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Sample records for conversions locating gene

  1. 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

  2. Gene Conversion Shapes Linear Mitochondrial Genome Architecture

    PubMed Central

    Smith, David Roy; Keeling, Patrick J.

    2013-01-01

    Recently, it was shown that gene conversion between the ends of linear mitochondrial chromosomes can cause telomere expansion and the duplication of subtelomeric loci. However, it is not yet known how widespread this phenomenon is and how significantly it has impacted organelle genome architecture. Using linear mitochondrial DNAs and mitochondrial plasmids from diverse eukaryotes, we argue that telomeric recombination has played a major role in fashioning linear organelle chromosomes. We find that mitochondrial telomeres frequently expand into subtelomeric regions, resulting in gene duplications, homogenizations, and/or fragmentations. We suggest that these features are a product of subtelomeric gene conversion, provide a hypothetical model for this process, and employ genetic diversity data to support the idea that the greater the effective population size the greater the potential for gene conversion between subtelomeric loci. PMID:23572386

  3. Polarized gene conversion at the bz locus of maize.

    PubMed

    Dooner, Hugo K; He, Limei

    2014-09-23

    Nucleotide diversity is greater in maize than in most organisms studied to date, so allelic pairs in a hybrid tend to be highly polymorphic. Most recombination events between such pairs of maize polymorphic alleles are crossovers. However, intragenic recombination events not associated with flanking marker exchange, corresponding to noncrossover gene conversions, predominate between alleles derived from the same progenitor. In these dimorphic heterozygotes, the two alleles differ only at the two mutant sites between which recombination is being measured. To investigate whether gene conversion at the bz locus is polarized, two large diallel crossing matrices involving mutant sites spread across the bz gene were performed and more than 2,500 intragenic recombinants were scored. In both diallels, around 90% of recombinants could be accounted for by gene conversion. Furthermore, conversion exhibited a striking polarity, with sites located within 150 bp of the start and stop codons converting more frequently than sites located in the middle of the gene. The implications of these findings are discussed with reference to recent data from genome-wide studies in other plants.

  4. Whole-Genome Analysis of Gene Conversion Events

    NASA Astrophysics Data System (ADS)

    Hsu, Chih-Hao; Zhang, Yu; Hardison, Ross; Miller, Webb

    Gene conversion events are often overlooked in analyses of genome evolution. In a conversion event, an interval of DNA sequence (not necessarily containing a gene) overwrites a highly similar sequence. The event creates relationships among genomic intervals that can confound attempts to identify orthologs and to transfer functional annotation between genomes. Here we examine 1,112,202 paralogous pairs of human genomic intervals, and detect conversion events in about 13.5% of them. Properties of the putative gene conversions are analyzed, such as the lengths of the paralogous pairs and the spacing between their sources and targets. Our approach is illustrated using conversion events in the beta-globin gene cluster.

  5. A double-strand break can trigger immunoglobulin gene conversion

    PubMed Central

    Bastianello, Giulia; Arakawa, Hiroshi

    2017-01-01

    All three B cell-specific activities of the immunoglobulin (Ig) gene re-modeling system—gene conversion, somatic hypermutation and class switch recombination—require activation-induced deaminase (AID). AID-induced DNA lesions must be further processed and dissected into different DNA recombination pathways. In order to characterize potential intermediates for Ig gene conversion, we inserted an I-SceI recognition site into the complementarity determining region 1 (CDR1) of the Ig light chain locus of the AID knockout DT40 cell line, and conditionally expressed I-SceI endonuclease. Here, we show that a double-strand break (DSB) in CDR1 is sufficient to trigger Ig gene conversion in the absence of AID. The pattern and pseudogene usage of DSB-induced gene conversion were comparable to those of AID-induced gene conversion; surprisingly, sometimes a single DSB induced multiple gene conversion events. These constitute direct evidence that a DSB in the V region can be an intermediate for gene conversion. The fate of the DNA lesion downstream of a DSB had more flexibility than that of AID, suggesting two alternative models: (i) DSBs during the physiological gene conversion are in the minority compared to single-strand breaks (SSBs), which are frequently generated following DNA deamination, or (ii) the physiological gene conversion is mediated by a tightly regulated DSB that is locally protected from non-homologous end joining (NHEJ) or other non-homologous DNA recombination machineries. PMID:27701075

  6. 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

  7. Location, location, location. Salmonella senses ethanolamine to gauge distinct host environments and coordinate gene expression

    PubMed Central

    Anderson, Christopher J.; Kendall, Melissa M.

    2016-01-01

    Chemical and nutrient signaling mediate all cellular processes, ensuring survival in response to changing environmental conditions. Ethanolamine is a component of phosphatidylethanolamine, a major phospholipid of mammalian and bacterial cell membranes. Ethanolamine is abundant in the gastrointestinal (GI) tract from dietary sources as well as from the normal turnover of intestinal epithelial and bacterial cells in the gut. Additionally, mammalian cells maintain intracellular ethanolamine concentrations through low and high-affinity uptake systems and the internal recycling of phosphatidylethanolamine; therefore, ethanolamine is ubiquitous throughout the mammalian host. Although ethanolamine has profound signaling activity within mammalian cells by modulating inflammatory responses and intestinal physiology, ethanolamine is best appreciated as a nutrient for bacteria that supports growth. In our recent work (Anderson, et al. PLoS Pathog (2015), 11: e1005278), we demonstrated that Salmonella enterica serovar Typhimurium (Salmonella) exploits ethanolamine signaling to adapt to distinct host environments to precisely coordinate expression of genes encoding metabolism and virulence, which ultimately enhances disease progression. PMID:28357338

  8. Genomic location and characterisation of MIC genes in cattle.

    PubMed

    Birch, James; De Juan Sanjuan, Cristina; Guzman, Efrain; Ellis, Shirley A

    2008-08-01

    Major histocompatibility complex (MHC) class I chain-related (MIC) genes have been previously identified and characterised in human. They encode polymorphic class I-like molecules that are stress-inducible, and constitute one of the ligands of the activating natural killer cell receptor NKG2D. We have identified three MIC genes within the cattle genome, located close to three non-classical MHC class I genes. The genomic position relative to other genes is very similar to the arrangement reported in the pig MHC region. Analysis of MIC cDNA sequences derived from a range of cattle cell lines suggest there may be four MIC genes in total. We have investigated the presence of the genes in distinct and well-defined MHC haplotypes, and show that one gene is consistently present, while configuration of the other three genes appears variable.

  9. 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.

  10. Human blood group genes 2004: chromosomal locations and cloning strategies.

    PubMed

    Lögdberg, Lennart; Reid, Marion E; Lamont, Ryan E; Zelinski, Teresa

    2005-01-01

    Of the 29 human blood group system genes, 27 have been localized to 14 autosomes and 2 have been assigned to the X chromosome. It is remarkable that 28 of the 29 system genes have now been localized to a single cytogenetic band on a specific chromosome. In this review, we summarize the chromosomal locations and cloning strategies used for those genes encoding blood group systems. We highlight such information about the 3 most recently defined blood group systems (I, GLOB, and GIL). In addition, we provide new information about 2 older blood group systems (SC and RAPH) whose polymorphisms have been defined in cloned genes.

  11. 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

  12. Gene conversions in the growth hormone gene family of primates: stronger homogenizing effects in the Hominidae lineage.

    PubMed

    Petronella, Nicholas; Drouin, Guy

    2011-09-01

    In humans, the growth hormone/chorionic somatomammotropin gene family is composed of five highly similar genes. We characterized the gene conversions that occurred between the growth hormone genes of 11 primate species. We detected 48 conversions using GENECONV and others were only detected using phylogenetic analyses. Gene conversions were detected in all species analyzed, their average size (±standard deviation) is 197.8±230.4 nucleotides, the size of the conversions is correlated with sequence similarity and converted regions are significantly more GC-rich than non-converted regions. Gene conversions have a stronger homogenizing effect in Hominidae genes than in other primate species. They are also less frequent in conserved gene regions and towards functionally important genes. This suggests that the high degree of sequence similarity observed between the growth hormone genes of primate species is a consequence of frequent gene conversions in gene regions which are under little selective constraints.

  13. The Location of Viability Genes within a Testcross Framework.

    PubMed

    Chapco, W

    1972-02-01

    The maximum likelihood method is applied to the problem of estimating the positions and effects of viability genes. Whenever testcross linkage data indicate the presence of differential viability, it is hypothesized that there exists one viability gene between each marker. Estimation is possible only for two-point data since the number of independent expectation expressions is less than the number of parameters for three or more markers. It is pointed out that within the two-point testcross system, it is impossible to distinguish between pleiotropic effects of the marker genes and the effect of a middle viability gene, if existent. The methods outlined will be useful in their application to experiments specifically designed to locate induced viability genes.

  14. Evidence for gene conversion among immunoglobulin heavy chain variable region genes.

    PubMed

    Clarke, S H; Rudikoff, S

    1984-03-01

    We have previously reported that the VH region amino acid sequence of a phosphocholine (PC)-binding hybridoma antibody of CBA/J origin, HP101 6G6 (6G6), differs extensively from the VH regions of other PC-binding antibodies. The sequence of 6G6 VH appears to be derived from a gene homologous to the BALB/c V11 gene, a member of the PC VH (T15 VH) gene family not normally used to encode PC-binding antibodies. The 6G6 VH sequence differs from the translated sequence of V11 by six amino acids, four of which occur at the same position in other members of this gene family. This coincidence led to the proposal that the 6G6 VH gene was derived by gene conversion involving three genes of the PC VH gene family. We report here the nucleic acid sequence of the rearranged VH gene of hybridoma 6G6. This sequence supports our previous suggestion of gene conversion by confirming those differences, relative to the BALB/c V11 gene sequence, that are encoded by other members of this gene family, and extends this correlation to include three silent base pair substitutions as well. In addition, 5' noncoding region sequence and Southern blot analysis using probes derived from the coding and 5' noncoding regions confirm that the 6G6 VH gene is likely to be derived from the V11 homologue in CBA/J mice, and suggest that all three genes believed to be involved in the generation of the 6G6 VH gene are present in the CBA/J genome, a prerequisite for their involvement in gene conversion.

  15. Gene conversion between red and defective green opsin gene in blue cone monochromacy

    SciTech Connect

    Reyniers, E.; Van Thienen, M.N.; De Boulle, K.; Willems, P.J.

    1995-09-20

    Blue cone monochromacy is an X-linked condition in which the function of both the red pigment gene (RCP) and the green pigment gene (GCP) is impaired. Blue cone monochromacy can be due to a red/green gene array rearrangement existing of a single red/green hybrid gene and an inactivating C203R point mutation in both RCP and GCP. The flanking sequences of the C230R mutation in exon 4 of RCP were characteristic for GCP, indicating that this mutation was transferred from GCP into RCP by gene conversion. 23 refs., 3 figs., 1 tab.

  16. Chromosome locations of human EMX and OTX genes

    SciTech Connect

    Kastury, K.; Druck, T.; Huebner, K.

    1994-07-01

    The authors have determined the chromosomal localization of four human homeobox-containing genes, EMX1, EMX2, OTX1, and OTX2, related to Drosophila genes expressed in the developing head of the fly. Murine homologs of these genes are expressed in specific nested domains in the developing rostral brain of midgestation embryos. DNAs from a panel of 19 rodent-human hybrids, each carrying one or a few human chromosomes such that most human chromosomes regions were presented, were tested for the presence of the four gene loci by filter hybridization to radiolabeled probes. Regional chromosomal localization was determined by similarly testing DNAs from hybrid mapping panels for each of the candidate chromosomes. Finally, fluorescence in situ hybridization of cosmid clones for these loci refined the locations, two of which were in the vicinity of previously mapped orphan homeobox genes and two of which were near each other. OTX2, the earliest and most widely expressed gene, maps to chromosome region 14q21-q22; the OTX1 locus maps to 2p13; EMX2 maps to 10q26.1; and EMX1, the most narrowly and lately expressed, maps to 2p14-p13. Thus, these homeobox-containing genes involved in brain development are not linked to any of the four HOX clusters on 7p15-p14, 17q21-q22, 12q12-q13, and 2q31. However, the OTX1 and EMX1 loci may be closely linked on or near 2p13, prompting speculation that a clustered gene structure could have functional significance, as is presumably the case for the HOX clusters. 33 refs., 2 figs.

  17. 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.

  18. 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

  19. 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.

  20. The rate of meiotic gene conversion varies by sex and age

    PubMed Central

    Halldorsson, Bjarni V.; Hardarson, Marteinn T.; Kehr, Birte; Styrkarsdottir, Unnur; Gylfason, Arnaldur; Thorleifsson, Gudmar; Zink, Florian; Jonasdottir, Adalbjorg; Jonasdottir, Aslaug; Sulem, Patrick; Masson, Gisli; Thorsteinsdottir, Unnur; Helgason, Agnar; Kong, Augustine; Gudbjartsson, Daniel F.; Stefansson, Kari

    2016-01-01

    Meiotic recombination involves a combination of gene conversion and crossover events that along with mutations produce germline genetic diversity. Here, we report the discovery of 3,176 SNP and 61 indel gene conversions. Our estimate of the non-crossover (NCO) gene conversion rate (G) is 7.0 for SNPs and 5.8 for indels per Mb per generation, and the GC bias is 67.6%. For indels we demonstrate a 65.6% preference for the shorter allele. NCO gene conversions from mothers are longer than those from fathers and G is 2.17 times greater in mothers. Notably, G increases with the age of mothers, but not fathers. A disproportionate number of NCO gene conversions in older mothers occur outside double strand break (DSB) regions and in regions with relatively low GC content. This points to age-related changes in the mechanisms of meiotic gene conversions in oocytes. PMID:27643539

  1. Genomic and Population-Level Effects of Gene Conversion in Caenorhabditis Paralogs

    PubMed Central

    Katju, Vaishali; Bergthorsson, Ulfar

    2010-01-01

    Interlocus gene conversion, the nonreciprocal exchange of genetic material between genes, is facilitated by high levels of sequence identity between DNA sequences and has the dual effect of homogenizing intergenic sequences while increasing intragenic variation. Gene conversion can have important consequences for the evolution of paralogs subsequent to gene duplication, as well as result in misinterpretations regarding their evolution. We review the current state of research on gene conversion in paralogs within Caenorhabditis elegans and its congeneric species, including the relative rates of gene conversion, the range of observable conversion tracts, the genomic variables that strongly influence the frequency of gene conversion and its contribution to concerted evolution of multigene families. Additionally, we discuss recent studies that examine the phenotypic and population-genetic effects of interlocus gene conversion between the sex-determination locus fog-2 and its paralog ftr-1 in natural and experimental populations of C. elegans. In light of the limitations of gene conversion detection methods that rely solely on the statistical distribution of identical nucleotides between paralogs, we suggest that analyses of gene conversion in C. elegans take advantage of mutation accumulation experiments and sequencing projects of related Caenorhabditis species. PMID:24710096

  2. 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

  3. Unusual mutation clusters provide insight into class I gene conversion mechanisms.

    PubMed Central

    Pease, L R; Horton, R M; Pullen, J K; Yun, T J

    1993-01-01

    Genetic diversity among the K and D alleles of the mouse major histocompatibility complex is generated by gene conversion among members of the class I multigene family. The majority of known class I mutants contain clusters of nucleotide changes that can be traced to linked family members. However, the details of the gene conversion mechanism are not known. The bm3 and bm23 mutations represent exceptions to the usual pattern and provide insight into intermediates generated during the gene conversion process. Both of these variants contain clusters of five nucleotide substitutions, but they differ from the classic conversion mutants in the important respect that no donor gene for either mutation could be identified in the parental genome. Nevertheless, both mutation clusters are composed of individual mutations that do exist within the parent. Therefore, they are not random and appear to be templated. Significantly, the bm3 and bm23 mutation clusters are divided into overlapping regions that match class I genes which have functioned as donor genes in other characterized gene conversion events. The unusual structure of the mutation clusters indicates an underlying gene conversion mechanism that can generate mutation clusters as a result of the interaction of three genes in a single genetic event. The unusual mutation clusters are consistent with a hypothetical gene conversion model involving extrachromosomal intermediates. Images PMID:8321237

  4. Somatic generation of hybrid antibody H chain genes in transgenic mice via interchromosomal gene conversion

    PubMed Central

    1994-01-01

    We have constructed lines of mice with transgenes containing an antibody heavy (H) chain variable region (VHDJH) gene and various amounts of natural immunoglobulin (Ig) and plasmid flanking DNA. In these lines, recombination of the transgene and the endogenous Igh locus takes place in B cells, leading to the expression of functional H chains partially encoded by the transgenic VHDJH gene. Here, we demonstrate that the transgenic VHDJH gene, and various amounts of flanking sequence are recombined with Igh locus DNA via interchromosomal gene conversion. The structures of the resulting "hybrid" transgene-Igh H chain loci are consistent with the 3' end of the conversion occurring in regions of sequence identity, and the 5' end taking place between regions of little or no homology. This mode of antibody transgene recombination with the Igh locus is fundamentally different from the previously reported "trans H chain class switching" that results in reciprocal translocations. In contrast, this recombination resembles events previously observed in mammalian tissue culture cells between adjacent homologous chromosomal sequences, or transfected DNA and a homologous chromosomal target. Our data indicate that this recombination takes place at a low frequency, and that the frequency is influenced by both the length and extent of homology between the transgene and the Igh locus, but is not greatly affected by transgene copy number. This recombination pathway provides a novel approach for the subtle alteration of the clonal composition of the mouse B cell compartment in vivo using VH genes with defined structures and functions. PMID:8270869

  5. 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.

  6. Duplication of chicken defensin7 gene generated by gene conversion and homologous recombination

    PubMed Central

    Lee, Mi Ok; Bornelöv, Susanne; Andersson, Leif; Lamont, Susan J.; Chen, Junfeng; Womack, James E.

    2016-01-01

    Defensins constitute an evolutionary conserved family of cationic antimicrobial peptides that play a key role in host innate immune responses to infection. Defensin genes generally reside in complex genomic regions that are prone to structural variation, and defensin genes exhibit extensive copy number variation in humans and in other species. Copy number variation of defensin genes was examined in inbred lines of Leghorn and Fayoumi chickens, and a duplication of defensin7 was discovered in the Fayoumi breed. Analysis of junction sequences confirmed the occurrence of a simple tandem duplication of defensin7 with sequence identity at the junction, suggesting nonallelic homologous recombination between defensin7 and defensin6. The duplication event generated two chimeric promoters that are best explained by gene conversion followed by homologous recombination. Expression of defensin7 was not elevated in animals with two genes despite both genes being transcribed in the tissues examined. Computational prediction of promoter regions revealed the presence of several putative transcription factor binding sites generated by the duplication event. These data provide insight into the evolution and possible function of large gene families and specifically, the defensins. PMID:27849592

  7. Duplication of chicken defensin7 gene generated by gene conversion and homologous recombination.

    PubMed

    Lee, Mi Ok; Bornelöv, Susanne; Andersson, Leif; Lamont, Susan J; Chen, Junfeng; Womack, James E

    2016-11-29

    Defensins constitute an evolutionary conserved family of cationic antimicrobial peptides that play a key role in host innate immune responses to infection. Defensin genes generally reside in complex genomic regions that are prone to structural variation, and defensin genes exhibit extensive copy number variation in humans and in other species. Copy number variation of defensin genes was examined in inbred lines of Leghorn and Fayoumi chickens, and a duplication of defensin7 was discovered in the Fayoumi breed. Analysis of junction sequences confirmed the occurrence of a simple tandem duplication of defensin7 with sequence identity at the junction, suggesting nonallelic homologous recombination between defensin7 and defensin6 The duplication event generated two chimeric promoters that are best explained by gene conversion followed by homologous recombination. Expression of defensin7 was not elevated in animals with two genes despite both genes being transcribed in the tissues examined. Computational prediction of promoter regions revealed the presence of several putative transcription factor binding sites generated by the duplication event. These data provide insight into the evolution and possible function of large gene families and specifically, the defensins.

  8. Deregulated HOX genes in ameloblastomas are located in physical contiguity to keratin genes.

    PubMed

    Schiavo, Giulia; D'Antò, Vincenzo; Cantile, Monica; Procino, Alfredo; Di Giovanni, Stefano; Valletta, Rossella; Terracciano, Luigi; Baumhoer, Daniel; Jundt, Gernot; Cillo, Clemente

    2011-11-01

    The expression of the HOX gene network in mid-stage human tooth development mostly concerns the epithelial tooth germ compartment and involves the C and D HOX loci. To further dissect the HOX gene implication with tooth epithelium differentiation we compared the expression of the whole HOX network in human ameloblastomas, as paradigm of epithelial odontogenic tumors, with tooth germs. We identified two ameloblastoma molecular types with respectively low and high number of active HOX C genes. The highly expressing HOX C gene ameloblastomas were characterized by a strong keratinized phenotype. Locus C HOX genes are located on chromosome 12q13-15 in physical contiguity with one of the two keratin gene clusters included in the human genome. The most posterior HOX C gene, HOX C13, is capable to interact with hair keratin genes located on the other keratin gene cluster in physical contiguity with the HOX B locus on chromosome 17q21-22. Inside the HOX C locus, a 2.2 kb ncRNA (HOTAIR) able to repress transcription, in cis, along the entire HOX C locus and, in trans, at the posterior region of the HOX D locus has recently been identified. Interestingly both loci are deregulated in ameloblastomas. Our finding support an important role of the HOX network in characterizing the epithelial tooth compartment. Furthermore, the physical contiguity between locus C HOX and keratin genes in normal tooth epithelium and their deregulation in the neoplastic counterparts suggest they may act on the same mechanism potentially involved with epithelial tumorigenesis.

  9. Gene conversion variations generate structurally distinct pilin polypeptides in Neisseria gonorrhoeae.

    PubMed

    Swanson, J; Robbins, K; Barrera, O; Koomey, J M

    1987-04-01

    Pilus+ to pilus- phenotype change occurs in Neisseria gonorrhoeae through gene conversion of the gonococcus' complete, expressed pilin gene by nucleotides homologous to the pilS1 copy 5 partial pilin gene; assembly missense pilin is synthesized but pili are not. Reversion to pilus+ occurs by a subsequent recombinational event that replaces the complete pilin gene's pilS1 copy 5-like sequence with nucleotides from a different partial gene to effect expression of an orthodox (i.e., pilus producing) pilin. Sibling pilus+ revertants of common parentage can carry different sequences in their expressed pilin genes because they have undergone nonidentical gene conversion events such as recombinations with sequences from different partial genes, or recombinations with different length nucleotide stretches of the same partial gene; either can yield structurally and antigenically variant pilin polypeptides.

  10. Hard Selective Sweep and Ectopic Gene Conversion in a Gene Cluster Affording Environmental Adaptation

    PubMed Central

    Trampczynska, Aleksandra; Bernal, María; Motte, Patrick; Clemens, Stephan; Krämer, Ute

    2013-01-01

    Among the rare colonizers of heavy-metal rich toxic soils, Arabidopsis halleri is a compelling model extremophile, physiologically distinct from its sister species A. lyrata, and A. thaliana. Naturally selected metal hypertolerance and extraordinarily high leaf metal accumulation in A. halleri both require Heavy Metal ATPase4 (HMA4) encoding a PIB-type ATPase that pumps Zn2+ and Cd2+ out of specific cell types. Strongly enhanced HMA4 expression results from a combination of gene copy number expansion and cis-regulatory modifications, when compared to A. thaliana. These findings were based on a single accession of A. halleri. Few studies have addressed nucleotide sequence polymorphism at loci known to govern adaptations. We thus sequenced 13 DNA segments across the HMA4 genomic region of multiple A. halleri individuals from diverse habitats. Compared to control loci flanking the three tandem HMA4 gene copies, a gradual depletion of nucleotide sequence diversity and an excess of low-frequency polymorphisms are hallmarks of positive selection in HMA4 promoter regions, culminating at HMA4-3. The accompanying hard selective sweep is segmentally eclipsed as a consequence of recurrent ectopic gene conversion among HMA4 protein-coding sequences, resulting in their concerted evolution. Thus, HMA4 coding sequences exhibit a network-like genealogy and locally enhanced nucleotide sequence diversity within each copy, accompanied by lowered sequence divergence between paralogs in any given individual. Quantitative PCR corroborated that, across A. halleri, three genomic HMA4 copies generate overall 20- to 130-fold higher transcript levels than in A. thaliana. Together, our observations constitute an unexpectedly complex profile of polymorphism resulting from natural selection for increased gene product dosage. We propose that these findings are paradigmatic of a category of multi-copy genes from a broad range of organisms. Our results emphasize that enhanced gene product dosage

  11. Targeted heritable mutation and gene conversion by Cas9-CRISPR in Caenorhabditis elegans.

    PubMed

    Katic, Iskra; Großhans, Helge

    2013-11-01

    We have achieved targeted heritable genome modification in Caenorhabditis elegans by injecting mRNA of the nuclease Cas9 and Cas9 guide RNAs. This system rapidly creates precise genomic changes, including knockouts and transgene-instructed gene conversion.

  12. Differential replication dynamics for large and small Vibrio chromosomes affect gene dosage, expression and location

    PubMed Central

    Dryselius, Rikard; Izutsu, Kaori; Honda, Takeshi; Iida, Tetsuya

    2008-01-01

    Background Replication of bacterial chromosomes increases copy numbers of genes located near origins of replication relative to genes located near termini. Such differential gene dosage depends on replication rate, doubling time and chromosome size. Although little explored, differential gene dosage may influence both gene expression and location. For vibrios, a diverse family of fast growing gammaproteobacteria, gene dosage may be particularly important as they harbor two chromosomes of different size. Results Here we examined replication dynamics and gene dosage effects for the separate chromosomes of three Vibrio species. We also investigated locations for specific gene types within the genome. The results showed consistently larger gene dosage differences for the large chromosome which also initiated replication long before the small. Accordingly, large chromosome gene expression levels were generally higher and showed an influence from gene dosage. This was reflected by a higher abundance of growth essential and growth contributing genes of which many locate near the origin of replication. In contrast, small chromosome gene expression levels were low and appeared independent of gene dosage. Also, species specific genes are highly abundant and an over-representation of genes involved in transcription could explain its gene dosage independent expression. Conclusion Here we establish a link between replication dynamics and differential gene dosage on one hand and gene expression levels and the location of specific gene types on the other. For vibrios, this relationship appears connected to a polarisation of genetic content between its chromosomes, which may both contribute to and be enhanced by an improved adaptive capacity. PMID:19032792

  13. Role of Biased Gene Conversion in One-Locus Neutral Theory and Genome Evolution

    PubMed Central

    Walsh, James Bruce

    1983-01-01

    The implications of biased gene conversion acting on selectively neutral alleles are investigated for a single diallelic locus in a finite population. Even a very slight conversion bias can significantly alter fixation probabilities. We argue that most newly arising mutants will be at a conversion disadvantage, resulting in a potentially greatly decreased substitution rate of new alleles compared with predictions from strict neutral theory. Thus, conversion bias potential allows for conservation of particular alleles without having to invoke selection. Conversely, we also show that bias can be important in the maintenance of repeated gene families without altering the substitution rate at other loci that experience the same amount of conversion bias, provided that the number of genes in the family is sufficiently large. Bias can, therefore, be important at the genomic level and yet be unimportant at the populational level. Finally, we discuss the role of biased gene conversion in speciation events, concluding that this type of molecular turnover acting independently at many individual loci is very unlikely to decrease the time required for two allopatric populations to speciate. PMID:17246166

  14. Inhibition of retinoic acid-induced activation of 3' human HOXB genes by antisense oligonucleotides affects sequential activation of genes located upstream in the four HOX clusters.

    PubMed Central

    Faiella, A; Zappavigna, V; Mavilio, F; Boncinelli, E

    1994-01-01

    Most homeobox genes belonging to the Hox family are sequentially activated in embryonal carcinoma cells upon treatment with retinoic acid. Genes located at the 3' end of each one of the four Hox clusters are activated first, whereas upstream Hox genes are activated progressively later. This activation has been extensively studied for human HOX genes in the NT2/D1 cell line and shown to take place at the transcriptional level. To understand the molecular mechanisms of sequential HOX gene activation in these cells, we tried to modulate the expression of 3' HOX genes through the use of antisense oligonucleotides added to the culture medium. We chose the HOXB locus. A 5- to 15-fold reduction of the expression of HOXB1 and HOXB3 was sufficient to produce a significant inhibition of the activation of the upstream HOXB genes, as well as of their paralogs in the HOXA, HOXC, and HOXD clusters. Conversely, no effect was detectable on downstream HOX genes. The extent of this inhibition increased for progressively more-5' genes. The stability of the corresponding mRNAs appeared to be unaffected, supporting the idea that the observed effect might be mediated at the transcriptional level. These data suggest a cascade model of progressive activation of Hox genes, with a 3'-to-5' polarity. Images PMID:7911240

  15. TK{sup {minus}} mutants attributable to localized gene conversion in a human cell line

    SciTech Connect

    Giver, C.R.; Grosovsky, A.J.

    1995-11-01

    The human lymphoblastoid cell line TK6 is heterozygous at the tk gene, carrying an inactivating frameshift near the end of the coding sequence, within exon 7 of the functional allele. Here, we describe our use of sequence analyses at these polymorphic sites to identify 8 x-ray induced mutations, out of 184 examined, which exhibit partial conversion of the tk functional allele to the non-functional sequence. These mutants are characterized by loss of heterozygosity at the exon 4 frameshift polymorphism, and remain heterozgousity at exon 7. No restriction fragment length alterations were observed by Southern blotting, and sequencing of the tk cDNA in these mutants revealed the presence of two full length tk transcripts, both having the sequence of the non-functional allele in exon 4, but representing the two different sequences in exon 7. Therefore, the results cannot be explained by a partial deletion of the functional tk allele. Polymorphic microsatellite markers located both proximally and distally to tk on the q arm of chromosome 17 were found to remain heterozygous, ruling out the possibility of a single homologous exchange event. These mutants may be explained by single strand invasion coupled with mismatch repair of the resultant heteroduplex, or by recombinationally mediated repair of a double strand break or gap. We also present microsatellite mapping data which localizes the human tk gene to a 1cM region between markers D17S802 and D17S937.

  16. Chromosomal locations of three Bacillus subtilis din genes

    SciTech Connect

    Gillespie, K.; Yasbin, R.E.

    1987-07-01

    Previously isolated DNA damage-inducible (din) genes of Bacillus subtilis have been mapped on the bacterial chromosome by bacteriophage PBS1-mediated transduction. The din genes have been localized to three positions on the B. subtilis map. dinA cotransduction with the hisA locus was 80%, while dinC cotransduction with this marker was about 56%. dinB is unlinked to hisA, but its cotransduction with the dal-1 and purB loci was 84 and 22%, respectively.

  17. Enhancer Complexes Located Downstream of Both Human Immunoglobulin Cα Genes

    PubMed Central

    Mills, Frederick C.; Harindranath, Nagaradona; Mitchell, Mary; Max, Edward E.

    1997-01-01

    To investigate regulation of human immunoglobulin heavy chain expression, we have cloned DNA downstream from the two human Cα genes, corresponding to the position in the mouse IgH cluster of a locus control region (LCR) that includes an enhancer which regulates isotype switching. Within 25 kb downstream of both the human immunoglobulin Cα1 and Cα2 genes we identified several segments of DNA which display B lymphoid–specific DNase I hypersensitivity as well as enhancer activity in transient transfections. The corresponding sequences downstream from each of the two human Cα genes are nearly identical to each other. These enhancers are also homologous to three regions which lie in similar positions downstream from the murine Cα gene and form the murine LCR. The strongest enhancers in both mouse and human have been designated HS12. Within a 135-bp core homology region, the human HS12 enhancers are ∼90% identical to the murine homolog and include several motifs previously demonstrated to be important for function of the murine enhancer; additional segments of high sequence conservation suggest the possibility of previously unrecognized functional motifs. On the other hand, certain functional elements in the murine enhancer, including a B cell–specific activator protein site, do not appear to be conserved in human HS12. The human homologs of the murine enhancers designated HS3 and HS4 show lower overall sequence conservation, but for at least two of the functional motifs in the murine HS4 (a κB site and an octamer motif  ) the human HS4 homologs are exactly conserved. An additional hypersensitivity site between human HS3 and HS12 in each human locus displays no enhancer activity on its own, but includes a region of high sequence conservation with mouse, suggesting the possibility of another novel functional element. PMID:9294139

  18. Gene conversion accounts for pilin structural changes and for reversible piliation "phase" changes in gonococci.

    PubMed

    Swanson, J; Bergstrom, S; Boslego, J; Koomey, M

    1987-01-01

    Pilus+ "wild-type" gonococci (Gc) frequently display gene conversion of their expressed complete pilin gene (CPG); a copy of DNA derived from one of the Gc genome's multiple silent partial pilin genes (PPG) is recombinationally-inserted into the CPG's central and 3' portions with formation of a new, chimeric CPG. Expression of that new CPG leads to either 1) retention of pilus+ phenotype but change in pilin primary structure/antigenicity, or 2) phase change to pilus- phenotype capable of reverting. This study utilizes pilus revertants of P-rp +/- Gc and P+ colony morphotype variants spawned by P++ Gc to examine pilin gene conversion in strain MS11mk Gc in greater detail. Each revertant's and variant's expressed pilin gene's sequence (as pilin mRNA) was defined to learn whether their differences are due to gene conversion by different PPGs, or by varying stretches from the same PPG, or both. Gene conversion by PPG pilS1 copy 2 has been documented in Gc recovered from a human volunteer's urethra previously inoculated with pilus Gc (strain MS11). The pilus+ Gc isolated expressed structurally/antigenically distinct pilins.

  19. Engineering the Caenorhabditis elegans genome by Mos1-induced transgene-instructed gene conversion.

    PubMed

    Robert, Valérie J P

    2012-01-01

    Mos1-induced transgene-instructed gene conversion (MosTIC) is a technique of choice to engineer the genome of the nematode Caenorhabditis elegans. MosTIC is initiated by the excision of Mos1, a DNA transposon of the Tc1/Mariner super family that can be mobilized in the germ line of C. elegans. Mos1 excision creates a DNA double-strand break that is repaired by several cellular mechanisms, including transgene-instructed gene conversion. For MosTIC, the transgenic repair template used by the gene conversion machinery is made of sequences that share DNA homologies with the genomic region to engineer and carries the modifications to be introduced in the genome. In this chapter, we present two MosTIC protocols routinely used.

  20. Structure, chromosome location, and expression of the human. gamma. -actin gene: Differential evolution, location, and expression of the cytoskeletal BETA- and. gamma. -actin genes

    SciTech Connect

    Erba, H.P.; Eddy, R.; Shows, T.; Kedes, L.; Gunning, P.

    1988-04-01

    The accumulation of the cytoskeletal ..beta..-and ..gamma..-actin mRNAs was determined in a variety of mouse tissues and organs. The ..beta..-iosform is always expressed in excess of the ..gamma..-isoform. However, the molar ratio of ..beta..- to ..gamma..-actin mRNA varies from 1.7 in kidney and testis to 12 in sarcomeric muscle to 114 in liver. The authors conclude that, whereas the cytoskeletal ..beta..- and ..gamma..-actins are truly coexpressed, their mRNA levels are subject to differential regulation between different cell types. The human ..gamma..-actin gene has been cloned and sequenced, and its chromosome location has been determined. The gene is located on human chromosome 17, unlike ..beta..-actin which is on chromosome 7. Thus, if these genes are also unlinked in the mouse, the coexpression of the ..beta..- and ..gamma..-actin genes in rodent tissues cannot be determined by gene linkage. Comparison of the human ..beta..- and ..gamma..-actin genes reveals that noncoding sequences in the 5'-flanking region and in intron III have been conserved since the duplication that gave rise to these two genes. In contrast, there are sequences in intron III and the 3'-untranslated region which are not present in the ..beta..-actin gene but are conserved between the human ..gamma..-actin and the Xenopus borealis type 1 actin genes. Such conserved noncoding sequences may contribute to the coexpression of ..beta..- and ..gamma..-actin or to the unique regulation and function of the ..gamma..-actin gene. Finally, the authors demonstrate that the human ..gamma..-actin gene is expressed after introduction into mouse L cells and C2 myoblasts and that, upon fusion of C2 cells to form myotubes, the human ..gamma..-actin gene is appropriately regulated.

  1. 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

  2. Chromosomal double-strand breaks induce gene conversion at high frequency in mammalian cells.

    PubMed Central

    Taghian, D G; Nickoloff, J A

    1997-01-01

    Double-strand breaks (DSBs) stimulate chromosomal and extrachromosomal recombination and gene targeting. Transcription also stimulates spontaneous recombination by an unknown mechanism. We used Saccharomyces cerevisiae I-SceI to stimulate recombination between neo direct repeats in Chinese hamster ovary (CHO) cell chromosomal DNA. One neo allele was controlled by the dexamethasone-inducible mouse mammary tumor virus promoter and inactivated by an insertion containing an I-SceI site at which DSBs were introduced in vivo. The other neo allele lacked a promoter but carried 12 phenotypically silent single-base mutations that create restriction sites (restriction fragment length polymorphisms). This system allowed us to generate detailed conversion tract spectra for recipient alleles transcribed at high or low levels. Transient in vivo expression of I-SceI increased homologous recombination 2,000- to 10,000-fold, yielding recombinants at frequencies as high as 1%. Strikingly, 97% of these products arose by gene conversion. Most products had short, bidirectional conversion tracts, and in all cases, donor neo alleles (i.e., those not suffering a DSB) remained unchanged, indicating that conversion was fully nonreciprocal. DSBs in exogenous DNA are usually repaired by end joining requiring little or no homology or by nonconservative homologous recombination (single-strand annealing). In contrast, we show that chromosomal DSBs are efficiently repaired via conservative homologous recombination, principally gene conversion without associated crossing over. For DSB-induced events, similar recombination frequencies and conversion tract spectra were found under conditions of low and high transcription. Thus, transcription does not further stimulate DSB-induced recombination, nor does it appear to affect the mechanism(s) by which DSBs induce gene conversion. PMID:9343400

  3. 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.

  4. Mosaic gene conversion after a tandem duplication of mtDNA sequence in Diomedeidae (albatrosses).

    PubMed

    Eda, Masaki; Kuro-o, Masaki; Higuchi, Hiroyoshi; Hasegawa, Hiroshi; Koike, Hiroko

    2010-04-01

    Although the tandem duplication of mitochondrial (mt) sequences, especially those of the control region (CR), has been detected in metazoan species, few studies have focused on the features of the duplicated sequence itself, such as the gene conversion rate, distribution patterns of the variation, and relative rates of evolution between the copies. To investigate the features of duplicated mt sequences, we partially sequenced the mt genome of 16 Phoebastria albatrosses belonging to three species (P. albatrus, P. nigripes, and P. immutabilis). More than 2,300 base pairs of tandemly-duplicated sequence were shared by all three species. The observed gene arrangement was shared in the three Phoebastria albatrosses and suggests that the duplication event occurred in the common ancestor of the three species. Most of the copies in each individual were identical or nearly identical, and were maintained through frequent gene conversions. By contrast, portions of CR domains I and III had different phylogenetic signals, suggesting that gene conversion had not occurred in those sections after the speciation of the three species. Several lines of data, including the heterogeneity of the rate of molecular evolution, nucleotide differences, and putative secondary structures, suggests that the two sequences in CR domain I are maintained through selection; however, additional studies into the mechanisms of gene conversion and mtDNA synthesis are required to confirm this hypothesis.

  5. Human urokinase gene is located on the long arm of chromosome 10.

    PubMed Central

    Tripputi, P; Blasi, F; Verde, P; Cannizzaro, L A; Emanuel, B S; Croce, C M

    1985-01-01

    Urokinase is one of the two plasminogen activators that catalyze the conversion of inactive plasminogen to plasmin. By combining somatic cell genetics, in situ hybridization, and Southern hybridization, we localized the human urokinase gene on the distal third of the long arm (q24-qter) of chromosome 10. Images PMID:2989821

  6. Harnessing gene conversion in chicken B cells to create a human antibody sequence repertoire.

    PubMed

    Schusser, Benjamin; Yi, Henry; Collarini, Ellen J; Izquierdo, Shelley Mettler; Harriman, William D; Etches, Robert J; Leighton, Philip A

    2013-01-01

    Transgenic chickens expressing human sequence antibodies would be a powerful tool to access human targets and epitopes that have been intractable in mammalian hosts because of tolerance to conserved proteins. To foster the development of the chicken platform, it is beneficial to validate transgene constructs using a rapid, cell culture-based method prior to generating fully transgenic birds. We describe a method for the expression of human immunoglobulin variable regions in the chicken DT40 B cell line and the further diversification of these genes by gene conversion. Chicken VL and VH loci were knocked out in DT40 cells and replaced with human VK and VH genes. To achieve gene conversion of human genes in chicken B cells, synthetic human pseudogene arrays were inserted upstream of the functional human VK and VH regions. Proper expression of chimeric IgM comprised of human variable regions and chicken constant regions is shown. Most importantly, sequencing of DT40 genetic variants confirmed that the human pseudogene arrays contributed to the generation of diversity through gene conversion at both the Igl and Igh loci. These data show that engineered pseudogene arrays produce a diverse pool of human antibody sequences in chicken B cells, and suggest that these constructs will express a functional repertoire of chimeric antibodies in transgenic chickens.

