 refs., 2 figs., 1 tab.

  2. The gene for the Ellis-van Creveld syndrome is located on chromosome 4p16.

    PubMed

    Polymeropoulos, M H; Ide, S E; Wright, M; Goodship, J; Weissenbach, J; Pyeritz, R E; Da Silva, E O; Ortiz De Luna, R I; Francomano, C A

    1996-07-01

    Ellis-van Creveld syndrome (EVC) is an autosomal recessive disorder characterized by disproportionate dwarfism, polydactyly, and congenital heart disease. This rare disorder is found with increased frequency among the Old Order Amish community in Lancaster County, Pennsylvania. We have used linkage analysis to localize the gene responsible for the EVC phenotype in nine interrelated Amish pedigrees and three unrelated families from Mexico, Ecuador, and Brazil. We now report the linkage for the Ellis-van Creveld syndrome gene to markers on the distal short arm of human chromosome 4, with Zmax = 6.91 at theta = 0.02 for marker HOX7, in a region proximal to the FGFR3 gene responsible for the achondroplasia phenotype. PMID:8661097

  3. Murine chromosomal location of five bHLH-Zip transcription factor genes

    SciTech Connect

    Steingrimsson, E.; Gilbert, D.J.; Copeland, N.G.; Jenkins, N.A.

    1995-07-20

    The genes for the bHLH-Zip transcription factors Tfap4, Mxi1, Tcfeb, Usf1, and Usf2 have been mapped in mouse by interspecific backcross analysis. Mxi1, Usf1, and Usf2 have been mapped previously by in situ hybridization, but their positions on the meiotic linkage map had not been determined. The other two genes have not previously been mapped in mouse. These transcription factors belong to a growing family of transcriptional regulators, some of which are known to form a complex network of interacting proteins that control cell proliferation and apoptosis. As expected, based on mapping studies of other bHLH-Zip genes, these loci were well distributed among mouse chromosomes. In addition, some of the probes used in this study detected multiple, independently segregating loci, suggesting the possible existence of additional family members or species-specific pseudogenes. 34 refs., 1 fig., 1 tab.

  4. Major Gene for Field Stem Rust Resistance Co-Locates with Resistance Gene Sr12 in ‘Thatcher’ Wheat

    PubMed Central

    Hiebert, Colin W.; Kolmer, James A.; McCartney, Curt A.; Briggs, Jordan; Fetch, Tom; Bariana, Harbans; Choulet, Frederic; Rouse, Matthew N.; Spielmeyer, Wolfgang

    2016-01-01

    Stem rust, caused by Puccinia graminis (Pgt), is a damaging disease of wheat that can be controlled by utilizing effective stem rust resistance genes. ‘Thatcher’ wheat carries complex resistance to stem rust that is enhanced in the presence of the resistance gene Lr34. The purpose of this study was to examine APR in ‘Thatcher’ and look for genetic interactions with Lr34. A RIL population was tested for stem rust resistance in field nurseries in Canada, USA, and Kenya. BSA was used to find SNP markers associated with reduced stem rust severity. A major QTL was identified on chromosome 3BL near the centromere in all environments. Seedling testing showed that Sr12 mapped to the same region as the QTL for APR. The SNP markers were physically mapped and the region carrying the resistance was searched for sequences with homology to members of the NB-LRR resistance gene family. SNP marker from one NB-LRR-like sequence, NB-LRR3 co-segregated with Sr12. Two additional populations, including one that lacked Lr34, were tested in field nurseries. NB-LRR3 mapped near the maximum LOD for reduction in stem rust severity in both populations. Lines from a population that segregated for Sr12 and Lr34 were tested for seedling Pgt biomass and infection type, as well as APR to field stem rust which showed an interaction between the genes. We concluded that Sr12, or a gene closely linked to Sr12, was responsible for ‘Thatcher’-derived APR in several environments and this resistance was enhanced in the presence of Lr34. PMID:27309724

  5. Major Gene for Field Stem Rust Resistance Co-Locates with Resistance Gene Sr12 in 'Thatcher' Wheat.

    PubMed

    Hiebert, Colin W; Kolmer, James A; McCartney, Curt A; Briggs, Jordan; Fetch, Tom; Bariana, Harbans; Choulet, Frederic; Rouse, Matthew N; Spielmeyer, Wolfgang

    2016-01-01

    Stem rust, caused by Puccinia graminis (Pgt), is a damaging disease of wheat that can be controlled by utilizing effective stem rust resistance genes. 'Thatcher' wheat carries complex resistance to stem rust that is enhanced in the presence of the resistance gene Lr34. The purpose of this study was to examine APR in 'Thatcher' and look for genetic interactions with Lr34. A RIL population was tested for stem rust resistance in field nurseries in Canada, USA, and Kenya. BSA was used to find SNP markers associated with reduced stem rust severity. A major QTL was identified on chromosome 3BL near the centromere in all environments. Seedling testing showed that Sr12 mapped to the same region as the QTL for APR. The SNP markers were physically mapped and the region carrying the resistance was searched for sequences with homology to members of the NB-LRR resistance gene family. SNP marker from one NB-LRR-like sequence, NB-LRR3 co-segregated with Sr12. Two additional populations, including one that lacked Lr34, were tested in field nurseries. NB-LRR3 mapped near the maximum LOD for reduction in stem rust severity in both populations. Lines from a population that segregated for Sr12 and Lr34 were tested for seedling Pgt biomass and infection type, as well as APR to field stem rust which showed an interaction between the genes. We concluded that Sr12, or a gene closely linked to Sr12, was responsible for 'Thatcher'-derived APR in several environments and this resistance was enhanced in the presence of Lr34.

  6. Major Gene for Field Stem Rust Resistance Co-Locates with Resistance Gene Sr12 in 'Thatcher' Wheat.

    PubMed

    Hiebert, Colin W; Kolmer, James A; McCartney, Curt A; Briggs, Jordan; Fetch, Tom; Bariana, Harbans; Choulet, Frederic; Rouse, Matthew N; Spielmeyer, Wolfgang

    2016-01-01

    Stem rust, caused by Puccinia graminis (Pgt), is a damaging disease of wheat that can be controlled by utilizing effective stem rust resistance genes. 'Thatcher' wheat carries complex resistance to stem rust that is enhanced in the presence of the resistance gene Lr34. The purpose of this study was to examine APR in 'Thatcher' and look for genetic interactions with Lr34. A RIL population was tested for stem rust resistance in field nurseries in Canada, USA, and Kenya. BSA was used to find SNP markers associated with reduced stem rust severity. A major QTL was identified on chromosome 3BL near the centromere in all environments. Seedling testing showed that Sr12 mapped to the same region as the QTL for APR. The SNP markers were physically mapped and the region carrying the resistance was searched for sequences with homology to members of the NB-LRR resistance gene family. SNP marker from one NB-LRR-like sequence, NB-LRR3 co-segregated with Sr12. Two additional populations, including one that lacked Lr34, were tested in field nurseries. NB-LRR3 mapped near the maximum LOD for reduction in stem rust severity in both populations. Lines from a population that segregated for Sr12 and Lr34 were tested for seedling Pgt biomass and infection type, as well as APR to field stem rust which showed an interaction between the genes. We concluded that Sr12, or a gene closely linked to Sr12, was responsible for 'Thatcher'-derived APR in several environments and this resistance was enhanced in the presence of Lr34. PMID:27309724

  7. The Y-located gonadoblastoma gene TSPY amplifies its own expression through a positive feedback loop in prostate cancer cells

    SciTech Connect

    Kido, Tatsuo; Lau, Yun-Fai Chris

    2014-03-28

    Highlights: • Y-encoded proto-oncoprotein TSPY amplifies its expression level via a positive feedback loop. • TSPY binds to the chromatin/DNA at exon 1 of TSPY gene. • TSPY enhances the gene expression in a TSPY exon 1 sequence dependent manner. • The conserved SET/NAP-domain is essential for TSPY transactivation. • Insights on probable mechanisms on TSPY exacerbation on cancer development in men. - Abstract: The testis-specific protein Y-encoded (TSPY) is a repetitive gene located on the gonadoblastoma region of the Y chromosome, and has been considered to be the putative gene for this oncogenic locus on the male-only chromosome. It is expressed in spermatogonial cells and spermatocytes in normal human testis, but abundantly in gonadoblastoma, testicular germ cell tumors and a variety of somatic cancers, including melanoma, hepatocellular carcinoma and prostate cancer. Various studies suggest that TSPY accelerates cell proliferation and growth, and promotes tumorigenesis. In this report, we show that TSPY could bind directly to the chromatin/DNA at exon 1 of its own gene, and greatly enhance the transcriptional activities of the endogenous gene in the LNCaP prostate cancer cells. Domain mapping analyses of TSPY have localized the critical and sufficient domain to the SET/NAP-domain. These results suggest that TSPY could efficiently amplify its expression and oncogenic functions through a positive feedback loop, and contribute to the overall tumorigenic processes when it is expressed in various human cancers.

  8. Dissection of the locus control function located on the chicken lysozyme gene domain in transgenic mice.

    PubMed Central

    Bonifer, C; Yannoutsos, N; Krüger, G; Grosveld, F; Sippel, A E

    1994-01-01

    The entire chicken lysozyme gene locus including all known cis-regulatory sequences and the 5' and 3' matrix attachment sites defining the borders of the DNase I sensitive chromatin domain, is expressed at a high level and independent of its chromosomal position in macrophages of transgenic mice. It was concluded that the lysozyme gene locus carries a locus control function. We analysed several cis-regulatory deletion mutants to investigate their influence on tissue specificity and level of expression. Position independent expression of the gene is lost whenever one of the upstream tissue specific enhancer regions is deleted, although tissue specific expression is usually retained. Deletion of the domain border fragments has no influence on copy number dependency of expression. However, without these regions an increased incidence of ectopic expression is observed. This suggests that the domain border fragments may help to suppress transgene expression in inappropriate tissues. We conclude, that position independent expression of the lysozyme gene is not controlled by a single specific region of the locus but is the result of the concerted action of several tissue specific upstream regulatory DNA elements with the promoter. Images PMID:7937146

  9. Gene conversion in yeast as a function of linear energy transfer (LET) for low-LET radiation

    SciTech Connect

    Unrau, P.; Morrison, D.P.; Johnson, J.R.

    1992-05-01

    The relative biological effectiveness (RBE) for low-LET radiation is known to depend on such factors as LET and dose rate. Microdosimetric calculations indicate that the biological target size could also be an important parameter, and calculations predict that the RBE for effects produced by hits in target sizes below about 100 nm should be unity for all low LET radiation. We have measured that RBE for gene conversion in yeast (a small target) for five different low LET photon sources, and the results were consistent with an RBE of unity, which agrees with microdosimetric predictions. 4 refs.

  10. Gene conversion causing human inherited disease: evidence for involvement of non-B-DNA-forming sequences and recombination-promoting motifs in DNA breakage and repair

    PubMed Central

    Chuzhanova, Nadia; Chen, Jian-Min; Bacolla, Albino; Patrinos, George P.; Férec, Claude; Wells, Robert D.; Cooper, David N.

    2009-01-01

    A variety of DNA sequence motifs including inverted repeats, minisatellites, and the χ recombination hotspot, have been reported in association with gene conversion in human genes causing inherited disease. However, no methodical statistically-based analysis has been performed to formalize these observations. We have performed an in silico analysis of the DNA sequence tracts involved in 27 non-overlapping gene conversion events in 19 different genes reported in the context of inherited disease. We found that gene conversion events tend to occur within (C+G)- and CpG-rich regions and that sequences with the potential to form non-B-DNA structures, and which may be involved in the generation of double-strand breaks that could in turn serve to promote gene conversion, occur disproportionately within maximal converted tracts and/or short flanking regions. Maximal converted tracts were also found to be enriched (p<0.01) in a truncated version of the χ-element (a TGGTGG motif), immunoglobulin heavy chain class switch repeats, translin target sites and several novel motifs including (or overlapping) the classical meiotic recombination hotspot, CCTCCCCT. Finally, gene conversions tend to occur in genomic regions that have the potential to fold into stable hairpin conformations. These findings support the concept that recombination-inducing motifs, in association with alternative DNA conformations, can promote recombination in the human genome. PMID:19431182

  11. Lipase genes in Mucor circinelloides: identification, sub-cellular location, phylogenetic analysis and expression profiling during growth and lipid accumulation.

    PubMed

    Zan, Xinyi; Tang, Xin; Chu, Linfang; Zhao, Lina; Chen, Haiqin; Chen, Yong Q; Chen, Wei; Song, Yuanda

    2016-10-01

    Lipases or triacylglycerol hydrolases are widely spread in nature and are particularly common in the microbial world. The filamentous fungus Mucor circinelloides is a potential lipase producer, as it grows well in triacylglycerol-contained culture media. So far only one lipase from M. circinelloides has been characterized, while the majority of lipases remain unknown in this fungus. In the present study, 47 potential lipase genes in M. circinelloides WJ11 and 30 potential lipase genes in M. circinelloides CBS 277.49 were identified by extensive bioinformatics analysis. An overview of these lipases is presented, including several characteristics, sub-cellular location, phylogenetic analysis and expression profiling of the lipase genes during growth and lipid accumulation. All of these proteins contained the consensus sequence for a classical lipase (GXSXG motif) and were divided into four types including α/β-hydrolase_1, α/β-hydrolase_3, class_3 and GDSL lipase (GDSL) based on gene annotations. Phylogenetic analyses revealed that class_3 family and α/β-hydrolase_3 family were the conserved lipase family in M. circinelloides. Additionally, some lipases also contained a typical acyltransferase motif of H-(X) 4-D, and these lipases may play a dual role in lipid metabolism, catalyzing both lipid hydrolysis and transacylation reactions. The differential expression of all lipase genes were confirmed by quantitative real-time PCR, and the expression profiling were analyzed to predict the possible biological roles of these lipase genes in lipid metabolism in M. circinelloides. We preliminarily hypothesized that lipases may be involved in triacylglycerol degradation, phospholipid synthesis and beta-oxidation. Moreover, the results of sub-cellular localization, the presence of signal peptide and transcriptional analyses of lipase genes indicated that four lipase in WJ11 most likely belong to extracellular lipases with a signal peptide. These findings provide a platform

  12. Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis.

    PubMed

    Enault, François; Suhre, Karsten; Poirot, Olivier; Abergel, Chantal; Claverie, Jean-Michel

    2004-07-01

    Phydbac (phylogenomic display of bacterial genes) implemented a method of phylogenomic profiling using a distance measure based on normalized BLAST scores. This method was able to increase the predictive power of phylogenomic profiling by about 25% when compared to the classical approach based on Hamming distances. Here we present a major extension of Phydbac (named here Phydbac2), that extends both the concept and the functionality of the original web-service. While phylogenomic profiles remain the central focus of Phydbac2, it now integrates chromosomal proximity and gene fusion analyses as two additional non-similarity-based indicators for inferring pairwise gene functional relationships. Moreover, all presently available (January 2004) fully sequenced bacterial genomes and those of three lower eukaryotes are now included in the profiling process, thus increasing the initial number of reference genomes (71 in Phydbac) to 150 in Phydbac2. Using the KEGG metabolic pathway database as a benchmark, we show that the predictive power of Phydbac2 is improved by 27% over the previous version. This gain is accounted for on one hand, by the increased number of reference genomes (11%) and on the other hand, as a result of including chromosomal proximity into the distance measure (16%). The expanded functionality of Phydbac2 now allows the user to query more than 50 different genomes, including at least one member of each major bacterial group, most major pathogens and potential bio-terrorism agents. The search for co-evolving genes based on consensus profiles from multiple organisms, the display of Phydbac2 profiles side by side with COG information, the inclusion of KEGG metabolic pathway maps the production of chromosomal proximity maps, and the possibility of collecting and processing results from different Phydbac queries in a common shopping cart are the main new features of Phydbac2. The Phydbac2 web server is available at http://igs-server.cnrs-mrs.fr/phydbac/.

  13. A major recombination hotspot in the XqYq pseudoautosomal region gives new insight into processing of human gene conversion events.

    PubMed

    Sarbajna, Shriparna; Denniff, Matthew; Jeffreys, Alec J; Neumann, Rita; Soler Artigas, María; Veselis, Amelia; May, Celia A

    2012-05-01

    Recombination plays a fundamental role in meiosis. Non-exchange gene conversion (non-crossover, NCO) may facilitate homologue pairing, while reciprocal crossover (CO) physically connects homologues so they orientate appropriately on the meiotic spindle. In males, X-Y homologous pairing and exchange occurs within the two pseudoautosomal regions (PARs) together comprising <5% of the human sex chromosomes. Successful meiosis depends on an obligatory CO within PAR1, while the nature and role of exchange within PAR2 is unclear. Here, we describe the identification and characterization of a typical ~1 kb wide recombination hotspot within PAR2. We find that both COs and NCOs are strongly modulated in trans by the presumed chromatin remodelling protein PRDM9, and in cis by a single nucleotide polymorphism (SNP) located at the hotspot centre that appears to influence recombination initiation and which causes biased gene conversion in SNP heterozygotes. This, the largest survey to date of human NCOs reveals for the first time substantial inter-individual variation in the NCO:CO ratio. Although the extent of biased transmission at the central marker in COs is similar across men, it is highly variable among NCO recombinants. This suggests that cis-effects are mediated not only through recombination initiation frequencies varying between haplotypes but also through subsequent processing, with the potential to significantly intensify meiotic drive of hotspot-suppressing alleles. The NCO:CO ratio and extent of transmission distortion among NCOs appear to be inter-related, suggesting the existence of two NCO pathways in humans. PMID:22291443

  14. Coalescent Times and Patterns of Genetic Diversity in Species with Facultative Sex: Effects of Gene Conversion, Population Structure, and Heterogeneity.

    PubMed

    Hartfield, Matthew; Wright, Stephen I; Agrawal, Aneil F

    2016-01-01

    Many diploid organisms undergo facultative sexual reproduction. However, little is currently known concerning the distribution of neutral genetic variation among facultative sexual organisms except in very simple cases. Understanding this distribution is important when making inferences about rates of sexual reproduction, effective population size, and demographic history. Here we extend coalescent theory in diploids with facultative sex to consider gene conversion, selfing, population subdivision, and temporal and spatial heterogeneity in rates of sex. In addition to analytical results for two-sample coalescent times, we outline a coalescent algorithm that accommodates the complexities arising from partial sex; this algorithm can be used to generate multisample coalescent distributions. A key result is that when sex is rare, gene conversion becomes a significant force in reducing diversity within individuals. This can reduce genomic signatures of infrequent sex (i.e., elevated within-individual allelic sequence divergence) or entirely reverse the predicted patterns. These models offer improved methods for assessing null patterns of molecular variation in facultative sexual organisms.

  15. MHC Class IIB Exon 2 Polymorphism in the Grey Partridge (Perdix perdix) Is Shaped by Selection, Recombination and Gene Conversion

    PubMed Central

    Bryjová, Anna; Albrecht, Tomáš; Bryja, Josef

    2013-01-01

    Among bird species, the most studied major histocompatibility complex (MHC) is the chicken MHC. Although the number of studies on MHC in free-ranging species is increasing, the knowledge on MHC variation in species closely related to chicken is required to understand the peculiarities of bird MHC evolution. Here we describe the variation of MHC class IIB (MHCIIB) exon 2 in a population of the Grey partridge (Perdix perdix), a species of high conservation concern throughout Europe and an emerging galliform model in studies of sexual selection. We found 12 alleles in 108 individuals, but in comparison to other birds surprisingly many sites show signatures of historical positive selection. Individuals displayed between two to four alleles both on genomic and complementary DNA, suggesting the presence of two functional MHCIIB loci. Recombination and gene conversion appear to be involved in generating MHCIIB diversity in the Grey partridge; two recombination breakpoints and several gene conversion events were detected. In phylogenetic analysis of galliform MHCIIB, the Grey partridge alleles do not cluster together, but are scattered through the tree instead. Thus, our results indicate that the Grey partridge MHCIIB is comparable to most other galliforms in terms of copy number and population polymorphism. PMID:23935938

  16. RAD51-dependent break-induced replication differs in kinetics and checkpoint responses from RAD51-mediated gene conversion.

    PubMed

    Malkova, Anna; Naylor, Maria L; Yamaguchi, Miyuki; Ira, Grzegorz; Haber, James E

    2005-02-01

    Diploid Saccharomyces cells experiencing a double-strand break (DSB) on one homologous chromosome repair the break by RAD51-mediated gene conversion >98% of the time. However, when extensive homologous sequences are restricted to one side of the DSB, repair can occur by both RAD51-dependent and RAD51-independent break-induced replication (BIR) mechanisms. Here we characterize the kinetics and checkpoint dependence of RAD51-dependent BIR when the DSB is created within a chromosome. Gene conversion products appear within 2 h, and there is little, if any, induction of the DNA damage checkpoint; however, RAD51-dependent BIR occurs with a further delay of 2 to 4 h and cells arrest in response to the G(2)/M DNA damage checkpoint. RAD51-dependent BIR does not require special facilitating sequences that are required for a less efficient RAD51-independent process. RAD51-dependent BIR occurs efficiently in G(2)-arrested cells. Once repair is initiated, the rate of repair replication during BIR is comparable to that of normal DNA replication, as copying of >100 kb is completed less than 30 min after repair DNA synthesis is detected close to the DSB.

  17. The human cell cycle gene CDC25B is located at 20 p13

    SciTech Connect

    Lane, S.A.; Baker, E.; Sutherland, G.R. ); Tonks, I.; Hayward, N.; Ellem, K. )

    1993-03-01

    Central to the onset of mitosis in all eucaryotic cells is the CDC2 protein kinase, the activity of which is negatively regulated by phosphorylation, and positively activated by dephosphorylation (5). The latter function is carried out by a novel phosphatase, cdc25 (4). There appear to be at least three human CDC25 genes that code for A (3), B (3), and C (6) forms of cdc25. The gene for cdc25C was recently mapped to chromosome band 5q31 by fluorescence in situ hybridization (FISH) (7); however, genes for cdc25A and cdc25B have not yet been chromosomally assigned. A cDNA clone (CentroV), isolated from a [lambda]gt11 expression library constructed from the human melanoma cell line A2058 (Clontech), contained a 2.6-kb insert upon partial digestion with EcoRI and fragments of 1.2 and 1.4-kb upon complete digestion. Sequencing of the cDNA clone showed it to be derived from part of the CDC25B mRNA corresponding to nucleotides 307 to 2898 of the previously sequence (3). The 1.2- and 1.4-kb fragments were nick-translated with biotin-14-dATP and hybridized in situ simultaneously at a final concentration of 5 ng/[mu]l to metaphases from two normal males. The FISH method was modified from that previously described (1) in that chromosomes were stained before analysis with both propidium iodide (as counterstain) and DAPI (for chromosome identification). Twenty metaphases from the first normal male were examined for fluorescent signal. Nineteen of these metaphases showed signal on one or both chromatids of chromosome 20 in the region 20p12-p13; 93% of this signal was at 20p13. There was a total of 17 nonspecific background dots observed in these 20 metaphases. A similar result was obtained from the hybridization to the second normal male.

  18. Structure, chromosome location, and expression of the mouse zinc finger gene Krox-20: multiple gene products and coregulation with the proto-oncogene c-fos.

    PubMed Central

    Chavrier, P; Janssen-Timmen, U; Mattéi, M G; Zerial, M; Bravo, R; Charnay, P

    1989-01-01

    We have analyzed the structure and the regulation of Krox-20, a mouse zinc finger-encoding gene which is transiently activated following serum stimulation of quiescent fibroblast cells in culture. The gene is localized on chromosome 10, band B5, in the mouse, and the homologous human gene also maps to chromosome 10 (region q21.1 to q22.1). Alternative splicing of the 5'-most intron of the Krox-20 gene gives rise to mRNAs encoding putative zinc finger proteins with different N termini. The first exon contains a sequence element with strong similarity to the c-fos proto-oncogene serum response element (SRE). This element can functionally substitute for the c-fos SRE, and it binds the same nuclear protein. It is probably responsible for the serum induction of Krox-20, possibly in combination with a weaker SRE located in the 5'-flanking region of the gene. Our findings suggest that c-fos, Krox-20, and a number of immediate-early serum response genes are coregulated and that the SRE and its cognate protein are essential components of this regulatory pathway. Images PMID:2496302

  19. Identification of chromosomal location of mupA gene, encoding low-level mupirocin resistance in staphylococcal isolates.

    PubMed Central

    Ramsey, M A; Bradley, S F; Kauffman, C A; Morton, T M

    1996-01-01

    Low- and high-level mupirocin resistance have been reported in Staphylococcus aureus. The expression of plasmid-encoded mupA is responsible for high-level mupirocin resistance. Low-level mupirocin-resistant strains do not contain plasmid-encoded mupA, and a chromosomal location for this gene has not previously been reported. We examined high- and low-level mupirocin-resistant S. aureus strains to determine if mupA was present on the chromosome of low-level-resistant isolates. Southern blot analysis of DNA from four mupirocin-resistant strains identified mupA in both high- and low-level mupirocin-resistant strains. Low-level mupirocin-resistant strains contained a copy of mupA on the chromosome, while the high-level mupirocin-resistant isolate contained a copy of the gene on the plasmid. PCR amplification of genomic DNA from each mupirocin-resistant strain resulted in a 1.65-kb fragment, the predicted product from the intragenic mupA primers. This is the first report of a chromosomal location for the mupA gene conferring low-level mupirocin resistance. PMID:9124848

  20. Annotation of differentially expressed genes in the somatic embryogenesis of musa and their location in the banana genome.

    PubMed

    Maldonado-Borges, Josefina Ines; Ku-Cauich, José Roberto; Escobedo-Graciamedrano, Rosa Maria

    2013-01-01

    Analysis of cDNA-AFLP was used to study the genes expressed in zygotic and somatic embryogenesis of Musa acuminata Colla ssp. malaccensis, and a comparison was made between their differential transcribed fragments (TDFs) and the sequenced genome of the double haploid- (DH-) Pahang of the malaccensis subspecies that is available in the network. A total of 253 transcript-derived fragments (TDFs) were detected with apparent size of 100-4000 bp using 5 pairs of AFLP primers, of which 21 were differentially expressed during the different stages of banana embryogenesis; 15 of the sequences have matched DH-Pahang chromosomes, with 7 of them being homologous to gene sequences encoding either known or putative protein domains of higher plants. Four TDF sequences were located in all Musa chromosomes, while the rest were located in one or two chromosomes. Their putative individual function is briefly reviewed based on published information, and the potential roles of these genes in embryo development are discussed. Thus the availability of the genome of Musa and the information of TDFs sequences presented here opens new possibilities for an in-depth study of the molecular and biochemical research of zygotic and somatic embryogenesis of Musa.

  1. Rice transglutaminase gene: Identification, protein expression, functionality, light dependence and specific cell location.

    PubMed

    Campos, N; Castañón, S; Urreta, I; Santos, M; Torné, J M

    2013-05-01

    Transglutaminases (TGases), that catalyze post-translational modification of proteins, are scarcely known in plants. As part of a project to characterize transglutaminase genes in new plant species, the identification and characterization of a TGase in rice is presented. Using differential primers, a cDNA (tgo) of 1767bp from genomic rice DNA amplification was obtained. The primers were designed from the rice DNA sequence relatively homologous to the gene encoding active maize chloroplast TGase. Amino acid sequence of the deduced rice TGase protein (TGO) indicated that it contains the enzyme catalytic triad (Cys-His-Asp), three repeats, myristoylation domains and a leucine zipper motif. The TGO recombinant protein was characterized, showing specific activity regulation, and indicating that tgo encoded for an authentic TGase. Substrate preference and Ca(2+) dependent activity were also detected. In the rice plant TGO protein was immunolocalized in the grana chloroplasts, in protein vesicles near them, and in the bulliform cells. Immunoblot analyses, tgo mRNA expression, and TGase activity indicated that TGO expression in rice was light dependent and regulated by the illumination period. This work increases significantly our plant TGase understanding. Its functional role in rice, which is a good model system for C3 plants, is discussed.

  2. Sequence Diversity in MIC6 Gene among Toxoplasma gondii Isolates from Different Hosts and Geographical Locations.

    PubMed

    Li, Zhong-Yuan; Song, Hui-Qun; Chen, Jia; Zhu, Xing-Quan

    2015-06-01

    Toxoplasma gondii is an opportunistic protozoan parasite that can infect almost all warm-blooded animals including humans with a worldwide distribution. Micronemes play an important role in invasion process of T. gondii, associated with the attachment, motility, and host cell recognition. In this research, sequence diversity in microneme protein 6 (MIC6) gene among 16 T. gondii isolates from different hosts and geographical regions and 1 reference strain was examined. The results showed that the sequence of all the examined T. gondii strains was 1,050 bp in length, and their A + T content was between 45.7% and 46.1%. Sequence analysis presented 33 nucleotide mutation positions (0-1.1%), resulting in 23 amino acid substitutions (0-2.3%) aligned with T. gondii RH strain. Moreover, T. gondii strains representing the 3 classical genotypes (Type I, II, and III) were separated into different clusters based on the locus of MIC6 using phylogenetic analyses by Bayesian inference (BI), maximum parsimony (MP), and maximum likelihood (ML), but T. gondii strains belonging to ToxoDB #9 were separated into different clusters. Our results suggested that MIC6 gene is not a suitable marker for T. gondii population genetic studies. PMID:26174829

  3. A novel HBA2 gene conversion in cis or trans: "α12 allele" in a Saudi population.

    PubMed

    Borgio, J Francis; AbdulAzeez, S; Al-Nafie, Awatif N; Naserullah, Zaki A; Al-Jarrash, Sana; Al-Madan, Mohammed S; Al-Muhanna, Fahad; Steinberg, Martin H; Al-Ali, Amein K

    2014-12-01

    Thalassemia and sickle cell disease are the most prevalent hemoglobin disorders in the populations of Dammam, Al-Qatif and Al-Ahsa regions in the Eastern Province of Saudi Arabia where our study cases originated. Increased HbF can modify these disorders. Direct sequencing of the HBA2 and HBA1 genes from 157 Saudi subjects revealed a new HBA2 gene conversion in cis or trans in 5.7% of the total. We refer to this new HBA2 gene convert as an α12 (HBA12) allele due to its combination of α1 (HBA1) and α2 (HBA2) sequences. Three genotypes, homozygous (-α12(3.7)/α1α12), heterozygous (α1α2/α1α12) and hemizygous (α1- (4.2)/α1α12) for the α12 allele were observed. The majority of individuals who were positive for the α12 allele had a reduction in the percentage of HbA2. Further studies are necessary to evaluate the possible effect of these changes on globin gene expression.

  4. A scaffold-associated DNA region is located downstream of the pea plastocyanin gene.

    PubMed Central

    Slatter, R E; Dupree, P; Gray, J C

    1991-01-01

    Chromosomal scaffold-associated DNA has been isolated from pea leaf nuclei treated with lithium diiodosalicylate to remove histones and then digested with restriction enzymes to remove the DNA in chromosomal loops. A scaffold-associated region (SAR) of DNA has been identified 8 to 9 kb downstream of the single-copy pea plastocyanin gene in proximity to a repetitive sequence present in 300 copies in the pea haploid genome. Isolated restriction fragments from within the SAR can bind to scaffold preparations in a binding assay in vitro. The nucleotide sequence of the SAR indicates a 540-bp 77% A+T-rich region containing many sequence elements in common with SARs from other organisms. Sequences with homology to topoisomerase II binding sites, A-box and T-box sequences, and replication origins are present within this AT-rich region. PMID:1821767

  5. Size and location of radish chromosome regions carrying the fertility restorer Rfk1 gene in spring turnip rape.

    PubMed

    Niemelä, Tarja; Seppänen, Mervi; Badakshi, Farah; Rokka, Veli-Matti; Heslop-Harrison, J S Pat

    2012-04-01

    In spring turnip rape (Brassica rapa L. spp. oleifera), the most promising F1 hybrid system would be the Ogu-INRA CMS/Rf system. A Kosena fertility restorer gene Rfk1, homolog of the Ogura restorer gene Rfo, was successfully transferred from oilseed rape into turnip rape and that restored the fertility in female lines carrying Ogura cms. The trait was, however, unstable in subsequent generations. The physical localization of the radish chromosomal region carrying the Rfk1 gene was investigated using genomic in situ hybridization (GISH) and bacterial artificial chromosome-fluorescence in situ hybridization (BAC-FISH) methods. The metaphase chromosomes were hybridized using radish DNA as the genomic probe and BAC64 probe, which is linked with Rfo gene. Both probes showed a signal in the chromosome spreads of the restorer line 4021-2 Rfk of turnip rape but not in the negative control line 4021B. The GISH analyses clearly showed that the turnip rape restorer plants were either monosomic (2n=2x=20+1R) or disomic (2n=2x=20+2R) addition lines with one or two copies of a single alien chromosome region originating from radish. In the BAC-FISH analysis, double dot signals were detected in subterminal parts of the radish chromosome arms showing that the fertility restorer gene Rfk1 was located in this additional radish chromosome. Detected disomic addition lines were found to be unstable for turnip rape hybrid production. Using the BAC-FISH analysis, weak signals were sometimes visible in two chromosomes of turnip rape and a homologous region of Rfk1 in chromosome 9 of the B. rapa A genome was verified with BLAST analysis. In the future, this homologous area in A genome could be substituted with radish chromosome area carrying the Rfk1 gene.

  6. Phylogenetic Diversity of Archaea and the Archaeal Ammonia Monooxygenase Gene in Uranium Mining-Impacted Locations in Bulgaria

    PubMed Central

    Radeva, Galina; Kenarova, Anelia; Bachvarova, Velina; Popov, Ivan; Selenska-Pobell, Sonja

    2014-01-01

    Uranium mining and milling activities adversely affect the microbial populations of impacted sites. The negative effects of uranium on soil bacteria and fungi are well studied, but little is known about the effects of radionuclides and heavy metals on archaea. The composition and diversity of archaeal communities inhabiting the waste pile of the Sliven uranium mine and the soil of the Buhovo uranium mine were investigated using 16S rRNA gene retrieval. A total of 355 archaeal clones were selected, and their 16S rDNA inserts were analysed by restriction fragment length polymorphism (RFLP) discriminating 14 different RFLP types. All evaluated archaeal 16S rRNA gene sequences belong to the 1.1b/Nitrososphaera cluster of Crenarchaeota. The composition of the archaeal community is distinct for each site of interest and dependent on environmental characteristics, including pollution levels. Since the members of 1.1b/Nitrososphaera cluster have been implicated in the nitrogen cycle, the archaeal communities from these sites were probed for the presence of the ammonia monooxygenase gene (amoA). Our data indicate that amoA gene sequences are distributed in a similar manner as in Crenarchaeota, suggesting that archaeal nitrification processes in uranium mining-impacted locations are under the control of the same key factors controlling archaeal diversity. PMID:24711725

  7. [Sop proteins can cause transcriptional silencing of genes located close to the centromere sites of linear plasmid N15].

    PubMed

    Mardanov, A V; Lane, D; Ravin, N V

    2010-01-01

    Stable inheritance of bacterial chromosomes and low copy number plasmids is ensured by accurate partitioning of replicated molecules between the daughter cells at division. Partitioning of the prophage of the temperate bacteriophage N15, which exists as a linear plasmid molecule with covalently closed ends, depends on the sop locus, comprising genes sopA and sopB, as well as four centromere sites located in different regions of the N15 genome essential for replication and the control of lysogeny. We found that binding of SopB to the centromere can silence centromere-proximal promoters, presumably due to subsequent polymerizing of SopB along the DNA. Close to the IR4 centromere site we identified a promoter, P59, able to drive expression of phage late genes encoding the structural proteins of virion. We found that following binding to IR4 the N15 Sop proteins can cause repression of this promoter. The repression depends on SopB and became stronger in the presence of SopA. Sop-dependent silencing of centromere-proximal promoters control gene expression in phage N15, particularly preventing undesired expression of late genes in the N15 prophage. Thus, the phage N15 sop system not only ensures plasmid partitioning but is also involved in the genetic network controlling prophage replication and the maintenance of lysogeny.

  8. Regulatory roles of spnT, a novel gene located within transposon TnTIR.

    PubMed

    Wei, Jun-Rong; Soo, Po-Chi; Horng, Yu-Tze; Hsieh, Shang-Chen; Tsai, Yu-Huan; Swift, Simon; Withers, Helen; Williams, Paul; Lai, Hsin-Chih

    2006-09-29

    The transposon TnTIR contains spnIR quorum-sensing system regulating sliding motility and the production of nuclease, biosurfactant, and prodigiosin in Serratia marcescens. Within TnTIR, a gene named spnT is upstream of and co-transcribed with spnI. SpnT is a cytoplasmic protein and its level peaks during early stationary phase. spnT over-expression resulted in inhibition of sliding motility and synthesis of prodigiosin, and biosurfactant similar to spnR. spnT but not spnR over-expression induced cell elongation and aberrant DNA replication in S. marcescens and Escherichia coli strains. In comparison with wild-type E. coli strain, over-expression of spnT in an E. coli priA and dnaC double-mutant strain did not lead to the aberrant cell morphology phenotypes, suggesting SpnT may act through the recombination-dependent DNA replication system. As spnT over-expression inhibited swarming but not swimming motility, SpnT may indirectly function as a negative regulator of surface-dependent migration and secondary metabolite production.

  9. Discrimination of Deletion and Duplication Subtypes of the Deleted in Azoospermia Gene Family in the Context of Frequent Interloci Gene Conversion

    PubMed Central

    Vaszkó, Tibor; Papp, János; Krausz, Csilla; Casamonti, Elena; Géczi, Lajos; Olah, Edith

    2016-01-01

    Due to its palindromic setup, AZFc (Azoospermia Factor c) region of chromosome Y is one of the most unstable regions of the human genome. It contains eight gene families expressed mainly in the testes. Several types of rearrangement resulting in changes in the cumulative copy number of the gene families were reported to be associated with diseases such as male infertility and testicular germ cell tumors. The best studied AZFc rearrangement is gr/gr deletion. Its carriers show widespread phenotypic variation from azoospermia to normospermia. This phenomenon was initially attributed to different gr/gr subtypes that would eliminate distinct members of the affected gene families. However, studies conducted to confirm this hypothesis have brought controversial results, perhaps, in part, due to the shortcomings of the utilized subtyping methodology. This proof-of-concept paper is meant to introduce here a novel method aimed at subtyping AZFc rearrangements. It is able to differentiate the partial deletion and partial duplication subtypes of the Deleted in Azoospermia (DAZ) gene family. The keystone of the method is the determination of the copy number of the gene family member-specific variant(s) in a series of sequence family variant (SFV) positions. Most importantly, we present a novel approach for the correct interpretation of the variant copy number data to determine the copy number of the individual DAZ family members in the context of frequent interloci gene conversion.Besides DAZ1/DAZ2 and DAZ3/DAZ4 deletions, not yet described rearrangements such as DAZ2/DAZ4 deletion and three duplication subtypes were also found by the utilization of the novel approach. A striking feature is the extremely high concordance among the individual data pointing to a certain type of rearrangement. In addition to being able to identify DAZ deletion subtypes more reliably than the methods used previously, this approach is the first that can discriminate DAZ duplication subtypes as well

  10. Taxonomic and gene-centric metagenomics of the fecal microbiome of low and high feed conversion ratio (FCR) broilers.

    PubMed

    Singh, K M; Shah, T M; Reddy, Bhaskar; Deshpande, S; Rank, D N; Joshi, C G

    2014-02-01

    Individual weight gain in broiler growers appears to vary, which may in part be due to variation in their gut microbiota. In this paper we analyse the fecal microbiota of low and high feed conversion ratio (FCR) broilers. After shotgun sequencing of the fecal microbiome, we used the SEED database to identify the microbial diversity and metabolic potential in low and high FCR birds. The domain-level breakdown of our samples was bacteria (>95 %), eukaryotes (>2 %), archaea (>0.2 %), and viruses (>0.2 %). At the phylum level, Proteobacteria (78.83 % in low and 52.04 % in high FCR), Firmicutes (11.97 % in low and 27.53 % in high FCR) and Bacteroidetes (7.10 % in low FCR and 17.53 % in high FCR) predominated in the fecal microbial community. Poultry fecal metagenomes revealed the sequences related to 33 genera in both low and high FCR with significantly different proportion. Functional analysis revealed that genes for the metabolism of carbohydrates, amino acids and derivatives and protein metabolism were most abundant in SEED subsystem in both samples. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Indeed, genes associated with sulphur assimilation, flagellum and flagellar motility were over represented in low FCR birds. This information could help in developing strategies to improve feed efficiency and feed formulation for broiler chickens.

  11. Chromosome Map of Xanthomonas campestris pv. campestris 17 with Locations of Genes Involved in Xanthan Gum Synthesis and Yellow Pigmentation

    PubMed Central

    Tseng, Yi-Hsiung; Choy, Ka-Tim; Hung, Chih-Hsin; Lin, Nien-Tsung; Liu, Jane-Yu; Lou, Chih-Hong; Yang, Bih-Ying; Wen, Fu-Shyan; Weng, Shu-Fen; Wu, Jung-Rung

    1999-01-01

    No plasmid was detected in Xanthomonas campestris pv. campestris 17, a strain of the causative agent of black rot in cruciferous plants isolated in Taiwan. Its chromosome was cut by PacI, PmeI, and SwaI into five, two, and six fragments, respectively, and a size of 4.8 Mb was estimated by summing the fragment lengths in these digests. Based on the data obtained from partial digestion and Southern hybridization using probes common to pairs of the overlapping fragments or prepared from linking fragments, a circular physical map bearing the PacI, PmeI, and SwaI sites was constructed for the X. campestris pv. campestris 17 chromosome. Locations of eight eps loci involved in exopolysaccharide (xanthan gum) synthesis, two rrn operons each possessing an unique I-CeuI site, one pig cluster required for yellow pigmentation, and nine auxotrophic markers were determined, using mutants isolated by mutagenesis with Tn5(pfm)CmKm. This transposon contains a polylinker with sites for several rare-cutting restriction endonucleases located between the chloramphenicol resistance and kanamycin resistance (Kmr) genes, which upon insertion introduced additional sites into the chromosome. The recA and tdh genes, with known sequences, were mapped by tagging with the polylinker-Kmr segment from Tn5(pfm)CmKm. This is the first map for X. campestris and would be useful for genetic studies of this and related Xanthomonas species. PMID:9864320

  12. Effects of dietary biotin and avidin on growth, survival, feed conversion, biotin status and gene expression of zebrafish Danio rerio.

    PubMed

    Yossa, Rodrigue; Sarker, Pallab K; Karanth, Santhosh; Ekker, Marc; Vandenberg, Grant W

    2011-12-01

    A study was conducted to investigate the effects of dietary avidin on growth, survival, food conversion, biotin status and gene expression of zebrafish (Danio rerio Hamilton-Buchanan) juveniles (average wet mass 0.178 g) fed 7 purified diets for 12 weeks. Experimental diets were formulated to provide 0×, 1×, 15×, 30×, 60× and 120× excess avidin versus biotin kg(-1) diet, on a molar basis; a control diet contained neither supplemental biotin nor avidin. Fish fed the control diet had the lowest percentage weight gain and the highest mortality, while the highest percentage weight gain and the lowest mortality was observed with the 0× diet (P<0.05). A linear relationship was observed between feed conversion ratio (FCR) and dietary avidin (r=0.876; P<0.0001). Fish fed diets with 120× more avidin than biotin had the highest whole-body biotin content, while the lowest value was obtained with the control and avidin-free diets (P<0.05). Elevated levels of acetyl CoA carboxylase-A (acca), methylcrotonyl CoA carboxylase (mcc) and propionyl CoA carboxylase-A (pcca) transcripts were recorded in fish fed the control diet, in comparison to the other diets. A broken-line analysis indicated that feeding zebrafish a diet with 60 times more avidin than the dietary biotin requirement level will cause biotin deficiency signs.

  13. Conversion of the pathogenic fungus Colletotrichum magna to a nonpathogenic, endophytic mutualist by gene disruption

    USGS Publications Warehouse

    Redman, R.S.; Ranson, J.C.; Rodriguez, R.J.

    1999-01-01

    Hygromycin-resistant transformants of the cucurbit pathogen Colletotrichum magna (teleomorph: Glomerella magna) were generated by restriction enzyme-mediated integration (REMI) transformation. A rapid pathogenicity assay involving watermelon (Citrullus lanatus) seedlings was developed and 14,400 REMI transformants were screened and assessed for their ability to cause disease, colonize plant tissues, and confer disease resistance against wild-type C. magna. A total of 176 nonpathogenic REMI mutants capable of colonizing cucurbit plants were isolated and assigned to three groups based on their ability to confer disease resistance: phenotype A, 80 to 100% disease protection; phenotype B, 10 to 65% disease protection; and phenotype C, 0 to 4% disease protection. Molecular and genetic analyses of one REMI mutant (R1) indicated that the nonpathogenic phenotype A resulted from a single-site integration. R1 showed a 1:1 segregation of hygromycin resistance and nonpathogenicity and all hygromycin-resistant progeny were nonpathogenic. The integrated vector and 5.5 kb of flanking fungal genomic DNA were isolated from R1 and designated pGMR1. To verify that pGMR1 contained pathogenicity gene sequences, a wild-type isolate of C. magna was transformed with pGMR1 to induce gene disruptions by homologous integration. Approximately 47% of the pGMR1 transformants expressed phenotype A, indicating homologous integration and gene disruption.

  14. Androgen response element of the glycine N-methyltransferase gene is located in the coding region of its first exon.

    PubMed

    Lee, Cheng-Ming; Yen, Chia-Hung; Tzeng, Tsai-Yu; Huang, Yu-Zen; Chou, Kuan-Hsien; Chang, Tai-Jay; Arthur Chen, Yi-Ming

    2013-01-01

    Androgen plays an important role in the pathogenesis of PCa (prostate cancer). Previously, we identified GNMT (glycine N-methyltransferase) as a tumour susceptibility gene and characterized its promoter region. Besides, its enzymatic product-sarcosine has been recognized as a marker for prognosis of PCa. The goals of this study were to determine whether GNMT is regulated by androgen and to map its AREs (androgen response elements). Real-time PCR analyses showed that R1881, a synthetic AR (androgen receptor) agonist induced GNMT expression in AR-positive LNCaP cells, but not in AR-negative DU145 cells. In silico prediction showed that there are four putative AREs in GNMT-ARE1, ARE2 and ARE3 are located in the intron 1 and ARE4 is in the intron 2. Consensus ARE motif deduced from published AREs was used to identify the fifth ARE-ARE5 in the coding region of exon 1. Luciferase reporter assay found that only ARE5 mediated the transcriptional activation of R1881. ARE3 overlaps with a YY1 [Yin and Yang 1 (motif (CaCCATGTT, +1118/+1126)] that was further confirmed by antibody supershift and ChIP (chromatin immunoprecipitation) assays. EMSA (electrophoretic mobility shift assay) and ChIP assay confirmed that AR interacts with ARE5 in vitro and in vivo. In summary, GNMT is an AR-targeted gene with its functional ARE located at +19/+33 of the first exon. These results are valuable for the study of the influence of androgen on the gene expression of GNMT especially in the pathogenesis of cancer. PMID:23883094

  15. De novo intrachromosomal gene conversion from OPN1MW to OPN1LW in the male germline results in Blue Cone Monochromacy

    PubMed Central

    Buena-Atienza, Elena; Rüther, Klaus; Baumann, Britta; Bergholz, Richard; Birch, David; De Baere, Elfride; Dollfus, Helene; Greally, Marie T.; Gustavsson, Peter; Hamel, Christian P.; Heckenlively, John R.; Leroy, Bart P.; Plomp, Astrid S.; Pott, Jan Willem R.; Rose, Katherine; Rosenberg, Thomas; Stark, Zornitza; Verheij, Joke B. G. M.; Weleber, Richard; Zobor, Ditta; Weisschuh, Nicole; Kohl, Susanne; Wissinger, Bernd

    2016-01-01

    X-linked cone dysfunction disorders such as Blue Cone Monochromacy and X-linked Cone Dystrophy are characterized by complete loss (of) or reduced L- and M- cone function due to defects in the OPN1LW/OPN1MW gene cluster. Here we investigated 24 affected males from 16 families with either a structurally intact gene cluster or at least one intact single (hybrid) gene but harbouring rare combinations of common SNPs in exon 3 in single or multiple OPN1LW and OPN1MW gene copies. We assessed twelve different OPN1LW/MW exon 3 haplotypes by semi-quantitative minigene splicing assay. Nine haplotypes resulted in aberrant splicing of ≥20% of transcripts including the known pathogenic haplotypes (i.e. ‘LIAVA’, ‘LVAVA’) with absent or minute amounts of correctly spliced transcripts, respectively. De novo formation of the ‘LIAVA’ haplotype derived from an ancestral less deleterious ‘LIAVS’ haplotype was observed in one family with strikingly different phenotypes among affected family members. We could establish intrachromosomal gene conversion in the male germline as underlying mechanism. Gene conversion in the OPN1LW/OPN1MW genes has been postulated, however, we are first to demonstrate a de novo gene conversion within the lineage of a pedigree. PMID:27339364

  16. Retroviral sequences located within an intron of the dilute gene alter dilute expression in a tissue-specific manner.

