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Sample records for artificial chromosome contig

  1. Construction of a yeast artificial chromosome contig encompassing the chromosome 14 Alzheimer`s disease locus

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    Sharma, V.; Bonnycastle, L.; Poorkai, P. [Univ. of Washington, Seattle, WA (United States)] [and others

    1994-09-01

    We have constructed a yeast artificial chromosome (YAC) contig of chromosome 14q24.3 which encompasses the chromosome 14 Alzheimer`s disease locus (AD3). Determined by linkage analysis of early-onset Alzheimer`s disease kindreds, this interval is bounded by the genetic markers D14S61-D14S63 and spans approximately 15 centimorgans. The contig consists of 29 markers and 74 YACs of which 57 are defined by one or more sequence tagged sites (STSs). The STS markers comprise 5 genes, 16 short tandem repeat polymorphisms and 8 cDNA clones. An additional number of genes, expressed sequence tags and cDNA fragments have been identified and localized to the contig by hybridization and sequence analysis of anonymous clones isolated by cDNA direct selection techniques. A minimal contig of about 15 YACs averaging 0.5-1.5 megabase in length will span this interval and is, at first approximation, in rough agreement with the genetic map. For two regions of the contig, our coverage has relied on L1/THE fingerprint and Alu-PCR hybridization data of YACs provided by CEPH/Genethon. We are currently developing sequence tagged sites from these to confirm the overlaps revealed by the fingerprint data. Among the genes which map to the contig are transforming growth factor beta 3, c-fos, and heat shock protein 2A (HSPA2). C-fos is not a candidate gene for AD3 based on the sequence analysis of affected and unaffected individuals. HSPA2 maps to the proximal edge of the contig and Calmodulin 1, a candidate gene from 4q24.3, maps outside of the region. The YAC contig is a framework physical map from which cosmid or P1 clone contigs can be constructed. As more genes and cDNAs are mapped, a highly resolved transcription map will emerge, a necessary step towards positionally cloning the AD3 gene.

  2. A 6. 5-Mb yeast artificial chromosome contig incorporating 33 DNA markers on the human X chromosome at Xq22

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    Vetrie, D.; Kendall, E.; Coffey, A.; Hassock, S.; Collins, J.; Todd, C.; Bobrow, M.; Bentley, D.R. (Paediatric Research Unit, London (United Kingdom)); Lehrach, H. (Imperial Cancer Research Fund, London (United Kingdom)); Harris, A. (John Radcliffe Hospital, Oxford (United Kingdom))

    1994-01-01

    The Xq22 region of the human X chromosome contains genes for a number of inherited disorders. Sixty-nine yeast artificial chromosome clones have been isolated and assembled into a 6.5-Mb contig that contains 33 DNA markers localized to this region. This contig extends distally from DXS366 to beyond DXS87 and includes the genes involved in X-linked agammaglobulinemia (btk), Fabry disease (GLA), and Pelizaeus-Merzbacher disease (PLP). The order of markers in this contig is consistent with the known genetic and physical mapping information of Xq22. This cloned material provides a source from which to isolate other genes located in this part of the X chromosome. 45 refs., 2 figs., 2 tabs.

  3. A yeast artificial chromosome contig of the critical region for cri-du-chat syndrome

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    Goodart, S.A.; Rojas, K.; Overhauser, J. [Thomas Jefferson Univ., Philadelphia, PA (United States)] [and others

    1994-11-01

    Cri-du-chat is a chromosomal deletion syndrome characterized by partial deletion of the short arm of chromosome 5. The clinical symptoms include growth and mental retardation, microcephaly, hypertelorism, epicanthal folds, hyptonia, and a high-pitched monochromatic cry that is usually considered diagnostic for the syndrome. Recently, a correlation between clinical features and the extent of the chromosome 5 deletions has identified two regions of the short arm that appear to be critical for the abnormal development manifested in this syndrome. Loss of a small region in 5p15.2 correlates with all of the clinical features of cri-du-chat with the exception of the cat-like cry, which maps to 5p15.3. Here the authors report the construction of a YAC contig that spans the chromosomal region in 5p15.2 that plays a major role in the etiology of the cri-du-chat syndrome. YACs that span the 2-Mb cri-du-chat critical region have been identified and characterized. This YAC contig lays the groundwork for the construction of a transcriptional map of this region and the eventual identification of genes involved in the clinical features associated with the cri-du-chat syndrome. It also provides a new diagnostic tool for cri-du-chat in the shape of a YAC clone that may span the entire critical region. 24 refs., 4 figs., 2 tabs.

  4. A BACTERIAL ARTIFICIAL CHROMOSOME CONTIG SPANNING THE MAJOR DOMESTICATION LOCUS Q IN WHEAT AND IDENTIFICATION OF A CANDIDATE GENE

    Science.gov (United States)

    The Q locus played a major role in the domestication of wheat because it confers the free-threshing character and influences many other agronomically important traits. We constructed a physical contig spanning the Q locus using a Triticum monococcum BAC library. Four chromosome walking steps were ...

  5. Bacterial Artificial Chromosome Mutagenesis Using Recombineering

    OpenAIRE

    Kumaran Narayanan; Qingwen Chen

    2011-01-01

    Gene expression from bacterial artificial chromosome (BAC) clones has been demonstrated to facilitate physiologically relevant levels compared to viral and nonviral cDNA vectors. BACs are large enough to transfer intact genes in their native chromosomal setting together with flanking regulatory elements to provide all the signals for correct spatiotemporal gene expression. Until recently, the use of BACs for functional studies has been limited because their large size has inherently presented...

  6. Bacterial Artificial Chromosome Mutagenesis Using Recombineering

    Directory of Open Access Journals (Sweden)

    Kumaran Narayanan

    2011-01-01

    Full Text Available Gene expression from bacterial artificial chromosome (BAC clones has been demonstrated to facilitate physiologically relevant levels compared to viral and nonviral cDNA vectors. BACs are large enough to transfer intact genes in their native chromosomal setting together with flanking regulatory elements to provide all the signals for correct spatiotemporal gene expression. Until recently, the use of BACs for functional studies has been limited because their large size has inherently presented a major obstacle for introducing modifications using conventional genetic engineering strategies. The development of in vivo homologous recombination strategies based on recombineering in E. coli has helped resolve this problem by enabling facile engineering of high molecular weight BAC DNA without dependence on suitably placed restriction enzymes or cloning steps. These techniques have considerably expanded the possibilities for studying functional genetics using BACs in vitro and in vivo.