  7. Gene conversion and crossing over along the 405-kb left arm of Saccharomyces cerevisiae chromosome VII.

    PubMed

    Malkova, Anna; Swanson, Johanna; German, Miriam; McCusker, John H; Housworth, Elizabeth A; Stahl, Franklin W; Haber, James E

    2004-09-01

    Gene conversions and crossing over were analyzed along 10 intervals in a 405-kb region comprising nearly all of the left arm of chromosome VII in Saccharomyces cerevisiae. Crossover interference was detected in all intervals as measured by a reduced number of nonparental ditypes. We have evaluated interference between crossovers in adjacent intervals by methods that retain the information contained in tetrads as opposed to single segregants. Interference was seen between intervals when the distance in the region adjacent to a crossover was < approximately 35 cM (90 kb). At the met13 locus, which exhibits approximately 9% gene conversions, those gene conversions accompanied by crossing over exerted interference in exchanges in an adjacent interval, whereas met13 gene conversions without an accompanying exchange did not show interference. The pattern of exchanges along this chromosome arm can be represented by a counting model in which there are three nonexchange events between adjacent exchanges; however, maximum-likelihood analysis suggests that approximately 8-12% of the crossovers on chromosome VII arise by a separate, noninterfering mechanism.

  8. 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.

  9. 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

  10. 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.

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

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2014-10-02

    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.

  12. 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.

  13. Conservative inheritance of newly synthesized DNA in double-strand break-induced gene conversion.

    PubMed

    Ira, Grzegorz; Satory, Dominik; Haber, James E

    2006-12-01

    To distinguish among possible mechanisms of repair of a double-strand break (DSB) by gene conversion in budding yeast, Saccharomyces cerevisiae, we employed isotope density transfer to analyze budding yeast mating type (MAT) gene switching in G2/M-arrested cells. Both of the newly synthesized DNA strands created during gene conversion are found at the repaired locus, leaving the donor unchanged. These results support suggestions that mitotic DSBs are primarily repaired by a synthesis-dependent strand-annealing mechanism. We also show that the proportion of crossing-over associated with DSB-induced ectopic recombination is not affected by the presence of nonhomologous sequences at one or both ends of the DSB or the presence of additional sequences that must be copied from the donor.

  14. The Superantigen Gene ypm Is Located in an Unstable Chromosomal Locus of Yersinia pseudotuberculosis

    PubMed Central

    Carnoy, Christophe; Floquet, Stephanie; Marceau, Michael; Sebbane, Florent; Haentjens-Herwegh, Stephanie; Devalckenaere, Annie; Simonet, Michel

    2002-01-01

    Yersinia pseudotuberculosis produces YPM (Y. pseudotuberculosis-derived mitogen), a superantigenic toxin that exacerbates the virulence of the bacterium in vivo. To date, three alleles of the superantigen gene (ypmA, ypmB, and ypmC) have been described. These genes are not found in all Y. pseudotuberculosis strains and have a low GC content, suggesting their location on mobile genetic elements. To elucidate this question, the genetic environment of the superantigen-encoding genes was characterized and 11 open reading frames (ORFs) were defined. Sequence analysis revealed that the ypm genes were not associated with plasmids, phages, transposons, or pathogenicity islands and that the superantigen genes were always located in the chromosome between ORF3 and ORF4. Nonsuperantigenic strains exhibited the same genetic organization of the locus but lacked the ypm gene between ORF3 and ORF4. A new insertion sequence, designated IS1398, which displays features of the Tn3 family, was characterized downstream of the ypmA and ypmC genes. A 13.3-kb region containing the ypm genes was not found in the genome of Y. pestis (CO92 and KIM 5 strains). We experimentally induced deletion of the ypm gene from a superantigen-expressing Y. pseudotuberculosis: using the association of aph(3′)-IIIa and sacB genes, we demonstrated that when these reporter genes were present in the ypm locus, deletion of these genes was about 250 times more frequent than when they were located in another region of the Y. pseudotuberculosis chromosome. These results indicate that unlike other superantigenic toxin genes, the Yersinia ypm genes are not associated with mobile genetic elements but are inserted in an unstable locus of the genome. PMID:12142419

  15. Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease.

    PubMed

    Casola, Claudio; Zekonyte, Ugne; Phillips, Andrew D; Cooper, David N; Hahn, Matthew W

    2012-03-01

    Establishing the molecular basis of DNA mutations that cause inherited disease is of fundamental importance to understanding the origin, nature, and clinical sequelae of genetic disorders in humans. The majority of disease-associated mutations constitute single-base substitutions and short deletions and/or insertions resulting from DNA replication errors and the repair of damaged bases. However, pathological mutations can also be introduced by nonreciprocal recombination events between paralogous sequences, a phenomenon known as interlocus gene conversion (IGC). IGC events have thus far been linked to pathology in more than 20 human genes. However, the large number of duplicated gene sequences in the human genome implies that many more disease-associated mutations could originate via IGC. Here, we have used a genome-wide computational approach to identify disease-associated mutations derived from IGC events. Our approach revealed hundreds of known pathological mutations that could have been caused by IGC. Further, we identified several dozen high-confidence cases of inherited disease mutations resulting from IGC in ∼1% of all genes analyzed. About half of the donor sequences associated with such mutations are functional paralogous genes, suggesting that epistatic interactions or differential expression patterns will determine the impact upon fitness of specific substitutions between duplicated genes. In addition, we identified thousands of hitherto undescribed and potentially deleterious mutations that could arise via IGC. Our findings reveal the extent of the impact of interlocus gene conversion upon the spectrum of human inherited disease.

  16. On the origins of tandemly repeated genes: does histone gene copy number in Drosophila reflect chromosomal location?

    PubMed

    Fitch, D H; Strausbaugh, L D; Barrett, V

    1990-04-01

    Widely regarded beliefs about Drosophila histone gene copy numbers and developmental requirements have been generalized from fairly limited data since studies on histone gene arrangements and copy numbers have been largely confined to a single species, D. melanogaster. Histone gene copy numbers and chromosomal locations were examined in three species: D. melangaster, D. hydei and D. hawaiiensis. Quantitative whole genome blot analysis of DNA from diploid tissues revealed a tenfold variability in histone gene copy numbers for these three species. In situ hybridization to polytene chromosomes showed that the histone DNA (hDNA) chromosomal location is different in all three species. These observations lead us to propose a relationship between histone gene reiteration and chromosomal position.

  17. 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.

  18. Location and characterization of two widely separated glucocorticoid response elements in the phosphoenolpyruvate carboxykinase gene

    SciTech Connect

    Petersen, D.D.; Magnuson, M.A.; Granner, D.K.

    1988-01-01

    Chimeric genes were constructed by fusion of various regions of the 5'-flanking sequence from the phosphoenolpyruvate carboxykinase (GTP) (PEPCK) gene to the chloramphenicol acetyltransferase-coding sequence and to simian virus 40 splice and polyadenylation sequences. These were used to demonstrate that two glucocorticoid regulatory elements (GREs) combine to confer glucocorticoid responsiveness upon the PEPCK gene in H4IIE hepatoma cells. Both elements, distal one whose 5' boundary is located between -1264 and -1111 base pairs and a proximal one located between -468 and -420 base pairs relative to the transcription initiation site, act independently, in various positions and orientations, and upon the heterologous thymidine kinase promoter. Each element accounts for half of the maximal response of the chimeric genes. Therefore, two widely separated enhancerlike elements contribute equally to the response of the PEPCK gene to glucocorticoid hormones. Neither of the PEPCK GREs contains the TGTTCT consensus sequence associated with most other GREs.

  19. Location and characterization of two widely separated glucocorticoid response elements in the phosphoenolpyruvate carboxykinase gene.

    PubMed Central

    Petersen, D D; Magnuson, M A; Granner, D K

    1988-01-01

    Chimeric genes were constructed by fusion of various regions of the 5'-flanking sequence from the phosphoenolpyruvate carboxykinase (GTP) (PEPCK) gene to the chloramphenicol acetyltransferase-coding sequence and to simian virus 40 splice and polyadenylation sequences. These were used to demonstrate that two glucocorticoid regulatory elements (GREs) combine to confer glucocorticoid responsiveness upon the PEPCK gene in H4IIE hepatoma cells. Both elements, a distal one whose 5' boundary is located between -1264 and -1111 base pairs and a proximal one located between -468 and -420 base pairs relative to the transcription initiation site, act independently, in various positions and orientations, and upon the heterologous thymidine kinase promoter. Each element accounts for half of the maximal response of the chimeric genes. Therefore, two widely separated enhancerlike elements contribute equally to the response of the PEPCK gene to glucocorticoid hormones. Neither of the PEPCK GREs contains the TGTTCT consensus sequence associated with most other GREs. Images PMID:3422101

  20. Transcriptional effects on double-strand break-induced gene conversion tracts.

    PubMed

    Weng, Y S; Xing, D; Clikeman, J A; Nickoloff, J A

    2000-10-16

    Transcription stimulates spontaneous homologous recombination, but prior studies have not investigated the effects of transcription on double-strand break (DSB)-induced recombination in yeast. We examined products of five ura3 direct repeat substrates in yeast using alleles that were transcribed at low or high levels. In each strain, recombination was stimulated by DSBs created in vivo at an HO site in one copy of ura3. Increasing transcription levels in donor or recipient alleles did not further stimulate DSB-induced recombination, nor did it alter the relative frequencies of conversion and deletion (pop-out) events. This result is consistent with the idea that transcription enhances spontaneous recombination by increasing initiation. Gene conversion tracts were measured using silent restriction fragment length polymorphisms (RFLPs) at approximately 100bp intervals. Transcription did not alter average tract lengths, but increased transcription in donor alleles increased both the frequency of promoter-proximal (5') unidirectional tracts and conversion of 5' markers. Increased transcription in recipient alleles increased the frequency of bidirectional tracts. We demonstrate that these effects are due to transcription per se, and not just transcription factor binding. These results suggest that transcription influences aspects of gene conversion after initiation, such as strand invasion and/or mismatch repair (MMR).

  1. Improved detection of differentially expressed genes through incorporation of gene locations.

    PubMed

    Xiao, Guanghua; Reilly, Cavan; Khodursky, Arkady B

    2009-09-01

    In determining differential expression in cDNA microarray experiments, the expression level of an individual gene is usually assumed to be independent of the expression levels of other genes, but many recent studies have shown that a gene's expression level tends to be similar to that of its neighbors on a chromosome, and differentially expressed (DE) genes are likely to form clusters of similar transcriptional activity along the chromosome. When modeled as a one-dimensional spatial series, the expression level of genes on the same chromosome frequently exhibit significant spatial correlation, reflecting spatial patterns in transcription. By modeling these spatial correlations, we can obtain improved estimates of transcript levels. Here, we demonstrate the existence of spatial correlations in transcriptional activity in the Escherichia coli (E. coli) chromosome across more than 50 experimental conditions. Based on this finding, we propose a hierarchical Bayesian model that borrows information from neighboring genes to improve the estimation of the expression level of a given gene and hence the detection of DE genes. Furthermore, we extend the model to account for the circular structure of E. coli chromosome and the intergenetic distance between gene neighbors. The simulation studies and analysis of real data examples in E. coli and yeast Saccharomyces cerevisiae show that the proposed method outperforms the commonly used significant analysis of microarray (SAM) t-statistic in detecting DE genes.

  2. 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

  3. Gene conversion involving the pilin structural gene correlates with pilus+ in equilibrium with pilus- changes in Neisseria gonorrhoeae.

    PubMed

    Swanson, J; Bergström, S; Robbins, K; Barrera, O; Corwin, D; Koomey, J M

    1986-10-24

    Gonococci (Gc) exhibit pilus+----pilus- "phase transitions" at high frequency, but only some of the pilus- Gc can revert to pilus+ phenotype. We examined reversible phase transitions between pilus+ Gc and a particular pilus- variant (P-rp+ phenotype) whose pilin mRNA carries a unique block of nucleotides encoding an "assembly missense" pilin polypeptide. The results show that Gc pilus+ in equilibrium with P-rp+ transitions can result from intragenic recombination in which there is nonreciprocal exchange of partially homologous DNA sequences from a partial pilin gene (in silent, storage form) into the expression locus' complete pilin gene. Hence Gc pilus phase variation, like pilus antigenic variation, can occur by gene conversion of the pilin structural gene expression locus.

  4. Molecular Evolution of the Small Subunit of Ribulose Bisphosphate Carboxylase: Nucleotide Substitution and Gene Conversion

    PubMed Central

    Meagher, R. B.; Berry-Lowe, S.; Rice, K.

    1989-01-01

    The nucleotide sequences encoding the mature portion of 31 ribulose 1,5-bisphosphate carboxylase small subunit (SSU) genes from 17 genera of plants, green algae and cyanobacteria were examined. Among the 465 pairwise sequence comparisons, SSU multigene family members within the same species were more similar to each other in nonsynonymous or replacement nucleotide substitutions (RNS) than they were to SSU sequences in any other organism. The concerted evolution of independent SSU gene lineages within closely related plant species suggests that homogenization of RNS positions has occurred at least once in the life of each genus. The rate of expected RNS among mature SSU sequences was calculated to be 1.25 X 10(-9)/site/yr for the first 70 million years (MY) of divergence with a significant slowing to 0.13 X 10(-9)/site/yr for the next 1,400 MY. The data suggest that mature SSU sequences do not accumulate more than 20% differences in the RNS positions without compensatory changes in other components of this enzyme system. During the first 70 MY of divergence between species, the rate of expected synonymous or silent nucleotide substitutions (SNS) is ~6.6 X 10(-9)/site/yr. This is five times the RNS rate and is similar to the silent rate observed in animals. In striking contrast, SNS and RNS do not show this correlation among SSU gene family members within a species. A mechanism involving gene conversion within the exons followed by selection for biased gene conversion products with conservation of RNS positions and divergence of SNS positions is discussed. A SSU gene tree based on corrected RNS for 31 SSU sequences is presented and agrees well with a species tree based on morphological and cytogenetic traits for the 17 genera examined. SSU gene comparisons may be useful in predicting phylogenetic relationships and in some cases divergence times of various plant, algal and cyanobacterial species. PMID:2515110

  5. Two human c-onc genes are located on the long arm of chromosome 8.

    PubMed Central

    Neel, B G; Jhanwar, S C; Chaganti, R S; Hayward, W S

    1982-01-01

    We have used in situ chromosome hybridization techniques to map the human cellular counterparts (c-onc genes) of the transforming genes of two RNA tumor viruses on human meiotic pachytene and somatic metaphase chromosomes. We find that the human c-mos gene is located on chromosome 8 at a position corresponding to band 8q22 on the somatic map. The human c-myc gene is found on chromosome 8 at position 8q24. These regions on the long arm of chromosome 8 have been previously reported to be involved in specific translocations found in the M-2 subset of acute nonlymphoblastic leukemias. Burkitt lymphoma, and other forms of non-Hodgkin lymphoma, and a familial abnormality that predisposes to renal cell carcinoma. These results suggest that translocations of the human c-mos or c-myc genes may be causally related to neoplastic transformation. Images PMID:6961456

  6. Conservation and Purifying Selection of Transcribed Genes Located in a Rice Centromere[W

    PubMed Central

    Fan, Chuanzhu; Walling, Jason G.; Zhang, Jianwei; Hirsch, Cory D.; Jiang, Jiming; Wing, Rod A.

    2011-01-01

    Recombination is strongly suppressed in centromeric regions. In chromosomal regions with suppressed recombination, deleterious mutations can easily accumulate and cause degeneration of genes and genomes. Surprisingly, the centromere of chromosome8 (Cen8) of rice (Oryza sativa) contains several transcribed genes. However, it remains unclear as to what selective forces drive the evolution and existence of transcribed genes in Cen8. Sequencing of orthologous Cen8 regions from two additional Oryza species, Oryza glaberrima and Oryza brachyantha, which diverged from O. sativa 1 and 10 million years ago, respectively, revealed a set of seven transcribed Cen8 genes conserved across all three species. Chromatin immunoprecipitation analysis with the centromere-specific histone CENH3 confirmed that the sequenced orthologous regions are part of the functional centromere. All seven Cen8 genes have undergone purifying selection, representing a striking phenomenon of active gene survival within a recombination-free zone over a long evolutionary time. The coding sequences of the Cen8 genes showed sequence divergence and mutation rates that were significantly reduced from those of genes located on the chromosome arms. This suggests that Oryza has a mechanism to maintain the fidelity and functionality of Cen8 genes, even when embedded in a sea of repetitive sequences and transposable elements. PMID:21856794

  7. 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.

  8. Contrasting evolutionary histories of MHC class I and class II loci in grouse--effects of selection and gene conversion.

    PubMed

    Minias, P; Bateson, Z W; Whittingham, L A; Johnson, J A; Oyler-McCance, S; Dunn, P O

    2016-05-01

    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.

  9. 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.

  10. Genes located in a chromosomal inversion are correlated with territorial song in white-throated sparrows.

    PubMed

    Zinzow-Kramer, W M; Horton, B M; McKee, C D; Michaud, J M; Tharp, G K; Thomas, J W; Tuttle, E M; Yi, S; Maney, D L

    2015-11-01

    The genome of the white-throated sparrow (Zonotrichia albicollis) contains an inversion polymorphism on chromosome 2 that is linked to predictable variation in a suite of phenotypic traits including plumage color, aggression and parental behavior. Differences in gene expression between the two color morphs, which represent the two common inversion genotypes (ZAL2/ZAL2 and ZAL2/ZAL2(m) ), may therefore advance our understanding of the molecular underpinnings of these phenotypes. To identify genes that are differentially expressed between the two morphs and correlated with behavior, we quantified gene expression and terrirorial aggression, including song, in a population of free-living white-throated sparrows. We analyzed gene expression in two brain regions, the medial amygdala (MeA) and hypothalamus. Both regions are part of a 'social behavior network', which is rich in steroid hormone receptors and previously linked with territorial behavior. Using weighted gene co-expression network analyses, we identified modules of genes that were correlated with both morph and singing behavior. The majority of these genes were located within the inversion, showing the profound effect of the inversion on the expression of genes captured by the rearrangement. These modules were enriched with genes related to retinoic acid signaling and basic cellular functioning. In the MeA, the most prominent pathways were those related to steroid hormone receptor activity. Within these pathways, the only gene encoding such a receptor was ESR1 (estrogen receptor 1), a gene previously shown to predict song rate in this species. The set of candidate genes we identified may mediate the effects of a chromosomal inversion on territorial behavior.

  11. Biased Gene Conversion in Rhizobium etli Is Caused by Preferential Double-Strand Breaks on One of the Recombining Homologs

    PubMed Central

    Yáñez-Cuna, Fares Osam; Castellanos, Mildred

    2015-01-01

    ABSTRACT Gene conversion, the nonreciprocal transfer of information during homologous recombination, is the main process that maintains identity between members of multigene families. Gene conversion in the nitrogenase (nifH) multigene family of Rhizobium etli was analyzed by using a two-plasmid system, where each plasmid carried a copy of nifH. One of the nifH copies was modified, creating restriction fragment length polymorphisms (RFLPs) spaced along the gene. Once the modified plasmid was introduced into R. etli, selection was done for cointegration with a resident plasmid lacking the RFLPs. Most of the cointegrate molecules harbor gene conversion events, biased toward a gain of RFLPs. This bias may be explained under the double-strand break repair model by proposing that the nifH gene lacking the RFLPs suffers a DNA double-strand break, so the incoming plasmid functions as a template for repairing the homolog on the resident plasmid. To support this proposal, we cloned an SceI site into the nifH homolog that had the RFLPs used for scoring gene conversion. In vivo expression of the meganuclease I-SceI allowed the generation of a double-strand break on this homolog. Upon introduction of this modified plasmid into an R. etli strain lacking I-SceI, biased gene conversion still favored the retention of markers on the incoming plasmid. In contrast, when the recipient strain ectopically expressed I-SceI, a dramatic reversal in gene conversion bias was seen, favoring the preservation of resident sequences. These results show that biased gene conversion is caused by preferential double-strand breaks on one of the recombining homologs. IMPORTANCE In this work, we analyzed gene conversion by using a system that entails horizontal gene transfer followed by homologous recombination in the recipient cell. Most gene conversion events are biased toward the acquisition of the incoming sequences, ranging in size from 120 bp to 800 bp. This bias is due to preferential cutting of

  12. Location of Promoter and Operator Sites in the Biotin Gene Cluster of Escherichia coli

    PubMed Central

    Cleary, Paul P.; Campbell, Allan; Chang, Robin

    1972-01-01

    Biotin independence in E. coli requires five closely linked genes, bioA, bioB, bioF, bioC, and bioD. The residual gene activity of deletion mutants has been studied by complementation and enzyme assays. Deletion of the left end of the bioA gene does not impair expression of the remaining genes, but deletions from the left extending into bioB abolish all gene expression. Nonsense mutations in bioB reduce expression of bioC, bioF, and bioD. Therefore, the four genes, bioB, bioF, bioC, and bioD, are transcribed as a unit from left to right, from a promotor located between bioA and bioB. Expression of the bio genes is repressible by added biotin. Deletions removing the left end of bioA do not affect repressibility of bioD. Therefore the operator, as well as the promoter, lie to the right of bioA. One deletion that removes bioA, bioB, and bioF renders the bioD gene constitutive, presumably by fusion to an unknown operon. Therefore, the operator lies to the left of bioC. PMID:4559599

  13. 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

  14. 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.

  15. 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

  16. A novel primate specific gene, CEI, is located in the homeobox gene IRXA2 promoter in Homo sapiens.

    PubMed

    Wu, Qingfa; Tommerup, Niels; Ming Wang, San; Hansen, Lars

    2006-04-26

    The Iroquois (IRX) homeobox gene family consists of six highly conserved transcription factors that are of importance for normal embryonic development. They are organized in two gene clusters in human, one on 5p15.33 and the other one on 16q12.2, respectively, and both the organization and the structure of the genes are highly conserved. An open reading frame coding for an unknown protein is identified in the promoter of IRXA2 on chromosome 5p. This new gene is composed of four exons and it is orientated in a head-to-head manner to IRXA2. Only a short 851 bp segment separates the two translation start codons and the two genes may share a bi-directional promoter. This bi-directional promoter is embedded in a large CpG-island, that also continues into both genes. RT-PCR analysis of the new gene reveals two alternative mRNA transcripts and a third mRNA transcript can be predicted from EST clones. The expression profile of the gene analysed in 9 different human tissues reveals that it is expressed in a coordinated fashion with IRXA2, which has led to the name CEI (Coordinated Expression to IRXA2). The CEI protein lacks homology to any known protein or protein domain in public databases, and a putative amino terminal signal peptide suggests the protein is secreted or ER compartment located. The gene is only found in the human and the chimpanzee genome, but not in the mouse or the rat genome, which suggests that CEI is unique for higher primates. As the identified bi-directional promoter not being a relic of an ancient compact genome, CEI may play an important role in the evolution of higher primates in coordination with the IRX genes.

  17. 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

  18. 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

    2015-03-12

    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.

  19. 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

  20. 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

  1. Genes located in a chromosomal inversion are correlated with territorial song in white-throated sparrows

    PubMed Central

    Zinzow-Kramer, Wendy M.; Horton, Brent M.; McKee, Clifton D.; Michaud, Justin M.; Tharp, Gregory K.; Thomas, James W.; Tuttle, Elaina M.; Yi, Soojin; Maney, Donna L.

    2016-01-01

    The genome of the white-throated sparrow (Zonotrichia albicollis) contains an inversion polymorphism on chromosome 2 that is linked to predictable variation in a suite of phenotypic traits including plumage color, aggression, and parental behavior. Differences in gene expression between the two color morphs, which represent the two common inversion genotypes (ZAL2/ZAL2 and ZAL2/ZAL2m), are therefore of potential interest toward understanding the molecular underpinnings of these phenotypes. To identify genes that are differentially expressed between the two morphs and correlated with behavior, we quantified both behavior and brain gene expression in a population of free-living white-throated sparrows. We quantified behavioral responses to simulated territorial intrusions (STIs) early during the breeding season. In the same birds, we then performed a transcriptome-wide analysis of gene expression in two regions, the medial amygdala and hypothalamus. Both regions are part of a ‘social behavior network’, which is rich in steroid hormone receptors and previously linked with territorial behavior. Using network analyses, we identified modules of genes that were correlated with both morph and STI-induced singing behavior. The majority of these genes were located within the inversion, demonstrating the profound effect the inversion has on the expression of genes captured by the rearrangement. Gene pathway analyses revealed that in the medial amygdala, the most prominent pathways were those related to steroid hormone receptor activity. Within these pathways, the only gene encoding such a receptor was ESR1 (estrogen receptor alpha). Our results thus suggest that ESR1 and related genes are important for behavioral differences between the morphs. PMID:26463687

  2. 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.

  3. First identification of a chromosomally located penicillinase gene in Kingella kingae species isolated in continental Europe.

    PubMed

    Basmaci, Romain; Bidet, Philippe; Berçot, Béatrice; Jost, Christelle; Kwon, Thérésa; Gaumetou, Elodie; Bonacorsi, Stéphane

    2014-10-01

    Kingella kingae is the major pathogen causing osteoarticular infections (OAI) in young children in numerous countries. Plasmid-borne TEM-1 penicillinase production has been sporadically detected in a few countries but not in continental Europe, despite a high prevalence of K. kingae infections. We describe here for the first time a K. kingae β-lactamase-producing strain in continental Europe and demonstrate the novel chromosomal location of the blaTEM-1 gene in K. kingae species.

  4. First Identification of a Chromosomally Located Penicillinase Gene in Kingella kingae Species Isolated in Continental Europe

    PubMed Central

    Basmaci, Romain; Bidet, Philippe; Berçot, Béatrice; Jost, Christelle; Kwon, Thérésa; Gaumetou, Elodie

    2014-01-01

    Kingella kingae is the major pathogen causing osteoarticular infections (OAI) in young children in numerous countries. Plasmid-borne TEM-1 penicillinase production has been sporadically detected in a few countries but not in continental Europe, despite a high prevalence of K. kingae infections. We describe here for the first time a K. kingae β-lactamase-producing strain in continental Europe and demonstrate the novel chromosomal location of the blaTEM-1 gene in K. kingae species. PMID:25049250

  5. Plasmid pCAR3 Contains Multiple Gene Sets Involved in the Conversion of Carbazole to Anthranilate†

    PubMed Central

    Urata, Masaaki; Uchimura, Hiromasa; Noguchi, Haruko; Sakaguchi, Tomoya; Takemura, Tetsuo; Eto, Kaori; Habe, Hiroshi; Omori, Toshio; Yamane, Hisakazu; Nojiri, Hideaki

    2006-01-01

    The carbazole degradative car-I gene cluster (carAaIBaIBbICIAcI) of Sphingomonas sp. strain KA1 is located on the 254-kb circular plasmid pCAR3. Carbazole conversion to anthranilate is catalyzed by carbazole 1,9a-dioxygenase (CARDO; CarAaIAcI), meta-cleavage enzyme (CarBaIBbI), and hydrolase (CarCI). CARDO is a three-component dioxygenase, and CarAaI and CarAcI are its terminal oxygenase and ferredoxin components. The car-I gene cluster lacks the gene encoding the ferredoxin reductase component of CARDO. In the present study, based on the draft sequence of pCAR3, we found multiple carbazole degradation genes dispersed in four loci on pCAR3, including a second copy of the car gene cluster (carAaIIBaIIBbIICIIAcII) and the ferredoxin/reductase genes fdxI-fdrI and fdrII. Biotransformation experiments showed that FdrI (or FdrII) could drive the electron transfer chain from NAD(P)H to CarAaI (or CarAaII) with the aid of ferredoxin (CarAcI, CarAcII, or FdxI). Because this electron transfer chain showed phylogenetic relatedness to that consisting of putidaredoxin and putidaredoxin reductase of the P450cam monooxygenase system of Pseudomonas putida, CARDO systems of KA1 can be classified in the class IIA Rieske non-heme iron oxygenase system. Reverse transcription-PCR (RT-PCR) and quantitative RT-PCR analyses revealed that two car gene clusters constituted operons, and their expression was induced when KA1 was exposed to carbazole, although the fdxI-fdrI and fdrII genes were expressed constitutively. Both terminal oxygenases of KA1 showed roughly the same substrate specificity as that from the well-characterized carbazole degrader Pseudomonas resinovorans CA10, although slight differences were observed. PMID:16672458

  6. Tissue polarity genes of Drosophila regulate the subcellular location for prehair initiation in pupal wing cells

    PubMed Central

    1993-01-01

    The Drosophila wing is decorated with a regular array of distally pointing hairs. In the pupal wing, the hairs are formed from micro- villus like prehairs that contain large bundles of actin filaments. The distal orientation of the actin bundles reveals the proximal-distal polarity within the pupal wing epithelium. We have used F-actin staining to examine early stages of prehair development in both wild- type and mutant pupal wings. We have found a striking correlation between hair polarity and the subcellular location for assembly of the prehair. In a wild-type wing, all of the distally pointing hairs are derived from prehairs that are formed at the distal vertex of the hexagonally shaped pupal wing cells. Mutations in six tissue polarity genes result in abnormal hair polarity on the adult wing, and all also alter the subcellular location for prehair initiation. Based on their cellular phenotypes, we can place these six genes into three phenotypic groups. Double mutant analysis indicates that these phenotypic groups correspond to epistasis groups. This suggests that the tissue polarity genes function in or on a pathway that controls hair polarity by regulating the subcellular location for prehair formation. PMID:8408199

  7. Induction of mitotic gene conversion by browning reaction products and its modulation by naturally occurring agents.

    PubMed

    Rosin, M P; Stich, H F; Powrie, W D; Wu, C H

    1982-05-01

    Mitotic gene conversion in the D7 strain of Saccharomyces cerevisiae was significantly enhanced by exposure to non-enzymatic browning reaction products. These products were formed during the heating of sugar (caramelization reaction) or sugar-amino acid mixtures (Maillard reaction) at temperatures normally used during the cooking of food. Several modulating factors of this convertogenic activity were identified. These factors included two main groups: (1) trace metals which are widely distributed in the environment; and (2) several cellular enzymatic systems. The convertogenic activities of a heated glucose-lysine mixture and a commercial caramel powder were completely suppresses when yeast were concurrently exposed to these products and to either FeIII or CuII. Equimolar concentrations of MnII or sodium selenite had no effect on the convertogenic activity of the products of either model system. Horse-radish peroxidase, beef liver catalase and rat liver S9 preparations each decreased the frequency of gene conversion induced by the caramel powder and the heated glucose-lysine products. This modulating activity of the enzymes was lost if they were heat-inactivated. These studies indicate the presence of a variety of protective mechanisms which can modify genotoxic components in complex food mixtures.

  8. Characterization of a cytochrome c gene located at the gene cluster for chlorate respiration in Ideonella dechloratans.

    PubMed

    Bohlin, Jan; Bäcklund, Anna Smedja; Gustavsson, Niklas; Wahlberg, Sara; Nilsson, Thomas

    2010-08-20

    Anaerobic chlorate respiration requires electron transport from the bacterial inner membrane to the soluble periplasmic chlorate reductase. We have recently demonstrated that soluble c cytochromes function as electron carriers for chlorate reduction in Ideonella dechloratans (Smedja Bäcklund et al. 2009). In the present work, we describe a gene encoding soluble c-type cytochrome [cyt; GenBank ID: EU768872] located close to the gene cluster for chlorate reduction in I. dechloratans. The predicted amino acid sequence does not match any of the peptide masses or partial sequences obtained earlier from periplasmic c cytochromes. The gene, without the predicted signal sequence, was expressed heterologously in E. coli and the recombinant protein was purified, refolded and reconstituted with heme. The reconstituted protein shows spectral properties characteristic for c cytochromes, with an absorption maximum at 553 nm for the alpha band in the reduced state. Pyridine hemochrome analysis demonstrates the formation of covalently bound heme.

  9. Genomic cloning, structure, expression pattern, and chromosomal location of the human SIX3 gene.

    PubMed

    Granadino, B; Gallardo, M E; López-Ríos, J; Sanz, R; Ramos, C; Ayuso, C; Bovolenta, P; Rodríguez de Córdoba, S

    1999-01-01

    The Drosophila gene sine oculis (so) is a nuclear homeoprotein that is required for eye development. Homologous genes to so, denoted SIX genes, have been found in vertebrates. Among the SIX genes, SIX3 is considered to be the functional homologue of so. To provide insight into the potential implications of SIX3 in human ocular malformations, we have cloned and characterized the human SIX3 gene. In human eye, SIX3 produces a 3-kb transcript that codes for a 332-amino-acid polypeptide that is virtually identical to its mouse and chick homologues. Expression of SIX3 was detected in human embryos as early as 5-7 weeks of gestation and found to be maintained in the eye throughout the entire period of fetal development. At 20 weeks of gestation, expression of SIX3 in the human retina was detected in the ganglion cells and in cells of the inner nuclear layer. The human SIX3 gene spans 4.4 kb of genomic DNA and is split in two exons separated by a 1659-bp intron. SIX3 was mapped to human chromosome 2p16-p21, between the genetic markers D2S119 and D2S288. Interestingly, the map position of human SIX3 overlaps the locations of two dominant disorders with ocular phenotypes that have been assigned to this chromosomal region, holoprosencephaly type 2 and Malattia Leventinese.

  10. 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

  11. 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.

  12. 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…

  13. 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

  14. The roles of gene duplication, gene conversion and positive selection in rodent Esp and Mup pheromone gene families with comparison to the Abp family.

    PubMed

    Karn, Robert C; Laukaitis, Christina M

    2012-01-01

    Three proteinaceous pheromone families, the androgen-binding proteins (ABPs), the exocrine-gland secreting peptides (ESPs) and the major urinary proteins (MUPs) are encoded by large gene families in the genomes of Mus musculus and Rattus norvegicus. We studied the evolutionary histories of the Mup and Esp genes and compared them with what is known about the Abp genes. Apparently gene conversion has played little if any role in the expansion of the mouse Class A and Class B Mup genes and pseudogenes, and the rat Mups. By contrast, we found evidence of extensive gene conversion in many Esp genes although not in all of them. Our studies of selection identified at least two amino acid sites in β-sheets as having evolved under positive selection in the mouse Class A and Class B MUPs and in rat MUPs. We show that selection may have acted on the ESPs by determining K(a)/K(s) for Exon 3 sequences with and without the converted sequence segment. While it appears that purifying selection acted on the ESP signal peptides, the secreted portions of the ESPs probably have undergone much more rapid evolution. When the inner gene converted fragment sequences were removed, eleven Esp paralogs were present in two or more pairs with K(a)/K(s) >1.0 and thus we propose that positive selection is detectable by this means in at least some mouse Esp paralogs. We compare and contrast the evolutionary histories of all three mouse pheromone gene families in light of their proposed functions in mouse communication.

  15. c-Ha-ras gene bidirectional promoter expressed in vitro: location and regulation.

    PubMed Central

    Lowndes, N F; Paul, J; Wu, J; Allan, M

    1989-01-01

    Increased transcriptional activity of the c-Ha-ras gene product is correlated with induction of several important human tumor types. For this reason, we have investigated the nature of the c-Ha-ras promoter and the factors that regulate its expression. Using S1 and primer extension analysis of c-Ha-ras RNA from EJ cells, we have identified 18 initiation sites within an upstream exon (exon -1) whose 3' end (the donor splice site [D]) is located 1,105 base pairs (bp) upstream of the ATG codon. The furthest-upstream initiation site is located -191 bp relative to D, and the furthest downstream is located -16 bp relative to D. Transient expression assays, in which a series of mutants spanning this region were ligated to a promoterless chloramphenicol acetyltransferase vector, functionally confirmed the position and extent of this promoter. Mutational analysis further located a 47-bp element located between -243 and -196 relative to D that up-regulated transcriptional activity of the promoter region by 20- to 40-fold. This region contained both a GC box known to bind SP1 and a CCAAT box. Insertion of a simian virus 40 enhancer 5' to the promoter up-regulated transcription from each initiation site by approximately 10- to 20-fold. We have also localized, both by chloramphenicol acetyltransferase assay and by S1 analysis, a strong promoter operating in the direction opposite that of the gene and originating immediately 5' to the 47-bp regulatory region. The reverse promoter was found to have nine initiation sites between -248 and -278 relative to D. Images PMID:2674682

  16. Concerted action of the MutLβ heterodimer and Mer3 helicase regulates the global extent of meiotic gene conversion

    PubMed Central

    Duroc, Yann; Kumar, Rajeev; Ranjha, Lepakshi; Adam, Céline; Guérois, Raphaël; Md Muntaz, Khan; Marsolier-Kergoat, Marie-Claude; Dingli, Florent; Laureau, Raphaëlle; Loew, Damarys; Llorente, Bertrand; Charbonnier, Jean-Baptiste; Cejka, Petr; Borde, Valérie

    2017-01-01

    Gene conversions resulting from meiotic recombination are critical in shaping genome diversification and evolution. How the extent of gene conversions is regulated is unknown. Here we show that the budding yeast mismatch repair related MutLβ complex, Mlh1-Mlh2, specifically interacts with the conserved meiotic Mer3 helicase, which recruits it to recombination hotspots, independently of mismatch recognition. This recruitment is essential to limit gene conversion tract lengths genome-wide, without affecting crossover formation. Contrary to expectations, Mer3 helicase activity, proposed to extend the displacement loop (D-loop) recombination intermediate, does not influence the length of gene conversion events, revealing non-catalytical roles of Mer3. In addition, both purified Mer3 and MutLβ preferentially recognize D-loops, providing a mechanism for limiting gene conversion in vivo. These findings show that MutLβ is an integral part of a new regulatory step of meiotic recombination, which has implications to prevent rapid allele fixation and hotspot erosion in populations. DOI: http://dx.doi.org/10.7554/eLife.21900.001 PMID:28051769

  17. Concerted action of the MutLβ heterodimer and Mer3 helicase regulates the global extent of meiotic gene conversion.

    PubMed

    Duroc, Yann; Kumar, Rajeev; Ranjha, Lepakshi; Adam, Céline; Guérois, Raphaël; Md Muntaz, Khan; Marsolier-Kergoat, Marie-Claude; Dingli, Florent; Laureau, Raphaëlle; Loew, Damarys; Llorente, Bertrand; Charbonnier, Jean-Baptiste; Cejka, Petr; Borde, Valérie

    2017-01-04

    Gene conversions resulting from meiotic recombination are critical in shaping genome diversification and evolution. How the extent of gene conversions is regulated is unknown. Here we show that the budding yeast mismatch repair related MutLβ complex, Mlh1-Mlh2, specifically interacts with the conserved meiotic Mer3 helicase, which recruits it to recombination hotspots, independently of mismatch recognition. This recruitment is essential to limit gene conversion tract lengths genome-wide, without affecting crossover formation. Contrary to expectations, Mer3 helicase activity, proposed to extend the displacement loop (D-loop) recombination intermediate, does not influence the length of gene conversion events, revealing non-catalytical roles of Mer3. In addition, both purified Mer3 and MutLβ preferentially recognize D-loops, providing a mechanism for limiting gene conversion in vivo. These findings show that MutLβ is an integral part of a new regulatory step of meiotic recombination, which has implications to prevent rapid allele fixation and hotspot erosion in populations.

  18. A second hypermutable DNA sequence is located within the fragile X gene

    SciTech Connect

    Zhong, N.; Dobkin, C.; Brown, W.T.

    1994-07-15

    The molecular basis for the Fragile X syndrome is a large expansion of an unstable triplet repeat (CGG)n at the 5{prime} untranslated end of the FMR-1 gene leading to a lack of gene expression. We have discovered that another DNA sequence located within the gene is hypermutable. The FRAXAC2 locus is a microsatellite marker located 10 kb downstream to the (CGG)n within FMR-1. PCR analysis of FRAXAC2 from 265 chromosomes showed 261 had lengths that differed by single bps from 146 to 153 bps and four had 155, 157, 158, and 159 bps. Sequence analysis showed three variable length subregions: a GT repeat followed by a constant C, a TA repeat and a poly(T), which could be represented as a (GT)x-C-(TA)y-(T)z complex, with x values of 13-17 and 19; y values of 6-8; and a z values 10-20 and 25, with a total of 40 different alleles and a heterozygosity of 90.1%. Inheritance studies of FRAXAC2 in 32 fragile X families showed 4 mutations among 2 fragile X families including 3 of 67 from female-carrier fragile X chromosomes and 1 of 54 from their normal chromosomes. Thus, 3.3% (4/121) of the fragile X derived meioses were unstable. No mutation was detected from 25 normal male spouses and 112 CEPH family meioses. The hypermutable FRAXAC2 appears to be the first identified microsatellite with three variable parts. The finding of two highly mutable sequences near each other and within the same gene suggests a related mutational mechanism exists with two targets in the FMR-1 gene.

  19. 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.