    PubMed Central

    Seperack, P K; Mercer, J A; Strobel, M C; Copeland, N G; Jenkins, N A

    1995-01-01

    The murine dilute coat color locus encodes an unconventional myosin heavy chain that is thought to be required for the elaboration or maintenance of dendrites or organelle transport in melanocytes and neurons. In previous studies we showed that the d mutation carried by many inbred strains of mice (now referred to as dilute viral, dv), is caused by the integration of an ecotropic murine leukemia virus (Emv-3) into the dilute gene and that phenotypic revertants of dv (termed d+) result from viral excision; a solo viral long terminal repeat (LTR) is all that remains in revertant DNA. In the studies described here we show that Emv-3 sequences are located within an intron of the dilute gene in a region of the C-terminal tail that is differentially spliced. We also show that these Emv-3 sequences result in the production of shortened and abnormally spliced dilute transcripts and that the level of this effect varies among tissues. This tissue-specific effect on dilute expression likely accounts for the absence of neurological abnormalities observed in dv mice. Surprisingly, we also found that the solo viral LTR present in revertant d+ DNA produces a tissue-specific effect on dilute expression, although this effect is less dramatic than with the full-length provirus and produces no obvious mutant phenotype. These findings have important implications for understanding the effects of viral sequences on mammalian gene expression. Images PMID:7774591

  17. Cystatin D locates in the nucleus at sites of active transcription and modulates gene and protein expression.

    PubMed

    Ferrer-Mayorga, Gemma; Alvarez-Díaz, Silvia; Valle, Noelia; De Las Rivas, Javier; Mendes, Marta; Barderas, Rodrigo; Canals, Francesc; Tapia, Olga; Casal, J Ignacio; Lafarga, Miguel; Muñoz, Alberto

    2015-10-30

    Cystatin D is an inhibitor of lysosomal and secreted cysteine proteases. Strikingly, cystatin D has been found to inhibit proliferation, migration, and invasion of colon carcinoma cells indicating tumor suppressor activity that is unrelated to protease inhibition. Here, we demonstrate that a proportion of cystatin D locates within the cell nucleus at specific transcriptionally active chromatin sites. Consistently, transcriptomic analysis show that cystatin D alters gene expression, including that of genes encoding transcription factors such as RUNX1, RUNX2, and MEF2C in HCT116 cells. In concordance with transcriptomic data, quantitative proteomic analysis identified 292 proteins differentially expressed in cystatin D-expressing cells involved in cell adhesion, cytoskeleton, and RNA synthesis and processing. Furthermore, using cytokine arrays we found that cystatin D reduces the secretion of several protumor cytokines such as fibroblast growth factor-4, CX3CL1/fractalkine, neurotrophin 4 oncostatin-M, pulmonary and activation-regulated chemokine/CCL18, and transforming growth factor B3. These results support an unanticipated role of cystatin D in the cell nucleus, controlling the transcription of specific genes involved in crucial cellular functions, which may mediate its protective action in colon cancer.

  18. Cystatin D Locates in the Nucleus at Sites of Active Transcription and Modulates Gene and Protein Expression*

    PubMed Central

    Ferrer-Mayorga, Gemma; Alvarez-Díaz, Silvia; Valle, Noelia; De Las Rivas, Javier; Mendes, Marta; Barderas, Rodrigo; Canals, Francesc; Tapia, Olga; Casal, J. Ignacio; Lafarga, Miguel; Muñoz, Alberto

    2015-01-01

    Cystatin D is an inhibitor of lysosomal and secreted cysteine proteases. Strikingly, cystatin D has been found to inhibit proliferation, migration, and invasion of colon carcinoma cells indicating tumor suppressor activity that is unrelated to protease inhibition. Here, we demonstrate that a proportion of cystatin D locates within the cell nucleus at specific transcriptionally active chromatin sites. Consistently, transcriptomic analysis show that cystatin D alters gene expression, including that of genes encoding transcription factors such as RUNX1, RUNX2, and MEF2C in HCT116 cells. In concordance with transcriptomic data, quantitative proteomic analysis identified 292 proteins differentially expressed in cystatin D-expressing cells involved in cell adhesion, cytoskeleton, and RNA synthesis and processing. Furthermore, using cytokine arrays we found that cystatin D reduces the secretion of several protumor cytokines such as fibroblast growth factor-4, CX3CL1/fractalkine, neurotrophin 4 oncostatin-M, pulmonary and activation-regulated chemokine/CCL18, and transforming growth factor B3. These results support an unanticipated role of cystatin D in the cell nucleus, controlling the transcription of specific genes involved in crucial cellular functions, which may mediate its protective action in colon cancer. PMID:26364852

  19. CYP7A1 Gene Polymorphism Located in the 5′ Upstream Region Modifies the Risk of Coronary Artery Disease

    PubMed Central

    Iwanicki, Tomasz; Balcerzyk, Anna; Niemiec, Pawel; Nowak, Tomasz; Ochalska-Tyka, Anna; Krauze, Jolanta; Kosiorz-Gorczynska, Sylwia; Grzeszczak, Wladyslaw; Zak, Iwona

    2015-01-01

    Background. 7-Alpha cholesterol hydroxylase (CYP7A1), the first enzyme of classic conversion pathway leading from cholesterol to bile acids synthesis, is encoded by CYP7A1 gene. Its single nucleotide polymorphisms (SNPs) influence serum lipid levels and may be related to impaired lipid profile leading to coronary artery disease (CAD). The aim of the present study was to analyze the possible association between the rs7833904 CYP7A1 polymorphism and premature CAD. Material and Methods. Serum lipid levels and rs7833904 SNP were determined in 419 subjects: 200 patients with premature CAD and 219 age and sex matched controls. Results. The A allele carrier state was associated with CAD (OR = 1.76, 95% CI; 1.14–2.71, P = 0.014). The effect was even stronger in the male subgroups (OR = 2.16, 95% CI; 1.28–3.65, P = 0.003). There was no effect in the females. Risk factors of CAD and clinical phenotype of atherosclerosis were not associated with genotype variants of the rs7833904 SNP. Lipid profiles also did not differ significantly between individual genotypes. Conclusion. The CYP7A1 rs7833904 polymorphism may modify the risk of CAD. This effect is especially strong in male subjects. The studied polymorphism does not significantly influence serum lipid levels, in the present study. PMID:25944972

  20. A split hand-split foot (SHFM3) gene is located at 10q24{yields}25

    SciTech Connect

    Gurrieri, F.; Genuardi, M.; Nanni, L.; Sangiorgi, E.; Garofalo, G.

    1996-04-24

    The split hand-split foot (SHSF) malformation affects the central rays of the upper and lower limbs. It presents either as an isolated defect or in association with other skeletal or non-skeletal abnormalities. An autosomal SHSF locus (SHFM1) was previously mapped to 7q22.1. We report the mapping of a second autosomal SHSF locus to 10q24{yields}25 region. Maximum lod scores of 3.73, 4.33 and 4.33 at a recombination fraction of zero were obtained for the loci D10S198, PAX2 and D10S1239, respectively. An 19 cM critical region could be defined by haplotype analysis and several genes with a potential role in limb morphogenesis are located in this region. Heterogeneity testing indicates the existence of at least one additional autosomal SHSF locus. 36 refs., 3 figs., 3 tabs.

  1. Sequence Variation in HSP40 Gene among 16 Toxoplasma gondii Isolates from Different Hosts and Geographical Locations.

    PubMed

    Li, Zhong-Yuan; Lu, Jing; Zhou, Dong-Hui; Chen, Jia; Zhu, Xing-Quan

    2015-01-01

    Toxoplasma gondii with worldwide distribution has received substantial medical and scientific attentions as it causes serious clinical and veterinary problems especially for pregnant women and immunocompromised patients. Heat shock protein 40 (HSP40) plays a variety of essential roles in the pathogenesis of this protozoan parasite. In order to detail the genetic diversity of HSP40 gene, 16 T. gondii strains from different hosts and geographical locations were used in this study. Our results showed that HSP40 sequence of the examined strains was between 6621 bp and 6644 bp in length, and their A+T content was from 48.54% to 48.80%. Furthermore, sequence analysis presented 195 nucleotide mutation positions (0.12%-1.14%) including 29 positions in CDS (0.02%-0.12%) compared with T. gondii ME49 strain (ToxoDB: TGME49_265310). Phylogenetic assay revealed that T. gondii strains representing three classical genotypes (Types I, II, and III) were completely separated into different clusters by maximum parsimony (MP) method, but Type II and ToxoDB#9 strains were grouped into the same cluster. These results suggested that HSP40 gene is not a suitable marker for T. gondii population genetic research, though three classical genotypes of T. gondii could be differentiated by restriction enzymes MscI and EarI existing in amplicon C. PMID:26613080

  2. Genomic sequence analysis of the 238-kb swine segment with a cluster of TRIM and olfactory receptor genes located, but with no class I genes, at the distal end of the SLA class I region.

    PubMed

    Ando, Asako; Shigenari, Atsuko; Kulski, Jerzy K; Renard, Christine; Chardon, Patrick; Shiina, Takashi; Inoko, Hidetoshi

    2005-12-01

    Continuous genomic sequence has been previously determined for the swine leukocyte antigen (SLA) class I region from the TNF gene cluster at the border between the major histocompatibility complex (MHC) class III and class I regions to the UBD gene at the telomeric end of the classical class I gene cluster (SLA-1 to SLA-5, SLA-9, SLA-11). To complete the genomic sequence of the entire SLA class I genomic region, we have analyzed the genomic sequences of two BAC clones carrying a continuous 237,633-bp-long segment spanning from the TRIM15 gene to the UBD gene located on the telomeric side of the classical SLA class I gene cluster. Fifteen non-class I genes, including the zinc finger and the tripartite motif (TRIM) ring-finger-related family genes and olfactory receptor genes, were identified in the 238-kilobase (kb) segment, and their location in the segment was similar to their apparent human homologs. In contrast, a human segment (alpha block) spanning about 375 kb from the gene ETF1P1 and from the HLA-J to HLA-F genes was absent from the 238-kb swine segment. We conclude that the gene organization of the MHC non-class I genes located in the telomeric side of the classical SLA class I gene cluster is remarkably similar between the swine and the human segments, although the swine lacks a 375-kb segment corresponding to the human alpha block.

  3. Genotyping of turkey coronavirus field isolates from various geographic locations in the Unites States based on the spike gene.

    PubMed

    Chen, Yi-Ning; Loa, Chien Chang; Ababneh, Mustafa Mohammed-Khair; Wu, Ching Ching; Lin, Tsang Long

    2015-11-01

    Turkey flocks have experienced turkey coronaviral enteritis sporadically in the United States since the 1990s. Twenty-four field isolates of turkey coronavirus (TCoV) from multiple states in the United States were recovered from 1994 to 2010 to determine the genetic relationships among them. The entire spike (S) gene of each TCoV isolate was amplified and sequenced. Pairwise comparisons were performed using the Clustal W program, revealing 90.0% to 98.4% sequence identity in the full-length S protein, 77.6% to 96.6% in the amino terminus of the S1 subunit (containing one hypervariable region in S1a), and 92.1% to 99.3% in the S2 subunit at the deduced amino acid sequence level. The conserved motifs, including two cleavage recognition sequences of the S protein, two heptad repeats, the transmembrane domain, and the Golgi retention signal were identified in all TCoV isolates. Phylogenetic analysis based on the full-length S gene was used to distinguish North American TCoV isolates from French TCoV isolates. Among the North American TCoV isolates, three distinct genetic groups with 100% bootstrap support were observed. North Carolina isolates formed group I, Texas isolates formed group II, and Minnesota isolates formed Group III. The S genes of 24 TCoV isolates from the United States remained conserved because they contained predominantly synonymous substitutions. The findings of the present study suggest endemic circulation of distinct TCoV genotypes in different geographic locations.

  4. Hellenic subduction earthquake locations including OBS, ocean bottom seismometers and hints at shallow slab structure from teleseismic conversions: A pilot experiment.

    NASA Astrophysics Data System (ADS)

    Sachpazi, M.; Laigle, M.; Charalampakis, M.; Diaz, J.; Gesret, A.; Sokos, E.; Petrou, P.; Flueh, E.; Nicolich, R.; Hirn, A.

    2010-05-01

    In the frame of the European Union "THALES WAS RIGHT" project on seismogenic zones in European subductions and of the European Union "SALVADOR" programme of IfM-GEOMAR for the access to OBS, ocean bottom seismometers, we have deployed in early June 2006 and for 5 months an onshore-offshore array in the SW part of the Hellenic subduction, the area between the south west tip of Peloponissos and Crete. The array consisted of 5, three component OBS and of up to 15 land seismometers. This provided for the first time a constraint on the hypocentral locations of local earthquakes offshore, that up to then were poorly located because of an insufficient azimuthal coverage, since all the permanent stations are on land on one side. Comparison of the routinely located hypocenters by the permanent array with those located by the special local onshore/offshore local array shows that some background seismicity may be mislocated by several tens of kilometers with for instance small earthquakes of the upper part of the plate boundary SW of Crete-Peloponissos having been located as deep earthquakes in the SW Aegean because of lack of constraint to the SW. This survey was organized early in the THALES WAS RIGHT project, in order to provide a reference observation period for the project. This proved a valuable effort since it provided this basis just a year before the major earthquake for decades in the region. This allows to reveal temporal patterns of seismicity, thus constrained by the addition of offshore observations. Indeed a very strong earthquake for the region occurred on February 14, 2008, SW offshore Methoni. Differential location of its hypocenter can be made by land stations, with respect to hypocenters of the pre-seismic period phase that had been accurately located with OBS nearby. This allows to constrain in retrospect the future hypocenter of the M=6.9 earthquake as a geographical gap in smaller earthquake occurrence in the months before. Preliminary results from the

  5. Molecular Evolution of the CYP2D Subfamily in Primates: Purifying Selection on Substrate Recognition Sites without the Frequent or Long-Tract Gene Conversion

    PubMed Central

    Yasukochi, Yoshiki; Satta, Yoko

    2015-01-01

    The human cytochrome P450 (CYP) 2D6 gene is a member of the CYP2D gene subfamily, along with the CYP2D7P and CYP2D8P pseudogenes. Although the CYP2D6 enzyme has been studied extensively because of its clinical importance, the evolution of the CYP2D subfamily has not yet been fully understood. Therefore, the goal of this study was to reveal the evolutionary process of the human drug metabolic system. Here, we investigate molecular evolution of the CYP2D subfamily in primates by comparing 14 CYP2D sequences from humans to New World monkey genomes. Window analysis and statistical tests revealed that entire genomic sequences of paralogous genes were extensively homogenized by gene conversion during molecular evolution of CYP2D genes in primates. A neighbor-joining tree based on genomic sequences at the nonsubstrate recognition sites showed that CYP2D6 and CYP2D8 genes were clustered together due to gene conversion. In contrast, a phylogenetic tree using amino acid sequences at substrate recognition sites did not cluster the CYP2D6 and CYP2D8 genes, suggesting that the functional constraint on substrate specificity is one of the causes for purifying selection at the substrate recognition sites. Our results suggest that the CYP2D gene subfamily in primates has evolved to maintain the regioselectivity for a substrate hydroxylation activity between individual enzymes, even though extensive gene conversion has occurred across CYP2D coding sequences. PMID:25808902

  6. Molecular evolution of the vertebrate TLR1 gene family - a complex history of gene duplication, gene conversion, positive selection and co-evolution

    PubMed Central

    2011-01-01

    Background The Toll-like receptors represent a large superfamily of type I transmembrane glycoproteins, some common to a wide range of species and others are more restricted in their distribution. Most members of the Toll-like receptor superfamily have few paralogues; the exception is the TLR1 gene family with four closely related genes in mammals TLR1, TLR2, TLR6 and TLR10, and four in birds TLR1A, TLR1B, TLR2A and TLR2B. These genes were previously thought to have arisen by a series of independent gene duplications. To understand the evolutionary pattern of the TLR1 gene family in vertebrates further, we cloned the sequences of TLR1A, TLR1B, TLR2A and TLR2B in duck and turkey, constructed phylogenetic trees, predicted codons under positive selection and identified co-evolutionary amino acid pairs within the TLR1 gene family using sequences from 4 birds, 28 mammals, an amphibian and a fish. Results This detailed phylogenetic analysis not only clarifies the gene gains and losses within the TLR1 gene family of birds and mammals, but also defines orthologues between these vertebrates. In mammals, we predict amino acid sites under positive selection in TLR1, TLR2 and TLR6 but not TLR10. We detect co-evolution between amino acid residues in TLR2 and the other members of this gene family predicted to maintain their ability to form functional heterodimers. In birds, we predict positive selection in the TLR2A and TLR2B genes at functionally significant amino acid residues. We demonstrate that the TLR1 gene family has mostly been subject to purifying selection but has also responded to directional selection at a few sites, possibly in response to pathogen challenge. Conclusions Our phylogenetic and structural analyses of the vertebrate TLR1 family have clarified their evolutionary origins and predict amino acid residues likely to be important in the host's defense against invading pathogens. PMID:21619680

  7. Gene array analysis of neural crest cells identifies transcription factors necessary for direct conversion of embryonic fibroblasts into neural crest cells

    PubMed Central

    Motohashi, Tsutomu; Watanabe, Natsuki; Nishioka, Masahiro; Nakatake, Yuhki; Yulan, Piao; Mochizuki, Hiromi; Kawamura, Yoshifumi; Ko, Minoru S. H.; Goshima, Naoki; Kunisada, Takahiro

    2016-01-01

    ABSTRACT Neural crest cells (NC cells) are multipotent cells that emerge from the edge of the neural folds and migrate throughout the developing embryo. Although the gene regulatory network for generation of NC cells has been elucidated in detail, it has not been revealed which of the factors in the network are pivotal to directing NC identity. In this study we analyzed the gene expression profile of a pure NC subpopulation isolated from Sox10-IRES-Venus mice and investigated whether these genes played a key role in the direct conversion of Sox10-IRES-Venus mouse embryonic fibroblasts (MEFs) into NC cells. The comparative molecular profiles of NC cells and neural tube cells in 9.5-day embryos revealed genes including transcription factors selectively expressed in developing trunk NC cells. Among 25 NC cell-specific transcription factor genes tested, SOX10 and SOX9 were capable of converting MEFs into SOX10-positive (SOX10+) cells. The SOX10+ cells were then shown to differentiate into neurons, glial cells, smooth muscle cells, adipocytes and osteoblasts. These SOX10+ cells also showed limited self-renewal ability, suggesting that SOX10 and SOX9 directly converted MEFs into NC cells. Conversely, the remaining transcription factors, including well-known NC cell specifiers, were unable to convert MEFs into SOX10+ NC cells. These results suggest that SOX10 and SOX9 are the key factors necessary for the direct conversion of MEFs into NC cells. PMID:26873953

  8. VH mutant rabbits lacking the VH1a2 gene develop a2+ B cells in the appendix by gene conversion-like alteration of a rearranged VH4 gene.

    PubMed

    Sehgal, D; Mage, R G; Schiaffella, E

    1998-02-01

    We investigated the molecular basis for the appearance of V(H)a2 allotype-bearing B cells in mutant Alicia rabbits. The mutation arose in an a2 rabbit; mutants exhibit altered expression of V(H) genes because of a small deletion encompassing V(H)1a2, the 3'-most gene in the V(H) locus. The V(H)1 gene is the major source of V(H)a allotype because this gene is preferentially rearranged in normal rabbits. In young homozygous ali/ali animals, the levels of a2 molecules found in the serum increase with age. In adult ali/ali rabbits, 20 to 50% of serum Igs and B cells bear a2 allotypic determinants. Previous studies suggested that positive selection results in expansion of a2 allotype-bearing B cells in the appendix of young mutant ali/ali rabbits. We separated appendix cells from a 6-wk-old Alicia rabbit by FACS based on the expression of surface IgM and a2 allotype. The VDJ portion of the expressed Ig mRNA was amplified from the IgM+ a2+ and IgM+ a2- populations by reverse transcriptase-PCR. The cDNAs from both populations were cloned and sequenced. Analysis of these sequences suggested that, in a2+ B cells, the first D proximal functional gene in Alicia rabbits, V(H)4a2, rearranged and was altered further by a gene conversion-like mechanism. Upstream V(H) genes were identified as potential gene sequence donors; V(H)9 was found to be the most frequently used gene donor. Among the a2- B cells, y33 was the most frequently rearranged gene.

  9. CYS3, a hotspot of meiotic recombination in Saccharomyces cerevisiae. Effects of heterozygosity and mismatch repair functions on gene conversion and recombination intermediates.

    PubMed Central

    Vedel, M; Nicolas, A

    1999-01-01

    We have examined meiotic recombination at the CYS3 locus. Genetic analysis indicates that CYS3 is a hotspot of meiotic gene conversion, with a putative 5'-3' polarity gradient of conversion frequencies. This gradient is relieved in the presence of msh2 and pms1 mutations, indicating an involvement of mismatch repair functions in meiotic recombination. To investigate the role of mismatch repair proteins in meiotic recombination, we performed a physical analysis of meiotic DNA in wild-type and msh2 pms1 strains in the presence or absence of allelic differences at CYS3. Neither the mutations in CYS3 nor the absence of mismatch repair functions affects the frequency and distribution of nearby recombination-initiating DNA double-strand breaks (DSBs). Processing of DSBs is also similar in msh2 pms1 and wild-type strains. We conclude that mismatch repair functions do not control the distribution of meiotic gene conversion events at the initiating steps. In the MSH2 PMS1 background, strains heteroallelic for frameshift mutations in CYS3 exhibit a frequency of gene conversion greater than that observed for either marker alone. Physical analysis revealed no modification in the formation of DSBs, suggesting that this marker effect results from subsequent processing events that are not yet understood. PMID:10101154

  10. DT40 knock-out and knock-in studies determine the regions necessary and sufficient for transcription and epigenetic conversion of the chicken Ig-β gene.

    PubMed

    Itaya, Kakeru; Chayahara, Kozue; Hirai, Takanori; Minbuta, Tomohiro; Uchikawa, Takafumi; Tanaka, Tomoki; Masaki, Shinya; Kuroda, Kosuke; Ono, Masao

    2011-03-01

    The chicken Ig-β locus is organized by three cell-type-specific genes and two ubiquitously expressed genes. B-cell-specific DNase I hypersensitive sites (DHS) in that locus, including three present inside the flanking gene, were grouped into six regions and deleted. The deletions decreased Ig-β mRNA content to <0.1% of that of normal DT40 cells and converted epigenetic parameters such as histone modifications, CG methylation and DNase I hypersensitivity into inactive states. Knocked-in DHS regions into knock-out cells reactivated both transcription of the Ig-β gene and epigenetic parameters. Thus, the collaboration of the scattered regulatory regions was essential and sufficient not only for B-cell-specific transcription of the Ig-β gene, but also for the conversion of epigenetic parameters. On the basis of the knock-in studies, we determined the regions involved in the conversion and maintenance of the epigenetic parameters. These scattered regulatory regions were limited in vicinity such as in an intron of the gene, in the intergenic regions and in the introns of a flanking gene.

  11. Inter- and intraspecies phylogenetic analyses reveal extensive X-Y gene conversion in the evolution of gametologous sequences of human sex chromosomes.

    PubMed

    Trombetta, Beniamino; Sellitto, Daniele; Scozzari, Rosaria; Cruciani, Fulvio

    2014-08-01

    It has long been believed that the male-specific region of the human Y chromosome (MSY) is genetically independent from the X chromosome. This idea has been recently dismissed due to the discovery that X-Y gametologous gene conversion may occur. However, the pervasiveness of this molecular process in the evolution of sex chromosomes has yet to be exhaustively analyzed. In this study, we explored how pervasive X-Y gene conversion has been during the evolution of the youngest stratum of the human sex chromosomes. By comparing about 0.5 Mb of human-chimpanzee gametologous sequences, we identified 19 regions in which extensive gene conversion has occurred. From our analysis, two major features of these emerged: 1) Several of them are evolutionarily conserved between the two species and 2) almost all of the 19 hotspots overlap with regions where X-Y crossing-over has been previously reported to be involved in sex reversal. Furthermore, in order to explore the dynamics of X-Y gametologous conversion in recent human evolution, we resequenced these 19 hotspots in 68 widely divergent Y haplogroups and used publicly available single nucleotide polymorphism data for the X chromosome. We found that at least ten hotspots are still active in humans. Hence, the results of the interspecific analysis are consistent with the hypothesis of widespread reticulate evolution within gametologous sequences in the differentiation of hominini sex chromosomes. In turn, intraspecific analysis demonstrates that X-Y gene conversion may modulate human sex-chromosome-sequence evolution to a greater extent than previously thought.

  12. A chloroplast DNA deletion located in RNA polymerase gene rpoC2 in CMS lines of sorghum.

    PubMed

    Chen, Z; Muthukrishnan, S; Liang, G H; Schertz, K F; Hart, G E

    1993-01-01

    Fertile lines of sorghum (Sorghum bicolor) were shown to differ from cytoplasmic male sterile (CMS) lines by the presence of a 3.8 kb HindIII chloroplast DNA fragment in the former and a smaller (3.7 kb) fragment in the latter. DNA/DNA hybridization studies showed that these two fragments are homologous. Fertile plants from S. versicolor, S. almum, S. halepense, and Sorghastrum nutans (Yellow Indiangrass) also have the 3.8 kb fragment, and CMS lines studied containing A1, A2 and A3 cytoplasms have the 3.7 kb fragment. The size difference between the two fragments was localized to a 1.0 kb SacI-HindIII fragment by restriction mapping. A 165 bp deletion, which is flanked by a 51 bp tandem repeat, was identified in the CMS lines by sequencing the clones. Comparison of the two sequences with those from maize, rice, tobacco, spinach, pea, and liverwort revealed that the deleted sequence is located in the middle of the RNA polymerase beta" subunit encoded by the gene rpoC2. The amino acid sequence deleted in the CMS lines is in a monocot-specific region which contains two protein motifs that are characteristic of several transcriptional activation factors, namely, a leucine zipper motif and an acidic domain capable of forming an amphipathic alpha-helix. Further studies designed to determine whether or not the deletion is involved in CMS of sorghum are underway.

  13. Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill-Robertson Interference, in an Avian System.

    PubMed

    Bolívar, Paulina; Mugal, Carina F; Nater, Alexander; Ellegren, Hans

    2016-01-01

    The ratio of nonsynonymous to synonymous substitution rates (ω) is often used to measure the strength of natural selection. However, ω may be influenced by linkage among different targets of selection, that is, Hill-Robertson interference (HRI), which reduces the efficacy of selection. Recombination modulates the extent of HRI but may also affect ω by means of GC-biased gene conversion (gBGC), a process leading to a preferential fixation of G:C ("strong," S) over A:T ("weak," W) alleles. As HRI and gBGC can have opposing effects on ω, it is essential to understand their relative impact to make proper inferences of ω. We used a model that separately estimated S-to-S, S-to-W, W-to-S, and W-to-W substitution rates in 8,423 avian genes in the Ficedula flycatcher lineage. We found that the W-to-S substitution rate was positively, and the S-to-W rate negatively, correlated with recombination rate, in accordance with gBGC but not predicted by HRI. The W-to-S rate further showed the strongest impact on both dN and dS. However, since the effects were stronger at 4-fold than at 0-fold degenerated sites, likely because the GC content of these sites is farther away from its equilibrium, ω slightly decreases with increasing recombination rate, which could falsely be interpreted as a consequence of HRI. We corroborated this hypothesis analytically and demonstrate that under particular conditions, ω can decrease with increasing recombination rate. Analyses of the site-frequency spectrum showed that W-to-S mutations were skewed toward high, and S-to-W mutations toward low, frequencies, consistent with a prevalent gBGC-driven fixation bias.

  14. The human intercellular adhesion molecule 3 (ICAM3) gene is located in the 19p13.2-p13.3 region, close to the ICAM1 gene

    SciTech Connect

    Bossy, D.; Simmons, D.L.; Mattei, M.G.

    1994-10-01

    The chromosomal location of the intercellular adhesion molecule 3 (ICAM3) gene, coding for a lymphocyte function-associated antigen (LFA)-1 counterreceptor and selectively expressed by human leukocytes, was analyzed by in situ hybridization with the cDNA coding sequence as a probe. This sequence mapped to the p13.2-p13.3 region of chromosome 19, close to the ICAM1 gene chromosomal location. 17 refs., 1 fig.

  15. Y chromosome haplotype diversity in Mongolic-speaking populations and gene conversion at the duplicated STR DYS385a,b in haplogroup C3-M407.

    PubMed

    Malyarchuk, Boris A; Derenko, Miroslava; Denisova, Galina; Woźniak, Marcin; Rogalla, Urszula; Dambueva, Irina; Grzybowski, Tomasz

    2016-06-01

    Y chromosome microsatellite (Y-STR) diversity has been studied in different Mongolic-speaking populations from South Siberia, Mongolia, North-East China and East Europe. The results obtained indicate that the Mongolic-speaking populations clustered into two groups, with one group including populations from eastern part of South Siberia and Central Asia (the Buryats, Barghuts and Khamnigans) and the other group including populations from western part of Central Asia and East Europe (the Mongols and Kalmyks). High frequency of haplogroup C3-M407 (>50%) is present in the Buryats, Barghuts and Khamnigans, whereas in the Mongols and Kalmyks its frequency is much lower. In addition, two allelic combinations in DYS385a,b loci of C3-M407 haplotypes have been observed: the combination 11,18 (as well as 11,17 and 11,19) is frequent in different Mongolic-speaking populations, but the 11,11 branch is present mainly in the Kalmyks and Mongols. Results of locus-specific sequencing suggest that the action of gene conversion is a more likely explanation for origin of homoallelic 11,11 combination. Moreover, analysis of median networks of Y-STR haplotypes demonstrates that at least two gene conversion events can be revealed-one of them has probably occurred among the Mongols, and the other event occurred in the Barghuts. These two events give an average gene conversion rate range of 0.24-7.1 × 10(-3) per generation. PMID:26911356

  16. Gene conversion is strongly induced in human cells by double-strand breaks and is modulated by the expression of BCL-x(L)

    NASA Technical Reports Server (NTRS)

    Wiese, Claudia; Pierce, Andrew J.; Gauny, Stacey S.; Jasin, Maria; Kronenberg, Amy; Chatterjee, A. (Principal Investigator)

    2002-01-01

    Homology-directed repair (HDR) of DNA double-strand breaks (DSBs) contributes to the maintenance of genomic stability in rodent cells, and it has been assumed that HDR is of similar importance in DSB repair in human cells. However, some outcomes of homologous recombination can be deleterious, suggesting that factors exist to regulate HDR. We demonstrated previously that overexpression of BCL-2 or BCL-x(L) enhanced the frequency of X-ray-induced TK1 mutations, including loss of heterozygosity events presumed to arise by mitotic recombination. The present study was designed to test whether HDR is a prominent DSB repair pathway in human cells and to determine whether ectopic expression of BCL-x(L) affects HDR. Using TK6-neo cells, we find that a single DSB in an integrated HDR reporter stimulates gene conversion 40-50-fold, demonstrating efficient DSB repair by gene conversion in human cells. Significantly, DSB-induced gene conversion events are 3-4-fold more frequent in TK6 cells that stably overexpress the antiapoptotic protein BCL-X(L). Thus, HDR plays an important role in maintaining genomic integrity in human cells, and ectopic expression of BCL-x(L) enhances HDR of DSBs. This is the first study to highlight a function for BCL-x(L) in modulating DSB repair in human cells.

  17. Molecular evidence that the genes for dioecism and monoecism in Spinacia oleracea L. are located at different loci in a chromosomal region.

    PubMed

    Yamamoto, K; Oda, Y; Haseda, A; Fujito, S; Mikami, T; Onodera, Y

    2014-03-01

    Spinach (Spinacia oleracea L.) is widely known to be dioecious. However, monoecious plants can also occur in this species. Sex expression in dioecious spinach plants is controlled by a single gene pair termed X and Y. Our previous study showed that a single, incompletely dominant gene, which controls the monoecious condition in spinach line 03-336, should be allelic or linked to X/Y. Here, we developed 19 AFLP markers closely linked to the monoecious gene. The AFLP markers were mapped to a 38.2-cM chromosomal region that included the monoecious gene, which is bracketed between flanking markers with a distance of 7.1 cM. The four AFLP markers developed in our studies were converted into sequence-characterized amplified region (SCAR) markers, which are linked to both the monoecious gene and Y and are common to both populations segregating for the genes. Linkage analysis using the SCAR markers suggested that the monoecious gene (M) and Y are located in different intervals, between different marker pairs. Analysis of populations segregating for both M and Y also directly demonstrates linkage of the genes at a distance of ~12 cM. The data presented in this study may be useful for breeding dioecious and highly male monoecious lines utilized as the pollen parents for hybrid seed production, as well as for studies of the evolutionary history of sexual systems in this species, and can provide a molecular basis for positional cloning of the sex-determining genes.

  18. A coniferyl aldehyde dehydrogenase gene from Pseudomonas sp. strain HR199 enhances the conversion of coniferyl aldehyde by Saccharomyces cerevisiae.

    PubMed

    Adeboye, Peter Temitope; Olsson, Lisbeth; Bettiga, Maurizio

    2016-07-01

    The conversion of coniferyl aldehyde to cinnamic acids by Saccharomyces cerevisiae under aerobic growth conditions was previously observed. Bacteria such as Pseudomonas have been shown to harbor specialized enzymes for converting coniferyl aldehyde but no comparable enzymes have been identified in S. cerevisiae. CALDH from Pseudomonas was expressed in S. cerevisiae. An acetaldehyde dehydrogenase (Ald5) was also hypothesized to be actively involved in the conversion of coniferyl aldehyde under aerobic growth conditions in S. cerevisiae. In a second S. cerevisiae strain, the acetaldehyde dehydrogenase (ALD5) was deleted. A prototrophic control strain was also engineered. The engineered S. cerevisiae strains were cultivated in the presence of 1.1mM coniferyl aldehyde under aerobic condition in bioreactors. The results confirmed that expression of CALDH increased endogenous conversion of coniferyl aldehyde in S. cerevisiae and ALD5 is actively involved with the conversion of coniferyl aldehyde in S. cerevisiae. PMID:27070284

  19. Development of a multiple bulked segregant analysis (MBSA) method used to locate a new stem rust resistance gene (Sr54) in the winter wheat cultivar Norin 40.

    PubMed

    Ghazvini, Habibollah; Hiebert, Colin W; Thomas, Julian B; Fetch, Thomas

    2013-02-01

    An important aspect of studying putative new genes in wheat is determining their position on the wheat genetic map. The primary difficulty in mapping genes is determining which chromosome carries the gene of interest. Several approaches have been developed to address this problem, each with advantages and disadvantages. Here we describe a new approach called multiple bulked segregant analysis (MBSA). A set of 423 simple sequence repeat (SSR) markers were selected based on profile simplicity, frequency of polymorphism, and distribution across the wheat genome. SSR primers were preloaded in 384-well PCR plates with each primer occupying 16 wells. In practice, 14 wells are reserved for "mini-bulks" that are equivalent to four gametes (e.g. two F(2) individuals) comprised of individuals from a segregated population that have a known homozygous genotype for the gene of interest. The remaining two wells are reserved for the parents of the population. Each well containing a mini-bulk can have one of three allele compositions for each SSR: only the allele from one parent, only the allele from the other parent, or both alleles. Simulation experiments were performed to determine the pattern of mini-bulk allele composition that would indicate putative linkage between the SSR in question and the gene of interest. As a test case, MBSA was employed to locate an unidentified stem rust resistance (Sr) gene in the winter wheat cultivar Norin 40. A doubled haploid (DH) population (n = 267) was produced from hybrids of the cross LMPG-6S/Norin 40. The DH population segregated for a single gene (χ (1:1) (2) = 0.093, p = 0.76) for resistance to Puccinia graminis f.sp. tritici race LCBN. Four resistant DH lines were included in each of the 14 mini-bulks for screening. The Sr gene was successfully located to the long arm of chromosome 2D using MBSA. Further mapping confirmed the chromosome location and revealed that the Sr gene was located in a linkage block that may represent an alien

  20. The structure of the human intron-containing S8 ribosomal protein gene and determination of its chromosomal location at 1p32-p32. 4

    SciTech Connect

    Davies, B.; Fried, M. )

    1993-01-01

    The intron-containing gene encoding human ribosomal protein SS (RPS8) has been cloned and characterized, and its chromosomal position determined. Using a PCR-based cloning strategy, we have isolated the intron-containing gene in the presence of its many processed pseudogenes and determined the DNA sequence of the entire gene and its upstream and downstream flanking regions. The human RPS8 gene is 3161 bp in length and comprises six exons. Despite lacking a consensus TATA box, primer extension analysis indicates that the start of transcription is precisely located at a C residue within an 11-bp oligopyrimidine tract. The first exon, which contains the ATG start codon, is just 27 bp in length. The DNA sequence 5[prime] to the RPS8 gene and within the first exon and intron shows several features of a CpG island. A combination of Southern blotting, PCR, and fluorescence in situ hybridization analyses has enabled the chromosomal location of the human RPSS gene to be determined as lp32-p34.1. 51 refs., 5 figs.

  1. Nucleotide sequencing analysis of the swine 433-kb genomic segment located between the non-classical and classical SLA class I gene clusters.

    PubMed

    Shigenari, Atsuko; Ando, Asako; Renard, Christine; Chardon, Patrick; Shiina, Takashi; Kulski, Jerzy K; Yasue, Hiroshi; Inoko, Hidetoshi

    2004-01-01

    Genome analysis of the swine leukocyte antigen ( SLA) region is needed to obtain information on the MHC genomic sequence similarities and differences between the swine and human, given the possible use of swine organs for xenotransplantation. Here, the genomic sequences of a 433-kb segment located between the non-classical and classical SLA class I gene clusters were determined and analyzed for gene organization and contents of repetitive sequences. The genomic organization and diversity of this swine non-class I gene region was compared with the orthologous region of the human leukocyte antigen ( HLA) complex. The length of the fully sequenced SLA genomic segment was 433 kb compared with 595 kb in the corresponding HLA class I region. This 162-kb difference in size between the swine and human genomic segments can be explained by indel activity, and the greater variety and density of repetitive sequences within the human MHC. Twenty-one swine genes with strong sequence similarity to the corresponding human genes were identified, with the gene order from the centromere to telomere of HCR - SPR1 - SEEK1 - CDSN - STG - DPCR1 - KIAA1885 - TFIIH - DDR - IER3 - FLOT1 - TUBB - KIAA0170 - NRM - KIAA1949 - DDX16 - FLJ13158 - MRPS18B - FB19 - ABCFI - CAT56. The human SEEK1 and DPCR1 genes are pseudogenes in swine. We conclude that the swine non-class I gene region that we have sequenced is highly conserved and therefore homologous to the corresponding region located between the HLA-C and HLA-E genes in the human.

  2. The human zinc-finger protein-7 gene is located 90 kb 3' of MYC and is not expressed in Burkitt lymphoma cell lines.

    PubMed

    Feduchi, E; Gallego, M I; Lazo, P A

    1994-09-15

    The zinc-finger gene-7 (ZNF7) was located 90 kb 3' of MYC on human chromosome 8 band q24 by pulsed-field gel electrophoresis (PFGE). This position lies between the MLV14 and BVR1 loci, 2 variant translocation breakpoints in Burkitt lymphomas. The structure of the ZNF7 gene was not altered by translocations in Burkitt-lymphoma cell lines as shown by its germline-restriction map configuration. The chromosomal region surrounding the ZNF7 gene was extensively methylated. The ZNF7 gene was not expressed in 19 BL cell lines. Expression was detected only in the BL41 and BL47 cell lines and in the SW756 cervical-carcinoma cell line. The RNA in each was of a different size. We postulate that the lack of ZNF7 expression in Burkitt lymphomas might contribute to the tumor phenotype.

  3. The New Macrolide-Lincosamide-Streptogramin B Resistance Gene erm(45) Is Located within a Genomic Island in Staphylococcus fleurettii

    PubMed Central

    Wipf, Juliette R. K.; Schwendener, Sybille; Nielsen, Jesper Boye; Westh, Henrik

    2015-01-01

    Genome alignment of a macrolide, lincosamide, and streptogramin B (MLSB)-resistant Staphylococcus fleurettii strain with an MLSB-susceptible S. fleurettii strain revealed a novel 11,513-bp genomic island carrying the new erythromycin resistance methylase gene erm(45). This gene was shown to confer inducible MLSB resistance when cloned into Staphylococcus aureus. The erm(45)-containing island was integrated into the housekeeping gene guaA in S. fleurettii and was able to form a circular intermediate but was not transmissible to S. aureus. PMID:25779586

  4. The genes for secretion and maturation of lactococcins are located on the chromosome of Lactococcus lactis IL1403.

    PubMed Central

    Venema, K; Dost, M H; Beun, P A; Haandrikman, A J; Venema, G; Kok, J

    1996-01-01

    Southern hybridization and PCR analysis were used to show that Lactococcus lactis IL1403, a plasmid-free strain that does not produce bacteriocin, contains genes on its chromosome that are highly homologous to lcnC and lcnD and encode the lactococcin secretion and maturation system. The lcnC and lcnD homologs on the chromosome of IL1403 were interrupted independently by Campbell-type integrations. Both insertion mutants were unable to secrete active lactococcin. Part of the chromosomal lcnC gene was cloned and sequenced. Only a few nucleotide substitutions occurred, compared with the plasmid-encoded lcnC gene, and these did not lead to changes in the deduced amino acid sequence. No genes homologous to those for lactococcin A, B, or M could be detected in IL1403, and the strain does not produce bacteriocin activity. PMID:8633867

  5. Refining the mouse chromosomal location of Cdm, the major gene associated with susceptibility to cadmium-induced testicular necrosis.

    PubMed

    Dalton, T P; Miller, M L; Wu, X; Menon, A; Cianciolo, E; McKinnon, R A; Smith, P W; Robinson, L J; Nebert, D W

    2000-03-01

    Cadmium (Cd++) is a widespread environmental pollutant and classifed as an IARC 'Category I' human carcinogen. Cd++ can also cause severe renal toxicity and may be involved clinically in cardiovascular disease and osteoporosis. Genetic differences in sensitivity to cadmium toxicity have been noted in humans, whereas, among inbred mouse strains, unequivocal genetic data exist. Resistance to cadmium-induced testicular damage was reported in 1973 to be associated with a single major recessive gene, named Cdm, which has now been localized to mouse chromosome (Chr) 3. Using polymorphic microsatellite markers and semiquantitative histological parameters, we have corroborated the original 1973 data concerning mendelian inheritance and have further refined the region containing the Cdm gene from more than 24 cM to 0.64 cM (estimated 40-80 genes). We phenotyped 26 recombinant inbred lines generated from C57BL/6J (B6, resistant) and DBA/2J (D2, sensitive) inbred mice, and determined that the Cdm gene maps between microsatellite markers D3Mit110 and D3Mit255. Although toxicity to numerous heavy metals is well known, virtually no molecular mechanisms have yet been uncovered either in humans or laboratory animals. Identification and characterization of the mouse Cdm gene should enhance our understanding of heavy metal toxicity by identifying and characterizing, for the first time, a major mammalian gene responsible for susceptibility to diseases caused by heavy metal toxicity. PMID:10762002

  6. Genetic analysis of RpL38 and RpL5, two minute genes located in the centric heterochromatin of chromosome 2 of Drosophila melanogaster.

    PubMed

    Marygold, Steven J; Coelho, Carmen M A; Leevers, Sally J

    2005-02-01

    The Minute mutations of Drosophila melanogaster are thought to disrupt genes that encode ribosomal proteins (RPs) and thus impair ribosome function and protein synthesis. However, relatively few Minutes have been tied to distinct RP genes and more Minute loci are likely to be discovered. We have identified point mutations in RpL38 and RpL5 in a screen for factors limiting for growth of the D. melanogaster wing. Here, we present the first genetic characterization of these loci. RpL38 is located in the centric heterochromatin of chromosome arm 2R and is identical to a previously identified Minute, M(2)41A, and also l(2)41Af. RpL5 is located in the 2L centric heterochromatin and defines a novel Minute gene. Both genes are haplo-insufficient, as heterozygous mutations cause the classic Minute phenotypes of small bristles and delayed development. Surprisingly, we find that RpL38(-)/+ and RpL5(-)/+ adult flies have abnormally large wings as a result of increased cell size, emphasizing the importance of translational regulation in the control of growth. Taken together, our data provide new molecular and genetic information on two previously uncharacterized Minute/RP genes, the heterochromatic regions in which they reside, and the role of their protein products in the control of organ growth.

  7. Molecular markers located on the DGAT1, CAST, and LEPR genes and their associations with milk production and fertility traits in Holstein cattle.

    PubMed

    Hill, R; Canal, A; Bondioli, K; Morell, R; Garcia, M D

    2016-03-31

    The objective of the present study was to investigate single nucleotide polymorphisms (SNPs) located in three candidate genes previously reported to have effects on fertility and milk production traits in a population of 123 Holstein cows. The milk production traits evaluated included lifetime averages of milk yield, protein concentration, and fat concentration. Fertility traits evaluated included lifetime averages of services per conception and days-open. Candidate genes included those encoding diacylglycerol acyltransferase (DGAT1), leptin receptor (LEPR), and calpastatin (CAST). A total of 60 SNPs were selected (20 per gene) at equidistant locations on each candidate gene to identify potential linkage with causative mutations. Four SNPs were identified as being significantly associated with the evaluated fertility traits. Specifically, SNPs rs109663724 and rs137673193 were significantly associated with lifetime average days-open, while rs109663724 and rs135560721 were significantly associated with lifetime average number of services per conception. Five SNP (rs109663724, rs132699547, rs135423283, rs135576599, and rs13675432) were significantly associated with lifetime averages of milk protein concentration and milk fat concentration, with only one SNP (rs109663724) being significantly associated with the average lifetime milk yield. Although multiple SNPs were identified in the current study as being significantly associated with milk production and fertility traits, it is essential that these SNPs are validated in larger populations, under more diverse environments, and that additional SNPs and candidate genes are evaluated prior to their implementation into selection strategies.

  8. A Solanum lycopersicum × Solanum pimpinellifolium Linkage Map of Tomato Displaying Genomic Locations of R-Genes, RGAs, and Candidate Resistance/Defense-Response ESTs

    PubMed Central

    Sharma, Arun; Zhang, Liping; Niño-Liu, David; Ashrafi, Hamid; Foolad, Majid R.

    2008-01-01

    We have identified an accession (LA2093) within the tomato wild species Solanum pimpinellifolium with many desirable characteristics, including biotic and abiotic stress tolerance and good fruit quality. To utilize the full genetic potential of LA2093 in tomato breeding, we have developed a linkage map based on an F2 population of a cross between LA2093 and a tomato breeding line, using 115 RFLP, 94 EST, and 41 RGA markers. The map spanned 1002.4 cM of the 12 tomato chromosomes with an average marker distance of 4.0 cM. The length of the map and linear order of the markers were in good agreement with the published maps of tomato. The ESTs were chosen based on their sequence similarities with known resistance or defense-response genes, signal-transduction factors, transcriptional regulators, and genes encoding pathogenesis-related proteins. Locations of several ESTs and RGAs coincided with locations of several known tomato resistance genes and quantitative resistance loci (QRLs), suggesting that candidate-gene approach may be effective in identifying and mapping new R genes. This map will be useful for marker-assisted exploitation of desirable traits in LA2093 and other S. pimpinellifolium accessions, and possibly for utilization of genetic variation within S. lycopersicum. PMID:19223983

  9. HLXB9 Gene Expression, and Nuclear Location during In Vitro Neuronal Differentiation in the SK-N-BE Neuroblastoma Cell Line

    PubMed Central

    Leotta, Claudia Giovanna; Federico, Concetta; Brundo, Maria Violetta; Tosi, Sabrina; Saccone, Salvatore

    2014-01-01

    Different parts of the genome occupy specific compartments of the cell nucleus based on the gene content and the transcriptional activity. An example of this is the altered nuclear positioning of the HLXB9 gene in leukaemia cells observed in association with its over-expression. This phenomenon was attributed to the presence of a chromosomal translocation with breakpoint proximal to the HLXB9 gene. Before becoming an interesting gene in cancer biology, HLXB9 was studied as a developmental gene. This homeobox gene is also known as MNX1 (motor neuron and pancreas homeobox 1) and it is relevant for both motor neuronal and pancreatic beta cells development. A spectrum of mutations in this gene are causative of sacral agenesis and more broadly, of what is known as the Currarino Syndrome, a constitutional autosomal dominant disorder. Experimental work on animal models has shown that HLXB9 has an essential role in motor neuronal differentiation. Here we present data to show that, upon treatment with retinoic acid, the HLXB9 gene becomes over-expressed during the early stages of neuronal differentiation and that this corresponds to a reposition of the gene in the nucleus. More precisely, we used the SK-N-BE human neuroblastoma cell line as an in vitro model and we demonstrated a transient transcription of HLXB9 at the 4th and 5th days of differentiation that corresponded to the presence, predominantly in the cell nuclei, of the encoded protein HB9. The nuclear positioning of the HLXB9 gene was monitored at different stages: a peripheral location was noted in the proliferating cells whereas a more internal position was noted during differentiation, that is while HLXB9 was transcriptionally active. Our findings suggest that HLXB9 can be considered a marker of early neuronal differentiation, possibly involving chromatin remodeling pathways. PMID:25136833

  10. HLXB9 gene expression, and nuclear location during in vitro neuronal differentiation in the SK-N-BE neuroblastoma cell line.