  7. [Cashmere goat bacterial artificial chromosome recombination and cell transfection system].

    Science.gov (United States)

    Huang, Tian; Cao, Zhongyang; Yang, Yaohui; Cao, Gengsheng

    2016-03-01

    The Cashmere goat is mainly used to produce cashmere, which is very popular for its delicate fiber, luscious softness and natural excellent warm property. Keratin associated protein (KAP) and bone morphogenetic protein (BMP) of the Cashmere goat play an important role in the proliferation and development of cashmere fiber follicle cells. Bacterial artificial chromosome containing kap6.3, kap8.1 and bmp4 genes were used to increase the production and quality of Cashmere. First, we constructed bacterial artificial chromosomes by homology recombination. Then Tol2 transposon was inserted into bacterial artificial chromosomes that were then transfected into Cashmere goat fibroblasts by Amaxa Nucleofector technology according to the manufacture's instructions. We successfully constructed the BAC-Tol2 vectors containing target genes. Each vector contained egfp report gene with UBC promoter, Neomycin resistant gene for cell screening and two loxp elements for resistance removing after transfected into cells. The bacterial artificial chromosome-Tol2 vectors showed a high efficiency of transfection that can reach 1% to 6% with a highest efficiency of 10%. We also obtained Cashmere goat fibroblasts integrated exogenous genes (kap6.3, kap8.1 and bmp4) preparing for the clone of Cashmere goat in the future. Our research demonstrates that the insertion of Tol2 transposons into bacterial artificial chromosomes improves the transfection efficiency and accuracy of bacterial artificial chromosome error-free recombination. PMID:27349114

  8. Sex Chromosome Evolution in Amniotes: Applications for Bacterial Artificial Chromosome Libraries

    OpenAIRE

    Janes, Daniel E.; Nicole Valenzuela; Tariq Ezaz; Chris Amemiya; Edwards, Scott V.

    2011-01-01

    Variability among sex chromosome pairs in amniotes denotes a dynamic history. Since amniotes diverged from a common ancestor, their sex chromosome pairs and, more broadly, sex-determining mechanisms have changed reversibly and frequently. These changes have been studied and characterized through the use of many tools and experimental approaches but perhaps most effectively through applications for bacterial artificial chromosome (BAC) libraries. Individual BAC clones carry 100–200 kb of seque...

  9. A high-throughput strategy for screening of bacterial artificial chromosome libraries and anchoring of clones on a genetic map constructed with single nucleotide polymorphisms

    OpenAIRE

    Deal Karin R; Ma Yaqin; Xu Kenong; Luo Ming-Cheng; Nicolet Charles M; Dvorak Jan

    2009-01-01

    Abstract Background Current techniques of screening bacterial artificial chromosome (BAC) libraries for molecular markers during the construction of physical maps are slow, laborious and often assign multiple BAC contigs to a single locus on a genetic map. These limitations are the principal impediment in the construction of physical maps of large eukaryotic genomes. It is hypothesized that this impediment can be overcome by screening multidimensional pools of BAC clones using the highly para...

  10. A high-throughput strategy for screening of bacterial artificial chromosome libraries and anchoring of clones on a genetic map constructed with single nucleotide polymorphisms

    OpenAIRE

    Luo, Ming-Cheng; Xu, Kenong; Ma, Yaqin; Karin R Deal; Nicolet, Charles M.; Dvorak, Jan

    2009-01-01

    Background Current techniques of screening bacterial artificial chromosome (BAC) libraries for molecular markers during the construction of physical maps are slow, laborious and often assign multiple BAC contigs to a single locus on a genetic map. These limitations are the principal impediment in the construction of physical maps of large eukaryotic genomes. It is hypothesized that this impediment can be overcome by screening multidimensional pools of BAC clones using the highly parallel Illu...

  11. Sex Chromosome Evolution in Amniotes: Applications for Bacterial Artificial Chromosome Libraries

    Science.gov (United States)

    Janes, Daniel E.; Valenzuela, Nicole; Ezaz, Tariq; Amemiya, Chris; Edwards, Scott V.

    2011-01-01

    Variability among sex chromosome pairs in amniotes denotes a dynamic history. Since amniotes diverged from a common ancestor, their sex chromosome pairs and, more broadly, sex-determining mechanisms have changed reversibly and frequently. These changes have been studied and characterized through the use of many tools and experimental approaches but perhaps most effectively through applications for bacterial artificial chromosome (BAC) libraries. Individual BAC clones carry 100–200 kb of sequence from one individual of a target species that can be isolated by screening, mapped onto karyotypes, and sequenced. With these techniques, researchers have identified differences and similarities in sex chromosome content and organization across amniotes and have addressed hypotheses regarding the frequency and direction of past changes. Here, we review studies of sex chromosome evolution in amniotes and the ways in which the field of research has been affected by the advent of BAC libraries. PMID:20981143

  12. A YAC contig encompassing the recessive Stargardt disease gene (STGD) on chromosome 1p

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    Anderson, K.L.; Lewis, R.A.; Chinault, A.C. [Baylor College of Medicine, Houston, TX (United States)] [and others

    1995-12-01

    Stargardt disease (STGD) and fundus flavimaculatus are infrequent autosomal recessive conditions characterized by a juvenile macular dystrophy and variable degrees of peripheral retinal changes. Linkage analysis performed in 47 STGD/fundus flavimaculatus families demonstrated significant linkage to 13 polymorphic DNA markers on chromosome 1p. The maximum combined two-point lod score was 32.7 (maximum recombination fraction [{theta}{sub max}] = .006) with the polymorphic marker D1S188. Our data demonstrate that STGD and fundus flavimaculatus are the same disorder clinically and genetically and provide further evidence for genetic homogeneity of this phenotype. Analysis of recombination on disease chromosomes placed the STGD gene within a 4-cM interval between markers D1S435 and D1S236. A physical map was constructed of a YAC contig flanking STGD, from markers D1S500 to D1S495, and includes the critical interval delineated by historical recombinants. This contig spans {approximately}31 cM, with one gap (3-5 cM) that is outside the 4-cM critical region. Localization of STGD to a single YAC contig will facilitate its positional cloning. 75 refs., 3 figs., 21 tabs.