  20. Codelivery of antitumor drug and gene by a pH-sensitive charge-conversion system.

    PubMed

    Guan, Xiuwen; Li, Yanhui; Jiao, Zixue; Lin, Lin; Chen, Jie; Guo, Zhaopei; Tian, Huayu; Chen, Xuesi

    2015-02-11

    In the present study, a gene and drug codelivery system was developed by electrostatic binding of polyethylenimine-poly(l-lysine)-poly(l-glutamic acid) (PELG), polyethylenimine (PEI), cis-aconityl-doxorubicin (CAD), and DNA. Zeta potential and drug release analysis confirmed the pH-responsive charge conversion and acid-sensitive drug release functional properties of the PELG/PEI/(DNA+CAD) system. Gel retardation assay and transfection experiment showed the codelivery system had effective DNA binding ability and good transfection efficiency on HepG2 cells. The therapeutic gene p53 was further employed to study its combinational effects with CAD. Cytotoxicity assay showed the half inhibitory concentration (IC50) of the PELG/PEI/(p53+CAD) codelivery system was lower than that of the gene or the drug delivery system. Confocal laser scanning microscopy (CLSM) showed that the drug and gene could be delivered into the cells simultaneously. A significant increase of p53 gene expression was achieved after HepG2 cells treated by PELG/PEI/(p53+CAD) codelivery system. The apoptosis experiment indicated clearly that the codelivery system could lead an effective apoptosis on tumor cells, which was beneficial for the treatment of cancer. The biodistribution and tumor accumulation of the codelivery system was explored via in vivo imaging in subcutaneous xenograft and in situ tumor models. The tumor and some major organs were excised and imaged, and the results showed that the codelivery system can accumulate efficiently in tumor for both tumor models. It can be suggested from the above results that the PELG/PEI/(DNA+CAD) codelivery system will have great potential applications in cancer therapy.

  1. The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana

    PubMed Central

    Wijnker, Erik; Velikkakam James, Geo; Ding, Jia; Becker, Frank; Klasen, Jonas R; Rawat, Vimal; Rowan, Beth A; de Jong, Daniël F; de Snoo, C Bastiaan; Zapata, Luis; Huettel, Bruno; de Jong, Hans; Ossowski, Stephan; Weigel, Detlef; Koornneef, Maarten; Keurentjes, Joost JB; Schneeberger, Korbinian

    2013-01-01

    Knowledge of the exact distribution of meiotic crossovers (COs) and gene conversions (GCs) is essential for understanding many aspects of population genetics and evolution, from haplotype structure and long-distance genetic linkage to the generation of new allelic variants of genes. To this end, we resequenced the four products of 13 meiotic tetrads along with 10 doubled haploids derived from Arabidopsis thaliana hybrids. GC detection through short reads has previously been confounded by genomic rearrangements. Rigid filtering for misaligned reads allowed GC identification at high accuracy and revealed an ∼80-kb transposition, which undergoes copy-number changes mediated by meiotic recombination. Non-crossover associated GCs were extremely rare most likely due to their short average length of ∼25–50 bp, which is significantly shorter than the length of CO-associated GCs. Overall, recombination preferentially targeted non-methylated nucleosome-free regions at gene promoters, which showed significant enrichment of two sequence motifs. DOI: http://dx.doi.org/10.7554/eLife.01426.001 PMID:24347547

  2. Complete conversion of antibiotic precursor to pristinamycin IIA by overexpression of Streptomyces pristinaespiralis biosynthetic genes.

    PubMed

    Sezonov, G; Blanc, V; Bamas-Jacques, N; Friedmann, A; Pernodet, J L; Guérineau, M

    1997-04-01

    A Streptomyces pristinaespiralis strain, which produces a streptogramin antibiotic pristinamycin II (PII) as a mixture of two biologically active molecules PIIB and PIIA, was genetically engineered to produce exclusively PIIA. The snaA,B genes, which encode a PIIA synthase that performs oxidation of the precursor (PIIB) to the final product (PIIA), were integrated in the chromosome of S. pristinaespiralis using an integrative derivative of the pSAM2 genetic element from Streptomyces ambofaciens. Integration was due to site-specific recombination at the attB site of S. pristinaespiralis, and no homologous recombination at the snaA,B locus was observed. The attB site of S. pristinaespiralis was sequenced and found to overlap the 3' end of a pro-tRNA gene. The integrants were stable in industrial conditions of pristinamycin production and showed no decrease in PII biosynthesis. Western blot analysis showed a constant production of the PIIA synthase in the overall fermentation process due to expression of the cloned snaA,B genes from the constitutive ermE promoter. This allows the complete conversion of the PIIB form into PIIA.

  3. The KUP gene, located on human chromosome 14, encodes a protein with two distant zinc fingers.

    PubMed

    Chardin, P; Courtois, G; Mattei, M G; Gisselbrecht, S

    1991-04-11

    We have isolated a human cDNA (kup), encoding a new protein with two distantly spaced zinc fingers of the C2H2 type. This gene is highly conserved in mammals and is expressed mainly in hematopoietic cells and testis. Its expression was not higher in the various transformed cells tested than in the normal corresponding tissues. The kup gene is located in region q23-q24 of the long arm of human chromosome 14. The kup protein is 433 a.a. long, has a M.W. close to 50 kD and binds to DNA. Although the structure of the kup protein is unusual, the isolated fingers resemble closely those of the Krüppel family, suggesting that this protein is also a transcription factor. The precise function and DNA motif recognized by the kup protein remain to be determined.

  4. High-frequency conversion to a "fluffy" developmental phenotype in Aspergillus spp. by 5-azacytidine treatment: evidence for involvement of a single nuclear gene.

    PubMed Central

    Tamame, M; Antequera, F; Villanueva, J R; Santos, T

    1983-01-01

    Transient exposure of mycelia from Aspergillus niger and Aspergillus nidulans to the cytidine analog 5-azacytidine, leading to no more than 0.3 to 0.5% substitution for cytosine by 5-azacytosine in A. nidulans DNA, resulted in the conversion of a high fraction of the cell population (more than 20%) to a mitotically and meiotically stable "fluffy" developmental phenotype. The phenotypic variants are characterized by the developmentally timed production of a profuse fluffy network of undifferentiated aerial hyphae that seem to escape signals governing vegetative growth. Genetic analysis with six different fluffy clones reveals that this trait is not cytoplasmically coded, is recessive in heterozygous diploids but codominant in heterokaryons, and exhibits a 1:1 Mendelian segregation pattern upon sexual sporulation of heterozygous diploids. Complementation and mitotic haploidization studies indicated that all variants are affected in the same gene, which can be tentatively located on chromosome VIII of A. nidulans. Molecular analysis to search for modified bases showed that DNA methylation is negligible in in both A. niger and A. nidulans and that no differences could be detected among DNAs from wild-type cells, fluffy clones, or mycelia exposed to 5-azacytidine. It thus appears that high-frequency conversion of fungal mycelia to a stable, variant developmental phenotype by 5-azacytidine is the result of some kind of target action on a single nuclear gene and that this conversion can occur in organisms virtually devoid of DNA methylation. Images PMID:6197627

  5. Ligands located within a cholesterol domain enhance gene delivery to the target tissue

    PubMed Central

    Xu, Long; Betker, Jamie; Yin, Hao; Anchordoquy, Thomas J.

    2012-01-01

    Targeted gene delivery provides enormous potential for clinical treatment of many incurable diseases. Liposomes formulated with targeting ligands have been tested extensively both in vitro and in vivo, and many studies have strived to identify more efficacious ligands. However, the environment of the ligand within the delivery vehicle is generally not considered, and this study assesses the effect of ligand micoenvironment by utilizing a lipoplex possessing a cholesterol domain. Our recent work has shown that the presence of the targeting ligand within the cholesterol domain promotes more productive transfection in cultured cells. In the present study, lipoplexes having the identical lipid composition were formulated with different conjugates of the folate ligand such that the ligand was included in, or excluded from, the cholesterol domain. The effect of locating the ligand within the cholesterol domain was then tested in a xenograft tumor model in mice. Lipoplexes that included the ligand within the cholesterol domain showed significantly higher luciferase expression and plasmid accumulation in tumors as compared to lipoplexes in which the ligand was excluded from the domain. These results demonstrate that the microenvironment of the ligand can affect gene delivery to tumors, and show that ligand-mediated delivery can be enhanced by locating targeting ligands within a cholesterol domain. PMID:22440429

  6. Effects of terminal nonhomology and homeology on double-strand-break-induced gene conversion tract directionality.

    PubMed Central

    Nelson, H H; Sweetser, D B; Nickoloff, J A

    1996-01-01

    Double-strand breaks (DSBs) greatly enhance gene conversion in the yeast Saccharomyces cerevisiae. In prior plasmid x chromosome crosses, conversion tracts were often short ( < 53 bp) and usually extended in only one direction from a DSB in an HO recognition sequence inserted into ura3. To allow fine-structure analysis of short and unidirectional tracts, phenotypically silent markers were introduced at 3- and 6-bp intervals flanking the HO site. These markers, which created a 70-bp homeologous region (71% homology), greatly increased the proportion of bidirectional tracts. Among products with short or unidirectional tracts, 85% were highly directional, converting markers on only one side (the nearest marker being 6 bp from the HO site). A DSB in an HO site insertion creates terminal nonhomologies. The high degree of directionality is a likely consequence of the precise cleavage at homology/nonhomology borders in hybrid DNA by Rad1/10 endonuclease. In contrast, terminal homeology alone yielded mostly unidirectional tracts. Thus, nonhomology flanked by homeology yields primarily bidirectional tracts, but terminal homeology or nonhomology alone yields primarily unidirectional tracts. These results are inconsistent with uni- and bidirectional tracts arising from one- and two-ended invasion mechanisms, respectively, as reduced homology would be expected to favor one-ended events. Tract spectra with terminal homeology alone with similar in RAD1 and rad1 cells, indicating that the high proportion of bidirectional tracts seen with homeology flanking nonhomology is not a consequence of Rad1/10 cleavage at homology/homeology boundaries. Instead, tract directionality appears to reflect the influence of the degree of broken-end homology on mismatch repair. PMID:8649406

  7. 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.

  8. Chromosomal divergence and evolutionary inferences in Rhodniini based on the chromosomal location of ribosomal genes

    PubMed Central

    Pita, Sebastián; Panzera, Francisco; Ferrandis, Inés; Galvão, Cleber; Gómez-Palacio, Andrés; Panzera, Yanina

    2013-01-01

    In this study, we used fluorescence in situ hybridisation to determine the chromosomal location of 45S rDNA clusters in 10 species of the tribe Rhodniini (Hemiptera: Reduviidae: Triatominae). The results showed striking inter and intraspecific variability, with the location of the rDNA clusters restricted to sex chromosomes with two patterns: either on one (X chromosome) or both sex chromosomes (X and Y chromosomes). This variation occurs within a genus that has an unchanging diploid chromosome number (2n = 22, including 20 autosomes and 2 sex chromosomes) and a similar chromosome size and genomic DNA content, reflecting a genome dynamic not revealed by these chromosome traits. The rDNA variation in closely related species and the intraspecific polymorphism in Rhodnius ecuadoriensis suggested that the chromosomal position of rDNA clusters might be a useful marker to identify recently diverged species or populations. We discuss the ancestral position of ribosomal genes in the tribe Rhodniini and the possible mechanisms involved in the variation of the rDNA clusters, including the loss of rDNA loci on the Y chromosome, transposition and ectopic pairing. The last two processes involve chromosomal exchanges between both sex chromosomes, in contrast to the widely accepted idea that the achiasmatic sex chromosomes of Heteroptera do not interchange sequences. PMID:23778665

  9. 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.

  10. 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.

  11. Non-crossover gene conversions show strong GC bias and unexpected clustering in humans

    PubMed Central

    Williams, Amy L; Genovese, Giulio; Dyer, Thomas; Altemose, Nicolas; Truax, Katherine; Jun, Goo; Patterson, Nick; Myers, Simon R; Curran, Joanne E; Duggirala, Ravi; Blangero, John; Reich, David; Przeworski, Molly

    2015-01-01

    Although the past decade has seen tremendous progress in our understanding of fine-scale recombination, little is known about non-crossover (NCO) gene conversion. We report the first genome-wide study of NCO events in humans. Using SNP array data from 98 meioses, we identified 103 sites affected by NCO, of which 50/52 were confirmed in sequence data. Overlap with double strand break (DSB) hotspots indicates that most of the events are likely of meiotic origin. We estimate that a site is involved in a NCO at a rate of 5.9 × 10−6/bp/generation, consistent with sperm-typing studies, and infer that tract lengths span at least an order of magnitude. Observed NCO events show strong allelic bias at heterozygous AT/GC SNPs, with 68% (58–78%) transmitting GC alleles (p = 5 × 10−4). Strikingly, in 4 of 15 regions with resequencing data, multiple disjoint NCO tracts cluster in close proximity (∼20–30 kb), a phenomenon not previously seen in mammals. DOI: http://dx.doi.org/10.7554/eLife.04637.001 PMID:25806687

  12. 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

  13. 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.

  14. 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

  15. 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.

  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. The case of the unreliable SNP: recurrent back-mutation of Y-chromosomal marker P25 through gene conversion.

    PubMed

    Adams, Susan M; King, Turi E; Bosch, Elena; Jobling, Mark A

    2006-05-25

    The Y-chromosomal binary marker P25 is a paralogous sequence variant, rather than a SNP: three copies of the P25 sequence lie within the giant palindromic repeats on Yq, and one copy has undergone a C to A transversion to define haplogroup R1b (designated C/C/A). Since gene conversion is known to be active in the palindromic repeats, we reasoned that P25 might be liable to back-mutation by gene conversion, yielding the ancestral state C/C/C. Through analysis of a set of binary markers in Y-chromosomes in two large samples from Great Britain and the Iberian Peninsula we show that such conversion events have occurred at least twice, and provide preliminary evidence that the reverse conversion event (yielding C/A/A) has also occurred. Because of its inherent instability, we suggest that P25 be used with caution in forensic studies, and perhaps replaced with the more reliable binary marker M269.

  18. 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.

  19. Analysis of crossover breakpoints yields new insights into the nature of the gene conversion events associated with large NF1 deletions mediated by nonallelic homologous recombination.

    PubMed

    Bengesser, Kathrin; Vogt, Julia; Mussotter, Tanja; Mautner, Victor-Felix; Messiaen, Ludwine; Cooper, David N; Kehrer-Sawatzki, Hildegard

    2014-02-01

    Large NF1 deletions are mediated by nonallelic homologous recombination (NAHR). An in-depth analysis of gene conversion operating in the breakpoint-flanking regions of large NF1 deletions was performed to investigate whether the rate of discontinuous gene conversion during NAHR with crossover is increased, as has been previously noted in NAHR-mediated rearrangements. All 20 germline type-1 NF1 deletions analyzed were mediated by NAHR associated with continuous gene conversion within the breakpoint-flanking regions. Continuous gene conversion was also observed in 31/32 type-2 NF1 deletions investigated. In contrast to the meiotic type-1 NF1 deletions, type-2 NF1 deletions are predominantly of post-zygotic origin. Our findings therefore imply that the mitotic as well as the meiotic NAHR intermediates of large NF1 deletions are processed by long-patch mismatch repair (MMR), thereby ensuring gene conversion tract continuity instead of the discontinuous gene conversion that is characteristic of short-patch repair. However, the single type-2 NF1 deletion not exhibiting continuous gene conversion was processed without MMR, yielding two different deletion-bearing chromosomes, which were distinguishable in terms of their breakpoint positions. Our findings indicate that MMR failure during NAHR, followed by post-meiotic/mitotic segregation, has the potential to give rise to somatic mosaicism in human genomic rearrangements by generating breakpoint heterogeneity.

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

    PubMed

    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

  1. 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

  2. The human corticosteroid binding globulin gene is located on chromosome 14q31-q32.1 near two other serine protease inhibitor genes.

    PubMed

    Seralini, G E; Bérubé, D; Gagné, R; Hammond, G L

    1990-11-01

    Human corticosteroid binding globulin (CBG) cDNA fragments were radiolabeled and hybridized in situ to metaphase chromosome preparations. The results localized the CBG gene to the q31-q32.1 region of human chromosome 14. This location also contains the genes for two closely related serine protease inhibitors: alpha 1-proteinase inhibitor and alpha 1-antichymotrypsin. It is therefore likely that these genes evolved by duplication events, and it would appear that this region contains a series of functionally related genes.

  3. Identification, expression pattern, cellular location and potential role of the caveolin-1 gene from Artemia sinica.

    PubMed

    Li, Xuejie; Yao, Feng; Zhang, Wei; Cheng, Cheng; Chu, Bing; Liu, Yan; Mei, Yanli; Wu, Yang; Zou, Xiangyang; Hou, Lin

    2014-05-01

    Caveolins are integral membrane proteins that serve as scaffolds to recruit numerous signaling molecules. Caveolins play an important role in membrane trafficking, signal transduction, substrate transport and endocytosis in differentiated cells. In this study, a caveolin-1 gene from Artemia sinica (As-cav-1) was successfully cloned for the first time. The full-length cDNA of As-cav-1 comprises 974 bp, with a 675 bp open reading frame (ORF) that encodes a polypeptide of 224 amino acids with a caveolin scaffolding domain (CSD) and two transmembrane domains. Multiple sequence alignment revealed that the putative As-CAV-1 protein sequence was relatively conserved across species, especially in the CSD domain. Real-time PCR revealed high levels of the As-cav-1 transcript at 0h of embryo development. Furthermore, As-cav-1 transcripts were highly upregulated under high salinity (200‰) and low temperature stresses (15°C). To further characterize As-cav-1, recombinant pET30a-cav-1 protein was expressed using a prokaryotic expression system. The recombinant protein comprised 290 amino acids with a theoretical molecular weight of 32kDa, and a predicted isoelectric point of 5.6. Western blotting of the expression levels of As-CAV-1 during different embryo development stages revealed that As-CAV-1 levels decreased gradually during development stages from 0 h to 40 h, and increased at 3d. Furthermore, western blotting showed that As-CAV-1 was upregulated to its highest expression level by low temperature stress (15°C) and high salinity. Confocal laser microscopy analysis, using antibodies generated against the recombinant As-CAV-1 protein, showed that As-CAV-1 was mostly located in the cell membrane. Our results suggested that As-cav-1 plays a vital role in protecting embryos from high salt damage and low temperature stress, especially during post-diapause embryonic development.

  4. 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.

  5. Effect of gene location, mRNA secondary structures, and RNase sites on expression of two genes in an engineered operon.

    PubMed

    Smolke, Christina D; Keasling, Jay D

    2002-12-30

    The effects of endoribonuclease sites, secondary structures in mRNA, and gene placement on protein production and mRNA stability and steady-state levels were tested in a dual-gene operon containing the genes encoding beta-galactosidase (lacZ) from Escherichia coli and green fluorescent protein (gfp) from Aequorea victoria. Two previously identified RNase E sites were placed separately between the coding regions to direct cleavage in this area and produce two secondary transcripts, each containing a single-gene coding region. Novel secondary structures were engineered into the 3' and 5' ends of each of the coding regions to protect the transcript from inactivation by endoribonucleases (5' hairpins) and degradation by exoribonucleases (3' hairpins). In addition, the effects of relative gene placement were examined by switching the locations of the two coding regions. Depending on the particular secondary structures and RNase E sites placed between the genes the relative steady-state transcript and protein levels encoded by the two reporter genes could be changed up to 2.5-fold and 4-fold, respectively. By changing gene location and incorporating secondary structures and RNase E sites the relative steady-state transcript and protein levels encoded by the two reporter genes could be changed up to 100-fold and 750-fold, respectively.

  6. 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.

  7. 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

  8. 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 ...

  9. The DNA sequence of the H-2kb gene: evidence for gene conversion as a mechanism for the generation of polymorphism in histocompatibilty antigens.

    PubMed Central

    Weiss, E; Golden, L; Zakut, R; Mellor, A; Fahrner, K; Kvist, S; Flavell, R A

    1983-01-01

    We have determined the DNA sequence of the H-2Kb gene of the C57B1/10 mouse. Comparison of this sequence with that of the allelic H-2Kd shows surprisingly that the exons have accumulated more mutations than their introns. Moreover, many of these changes in the exons are clustered in short regions or hot spots. Additional comparison of these sequences with the H-2Ld and H-2Db sequences shows that, in several cases, the altered sequence generated at the hot spot is identical to the corresponding region of a non-allelic H-2 gene. The clustered changes are responsible for 60% of the amino acid differences between the H-2Kb and H-2Kd genes and suggest that micro-gene conversion events occurring within the exons and involving only tens of nucleotides are an important mechanism for the generation of polymorphic differences between natural H-2 alleles. Images Fig. 3. PMID:11894963

  10. Structure, Expression, Chromosomal Location and Product of the Gene Encoding Adh2 in Petunia

    PubMed Central

    Gregerson, R. G.; Cameron, L.; McLean, M.; Dennis, P.; Strommer, J.

    1993-01-01

    In most higher plants the genes encoding alcohol dehydrogenase comprise a small gene family, usually with two members. The Adh1 gene of Petunia has been cloned and analyzed, but a second identifiable gene was not recovered from any of three genomic libraries. We have therefore employed the polymerase chain reaction to obtain the major portion of a second Adh gene. From sequence, mapping and northern data we conclude this gene encodes ADH2, the major anaerobically inducible Adh gene of Petunia. The availability of both Adh1 and Adh2 from Petunia has permitted us to compare their structures and patterns of expression to those of the well-studied Adh genes of maize, of which one is highly expressed developmentally, while both are induced in response to hypoxia. Despite their evolutionary distance, evidenced by deduced amino acid sequence as well as taxonomic classification, the pairs of genes are regulated in strikingly similar ways in maize and Petunia. Our findings suggest a significant biological basis for the regulatory strategy employed by these distant species for differential expression of multiple Adh genes. PMID:8096485

  11. 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.

  12. Cloning of the bile salt hydrolase (bsh) gene from Enterococcus faecium FAIR-E 345 and chromosomal location of bsh genes in food enterococci.

    PubMed

    Wijaya, Agus; Hermann, Anette; Abriouel, Hikmate; Specht, Ingrid; Yousif, Nuha M K; Holzapfel, Wilhelm H; Franz, Charles M A P

    2004-12-01

    Enterococcus faecium strain FAIR-E 345 isolated from food was shown to possess bile salt hydrolase (Bsh) activity in a plate screening assay and by high-performance liquid chromatography analysis. The bsh gene was cloned and sequenced. DNA sequence analysis revealed that it encoded a protein of 324 amino acids, with pI 4.877. A bsh gene probe was prepared from the cloned bsh gene and was used for probing plasmid and total genomic DNA of Bsh-positive enterococci isolated from food to determine the genomic location of their bsh genes. This probe was able to detect the bsh gene among total genomic DNA preparations but not from plasmid preparations of 10 plasmid-bearing Enterococcus strains. However, the probe could detect the bsh gene from total genomic DNA preparations of 12 Enterococcus strains that did not contain detectable plasmid DNA. In no cases did the probe hybridize with plasmid DNA preparations, suggesting that the bsh gene among enterococci is probably generally chromosomally encoded. This presumptive chromosomal location of bsh genes among food enterococci suggests that transfer of this trait by conjugative plasmids is unlikely.

  13. ord1, an oxidoreductase gene responsible for conversion of O-methylsterigmatocystin to aflatoxin in Aspergillus flavus.

    PubMed Central

    Prieto, R; Woloshuk, C P

    1997-01-01

    Among the enzymatic steps in the aflatoxin biosynthetic pathway, the conversion of O-methylsterigmatocystin to aflatoxin has been proposed to be catalyzed by an oxidoreductase. Transformants of Aspergillus flavus 649WAF2 containing a 3.3-kb genomic DNA fragment and the aflatoxin biosynthesis regulatory gene aflR converted exogenously supplied O-methylsterigmatocystin to aflatoxin B1. A gene, ord1, corresponding to a transcript of about 2 kb was identified within the 3.3-kb DNA fragment. The promoter region presented a putative AFLR binding site and a TATA sequence. The nucleotide sequence of the gene revealed an open reading frame encoding a protein of 528 amino acids with a deduced molecular mass of 60.2 kDa. The gene contained six introns and seven exons. Heterologous expression of the ord1 open reading frame under the transcriptional control of the Saccharomyces cerevisiae galactose-inducible gal1 promoter results in the ability to convert O-methylsterigmatocystin to aflatoxin B1. The data indicate that ord1 is sufficient to accomplish the last step of the aflatoxin biosynthetic pathway. A search of various databases for similarity indicated that ord1 encodes a cytochrome P-450-type monooxygenase, and the gene has been assigned to a new P-450 gene family named CYP64. PMID:9143099

  14. 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 ...

  15. 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.

  16. Transcription of a donor enhances its use during double-strand break-induced gene conversion in human cells.

    PubMed

    Schildkraut, Ezra; Miller, Cheryl A; Nickoloff, Jac A

    2006-04-01

    Homologous recombination (HR) mediates accurate repair of double-strand breaks (DSBs) but carries the risk of large-scale genetic change, including loss of heterozygosity, deletions, inversions, and translocations. Nearly one-third of the human genome consists of repetitive sequences, and DSB repair by HR often requires choices among several homologous repair templates, including homologous chromosomes, sister chromatids, and linked or unlinked repeats. Donor preference during DSB-induced gene conversion was analyzed by using several HR substrates with three copies of neo targeted to a human chromosome. Repair of I-SceI nuclease-induced DSBs in one neo (the recipient) required a choice between two donor neo genes. When both donors were downstream, there was no significant bias for proximal or distal donors. When donors flanked the recipient, we observed a marked (85%) preference for the downstream donor. Reversing the HR substrate in the chromosome eliminated this preference, indicating that donor choice is influenced by factors extrinsic to the HR substrate. Prior indirect evidence suggested that transcription might increase donor use. We tested this question directly and found that increased transcription of a donor enhances its use during gene conversion. A preference for transcribed donors would minimize the use of nontranscribed (i.e., pseudogene) templates during repair and thus help maintain genome stability.

  17. A novel approach to locate Phytophthora infestans resistance genes on the potato genetic map.

    PubMed

    Jacobs, Mirjam M J; Vosman, Ben; Vleeshouwers, Vivianne G A A; Visser, Richard G F; Henken, Betty; van den Berg, Ronald G

    2010-02-01

    Mapping resistance genes is usually accomplished by phenotyping a segregating population for the resistance trait and genotyping it using a large number of markers. Most resistance genes are of the NBS-LRR type, of which an increasing number is sequenced. These genes and their analogs (RGAs) are often organized in clusters. Clusters tend to be rather homogenous, viz. containing genes that show high sequence similarity with each other. From many of these clusters the map position is known. In this study we present and test a novel method to quickly identify to which cluster a new resistance gene belongs and to produce markers that can be used for introgression breeding. We used NBS profiling to identify markers in bulked DNA samples prepared from resistant and susceptible genotypes of small segregating populations. Markers co-segregating with resistance can be tested on individual plants and directly used for breeding. To identify the resistance gene cluster a gene belongs to, the fragments were sequenced and the sequences analyzed using bioinformatics tools. Putative map positions arising from this analysis were validated using markers mapped in the segregating population. The versatility of the approach is demonstrated with a number of populations derived from wild Solanum species segregating for P. infestans resistance. Newly identified P. infestans resistance genes originating from S. verrucosum, S. schenckii, and S. capsicibaccatum could be mapped to potato chromosomes 6, 4, and 11, respectively.

  18. 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.

  19. Role of Ectopic Gene Conversion in the Evolution of a Candida krusei Pleiotropic Drug Resistance Transporter Family

    PubMed Central

    Lamping, Erwin; Zhu, Jing-yi; Niimi, Masakazu; Cannon, Richard David

    2017-01-01

    Gene duplications enable the evolution of novel gene function, but strong positive selection is required to preserve advantageous mutations in a population. This is because frequent ectopic gene conversions (EGCs) between highly similar, tandem-duplicated, sequences, can rapidly remove fate-determining mutations by replacing them with the neighboring parent gene sequences. Unfortunately, the high sequence similarities between tandem-duplicated genes severely hamper empirical studies of this important evolutionary process, because deciphering their correct sequences is challenging. In this study, we employed the eukaryotic model organism Saccharomyces cerevisiae to clone and functionally characterize all 30 alleles of an important pair of tandem-duplicated multidrug efflux pump genes, ABC1 and ABC11, from seven strains of the diploid pathogenic yeast Candida krusei. Discovery and functional characterization of their closest ancestor, C. krusei ABC12, helped elucidate the evolutionary history of the entire gene family. Our data support the proposal that the pleiotropic drug resistance (PDR) transporters Abc1p and Abc11p have evolved by concerted evolution for ∼134 MY. While >90% of their sequences remained identical, very strong purifying selection protected six short DNA patches encoding just 18 core amino acid (aa) differences in particular trans membrane span (TMS) regions causing two distinct efflux pump functions. A proline-kink change at the bottom of Abc11p TMS3 was possibly fate determining. Our data also enabled the first empirical estimates for key parameters of eukaryotic gene evolution, they provided rare examples of intron loss, and PDR transporter phylogeny confirmed that C. krusei belongs to a novel, yet unnamed, third major Saccharomycotina lineage. PMID:28159755

  20. Chromosomal integration of recombinant alpha-amylase and glucoamylase genes in saccharomyces cerevisiae for starch conversion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recombinant constructs of barley '-amylase and Lentinula edodes glucoamylase genes were integrated into the chromosomes of Saccharomyces cerevisiae. The insertion was confirmed by PCR amplification of the gene sequence in the chromosomes. The expression was analyzed by SDS-PAGE of the enzymes puri...

  1. Locations of human and mouse genes encoding the RFX1 and RFX2 transcription factor proteins.

    PubMed

    Doyle, J; Hoffman, S; Ucla, C; Reith, W; Mach, B; Stubbs, L

    1996-07-01

    RFX transcription factors constitute a highly conserved family of site-specific DNA binding proteins involved in the expression of a variety of cellular and viral genes, including major histocompatibility complex class II genes and genes in human hepatitis B virus. Five members of the RFX gene family have been isolated from human and mouse, and all share a highly characteristic DNA binding domain that is distinct from other known DNA binding motifs. The human RFX1 and RFX2 genes have been assigned by in situ hybridization to chromosome 19p13.1 and 19p13.3, respectively. In this paper, we present data that localize RFX1 and RFX2 precisely within the detailed physical map of human chromosome 19 and genetic data that assign Rfx1 and Rfx2 to homologous regions of mouse chromosomes 8 and 17, respectively. These data define the established relationships between these homologous mouse and human regions in further detail and provide new tools for linking cloned genes to phenotypes in both species.

  2. Gene conversion events and variable degree of homogenization of rDNA loci in cultivars of Brassica napus

    PubMed Central

    Sochorová, Jana; Coriton, Olivier; Kuderová, Alena; Lunerová, Jana; Chèvre, Anne-Marie; Kovařík, Aleš

    2017-01-01

    Background and aims Brassica napus (AACC, 2n = 38, oilseed rape) is a relatively recent allotetraploid species derived from the putative progenitor diploid species Brassica rapa (AA, 2n = 20) and Brassica oleracea (CC, 2n = 18). To determine the influence of intensive breeding conditions on the evolution of its genome, we analysed structure and copy number of rDNA in 21 cultivars of B. napus, representative of genetic diversity. Methods We used next-generation sequencing genomic approaches, Southern blot hybridization, expression analysis and fluorescence in situ hybridization (FISH). Subgenome-specific sequences derived from rDNA intergenic spacers (IGS) were used as probes for identification of loci composition on chromosomes. Key Results Most B. napus cultivars (18/21, 86 %) had more A-genome than C-genome rDNA copies. Three cultivars analysed by FISH (‘Darmor’, ‘Yudal’ and ‘Asparagus kale’) harboured the same number (12 per diploid set) of loci. In B. napus ‘Darmor’, the A-genome-specific rDNA probe hybridized to all 12 rDNA loci (eight on the A-genome and four on the C-genome) while the C-genome-specific probe showed weak signals on the C-genome loci only. Deep sequencing revealed high homogeneity of arrays suggesting that the C-genome genes were largely overwritten by the A-genome variants in B. napus ‘Darmor’. In contrast, B. napus ‘Yudal’ showed a lack of gene conversion evidenced by additive inheritance of progenitor rDNA variants and highly localized hybridization signals of subgenome-specific probes on chromosomes. Brassica napus ‘Asparagus kale’ showed an intermediate pattern to ‘Darmor’ and ‘Yudal’. At the expression level, most cultivars (95 %) exhibited stable A-genome nucleolar dominance while one cultivar (‘Norin 9’) showed co-dominance. Conclusions The B. napus cultivars differ in the degree and direction of rDNA homogenization. The prevalent direction of gene conversion (towards the A-genome) correlates

  3. Endometriosis Located Proximal to or Remote From the Uterus Differentially Affects Uterine Gene Expression.

    PubMed

    Naqvi, Hanyia; Mamillapalli, Ramanaiah; Krikun, Graciela; Taylor, Hugh S

    2016-02-01

    The mechanisms that lead to the altered uterine gene expression in women with endometriosis are poorly understood. Are these changes in gene expression mediated by proximity to endometriotic lesions or is endometriosis a systemic disease where the effect is independent of proximity to the uterus? To answer this question, we created endometriosis in a murine model either in the peritoneal cavity (proximal) or at a subcutaneous remote site (distal). The expression of several genes that are involved in endometrial receptivity (homeobox A10 [Hoxa10], homeobox A11 [Hoxa11], insulin-like growth factor binding protein 1 [Igfbp1], Kruppel-like factor 9 [Klf9], and progesterone receptor [Pgr]) was measured in the eutopic endometrium of mice transplanted with either proximal or distal endometriosis lesions. Decreased expression of Hoxa10, Igfbp1, Klf9, and total Pgr genes was observed in the eutopic endometrium of mice with peritoneal endometriosis. In the mice with distal lesions, overall expression of these genes was not as severely affected, however, Igfbp1 expression was similarly decreased and the effect on Pgr was more pronounced. Endometriosis does have a systemic effect that varies with distance to the end organ. However, even remote disease selectively and profoundly alters the expression of genes such as Pgr. This is the first controlled experiment demonstrating that endometriosis is not simply a local peritoneal disease. Selective alteration of genes critical for endometrial receptivity and endometriosis propagation may be systemic. Similarly, systemic effects of endometriosis on other organs may also be responsible for the widespread manifestations of the disease.

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

    PubMed Central

    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. PMID:26584902

  5. The Wnt-target gene Dlk-1 is regulated by the Prmt5-associated factor Copr5 during adipogenic conversion

    PubMed Central

    Paul, Conception; Sardet, Claude; Fabbrizio, Eric

    2015-01-01

    ABSTRACT Protein arginine methyl transferase 5 (Prmt5) regulates various differentiation processes, including adipogenesis. Here, we investigated adipogenic conversion in cells and mice in which Copr5, a Prmt5- and histone-binding protein, was genetically invalidated. Compared to control littermates, the retroperitoneal white adipose tissue (WAT) of Copr5 KO mice was slightly but significantly reduced between 8 and 16 week/old and contained fewer and larger adipocytes. Moreover, the adipogenic conversion of Copr5 KO embryoid bodies (EB) and of primary embryo fibroblasts (Mefs) was markedly delayed. Differential transcriptomic analysis identified Copr5 as a negative regulator of the Dlk-1 gene, a Wnt target gene involved in the control of adipocyte progenitors cell fate. Dlk-1 expression was upregulated in Copr5 KO Mefs and the Vascular Stromal Fraction (VSF) of Copr5 KO WAT. Chromatin immunoprecipitation (ChIP) show that the ablation of Copr5 has impaired both the recruitment of Prmt5 and β-catenin at the Dlk-1 promoter. Overall, our data suggest that Copr5 is involved in the transcriptional control exerted by the Wnt pathway on early steps of adipogenesis. PMID:25681392

  6. 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.

  7. 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.

  8. Homology Requirements and Competition between Gene Conversion and Break-Induced Replication during Double-Strand Break Repair.

    PubMed

    Mehta, Anuja; Beach, Annette; Haber, James E

    2017-02-02

    Saccharomyces cerevisiae mating-type switching is initiated by a double-strand break (DSB) at MATa, leaving one cut end perfectly homologous to the HMLα donor, while the second end must be processed to remove a non-homologous tail before completing repair by gene conversion (GC). When homology at the matched end is ≤150 bp, efficient repair depends on the recombination enhancer, which tethers HMLα near the DSB. Thus, homology shorter than an apparent minimum efficient processing segment can be rescued by tethering the donor near the break. When homology at the second end is ≤150 bp, second-end capture becomes inefficient and repair shifts from GC to break-induced replication (BIR). But when pol32 or pif1 mutants block BIR, GC increases 3-fold, indicating that the steps blocked by these mutations are reversible. With short second-end homology, absence of the RecQ helicase Sgs1 promotes gene conversion, whereas deletion of the FANCM-related Mph1 helicase promotes BIR.

  9. Sequence analysis of 21 genes located in the Kartagener syndrome linkage region on chromosome 15q.

    PubMed

    Geremek, Maciej; Schoenmaker, Frederieke; Zietkiewicz, Ewa; Pogorzelski, Andrzej; Diehl, Scott; Wijmenga, Cisca; Witt, Michal

    2008-06-01

    Primary ciliary dyskinesia (PCD) is a rare genetic disorder, which shows extensive genetic heterogeneity and is mostly inherited in an autosomal recessive fashion. There are four genes with a proven pathogenetic role in PCD. DNAH5 and DNAI1 are involved in 28 and 10% of PCD cases, respectively, while two other genes, DNAH11 and TXNDC3, have been identified as causal in one PCD family each. We have previously identified a 3.5 cM (2.82 Mb) region on chromosome 15q linked to Kartagener syndrome (KS), a subtype of PCD characterized by the randomization of body organ positioning. We have now refined the KS candidate region to a 1.8 Mb segment containing 18 known genes. The coding regions of these genes and three neighboring genes were subjected to sequence analysis in seven KS probands, and we were able to identify 60 single nucleotide sequence variants, 35 of which resided in mRNA coding sequences. However, none of the variations alone could explain the occurrence of the disease in these patients.

  10. 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.

  11. 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.

  12. CHROMOSOMAL LOCATION AND GENE PAUCITY IN THE MALE SPECIFIC REGION ON PAPAYA Y CHROMOSOME

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sex chromosomes in flowering plants evolved recently and many of them remain homomorphic, including those in papaya. We investigated the chromosomal location of papaya’s small male specific region of the hermaphrodite Y (Yh) chromosome (MSY) and its genomic features. We conducted chromosome fluoresc...

  13. A family of MHC class I-like genes located in the vicinity of the mouse leukocyte receptor complex

    PubMed Central

    Kasahara, Masanori; Watanabe, Yutaka; Sumasu, Motoko; Nagata, Taeko

    2002-01-01

    Some members of the major histocompatibility complex (MHC) class I gene family are encoded outside the MHC. Here we describe a family of mouse class I-like genes mapping to the vicinity of the leukocyte receptor complex (LRC) on chromosome 7. This family, which we call Mill (MHC class I-like located near the LRC), has two members designated Mill1 and Mill2. Both genes are predicted to encode membrane glycoproteins with domain organization essentially similar to that of MHC class I heavy chains. The following features of Mill are noteworthy. (i) The deduced MILL proteins lack most of the residues known to be involved in the docking of peptides in classical MHC class I molecules. (ii) Among the known members of the class I gene family, MILL1 and MILL2 are related most closely to MICA/MICB encoded in the human MHC. (iii) Unlike all other known members of the class I gene family, Mill1 and Mill2 have an exon between those coding for the signal peptide and the α1 domain. (iv) Mill1 has a more restricted expression profile than Mill2. (v) The gene orthologous to Mill1 or Mill2 apparently is absent in the human. (vi) Mill1 and Mill2 show a limited degree of polymorphism in laboratory mice. The observation that the Mill family is related most closely to the MIC family, together with its apparent absence in the human, suggests its involvement in innate immunity. PMID:12370446

  14. FCER1B, a candidate gene for atopy, is located in 11q13 between CD20 and TCN1

    SciTech Connect

    Szepetowski, P.; Gaudray, P. )

    1994-01-15

    It is now well established that syntenic regions of the genome such as the pericentromeric region of mouse chromosome 19 and band q12 of human chromosome 11 are conserved in mice and men. One study has linked genetically familial forms of allergic asthma and rhinitis (atopy) to this human chromosome region. The murine gene encoding the [beta]-chain of the high-affinity receptor for IgE (Fce1b) has been mapped to chromosome 19. It is conceivable that this gene could be involved in allergic responses. The authors have thus hypothesized that the human homolog of this gene should be situated in chromosome band 11q13 and could be a good candidate for the atopy gene itself. While work was in progress, the human homolog of Fce1b, which had been cloned and sequenced by Kuester et al., was localized genetically in 11q13, and a dinucleotide (CA) repeat located nearby was strongly linked to familial atopy. However, the precise mapping of this gene and the actual distances separating it from neighboring sequences have not been determined. The authors describe the precise mapping of this gene using fluorescence in situ hybridization and pulsed-field electrophoresis. 11 refs., 1 fig.

  15. Combination of microdissection and microarray analysis to identify gene expression changes between differentially located tumour cells in breast cancer.

    PubMed

    Zhu, Gang; Reynolds, Louise; Crnogorac-Jurcevic, Tatjana; Gillett, Cheryl E; Dublin, Edwin A; Marshall, John F; Barnes, Diana; D'Arrigo, Corrado; Van Trappen, Philippe O; Lemoine, Nicholas R; Hart, Ian R

    2003-06-12

    Comparison of gene expression changes between cancer cells at the periphery and in the centre of breast cancers was performed using a combination of microdissection and microarray analysis. Cancer cells from the two areas were pooled separately from five patients with ductal carcinoma in situ and separately from five patients with frankly invasive cancer. Limited total RNA, 100-200 ng, from this microdissected tissue required use of the Atlas SMART trade mark Probe Amplification Kit to synthesize and amplify cDNA and make (33)P-labelled probes. Probes were then hybridized to Atlas Human Cancer 1.2 Arrays containing 1176 known genes. Triplicate analysis revealed that 22 genes changed their expression levels in the periphery relative to the central region: 15 upregulated and seven downregulated (arbitrary threshold of 1.5-fold or greater). Differences in RNA levels were confirmed by quantitative real-time PCR for two of the genes and by changes in protein levels, detected by immunohistochemistry, for a couple of representative gene products. Thus, changes in gene expression associated with variation in microanatomical location of neoplastic cells can be detected within even small developing tumour masses.