    PubMed

    Leotta, Claudia Giovanna; Federico, Concetta; Brundo, Maria Violetta; Tosi, Sabrina; Saccone, Salvatore

    2014-01-01

    Different parts of the genome occupy specific compartments of the cell nucleus based on the gene content and the transcriptional activity. An example of this is the altered nuclear positioning of the HLXB9 gene in leukaemia cells observed in association with its over-expression. This phenomenon was attributed to the presence of a chromosomal translocation with breakpoint proximal to the HLXB9 gene. Before becoming an interesting gene in cancer biology, HLXB9 was studied as a developmental gene. This homeobox gene is also known as MNX1 (motor neuron and pancreas homeobox 1) and it is relevant for both motor neuronal and pancreatic beta cells development. A spectrum of mutations in this gene are causative of sacral agenesis and more broadly, of what is known as the Currarino Syndrome, a constitutional autosomal dominant disorder. Experimental work on animal models has shown that HLXB9 has an essential role in motor neuronal differentiation. Here we present data to show that, upon treatment with retinoic acid, the HLXB9 gene becomes over-expressed during the early stages of neuronal differentiation and that this corresponds to a reposition of the gene in the nucleus. More precisely, we used the SK-N-BE human neuroblastoma cell line as an in vitro model and we demonstrated a transient transcription of HLXB9 at the 4th and 5th days of differentiation that corresponded to the presence, predominantly in the cell nuclei, of the encoded protein HB9. The nuclear positioning of the HLXB9 gene was monitored at different stages: a peripheral location was noted in the proliferating cells whereas a more internal position was noted during differentiation, that is while HLXB9 was transcriptionally active. Our findings suggest that HLXB9 can be considered a marker of early neuronal differentiation, possibly involving chromatin remodeling pathways. PMID:25136833

  11. Conversational Dominance.

    ERIC Educational Resources Information Center

    Esau, Helmut; Poth, Annette

    Details of conversational behavior can often not be interpreted until the social interaction, including the rights and obligations of the participants, their intent, the topic, etc., has been defined. This paper presents a model of conversation in which the conversational image a person presents in a given conversational situation is a function of…

  12. Detection of new HLA-DPB1 alleles generated by interallelic gene conversion using PCR amplification of DPB1 second exon sequences from sperm

    SciTech Connect

    Erlich, H.; Zangenberg, G.; Bugawan, T.

    1994-09-01

    The rate at which allelic diversity at the HLA class I and class II loci evolves has been the subject of considerable controversy as have the mechanisms which generate new alleles. The patchwork pattern of polymorphism, particularly within the second exon of the HLA-DPB1 locus where the polymorphic sequence motifs are localized to 6 discrete regions, is consistent with the hypothesis that much of the allelic sequence variation may have been generated by segmental exchange (gene conversion). To measure the rate of new DPB1 variant generation, we have developed a strategy in which DPB1 second exon sequences are amplified from pools of FACS-sorted sperm (n=50) from a heterozygous sperm donor. Pools of sperm from these heterozygous individuals are amplified with an allele-specific primer for one allele and analyzed with sequence-specific oligonucleotide probes (SSOP) complementary to the other allele. This screening procedure, which is capable of detecting a single variant molecule in a pool of parental alleles, allows the identification of new variants that have been generated by recombination and/or gene conversion between the two parental alleles. To control for potential PCR artifacts, the same screening procedure was carried out with mixtures of sperm from DPB1 *0301/*0301 and DPB1 *0401/ 0401 individuals. Pools containing putative new variants DPB1 alleles were analyzed further by cloning into M13 and sequencing the M13 clones. Our current estimate is that about 1/10,000 sperm from these heterozygous individuals represents a new DPB1 allele generated by micro-gene conversion within the second exon.

  13. Gene conversion is strongly induced in human cells by double-strand breaks and is modulated by the expression of BCL-XL

    SciTech Connect

    Wiese, Claudia; Pierce, Andrew J.; Gauny, Stacey S.; Jasin, Maria; Kronenberg, Amy

    2001-09-25

    Homology-directed repair (HDR) of DNA double-strand breaks (DSBs) is a well-established mechanism that contributes to the maintenance of genomic stability in rodent cells, and it has been assumed that HDR is of similar importance in the repair of DSBs in human cells. However, in addition to promoting genomic stability, some outcomes of homologous recombination can be deleterious, suggesting that factors exist to regulate HDR. We previously demonstrated that overexpression of BCL-2 or BCL-xL enhanced the frequency of x-ray-induced mutations involving the TK1 locus, including loss of heterozygosity (LOH) events presumed to arise by mitotic recombination. The present study was designed to test whether HDR is a prominent DSB repair pathway in human cells, and to directly determine whether ectopic expression of BCL-xL affects HDR. We used the B-lymphoblastoid cell line TK6, which expresses wild-type TP53 and resembles normal lymphocytes in undergoing apoptosis following! genotoxic stress. U sing isogenic derivatives of TK6 cells (TK6-neo, TK6-bcl-xL), we find that a DSB in an integrated HDR reporter stimulates gene conversion 40-50-fold in TK6-neo cells, demonstrating that a DSB can be efficiently repaired by gene conversion in human cells. Significantly, DSB-induced gene conversion events are 3- to 4-fold more frequent in BCL-xL overexpressing cells. The results demonstrate that HDR plays an important role in maintaining genomic integrity in human cells and that ectopic expression of BCL-xL enhances HDR of DSBs. To our knowledge, this is the first study to highlight a function for BCL-xL in modulating DSB repair in human cells.

  14. FKHL15, a new human member of the forkhead gene family located on chromosome 9q22

    SciTech Connect

    Chadwick, B.P.; Obermayr, F.; Frischauf, A.M.

    1997-05-01

    FKHL15 was isolated from a cDNA library enriched for transcripts from 9q22. Isolation and sequencing of a 3.5-kb cDNA clone identified a putative 376-amino-acid protein with greater than 80% homology over a 100-amino-acid stretch to the forkhead DNA-binding domain. The FKHL15 gene contains a region rich in alanine residues, frequently associated with transcriptional repression. The forkhead genes are believed to play important roles in development and differentiation in many different organisms and have also been implicated in the development of some tumors. The map position of FKHL15 on 9q22 places the gene within the candidate regions for the cancer predisposition syndrome multiple self-healing squamous epitheliomata and the degenerative neurological disorder hereditary sensory neuropathy type 1. This is a region frequently lost in squamous cell cancer. 47 refs., 5 figs.

  15. Chromatin studies reveal that an ERE is located far upstream of a vitellogenin gene and that a distal tissue-specific hypersensitive site is conserved for two coordinately regulated vitellogenin genes.

    PubMed Central

    Burch, J B; Fischer, A H

    1990-01-01

    Estrogen induces the expression of three vitellogenin genes in chicken hepatocytes. To survey the vitellogenin III (VTGIII) gene region for possible distal regulatory sequences, we identified tissue-specific hypersensitive (HS) sites within a 45 kb chromatin region spanning this gene. Five constitutive HS sites were found to mark the VTGIII gene region in hormone-naive hepatocytes. Strikingly, the constitutive HS site located 5.5 kb upstream of the VTGIII gene and a previously identified HS site located within the coordinately regulated VTGII gene mapped to nearly identical copies of a 72 bp sequence. Moreover, it would appear that there has been evolutionary pressure to retain specifically this 72 bp of VTGII-like sequence near the VTGIII gene subsequent to the VTGIII and VTGII genes becoming unlinked approximately 16 Myr ago. Two additional sets of HS sites were induced in the VTGIII gene region in response to estrogen. One set mapped immediately upstream of the gene in the vicinity of what we show to be a functional estrogen response element (ERE). The other induced HS site mapped 7.5 kb upstream of the gene. This far-upstream region was sequenced and was found to contain two imperfect ERE consensus sequences spaced 88 bp apart. In transient expression assays neither of these individual imperfect ERE sequences was functional, but a fragment spanning both sequences behaved as a strong ERE. In contrast to this synergism between imperfect ERE sequences, the presence of an NF-1 binding site 23 bp away from the more distal imperfect ERE sequence was not sufficient to render the latter a functional ERE in our assays. Images PMID:2377458

  16. Molecular evidence that the genes for dioecism and monoecism in Spinacia oleracea L. are located at different loci in a chromosomal region

    PubMed Central

    Yamamoto, K; Oda, Y; Haseda, A; Fujito, S; Mikami, T; Onodera, Y

    2014-01-01

    Spinach (Spinacia oleracea L.) is widely known to be dioecious. However, monoecious plants can also occur in this species. Sex expression in dioecious spinach plants is controlled by a single gene pair termed X and Y. Our previous study showed that a single, incompletely dominant gene, which controls the monoecious condition in spinach line 03–336, should be allelic or linked to X/Y. Here, we developed 19 AFLP markers closely linked to the monoecious gene. The AFLP markers were mapped to a 38.2-cM chromosomal region that included the monoecious gene, which is bracketed between flanking markers with a distance of 7.1 cM. The four AFLP markers developed in our studies were converted into sequence-characterized amplified region (SCAR) markers, which are linked to both the monoecious gene and Y and are common to both populations segregating for the genes. Linkage analysis using the SCAR markers suggested that the monoecious gene (M) and Y are located in different intervals, between different marker pairs. Analysis of populations segregating for both M and Y also directly demonstrates linkage of the genes at a distance of ∼12 cM. The data presented in this study may be useful for breeding dioecious and highly male monoecious lines utilized as the pollen parents for hybrid seed production, as well as for studies of the evolutionary history of sexual systems in this species, and can provide a molecular basis for positional cloning of the sex-determining genes. PMID:24169648

  17. Gene encoding the collagen type I and thrombospondin receptor CD36 is located on chromosome 7q11. 2

    SciTech Connect

    Fernandez-Ruiz, E.; Armesilla, A.L.; Sanchez-Madrid, F.; Vega, M.A. )

    1993-09-01

    The human CD36 is a member of a gene family of structurally related glycoproteins and functions as a receptor for collagen type I and thrombospondin. CD36 also binds to red blood cells infected with the human malaria parasite Plasmodium falciparum. In the present study, the CD36 gene was assigned to chromosome 7 by using the polymerase chain reaction with DNA from human-hamster somatic cell hybrids. Furthermore, the use of a CD36 genomic probe has allowed the localization of the CD36 locus to the 7q11.2 band by fluorescence in situ hybridization coupled with GTG-banding. 14 refs., 2 figs.

  18. Genetic polymorphisms located in genes related to immune and inflammatory processes are associated with end-stage renal disease: a preliminary study

    PubMed Central

    2012-01-01

    Background Chronic kidney disease progression has been linked to pro-inflammatory cytokines and markers of inflammation. These markers are also elevated in end-stage renal disease (ESRD), which constitutes a serious public health problem. Objective To investigate whether single nucleotide polymorphisms (SNPs) located in genes related to immune and inflammatory processes, could be associated with ESRD development. Design and methods A retrospective case-control study was carried out on 276 patients with ESRD and 288 control subjects. Forty-eight SNPs were genotyped via SNPlex platform. Logistic regression was used to assess the relationship between each sigle polymorphism and the development of ESRD. Results Four polymorphisms showed association with ESRD: rs1801275 in the interleukin 4 receptor (IL4R) gene (OR: 0.66 (95%CI = 0.46-0.95); p = 0.025; overdominant model), rs4586 in chemokine (C-C motif) ligand 2 (CCL2) gene (OR: 0.70 (95%CI = 0.54-0.90); p = 0.005; additive model), rs301640 located in an intergenic binding site for signal transducer and activator of transcription 4 (STAT4) (OR: 1.82 (95%CI = 1.17-2.83); p = 0.006; additive model) and rs7830 in the nitric oxide synthase 3 (NOS3) gene (OR: 1.31 (95%CI = 1.01-1.71); p = 0.043; additive model). After adjusting for multiple testing, results lost significance. Conclusion Our preliminary data suggest that four genetic polymorphisms located in genes related to inflammation and immune processes could help to predict the risk of developing ESRD. PMID:22817530

  19. Locating a modifier gene of Ovum mutant through crosses between DDK and C57BL/6J inbred strains in mice.

    PubMed

    Tan, Jing; Song, Gen Di; Song, Jia Sheng; Ren, Shi Hao; Li, Chun Li; Zheng, Zhen Yu; Zhao, Wei Dong

    2016-06-01

    A striking infertile phenotype has been discovered in the DDK strain of mouse. The DDK females are usually infertile when crossed with males of other inbred strains, whereas DDK males exhibit normal fertility in reciprocal crosses. This phenomenon is caused by mutation in the ovum (Om) locus on chromosome 11 and known as the DDK syndrome. Previously, some research groups reported that the embryonic mortality deviated from the semilethal rate in backcrosses between heterozygous (Om/+) females and males of other strains. This embryonic mortality exhibited an aggravated trend with increasing background genes of other strains. These results indicated that some modifier genes of Om were present in other strains. In the present study, a population of N₂2 (Om/+) females from the backcrosses between C57BL/6J (B6) and F₁ (B6♀ × DDK♂) was used to map potential modifier genes of Om. Quantitative trait locus showed that a major locus, namely Amom1 (aggravate modifier gene of Om 1), was located at the middle part of chromosome 9 in mice. The Amom1 could increase the expressivity of Om gene, thereby aggravating embryonic lethality when heterozygous (Om/+) females mated with males of B6 strain. Further, the 1.5 LOD-drop analysis indicated that the confidence interval was between 37.54 and 44.46 cM, ~6.92 cM. Amom1 is the first modifier gene of Om in the B6 background.

  20. Locating a modifier gene of Ovum mutant through crosses between DDK and C57BL/6J inbred strains in mice.

    PubMed

    Tan, Jing; Song, Gen Di; Song, Jia Sheng; Ren, Shi Hao; Li, Chun Li; Zheng, Zhen Yu; Zhao, Wei Dong

    2016-06-01

    A striking infertile phenotype has been discovered in the DDK strain of mouse. The DDK females are usually infertile when crossed with males of other inbred strains, whereas DDK males exhibit normal fertility in reciprocal crosses. This phenomenon is caused by mutation in the ovum (Om) locus on chromosome 11 and known as the DDK syndrome. Previously, some research groups reported that the embryonic mortality deviated from the semilethal rate in backcrosses between heterozygous (Om/+) females and males of other strains. This embryonic mortality exhibited an aggravated trend with increasing background genes of other strains. These results indicated that some modifier genes of Om were present in other strains. In the present study, a population of N₂2 (Om/+) females from the backcrosses between C57BL/6J (B6) and F₁ (B6♀ × DDK♂) was used to map potential modifier genes of Om. Quantitative trait locus showed that a major locus, namely Amom1 (aggravate modifier gene of Om 1), was located at the middle part of chromosome 9 in mice. The Amom1 could increase the expressivity of Om gene, thereby aggravating embryonic lethality when heterozygous (Om/+) females mated with males of B6 strain. Further, the 1.5 LOD-drop analysis indicated that the confidence interval was between 37.54 and 44.46 cM, ~6.92 cM. Amom1 is the first modifier gene of Om in the B6 background. PMID:27350672

  1. Autosomal location of genes from the conserved mammalian X in the platypus (Ornithorhynchus anatinus): implications for mammalian sex chromosome evolution.

    PubMed

    Waters, Paul D; Delbridge, Margaret L; Deakin, Janine E; El-Mogharbel, Nisrine; Kirby, Patrick J; Carvalho-Silva, Denise R; Graves, Jennifer A Marshall

    2005-01-01

    Mammalian sex chromosomes evolved from an ancient autosomal pair. Mapping of human X- and Y-borne genes in distantly related mammals and non-mammalian vertebrates has proved valuable to help deduce the evolution of this unique part of the genome. The platypus, a monotreme mammal distantly related to eutherians and marsupials, has an extraordinary sex chromosome system comprising five X and five Y chromosomes that form a translocation chain at male meiosis. The largest X chromosome (X1), which lies at one end of the chain, has considerable homology to the human X. Using comparative mapping and the emerging chicken database, we demonstrate that part of the therian X chromosome, previously thought to be conserved across all mammals, was lost from the platypus X1 to an autosome. This region included genes flanking the XIST locus, and also genes with Y-linked homologues that are important to male reproduction in therians. Since these genes lie on the X in marsupials and eutherians, and also on the homologous region of chicken chromosome 4, this represents a loss from the monotreme X rather than an additional evolutionary stratum of the human X. PMID:15973504

  2. Collection of mitochondrial cytochrome oxidase I gene sequences from Rhipicephalus ticks from various geographic locations around the world

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Determining the origin of the cattle tick, Rhipicephalus microplus, will be helpful to the effort to find biological control agents. Molecular phylogenetics can assist in this determination. Thus, we sequenced and assembled partial gene sequences from the mitochondrial cytochrome oxidase I coding r...

  3. The human gene (CSNK2A1) coding for the casein kinase II subunit [alpha] is located on chromosome 20 and contains tandemly arranged Alu repeats

    SciTech Connect

    Wirkner, U.; Lichter, P.; Pyerin, W. ); Voss, H.; Ansorge, W. )

    1994-01-15

    The authors have isolated and characterized an 18.9-kb genomic clone representing a central portion of the human casein kinase II (CKII) subunit [alpha] gene (CSNK2A1). Using the whole clone as a probe, the gene was localized on chromosome 20p13. The clone contains eight exons whose sequences comprise bases 102 to 824 of the coding region of the human CKII[alpha]. The exon/intron splice junctions conform to the gt/ag rule. Three of the nine introns are located at positions corresponding to those in the CKII[alpha] gene of the nematode Caenorhabditis elegans. The introns contain eight complete and eight incomplete Alu repeats. Some of the Alu sequences are arranged in tandems of two or three, which seem to originate from insertions of younger Alu sequences into the poly(A) region of previously integrated Alu sequences, as indicated by flanking direct repeats. 50 refs., 5 figs., 1 tab.

  4. Genetic homogeneity among Listeria monocytogenes strains from infected patients and meat products from two geographic locations determined by phenotyping, ribotyping and PCR analysis of virulence genes.

    PubMed

    Jaradat, Z W; Schutze, G E; Bhunia, A K

    2002-06-01

    Thirty Listeria monocytogenes isolates from human patients and foods originated from two different geographic locations without any epidemiological relations were analyzed for their genotypic and phenotypic virulence gene expressions and genetic relatedness. All strains contained virulence genes, inlA, inlB, actA, hlyA, plcA and plcB, with expected product size in PCR assay except for the actA gene. Some strains produced actA gene product of 268 and others 385 bp. Phenotypically, all were hemolytic but showed variable expressions of phospholipase activity. Ribotyping classified isolates into 12 different groups based on the similarity to DuPont Identification numbers (DID), which consisted primarily of clinical or food isolates or both. Cluster analysis also indicated possible existence of clones of L. monocytogenes that are found in food or human hosts or are evenly distributed between these two. Two isolates (F1 from food and CHL1250 from patient) had unique ribotype patterns that were not previously reported in the RiboPrinter database. This study indicates distribution of diverse L. monocytogenes strains in clinical and food environments. The isolates showed 92-99% genetic homogeneity, in spite of their origins from two different geographic locations and environments.

  5. Opossum alcohol dehydrogenases: Sequences, structures, phylogeny and evolution: evidence for the tandem location of ADH genes on opossum chromosome 5.

    PubMed

    Holmes, Roger S

    2009-03-16

    BLAT (BLAST-Like Alignment Tool) analyses and interrogations of the recently published opossum genome were undertaken using previously reported rat ADH amino acid sequences. Evidence is presented for six opossum ADH genes localized on chromosome 5 and organized in a comparable ADH gene cluster to that reported for human and rat ADH genes. The predicted amino acid sequences and secondary structures for the opossum ADH subunits and the intron-exon boundaries for opossum ADH genes showed a high degree of similarity with other mammalian ADHs, and four opossum ADH classes were identified, namely ADH1, ADH3, ADH6 and ADH4 (for which three genes were observed: ADH4A, ADH4B and ADH4C). Previous biochemical analyses of opossum ADHs have reported the tissue distribution and properties for these enzymes: ADH1, the major liver enzyme; ADH3, widely distributed in opossum tissues with similar kinetic properties to mammalian class 3 ADHs; and ADH4, for which several forms were localized in extrahepatic tissues, especially in the digestive system and in the eye. These ADHs are likely to perform similar functions to those reported for other mammalian ADHs in the metabolism of ingested and endogenous alcohols and aldehydes. Phylogenetic analyses examined opossum, human, rat, chicken and cod ADHs, and supported the proposed designation of opossum ADHs as class I (ADH1), class III (ADH3), class IV (ADH4A, ADH4B and ADH4C) and class VI (ADH6). Percentage substitution rates were examined for ADHs during vertebrate evolution which indicated that ADH3 is evolving at a much slower rate to that of the other ADH classes.

  6. Independent stratum formation on the avian sex chromosomes reveals inter-chromosomal gene conversion and predominance of purifying selection on the W chromosome.

    PubMed

    Wright, Alison E; Harrison, Peter W; Montgomery, Stephen H; Pointer, Marie A; Mank, Judith E

    2014-11-01

    We used a comparative approach spanning three species and 90 million years to study the evolutionary history of the avian sex chromosomes. Using whole transcriptomes, we assembled the largest cross-species dataset of W-linked coding content to date. Our results show that recombination suppression in large portions of the avian sex chromosomes has evolved independently, and that long-term sex chromosome divergence is consistent with repeated and independent inversions spreading progressively to restrict recombination. In contrast, over short-term periods we observe heterogeneous and locus-specific divergence. We also uncover four instances of gene conversion between both highly diverged and recently evolved gametologs, suggesting a complex mosaic of recombination suppression across the sex chromosomes. Lastly, evidence from 16 gametologs reveal that the W chromosome is evolving with a significant contribution of purifying selection, consistent with previous findings that W-linked genes play an important role in encoding sex-specific fitness.

  7. Divergent location of ribosomal genes in chromosomes of fish thorny-headed worms, Pomphorhynchus laevis and Pomphorhynchus tereticollis (Acanthocephala).

    PubMed

    Bombarová, Marta; Marec, Frantisek; Nguyen, Petr; Spakulová, Marta

    2007-10-01

    We studied distribution of ribosomal DNA (rDNA) sequences along with chromosomal location of the nucleolar organizer regions (NORs) in males of two fish parasites, Pomphorhynchus laevis and Pomphorhynchus tereticollis (Acanthocephala). Fluorescence in situ hybridization with 18S rDNA probe identified two clusters of rDNA in each species, but revealed a remarkable difference in their location on chromosomes. In P. laevis, the rDNA-FISH signals were found in long arms of the first chromosome pair and in short arms of the second pair. Whereas in P. tereticollis, rDNA clusters were located in long arms of both the first and second chromosome pairs. The divergent location of rDNA clusters in the chromosome No. 2 supports current classification of P. tereticollis, previously considered a synonym of P. laevis, as a separate species. A possible scenario of the second chromosome rearrangement during karyotype evolution of the two species involves two successive pericentric inversions. In both species, one or two prominent nucleoli were apparent within interphase nuclei stained with either silver nitrate or a fluorescent dye YOYO-1. However, a single large nucleolus was observed in early stages of mitosis and meiosis I regardless the number of rDNA clusters. Nevertheless, two bivalents with silver-stained NORs in diakinesis and two silver-stained sites in early prophase II nuclei indicated that all NORs are active. This means that each Pomphorhynchus NOR generates a nucleolus, but the resulting nucleoli have a strong tendency to associate in a large body.

  8. Analysis of the promoter region of a cardiac specific phospholipase A{sub 2} gene located at 1p35

    SciTech Connect

    Winstead, M.V.; Chen, J.; Tischfield, J.A.

    1994-09-01

    Phospholipases may play an important role in the pathology of tissue damage and in membrane remodeling. We have previously shown that the Group II PLA{sub 2} gene and two PLA{sub 2}-like gene fragments map to 1p35. We have since shown that at least one of the fragments is part of a cardiac-specific PLA{sub 2} gene. Thus the identification and characterization of the regulatory regions of this new phospholipase A{sub 2} (PLA{sub 2}) may be important for understanding the regulation of this gene under normal and pathologic conditions. HPLA2-10, mainly expressed in heart, is a low molecular weight, Ca{sup 2+}-dependent PLA{sub 2} that we have classified as a new group (Group III) based on structural considerations. The 5{prime} regulatory region of HPLA2-10 was isolated from a human genomic DNA bacteriophage library and cloned into pUC19. Computer analysis of the region`s DNA sequence indicates the presence of multiple transcription factor binding sites. A comparison between the human promoter region and the promoter region of the rat homologue, RPLA2-10, indicates that at least two putative transcription factor binding sites are conserved between the two species. These include a CCAAT box and an AGTCCT hexanucleotide, which has been implicated as a binding site for the glucocorticoid receptor. DNA footprint analysis is being performed to determine whether or not these putative regions are sites of protein binding. Also, a proposed view of the evolution of the distinct groups of low molecular weight PLA{sub 2}s will be presented.

  9. Occupancy of RNA Polymerase II Phosphorylated on Serine 5 (RNAP S5P) and RNAP S2P on Varicella-Zoster Virus Genes 9, 51, and 66 Is Independent of Transcript Abundance and Polymerase Location within the Gene

    PubMed Central

    Henderson, Heather H.; Timberlake, Kensey B.; Austin, Zoe A.; Badani, Hussain; Sanford, Bridget; Tremblay, Keriann; Baird, Nicholas L.; Jones, Kenneth; Rovnak, Joel; Frietze, Seth; Gilden, Don

    2015-01-01

    ABSTRACT Regulation of gene transcription in varicella-zoster virus (VZV), a ubiquitous human neurotropic alphaherpesvirus, requires coordinated binding of multiple host and virus proteins onto specific regions of the virus genome. Chromatin immunoprecipitation (ChIP) is widely used to determine the location of specific proteins along a genomic region. Since the size range of sheared virus DNA fragments governs the limit of accurate protein localization, particularly for compact herpesvirus genomes, we used a quantitative PCR (qPCR)-based assay to determine the efficiency of VZV DNA shearing before ChIP, after which the assay was used to determine the relationship between transcript abundance and the occupancy of phosphorylated RNA polymerase II (RNAP) on the gene promoter, body, and terminus of VZV genes 9, 51, and 66. The abundance of VZV gene 9, 51, and 66 transcripts in VZV-infected human fetal lung fibroblasts was determined by reverse transcription-linked quantitative PCR. Our results showed that the C-terminal domain of RNAP is hyperphosphorylated at serine 5 (S5P) on VZV genes 9, 51, and 66 independently of transcript abundance and the location within the virus gene at both 1 and 3 days postinfection (dpi). In contrast, phosphorylated serine 2 (S2P)-modified RNAP was not detected at any virus gene location at 3 dpi and was detected at levels only slightly above background levels at 1 dpi. IMPORTANCE Regulation of herpesvirus gene transcription is an elaborate choreography between proteins and DNA that is revealed by chromatin immunoprecipitation (ChIP). We used a quantitative PCR-based assay to determine fragment size after DNA shearing, a critical parameter in ChIP assays, and exposed a basic difference in the mechanism of transcription between mammalian cells and VZV. We found that hyperphosphorylation at serine 5 of the C-terminal domain of RNAP along the lengths of VZV genes (the promoter, body, and transcription termination site) was independent of m

  10. The Z-DNA motif d(TG)30 promotes reception of information during gene conversion events while stimulating homologous recombination in human cells in culture.

    PubMed

    Wahls, W P; Wallace, L J; Moore, P D

    1990-02-01

    Tracts of the alternating dinucleotide polydeoxythymidylic-guanylic [d(TG)].polydeoxyadenylic-cytidylic acid [d(AC)], present throughout the human genome, are capable of readily forming left-handed Z-DNA in vitro. We have analyzed the effects of the Z-DNA motif d(TG)30 upon homologous recombination between two nonreplicating plasmid substrates cotransfected into human cells in culture. In this study, the sequence d(TG)30 is shown to stimulate homologous recombination up to 20-fold. Enhancement is specific to the Z-DNA motif; a control DNA fragment of similar size does not alter the recombination frequency. The stimulation of recombination is observed at a distance (237 to 1,269 base pairs away from the Z-DNA motif) and involves both gene conversion and reciprocal exchange events. Maximum stimulation is observed when the sequence is present in both substrates, but it is capable of stimulating when present in only one substrate. Analysis of recombination products indicates that the Z-DNA motif increases the frequency and alters the distribution of multiple, unselected recombination events. Specifically designed crosses indicate that the substrate containing the Z-DNA motif preferentially acts as the recipient of genetic information during gene conversion events. Models describing how left-handed Z-DNA sequences might promote the initiation of homologous recombination are presented. PMID:2405255

  11. The zinc finger domain of Tzfp binds to the tbs motif located at the upstream flanking region of the Aie1 (aurora-C) kinase gene.

    PubMed

    Tang, C J; Chuang, C K; Hu, H M; Tang, T K

    2001-06-01

    Our previous studies showed that Aie1 (aurora-C), is a novel testis kinase belonging to the aurora kinase family (). In this report, we describe a testis zinc finger protein (Tzfp) that binds to the upstream flanking sequence of the Aie1 gene. The mouse Tzfp gene, mapped to chromosome 7 B2-B3, encodes a 465-amino acid transcription factor containing a conserved N-terminal BTB/POZ domain and three C-terminal PLZF-like C(2)H(2) zinc fingers. The zinc finger domain of Tzfp binds to the TGTACAGTGT motif (Tzfp binding site, termed tbs) located at the upstream flanking sequence of the Aie1 gene by gel mobility shift, DNase I footprinting, and competition analyses. When the C-terminal zinc fingers of Tzfp were fused to the transactivation domain of VP16, the chimera activated transcription of a reporter construct containing multiple copies of the tbs. In contrast, the same chimera did not activate the reporter gene when an essential nucleotide fifth C was mutated to A at the tbs. Furthermore, we showed that the N-terminal BTB/POZ domain of TZFP has a repressor activity. Taken together, our results indicate that Tzfp recognizes a sequence-specific motif (tbs) and may play a role in the regulation of the genes carrying the tbs.

  12. Novel application of pH-sensitive firefly luciferases as dual reporter genes for simultaneous ratiometric analysis of intracellular pH and gene expression/location.

    PubMed

    Gabriel, Gabriele V M; Viviani, Vadim R

    2014-12-01

    Firefly luciferases are widely used as bioluminescent reporter genes for bioimaging and biosensors. Aiming at simultaneous analyses of different gene expression and cellular events, luciferases and GFPs that exhibit distinct bioluminescence and fluorescence colors have been coupled with each promoter, making dual and multicolor reporter systems. Despite their wide use, firefly luciferase bioluminescence spectra are pH-sensitive, resulting in a typical large red shift at acidic pH, a side-effect that may affect some bioanalytical purposes. Although some intracellular pH-indicators employ dual color and fluorescent dyes, none has been considered to benefit from the characteristic spectral pH-sensitivity of firefly luciferases to monitor intracellular pH-associated stress, an important indicator of cell homeostasis. Here we demonstrate a linear relationship between the ratio of intensities in the green and red regions of the bioluminescence spectra and pH using firefly luciferases cloned in our laboratory (Macrolampis sp2 and Cratomorphus distinctus), allowing estimation of E. coli intracellular pH, thus providing a new analytical method for ratiometric intracellular pH-sensing. This is the first dual reporter system that employs a single luciferase gene to simultaneously monitor intracellular pH using spectral changes, and gene expression and/or ATP concentration using the bioluminescence intensity, showing great potential for real time bioanalysis of intracellular processes associated with metabolic changes such as apoptosis, cell death, inflammation and tissue acidification, among the other physiological changes.

  13. Adipose and muscle tissue gene expression of two genes (NCAPG and LCORL) located in a chromosomal region associated with cattle feed intake and gain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A region on bovine chromosome 6 has been implicated in cattle birth weight, growth, and length. Non-SMC conodensin I complex subunit G (NCAPG) and ligand dependent nuclear receptor corepressor-like protein (LCORL) are positional candidate genes within this region. Previously identified genetic mark...

  14. A downstream regulatory element located within the coding sequence mediates autoregulated expression of the yeast fatty acid synthase gene FAS2 by the FAS1 gene product.

    PubMed

    Wenz, P; Schwank, S; Hoja, U; Schüller, H J

    2001-11-15

    The fatty acid synthase genes FAS1 and FAS2 of the yeast Saccharomyces cerevisiae are transcriptionally co-regulated by general transcription factors (such as Reb1, Rap1 and Abf1) and by the phospholipid-specific heterodimeric activator Ino2/Ino4, acting via their corresponding upstream binding sites. Here we provide evidence for a positive autoregulatory influence of FAS1 on FAS2 expression. Even with a constant FAS2 copy number, a 10-fold increase of FAS2 transcript amount was observed in the presence of FAS1 in multi-copy, compared to a fas1 null mutant. Surprisingly, the first 66 nt of the FAS2 coding region turned out as necessary and sufficient for FAS1-dependent gene expression. FAS2-lacZ fusion constructs deleted for this region showed high reporter gene expression even in the absence of FAS1, arguing for a negatively-acting downstream repression site (DRS) responsible for FAS1-dependent expression of FAS2. Our data suggest that the FAS1 gene product, in addition to its catalytic function, is also required for the coordinate biosynthetic control of the yeast FAS complex. An excess of uncomplexed Fas1 may be responsible for the deactivation of an FAS2-specific repressor, acting via the DRS. PMID:11713312

  15. Determination of n+1 gamete transmission rate of trisomics and location of gene controlling 2n gamete formation in Chinese cabbage (Brassica rapa).

    PubMed

    Zhang, Cheng-He; Li, Xiao-Feng; Shen, Shu-Xing; Yuan, He; Xuan, Shu-Xin

    2009-01-01

    A set of trisomics of Chinese cabbage was used for determining the n+1 gamete transmission rate and locating the gene controlling 2n gamete formation on the corresponding chromosome. The results showed that the transmission rates of extra chromosomes in different trisomics varied from 0% to 15.38% by male gametes and from 0% to 17.39% by female gametes. Of the nine F(2) populations derived from the hybridizations between each trisomic and Bp058 (2n gamete material), only Tri-4xBp058 showed that the segregation ratio of plants without 2n gamete formation to plants with 2n gamete formation was 10.38:1, which fitted the expected segregation ratio of the trisomics (AAa) based on the 7.37% of n+1 gamete transmission through female and 5.88% through male. In other populations the segregation ratios varied from 2.48:1 to 3.72:1, which fitted the expected 3:1 segregation ratio of the bisomics (Aa). These results suggested that the gene controlling 2n gamete formation in Chinese cabbage Bp058 was located on chromosome 4. Further trisomic analysis based on the chromosome segregation and the incomplete stochastic chromatid segregation indicated that the gene locus was tightly linked to the centromere.

  16. Plasminogen activator inhibitor type 1 gene is located at region q21. 3-q22 of chromosome 7 and genetically linked with cystic fibrosis

    SciTech Connect

    Klinger, K.W.; Winqvist, R.; Riccio, A.; Andreasen, P.A.; Sartorio, R.; Nielsen, L.S.; Stuart, N.; Stanislovitis, P.; Watkins, P.; Douglas, R.

    1987-12-01

    The regional chromosomal location of the human gene for plasminogen activator inhibitor type 1 (PAI1) was determined by three independent methods of gene mapping. PAI1 was localized first to 7cen-q32 and then to 7q21.3-q22 by Southern blot hybridization analysis of a panel of human and mouse somatic cell hybrids with a PAI1 cDNA probe and in situ hybridization, respectively. The authors frequent HindIII restriction fragment length polymorphism (RFLP) of the PAI1 gene with an information content of 0.369. In family studies using this polymorphism, genetic linkage was found between PAI1 and the loci for erythropoietin (EPO), paraoxonase (PON), the met protooncogene (MET), and cystic fibrosis (CF), all previously assigned to the middle part of the long arm of chromosome 7. The linkage with EPO was closest with an estimated genetic distance of 3 centimorgans, whereas that to CF was 20 centimorgans. A three-point genetic linkage analysis and data from previous studies showed that the most likely order of these loci is EPO, PAI1, PON, (MET, CF), with PAI1 being located centromeric to CF. The PAI1 RFLP may prove to be valuable in ordering genetic markers in the CF-linkage group and may also be valuable in genetic analysis of plasminogen activation-related diseases, such as certain thromboembolic disorders and cancer.

  17. A New Aspergillus fumigatus Typing Method Based on Hypervariable Tandem Repeats Located within Exons of Surface Protein Coding Genes (TRESP)

    PubMed Central

    Garcia-Rubio, Rocio; Gil, Horacio; Monteiro, Maria Candida; Pelaez, Teresa; Mellado, Emilia

    2016-01-01

    Aspergillus fumigatus is a saprotrophic mold fungus ubiquitously found in the environment and is the most common species causing invasive aspergillosis in immunocompromised individuals. For A. fumigatus genotyping, the short tandem repeat method (STRAf) is widely accepted as the first choice. However, difficulties associated with PCR product size and required technology have encouraged the development of novel typing techniques. In this study, a new genotyping method based on hypervariable tandem repeats within exons of surface protein coding genes (TRESP) was designed. A. fumigatus isolates were characterized by PCR amplification and sequencing with a panel of three TRESP encoding genes: cell surface protein A; MP-2 antigenic galactomannan protein; and hypothetical protein with a CFEM domain. The allele sequence repeats of each of the three targets were combined to assign a specific genotype. For the evaluation of this method, 126 unrelated A. fumigatus strains were analyzed and 96 different genotypes were identified, showing a high level of discrimination [Simpson’s index of diversity (D) 0.994]. In addition, 49 azole resistant strains were analyzed identifying 26 genotypes and showing a lower D value (0.890) among them. This value could indicate that these resistant strains are closely related and share a common origin, although more studies are needed to confirm this hypothesis. In summary, a novel genotyping method for A. fumigatus has been developed which is reproducible, easy to perform, highly discriminatory and could be especially useful for studying outbreaks. PMID:27701437

  18. Polymorphism and chromosomal location of the MC4R (melanocortin-4 receptor) gene in the dog and red fox.

    PubMed

    Skorczyk, Anna; Stachowiak, Monika; Szczerbal, Izabela; Klukowska-Roetzler, Jolanta; Schelling, Claude; Dolf, Gaudenz; Switonski, Marek

    2007-05-01

    The melanocortin-4 receptor (MC4R) is expressed in the hypothalamus and regulates energy intake and body weight. In silico screening of the canine chromosome 1 sequence and a comparison with the porcine MC4R sequence by BLAST were performed. The nucleotide sequence of the whole coding region and 3'- and 5'-flanking regions of the dog (1214 bp) and red fox (1177 bp) MC4R gene was established and high conservation of the nucleotide sequences was revealed (99%). Five sets of PCR primers were designed and a search for polymorphism was performed by the SSCP technique in a group of 31 dogs representing nineteen breeds and 35 farm red foxes. Sequencing of DNA fragments, representing the identified SSCP patterns, revealed three single nucleotide polymorphisms (including a missense one) in dogs and four silent SNPs in red foxes. An average SNP frequency was approx. 1/400 bp in the dog and 1/300 bp in the red fox. We mapped the MC4R gene by FISH to the canine chromosome 1 (CFA1q1.1) and to the red fox chromosome 5 (VVU5p1.2).

  19. A phosphorylation site located in the NH2-terminal domain of c-Myc increases transactivation of gene expression.

    PubMed

    Seth, A; Alvarez, E; Gupta, S; Davis, R J

    1991-12-15

    The c-myc gene encodes a sequence-specific DNA-binding protein (c-Myc) that forms leucine zipper complexes and can act as a transcription factor. Growth factor stimulation of cells causes the phosphorylation of the c-Myc transcriptional activation domain at Ser62 within a proline-rich region that is highly conserved among members of the Myc family (Alvarez, E., Northwood, I.C., Gonzalez, F. A., Latour, D. A., Seth, A., Abate, C., Curran, T., and Davis, R. J. (1991) J. Biol. Chem. 266, 15277-15285). This phosphorylation site is a substrate for growth factor-regulated MAP kinases and for the cell cycle-dependent protein kinase p34cdc2. We report that serum treatment of cells results in a marked increase in the transactivation of gene expression mediated by the c-Myc transcriptional activation domain. A point mutation at the site of growth factor-stimulated phosphorylation (Ser62) decreases the serum induction of transactivation. These data indicate that the c-Myc transcriptional activation domain may be a direct target of signal transduction pathways. PMID:1748630

  20. Adipose and Muscle Tissue Gene Expression of Two Genes (NCAPG and LCORL) Located in a Chromosomal Region Associated with Cattle Feed Intake and Gain

    PubMed Central

    Lindholm-Perry, Amanda K.; Kuehn, Larry A.; Oliver, William T.; Sexten, Andrea K.; Miles, Jeremy R.; Rempel, Lea A.; Cushman, Robert A.; Freetly, Harvey C.

    2013-01-01

    A region on bovine chromosome 6 has been implicated in cattle birth weight, growth, and length. Non-SMC conodensin I complex subunit G (NCAPG) and ligand dependent nuclear receptor corepressor-like protein (LCORL) are positional candidate genes within this region. Previously identified genetic markers in both genes were associated with average daily gain (ADG) and average daily feed intake (ADFI) in a crossbred population of beef steers. These markers were also associated with hot carcass weight, ribeye area and adjusted fat thickness suggesting that they may have a role in lean muscle growth and/or fat deposition. The purpose of this study was to determine whether the transcript abundance of either of these genes in cattle adipose and muscle tissue was associated with variation in feed intake and average daily gain phenotypes. Transcript abundance for NCAPG and LCORL in adipose and muscle tissue was measured in heifers (adipose only), cows and steers using real-time polymerase chain reaction. In the adipose tissue from cows and heifers, a negative correlation between LCORL transcript abundance and ADFI were detected (P = 0.05). In the muscle tissue from cows, transcript abundance of NCAPG was associated with ADG (r = 0.26; P = 0.009). A positive correlation between LCORL transcript abundance from muscle tissue of steers and ADFI was detected (P = 0.04). LCORL protein levels in the muscle of steers were investigated and were associated with ADFI (P = 0.01). These data support our earlier genetic associations with ADFI and ADG within this region and represent the potential for biological activity of these genes in the muscle and adipose tissues of beef cattle; however, they also suggest that sex, age and/or nutrition-specific interactions may affect the expression of NCAPG and LCORL in these tissues. PMID:24278337

  1. Adipose and muscle tissue gene expression of two genes (NCAPG and LCORL) located in a chromosomal region associated with cattle feed intake and gain.

    PubMed

    Lindholm-Perry, Amanda K; Kuehn, Larry A; Oliver, William T; Sexten, Andrea K; Miles, Jeremy R; Rempel, Lea A; Cushman, Robert A; Freetly, Harvey C

    2013-01-01

    A region on bovine chromosome 6 has been implicated in cattle birth weight, growth, and length. Non-SMC conodensin I complex subunit G (NCAPG) and ligand dependent nuclear receptor corepressor-like protein (LCORL) are positional candidate genes within this region. Previously identified genetic markers in both genes were associated with average daily gain (ADG) and average daily feed intake (ADFI) in a crossbred population of beef steers. These markers were also associated with hot carcass weight, ribeye area and adjusted fat thickness suggesting that they may have a role in lean muscle growth and/or fat deposition. The purpose of this study was to determine whether the transcript abundance of either of these genes in cattle adipose and muscle tissue was associated with variation in feed intake and average daily gain phenotypes. Transcript abundance for NCAPG and LCORL in adipose and muscle tissue was measured in heifers (adipose only), cows and steers using real-time polymerase chain reaction. In the adipose tissue from cows and heifers, a negative correlation between LCORL transcript abundance and ADFI were detected (P = 0.05). In the muscle tissue from cows, transcript abundance of NCAPG was associated with ADG (r = 0.26; P = 0.009). A positive correlation between LCORL transcript abundance from muscle tissue of steers and ADFI was detected (P = 0.04). LCORL protein levels in the muscle of steers were investigated and were associated with ADFI (P = 0.01). These data support our earlier genetic associations with ADFI and ADG within this region and represent the potential for biological activity of these genes in the muscle and adipose tissues of beef cattle; however, they also suggest that sex, age and/or nutrition-specific interactions may affect the expression of NCAPG and LCORL in these tissues.

  2. Functional dissection of an enhancer-like element located within the second intron of the human U2AF1L4 gene.

    PubMed

    Didych, D A; Smirnov, N A; Kotova, E S; Akopov, S B; Nikolaev, L G; Sverdlov, E D

    2011-08-01

    A detailed functional and evolutionary analysis of an enhancer element of the human genome (enhancer 12) located in the second intron of the U2AF1L4 gene, which we identified earlier, is presented. Overlapping fragments of the studied genome region were analyzed for enhancer activity, and the site responsible for the activity of this element was identified using transient transfections of HeLa cells. Comparison of the enhancer 12 sequence with orthologous sequences from seven primate species revealed the existence of evolutionarily conserved sequences within this element. One of the identified conservative regions is likely responsible for the enhancer activity and is able to specifically interact in vitro with proteins of HeLa cell nuclear extract. The ability of orthologous primate sequences to compete with enhancer 12 for binding with HeLa cell nuclear extract proteins and to enhance the activity of the reporter gene in transient transfection of HeLa cells is demonstrated. PMID:22022969

  3. Association study of genes associated to asthma in a specific environment, in an asthma familial collection located in a rural area influenced by different industries.

    PubMed

    Morin, Andréanne; Brook, Jeffrey R; Duchaine, Caroline; Laprise, Catherine

    2012-08-01

    Eight candidate genes selected in this study were previously associated with gene-environment interactions in asthma in an urban area. These genes were analyzed in a familial collection from a founder and remote population (Saguenay-Lac-Saint-Jean; SLSJ) located in an area with low air levels of ozone but with localized areas of relatively high air pollutant levels, such as sulphur dioxide, when compared to many urban areas. Polymorphisms (SNPs) were extracted from the genome-wide association study (GWAS) performed on the SLSJ familial collection. A transmission disequilibrium test (TDT) was performed using the entire family sample (1,428 individuals in 254 nuclear families). Stratification according to the proximity of aluminium, pulp and paper industries was also analyzed. Two genes were associated with asthma in the entire sample before correction (CAT and NQO1) and one was associated after correction for multiple analyses (CAT). Two genes were associated when subjects were stratified according to the proximity of aluminium industries (CAT and NQO1) and one according to the proximity of pulp and paper industries (GSTP1). However, none of them resisted correction for multiple analyses. Given that the spatial pattern of environmental exposures can be complex and inadequately represented by a few stationary monitors and that exposures can also come from sources other than the standard outdoor air pollution (e.g., indoor air, occupation, residential wood smoke), a new approach and new tools are required to measure specific and individual pollutant exposures in order to estimate the real impact of gene-environment interactions on respiratory health. PMID:23066387

  4. Transcriptional and preliminary functional analysis of the six genes located in divergence of phoR/phoP in Streptomyces lividans.

    PubMed

    Darbon, Emmanuelle; Martel, Cécile; Nowacka, Aleksandra; Pegot, Sylvine; Moreau, Patrice L; Virolle, Marie-Joëlle

    2012-09-01

    Streptomyces lividans senses and adjusts to a situation of Pi limitation via the expression of genes of the pho regulon controlled by the two-component system PhoR/PhoP. Interestingly, an in silico analysis of the proteins encoded by the six genes located in divergence of phoR/phoP revealed that the latter bear features often found in metalloproteins involved in the sensing/resistance to oxidative stress. We determined whether genes of this region were belonging to the pho regulon and whether the encoded proteins do play a role in the resistance to oxidative stress. For this purpose, a transcriptional analysis of these genes was carried out on the carbon and nitrogen rich medium R2YE and on a minimal medium (MM). On R2YE, the expression of the genes phoU to sco4225 was much higher than on MM and constant throughout growth. On this medium, the expression of phoU was totally PhoP-dependent whereas the expression of sco4227 and sco4226 was partially PhoP-dependent, taking place from the phoU promoter region. In contrast, on MM, the expression of sco4227 and sco4226 was PhoP-independent whereas that of phoU remained PhoP-dependent and showed, as phoR/phoP, a peak of expression at 48 h. sco4225, sco4224, and sco4223 were transcribed from their own promoter independently of PhoP in both media. The mutants of five out of six genes of the region (Δsco4226 mutant could not be obtained) grew poorly in the presence of exogenous oxidants, suggesting a role of the encoded proteins in the resistance to oxidative stress, especially on the rich medium R2YE.

  5. The gene for the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase is located close to the gene for the large subunit in the cyanobacterium Anacystis nidulans 6301.