  13. A YAC contig of the human CC chemokine genes clustered on chromosome 17q11.2

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    Naruse, Kuniko [Kumamoto Univ. Medical School, Honjo (Japan)]|[Prefectural Univ. of Kumamoto, Tsukide (Japan); Nomiyama, Hisayuki; Miura, Retsu [Kumamoto Univ. Medical School, Honjo (Japan)] [and others

    1996-06-01

    CC chemokines are cytokines that attract and activate leukocytes. The human genes for the CC chemokines are clustered on chromosome 17. To elucidate the genomic organization of the CC chemokine genes, we constructed a YAC contig comprising 34 clones. The contig was shown to contain all 10 CC chemokine genes reported so far, except for one gene whose nucleotide sequence is not available. The contig also contains 4 CC chemokine-like genes, which were deposited in GenBank as ESTs and are here referred to as NCC-1, NCC-2, NCC-3, and NCC-4. Within the contig, the CC chemokine genes were localized in two regions. In addition, the CC chemokine genes were localized in two regions. In addition, the CC chemokine genes were more precisely mapped on chromosome 17q11.2 using a somatic cell hybrid cell DNA panel containing various portions of human chromosome 17. Interestingly, a reciprocal translocation t(Y;17) breakpoint, contained in the hybrid cell line Y1741, lay between the two chromosome 17 chemokine gene regions covered by our YAC contig. From these results, the order and the orientation of CC chemokine genes on chromosome 17 were determined as follows: centromere-neurofibromatosis 1-(MCP-3, MCP-1, NCC-1, I-309)-Y1741 breakpoint-RANTES-(LD78{gamma}, AT744.2, LD78{beta})-(NCC-3, NCC-2, AT744.1, LD78{alpha})-NCC-4-retinoic acid receptor {alpha}-telomere. 22 refs., 1 fig., 2 tabs.

  14. A Yeast Artificial Chromosome Library Database: Design Considerations

    OpenAIRE

    Frisse, Mark E.; Ge, NengJie; Langenbacher, JulieM.; Kahn, Michael G.; Brownstein, Bernard H

    1990-01-01

    This paper first describes a simple collection of HyperCard stacks created and used by genetics researchers to catalog information in a human yeast artificial chromosome (YAC) library. Although an intuitive human-computer interface made the HyperCard program easy to use, the program was neither an efficient nor a secure primary database for vital laboratory data. This paper subsequently describes a relational database implementation prototype that overcomes HyperCard's deficiencies as a datab...

  15. Integrative bacterial artificial chromosomes for DNA integration into the Bacillus subtilis chromosome.

    Science.gov (United States)

    Juhas, Mario; Ajioka, James W

    2016-06-01

    Bacillus subtilis is a well-characterized model bacterium frequently used for a number of biotechnology and synthetic biology applications. Novel strategies combining the advantages of B. subtilis with the DNA assembly and editing tools of Escherichia coli are crucial for B. subtilis engineering efforts. We combined Gibson Assembly and λ red recombineering in E. coli with RecA-mediated homologous recombination in B. subtilis for bacterial artificial chromosome-mediated DNA integration into the well-characterized amyE target locus of the B. subtilis chromosome. The engineered integrative bacterial artificial chromosome iBAC(cav) can accept any DNA fragment for integration into B. subtilis chromosome and allows rapid selection of transformants by B. subtilis-specific antibiotic resistance and the yellow fluorescent protein (mVenus) expression. We used the developed iBAC(cav)-mediated system to integrate 10kb DNA fragment from E. coli K12 MG1655 into B. subtilis chromosome. iBAC(cav)-mediated chromosomal integration approach will facilitate rational design of synthetic biology applications in B. subtilis. PMID:27033694

  16. A YAC contig and an EST map in the pericentromeric region of chromosome 13 surrounding the loci for neurosensory nonsyndromic deafness (DFNB1 and DFNA3) and Limb-Girdle muscular dystrophy type 2C (LGMD2C)

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    Guilford, P.; Crozet, F.; Blanchard, S. [Institut Pasteur, Paris (France)] [and others

    1995-09-01

    Two forms of inherited childhood nonsyndromic deafness (DFNB1 and DFNA3) and a Duchenne-like form of progressive muscular dystrophy (LGMD2C) have been mapped to the pericentromeric region of chromosome 13. To clone the genes responsible for these diseases we constructed a yeast artificial chromosome (YAC) contig spanning an 8-cM region between the polymorphic markers D13S221. The contig comprises 24 sequence-tagged sites, among which 15 were newly obtained. This contig allowed us to order the polymorphic markers centromere- D13S175-D13S141-D13S143-D13S115-AFM128yc1-D13S292-D13S283-AFM323vh5-D13S221-telomere. Eight expressed sequence tags, previously assigned to 13q11-q12 (D13S182E, D13S183E, D13S502E, D13S504E, D13S505E, D13S837E, TUBA2, ATP1AL1), were localized on the YAC contig. YAC screening of a cDNA library derived from mouse cochlea allowed us to identify an {alpha}-tubulin gene (TUBA2) that was subsequently precisely mapped within the candidate region. 36 refs., 2 figs., 2 tabs.

  17. Construction and Characterization of Three Wheat Bacterial Artificial Chromosome Libraries

    Directory of Open Access Journals (Sweden)

    Wenjin Cao

    2014-11-01

    Full Text Available We have constructed three bacterial artificial chromosome (BAC libraries of wheat cultivar Triticum aestivum Wangshuibai, germplasms T. monococcum TA2026 and TA2033. A total of 1,233,792,170,880 and 263,040 clones were picked and arrayed in 384-well plates. On the basis of genome sizes of 16.8 Gb for hexaploid wheat and 5.6 Gb for diploid wheat, the three libraries represented 9.05-, 2.60-, and 3.71-fold coverage of the haploid genomes, respectively. An improved descending pooling system for BAC libraries screening was established. This improved strategy can save 80% of the time and 68% of polymerase chain reaction (PCR with the same successful rate as the universal 6D pooling strategy.

  18. Human artificial chromosomes for Duchenne muscular dystrophy and beyond: challenges and hopes.

    OpenAIRE

    Tedesco, F. S.

    2015-01-01

    Safe and efficacious vectors able to carry large or several transgenes are of key importance for gene therapy. Human artificial chromosomes can fulfil this essential requirement; moreover, they do not integrate into the host genome. However, drawbacks such as the low efficiency of chromosome transfer and their relatively complex engineering still limit their widespread use. In this article, I summarise the key steps that brought human artificial chromosomes into preclinical research for Duche...

  19. Refined human artificial chromosome vectors for gene therapy and animal transgenesis

    OpenAIRE

    Kazuki, Y; Hoshiya, H.; Takiguchi, M.; S. Abe; Iida, Y; Osaki, M.; Katoh, M; Hiratsuka, M; Shirayoshi, Y; Hiramatsu, K; Ueno, E; N. Kajitani; Yoshino, T.; Kazuki, K; Ishihara, C.