  16. 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.

  17. Gene conversion and deletion frequencies during double-strand break repair in human cells are controlled by the distance between direct repeats.

    PubMed

    Schildkraut, Ezra; Miller, Cheryl A; Nickoloff, Jac A

    2005-01-01

    Homologous recombination (HR) repairs DNA double-strand breaks and maintains genome stability. HR between linked, direct repeats can occur by gene conversion without an associated crossover that maintains the gross repeat structure. Alternatively, direct repeat HR can occur by gene conversion with a crossover, or by single-strand annealing (SSA), both of which delete one repeat and the sequences between the repeats. Prior studies of different repeat structures in yeast and mammalian cells revealed disparate conversion:deletion ratios. Here, we show that a key factor controlling this ratio is the distance between the repeats, with conversion frequency increasing linearly with the distances from 850 to 3800 bp. Deletions are thought to arise primarily by SSA, which involves extensive end-processing to reveal complementary single-strands in each repeat. The results can be explained by a model in which strand-invasion leading to gene conversion competes more effectively with SSA as more extensive end-processing is required for SSA. We hypothesized that a transcription unit between repeats would inhibit end-processing and SSA, thereby increasing the fraction of conversions. However, conversion frequencies were identical for direct repeats separated by 3800 bp of transcriptionally silent or active DNA, indicating that end-processing and SSA are not affected by transcription.

  18. 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

  19. Chromosome location, DNA markers and rust resistance of the sunflower gene R5

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sunflower rust, incited by the fungus Puccinia helianthi Schwein., has not been a serious problem for many decades because of successful deployment of effective genes in commercial sunflower hybrids in North America. In the 1980s and early 1990s, however, a shift in virulence of the rust race popula...

  20. Mapping platypus SOX genes; autosomal location of SOX9 excludes it from sex determining role.

    PubMed

    Wallis, M C; Delbridge, M L; Pask, A J; Alsop, A E; Grutzner, F; O'Brien, P C M; Rens, W; Ferguson-Smith, M A; Graves, J A M

    2007-01-01

    In the absence of an SRY orthologue the platypus sex determining gene is unknown, so genes in the human testis determining pathway are of particular interest as candidates. SOX9 is an attractive choice because SOX9 deletions cause male-to-female sex reversal in humans and mice, and SOX9 duplications cause female-to-male sex reversal. We have localized platypus SOX9, as well as the related SOX10, to platypus chromosomes 15 and 10, respectively, the first assignments to these platypus chromosomes, and the first comparative mapping markers from human chromosomes 17 and 22. The autosomal localization of platypus SOX9 in this study contradicts the hypothesis that SOX9 acts as the sex determining switch in platypus.

  1. 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/.

  2. The human cytochrome b561 gene (CYB561) is located at 17q11-qter

    SciTech Connect

    McBride, O.W.; Yi, H.F.; Srivastava, M.

    1994-06-01

    Cytochrome b561 is a major transmembrane protein that is specific to catacholamine and neuropeptide secretory vesicles of the adrenal medulla, pituitary gland, and other neuroendocrine tissues. This 30-kDa cytochrome is present in both the small synaptic vesicles and the large dense core vesicles (chromaffin granules) of the tissues. In this paper, we report that the human gene encoding cytochrome b561 (CYB561; GenBank Accession No. U06715) is localized to 17q11-qter.

  3. Sizes, locations, and directions of transcription of two genes on a cloned maize chloroplast DNA sequence

    PubMed Central

    Link, Gerhard; Bogorad, Lawrence

    1980-01-01

    mRNA for the large subunit (LS) of ribulose-1,5-bisphosphate carboxylase [3-phospho-D-glycerate carboxylase (dimerizing), EC 4.1.1.39] of Zea mays is complementary to an uninterrupted 1600-base-pair-long chloroplast DNA sequence that has been mapped precisely within the 4350-base-pair-long chloroplast DNA fragment Bam 9 to which it had been traced earlier [Bedbrook, J. R., Coen, D. M., Beaton, A. R., Bogorad, L. & Rich, A. (1979) J. Biol. Chem. 254, 905-910]. An additional 1400-base-pair-long uninterrupted region that is colinear with a chloroplast RNA has been detected on Bam 9. The transcript from this region is part of a 2200-nucleotide-long RNA. The remainder of the DNA sequence for the 2200-base-pair RNA maps outside Bam 9. The 1600-base-pair LS gene and the gene for the 2200-nucleotide transcript are close to one another. They are separated by an untranscribed intercistronic “gap” about 330 base pairs long. These two closely packed genes are inverted on the chromosome—i.e., their 3′ termini are at opposite ends of the untranscribed gap and they map on opposite strands. Images PMID:16592800

  4. A transcriptional repressor of the ERF family confers drought tolerance to rice and regulates genes preferentially located on chromosome 11.

    PubMed

    Joo, Joungsu; Choi, Hae Jong; Lee, Youn Hab; Kim, Yeon-Ki; Song, Sang Ik

    2013-07-01

    Plant-specific ethylene response factors (ERFs) play important roles in abiotic and biotic stress responses in plants. Using a transgenic approach, we identified two rice ERF genes, OsERF4a and OsERF10a, which conferred drought stress tolerance. In particular, OsERF4a contains a conserved ERF-associated amphiphilic repression (EAR) motif in its C-terminal region that has been shown to function as a transcriptional repression domain. Expression profiling of transgenic rice plants over-expressing OsERF4a using either a constitutively active or an ABA-inducible promoter identified 45 down-regulated and 79 up-regulated genes in common. The increased stress tolerance by over-expression of the EAR domain-containing protein OsERF4a could result from suppression of a repressor of the defense response. Expression of the putative silent information regulator 2 (Sir2) repressor protein was repressed, and expression of several stress-response genes were induced by OsERF4a over-expression. The Sir2 and 7 out of 9 genes that were down-regulated by OsERF4a over-expression were induced by high salinity and drought treatments in non-transgenic control plants. Genes that were down- and up-regulated by OsERF4a over-expression were highly biased toward chromosome 11. Rice chromosome 11 has several large clusters of disease-resistance and defense-response genes. Taken together, our results suggest that OsERF4a is a positive regulator of shoot growth and water-stress tolerance in rice during early growth stages. We propose that OsERF4a could work by suppressing a repressor of the defense responses and/or by controlling the expression of a large number of genes located on chromosome 11.

  5. 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.

  6. Annotation of Differentially Expressed Genes in the Somatic Embryogenesis of Musa and Their Location in the Banana Genome

    PubMed Central

    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. PMID:24027442

  7. 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

  8. 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.

  9. Location of 45S Ribosomal Genes in Mitotic and Meiotic Chromosomes of Buthid Scorpions.

    PubMed

    Mattos, Viviane Fagundes; Carvalho, Leonardo Sousa; Cella, Doralice Maria; Schneider, Marielle Cristina

    2014-09-01

    Buthid scorpions exhibit a high variability in diploid number within genera and even within species. Cytogenetically, Buthidae differs from other families of Scorpiones based on its low diploid numbers, holocentric chromosomes, and complex chromosomal chains, which form during meiosis. In this study, we analyzed the distribution of the 45S ribosomal DNA (rDNA) genes in the mitotic and meiotic chromosomes of seven buthid species belonging to the genera Rhopalurus and Tityus with the ultimate goal of elucidating the chromosome organization in these scorpions. The chromosome number ranged from 2n=6 to 2n=28. Despite the high variance in diploid number, all species examined carried their 45S rDNA sites in the terminal region of exactly two chromosomes. Analyses of meiotic cells revealed 45S rDNA clusters in the chromosomal chains of Rhopalurus agamemnon, Tityus bahiensis, Tityus confluens, and Tityus martinpaechi, or in bivalent-like configuration in Rhopalurus rochai, Tityus bahiensis, Tityus confluens, Tityus fasciolatus, and Tityus paraguayensis. In the species examined, the 45S rDNA sites colocalized with constitutive heterochromatin regions. In light of the high chromosome variability and maintenance of number and terminal position of 45S rDNA sites in buthids, the heterochromatin may act to conserve the integrity of the ribosomal genes.

  10. Conversion of a gene-specific repressor to a regional silencer

    PubMed Central

    Rine, Laura N. Rusché and Jasper

    2001-01-01

    In Saccharomyces cerevisiae, gene silencing at the HMR and HML loci is normally dependent on Sir2p, Sir3p, and Sir4p, which are structural components of silenced chromatin. Sir2p is a NAD+-dependent histone deacetylase required for silencing. Silencing can be restored in cells lacking Sir proteins by a dominant mutation in SUM1, which normally acts as a mitotic repressor of meiotic genes. This study found that mutant Sum1-1p, but not wild-type Sum1p, associated directly with HM loci. The origin recognition complex (ORC) was required for Sum1-1p-mediated silencing, and mutations in ORC genes reduced association of Sum1-1p with the HM loci. Sum1-1p-mediated silencing also depended on HST1, a paralog of SIR2. Both Sum1-1p and wild-type Sum1p interacted with Hst1p in coimmunoprecipitation experiments. Therefore, the SUM1-1 mutation did not change the affinity of Sum1p for Hst1p, but rather relocalized Sum1p to the HM loci. Sum1-1–Hst1p action led to hypoacetylation of the nucleosomes at HM loci. Thus, Sum1-1p and Hst1p could substitute for Sir proteins to achieve silencing through formation of a compositionally distinct type of heterochromatin. PMID:11316790

  11. 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.

  12. Vertical datum conversion process for the inland and coastal gage network located in the New England, Mid-Atlantic, and South Atlantic-Gulf hydrologic regions

    USGS Publications Warehouse

    Rydlund, Jr., Paul H.; Noll, Michael L.

    2017-03-07

    Datum conversions from the National Geodetic Vertical Datum of 1929 to the North American Vertical Datum of 1988 among inland and coastal gages throughout the hydrologic regions of New England, the Mid-Atlantic, and the South Atlantic-Gulf have implications among river and storm surge forecasting, general commerce, and water-control operations. The process of data conversions may involve the application of a recovered National Geodetic Vertical Datum of 1929–North American Vertical Datum of 1988 offset, a simplistic datum transformation using VDatum or VERTCON software, or a survey, depending on a gaging network datum evaluation, anticipated uncertainties for data use among the cooperative water community, and methods used to derive the conversion. Datum transformations from National Geodetic Vertical Datum of 1929 to North American Vertical Datum of 1988 using VERTCON purport errors of ± 0.13 foot at the 95 percent confidence level among modeled points, claiming more consistency along the east coast. Survey methods involving differential and trigonometric leveling, along with observations using Global Navigation Satellite System technology, afford a variety of approaches to establish or perpetuate a datum during a survey. Uncertainties among leveling approaches are generally < 0.1 foot, and and Global Navigation Satellite System approaches may be categorized with uncertainties of ≤0.1 foot for a Level I quality category and ≥0.1 foot for Level II or III quality categories (defined by the U.S. Geological Survey) by observation and review of experienced practice. The conversion process is initiated with an evaluation of the inland and coastal gage network datum, beginning with altitude datum components and the history of those components queried through the U.S. Geological Survey Groundwater Site Inventory database. Subsequent edits to the Groundwater Site Inventory database may be required and a consensus reached among the U.S. Geological Survey Water

  13. 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

  14. A gene for nonspecific X-linked mental retardation (MRX41) is located in the distal segment of Xq28

    SciTech Connect

    Hamel, B.C.J.; Kremer, H.; Helm, B. van den

    1996-07-12

    We report on a family in which non-syndromal mild to moderate mental retardation segregates as an X-linked trait (MRX41). Two point linkage analysis demonstrated linkage between the disorder and marker DXS3 in Xq21.33 with a lod score of 2.56 at {theta} = 0.0 and marker DXS1108 in Xq28 with a lod score of 3.82 at {theta} = 0.0. Multipoint linkage analysis showed that the odds for a location of the gene in Xq28 vs. Xq21.33 are 100:1. This is the fourth family with non-specific X-linked mental retardation with Xq28-qter as the most likely gene localization. 16 refs., 2 figs., 1 tab.

  15. The nitrate reductase-encoding gene of Volvox carteri: map location, sequence and induction kinetics.

    PubMed

    Gruber, H; Goetinck, S D; Kirk, D L; Schmitt, R

    1992-10-12

    The nitrate reductase (NR) structural gene (nitA) of Volvox carteri has been cloned and characterized. There is a single copy of this gene in the genome, and RFLP (restriction-fragment length polymorphism) analysis assigns it to the previously defined nitA/chlR locus on linkage group IX, 20-30 cM from the two beta-tubulin-encoding loci. Determination of the 5871-nt sequence of the coding region of genomic clones, and comparisons to a cDNA sequence, revealed ten introns and eleven exons that encode a 864-aa polypeptide. Detailed comparisons with higher-plant and fungal NRs indicate that, whereas the aa sequence is strongly conserved within functional domains for the flavin adenine dinucleotide-, heme- and molybdenum-pterin cofactor-binding sites, substantial differences in the aa sequence occur in the N-terminal end and the two inter-domain regions. Two potential transcription start points 439 and 452 nt upstream from the start codon and a polyadenylation signal 355 nt downstream from the stop codon have been identified by primer-extension analysis and cDNA sequencing, respectively. Accumulation of the nitA transcript is both induced by nitrate and repressed by ammonium and urea: after the organism is transferred from ammonium to nitrate as the nitrogen source, a 3.6-kb NR transcript is readily detectable on Northern blots by 10 min, reaches maximum abundance by 30 min, and then rapidly declines to an intermediate level that is subsequently maintained. Substantial induction by nitrate is observed at the end of the dark portion of the daily light/dark cycle, but the inductive response peaks in the first hour of the light period.(ABSTRACT TRUNCATED AT 250 WORDS)

  16. 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

  17. 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

  18. Phylogenetic diversity of archaea and the archaeal ammonia monooxygenase gene in uranium mining-impacted locations in Bulgaria.

    PubMed

    Radeva, Galina; Kenarova, Anelia; Bachvarova, Velina; Flemming, Katrin; Popov, Ivan; Vassilev, Dimitar; 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.

  19. [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.

  20. Reporter system for the detection of in vivo gene conversion: changing colors from blue to green using GFP variants.

    PubMed

    Sommer, Jeffrey R; Alderson, Jon; Laible, Goetz; Petters, Robert M

    2006-06-01

    We have devised a system for the study of in vivo gene correction based on the detection of color variants of the green fluorescent protein (GFP) from the jellyfish Aequorea victoria. The intensity and spectra of the fluorescence emitted by the blue (BFP) and red-shifted (EGFP) variants of GFP differ from each other. We modified one nucleotide from an EGFP expression vector that we predicted would yield a blue variant (TAC-CAC, Tyr(66)-His(66)). Cells that were either transiently or stably transfected with the reporter system were used to test the functionality and feasibility of the detection of in vivo gene correction. A thio-protected single-stranded oligonucleotide designed to convert the genotype of the blue variant to that of the EGFP variant by the correction of a single base pair was delivered to the reporter cells using a variety of methodologies and strategies.Conversion events were easily observed using fluorescent microscopy because of the enhanced emission intensity and different spectra of the EGFP variant.

  1. Evolutionary dynamics of triosephosphate isomerase gene intron location pattern in Metazoa: A new perspective on intron evolution in animals.

    PubMed

    Chen, Bing; Shao, Jingru; Zhuang, Huifu; Wen, Jianfan

    2017-02-20

    Intron evolution, including its dynamics in the evolutionary transitions and diversification of eukaryotes, remains elusive. Inadequate taxon sampling due to data shortage, unclear phylogenetic framework, and inappropriate outgroup application might be among the causes. Besides, the integrity of all the introns within a gene was often neglected previously. Taking advantage of the ancient conserved triosephosphate isomerase gene (tim), the relatively robust phylogeny of Metazoa, and choanoflagellates as outgroup, the evolutionary dynamics of tim intron location pattern (ILP) in Metazoa was investigated. From 133 representative species of ten phyla, 30 types of ILPs were identified. A most common one, which harbors the maximum six intron positions, is deduced to be the common ancestral tim ILP of Metazoa, which almost had formed in their protozoan ancestor and was surprisingly retained and passed down till to each ancestors of metazoan phyla. In the subsequent animal diversification, it underwent different evolutionary trajectories: within Deuterostomia, it was almost completely retained only with changes in a few species with relatively recently fast-evolving histories, while within the rapidly radiating Protostomia, besides few but remarkable retention, it usually displayed extensive intron losses and a few gains. Therefore, a common ancestral exon-intron arrangement pattern of an animal gene is definitely discovered; besides the 'intron-rich view' of early animal genes being confirmed, the novel insight that high exon-intron re-arrangements of genes seem to be associated with the relatively recently rapid evolution of lineages/species/genomes but have no correlation with the ancient major evolutionary transitions in animal evolution, is revealed.

  2. Allelic variation of polyphenol oxidase (PPO) genes located on chromosomes 2A and 2D and development of functional markers for the PPO genes in common wheat.

    PubMed

    He, X Y; He, Z H; Zhang, L P; Sun, D J; Morris, C F; Fuerst, E P; Xia, X C

    2007-06-01

    Polyphenol oxidase (PPO) activity is highly related to the undesirable browning of wheat-based end products, especially Asian noodles. Characterization of PPO genes and the development of their functional markers are of great importance for marker-assisted selection in wheat breeding. In the present study, complete genomic DNA sequences of two PPO genes, one each located on chromosomes 2A and 2D and their allelic variants were characterized by means of in silico cloning and experimental validation. Sequences were aligned at both DNA and protein levels. Two haplotypes on chromosome 2D showed 95.2% sequence identity at the DNA level, indicating much more sequence diversity than those on chromosome 2A with 99.6% sequence identity. Both of the PPO genes on chromosomes 2A and 2D contain an open reading frame (ORF) of 1,731 bp, encoding a PPO precursor peptide of 577 amino acids with a predicted molecular mass of approximately 64 kD. Two complementary dominant STS markers, PPO16 and PPO29, were developed based on the PPO gene haplotypes located on chromosome 2D; they amplify a 713-bp fragment in cultivars with low PPO activity and a 490-bp fragment in those with high PPO activity, respectively. The two markers were mapped on chromosome 2DL using a doubled haploid population derived from the cross Zhongyou 9507/CA9632, and a set of nullisomic-tetrasomic lines and ditelosomic line 2DS of Chinese Spring. QTL analysis indicated that the PPO gene co-segregated with the two STS markers and was closely linked to SSR marker Xwmc41 on chromosome 2DL, explaining from 9.6 to 24.4% of the phenotypic variance for PPO activity across three environments. In order to simultaneously detect PPO loci on chromosomes 2A and 2D, a multiplexed marker combination PPO33/PPO16 was developed and yielded distinguishable DNA patterns in a number of cultivars. The STS marker PPO33 for the PPO gene on chromosome 2A was developed from the same gene sequences as PPO18 that we reported previously, and

  3. 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

  4. 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

  5. ATP binding and hydrolysis and autophosphorylation of CbbQ encoded by the gene located downstream of RubisCO genes.

    PubMed

    Hayashi, Nobuhiro R; Igarashi, Yasuo

    2002-02-08

    CbbQ is encoded by the gene located downstream of ribulose 1,5-bisphosphate carboxylase/oxygenase genes (cbbLS) in the thermophilic hydrogen-oxidizing bacterium, Hydrogenophilus thermoluteolus. The protein possesses two nucleotide-binding motifs in its amino acid sequence, and it posttranslationally activates RubisCO. We present ATP hydrolysis and binding of CbbQ. CbbQ releases P(i) from ATP only in the presence of Mg(2+). CbbQ interacts with an 2'(3')-O-(2,4,6-trinitrophenyl)adenosine 5'-triphosphate in the presence or absence of Mg(2+). The interaction with Mg(2+) and/or a nucleotide induces a conformational change in CbbQ. Autophosphorylation of CbbQ occurs only in the absence of Mg(2+).

  6. Recurrent mutation, gene conversion, or recombination at the human phenylalanine hydroxylase locus: evidence in French-Canadians and a catalog of mutations.

    PubMed Central

    John, S W; Rozen, R; Scriver, C R; Laframboise, R; Laberge, C

    1990-01-01

    The codon 408 mutation (CGG----TGG, Arg----Trp) in exon 12 of the phenylalanine hydroxylase (PAH) gene occurs on haplotype 1 in French-Canadians; elsewhere this mutation (R408W) occurs on haplotype 2. A CpG dinucleotide is involved. The finding is compatible with a recurrent mutation, gene conversion, or a single recombination between haplotypes 2 and 1. A tabulation of 20 known mutations at the PAH locus reveals three instances of putative recurrent mutation. PMID:1971147

  7. High efficiency myogenic conversion of human fibroblasts by adenoviral vector-mediated MyoD gene transfer. An alternative strategy for ex vivo gene therapy of primary myopathies.

    PubMed Central

    Lattanzi, L; Salvatori, G; Coletta, M; Sonnino, C; Cusella De Angelis, M G; Gioglio, L; Murry, C E; Kelly, R; Ferrari, G; Molinaro, M; Crescenzi, M; Mavilio, F; Cossu, G

    1998-01-01

    Ex vivo gene therapy of primary myopathies, based on autologous transplantation of genetically modified myogenic cells, is seriously limited by the number of primary myogenic cells that can be isolated, expanded, transduced, and reimplanted into the patient's muscles. We explored the possibility of using the MyoD gene to induce myogenic conversion of nonmuscle, primary cells in a quantitatively relevant fashion. Primary human and murine fibroblasts from skin, muscle, or bone marrow were infected by an E1-deleted adenoviral vector carrying a retroviral long terminal repeat-promoted MyoD cDNA. Expression of MyoD caused irreversible withdrawal from the cell cycle and myogenic differentiation in the majority (from 60 to 90%) of cultured fibroblasts, as defined by activation of muscle-specific genes, fusion into contractile myotubes, and appearance of ultrastructurally normal sarcomagenesis in culture. 24 h after adenoviral exposure, MyoD-converted cultures were injected into regenerating muscle of immunodeficient (severe combined immunodeficiency/beige) mice, where they gave rise to beta-galactosidase positive, centrally nucleated fibers expressing human myosin heavy chains. Fibers originating from converted fibroblasts were indistinguishable from those obtained by injection of control cultures of lacZ-transduced satellite cells. MyoD-converted murine fibroblasts participated to muscle regeneration also in immunocompetent, syngeneic mice. Although antibodies from these mice bound to adenoviral infected cells in vitro, no inflammatory infiltrate was present in the graft site throughout the 3-wk study period. These data support the feasibility of an alternative approach to gene therapy of primary myopathies, based on implantation of large numbers of genetically modified primary fibroblasts massively converted to myogenesis by adenoviral delivery of MyoD ex vivo. PMID:9593768

  8. 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

  9. A putatively phase variable gene (dca) required for natural competence in Neisseria gonorrhoeae but not Neisseria meningitidis is located within the division cell wall (dcw) gene cluster.

    PubMed

    Snyder, L A; Saunders, N J; Shafer, W M

    2001-02-01

    A cluster of 18 open reading frames (ORFs), 15 of which are homologous to genes involved in division and cell wall synthesis, has been identified in Neisseria gonorrhoeae and Neisseria meningitidis. The three additional ORFs, internal to the dcw cluster, are not homologous to dcw-related genes present in other bacterial species. Analysis of the N. meningitidis strain MC58 genome for foreign DNA suggests that these additional ORFs have not been acquired by recent horizontal exchange, indicating that they are a long-standing, integral part of the neisserial dcw gene cluster. Reverse transcription-PCR analysis of RNA extracted from N. gonorrhoeae strain FA19 confirmed that all three ORFs are transcribed in gonococci. One of these ORFs (dca, for division cluster competence associated), located between murE and murF, was studied in detail and found to be essential for competence in the gonococcal but not in the meningococcal strains tested. Computer analysis predicts that dca encodes an inner membrane protein similar to hypothetical proteins produced by other gram-negative bacteria. In some meningococcal strains dca is prematurely terminated following a homopolymeric tract of G's, the length of which differs between isolates of N. meningitidis, suggesting that dca is phase variable in this species. A deletion and insertional mutation was made in the dca gene of N. gonorrhoeae strain FA19 and N. meningitidis strain NMB. This mutation abrogated the ability of the gonococci to be transformed with chromosomal DNA. Thus, we conclude that the dca-encoded gene product is an essential competence factor for gonococci.

  10. Lack of neighborhood effects from a transcriptionally active phosphoglycerate kinase-neo cassette located between the murine beta-major and beta-minor globin genes.

    PubMed

    Kaufman, R M; Lu, Z H; Behl, R; Holt, J M; Ackers, G K; Ley, T J

    2001-07-01

    For the treatment of beta-globin gene defects, a homologous recombination-mediated gene correction approach would provide advantages over random integration-based gene therapy strategies. However, "neighborhood effects" from retained selectable marker genes in the targeted locus are among the key issues that must be taken into consideration for any attempt to use this strategy for gene correction. An Ala-to-Ile mutation was created in the beta6 position of the mouse beta-major globin gene (beta(6I)) as a step toward the development of a murine model system that could serve as a platform for therapeutic gene correction studies. The marked beta-major gene can be tracked at the level of DNA, RNA, and protein, allowing investigation of the impact of a retained phosphoglycerate kinase (PGK)-neo cassette located between the mutant beta-major and beta-minor globin genes on expression of these 2 neighboring genes. Although the PGK-neo cassette was expressed at high levels in adult erythroid cells, the abundance of the beta(6I) mRNA was indistinguishable from that of the wild-type counterpart in bone marrow cells. Similarly, the output from the beta-minor globin gene was also normal. Therefore, in this specific location, the retained, transcriptionally active PGK-neo cassette does not disrupt the regulated expression of the adult beta-globin genes. (Blood. 2001;98:65-73)

  11. 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

  12. Molecular mapping re-locates the Stb2 gene for resistance to Septoria tritici blotch derived from cultivar Veranopolis on wheat chromosome 1BS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Septoria tritici blotch (STB) is one of the most destructive foliar diseases in many of the wheat (Triticum aestivum L.) growing regions of the world. Gene Stb2, derived from cv. ‘Veranopolis’, provides effective resistance against STB. Attempts to refine the map location of this resistance gene cou...

  13. Molecular cloning and expression analysis of a novel gene DGCR8 located in the DiGeorge syndrome chromosomal region.

    PubMed

    Shiohama, Aiko; Sasaki, Takashi; Noda, Setsuko; Minoshima, Shinsei; Shimizu, Nobuyoshi

    2003-04-25

    We have identified and cloned a novel gene (DGCR8) from the human chromosome 22q11.2. This gene is located in the DiGeorge syndrome chromosomal region (DGCR). It consists of 14 exons spanning over 35kb and produces transcripts with ORF of 2322bp, encoding a protein of 773 amino acids. We also isolated a mouse ortholog Dgcr8 and found it has 95.3% identity with human DGCR8 at the amino acid sequence level. Northern blot analysis of human and mouse tissues from adult and fetus showed rather ubiquitous expression. However, the in situ hybridization of mouse embryos revealed that mouse Dgcr8 transcripts are localized in neuroepithelium of primary brain, limb bud, vessels, thymus, and around the palate during the developmental stages of embryos. The expression profile of Dgcr8 in developing mouse embryos is consistent with the clinical phenotypes including congenital heart defects and palate clefts associated with DiGeorge syndrome (DGS)/conotruncal anomaly face syndrome (CAFS)/velocardiofacial syndrome (VCFS), which are caused by monoallelic microdeletion of chromosome 22q11.2.

  14. The HLA-B*83:01 allele is generated by a gene conversion event including whole of exon 2 and partial introns 1 and 2 between B*44 and B*56 alleles.

    PubMed

    Cervera, I; Herraiz, M A; Vidart, J A; Peñaloza, J; Martinez-Laso, J

    2011-02-01

    Several studies have indicated the gene conversion as the most important mechanism about the MHC polymorphism generation when intron sequences are studied. The data obtained confirm that the B*83:01 allele is generated by gene conversion event including exon 2 and partial intron 1 and 2 between B*44 and B*56 alleles.

  15. A Gene Cluster Encoding Steps in Conversion of Naphthalene to Gentisate in Pseudomonas sp. Strain U2

    PubMed Central

    Fuenmayor, Sergio L.; Wild, Mark; Boyes, Alastair L.; Williams, Peter A.

    1998-01-01

    Pseudomonas sp. strain U2 was isolated from oil-contaminated soil in Venezuela by selective enrichment on naphthalene as the sole carbon source. The genes for naphthalene dioxygenase were cloned from the plasmid DNA of strain U2 on an 8.3-kb BamHI fragment. The genes for the naphthalene dioxygenase genes nagAa (for ferredoxin reductase), nagAb (for ferredoxin), and nagAc and nagAd (for the large and small subunits of dioxygenase, respectively) were located by Southern hybridizations and by nucleotide sequencing. The genes for nagB (for naphthalene cis-dihydrodiol dehydrogenase) and nagF (for salicylaldehyde dehydrogenase) were inferred from subclones by their biochemical activities. Between nagAa and nagAb were two open reading frames, homologs of which have also been identified in similar locations in two nitrotoluene-using strains (J. V. Parales, A. Kumar, R. E. Parales, and D. T. Gibson, Gene 181:57–61, 1996; W.-C. Suen, B. Haigler, and J. C. Spain, J. Bacteriol. 178:4926–4934, 1996) and a naphthalene-using strain (G. J. Zylstra, E. Kim, and A. K. Goyal, Genet. Eng. 19:257–269, 1997). Recombinant Escherichia coli strains with plasmids carrying this region were able to convert salicylate to gentisate, which was identified by a combination of gas chromatography-mass spectrometry and nuclear magnetic resonance. The first open reading frame, designated nagG, encodes a protein with characteristics of a Rieske-type iron-sulfur center homologous to the large subunits of dihydroxylating dioxygenases, and the second open reading frame, designated nagH, encodes a protein with limited homology to the small subunits of the same dioxygenases. Cloned together in E. coli, nagG, nagH, and nagAb, were able to convert salicylate (2-hydroxybenzoate) into gentisate (2,5-dihydroxybenzoate) and therefore encode a salicylate 5-hydroxylase activity. Single-gene knockouts of nagG, nagH, and nagAb demonstrated their functional roles in the formation of gentisate. It is proposed

  16. 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.

  17. Characterization of divIVA and other genes located in the chromosomal region downstream of the dcw cluster in Streptococcus pneumoniae.

    PubMed

    Fadda, Daniela; Pischedda, Carla; Caldara, Fabrizio; Whalen, Michael B; Anderluzzi, Daniela; Domenici, Enrico; Massidda, Orietta

    2003-10-01

    We analyzed the chromosome region of Streptococcus pneumoniae located downstream of the division and cell wall (dcw) cluster that contains the homolog of the Bacillus subtilis cell division gene divIVA and some genes of unknown function. Inactivation of divIVA in S. pneumoniae resulted in severe growth inhibition and defects in cell shape, nucleoid segregation, and cell division. Inactivation of the ylm genes resulted in some morphological and/or division abnormalities, depending on the inactivated gene. Transcriptional analysis revealed a relationship between these genes and the ftsA and ftsZ cell division genes, also indicating that the connection between the dcw cluster and the divIVA region is more extensive than just chromosomal position and gene organization.

  18. HybridGO-Loc: mining hybrid features on gene ontology for predicting subcellular localization of multi-location proteins.

    PubMed

    Wan, Shibiao; Mak, Man-Wai; Kung, Sun-Yuan

    2014-01-01

    Protein subcellular localization prediction, as an essential step to elucidate the functions in vivo of proteins and identify drugs targets, has been extensively studied in previous decades. Instead of only determining subcellular localization of single-label proteins, recent studies have focused on predicting both single- and multi-location proteins. Computational methods based on Gene Ontology (GO) have been demonstrated to be superior to methods based on other features. However, existing GO-based methods focus on the occurrences of GO terms and disregard their relationships. This paper proposes a multi-label subcellular-localization predictor, namely HybridGO-Loc, that leverages not only the GO term occurrences but also the inter-term relationships. This is achieved by hybridizing the GO frequencies of occurrences and the semantic similarity between GO terms. Given a protein, a set of GO terms are retrieved by searching against the gene ontology database, using the accession numbers of homologous proteins obtained via BLAST search as the keys. The frequency of GO occurrences and semantic similarity (SS) between GO terms are used to formulate frequency vectors and semantic similarity vectors, respectively, which are subsequently hybridized to construct fusion vectors. An adaptive-decision based multi-label support vector machine (SVM) classifier is proposed to classify the fusion vectors. Experimental results based on recent benchmark datasets and a new dataset containing novel proteins show that the proposed hybrid-feature predictor significantly outperforms predictors based on individual GO features as well as other state-of-the-art predictors. For readers' convenience, the HybridGO-Loc server, which is for predicting virus or plant proteins, is available online at http://bioinfo.eie.polyu.edu.hk/HybridGoServer/.

  19. HybridGO-Loc: Mining Hybrid Features on Gene Ontology for Predicting Subcellular Localization of Multi-Location Proteins

    PubMed Central

    Wan, Shibiao; Mak, Man-Wai; Kung, Sun-Yuan

    2014-01-01

    Protein subcellular localization prediction, as an essential step to elucidate the functions in vivo of proteins and identify drugs targets, has been extensively studied in previous decades. Instead of only determining subcellular localization of single-label proteins, recent studies have focused on predicting both single- and multi-location proteins. Computational methods based on Gene Ontology (GO) have been demonstrated to be superior to methods based on other features. However, existing GO-based methods focus on the occurrences of GO terms and disregard their relationships. This paper proposes a multi-label subcellular-localization predictor, namely HybridGO-Loc, that leverages not only the GO term occurrences but also the inter-term relationships. This is achieved by hybridizing the GO frequencies of occurrences and the semantic similarity between GO terms. Given a protein, a set of GO terms are retrieved by searching against the gene ontology database, using the accession numbers of homologous proteins obtained via BLAST search as the keys. The frequency of GO occurrences and semantic similarity (SS) between GO terms are used to formulate frequency vectors and semantic similarity vectors, respectively, which are subsequently hybridized to construct fusion vectors. An adaptive-decision based multi-label support vector machine (SVM) classifier is proposed to classify the fusion vectors. Experimental results based on recent benchmark datasets and a new dataset containing novel proteins show that the proposed hybrid-feature predictor significantly outperforms predictors based on individual GO features as well as other state-of-the-art predictors. For readers' convenience, the HybridGO-Loc server, which is for predicting virus or plant proteins, is available online at http://bioinfo.eie.polyu.edu.hk/HybridGoServer/. PMID:24647341

  20. 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.

  1. 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.

  2. A common transcriptional activator is located in the coding region of two replication-dependent mouse histone genes.

    PubMed Central

    Hurt, M M; Bowman, T L; Marzluff, W F

    1991-01-01

    There is a region in the mouse histone H3 gene protein-encoding sequence required for high expression. The 110-nucleotide coding region activating sequence (CRAS) from codons 58 to 93 of the H3.2 gene restored expression when placed 520 nucleotides 5' of the start of transcription in the correct orientation. Since identical mRNA molecules are produced by transcription of the original deletion gene and the deletion gene with the CRAS at -520, effects of the deletions on mRNA stability or other posttranscriptional events are completely ruled out. Inversion of the CRAS sequence in its proper position in the H3 gene resulted in only a threefold increase in expression, and placing the CRAS sequence 5' of the deleted gene in the wrong orientation had no effect on expression. In-frame deletions in the coding region of an H2a.2 gene led to identification of a 105-nucleotide sequence in the coding region between amino acids 50 and 85 necessary for high expression of the gene. Additionally, insertion of the H3 CRAS into the deleted region of the H2a.2 gene restored expression of the H2a gene. Thus, the CRAS element has an orientation-dependent, position-independent effect. Gel mobility shift competition studies indicate that the same proteins interact with both the H3 and H2a CRAS elements, suggesting that a common factor is involved in expression of histone genes. Images PMID:2038312

  3. 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.

  4. 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

  5. A clustered set of three Sp-family genes is ancestral in the Metazoa: evidence from sequence analysis, protein domain structure, developmental expression patterns and chromosomal location

    PubMed Central

    2010-01-01

    Background The Sp-family of transcription factors are evolutionarily conserved zinc finger proteins present in many animal species. The orthology of the Sp genes in different animals is unclear and their evolutionary history is therefore controversially discussed. This is especially the case for the Sp gene buttonhead (btd) which plays a key role in head development in Drosophila melanogaster, and has been proposed to have originated by a recent gene duplication. The purpose of the presented study was to trace orthologs of btd in other insects and reconstruct the evolutionary history of the Sp genes within the metazoa. Results We isolated Sp genes from representatives of a holometabolous insect (Tribolium castaneum), a hemimetabolous insect (Oncopeltus fasciatus), primitively wingless hexapods (Folsomia candida and Thermobia domestica), and an amphipod crustacean (Parhyale hawaienis). We supplemented this data set with data from fully sequenced animal genomes. We performed phylogenetic sequence analysis with the result that all Sp factors fall into three monophyletic clades. These clades are also supported by protein domain structure, gene expression, and chromosomal location. We show that clear orthologs of the D. melanogaster btd gene are present even in the basal insects, and that the Sp5-related genes in the genome sequence of several deuterostomes and the basal metazoans Trichoplax adhaerens and Nematostella vectensis are also orthologs of btd. Conclusions All available data provide strong evidence for an ancestral cluster of three Sp-family genes as well as synteny of this Sp cluster and the Hox cluster. The ancestral Sp gene cluster already contained a Sp5/btd ortholog, which strongly suggests that btd is not the result of a recent gene duplication, but directly traces back to an ancestral gene already present in the metazoan ancestor. PMID:20353601

  6. Three human glutamate dehydrogenase genes (GLUD1, GLUDP2, and GLUDP3) are located on chromosome 10q, but are not closely physically linked

    SciTech Connect

    Deloukas, P.; Loon, A.P.G.M. van ); Dauwerse, J.G.; Ommen, G.J.B. van ); Moschonas, N.K. )

    1993-09-01

    Yeast artificial chromosomes (YACs) of 340 and 370 kb that contain the functional human glutamate dehydrogenase gene (GLUD1) and the pseudogene GLUDP2, respectively, were isolated. These genes were not physically linked to each other nor to any other sequences homologous to the exons of GLUD1. No additional GLUD sequences were found within at least 70 kb of the 5[prime] and 175 kb of the 3[prime] end of GLUD1 or 150 kb of either end of GLUDP2. By in situ hybridization, GLUD1 was located at 10q23.3, GLUDP2 at 10q11.2, and another pseudogene of the GLUD gene family, GLUDP3, at 10q22.1. DNA fragments of these three genes showed cross-hybridization to the loci assigned to the other two genes, but not to any other chromosomal locus. Thus, these three genes are located at distinct positions on chromosome 10q. 19 refs., 3 figs., 1 tab.

  7. 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.

  8. Lr41, Lr39, and a leaf rust resistance gene from Aegilops cylindrica may be allelic and are located on wheat chromosome 2DS.

    PubMed

    Singh, Sukhwinder; Franks, C D; Huang, L; Brown-Guedira, G L; Marshall, D S; Gill, B S; Fritz, A

    2004-02-01

    The leaf rust resistance gene Lr41 in wheat germplasm KS90WGRC10 and a resistance gene in wheat breeding line WX93D246-R-1 were transferred to Triticum aestivum from Aegilops tauschii and Ae. cylindrica, respectively. The leaf rust resistance gene in WX93D246-R-1 was located on wheat chromosome 2D by monosomic analysis. Molecular marker analysis of F(2) plants from non-critical crosses determined that this gene is 11.2 cM distal to marker Xgwm210 on the short arm of 2D. No susceptible plants were detected in a population of 300 F(2) plants from a cross between WX93D246-R-1 and TA 4186 ( Lr39), suggesting that the gene in WX93D246-R-1 is the same as, or closely linked to, Lr39. In addition, no susceptible plants were detected in a population of 180 F(2) plants from the cross between KS90WGRC10 and WX93D246-R-1. The resistance gene in KS90WGRC10, Lr41, was previously reported to be located on wheat chromosome 1D. In this study, no genetic association was found between Lr41 and 51 markers located on chromosome 1D. A population of 110 F(3 )lines from a cross between KS90WGRC10 and TAM 107 was evaluated with polymorphic SSR markers from chromosome 2D and marker Xgdm35 was found to be 1.9 cM proximal to Lr41. When evaluated with diverse isolates of Puccinia triticina, similar reactions were observed on WX93D246-R-1, KS90WGRC10, and TA 4186. The results of mapping, allelism, and race specificity test indicate that these germplasms likely have the same gene for resistance to leaf rust.

  9. 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.

  10. 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.

  11. The Nine Genes of the Nocardia lactamdurans Cephamycin Cluster Are Transcribed into Large mRNAs from Three Promoters, Two of Them Located in a Bidirectional Promoter Region

    PubMed Central

    Enguita, Francisco J.; Coque, Juan Jose R.; Liras, Paloma; Martin, Juan F.