    PubMed Central

    Shinozaki, K; Sugiura, M

    1983-01-01

    The gene for the small subunit (SS) of ribulose-1,5-bisphosphate carboxylase/oxygenase from a cyanobacterium, Anacystis nidulans 6301, has been cloned and subjected to sequence analysis. The SS coding region is located close to and downstream from the large subunit (LS) coding region on the same DNA strand. The spacer region between the LS and the SS coding regions contains 93 base pairs (bp), and has no promoter-like sequences. The coding region of A. nidulans SS gene contains 333 bp (111 codons). The deduced amino acid sequence of the A. nidulans SS protein shows 40% homology with those of higher plants. Images PMID:6415615

  6. Investigation on the formation, conversion and bioactivity of a G-quadruplex structure in the PALB2 gene.

    PubMed

    Li, Fangyuan; Zhou, Jiang; Xu, Ming; Yuan, Gu

    2016-02-01

    There is a putative G-quadruplex sequence (PGS), 5'-G3ACAG4TTG2TG4 TAG4CAG2TTG3-3', in the promoter region of the PALB2 gene. According to the importance of PALB2 in the process of homologous recombination and breast cancer, and the hypothesis that G-quadruplexes might play a role in transcriptional regulation, we evaluated the formation of G-quadruplex from this complex sequence, as well as its structural information and importance for PALB2 transcription. The G-rich sequence was suggested to form G-quadruplex structure in the NH4OAc solution with 3NH4+ ion by ESI-MS spectrometry, and it was testified in the KCl solution by CD experiments which showed the typical 290 nm band and a high melting temperature. We also classified the guanines in the sequence into four types and demonstrated their roles in the formation of the G-quadruplex structure. In addition, a luciferase assay proved that the formation of the G-quadruplex down-regulate the transcription of the gene. Therefore, our findings provided a foundation for the formation and bioactivity of the G-quadruplex in the promoter region of PALB2 gene and a novel insight for understanding PALB2 gene regulation.

  7. Investigation on the formation, conversion and bioactivity of a G-quadruplex structure in the PALB2 gene.

    PubMed

    Li, Fangyuan; Zhou, Jiang; Xu, Ming; Yuan, Gu

    2016-02-01

    There is a putative G-quadruplex sequence (PGS), 5'-G3ACAG4TTG2TG4 TAG4CAG2TTG3-3', in the promoter region of the PALB2 gene. According to the importance of PALB2 in the process of homologous recombination and breast cancer, and the hypothesis that G-quadruplexes might play a role in transcriptional regulation, we evaluated the formation of G-quadruplex from this complex sequence, as well as its structural information and importance for PALB2 transcription. The G-rich sequence was suggested to form G-quadruplex structure in the NH4OAc solution with 3NH4+ ion by ESI-MS spectrometry, and it was testified in the KCl solution by CD experiments which showed the typical 290 nm band and a high melting temperature. We also classified the guanines in the sequence into four types and demonstrated their roles in the formation of the G-quadruplex structure. In addition, a luciferase assay proved that the formation of the G-quadruplex down-regulate the transcription of the gene. Therefore, our findings provided a foundation for the formation and bioactivity of the G-quadruplex in the promoter region of PALB2 gene and a novel insight for understanding PALB2 gene regulation. PMID:26645143

  8. Establishment of Cloned Anaplasma phagocytophilum and Analysis of p44 Gene Conversion within an Infected Horse and Infected SCID Mice

    PubMed Central

    Lin, Quan; Rikihisa, Yasuko

    2005-01-01

    Diverse p44 alleles at the p44 expression locus (p44Es) encoding surface-exposed major membrane proteins, P44s, of Anaplasma phagocytophilum were hypothesized to be garnered by recombination to enact antigenic variation. However, this hypothesis has not been proven so far, due to inability to clone this obligate intragranulocytic rickettsia. To define the p44E recombination, we developed a novel method to clone A. phagocytophilum. This isogenic cloned population containing a defined p44E was used to infect a naive horse and severe combined immunodeficiency (SCID) mice. During a 58-day infection period in the blood of the horse, p44E conversion was evident in a total of 11 new p44Es, 48% (115/242) of the sequenced p44E population. During a 50-day infection period in the blood of SCID mice, p44E conversion was manifested in a total of 13 new p44Es, 42% (192/460) of the p44E population. Thus, similar levels of p44E convertants were detected in either the presence or absence of an acquired immune system, suggesting that T- and B-cell immune pressure was not essential for recombination and/or selection of the p44E variants. Analysis of sequentially changed p44Es revealed that the entire central hypervariable region of donor p44 pseudogenes or of donor full-length p44s replaced the same region of the resident p44E as a cassette. Putative recombination points were detected within p44 conserved regions flanking the central hypervariable region by the TOPALi analysis. Our results unambiguously demonstrated p44E recombination. The cloning method developed would facilitate precise analysis of the recombination process and the extent of diversity which the recombination creates in the antigenic repertoire. PMID:16041027

  9. Direct conversion of mouse embryonic fibroblasts into functional keratinocytes through transient expression of pluripotency-related genes.

    PubMed

    Iacovides, Demetris; Rizki, Gizem; Lapathitis, Georgios; Strati, Katerina

    2016-01-01

    The insufficient ability of specialized cells such as neurons, cardiac myocytes, and epidermal cells to regenerate after tissue damage poses a great challenge to treat devastating injuries and ailments. Recent studies demonstrated that a diverse array of cell types can be directly derived from embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), or somatic cells by combinations of specific factors. The use of iPSCs and direct somatic cell fate conversion, or transdifferentiation, holds great promise for regenerative medicine as these techniques may circumvent obstacles related to immunological rejection and ethical considerations. However, producing iPSC-derived keratinocytes requires a lengthy two-step process of initially generating iPSCs and subsequently differentiating into skin cells, thereby elevating the risk of cellular damage accumulation and tumor formation. In this study, we describe the reprogramming of mouse embryonic fibroblasts into functional keratinocytes via the transient expression of pluripotency factors coupled with directed differentiation. The isolation of an iPSC intermediate is dispensable when using this method. Cells derived with this approach, termed induced keratinocytes (iKCs), morphologically resemble primary keratinocytes. Furthermore they express keratinocyte-specific markers, downregulate mesenchymal markers as well as the pluripotency factors Oct4, Sox2, and Klf4, and they show important functional characteristics of primary keratinocytes. iKCs can be further differentiated by high calcium administration in vitro and are capable of regenerating a fully stratified epidermis in vivo. Efficient conversion of somatic cells into keratinocytes could have important implications for studying genetic skin diseases and designing regenerative therapies to ameliorate devastating skin conditions. PMID:27473056

  10. Association of variation in hepatic lipase activity with promoter variation in the hepatic lipase gene. The LOCAT Study Invsestigators.

    PubMed Central

    Tahvanainen, E; Syvanne, M; Frick, M H; Murtomaki-Repo, S; Antikainen, M; Kesaniemi, Y A; Kauma, H; Pasternak, A; Taskinen, M R; Ehnholm, C

    1998-01-01

    The associations between six genetic polymorphisms in the hepatic lipase (HL) gene (LIPC) and variation in postheparin HL activity and fasting serum lipoproteins were evaluated in 395 male Finnish coronary heart disease patients with HDL cholesterol concentrations

  11. Induced rates of mitotic crossing over and possible mitotic gene conversion per wing anlage cell in Drosophila melanogaster by X rays and fission neutrons

    SciTech Connect

    Ayaki, T.; Fujikawa, K.; Ryo, H.; Itoh, T.; Kondo, S. )

    1990-09-01

    As a model for chromosome aberrations, radiation-induced mitotic recombination of mwh and flr genes in Drosophila melanogaster strain (mwh +/+ flr) was quantitatively studied. Fission neutrons were five to six times more effective than X rays per unit dose in producing either crossover-mwh/flr twins and mwh singles-or flr singles, indicating that common processes are involved in the production of crossover and flr singles. The X-ray-induced rate/wing anlage cell/Gy for flr singles was 1 X 10(-5), whereas that of crossover was 2 x 10(-4); the former and the latter rate are of the same order of magnitude as those of gene conversion and crossover in yeast, respectively. Thus, we conclude that proximal-marker flr singles induced in the transheterozygote are gene convertants. Using the model based on yeast that recombination events result from repair of double-strand breaks or gaps, we propose that mitotic recombination in the fly is a secondary result of recombinational DNA repair. Evidence for recombinational misrepair in the fly is given. The relative ratio of radiation-induced mitotic crossover to spontaneous meiotic crossover is one order of magnitude higher in the fly than in yeast and humans.

  12. Is GC bias in the nuclear genome of the carnivorous plant Utricularia driven by ROS-based mutation and biased gene conversion?

    PubMed

    Ibarra-Laclette, Enrique; Albert, Victor A; Herrera-Estrella, Alfredo; Herrera-Estrella, Luis

    2011-11-01

    At less than 90 Mbp, the tiny nuclear genome of the carnivorous bladderwort plant Utricularia is an attractive model system for studying molecular evolutionary processes leading to genome miniaturization. Recently, we reported that expression of genes encoding DNA repair and reactive oxygen species (ROS) detoxification enzymes is highest in Utricularia traps, and we argued that ROS mutagenic action correlates with the high nucleotide substitution rates observed in the Utricularia plastid, mitochondrial, and nuclear genomes. Here, we extend our analysis of 100 nuclear genes from Utricularia and related asterid eudicots to examine nucleotide substitution biases and their potential correlation with ROS-induced DNA lesions. We discovered an unusual bias toward GC nucleotides, most prominently in transition substitutions at the third position of codons, which are presumably silent with respect to adaptation. Given the general tendency of biased gene conversion to drive GC bias, and of ROS to induce double strand breaks requiring recombinational repair, we propose that some of the unusual features of the bladderwort and its genome may be more reflective of these nonadaptive processes than of natural selection.

  13. Is GC bias in the nuclear genome of the carnivorous plant Utricularia driven by ROS-based mutation and biased gene conversion?

    PubMed

    Ibarra-Laclette, Enrique; Albert, Victor A; Herrera-Estrella, Alfredo; Herrera-Estrella, Luis

    2011-11-01

    At less than 90 Mbp, the tiny nuclear genome of the carnivorous bladderwort plant Utricularia is an attractive model system for studying molecular evolutionary processes leading to genome miniaturization. Recently, we reported that expression of genes encoding DNA repair and reactive oxygen species (ROS) detoxification enzymes is highest in Utricularia traps, and we argued that ROS mutagenic action correlates with the high nucleotide substitution rates observed in the Utricularia plastid, mitochondrial, and nuclear genomes. Here, we extend our analysis of 100 nuclear genes from Utricularia and related asterid eudicots to examine nucleotide substitution biases and their potential correlation with ROS-induced DNA lesions. We discovered an unusual bias toward GC nucleotides, most prominently in transition substitutions at the third position of codons, which are presumably silent with respect to adaptation. Given the general tendency of biased gene conversion to drive GC bias, and of ROS to induce double strand breaks requiring recombinational repair, we propose that some of the unusual features of the bladderwort and its genome may be more reflective of these nonadaptive processes than of natural selection. PMID:22057327

  14. High Throughput Sequencing of Entamoeba 27nt Small RNA Population Reveals Role in Permanent Gene Silencing But No Effect on Regulating Gene Expression Changes during Stage Conversion, Oxidative, or Heat Shock Stress.

    PubMed

    Zhang, Hanbang; Ehrenkaufer, Gretchen M; Manna, Dipak; Hall, Neil; Singh, Upinder

    2015-01-01

    The human parasite Entamoeba histolytica has an active RNA interference (RNAi) pathway with an extensive repertoire of 27nt small RNAs that silence genes. However the role of this pathway in regulating amebic biology remains unknown. In this study, we address whether silencing via 27nt small RNAs may be a mechanism for controlling gene expression changes during conversion between the trophozoite and cyst stages of the parasite. We sequenced small RNA libraries generated from trophozoites, early cysts, mature cysts, and excysting cells and mapped them to the E. invadens genome. Our results show that, as in E. histolytica, small RNAs in E. invadens are largely ~27nt in length, have an unusual 5'-polyphosphate structure and mediate gene silencing. However, when comparing the libraries from each developmental time-point we found few changes in the composition of the small RNA populations. Furthermore, genes targeted by small RNAs were permanently silenced with no changes in transcript abundance during development. Thus, the E. invadens 27nt small RNA population does not mediate gene expression changes during development. In order to assess the generalizability of our observations, we examined whether small RNAs may be regulating gene expression changes during stress response in E. histolytica. Comparison of the 27nt small RNA populations from E. histolytica trophozoites from basal conditions, or after heat shock or exposure to oxidative stress showed few differences. Similar to data in E. invadens development, genes targeted by small RNAs were consistently silenced and did not change expression under tested stress conditions. Thus, the biological roles of the 27nt small RNA population in Entamoeba remain elusive. However, as the first characterization of the RNAi pathway in E. invadens these data serve as a useful resource for the study of Entamoeba development and open the door to the development of RNAi-based gene silencing tools in E. invadens.

  15. Analysis of Human Rotaviruses from a Single Location Over an 18-Year Time Span Suggests that Protein Coadaption Influences Gene Constellations

    PubMed Central

    Zhang, Shu; McDonald, Paul W.; Thompson, Travis A.; Dennis, Allison F.; Akopov, Asmik; Kirkness, Ewen F.; Patton, John T.

    2014-01-01

    ABSTRACT Rotaviruses (RVs) are 11-segmented, double-stranded RNA viruses that cause severe gastroenteritis in children. In addition to an error-prone genome replication mechanism, RVs can increase their genetic diversity by reassorting genes during host coinfection. Such exchanges allow RVs to acquire advantageous genes and adapt in the face of selective pressures. However, reassortment may also impose fitness costs if it unlinks genes/proteins that have accumulated compensatory, coadaptive mutations and that operate best when kept together. To better understand human RV evolutionary dynamics, we analyzed the genome sequences of 135 strains (genotype G1/G3/G4-P[8]-I1-C1-R1-A1-N1-T1-E1-H1) that were collected at a single location in Washington, DC, during the years 1974 to 1991. Intragenotypic phylogenetic trees were constructed for each viral gene using the nucleotide sequences, thereby defining novel allele level gene constellations (GCs) and illuminating putative reassortment events. The results showed that RVs with distinct GCs cocirculated during the vast majority of the collection years and that some of these GCs persisted in the community unchanged by reassortment. To investigate the influence of protein coadaptation on GC maintenance, we performed a mutual information-based analysis of the concatenated amino acid sequences and identified an extensive covariance network. Unexpectedly, amino acid covariation was highest between VP4 and VP2, which are structural components of the RV virion that are not thought to directly interact. These results suggest that GCs may be influenced by the selective constraints placed on functionally coadapted, albeit noninteracting, viral proteins. This work raises important questions about mutation-reassortment interplay and its impact on human RV evolution. IMPORTANCE Rotaviruses are devastating human pathogens that cause severe diarrhea and kill >450,000 children each year. The virus can evolve by accumulating mutations and by

  16. Deduced amino acid sequence, gene structure and chromosomal location of a novel human class Mu glutathione S-transferase, GSTM4.

    PubMed Central

    Zhong, S; Spurr, N K; Hayes, J D; Wolf, C R

    1993-01-01

    The Mu-Class glutathione S-transferases (GSTs) are subject to marked inter-individual variation in man, owing to the fact that 40-50% of the population fail to express M1 subunits. Mu-Class GST from two lymphoblastoid cell lines (expressing M1 subunits and the other 'nulled' for M1) have been studied. Both cell lines were found to express a Mu-Class GST that has not been described previously. The cDNA encoding this novel transferase, designated 'GSTM4' has been isolated and the enzyme shown to be comprised of 218 amino acids (including the initiator methionine residue) with an M(r) of approx. 25.5 kDa. Molecular cloning demonstrated that the lymphoblastoid cell line which expressed GSTM1 possessed the b allelic variant (i.e. that with an asparagine residue at position 173). The genes for GSTM4 and GSTM1b have been cloned and found to contain seven introns and eight exons. The coding region of the GSTM4 gene, including the seven introns, encompasses 5.0 kb, whereas the same region of GSTM1b is 5.5 kb; the difference in the size of the two genes is due to the length of intron 7. DNA sequencing allowed a GSTM4-gene-specific oligo-primer to be designed which has been utilized in a PCR-based assay to determine that the GSTM4 gene is located on chromosome 1. Images Figure 1 Figure 3 Figure 6 PMID:8471052

  17. Locations and contexts of sequences that hybridize to poly(dG-dT).(dC-dA) in mammalian ribosomal DNAs and two X-linked genes.

    PubMed Central

    Braaten, D C; Thomas, J R; Little, R D; Dickson, K R; Goldberg, I; Schlessinger, D; Ciccodicola, A; D'Urso, M

    1988-01-01

    Sequences located several kilobases both 5' and 3' of the stably transcribed portion of several genes hybridize to radio-labeled pure fragments of the alternating sequence poly (dG-dT) (dC-dA) ["poly(GT)"]. The genes include the ribosomal DNA of mouse, rat, and human, and also human glucose-6-phosphate dehydrogenase (G6PD) and mouse hypoxanthine-guanine phosphoribosyl transferase (HPRT). HPRT has additional hybridizing sequences in introns. Fragments that include the hybridizing sequences and up to 300 bp of adjoining DNA show perfect runs of poly(GT) (greater than 30bp) in all but the human 5' region of rDNA, which shows a somewhat different alternating purine:pyrimidine sequence, poly(GTAT) (36bp). Within 150 bp of these sequences in various instances are found a number of other sequences reported to affect DNA conformation in model systems. Most marked is an enhancement of sequences matching at least 67% to the consensus binding sequence for topoisomerase II. Two to ten-fold less of such sequences were found in other sequenced portions of the nontranscribed spacer or in the transcribed portion of rDNA. The conservation of the locations of tracts of alternating purine:pyrimidine between evolutionarily diverse species is consistent with a possible functional role for these sequences. Images PMID:3267216

  18. Down-regulation of the cytoglobin gene, located on 17q25, in tylosis with oesophageal cancer (TOC): evidence for trans-allele repression.

    PubMed

    McRonald, Fiona E; Liloglou, Triantafillos; Xinarianos, George; Hill, Laura; Rowbottom, Lynn; Langan, Joanne E; Ellis, Anthony; Shaw, Joan M; Field, John K; Risk, Janet M

    2006-04-15

    Tylosis (focal non-epidermolytic palmoplantar keratoderma) is an autosomal dominant skin disorder that is associated with the early onset of squamous cell oesophageal cancer (SCOC) in three families. Our previous linkage and haplotype analyses have mapped the tylosis with oesophageal cancer (TOC) locus to a 42.5 kb region on chromosome 17q25 that has also been implicated in the aetiology of sporadically occurring SCOC from a number of different geographical populations. Oesophageal cancer is one of the 10 leading causes of cancer mortality worldwide. No inherited disease-causing mutations have been identified in the genes located in the 42.5 kb minimal region. We now show that cytoglobin gene expression in oesophageal biopsies from tylotic patients is dramatically reduced by approximately 70% compared with normal oesophagus. Furthermore, both alleles are equally repressed. Given the autosomal dominant nature of the disease, these results exclude haploinsufficiency as a mechanism of the disease and instead suggest a novel trans-allele interaction. We also show that the promoter is hypermethylated in sporadic oesophageal cancer samples: this may constitute the 'second hit' of a gene previously implicated in this disease by allelic imbalance studies.

  19. Contentious Conversations

    ERIC Educational Resources Information Center

    Zuidema, Leah A.

    2011-01-01

    The idea of joining a conversation through reading and writing is not new; in his 1941 book "The Philosophy of Literary Form: Studies in Symbolic Action," Kenneth Burke suggests that the acts of reading and writing are like entering a parlor where others are already conversing. The author explores the place of professional debate within NCTE and…

  20. Molecular Cytogenetic Analysis of the European Hake Merluccius merluccius (Merlucciidae, Gadiformes): U1 and U2 snRNA Gene Clusters Map to the Same Location.

    PubMed

    García-Souto, Daniel; Troncoso, Tomás; Pérez, Montse; Pasantes, Juan José

    2015-01-01

    The European hake (Merluccius merluccius) is a highly valuable and intensely fished species in which a long-term alive stock has been established in captivity for aquaculture purposes. Due to their huge economic importance, genetic studies on hakes were mostly focused on phylogenetic and phylogeographic aspects; however chromosome numbers are still not described for any of the fifteen species in the genus Merluccius. In this work we report a chromosome number of 2n = 42 and a karyotype composed of three meta/submetacentric and 18 subtelo/telocentric chromosome pairs. Telomeric sequences appear exclusively at both ends of every single chromosome. Concerning rRNA genes, this species show a single 45S rDNA cluster at an intercalary location on the long arm of subtelocentric chromosome pair 12; the single 5S rDNA cluster is also intercalary to the long arm of chromosome pair 4. While U2 snRNA gene clusters map to a single subcentromeric position on chromosome pair 13, U1 snRNA gene clusters seem to appear on almost all chromosome pairs, but showing bigger clusters on pairs 5, 13, 16, 17 and 19. The brightest signals on pair 13 are coincident with the single U2 snRNA gene cluster signals. Therefore, the use of these probes allows the unequivocal identification of at least 7 of the chromosome pairs that compose the karyotype of Merluccius merluccius thus opening the way to integrate molecular genetics and cytological data on the study of the genome of this important species. PMID:26716701

  1. Molecular Cytogenetic Analysis of the European Hake Merluccius merluccius (Merlucciidae, Gadiformes): U1 and U2 snRNA Gene Clusters Map to the Same Location

    PubMed Central

    García-Souto, Daniel; Troncoso, Tomás; Pérez, Montse; Pasantes, Juan José

    2015-01-01

    The European hake (Merluccius merluccius) is a highly valuable and intensely fished species in which a long-term alive stock has been established in captivity for aquaculture purposes. Due to their huge economic importance, genetic studies on hakes were mostly focused on phylogenetic and phylogeographic aspects; however chromosome numbers are still not described for any of the fifteen species in the genus Merluccius. In this work we report a chromosome number of 2n = 42 and a karyotype composed of three meta/submetacentric and 18 subtelo/telocentric chromosome pairs. Telomeric sequences appear exclusively at both ends of every single chromosome. Concerning rRNA genes, this species show a single 45S rDNA cluster at an intercalary location on the long arm of subtelocentric chromosome pair 12; the single 5S rDNA cluster is also intercalary to the long arm of chromosome pair 4. While U2 snRNA gene clusters map to a single subcentromeric position on chromosome pair 13, U1 snRNA gene clusters seem to appear on almost all chromosome pairs, but showing bigger clusters on pairs 5, 13, 16, 17 and 19. The brightest signals on pair 13 are coincident with the single U2 snRNA gene cluster signals. Therefore, the use of these probes allows the unequivocal identification of at least 7 of the chromosome pairs that compose the karyotype of Merluccius merluccius thus opening the way to integrate molecular genetics and cytological data on the study of the genome of this important species. PMID:26716701

  2. C-terminal region of activation-induced cytidine deaminase (AID) is required for efficient class switch recombination and gene conversion.

    PubMed

    Sabouri, Somayeh; Kobayashi, Maki; Begum, Nasim A; Xu, Jianliang; Hirota, Kouji; Honjo, Tasuku

    2014-02-11

    Activation-induced cytidine deaminase (AID) introduces single-strand breaks (SSBs) to initiate class switch recombination (CSR), gene conversion (GC), and somatic hypermutation (SHM). CSR is mediated by double-strand breaks (DSBs) at donor and acceptor switch (S) regions, followed by pairing of DSB ends in two S regions and their joining. Because AID mutations at its C-terminal region drastically impair CSR but retain its DNA cleavage and SHM activity, the C-terminal region of AID likely is required for the recombination step after the DNA cleavage. To test this hypothesis, we analyzed the recombination junctions generated by AID C-terminal mutants and found that 0- to 3-bp microhomology junctions are relatively less abundant, possibly reflecting the defects of the classical nonhomologous end joining (C-NHEJ). Consistently, the accumulation of C-NHEJ factors such as Ku80 and XRCC4 was decreased at the cleaved S region. In contrast, an SSB-binding protein, poly (ADP)-ribose polymerase1, was recruited more abundantly, suggesting a defect in conversion from SSB to DSB. In addition, recruitment of critical DNA synapse factors such as 53BP1, DNA PKcs, and UNG at the S region was reduced during CSR. Furthermore, the chromosome conformation capture assay revealed that DNA synapse formation is impaired drastically in the AID C-terminal mutants. Interestingly, these mutants showed relative reduction in GC compared with SHM in chicken DT40 cells. Collectively, our data indicate that the C-terminal region of AID is required for efficient generation of DSB in CSR and GC and thus for the subsequent pairing of cleaved DNA ends during recombination in CSR.

  3. Adult mice maintained on a high-fat diet exhibit object location memory deficits and reduced hippocampal SIRT1 gene expression.

    PubMed

    Heyward, Frankie D; Walton, R Grace; Carle, Matthew S; Coleman, Mark A; Garvey, W Timothy; Sweatt, J David

    2012-07-01

    Mounting evidence has established that diet-induced obesity (DIO) is associated with deficits in hippocampus-dependent memory. The bulk of research studies dealing with this topic have utilized rats fed a high-fat diet as an experimental model. To date, there has been a paucity of research studies that have established whether the memory deficits exhibited in DIO rats can be recapitulated in mice. Moreover, the majority of experiments that have evaluated memory performance in rodent models of DIO have utilized memory tests that are essentially aversive in nature (i.e., Morris water maze). The current study sought to fill an empirical void by determining if mice maintained on a high-fat diet exhibit deficits in two non-aversive memory paradigms: novel object recognition (NOR) and object location memory (OLM). Here we report that mice fed a high-fat diet over 23 weeks exhibit intact NOR, albeit a marked impairment in hippocampus-dependent OLM. We also determined the existence of corresponding aberrations in gene expression within the hippocampus of DIO mice. DIO mice exhibited significant reductions in both SIRT1 and PP1 mRNA within the hippocampus. Our data suggest that mice maintained on a high-fat diet present with impaired hippocampus-dependent spatial memory and a corresponding alteration in the expression of genes that have been implicated in memory consolidation.

  4. A matrix attachment region is located upstream from the high-molecular-weight glutenin gene Bx7 in wheat (Triticum aestivum L.).

    PubMed

    Rampitsch, C; Jordan, M C; Cloutier, S

    2000-06-01

    A 2.2-kb nucleotide sequence rich in AT, located upstream from the Bx7 allele of the high-molecular-weight glutenin Glu-B1 locus in wheat (Triticum aestivum cv. Glenlea) was cloned following amplification by PCR. The 5' region of this sequence contains motifs typically found in matrix attachment regions (MARs) in other plants. We have shown that part of the 2.2-kb DNA binds to wheat nuclear matrix (NM) in vitro, at least as strongly as a known MAR (Adh1) from maize suggesting that there is a MAR upstream of Bx7. This MAR is approximately 800 bases in length running from -750 to -1560 bases, relative to the start codon. Although the MAR is associated with a tissue-specific gene and is beside a strong tissue-specific promoter, the MAR sequence did not lead to tissue-specific expression of the beta-glucuronidase marker gene under the control of the rice actin promoter in various tissues. Presence of the MAR was only slightly beneficial with respect to expression levels, which were not greatly altered in transient expression assays in various wheat tissues although a slight increase in the number of foci was observed in leaves, which have low transformation efficiencies.

  5. Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression.

    PubMed

    Eiberg, Hans; Troelsen, Jesper; Nielsen, Mette; Mikkelsen, Annemette; Mengel-From, Jonas; Kjaer, Klaus W; Hansen, Lars

    2008-03-01

    The human eye color is a quantitative trait displaying multifactorial inheritance. Several studies have shown that the OCA2 locus is the major contributor to the human eye color variation. By linkage analysis of a large Danish family, we finemapped the blue eye color locus to a 166 Kbp region within the HERC2 gene. By association analyses, we identified two SNPs within this region that were perfectly associated with the blue and brown eye colors: rs12913832 and rs1129038. Of these, rs12913832 is located 21.152 bp upstream from the OCA2 promoter in a highly conserved sequence in intron 86 of HERC2. The brown eye color allele of rs12913832 is highly conserved throughout a number of species. As shown by a Luciferase assays in cell cultures, the element significantly reduces the activity of the OCA2 promoter and electrophoretic mobility shift assays demonstrate that the two alleles bind different subsets of nuclear extracts. One single haplotype, represented by six polymorphic SNPs covering half of the 3' end of the HERC2 gene, was found in 155 blue-eyed individuals from Denmark, and in 5 and 2 blue-eyed individuals from Turkey and Jordan, respectively. Hence, our data suggest a common founder mutation in an OCA2 inhibiting regulatory element as the cause of blue eye color in humans. In addition, an LOD score of Z = 4.21 between hair color and D14S72 was obtained in the large family, indicating that RABGGTA is a candidate gene for hair color.

  6. Conversation Analysis.

    ERIC Educational Resources Information Center

    Schiffrin, Deborah

    1990-01-01

    Summarizes the current state of research in conversation analysis, referring primarily to six different perspectives that have developed from the philosophy, sociology, anthropology, and linguistics disciplines. These include pragmatics; speech act theory; interactional sociolinguistics; ethnomethodology; ethnography of communication; and…

  7. Genetic Analysis of a Chromosomal Region Containing vanA and vanB, Genes Required for Conversion of Either Ferulate or Vanillate to Protocatechuate in Acinetobacter†

    PubMed Central

    Segura, Ana; Bünz, Patricia V.; D’Argenio, David A.; Ornston, L. Nicholas

    1999-01-01

    VanA and VanB form an oxygenative demethylase that converts vanillate to protocatechuate in microorganisms. Ferulate, an abundant phytochemical, had been shown to be metabolized through a vanillate intermediate in several Pseudomonas isolates, and biochemical evidence had indicated that vanillate also is an intermediate in ferulate catabolism by Acinetobacter. Genetic evidence supporting this conclusion was obtained by characterization of mutant Acinetobacter strains blocked in catabolism of both ferulate and vanillate. Cloned Acinetobacter vanA and vanB were shown to be members of a chromosomal segment remote from a supraoperonic cluster containing other genes required for completion of the catabolism of ferulate and its structural analogs, caffeate and coumarate, through protocatechuate. The nucleotide sequence of DNA containing vanA and vanB demonstrated the presence of genes that, on the basis of nucleotide sequence similarity, appeared to be associated with transport of aromatic compounds, metabolism of such compounds, or iron scavenging. Spontaneous deletion of 100 kb of DNA containing this segment does not impede the growth of cells with simple carbon sources other than vanillate or ferulate. Additional spontaneous mutations blocking vanA and vanB expression were shown to be mediated by IS1236, including insertion of the newly discovered composite transposon Tn5613. On the whole, vanA and vanB appear to be located within a nonessential genetic region that exhibits considerable genetic malleability in Acinetobacter. The overall organization of genes neighboring Acinetobacter vanA and vanB, including a putative transcriptional regulatory gene that is convergently transcribed and overlaps vanB, is conserved in Pseudomonas aeruginosa but has undergone radical rearrangement in other Pseudomonas species. PMID:10348863

  8. Whole-Genome Analysis of Individual Meiotic Events in Drosophila melanogaster Reveals That Noncrossover Gene Conversions Are Insensitive to Interference and the Centromere Effect

    PubMed Central

    Miller, Danny E.; Smith, Clarissa B.; Kazemi, Nazanin Yeganeh; Cockrell, Alexandria J.; Arvanitakis, Alexandra V.; Blumenstiel, Justin P.; Jaspersen, Sue L.; Hawley, R. Scott

    2016-01-01

    A century of genetic analysis has revealed that multiple mechanisms control the distribution of meiotic crossover events. In Drosophila melanogaster, two significant positional controls are interference and the strongly polar centromere effect. Here, we assess the factors controlling the distribution of crossovers (COs) and noncrossover gene conversions (NCOs) along all five major chromosome arms in 196 single meiotic divisions to generate a more detailed understanding of these controls on a genome-wide scale. Analyzing the outcomes of single meiotic events allows us to distinguish among different classes of meiotic recombination. In so doing, we identified 291 NCOs spread uniformly among the five major chromosome arms and 541 COs (including 52 double crossovers and one triple crossover). We find that unlike COs, NCOs are insensitive to the centromere effect and do not demonstrate interference. Although the positions of COs appear to be determined predominately by the long-range influences of interference and the centromere effect, each chromosome may display a different pattern of sensitivity to interference, suggesting that interference may not be a uniform global property. In addition, unbiased sequencing of a large number of individuals allows us to describe the formation of de novo copy number variants, the majority of which appear to be mediated by unequal crossing over between transposable elements. This work has multiple implications for our understanding of how meiotic recombination is regulated to ensure proper chromosome segregation and maintain genome stability. PMID:26944917

  9. Genetically Based Location from Triploid Populations and Gene Ontology of a 3.3-Mb Genome Region Linked to Alternaria Brown Spot Resistance in Citrus Reveal Clusters of Resistance Genes

    PubMed Central

    Cuenca, José; Aleza, Pablo; Vicent, Antonio; Brunel, Dominique; Ollitrault, Patrick; Navarro, Luis

    2013-01-01

    Genetic analysis of phenotypical traits and marker-trait association in polyploid species is generally considered as a challenge. In the present work, different approaches were combined taking advantage of the particular genetic structures of 2n gametes resulting from second division restitution (SDR) to map a genome region linked to Alternaria brown spot (ABS) resistance in triploid citrus progeny. ABS in citrus is a serious disease caused by the tangerine pathotype of the fungus Alternaria alternata. This pathogen produces ACT-toxin, which induces necrotic lesions on fruit and young leaves, defoliation and fruit drop in susceptible genotypes. It is a strong concern for triploid breeding programs aiming to produce seedless mandarin cultivars. The monolocus dominant inheritance of susceptibility, proposed on the basis of diploid population studies, was corroborated in triploid progeny. Bulk segregant analysis coupled with genome scan using a large set of genetically mapped SNP markers and targeted genetic mapping by half tetrad analysis, using SSR and SNP markers, allowed locating a 3.3 Mb genomic region linked to ABS resistance near the centromere of chromosome III. Clusters of resistance genes were identified by gene ontology analysis of this genomic region. Some of these genes are good candidates to control the dominant susceptibility to the ACT-toxin. SSR and SNP markers were developed for efficient early marker-assisted selection of ABS resistant hybrids. PMID:24116149

  10. Genetically based location from triploid populations and gene ontology of a 3.3-mb genome region linked to Alternaria brown spot resistance in citrus reveal clusters of resistance genes.

    PubMed

    Cuenca, José; Aleza, Pablo; Vicent, Antonio; Brunel, Dominique; Ollitrault, Patrick; Navarro, Luis

    2013-01-01

    Genetic analysis of phenotypical traits and marker-trait association in polyploid species is generally considered as a challenge. In the present work, different approaches were combined taking advantage of the particular genetic structures of 2n gametes resulting from second division restitution (SDR) to map a genome region linked to Alternaria brown spot (ABS) resistance in triploid citrus progeny. ABS in citrus is a serious disease caused by the tangerine pathotype of the fungus Alternaria alternata. This pathogen produces ACT-toxin, which induces necrotic lesions on fruit and young leaves, defoliation and fruit drop in susceptible genotypes. It is a strong concern for triploid breeding programs aiming to produce seedless mandarin cultivars. The monolocus dominant inheritance of susceptibility, proposed on the basis of diploid population studies, was corroborated in triploid progeny. Bulk segregant analysis coupled with genome scan using a large set of genetically mapped SNP markers and targeted genetic mapping by half tetrad analysis, using SSR and SNP markers, allowed locating a 3.3 Mb genomic region linked to ABS resistance near the centromere of chromosome III. Clusters of resistance genes were identified by gene ontology analysis of this genomic region. Some of these genes are good candidates to control the dominant susceptibility to the ACT-toxin. SSR and SNP markers were developed for efficient early marker-assisted selection of ABS resistant hybrids.

  11. Four genes located on a SSC2 meat quality QTL region are associated with different meat quality traits in Landrace × Chinese-European crossbred population.

    PubMed

    Cepica, S; Ovilo, C; Masopust, M; Knoll, A; Fernandez, A; Lopez, A; Rohrer, G A; Nonneman, D

    2012-06-01

    Several quantitative trait loci (QTL) for different meat quality traits have been localized on the q arm of porcine chromosome 2 at position 55-78 cM. Association analyses were performed in a commercial Landrace × Chinese-European (LCE) crossbred population (n = 446) slaughtered at approximately 127 kg and an average age of 198 days with records for performance (growth, fat and meat accretion) and meat quality [intramuscular fat (IMF), Minolta L*, Minolta a*, Minolta b* and pH at 45 m]. Polymorphisms within positional candidate genes cloned from homologous regions on human chromosome 19, ubiquitin-like 5 (UBL5- AM950288:g.566G>A), resistin (RETN- AM157180:g.1473A>G causing substitution p.Ala36Thr), insulin receptor (INSR- AM950289:g.589T>C) and complement factor D (adipsin) (CFD- AM950287:g. 306C>T) were located at positions 62.1, 64.0, 68.0 and 70.7 cM respectively on the current USDA USMARC map of porcine chromosome 2 and had the following allele frequencies in the LCE: UBL5 566G - 0.57; RETN 1473G - 0.84; INSR 589C - 0.70; and CFD 306C - 0.73. The effects of alleles within the candidate genes on the recorded traits were estimated using an animal model. Significant effects (P < 0.05) were found for pH(45) in m. semimembranosus (m. sm.) (UBL5), IMF (RETN) and Minolta L* (RETN, CFD). Differences between phenotypic means of homozygotes at UBL5, RETN and either RETN or CFD explained 0.34 SD for pH(45) in m. sm., 0.47 SD for IMF and 0.68 SD for Minolta L* respectively. Suggestive effects (P < 0.10) on IMF (UBL5, CFD), Minolta a* (INSR, CFD) and Minolta b* (INSR) were also observed. Our results support the localization of further QTL for meat quality traits in this region and suggest that there are several genes affecting different meat quality traits.

  12. Localization of two human autoantigen genes by PCR screening and in situ hybridization-glycyl-tRNA synthetase locates to 7p15 and Alanyl-tRNA synthetase locates to 16q22

    SciTech Connect

    Nichols, R.C.; Pai, S.I.; Liu, P.; Ge, Q.; Targoff, I.N.

    1995-11-01

    Aminoacyl-tRNA synthetases (aminoacyl-RS) catalyze the attachment of an amino acid to its cognate tRNA. Five of 20 human aminoacyl-RS (histidyl-RS, threonyl-RS, isoleucyl-RS, glycyl-RS, and alanyl-RS) have been identified as targets of autoantibodies in the autoimmune disease polymyositis/dermatomyositis (PM/DM; 9). A sixth autoantigenic amino-acyl-RS, lysyl-RS, was recently reported. The genes for histidyl-RS and threonyl-RS have been assigned to chromosome 5, as have the genes for leucyl-RS and arginyl-RS. Six other aminoacyl-RS (glutamyl-prolyl-RS, valyl-RS, cysteinyl-RS, methionyl-RS, tryptophanyl-RS, and asparaginyl-RS) were assigned to chromosomes 1, 6, 11, 12, 14, and 18, respectively. The reason for a preponderance of aminoacyl-RS genes on chromosome 5 is unknown, but it has been suggested that regulatory relatedness might be a factor. Recently the entire or partial cDNA sequences for two autoantigenic aminoacyl-RS genes, glycyl-RS (gene symbol GARS; 4) and alanyl-RS (gene symbol AARS; 1), were reported. To understand further the genesis of autoimmune responses to aminoacyl-RS and to determine whether genes for autoantigenic aminoacyl-RS colocalize to chromosome 5, we have determined the chromosomal site of the GARS and AARS genes by PCR-based screening of somatic cell hybrid panels and by fluorescence in situ hybridization (FISH) analysis. 10 refs., 1 fig.

  13. Fine mapping and DNA fiber FISH analysis locates the tobamovirus resistance gene L3 of Capsicum chinense in a 400-kb region of R-like genes cluster embedded in highly repetitive sequences.

    PubMed

    Tomita, R; Murai, J; Miura, Y; Ishihara, H; Liu, S; Kubotera, Y; Honda, A; Hatta, R; Kuroda, T; Hamada, H; Sakamoto, M; Munemura, I; Nunomura, O; Ishikawa, K; Genda, Y; Kawasaki, S; Suzuki, K; Meksem, K; Kobayashi, K

    2008-11-01

    The tobamovirus resistance gene L(3) of Capsicum chinense was mapped using an intra-specific F2 population (2,016 individuals) of Capsicum annuum cultivars, into one of which had been introduced the C. chinense L(3) gene, and an inter-specific F2 population (3,391 individuals) between C. chinense and Capsicum frutescence. Analysis of a BAC library with an AFLP marker closely linked to L(3)-resistance revealed the presence of homologs of the tomato disease resistance gene I2. Partial or full-length coding sequences were cloned by degenerate PCR from 35 different pepper I2 homologs and 17 genetic markers were generated in the inter-specific combination. The L(3) gene was mapped between I2 homolog marker IH1-04 and BAC-end marker 189D23M, and located within a region encompassing two different BAC contigs consisting of four and one clones, respectively. DNA fiber FISH analysis revealed that these two contigs are separated from each other by about 30 kb. DNA fiber FISH results and Southern blotting of the BAC clones suggested that the L(3) locus-containing region is rich in highly repetitive sequences. Southern blot analysis indicated that the two BAC contigs contain more than ten copies of the I2 homologs. In contrast to the inter-specific F2 population, no recombinant progeny were identified to have a crossover point within two BAC contigs consisting of seven and two clones in the intra-specific F2 population. Moreover, distribution of the crossover points differed between the two populations, suggesting linkage disequilibrium in the region containing the L locus.

  14. Assignment of two human autoantigen genes-isoleucyl-tRNA synthetase locates to 9q21 and lysyl-tRNA synthetase locates to 16q23-q24

    SciTech Connect

    Nichols, R.C.; Blinder, J.; Pai, S.I.

    1996-08-15

    Protein synthesis is initiated by the attachment of amino acids to cognate tRNAs by aminoacyl-tRNA synthetases (aaRS). Five of twenty human aaRS (histidyl-RS, threonyl-RS, alanyl-RS, glycyl-RS, and isoleucyl-RS) have been identified as targets of autoantibodies in the autoimmune disease polymyositis/dermatomyositis. Autoantibodies to human lysyl-RS, a sixth autoantigenic aminoacyl-RS, were recently identified. The genes for histidyl-RS and threonyl-RS have been localized to chromosome 5, and we recently reported that the genes for alanyl-RS and glycyl-RS localize to chromosomes 16 and 7, respectively. To understand the genesis of autoimmune responses to aaRS better, we have used PCR-based screening of somatic cell hybrid panels and fluorescence in situ hybridization (FISH) to assign the genes for isoleucyl-RS and lysyl-RS. 19 refs., 1 fig.

  15. Conversion of 5-formyltetrahydrofolic acid to 5-methyltetrahydrofolic acid is unimpaired in folate-adequate persons homozygous for the C677T mutation in the methylenetetrahydrofolate reductase gene.

    PubMed

    Stern, L L; Bagley, P J; Rosenberg, I H; Selhub, J

    2000-09-01

    Methylenetetrahydrofolate reductase (MTHFR) catalyzes the synthesis of 5-methyltetrahydrofolic acid (5-CH(3)-H(4) folic acid), the methyl donor for the formation of methionine from homocysteine. A common C677T transition in the MTHFR gene results in a variant with a lower specific activity and a greater sensitivity to heat than the normal enzyme, as measured in vitro. This study was undertaken to determine the capacity of homozygotes for the MTHFR C677T transition to convert 5-formyltetrahydrofolic acid (5-HCO-H(4) folic acid) to 5-CH(3)-H(4) folic acid, a process that requires the action of MTHFR. Six subjects homozygous for the C677T transition (T/T) and 6 subjects with wild-type MTHFR (C/C) were given a 5-mg oral dose of (6R:,S:)-5-HCO-H(4) folic acid. Plasma and urine were analyzed for 5-CH(3)-H(4) folic acid concentrations using affinity/HPLC coupled with fluorescence or UV detection. The mean areas under the curves created by the rise and fall of plasma 5-CH(3)-H(4) folic acid after the oral dose did not differ between the two genotypes, 424.5 +/- 140.3 (T/T) vs. 424.1+/- 202.4 h.nmol/L (C/C). There also was no significant difference in the mean cumulative 7-h urinary excretion of 5-CH(3)-H(4) folic acid between the T/T (2.5 +/- 1.4 micromol) and C/C (1.9 +/- 1.0 micromol) genotypes. Under the conditions employed, the conversion of oral 5-HCO-H(4) folic acid to 5-CH(3)-H(4) folic acid is not impaired in persons with the T/T MTHFR genotype. Possible reasons for these findings are discussed. PMID:10958818

  16. Conversational sensemaking

    NASA Astrophysics Data System (ADS)

    Preece, Alun; Webberley, Will; Braines, Dave

    2015-05-01

    Recent advances in natural language question-answering systems and context-aware mobile apps create opportunities for improved sensemaking in a tactical setting. Users equipped with mobile devices act as both sensors (able to acquire information) and effectors (able to act in situ), operating alone or in collectives. The currently- dominant technical approaches follow either a pull model (e.g. Apple's Siri or IBM's Watson which respond to users' natural language queries) or a push model (e.g. Google's Now which sends notifications to a user based on their context). There is growing recognition that users need more flexible styles of conversational interaction, where they are able to freely ask or tell, be asked or told, seek explanations and clarifications. Ideally such conversations should involve a mix of human and machine agents, able to collaborate in collective sensemaking activities with as few barriers as possible. Desirable capabilities include adding new knowledge, collaboratively building models, invoking specific services, and drawing inferences. As a step towards this goal, we collect evidence from a number of recent pilot studies including natural experiments (e.g. situation awareness in the context of organised protests) and synthetic experiments (e.g. human and machine agents collaborating in information seeking and spot reporting). We identify some principles and areas of future research for "conversational sensemaking".

  17. Conversational sensing

    NASA Astrophysics Data System (ADS)

    Preece, Alun; Gwilliams, Chris; Parizas, Christos; Pizzocaro, Diego; Bakdash, Jonathan Z.; Braines, Dave

    2014-05-01

    Recent developments in sensing technologies, mobile devices and context-aware user interfaces have made it pos- sible to represent information fusion and situational awareness for Intelligence, Surveillance and Reconnaissance (ISR) activities as a conversational process among actors at or near the tactical edges of a network. Motivated by use cases in the domain of Company Intelligence Support Team (CoIST) tasks, this paper presents an approach to information collection, fusion and sense-making based on the use of natural language (NL) and controlled nat- ural language (CNL) to support richer forms of human-machine interaction. The approach uses a conversational protocol to facilitate a ow of collaborative messages from NL to CNL and back again in support of interactions such as: turning eyewitness reports from human observers into actionable information (from both soldier and civilian sources); fusing information from humans and physical sensors (with associated quality metadata); and assisting human analysts to make the best use of available sensing assets in an area of interest (governed by man- agement and security policies). CNL is used as a common formal knowledge representation for both machine and human agents to support reasoning, semantic information fusion and generation of rationale for inferences, in ways that remain transparent to human users. Examples are provided of various alternative styles for user feedback, including NL, CNL and graphical feedback. A pilot experiment with human subjects shows that a prototype conversational agent is able to gather usable CNL information from untrained human subjects.

  18. Predictability of Conversation Partners

    NASA Astrophysics Data System (ADS)

    Takaguchi, Taro; Nakamura, Mitsuhiro; Sato, Nobuo; Yano, Kazuo; Masuda, Naoki

    2011-08-01

    Recent developments in sensing technologies have enabled us to examine the nature of human social behavior in greater detail. By applying an information-theoretic method to the spatiotemporal data of cell-phone locations, [C. Song , ScienceSCIEAS0036-8075 327, 1018 (2010)] found that human mobility patterns are remarkably predictable. Inspired by their work, we address a similar predictability question in a different kind of human social activity: conversation events. The predictability in the sequence of one’s conversation partners is defined as the degree to which one’s next conversation partner can be predicted given the current partner. We quantify this predictability by using the mutual information. We examine the predictability of conversation events for each individual using the longitudinal data of face-to-face interactions collected from two company offices in Japan. Each subject wears a name tag equipped with an infrared sensor node, and conversation events are marked when signals are exchanged between sensor nodes in close proximity. We find that the conversation events are predictable to a certain extent; knowing the current partner decreases the uncertainty about the next partner by 28.4% on average. Much of the predictability is explained by long-tailed distributions of interevent intervals. However, a predictability also exists in the data, apart from the contribution of their long-tailed nature. In addition, an individual’s predictability is correlated with the position of the individual in the static social network derived from the data. Individuals confined in a community—in the sense of an abundance of surrounding triangles—tend to have low predictability, and those bridging different communities tend to have high predictability.

  19. A Novel NADPH-Dependent Aldehyde Reductase Gene from Saccharomyces cerevisiae NRRL Y-12632 Involved in the Detoxification of Aldehyde Inhibitors Derived from Lignocellulosic Biomass Conversion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aldehyde inhibitors such as furfural, 5-hydroxymethylfurfural (HMF), anisaldehyde, benzaldehyde, cinnamaldehyde, and phenylaldehyde are commonly generated during lignocellulosic biomass conversion process for low-cost cellulosic ethanol production that interferes with subsequent microbial growth and...

  20. The Solanum pimpinellifolium Cf-ECP1 and Cf-ECP4 genes for resistance to Cladosporium fulvum are located at the Milky Way locus on the short arm of chromosome 1.