    2010-01-01

    Human artificial chromosomes (HACs) have several advantages as gene therapy vectors, including stable episomal maintenance, and the ability to carry large gene inserts. We previously developed HAC vectors from the normal human chromosomes using a chromosome engineering technique. However, endogenous genes were remained in these HACs, limiting their therapeutic applications. In this study, we refined a HAC vector without endogenous genes from human chromosome 21 in homologous recombination-pro...

  20. A 11 Mb YAC-based contig spanning the familial juvenile nephronophthisis region (NPH1) located on chromosome 2q

    Energy Technology Data Exchange (ETDEWEB)

    Konrad, M.; Saunier, S.; Silbermann, F. [INSERM, Paris (France)] [and others

    1995-12-10

    A gene (NPH1) responsible for approximately 90% of the purely renal form of familial juvenile nephronophthisis, a progressive tubulo-interstitial kidney disorder, maps to human chromosome 2. We report the construction of a YAC-based contig spanning the critical NPH1 region and the flanking genetic markers. This physical map was integrated with a refined genetic map that restricted the NPH1 interval to about 2 cM; this interval corresponds to a maximum physical distance of 3.5 Mb. The entire contig covers 9 cM between the loci D2S135 and D2S121. The maximum physical distance between these two markers is approximately 11.3 Mb. Forty-five sequence-tagged sites, including six genes, have been located within this contig. PAX8, a member of the human paired box gene family, that is expressed in the developing kidney, was assigned outside the restricted NPH1 critical region and cannot therefore be regarded as a candidate gene. This set of overlapping clones represents a useful resource for further targeted development of genetic markers and for the characterization of candidate genes responsible for juvenile nephronophthisis. 26 refs., 2 figs., 3 tabs.

  1. Rescue of end fragments of yeast artificial chromosomes by homologous recombination in yeast.

    OpenAIRE

    Hermanson, G G; Hoekstra, M F; McElligott, D. L.; Evans, G A

    1991-01-01

    Yeast artificial chromosomes (YACs) provide a powerful tool for the isolation and mapping of large regions of mammalian chromosomes. We developed a rapid and efficient method for the isolation of DNA fragments representing the extreme ends of YAC clones by the insertion of a rescue plasmid into the YAC vector by homologous recombination. Two rescue vectors were constructed containing a yeast LYS2 selectable gene, a bacterial origin of replication, an antibiotic resistance gene, a polylinker c...

  2. Organization of the Bacillus subtilis 168 chromosome between kdg and the attachment site of the SP beta prophage: use of Long Accurate PCR and yeast artificial chromosomes for sequencing.

    Science.gov (United States)

    Capuano, V; Galleron, N; Pujic, P; Sorokin, A; Ehrlich, S D

    1996-11-01

    Within the Bacillus subtilis genome sequencing project, the region between lysA and ilvA was assigned to our laboratory. In this report we present the sequence of the last 36 kb of this region, between the kdg operon and the attachment site of the SP beta prophage. A two-step strategy was used for the sequencing. In the first step, total chromosomal DNA was cloned in phage M13-based vectors and the clones carrying inserts from the target region were identified by hybridization with a cognate yeast artificial chromosome (YAC) from our collection. Sequencing of the clones allowed us to establish a number of contigs. In the second step the contigs were mapped by Long Accurate (LA) PCR and the remaining gaps closed by sequencing of the PCR products. The level of sequence inaccuracy due to LA PCR errors appeared to be about 1 in 10,000, which does not affect significantly the final sequence quality. This two-step strategy is efficient and we suggest that it can be applied to sequencing of longer chromosomal regions. The 36 kb sequence contains 38 coding sequences (CDSs), 19 of which encode unknown proteins. Seven genetic loci already mapped in this region, xpt, metB, ilvA, ilvD, thyB, dfrA and degR were identified. Eleven CDSs were found to display significant similarities to known proteins from the data banks, suggesting possible functions for some of the novel genes: cspD may encode a cold shock protein; bcsA, the first bacterial homologue of chalcone synthase; exol, a 5' to 3' exonuclease, similar to that of DNA polymerase I of Escherichia coli; and bsaA, a stress-response-associated protein. The protein encoded by yplP has homology with the transcriptional NifA-like regulators. The arrangement of the genes relative to possible promoters and terminators suggests 19 potential transcription units. PMID:8969496

  3. Construction of an American mink Bacterial Artificial Chromosome (BAC library and sequencing candidate genes important for the fur industry

    Directory of Open Access Journals (Sweden)

    Christensen Knud

    2011-07-01

    Full Text Available Abstract Background Bacterial artificial chromosome (BAC libraries continue to be invaluable tools for the genomic analysis of complex organisms. Complemented by the newly and fast growing deep sequencing technologies, they provide an excellent source of information in genomics projects. Results Here, we report the construction and characterization of the CHORI-231 BAC library constructed from a Danish-farmed, male American mink (Neovison vison. The library contains approximately 165,888 clones with an average insert size of 170 kb, representing approximately 10-fold coverage. High-density filters, each consisting of 18,432 clones spotted in duplicate, have been produced for hybridization screening and are publicly available. Overgo probes derived from expressed sequence tags (ESTs, representing 21 candidate genes for traits important for the mink industry, were used to screen the BAC library. These included candidate genes for coat coloring, hair growth and length, coarseness, and some receptors potentially involved in viral diseases in mink. The extensive screening yielded positive results for 19 of these genes. Thirty-five clones corresponding to 19 genes were sequenced using 454 Roche, and large contigs (184 kb in average were assembled. Knowing the complete sequences of these candidate genes will enable confirmation of the association with a phenotype and the finding of causative mutations for the targeted phenotypes. Additionally, 1577 BAC clones were end sequenced; 2505 BAC end sequences (80% of BACs were obtained. An excess of 2 Mb has been analyzed, thus giving a snapshot of the mink genome. Conclusions The availability of the CHORI-321 American mink BAC library will aid in identification of genes and genomic regions of interest. We have demonstrated how the library can be used to identify specific genes of interest, develop genetic markers, and for BAC end sequencing and deep sequencing of selected clones. To our knowledge, this is the

  4. Delineating Rearrangements in Single Yeast Artificial Chromosomes by Quantitative DNA Fiber Mapping

    OpenAIRE

    Weier, Heinz-Ulrich G.; Greulich-Bode, Karin M.; Wu, Jenny; Duell, Thomas

    2009-01-01

    Cloning of large chunks of human genomic DNA in recombinant systems such as yeast or bacterial artificial chromosomes has greatly facilitated the construction of physical maps, the positional cloning of disease genes or the preparation of patient-specific DNA probes for diagnostic purposes. For this process to work efficiently, the DNA cloning process and subsequent clone propagation need to maintain stable inserts that are neither deleted nor otherwise rearranged. Some regions of the human g...