    1998-01-01

    The nine biosynthesis genes of the Nocardia lactamdurans cephamycin cluster are expressed as three different mRNAs initiating at promoters latp, cefDp, and pcbABp, as shown by low-resolution S1 nuclease protection assays and Northern blotting analysis. Bidirectional expression occurred from divergent promoters (latp and cefDp) located in a 629-bp intergenic region that contains three heptameric direct repeats similar to those recognized by members of the SARP (Streptomyces antibiotic regulatory proteins) family. The lat gene is transcribed in a single monocistronic transcript initiating at latp. A second unusually long polycistronic mRNA (more than 16 kb) corresponding to six biosynthesis genes (pcbAB, pcbC, cmcI, cmcJ, cefF, and cmcH) started at pcbABp. A third polycistronic mRNA corresponding to the cefD and cefE genes started at cefDp. PMID:9765587

  12. 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.

  13. Homologous and homeologous intermolecular gene conversion are not differentially affected by mutations in the DNA damage or the mismatch repair genes RAD1, RAD50, RAD51, RAD52, RAD54, PMS1 and MSH2

    SciTech Connect

    Porter, G.; Westmoreland, J.; Priebe, S.

    1996-06-01

    Mismatch repair (MMR) genes or genes involved in both DNA damage repair and homologous recombination might affect homeologous vs. homologous recombination differentially. Spontaneous mitotic gene conversion between a chromosome and a homologous or homeologous donor sequence (14% diverged) on a single copy plasmid was examined in wild-type Saccharomyces cerevisiae strains and in MMR or DNA damage repair mutants. Homologous recombination in rad51, rad52 and rad54 mutants was considerably reduced, while there was little effect of rad1, rad50, pms1 and msh2 null mutations. DNA divergence resulted in no differential effect on recombination rates in the wild type or the mutants; there was only a five- to 10-fold reduction in homeologous relative to homologous recombination regardless of background. Since DNA divergence is known to affect recombination in some systems, we propose that differences in the role of MMR depends on the mode of recombination and/or the level of divergence. Based on analysis of the recombination breakpoints, there is a minimum of three homologous bases required at a recombination junction. A comparison of Rad{sup +} vs. rad52 strains revealed that while all conversion tracts are continuous, elimination of RAD52 leads to the appearance of a novel class of very short conversion tracts. 67 refs., 5 figs., 4 tabs.

  14. Homologous and Homeologous Intermolecular Gene Conversion Are Not Differentially Affected by Mutations in the DNA Damage or the Mismatch Repair Genes Rad1, Rad50, Rad51, Rad52, Rad54, Pms1 and Msh2

    PubMed Central

    Porter, G.; Westmoreland, J.; Priebe, S.; Resnick, M. A.

    1996-01-01

    Mismatch repair (MMR) genes or genes involved in both DNA damage repair and homologous recombination might affect homeologous vs. homologous recombination differentially. Spontaneous mitotic gene conversion between a chromosome and a homologous or homeologous donor sequence (14% diverged) on a single copy plasmid was examined in wild-type Saccharomyces cerevisiae strains and in MMR or DNA damage repair mutants. Homologous recombination in rad51, rad52 and rad54 mutants was considerably reduced, while there was little effect of rad1, rad50, pms1 and msh2 null mutations. DNA divergence resulted in no differential effect on recombination rates in the wild type or the mutants; there was only a five- to 10-fold reduction in homeologous relative to homologous recombination regardless of background. Since DNA divergence is known to affect recombination in some systems, we propose that differences in the role of MMR depends on the mode of recombination and/or the level of divergence. Based on analysis of the recombination breakpoints, there is a minimum of three homologous bases required at a recombination junction. A comparison of Rad(+) vs. rad52 strains revealed that while all conversion tracts are continuous, elimination of RAD52 leads to the appearance of a novel class of very short conversion tracts. PMID:8725224

  15. Chromosomal location and comparative genomics analysis of powdery mildew resistance gene Pm51 in a putative wheat-Thinopyrum ponticum introgression line.

    PubMed

    Zhan, Haixian; Li, Guangrong; Zhang, Xiaojun; Li, Xin; Guo, Huijuan; Gong, Wenping; Jia, Juqing; Qiao, Linyi; Ren, Yongkang; Yang, Zujun; Chang, Zhijian

    2014-01-01

    Powdery mildew (PM) is a very destructive disease of wheat (Triticum aestivum L.). Wheat-Thinopyrum ponticum introgression line CH7086 was shown to possess powdery mildew resistance possibly originating from Th. ponticum. Genomic in situ hybridization and molecular characterization of the alien introgression failed to identify alien chromatin. To study the genetics of resistance, CH7086 was crossed with susceptible genotypes. Segregation in F2 populations and F2:3 lines tested with Chinese Bgt race E09 under controlled conditions indicated that CH7086 carries a single dominant gene for powdery mildew resistance. Fourteen SSR and EST-PCR markers linked with the locus were identified. The genetic distances between the locus and the two flanking markers were 1.5 and 3.2 cM, respectively. Based on the locations of the markers by nullisomic-tetrasomic and deletion lines of 'Chinese Spring', the resistance gene was located in deletion bin 2BL-0.89-1.00. Conserved orthologous marker analysis indicated that the genomic region flanking the resistance gene has a high level of collinearity to that of rice chromosome 4 and Brachypodium chromosome 5. Both resistance specificities and tests of allelism suggested the resistance gene in CH7086 was different from previously reported powdery mildew resistance genes on 2BL, and the gene was provisionally designated PmCH86. Molecular analysis of PmCH86 compared with other genes for resistance to Bgt in the 2BL-0.89-1.00 region suggested that PmCH86 may be a new PM resistance gene, and it was therefore designated as Pm51. The closely linked flanking markers could be useful in exploiting this putative wheat-Thinopyrum translocation line for rapid transfer of Pm51 to wheat breeding programs.

  16. 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

  17. qnrE1, a Member of a New Family of Plasmid-located Quinolone Resistance Genes Originated from the Chromosome of Enterobacter spp.

    PubMed

    Albornoz, Ezequiel; Tijet, Nathalie; De Belder, Denise; Gomez, Sonia; Martino, Florencia; Corso, Alejandra; Melano, Roberto G; Petroni, Alejandro

    2017-02-13

    qnrE1, found in a clinical Klebsiella pneumoniae, resulted undetectable by PCR assays used for the six qnr families. qnrE1 was located on a conjugative plasmid (ca. 185 kb) and differed from qnrB alleles by 25%. Phylogenetic reconstructions of qnr genes and proteins, and analysis of the qnrE1 surroundings showed that this gene belongs to a new qnr family and was likely mobilized by ISEcp1 from the chromosome of Enterobacter spp. to plasmids of K. pneumoniae.

  18. The Ah receptor nuclear translocator gene (ARNT) is located on q21 of human chromosome 1 and on mouse chromosome 3 near Cf-3

    SciTech Connect

    Johnson, B.; Brooks, B.A.; Heinzmann, C. ); Mohandas, T. )

    1993-09-01

    The authors have mapped the Ah (aryl hydrocarbon) receptor nuclear translocator (ARNT) gene to a conserved linkage group located on mouse chromosome 3 and human chromosome 1. EcoRi-digested DNA from a panel of 17 human x mouse somatic cell hybrids was probed with a cDNA fragment of the human ARNT gene. Six of the 17 independent mouse x human hybrids were positive for human bands. Human chromosome 1 showed complete cosegregation with the gene, whereas discordant segregation was observed for all other human chromosomes. The human gene was localized to 1q21 by using DNA from mouse x human hybrid clones that retain translocations involving human chromosome 1, by segregation analysis in nine informative CEPH families, and by in situ hybridization. The mouse homologue was mapped to mouse chromosome 3 using a panel of 16 hamster x mouse somatic cell hybrids. Six of 16 mouse x hamster hybrids were positive for mouse bands, showing complete concordance with mouse chromosome 3. The mouse Arnt gene was regionally mapped on chromosome 3, using linkage analysis in an interspecific backcross. The results indicate that the mouse gene resides about 40 cM from the centromere and about 10 cM proximal to Cf-3, the gene for tissue factor. 41 refs., 4 figs., 5 tabs.

  19. 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

  20. 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.

  1. 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.

  2. Gene conversion in the CYP11B2 gene encoding P450c11AS is associated with, but does not cause, the syndrome of corticosterone methyloxidase II deficiency

    SciTech Connect

    Fardella, C.E.; Hum, D.W.; Rodriguez, H. |

    1996-01-01

    Cytochrome P450c11AS (aldosterone synthase) has 11{beta}hydroxylase, 18-hydroxylase, and 18-oxidase activities and is expressed solely in the adrenal zona glomerulosa. Corticosterone methyloxidase II (CMOII) deficiency denotes a rare disorder of adrenal steroidogenesis in which only the 18-oxidase activity of P450c11AS is disrupted, while the 11{beta}-hydroxylase and 18-hydroxylase activities persist. Such patients have elevated serum concentrations of corticosterone and 18-hydroxycorticosterone and very low or unmeasurable concentrations of aldosterone, often resulting in a clinical salt-losing crisis in infancy. We have sought mutations causing CMOII deficiency in outbred populations. In three of four unrelated P450c11AS alleles from two unrelated patients with CMOII deficiency, we found a gene conversion event in which exons 3 and 4 of the CYP11B2 gene encoding P450c11AS were changed to the sequence of the nearby CYP11B1 gene, which encodes the related enzyme P450c11{beta}. This conversion resulted in a mutant P450c11AS protein carrying three changes. We built seven vectors expressing P450c11AS carrying each mutation singly, each of the three possible pairs of mutations, and the triple mutation as found in the proband. The activities in steroidogenic MA-10 and JEG-3 cells were 10- to 20-fold higher. In these systems all of the mutants retained normal 18-oxidase activity, indicating that the detected gene conversion event is associated with but does not cause CMOII deficiency. None of the four CPY11B2 alleles in these two patients bore other identifiable mutations. These patients might have mutations in the promoters or other noncoding regions, or mutations in genes other than CYP11B2 may cause the syndrome of CMOII deficiency. 37 refs., 2 figs., 2 tabs.

  3. Gene cloning of an efficiency oleate hydratase from Stenotrophomonas nitritireducens for polyunsaturated fatty acids and its application in the conversion of plant oils to 10-hydroxy fatty acids.

    PubMed

    Kang, Woo-Ri; Seo, Min-Ju; Shin, Kyung-Chul; Park, Jin-Byung; Oh, Deok-Kun

    2017-01-01

    Hydroxy fatty acids are used as precursors of lactones and dicarboxylic acids, as starting materials of polymers, and as additives in coatings and paintings. Stenotrophomonas nitritireducens efficiently converts cis-9 polyunsaturated fatty acids (PUFAs) to 10-hydroxy fatty acids. However, gene encoding enzyme involved in this conversion has not been identified to date. We purified a putative fatty acid double-bond hydratase from S. nitritireducens by ultrafiltration and HiPrep DEAE FF and Resource Q ion exchange chromatographies. Peptide sequences of the purified enzyme were obtained by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) analysis. Sequence of the partial gene encoding this putative fatty acid double-bond hydratase was determined by degenerate polymerase chain reaction (PCR) based on the peptide sequences. The remaining gene sequence was identified by rapid amplification of cDNA ends using cDNA of S. nitritireducens as a template, and the full-length gene was cloned subsequently. The expressed enzyme was identified as an oleate hydratase by determining its kinetic parameters toward unsaturated fatty acids. S. nitritireducens oleate hydratase showed higher activity toward PUFAs compared with other available oleate hydratases. This suggested that the enzyme could be used effectively to convert plant oils to 10-hydroxy fatty acids because these oils contained unsaturated fatty acids such as oleic acid (OA) and linoleic acid (LA) and PUFAs such as α-linolenic acid and/or γ-linolenic acid. The enzyme converted soybean oil and perilla seed oil hydrolyzates containing 10 mM total unsaturated fatty acids, including OA, LA, and ALA, to 8.87 and 8.70 mM total 10-hydroxy fatty acids, respectively, in 240 min. To our knowledge, this is the first study on the biotechnological conversion of PUFA-containing oils to hydroxy fatty acids. Biotechnol. Bioeng. 2017;114: 74-82. © 2016 Wiley Periodicals, Inc.

  4. Within- and between-individual sequence variation among ITS1 copies in the meadow grasshopper Chorthippus parallelus indicates frequent intrachromosomal gene conversion.

    PubMed

    Parkin, Emma J; Butlin, Roger K

    2004-08-01

    Sequencing multiple copies of the ITS1 region revealed the coexistence of two or more haplotypes within the genome of Chorthippus parallelus. Using a PCR-RFLP approach, the ITS1 numbers and frequencies of haplotypes present in each of 40 individuals were investigated, revealing a consistent lack of homogeneity. For each individual, the level of intra-individual variation was estimated from a sample of 20 ITS1 copies. The level of differentiation in haplotype frequency among individuals was then estimated by maximum likelihood using models based on the Dirichlet distribution. This confirmed the existence of significant levels of variation among individuals within each population studied. The most likely turnover mechanism that could generate this pattern of variation is gene conversion, operating at the intrachromosomal level. Furthermore, the discovery of linkage disequilibrium among the ITS1 haplotypes of C. parallelus suggests that intrachromosomal gene conversion occurs more frequently than interchromosomal recombination. Subspecies of C. parallelus showed significantly different haplotype distributions following about 0.5 Myr of divergence. With respect to the process of concerted evolution, we show that homogenization of repeats is slow relative to speciation, and the standing variation among individuals is sufficient for selection to operate.

  5. 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

  6. 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.

  7. The human c-ros gene (ROS) is located at chromosome region 6q16----6q22.

    PubMed

    Nagarajan, L; Louie, E; Tsujimoto, Y; Balduzzi, P C; Huebner, K; Croce, C M

    1986-09-01

    The human homolog, c-ros, of the transforming gene, v-ros, of the avian sarcoma virus, UR2, has been isolated from a human genomic library. A single-copy fragment from the human c-ros genomic clone has been used to map the human c-ros homolog (ROS) to human chromosome region 6q16----6q22 by somatic cell hybrid analysis and chromosomal in situ hybridization. Thus, the c-ros gene joins the c-myb oncogene, which is distal to the c-ros gene on the long arm of human chromosome 6, as a candidate for involvement in chromosome 6q deletions and rearrangements seen in various malignancies.

  8. 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

  9. Transcriptional regulation by activation and repression elements located at the 5'-noncoding region of the human alpha9 nicotinic receptor subunit gene.

    PubMed

    Valor, Luis M; Castillo, Mar; Ortiz, José A; Criado, Manuel

    2003-09-26

    The alpha9 subunit is a component of the neuronal nicotinic acetylcholine receptor gene superfamily that is expressed in very restricted locations. The promoter of the human gene has been analyzed in the human neuroblastoma SH-SY5Y, where alpha9 subunit expression was detected, and in C2C12 cells that do not express alpha9. A proximal promoter region (from -322 to +113) showed maximal transcriptional activity in SH-SY5Y cells, whereas its activity in C1C12 cells was much lower. Two elements unusually located at the 5'-noncoding region exhibited opposite roles. A negative element located between +15 and +48 appears to be cell-specific because it was effective in C2C12 but not in SH-SY5Y cells, where it was counterbalanced by the presence of the promoter region 5' to the initiation site. An activating element located between +66 and +79 and formed by two adjacent Sox boxes increased the activity of the alpha9 promoter about 4-fold and was even able to activate other promoters. This element interacts with Sox proteins, probably through a cooperative mechanism in which the two Sox boxes are necessary. We propose that the Sox complex provides an initial scaffold that facilitates the recruiting of the transcriptional machinery responsible for alpha9 subunit expression.

  10. 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.

  11. 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.

  12. 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...

  13. 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.

  14. Development of a Bioinformatics Framework for the Detection of Gene Conversion and the Analysis of Combinatorial Diversity in Immunoglobulin Heavy Chains in Four Cattle Breeds

    PubMed Central

    Czerny, Claus-Peter; König, Sven; Diesterbeck, Ulrike S.

    2016-01-01

    We have developed a new bioinformatics framework for the analysis of rearranged bovine heavy chain immunoglobulin (Ig) variable regions by combining and refining widely used alignment algorithms. This bioinformatics framework allowed us to investigate alignments of heavy chain framework regions (FRHs) and the separate alignments of FRHs and heavy chain complementarity determining regions (CDRHs) to determine their germline origin in the four cattle breeds Aubrac, German Black Pied, German Simmental, and Holstein Friesian. Now it is also possible to specifically analyze Ig heavy chains possessing exceptionally long CDR3Hs. In order to gain more insight into breed specific differences in Ig combinatorial diversity, somatic hypermutations and putative gene conversions of IgG, we compared the dominantly transcribed variable (IGHV), diversity (IGHD), and joining (IGHJ) segments and their recombination in the four cattle breeds. The analysis revealed the use of 15 different IGHV segments, 21 IGHD segments, and two IGHJ segments with significant different transcription levels within the breeds. Furthermore, there are preferred rearrangements within the three groups of CDR3H lengths. In the sequences of group 2 (CDR3H lengths (L) of 11–47 amino acid residues (aa)) a higher number of recombination was observed than in sequences of group 1 (L≤10 aa) and 3 (L≥48 aa). The combinatorial diversity of germline IGHV, IGHD, and IGHJ-segments revealed 162 rearrangements that were significantly different. The few preferably rearranged gene segments within group 3 CDR3H regions may indicate specialized antibodies because this length is unique in cattle. The most important finding of this study, which was enabled by using the bioinformatics framework, is the discovery of strong evidence for gene conversion as a rare event using pseudogenes fulfilling all definitions for this particular diversification mechanism. PMID:27828971

  15. The importance of location and orientation of male specific lethal complex binding sites of differing affinities on reporter gene dosage compensation in Drosophila.

    PubMed

    Schiemann, Anja H; Weake, Vikki M; Li, Fang; Laverty, Corey; Belikoff, Esther J; Scott, Maxwell J

    2010-11-26

    The male specific lethal (MSL) complex is required for X chromosome dosage compensation in Drosophila. The complex binds to most actively transcribed X-linked genes in males and upregulates expression. High resolution chromatin immunoprecipitation assays have identified over one hundred high affinity binding sites on the X chromosome. One of the first high affinity sites discovered is at cytological location 18D11. The MSL complex binds weakly to a single copy of a 510bp fragment from 18D11 but strongly to a tetramer of the fragment. Here we have investigated the effect of insertion of sites of differing affinities, either upstream or within the transcribed gene, on complex binding and transcription upregulation. Insertion of four copies of the 18D11 fragment upstream or at the 3' end of a reporter gene led to strong MSL complex binding and increased expression in males. In contrast, the MSL complex did not bind consistently to autosomal transgenes that contained a single copy of the 18D11 site upstream of the gene promoter. However, MSL complex binding was observed in all lines if the single 18D11 fragment was inserted into the 3' end of the reporter gene in either orientation. This is consistent with previous studies that showed gene transcription facilitates MSL complex binding. Surprisingly, transcription elevation in males was only observed if the 18D11 fragment was in the forward orientation and only in some lines. Our results suggest that MSL complex binding to weaker sites and transcription enhancement is influenced by gene transcription, binding site orientation and the local chromatin environment. In contrast, strong binding sites do not need to be transcribed to recruit sufficient complex to cause transcription elevation of nearby genes.

  16. 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.

  17. A molecular linkage map of tomato displaying chromosomal locations of resistance gene analogs based on a Lycopersicon esculentum x Lycopersicon hirsutum cross.

    PubMed

    Zhang, L P; Khan, A; Niño-Liu, D; Foolad, M R

    2002-02-01

    A molecular linkage map of tomato was constructed based on a BC1 population (N = 145) of a cross between Lycopersicon esculentum Mill. line NC84173 (maternal and recurrent parent) and Lycopersicon hirsutum Humb. and Bonpl. accession PI126445. NC84173 is an advanced breeding line that is resistant to several tomato diseases, not including early blight (EB) and late blight (LB). PI126445 is a self-incompatible accession that is resistant to many tomato diseases, including EB and LB. The map included 142 restriction fragment length polymorphism (RFLP) markers and 29 resistance gene analogs (RGAs). RGA loci were identified by PCR amplification of genomic DNA from the BC1 population, using ten pairs of degenerate oligonucleotide primers designed based on conserved leucine-rich repeat (LRR), nucleotide binding site (NBS), and serine (threonine) protein kinase (PtoKin) domains of known resistance genes (R genes). The PCR-amplified DNAs were separated by denaturing polyacrylamide gel electrophoresis (PAGE), which allowed separation of heterogeneous products and identification and mapping of individual RGA loci. The map spanned 1469 cM of the 12 tomato chromosomes with an average marker distance of 8.6 cM. The RGA loci were mapped to 9 of the 12 tomato chromosomes. Locations of some RGAs coincided with locations of several known tomato R genes or quantitative resistance loci (QRLs), including Cf-1, Cf-4, Cf-9, Cf-ECP2, rx-1, and Cm1.1 (chromosome 1); Tm-1 (chromosome 2); Asc (chrromosme 3); Pto, Fen, and Prf (chromosome 5); 01-1, Mi, Ty-1, Cm6.1, Cf-2, CF-5, Bw-5, and Bw-1 (chromosome 6); I-1, 1-3, and Ph-1 (chromosome 7); Tm-2a and Fr1 (chromosome 9); and Lv (chromosome 12). These co-localizations indicate that the RGA loci were either linked to or part of the known R genes. Furthermore, similar to that for many R gene families, several RGA loci were found in clusters, suggesting their potential evolutionary relationship with R genes. Comparisons of the present map with

  18. 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

  19. 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

  20. 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…

  1. Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle.

    PubMed

    de Almeida Santana, Miguel Henrique; Junior, Gerson Antônio Oliveira; Cesar, Aline Silva Mello; Freua, Mateus Castelani; da Costa Gomes, Rodrigo; da Luz E Silva, Saulo; Leme, Paulo Roberto; Fukumasu, Heidge; Carvalho, Minos Esperândio; Ventura, Ricardo Vieira; Coutinho, Luiz Lehmann; Kadarmideen, Haja N; Ferraz, José Bento Sterman

    2016-11-01

    The use of genome-wide association results combined with other genomic approaches may uncover genes and metabolic pathways related to complex traits. In this study, the phenotypic and genotypic data of 1475 Nellore (Bos indicus) cattle and 941,033 single nucleotide polymorphisms (SNPs) were used for genome-wide association study (GWAS) and copy number variations (CNVs) analysis in order to identify candidate genes and putative pathways involved with the feed conversion ratio (FCR). The GWAS was based on the Bayes B approach analyzing genomic windows with multiple regression models to estimate the proportion of genetic variance explained by each window. The CNVs were detected with PennCNV software using the log R ratio and B allele frequency data. CNV regions (CNVRs) were identified with CNVRuler and a linear regression was used to associate CNVRs and the FCR. Functional annotation of associated genomic regions was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) and the metabolic pathways were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG). We showed five genomic windows distributed over chromosomes 4, 6, 7, 8, and 24 that explain 12 % of the total genetic variance for FCR, and detected 12 CNVRs (chromosomes 1, 5, 7, 10, and 12) significantly associated [false discovery rate (FDR) < 0.05] with the FCR. Significant genomic regions (GWAS and CNV) harbor candidate genes involved in pathways related to energetic, lipid, and protein metabolism. The metabolic pathways found in this study are related to processes directly connected to feed efficiency in beef cattle. It was observed that, even though different genomic regions and genes were found between the two approaches (GWAS and CNV), the metabolic processes covered were related to each other. Therefore, a combination of the approaches complement each other and lead to a better understanding of the FCR.

  2. The murine homeobox genes Nkx2.3 and Nkx2.6 are located on chromosomes 19 and 14, respectively

    SciTech Connect

    Copeland, N.G.; Jenkins, N.A.; Harvey, R.P.

    1994-08-01

    The mouse chromosomal locations of two murine homeobox genes, Nkx2.3 and Nkx2.6, were determined by interspecific backcross analysis using progeny derived from matings of [(C57BL/6J x Mus spretus) F1 x C57BL/6J] mice. This interspecific backcross mapping panel has been typed for over 1400 loci that are well distributed among all the autosomes as well as the X chromosomes. The mapping data indicated that Nkx2.3 is located in the distal region of mouse chromosome 19. This distal region of mouse chromosome 19 shares homology with human chromosome 10q, suggesting that the human homologue of Nkx2.3 will map to this region of chromosome 10. The mapping data indicated that the Nkx2.6 gene is located in the middle region of chromosome 14. This region of mouse chromosome 14 shares homology with human chromosome 8p, suggesting that the human homologue of Nkx2.6 will map to this region of human chromosome 8.

  3. 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.

  4. An imprinted long noncoding RNA located between genes Meg8 and Meg9 in the cattle Dlk1-Dio3 domain.

    PubMed

    Zhang, Mingyue; Zhao, Yupeng; Wang, Guannan; Li, Dongjie; Chen, Weina; Zhang, Cui; Li, Shijie

    2017-02-01

    The Dlk1-Dio3 imprinted domain is located on the cattle chromosome 21 and contains three paternally expressed protein-coding genes and a number of maternally expressed short or long noncoding RNA genes. We have previously obtained two maternally expressed long noncoding RNA genes, Meg8 and Meg9, from the cattle. In this study, we identified a novel noncoding RNA located between Meg8 and Meg9 known as LINC24061 according to the GENCODE annotated bibliography. Two alternatively spliced transcripts (LINC24061-v1 and LINC24061-v2) were obtained using RT-PCR and RACE, and the expression pattern of LINC24061-v1 and LINC24061-v2 was shown to be tissue-specific. The LINC24061-v1 splice variant was expressed in only three types of tissues: heart, kidney and muscle; in contrast, LINC24061-v2 was expressed in all eight tissues examined, including heart, liver, spleen, lung, kidney, skeletal muscle, subcutaneous fat, and brain of adult cattle. The allele-specific expression of LINC24061 was identified based on a single nucleotide polymorphism (SNP) in exon 2 of LINC24061. The results showed that LINC24061 exhibited monoallelic expression in all the examined cattle tissues.

  5. 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.

  6. Identification of the cluster control region for the protocadherin-beta genes located beyond the protocadherin-gamma cluster.

    PubMed

    Yokota, Shinnichi; Hirayama, Teruyoshi; Hirano, Keizo; Kaneko, Ryosuke; Toyoda, Shunsuke; Kawamura, Yoshimi; Hirabayashi, Masumi; Hirabayashi, Takahiro; Yagi, Takeshi

    2011-09-09

    The clustered protocadherins (Pcdhs), Pcdh-α, -β, and -γ, are transmembrane proteins constituting a subgroup of the cadherin superfamily. Each Pcdh cluster is arranged in tandem on the same chromosome. Each of the three Pcdh clusters shows stochastic and combinatorial expression in individual neurons, thus generating a hugely diverse set of possible cell surface molecules. Therefore, the clustered Pcdhs are candidates for determining neuronal molecular diversity. Here, we showed that the targeted deletion of DNase I hypersensitive (HS) site HS5-1, previously identified as a Pcdh-α regulatory element in vitro, affects especially the expression of specific Pcdh-α isoforms in vivo. We also identified a Pcdh-β cluster control region (CCR) containing six HS sites (HS16, 17, 17', 18, 19, and 20) downstream of the Pcdh-γ cluster. This CCR comprehensively activates the expression of the Pcdh-β gene cluster in cis, and its deletion dramatically decreases their expression levels. Deleting the CCR nonuniformly down-regulates some Pcdh-γ isoforms and does not affect Pcdh-α expression. Thus, the CCR effect extends beyond the 320-kb region containing the Pcdh-γ cluster to activate the upstream Pcdh-β genes. Thus, we concluded that the CCR is a highly specific regulatory unit for Pcdh-β expression on the clustered Pcdh genomic locus. These findings suggest that each Pcdh cluster is controlled by distinct regulatory elements that activate their expression and that the stochastic gene regulation of the clustered Pcdhs is controlled by the complex chromatin architecture of the clustered Pcdh locus.

  7. Upregulation of Oxidative Stress Related Genes in a Chronic Kidney Disease Attributed to Specific Geographical Locations of Sri Lanka

    PubMed Central

    Sayanthooran, Saravanabavan; Gunerathne, Lishanthe; Abeysekera, Tilak D. J.; Sooriyapathirana, Suneth S.

    2016-01-01

    Objective. To infer the influence of internal and external oxidative stress in chronic kidney disease patients of unknown etiology (CKDu) in Sri Lanka, by analyzing expression of genes related directly or indirectly to oxidative stress: glutamate-cysteine ligase catalytic subunit (GCLC), glutathione S-transferase mu 1 (GSTM1), glucose-6-phosphate dehydrogenase (G6PD), fibroblast growth factor-23 (FGF23), and NLR family pyrin domain containing 3 (NLRP3). Methods. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was carried out for the selected populations: CKDu patients (n = 43), chronic kidney disease patients (CKD; n = 14), healthy individuals from a CKDu endemic area (GHI; n = 9), and nonendemic area (KHI; n = 16). Fold changes were quantified relative to KHI. Results. GCLC had greater than threefold upregulation in all three study groups, with a maximum of 7.27-fold upregulation in GHI (p = 0.000). GSTM1 was not expressed in 25.6% of CKDu and 42.9% of CKD patients, but CKDu patients expressing GSTM1 showed upregulation of 2.60-fold (p < 0.05). Upregulation of FGF23 and NLRP3 genes in CKD and CKDu was observed (p < 0.01), with greater fold changes in CKD. Conclusion. Results suggest higher influence of external sources of oxidative stress in CKDu, possibly owing to environmental conditions. PMID:27975059

  8. 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).

  9. 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

  10. Human homeo box-containing genes located at chromosome regions 2q31----2q37 and 12q12----12q13.

    PubMed Central

    Cannizzaro, L A; Croce, C M; Griffin, C A; Simeone, A; Boncinelli, E; Huebner, K

    1987-01-01

    Four human homeo box-containing cDNAs isolated from mRNA of an SV40-transformed human fibroblast cell line have been regionally localized on the human gene map. One cDNA clone, c10, was found to be nearly identical to the previously mapped Hox-2.1 gene at 17q21. A second cDNA clone, c1, which is 87% homologous to Hox-2.2 at the nucleotide level but is distinct from Hox-2.1 and Hox-2.2, also maps to this region of human chromosome 17 and is probably another member of the Hox-2 cluster of homeo box-containing genes. The third cDNA clone, c8, in which the homeo box is approximately 84% homologous to the mouse Hox-1.1 homeo box region on mouse chromosome 6, maps to chromosome region 12q12----12q13, a region that is involved in chromosome abnormalities in human seminomas and teratomas. The fourth cDNA clone, c13, whose homeo box is approximately 73% homologous to the Hox-2.2 homeo box sequence, is located at chromosome region 2q31----q37. The human homeo box-containing cluster of genes at chromosome region 17q21 is the human cognate of the mouse homeo box-containing gene cluster on mouse chromosome 11. Other mouse homeo box-containing genes of the Antennapedia class (class I) map to mouse chromosomes 6 (Hox-1, proximal to the IgK locus) and 15 (Hox-3). A mouse gene, En-1, with an engrailed-like homeo box (class II) and flanking region maps to mouse chromosome 1 (near the dominant hemimelia gene). Neither of the class I homeo box-containing genes--c8 and c13--maps to a region of obvious homology to chromosomal positions of the presently known mouse homeo box-containing genes. Images Fig. 2 Fig. 3 Fig. 5 PMID:2886047

  11. 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...

  12. 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.

  13. Location Privacy

    NASA Astrophysics Data System (ADS)

    Meng, Xiaofeng; Chen, Jidong

    With rapid development of sensor and wireless mobile devices, it is easy to access mobile users' location information anytime and anywhere. On one hand, LBS is becoming more and more valuable and important. On the other hand, location privacy issues raised by such applications have also gained more attention. However, due to the specificity of location information, traditional privacy-preserving techniques in data publishing cannot be used. In this chapter, we will introduce location privacy, and analyze the challenges of location privacy-preserving, and give a survey of existing work including the system architecture, location anonymity and query processing.

  14. Oncogenic properties of a novel gene JK-1 located in chromosome 5p and its overexpression in human esophageal squamous cell carcinoma.

    PubMed

    Tang, Wing K; Chui, Chung H; Fatima, Sarwat; Kok, Stanton H L; Pak, Kai C; Ou, Tian M; Hui, Kin S; Wong, Mei M; Wong, John; Law, Simon; Tsao, S W; Lam, King Y; Beh, Philip S L; Srivastava, Gopesh; Chan, Albert S C; Ho, Kwok P; Tang, Johnny C O

    2007-06-01

    Esophageal squamous cell carcinoma (ESCC) shows high frequency and mortality in Asian regions, including China. Previous analysis of genomic DNA of ESCC using comparative genomic hybridization indicated that amplification of the chromosome 5p regions is a common event in ESCC cell lines and patient cases of Hong Kong Chinese origin, and the results suggested that the genes located in the chromosome 5p regions may play crucial roles in the molecular pathogenesis of ESCC. Our previous studies on ESCC confirmed the tumorigenic and overexpression properties of a novel gene JS-1 located in chromosome 5p15.2 upstream to delta-catenin. In the present study, another novel gene JK-1 which is located at 5p15.1 downstream to delta-catenin was characterized for its roles in the pathogenesis of ESCC. Thirteen ESCC cell lines and 30 surgical specimens of esophageal tumors were studied for the overexpression of JK-1 using multiplex RT-PCR analysis. The transforming capacity of overexpression of JK-1 was also investigated by transfecting NIH 3T3 and HEK 293 cells with the expression vector cloned with JK-1, followed by the soft agar and foci formation assays. JK-1 was overexpressed in 9/13 (69%) of the ESCC cell lines and 9/30 (30%) of the ESCC patient cases. Both NIH 3T3 and HEK 293 cells acquired the properties of anchorage-dependent and -independent growth when JK-1 was overexpressed. Most significantly, subcutaneous sarcomas were formed in all (3/3) the athymic nude mice after NIH 3T3 cells overexpressing JK-1 were injected subcutaneously. Our results thus indicated that JK-1 is commonly overexpressed in ESCC and has a prominent capacity to transform normal cells. Our overall results thus provide the first evidence that the overexpression of JK-1 and its transforming capacity in normal cells may play a critical role in the molecular pathogenesis of ESCC.

  15. Impact of the location of CpG methylation within the GSTP1 gene on its specificity as a DNA marker for hepatocellular carcinoma.

    PubMed

    Jain, Surbhi; Chen, Sitong; Chang, Kung-Chao; Lin, Yih-Jyh; Hu, Chi-Tan; Boldbaatar, Batbold; Hamilton, James P; Lin, Selena Y; Chang, Ting-Tsung; Chen, Shun-Hua; Song, Wei; Meltzer, Stephen J; Block, Timothy M; Su, Ying-Hsiu

    2012-01-01

    Hypermethylation of the glutathione S-transferase π 1 (GSTP1) gene promoter region has been reported to be a potential biomarker to distinguish hepatocellular carcinoma (HCC) from other liver diseases. However, reports regarding how specific a marker it is have ranged from 100% to 0%. We hypothesized that, to a large extent, the variation of specificity depends on the location of the CpG sites analyzed. To test this hypothesis, we compared the methylation status of the GSTP1 promoter region of the DNA isolated from HCC, cirrhosis, hepatitis, and normal liver tissues by bisulfite-PCR sequencing. We found that the 5' region of the position -48 nt from the transcription start site of the GSTP1 gene is selectively methylated in HCC, whereas the 3' region is methylated in all liver tissues examined, including normal liver and the HCC tissue. Interestingly, when DNA derived from fetal liver and 11 nonhepatic normal tissue was also examined by bisulfite-PCR sequencing, we found that methylation of the 3' region of the promoter appeared to be liver-specific. A methylation-specific PCR assay targeting the 5' region of the promoter was developed and used to quantify the methylated GSTP1 gene in various diseased liver tissues including HCC. When we used an assay targeting the 3' region, we found that the methylation of the 5'-end of the GSTP1 promoter was significantly more specific than that of the 3'-end (97.1% vs. 60%, p<0.0001 by Fisher's exact test) for distinguishing HCC (n = 120) from hepatitis (n = 35) and cirrhosis (n = 35). Encouragingly, 33.8% of the AFP-negative HCC contained the methylated GSTP1 gene. This study clearly demonstrates the importance of the location of CpG site methylation for HCC specificity and how liver-specific DNA methylation should be considered when an epigenetic DNA marker is studied for detection of HCC.

  16. Identification of a TXREB pseudogene (TXREBP) located between the genes for p55 (MPP1) and G6PD on Xq28

    SciTech Connect

    Das, S.; Gitschier, J. )

    1994-05-01

    A fibroblast cDNA library was screened by hybridization to a yeast artificial chromosome containing genomic sequences from human Xq28. The majority of positive cDNA clones were found to correspond to the cDNA coding for TXREB, an HTLV-1 enhancer-binding protein. Sequence analysis of the Xq28 genomic DNA revealed a number of deleterious changes compared to the previously reported cDNA. In addition, both the genomic DNA and cDNA isolates were found to be lacking a 599-bp sequence, bracketed by GT and AG, in the 5[prime] untranslated region. These results suggest that the Xq28-linked gene is a processed pseudogene for TXREB and that the previously reported cDNA was only partially processed. Southern blot analysis on a hybrid mapping panel confirmed the presence of at least one autosomal gene for TXREB, and Northern blot hybridization with the 599-bp putative intron probe confirmed that the sequence is not part of the mature mRNA. Further analysis showed that the gene is expressed in a variety of human tissues and that the pseudogene is located between the genes for the proteins p55 and G5PD. 7 refs., 3 figs.

  17. 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

  18. The first gene-based map of Lupinus angustifolius L.-location of domestication genes and conserved synteny with Medicago truncatula.

    PubMed

    Nelson, Matthew N; Phan, Huyen T T; Ellwood, Simon R; Moolhuijzen, Paula M; Hane, James; Williams, Angela; O'Lone, Clare E; Fosu-Nyarko, John; Scobie, Marie; Cakir, Mehmet; Jones, Michael G K; Bellgard, Matthew; Ksiazkiewicz, Michał; Wolko, Bogdan; Barker, Susan J; Oliver, Richard P; Cowling, Wallace A

    2006-07-01

    We report the first gene-based linkage map of Lupinus angustifolius (narrow-leafed lupin) and its comparison to the partially sequenced genome of Medicago truncatula. The map comprises 382 loci in 20 major linkage groups, two triplets, three pairs and 11 unlinked loci and is 1,846 cM in length. The map was generated from the segregation of 163 RFLP markers, 135 gene-based PCR markers, 75 AFLP and 4 AFLP-derived SCAR markers in a mapping population of 93 recombinant inbred lines, derived from a cross between domesticated and wild-type parents. This enabled the mapping of five major genes controlling key domestication traits in L. angustifolius. Using marker sequence data, the L. angustifolius genetic map was compared to the partially completed M. truncatula genome sequence. We found evidence of conserved synteny in some regions of the genome despite the wide evolutionary distance between these legume species. We also found new evidence of widespread duplication within the L. angustifolius genome.

  19. Metric Conversion

    Atmospheric Science Data Center

    2013-03-12

    ... petabyte = one quadrillion bytes The Bureau International Poids et Measures (BIPM) brochure on the International System ... For accurate conversions, see the National Institute of Standards and Technology (NIST) Special Publications: NIST Guide to ...

  20. Conversion Disorder

    MedlinePlus

    ... Recent significant stress or emotional trauma Being female — women are much more likely to develop conversion disorder Having a mental health condition, such as mood or anxiety disorders, dissociative disorder or certain personality disorders Having ...

  1. Implication of nifA in regulation of genes located on a Rhizobium meliloti cryptic plasmid that affect nodulation efficiency.

    PubMed Central

    Sanjuan, J; Olivares, J

    1989-01-01

    We examined the contribution of a cryptic plasmid, pRmeGR4b, to the nodulation of Medicago sativa by strain GR4 of Rhizobium meliloti. A 905-base-pair PstI DNA fragment in pRmeGR4b was found to hybridize DNA of the R. meliloti fixA promoter region as a probe. Sequence analysis of the PstI fragment showed a 206-base-pair region displaying high homology with the DNA upstream of the RNA start points of the P1 and P2 symbiotic promoters. Putative nif promoter consensus sequences were conserved in this DNA segment. Expression of DNA downstream of the nif promoterlike sequence, monitored by beta-galactosidase activity of different lacZ fusions, was demonstrated to depend on a functional nifA gene, both in microaerobically free-living cells and in nodules. Individual transposon Tn3-HoHo1 insertions in this DNA region caused a reduced nodulation competitiveness. This new symbiotic region, occupying approximately 5 kilobases of pRmeGR4b DNA, was called nfe (nodule formation efficiency). Images PMID:2546913

  2. Locating overlapping dense subgraphs in gene (protein) association networks and predicting novel protein functional groups among these subgraphs

    NASA Astrophysics Data System (ADS)

    Palla, Gergely; Derenyi, Imre; Farkas, Illes J.; Vicsek, Tamas

    2006-03-01

    Most tasks in a cell are performed not by individual proteins, but by functional groups of proteins (either physically interacting with each other or associated in other ways). In gene (protein) association networks these groups show up as sets of densely connected nodes. In the yeast, Saccharomyces cerevisiae, known physically interacting groups of proteins (called protein complexes) strongly overlap: the total number of proteins contained by these complexes by far underestimates the sum of their sizes (2750 vs. 8932). Thus, most functional groups of proteins, both physically interacting and other, are likely to share many of their members with other groups. However, current algorithms searching for dense groups of nodes in networks usually exclude overlaps. With the aim to discover both novel functions of individual proteins and novel protein functional groups we combine in protein association networks (i) a search for overlapping dense subgraphs based on the Clique Percolation Method (CPM) (Palla, G., et.al. Nature 435, 814-818 (2005), http://angel.elte.hu/clustering), which explicitly allows for overlaps among the groups, and (ii) a verification and characterization of the identified groups of nodes (proteins) with the help of standard annotation databases listing known functions.