    PubMed

    Soumpourou, Eleni; Iakovidis, Michael; Chartrain, Laetitia; Lyall, Verity; Thomas, Colwyn M

    2007-11-01

    The interaction between tomato and the leaf mould pathogen Cladosporium fulvum is an excellent model to study gene-for-gene interactions and plant disease resistance gene evolution. Most Cf genes were introgressed into cultivated tomato (Solanum lycopersicum) from wild relatives such as S. pimpinellifolium and novel Cf-ECP genes were recently identified in this species. Our objective is to isolate Cf-ECP1, Cf-ECP2, Cf-ECP4 and Cf-ECP5 to increase our understanding of Cf gene evolution, and the molecular basis for recognition specificity in Cf proteins. The map locations of Cf-ECP2 and Cf-ECP5 have been reported previously and we report here that Cf-ECP1 and Cf-ECP4 map to a different locus on the short arm of chromosome 1. The analysis of selected recombinants and allelism tests showed both genes are located at Milky Way together with Cf-9 and Cf-4. Our results emphasise the importance of this locus in generating novel Cf genes for resistance to C. fulvum. Candidate genes for Cf-ECP1 and Cf-ECP4 were also identified by DNA gel blot analysis of bulked segregant pools. In addition, we generated functional cassettes for expression of the C. fulvum ECP1, ECP2, ECP4 and ECP5 proteins using recombinant Potato Virus X, and three ECPs were also expressed in stable transformed plants. Using marker-assisted selection we have also identified recombinants containing Cf-ECP1, Cf-ECP2, Cf-ECP4 or Cf-ECP5 in cis with a linked T-DNA carrying the non-autonomous Zea mays transposon Dissociation. Using these resources it should now be possible to isolate all four Cf-ECPs using transposon tagging, or a candidate gene strategy.

  1. Polymerase chain reaction (PCR)-based methods for detection/identification of mycotoxigenic fungi targeting fumonisin biosynthetic genes: Use of variation in FUM cluster location to distinguish between and quantify

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The fungus Fusarium is an agricultural problem because it can cause disease on most crop plants and can contaminate crops with mycotoxins. There is considerable variation in the presence/absence and genomic location of gene clusters responsible for synthesis of mycotoxins and other secondary metabol...

  2. Tissue specificity of methylation of cytosines in regulatory regions of four genes located in the locus FXYD5-COX7A1 of human chromosome 19: correlation with their expression level.

    PubMed

    Chalaya, T V; Akopov, S B; Nikolaev, L G; Sverdlov, E D

    2006-03-01

    In this study, we compared degree of methylation of selected CpG sites in CCGG sequences located in promoter regions of four human genes with expression level of these genes in several human cell lines and tissues. These genes were subdivided into two groups according to the dependence of their expression on CpG methylation in the 5 -regions. The first group, characterized by clear correlation of methylation with the transcription level, includes housekeeping gene COX6B (the absence of methylation unambiguously correlates with expression) and urothelium-specific uroplakin gene (the methylation coincides with absence of expression). The second group includes genes that are expressed in many, but not all tissues and cells. For these genes (LEAP-1 and ATP4A), there was no correlation between methylation and expression. It is possible that methylation provides some basal level of gene repression, which is overcome by binding of tissue-specific transcription factors, whereas lack of methylation gives the opportunity for gene expression in various cells and tissues. PMID:16545066

  3. Chromosomal locations of the human and mouse genes for precursors of epidermal growth factor and the. beta. subunit of nerve growth factor

    SciTech Connect

    Zabel, B.U.; Eddy, R.L.; Lalley, P.A.; Scott, J.; Bell, G.I.; Shows, T.B.

    1985-01-01

    DNA probes for pre-pro-epidermal growth factor (EGF) and the precursor of the ..beta.. subunit of nerve growth factor (NGF) were used to chromosomally map human and mouse EGF and NGF genes in panels of human-mouse and mouse-Chinese hamster somatic cell hybrids. The EGF and NGF genes were mapped to human chromosomes 4 and 1, respectively, by using human-mouse cell hybrids. A combination of regional mapping using a chromosome 1 translocation and comparative gene mapping suggests that the human NGF gene is in the p21-p22.1 region of chromosome 1. In mouse-Chinese hamster cell hybrids, both genes were assigned to mouse chromosome 3. A knowledge of the chromosomal assignment of these genes should help in our understanding of their regulation and role in development and disease.

  4. DIORAMA Location Type User's Guide

    SciTech Connect

    Terry, James Russell

    2015-01-29

    The purpose of this report is to present the current design and implementation of the DIORAMA location type object (LocationType) and to provide examples and use cases. The LocationType object is included in the diorama-app package in the diorama::types namespace. Abstractly, the object is intended to capture the full time history of the location of an object or reference point. For example, a location may be speci ed as a near-Earth orbit in terms of a two-line element set, in which case the location type is capable of propagating the orbit both forward and backward in time to provide a location for any given time. Alternatively, the location may be speci ed as a xed set of geodetic coordinates (latitude, longitude, and altitude), in which case the geodetic location of the object is expected to remain constant for all time. From an implementation perspective, the location type is de ned as a union of multiple independent objects defi ned in the DIORAMA tle library. Types presently included in the union are listed and described in subsections below, and all conversions or transformation between these location types are handled by utilities provided by the tle library with the exception of the \\special-values" location type.

  5. Chromosomal location of Pm35, a novel Aegilops tauschii derived powdery mildew resistance gene introgressed into common wheat (Triticum aestivum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A single gene controlling powdery mildew resistance was identified in the North Carolina germplasm line NC96BGTD3 (NCD3) using genetic analysis of F2 derived lines from a NCD3 X Saluda cross. Microsatellite markers linked to this Pm gene were identified and their most likely order was Xcfd7, 10.3cM,...

  6. Touch-inducible genes for calmodulin and a calmodulin-related protein are located in tandem on a chromosome of Arabidopsis thaliana.

    PubMed

    Ito, T; Hirano, M; Akama, K; Shimura, Y; Okada, K

    1995-10-01

    Genes for calmodulin and calmodulin-related proteins in Arabidopsis are up-regulated by a variety of physical stimuli, which include rain, wind and touch [Braam and Davis (1990) Cell 60: 357]. We have isolated five genes for calmodulin (AtCAL1, 2, 3, 5, 6) and one gene for a calmodulin-related protein (AtCAL4) from an Arabidopsis genomic library. Touch stimulus of Arabidopsis plants induces the accumulation of mRNA transcribed from AtCAL4 and AtCAL5, but not from the other isolated genes. The two touch-inducible genes are arrayed in tandem with a short intergenic region of 700 bp but they show different organ-specific patterns of expression.

  7. The primary structure and genomic organization of five novel transcripts located close to the Huntington's disease gene on human chromosome 4p16.3.

    PubMed

    Hadano, S; Ishida, Y; Ikeda, J E

    1998-06-30

    Five distinct novel transcripts (RES4-22, -23, -24, -25 and -26) that mapped to the 1-Mb interval between D4S180 and D4S183 on human chromosome 4p16.3 close to the Huntington's disease (HD) gene were isolated, and the structure and exon/intron organization of each gene were thoroughly analyzed. The transcripts of the RES4-22, -23 and -24 genes each have several isoforms by alternative splicing and these have also been defined. Two transcripts, RES4-24 and RES4-25, reside in the same genomic region with opposite polarities and they also clearly overlap. Among these transcripts, RES4-26 was found to encode a novel zinc finger protein. The transcript map based upon our current level of analysis combined with data from previous studies reveals the gene-rich nature and the intricate organization of the genes in the HD locus.

  8. The CD36, CLA-1(CD36L1), and LIMPII (CD36L2) gene family: Cellular distribution, chromosomal location, and genetic evolution

    SciTech Connect

    Calvo, D.; Vega, M.A.; Dopazo, J.

    1995-01-01

    CD36, CLA-1, and LIMPII are single polypeptide membrane glycoproteins, and the genes encoding them constitute a recently described gene family. In the present paper, a cDNA encoding the human lysosomal membrane protein LIMPII was used to determine its expression pattern in cells of various lineages. Like CLA-1, and in contrast with the restricted expression of CD36, the expression of LIMPII is widespread. Mapping of the human LIMPII and CLA-1 genes (gene symbols CD36L2 and CD36L1, respectively) to specific chromosomes revealed that CLA-1, LIMPII, and CD36 do not form a gene cluster, but are found dispersed on chromosomes 12, 4, and 7, respectively. These data, together with the phylogenetic analysis carried out for the members of this family, indicate that the LIMPII, CIA-1, and CD36 genes diverged early in evolution from an ancestor gene, possibly before the divergence between the arthropods and the vertebrates. 48 refs., 5 figs.

  9. Genomic organization, complete sequence, and chromosomal location of the gene for human eotaxin (SCYA11), an eosinophil-specific CC chemokine

    SciTech Connect

    Garcia-Zepeda, E.A.; Sarafi, M.N.; Luster, A.D. |

    1997-05-01

    Eotaxin is a CC chemokine that is a specific chemoattractant for eosinophils and is implicated in the pathogenesis of eosinophilic inflammatory diseases, such as asthma. We describe the genomic organization, complete sequence, including 1354 bp 5{prime} of the RNA initiation site, and chromosomal localization of the human eotaxin gene. Fluorescence in situ hybridization analysis localized eotaxin to human chromosome 17, in the region q21.1-q21.2, and the human gene name SCYA11 was assigned. We also present the 5{prime} flanking sequence of the mouse eotaxin gene and have identified several regulatory elements that are conserved between the murine and the human promoters. In particular, the presence of elements such as NF-{Kappa}B, interferon-{gamma} response element, and glucocorticoid response element may explain the observed regulation of the eotaxin gene by cytokines and glucocorticoids. 17 refs., 4 figs., 1 tab.

  10. The leukemia inhibitory factor receptor (LIFR) gene is located within a cluster of cytokine receptor loci on mouse chromosome 15 and human chromosome 5p12-p13

    SciTech Connect

    Gearing, D.P. ); Druck, T.; Huebner, K. ); Overhauser, J. ); Gilbert, D.J.; Copeland, N.G.; Jenkins, N.A. )

    1993-10-01

    The leukemia inhibitory factor receptor (LIFR) gene was localized to human chromosome 5p12-p13 by somatic cell hybrid analysis. Interspecific backcross analysis revealed that the murine locus was on chromosome 15 in a region of homology with human chromosome 5p. In both human and mouse genomes, the LIFR locus was linked to the genes encoding the receptors for interleukin-7, prolactin, and growth hormone. 13 refs., 1 fig.

  11. Identification and Characterization of a Gene stp17 Located on the Linear Plasmid pBSSB1 as an Enhanced Gene of Growth and Motility in Salmonella enterica Serovar Typhi

    PubMed Central

    Zhang, Haifang; Zhu, Yunxia; Xie, Xiaofang; Wang, Min; Du, Hong; Xu, Shungao; Zhang, Ying; Gong, Mingyu; Ni, Bin; Xu, Huaxi; Huang, Xinxiang

    2016-01-01

    The linear plasmid pBSSB1 mediates the flagellar phase variation in H:z66 positive Salmonella enterica serovar Typhi (S. Typhi). The gene named stp17 (S. Typhi plasmid number 17 gene) is located on pBSSB1 and encodes the protein STP17. The expression pattern at the protein-level and function of STP17 remains unknown. In this study, the recombinant protein STP17His6 was expressed, purified and used to prepare the polyclonal anti-STP17 antibody. We detected protein-level expression of stp17 in S. Typhi and further investigated the protein expression characteristics of stp17 in different growth phases by western blot analysis. The effects of STP17 on bacterial growth and motility were analyzed. In addition, the structure of STP17 was predicted and the active site of STP17 was identified by site-directed mutagenesis. The results showed that STP17 was expressed stably in the wild type strain of S. Typhi. STP17 expression at the protein level peaks when cultures reach an OD600 value of 1.2. The growth rate and motility of the Δstp17 strain were significantly decreased compared with the wild type strain (P < 0.05) and this phenotype was restored in the stp17 complementary strain. Moreover, the growth rate and motility of the stp17 over-expression strain was greater than the wild type strain. STP17 contains nine Helix segments, six Stand segments and some Coil segments in the secondary structural level. The top-ranked 3-D structure of STP17 predicted by I-TASSER contains a putative ATPase domain and the amino acid residues of GLY16, GLY19, LYS20, ASN133, LYS157, and LYS158 may be the active site residues of STP17. Finally, STP17 was able to catalyze the ATP to ADP reaction, suggesting that STP17 may be an ATPase. To our knowledge, this is the first report describing the protein expression characteristics of STP17 in S. Typhi, showing that STP17 promotes bacterial growth and motility, which may be associated with its potential ATPase activity. PMID:27761429

  12. The gene encoding human intestinal trefoil factor (TFF3) is located on chromosome 21q22.3 clustered with other members of the trefoil peptide family

    SciTech Connect

    Chinery, R.; Williamson, J.; Poulsom, R.

    1996-03-01

    The gene coding for human intestinal trefoil factor (hITF), a recently described cellular motogen produced by gastrointestinal goblet cells and epithelia elsewhere, is a member of the rapidly growing trefoil peptide family. In a rodent-human somatic cell hybrid panel, the hITF (HGMW-approved symbol TFF3) genomic locus segregated with human chromosome 21q. Fluorescence in situ hybridization with a 2.1-kb genomic probe of the hITF gene mapped this locus more precisely to the q22.3 region. Triple fluorescence in situ hybridization, together with physical mapping of human genomic DNA using pulsed-field gel electrophoresis, revealed that the hITF gene is tightly linked to those encoding the other known human trefoil peptides, namely the breast cancer estrogen-inducable gene pS2 (BCEI) and human spasmolytic polypeptide (hSP/SML1). This gene family could become a useful marker for the genetic and physical mapping of chromosome 21 and for a better definition of the region involved in the clinical phenotype of several genetic diseases. 17 refs., 2 figs.

  13. Chromosomal locations and modes of action of genes of the retinoid (vitamin A) system support their involvement in the etiology of schizophrenia

    SciTech Connect

    Goodman, A.B.

    1995-08-14

    Vitamin A (retinoid), an essential nutrient for fetal and subsequent mammalian development, is involved in gene expression, cell differentiation, proliferation, migration, and death. Retinoic acid (RA) the morphogenic derivative of vitamin A is highly teratogenic. In humans retinoid excess or deficit can result in brain anomalies and psychosis. This review discusses chromosomal loci of genes that control the retinoid cascade in relation to some candidate genes in schizophrenia. The paper relates the knowledge about the transport, delivery, and action of retinoids to what is presently known about the pathology of schizophrenia, with particular reference to the dopamine hypothesis, neurotransmitters, the glutamate hypothesis, neurotransmitters, the glutamate hypothesis, retinitis pigmentosa, dermatologic disorders, and craniofacial anomalies. 201 refs., 1 tab.

  14. The Podospora rmp1 gene implicated in nucleus-mitochondria cross-talk encodes an essential protein whose subcellular location is developmentally regulated.

    PubMed Central

    Contamine, Véronique; Zickler, Denise; Picard, Marguerite

    2004-01-01

    It has been previously reported that, at the time of death, the Podospora anserina AS1-4 mutant strains accumulate specific deleted forms of the mitochondrial genome and that their life spans depend on two natural alleles (variants) of the rmp1 gene: AS1-4 rmp1-2 strains exhibit life spans strikingly longer than those of AS1-4 rmp1-1. Here, we show that rmp1 is an essential gene. In silico analyses of eight rmp1 natural alleles present in Podospora isolates and of the putative homologs of this orphan gene in other filamentous fungi suggest that rmp1 evolves rapidly. The RMP1 protein is localized in the mitochondrial and/or the cytosolic compartment, depending on cell type and developmental stage. Strains producing RMP1 without its mitochondrial targeting peptide are viable but exhibit vegetative and sexual defects. PMID:15020413

  15. Identification of a novel first exon in the human dystrophin gene and of a new promoter located more than 500 kb upstream of the nearest known promoter

    SciTech Connect

    Yanagawa, H.; Nishio, H.; Takeshima, Y.

    1994-09-01

    The dystrophin gene, which is muted in patients with Duchenne and Becker muscular dystrophies, is the largest known human gene. Five alternative promoters have been characterized until now. Here we show that a novel dystrophin isoform with a different first exon can be produced through transcription initiation at a previously-unidentified alternative promoter. The case study presented is that of patient with Duchenne muscular dystrophy who had a deletion extending from 5{prime} end of the dystrophin gene to exon 2, including all promoters previously mapped in the 5{prime} part of the gene. Transcripts from lymphoblastoid cells were found to contain sequences corresponding to exon 3, indicating the presence of new promoter upstream of this exon. The nucleotide sequence of amplified cDNA corresponding to the 5{prime} end of the new transcript indicated that the 5{prime} end of exon 3 was extended by 9 codons, only the last (most 3{prime}) of which codes for methionine. The genomic nucleotide sequence upstream from the new exon, as determined using inverse polymerase chain reaction, revealed the presence of sequences similar to a TATA box, an octamer motif and an MEF-2 element. The identified promoter/exon did not map to intron 2, as might have been expected, but to a position more than 500 kb upstream of the most 5{prime} of the previously-identified promoters, thereby adding 500 kb to the dystrophin gene. The sequence of part of the new promoter region is very similar to that of certain medium reiteration frequency repetitive sequences. These findings may help us understand the molecular evolution of the dystrophin gene.

  16. In Search of ‘Birth Month Genes’: Using Existing Data Repositories to Locate Genes Underlying Birth Month-Disease Relationships

    PubMed Central

    Boland, Mary Regina; Tatonetti, Nicholas P

    2016-01-01

    Prenatal and perinatal exposures vary seasonally (e.g., sunlight, allergens) and many diseases are linked with variance in exposure. Epidemiologists often measure these changes using birth month as a proxy for seasonal variance. Likewise, Genome-Wide Association Studies have associated or implicated these same diseases with many genes. Both disparate data types (epidemiological and genetic) can provide key insights into the underlying disease biology. We developed an algorithm that links 1) epidemiological data from birth month studies with 2) genetic data from published gene-disease association studies. Our framework uses existing data repositories — PubMed, DisGeNET and Gene Ontology — to produce a bipartite network that connects enriched seasonally varying biofactorss with birth month dependent diseases (BMDDs) through their overlapping developmental gene sets. As a proof-of-concept, we investigate 7 known BMDDs and highlight three important biological networks revealed by our algorithm and explore some interesting genetic mechanisms potentially responsible for the seasonal contribution to BMDDs. PMID:27570668

  17. 3pK, a new mitogen-activated protein kinase-activated protein kinase located in the small cell lung cancer tumor suppressor gene region.

    PubMed Central

    Sithanandam, G; Latif, F; Duh, F M; Bernal, R; Smola, U; Li, H; Kuzmin, I; Wixler, V; Geil, L; Shrestha, S

    1996-01-01

    NotI linking clones, localized to the human chromosome 3p21.3 region and homozygously deleted in small cell lung cancer cell lines NCI-H740 and NCI-H1450, were used to search for a putative tumor suppressor gene(s). One of these clones, NL1G210, detected a 2.5-kb mRNA in all examined human tissues, expression being especially high in the heart and skeletal muscle. Two overlapping cDNA clones containing the entire open reading frame were isolated from a human heart cDNA library and fully characterized. Computer analysis and a search of the GenBank database to reveal high sequence identity of the product of this gene to serine-threonine kinases, especially to mitogen-activated protein kinase-activated protein kinase 2, a recently described substrate of mitogen-activated kinases. Sequence identitiy was 72% at the nucleotide level and 75% at the amino acid level, strongly suggesting that this protein is a serine-threonine kinase. Here we demonstrate that the new gene, referred to as 3pK (for chromosome 3p kinase), in fact encodes a mitogen-activated protein kinase-regulated protein serine-threonine kinase with a novel substrate specificity. PMID:8622688

  18. Mutations in the unc-52 gene responsible for body wall muscle defects in adult Caenorhabditis elegans are located in alternatively spliced exons

    SciTech Connect

    Rogalski, T.M.; Gilchrist, E.J.; Mullen, G.P.

    1995-01-01

    The unc-52 gene in Caenorhabditis elegans produces several large proteins that function in the basement membrane underlying muscle cells. Mutations in this gene result in defects in myofilament assembly and in the attachment of the myofilament lattice to the muscle cell membrane. The st549 and ut111 alleles of unc-52 produce a lethal (Pat) terminal phenotype whereas the e444, e669, e998, e1012 and e1421 mutations result in viable, paralyzed animals. We have identified the sequence alterations responsible for these mutant phenotypes. The st549 allele has a premature stop codon in exon 7 that should result in the complete elimination of unc-52 gene function, and the ut111 allele has a Tc1 transposon inserted into the second exon of the gene. The five remaining mutations are clustered in a small interval containing three adjacent, alternatively spliced exons (16, 17 and 18). These mutations affect some, but not all of the unc-52-encoded proteins. Thirteen intragenic revertants of the e669, e998, e1012 and e1421 alleles have also been sequenced. The majority of these carry the original mutation plus a G to A transition in the conserved splice acceptor site of the affected exon. This result suggests that reversion of the mutant phenotype in these strains may be the result of exon-skipping. 38 refs., 6 figs., 2 tabs.

  19. Adipose and muscle tissue expression of two genes (NCAPG and LCORL) located in a chromosomal region associated with cattle feed intake and gain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A region on bovine chromosome 6 has been implicated in cattle birth weight, growth, and length. Non-SMC conodensin I complex subunit G (NCAPG) and ligand dependent nuclear receptor corepressor-like protein (LCORL) are positional candidate genes within this region. We previously identified genetic ...

  20. The interleukin 3 gene is located on human chromosome 5 and is deleted in myeloid leukemias with a deletion of 5q.

    PubMed Central

    Le Beau, M M; Epstein, N D; O'Brien, S J; Nienhuis, A W; Yang, Y C; Clark, S C; Rowley, J D

    1987-01-01

    The gene IL-3 encodes interleukin 3, a hematopoietic colony-stimulating factor (CSF) that is capable of supporting the proliferation of a broad range of hematopoietic cell types. By using somatic cell hybrids and in situ chromosomal hybridization, we localized this gene to human chromosome 5 at bands q23-31, a chromosomal region that is frequently deleted [del(5q)] in patients with myeloid disorders. By in situ hybridization, IL-3 was found to be deleted in the 5q-chromosome of one patient with refractory anemia who had a del(5)(q15q33.3), of three patients with refractory anemia (two patients) or acute nonlymphocytic leukemia (ANLL) de novo who had a similar distal breakpoint [del(5)(q13q33.3)], and of a fifth patient, with therapy-related ANLL, who had a similar distal breakpoint in band q33 [del(5)(q14q33.3)]. Southern blot analysis of somatic cell hybrids retaining the normal or the deleted chromosome 5 from two patients with the refractory anemia 5q- syndrome indicated that IL-3 sequences were absent form the hybrids retaining the deleted chromosome 5 but not from hybrids that had a cytologically normal chromosome 5. Thus, a small segment of chromosome 5 contains IL-3, GM-CSF (the gene encoding granulocyte-macrophage-CSF), CSF-1 (the gene encoding macrophage-CSF), and FMS (the human c-fms protooncogene, which encodes the CSF-1 receptor). Our findings and earlier results indicating that GM-CSF, CSF-1, and FMS were deleted in the 5q-chromosome, suggest that loss of IL-3 or of other CSF genes may play an important role in the pathogenesis of hematologic disorders associated with a del(5q). Images PMID:3497400

  1. Structure, expression, and chromosome location of the gene for the beta subunit of brain-specific Ca2+/calmodulin-dependent protein kinase II identified by transgene integration in an embryonic lethal mouse mutant.

    PubMed Central

    Karls, U; Müller, U; Gilbert, D J; Copeland, N G; Jenkins, N A; Harbers, K

    1992-01-01

    The transgenic mouse strain CAT40 carries in its germ line one copy of a DNA construct consisting of the chloramphenicol acetyltransferase gene and the immunoglobulin heavy-chain enhancer. We show that transgene integration has resulted in a recessive lethal mutation that leads to death of homozygous CAT40 embryos shortly after implantation. The transgene has integrated adjacent to the 3' end of the gene coding for the beta subunit of the brain-specific Ca2+/calmodulin-dependent protein kinase II (Camk-2). The complete cDNA sequence of the Camk-2 gene and most of its exon/intron structure was determined. The deduced amino acid sequence is highly homologous to the previously described rat protein. The chromosomal location of the Camk-2 locus was mapped by interspecific backcross analysis to the proximal region of mouse chromosome 11. This region lacks previously identified recessive embryonic lethal mutations. During embryonic development, Camk-2-specific transcripts are first seen in the head section of 12.5-day-old embryos, and in adult mice the gene is expressed almost exclusively in the brain. Although transcription of the Camk-2 gene in heterozygous CAT40 mice is affected by transgene integration, it is unlikely that this gene is responsible for the mutant phenotype, since it is not expressed in blastocysts and the first transcripts during normal development are detected after the death of homozygous CAT40 embryos. Transgene integration is accompanied by a large deletion of cellular DNA; death is therefore most likely caused by the loss of a gene or genes that are important for early postimplantation development. Images PMID:1321343

  2. Preferrential rearrangement in normal rabbits of the 3' VHa allotype gene that is deleted in Alicia mutants; somatic hypermutation/conversion may play a major role in generating the heterogeneity of rabbit heavy chain variable region sequences.

    PubMed

    Allegrucci, M; Young-Cooper, G O; Alexander, C B; Newman, B A; Mage, R G

    1991-02-01

    The rabbit is unique in having well-defined allotypes in the variable region of the heavy chain. Products of the VHa locus, (with alleles a1, a2, and a3), account for the majority of the serum immunoglobulins. A small percentage of the serum immunoglobulins are a-negative. In 1986, Kelus and Weiss described a mutation that depressed the expression of the Ig VH a2 genes in an a1/a2 rabbit. From this animal the Alicia rabbit strain was developed and the mutation was termed ali. We previously showed, using Southern analysis and the transverse alternating field electrophoresis technique, that the difference between the ali rabbit and normal is a relatively small deletion including some of the most 3' VH genes. The most JH proximal 3' VH1 genes in DNA from normal rabbits of a1, a2 and a3 haplotypes encode a1, a2 and a3 molecules respectively, and it has been suggested that these genes are responsible for allelic inheritance of VHa allotypes. The present study suggests that the 3' end of the VH locus probably plays a key role in regulation of VH gene expression in rabbits because VH gene(s) in this region are the target(s) of preferential VDJ rearrangements. This raises the possibility that mechanisms such as somatic gene conversion and hypermutation are at work to generate the antibody repertoire in this species. Our data support the view that the 3' VH1 gene may be the preferred target for rearrangement in normal rabbits, and for the normal chromosome in heterozygous ali animals. However, homozygous ali rabbits with a deletion that removed the a2-encoding VH1 on both chromosomes do survive, rearrange other VH genes and produce normal levels of immunoglobulins as well as a significant percentage of B cells which bear the a2 allotype. This challenges the view that one VH gene, VH1, is solely responsible for the inheritance pattern of VHa allotypes.

  3. c-Myc/Max heterodimers bind cooperatively to the E-box sequences located in the first intron of the rat ornithine decarboxylase (ODC) gene.

    PubMed

    Walhout, A J; Gubbels, J M; Bernards, R; van der Vliet, P C; Timmers, H T

    1997-04-15

    The oncoprotein c-Myc plays an important role in cell proliferation, transformation, inhibition of differentiation and apoptosis. These functions most likely result from the transcription factor activity of c-Myc. As a heterodimer with Max, the c-Myc protein binds to the E-box sequence (CACGTG), which is also recognized by USF dimers. In order to test differences in target gene recognition of c-Myc/Max, Max and USF dimers, we compared the DNA binding characteristics of these proteins in vitro using vaccinia viruses expressing full-length c-Myc and Max proteins. As expected, purified c-Myc/max binds specifically to a consensus E-box. The optimal conditions for DNA binding by either c-Myc/Max, Max or USF dimers differ with respect to ionic strength and Mg2+ ion concentration. Most interestingly, the c-Myc/Max complex binds with a high affinity to its natural target, the rat ODC gene, which contains two adjacent, consensus E-boxes. High affinity binding results from teh ability of c-Myc/Max dimers to bind cooperatively to these E-boxes. We propose that differential cooperative binding by E-box binding transcription factors could contribute to target gene specificity.

  4. The gene for severe combined immunodeficiency disease in Athabascan-speaking Native Americans is located on chromosome 10p.

    PubMed Central

    Li, L; Drayna, D; Hu, D; Hayward, A; Gahagan, S; Pabst, H; Cowan, M J

    1998-01-01

    Severe combined immunodeficiency disease (SCID) consists of a group of heterogeneous genetic disorders. The most severe phenotype, T-B- SCID, is inherited as an autosomal recessive trait and is characterized by a profound deficiency of both T cell and B cell immunity. There is a uniquely high frequency of T-B- SCID among Athabascan-speaking Native Americans (A-SCID). To localize the A-SCID gene, we conducted a genomewide search, using linkage analysis of approximately 300 microsatellite markers in 14 affected Athabascan-speaking Native American families. We obtained conclusive evidence for linkage of the A-SCID locus to markers on chromosome 10p. The maximum pairwise LOD scores 4.53 and 4.60 were obtained from two adjacent markers, D10S191 and D10S1653, respectively, at a recombination fraction of straight theta=.00. Recombination events placed the gene in an interval of approximately 6.5 cM flanked by D10S1664 and D10S674. Multipoint analysis positioned the gene for the A-SCID phenotype between D10S191 and D10S1653, with a peak LOD score of 5.10 at D10S191. Strong linkage disequilibrium was found in five linked markers spanning approximately 6.5 cM in the candidate region, suggesting a founder effect with an ancestral mutation that occurred sometime before 1300 A.D. PMID:9443881

  5. Conjugative transfer of plasmid-located antibiotic resistance genes within the gastrointestinal tract of lesser mealworm larvae, Alphitobius diaperinus (Coleoptera: Tenebrionidae).

    PubMed

    Crippen, Tawni L; Poole, Toni L

    2009-09-01

    The frequency of conjugative transfer of antimicrobial resistance plasmids between bacteria within the gastrointestinal tract of lesser mealworm larvae, a prevalent pest in poultry production facilities, was determined. Lesser mealworm larvae were exposed to a negative bacterial control, a donor Salmonella enterica serotype Newport strain, a recipient Escherichia coli, or both donor and recipient to examine horizontal gene transfer of plasmids. Horizontal gene transfer was validated post external disinfection, via a combination of selective culturing, testing of indole production by spot test, characterization of incompatibility plasmids by polymerase chain reaction, and profiling antibiotic susceptibility by a minimum inhibitory concentration (MIC) assay. Transconjugants were produced in all larvae exposed to both donor and recipient bacteria at frequencies comparable to control in vitro filter mating conjugation studies run concurrently. Transconjugants displayed resistance to seven antibiotics in our MIC panel and, when characterized for incompatibility plasmids, were positive for the N replicon and negative for the A/C replicon. The transconjugants did not display resistance to expanded-spectrum cephalosporins, which were associated with the A/C plasmid. This study demonstrates that lesser mealworm larvae, which infest poultry litter, are capable of supporting the horizontal transfer of antibiotic resistance genes and that this exchange can occur within their gastrointestinal tract and between different species of bacteria under laboratory conditions. This information is essential to science-based risk assessments of industrial antibiotic usage and its impact on animal and human health. PMID:19425825

  6. Evaluation of rs62527607 [GT] single nucleotide polymorphism located in BAALC gene in children with acute leukemia using mismatch PCR-RFLP.

    PubMed

    Nadimi, Motahareh; Rahgozar, Soheila; Moafi, Alireza; Tavassoli, Manoochehr; Mesrian Tanha, Hamzeh

    2016-01-01

    Acute leukemia is the most common cancer in children and involves several factors that contribute to the development of multidrug resistance and treatment failure. According to our recent studies, the BAALC gene is identified to have high mRNA expression levels in childhood acute lymphoblastic leukemia (ALL) and those with multidrug resistance. Several polymorphisms are associated with the expression of this gene. To date, there has been no study on the rs62527607 [GT] single nucleotide polymorphism (SNP) of BAALC gene and its link with childhood acute lymphoblastic and myeloid leukemia (AML). The purpose of this study is to evaluate the prevalence of this polymorphism in pediatric acute leukemia, as well as its relationship with prognosis. DNA samples were extracted from bone marrow slides of 129 children with ALL and 16 children with AML. The rs62527607 [GT] SNP was evaluated using mismatch polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)-based analysis. The association between the SNP alleles and patient disease-free survival was then assessed. The prevalence of the T-allele of rs62527607 [GT] SNP in childhood T-ALL and pre-B-ALL was 28.3% and 11.2%, respectively. In the pre-B-ALL patients, 3 year disease free survival was associated with the GG genotype. Results showed a robust association between the rs62527607 SNP and the risk of relapse in ALL, but not AML, patients. T-ALL patients with the GT genotype had an 8.75 fold higher risk of relapse. The current study demonstrates a significant association between the genotype GT and the polymorphic allele G424T, and introduces this SNP as a negative prognostic factor in children with ALL.

  7. Interleukin 3 gene is located on human chromosome 5 and is deleted in myeloid leukemias with a deletion of 5q

    SciTech Connect

    Le Beau, M.M.; Epstein, N.D.; O'Brien, S.J.; Nienhuis, A.W.; Yang, Y.C.; Clark, S.C.; Rowley, J.D.

    1987-08-01

    The gene IL-3 encodes interleukin 3, a hematopoietic colony-stimulating factor (CSF) that is capable of supporting the proliferation of a broad range of hematopoietic cell types. By using somatic cell hybrids and in situ chromosomal hybridization, the authors localized this gene to human chromosome 5 at bands q23-31, a chromosomal region that is frequently deleted (del(5q)) in patients with myeloid disorders. By in situ hybridization, IL-3 was found to be deleted in the 5q-chromosome of one patient with refractory anemia who had a del(5)(q15q33.3), of three patients with refractory anemia (two patients) or acute nonlymphocytic leukemia (ANLL) de novo who had a similar distal breakpoint (del(5)(q13q33.3)), and of a fifth patient, with therapy-related ANLL, who had a similar distal breakpoint in band q33(del(5)(q14q33.3)). Southern blot analysis of somatic cell hybrids retaining the normal or the deleted chromosome 5 from two patients with the refractory anemia 5q- syndrome indicated that IL-3 sequences were absent from the hybrids retaining the deleted chromosome 5 but not from hybrids that had a cytologically normal chromosome 5. Thus, a small segment of chromosome 5 contains IL-3, GM-CSF, CSF-1, and FMS. The findings and earlier results indicating that GM-CSF, CSF-1, and FMS were deleted in the 5q- chromosome, suggest that loss of IL-3 or of other CSF genes may play an important role in the pathogenesis of hematologic disorders associated with a del(5q).

  8. Chromosomal location of a pollen fertility-restoring gene, Rf, for CMS in Japanese bunching onion (Allium fistulosum L.) possessing the cytoplasm of A. galanthum Kar. et Kir. revealed by genomic in situ hybridization.

    PubMed

    Yamashita, Ken-Ichiro; Takatori, Yuka; Tashiro, Yosuke

    2005-06-01

    In a previous study, we developed cytoplasmic male sterile lines of Allium fistulosum possessing the cytoplasm of A. galanthum, a wild species, by continuous backcrossing. Furthermore, we reported the presence of a pollen fertility-restoring gene (Rf) for cytoplasmic male sterility (CMS) in A. fistulosum from segregation of pollen fertility of backcross progenies. In the present study, genomic in situ hybridization (GISH), using genomic DNA of A. galanthum as the probe DNA and that of A. fistulosum as the blocking DNA, was applied to F(1) hybrids between both species and backcross progenies to determine the chromosomal location of the Rf locus. By means of GISH, eight chromosomes from A. galanthum were clearly discriminated from those of A. fistulosum in the F(1) hybrids, and chromosome substitution process through continuous backcrossing was visualized. Interestingly, the chromosome region from A. galanthum, specific to male fertile plants, was detected in one chromosome of BC(4) to BC(7) generations. Based on the karyotype analysis of the male fertile plants, the chromosome was identified as the 5F chromosome. Our results confirm that the Rf locus is located on the 5F chromosome of the male fertile plants. This is the first report that identified the chromosomal location of the pollen fertility-restoring gene in A. fistulosum. PMID:15883793

  9. Genetic mutations in the K1 and K10 genes of patients with epidermolytic hyperkeratosis. Correlation between location and disease severity.

    PubMed Central

    Syder, A J; Yu, Q C; Paller, A S; Giudice, G; Pearson, R; Fuchs, E

    1994-01-01

    Epidermolytic hyperkeratosis (EH) is a skin disease caused by mutations in the genes encoding K1 and K10, the differentiation-specific keratins of epidermis. To explore the heterogeneity of mutations and to assess whether a correlation exists between disease severity and the extent to which a mutation interferes with keratin network formation, we determined the genetic bases of four severe incidences of EH and one unusually mild case. Two severe cases have the same mutation, K10-R156:C, at a conserved arginine that we previously showed was mutated to a histidine in two unrelated EH families. An additional severe case has a mutation six residues away, still within the amino end of the alpha-helical rod domain of K10. The other severe case has a mutation in the conserved carboxy end of the K1 rod. In contrast, affected members of the atypically mild family have a mutation just proximal to the conserved carboxy end of the K10 rod. By genetic engineering and gene transfection, we demonstrate that each mutation is functionally responsible for the keratin filament aberrations that are typical of keratinocytes cultured from these patients. Moreover, we show that the mild EH mutation less severely affects filament network formation. Taken together, our studies strengthen the link between filament perturbations, cell fragility, and degeneration. Images PMID:7512983

  10. Identification and characterization of a GDSL esterase gene located proximal to the swr quorum-sensing system of Serratia liquefaciens MG1.

    PubMed

    Riedel, Kathrin; Talker-Huiber, Daniela; Givskov, Michael; Schwab, Helmut; Eberl, Leo

    2003-07-01

    Serratia liquefaciens MG1 employs the swr quorum-sensing system to control various functions, including production of extracellular enzymes and swarming motility. Here we report the sequencing of the swr flanking DNA regions. We identified a gene upstream of swrR and transcribed in the same direction, designated estA, which encodes an esterase that belongs to family II of lipolytic enzymes. EstA was heterologously expressed in Escherichia coli, and the substrate specificity of the enzyme was determined in crude extracts. With the aid of zymograms visualizing EstA on polyacrylamide gels and by the analysis of a transcriptional fusion of the estA promoter to the promoterless luxAB genes, we showed that expression of the esterase is not regulated by the swr quorum-sensing system. An estA mutant was generated and was found to exhibit growth defects on minimal medium containing Tween 20 or Tween 80 as the sole carbon source. Moreover, we show that the mutant produces greatly reduced amounts of N-acyl-homoserine lactone (AHL) signal molecules on Tween-containing medium compared with the wild type, suggesting that under certain growth conditions EstA may be important for providing the cell with precursors required for AHL biosynthesis.

  11. Wind energy conversion system

    SciTech Connect

    Longrigg, P.

    1987-03-17

    This patent describes a wind energy conversion system comprising: a propeller rotatable by force of wind; a generator of electricity mechanically coupled to the propeller for converting power of the wind to electric power for use by an electric load; means coupled between the generator and the electric load for varying the electric power drawn by the electric load to alter the electric loading of the generator; means for electro-optically sensing the speed of the wind at a location upwind from the propeller; and means coupled between the sensing means and the power varying means for operating the power varying means to adjust the electric load of the generator in accordance with a sensed value of wind speed to thereby obtain a desired ratio of wind speed to the speed of a tip of a blade of the propeller.

  12. Location of phosphorylation site and DNA-binding site of a positive regulator, OmpR, involved in activation of the osmoregulatory genes of Escherichia coli.

    PubMed

    Kato, M; Aiba, H; Tate, S; Nishimura, Y; Mizuno, T

    1989-06-01

    The OmpR protein of Escherichia coli is a positive regulator involved in activation of the ompF and ompC genes which encode the major outer membrane proteins OmpF and OmpC, respectively. By employing recombinant DNA techniques, we isolated the N- and C-terminal halves of the OmpR molecule. From the results of biochemical analyses of these fragments, it was concluded that the N-terminal portion contains a site involved in phosphorylation by an OmpR-specific protein kinase EnvZ, whereas the C-terminal part possesses a DNA-binding site for the ompC and ompF promoters.

  13. Stripe rust resistance and dough quality of new wheat - Dasypyrum villosum translocation lines T1DL•1V#3S and T1DS•1V#3L and the location of HMW-GS genes.

    PubMed

    Zhao, W C; Gao, X; Dong, J; Zhao, Z J; Chen, Q G; Chen, L G; Shi, Y G; Li, X Y

    2015-07-17

    The transfer of agronomically useful genes from wild wheat species into cultivated wheat is one of the most effective approaches to improvement of wheat varieties. To evaluate the transfer of genes from Dasypyrum villosum into Triticum aestivum, wheat quality and disease resistance was evaluated in two new translocation lines, T1DL•1V#3S and T1DS•1V#3L. We examined the levels of stripe rust resistance and dough quality in the two lines, and identified and located the stripe rust resistant genes and high molecular weight glutenin subunit (HMW-GS) genes Glu-V1 of D. villosum. Compared to the Chinese Spring (CS) variety, T1DL•1V#3S plants showed moderate resistance to moderate susceptibility to the stripe rust races CYR33 and Su11-4. However, T1DS•1V#3L plants showed high resistance or immunity to these stripe rusts. The genes for resistance to stripe rust were located on 1VL of D. villosum. In comparison to CS, the dough from T1DS•1V#3L had a significantly shorter developing time (1.45 min) and stable time (1.0 min), a higher weakness in gluten strength (208.5 FU), and a lower farinograph quality index (18). T1DL•1V#3S had a significantly longer developing time (4.2 min) and stable time (5.25 min), a lower weakness in gluten strength (53 FU) and a higher farinograph quality index (78.5). We also found that T1DS•1V#3L had reduced gluten strength and dough quality compared to CS, but T1DL•1V#3S had increased gluten strength and dough quality. The results of SDS-PAGE analysis indicated that Glu-V1 of D. villosum was located on short arm 1VS and long arm 1VL. These results prove that the new translocation lines, T1DS•1V#3L and T1DS•1V#3L, have valuable stripe rust resistance and dough quality traits that will be important for improving wheat quality and resistance in future wheat breeding programs.

  14. Evidence for an association between nonsyndromic cleft lip with or without cleft palate and a gene located on the long arm of chromosome 4

    SciTech Connect

    Mitchell, L.E.; Healey, S.C.; Chenevix-Trench, G. |

    1995-11-01

    Recent studies suggest that the familial aggregation of nonsyndromic cleft lip with or without cleft palate (CL{+-}P) is likely to be attributable to the effects of several susceptibility loci, acting in a multiplicative fashion. Two potential CL{+-}P susceptibility loci (CSL), transforming growth factor alpha (TGFA) and retinoic acid receptor (RARA), have been identified through association studies. In addition, recent evidence of linkage between CL{+-}P and two markers (D4S175 and D4S192) in the region 4q25-4q31.3 raised the possibility that a CSL, with a larger effect than either TGFA or RARA, may reside within this region of the human genome. The present analyses were undertaken to determine whether D4S175 or D4S192 is significantly associated with CL{+-}P in a sample of unrelated patients that have previously provided evidence of associations between CL{+-}P and both TGFA and RARA. The results of these analyses provide further, tentative, evidence for the presence of a CSL locus on the long arm of chromosome 4 and help to refine the location of this locus in the region of D4S175 and D4S192. 28 refs., 4 tabs.

  15. Genes for alkaline/neutral invertase in rice: alkaline/neutral invertases are located in plant mitochondria and also in plastids.

    PubMed

    Murayama, Seiji; Handa, Hirokazu

    2007-04-01

    Two cDNA clones (OsNIN1 and OsNIN3) encoding an alkaline/neutral invertase localized in organelles were identified from rice. The deduced amino acid sequences of these cDNA clones showed high homology to other plant alkaline/neutral invertases. Semi-quantitative reverse transcription polymerase chain reaction revealed that the expression of OsNIN1 was constitutive and independent of organ difference, although its expression level was low. Analyses using five types of web software for the prediction of protein localization in the cell, Predotar, PSORT, Mitoprot, TargetP, and ChloroP, strongly supported the possibility that OsNIN1 is transported into the mitochondria and that OsNIN3 is transported into plastids. Transient expression of fusion proteins combining the amino terminal region of these two proteins with sGFP demonstrated that N-OsNIN1::GFP and N-OsNIN3::GFP fusion proteins were transported into the mitochondria and plastids, respectively. We expressed the OsNIN1 protein in vitro and revealed that the translated protein had an invertase activity. These results clearly indicate that some of alkaline/neutral invertases are located in plant organelles, mitochondria and plastids, and that they might have a novel physiological function in plant organelles.

  16. IL-4 and IL-13 induce SOCS-1 gene expression in A549 cells by three functional STAT6-binding motifs located upstream of the transcription initiation site.

    PubMed

    Hebenstreit, Daniel; Luft, Petra; Schmiedlechner, Angela; Regl, Gerhard; Frischauf, Anna-Maria; Aberger, Fritz; Duschl, Albert; Horejs-Hoeck, Jutta

    2003-12-01

    Proteins of the suppressors of cytokine signaling (SOCS) family have important functions as negative regulators of cytokine signaling. We show here that SOCS-1 expression can be induced in the human epithelial lung cell line A549 by IL-4 and IL-13. Analysis of reporter gene constructs under control of the SOCS-1 promoter provides evidence that IL-4- and IL-13-induced up-regulation is dependent on three IFN-gamma-activated sequence motifs of the sequence TTC(N)(4)GAA, which is known for binding STAT6. The three motifs are situated close to each other approximately 600 bp upstream of the transcriptional initiation site. When mutations were inserted into all three IFN-gamma-activated sequence motifs at the same time, IL-4-IL-13-induced luciferase activity was abrogated. With single and double mutants, promoter activity was diminished in comparison with the wild-type promoter. STAT6 is therefore required for IL-4-IL-13-dependent SOCS-1 expression in A549 cells, and the three identified binding motifs cooperate to induce maximal transcription. EMSAs conducted with nuclear extracts of IL-4- and IL-13-stimulated A549 cells showed that STAT6 was able to bind to each of the three binding motifs. Finally, cotransfection of a SOCS-1 expression vector inhibited activation of SOCS-1 promoter luciferase constructs. Thus, SOCS-1 is able to autoregulate its expression via a negative feedback loop.

  17. NAB2-STAT6 gene fusion and STAT6 immunoexpression in extrathoracic solitary fibrous tumors: the association between fusion variants and locations.

    PubMed

    Chuang, I-Chieh; Liao, Kuan-Cho; Huang, Hsuan-Ying; Kao, Yu-Chien; Li, Chien-Feng; Huang, Shih-Chiang; Tsai, Jen-Wei; Chen, Ko-Chin; Lan, Jui; Lin, Po-Chun

    2016-05-01

    Solitary fibrous tumor (SFT) is a rare mesenchymal neoplasm harboring NAB2-STAT6 fusion, which drives STAT6 nuclear relocation. For extrathoracic SFTs, the clinical relevance of this molecular hallmark remains obscure. We assessed STAT6 immunoexpression for 61 extrathoracic SFTs exclusive of the meninges and head and neck, and 25 had analyzable RNAs to distinguish fusion variants by RT-PCR. The immunohistochemical and molecular findings were correlated with clincopathological features and disease-free survival (DFS). Twenty-eight males and 33 females had SFTs in the body cavities (n = 31), extremities (n = 17), and trunk (n = 13), categorized into 53 non-malignant and 8 malignant tumors. The vast majority (n = 57, 93%) exhibited distinctive STAT6 nuclear expression, including malignant ones. The common fusion variants were NAB2ex6-STAT6ex16/17 in 13 SFTs and NAB2ex4-STAT6ex2 in 8, while miscellaneous variants were detected only in 4 SFTs in the limbs and trunk but not in any body cavity-based cases (P = 0.026). The worse DFS was univariately associated with malignant histology (P = 0.04) but unrelated to tumor size, location, or fusion variant. Conclusively, extrathoracic SFTs mostly harbor NAB2ex6-STAT6ex16/17, followed by NAB2ex4-STAT6ex2. Miscellaneous variants are significantly rare in SFTs within the body cavities. The clinical aggressiveness of extrathoraic SFTs is associated with malignant histology but unrelated to the NAB2-STAT6 fusion variants. PMID:27039712

  18. NAB2-STAT6 gene fusion and STAT6 immunoexpression in extrathoracic solitary fibrous tumors: the association between fusion variants and locations.

    PubMed

    Chuang, I-Chieh; Liao, Kuan-Cho; Huang, Hsuan-Ying; Kao, Yu-Chien; Li, Chien-Feng; Huang, Shih-Chiang; Tsai, Jen-Wei; Chen, Ko-Chin; Lan, Jui; Lin, Po-Chun

    2016-05-01

    Solitary fibrous tumor (SFT) is a rare mesenchymal neoplasm harboring NAB2-STAT6 fusion, which drives STAT6 nuclear relocation. For extrathoracic SFTs, the clinical relevance of this molecular hallmark remains obscure. We assessed STAT6 immunoexpression for 61 extrathoracic SFTs exclusive of the meninges and head and neck, and 25 had analyzable RNAs to distinguish fusion variants by RT-PCR. The immunohistochemical and molecular findings were correlated with clincopathological features and disease-free survival (DFS). Twenty-eight males and 33 females had SFTs in the body cavities (n = 31), extremities (n = 17), and trunk (n = 13), categorized into 53 non-malignant and 8 malignant tumors. The vast majority (n = 57, 93%) exhibited distinctive STAT6 nuclear expression, including malignant ones. The common fusion variants were NAB2ex6-STAT6ex16/17 in 13 SFTs and NAB2ex4-STAT6ex2 in 8, while miscellaneous variants were detected only in 4 SFTs in the limbs and trunk but not in any body cavity-based cases (P = 0.026). The worse DFS was univariately associated with malignant histology (P = 0.04) but unrelated to tumor size, location, or fusion variant. Conclusively, extrathoracic SFTs mostly harbor NAB2ex6-STAT6ex16/17, followed by NAB2ex4-STAT6ex2. Miscellaneous variants are significantly rare in SFTs within the body cavities. The clinical aggressiveness of extrathoraic SFTs is associated with malignant histology but unrelated to the NAB2-STAT6 fusion variants.