  5. The development and characterisation of a bacterial artificial chromosome library for Fragaria vesca

    OpenAIRE

    Abbott Albert G; Monfort Amparo; Muñoz-Torres Monica C; Sargent Daniel J; Girona Elena; Bonet Julio; Arús Pere; Simpson David W; Davik Jahn

    2009-01-01

    Abstract Background The cultivated strawberry Fragaria ×ananassa is one of the most economically-important soft-fruit species. Few structural genomic resources have been reported for Fragaria and there exists an urgent need for the development of physical mapping resources for the genus. The first stage in the development of a physical map for Fragaria is the construction and characterisation of a high molecular weight bacterial artificial chromosome (BAC) library. Methods A BAC library, cons...

  6. Efficient manipulation of the human adenovirus genome as an infectious yeast artificial chromosome clone.

    OpenAIRE

    Ketner, G; Spencer, F; Tugendreich, S; C. Connelly; Hieter, P

    1994-01-01

    A yeast artificial chromosome (YAC) containing a complete human adenovirus type 2 genome was constructed, and viral DNA derived from the YAC was shown to be infectious upon introduction into mammalian cells. The adenovirus YAC could be manipulated efficiently using homologous recombination-based methods in the yeast host, and mutant viruses, including a variant that expresses the human analog of the Saccharomyces cerevisiae CDC27 gene, were readily recovered from modified derivatives of the Y...

  7. Generalized Gap Model for Bacterial Artificial Chromosome Clone Fingerprint Mapping and Shotgun Sequencing

    OpenAIRE

    Wendl, Michael C; Robert H Waterston

    2002-01-01

    We develop an extension to the Lander-Waterman theory for characterizing gaps in bacterial artificial chromosome fingerprint mapping and shotgun sequencing projects. It supports a larger set of descriptive statistics and is applicable to a wider range of project parameters. We show that previous assertions regarding inconsistency of the Lander-Waterman theory at higher coverages are incorrect and that another well-known but ostensibly different model is in fact the same. The apparent paradox ...

  8. Complete Genomes of Classical Swine Fever Virus Cloned into Bacterial Artificial Chromosomes

    OpenAIRE

    Rasmussen, Thomas Bruun; Reimann, I; Uttenthal, Åse; De Beer, M.

    2011-01-01

    Complete genome amplification of viral RNA provides a new tool for the generation of modified pestiviruses. We have used our full-genome amplification strategy for generation of amplicons representing complete genomes of classical swine fever virus. The amplicons were cloned directly into a stable single-copy bacterial artificial chromosome (BAC) generating full-length pestivirus DNAs from which infectious RNA transcripts could be also derived. Our strategy allows construction of stable infec...

  9. Bacterial Artificial Chromosome Clones of Viruses Comprising the Towne Cytomegalovirus Vaccine

    OpenAIRE

    Xiaohong Cui; Adler, Stuart P.; Davison, Andrew J.; Larry Smith; EL-Sayed E. Habib; McVoy, Michael A.

    2012-01-01

    Bacterial artificial chromosome (BAC) clones have proven invaluable for genetic manipulation of herpesvirus genomes. BAC cloning can also be useful for capturing representative genomes that comprise a viral stock or mixture. The Towne live attenuated cytomegalovirus vaccine was developed in the 1970s by serial passage in cultured fibroblasts. Although its safety, immunogenicity, and efficacy have been evaluated in nearly a thousand human subjects, the vaccine itself has been little studied. I...

  10. Generating Transgenic Mice from Bacterial Artificial Chromosomes: Transgenesis Efficiency, Integration and Expression Outcomes

    OpenAIRE

    Van Keuren, Margaret L.; Gavrilina, Galina B.; Filipiak, Wanda E.; Zeidler, Michael G.; Saunders, Thomas L.

    2009-01-01

    Transgenic mice are widely used in biomedical research to study gene expression, developmental biology, and gene therapy models. Bacterial artificial chromosome (BAC) transgenes direct gene expression at physiological levels with the same developmental timing and expression patterns as endogenous genes in transgenic animal models. We generated 707 transgenic founders from 86 BAC transgenes purified by three different methods. Transgenesis efficiency was the same for all BAC DNA purification m...

  11. YAC contigs of the Rab1 and wobbler (wr) spinal muscular atrophy gene region on proximal mouse chromosome 11 and of the homologous region on human chromosome 2p

    Energy Technology Data Exchange (ETDEWEB)

    Wedemeyer, N.; Lengeling, A.; Ronsiek, M. [Univ. of Bielefeld (Germany)] [and others

    1996-03-05

    Despite rapid progress in the physical characterization of murine and human genomes, little molecular information is available on certain regions, e.g., proximal mouse chromosome 11 (Chr 11) and human chromosome 2p (Chr2p). We have localized the wobbler spinal atrophy gene wr to proximal mouse Chr 11, tightly linked to Rab1, a gene coding for a small GTP-binding protein, and Glns-ps1, an intronless pseudogene of the glutamine synthetase gene. We have not used these markers to construct a 1.3-Mb yeast artificial chromosome (YAC) contig of the Rab1 region on mouse Chr 11. Four YAC clones isolated from two independent YAC libraries were characterized by rare-cutting analysis, fluorescence in situ hybridization (FISH), and sequence-tagged site (STS) isolation and mapping. Rab1 and Glns-ps1 were found to be only 200 kb apart. A potential CpG island near a methylated NarI site and a trapped exon, ETG1.1, were found over 250 kb from Rab1. Two overlapping YACs were identified that contained a 150-kb region of human Chr 2p, comprising the RAB1 locus, AHY1.1, and the human homologue of ETG1.1, indicating a high degree of conservation of this region in the two species. We mapped AHY1.1 and thus human RAB1 on Chr 2p13.4-p14 using somatic cell hybrids and a radiation hybrid panel, thus extending a known region of conserved synteny between mouse Chr 11 and human Chr 2p. Recently, the gene LMGMD2B for a human recessive neuromuscular disease, limb girdle muscular dystrophy type 2B, has been mapped to 2p13-p16. The conservation between the mouse Rab1 and human RAB1 regions will be helpful in identifying candidate genes for the wobbler spinal muscular atrophy and in clarifying a possible relationship between wr and LMGMD2B. 33 refs., 7 figs., 3 tabs.

