1,884 research outputs found
Bioinformatics' approaches to detect genetic variation in whole genome sequencing data
No full textCurrent genetic marker repositories are not sufficient or even are completely lacking for most farm animals. However, genetic markers are essential for the development of a research tool facilitating discovery of genetic factors that contribute to resistance to disease and the overall welfare and performance in farm animals. By large scale identification of Single Nucleotide Polymorphisms (SNPs) and Structural Variants (SVs) we aimed to contribute to the development of a repository of genetic variants for farm animals. For this purpose bioinformatics data pipelines were designed and validated to address the challenge of the cost effective identification of genetic markers in DNA sequencing data even in absence of a fully sequenced reference genome. To find SNPs in pig, we analysed publicly available whole genome shotgun sequencing datasets by sequence alignment and clustering. Sequence clusters were assigned to genomic locations using publicly available BAC sequencing and BAC mapping data. Within the sequence clusters thousands of SNPs were detected of which the genomic location is roughly known. For turkey and duck, species that both were lacking a sufficient sequence data repository for variant discovery, we applied next-generation sequencing (NGS) on a reduced genome representation of a pooled DNA sample. For turkey a genome reference was reconstructed from our sequencing data and available public sequencing data whereas in duck the reference genome constructed by a (NGS) project was used. SNPs obtained by our cost-effective SNP detection procedure still turned out to cover, at intervals, the whole turkey and duck genomes and are of sufficient quality to be used in genotyping studies. Allele frequencies, obtained by genotyping animal panels with a subset our SNPs, correlated well with those observed during SNP detection. The availability of two external duck SNP datasets allowed for the construction of a subset of SNPs which we had in common with these sets. Genotyping turned out that this subset was of outstanding quality and can be used for benchmarking other SNPs that we identified within duck. Ongoing developments in (NGS) allowed for paired end sequencing which is an extension on sequencing analysis that provides information about which pair of reads are coming from the outer ends of one sequenced DNA fragment. We applied this technique on a reduced genome representation of four chicken breeds to detect SVs. Paired end reads were mapped to the chicken reference genome and SVs were identified as abnormally aligned read pairs that have orientation or span sizes discordant from the reference genome. SV detection parameters, to distinguish true structural variants from false positives, were designed and optimized by validation of a small representative sample of SVs using PCR and traditional capillary sequencing. To conclude: we developed SNP repositories which fulfils a requirement for SNPs to perform linkage analysis, comparative genomics QTL studies and ultimately GWA studies in a range of farm animals. We also set the first step in developing a repository for SVs in chicken, a relatively new genetic marker in animal sciences. <br/
The development and characterization of a 60K SNP chip for chicken
No full textAbstract Background In livestock species like the chicken, high throughput single nucleotide polymorphism (SNP) genotyping assays are increasingly being used for whole genome association studies and as a tool in breeding (referred to as genomic selection). To be of value in a wide variety of breeds and populations, the success rate of the SNP genotyping assay, the distribution of the SNP across the genome and the minor allele frequencies (MAF) of the SNPs used are extremely important. Results We describe the design of a moderate density (60k) Illumina SNP BeadChip in chicken consisting of SNPs known to be segregating at high to medium minor allele frequencies (MAF) in the two major types of commercial chicken (broilers and layers). This was achieved by the identification of 352,303 SNPs with moderate to high MAF in 2 broilers and 2 layer lines using Illumina sequencing on reduced representation libraries. To further increase the utility of the chip, we also identified SNPs on sequences currently not covered by the chicken genome assembly (Gallus_gallus-2.1). This was achieved by 454 sequencing of the chicken genome at a depth of 12x and the identification of SNPs on 454-derived contigs not covered by the current chicken genome assembly. In total we added 790 SNPs that mapped to 454-derived contigs as well as 421 SNPs with a position on Chr_random of the current assembly. The SNP chip contains 57,636 SNPs of which 54,293 