  19. Genetic variability among Syphacia obvelata isolates from laboratory mice in four different geographical locations of China revealed by sequence analyses of five mitochondrial genes.

    PubMed

    Wang, Chun-Ren; Lou, Yan; Zhang, Yan; Wang, Wen-Tao; Zheng, Xu; Xu, Wen-Wen; Zhang, Ying; Tian, Si-Qin; Na, Lu; Chang, Qiao-Cheng

    2015-04-01

    Syphacia obvelata is a rodent nematode with high prevalence in laboratory mice. In the present study, we examined the genetic variability of S. obvelata from naturally infected laboratory mice in four different provinces, China. Five mitochondrial (mt) DNA regions, namely cytochrome c oxidase subunit 1 (pcox1), cytochrome b (pcytb), large subunit ribosomal RNA (prrnL) and NADH dehydrogenase subunits 1 and 5 (pnad1 and pnad5), were amplified separately from individual nematodes by PCR, and then sequenced directly. The size of the sequences of pcox1, pcytb, prrnL, pnad1 and pnad5 was 628 bp, 555 bp, 548 bp, 548 bp and 561 bp, respectively. While the intra-specific sequence variations within S. obvelata were 0-1.0% for pcox1, 0-1.6% for pcytb, 0-2.8% for prrnL, 0-2.0% for pnad1 and 0-1.8% for pnad5, the inter-specific sequence differences among members of the Oxyuridae were significantly higher, being 14.0-17.5% for pcox1, 27.5-32.9% for pcytb, 35.8-37.2% for prrnL, 22.2-26.8% for pnad1 and 22.3-25.2% for pnad5, respectively. Phylogenetic analyses based on combined sequences of four mt protein-coding genes, using Bayesian inference (BI), maximum likelihood (ML) and maximum parsimony (MP) methods, indicated that all of the S. obvelata samples grouped together with high statistical support, but samples from the same geographical origin did not always cluster together. These findings demonstrated the existence of low-level intra-specific variation in five mtDNA sequences among S. obvelata isolates from laboratory mice, but no obvious geographical distinction among S. obvelata isolates from laboratory mice in different geographic regions in China. These results provide basic information for further studies of systematics and population genetics of S. obvelata.

  20. Expansion of the. alpha. sub 2 -adrenergic receptor family: Cloning and characterization of a human. alpha. sub 2 -adrenergic receptor subtype, the gene for which is located on chromosome 2

    SciTech Connect

    Lomasney, J.W.; Lorenz, W.; Allen, L.F.; King, K.; Caron, M.G.; Lefkowitz, R.J. ); Regan, J.W. ); Yang-Feng, T.L. )

    1990-07-01

    Pharmacologic, biochemical, and genetic analyses have demonstrated the existence of multiple {alpha}{sub 2}-adrenergic receptor ({alpha}{sub 2}AR) subtypes. The authors have cloned a human {alpha}{sub 2}AR by using the polymerase chain reaction with oligonucleotide primers homologous to conserved regions of the previously cloned {alpha}{sub 2}ARs, the genes for which are located on human chromosomes 4 (C4) and 10 (C10). The deduced amino acid sequence encodes a protein of 450 amino acids whose putative topology is similar to that of the family of guanine nucleotide-binding protein-coupled receptors, but whose structure most closely resembles that of the {alpha}{sub 2}ARs. Competition curve analysis of the binding properties of the receptor expressed in COS-7 cells with a variety of adrenergic ligands demonstrates a unique {alpha}{sub 2}AR pharmacology. Hybridization with somatic cell hybrids shows that the gene for this receptor is located on chromosome 2. Northern blot analysis of various rat tissues shows expression in liver and kidney. The unique pharmacology and tissue localization of this receptor suggest that this is an {alpha}{sub 2}AR subtype not previously identified by classical pharmacological or ligand binding approaches.

  1. Overexpression of the genes PDC1 and ADH1 activates glycerol conversion to ethanol in the thermotolerant yeast Ogataea (Hansenula) polymorpha.

    PubMed

    Kata, Iwona; Semkiv, Marta V; Ruchala, Justyna; Dmytruk, Kostyantyn V; Sibirny, Andriy A

    2016-08-01

    Conversion of byproduct from biodiesel production glycerol to high-value compounds is of great importance. Ethanol is considered a promising product of glycerol bioconversion. The methylotrophic thermotolerant yeast Ogataea (Hansenula) polymorpha is of great interest for this purpose as the glycerol byproduct contains methanol and heavy metals as contaminants, and this yeast utilizes methanol and is relatively resistant to heavy metals. Besides, O. polymorpha shows robust growth on glycerol and produces ethanol from various carbon sources. The thermotolerance of this yeast is an additional advantage, allowing increased fermentation temperature to 45-48 °C, leading to increased rate of the fermentation process and a fall in the cost of distillation. The wild-type strain of O. polymorpha produces insignificant amounts of ethanol from glycerol (0.8 g/l). Overexpression of PDC1 coding for pyruvate decarboxylase enhanced ethanol production up to 3.1 g/l, whereas simultaneous overexpression of PDC1 and ADH1 (coding for alcohol dehydrogenase) led to further increase in ethanol production from glycerol. Moreover, the increased temperature of fermentation up to 45 °C stimulated the production of ethanol from glycerol used as the only carbon source up to 5.0 g/l, which exceeds the data obtained by methylotrophic yeast strains reported so far. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27256876

  2. Evidence for an association between non-syndromic cleft lip with or without cleft palate and a gene located on the long arm of chromosome 4

    SciTech Connect

    Healey, S.C.; Chenevix-Trench, G.; Mitchell, L.E.

    1994-09-01

    Evidence of linkage has been reported for non-syndromic cleft lip with or without cleft palate (CL{+-}P) and two markers (D4S175 and D4S192) in the region 4q25-4q31.3. The linkage evidence comes from a single Caucasian pedigree with multiple cases of CL{+-}P in five generations. High-density pedigrees are, however, atypical of CL{+-}P and linkage evidence obtained from such a family may not be relevant to the majority of CL{+-}P families. We have, therefore, examined the association of CL{+-}P with both D4S175 and D4S192 in 95 unrelated CL{+-}P patients and 161 unselected controls. There was no evidence for an association between D4S175 and CL{+-}P in these data. There was, however, a significant association between D4S192 and CL{+-}P ({chi}{sup 2}{sub 4}=15.5,P=0.006), and the genotypic distribution was significantly heterogeneous between CL{+-}P patients and controls (P=0.025). Comparison of each of the four most common alleles (i.e A87, A89, A91 and A95), to all other alleles combined, indicated that A87 was significantly less common (OR=0.56,95% C.I. 0.34-0.90), and A95 was significantly more common (OR=1.88,95% C.I. 1.03-3.43) among the CL{+-}P patients than the controls. Although of only borderline significance, A89 also appeared to be more common among patients than controls (OR=1.43,95% C.I. 0.99-2.60). Hence, it appears that genetic variation at a CL{+-}P susceptibility locus (CSL) linked to D4S192 may be associated with both increased and decreased risk of CL{+-}P. In combination, A89 and A95 are significantly more common in CL{+-}P patients than in controls (OR=1.80;95% C.I. 1.24-2.60) and account for a risk ratio of 1.08 in the first degree relatives of CL{+-}P patients. These results provide further evidence for the presence of a CSL in the region 4q25-4q31.1, and indicate that the putative CSL is located closer to D4S192 than to D4S175.

  3. Conversion of MDCK cell line to suspension culture by transfecting with human siat7e gene and its application for influenza virus production.

    PubMed

    Chu, Chia; Lugovtsev, Vladimir; Golding, Hana; Betenbaugh, Michael; Shiloach, Joseph

    2009-09-01

    MDCK cells are currently being considered as an alternative to embryonated eggs for influenza virus propagation and hemagglutinin (HA) production intended for vaccine manufacturing. MDCK cells were found suitable for the virus production but their inability to grow in suspension burdens the process of scale up and hence their production capability. Anchorage-dependent MDCK cells were converted to anchorage-independent cells, capable of growing in suspension as a result of transfection with the human siat7e gene (ST6GalNac V). This gene was previously identified as having an important role in cellular adhesion when the transcriptions of genes from anchorage-dependent and anchorage-independent HeLa cells were compared. Unlike the parental MDCK cells, the siat7e-expressing cells were capable of growing in shake flasks as suspension cultures, achieving maximum concentration of 7 x 10(5) cells/mL while keeping close to 100% viability throughout the growth phase. In production experiments, the siat7e-expressing cells were infected with the Influenza B/Victoria/504/2000 strain. It was determined that the cell-derived viruses retained similar antigenic properties as those obtained from egg-derived viruses and their nucleotide sequences were identical. The specific production of hemagglutinin (expressed in hemagglutination units per 10(6) cells) from the siat7e-expressing cells was approximately 20 times higher than the specific production from the parental MDCK cells. If this suspension process scales up, the production potential of HA from 10 L of siat7e-expressing cells at a concentration of 10(6) cells/mL would be equivalent to the amount of HA obtained from 10,000 embryonated eggs. PMID:19706449

  4. Conversion of MDCK cell line to suspension culture by transfecting with human siat7e gene and its application for influenza virus production

    PubMed Central

    Chu, Chia; Lugovtsev, Vladimir; Golding, Hana; Betenbaugh, Michael; Shiloach, Joseph

    2009-01-01

    MDCK cells are currently being considered as an alternative to embryonated eggs for influenza virus propagation and hemagglutinin (HA) production intended for vaccine manufacturing. MDCK cells were found suitable for the virus production but their inability to grow in suspension burdens the process of scale up and hence their production capability. Anchorage-dependent MDCK cells were converted to anchorage-independent cells, capable of growing in suspension as a result of transfection with the human siat7e gene (ST6GalNac V). This gene was previously identified as having an important role in cellular adhesion when the transcriptions of genes from anchorage-dependent and anchorage-independent HeLa cells were compared. Unlike the parental MDCK cells, the siat7e-expressing cells were capable of growing in shake flasks as suspension cultures, achieving maximum concentration of 7 × 105 cells/mL while keeping close to 100% viability throughout the growth phase. In production experiments, the siat7e-expressing cells were infected with the Influenza B/Victoria/504/2000 strain. It was determined that the cell-derived viruses retained similar antigenic properties as those obtained from egg-derived viruses and their nucleotide sequences were identical. The specific production of hemagglutinin (expressed in hemagglutination units per 106 cells) from the siat7e-expressing cells was approximately 20 times higher than the specific production from the parental MDCK cells. If this suspension process scales up, the production potential of HA from 10 L of siat7e-expressing cells at a concentration of 106 cells/mL would be equivalent to the amount of HA obtained from 10,000 embryonated eggs. PMID:19706449

  5. Direct comparison between genomic constitution and flavonoid contents in Allium multiple alien addition lines reveals chromosomal locations of genes related to biosynthesis from dihydrokaempferol to quercetin glucosides in scaly leaf of shallot (Allium cepa L.).

    PubMed

    Masuzaki, S; Shigyo, M; Yamauchi, N

    2006-02-01

    The extrachromosome 5A of shallot (Allium cepa L., genomes AA) has an important role in flavonoid biosynthesis in the scaly leaf of Allium fistulosum-shallot monosomic addition lines (FF+nA). This study deals with the production and biochemical characterisation of A. fistulosum-shallot multiple alien addition lines carrying at least 5A to determine the chromosomal locations of genes for quercetin formation. The multiple alien additions were selected from the crossing between allotriploid FFA (female symbol) and A. fistulosum (male symbol). The 113 plants obtained from this cross were analysed by a chromosome 5A-specific PGI isozyme marker of shallot. Thirty plants were preliminarily selected for an alien addition carrying 5A. The chromosome numbers of the 30 plants varied from 18 to 23. The other extrachromosomes in 19 plants were completely identified by using seven other chromosome markers of shallot. High-performance liquid chromatography analyses of the 19 multiple additions were conducted to identify the flavonoid compounds produced in the scaly leaves. Direct comparisons between the chromosomal constitution and the flavonoid contents of the multiple alien additions revealed that a flavonoid 3'-hydroxylase (F3'H) gene for the synthesis of quercetin from kaempferol was located on 7A and that an anonymous gene involved in the glucosidation of quercetin was on 3A or 4A. As a result of supplemental SCAR analyses by using genomic DNAs from two complete sets of A. fistulosum-shallot monosomic additions, we have assigned F3'H to 7A and flavonol synthase to 4A.

  6. Direct comparison between genomic constitution and flavonoid contents in Allium multiple alien addition lines reveals chromosomal locations of genes related to biosynthesis from dihydrokaempferol to quercetin glucosides in scaly leaf of shallot (Allium cepa L.).

    PubMed

    Masuzaki, S; Shigyo, M; Yamauchi, N

    2006-02-01

    The extrachromosome 5A of shallot (Allium cepa L., genomes AA) has an important role in flavonoid biosynthesis in the scaly leaf of Allium fistulosum-shallot monosomic addition lines (FF+nA). This study deals with the production and biochemical characterisation of A. fistulosum-shallot multiple alien addition lines carrying at least 5A to determine the chromosomal locations of genes for quercetin formation. The multiple alien additions were selected from the crossing between allotriploid FFA (female symbol) and A. fistulosum (male symbol). The 113 plants obtained from this cross were analysed by a chromosome 5A-specific PGI isozyme marker of shallot. Thirty plants were preliminarily selected for an alien addition carrying 5A. The chromosome numbers of the 30 plants varied from 18 to 23. The other extrachromosomes in 19 plants were completely identified by using seven other chromosome markers of shallot. High-performance liquid chromatography analyses of the 19 multiple additions were conducted to identify the flavonoid compounds produced in the scaly leaves. Direct comparisons between the chromosomal constitution and the flavonoid contents of the multiple alien additions revealed that a flavonoid 3'-hydroxylase (F3'H) gene for the synthesis of quercetin from kaempferol was located on 7A and that an anonymous gene involved in the glucosidation of quercetin was on 3A or 4A. As a result of supplemental SCAR analyses by using genomic DNAs from two complete sets of A. fistulosum-shallot monosomic additions, we have assigned F3'H to 7A and flavonol synthase to 4A. PMID:16411131

  7. The Drosophila melanogaster homologue of the Xeroderma pigmentosum D gene product is located in euchromatic regions and has a dynamic response to UV light-induced lesions in polytene chromosomes.

    PubMed

    Reynaud, E; Lomelí, H; Vázquez, M; Zurita, M

    1999-04-01

    The XPD/ERCC2/Rad3 gene is required for excision repair of UV-damaged DNA and is an important component of nucleotide excision repair. Mutations in the XPD gene generate the cancer-prone syndrome, xeroderma pigmentosum, Cockayne's syndrome, and trichothiodystrophy. XPD has a 5'- to 3'-helicase activity and is a component of the TFIIH transcription factor, which is essential for RNA polymerase II elongation. We present here the characterization of the Drosophila melanogaster XPD gene (DmXPD). DmXPD encodes a product that is highly related to its human homologue. The DmXPD protein is ubiquitous during development. In embryos at the syncytial blastoderm stage, DmXPD is cytoplasmic. At the onset of transcription in somatic cells and during gastrulation in germ cells, DmXPD moves to the nuclei. Distribution analysis in polytene chromosomes shows that DmXPD is highly concentrated in the interbands, especially in the highly transcribed regions known as puffs. UV-light irradiation of third-instar larvae induces an increase in the signal intensity and in the number of sites where the DmXPD protein is located in polytene chromosomes, indicating that the DmXPD protein is recruited intensively in the chromosomes as a response to DNA damage. This is the first time that the response to DNA damage by UV-light irradiation can be visualized directly on the chromosomes using one of the TFIIH components.

  8. Biotechnology of biomass conversion

    SciTech Connect

    Wayman, M.; Parekh, S.R.

    1990-01-01

    This book covers: An introduction to biomass crops; The microbiology of fermentation processes; The production of ethanol from biomass crops, such as sugar cane and rubbers; The energy of biomass conversion; and The economics of biomass conversion.

  9. IncM Plasmid R1215 Is the Source of Chromosomally Located Regions Containing Multiple Antibiotic Resistance Genes in the Globally Disseminated Acinetobacter baumannii GC1 and GC2 Clones

    PubMed Central

    Blackwell, Grace A.

    2016-01-01

    ABSTRACT Clear similarities between antibiotic resistance islands in the chromosomes of extensively antibiotic-resistant isolates from the two dominant, globally distributed Acinetobacter baumannii clones, GC1 and GC2, suggest a common origin. A close relative of the likely progenitor of both of these regions was found in R1215, a conjugative IncM plasmid from a Serratia marcescens strain isolated prior to 1980. The 37.8-kb resistance region in R1215 lies within the mucB gene and includes aacC1, aadA1, aphA1b, blaTEM, catA1, sul1, and tetA(A), genes that confer resistance to gentamicin, streptomycin and spectinomycin, kanamycin and neomycin, ampicillin, chloramphenicol, sulfamethoxazole, and tetracycline, respectively. The backbone of this region is derived from Tn1721 and is interrupted by a hybrid Tn2670 (Tn21)-Tn1696-type transposon, Tn6020, and an incomplete Tn1. After minor rearrangements, this R1215 resistance island can generate AbGRI2-0*, the predicted earliest form of the IS26-bounded AbGRI2-type resistance island of GC2 isolates, and to the multiple antibiotic resistance region (MARR) of AbaR0, the precursor of this region in AbaR-type resistance islands in the GC1 group. A 29.9-kb circle excised by IS26 has been inserted into the A. baumannii chromosome to generate AbGRI2-0*. To create the MARR of AbaR0, a different circular form, again generated by IS26 from an R1215 resistance region variant, has been opened at a different point by recombination with a copy of the sul1 gene already present in the AbaR precursor. Recent IncM plasmids related to R1215 have a variant resistance island containing a blaSHV gene in the same location. IMPORTANCE Two lineages of extensively antibiotic-resistant A. baumannii currently plaguing modern medicine each acquired resistance to all of the original antibiotics (ampicillin, tetracycline, kanamycin, and sulfonamides) by the end of the 1970s and then became resistant to antibiotics from newer families after they were

  10. Direct Conversion of Energy.

    ERIC Educational Resources Information Center

    Corliss, William R.

    This publication is one of a series of information booklets for the general public published by the United States Atomic Energy Commission. Direct energy conversion involves energy transformation without moving parts. The concepts of direct and dynamic energy conversion plus the laws governing energy conversion are investigated. Among the topics…

  11. Engineering the central pathways in Lactococcus lactis: functional expression of the phosphofructokinase (pfk) and alternative oxidase (aox1) genes from Aspergillus niger in Lactococcus lactis facilitates improved carbon conversion rates under oxidizing conditions.

    PubMed

    Papagianni, Maria; Avramidis, Nicholaos

    2012-08-10

    The present work describes a novel central pathway engineering method that has been designed with the aim to increase the carbon conversion rates under oxidizing conditions in L. lactis fermentations. The nisin producer L. lactis ATCC11454 strain has been genetically engineered by cloning a truncated version of the phosphofructokinase gene (pfk13), along with the pkaC, encoding for the catalytic subunit of cAMP-dependent protein kinase, and the alternative oxidase (aox1) genes of A. niger. Functional expression of the above genes resulted in enhanced PFK activity and the introduction of AOX activity and alternative respiration in the presence of a source of heme in the substrate, under fully aerobic growth conditions. The constructed strain is capable of fermenting high concentrations of glucose as was demonstrated in a series of glucostat fed-batch fermentations with glucose levels maintained at 55, 138 and 277 mM. The high maximum specific uptake rate of glucose of 1.8 mMs(-1)gCDW(-1) at 277 mM glucose is characteristic of the improved ability of the microorganism to handle elevated glucose concentrations under conditions otherwise causing severe reduction of PFK activity. The increased carbon flow through glycolysis led to increased protein synthesis that was reflected in increased biomass and nisin levels. The pfk 13-pkaC-aox1-transformant strain's fermentation at 277 mM glucose gave a final biomass concentration of 7.5 g/l and nisin activity of 14,000 IU/ml which is, compared to the parental strain's production levels at its optimal 55 mM glucose, increased by a factor of 2.34 for biomass and 4.37 for nisin. PMID:22759530

  12. Automatic microscopy for mitotic cell location.

    NASA Technical Reports Server (NTRS)

    Herron, J.; Ranshaw, R.; Castle, J.; Wald, N.

    1972-01-01

    Advances are reported in the development of an automatic microscope with which to locate hematologic or other cells in mitosis for subsequent chromosome analysis. The system under development is designed to perform the functions of: slide scanning to locate metaphase cells; conversion of images of selected cells into binary form; and on-line computer analysis of the digitized image for significant cytogenetic data. Cell detection criteria are evaluated using a test sample of 100 mitotic cells and 100 artifacts.

  13. Static conversion systems

    NASA Astrophysics Data System (ADS)

    Ewell, R.; Mondt, J.

    Historically, all space power systems that have actually flown in space have relied on static energy conversion technology. Thus, static conversion is being considered for space nuclear power systems as well. There are four potential static conversion technologies which should be considered. These include: the alkali metal thermoelectric converter (AMTEC), the thermionic converter, the thermoelectric converter, and the thermophotovoltaic converter (TPV). These four conversion technologies will be described in brief detail along with their current status and development needs. In addition, the systems implications of using each of these conversion technologies with a space nuclear reactor power system will be evaluated and some comparisons made.

  14. Nucleotide sequences of the fecBCDE genes and locations of the proteins suggest a periplasmic-binding-protein-dependent transport mechanism for iron(III) dicitrate in Escherichia coli.

    PubMed Central

    Staudenmaier, H; Van Hove, B; Yaraghi, Z; Braun, V

    1989-01-01

    The fec region of the Escherichia coli chromosome determines a citrate-dependent iron(III) transport system. The nucleotide sequence of fec revealed five genes, fecABCDE, which are transcribed from fecA to fecE. The fecA gene encodes a previously described outer membrane receptor protein. The fecB gene product is formed as a precursor protein with a signal peptide of 21 amino acids; the mature form, with a molecular weight of 30,815, was previously found in the periplasm. The fecB genes of E. coli B and E. coli K-12 differed in 3 nucleotides, of which 2 gave rise to conservative amino acid exchanges. The fecC and fecD genes were found to encode very hydrophobic polypeptides with molecular weights of 35,367 and 34,148, respectively, both of which are localized in the cytoplasmic membrane. The fecE product was a rather hydrophilic but cytoplasmic membrane-bound protein of Mr 28,189 and contained regions of extensive homology to ATP-binding proteins. The number, structural characteristics, and locations of the FecBCDE proteins were typical for a periplasmic-binding-protein-dependent transport system. It is proposed that after FecA- and TonB-dependent transport of iron(III) dicitrate across the outer membrane, uptake through the cytoplasmic membrane follows the binding-protein-dependent transport mechanism. FecC and FecD exhibited homologies to each other, to the N- and C-terminal halves of FhuB of the iron(III) hydroxamate transport system, and to BtuC of the vitamin B12 transport system. FecB showed some homology to FhuD, suggesting that the latter may function in the same manner as a binding protein in iron(III) hydroxamate transport. The close homology between the proteins of the two iron transport systems and of the vitamin B12 transport system indicates a common evolution for all three systems. Images PMID:2651410

  15. Molecular cloning and tissue expression of FAT, the human homologue of the Drosophila fat gene that is located on chromosome 4q34-q35 and encodes a putative adhesion molecule

    SciTech Connect

    Dunne, P. Owen, M.J.; Hanby, A.M.; Poulsom, R.

    1995-11-20

    FAT, a new member of the human cadherin super-family, has been isolated from the T-leukemia cell line J6. The predicted protein closely resembles the Drosophila tumor suppressor fat, which is essential for controlling cell proliferation during Drosophila development. The gene has the potential to encode a large transmembrane protein of nearly 4600 residues with 34 tandem cadherin repeats, five EGF-like repeats, and a laminin A-G domain. The cytoplasmic sequence contains two domains with distant homology to the cadherin catenin-binding region. Northern blotting analysis of J6 mRNA demonstrated full-length, approximately 15-kb, FAT message in addition to several 5{prime}-truncated transcripts. In addition to its presence in J6 cells, in situ hybridization revealed FAT mRNA expression in epithelia and in some mesenchymal compartments. Furthermore, higher levels of expression were observed in fetal, as opposed to adult, tissue, suggesting that its expression may be developmentally regulated in these tissues. FAT shows homologies with a number of proteins important in developmental decisions and cell:cell communication and is the first fat-like protein reported in vertebrates. The gene encoding FAT was located by in situ hybridization on chromosome 4q34-q35. We propose that this family of molecules is likely to be important in mammalian developmental processes and cell communication. 80 refs., 10 figs., 1 tab.

  16. Location, Location, Location: Development of Spatiotemporal Sequence Learning in Infancy

    ERIC Educational Resources Information Center

    Kirkham, Natasha Z.; Slemmer, Jonathan A.; Richardson, Daniel C.; Johnson, Scott P.

    2007-01-01

    We investigated infants' sensitivity to spatiotemporal structure. In Experiment 1, circles appeared in a statistically defined spatial pattern. At test 11-month-olds, but not 8-month-olds, looked longer at a novel spatial sequence. Experiment 2 presented different color/shape stimuli, but only the location sequence was violated during test;…

  17. Unique class 1 integron and multiple resistance genes co-located on IncHI2 plasmid is associated with the emerging multidrug resistance of Salmonella Indiana isolated from chicken in China.

    PubMed

    Lai, Jing; Wang, Yang; Shen, Jianzhong; Li, Ruichao; Han, Jing; Foley, Steven L; Wu, Congming

    2013-07-01

    The objective of this study was to clarify the molecular antimicrobial resistance mechanisms of Salmonella enterica serovar Indiana isolated from chickens in China. A total of 327 chicken intestinal content and feces were collected in Shandong, China in 2009. Isolates were serotyped and antimicrobial susceptibility testing was performed. Thirty-five (10.7%) Salmonella isolates were recovered, and 16 (45.7%) were Salmonella enterica serovar Indiana, which were resistant to at least 14 of 15 antimicrobial agents. The 16 Salmonella enterica serovar Indiana detected and other 13 Salmonella enterica serovar Indiana that were selected from 133 Salmonella enterica serovar Indiana isolated in 2008 were subjected to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Then class 1 integron and drug resistance genes were detected by polymerase chain reaction. Linkage between plasmids and resistance components was determined by conjugation, electrotransformation, S1 nuclease-PFGE, polymerase chain reaction-based replicon typing and Southern blot assays. Regions flanking integrons were sequenced by modified random primer walking strategy. PFGE and MLST suggested that all the 29 Salmonella enterica serovar Indiana isolates that shared >78% similarity in PFGE patterns were of the same MLST type, ST17. Two kinds of class 1 integrons had different integrase genes and the same variable region (dfrA7/aadA4/IS26/aac(6')-Ib/blaOXA-1/catB3/arr-3), and additional antimicrobial resistance genes such as blaCTX-M-24, floR, and so on were detected on IncHI2 plasmids in 29 Salmonella enterica serovar Indiana, and seven plasmids were conjugative. Analysis of the genetic environment of the integrons suggested that these integrons might have been formed by the help of IS26. To our knowledge, the variable region in class 1 integrons is the longest reported in Salmonella to date. The unique integrons and multiple resistance genes co-located on the IncHI2 plasmid

  18. Conversing with Computers

    NASA Technical Reports Server (NTRS)

    2004-01-01

    I/NET, Inc., is making the dream of natural human-computer conversation a practical reality. Through a combination of advanced artificial intelligence research and practical software design, I/NET has taken the complexity out of developing advanced, natural language interfaces. Conversational capabilities like pronoun resolution, anaphora and ellipsis processing, and dialog management that were once available only in the laboratory can now be brought to any application with any speech recognition system using I/NET s conversational engine middleware.

  19. Locating Continuing Education Programs.

    ERIC Educational Resources Information Center

    Mason, Robert C.

    1986-01-01

    Emphasizes program location as an important component of the marketing plan for continuing education. Also discusses relations among program location and quality, costs, supportive services, and economies of scale. (CH)

  20. Cable-fault locator

    NASA Technical Reports Server (NTRS)

    Cason, R. L.; Mcstay, J. J.; Heymann, A. P., Sr.

    1979-01-01

    Inexpensive system automatically indicates location of short-circuited section of power cable. Monitor does not require that cable be disconnected from its power source or that test signals be applied. Instead, ground-current sensors are installed in manholes or at other selected locations along cable run. When fault occurs, sensors transmit information about fault location to control center. Repair crew can be sent to location and cable can be returned to service with minimum of downtime.

  1. Analysis of in vivo oocyte maturation, in vitro embryo development and gene expression in cumulus cells of dairy cows and heifers selected for one fertility quantitative trait loci (QTL) located on BTA3.

    PubMed

    Coyral-Castel, S; Brisard, D; Touzé, J-L; Dupont, M; Ramé, C; Uzbekova, S; Dupont, J

    2012-06-01

    We have previously shown that Holstein cows selected for their homozygous favorable ("fertil+") or unfavorable ("fertil-") haplotype at one quantitative trait loci (QTL) of female fertility located on chromosome 3 (QTL-F-Fert-BTA3) had a different success rate 35 and 90 days after the first artificial insemination. To determine whether the lower fertility in "fertil-" animals could be related to oocyte quality, we analyzed the embryo development rate in vitro and the oocyte meiotic maturation in vivo in "fertil+" and "fertil-" heifers. In vitro maturation and fertilization of immature oocytes recovered by ovum pick-up from "fertil+" and "fertil-" heifers resulted in similar cleavage and blastocyst rates in the two haplotypes. However the percentage of expanded blastocysts and the number of cells per blastocyst were significantly higher in "fertil+". Oocytes from presumptive preovulatory follicles were analyzed after ovarian stimulation. A similar rate of immature (from prophase to metaphase-I) and mature oocytes (metaphase-II) was obtained in the two haplotypes, whereas a significantly higher percentage of oocytes from metaphase-I to metaphase-II was observed in "fertil+" compared to "fertil-" heifers. Since cumulus cells (CCs) could reflect the developmental competence of oocytes, we analyzed the expression of seven genes included in the QTL-F-Fert-BTA3 using real-time PCR in bovine CCs after in vivo or in vitro maturation, as a model of higher and lower competence, respectively. Transcript levels of TAGLN2, EEF1A1 and PIGM were higher in CCs after in vitro maturation (IVM) compared to in vivo maturation, whereas no difference was observed for IFI16, KIRREL, SPTA1 and PEX19 expression. The expression levels of all these genes in in preovulatory CCs were not significantly different between "fertil+" and "fertil-" heifers. In conclusion, the lower fertility of "fertil-" females could be partially due to a lowest quality of the oocytes and consequently of

  2. Deletion 6(p25.1) in a child with mild dysmorphic features and absence of major eye malformations: Implications for the location of genes involved in ocular development

    SciTech Connect

    Tepperberg, J.H.; Rao, K.W.; Albright, S.G.

    1994-09-01

    The authors describe a young girl with an apparently terminal deletion of chromosome 6 at p25.1 Fluorescence in situ hybridization with a chromosome 6 painting probe (ONCOR), showed that the abnormal chromosome 6 is composed entirely of chromosome 6 material. Analysis of the parents chromosomes with the same paint probe ruled out an inherited structural abnormality. To our knowledge, this case is the smallest terminal deletion of 6p yet reported. The patient is a 4 year, 6 month old female who was 3300g at birth. She has global developmental delay and little intelligible speech. Her weight is at the 25th centile, height at the 50th centile for a 3 1/2-year-old, and head circumference at the 25th centile. The eyes are prominent with shallow orbits. She has mild hyperopia and astigmatism. The philtrum is short and the vermillion border is thin. The midface is hypoplastic and there is dental malocclusion. Some of the common features reported in individuals with larger 6p terminal deletions include mental retardation, microcephaly, eye and ear abnormalities, short neck/excess nuchal skin, and flat broad nasal bridge. Our patient lacks several of the features reported in patients with larger deletions of 6p, including the more severe eye defects (e.g., anterior segment malformations including Peters and Rieger anomalies) described in individuals with 6p23 or 24 terminal deletions. This patient could be important in mapping the critical region for 6p deletion syndrome and for localizing clinical findings to a specific area of 6p. This case also raises the possibility that the gene(s) on 6p important for ocular growth and development are located proximal to 6p25.1.

  3. Location, Location, Location: Where Do Location-Based Services Fit into Your Institution's Social Media Mix?

    ERIC Educational Resources Information Center

    Nekritz, Tim

    2011-01-01

    Foursquare is a location-based social networking service that allows users to share their location with friends. Some college administrators have been thinking about whether and how to take the leap into location-based services, which are also known as geosocial networking services. These platforms, which often incorporate gaming elements like…

  4. The Conversation Class

    ERIC Educational Resources Information Center

    Jackson, Acy L.

    2012-01-01

    The conversation class occupies a unique place in the process of learning English as a second or foreign language. From the author's own experience in conducting special conversation classes with Persian-speaking adults, he has drawn up a number of simple but important guidelines, some of which he hopes may provide helpful suggestions for the…

  5. NUCLEAR CONVERSION APPARATUS

    DOEpatents

    Seaborg, G.T.

    1960-09-13

    A nuclear conversion apparatus is described which comprises a body of neutron moderator, tubes extending therethrough, uranium in the tubes, a fluid- circulating system associated with the tubes, a thorium-containing fluid coolant in the system and tubes, and means for withdrawing the fluid from the system and replacing it in the system whereby thorium conversion products may be recovered.

  6. Energy conversion alternatives study

    NASA Technical Reports Server (NTRS)

    Shure, L. T.

    1979-01-01

    Comparison of coal based energy systems is given. Study identifies and compares various advanced energy conversion systems using coal or coal derived fuels for baselaoad electric power generation. Energy Conversion Alternatives Study (ECAS) reports provede government, industry, and general public with technically consistent basis for comparison of system's options of interest for fossilfired electric-utility application.

  7. Common conversion factors.

    PubMed

    2001-05-01

    This appendix presents tables of some of the more common conversion factors for units of measure used throughout Current Protocols manuals, as well as prefixes indicating powers of ten for SI units. Another table gives conversions between temperatures on the Celsius (Centigrade) and Fahrenheit scales. PMID:18770653

  8. Assessment through Conversation.

    ERIC Educational Resources Information Center

    Fu, Danling; Lamme, Linda L.

    2002-01-01

    Presents conversations with parents, teachers, and children around portfolios that provide a better picture of a child's growth and understanding than standardized test scores ever can. Concludes that the involvement of students, teachers, and parents in conversation about children's literacy development brings the potential of a common vision and…

  9. 36 CFR 72.72 - Conversion requirements.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... converted to other than public recreation uses. A conversion will only be approved if it is found to be in... permission to convert UPARR assisted properties in whole or in part to other than public recreation uses must... converted property. Equivalent usefulness and location will be determined based on the following...

  10. Homologs of Escherichia coli recJ, gltX and of a putative 'early' gene of avian Chlamydia psittaci are located upstream of the 'late' omp2 locus of Chlamydia psittaci strain guinea pig inclusion conjunctivitis.

    PubMed

    Hsia, R C; Bavoil, P M

    1996-10-17

    The nucleotide sequence of nearly 6 kb of genomic DNA located immediately upstream of the omp3-omp2 operon of Chlamydia psittaci strain GPIC was obtained, revealing four significant open reading frames (ORFs), named ORF1, ORF2, ORF4 and ORF5. Searches for homologous sequences in the GenBank/EMBL databases have revealed that: (a) the open-ended ORF1 putatively encodes an homolog of RecJ of Escherichia coli, thought to be required for RecBCD-independent and conjugational recombination, and for UV repair; (b) the predicted translation product of ORF4 is highly homologous to the putative product of EUO, a previously described ORF of avian C. psittaci strain 6BC which is preferentially transcribed early during the life cycle; and (c) ORF5 putatively encodes an homolog of bacterial glutamyl-tRNA synthetases. This analysis establishes the genetic linkage of late (omp3-omp2) and of a proposed early (EUO) genes in Chlamydia.

  11. Postoperative conversion disorder.

    PubMed

    Afolabi, Kola; Ali, Sameer; Gahtan, Vivian; Gorji, Reza; Li, Fenghua; Nussmeier, Nancy A

    2016-05-01

    Conversion disorder is a psychiatric disorder in which psychological stress causes neurologic deficits. A 28-year-old female surgical patient had uneventful general anesthesia and emergence but developed conversion disorder 1 hour postoperatively. She reported difficulty speaking, right-hand numbness and weakness, and right-leg paralysis. Neurologic examination and imaging revealed no neuronal damage, herniation, hemorrhage, or stroke. The patient mentioned failing examinations the day before surgery and discontinuing her prescribed antidepressant medication, leading us to diagnose conversion disorder, with eventual confirmation by neuroimaging and follow-up examinations.

  12. Postoperative conversion disorder.

    PubMed

    Afolabi, Kola; Ali, Sameer; Gahtan, Vivian; Gorji, Reza; Li, Fenghua; Nussmeier, Nancy A

    2016-05-01

    Conversion disorder is a psychiatric disorder in which psychological stress causes neurologic deficits. A 28-year-old female surgical patient had uneventful general anesthesia and emergence but developed conversion disorder 1 hour postoperatively. She reported difficulty speaking, right-hand numbness and weakness, and right-leg paralysis. Neurologic examination and imaging revealed no neuronal damage, herniation, hemorrhage, or stroke. The patient mentioned failing examinations the day before surgery and discontinuing her prescribed antidepressant medication, leading us to diagnose conversion disorder, with eventual confirmation by neuroimaging and follow-up examinations. PMID:27041258

  13. Reversible micromachining locator

    DOEpatents

    Salzer, Leander J.; Foreman, Larry R.

    1999-01-01

    This invention provides a device which includes a locator, a kinematic mount positioned on a conventional tooling machine, a part carrier disposed on the locator and a retainer ring. The locator has disposed therein a plurality of steel balls, placed in an equidistant position circumferentially around the locator. The kinematic mount includes a plurality of magnets which are in registry with the steel balls on the locator. In operation, a blank part to be machined is placed between a surface of a locator and the retainer ring (fitting within the part carrier). When the locator (with a blank part to be machined) is coupled to the kinematic mount, the part is thus exposed for the desired machining process. Because the locator is removably attachable to the kinematic mount, it can easily be removed from the mount, reversed, and reinserted onto the mount for additional machining. Further, the locator can likewise be removed from the mount and placed onto another tooling machine having a properly aligned kinematic mount. Because of the unique design and use of magnetic forces of the present invention, positioning errors of less than 0.25 micrometer for each machining process can be achieved.

  14. Reversible micromachining locator

    DOEpatents

    Salzer, L.J.; Foreman, L.R.

    1999-08-31

    This invention provides a device which includes a locator, a kinematic mount positioned on a conventional tooling machine, a part carrier disposed on the locator and a retainer ring. The locator has disposed therein a plurality of steel balls, placed in an equidistant position circumferentially around the locator. The kinematic mount includes a plurality of magnets which are in registry with the steel balls on the locator. In operation, a blank part to be machined is placed between a surface of a locator and the retainer ring (fitting within the part carrier). When the locator (with a blank part to be machined) is coupled to the kinematic mount, the part is thus exposed for the desired machining process. Because the locator is removably attachable to the kinematic mount, it can easily be removed from the mount, reversed, and reinserted onto the mount for additional machining. Further, the locator can likewise be removed from the mount and placed onto another tooling machine having a properly aligned kinematic mount. Because of the unique design and use of magnetic forces of the present invention, positioning errors of less than 0.25 micrometer for each machining process can be achieved. 7 figs.

  15. Semantic Location Extraction from Crowdsourced Data

    NASA Astrophysics Data System (ADS)

    Koswatte, S.; Mcdougall, K.; Liu, X.

    2016-06-01

    Crowdsourced Data (CSD) has recently received increased attention in many application areas including disaster management. Convenience of production and use, data currency and abundancy are some of the key reasons for attracting this high interest. Conversely, quality issues like incompleteness, credibility and relevancy prevent the direct use of such data in important applications like disaster management. Moreover, location information availability of CSD is problematic as it remains very low in many crowd sourced platforms such as Twitter. Also, this recorded location is mostly related to the mobile device or user location and often does not represent the event location. In CSD, event location is discussed descriptively in the comments in addition to the recorded location (which is generated by means of mobile device's GPS or mobile communication network). This study attempts to semantically extract the CSD location information with the help of an ontological Gazetteer and other available resources. 2011 Queensland flood tweets and Ushahidi Crowd Map data were semantically analysed to extract the location information with the support of Queensland Gazetteer which is converted to an ontological gazetteer and a global gazetteer. Some preliminary results show that the use of ontologies and semantics can improve the accuracy of place name identification of CSD and the process of location information extraction.

  16. Responsive Teaching through Conversation

    ERIC Educational Resources Information Center

    Dozier, Cheryl; Garnett, Susan; Tabatabai, Simeen

    2011-01-01

    Conversations are the heart of responsive teaching. By talking with struggling learners, teachers can find out about their interests in order to design effective, personalized instruction; build relationships; work through complexities in teaching and learning; and celebrate successes.

  17. Photochemical Energy Conversion.

    ERIC Educational Resources Information Center

    Batschelet, William H.; George, Arnold

    1986-01-01

    Describes procedures for two demonstrations: (1) photochemical energy conversion using ferric oxalate actinometry and (2) liquification of gases using Freon 114. Safety precautions are given for both demonstrations, as are procedures and material specifications. (JM)

  18. Methane conversion process

    SciTech Connect

    Gaffney, A.M.; Jones, C.A.; Sofranko, J.A.

    1989-01-03

    This patent describes a process for the conversion of methane to higher hydrocarbons and coproduct water wherein methane is contacted at reactive conditions with a conversion catalyst comprised of a reducible metal oxide selected from the group consisting of an oxide of manganese, tin, indium, germanium, antimony, leads, bismuth, cerium, praseodymium, terbium, iron, and ruthenium. The improvement consists of: pretreating the catalyst before use in the conversion of methane to higher hydrocarbons and coproduct water with a reducing agent at 650/sup 0/C to 1200/sup 0/C for a time sufficient to improve the bulk density and attrition resistance of the catalyst and thereafter contacting the pretreated catalyst with methane at methane conversion conditions effective to form higher hydrocarbons and coproduct water.

  19. Structured luminescence conversion layer

    DOEpatents

    Berben, Dirk; Antoniadis, Homer; Jermann, Frank; Krummacher, Benjamin Claus; Von Malm, Norwin; Zachau, Martin

    2012-12-11

    An apparatus device such as a light source is disclosed which has an OLED device and a structured luminescence conversion layer deposited on the substrate or transparent electrode of said OLED device and on the exterior of said OLED device. The structured luminescence conversion layer contains regions such as color-changing and non-color-changing regions with particular shapes arranged in a particular pattern.

  20. Conversion of solar energy

    NASA Astrophysics Data System (ADS)

    Semenov, N. N.; Shilov, A. E.

    The papers presented in this volume provide an overview of current theoretical and experimental research related to the conversion and practical utilization of solar energy. Topics discussed include semiconductor photovoltaic cells, orbital solar power stations, chemical and biological methods of solar energy conversion, and solar energy applications. Papers are included on new theoretical models of solar cells and prospects for increasing their efficiency, metrology and optical studies of solar cells, and some problems related to the thermally induced deformations of large space structures.

  1. Object locating system

    DOEpatents

    Novak, James L.; Petterson, Ben

    1998-06-09

    A sensing system locates an object by sensing the object's effect on electric fields. The object's effect on the mutual capacitance of electrode pairs varies according to the distance between the object and the electrodes. A single electrode pair can sense the distance from the object to the electrodes. Multiple electrode pairs can more precisely locate the object in one or more dimensions.

  2. Reversible micromachining locator

    DOEpatents

    Salzer, Leander J.; Foreman, Larry R.

    2002-01-01

    A locator with a part support is used to hold a part onto the kinematic mount of a tooling machine so that the part can be held in or replaced in exactly the same position relative to the cutting tool for machining different surfaces of the part or for performing different machining operations on the same or different surfaces of the part. The locator has disposed therein a plurality of steel balls placed at equidistant positions around the planar surface of the locator and the kinematic mount has a plurality of magnets which alternate with grooves which accommodate the portions of the steel balls projecting from the locator. The part support holds the part to be machined securely in place in the locator. The locator can be easily detached from the kinematic mount, turned over, and replaced onto the same kinematic mount or another kinematic mount on another tooling machine without removing the part to be machined from the locator so that there is no need to touch or reposition the part within the locator, thereby assuring exact replication of the position of the part in relation to the cutting tool on the tooling machine for each machining operation on the part.

  3. Sensors Locate Radio Interference

    NASA Technical Reports Server (NTRS)

    2009-01-01

    After receiving a NASA Small Business Innovation Research (SBIR) contract from Kennedy Space Center, Soneticom Inc., based in West Melbourne, Florida, created algorithms for time difference of arrival and radio interferometry, which it used in its Lynx Location System (LLS) to locate electromagnetic interference that can disrupt radio communications. Soneticom is collaborating with the Federal Aviation Administration (FAA) to install and test the LLS at its field test center in New Jersey in preparation for deploying the LLS at commercial airports. The software collects data from each sensor in order to compute the location of the interfering emitter.

  4. Object locating system

    DOEpatents

    Novak, J.L.; Petterson, B.

    1998-06-09

    A sensing system locates an object by sensing the object`s effect on electric fields. The object`s effect on the mutual capacitance of electrode pairs varies according to the distance between the object and the electrodes. A single electrode pair can sense the distance from the object to the electrodes. Multiple electrode pairs can more precisely locate the object in one or more dimensions. 12 figs.

  5. Lunar Impact Flash Locations

    NASA Technical Reports Server (NTRS)

    Moser, D. E.; Suggs, R. M.; Kupferschmidt, L.; Feldman, J.

    2015-01-01

    A bright impact flash detected by the NASA Lunar Impact Monitoring Program in March 2013 brought into focus the importance of determining the impact flash location. A process for locating the impact flash, and presumably its associated crater, was developed using commercially available software tools. The process was successfully applied to the March 2013 impact flash and put into production on an additional 300 impact flashes. The goal today: provide a description of the geolocation technique developed.

  6. Isomolybdate conversion coatings

    NASA Technical Reports Server (NTRS)

    Minevski, Zoran (Inventor); Maxey, Jason (Inventor); Nelson, Carl (Inventor); Eylem, Cahit (Inventor)

    2002-01-01

    A conversion coating solution and process forms a stable and corrosion-resistant layer on metal substrates or layers or, more preferably, on a boehmite layer or other base conversion coating. The conversion coating process involves contacting the substrate, layer or coating with an aqueous alkali metal isomolybdate solution in order to convert the surface of the substrate, layer or coating to a stable conversion coating. The aqueous alkali metal molybdates are selected from sodium molybdate (Na.sub.2 MoO.sub.4), lithium molybdate (Li.sub.2 MoO.sub.4), potassium molybdate (K.sub.2 MoO.sub.4), or combinations thereof, with the most preferred alkali metal molybdate being sodium molybdate. The concentration of alkali metal molybdates in the solution is preferably less than 5% by weight. In addition to the alkali metal molybdates, the conversion coating solution may include alkaline metal passivators selected from lithium nitrate (LiNO.sub.3), sodium nitrate (NaNO.sub.3), ammonia nitrate (NH.sub.4 NO.sub.3), and combinations thereof; lithium chloride, potassium hexafluorozirconate (K.sub.2 ZrF.sub.6) or potassium hexafluorotitanate (K.sub.2 TiF.sub.6).

  7. Laser energy conversion

    NASA Technical Reports Server (NTRS)

    Jalufka, N. W.

    1989-01-01

    The conversion of laser energy to other, more useful, forms is an important element of any space power transmission system employing lasers. In general the user, at the receiving sight, will require the energy in a form other than laser radiation. In particular, conversion to rocket power and electricity are considered to be two major areas where one must consider various conversion techniques. Three systems (photovoltaic cells, MHD generators, and gas turbines) have been identified as the laser-to-electricity conversion systems that appear to meet most of the criteria for a space-based system. The laser thruster also shows considerable promise as a space propulsion system. At this time one cannot predict which of the three laser-to-electric converters will be best suited to particular mission needs. All three systems have some particular advantages, as well as disadvantages. It would be prudent to continue research on all three systems, as well as the laser rocket thruster. Research on novel energy conversion systems, such as the optical rectenna and the reverse free-electron laser, should continue due to their potential for high payoff.

  8. Frequency conversion system

    NASA Technical Reports Server (NTRS)

    Sanders, Steven (Inventor); Waarts, Robert G. (Inventor)

    2001-01-01

    A frequency conversion system comprises first and second gain sources providing first and second frequency radiation outputs where the second gain source receives as input the output of the first gain source and, further, the second gain source comprises a Raman or Brillouin gain fiber for wave shifting a portion of the radiation of the first frequency output into second frequency radiation output to provided a combined output of first and second frequencies. Powers are gain enhanced by the addition of a rare earth amplifier or oscillator, or a Raman/Brillouin amplifier or oscillator between the high power source and the NFM device. Further, polarization conversion using Raman or Brillouin wavelength shifting is provided to optimize frequency conversion efficiency in the NFM device.