  12. Final report. Human artificial episomal chromosome (HAEC) for building large genomic libraries

    Energy Technology Data Exchange (ETDEWEB)

    Jean-Michael H. Vos

    1999-12-09

    Collections of human DNA fragments are maintained for research purposes as clones in bacterial host cells. However for unknown reasons, some regions of the human genome appear to be unclonable or unstable in bacteria. Their team has developed a system using episomes (extrachromosomal, autonomously replication DNA) that maintains large DNA fragments in human cells. This human artificial episomal chromosomal (HAEC) system may prove useful for coverage of these especially difficult regions. In the broader biomedical community, the HAEC system also shows promise for use in functional genomics and gene therapy. Recent improvements to the HAEC system and its application to mapping, sequencing, and functionally studying human and mouse DNA are summarized. Mapping and sequencing the human genome and model organisms are only the first steps in determining the function of various genetic units critical for gene regulation, DNA replication, chromatin packaging, chromosomal stability, and chromatid segregation. Such studies will require the ability to transfer and manipulate entire functional units into mammalian cells.

  13. In situ hybridization to cytogenetic bands of yeast artificial chromosomes covering 50% of human Xq24-Xq28 DNA

    OpenAIRE

    Montanaro, Vittorio; Casamassimi, Amelia; D'Urso, Michele; Yoon, Jae-Young; Freije, Wadiha; Schlessinger, David; Muenke, Maximilian; Nussbaum, Robert L.; Saccone, Salvatore; Maugeri, Silvana; Santoro, Anna Maria; Motta, Salvatore; Della Valle, Giuliano

    1991-01-01

    From the collection described by Abidi et al., 102 yeast artificial chromosomes (YACs) with human DNA inserts more than 300 kb in length were assigned to chromosomal band positions on early metaphase chromosomes by in situ hybridization using the biotin-avidin method. All the YACs hybridized within the Xq24-Xqter region, supporting the origin of the vast majority of the YACs from single human X-chromosomal sites. With assignments precise to ±0.5 bands, YACs were distributed among cytogenetic ...

  14. A new vector for recombination-based cloning of large DNA fragments from yeast artificial chromosomes.

    OpenAIRE

    Bradshaw, M S; Bollekens, J A; Ruddle, F H

    1995-01-01

    The functional analysis of genes frequently requires manipulation of large genomic regions embedded in yeast artificial chromosomes (YACs). We have designed a yeast-bacteria shuttle vector, pClasper, that can be used to clone specific regions of interest from YACs by homologous recombination. The important feature of pClasper is the presence of the mini-F factor replicon. This leads to a significant increase in the size of the plasmid inserts that can be maintained in bacteria after cloning b...

  15. Cloning the simian varicella virus genome in E. coli as an infectious bacterial artificial chromosome

    OpenAIRE

    Gray, Wayne L.; Zhou, Fuchun; Noffke, Juliane; Tischer, B Karsten

    2011-01-01

    Simian varicella virus (SVV) is closely related to human varicella-zoster virus and causes varicella and zoster-like disease in nonhuman primates. In this study, a mini-F replicon was inserted into a SVV cosmid and infectious SVV was generated by co-transfection of Vero cells with overlapping SVV cosmids. The entire SVV genome, cloned as a bacterial artificial chromosome (BAC), was stably propagated upon serial passage in E. coli. Transfection of pSVV-BAC DNA into Vero cells yielded infectiou...

  16. Construction and characterization of a bacterial artificial chromosome library of the maize inbred line Qi319

    Directory of Open Access Journals (Sweden)

    Chun Hua Mu

    2016-03-01

    Full Text Available Zea mays L. has been the most cultivated crop and the crop with the largest yield in China since 2012. We constructed a bacterial artificial chromosome (BAC library for the maize inbred line Qi319, which may be used as a key source for disease-resistant maize breeding in China. The BAC contains 270,720 clones, with an average insert size of 90 kb. The coverage of the library is about 10.43 genome equivalents when considering a haploid genome size of 2300 Mb, providing a 99.99% likelihood of isolating any maize gene or sequence in the library. An average of 12 clones were obtained by polymerase chain reaction screening by using primer pairs linked to the genes for resistance to maize southern rust and rough dwarf. The results indicate that the library can satisfy the requirements for recovering specific sequences. The library is available to researchers to whom it may be of interest.

  17. Construction and characterization of bacterial artificial chromosomes (BACs) containing herpes simplex virus full-length genomes.

    Science.gov (United States)

    Nagel, Claus-Henning; Pohlmann, Anja; Sodeik, Beate

    2014-01-01

    Bacterial artificial chromosomes (BACs) are suitable vectors not only to maintain the large genomes of herpesviruses in Escherichia coli but also to enable the traceless introduction of any mutation using modern tools of bacterial genetics. To clone a herpes simplex virus genome, a BAC replication origin is first introduced into the viral genome by homologous recombination in eukaryotic host cells. As part of their nuclear replication cycle, genomes of herpesviruses circularize and these replication intermediates are then used to transform bacteria. After cloning, the integrity of the recombinant viral genomes is confirmed by restriction length polymorphism analysis and sequencing. The BACs may then be used to design virus mutants. Upon transfection into eukaryotic cells new herpesvirus strains harboring the desired mutations can be recovered and used for experiments in cultured cells as well as in animal infection models. PMID:24671676

  18. A Plasmid Set for Efficient Bacterial Artificial Chromosome (BAC) Transgenesis in Zebrafish.

    Science.gov (United States)

    Fuentes, Fernando; Reynolds, Eric; Lewellis, Stephen W; Venkiteswaran, Gayatri; Knaut, Holger

    2016-01-01

    Transgenesis of large DNA constructs is essential for gene function analysis. Recently, Tol2 transposase-mediated transgenesis has emerged as a powerful tool to insert bacterial artificial chromosome (BAC) DNA constructs into the genome of zebrafish. For efficient transgenesis, the genomic DNA piece in the BAC construct needs to be flanked by Tol2 transposon sites, and the constructs should contain a transgenesis marker for easy identification of transgenic animals. We report a set of plasmids that contain targeting cassettes that allow the insertion of Tol2 sites and different transgenesis markers into BACs. Using BACs containing these targeting cassettes, we show that transgenesis is as efficient as iTol2, that preselecting for expression of the transgenesis marker increases the transgenesis rate, and that BAC transgenics faithfully recapitulate the endogenous gene expression patterns and allow for the estimation of the endogenous gene expression levels. PMID:26818072