could be genotyped and were shown to be segregating in chicken populations. Our SNP identification procedure appeared to be highly reliable and the overall validation rate of the SNPs on the chip was 94%. We were able to map 328 SNPs derived from the 454 sequence contigs on the chicken genome. The majority of these SNPs map to chromosomes that are already represented in genome build Gallus_gallus-2.1.0. Twenty-eight SNPs were used to construct two new linkage groups most likely representing two micro-chromosomes not covered by the current genome assembly. Conclusions The high success rate of the SNPs on the Illumina chicken 60K Beadchip emphasizes the power of Next generation sequence (NGS) technology for the SNP identification and selection step. The identification of SNPs from sequence contigs derived from NGS sequencing resulted in improved coverage of the chicken genome and the construction of two new linkage groups most likely representing two chicken micro-chromosomes.</p
Regional differences in recombination hotspots between two chicken populations
No full textAbstract Background Although several genetic linkage maps of the chicken genome have been published, the resolution of these maps is limited and does not allow the precise identification of recombination hotspots. The availability of more than 3.2 million SNPs in the chicken genome and the recent advances in high throughput genotyping techniques enabled us to increase marker density for the construction of a high-resolution linkage map of the chicken genome. This high-resolution linkage map allowed us to study recombination hotspots across the genome between two chicken populations: a purebred broiler line and a broiler × broiler cross. In total, 1,619 animals from the two different broiler populations were genotyped with 17,790 SNPs. Results The resulting linkage map comprises 13,340 SNPs. Although 360 polymorphic SNPs that had not been assigned to a known chromosome on chicken genome build WASHUC2 were included in this study, no new linkage groups were found. The resulting linkage map is composed of 31 linkage groups, with a total length of 3,054 cM for the sex-average map of the combined population. The sex-average linkage map of the purebred broiler line is 686 cM smaller than the linkage map of the broiler × broiler cross. Conclusions In this study, we present a linkage map of the chicken genome at a substantially higher resolution than previously published linkage maps. Regional differences in recombination hotspots between the two mapping populations were observed in several chromosomes near the telomere of the p arm; the sex-specific analysis revealed that these regional differences were mainly caused by female-specific recombination hotspots in the broiler × broiler cross.</p
Martin Buber Collection 1897-1980 Bulk dates: 1921-1929
No full textThe Martin Buber Collection holds various papers of this philosopher, with a focus on his work. More than half the collection consists of his letters to Franz Rosenzweig, including a number of them devoted to their collaborative translation of the Bible; lectures he gave at the Freies Jüdisches Lehrhaus in Frankfurt am Main; and a discussion of Buber’s book Ich und Du (I and Thou). In addition the collection holds texts of some of Martin Buber's lectures, photographs, a few letters to others, invitations and an article.The following individuals are mentioned in this collection:Ahren, Yitzhak; Balthasar, H. von; Billigheimer, Samuel; Diamond, Malcolm; Fackenheim, Emil; Farber, Leslie; Fox, Marvin; Friedman, Maurice; Galliner, Arthur; Galliner, Helmut; Gandhi, Mohandas K.; Glatzer, Nahum; Goes, Albrecht; Guggenheim, Siegfried; Heinemann, F.; Hesse, Ninon; Hocking, William Ernst; Hohoff, Curt; Kaplan, Mordechai; Kaufmann, Fritz; Kerenyi, Karl; Klotz, Elena; Kohn, Hans; Kreutzberger, Max; Kuhn, Helmuth; Landauer, Gustav; Levin, Meyer; Levinas, Emmanuel; Loewenberg, Frank; Mailenburg, James; Marcel, Gabriel; Michael, Max; Newman, Louis; Niebuhr, Reinhold; Pfuetze, Paul; Porter, Jack Nusan; Ross, Irvin; Rotenstreich, Nathan; Schneider, Herbert; Scholem, Gershom; Schorsch, Ismar; Sholem, Gershom; Simon, Ernst; Simon, Isidor; Stahr, Adolf; Tagore, Rabindranath; Taubes, Jacob; Weltmann, Lutz; Weltsch, Robert; Wheelwright, Philip; Wilkers, KarldigitizedDigital ImageBorn in Vienna on February 2, 1878, Martin Buber studied philosophy and art history at various European universities, became active in the Zionist movement, and worked as an author, editor, and publisher. Moving to Berlin in 1906, and to Heppenheim near Frankfurt am Main in 1916, he published highly regarded philosophical and theological works. Buber emigrated to Palestine in 1938, where he taught at the Hebrew University in Jerusalem until his death on June 13, 1965.Articles on Martin Buber may be found in ‘Manuscripts about Martin Buber’, MF 189 (available online), and in the Martin Buber Clippings Collection.Photographs removed to Photograph CollectionProcesse