  3. Spatial language and converseness.

    PubMed

    Burigo, Michele; Coventry, Kenny R; Cangelosi, Angelo; Lynott, Dermot

    2016-12-01

    Typical spatial language sentences consist of describing the location of an object (the located object) in relation to another object (the reference object) as in "The book is above the vase". While it has been suggested that the properties of the located object (the book) are not translated into language because they are irrelevant when exchanging location information, it has been shown that the orientation of the located object affects the production and comprehension of spatial descriptions. In line with the claim that spatial language apprehension involves inferences about relations that hold between objects it has been suggested that during spatial language apprehension people use the orientation of the located object to evaluate whether the logical property of converseness (e.g., if "the book is above the vase" is true, then also "the vase is below the book" must be true) holds across the objects' spatial relation. In three experiments using sentence acceptability rating tasks we tested this hypothesis and demonstrated that when converseness is violated people's acceptability ratings of a scene's description are reduced indicating that people do take into account geometric properties of the located object and use it to infer logical spatial relations.

  4. The chicken beta 2-microglobulin gene is located on a non-major histocompatibility complex microchromosome: a small, G+C-rich gene with X and Y boxes in the promoter.

    PubMed Central

    Riegert, P; Andersen, R; Bumstead, N; Döhring, C; Dominguez-Steglich, M; Engberg, J; Salomonsen, J; Schmid, M; Schwager, J; Skjødt, K; Kaufman, J

    1996-01-01

    beta 2-Microglobulin is an essential subunit of major histocompatibility complex (Mhc) class I molecules, which present antigenic peptides to T lymphocytes. We sequenced a number of cDNAs and two genomic clones corresponding to chicken beta 2-microglobulin. The chicken beta 2-microglobulin gene has a similar genomic organization but smaller introns and higher G+C content than mammalian beta 2-microglobulin genes. The promoter region is particularly G+C-rich and contains, in addition to interferon regulatory elements, potential S/W, X, and Y boxes that were originally described for mammalian class II but not class I alpha or beta 2-microglobulin genes. There is a single chicken beta 2-microglobulin gene that has little polymorphism in the coding region. Restriction fragment length polymorphisms from Mhc homozygous lines, Mhc congenic lines, and backcross families, as well as in situ hybridization, show that the beta 2-microglobulin gene is located on a microchromosome different from the one that contains the chicken Mhc. We propose that the structural similarities between the beta 2-microglobulin and Mhc genes in the chicken are due to their presence on microchromosomes and suggest that these features and the microchromosomes appeared by deletion of DNA in the lineage leading to the birds. Images Fig. 4 Fig. 5 PMID:8577748

  5. Hydroxylamine assimilation by Rhodobacter capsulatus E1F1. requirement of the hcp gene (hybrid cluster protein) located in the nitrate assimilation nas gene region for hydroxylamine reduction.

    PubMed

    Cabello, Purificación; Pino, Carmen; Olmo-Mira, M Francisca; Castillo, Francisco; Roldán, M Dolores; Moreno-Vivián, Conrado

    2004-10-29

    Rhodobacter capsulatus E1F1 grows phototrophically with nitrate as nitrogen source. Using primers designed for conserved motifs in bacterial assimilatory nitrate reductases, a 450-bp DNA was amplified by PCR and used for the screening of a genomic library. A cosmid carrying an insert with four SalI fragments of 2.8, 4.1, 4.5, and 5.8 kb was isolated, and DNA sequencing revealed that it contains a nitrate assimilation (nas) gene region, including the hcp gene coding for a hybrid cluster protein (HCP). Expression of hcp is probably regulated by a nitrite-sensitive repressor encoded by the adjacent nsrR gene. A His(6)-HCP was overproduced in Escherichia coli and purified. HCP contained about 6 iron and 4 labile sulfide atoms per molecule, in agreement with the presence of both [2Fe-2S] and [4Fe-2S-2O] clusters, and showed hydroxylamine reductase activity, forming ammonia in vitro with methyl viologen as reductant. The apparent K(m) values for NH(2)OH and methyl viologen were 1 mM and 7 microM, respectively, at the pH and temperature optima (9.3 and 40 degrees C). The activity was oxygen-sensitive and was inhibited by sulfide and iron reagents. R. capsulatus E1F1 grew phototrophically, but not heterotrophically, with 1 mM NH(2)OH as nitrogen source, and up to 10 mM NH(2)OH was taken up by anaerobic resting cells. Ammonium was transiently accumulated in the media, and its assimilation was prevented by L-methionine-D,L-sulfoximine, a glutamine synthetase inhibitor. In addition, hydroxylamine- or nitrite-grown cells showed the higher hydroxylamine reductase activities. However, R. capsulatus B10S, a strain lacking the whole hcp-nas region, did not grow with 1 mM NH(2)OH. Also, E. coli cells overproducing HCP tolerate hydroxyl-amine better during anaerobic growth. These results suggest that HCP is involved in assimilation of NH(2)OH, a toxic product that could be formed during nitrate assimilation, probably in the nitrite reduction step.

  6. 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.

  7. 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

  8. A molecular-cytogenetic method for locating genes to pericentromeric regions facilitates a genomewide comparison of synteny between the centromeric regions of wheat and rice.

    PubMed

    Qi, Lili; Friebe, Bernd; Zhang, Peng; Gill, Bikram S

    2009-12-01

    Centromeres, because of their repeat structure and lack of sequence conservation, are difficult to assemble and compare across organisms. It was recently discovered that rice centromeres often contain genes. This suggested a method for studying centromere homologies between wheat and rice chromosomes by mapping rice centromeric genes onto wheat aneuploid stocks. Three of the seven cDNA clones of centromeric genes from rice centromere 8 (Cen8), 6729.t09, 6729.t10, and 6730.t11 which lie in the Cen8 kinetochore region, and three wheat ESTs, BJ301191, BJ305475, and BJ280500, with similarity to sequences of rice centromeric genes, were mapped to the centromeric regions of the wheat group-7 (W7) chromosomes. A possible pericentric inversion in chromosome 7D was detected. Genomewide comparison of wheat ESTs that mapped to centromeric regions against rice genome sequences revealed high conservation and a one-to-one correspondence of centromeric regions between wheat and rice chromosome pairs W1-R5, W2-R7, W3-R1, W5-R12, W6-R2, and W7-R8. The W4 centromere may share homology with R3 only or with R3 + R11. Wheat ESTs that mapped to the pericentromeric region of the group-5 long arm anchored to the rice BACs located in the recently duplicated region at the distal ends of the short arms of rice chromosomes 11 and 12. A pericentric inversion specific to the rice lineage was detected. The depicted framework provides a working model for further studies on the structure and evolution of cereal chromosome centromeres.

  9. Long non-coding RNAs differentially expressed between normal versus primary breast tumor tissues disclose converse changes to breast cancer-related protein-coding genes.

    PubMed

    Reiche, Kristin; Kasack, Katharina; Schreiber, Stephan; Lüders, Torben; Due, Eldri U; Naume, Bjørn; Riis, Margit; Kristensen, Vessela N; Horn, Friedemann; Børresen-Dale, Anne-Lise; Hackermüller, Jörg; Baumbusch, Lars O

    2014-01-01

    Breast cancer, the second leading cause of cancer death in women, is a highly heterogeneous disease, characterized by distinct genomic and transcriptomic profiles. Transcriptome analyses prevalently assessed protein-coding genes; however, the majority of the mammalian genome is expressed in numerous non-coding transcripts. Emerging evidence supports that many of these non-coding RNAs are specifically expressed during development, tumorigenesis, and metastasis. The focus of this study was to investigate the expression features and molecular characteristics of long non-coding RNAs (lncRNAs) in breast cancer. We investigated 26 breast tumor and 5 normal tissue samples utilizing a custom expression microarray enclosing probes for mRNAs as well as novel and previously identified lncRNAs. We identified more than 19,000 unique regions significantly differentially expressed between normal versus breast tumor tissue, half of these regions were non-coding without any evidence for functional open reading frames or sequence similarity to known proteins. The identified non-coding regions were primarily located in introns (53%) or in the intergenic space (33%), frequently orientated in antisense-direction of protein-coding genes (14%), and commonly distributed at promoter-, transcription factor binding-, or enhancer-sites. Analyzing the most diverse mRNA breast cancer subtypes Basal-like versus Luminal A and B resulted in 3,025 significantly differentially expressed unique loci, including 682 (23%) for non-coding transcripts. A notable number of differentially expressed protein-coding genes displayed non-synonymous expression changes compared to their nearest differentially expressed lncRNA, including an antisense lncRNA strongly anticorrelated to the mRNA coding for histone deacetylase 3 (HDAC3), which was investigated in more detail. Previously identified chromatin-associated lncRNAs (CARs) were predominantly downregulated in breast tumor samples, including CARs located in the

  10. Long Non-Coding RNAs Differentially Expressed between Normal versus Primary Breast Tumor Tissues Disclose Converse Changes to Breast Cancer-Related Protein-Coding Genes

    PubMed Central

    Reiche, Kristin; Kasack, Katharina; Schreiber, Stephan; Lüders, Torben; Due, Eldri U.; Naume, Bjørn; Riis, Margit; Kristensen, Vessela N.; Horn, Friedemann; Børresen-Dale, Anne-Lise; Hackermüller, Jörg; Baumbusch, Lars O.

    2014-01-01

    Breast cancer, the second leading cause of cancer death in women, is a highly heterogeneous disease, characterized by distinct genomic and transcriptomic profiles. Transcriptome analyses prevalently assessed protein-coding genes; however, the majority of the mammalian genome is expressed in numerous non-coding transcripts. Emerging evidence supports that many of these non-coding RNAs are specifically expressed during development, tumorigenesis, and metastasis. The focus of this study was to investigate the expression features and molecular characteristics of long non-coding RNAs (lncRNAs) in breast cancer. We investigated 26 breast tumor and 5 normal tissue samples utilizing a custom expression microarray enclosing probes for mRNAs as well as novel and previously identified lncRNAs. We identified more than 19,000 unique regions significantly differentially expressed between normal versus breast tumor tissue, half of these regions were non-coding without any evidence for functional open reading frames or sequence similarity to known proteins. The identified non-coding regions were primarily located in introns (53%) or in the intergenic space (33%), frequently orientated in antisense-direction of protein-coding genes (14%), and commonly distributed at promoter-, transcription factor binding-, or enhancer-sites. Analyzing the most diverse mRNA breast cancer subtypes Basal-like versus Luminal A and B resulted in 3,025 significantly differentially expressed unique loci, including 682 (23%) for non-coding transcripts. A notable number of differentially expressed protein-coding genes displayed non-synonymous expression changes compared to their nearest differentially expressed lncRNA, including an antisense lncRNA strongly anticorrelated to the mRNA coding for histone deacetylase 3 (HDAC3), which was investigated in more detail. Previously identified chromatin-associated lncRNAs (CARs) were predominantly downregulated in breast tumor samples, including CARs located in the

  11. Impact of the Location of CpG Methylation within the GSTP1 Gene on Its Specificity as a DNA Marker for Hepatocellular Carcinoma

    PubMed Central

    Jain, Surbhi; Boldbaatar, Batbold; Hamilton, James P.; Lin, Selena Y.; Chang, Ting-Tsung; Chen, Shun-Hua; Song, Wei; Meltzer, Stephen J.; Block, Timothy M.; Su, Ying-Hsiu

    2012-01-01

    Hypermethylation of the glutathione S-transferase π 1 (GSTP1) gene promoter region has been reported to be a potential biomarker to distinguish hepatocellular carcinoma (HCC) from other liver diseases. However, reports regarding how specific a marker it is have ranged from 100% to 0%. We hypothesized that, to a large extent, the variation of specificity depends on the location of the CpG sites analyzed. To test this hypothesis, we compared the methylation status of the GSTP1 promoter region of the DNA isolated from HCC, cirrhosis, hepatitis, and normal liver tissues by bisulfite–PCR sequencing. We found that the 5′ region of the position −48 nt from the transcription start site of the GSTP1 gene is selectively methylated in HCC, whereas the 3′ region is methylated in all liver tissues examined, including normal liver and the HCC tissue. Interestingly, when DNA derived from fetal liver and 11 nonhepatic normal tissue was also examined by bisulfite-PCR sequencing, we found that methylation of the 3′ region of the promoter appeared to be liver-specific. A methylation-specific PCR assay targeting the 5′ region of the promoter was developed and used to quantify the methylated GSTP1 gene in various diseased liver tissues including HCC. When we used an assay targeting the 3′ region, we found that the methylation of the 5′-end of the GSTP1 promoter was significantly more specific than that of the 3′-end (97.1% vs. 60%, p<0.0001 by Fisher's exact test) for distinguishing HCC (n = 120) from hepatitis (n = 35) and cirrhosis (n = 35). Encouragingly, 33.8% of the AFP-negative HCC contained the methylated GSTP1 gene. This study clearly demonstrates the importance of the location of CpG site methylation for HCC specificity and how liver-specific DNA methylation should be considered when an epigenetic DNA marker is studied for detection of HCC. PMID:22536438

  12. Conversational Telugu.

    ERIC Educational Resources Information Center

    Beinstein, Judith; And Others

    The purpose of this text is to develop elementary conversational skills in Telugu. The language materials consist of four types of language learning activities. The first, and most predominant, is the unit microwave cycle. These cycles divide the learning process into two basic phases, the first of which involves mimicry, memorization, and…

  13. Conversational Tamil.

    ERIC Educational Resources Information Center

    Beinstein, Judith; And Others

    The purpose of this text is to develop conversational skills in Tamil. It is to be used as a review of what has been learned in class and not as a teaching device. The language materials consist of four types of language learning activities. The unit microwave cycle divides the learning process into two basic phases. The first phase involves…

  14. A new carboxylesterase from Brevibacterium linens IFO 12171 responsible for the conversion of 1,4-butanediol diacrylate to 4-hydroxybutyl acrylate: purification, characterization, gene cloning, and gene expression in Escherichia coli.

    PubMed

    Sakai, Y; Ishikawa, J; Fukasaka, S; Yurimoto, H; Mitsui, R; Yanase, H; Kato, N

    1999-04-01

    A carboxylesterase that is responsible for conversion of 1,4-butanediol diacrylate (BDA) to 4-hydroxybutyl acrylate (4HBA) was found in Brevibacterium lines IFO 12171, and purified to homogeneity. The purified enzyme was active toward a variety of diesters of ethylene glycol, 1,4-butanediol, and 1,6-hexanediol. The K(m) and kcat of the enzyme for BDA were 3.04 mM and 203,000 s-1, respectively. The reaction with the purified enzyme gave 98 mM 4HBA from 100 mM BDA for 60 min. The enzyme gene was cloned from the chromosomal DNA of the bacterium. The open reading frame encoding the enzyme was 1176 bp long, corresponding to a protein of 393 amino acid residues (molecular mass = 42,569 Da). The deduced amino acid sequence contained the tetra peptide motif sequence, STTK, and the serine residue was confirmed to be the catalytic center of BDA esterase by site-directed mutagenesis for several amino acid residues. The gene was expressed in Escherichia coli under the control of the lac promoter, and the gene product (a fusion protein with 6 amino acid residues from beta-galactosidase) showed the same catalytic properties as the enzyme from the parent strain.

  15. 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

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

    PubMed

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

    2016-05-01

    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.

  17. Restoration of senescence in breast and ovarian cancer cells following the transfer of the YAC carrying SEN6A gene located at 6q16.3.

    PubMed

    Rane, Neena S; Sandhu, Arbansjit K; Zhawar, Vikramjit S; Kaur, Gurpreet; Popescu, Nicholas C; Kandpal, Raj P; Jhanwar-Uniyal, Meena; Athwal, Raghbir S

    2011-01-01

    We previously located a senescence gene locus (SEN6A), at chromosome 6q14-21 by a functional strategy using chromosome transfer into immortal ovarian tumor cells. To further elucidate the SEN6A locus, intact chromosome 6 or 6q was transferred into rat ovarian tumor cells and a panel of immortal revertant clones of senescent cells was generated. The panel of independent colonies as well as mixed populations of revertant cells was analyzed for the presence or absence of chromosome 6 specific markers. These investigations led to the identification of a fine deletion of approximately 1cM at chromosomal interval 6q16.3. A contiguous stretch containing five yeast artificial chromosome (YAC) clones was constructed across the deleted region. The non-chimeric YAC clones were retrofitted and transferred into mouse A9 cells by spheroplast fusion to generate YAC/A9 hybrids. YAC DNA present in YAC/A9 hybrids was subsequently transferred by microcell fusion into immortal tumor cells, and the hybrid cells were characterized for their senescence phenotype. Using this functional strategy, the transfer of YAC clone 966b10 was shown to restore senescence in both rat and human ovarian and breast tumor cells. Our results demonstrate that the SEN6A gene is carried on a 1 Mb YAC, 966b10, which maps at 6q16.3.

  18. 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.

  19. The location of Z- and W-linked marker genes and sequence on the homomorphic sex chromosomes of the ostrich and the emu

    PubMed Central

    Ogawa, Akira; Murata, Koichi; Mizuno, Shigeki

    1998-01-01

    Perhaps the most striking fact about early Cenozoic avian history some 70 million years ago was the rapid radiation of large, flightless, ground-living birds. It has been suggested that, for a time, there was active competition between these large terrestrial birds and the early mammals. Probably reflecting the above noted early start of Ratitae of the infraclass Eoaves, the presumptive sex chromosomes of their present day survivors, such as the emu and the ostrich, largely remained homomorphic. The signs of genetic differentiation between their still-homomorphic Z and W chromosomes were tested by using two marker genes (Z-linked ZOV3 and the gene for the iron-responsive element-binding protein) and one marker sequence of a part of a presumptive pseudogene (W-linked EE0.6 of the chicken). Their homologues, maintaining 71–92% identities to the chicken counterparts, were found in both the emu (Dromaius novaehollandiae) and the ostrich (Struthio camelus). Their locations were visualized on chromosome preparations by fluorescence in situ hybridization. In the case of the emu, these three marker sequences were localized on both members of the fifth pair of a female, thus revealing no sign yet of genetic differentiation between the Z and the W. The finding was the same with regard to both members of the fourth pair of male ostriches. In the female ostrich, however, the sequence of the gene for the iron-responsive element-binding protein was missing from one of the pairs, thus revealing the differentiation by a small deletion of the W from the Z. PMID:9539751

  20. 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.

  1. 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".

  2. 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.

  3. Subcellular location of Arabidopsis thaliana subfamily a1 β-galactosidases and developmental regulation of transcript levels of their coding genes.

    PubMed

    Moneo-Sánchez, María; Izquierdo, Lucía; Martín, Ignacio; Labrador, Emilia; Dopico, Berta

    2016-12-01

    The aim of this work is to gain insight into the six members of the a1 subfamily of the β-galactosidases (BGAL) from Arabidopsis thaliana. First, the subcellular location of all these six BGAL proteins from a1 subfamily has been established in the cell wall by the construction of transgenic plants producing the enhanced green fluorescent protein (eGFP) fused to the BGAL proteins. BGAL12 is also located in the endoplasmic reticulum. Our study of the AtBGAL transcript accumulation along plant development indicated that all AtBGAL transcript appeared in initial stages of development, both dark- and light-grown seedlings, being AtBGAL1, AtBGAL2 and AtBGAL3 transcripts the predominant ones in the latter condition, mainly in the aerial part and with levels decreasing with age. The high accumulation of transcript of AtBGAL4 in basal internodes and in leaves at the end of development, and their strong increase after treatment both with BL and H3BO3 point to an involvement of BGAL4 in cell wall changes leading to the cease of elongation and increased rigidity. The changes of AtBGAL transcript accumulation in relation to different stages and conditions of plant development, suggest that each of the different gene products have a plant-specific function and provides support for the proposed function of the subfamily a1 BGAL in plant cell wall remodelling for cell expansion or for cell response to stress conditions.

  4. 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.

  5. 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

  6. 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.

  7. A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes.

    PubMed

    Bazak, Lily; Haviv, Ami; Barak, Michal; Jacob-Hirsch, Jasmine; Deng, Patricia; Zhang, Rui; Isaacs, Farren J; Rechavi, Gideon; Li, Jin Billy; Eisenberg, Eli; Levanon, Erez Y

    2014-03-01

    RNA molecules transmit the information encoded in the genome and generally reflect its content. Adenosine-to-inosine (A-to-I) RNA editing by ADAR proteins converts a genomically encoded adenosine into inosine. It is known that most RNA editing in human takes place in the primate-specific Alu sequences, but the extent of this phenomenon and its effect on transcriptome diversity are not yet clear. Here, we analyzed large-scale RNA-seq data and detected ∼1.6 million editing sites. As detection sensitivity increases with sequencing coverage, we performed ultradeep sequencing of selected Alu sequences and showed that the scope of editing is much larger than anticipated. We found that virtually all adenosines within Alu repeats that form double-stranded RNA undergo A-to-I editing, although most sites exhibit editing at only low levels (<1%). Moreover, using high coverage sequencing, we observed editing of transcripts resulting from residual antisense expression, doubling the number of edited sites in the human genome. Based on bioinformatic analyses and deep targeted sequencing, we estimate that there are over 100 million human Alu RNA editing sites, located in the majority of human genes. These findings set the stage for exploring how this primate-specific massive diversification of the transcriptome is utilized.

  8. 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.

  9. 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.

  10. 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...

  11. Transcriptional regulation of the human, porcine and bovine OCTN2 gene by PPARα via a conserved PPRE located in intron 1

    PubMed Central

    2014-01-01

    Background The novel organic cation transporter 2 (OCTN2) is the physiologically most important carnitine transporter in tissues and is responsible for carnitine absorption in the intestine, carnitine reabsorption in the kidney and distribution of carnitine between tissues. Genetic studies clearly demonstrated that the mouse OCTN2 gene is directly regulated by peroxisome proliferator-activated receptor α (PPARα). Despite its well conserved role as an important regulator of lipid catabolism in general, the specific genes under control of PPARα within each lipid metabolic pathway were shown to differ between species and it is currently unknown whether the OCTN2 gene is also a PPARα target gene in pig, cattle, and human. In the present study we examined the hypothesis that the porcine, bovine, and human OCTN2 gene are also PPARα target genes. Results Using positional cloning and reporter gene assays we identified a functional PPRE, each in the intron 1 of the porcine, bovine, and human OCTN2 gene. Gel shift assay confirmed binding of PPARα to this PPRE in the porcine, bovine, and the human OCTN2 gene. Conclusions The results of the present study show that the porcine, bovine, and human OCTN2 gene, like the mouse OCTN2 gene, is directly regulated by PPARα. This suggests that regulation of genes involved in carnitine uptake by PPARα is highly conserved across species. PMID:25299939

  12. 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.

  13. 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...

  14. 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.

  15. Transforming capacity of two novel genes JS-1 and JS-2 located in chromosome 5p and their overexpression in human esophageal squamous cell carcinoma.

    PubMed

    Fatima, Sarwat; Chui, Chung H; Tang, Wing K; Hui, Kin S; Au, Ho W; Li, Wing Y; Wong, Mei M; Cheung, Filly; Tsao, S W; Lam, King Y; Beh, Philip S L; Wong, John; Law, Simon; Srivastava, Gopesh; Ho, Kwok P; Chan, Albert S C; Tang, Johnny C O

    2006-01-01

    Esophageal squamous cell carcinoma (ESCC) has a high mortality rate and geographic differences in incidence. Previous studies of comparative genomic hybridization (CGH) showed that chromosomal 5p is frequently amplified in cell lines and primary ESCC of Hong Kong Chinese origin. In this report, attempt was made to study two novel genes, named as JS-1 and JS-2, which are located in chromosome 5p15.2 and are 5' upstream to delta catenin for their roles in molecular pathogenesis of ESCC. Eleven cell lines, 27 primary ESCC cases and multiple human tissue cDNA panels (MTC) of digestive system were studied for the expression level of JS-1 and JS-2 by RT-PCR. The full-length cDNA sequences of JS-1 and JS-2 were determined from a non-tumor esophageal epithelial cell line by 3' and 5' rapid amplification of cDNA ends (RACE). The transforming capacity of JS-1 and JS-2 was also investigated by transfecting NIH 3T3 cells with the expression vector pcDNA3.1(-) cloned with the full coding sequences and it was followed by the study of foci formation of the transfected cells under confluence growth and the anchorage-independent growth in soft agar. Forty-five percent (5/11) and 18% (2/11) of the ESCC cell lines showed overexpression of JS-1 and JS-2 respectively, while 55% (15/27) and 14% (3/22) primary ESCC cases showed overexpression of JS-1 and JS-2 respectively. JS-1 overexpression was most common in patients with stage II ESCC (6/27; 22%) whereas JS-2 was only overexpressed in a dysplastic lesion (1/22; 4%) and stage III tumors (2/22; 9%). The expression levels of JS-1 and JS-2 are both low in normal esophageal tissues. Overexpression of JS-1 in NIH 3T3 cells caused foci formation in confluence growth and colony formation in soft agar but not for JS-2. A high grade sarcoma was formed in the athymic nude mice when NIH 3T3 cells overexpressing JS-1 were injected subcutaneously. Our results thus indicate that the frequent overexpression of JS-1 in ESCC and its transforming

  16. The C/ebp-Atf response element (CARE) location reveals two distinct Atf4-dependent, elongation-mediated mechanisms for transcriptional induction of aminoacyl-tRNA synthetase genes in response to amino acid limitation

    PubMed Central

    Shan, Jixiu; Zhang, Fan; Sharkey, Jason; Tang, Tiffany A.; Örd, Tönis; Kilberg, Michael S.

    2016-01-01

    The response to amino acid (AA) limitation of the entire aminoacyl-tRNA synthetase (ARS) gene family revealed that 16/20 of the genes encoding cytoplasmic-localized enzymes are transcriptionally induced by activating transcription factor 4 (Atf4) via C/ebp-Atf-Response-Element (CARE) enhancers. In contrast, only 4/19 of the genes encoding mitochondrial-localized ARSs were weakly induced. Most of the activated genes have a functional CARE near the transcription start site (TSS), but for others the CARE is downstream. Regardless of the location of CARE enhancer, for all ARS genes there was constitutive association of RNA polymerase II (Pol II) and the general transcription machinery near the TSS. However, for those genes with a downstream CARE, Atf4, C/ebp-homology protein (Chop), Pol II and TATA-binding protein exhibited enhanced recruitment to the CARE during AA limitation. Increased Atf4 binding regulated the association of elongation factors at both the promoter and the enhancer regions, and inhibition of cyclin-dependent kinase 9 (CDK9), that regulates these elongation factors, blocked induction of the AA-responsive ARS genes. Protein pull-down assays indicated that Atf4 directly interacts with CDK9 and its associated protein cyclin T1. The results demonstrate that AA availability modulates the ARS gene family through modulation of transcription elongation. PMID:27471030

  17. Two thyroid hormone regulated genes, the beta-subunits of nerve growth factor (NGFB) and thyroid stimulating hormone (TSHB), are located less than 310 kb apart in both human and mouse genomes.

    PubMed

    Dracopoli, N C; Rose, E; Whitfield, G K; Guidon, P T; Bale, S J; Chance, P A; Kourides, I A; Housman, D E

    1988-08-01

    Two thyroid hormone regulated genes, the beta-subunits of nerve growth factor (NGFB) and thyroid stimulating hormone (TSHB), have been assigned to mouse chromosome 3 and human chromosome 1p22. We have used the techniques of linkage analysis and pulsed field gel electrophoresis to determine the proximity of these two antithetically regulated genes in this conserved linkage group. Four novel restriction fragment length polymorphisms were identified at the human TSHB gene. Two-point linkage analysis between TSHB and NGFB in 46 families, including the Centre d'Etude du Polymorphisme Humain (CEPH) reference panel, demonstrated no recombination (theta = 0.00, Z = 42.8). Analysis of this region by pulsed field gel electrophoresis showed that the genes for TSHB and NGFB are located less than 310 kb apart in man and 220 kb in the mouse.

  18. 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.

  19. Multi-location gram-positive and gram-negative bacterial protein subcellular localization using gene ontology and multi-label classifier ensemble

    PubMed Central

    2015-01-01

    Background It has become a very important and full of challenge task to predict bacterial protein subcellular locations using computational methods. Although there exist a lot of prediction methods for bacterial proteins, the majority of these methods can only deal with single-location proteins. But unfortunately many multi-location proteins are located in the bacterial cells. Moreover, multi-location proteins have special biological functions capable of helping the development of new drugs. So it is necessary to develop new computational methods for accurately predicting subcellular locations of multi-location bacterial proteins. Results In this article, two efficient multi-label predictors, Gpos-ECC-mPLoc and Gneg-ECC-mPLoc, are developed to predict the subcellular locations of multi-label gram-positive and gram-negative bacterial proteins respectively. The two multi-label predictors construct the GO vectors by using the GO terms of homologous proteins of query proteins and then adopt a powerful multi-label ensemble classifier to make the final multi-label prediction. The two multi-label predictors have the following advantages: (1) they improve the prediction performance of multi-label proteins by taking the correlations among different labels into account; (2) they ensemble multiple CC classifiers and further generate better prediction results by ensemble learning; and (3) they construct the GO vectors by using the frequency of occurrences of GO terms in the typical homologous set instead of using 0/1 values. Experimental results show that Gpos-ECC-mPLoc and Gneg-ECC-mPLoc can efficiently predict the subcellular locations of multi-label gram-positive and gram-negative bacterial proteins respectively. Conclusions Gpos-ECC-mPLoc and Gneg-ECC-mPLoc can efficiently improve prediction accuracy of subcellular localization of multi-location gram-positive and gram-negative bacterial proteins respectively. The online web servers for Gpos-ECC-mPLoc and Gneg

  20. 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.

  1. Chloroplast-located BjFer1 together with anti-oxidative genes alleviate hydrogen peroxide and hydroxyl radical injury in cytoplasmic male-sterile Brassica juncea.

    PubMed

    Yang, Jinghua; Liu, Shan; Yang, Xiaodong; Zhang, Mingfang

    2012-04-01

    We studied how plant cell modulated redox homeostasis in cytoplasmic male-sterility (CMS) Brassica juncea. The CMS Brassica juncea was identified to be mutated in several mitochondrial genes that suggested the changes of cell redox homeostasis. We observed that it was not associated with increased oxidative stress as shown by decreased H(2)O(2) and (∙)OH contents in this type of CMS. The expressions of several anti-oxidative genes were up-regulated in 5-day-old seedlings of CMS than MF lines under light and dark conditions. The mitochondrial alternative oxidase pathway was not activated, as indicated by no increased expression of AOX1a gene in CMS. Interestingly, the expression of Ferritin1 gene was markedly activated in 5-day-old seedlings of CMS than MF line under light and dark conditions. Consequently, we detected increased content of total iron in 30-day-old leaves in CMS than MF line. We isolated Ferritin1 orthologous gene from Brassica juncea, which was targeted to the chloroplast and induced by Fe-citrate and H(2)O(2), not ABA. Taken together, we proposed that increased expressions of BjFer1 and several antioxidant genes protected cell from oxidative stress in CMS Brassica juncea.

  2. Evolutionary conservation and genomic organization of XAP-4, an Xq28 located gene coding for a human rab GDP-dissociation inhibitor (GDI).

    PubMed

    Sedlacek, Z; Konecki, D S; Korn, B; Klauck, S M; Poustka, A

    1994-10-01

    After the development of efficient methods for the construction of transcription maps of defined genomic regions, the rate-limiting step in the analysis of the coding potentials of these regions is the elucidation of function of the novel genes and the examination of their possible involvement in hereditary diseases localized to the region. This can be greatly facilitated by the detection of sequence homology to a gene of known function. XAP-4 is one of the genes identified in the G6PD region of the human Xq28 by direct cDNA selection. The rapid assembly of this gene and the determination of its function was possible because of its sequence homology with the bovine smg p25A/rab3A GDP dissociation inhibitor (GDI). Sequence comparison with other GDIs in the databases has revealed that XAP-4 belongs to one of at least two distinct classes of mammalian rab GDIs. The rab GDIs, which play an important role in the regulation of cellular transport, are highly evolutionarily conserved, as are several other genes identified in the neighborhood of XAP-4. This genomic region is very gene dense, and all the cDNA clones from the approximately 2.5-kb-long transcript of XAP-4 map to a single 7.5-kb genomic EcoRI fragment. The genomic organization of XAP-4 has been examined to determine the distribution of the exonic sequences within this short segment of genomic DNA. It was found that, similar to several other genes from the region, XAP-4 is split into exons of average size, which are interrupted by very short introns.

  3. A novel ankyrin repeat-containing gene (Kank) located at 9p24 is a growth suppressor of renal cell carcinoma.

    PubMed

    Sarkar, Shubhashish; Roy, Badal Chandra; Hatano, Naoya; Aoyagi, Teiichiro; Gohji, Kazuo; Kiyama, Ryoiti

    2002-09-27

    By a combination of genome subtraction and comprehensive analysis of loss of heterozygosity based on mapping hemizygous deletions for a potential tumor-related locus, a minimum overlapping region of deletions at 9p24 the size of 165 kb was identified and found to harbor a new potential tumor suppressor gene for renal cell carcinoma, the Kank gene. Kank (for kidney ankyrin repeat-containing protein) contains four ankyrin repeats at its C terminus. Expression of the gene was suppressed in 6 of 8 or 6 of 10 cancer tissues examined by reverse transcription-PCR or Western blotting, respectively, and in several kidney tumor cell lines due to methylation at CpG sites in the gene. Epigenetic methylation or imprinting seemed to be the first hit, which was followed by a second hit of deletion, resulting in loss of function in many of these deletion cases. Expression of this gene in expression-negative HEK293 cells induced growth retardation at G(0)/G(1) as well as morphological changes.

  4. Heterogeneity of nervous system mitochondria: location, location, location!

    PubMed

    Dubinsky, Janet M

    2009-08-01

    Mitochondrial impairments have been associated with many neurological disorders, from inborn errors of metabolism or genetic disorders to age and environmentally linked diseases of aging (DiMauro S., Schon E.A. 2008. Mitochondrial disorders in the nervous system. Annu. Rev., Neurosci. 31, 91-123.). In these disorders, specific nervous system components or brain regions appear to be initially more susceptible to the triggering event or pathological process. Such regional variation in susceptibility to multiple types of stressors raises the possibility that inherent differences in mitochondrial function may mediate some aspect of pathogenesis. Regional differences in the distribution or number of mitochondria, mitochondrial enzyme activities, enzyme expression levels, mitochondrial genes or availability of necessary metabolites become attractive explanations for selective vulnerability of a nervous system structure. While regionally selective mitochondrial vulnerability has been documented, regional variations in other cellular and tissue characteristics may also contribute to metabolic impairment. Such environmental variables include high tonic firing rates, neurotransmitter phenotype, location of mitochondria within a neuron, or the varied tissue perfusion pressure of different cerebral arterial branches. These contextual variables exert regionally distinct regulatory influences on mitochondria to tune their energy production to local demands. Thus to understand variations in mitochondrial functioning and consequent selective vulnerability to injury, the organelle must be placed within the context of its cellular, functional, developmental and neuroanatomical environment.

  5. 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

  6. The human genes for desmogleins (DSG1 and DSG3) are located in a small region on chromosome 18q12

    SciTech Connect

    Wang, Yimin; Amagai, Masayuki; Minoshima, Shinsei; Sakai, Kosuke; Nishikawa, Takeji; Shimizu, Nobuyoshi ); Green, K.J. )

    1994-04-01

    Desmoglein is a transmembrane glycoprotein component of desmosomes in vertebrate epithelial cells. Two of the three currently known desmogleins are the autoantigens of autoimmune skin blistering diseases, pemphigus vulgaris and pemphigus foliaceus, in which autoantibodies cause the loss of cell adhesion of keratinocytes with resultant blister formation. In this study, the genes for two autoantigens (DSG1 for pemphigus foliaceus and DSG3 for pemphigus vulgaris) were mapped on band q12 of human chromosome 18 by fluorescence in situ hybridization. Furthermore, both genes were localized on a 320-kb genomic fragment separated by pulsed-field gel electrophoresis. These results suggest the possibility of a cluster for the desmoglein gene family on chromosome 18. 29 refs., 2 figs.

  7. 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.

  8. Identification of Multiresistance Gene cfr in Methicillin-Resistant Staphylococcus aureus from Pigs: Plasmid Location and Integration into a Staphylococcal Cassette Chromosome mec Complex

    PubMed Central

    Li, Dexi; Wu, Congming; Wang, Yang; Fan, Run

    2015-01-01

    The multiresistance gene cfr was found in 8/231 porcine methicillin-resistant Staphylococcus aureus isolates. They were characterized by multilocus sequence typing, spa typing, dru typing, and staphylococcal cassette chromosome mec (SCCmec) typing as ST627-t002-dt12w-IVb, ST6-t304-dt12w-IVb, ST9-t899-dt12w-IVb, ST9-t899-dt12ae-IVb, or ST63-t899-dt12v-IVb. Different cfr gene regions were detected on plasmids of ca. 35 kb in seven isolates. For the first time, an ISEnfa4-cfr-IS256 fragment was found to be inserted upstream of the ccr genes in a chromosomal SCCmec IVb element of the remaining isolate. PMID:25824234

  9. 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.

  10. The location of four fimbrin-encoding genes, agfA, fimA, sefA and sefD, on the Salmonella enteritidis and/or S. typhimurium XbaI-BlnI genomic restriction maps.

    PubMed

    Collinson, S K; Liu, S L; Clouthier, S C; Banser, P A; Doran, J L; Sanderson, K E; Kay, W W

    1996-02-22

    Four fimbrin-encoding genes, fimA (type-1 or SEF21 fimbriae), agfA (thin aggregative or SEF17 fimbriae), sefA (SEF14 fimbriae and sefD (SEF18 fimbriae) from Salmonella enteritidis (Se) 27655-3b were located onto the XbaI-BlnI genomic restriction maps of Salmonella typhimurium (St) LT2 and Se strains SSU7998 and 27655-3b. The XbaI or BlnI genomic fragments carrying these genes were identified by hybridization with labeled oligodeoxyribonucleotides or fimbrin-encoding genes. The fimbrin-encoding genes were not encoded by the virulence plasmids, but were located on chromosomal DNA fragments. The position of each gene on a given XbaI fragment was determined by hybridization of a series of XbaI-digested genomic DNA samples from previously characterized Tn10 mutants of Se and St with its respective probe. The fimA gene mapped near 13 centisomes (Cs) between purE884::Tn10 at 12.6 Cs (11.8 min) and apeE2::Tn10 at 12.8 Cs (12.3 min) beside the first XbaI site at 13.0 Cs in St or between purE884::Tn10 at 12.6 Cs and the XbaI site at 13.6 Cs in Se. The agfA gene mapped near 26 Cs between putA::Tn10 and pyrC691::Tn10 in St, but near 40 Cs between pncX::Tn10 and the XbaI site at 43.3 Cs in Se. This difference in map position was due to the location of agfA near one end of the 815-kb chromosomal fragment inverted between Se and St. The sefA and sefD genes mapped precisely at 97.6 Cs in Se, but were absent from the genome of St LT2. To verify the mapping procedures used herein, tctC was also mapped in both Salmonella serovars. As expected, tctC mapped near 60 Cs in both St and Se, thereby confirming previous studies.

  11. Cloning and analysis of structural genes from Streptomyces pristinaespiralis encoding enzymes involved in the conversion of pristinamycin IIB to pristinamycin IIA (PIIA): PIIA synthase and NADH:riboflavin 5'-phosphate oxidoreductase.

    PubMed Central

    Blanc, V; Lagneaux, D; Didier, P; Gil, P; Lacroix, P; Crouzet, J

    1995-01-01

    In Streptomyces pristinaespiralis, two enzymes are necessary for conversion of pristinamycin IIB (PIIB) to pristinamycin IIA (PIIA), the major component of pristinamycin (D. Thibaut, N. Ratet, D. Bisch, D. Faucher, L. Debussche, and F. Blanche, J. Bacteriol. 177:5199-5205, 1995); these enzymes are PIIA synthase, a heterodimer composed of the SnaA and SnaB proteins, which catalyzes the oxidation of PIIB to PIIA, and the NADH:riboflavin 5'-phosphate oxidoreductase (hereafter called FMN reductase), the SnaC protein, which provides the reduced form of flavin mononucleotide for the reaction. By using oligonucleotide probes designed from limited peptide sequence information of the purified proteins, the corresponding genes were cloned from a genomic library of S. pristinaespiralis. SnaA and SnaB showed no significant similarity with proteins from databases, but SnaA and SnaB had similar protein domains. Disruption of the snaA gene in S. pristinaespiralis led to accumulation of PIIB. Complementation of a S. pristinaespiralis PIIA-PIIB+ mutant with the snaA and snaB genes, cloned in a low-copy-number plasmid, partially restored production of PIIA. The deduced amino acid sequence of the snaC gene showed no similarity to the sequences of other FMN reductases but was 39% identical with the product of the actVB gene of the actinorhodin cluster of Streptomyces coelicolor A(3)2, likely to be involved in the dimerization step of actinorhodin biosynthesis. Furthermore, an S. coelicolor A(3)2 mutant blocked in this step was successfully complemented by the snaC gene, restoring the production of actinorhodin. PMID:7665509

  12. 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

  13. Clustering, haplotype diversity and locations of MIC-3: a unique root-specific defense-related gene family in upland cotton (Gossypium hirsutum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    MIC-3-related genes of cotton (Gossypium spp.) were identified and shown to have root-specific expression, associated with pathogen defense-related function and specifically increased expression in root-knot nematode (RKN) resistant plants after nematode infection. Here we cloned and sequenced MIC-...