  19. Construction of bacterial artificial chromosome libraries for Zhikong Scallop Chlamys farreri

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yang; ZHANG Xiaojun; Chantel F.SCHEURING; ZHANG Hongbin; LI Fuhua; XIANG Jianhai

    2008-01-01

    Two Large-insert genomic bacterial artificial chromosome (BAC) libraries of Zhikong scallop Chlamys farreri were constructed to promote our genetic and genomic research.High-quality megabase-sized DNA was isolated from the adductor muscle of the scallop and partially digested by BamH I and Mbo I,respectively.The BamH I library consisted of 53760 clones while the Mbo I library consisted of 7680 clones.Approximately 96% of the clones in BamH I library contained nuclear DNA inserts in average size of 100 kb,providing a coverage of 5.3 haploid genome equivalents.Similarly,the Mbo I library with an average insert of 145 kb and no insert-empty clones,thus providing a genome coverage of 1.1 haploid genome equivalents.

  20. DNA immunization with a herpes simplex virus 2 bacterial artificial chromosome

    International Nuclear Information System (INIS)

    Construction of a herpes simplex virus 2 (HSV-2) bacterial artificial chromosome (BAC) is described. BAC vector sequences were inserted into the thymidine kinase gene of HSV-2 by homologous recombination. DNA from cells infected with the resulting recombinant virus was transformed into E. coli, and colonies containing the HSV-2 BAC (HSV2-BAC) were isolated and analyzed for the expected genotype. HSV2-BAC DNA was infectious when transfected back into mammalian cells and the resulting virus was thymidine kinase negative. When used to immunize mice, the HSV2-BAC DNA elicited a strong HSV-2 specific antibody response that was equal to or greater than live virus immunization. Further, HSV2-BAC immunization was protective when animals were challenged with a lethal dose of virus. The utility of the HSV2-BAC for construction of recombinant virus genomes was demonstrated by elimination of the HSV-2 glycoprotein D (gD) gene. A recombinant HSV-2 BAC with the gD gene deleted was isolated and shown to be incapable of producing infectious virus following transfection unless an HSV gD gene was expressed in a complementing cell line. Immunization of mice with the HSV2 gD-BAC also elicited an HSV-2 specific antibody response and was protective. The results demonstrate the feasibility of DNA immunization with HSV-2 bacterial artificial chromosomes for replicating and nonreplicating candidate HSV-2 vaccines, as well as the utility of BAC technology for construction and maintenance of novel HSV-2 vaccines. The results further suggest that such technology will be a powerful tool for dissecting the immune response to HSV-2

  1. Efficient assembly of de novo human artificial chromosomes from large genomic loci

    Directory of Open Access Journals (Sweden)

    Stromberg Gregory

    2005-07-01

    Full Text Available Abstract Background Human Artificial Chromosomes (HACs are potentially useful vectors for gene transfer studies and for functional annotation of the genome because of their suitability for cloning, manipulating and transferring large segments of the genome. However, development of HACs for the transfer of large genomic loci into mammalian cells has been limited by difficulties in manipulating high-molecular weight DNA, as well as by the low overall frequencies of de novo HAC formation. Indeed, to date, only a small number of large (>100 kb genomic loci have been reported to be successfully packaged into de novo HACs. Results We have developed novel methodologies to enable efficient assembly of HAC vectors containing any genomic locus of interest. We report here the creation of a novel, bimolecular system based on bacterial artificial chromosomes (BACs for the construction of HACs incorporating any defined genomic region. We have utilized this vector system to rapidly design, construct and validate multiple de novo HACs containing large (100–200 kb genomic loci including therapeutically significant genes for human growth hormone (HGH, polycystic kidney disease (PKD1 and ß-globin. We report significant differences in the ability of different genomic loci to support de novo HAC formation, suggesting possible effects of cis-acting genomic elements. Finally, as a proof of principle, we have observed sustained ß-globin gene expression from HACs incorporating the entire 200 kb ß-globin genomic locus for over 90 days in the absence of selection. Conclusion Taken together, these results are significant for the development of HAC vector technology, as they enable high-throughput assembly and functional validation of HACs containing any large genomic locus. We have evaluated the impact of different genomic loci on the frequency of HAC formation and identified segments of genomic DNA that appear to facilitate de novo HAC formation. These genomic loci

  2. Cloning of a very virulent plus, 686 strain of Marek’s disease virus as a bacterial artificial chromosome

    Science.gov (United States)

    Bacterial artificial chromosome (BAC) vectors were first developed to facilitate propagation and manipulation of large DNA fragments. This technology was later used to clone full-length genomes of large DNA viruses to study viral gene function. Marek’s disease virus (MDV) is a highly oncogenic herpe...

  3. Plant artificial chromosome technology and its potential application in genetic engineering.

    Science.gov (United States)

    Yu, Weichang; Yau, Yuan-Yeu; Birchler, James A

    2016-05-01

    Genetic engineering with just a few genes has changed agriculture in the last 20 years. The most frequently used transgenes are the herbicide resistance genes for efficient weed control and the Bt toxin genes for insect resistance. The adoption of the first-generation genetically engineered crops has been very successful in improving farming practices, reducing the application of pesticides that are harmful to both human health and the environment, and producing more profit for farmers. However, there is more potential for genetic engineering to be realized by technical advances. The recent development of plant artificial chromosome technology provides a super vector platform, which allows the management of a large number of genes for the next generation of genetic engineering. With the development of other tools such as gene assembly, genome editing, gene targeting and chromosome delivery systems, it should become possible to engineer crops with multiple genes to produce more agricultural products with less input of natural resources to meet future demands. PMID:26369910

  4. Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A.