The SF-36: a simple, effective measure of mobility disability for epidemiological studies
No full textBackgroundMobility disability is a major problem in older people. Numerous scales exist for the measurement of disability but often these do not permit comparisons between study groups. The physical functioning (PF) domain of the established and widely used Short Form-36 (SF-36) questionnaire asks about limitations on ten mobility activities.ObjectivesTo describe prevalence of mobility disability in an elderly population, investigate the validity of the SF-36 PF score as a measure of mobility disability, and to establish age and sex specific norms for the PF score.MethodsWe explored relationships between the SF-36 PF score and objectively measured physical performance variables among 349 men and 280 women, 59-72 years of age, who participated in the Hertfordshire Cohort Study (HCS). Normative data were derived from the Health Survey for England (HSE) 1996.Results32% of men and 46% of women had at least some limitation in PF scale items. Poor SF-36 PF scores (lowest fifth of the gender-specific distribution) were related to: lower grip strength; longer timed-up-and-go, 3m walk, and chair rises test times in men and women; and lower quadriceps peak torque in women but not men. HSE normative data showed that median PF scores declined with increasing age in men and women.ConclusionOur results are consistent with the SF-36 PF score being a valid measure of mobility disability in epidemiological studies. This approach might be a first step towards enabling simple comparisons of prevalence of mobility disability between different studies of older people. The SF-36 PF score could usefully complement existing detailed schemes for classification of disability and it now requires validation against them
Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping
No full textBACKGROUND:
The publication of the first draft chicken sequence assembly became available in 2004 and was updated in 2006. However, this does not constitute a definitive and complete sequence of the chicken genome, since the microchromosomes are notably under-represented. In an effort to develop maps for the microchromosomes absent from the chicken genome assembly, we developed radiation hybrid (RH) and genetic maps with markers isolated from sequence currently assigned to "chromosome Unknown" (chrUn). The chrUn is composed of sequence contigs not assigned to named chromosomes. To identify and map sequence belonging to the microchromosomes we used a comparative mapping strategy, and we focused on the small linkage group E26C13.
RESULTS:
In total, 139 markers were analysed with the chickRH6 panel, of which 120 were effectively assigned to the E26C13 linkage group, the remainder mapping elsewhere in the genome. The final RH map is composed of 22 framework markers extending over a 245.6 cR distance. A corresponding genetic map was developed, whose length is 103 cM in the East Lansing reference population. The E26C13 group was assigned to GGA25 (Gallus gallus chromosome 25) by FISH (fluorescence in situ hybridisation) mapping.
CONCLUSION:
The high-resolution RH framework map obtained here covers the entire chicken chromosome 25 and reveals the existence of a high number of intrachromosomal rearrangements when compared to the human genome. The strategy used here for the characterization of GGA25 could be used to improve knowledge on the other uncharacterized small, yet gene-rich microchromosomes
"To me, the poor and the powerless – and I am that – are always the ones that know what is going on": Interview with Irish writer Emer Martin
No full textEmer Martin is an Irish author, artist and teacher who lives in California. She has produced a strikingly diverse range of work: novels, poems, literary journalism, paintings, and short films. She is also an active writer for newspapers and on social media. Her first novel, Breakfast in Babylon (1995), won Book of the Year 1996 at the prestigious Listowel Writers’ Week in her native Ireland. This novel and her next, More Bread Or I’ll Appear (1999), were published internationally and widely acclaimed. Her third novel, Baby Zero, was published in the UK and Ireland in March 2007 by Dingle, and released in the US in 2014 by Rawmeash, an artist-led publishing cooperative run by artists for artists and based between USA and Ireland. Rawmeash was founded by Emer Martin in 2012. Emer Martin is an extremely political and expressive artist. In this interview, she shares her views on such cultural matters and the idea of art as resistance; or contemporary concerns, such as the politics of capitalism, the