  14. G-quadruplex (G4) motifs in the maize (Zea mays L.) genome are enriched at specific locations in thousands of genes coupled to energy status, hypoxia, low sugar, and nutrient deprivation.

    PubMed

    Andorf, Carson M; Kopylov, Mykhailo; Dobbs, Drena; Koch, Karen E; Stroupe, M Elizabeth; Lawrence, Carolyn J; Bass, Hank W

    2014-12-20

    The G-quadruplex (G4) elements comprise a class of nucleic acid structures formed by stacking of guanine base quartets in a quadruple helix. This G4 DNA can form within or across single-stranded DNA molecules and is mutually exclusive with duplex B-form DNA. The reversibility and structural diversity of G4s make them highly versatile genetic structures, as demonstrated by their roles in various functions including telomere metabolism, genome maintenance, immunoglobulin gene diversification, transcription, and translation. Sequence motifs capable of forming G4 DNA are typically located in telomere repeat DNA and other non-telomeric genomic loci. To investigate their potential roles in a large-genome model plant species, we computationally identified 149,988 non-telomeric G4 motifs in maize (Zea mays L., B73 AGPv2), 29% of which were in non-repetitive genomic regions. G4 motif hotspots exhibited non-random enrichment in genes at two locations on the antisense strand, one in the 5' UTR and the other at the 5' end of the first intron. Several genic G4 motifs were shown to adopt sequence-specific and potassium-dependent G4 DNA structures in vitro. The G4 motifs were prevalent in key regulatory genes associated with hypoxia (group VII ERFs), oxidative stress (DJ-1/GATase1), and energy status (AMPK/SnRK) pathways. They also showed statistical enrichment for genes in metabolic pathways that function in glycolysis, sugar degradation, inositol metabolism, and base excision repair. Collectively, the maize G4 motifs may represent conditional regulatory elements that can aid in energy status gene responses. Such a network of elements could provide a mechanistic basis for linking energy status signals to gene regulation in maize, a model genetic system and major world crop species for feed, food, and fuel.

  15. The Broken MLL Gene Is Frequently Located Outside the Inherent Chromosome Territory in Human Lymphoid Cells Treated with DNA Topoisomerase II Poison Etoposide

    PubMed Central

    Glukhov, Sergey I.; Rubtsov, Mikhail A.; Alexeyevsky, Daniil A.; Alexeevski, Andrei V.; Razin, Sergey V.; Iarovaia, Olga V.

    2013-01-01

    The mixed lineage leukaemia (MLL) gene is frequently rearranged in secondary leukaemias, in which it could fuse to a variety of different partners. Breakage in the MLL gene preferentially occurs within a ~8 kb region that possesses a strong DNA topoisomerase II cleavage site. It has been proposed that DNA topoisomerase II-mediated DNA cleavage within this and other regions triggers translocations that occur due to incorrect joining of broken DNA ends. To further clarify a possible mechanism for MLL rearrangements, we analysed the frequency of MLL cleavage in cells exposed to etoposide, a DNA topoisomerase II poison commonly used as an anticancer drug, and positioning of the broken 3’-end of the MLL gene in respect to inherent chromosomal territories. It was demonstrated that exposure of human Jurkat cells to etoposide resulted in frequent cleavage of MLL genes. Using MLL-specific break-apart probes we visualised cleaved MLL genes in ~17% of nuclei. Using confocal microscopy and 3D modelling, we demonstrated that in cells treated with etoposide and cultivated for 1 h under normal conditions, ~9% of the broken MLL alleles were present outside the chromosome 11 territory, whereas in both control cells and cells inspected immediately after etoposide treatment, virtually all MLL alleles were present within the chromosomal territory. The data are discussed in the framework of the “breakage first” model of juxtaposing translocation partners. We propose that in the course of repairing DNA topoisomerase II-mediated DNA lesions (removal of stalled DNA topoisomerase II complexes and non-homologous end joining), DNA ends acquire additional mobility, which allows the meeting and incorrect joining of translocation partners. PMID:24086652

  16. Pashto Conversation Manual and Pashto Conversation Tapescript.

    ERIC Educational Resources Information Center

    Tegey, Habibullah; Robson, Barbara

    This conversation manual and tapescript are part of a set of materials that have been developed to teach oral and written Afghan Pashto to English speakers. In addition to the conversation manual and tapescript, the set consists of a beginning textbook, an intermediate textbook, a reader, and a set of taped lessons that correlate with the…

  17. The tyrosyl-tRNA synthetase like gene located in the tyramine biosynthesis cluster of Enterococcus durans is transcriptionally regulated by tyrosine concentration and extracellular pH

    PubMed Central

    2012-01-01

    Background The tyramine producer Enterococcus durans IPLA655 contains all the necessary genes for tyramine biosynthesis, grouped in the TDC cluster. This cluster includes tyrS, an aminoacyl-tRNA synthetase like gene. Results This work shows that tyrS was maximally transcribed in absence of tyrosine at acidic pH, showing a greater than 10-fold induction in mRNA levels over levels occurring in presence of tyrosine. Mapping of the tyrS transcriptional start site revealed an unusually long untranslated leader region of 322 bp, which displays the typical features of the T box transcriptional attenuation mechanism. The tyrosine concentration regulation of tyrS was found to be mediated by a transcription antitermination system, whereas the specific induction at acidic pH was regulated at transcription initiation level. Conclusions The expression of the tyrS gene present in the TDC cluster of E. durans is transcriptionally regulated by tyrosine concentration and extracelular pH. The regulation is mediated by both an antitermination system and the promoter itself. PMID:22333391

  18. Control elements targeting Tgfb3 expression to the palatal epithelium are located intergenically and in introns of the upstream Ift43 gene

    PubMed Central

    Lane, Jamie; Yumoto, Kenji; Pisano, Justin; Azhar, Mohamad; Thomas, Penny S.; Kaartinen, Vesa

    2014-01-01

    Tgfb3 is strongly and specifically expressed in the epithelial tips of pre-fusion palatal shelves where it plays a critical non-redundant role in palatal fusion in both medial edge epithelial (MEE) cells and in a thin layer of flattened peridermal cells that covers the MEE. It is not known how Tgfb3 expression is regulated in these specific cell types. Using comparative genomics and transgenic reporter assays, we have identified cis-regulatory elements that could control Tgfb3 expression during palatogenesis. Our results show that a 61-kb genomic fragment encompassing the Tgfb3 gene drives remarkably specific reporter expression in the MEE and adjacent periderm. Within this fragment, we identified two small, non-coding, evolutionarily conserved regions in intron 2 of the neighboring Ift43 gene, and a larger region in the intervening sequence between the Ift43 and Tgfb3 genes, each of which could target reporter activity to the tips of pre-fusion/fusing palatal shelves. Identification of the cis-regulatory sequences controlling spatio-temporal Tgfb3 expression in palatal shelves is a key step toward understanding upstream regulation of Tgfb3 expression during palatogenesis and should enable the development of improved tools to investigate palatal epithelial fusion. PMID:25071603

  19. c-Myc/Max heterodimers bind cooperatively to the E-box sequences located in the first intron of the rat ornithine decarboxylase (ODC) gene.

    PubMed Central

    Walhout, A J; Gubbels, J M; Bernards, R; van der Vliet, P C; Timmers, H T

    1997-01-01

    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. PMID:9162900

  20. c-Myc/Max heterodimers bind cooperatively to the E-box sequences located in the first intron of the rat ornithine decarboxylase (ODC) gene

    PubMed Central

    Walhout, AJM; Gubbels, JM; Bernards, R; van der Vliet PC; Timmers, HTM

    1997-01-01

    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 the 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. PMID:9106360

  1. A gene encoding lysine 6-aminotransferase, which forms the beta-lactam precursor alpha-aminoadipic acid, is located in the cluster of cephamycin biosynthetic genes in Nocardia lactamdurans.

    PubMed Central

    Coque, J J; Liras, P; Laiz, L; Martín, J F

    1991-01-01

    A gene (lat) encoding lysine 6-aminotransferase was found upstream of the pcbAB (encoding alpha-aminoadipylcysteinyl-valine synthetase) and pcbC (encoding isopenicillin N synthase) genes in the cluster of early cephamycin biosynthetic genes in Nocardia lactamdurans. The lat gene was separated by a small intergenic region of 64 bp from the 5' end of the pcbAB gene. The lat gene contained an open reading frame of 1,353 nucleotides (71.4% G + C) encoding a protein of 450 amino acids with a deduced molecular mass of 48,811 Da. Expression of DNA fragments carrying the lat gene in Streptomyces lividans led to a high lysine 6-aminotransferase activity which was absent from untransformed S. lividans. The enzyme was partially purified from S. lividans(pULBS8) and showed a molecular mass of 52,800 Da as calculated by Sephadex gel filtration and polyacrylamide gel electrophoresis. DNA sequences which hybridized strongly with the lat gene of N. lactamdurans were found in four cephamycin-producing Streptomyces species but not in four other actinomycetes which are not known to produce beta-lactams, suggesting that the gene is specific for beta-lactam biosynthesis and is not involved in general lysine catabolism. The protein encoded by the lat gene showed similarity to ornithine-5-aminotransferases and N-acetylornithine-5-aminotransferases and contained a pyridoxal phosphate-binding consensus amino acid sequence around Lys-300 of the protein. The evolutionary implications of the lat gene as a true beta-lactam biosynthetic gene are discussed. Images PMID:1917857

  2. The human NOTCH1, 2, and 3 genes are located at chromosome positions 9q34, 1p13-11, and 19p13.2-p13.1 in regions of neoplasia-associated translocation

    SciTech Connect

    Larsson, C.; White, I.; Lendahl, U.

    1994-11-15

    In Drosophila the Notch gene controls differentiation to various cell fates in many tissues. Three mammalian Notch 1, 2, and 3. All three homologs are very highly conserved relative to the Drosophila Notch gene, which suggests that they are important for cell differentiation in mammals. This notion is supported by the previous finding of a truncated, translocated form of the human NOTCH1 gene (formerly TAN1) in three cases of leukemia. Given this genetic link between NOTCH1 and tumor formation, it is of interest to establish the chromosomal positions of the other two homologs. The authors report the identification of cosmid clones for the human NOTCH1, 2, and 3 genes. These clones were used as probes in fluorescence in situ hybridization to human metaphase chromosomes, and the results, combined with data from somatic cell hybrid panels, show that the NOTCH 2 and 3 genes are located at positions 1p13-p11 and 19p13.2-p13.1, respectively, which are regions of neoplasia-associated translocation. 41 refs., 4 figs.

  3. The lung enriched transcription factor TTF-1 and the ubiquitously expressed proteins Sp1 and Sp3 interact with elements located in the minimal promoter of the rat Clara cell secretory protein gene.

    PubMed Central

    Toonen, R F; Gowan, S; Bingle, C D

    1996-01-01

    The mechanisms that direct expression of the Clara cell secretory protein (CCSP) gene to the bronchiolar epithelial cells of the lung remain to be elucidated. Previous studies have identified a number of proteins which bind to a functionally important region (Region 1) located -132 to -76 bp from the transcription start site in the rat CCSP gene. Subsequently we have shown that while Region 1 is an important positive regulator of CCSP gene expression, sequences 3' of this region (-75 to +38) are sufficient to confer tissue-specific expression of a reporter gene. In the present study we have used transient transfections with a deletion series of CCSP-CAT reporter plasmids (where CAT is chloramphenicol acetyltransferase) and gel mobility shift assays with a series of overlapping oligonucleotides covering the whole minimal promoter region to study protein-DNA interactions within this region. These studies have identified a conserved functional binding site for the lung and thyroid enriched homeodomain transcription factor TTF-1, located between positions -51 and -42 from the transcription start site. CCSP-CAT chimaeric reporters containing this region are specifically activated by TTF-1 in co-transfection assays, and nuclear extracts from cells which express TTF-1 bind to this region, as does in vitro translated rat TTF-1. Three additional conserved regions were identified, and in further gel mobility shift studies with an oligonucleotide spanning the conserved region immediately 5' to the TTF-1 site we identified a binding site for the ubiquitously expressed zinc-finger-containing proteins Sp1 and Sp3. These studies suggest that cell-type-restricted and ubiquitous nuclear proteins may play a combined role in the regulation of the CCSP gene within the bronchiolar epithelium by interacting with the minimal promoter region. PMID:8687389

  4. 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.

  5. 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).

  6. 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

  7. 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…

  8. Learning through Conversation.

    ERIC Educational Resources Information Center

    Kelly, Patricia R.; Klein, Adria F.; Pinnell, Gay Su

    1996-01-01

    Through teacher-child conversation, experts use oral language to help novices take on more complex tasks; and Reading Recovery children, who are obviously having difficulty with school-based learning, are especially in need of significant conversations with adults. Reading and writing processes are supported through conversation with Reading…

  9. The First Rule of Plant Transposable Element Silencing: Location, Location, Location

    PubMed Central

    Sigman, Meredith J.; Slotkin, R. Keith

    2016-01-01

    Transposable elements (TEs) are mobile units of DNA that comprise large portions of plant genomes. Besides creating mutations via transposition and contributing to genome size, TEs play key roles in chromosome architecture and gene regulation. TE activity is repressed by overlapping mechanisms of chromatin condensation, epigenetic transcriptional silencing, and targeting by small interfering RNAs. The specific regulation of different TEs, as well as their different roles in chromosome architecture and gene regulation, is specified by where on the chromosome the TE is located: near a gene, within a gene, in a pericentromere/TE island, or at the centromere core. In this Review, we investigate the silencing mechanisms responsible for inhibiting TE activity for each of these chromosomal contexts, emphasizing that chromosomal location is the first rule dictating the specific regulation of each TE. PMID:26869697

  10. Two wheat glutathione peroxidase genes whose products are located in chloroplasts improve salt and H2O2 tolerances in Arabidopsis.

    PubMed

    Zhai, Chao-Zeng; Zhao, Lei; Yin, Li-Juan; Chen, Ming; Wang, Qing-Yu; Li, Lian-Cheng; Xu, Zhao-Shi; Ma, You-Zhi

    2013-01-01

    Oxidative stress caused by accumulation of reactive oxygen species (ROS) is capable of damaging effects on numerous cellular components. Glutathione peroxidases (GPXs, EC 1.11.1.9) are key enzymes of the antioxidant network in plants. In this study, W69 and W106, two putative GPX genes, were obtained by de novo transcriptome sequencing of salt-treated wheat (Triticum aestivum) seedlings. The purified His-tag fusion proteins of W69 and W106 reduced H2O2 and t-butyl hydroperoxide (t-BHP) using glutathione (GSH) or thioredoxin (Trx) as an electron donor in vitro, showing their peroxidase activity toward H2O2 and toxic organic hydroperoxide. GFP fluorescence assays revealed that W69 and W106 are localized in chloroplasts. Quantitative real-time PCR (Q-RT-PCR) analysis showed that two GPXs were differentially responsive to salt, drought, H2O2, or ABA. Isolation of the W69 and W106 promoters revealed some cis-acting elements responding to abiotic stresses. Overexpression of W69 and W106 conferred strong tolerance to salt, H2O2, and ABA treatment in Arabidopsis. Moreover, the expression levels of key regulator genes (SOS1, RbohD and ABI1/ABI2) involved in salt, H2O2 and ABA signaling were altered in the transgenic plants. These findings suggest that W69 and W106 not only act as scavengers of H2O2 in controlling abiotic stress responses, but also play important roles in salt and ABA signaling.

  11. 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.

  12. NGL data conversion system

    NASA Astrophysics Data System (ADS)

    Shoji, Masahiro; Horiuchi, Nobuyasu

    2005-06-01

    We are developing a NGL data conversion system for EPL, for LEEPL, and for EBDW, which is based on our established photomask data conversion system, PATACON PC-cluster. For EPL data conversion, it has SF division, Complementary division, Stitching, Proximity effect correction, Alignment mark insertion, EB stepper control data creation, and Mask inspection data creation. For LEEPL data conversion, it has Pattern checking, Complementary division, Stitching, Stress distortion correction, Alignment mark insertion, and Mask inspection data creation. For EB direct-writing data conversion, it has Proximity effect correction and Extraction of aperture pattern for cell projection exposure.

  13. Iterated multidimensional wave conversion

    SciTech Connect

    Brizard, A. J.; Tracy, E. R.; Johnston, D.; Kaufman, A. N.; Richardson, A. S.; Zobin, N.

    2011-12-23

    Mode conversion can occur repeatedly in a two-dimensional cavity (e.g., the poloidal cross section of an axisymmetric tokamak). We report on two novel concepts that allow for a complete and global visualization of the ray evolution under iterated conversions. First, iterated conversion is discussed in terms of ray-induced maps from the two-dimensional conversion surface to itself (which can be visualized in terms of three-dimensional rooms). Second, the two-dimensional conversion surface is shown to possess a symplectic structure derived from Dirac constraints associated with the two dispersion surfaces of the interacting waves.

  14. etramps, a New Plasmodium falciparum Gene Family Coding for Developmentally Regulated and Highly Charged Membrane Proteins Located at the Parasite–Host Cell Interface

    PubMed Central

    Spielmann, Tobias; Fergusen, David J. P.; Beck, Hans-Peter

    2003-01-01

    After invasion of erythrocytes, the human malaria parasite Plasmodium falciparum resides within a parasitophorous vacuole and develops from morphologically and metabolically distinct ring to trophozoite stages. During these developmental phases, major structural changes occur within the erythrocyte, but neither the molecular events governing this development nor the molecular composition of the parasitophorous vacuole membrane (PVM) is well known. Herein, we describe a new family of highly cationic proteins from P. falciparum termed early transcribed membrane proteins (ETRAMPs). Thirteen members were identified sharing a conserved structure, of which six were found only during ring stages as judged from Northern and Western analysis. Other members showed different stage-specific expression patterns. Furthermore, ETRAMPs were associated with the membrane fractions in Western blots, and colocalization and selective permeabilization studies demonstrated that ETRAMPs were located in the PVM. This was confirmed by immunoelectron microscopy where the PVM and tubovesicular extensions of the PVM were labeled. Early expressed ETRAMPs clearly defined separate PVM domains compared with the negatively charged integral PVM protein EXP-1, suggesting functionally different domains in the PVM with an oppositely charged surface coat. We also show that the dynamic change of ETRAMP composition in the PVM coincides with the morphological changes during development. The P. falciparum PVM is an important structure for parasite survival, and its analysis might provide better understanding of the requirements of intracellular parasites. PMID:12686607

  15. An internal ribosome entry site located upstream of the crucifer-infecting tobamovirus coat protein (CP) gene can be used for CP synthesis in vivo.

    PubMed

    Dorokhov, Yu L; Ivanov, P A; Komarova, T V; Skulachev, M V; Atabekov, J G

    2006-09-01

    It was previously shown that, unlike the type member of the genus Tobamovirus (TMV U1), a crucifer-infecting tobamovirus (crTMV) contains a 148 nt internal ribosome entry site (IRES)(CP,148)(CR) upstream of the coat protein (CP) gene. Here, viral vectors with substitutions in the stem-loop (SL) region of CP subgenomic promoters (TMV U1-CP-GFP/SL-mut and crTMV-CP-GFP/SL-mut) were constructed and the levels of CP synthesis in agroinoculation experiments were compared. No CP-GFP (green fluorescent protein) synthesis was detected in Nicotiana benthamiana leaves inoculated with TMV U1-CP-GFP/SL-mut, whereas a small amount of CP-GFP synthesis was obtained in crTMV-CP-GFP/SL-mut-injected leaves. Northern blots proved that both promoters were inactive. It could be hypothesized that IRES-mediated early production of the CP by crTMV is needed for realization of its crucifer-infecting capacity.

  16. Streptomyces venezuelae ISP5230 Maintains Excretion of Jadomycin upon Disruption of the MFS Transporter JadL Located within the Natural Product Biosynthetic Gene Cluster

    PubMed Central

    Forget, Stephanie M.; McVey, Jennifer; Vining, Leo C.

    2017-01-01

    JadL was identified as a Major Facilitator Superfamily (MFS) transporter (T.C. 2.A.1) through sequence homology. The protein is encoded by jadL, situated within the jadomycin biosynthetic gene cluster. JadL has, therefore, been assigned a putative role in host defense by exporting its probable substrates, the jadomycins, a family of secondary metabolites produced by Streptomyces venezuelae ISP5230. Herein, we evaluate this assumption through the construction and analysis of a jadL disrupted mutant, S. venezuelae VS678 (ΔjadL::aac(3)IV). Quantitative determination of jadomycin production with the jadL disrupted mutant did not show a significant decrease in production in comparison to the wildtype strain, as determined by HPLC and by tandem mass spectrometry. These results suggest that efflux of jadomycin occurs upon disruption of jadL, or that JadL is not involved in jadomycin efflux. Potentially, other transporters within S. venezuelae ISP5230 may adopt this role upon inactivation of JadL to export jadomycins. PMID:28377749

  17. Association of rs7719175, located in the IL13 gene promoter, with Schistosoma haematobium infection levels and identification of a susceptibility haplotype.

    PubMed

    Isnard, A; Kouriba, B; Doumbo, O; Chevillard, C

    2011-01-01

    Urinary schistosomiasis is a parasitic disease caused by Schistosoma haematobium helminths. S. haematobium eggs may remain trapped within the bladder or the ureter walls, causing major pathological disorders in the urogenital system. The polymorphism rs1800925(C/T) of the IL13 gene promoter, which is functional, has previously been associated with susceptibility to S. haematobium infection. The aim of this study was to further our understanding and to determine whether, in the 5q31-q33 region, rs1800925 affects infection levels alone or in synergy with other polymorphisms. After sequencing the IL13 promoter and increasing the single-nucleotide polymorphism density, we performed a linkage disequilibrium analysis between rs1800925 and the other markers in a Malian population. Multivariate linear regression analysis and electrophoretic mobility shift assay (EMSA) were performed to characterized markers in linkage disequilibrium with rs1800925. An additional polymorphism, rs7719175, in the IL13 promoter was associated with controlling infection levels in multivariate analysis. The haplotype rs7719175T-rs1800925C was associated with high infection levels. EMSA indicated that rs7719175 affects the binding of transcriptional factors to the promoter region. Polymorphisms rs7719175 and rs1800925 have a synergistic role in the control of infection levels caused by S. haematobium and using them as a haplotype allows a better discrimination between infected subjects.

  18. Cloning of the cDNAs for the small subunits of bovine and human DNA polymerase {delta} and chromosomal location of the human gene (POLD2)

    SciTech Connect

    Zhang, Jian; Tan, Cheng-Keat; Downey, K.M.

    1995-09-01

    cDNAs encoding the small subunit of bovine and human DNA polymerase {delta} have been cloned and sequenced. The predicted polypeptides, 50,885 and 51,289 Daltons, respectively, are 94% identical, similar to the catalytic subunits. The high degree of conservation of the polypeptides suggests an essential function for the small subunit in the heterodimeric core enzyme. Although the catalytic subunit of DNA polymerase 5 shares significant homology with those of the herpes virus family of DNA polymerases, the small subunit of mammalian DNA polymerase 6 is not homologous to the small subunit of either herpes simplex virus type 1 DNA polymerase (UL42 protein) or the Epstein-Barr virus DNA polymerase (BMRF1 protein). Searches of the protein databases failed to detect significant homology with any protein sequenced thus far. PCR analysis of DNA from a panel of human-hamster hybrid cell lines localized the gene (POLD2) for the small subunit of DNA polymerase 5 to human chromosome 7. 45 refs., 2 figs., 2 tabs.

  19. Biocatalytic Conversion of Avermectin to 4"-Oxo-Avermectin: Characterization of Biocatalytically Active Bacterial Strains and of Cytochrome P450 Monooxygenase Enzymes and Their Genes

    PubMed Central

    Jungmann, Volker; Molnár, István; Hammer, Philip E.; Hill, D. Steven; Zirkle, Ross; Buckel, Thomas G.; Buckel, Dagmar; Ligon, James M.; Pachlatko, J. Paul

    2005-01-01

    4"-Oxo-avermectin is a key intermediate in the manufacture of the agriculturally important insecticide emamectin benzoate from the natural product avermectin. Seventeen biocatalytically active Streptomyces strains with the ability to oxidize avermectin to 4"-oxo-avermectin in a regioselective manner have been discovered in a screen of 3,334 microorganisms. The enzymes responsible for this oxidation reaction in these biocatalytically active strains were found to be cytochrome P450 monooxygenases (CYPs) and were termed Ema1 to Ema17. The genes for Ema1 to Ema17 have been cloned, sequenced, and compared to reveal a new subfamily of CYPs. Ema1 to Ema16 have been overexpressed in Escherichia coli and purified as His-tagged recombinant proteins, and their basic enzyme kinetic parameters have been determined. PMID:16269732

  20. 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.

  1. Post-transcriptional regulation of cytokine genes in fish: A role for conserved AU-rich elements located in the 3'-untranslated region of their mRNAs.

    PubMed

    Roca, Francisco J; Cayuela, María L; Secombes, Chris J; Meseguer, José; Mulero, Victoriano

    2007-01-01

    The overproduction of cytokines, such us interleukin-1beta (IL-1beta) and tumor necrosis factor alpha (TNFalpha), contributes to the pathological complications observed in many inflammatory diseases caused by bacterial endotoxins. The synthesis of these cytokines is tightly regulated at both transcriptional and post-transcriptional levels. Post-transcriptional regulation of gene expression depends on specific cis-acting sequences and trans-acting factors. Thus, the presence of adenylate- and uridylate-rich (AU-rich) elements (AREs) has been described in the 3'-untranslated regions (UTRs) of many unstable mammalian mRNAs. Although, it represents the most widespread, phylogenetically conserved and efficient determinant of mRNA stability among those so far characterized in mammalian cells, no studies are available on the functional relevance of this sequence in non-mammalian vertebrates. In this contribution, we study the enzymatic activity of various luciferase reporter constructs, containing or lacking the 3'UTR of IL-1beta and TNFalpha from different fish species, and report the finding that bony fish AREs are able to decrease luciferase activity but are less potent than their mammalian counterparts. Surprisingly, the 3'UTR of the IL-1beta from the cartilaginous fish small spotted catshark had the greatest ability to decrease luciferase activity. Lastly, the functional significance of the above was confirmed by measuring the half-life of IL-1beta and TNFalpha mRNAs in gilthead seabream leukocytes by blocking transcription with actinomycin D. Both cytokine mRNAs were unstable with an estimated half-life of about 45 min in control and activated cells.

  2. Early expression of a Trypanosoma brucei VSG gene duplicated from an incomplete basic copy.

    PubMed

    Aline, R F; Myler, P J; Gobright, E; Stuart, K D

    1994-01-01

    Intrachromosomal variant surface glycoprotein (VSG) genes in Trypanosoma brucei are expressed by a mechanism involving gene conversion. The 3' boundary of gene conversion is usually within the last 130 bp of the VSG gene, a region of partially conserved sequences. We report here the loss of the predominant telomeric A VSG gene in the cloned variant antigenic type (VAT) 5A3, leaving only an intrachromosomal A VSG gene (the A-B gene). The nucleotide sequence of the A-B VSG gene reveals that it lacks the normal VSG 3' sequence. Surprisingly, we find cells expressing this A-B VSG gene in relapse populations arising from VAT 5A3. Since the A VSG mRNAs from these cells have a normal 3' sequence, the incomplete A-B VSG gene must be expressed via a partial gene conversion that supplies the functional 3' end. Although the A-B VSG gene is no longer predominant like the telomeric A VSG gene, it is still expressed more frequently than other intrachromosomal VSG genes, suggesting that factors other than a telomeric location determine whether a VSG gene is expressed early in a serodeme.

  3. 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.

  4. High affinity human IFN-gamma-binding capacity is encoded by a single receptor gene located in proximity to c-ros on human chromosome region 6q16 to 6q22.

    PubMed

    Pfizenmaier, K; Wiegmann, K; Scheurich, P; Krönke, M; Merlin, G; Aguet, M; Knowles, B B; Ucer, U

    1988-08-01

    We have used human-rodent somatic cell hybrids to investigate the regional localization of the IFN-gamma R gene on human chromosome 6 and studied functional and antigenic characteristics of the expressed IFN-gamma R by Scatchard analyses of 125I-IFN-gamma binding and binding of an anti-receptor mAb (A6C5). The data obtained revealed coordinate expression of IFN-gamma- and A6C5-binding capacity as well as competition in binding to chromosome 6-positive hybrids and normal cells, indicating that the A6C5-defined protein is by itself capable of high affinity IFN-gamma binding and, thus, is likely to constitute the major IFN-gamma R protein of distinct cell types. The receptor gene could be allocated to region 6q16 to 6q22, which also contains the c-ros oncogene. Genetic linkage of the IFN-gamma R gene to an oncogene located in a region of non-random chromosomal aberrations may have a causal relationship to the deregulated IFN-gamma R expression in several malignancies.

  5. 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.

  6. 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.

  7. 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

  8. Conversations in Child Care

    ERIC Educational Resources Information Center

    Bardige, Betty; Segal, Marilyn

    2004-01-01

    In this article, Bardige and Segal discuss how teachers can help a toddler's language and literacy development through conversation. They suggest an array of tactics, from asking young children open-ended, intellectually challenging questions to going beyond the here and now when carrying on a conversation. Research has shown that the practice of…

  9. Recording Conversations in Schools.

    ERIC Educational Resources Information Center

    Gluckman, Ivan B.; Koerner, Thomas J., Jr.

    1988-01-01

    In general, because of varying federal and state legislation and a paucity of court decisions, the law governing the recording of conversations is in considerable flux. School personnel desiring to record conversations in school without the consent or knowledge of all parties involved must proceed with considerable caution. (Author)

  10. 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.

  11. 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…

  12. 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.

  13. Content for Conversation Partners.

    ERIC Educational Resources Information Center

    Olson, Kathleen

    2002-01-01

    Suggests that a good strategy for helping English language learners to develop communicative competence in English is by pairing them with native English speakers. In such conversation programs, conversation partners should be provided with topics and activities that incorporate the goals, interests, and experiences of the learners. Recommends…

  14. Locative Inversion in Cantonese.

    ERIC Educational Resources Information Center

    Mok, Sui-Sang

    This study investigates the phenomenon of "Locative Inversion" in Cantonese. The term "Locative Inversion" indicates that the locative phrase (LP) syntactic process in Cantonese and the appears at the sentence-initial position and its logical subject occurs postverbally. It is demonstrated that this Locative Inversion is a…

  15. 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;…

  16. Genes

    MedlinePlus

    ... Search Search MedlinePlus GO GO About MedlinePlus Site Map FAQs Customer Support Health Topics Drugs & Supplements Videos & Tools Español You Are Here: Home → Medical Encyclopedia → Genes URL of this page: //medlineplus.gov/ency/article/ ...

  17. A {open_quotes}balanced{close_quotes} Y:16 translocation with the Y breakpoint just proximal to the Yq heterochromatin boundary associated with Turner-like neonatal lymphedema suggests the location of a potential anti-Turner gene

    SciTech Connect

    Erickson, R.P.; Hudgins, L.; Stone, J.F.

    1994-09-01

    A male patient with Turner-like hydrops in the newborn period (Bonnevie-Ullrich syndrome) was studied. The extensive nucchal cystic hygroma and hydrops resolved over several weeks. The karyotype was 46,X,t(Y;16)(q11.2;q24). The paternal karyotype was normal. Chromosome painting with the heterochromatic long arm repeat DYZ2 disclosed that all the hybridization was on the derivative 16. This was confirmed by chromosome painting with DYZ1, the other major Y long arm heterochromatic repeat, and DYZ3, the Y alphoid, centromeric repeat, which showed chromosomal separation of the 2 stained regions. A {open_quotes}FISHing trip{close_quotes} was performed using the Y YAC contig created in Dr. David Page`s laboratory. This disclosed 2 YACs located just proximal to the Y heterochromatin which {open_quotes}jumped{close_quotes} the translocation. The recent discovery of a candidate gene for the azoospermia factor (AZF) in this region suggests the possibility that there are several Y-expressed genes adjacent to the heterochromatin boundary as there are near the pseudoautosomal boundary.

  18. Sleeping at work: not all about location, location, location.

    PubMed

    Jay, Sarah M; Aisbett, Brad; Sprajcer, Madeline; Ferguson, Sally A

    2015-02-01

    Working arrangements in industries that use non-standard hours sometimes necessitate an 'onsite' workforce where workers sleep in accommodation within or adjacent to the workplace. Of particular relevance to these workers is the widely held (and largely anecdotal) assumption that sleep at home is better than sleep away, particularly when away for work. This narrative review explores the idea that sleep outcomes in these unique work situations are the product of an interaction between numerous factors including timing and duration of breaks, commute length, sleeping environment (noise, movement, vibration, light), circadian phase, demographic factors and familiarity with the sleep location. Based on the data presented in this review, it is our contention that the location of sleep, whilst important, is secondary to other factors such as the timing and duration of sleep periods. We suggest that future research should include measures that allow conceptualisation of other critical factors such as familiarity with the sleeping environment.

  19. Multiple binding sites for nuclear proteins of the anterior pituitary are located in the 5'-flanking region of the porcine follicle-stimulating hormone (FSH) beta-subunit gene.

    PubMed

    Kato, Y; Tomizawa, K; Kato, T

    1999-12-20

    Gonadotropins, follicle-stimulating hormone (FSH), and luteinizing hormone (LH), are synthesized specifically in the gonadotropes of the anterior pituitary. The aim of this study was to investigate nuclear factors that bind specifically to the porcine FSH beta-subunit gene. We examined nuclear protein binding to 2.75 kilobase pairs (kbp) of DNA adjacent to the porcine FSH beta-subunit gene: about 2.32 kbp of upstream DNA and 0.43 kbp of downstream DNA. The upstream region contains only TATA box, CACCC element, and some imperfect sequences of cAMP-responsive element, activator protein-1 binding site, and activator protein-2 binding site. Gel mobility shift assay using nuclear proteins extracted from the porcine anterior pituitary revealed that the proteins bound to a limited region of DNA, 107 bp long (designated as Fd2), located about -800 bp upstream from the transcription initiation site. Competitive binding assays demonstrated that the protein binding was sequence specific; the addition of excess amounts of several putative regulatory sequences and plasmid (non-homologous) DNA fragments did not reduce the binding. Furthermore, all five subfragments of Fd2 were also bound by the pituitary nuclear proteins, showing that the entire region of Fd2 is involved in this interaction. Southwestern blotting demonstrated that at least seven protein species of 110, 98, 78, 63, 52, 42, and 35 kDa recognize Fd2. Nuclear proteins from several other porcine tissues were also able to bind to the Fd2 fragment but the gel shift patterns were different and the bindings were weak, although only the cerebellum showed a pattern of binding that was similar to that of the anterior pituitary. These data suggest that multiple proteins of the anterior pituitary recognize a specific region of the porcine FSH beta-subunit gene.

  20. Solar Thermal Conversion

    SciTech Connect

    Kreith, F.; Meyer, R. T.

    1982-11-01

    The thermal conversion process of solar energy is based on well-known phenomena of heat transfer (Kreith 1976). In all thermal conversion processes, solar radiation is absorbed at the surface of a receiver, which contains or is in contact with flow passages through which a working fluid passes. As the receiver heats up, heat is transferred to the working fluid which may be air, water, oil, or a molten salt. The upper temperature that can be achieved in solar thermal conversion depends on the insolation, the degree to which the sunlight is concentrated, and the measures taken to reduce heat losses from the working fluid.

  1. 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.

  2. 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.

  3. Evolutionarily Engineered Ethanologenic Yeast Detoxifies Lignocellulosic Biomass Conversion Inhibitors by Reprogrammed Pathways

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lignocellulosic biomass conversion inhibitors furfural and HMF inhibit microbial growth and interfere with subsequent fermentation of ethanol, posing significant challenges for a sustainable cellulosic ethanol conversion industry. Numerous yeast genes were found to be associated with the inhibitor ...

  4. 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.

  5. Conversational flow promotes solidarity.

    PubMed

    Koudenburg, Namkje; Postmes, Tom; Gordijn, Ernestine H

    2013-01-01

    Social interaction is fundamental to the development of various aspects of "we-ness". Previous research has focused on the role the content of interaction plays in establishing feelings of unity, belongingness and shared reality (a cluster of variables referred to as solidarity here). The present paper is less concerned with content, but focuses on the form of social interaction. We propose that the degree to which conversations flow smoothly or not is, of itself, a cue to solidarity. We test this hypothesis in samples of unacquainted and acquainted dyads who communicate via headsets. Conversational flow is disrupted by introducing a delay in the auditory feedback (vs. no delay). Results of three studies show that smoothly coordinated conversations (compared with disrupted conversations and a control condition) increase feelings of belonging and perceptions of group entitativity, independently of conversation content. These effects are driven by the subjective experience of conversational flow. Our data suggest that this process occurs largely beyond individuals' control. We conclude that the form of social interaction is a powerful cue for inferring group solidarity. Implications for the impact of modern communication technology on developing a shared social identity are discussed.

  6. 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…

  7. Locatives in Kpelle.

    ERIC Educational Resources Information Center

    Kuha, Mai

    This paper examines the differences between locative expressions in Kpelle and English, based on the dialect of one native speaker of Kpelle. It discusses the crucial role of the reference object in defining the meaning of locatives in Kpelle, in contrast to English, where the characteristics of the object to be located are less important. An…

  8. Analysis of Linear Conversion to Two Modes

    NASA Astrophysics Data System (ADS)

    Brizard, Alain J.; Jaun, Andre; Kaufman, Allan N.; Tracy, Eugene R.

    2003-10-01

    Recent experimental observations [1] and computer simulations [2] show that, in a tokamak plasma with multispecies ions, an incident magnetosonic wave converts either to an ion-hybrid Bernstein wave or to an ion-cyclotron wave, depending on the location of the conversion region in the poloidal cross section. We present a cold-plasma model of simultaneous conversion to these two modes, and obtain explicit expressions for transmission and conversion coefficients. Our approach is based on phase-space analysis of multiple conversion [3], in two or four phase-space dimensions (i.e., one or two spatial dimensions).Our ray-tracing algorithm [4], for detection of conversion and for treatment of ray-splitting due to conversion, will be applied to this process. 1.E Nelson-Melby, M Porkolab, P T Bonoli, Y Lin, A Mazurenko, S J Wukitch, Phys Rev Lett 90 (2003) 155004 2.E F Jaeger, L A Berry, J R Myra, D B Batchelor, E D'Azevedo, P T Bonoli, C K Phillips, D N Smithe, D A D'Ippolito, M D Carter, R J Dumont, J C Wright, R W Harvey, Phys Rev Lett 90 (2003) 195001 3. Y-M Liang, J J Morehead, D R Cook, T Fla, A N Kaufman, Physics Letters A193 (1994) 82 4. E R Tracy, A N Kaufman, A Jaun, Physics Letters A290 (2001) 309

  9. 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.

  10. 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).

  11. 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.

  12. Reconstruction errors in digital-to-analog conversion.

    NASA Technical Reports Server (NTRS)

    Dotson, W. P., Jr.

    1972-01-01

    Error could theoretically be found as a function of time, midway between any two arbitrarily placed sample points. However, the analysis and the result would be difficult to use. As an alternative, worst-case instantaneous errors can be evaluated near the base-line crossing and at the peak of the analog signal. Location of sample points affects the error values obtained, but use of the points provides a means of comparing different reconstruction techniques. Zero-order conversion is discussed together with first-order conversion, second-order conversion, and third-order conversion.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Power conversion technologies

    SciTech Connect

    Haigh, R E

    1998-01-01

    The Power Conservation Technologies thrust area supports initiatives that enhance the core competencies of the Lawrence Livermore National Laboratory (LLNL) Engineering Directorate in the area of solid-state power electronics. Through partnerships with LLNL programs, projects focus on the development of enabling technologies for existing and emerging programs that have unique power conversion requirements. This year, a multi-disciplinary effort was supported which demonstrated solid-state, high voltage generation by using a dense, monolithic photovoltaic array. This effort builds upon Engineering's strengths in the core technology areas of power conversion, photonics, and microtechnologies.

  19. Reversible micromachining locator

    SciTech Connect

    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.

  20. Automatic vehicle location system

    NASA Technical Reports Server (NTRS)

    Hansen, G. R., Jr. (Inventor)

    1973-01-01

    An automatic vehicle detection system is disclosed, in which each vehicle whose location is to be detected carries active means which interact with passive elements at each location to be identified. The passive elements comprise a plurality of passive loops arranged in a sequence along the travel direction. Each of the loops is tuned to a chosen frequency so that the sequence of the frequencies defines the location code. As the vehicle traverses the sequence of the loops as it passes over each loop, signals only at the frequency of the loop being passed over are coupled from a vehicle transmitter to a vehicle receiver. The frequencies of the received signals in the receiver produce outputs which together represent a code of the traversed location. The code location is defined by a painted pattern which reflects light to a vehicle carried detector whose output is used to derive the code defined by the pattern.

  1. 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)

  2. 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…

  3. Conversations and Collaborations

    ERIC Educational Resources Information Center

    Korpan, Cynthia

    2010-01-01

    This paper looks at how a series of conversations contributed to the development of a newly formed role at the University of Victoria--Teaching Assistant Consultants (TACs). TACs act as departmental mentors for teaching assistants (TAs) in their respective departments, charged with providing support in the form of discipline-specific workshops…

  4. 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)

  5. 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.