  9. Direct conversion technology

    NASA Technical Reports Server (NTRS)

    Massier, Paul F.; Bankston, C. P.; Williams, R.; Underwood, M.; Jeffries-Nakamura, B.; Fabris, G.

    1989-01-01

    The overall objective of the Direct Conversion Technology task is to develop an experimentally verified technology base for promising direct conversion systems that have potential application for energy conservation in the end-use sectors. This report contains progress of research on the Alkali Metal Thermal-to-Electric Converter (AMTEC), and on the Two-Phase Liquid-Metal Magnetohydrodynamic Electrical Generator (LMMHD) for the period January 1, 1989 through December 31, 1989. Research on these concepts was initiated during October 1987. Reports prepared on previous occasions contain discussions on the following other direct conversion concepts: thermoelectric, pyroelectric, thermionic, thermophotovoltaic, thermoacoustic, thermomagnetic, thermoelastic (nitinol heat engines); and also, more complete discussions of AMTEC and LMMHD systems.

  10. Direct conversion technology

    SciTech Connect

    Massier, P.F.; Back, L.H.; Ryan, M.A.; Fabris, G.

    1992-01-07

    The overall objective of the Direct Conversion Technology task is to develop an experimentally verified technology base for promising direct conversion systems that have potential application for energy conservation in the end-use sectors. This report contains progress of research on the Alkali Metal Thermal-to-Electric Converter (AMTEC) and on the Two-Phase Liquid-Metal MHD Electrical Generator (LMMHD) for the period January 1, 1991 through December 31, 1991. Research on AMTEC and on LMMHD was initiated during October 1987. Reports prepared on previous occasions (Refs. 1--5) contain descriptive and performance discussions of the following direct conversion concepts: thermoelectric, pyroelectric, thermionic, thermophotovoltaic, thermoacoustic, thermomagnetic, thermoelastic (Nitionol heat engine); and also, more complete descriptive discussions of AMTEC and LMMHD systems.

  11. Digital optical conversion module

    DOEpatents

    Kotter, D.K.; Rankin, R.A.

    1988-07-19

    A digital optical conversion module used to convert an analog signal to a computer compatible digital signal including a voltage-to-frequency converter, frequency offset response circuitry, and an electrical-to-optical converter. Also used in conjunction with the digital optical conversion module is an optical link and an interface at the computer for converting the optical signal back to an electrical signal. Suitable for use in hostile environments having high levels of electromagnetic interference, the conversion module retains high resolution of the analog signal while eliminating the potential for errors due to noise and interference. The module can be used to link analog output scientific equipment such as an electrometer used with a mass spectrometer to a computer. 2 figs.

  12. Digital optical conversion module

    DOEpatents

    Kotter, Dale K.; Rankin, Richard A.

    1991-02-26

    A digital optical conversion module used to convert an analog signal to a computer compatible digital signal including a voltage-to-frequency converter, frequency offset response circuitry, and an electrical-to-optical converter. Also used in conjunction with the digital optical conversion module is an optical link and an interface at the computer for converting the optical signal back to an electrical signal. Suitable for use in hostile environments having high levels of electromagnetic interference, the conversion module retains high resolution of the analog signal while eliminating the potential for errors due to noise and interference. The module can be used to link analog output scientific equipment such as an electrometer used with a mass spectrometer to a computer.

  13. Somatization and conversion disorder.

    PubMed

    Hurwitz, Trevor A

    2004-03-01

    Somatization is the psychological mechanism whereby psychological distress is expressed in the form of physical symptoms. The psychological distress in somatization is most commonly caused by a mood disorder that threatens mental stability. Conversion disorder occurs when the somatic presentation involves any aspect of the central nervous system over which voluntary control is exercised. Conversion reactions represent fixed ideas about neurologic malfunction that are consciously enacted, resulting in psychogenic neurologic deficits. Treatment is complex and lengthy; it includes recovery of neurologic function aided by narcoanalysis and identification and treatment of the primary psychiatric disorder, usually a mood disorder. PMID:15101499

  14. ADEPT: Efficient Power Conversion

    SciTech Connect

    2011-01-01

    ADEPT Project: In today’s increasingly electrified world, power conversion—the process of converting electricity between different currents, voltage levels, and frequencies—forms a vital link between the electronic devices we use every day and the sources of power required to run them. The 14 projects that make up ARPA-E’s ADEPT Project, short for “Agile Delivery of Electrical Power Technology,” are paving the way for more energy efficient power conversion and advancing the basic building blocks of power conversion: circuits, transistors, inductors, transformers, and capacitors.

  15. Geostar - Navigation location system

    NASA Astrophysics Data System (ADS)

    Keyser, Donald A.

    The author describes the Radiodetermination Satellite Service (RDSS). The initial phase of the RDSS provides for a unique service enabling central offices and headquarters to obtain position-location information and receive short digital messages from mobile user terminals throughout the contiguous United States, southern Canada, and northern Mexico. The system employs a spread-spectrum, CDMA modulation technique allowing multiple customers to use the system simultaneously, without preassigned coordination with fellow users. Position location is currently determined by employing an existing radio determination receiver, such as Loran-C, GPS, or Transit, in the mobile user terminal. In the early 1990s position location will be determined at a central earth station by time-differential ranging of the user terminals via two or more geostationary satellites. A brief overview of the RDSS system architecture is presented with emphasis on the user terminal and its diverse applications.

  16. Marine cable location system

    SciTech Connect

    Zachariadis, R.G.

    1984-05-01

    An acoustic positioning system locates a marine cable at an exploration site, such cable employing a plurality of hydrophones at spaced-apart positions along the cable. A marine vessel measures water depth to the cable as the vessel passes over the cable and interrogates the hydrophones with sonar pulses along a slant range as the vessel travels in a parallel and horizontally offset path to the cable. The location of the hydrophones is determined from the recordings of water depth and slant range.

  17. Catalyst increases COS conversion

    SciTech Connect

    Goodboy, K.P.

    1985-02-18

    Increasingly stringent air quality legislation is placing greater emphasis on conversion of COS and CS/sub 2/ in Claus plants for the maximum sulfur recovery. Overall sulfur recovery goals are dependent upon outstanding service from the Claus catalyst in each reactor because catalyst activity is a major factor influencing plant performance. Today's catalyst are much improved over those used 10 years ago for the Claus (H/sub 2/S/SO/sub 2/) reaction. Recent technical efforts have focused on the conversion of COS and CS/sub 2/. These carbon-sulfur compounds can account for as much as 50% of the sulfur going to the incinerator, which essentially converts all remaining sulfur species to SO/sub 2/ for atmospheric dispersion. Previously, the mechanism of Claus COS conversion, i.e., hydrolysis or oxidation by SO/sub 2/, was studied and the conclusion was that oxidation by SO/sub 2/ appears to be the predominate mode of COS conversion on sulfated alumina catalysts.

  18. Ocean thermal energy conversion

    SciTech Connect

    Avery, W.H.

    1983-03-17

    A brief explanation of the Ocean Thermal Energy Conversion (OTEC) concept and an estimate of the amount of energy that can be produced from the ocean resource without introducing environmental concerns are presented. Use of the OTEC system to generate electric power and products which can replace fossil fuels is shown. The OTEC program status and its prospects for the future are discussed.

  19. Clinical Linguistics: Conversational Reflections

    ERIC Educational Resources Information Center

    Crystal, David

    2013-01-01

    This is a report of the main points I made in an informal "conversation" with Paul Fletcher and the audience at the 14th ICPLA conference in Cork. The observations arose randomly, as part of an unstructured 1-h Q&A, so they do not provide a systematic account of the subject, but simply reflect the issues which were raised by the conference…

  20. Evaluating Energy Conversion Efficiency

    NASA Technical Reports Server (NTRS)

    Byvik, C. E.; Smith, B. T.; Buoncristiani, A. M.

    1983-01-01

    Devices that convert solar radiation directly into storable chemical or electrical energy, have characteristic energy absorption spectrum; specifically, each of these devices has energy threshold. The conversion efficiency of generalized system that emcompasses all threshold devices is analyzed, resulting in family of curves for devices of various threshold energies operating at different temperatures.

  1. National conversion pilot project

    SciTech Connect

    Floyd, D.; Nichols, F.; Lily, A.

    1994-12-31

    Manufacturing Sciences Corporation (MSC) has undertaken a project from the U.S. Department of Energy (DOE) to convert buildings that are currently contaminated at Rocky Flats into buildings that are capable of producing commercial products. This conversion project is called the National Conversion Pilot Project (NCPP). The mission of the NCPP is to explore and demonstrate at the Rocky Flats site the feasibility of economic conversion at DOE facilities. This project was officially started on April 1 with the signing of a Cooperative Assistance Agreement between MSC and the DOE. The NCPP was jointly announced by Roy Romer, Governor of the State of Colorado; Mark Silverman, Manager of the Department of Energy Rocky Flats Office; Jack McGraw, Activity Administrator for U.S. Environmental Protection Agency (EPA) Region 8; and Tom Looby, Director of the Office of Environment from the Colorado Department of Health. On March 25, 1994, Hazel O`Leary, the Secretary of the DOE, toured the site of the NCPP and heartily endorsed the project as an example of how the DOE and commercial industry can jointly accomplish the conversion and cleanup of government facilities into productive commercial ventures.

  2. Mechanochemical Energy Conversion

    ERIC Educational Resources Information Center

    Pines, E.; And Others

    1973-01-01

    Summarizes the thermodynamics of macromolecular systems, including theories and experiments of cyclic energy conversion with rubber and collagen as working substances. Indicates that an early introduction into the concept of chemical potential and solution thermodynamics is made possible through the study of the cyclic processes. (CC)

  3. Teaching Conversation with Trivia.

    ERIC Educational Resources Information Center

    Crawford, Michael J.

    2002-01-01

    Presents a rationale for utilizing trivia to teach conversation. Shows how trivia-based materials fit into communicative language teaching approaches and provides examples of trivia-based activities and explains how to use them in the classroom. (Author/VWL)

  4. Planetary image conversion task

    NASA Technical Reports Server (NTRS)

    Martin, M. D.; Stanley, C. L.; Laughlin, G.

    1985-01-01

    The Planetary Image Conversion Task group processed 12,500 magnetic tapes containing raw imaging data from JPL planetary missions and produced an image data base in consistent format on 1200 fully packed 6250-bpi tapes. The output tapes will remain at JPL. A copy of the entire tape set was delivered to US Geological Survey, Flagstaff, Ariz. A secondary task converted computer datalogs, which had been stored in project specific MARK IV File Management System data types and structures, to flat-file, text format that is processable on any modern computer system. The conversion processing took place at JPL's Image Processing Laboratory on an IBM 370-158 with existing software modified slightly to meet the needs of the conversion task. More than 99% of the original digital image data was successfully recovered by the conversion task. However, processing data tapes recorded before 1975 was destructive. This discovery is of critical importance to facilities responsible for maintaining digital archives since normal periodic random sampling techniques would be unlikely to detect this phenomenon, and entire data sets could be wiped out in the act of generating seemingly positive sampling results. Reccomended follow-on activities are also included.

  5. A Conversation about Observation

    NASA Technical Reports Server (NTRS)

    Mather, John C.; Mao, Minnie Yuan

    2012-01-01

    In the spirit of the Lindau Meeting, we present a dialogue between a Nobel laureate and a young researcher. This interchange started online, where it continues to unfold. Here is a digest of this conversation, which has developed across time and space.

  6. Leadership is a conversation.

    PubMed

    Groysberg, Boris; Slind, Michael

    2012-06-01

    Globalization and new technologies have sharply reduced the efficacy of command-and-control management and its accompanying forms of corporate communication. In the course of a recent research project, the authors concluded that by talking with employees, rather than simply issuing orders, leaders can promote operational flexibility, employee engagement, and tight strategic alignment. Groysberg and Slind have identified four elements of organizational conversation that reflect the essential attributes of interpersonal conversation: intimacy, interactivity, inclusion, and intentionality. Intimacy shifts the focus from a top-down distribution of information to a bottom-up exchange of ideas. Organizational conversation is less corporate in tone and more casual. And it's less about issuing and taking orders than about asking and answering questions. Interactivity entails shunning the simplicity of monologue and embracing the unpredictable vitality of dialogue. Traditional one-way media-print and broadcast, in particular-give way to social media buttressed by social thinking. Inclusion turns employees into full-fledged conversation partners, entitling them to provide their own ideas, often on company channels. They can create content and act as brand ambassadors, thought leaders, and storytellers. Intentionality enables leaders and employees to derive strategically relevant action from the push and pull of discussion and debate. PMID:22741420

  7. Conversation with Copland

    ERIC Educational Resources Information Center

    Music Educators Journal, 1973

    1973-01-01

    Records a conversation between American composer Aaron Copland and Malcolm E. Besson, editor of Music Educators Journal. Mr. Copland discusses teaching, American music, and notes the greater number of composers writing today, and the livelier atmosphere of college music departments. (DS)

  8. Leadership is a conversation.

    PubMed

    Groysberg, Boris; Slind, Michael

    2012-06-01

    Globalization and new technologies have sharply reduced the efficacy of command-and-control management and its accompanying forms of corporate communication. In the course of a recent research project, the authors concluded that by talking with employees, rather than simply issuing orders, leaders can promote operational flexibility, employee engagement, and tight strategic alignment. Groysberg and Slind have identified four elements of organizational conversation that reflect the essential attributes of interpersonal conversation: intimacy, interactivity, inclusion, and intentionality. Intimacy shifts the focus from a top-down distribution of information to a bottom-up exchange of ideas. Organizational conversation is less corporate in tone and more casual. And it's less about issuing and taking orders than about asking and answering questions. Interactivity entails shunning the simplicity of monologue and embracing the unpredictable vitality of dialogue. Traditional one-way media-print and broadcast, in particular-give way to social media buttressed by social thinking. Inclusion turns employees into full-fledged conversation partners, entitling them to provide their own ideas, often on company channels. They can create content and act as brand ambassadors, thought leaders, and storytellers. Intentionality enables leaders and employees to derive strategically relevant action from the push and pull of discussion and debate.

  9. Solar energy conversion.

    SciTech Connect

    Crabtree, G. W.; Lewis, N. S.

    2008-03-01

    If solar energy is to become a practical alternative to fossil fuels, we must have efficient ways to convert photons into electricity, fuel, and heat. The need for better conversion technologies is a driving force behind many recent developments in biology, materials, and especially nanoscience. The Sun has the enormous untapped potential to supply our growing energy needs. The barrier to greater use of the solar resource is its high cost relative to the cost of fossil fuels, although the disparity will decrease with the rising prices of fossil fuels and the rising costs of mitigating their impact on the environment and climate. The cost of solar energy is directly related to the low conversion efficiency, the modest energy density of solar radiation, and the costly materials currently required. The development of materials and methods to improve solar energy conversion is primarily a scientific challenge: Breakthroughs in fundamental understanding ought to enable marked progress. There is plenty of room for improvement, since photovoltaic conversion efficiencies for inexpensive organic and dye-sensitized solar cells are currently about 10% or less, the conversion efficiency of photosynthesis is less than 1%, and the best solar thermal efficiency is 30%. The theoretical limits suggest that we can do much better. Solar conversion is a young science. Its major growth began in the 1970s, spurred by the oil crisis that highlighted the pervasive importance of energy to our personal, social, economic, and political lives. In contrast, fossil-fuel science has developed over more than 250 years, stimulated by the Industrial Revolution and the promise of abundant fossil fuels. The science of thermodynamics, for example, is intimately intertwined with the development of the steam engine. The Carnot cycle, the mechanical equivalent of heat, and entropy all played starring roles in the development of thermodynamics and the technology of heat engines. Solar-energy science faces

  10. Alpine radar conversion for LAWR

    NASA Astrophysics Data System (ADS)

    Savina, M.; Burlando, P.

    2012-04-01

    The Local Area Weather Radar (LAWR) is a ship-born weather radar system operating in X-band developed by the DHI Group to detect precipitation in urban areas. To date more than thirty units are installed in different settings around the world. A LAWR was also deployed in the Alps, at 3883 m a.s.l. on the Kl. Matterhorn (Valais, Switzerland). This was the highest LAWR of the world and it led to the development of an Alpine LAWR system that, besides featuring important technological improvements needed to withstand the severe Alpine conditions, required the development of a new Alpine Radar COnversion Model (ARCOM), which is the main focus of this contribution. The LAWR system is equipped with the original FURUNO fan-beam slotted antenna and the original logarithmic receiver, which limits the radar observations to the video signal (L) withour providing the reflectivity (Z). The beam is 0.95 deg wide and 20 deg high. It can detect precipitation to a max range of 60 km. In order to account for the limited availability of raw signal and information and the specific mountain set-up, the conversion model had to be developed differently from the state-of-the-art radar conversion technique used for this class of radars. In particular, the ARCOM is based on a model used to simulate a spatial dependent factor, hereafter called ACF, which is in turn function of parameters that take in account climatological conditions, also used in other conversion methods, but additionally accounting for local radar beam features and for orographic forcings such as the effective sampling power (sP), which is modelled by means of antenna pattern, geometric ground clutter and their interaction. The result is a conversion factor formulated to account for a range correction that is based on the increase of the sampling volume, partial beam blocking and local climatological conditions. The importance of the latter in this study is double with respect to the standard conversion technique for this

  11. Location of Geothermal Resources

    SciTech Connect

    2004-07-01

    Geothermal resources, which utilize the heat of the earth, are located throughout the plant's crust. Those closer to the surface are most commonly used because geothermal drilling costs are currently prohibitive below depths of between 10,000 and 15,000 feet.

  12. Birefringent Stress Location Sensor

    NASA Astrophysics Data System (ADS)

    Franks, R. B.; Torruellas, W.; Youngquist, R. C.

    1986-08-01

    A new type of stress location sensor is discussed in which the FMCW technique is used to detect the difference in propagation time between two optical paths in an optical fiber due to stress induced modal coupling. Two versions of the system are included, and experimental results are presented for each system.

  13. LOCATING AREAS OF CONCERN

    EPA Science Inventory

    A simple method to locate changes in vegetation cover, which can be used to identify areas under stress. The method only requires inexpensive NDVI data. The use of remotely sensed data is far more cost-effective than field studies and can be performed more quickly. Local knowledg...

  14. Particle impact location detector

    NASA Technical Reports Server (NTRS)

    Auer, S. O.

    1974-01-01

    Detector includes delay lines connected to each detector surface strip. When several particles strike different strips simultaneously, pulses generated by each strip are time delayed by certain intervals. Delay time for each strip is known. By observing time delay in pulse, it is possible to locate strip that is struck by particle.

  15. Chromosomal location of two human genes encoding tetrahydrobiopterin-metabolizing enzymes: 6-pyruvoyl-tetrahydropterin synthase maps to 11q22. 3-q23. 3, and pterin-4[alpha]-carbinolamine dehydratase maps to 10q22

    SciTech Connect

    Thoeny, B.; Heizmann, C.W. ); Mattei, M.G. )

    1994-01-15

    Tetrahydrobiopterin (BH[sub 4]) is the redox cofactor for the aromatic amino acid hydroxylases such as phenylalanine hydroxylase. At least five enzymes are known to be involved in BH[sub 4] biosynthesis and regeneration. A deficiency in several of the BH[sub 4] metabolic enzymes causes variant types of hyperphenylalaninemias in man. Recently, the authors cloned and expressed the human cDNAs for two of the BH[sub 4] enzymes, the 6-pyruvoyl-tetrahydropterin synthase and the pterin-4[alpha]-carbinolamine dehydratase (gene symbols PTS and PCD/DCOH, respectively). In this report, they localized the two genes on the human chromsomes by in situ hybridization. The PTS gene was mapped to the chromosomal region 11q22.3-q23.3, and the PCD/DCOH gene was mapped to the 10q22 band of the genome. 18 refs., 2 figs.

  16. Interferometric locating system

    NASA Technical Reports Server (NTRS)

    Macdoran, P. F. (Inventor)

    1980-01-01

    A system is described for determining the position of a vehicle or other target that emits radio waves and which is of the type that senses the difference in time of arrival at spaced ground stations of signals from the vehicle to locate the vehicle on a set of intersecting hyperbolas. A network of four ground stations detects the radio emissions from the vehicle and by means of cross correlation derives the relative signal delay at the ground stations from which the vehicle position is deduced. Because the signal detection is by cross correlation, no knowledge of the emission is needed, which makes even unintentional radio noise emissions usable as a locator beacon. By positioning one of the four ground stations at an elevation significantly above the plane of the other three stations, a three dimensional fix on the vehicle is possible.

  17. Dipole Well Location

    1998-08-03

    The problem here is to model the three-dimensional response of an electromagnetic logging tool to a practical situation which is often encountered in oil and gas exploration. The DWELL code provide the electromagnetic fields on the axis of a borehole due to either an electric or a magnetic dipole located on the same axis. The borehole is cylindrical, and is located within a stratified formation in which the bedding planes are not horizontal. The anglemore » between the normal to the bedding planes and the axis of the borehole may assume any value, or in other words, the borehole axis may be tilted with respect to the bedding planes. Additionally, all of the formation layers may have invasive zones of drilling mud. The operating frequency of the source dipole(s) extends from a few Hertz to hundreds of Megahertz.« less

  18. Electric current locator

    DOEpatents

    King, Paul E.; Woodside, Charles Rigel

    2012-02-07

    The disclosure herein provides an apparatus for location of a quantity of current vectors in an electrical device, where the current vector has a known direction and a known relative magnitude to an input current supplied to the electrical device. Mathematical constants used in Biot-Savart superposition equations are determined for the electrical device, the orientation of the apparatus, and relative magnitude of the current vector and the input current, and the apparatus utilizes magnetic field sensors oriented to a sensing plane to provide current vector location based on the solution of the Biot-Savart superposition equations. Description of required orientations between the apparatus and the electrical device are disclosed and various methods of determining the mathematical constants are presented.

  19. Underwater hydrophone location survey

    NASA Technical Reports Server (NTRS)

    Cecil, Jack B.

    1993-01-01

    The Atlantic Undersea Test and Evaluation Center (AUTEC) is a U.S. Navy test range located on Andros Island, Bahamas, and a Division of the Naval Undersea Warfare Center (NUWC), Newport, RI. The Headquarters of AUTEC is located at a facility in West Palm Beach, FL. AUTEC's primary mission is to provide the U.S. Navy with a deep-water test and evaluation facility for making underwater acoustic measurements, testing and calibrating sonars, and providing accurate underwater, surface, and in-air tracking data on surface ships, submarines, aircraft, and weapon systems. Many of these programs are in support of Antisubmarine Warfare (ASW), undersea research and development programs, and Fleet assessment and operational readiness trials. Most tests conducted at AUTEC require precise underwater tracking (plus or minus 3 yards) of multiple acoustic signals emitted with the correct waveshape and repetition criteria from either a surface craft or underwater vehicle.

  20. Optimal Facility-Location

    PubMed Central

    Goldman, A. J.

    2006-01-01

    Dr. Christoph Witzgall, the honoree of this Symposium, can count among his many contributions to applied mathematics and mathematical operations research a body of widely-recognized work on the optimal location of facilities. The present paper offers to non-specialists a sketch of that field and its evolution, with emphasis on areas most closely related to Witzgall’s research at NBS/NIST. PMID:27274920

  1. Ammonia Leak Locator Study

    NASA Technical Reports Server (NTRS)

    Dodge, Franklin T.; Wuest, Martin P.; Deffenbaugh, Danny M.

    1995-01-01

    The thermal control system of International Space Station Alpha will use liquid ammonia as the heat exchange fluid. It is expected that small leaks (of the order perhaps of one pound of ammonia per day) may develop in the lines transporting the ammonia to the various facilities as well as in the heat exchange equipment. Such leaks must be detected and located before the supply of ammonia becomes critically low. For that reason, NASA-JSC has a program underway to evaluate instruments that can detect and locate ultra-small concentrations of ammonia in a high vacuum environment. To be useful, the instrument must be portable and small enough that an astronaut can easily handle it during extravehicular activity. An additional complication in the design of the instrument is that the environment immediately surrounding ISSA will contain small concentrations of many other gases from venting of onboard experiments as well as from other kinds of leaks. These other vapors include water, cabin air, CO2, CO, argon, N2, and ethylene glycol. Altogether, this local environment might have a pressure of the order of 10(exp -7) to 10(exp -6) torr. Southwest Research Institute (SwRI) was contracted by NASA-JSC to provide support to NASA-JSC and its prime contractors in evaluating ammonia-location instruments and to make a preliminary trade study of the advantages and limitations of potential instruments. The present effort builds upon an earlier SwRI study to evaluate ammonia leak detection instruments [Jolly and Deffenbaugh]. The objectives of the present effort include: (1) Estimate the characteristics of representative ammonia leaks; (2) Evaluate the baseline instrument in the light of the estimated ammonia leak characteristics; (3) Propose alternative instrument concepts; and (4) Conduct a trade study of the proposed alternative concepts and recommend promising instruments. The baseline leak-location instrument selected by NASA-JSC was an ion gauge.

  2. Magnetic Location Indicator

    NASA Technical Reports Server (NTRS)

    Stegman, Thomas W.

    1992-01-01

    Ferrofluidic device indicates point of highest magnetic-flux density in workspace. Consists of bubble of ferrofluid in immiscible liquid carrier in clear plastic case. Used in flat block or tube. Axes of centering circle on flat-block version used to mark location of maximum flux density when bubble in circle. Device used to find point on wall corresponding to known point on opposite side of wall.

  3. Coso MT Site Locations

    SciTech Connect

    Doug Blankenship

    2011-05-04

    This data includes the locations of the MT data collected in and around the Coso Geothermal field that covered the West Flank area. These are the data that the 3D MT models were created from that were discussed in Phase 1 of the West Flank FORGE project. The projected coordinate system is NAD 1927 State Plane California IV FIPS 0404 and the Projection is Lambert Conformal Conic. Units are in feet.

  4. Frequency conversion system

    NASA Technical Reports Server (NTRS)

    Sanders, Steven (Inventor); Lang, Robert J. (Inventor)

    2001-01-01

    Laser diode pumped mid-IR wavelength sources include at least one high power, near-IR wavelength, injection and/or sources wherein one or both of such sources may be tunable providing a pump wave output beam to a quasi-phase matched (QPM) nonlinear frequency mixing (NFM) device. The NFM device may be a difference frequency mixing (DFM) device or an optical parametric oscillation (OPO) device. Wavelength tuning of at least one of the sources advantageously provides the ability for optimizing pump or injection wavelengths to match the QPM properties of the NFM device enabling a broad range of mid-IR wavelength selectivity. Also, pump powers are gain enhanced by the addition of a rare earth amplifier or oscillator, or a Raman/Brillouin amplifier or oscillator between the high power source and the NFM device. Further, polarization conversion using Raman or Brillouin wavelength shifting is provided to optimize frequency conversion efficiency in the NFM device.

  5. Movement coordination during conversation.

    PubMed

    Latif, Nida; Barbosa, Adriano V; Vatikiotis-Bateson, Eric; Vatiokiotis-Bateson, Eric; Castelhano, Monica S; Munhall, K G

    2014-01-01

    Behavioral coordination and synchrony contribute to a common biological mechanism that maintains communication, cooperation and bonding within many social species, such as primates and birds. Similarly, human language and social systems may also be attuned to coordination to facilitate communication and the formation of relationships. Gross similarities in movement patterns and convergence in the acoustic properties of speech have already been demonstrated between interacting individuals. In the present studies, we investigated how coordinated movements contribute to observers' perception of affiliation (friends vs. strangers) between two conversing individuals. We used novel computational methods to quantify motor coordination and demonstrated that individuals familiar with each other coordinated their movements more frequently. Observers used coordination to judge affiliation between conversing pairs but only when the perceptual stimuli were restricted to head and face regions. These results suggest that observed movement coordination in humans might contribute to perceptual decisions based on availability of information to perceivers. PMID:25119189

  6. Movement Coordination during Conversation

    PubMed Central

    Latif, Nida; Barbosa, Adriano V.; Vatiokiotis-Bateson, Eric; Castelhano, Monica S.; Munhall, K. G.

    2014-01-01

    Behavioral coordination and synchrony contribute to a common biological mechanism that maintains communication, cooperation and bonding within many social species, such as primates and birds. Similarly, human language and social systems may also be attuned to coordination to facilitate communication and the formation of relationships. Gross similarities in movement patterns and convergence in the acoustic properties of speech have already been demonstrated between interacting individuals. In the present studies, we investigated how coordinated movements contribute to observers’ perception of affiliation (friends vs. strangers) between two conversing individuals. We used novel computational methods to quantify motor coordination and demonstrated that individuals familiar with each other coordinated their movements more frequently. Observers used coordination to judge affiliation between conversing pairs but only when the perceptual stimuli were restricted to head and face regions. These results suggest that observed movement coordination in humans might contribute to perceptual decisions based on availability of information to perceivers. PMID:25119189

  7. Wind energy conversion system

    SciTech Connect

    Longrigg, Paul

    1987-01-01

    The wind energy conversion system includes a wind machine having a propeller connected to a generator of electric power, the propeller rotating the generator in response to force of an incident wind. The generator converts the power of the wind to electric power for use by an electric load. Circuitry for varying the duty factor of the generator output power is connected between the generator and the load to thereby alter a loading of the generator and the propeller by the electric load. Wind speed is sensed electro-optically to provide data of wind speed upwind of the propeller, to thereby permit tip speed ratio circuitry to operate the power control circuitry and thereby optimize the tip speed ratio by varying the loading of the propeller. Accordingly, the efficiency of the wind energy conversion system is maximized.

  8. Clinical linguistics: conversational reflections.

    PubMed

    Crystal, David

    2013-04-01

    This is a report of the main points I made in an informal "conversation" with Paul Fletcher and the audience at the 14th ICPLA conference in Cork. The observations arose randomly, as part of an unstructured 1-h Q&A, so they do not provide a systematic account of the subject, but simply reflect the issues which were raised by the conference participants during that time.

  9. Starch conversion technology

    SciTech Connect

    Van Beynum, G.M.A.; Roels, J.A.

    1985-01-01

    This volume with contributions by 17 international experts provides an overview of processes by which starch is converted to a form which makes it more suitable for other applications. Products from starch biochemical conversions include organic acids, alcohol, bipolymers, enzymes, amino acids, antibiotics and hormones. Alcohol produced from starch can be used to reduce dependency on petroleum for energy. Literature references and a subject index are provided.

  10. Session: Energy Conversion

    SciTech Connect

    Robertson, David; LaSala, Raymond J.; Kukacka, Lawrence E.; Bliem, Carl J.; Premuzic, Eugene T.; Weare, John H.

    1992-01-01

    This session at the Geothermal Energy Program Review X: Geothermal Energy and the Utility Market consisted of five presentations: ''Hydrothermal Energy Conversion Technology'' by David Robertson and Raymond J. LaSala; ''Materials for Geothermal Production'' by Lawrence E. Kukacka; ''Supersaturated Turbine Expansions for Binary Geothermal Power Plants'' by Carl J. Bliem; ''Geothermal Waster Treatment Biotechnology: Progress and Advantages to the Utilities'' by Eugen T. Premuzic; and ''Geothermal Brine Chemistry Modeling Program'' by John H. Weare.

  11. Direct conversion technology

    NASA Technical Reports Server (NTRS)

    Massier, P. F.; Bankston, C. P.; Fabris, G.; Kirol, L. D.

    1988-01-01

    The overall objective of the Direct Conversion Technology task is to develop an experimentally verified technology base for promising direct thermal-to-electric energy conversion systems that have potential application for energy conservation in the end-use sectors. This report contains progress of research on the Alkali Metal Thermal-to-Electric Converter (AMTEC), and on the Two-Phase Liquid-Metal MHD Electrical Generator (LMMHD) for the period January 1988 through December 1988. Research on these concepts was initiated during October 1987. In addition, status reviews and assessments are presented for thermomagnetic converter concepts and for thermoelastic converters (Nitinol heat engines). Reports prepared on previous occasions contain discussions on the following other direct conversion concepts: thermoelectric, pyroelectric, thermionic thermophotovoltaic and thermoacoustic; and also, more complete discussions of AMTEC and LMMHD systems. A tabulated summary of the various systems which have been reviewed thus far has been prepared. Some of the important technical research needs are listed and a schematic of each system is shown.

  12. Conversion of Questionnaire Data

    SciTech Connect

    Powell, Danny H; Elwood Jr, Robert H

    2011-01-01

    During the survey, respondents are asked to provide qualitative answers (well, adequate, needs improvement) on how well material control and accountability (MC&A) functions are being performed. These responses can be used to develop failure probabilities for basic events performed during routine operation of the MC&A systems. The failure frequencies for individual events may be used to estimate total system effectiveness using a fault tree in a probabilistic risk analysis (PRA). Numeric risk values are required for the PRA fault tree calculations that are performed to evaluate system effectiveness. So, the performance ratings in the questionnaire must be converted to relative risk values for all of the basic MC&A tasks performed in the facility. If a specific material protection, control, and accountability (MPC&A) task is being performed at the 'perfect' level, the task is considered to have a near zero risk of failure. If the task is performed at a less than perfect level, the deficiency in performance represents some risk of failure for the event. As the degree of deficiency in performance increases, the risk of failure increases. If a task that should be performed is not being performed, that task is in a state of failure. The failure probabilities of all basic events contribute to the total system risk. Conversion of questionnaire MPC&A system performance data to numeric values is a separate function from the process of completing the questionnaire. When specific questions in the questionnaire are answered, the focus is on correctly assessing and reporting, in an adjectival manner, the actual performance of the related MC&A function. Prior to conversion, consideration should not be given to the numeric value that will be assigned during the conversion process. In the conversion process, adjectival responses to questions on system performance are quantified based on a log normal scale typically used in human error analysis (see A.D. Swain and H.E. Guttmann

  13. Sonar Locator Systems

    NASA Technical Reports Server (NTRS)

    1985-01-01

    An underwater locator device called a Pinger is attached to an airplane's flight recorder for recovery in case of a crash. Burnett Electronics Pinger Model 512 resulted from a Burnett Electronics Laboratory, Inc./Langley Research Center contract for development of a search system for underwater mines. The Pinger's battery-powered transmitter is activated when immersed in water, and sends multidirectional signals for up to 500 hours. When a surface receiver picks up the signal, a diver can retrieve the pinger and the attached airplane flight recorder. Other pingers are used to track whales, mark underwater discoveries and assist oil drilling vessels.

  14. Location of Planet X

    SciTech Connect

    Harrington, R.S.

    1988-10-01

    Observed positions of Uranus and Neptune along with residuals in right ascension and declination are used to constrain the location of a postulated tenth planet. The residuals are converted into residuals in ecliptic longitude and latitude. The results are then combined into seasonal normal points, producing average geocentric residuals spaced slightly more than a year apart that are assumed to represent the equivalent heliocentric average residuals for the observed oppositions. Such a planet is found to most likely reside in the region of Scorpius, with considerably less likelihood that it is in Taurus. 8 references.

  15. Microbial Energy Conversion

    SciTech Connect

    Buckley, Merry; Wall, Judy D.

    2006-10-01

    The American Academy of Microbiology convened a colloquium March 10-12, 2006, in San Francisco, California, to discuss the production of energy fuels by microbial conversions. The status of research into various microbial energy technologies, the advantages and disadvantages of each of these approaches, research needs in the field, and education and training issues were examined, with the goal of identifying routes for producing biofuels that would both decrease the need for fossil fuels and reduce greenhouse gas emissions. Currently, the choices for providing energy are limited. Policy makers and the research community must begin to pursue a broader array of potential energy technologies. A diverse energy portfolio that includes an assortment of microbial energy choices will allow communities and consumers to select the best energy solution for their own particular needs. Funding agencies and governments alike need to prepare for future energy needs by investing both in the microbial energy technologies that work today and in the untested technologies that will serve the world’s needs tomorrow. More mature bioprocesses, such as ethanol production from starchy materials and methane from waste digestors, will find applications in the short term. However, innovative techniques for liquid fuel or biohydrogen production are among the longer term possibilities that should also be vigorously explored, starting now. Microorganisms can help meet human energy needs in any of a number of ways. In their most obvious role in energy conversion, microorganisms can generate fuels, including ethanol, hydrogen, methane, lipids, and butanol, which can be burned to produce energy. Alternatively, bacteria can be put to use in microbial fuel cells, where they carry out the direct conversion of biomass into electricity. Microorganisms may also be used some day to make oil and natural gas technologies more efficient by sequestering carbon or by assisting in the recovery of oil and

  16. Communication Access to Conversational Narrative

    ERIC Educational Resources Information Center

    Waller, Annalu

    2006-01-01

    This article describes methods that have been developed to provide augmentative and alternative communication communicators with better access to narrative conversation. It begins by highlighting the need to provide access to conversational narrative for people with complex communication needs, arguing that this type of conversation plays an…

  17. Special Features in Children's Conversations.

    ERIC Educational Resources Information Center

    Karjalainen, Merja

    In a study of features that seem to be typical of children's conversations, 10 Finnish preschool children's conversations were videotaped and audiotaped over a period of 10 hours. The children were taped in conversation, play, fairy tale, and eating situations. Among the findings are that all children enjoy playing with language, but some initiate…

  18. Crucial Conversations about America's Schools

    ERIC Educational Resources Information Center

    Draper, John C.; Protheroe, Nancy

    2010-01-01

    It's up to school leaders to shift the momentum away from conversations based on misperceptions and toward those that study critical issues about school improvement. "Crucial Conversations About America's Schools" talks about how to do this and provides examples of how to reframe conversations on the hot-button but important topics of…

  19. METHOD OF LOCATING GROUNDS

    DOEpatents

    Macleish, K.G.

    1958-02-11

    ABS>This patent presents a method for locating a ground in a d-c circult having a number of parallel branches connected across a d-c source or generator. The complete method comprises the steps of locating the ground with reference to the mildpoint of the parallel branches by connecting a potentiometer across the terminals of the circuit and connecting the slider of the potentiometer to ground through a current indicating instrument, adjusting the slider to right or left of the mildpoint so as to cause the instrument to indicate zero, connecting the terminal of the network which is farthest from the ground as thus indicated by the potentiometer to ground through a condenser, impressing a ripple voltage on the circuit, and then measuring the ripple voltage at the midpoint of each parallel branch to find the branch in which is the lowest value of ripple voltage, and then measuring the distribution of the ripple voltage along this branch to determine the point at which the ripple voltage drops off to zero or substantially zero due to the existence of a ground. The invention has particular application where a circuit ground is present which will disappear if the normal circuit voltage is removed.

  20. CD137, a member of the tumor necrosis factor receptor family, is located on chromosome 1p36, in a cluster of related genes, and colocalizes with several malignancies.

    PubMed

    Schwarz, H; Arden, K; Lotz, M

    1997-06-27

    CD137 (ILA/4-1BB) is a member of the tumor-necrosis-factor receptor family. Members of this receptor family and their structurally related ligands are important regulators of a wide variety of physiological processes and play an especially important role in the regulation of immune responses. CD137 regulates cell proliferation and survival of T-lymphocytes. Using Southern blot analysis and polymerase chain reaction, we localized the CD137 gene to chromosome 1p36. This chromosomal region harbors the genes of several other members of this receptor family and is associated with deletions and rearrangements in several malignancies.

  1. Methylation of miRNA genes and oncogenesis.

    PubMed

    Loginov, V I; Rykov, S V; Fridman, M V; Braga, E A

    2015-02-01

    Interaction between microRNA (miRNA) and messenger RNA of target genes at the posttranscriptional level provides fine-tuned dynamic regulation of cell signaling pathways. Each miRNA can be involved in regulating hundreds of protein-coding genes, and, conversely, a number of different miRNAs usually target a structural gene. Epigenetic gene inactivation associated with methylation of promoter CpG-islands is common to both protein-coding genes and miRNA genes. Here, data on functions of miRNAs in development of tumor-cell phenotype are reviewed. Genomic organization of promoter CpG-islands of the miRNA genes located in inter- and intragenic areas is discussed. The literature and our own results on frequency of CpG-island methylation in miRNA genes from tumors are summarized, and data regarding a link between such modification and changed activity of miRNA genes and, consequently, protein-coding target genes are presented. Moreover, the impact of miRNA gene methylation on key oncogenetic processes as well as affected signaling pathways is discussed.

  2. Zinc phosphate conversion coatings

    DOEpatents

    Sugama, T.

    1997-02-18

    Zinc phosphate conversion coatings for producing metals which exhibit enhanced corrosion prevention characteristics are prepared by the addition of a transition-metal-compound promoter comprising a manganese, iron, cobalt, nickel, or copper compound and an electrolyte such as polyacrylic acid, polymethacrylic acid, polyitaconic acid and poly-L-glutamic acid to a phosphating solution. These coatings are further improved by the incorporation of Fe ions. Thermal treatment of zinc phosphate coatings to generate {alpha}-phase anhydrous zinc phosphate improves the corrosion prevention qualities of the resulting coated metal. 33 figs.

  3. Zinc phosphate conversion coatings

    DOEpatents

    Sugama, Toshifumi

    1997-01-01

    Zinc phosphate conversion coatings for producing metals which exhibit enhanced corrosion prevention characteristics are prepared by the addition of a transition-metal-compound promoter comprising a manganese, iron, cobalt, nickel, or copper compound and an electrolyte such as polyacrylic acid, polymethacrylic acid, polyitaconic acid and poly-L-glutamic acid to a phosphating solution. These coatings are further improved by the incorporation of Fe ions. Thermal treatment of zinc phosphate coatings to generate .alpha.-phase anhydrous zinc phosphate improves the corrosion prevention qualities of the resulting coated metal.

  4. Pregnancy of unknown location.

    PubMed

    Schuneman, Margaret; Von Wald, Tiffany; Hansen, Keith

    2015-04-01

    The development of highly sensitive and accurate human chorionic gonadotropin assays as well as the improvement of vaginal ultrasound have allowed for the early detection of pregnancy and have reduced the morbidity and mortality associated with ectopic gestations. One of the byproducts of this increased sensitivity is pregnancy of unknown location (PUL), a term which is used to describe pregnancy in a woman with a positive pregnancy test but no signs of intrauterine or extrauterine pregnancy. A PUL can include an early intrauterine pregnancy, a failing intrauterine/extrauterine pregnancy or ectopic pregnancy. Modern medical management has improved the diagnosis and treatment of early pregnancy and pregnancy loss. In the hemodynamically stable patient with PUL, expectant management has been shown to be safe and allows for confirmatory studies before proceeding with therapy.

  5. Quantum Image Location

    NASA Astrophysics Data System (ADS)

    Jiang, Nan; Dang, Yijie; Zhao, Na

    2016-10-01

    Quantum image processing has been a hot topic as a consequence of the development of quantum computation. Many quantum image processing algorithms have been proposed, whose efficiency are theoretically higher than their corresponding classical algorithms. However, most of the quantum schemes do not consider the problem of measurement. If users want to get the results, they must measure the final state many times to get all the pixels' values. Moreover, executing the algorithm one time, users can only measure the final state one time. In order to measure it many times, users must execute the algorithms many times. If the measurement process is taken into account, whether or not the algorithms are really efficient needs to be reconsidered. In this paper, we try to solve the problem of measurement and give a quantum image location algorithm. This scheme modifies the probability of pixels to make the target pixel to be measured with higher probability. Furthermore, it only has linear complexity.

  6. Drivers of Wetland Conversion: a Global Meta-Analysis

    PubMed Central

    van Asselen, Sanneke; Verburg, Peter H.; Vermaat, Jan E.; Janse, Jan H.

    2013-01-01

    Meta-analysis of case studies has become an important tool for synthesizing case study findings in land change. Meta-analyses of deforestation, urbanization, desertification and change in shifting cultivation systems have been published. This present study adds to this literature, with an analysis of the proximate causes and underlying forces of wetland conversion at a global scale using two complementary approaches of systematic review. Firstly, a meta-analysis of 105 case-study papers describing wetland conversion was performed, showing that different combinations of multiple-factor proximate causes, and underlying forces, drive wetland conversion. Agricultural development has been the main proximate cause of wetland conversion, and economic growth and population density are the most frequently identified underlying forces. Secondly, to add a more quantitative component to the study, a logistic meta-regression analysis was performed to estimate the likelihood of wetland conversion worldwide, using globally-consistent biophysical and socioeconomic location factor maps. Significant factors explaining wetland conversion, in order of importance, are market influence, total wetland area (lower conversion probability), mean annual temperature and cropland or built-up area. The regression analyses results support the outcomes of the meta-analysis of the processes of conversion mentioned in the individual case studies. In other meta-analyses of land change, similar factors (e.g., agricultural development, population growth, market/economic factors) are also identified as important causes of various types of land change (e.g., deforestation, desertification). Meta-analysis helps to identify commonalities across the various local case studies and identify which variables may lead to individual cases to behave differently. The meta-regression provides maps indicating the likelihood of wetland conversion worldwide based on the location factors that have determined historic

  7. Averaged particle dose conversion coefficients in air crew dosimetry.

    PubMed

    Mares, V; Roesler, S; Schraube, H

    2004-01-01

    The MCNPX Monte Carlo code was used to calculate energy-dependent fluence-to-effective dose conversion coefficients for neutrons, protons, electrons, photons, charged pions and muons. The FLUKA Monte Carlo code was used to calculate the spectral particle fluences of secondary cosmic rays for different altitudes, and for different combinations of solar modulation and vertical cut-off rigidity parameters. The energy-averaged fluence-to-dose conversion coefficients were obtained by folding the particle fluence spectra with the conversion coefficients for effective dose and ambient dose equivalent. They show a slight dependence on altitude, solar activity and location in the geomagnetic field.

  8. Averaged particle dose conversion coefficients in air crew dosimetry.

    PubMed

    Mares, V; Roesler, S; Schraube, H

    2004-01-01

    The MCNPX Monte Carlo code was used to calculate energy-dependent fluence-to-effective dose conversion coefficients for neutrons, protons, electrons, photons, charged pions and muons. The FLUKA Monte Carlo code was used to calculate the spectral particle fluences of secondary cosmic rays for different altitudes, and for different combinations of solar modulation and vertical cut-off rigidity parameters. The energy-averaged fluence-to-dose conversion coefficients were obtained by folding the particle fluence spectra with the conversion coefficients for effective dose and ambient dose equivalent. They show a slight dependence on altitude, solar activity and location in the geomagnetic field. PMID:15353676

  9. Conversion to eslicarbazepine acetate monotherapy

    PubMed Central

    French, Jacqueline; Jacobson, Mercedes P.; Pazdera, Ladislav; Gough, Mallory; Cheng, Hailong; Grinnell, Todd; Blum, David

    2016-01-01

    Objective: To assess the efficacy and safety of eslicarbazepine acetate (ESL) monotherapy. Methods: This post hoc pooled analysis of 2 randomized double-blind studies (093-045 and -046) included adults with partial-onset seizures medically uncontrolled by 1 or 2 antiepileptic drugs (AEDs). Following the baseline period (8 weeks), eligible patients were randomized 2:1 to receive ESL 1,600 mg or 1,200 mg once daily for 18 weeks; the primary endpoint was study exit by meeting predefined exit criteria (signifying worsening seizure control). In each study, treatment was considered effective if the upper 95% confidence limit for exit rate was lower than the historical control threshold (65.3%). Results: Pooled exit rates were as follows: ESL 1,600 mg = 20.6% (95% confidence interval: 15.6%–26.8%); ESL 1,200 mg = 30.8% (23.0%–40.5%). Use of 2 baseline AEDs or rescue medication, US location, epilepsy duration ≥20 years, and higher maximum baseline seizure frequency were associated with higher exit risks. Median percent reductions in standardized seizure frequency between baseline and the 18-week double-blind period were as follows: ESL 1,600 mg = 43.2%; ESL 1,200 mg = 35.7%; baseline carbamazepine use was associated with smaller reductions. Safety profiles were similar between ESL doses. Conclusions: Exit rates for ESL monotherapy (1,600 mg and 1,200 mg once daily) were lower than the historical control threshold, irrespective of baseline AED use and region, with no additional safety concerns identified. Clinical factors and location clearly influence treatment responses in conversion-to-monotherapy trials. Classification of evidence: This pooled analysis provides Class IV evidence that for adults with medically uncontrolled partial-onset seizures, ESL monotherapy is well tolerated and effective. PMID:26911639

  10. Micromechanical power conversion

    NASA Astrophysics Data System (ADS)

    Noworolski, J. Mark

    A new concept in power conversion, based on electromechanical energy storage, is developed. Mechanical energy storage using Silicon offers a 2 order of magnitude improvement in volumetric energy storage density over conventional approaches using magnetic components. Two broad classes of electromechanical power converter topologies are introduced and analyzed: resonant and boost. Both are shown to scale well to smaller electromechanical device dimensions. A novel self-aligned micromachined polysilicon on nitride (SAMPSON) process flow was developed to fabricate mumechanical devices suitable for the boost conversion function. The process utility includes simplified fabrication of conventional surface micromachined resonators. Calculations showed that well-designed boost converters can achieve step-up factors in excess of 10 while using only a single mumechanical device. Boost converter tests utilizing discrete devices and the fabricated mumechanical elements demonstrated a step-up factor of 1.7. Measurements conducted on representative test devices indicate that power densities an order of magnitude higher than those in conventional power converters are attainable.