COVID-19 crisis or climate change. She also argues about her latest novel, The Cruelty Men, which in 2019 was shortlisted for best Irish novel the same year.Emer Martin é uma autora, artista e professora irlandesa que vive na Califórnia. Ela produziu uma gama surpreendentemente diversa de trabalhos: romances, poemas, jornalismo literário, pinturas e curtas-metragens. Ela também é redatora ativa de jornais e redes sociais. Seu primeiro romance, Breakfast in Babylon(1995), ganhou o prêmoio Livro do Ano de 1996 na prestigiosa Listowel Writers’ Week na sua terra natal Irlanda. Esse romance e o seu seguinte, More Bread Or I’ll Appear(1999), foram publicados internacionalmente e amplamente aclamados. Seu terceiro romance, Baby Zero, foi publicado no Reino Unido e na Irlanda em março de 2007 pela Dingle, e lançado nos Estados Unidos em 2014 pela Rawmeash, uma cooperativa de publicação liderada e dirigida por artistas para artistas e com sede entre os EUA e a Irlanda. Rawmeash foi fundada por Emer Martin em 2012. Emer Martin é uma artista extremamente política e expressiva. Nesta entrevista, ela compartilha suas opiniões sobre questões culturais e a ideia da arte como resistência; ou preocupações contemporâneas, como a política do capitalismo, a crise do COVID-19 ou as mudanças climáticas. Ela também discute sobre seu último romance, The Cruelty Men, que em 2019 foi selecionado para melhor romance irlandês no mesmo ano
Behavior of carbonyl ylide generated from 3-chloro-3-(p-nitrophenyl)diazirine and acetone 1,3-dipolar cycloaddition to benzaldehyde and epoxide formation
No full textPT: J; CR: DEMARCH P, 1982, J AM CHEM SOC, V104, P4952 DEMARCH P, 1982, J AM CHEM SOC, V104, P4953 GILL HS, 1983, J ORG CHEM, V48, P1051 HOUK KN, 1973, J AM CHEM SOC, V95, P7302 HUISGEN R, 1977, ANGEW CHEM INT EDIT, V16, P572 IBATA T, 1986, TETRAHEDRON LETT, V27, P4383 LIU MTH, 1974, TETRAHEDRON LETT, P1329 LIU MTH, 1987, TETRAHEDRON LETT, V28, P1011 MARTIN CW, 1971, J CHEM SOC CHEM COMM, P1438 MARTIN CW, 1971, J CHEM SOC CHEM COMM, P15 MARTIN CW, 1985, J ORG CHEM, V50, P2050 PADWA A, 1969, J ORG CHEM, V34, P2728 SEYFERTH D, 1974, J ORGANOMET CHEM, V67, P341 UEDA K, 1972, B CHEM SOC JPN, V45, P2779; NR: 14; TC: 8; J9: CHEM LETT; PG: 4; GA: L0892Source type: Electronic(1
Author children's picture book
No full textBímová, Š.: Author children's picture book. [Diploma thesis] Prague 2015 - Charles University - Faculty of education, 91 s. How was perceived book in the history and today? Selection of several authors I am try to explain past and present trends in the children and children's authors book. Didactic part is mainly focuse on the status of the book in the context with art lessons and not only in the motivation part of the lesson, but also in topic of lesson. Both principles are use in the didactic project, which was built on the theoretical content of the work. Everything closes the practical part, which was applied as a result of a reaction to previous two parts. KEYWORDS author's book, children's book, book illustration, fantasy, material, imaginatio
The gene order on Human Chromosome 15 and Chicken Chromosome 10 reveal multiple inter- and intrachromosomal rearrangements
No full textComparative mapping between the human and chicken genomes has revealed a striking conservation of synteny between the genomes of these two species, but the results have been based on low-resolution comparative maps. To address this conserved synteny in much more detail, a high-resolution human-chicken comparative map was constructed from human chromosome 15. Mapping, sequencing, and ordering of specific chicken bacterial artificial chromosomes has improved the comparative map of chromosome 15 (Hsa15) and the homologous regions in chicken with almost 100 new genes and/or expressed sequence tags. A comparison of Hsa15 with chicken identified seven conserved chromosomal segments between the two species. In chicken, these were on chromosome 1 (Gga1; two segments), Gga5 (two segments), and Gga10 (three segments). Although four conserved segments were also observed between Hsa15 and mouse, only one of the underlying rearrangement breakpoints was located at the same position as in chicken, indicating that the rearrangements generating the other three breakpoints occurred after the divergence of the rodent and the primate lineages. A high-resolution comparison of Gga10 with Hsa15 identified 19 conserved blocks, indicating the presence of at least 16 intrachromosomal rearrangement breakpoints in the bird lineage after the separation of birds and mammals. These results improve our knowledge of the evolution and dynamics of the vertebrate genomes and will aid in the clarification of the mechanisms that underlie the differentiation between the vertebrate species
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