  6. Electromechanical Energy Conversion.

    ERIC Educational Resources Information Center

    LePage, Wilbur R.

    This programed text on electromechanical energy conversion (motors and generators) was developed under contract with the U.S. Office of Education as Number 12 in a series of materials for use in an electrical engineering sequence. It is intended to be used in conjunction with other materials and with other short texts in the series. (DH)

  7. Conversion or New Building?

    ERIC Educational Resources Information Center

    Berkeley, Phil

    1970-01-01

    Examined first is "the overall problem of housing a TV studio complex to see what particular sorts of buildings are required and how they must be related," and then considered are "the relative merits and particular problems of new studio building or a conversion." (LS)

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. Electronic apex locators.

    PubMed

    Gordon, M P J; Chandler, N P

    2004-07-01

    Prior to root canal treatment at least one undistorted radiograph is required to assess canal morphology. The apical extent of instrumentation and the final root filling have a role in treatment success, and are primarily determined radiographically. Electronic apex locators reduce the number of radiographs required and assist where radiographic methods create difficulty. They may also indicate cases where the apical foramen is some distance from the radiographic apex. Other roles include the detection of root canal perforation. A review of the literature focussed first on the subject of electronic apex location. A second review used the names of apex location devices. From the combined searches, 113 pertinent articles in English were found. This paper reviews the development, action, use and types of electronic apex locators.

  16. Smart Location Mapping

    EPA Pesticide Factsheets

    The Smart Location Database, Access to Jobs and Workers via Transit, and National Walkability Index tools can help assess indicators related to the built environment, transit accessibility, and walkability.

  17. Uranium Location Database Compilation

    EPA Pesticide Factsheets

    EPA has compiled mine location information from federal, state, and Tribal agencies into a single database as part of its investigation into the potential environmental hazards of wastes from abandoned uranium mines in the western United States.

  18. 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.

  19. Wind energy conversion system

    DOEpatents

    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.

  20. Persuasion Detection in Conversation

    DTIC Science & Technology

    2010-03-01

    is the first step in developing machine learning systems that can automatically detect persuasion in conversations. This corpus was developed from...requires some form of persuasion. Based on this research, it may be possible to construct a machine learning system that can automatically detect...specific markers, can these markers be learned and identified by annotators? Our research attempted to answer all of these questions by annotating a

  1. Advanced Thermal Conversion Systems

    DTIC Science & Technology

    2015-03-18

    BAA09-31 3  Figure 1. (a) Energy diagram of the PETE process. Photo -excitation leads to enhanced...photovoltaic cells at 3000x concentration (~38%). As shown in Fig. 2(b), the highest conversion efficiencies are obtained by using photo -cathodes...p-type 4H-SiC (left) and polycrystalline n-type 3C-SiC (right). The fabrication process for p-type devices used bulk p- doped 4H-SiC wafers from

  2. 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.

  3. 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.

  4. 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.

  5. Natural gas conversion process

    SciTech Connect

    Not Available

    1992-01-01

    The experimental apparatus was dismantled and transferred to a laboratory space provided by Lawrence Berkeley Laboratory (LBL) which is already equipped with a high-ventilation fume hood. This will enable us to make tests at higher gas flow rates in a safe environment. Three papers presented at the ACS meeting in San Francisco (Symposium on Natural Gas Upgrading II) April 5--10, 1992 show that the goal of direct catalytic conversion of Methane into heavier Hydrocarbons in a reducing atmosphere is actively pursued in three other different laboratories. There are similarities in their general concept with our own approach, but the temperature range of the experiments reported in these recent papers is much lower and this leads to uneconomic conversion rates. This illustrates the advantages of Methane activation by a Hydrogen plasma to reach commercial conversion rates. A preliminary process flow diagram was established for the Integrated Process, which was outlined in the previous Quarterly Report. The flow diagram also includes all the required auxiliary facilities for product separation and recycle of the unconverted feed as well as for the preparation and compression of the Syngas by-product.

  6. 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

  7. RFI emitter location techniques

    NASA Technical Reports Server (NTRS)

    Rao, B. L. J.

    1973-01-01

    The possibility is discussed of using Doppler techniques for determining the location of ground based emitters causing radio frequency interference with low orbiting satellites. An error analysis indicates that it is possible to find the emitter location within an error range of 2 n.mi. The parameters which determine the required satellite receiver characteristic are discussed briefly along with the non-real time signal processing which may by used in obtaining the Doppler curve. Finally, the required characteristics of the satellite antenna are analyzed.

  8. 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.

  9. 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

  10. 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…

  11. 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…

  12. Uranium Location Database

    EPA Pesticide Factsheets

    A GIS compiled locational database in Microsoft Access of ~15,000 mines with uranium occurrence or production, primarily in the western United States. The metadata was cooperatively compiled from Federal and State agency data sets and enables the user to conduct geographic and analytical studies on mine impacts on the public and environment.

  13. Optimal Facility-Location.

    PubMed

    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.

  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. 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...

  16. Locating gravitational potential energy

    NASA Astrophysics Data System (ADS)

    Keeports, David

    2017-01-01

    Where does gravitational potential energy reside when a ball is in the air? The perfectly correct answer is that it is located in the ball-Earth system. Still, mechanical energy conservation problems are routinely solved by assigning a potential energy to the ball alone. Provided here is a proof that such an assignment introduces only an entirely undetectable error.

  17. 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.

  18. 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.

  19. VA Health Care Facilities Locator

    MedlinePlus

    ... VA » Locations » Find Locations Locations Find Locations The javascript used here is for validation purpose only. Your browser doesn't seem to support javascript or has it disabled. This site is a ...

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. Direct somatic lineage conversion

    PubMed Central

    Tanabe, Koji; Haag, Daniel; Wernig, Marius

    2015-01-01

    The predominant view of embryonic development and cell differentiation has been that rigid and even irreversible epigenetic marks are laid down along the path of cell specialization ensuring the proper silencing of unrelated lineage programmes. This model made the prediction that specialized cell types are stable and cannot be redirected into other lineages. Accordingly, early attempts to change the identity of somatic cells had little success and was limited to conversions between closely related cell types. Nuclear transplantation experiments demonstrated, however, that specialized cells even from adult mammals can be reprogrammed into a totipotent state. The discovery that a small combination of transcription factors can reprogramme cells to pluripotency without the need of oocytes further supported the view that these epigenetic barriers can be overcome much easier than assumed, but the extent of this flexibility was still unclear. When we showed that a differentiated mesodermal cell can be directly converted to a differentiated ectodermal cell without a pluripotent intermediate, it was suggested that in principle any cell type could be converted into any other cell type. Indeed, the work of several groups in recent years has provided many more examples of direct somatic lineage conversions. Today, the question is not anymore whether a specific cell type can be generated by direct reprogramming but how it can be induced. PMID:26416679

  5. 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).

  6. 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.

  7. 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.

  8. 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

  9. Drivers of wetland conversion: a global meta-analysis.

    PubMed

    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

  10. Aquatic Nuisance Species Locator

    EPA Pesticide Factsheets

    Data in this map has been collected by the United States Geological Survey's Nonindigenous Aquatic Species program located in Gainesville, Florida (http://nas.er.usgs.gov/default.aspx). This dataset may have some inaccuracies and is only current to June 15, 2012. The species identified in this dataset are not inclusive of all aquatic nuisance species, but rather a subset identified to be at risk for transport by recreational activities such as boating and angling. Additionally, the locations where organisims have been identified are also not inclusive and should be treated as a guide. Organisms are limited to the following: American bullfrog, Asian clam, Asian shore crab, Asian tunicate, Australian spotted jellyfish, Chinese mitten crab, New Zealand mudsnail, Colonial sea squirt, Alewife, Bighead carp, Black carp, Flathead catfish, Grass carp, Green crab, Lionfish, Northern snakehead, Quagga mussel, Round Goby, Ruffe, Rusty crayfish, Sea lamprey, Silver carp, Spiny water flea, Veined rapa whelk, Zebra mussel

  11. 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.

  12. Electric current locator

    DOEpatents

    King, Paul E [Corvallis, OR; Woodside, Charles Rigel [Corvallis, OR

    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.

  13. Coso MT Site Locations

    DOE Data Explorer

    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.

  14. 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.

  15. 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.

  16. Separatrix location in NSTX

    NASA Astrophysics Data System (ADS)

    Kelly, Frederick; Maingi, Rajesh; Maqueda, Ricky; Menard, Jon; Leblanc, Ben; Bell, Ron; Paul, Stephen

    2008-11-01

    The separatrix location and corresponding plasma parameters in NSTX were estimated for H-mode discharge 117125 containing both MARFEs and ELMs and for Type V ELMy H-mode discharge 128337. Since equilibrium reconstructions with LRDFIT did not accurately locate the LFS separatrix, a method based on the strong electron parallel heat conductivity was used to map the LFS magnetic flux surfaces to the HFS since the innermost Thomson scattering measurement of Te(R) is the most accurate. During a MARFE or at MARFE onset in NSTX shot 117125, this method estimated the electron temperature at the LFS separatrix, Te,sep, to vary between 31 and 41 eV. At times with no MARFE or ELM, Te,sep ranged between 41 and 93 eV. These Te,sep values compare well with Te,sep values (28-35 eV) in TEXTOR just before MARFE onset.^1 In NSTX shot 128337 late in the Type V ELMy phase, Te,sep was estimated to be ˜100 eV. These separatrix locations place the Er well outside the separatrix. [1] F.A. Kelly, W.M. Stacey, J. Rapp and M. Brix, Phys. Plasmas 8 (2001) 3382.

  17. Locating the stranger rapist.

    PubMed

    Davies, A; Dale, A

    1996-04-01

    As part of a larger project evaluating aspects of offender profiling, an initial study was undertaken of the geographic aspects of approximately 300 sexual offences carried out by 79 stranger rapists. The objective was to focus further research on the topic into potentially useful channels, but information thought to be of immediate use to investigating officers was also produced. It was ascertained that at least one-fifth of the sample of stranger rapists were itinerant to a greater or lesser extent. Analysis of the cases where both the offender's address and the location where he approached the victim were known, indicated that the majority of attacks (75 per cent) were initiated within five miles of the offenders' homes. The apparent reasons for victims being approached unusually far away included targeting of locations where numbers of suitable victims were available; raping during relatively sophisticated property offences; 'prowling' or 'hunting' over large areas by subjects who spent considerable amounts of time so doing; access to transport; and familiarity with widely dispersed neighbourhoods, often due to the offender having lived in two or more locations. As a result of this work, future research on the geography of rape will be directed towards those aspects of the offences which have been identified as relevant to the distance between an offender's base and the site where he approached his victim.

  18. 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.

  19. 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.

  20. The Role of Conversation Policy in Carrying Out Agent Conversations

    SciTech Connect

    Link, Hamilton E.; Phillips, Laurence R.

    1999-05-20

    Structured conversation diagrams, or conversation specifications, allow agents to have predictable interactions and achieve predefined information-based goals, but they lack the flexibility needed to function robustly in an unpredictable environment. We propose a mechanism that combines a typical conversation structure with a separately established policy to generate an actual conversation. The word "policy" connotes a high-level direction external to a specific planned interaction with the environment. Policies, which describe acceptable procedures and influence decisions, can be applied to broad sets of activity. Based on their observation of issues related to a policy, agents may dynamically adjust their communication patterns. The policy object describes limitations, constraints, and requirements that may affect the conversation in certain circumstances. Using this new mechanism of interaction simplifies the description of individual conversations and allows domain-specific issues to be brought to bear more easily during agent communication. By following the behavior of the conversation specification when possible and deferring to the policy to derive behavior in exceptional circumstances, an agent is able to function predictably under normal situations and still act rationally in abnormal situations. Different conversation policies applied to a given conversation specification can change the nature of the interaction without changing the specification.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. MGC9753 gene, located within PPP1R1B-STARD3-ERBB2-GRB7 amplicon on human chromosome 17q12, encodes the seven-transmembrane receptor with extracellular six-cystein domain.

    PubMed

    Katoh, Masuko; Katoh, Masaru

    2003-06-01

    MYC, ERBB2, MET, FGFR2, CCNE1, MYCN, WNT2, CD44, MDM2, NCOA3, IQGAP1 and STK6 loci are amplified in human gastric cancer. It has been reported that the gene corresponding to EST H16094 is co-amplified with ERBB2 gene in human gastric cancer. Here, we identified and characterized the gene corresponding to EST H16094 by using bioinformatics. BLAST programs revealed that EST H16094 was derived from the uncharacterized MGC9753 gene. Two ORFs were predicted within human MGC9753 mRNA, and ORF1 (nucleotide position 18-980 of NM_033419.1) was predicted as the coding region of human MGC9753 mRNA based on comparative genomics. Nucleotide sequence of mouse Mgc9753 mRNA was next determined in silico by modification of AK052486 cDNA (deleting C at the nucleotide position 37). Human MGC9753 and mouse Mgc9753 proteins were 320-amino-acid seven-transmembrane receptors with the N-terminal six-cysteine domain and an N-glycosylation site (85.0% total-amino-acid identity). Human MGC9753 protein showed 90.6% total-amino-acid identity with human CAB2 aberrant protein, which lacked the third-transmembrane domain of MGC9753 due to frame shifts within ORF. Human MGC9753 gene, consisting of eight exons, were clustered with PPP1R1B, STARD3, TCAP, PNMT, ERBB2, MGC14832 and GRB7 genes within the 120-kb region. PPP1R1B, STARD3, MGC9753, ERBB2 and GRB7 genes are co-amplified in several cases of gastric cancer. This is the first report on comprehensive characterization of the amplicon around the PPP1R1B-STARD3-TCAP-PNMT-MGC9753-ERBB2-MGC14832-GRB7 locus on human chromosome 17q12.

  7. Energy conversion apparatus

    SciTech Connect

    Porter, D.R.

    1988-10-18

    This patent describes an energy conversion apparatus comprising: an engine, the engine comprising a cylinder and a piston reciprocally mounted therein, the cylinder defining a combustion chamber on one side of the piston for receiving a fuel mixture and a fluid drive chamber on the other side of the piston for receiving hydraulic fluid, a turbine, the turbine comprising a housing and a vaned turbine wheel rotatably mounted on a drive shaft journalled in the housing, hydraulic means for coupling fluid in the fluid drive chamber of the cylinder with the housing for rotatably driving the turbine wheel and the drive shaft upon a given movement of the piston, means for providing the combustion chamber of the engine with a fuel mixture comprising hydrogen and oxygen, an ignition means for selectively igniting the mixture in the combustion chamber, and purging means for selectively rotating the turbine prior to ignition of the fuel mixture in the engine to remove air therefrom, the purging means comprising a pump means for moving fluid from the reservoir into the fluid drive chambers, the conduit means and the turbine housing, whereby the piston driven by the ignited fuel mixture forces fluid in the fluid drive chamber against the vanes of the turbine wheel to rotate the drive shaft.

  8. 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.

  9. Microbial conversion of coal

    SciTech Connect

    Bean, R.M. )

    1989-10-01

    The objectives of this project were to describe in detail the degradation of coals by fungi and microbes, to expand the range of applicability of the process to include new microbes and other coal types, to identify the means by which biosolubilization of coal is accomplished, and to explore means to enhance the rates and extent of coal bioconversion. The project was initiated in a response to the discovery by Dr. Martin Cohen at the University of Hartford, of a fungal strain of Coriolus versicolor that would render a solid coal substance, leonardite, into a liquid product. The project has identified the principal agent of leonardite solubilization as a powerful metal chelator, most likely a fungal-produced siderophore. Another nonlaccase enzyme has also been identified as a unique biosolubilizing agent produced by C. versicolor. Assays were developed for the quantitative determination of biological coal conversion, and for the determination of potency of biosolubilizing agent. Screening studies uncovered several microbial organisms capable of coal biodegradation, and led to the discovery that prolonged heating in air at the moderate temperature of 150{degree}C allowed the biodegradation of Illinois {number sign}6 coal to material soluble in dilute base. Chemical studies showed that leonardite biosolubilization was accompanied by relatively small change in composition, while solubilization of Illinois {number sign}6 coal involves considerable oxidation of the coal. 24 refs., 32 figs., 27 tabs.

  10. Solar energy conversion apparatus

    SciTech Connect

    Nash, S.G.

    1983-10-18

    Solar energy conversion apparatus is disclosed including a housing portion, an energy absorbing portion, a fluid directing portion and a cover portion; the housing portion including a molded plastic pan member including a base section with upwardly extending spaced spacer sections, the pan member including outwardly inclined sidewall sections having spaced inner and outer wall sections with a top section including an outwardly extending flange section and an inwardly extending slotted frame section; the energy absorbing portion including a conductive metal liner member positioned within the housing portion and resting on the upper surfaces of the spacer sections, a conductive metal separator section extending between the liner sidewall sections adjacent the upper ends thereof and enclosing the liner member; the fluid directing portion including a plurality of parallel spaced longitudinal baffle members arranged in a staggered relationship to provide a tortuous fluid path through the apparatus, an inlet opening and an outlet opening to the tortuous path, the baffle members extending upwardly from the liner bottom to the separator section; the cover portion including transparent impact resistant flat and dome members, the edges of the flat member being secured to the top section, the dome member being disposed over the flat member with its edges engaged with the flange section slots, the dome member including flat sections extending upwardly at an angle of 20/sup 0/ to 30/sup 0/ and a convex central section joining the flat sections.

  11. 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.

  12. Selecting a Retrospective Conversion Vendor.

    ERIC Educational Resources Information Center

    Lisowski, Andrew; Sessions, Judith

    1984-01-01

    Discussion of using vendors for retrospective conversion of library catalogs rather than in-house projects highlights reasons to consider vendors, four conversion methodologies, and vendor selection criteria (database, non-matches, local data, accuracy, charging, schedule, product delivery time, local system compatibility, MARC format, impact on…

  13. 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,…

  14. Language Teacher Educators Collaborative Conversations.

    ERIC Educational Resources Information Center

    Bailey, Francis; Hawkins, Maggie; Irujo, Suzanne; Larsen-Freeman, Diane; Rintell, Ellen; Willett, Jerri

    1998-01-01

    Conveys the power and value of collaborative conversation among a small group of language teacher educators who meet regularly to discuss practice. Excerpts from a discussion are presented to show a sample of real issues the teachers face and illustrate how the conversations allow ongoing feedback about real dilemmas from a supportive community of…

  15. Older Siblings as Conversational Partners.

    ERIC Educational Resources Information Center

    Hoff-Ginsberg, Erika; Krueger, Wendy M.

    1991-01-01

    Discusses a study of conversational dyadic interaction between children aged 1.5 to 3 years; their 4-, 5-, 7-, or 8-year-old siblings; and their mothers. Mothers were more supportive conversational partners and adapted their level of speech more than siblings. (GH)

  16. 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.…

  17. 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…

  18. 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…

  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. 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.

  2. 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

  3. 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.

  4. 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

  5. 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)

  6. Roadmap on optical energy conversion

    SciTech Connect

    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

    2016-06-24

    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

  7. 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

  8. 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

  9. stcS, a putative P-450 monooxygenase, is required for the conversion of versicolorin A to sterigmatocystin in Aspergillus nidulans.

    PubMed Central

    Keller, N P; Segner, S; Bhatnagar, D; Adams, T H

    1995-01-01

    Sterigmatocystin (ST) and aflatoxin are carcinogenic end point metabolites derived from the same biochemical pathway, which is found in several Aspergillus spp. Recently, an ST gene cluster, containing approximately 25 distinct genes that are each proposed to function specifically in ST biosynthesis, has been identified in Aspergillus nidulans. Each of these structural genes is named stc (sterigmatocystin) followed by a consecutive letter of the alphabet. We have previously described stcU (formerly verA) as encoding a keto-reductase required for the conversion of versicolorin A to ST. We now describe a second A. nidulans gene, stcS (formerly verB), that is located within 2 kb of stcU in the ST gene cluster. An stcS-disrupted strain of A. nidulans, TSS17, was unable to produce ST and converted ST/aflatoxin precursors to versicolorin A rather than ST, indicating that stcS functions at the same point in the pathway as stcU. Genomic sequence analysis of stcS shows that it encodes a cytochrome P-450 monooxygenase and constitutes a novel P-450 family, CYP59. Assuming that StcU activity mimics that of similar P-450s, it is likely that StcU catalyzes one of the proposed oxidation steps necessary to convert versicolorin A to ST. These results constitute the first genetic proof that the conversion of versicolorin A to ST requires more than one enzymatic activity. PMID:7486998

  10. Energy conversion and storage program

    NASA Astrophysics Data System (ADS)

    1990-12-01

    The Energy Conversion and Storage Program applies chemical and chemical engineering principles to solve problems in (1) production of new synthetic fuels; (2) development of high-performance rechargeable batteries and fuel cells; (3) development of advanced thermochemical processes for energy storage; (4) characterization of complex chemical processes; and (5) the application of novel materials for energy conversion and transmission. Projects focus on transport-process principles, chemical kinetics, thermodynamics, separation processes, organic and physical chemistry, and advanced methods of analysis. The following five areas are discussed: electrochemical energy storage and conversion; microstructured materials; biotechnology; fossil fuels; and high temperature superconducting processing. Papers have been processed separately for inclusion on the data base.

  11. Multisource thermophotovoltaic energy conversion

    NASA Astrophysics Data System (ADS)

    Regan, Thomas M.; Martin, Jose G.; Riccobono, Juanita R.; Ludman, Jacques E.

    1995-09-01

    Recently, at the University of Massachusetts Lowell, promising Thermophotovoltaic (TPV) experimental results have been produced utilizing an experimental system that incorporates holographic optical elements and tubular geometry thermal sources. The results and concepts presented in this paper bring to light a unique merging of combustion and solar energy sources. The holographic elements provide a mechanism for spectral splitting, as well as concentration, while the tubular thermal source provides a flexible TPV photon emitter geometry that is capable of utilizing various thermal sources. The work reported here details the experiments as well as the concepts that indicate that such a TPV system could readily produce electricity utilizing 'dual' thermal sources. A tubular photon source was located in the focus of parabolic assembly to 'collimate' the photons emitted by a lamp simulating a TPV photon emitter. The collimated photons were directed onto the holographic element and spectrally redirected as a function of the photon energy. Components of a system constructed in this geometry can be readily converted to produce a highly concentrating solar photovoltaic electrical power source.

  12. Chromosomal evolution of the PKD1 gene family in primates

    PubMed Central

    2008-01-01

    Background The autosomal dominant polycystic kidney disease (ADPKD) is mostly caused by mutations in the PKD1 (polycystic kidney disease 1) gene located in 16p13.3. Moreover, there are six pseudogenes of PKD1 that are located proximal to the master gene in 16p13.1. In contrast, no pseudogene could be detected in the mouse genome, only a single copy gene on chromosome 17. The question arises how the human situation originated phylogenetically. To address this question we applied comparative FISH-mapping of a human PKD1-containing genomic BAC clone and a PKD1-cDNA clone to chromosomes of a variety of primate species and the dog as a non-primate outgroup species. Results Comparative FISH with the PKD1-cDNA clone clearly shows that in all primate species studied distinct single signals map in subtelomeric chromosomal positions orthologous to the short arm of human chromosome 16 harbouring the master PKD1 gene. Only in human and African great apes, but not in orangutan, FISH with both BAC and cDNA clones reveals additional signal clusters located proximal of and clearly separated from the PKD1 master genes indicating the chromosomal position of PKD1 pseudogenes in 16p of these species, respectively. Indeed, this is in accordance with sequencing data in human, chimpanzee and orangutan. Apart from the master PKD1 gene, six pseudogenes are identified in both, human and chimpanzee, while only a single-copy gene is present in the whole-genome sequence of orangutan. The phylogenetic reconstruction of the PKD1-tree reveals that all human pseudogenes are closely related to the human PKD1 gene, and all chimpanzee pseudogenes are closely related to the chimpanzee PKD1 gene. However, our statistical analyses provide strong indication that gene conversion events may have occurred within the PKD1 family members of human and chimpanzee, respectively. Conclusion PKD1 must have undergone amplification very recently in hominid evolution. Duplicative transposition of the PKD1 gene and

  13. Dynamic Conversion Working Group Summary

    NASA Technical Reports Server (NTRS)

    Chaffee, N.; Sovie, R. J.

    1984-01-01

    The potential of dynamic conversion devices for use in solar and nuclear dynamic space power systems was addressed. Conversion systems considered were based on the use of Brayton, Stirling and Rankine cycles. Both organic and liquid metal Rankine cycles were included. The basic system considerations were: mission requirements, system attributes, system options, technology issues and constraints, and priorities of needed technology development. Mission requirements, where dynamic conversion was considered enabling technology, were identified along with the associated power levels and potential energy sources. When considering the system options special attention was given to recommend operating temperatures and other significant discriminators. A list of prioritized tasks considered important for the successful development of dynamic conversion systems for 1995 and beyond was compiled.

  14. Conversational topics in transsexual persons.

    PubMed

    Van Borsel, John; Cayzeele, Miet; Heirman, Eva; T'sjoen, Guy

    2014-06-01

    Abstract In general, speech language therapy for transsexual persons focuses on pitch and pitch variation and more recently also on resonance. Other communicative aspects are dealt with far less often, especially language. This study investigated to what extent conversational topics might need attention in therapy for transsexual persons. A total of 111 males, 116 females, 28 male-to-female and 18 female-to-male transsexuals were asked to indicate on a list with 34 topics how often they speak about each topic (never, sometimes, often) in conversations with males, with females and in a gender mixed group. Results showed that transsexual persons behave in accordance with the desired gender. However, they also tend to adopt a position depending on the gender of their conversational partner. It can be concluded that in general it is not necessary to pay attention to conversational topics in therapy for transsexual persons.

  15. Energy conversion at dipolarization fronts

    NASA Astrophysics Data System (ADS)

    Khotyaintsev, Yu. V.; Divin, A.; Vaivads, A.; André, M.; Markidis, S.

    2017-02-01

    We use multispacecraft observations by Cluster in the Earth's magnetotail and 3-D particle-in-cell simulations to investigate conversion of electromagnetic energy at the front of a fast plasma jet. We find that the major energy conversion is happening in the Earth (laboratory) frame, where the electromagnetic energy is being transferred from the electromagnetic field to particles. This process operates in a region with size of the order several ion inertial lengths across the jet front, and the primary contribution to E·j is coming from the motional electric field and the ion current. In the frame of the front we find fluctuating energy conversion with localized loads and generators at sub-ion scales which are primarily related to the lower hybrid drift instability excited at the front; however, these provide relatively small net energy conversion.

  16. Enzymes for improved biomass conversion

    SciTech Connect

    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.

  17. Virginia Hamilton: Continuing the Conversation.

    ERIC Educational Resources Information Center

    Mikkelsen, Nina

    1995-01-01

    Relates the latest installment of a continuing conversation between the author and Virginia Hamilton. Discusses ethnicity and identity, environmental issues, the creative process, and the way heritage, history, and family storytelling affect a writer's work. (RS)

  18. NASA thermionic-conversion program

    NASA Technical Reports Server (NTRS)

    Morris, J. F.

    1977-01-01

    Technological processes in out-of-core thermionic energy conversion are described. The emphasis was on high temperature electrode materials and system engineering of converter geometries to produce practical power densities.

  19. Effective communication during difficult conversations.

    PubMed

    Polito, Jacquelyn M

    2013-06-01

    A strong interest and need exist in the workplace today to master the skills of conducting difficult conversations. Theories and strategies abound, yet none seem to have found the magic formula with universal appeal and success. If it is such an uncomfortable skill to master is it better to avoid or initiate such conversations with employees? Best practices and evidence-based management guide us to the decision that quality improvement dictates effective communication, even when difficult. This brief paper will offer some suggestions for strategies to manage difficult conversations with employees. Mastering the skills of conducting difficult conversations is clearly important to keeping lines of communication open and productive. Successful communication skills may actually help to avert confrontation through employee engagement, commitment and appropriate corresponding behavior

  20. 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.

  1. Development of Geodetic Conversion Routines

    DTIC Science & Technology

    2001-09-01

    horizontal and vertical datums in the United States. It provides examples to invoke the Dynamic Link Library and use conversion functions in various programming languages, such as Visual Basic , C, and C++.

  2. Chromosomal location of the fosA3 and blaCTX-M genes in Proteus mirabilis and clonal spread of Escherichia coli ST117 carrying fosA3-positive IncHI2/ST3 or F2:A-:B- plasmids in a chicken farm.

    PubMed

    He, Dandan; Liu, Lanping; Guo, Baowei; Wu, Shengjun; Chen, Xiaojie; Wang, Jing; Zeng, Zhenling; Liu, Jian-Hua

    2017-04-01

    The aim of this study was to investigate the spread and location of the fosA3 gene among Enterobacteriaceae from diseased broiler chickens. Twenty-nine Escherichia coli and seven Proteus mirabilis isolates recovered from one chicken farm were screened for the presence of plasmid-mediated fosfomycin resistance genes by PCR. The clonal relatedness of fosA3-positive isolates, the transferability and location of fosA3, and the genetic context of the fosA3 gene were determined. Seven P. mirabilis isolates with three different pulsed-field gel electrophoresis (PFGE) patterns and five E. coli isolates belonging to sequence type 117 (ST117) and phylogenetic group D were positive for fosA3 and all carried the blaCTX-M gene. In E. coli, the genetic structures IS26-ISEcp1-blaCTX-M-65-IS26-fosA3-1758 bp-IS26 and IS26-ISEcp1-blaCTX-M-3-blaTEM-1-IS26-fosA3-1758 bp-IS26 were present on transferable IncHI2/ST3 and F2:A-:B- plasmids, respectively. However, fosA3 was located on the chromosome of the seven P. mirabilis isolates. IS26-ISEcp1-blaCTX-M-65-IS26-fosA3-1758 bp-IS26 and IS26-blaCTX-M-14-611 bp-fosA3-1222 bp-IS26 were detected in three and four P. mirabilis isolates, respectively. Minicircles that contained both fosA3 and blaCTX-M-65 were shared between E. coli and P. mirabilis. This is the first report of the fosA3 gene integrated into the chromosome of P. mirabilis isolates with the blaCTX-M gene. The emergence and clonal spread of avian pathogenic E. coli ST117 with the feature of multidrug resistance and high virulence are a serious problem.

  3. Frequency conversion of structured light.

    PubMed

    Steinlechner, Fabian; Hermosa, Nathaniel; Pruneri, Valerio; Torres, Juan P

    2016-02-15

    Coherent frequency conversion of structured light, i.e. the ability to manipulate the carrier frequency of a wave front without distorting its spatial phase and intensity profile, provides the opportunity for numerous novel applications in photonic technology and fundamental science. In particular, frequency conversion of spatial modes carrying orbital angular momentum can be exploited in sub-wavelength resolution nano-optics and coherent imaging at a wavelength different from that used to illuminate an object. Moreover, coherent frequency conversion will be crucial for interfacing information stored in the high-dimensional spatial structure of single and entangled photons with various constituents of quantum networks. In this work, we demonstrate frequency conversion of structured light from the near infrared (803 nm) to the visible (527 nm). The conversion scheme is based on sum-frequency generation in a periodically poled lithium niobate crystal pumped with a 1540-nm Gaussian beam. We observe frequency-converted fields that exhibit a high degree of similarity with the input field and verify the coherence of the frequency-conversion process via mode projection measurements with a phase mask and a single-mode fiber. Our results demonstrate the suitability of exploiting the technique for applications in quantum information processing and coherent imaging.

  4. Frequency conversion of structured light

    PubMed Central

    Steinlechner, Fabian; Hermosa, Nathaniel; Pruneri, Valerio; Torres, Juan P.

    2016-01-01

    Coherent frequency conversion of structured light, i.e. the ability to manipulate the carrier frequency of a wave front without distorting its spatial phase and intensity profile, provides the opportunity for numerous novel applications in photonic technology and fundamental science. In particular, frequency conversion of spatial modes carrying orbital angular momentum can be exploited in sub-wavelength resolution nano-optics and coherent imaging at a wavelength different from that used to illuminate an object. Moreover, coherent frequency conversion will be crucial for interfacing information stored in the high-dimensional spatial structure of single and entangled photons with various constituents of quantum networks. In this work, we demonstrate frequency conversion of structured light from the near infrared (803 nm) to the visible (527 nm). The conversion scheme is based on sum-frequency generation in a periodically poled lithium niobate crystal pumped with a 1540-nm Gaussian beam. We observe frequency-converted fields that exhibit a high degree of similarity with the input field and verify the coherence of the frequency-conversion process via mode projection measurements with a phase mask and a single-mode fiber. Our results demonstrate the suitability of exploiting the technique for applications in quantum information processing and coherent imaging. PMID:26875448

  5. Frequency conversion of structured light

    NASA Astrophysics Data System (ADS)

    Steinlechner, Fabian; Hermosa, Nathaniel; Pruneri, Valerio; Torres, Juan P.

    2016-02-01

    Coherent frequency conversion of structured light, i.e. the ability to manipulate the carrier frequency of a wave front without distorting its spatial phase and intensity profile, provides the opportunity for numerous novel applications in photonic technology and fundamental science. In particular, frequency conversion of spatial modes carrying orbital angular momentum can be exploited in sub-wavelength resolution nano-optics and coherent imaging at a wavelength different from that used to illuminate an object. Moreover, coherent frequency conversion will be crucial for interfacing information stored in the high-dimensional spatial structure of single and entangled photons with various constituents of quantum networks. In this work, we demonstrate frequency conversion of structured light from the near infrared (803 nm) to the visible (527 nm). The conversion scheme is based on sum-frequency generation in a periodically poled lithium niobate crystal pumped with a 1540-nm Gaussian beam. We observe frequency-converted fields that exhibit a high degree of similarity with the input field and verify the coherence of the frequency-conversion process via mode projection measurements with a phase mask and a single-mode fiber. Our results demonstrate the suitability of exploiting the technique for applications in quantum information processing and coherent imaging.

  6. 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.

  7. 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.

  8. 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.

  9. Conversion of borehole Stoneley waves to channel waves in coal

    SciTech Connect

    Johnson, P.A.; Albright, J.N.

    1987-01-01

    Evidence for the mode conversion of borehole Stoneley waves to stratigraphically guided channel waves was discovered in data from a crosswell acoustic experiment conducted between wells penetrating thin coal strata located near Rifle, Colorado. Traveltime moveout observations show that borehole Stoneley waves, excited by a transmitter positioned at substantial distances in one well above and below a coal stratum at 2025 m depth, underwent partial conversion to a channel wave propagating away from the well through the coal. In an adjacent well the channel wave was detected at receiver locations within the coal, and borehole Stoneley waves, arising from a second partial conversion of channel waves, were detected at locations above and below the coal. The observed channel wave is inferred to be the third-higher Rayleigh mode based on comparison of the measured group velocity with theoretically derived dispersion curves. The identification of the mode conversion between borehole and stratigraphically guided waves is significant because coal penetrated by multiple wells may be detected without placing an acoustic transmitter or receiver within the waveguide. 13 refs., 6 figs., 1 tab.

  10. mdv1-miR-M7-5p, located in the newly identified first intron of the latency-associated transcript of Marek's disease virus, targets the immediate-early genes ICP4 and ICP27.

    PubMed

    Strassheim, S; Stik, G; Rasschaert, D; Laurent, S

    2012-08-01

    Marek's disease virus serotype 1 (MDV-1) is an oncogenic alphaherpesvirus causing fatal T-cell lymphoma in chickens. MDV latency is characterized by the production of latency-associated transcripts (LATs), a family of non-protein-coding spliced RNAs. A cluster of four microRNAs (cluster mdv1-miR-M8-M10) was identified, but not formally mapped, at the predicted LAT 5' end. We established a LAT cDNA library from latently MDV-infected cell line MSB-1. We identified 22 highly variable LATs, which were due to the extensive alternative splicing of a total of 14 introns. RACE PCR confirmed the predicted 3' end and allowed identification of the 5' end, 400 nt upstream of the previously predicted LAT end. The LATs share their transcription start site with the microRNA-expressing transcript described previously, localizing the microRNAs to the first LAT intron and identifying the LATs as the primary transcripts of the microRNAs. We identified MDV immediate-early (IE) genes ICP4 and ICP27 as putative targets of mdv1-miR-M7-5p, the third microRNA of the cluster mdv1-miR-M8-M10. Endogenously expressed mdv1-miR-M7-5p in MSB-1 cells reduced luciferase activity significantly when microRNA-responsive elements from ICP4 or ICP27 were cloned in the 3' UTR of the firefly luciferase gene. ICP27 protein levels were decreased by 70 % when the mdv1-miR-M7-5p precursor was co-expressed with an ICP27 expression plasmid. Additionally, we showed a negative correlation between the decreased expression of mdv1-miR-M7-5p and an increase in ICP27 expression during virus reactivation. Our results suggest that, by targeting two IE genes, MDV microRNAs produced from LAT transcripts may contribute to establish and/or maintain latency.

  11. Conversion of sunflower multiband radiometer polarization measurements to polarization parameters

    NASA Technical Reports Server (NTRS)

    Biehl, Larry L.

    1995-01-01

    The data processing analysis and conversion of polarization measurements to polarization parameters from the Sunflower multiband radiometer is presented in this final report. Included is: (1) the actual data analysis; (2) the comparison of the averaging techniques and the percent polarization derived from the original and averaged I, Q, U parameters; (3) the polarizer angles used in conversion; (4) the Matlab files; (5) the relative ground size, field of view location, and view zenith angles, and (6) the summary of all the sky data for all dates.

  12. The gene for the serpin thrombin inhibitor (P17), protease nexin I, is located on human chromosome 2q33-q35 and on syntenic regions in the mouse and sheep genomes

    SciTech Connect

    Carter, R.E.; Burkin, D.J.; Fournier, R.E.K.

    1995-05-01

    Protease nexin I (PNI) is the most important physiologic regulator of {alpha}-thrombin in tissues. PNI is highly expressed and developmentally regulated in the nervous system where it is concentrated at neuromuscular junctions and also central synapses in the hippocampus and striatum. Approximately 10% of identified proteins at mammalian neuromuscular junctions are serine protease inhibitors, consistent with their central role in balancing serine protease activity to develop, maintain, and remodel synapses. Southern blot hybridization of PNI cDNA to somatic cell hybrids placed the structural gene for PNI (locus PI7) on human chromosome 2q33-q35 and to syntenic chromosomes in the mouse (chromosome 1) and sheep (chromosome 2). 30 refs., 2 figs.

  13. Serious Illness Conversations in ESRD.

    PubMed

    Mandel, Ernest I; Bernacki, Rachelle E; Block, Susan D

    2016-12-28

    Dialysis-dependent ESRD is a serious illness with high disease burden, morbidity, and mortality. Mortality in the first year on dialysis for individuals over age 75 years old approaches 40%, and even those with better prognoses face multiple hospitalizations and declining functional status. In the last month of life, patients on dialysis over age 65 years old experience higher rates of hospitalization, intensive care unit admission, procedures, and death in hospital than patients with cancer or heart failure, while using hospice services less. This high intensity of care is often inconsistent with the wishes of patients on dialysis but persists due to failure to explore or discuss patient goals, values, and preferences in the context of their serious illness. Fewer than 10% of patients on dialysis report having had a conversation about goals, values, and preferences with their nephrologist, although nearly 90% report wanting this conversation. Many nephrologists shy away from these conversations, because they do not wish to upset their patients, feel that there is too much uncertainty in their ability to predict prognosis, are insecure in their skills at broaching the topic, or have difficulty incorporating the conversations into their clinical workflow. In multiple studies, timely discussions about serious illness care goals, however, have been associated with enhanced goal-consistent care, improved quality of life, and positive family outcomes without an increase in patient distress or anxiety. In this special feature article, we will (1) identify the barriers to serious illness conversations in the dialysis population, (2) review best practices in and specific approaches to conducting serious illness conversations, and (3) offer solutions to overcome barriers as well as practical advice, including specific language and tools, to implement serious illness conversations in the dialysis population.

  14. In Vivo Selection of a Missense Mutation in adeR and Conversion of the Novel blaOXA-164 Gene into blaOXA-58 in Carbapenem-Resistant Acinetobacter baumannii Isolates from a Hospitalized Patient▿

    PubMed Central

    Higgins, Paul G.; Schneiders, Thamarai; Hamprecht, Axel; Seifert, Harald

    2010-01-01

    The mechanism of stepwise acquired multidrug resistance in Acinetobacter baumannii isolates from a hospitalized patient was investigated. Thirteen consecutive multidrug-resistant isolates were recovered from the same patient over a 2-month period. The Vitek 2 system identified the isolates as meropenem-sensitive Acinetobacter lwoffii; however, molecular identification showed that the isolates were A. baumannii. Etest revealed that the isolates were meropenem resistant. The presence of oxacillinase (OXA)-type enzymes were investigated by sequencing. The clonal relatedness of isolates was assessed by pulsed-field gel electrophoresis (PFGE). Expression of the genes encoding the efflux pumps AdeB and AdeJ was performed by semiquantitative real-time reverse transcription-PCR (qRT-PCR). The adeRS two-component system was sequenced. All isolates had identical PFGE fingerprints, suggesting clonal identity. The first six isolates were positive for the novel blaOXA-164 gene. The following seven isolates, recovered after treatment with a combination of meropenem, amikacin, ciprofloxacin, and co-trimoxazole showed an increas