  11. Mode conversion in ITER

    NASA Astrophysics Data System (ADS)

    Jaeger, E. F.; Berry, L. A.; Myra, J. R.

    2006-10-01

    Fast magnetosonic waves in the ion cyclotron range of frequencies (ICRF) can convert to much shorter wavelength modes such as ion Bernstein waves (IBW) and ion cyclotron waves (ICW) [1]. These modes are potentially useful for plasma control through the generation of localized currents and sheared flows. As part of the SciDAC Center for Simulation of Wave-Plasma Interactions project, the AORSA global-wave solver [2] has been ported to the new, dual-core Cray XT-3 (Jaguar) at ORNL where it demonstrates excellent scaling with the number of processors. Preliminary calculations using 4096 processors have allowed the first full-wave simulations of mode conversion in ITER. Mode conversion from the fast wave to the ICW is observed in mixtures of deuterium, tritium and helium3 at 53 MHz. The resulting flow velocity and electric field shear will be calculated. [1] F.W. Perkins, Nucl. Fusion 17, 1197 (1977). [2] E.F. Jaeger, L.A. Berry, J.R. Myra, et al., Phys. Rev. Lett. 90, 195001-1 (2003).

  12. Conversion program in Sweden

    SciTech Connect

    Jonsson, E.B.

    1997-08-01

    The conversion of the Swedish 50 MW R2 reactor from HEU to LEU fuel has been successfully accomplished over a 16 cycles long process. The conversion started in January 1991 with the introduction of 6 LEU assemblies in the 8*8 core. The first all LEU core was loaded in March 1993 and physics measurements were performed for the final licensing reports. A total of 142 LEU fuel assemblies have been irradiated up until September 1994 without any fuel incident. The operating licence for the R2 reactor was renewed in mid 1994 taking into account new fuel type. The Swedish Nuclear Inspectorate (SKI) pointed out one crucial problem with the LEU operation, that the back end of the LEU fuel cycle has not yet been solved. For the HEU fuel Sweden had the reprocessing alternative. The country is now relying heavily on the success of the USDOEs Off Site Fuels Policy to take back the spent fuel from the research reactors. They have in the meantime increased their intermediate storage facilities. There is, however, a limit both in time and space for storage of MTR-type of assemblies in water. The penalty of the lower thermal neutron flux in LEU cores has been reduced by improvements of the new irradiation rigs and by fine tuning the core calculations. The Studsvik code package, CASMO-SIMULATE, widely used for ICFM in LWRs has been modified to suit the compact MTR type of core.

  13. Energy conversion system

    DOEpatents

    Murphy, L.M.

    1985-09-16

    The energy conversion system includes a photo-voltaic array for receiving solar radiation and converting such radiation to electrical energy. The photo-voltaic array is mounted on a stretched membrane that is held by a frame. Tracking means for orienting the photo-voltaic array in predetermined positions that provide optimal exposure to solar radiation cooperate with the frame. An enclosure formed of a radiation transmissible material includes an inside containment space that accommodates the photo-voltaic array on the stretched membrane, the frame and the tracking means, and forms a protective shield for all such components. The enclosure is preferably formed of a flexible inflatable material and maintains its preferred form, such as a dome, under the influence of a low air pressure furnished to the dome. Under this arrangement the energy conversion system is streamlined for minimizing wind resistance, sufficiently weathproof for providing protection against weather hazards such as hail, capable of using diffused light, lightweight for low-cost construction and operational with a minimal power draw.

  14. Energy conversion system

    DOEpatents

    Murphy, Lawrence M.

    1987-01-01

    The energy conversion system includes a photo-voltaic array for receiving solar radiation and converting such radiation to electrical energy. The photo-voltaic array is mounted on a stretched membrane that is held by a frame. Tracking means for orienting the photo-voltaic array in predetermined positions that provide optimal exposure to solar radiation cooperate with the frame. An enclosure formed of a radiation transmissible material includes an inside containment space that accommodates the photo-voltaic array on the stretched membrane, the frame and the tracking means, and forms a protective shield for all such components. The enclosure is preferably formed of a flexible inflatable material and maintains its preferred form, such as a dome, under the influence of a low air pressure furnished to the dome. Under this arrangement the energy conversion system is streamlined for minimizing wind resistance, sufficiently weatherproof for providing protection against weather hazards such as hail, capable of using diffused light, lightweight for low-cost construction, and operational with a minimal power draw.

  15. Natural gas conversion process

    SciTech Connect

    Not Available

    1991-01-01

    The main objective is to design and operate a laboratory apparatus for the catalytic reforming of natural gas in order to provide data for a large-scale process. To accelerate the assembly and calibration of this equipment, a request has been made to the Lawrence Berkeley Laboratory for assistance, under the DOE's Industrial Visitor Exchange Program. Pr. Heinz Heinemann (Catalysis), Dr. John Apps (Geochemistry) and Dr. Robert Fulton (Mechanical Engineering) have expressed interest in supporting our request. Pr. Heinemann's recent results on the conversion of Petroleum Coke residues into CO2 and H2 mixtures using highly basic metal oxides catalysts, similar to ours, are very encouraging regarding the possibility of converting the Coke residue on our catalyst into Syngas in the Regenerator/riser, as proposed. To minimize Coke formation in the vapor phase, by the Plasmapyrolytic Methane Conversion reactions, the experimental data of H. Drost et al. (Ref. 12) have been reviewed. Work is underway to design equipment for the safe and non-polluting disposal of the two gaseous product streams of the flow loop. 2 refs.

  16. Light alkane conversion

    SciTech Connect

    Harandi, M.N.; Owen, H.

    1991-07-09

    This patent describes a process for the aromatization of an aliphatic feedstream. It comprises fluidizing finely divided solid particles in a combustion zone; charging oxygen-containing combustion gas and fuel to the combustion zone under combustion conditions; withdrawing a stream of finely divided particles from the combustion zone; flowing the withdrawn stream of finely divided particles above to a cracking/dehydrogenation zone; fluidizing the finely divided particles above in an aliphatic feedstream under conditions within the cracking/dehydrogenation zone controlled to at least partially crack and at least partially dehydrogenate the aliphatic feedstream to form an intermediate product stream containing a quantity of C{sub 4}-olefins such that the exothermic catalytic conversion of the C{sub 4}-olefins is sufficient to supply a portion of the endothermic heat of reaction for the endothermic catalytic conversion of paraffins contained in the intermediate feedstream to aromatics; contacting the intermediate product stream with an aromatization catalyst under aromatization conditions sufficient to evolve an aromatics-rich products stream.

  17. Care, communication and conversation.

    PubMed

    De Dijn, Herman

    2005-09-01

    The professionalisation of care has resulted in ever increasing specialisation, use of technical innovations and informatisation. This has had consequences for the level and way of involvement of the care provider vis-a-vis the patient. The result has been growing alienation on the part of the patient and flight into non-classical medicine, as well as frustration on the part of medical personnel, likewise with respect to the reactions of patients. A solution is usually sought in more communication. This might be styled the professional answer to alienation and frustration, whereby 'the human factor', it is hoped, can be better accounted for. Enhanced communication implies two elements: 1) to better cater for the feelings of patients by trained communicators, i.e. more openness, more client satisfaction; 2) to better take into account patient rights and to actually implement them. The question is whether measures in terms of communication, geared at enhancing client satisfaction and the implementation of patient rights, are the real answer to the above mentioned alienation and frustration. Perhaps the trouble has deeper reasons and requires taking other dimensions into account such as decency and human dignity, which cannot be captured simply in terms of satisfaction and rights. This would mean that the answer must be sought at a deeper level than communication. This level might be called 'conversation' (using a concept analysed by Michael Oakeshott). In the second part of the paper, the possible relationship between care and conversation will be briefly analysed.

  18. GREAM: A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species

    PubMed Central

    Chandrashekar, Darshan Shimoga; Dey, Poulami; Acharya, Kshitish K.

    2015-01-01

    Background Genome-wide repeat sequences, such as LINEs, SINEs and LTRs share a considerable part of the mammalian nuclear genomes. These repeat elements seem to be important for multiple functions including the regulation of transcription initiation, alternative splicing and DNA methylation. But it is not possible to study all repeats and, hence, it would help to short-list before exploring their potential functional significance via experimental studies and/or detailed in silico analyses. Result We developed the ‘Genomic Repeat Element Analyzer for Mammals’ (GREAM) for analysis, screening and selection of potentially important mammalian genomic repeats. This web-server offers many novel utilities. For example, this is the only tool that can reveal a categorized list of specific types of transposons, retro-transposons and other genome-wide repetitive elements that are statistically over-/under-represented in regions around a set of genes, such as those expressed differentially in a disease condition. The output displays the position and frequency of identified elements within the specified regions. In addition, GREAM offers two other types of analyses of genomic repeat sequences: a) enrichment within chromosomal region(s) of interest, and b) comparative distribution across the neighborhood of orthologous genes. GREAM successfully short-listed a repeat element (MER20) known to contain functional motifs. In other case studies, we could use GREAM to short-list repetitive elements in the azoospermia factor a (AZFa) region of the human Y chromosome and those around the genes associated with rat liver injury. GREAM could also identify five over-represented repeats around some of the human and mouse transcription factor coding genes that had conserved expression patterns across the two species. Conclusion GREAM has been developed to provide an impetus to research on the role of repetitive sequences in mammalian genomes by offering easy selection of more interesting

  19. Object Locating System

    NASA Technical Reports Server (NTRS)

    Arndt, G. Dickey (Inventor); Carl, James R. (Inventor)

    2000-01-01

    A portable system is provided that is operational for determining, with three dimensional resolution, the position of a buried object or approximately positioned object that may move in space or air or gas. The system has a plurality of receivers for detecting the signal front a target antenna and measuring the phase thereof with respect to a reference signal. The relative permittivity and conductivity of the medium in which the object is located is used along with the measured phase signal to determine a distance between the object and each of the plurality of receivers. Knowing these distances. an iteration technique is provided for solving equations simultaneously to provide position coordinates. The system may also be used for tracking movement of an object within close range of the system by sampling and recording subsequent position of the object. A dipole target antenna. when positioned adjacent to a buried object, may be energized using a separate transmitter which couples energy to the target antenna through the medium. The target antenna then preferably resonates at a different frequency, such as a second harmonic of the transmitter frequency.

  20. AOTV bow shock location

    NASA Technical Reports Server (NTRS)

    Desautel, D.

    1985-01-01

    Hypersonic bow-shock location and geometry are of central importance to the aerodynamics and aerothermodynamics of aeroassisted orbital transfer vehicles (AOTVs), but they are difficult to predict for a given vehicle configuration. This paper reports experimental measurements of shock standoff distance for the 70 deg cone AOTV configuration in shock-tunnel-test flows at Mach numbers of 3.8 to 7.9 and for angles of attack from 0 deg to 20 deg. The controlling parameter for hypersonic bow-shock standoff distance (for a given forebody shape) is the mean normal-shock density ratio. Values for this parameter in the tests reported are in the same range as those of the drag-brake AOTV perigee regime. Results for standoff distance are compared with those previously reported in the literature for this AOTV configuration. It is concluded that the AOTV shock standoff distance for the conical configuration, based on frustrum (base) radius, is equivalent to that of a sphere with a radius about 35 percent greater than that of the cone; the distance is, therefore, much less than reported in previous studies. Some reasons for the discrepancies between the present and previous are advanced. The smaller standoff distance determined here implies there will be less radiative heat transfer than was previously expected.

  1. Dental School of Graduation in Relation to Dentist Location.

    ERIC Educational Resources Information Center

    Johnson, Donald W.; And Others

    1979-01-01

    A statistical study is presented of the 1976 location, by region and state, of the active civilian dentists of the United States in relation to the dental schools from which they graduated. A master matrix table shows state-by-state distribution of the graduates of each school and, conversely, where each state obtained its dentists. (Author/JMD)

  2. Power conversion technologies

    SciTech Connect

    Newton, M. A.

    1997-02-01

    The Power Conversion Technologies thrust area identifies and sponsors development activities that enhance the capabilities of engineering at Lawrence Livermore National Laboratory (LLNL) in the area of solid- state power electronics. Our primary objective is to be a resource to existing and emerging LLNL programs that require advanced solid-state power electronic technologies.. Our focus is on developing and integrating technologies that will significantly impact the capability, size, cost, and reliability of future power electronic systems. During FY-96, we concentrated our research efforts on the areas of (1) Micropower Impulse Radar (MIR); (2) novel solid-state opening switches; (3) advanced modulator technology for accelerators; (4) compact accelerators; and (5) compact pulse generators.

  3. Optomechanical down-conversion

    NASA Astrophysics Data System (ADS)

    Groeblacher, Simon; Hofer, Sebastian; Wieczorek, Witlef; Vanner, Michael; Hammerer, Klemens; Aspelmeyer, Markus

    2011-03-01

    One of the central interactions in quantum optics is two-mode squeezing, also known as down-conversion. It has been used in a multitude of pioneering experiments to demonstrate non-classical states of light and it is at the heart of generating quantum entanglement in optical fields. Here we demonstrate first experimental results towards the optomechanical analogue, in which an optical and a mechanical mode interact via a two-mode squeezing operation. In addition, we make use of the fact that large optomechanical coupling strengths provide access to an interaction regime beyond the rotating wave approximation. This allows for simultaneous cooling of the mechanical mode, which will eventually enable the preparation of pure initial mechanical states and is hence an important precondition to achieve the envisioned optomechanical entanglement.

  4. Automated FORTRAN conversion

    NASA Technical Reports Server (NTRS)

    Aharonian, Gregory

    1986-01-01

    The most pratical solution to the conversion of FORTRAN to other programming languages which STO and a few others have adopted, uses an intermediate language that is easy to translate FORTRAN into, and allows for source codes in other languages to be generated automatically. The intermediate language is the union of all other programming languages (and the trick is to create a useful union) with some extensions that reflect the nature of the algorithms. The benefits of this approach are many. First the original FORTRAN program has to be rewritten only once, and then only parts of the program: most FORTRAN code passes through without and change (i.e., assignment and simple IF statements). Software tools are provided to ease this initial translation. Once in the intermediate language, the algorithm can then be obtained in any other language automatically. An example of a subroutine from the Rispack library in ten different languages is given.

  5. Thermal Energy Conversion Branch

    NASA Technical Reports Server (NTRS)

    Bielozer, Matthew C.; Schreiber, Jeffrey, G.; Wilson, Scott D.

    2004-01-01

    The Thermal Energy Conversion Branch (5490) leads the way in designing, conducting, and implementing research for the newest thermal systems used in space applications at the NASA Glenn Research Center. Specifically some of the most advanced technologies developed in this branch can be broken down into four main areas: Dynamic Power Systems, Primary Solar Concentrators, Secondary Solar Concentrators, and Thermal Management. Work was performed in the Dynamic Power Systems area, specifically the Stirling Engine subdivision. Today, the main focus of the 5490 branch is free-piston Stirling cycle converters, Brayton cycle nuclear reactors, and heat rejection systems for long duration mission spacecraft. All space exploring devices need electricity to operate. In most space applications, heat energy from radioisotopes is converted to electrical power. The Radioisotope Thermoelectric Generator (RTG) already supplies electricity for missions such as the Cassini Spacecraft. The focus of today's Stirling research at GRC is aimed at creating an engine that can replace the RTG. The primary appeal of the Stirling engine is its high system efficiency. Because it is so efficient, the Stirling engine will significantly reduce the plutonium fuel mission requirements compared to the RTG. Stirling is also being considered for missions such as the lunar/Mars bases and rovers. This project has focused largely on Stirling Engines of all types, particularly the fluidyne liquid piston engine. The fluidyne was developed by Colin D. West. This engine uses the same concepts found in any type of Stirling engine, with the exception of missing mechanical components. All the working components are fluid. One goal was to develop and demonstrate a working Stirling Fluidyne Engine at the 2nd Annual International Energy Conversion Engineering Conference in Providence, Rhode Island.

  6. No Distinction of Orthology/Paralogy between Human and Chimpanzee Rh Blood Group Genes

    PubMed Central

    Kitano, Takashi; Kim, Choong-Gon; Blancher, Antoine; Saitou, Naruya

    2016-01-01

    On human (Homo sapiens) chromosome 1, there is a tandem duplication encompassing Rh blood group genes (Hosa_RHD and Hosa_RHCE). This duplication occurred in the common ancestor of humans, chimpanzees (Pan troglodytes), and gorillas, after splitting from their common ancestor with orangutans. Although several studies have been conducted on ape Rh blood group genes, the clear genome structures of the gene clusters remain unknown. Here, we determined the genome structure of the gene cluster of chimpanzee Rh genes by sequencing five BAC (Bacterial Artificial Chromosome) clones derived from chimpanzees. We characterized three complete loci (Patr_RHα, Patr_RHβ, and Patr_RHγ). In the Patr_RHβ locus, a short version of the gene, which lacked the middle part containing exons 4–8, was observed. The Patr_RHα and Patr_RHβ genes were located on the locations corresponding to Hosa_RHD and Hosa_RHCE, respectively, and Patr_RHγ was in the immediate vicinity of Patr_RHβ. Sequence comparisons revealed high sequence similarity between Patr_RHβ and Hosa_RHCE, while the chimpanzee Rh gene closest to Hosa_RHD was not Patr_RHα but rather Patr_RHγ. The results suggest that rearrangements and gene conversions frequently occurred between these genes and that the classic orthology/paralogy dichotomy no longer holds between human and chimpanzee Rh blood group genes. PMID:26872772

  7. Immunoglobulin gene diversification in cattle.

    PubMed

    Meyer, A; Parng, C L; Hansal, S A; Osborne, B A; Goldsby, R A

    1997-01-01

    Research in several species has revealed that different types of mammals have evolved divergent molecular and cellular strategies for generating immunoglobulin diversity. Other chapters in this text have highlighted the specific characteristics unique to chicken, rabbit, mouse, human and sheep B lymphocyte development; namely indicating differences in the mechanisms of diversity and the site of primary B cell development. Studies of the bovine system have indicated that like the sheep system, the ileal Peyer's patch (IPP) is a likely chicken bursal equivalent, and is a site of primary B lymphocyte development. Substantial investigation in sheep has indicated that Ig diversity is created by untemplated somatic mutation and intense selective pressure (Reynaud et al., 1991). The frequency of alteration in the sheep Ig light chain gene locus also is characteristic of the bovine system, however, recent evidence from sequencing of bovine lambda light chain genes indicates that one mechanism that contributes to diversity is gene conversion, utilizing several pseudogenes located in the Ig locus (Parng et al., 1996). The mechanism by which this hyperalteration of Ig genes occurs in both sheep and cattle is poorly understood and is thus the focus of considerable investigation. The study of events in the IPP may also have informative ramifications for secondary diversification of the Ig repertoire by somatic hyperalteration in germinal centers.

  8. The gene for spinal cerebellar ataxia 3 (SCA3) is located in a region of {approximately} 3 cM on chromosome 14q24.3-q32.2

    SciTech Connect

    Stevanin, G.; Cancel, G.; Duerr, A.; Dubourg, O.; Agid, Y.; Brice, A.; Chneiweiss, H.; Weissenbach, J.; Cann, H.M.

    1995-01-01

    SCA3, the gene for spinal cerebellar ataxia 3, was recently mapped to a 15-cM interval between D14S67 and D14S81 on chromosome 14q, by linkage analysis in two families of French ancestry. The SCA3 candidate region has now been refined by linkage analysis with four new microsatellite markers (D14S256, D14S291, D14S280, and AFM343vf1) in the same two families, in which 19 additional individuals were genotyped, and in a third French family. Combined two-point linkage analyses show that the new markers, D14S280 and AFM343vf1, are tightly linked to the SCA3 locus, with maximal lod scores, at recombination fraction, ({theta}) = .00, of 7.05 and 13.70, respectively. Combined multipoint and recombinant haplotype analyses localize the SCA3 locus to a 3-cM interval flanked by D14S291 and D14S81. The same allele for D14S280 segregates with the disease locus in the three kindreds. This allele is frequent in the French population, however, and linkage disequilibrium is not clearly established. The SCA3 locus remains within the 29-cM region on 14q24.3-q32.2 containing the gene for the Machado-Joseph disease, which is clinically related to the phenotype determined by SCA3, but it cannot yet be concluded that both diseases result from alterations of the same gene. 30 refs., 3 figs., 3 tabs.

  9. Carbon aerogel electrodes for direct energy conversion

    DOEpatents

    Mayer, Steven T.; Kaschmitter, James L.; Pekala, Richard W.

    1997-01-01

    A direct energy conversion device, such as a fuel cell, using carbon aerogel electrodes, wherein the carbon aerogel is loaded with a noble catalyst, such as platinum or rhodium and soaked with phosphoric acid, for example. A separator is located between the electrodes, which are placed in a cylinder having plate current collectors positioned adjacent the electrodes and connected to a power supply, and a pair of gas manifolds, containing hydrogen and oxygen positioned adjacent the current collectors. Due to the high surface area and excellent electrical conductivity of carbon aerogels, the problems relative to high polarization resistance of carbon composite electrodes conventionally used in fuel cells are overcome.

  10. Carbon aerogel electrodes for direct energy conversion

    DOEpatents

    Mayer, S.T.; Kaschmitter, J.L.; Pekala, R.W.

    1997-02-11

    A direct energy conversion device, such as a fuel cell, using carbon aerogel electrodes is described, wherein the carbon aerogel is loaded with a noble catalyst, such as platinum or rhodium and soaked with phosphoric acid, for example. A separator is located between the electrodes, which are placed in a cylinder having plate current collectors positioned adjacent the electrodes and connected to a power supply, and a pair of gas manifolds, containing hydrogen and oxygen positioned adjacent the current collectors. Due to the high surface area and excellent electrical conductivity of carbon aerogels, the problems relative to high polarization resistance of carbon composite electrodes conventionally used in fuel cells are overcome. 1 fig.

  11. Enzymatic Upgrading of Heavy Crudes via Partial Oxidation or Conversion of PAHs

    SciTech Connect

    Borole, A P; Davison, B H; Kuritz, T

    2002-07-01

    The objective of this program was to investigate new enzyme-based technologies for upgrading of heavy oils. Enzymes were selected for screening from those capable of conversion of polyaromatic hydrocarbons (PAHs) reported in the literature. Oxidative reactions of PAHs using hydrogen peroxide as an oxidant with conversion to partially oxidized products were used. The enzymes (lignin peroxidase, cytochrome c) were tested in various organic solvents and found to loose activity in pure organic solvents. A thermodynamic analysis revealed lack of effective interaction between the substrate and enzyme as the cause for low activity. The protein cytochrome c was modified to work in organic media by chemical hydrophobic group attachment. Two different modifications were made: attachment of polyethylene glycol (PEG) and alkyl groups. Alkyl groups, being small could be attached at interior locations within the core of the enzyme and possibly near the active site. Increase in the threshold solvent concentration where maximum enzyme activity occurred indicated potential of this strategy for effective enzyme-substrate interaction. Further improvements in enzyme activity called for other diverse methods due to the unavailability of sufficient chemical modification sites. Genetic techniques were therefore explored for further improvements. These experiments focused on cloning of a gene for the fungal enzyme lignin peroxidase (lip) into yeast Pichia pastoris, which would allow easy manipulation of the gene. However, differences in the fungal and yeast cellular machinery impeded significant expression of the fungal enzyme. Several strategies were explored to allow higher-level expression of the enzyme, which was required for enzyme improvement. The strategies used in this investigation are described in the report. Industrial in-kind support was available throughout the project period. review of the research results was carried out on a regular basis (bimonthly reports and annual

  12. Geothermal energy conversion facility

    SciTech Connect

    Kutscher, C.F.

    1997-12-31

    With the termination of favorable electricity generation pricing policies, the geothermal industry is exploring ways to improve the efficiency of existing plants and make them more cost-competitive with natural gas. The Geothermal Energy Conversion Facility (GECF) at NREL will allow researchers to study various means for increasing the thermodynamic efficiency of binary cycle geothermal plants. This work has received considerable support from the US geothermal industry and will be done in collaboration with industry members and utilities. The GECF is being constructed on NREL property at the top of South Table Mountain in Golden, Colorado. As shown in Figure 1, it consists of an electrically heated hot water loop that provides heating to a heater/vaporizer in which the working fluid vaporizes at supercritical or subcritical pressures as high as 700 psia. Both an air-cooled and water-cooled condenser will be available for condensing the working fluid. In order to minimize construction costs, available equipment from the similar INEL Heat Cycle Research Facility is being utilized.

  13. GPU color space conversion

    NASA Astrophysics Data System (ADS)

    Chase, Patrick; Vondran, Gary

    2011-01-01

    Tetrahedral interpolation is commonly used to implement continuous color space conversions from sparse 3D and 4D lookup tables. We investigate the implementation and optimization of tetrahedral interpolation algorithms for GPUs, and compare to the best known CPU implementations as well as to a well known GPU-based trilinear implementation. We show that a 500 NVIDIA GTX-580 GPU is 3x faster than a 1000 Intel Core i7 980X CPU for 3D interpolation, and 9x faster for 4D interpolation. Performance-relevant GPU attributes are explored including thread scheduling, local memory characteristics, global memory hierarchy, and cache behaviors. We consider existing tetrahedral interpolation algorithms and tune based on the structure and branching capabilities of current GPUs. Global memory performance is improved by reordering and expanding the lookup table to ensure optimal access behaviors. Per multiprocessor local memory is exploited to implement optimally coalesced global memory accesses, and local memory addressing is optimized to minimize bank conflicts. We explore the impacts of lookup table density upon computation and memory access costs. Also presented are CPU-based 3D and 4D interpolators, using SSE vector operations that are faster than any previously published solution.

  14. Static Scale Conversion (SSC)

    2007-01-19

    The Static Scale Conversion (SSC) software is a unique enhancement to the AIMVEE system. It enables a SSC to weigh and measure vehicles and cargo dynamically (i.e., as they pass over the large scale. Included in the software is the AIMVEE computer code base. The SSC and AIMVEE computer system electronically continue to retrieve deployment information, identify vehicle automatically and determine total weight, individual axle weights, axle spacing and center-of-balance for any wheeled vehicle inmore » motion. The AIMVEE computer code system can also perform these functions statically for both wheel vehicles and cargo with information. The AIMVEE computer code system incorporates digital images and applies cubing algorithms to determine length, width, height for cubic dimensions of both vehicle and cargo. Once all this information is stored, it electronically links to data collection and dissemination systems to provide “actual” weight and measurement information for planning, deployment, and in-transit visibility.« less

  15. Static Scale Conversion (SSC)

    SciTech Connect

    2007-01-19

    The Static Scale Conversion (SSC) software is a unique enhancement to the AIMVEE system. It enables a SSC to weigh and measure vehicles and cargo dynamically (i.e., as they pass over the large scale. Included in the software is the AIMVEE computer code base. The SSC and AIMVEE computer system electronically continue to retrieve deployment information, identify vehicle automatically and determine total weight, individual axle weights, axle spacing and center-of-balance for any wheeled vehicle in motion. The AIMVEE computer code system can also perform these functions statically for both wheel vehicles and cargo with information. The AIMVEE computer code system incorporates digital images and applies cubing algorithms to determine length, width, height for cubic dimensions of both vehicle and cargo. Once all this information is stored, it electronically links to data collection and dissemination systems to provide “actual” weight and measurement information for planning, deployment, and in-transit visibility.

  16. PDB to AMPL Conversion

    2002-09-01

    PDB to AMPL Conversion was written to convert protein data base files to AMPL files. The protein data bases on the internet contain a wealth of information about the structue and makeup of proteins. Each file contains information derived by one or more experiments and contains information on how the experiment waw performed, the amino acid building blocks of each chain, and often the three-dimensional structure of the protein extracted from the experiments. The waymore » a protein folds determines much about its function. Thus, studying the three-dimensional structure of the protein is of great interest. Analysing the contact maps is one way to examine the structure. A contact map is a graph which has a linear back bone of amino acids for nodes (i.e., adjacent amino acids are always connected) and vertices between non-adjacent nodes if they are close enough to be considered in contact. If the graphs are similar then the folds of the protein and their function should also be similar. This software extracts the contact maps from a protein data base file and puts in into AMPL data format. This format is designed for use in AMPL, a programming language for simplifying linear programming formulations.« less

  17. High diversity of the 'Spumella-like' flagellates: an investigation based on the SSU rRNA gene sequences of isolates from habitats located in six different geographic regions.

    PubMed

    Boenigk, Jens; Pfandl, Karin; Stadler, Peter; Chatzinotas, Antonis

    2005-05-01

    We isolated 28 strains of 'Spumella-like' flagellates from different freshwater and soil habitats in Austria, People's Republic of China, Nepal, New Zealand, Uganda, Kenya, Tanzania and Hawaii by use of a modified filtration-acclimatization method. 'Spumella-like' flagellates were found in all of the samples and were often among the dominant bacterivorous flagellates in the respective environments. The small subunit ribosomal RNA (SSU rRNA) gene sequence of the isolates was determined and aligned with previously published sequences of members belonging to the Chrysophyceae sensu stricto. Phylogenetic analysis of the 28 new sequences confirmed their position within the Chrysophyceae sensu stricto and positioned them within different clades. Most of the sequences grouped within clade C and formed several subclusters separated from each other by green taxa including flagellates belonging to Ochromonas, Dinobryon, Poterioochromonas and others. All soil isolates clustered together (subcluster C1) with the soil strain Spumella elongata and the undescribed soil strain 'Spumella danica'. Aquatic isolates were affiliated with at least two branches (C2 and C3). Sequence similarity to the closest related member of the Chrysophyceae ranged between 92% and 99.6%, sequence divergence among the 'Spumella-like' flagellates was as high as 10%. We conclude that (i) the 'Spumella-like' flagellates are a diverse group both in terms of sequence dissimilarity between isolates and in terms of the number of genotypes, (ii) Spumella and Ochromonas are polyphyletic, and (iii) based on the SSU rRNA gene no biogeographical restriction of certain branches could be observed even though different ecotypes may be represented by the same genotype.

  18. Macrophage response to methacrylate conversion using a gradient approach.

    PubMed

    Lin, Nancy J; Bailey, LeeAnn O; Becker, Matthew L; Washburn, Newell R; Henderson, Lori A

    2007-03-01

    Incomplete conversion, an ongoing challenge facing photopolymerized methacrylate-based polymers, affects leachables as well as the resulting polymer network. As novel polymers and composites are developed, methods to efficiently screen cell response to these materials and their properties, including conversion, are needed. In this study, an in vitro screening methodology was developed to assess cells cultured directly on cross-linked polymer networks. A gradient in methacrylate double bond conversion was used to increase the experimental throughput. A substrate of 2,2-bis[4-(2-hydroxy-3-methacryloxypropoxy)phenyl] propane (BisGMA) and triethylene glycol dimethacrylate (TEGDMA) was prepared with a conversion ranging from 43.0% to 61.2%. Substrates aged for 7 days had no significant differences in surface roughness or hydrophilicity as a function of conversion. Leachables were detectable for at least 7 days using UV absorption, but their global cytotoxicity was insignificant after 5 days of aging. Thus, RAW 264.7 macrophage-like cells were cultured on aged substrates to evaluate the cell response to conversion, with possible contributions from the polymer network and local leachables. Conversions of 45% and 50% decreased viability (via calcein/ethidium staining) and increased apoptosis (via annexin-V staining). No significant changes (p>0.05) in tumor necrosis factor-alpha and interleukin-1beta gene expression, as measured by quantitative, real-time reverse transcription-polymerase chain reaction, were seen as conversion increased. Thus, conversions greater than 50% are recommended for equimolar BisGMA/TEGDMA. The ability to distinguish cell response as a function of conversion is useful as an initial biological screening platform to optimize dental polymers.

  19. Structure and Evolution of Genes Encoding Polyubiquitin and Ubiquitin-like Proteins in Arabidopsis Thaliana Ecotype Columbia

    PubMed Central

    Callis, J.; Carpenter, T.; Sun, C. W.; Vierstra, R. D.

    1995-01-01

    The Arabidopsis thaliana ecotype Columbia ubiquitin gene family consists of 14 members that can be divided into three types of ubiquitin genes; polyubiquitin genes, ubiquitin-like genes and ubiquitin extension genes. The isolation and characterization of eight ubiquitin sequences, consisting of four polyubiquitin genes and four ubiquitin-like genes, are described here, and their relationships to each other and to previously identified Arabidopsis ubiquitin genes were analyzed. The polyubiquitin genes, UBQ3, UBQ10, UBQ11 and UBQ14, contain tandem repeats of the 228-bp ubiquitin coding region. Together with a previously described polyubiquitin gene, UBQ4, they differ in synonymous substitutions, number of ubiquitin coding regions, number and nature of nonubiquitin C-terminal amino acid(s) and chromosomal location, dividing into two subtypes; the UBQ3/UBQ4 and UBQ10/UBQ11/UBQ14 subtypes. Ubiquitin-like genes, UBQ7, UBQ8, UBQ9 and UBQ12, also contain tandem repeats of the ubiquitin coding region, but at least one repeat per gene encodes a protein with amino acid substitutions. Nucleotide comparisons, K(s) value determinations and neighbor-joining analyses were employed to determine intra- and intergenic relationships. In general, the rate of synonymous substitution is too high to discern related repeats. Specific exceptions provide insight into gene relationships. The observed nucleotide relationships are consistent with previously described models involving gene duplications followed by both unequal crossing-over and gene conversion events. PMID:7713442

  20. In Conversation with Jim Blair

    ERIC Educational Resources Information Center

    Holman, Andrew

    2012-01-01

    Jim Blair is the only consultant nurse working with people with learning disabilities in the country. His job helps make people better and saves money. This article shares a conversation with Jim Blair. In the conversation, Blair says he is unhappy Valuing People programme did not do as much as it could have done. Jim is worried all the changes,…

  1. Conversational Competence in Academic Settings

    ERIC Educational Resources Information Center

    Bowman, Richard F.

    2014-01-01

    Conversational competence is a process, not a state. Ithaca does not exist, only the voyage to Ithaca. Vibrant campuses are a series of productive conversations. At its core, communicative competence in academic settings mirrors a collective search for meaning regarding the purpose and direction of a campus community. Communicative competence…

  2. The Practicalities of Document Conversion.

    ERIC Educational Resources Information Center

    Galbraith, Ian

    1993-01-01

    Describes steps involved in the conversion of source documents to scanned digital image format. Topics addressed include document preparation, including photographs and oversized material; indexing procedures, including automatic indexing possibilities; scanning documents, including resolution and throughput; quality control; backfile conversion;…

  3. Record Conversion at Oregon State.

    ERIC Educational Resources Information Center

    Watkins, Deane

    1985-01-01

    Describes the conversion of card catalog records at William Jasper Kerr Library, Oregon State University, to an online system. Discussion covers the use of OCLC and student assistants, procedures and specifications, and problems associated with massive retrospective conversion needs and uncertain budget allocations. Eight sources are recommended.…

  4. Intercultural Conversation: Building Understanding Together

    ERIC Educational Resources Information Center

    Dooley, Karen

    2009-01-01

    As schools in English-speaking countries become increasingly diverse, there are new and increasing opportunities for students to engage in intercultural conversations. Although such conversations have the potential to enrich the learning experience of all in the classroom, difficulties of understanding are likely to arise. The challenge is to…

  5. Faculty Meetings: Hidden Conversational Dynamics

    ERIC Educational Resources Information Center

    Bowman, Richard F.

    2015-01-01

    In the everydayness of faculty meetings, collegial conversations mirror distinctive dynamics and practices, which either enhance or undercut organizational effectiveness. A cluster of conversational practices affect how colleagues connect, engage, interact, and influence others during faculty meetings in diverse educational settings. The…

  6. Conversing Life: An Autoethnographic Construction

    ERIC Educational Resources Information Center

    Hoelson, Christopher N.; Burton, Rod

    2012-01-01

    This autoethnography is a constructed account of a co-exploration into the nature and effects of a longitudinal dyadic conversation process from a relational constructionist perspective. The conversations, between me as participant autoethnographer and a co-participant, aimed at maximising personal learning for both. Through co-created contexts of…

  7. FFTF Asbestos Location Tracking Program

    SciTech Connect

    Reynolds, J.A.

    1994-09-15

    An Asbestos Location Tracking Program was prepared to list, locate, and determine Asbestos content and to provide baseline {open_quotes}good faith{close_quotes} for yearly condition inspections for the FFTF Plant and buildings and grounds.

  8. Culture and conversion disorder: implications for DSM-5.

    PubMed

    Brown, Richard J; Lewis-Fernández, Roberto

    2011-01-01

    The diagnostic criteria and related features of conversion disorder are under revision for DSM-5, including the requirement that psychological factors accompany the symptoms or deficits in question (Criterion B) and whether conversion disorder should be re-labeled as a dissociative, rather than a somatoform, condition. We examined the cross-cultural evidence on the prevalence, characteristics, and associated features of pseudoneurological symptoms more generally, and conversion disorder in particular, in order to inform the ongoing re-evaluation of the conversion disorder category. We also examined the relationship between these constructs and dissociative symptoms and disorders across cultural groups. Searches were conducted of the mental health literature, particularly since 1994, regarding culture, race, or ethnicity factors related to conversion disorder. Many proposed DSM-5 revisions were supported, such as the elimination of Criterion B. We also found cross-cultural variability in predominant symptoms, disorder prevalence, and relationship with cultural syndromes. Additional information that may contribute to DSM-5 includes the elevated rates across cultures of traumatic exposure and psychiatric comorbidity in conversion disorder. Cross-culturally, conversion disorder is associated strongly with both dissociative and somatoform presentations, revealing no clear basis on which to locate the disorder in DSM-5. Careful consideration should be given to the possible alternatives.

  9. Spring loaded locator pin assembly

    DOEpatents

    Groll, Todd A.; White, James P.

    1998-01-01

    This invention deals with spring loaded locator pins. Locator pins are sometimes referred to as captured pins. This is a mechanism which locks two items together with the pin that is spring loaded so that it drops into a locator hole on the work piece.

  10. Spring loaded locator pin assembly

    DOEpatents

    Groll, T.A.; White, J.P.

    1998-03-03

    This invention deals with spring loaded locator pins. Locator pins are sometimes referred to as captured pins. This is a mechanism which locks two items together with the pin that is spring loaded so that it drops into a locator hole on the work piece. 5 figs.

  11. Impact-Locator Sensor Panels

    NASA Technical Reports Server (NTRS)

    Christiansen, Eric L.; Byers, Terry; Gibbons, Frank

    2008-01-01

    Electronic sensor systems for detecting and locating impacts of rapidly moving particles on spacecraft have been invented. Systems of this type could also be useful on Earth in settings in which the occurrence of impacts and/or the locations of impacts are not immediately obvious and there are requirements to detect and quickly locate impacts to prevent or minimize damage.

  12. Quantitative evaluation of ocean thermal energy conversion (OTEC): executive briefing

    SciTech Connect

    Gritton, E.C.; Pei, R.Y.; Hess, R.W.

    1980-08-01

    Documentation is provided of a briefing summarizing the results of an independent quantitative evaluation of Ocean Thermal Energy Conversion (OTEC) for central station applications. The study concentrated on a central station power plant located in the Gulf of Mexico and delivering power to the mainland United States. The evaluation of OTEC is based on three important issues: resource availability, technical feasibility, and cost.

  13. The Use of Conversational Repairs by African American Preschoolers

    ERIC Educational Resources Information Center

    Stockman, Ida J.; Karasinski, Laura; Guillory, Barbara

    2008-01-01

    Purpose: This study aimed to describe the types and frequency of conversational repairs used by African American (AA) children in relationship to their geographic locations and levels of performance on commonly used speech-language measures. Method: The strategies used to initiate repairs and respond to repair requests were identified in…

  14. Kcna1 gene deletion lowers the behavioral sensitivity of mice to small changes in sound location and increases asynchronous brainstem auditory evoked potentials, but does not affect hearing thresholds

    PubMed Central

    Allen, Paul D.; Ison, James R.

    2012-01-01

    Sound localization along the azimuth depends on the sensitivity of binaural nuclei in the auditory brainstem to small differences in interaural level and timing occurring within a sub-millisecond epoch, and on monaural pathways that transmit level and timing cues with high temporal fidelity to insure their coincident arrival at the binaural targets. The soma and axons of these brainstem neurons are heavily invested with ion channels containing the low-threshold potassium channel subunit Kv1.1, which previous in-vitro and in-vivo studies suggest are important for regulating their high input-output correspondence and temporal synchrony. We compared awake Kcna1 null mutant (−/−) mice lacking Kv1.1 with +/+ mice to determine if Kv1.1 activity contributes to sound localization, and examined anesthetized mice for absolute hearing thresholds for suprathreshold differences that may be revealed in the waveforms of auditory brainstem response potentials. The awake −/− mice tested with reflex modification audiometry had reduced sensitivity to an abrupt change in the location of a broad band noise compared to +/+ mice, while anesthetized −/− mice had normal absolute thresholds for tone pips but a high level of stimulus-evoked but asynchronous background activity. Evoked potential waveforms had progressively earlier peaks and troughs in −/− mice but the amplitude excursions between adjacent features were identical in the two groups. Their greater excitability and asynchrony in suprathreshold evoked potentials coupled with their normal thresholds suggests that a disruption in central neural processing in −/− mice and not peripheral hearing loss is responsible for their poor sound localization. PMID:22396426

  15. Petite fabrique de conversation francaise (Little Factory of French Conversation).

    ERIC Educational Resources Information Center

    Dubroca, Danielle

    1987-01-01

    A technique using dialogues and realistic prose passages from the works of Georges Simenon and Simone de Beauvoir to teach French conversational skills at the college level is explained and illustrated. (MSE)

  16. Roadmap on optical energy conversion

    NASA Astrophysics Data System (ADS)

    Boriskina, Svetlana V.; Green, Martin A.; Catchpole, Kylie; Yablonovitch, Eli; Beard, Matthew C.; Okada, Yoshitaka; Lany, Stephan; Gershon, Talia; Zakutayev, Andriy; Tahersima, Mohammad H.; Sorger, Volker J.; Naughton, Michael J.; Kempa, Krzysztof; Dagenais, Mario; Yao, Yuan; Xu, Lu; Sheng, Xing; Bronstein, Noah D.; Rogers, John A.; Alivisatos, A. Paul; Nuzzo, Ralph G.; Gordon, Jeffrey M.; Wu, Di M.; Wisser, Michael D.; Salleo, Alberto; Dionne, Jennifer; Bermel, Peter; Greffet, Jean-Jacques; Celanovic, Ivan; Soljacic, Marin; Manor, Assaf; Rotschild, Carmel; Raman, Aaswath; Zhu, Linxiao; Fan, Shanhui; Chen, Gang

    2016-07-01

    For decades, progress in the field of optical (including solar) energy conversion was dominated by advances in the conventional concentrating optics and materials design. In recent years, however, conceptual and technological breakthroughs in the fields of nanophotonics and plasmonics combined with a better understanding of the thermodynamics of the photon energy-conversion processes reshaped the landscape of energy-conversion schemes and devices. Nanostructured devices and materials that make use of size quantization effects to manipulate photon density of states offer a way to overcome the conventional light absorption limits. Novel optical spectrum splitting and photon-recycling schemes reduce the entropy production in the optical energy-conversion platforms and boost their efficiencies. Optical design concepts are rapidly expanding into the infrared energy band, offering new approaches to harvest waste heat, to reduce the thermal emission losses, and to achieve noncontact radiative cooling of solar cells as well as of optical and electronic circuitries. Light–matter interaction enabled by nanophotonics and plasmonics underlie the performance of the third- and fourth-generation energy-conversion devices, including up- and down-conversion of photon energy, near-field radiative energy transfer, and hot electron generation and harvesting. Finally, the increased market penetration of alternative solar energy-conversion technologies amplifies the role of cost-driven and environmental considerations. This roadmap on optical energy conversion provides a snapshot of the state of the art in optical energy conversion, remaining challenges, and most promising approaches to address these challenges. Leading experts authored 19 focused short sections of the roadmap where they share their vision on a specific aspect of this burgeoning research field. The roadmap opens up with a tutorial section, which introduces major concepts and terminology. It is our hope that the

  17. Roadmap on optical energy conversion

    NASA Astrophysics Data System (ADS)

    Boriskina, Svetlana V.; Green, Martin A.; Catchpole, Kylie; Yablonovitch, Eli; Beard, Matthew C.; Okada, Yoshitaka; Lany, Stephan; Gershon, Talia; Zakutayev, Andriy; Tahersima, Mohammad H.; Sorger, Volker J.; Naughton, Michael J.; Kempa, Krzysztof; Dagenais, Mario; Yao, Yuan; Xu, Lu; Sheng, Xing; Bronstein, Noah D.; Rogers, John A.; Alivisatos, A. Paul; Nuzzo, Ralph G.; Gordon, Jeffrey M.; Wu, Di M.; Wisser, Michael D.; Salleo, Alberto; Dionne, Jennifer; Bermel, Peter; Greffet, Jean-Jacques; Celanovic, Ivan; Soljacic, Marin; Manor, Assaf; Rotschild, Carmel; Raman, Aaswath; Zhu, Linxiao; Fan, Shanhui; Chen, Gang

    2016-07-01

    For decades, progress in the field of optical (including solar) energy conversion was dominated by advances in the conventional concentrating optics and materials design. In recent years, however, conceptual and technological breakthroughs in the fields of nanophotonics and plasmonics combined with a better understanding of the thermodynamics of the photon energy-conversion processes reshaped the landscape of energy-conversion schemes and devices. Nanostructured devices and materials that make use of size quantization effects to manipulate photon density of states offer a way to overcome the conventional light absorption limits. Novel optical spectrum splitting and photon-recycling schemes reduce the entropy production in the optical energy-conversion platforms and boost their efficiencies. Optical design concepts are rapidly expanding into the infrared energy band, offering new approaches to harvest waste heat, to reduce the thermal emission losses, and to achieve noncontact radiative cooling of solar cells as well as of optical and electronic circuitries. Light-matter interaction enabled by nanophotonics and plasmonics underlie the performance of the third- and fourth-generation energy-conversion devices, including up- and down-conversion of photon energy, near-field radiative energy transfer, and hot electron generation and harvesting. Finally, the increased market penetration of alternative solar energy-conversion technologies amplifies the role of cost-driven and environmental considerations. This roadmap on optical energy conversion provides a snapshot of the state of the art in optical energy conversion, remaining challenges, and most promising approaches to address these challenges. Leading experts authored 19 focused short sections of the roadmap where they share their vision on a specific aspect of this burgeoning research field. The roadmap opens up with a tutorial section, which introduces major concepts and terminology. It is our hope that the roadmap

  18. Interleukin-1 beta inhibits the endogenous expression of the early gene c-fos located within the nucleus of LH-RH neurons and interferes with hypothalamic LH-RH release during proestrus in the rat.

    PubMed

    Rivest, S; Rivier, C

    1993-06-01

    The ability of central interleukin-1 beta (IL-1 beta) administration to modulate the hypothalamic LH-RH release as well as the endogenous expression of the c-fos protein located within the nucleus of LH-RH neurons was examined during the afternoon of proestrus in rats. In a first series of experiments, 50 or 100 ng IL-1 beta were infused into the lateral ventricle of the rat brain at either 08.30, 12.00, 14.30, or 17.00 h of proestrus. The animals were then perfused transcardially with a solution of 4% paraformaldehyde from 17.30 and 18.00 h. In a second series of experiments, the rats were equipped with an intracerebroventricular (i.c.v.) cannula in the lateral ventricle and a push-pull cannula into the median eminence (ME), and LH-RH secretion was measured during the afternoon of proestrus. The third experiment investigated the putative role of corticotropin-releasing factor (CRF) in modulating the inhibitory effect of IL-1 beta on LH secretion by infusing CRF antagonists before the i.c.v. administration of the cytokine to gonadectomized male and female rats. The central infusion of 50 or 100 ng IL-1 beta at 12.00 h completely blocked the spontaneous expression of c-fos protein which normally occurs in the nucleus of LH-RH neurons between 17.30 and 18.00 h on proestrus. In contrast, 50 ng IL-1 beta was less effective (P < 0.05) when administered at 08.30 h, and totally without effect when infused at 14.30 h. Infusion of 50 ng IL-1 beta also markedly suppressed the hypothalamic release of LH-RH in proestrus rats bearing a push-pull cannula into the ME, and significantly decreased plasma LH levels in both gonadectomized male and female rats. Finally, we observed that the central administration of CRF antagonists did not modify the inhibitory effects of the cytokine on the activity of the hypothalamic-pituitary-gonadal (HPG) axis. These results provide the first direct evidence that IL-1 beta is a potent inhibitor of LH-RH neuronal activity during the proestrus LH

  19. A Conversation Well Worth Remembering

    ERIC Educational Resources Information Center

    Woolven-Allen, John

    2009-01-01

    To mark the 200th anniversary of Charles Darwin's birth, a special event was held at Oxford, which included a "Conversation" between Professor Richard Dawkins and Bishop Richard Harries. Here we present a personal reminiscence of the event.

  20. Enzymes for improved biomass conversion

    DOEpatents

    Brunecky, Roman; Himmel, Michael E.

    2016-02-02

    Disclosed herein are enzymes and combinations of the enzymes useful for the hydrolysis of cellulose and the conversion of biomass. Methods of degrading cellulose and biomass using enzymes and cocktails of enzymes are also disclosed.