    Science.gov (United States)

    Poursarebani, Naser; Nussbaumer, Thomas; Simková, Hana; Safář, Jan; Witsenboer, Hanneke; van Oeveren, Jan; Doležel, Jaroslav; Mayer, Klaus F X; Stein, Nils; Schnurbusch, Thorsten

    2014-07-01

    Bread wheat (Triticum aestivum L.) is the most important staple food crop for 35% of the world's population. International efforts are underway to facilitate an increase in wheat production, of which the International Wheat Genome Sequencing Consortium (IWGSC) plays an important role. As part of this effort, we have developed a sequence-based physical map of wheat chromosome 6A using whole-genome profiling (WGP™). The bacterial artificial chromosome (BAC) contig assembly tools fingerprinted contig (fpc) and linear topological contig (ltc) were used and their contig assemblies were compared. A detailed investigation of the contigs structure revealed that ltc created a highly robust assembly compared with those formed by fpc. The ltc assemblies contained 1217 contigs for the short arm and 1113 contigs for the long arm, with an L50 of 1 Mb. To facilitate in silico anchoring, WGP™ tags underlying BAC contigs were extended by wheat and wheat progenitor genome sequence information. Sequence data were used for in silico anchoring against genetic markers with known sequences, of which almost 79% of the physical map could be anchored. Moreover, the assigned sequence information led to the 'decoration' of the respective physical map with 3359 anchored genes. Thus, this robust and genetically anchored physical map will serve as a framework for the sequencing of wheat chromosome 6A, and is of immediate use for map-based isolation of agronomically important genes/quantitative trait loci located on this chromosome. PMID:24813060

  5. Physical map and organization of chromosome 7 in the rice blast fungus, Magnaporthe grisea.

    Science.gov (United States)

    Zhu, H; Blackmon, B P; Sasinowski, M; Dean, R A

    1999-08-01

    The rice blast fungus Magnaporthe grisea is a highly destructive plant pathogen and one of the most important for studying various aspects of host-plant interactions. It has been widely adopted as a model organism because it is ideally suited for genetic and biological studies. To facilitate map-based cloning, chromosome walking, and genome organization studies of M. grisea, a complete physical map of chromosome 7 was constructed using a large-insert (130 kb) bacterial artificial chromosome (BAC) library. Using 147 chromosome 7-specific single-copy BAC clones and 20 RFLP markers on chromosome 7, 625 BAC clones were identified by hybridization. BAC clones were digested with HindIII, and fragments were size separated on analytical agarose gels to create DNA fingerprints. Hybridization contigs were constructed using a random cost algorithm, whereas fingerprinting contigs were constructed using the software package FPC. Results from both methods were generally in agreement, but numerous anomalies were observed. The combined data produced five robust anchored contigs after gap closure by chromosomal walking. The genetic and physical maps agreed closely. The final physical map was estimated to cover >95% of the 4.2 Mb of chromosome 7. Based on the contig maps, a minimum BAC tile containing 42 BAC clones was created, and organization of repetitive elements and expressed genes of the chromosome was investigated. PMID:10447509

  6. A bacterial artificial chromosome library for Biomphalaria glabrata, intermediate snail host of Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Coen M Adema

    2006-10-01

    Full Text Available To provide a novel resource for analysis of the genome of Biomphalaria glabrata, members of the international Biomphalaria glabrata Genome Initiative (biology.unm.edu/biomphalaria-genome.html, working with the Arizona Genomics Institute (AGI and supported by the National Human Genome Research Institute (NHGRI, produced a high quality bacterial artificial chromosome (BAC library. The BB02 strain B. glabrata, a field isolate (Belo Horizonte, Minas Gerais, Brasil that is susceptible to several strains of Schistosoma mansoni, was selfed for two generations to reduce haplotype diversity in the offspring. High molecular weight DNA was isolated from ovotestes of 40 snails, partially digested with HindIII, and ligated into pAGIBAC1 vector. The resulting B. glabrata BAC library (BG_BBa consists of 61824 clones (136.3 kb average insert size and provides 9.05 × coverage of the 931 Mb genome. Probing with single/low copy number genes from B. glabrata and fingerprinting of selected BAC clones indicated that the BAC library sufficiently represents the gene complement. BAC end sequence data (514 reads, 299860 nt indicated that the genome of B. glabrata contains ~ 63% AT, and disclosed several novel genes, transposable elements, and groups of high frequency sequence elements. This BG_BBa BAC library, available from AGI at cost to the research community, gains in relevance because BB02 strain B. glabrata is targeted whole genome sequencing by NHGRI.

  7. Delineating Rearrangements in Single Yeast Artificial Chromosomes by Quantitative DNA Fiber Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Heinz-Ulrich G.; Greulich-Bode, Karin M.; Wu, Jenny; Duell, Thomas

    2009-09-18

    Cloning of large chunks of human genomic DNA in recombinant systems such as yeast or bacterial artificial chromosomes has greatly facilitated the construction of physical maps, the positional cloning of disease genes or the preparation of patient-specific DNA probes for diagnostic purposes. For this process to work efficiently, the DNA cloning process and subsequent clone propagation need to maintain stable inserts that are neither deleted nor otherwise rearranged. Some regions of the human genome; however, appear to have a higher propensity than others to rearrange in any host system. Thus, techniques to detect and accurately characterize such rearrangements need to be developed. We developed a technique termed 'Quantitative DNA Fiber Mapping (QDFM)' that allows accurate tagging of sequence elements of interest with near kilobase accuracy and optimized it for delineation of rearrangements in recombinant DNA clones. This paper demonstrates the power of this microscopic approach by investigating YAC rearrangements. In our examples, high-resolution physical maps for regions within the immunoglobulin lambda variant gene cluster were constructed for three different YAC clones carrying deletions of 95 kb and more. Rearrangements within YACs could be demonstrated unambiguously by pairwise mapping of cosmids along YAC DNA molecules. When coverage by YAC clones was not available, distances between cosmid clones were estimated by hybridization of cosmids onto DNA fibers prepared from human genomic DNA. In addition, the QDFM technology provides essential information about clone stability facilitating closure of the maps of the human genome as well as those of model organisms.

  8. Construction of an infectious clone of canine herpesvirus genome as a bacterial artificial chromosome.

    Science.gov (United States)

    Arii, Jun; Hushur, Orkash; Kato, Kentaro; Kawaguchi, Yasushi; Tohya, Yukinobu; Akashi, Hiroomi

    2006-04-01

    Canine herpesvirus (CHV) is an attractive candidate not only for use as a recombinant vaccine to protect dogs from a variety of canine pathogens but also as a viral vector for gene therapy in domestic animals. However, developments in this area have been impeded by the complicated techniques used for eukaryotic homologous recombination. To overcome these problems, we used bacterial artificial chromosomes (BACs) to generate infectious BACs. Our findings may be summarized as follows: (i) the CHV genome (pCHV/BAC), in which a BAC flanked by loxP sites was inserted into the thymidine kinase gene, was maintained in Escherichia coli; (ii) transfection of pCHV/BAC into A-72 cells resulted in the production of infectious virus; (iii) the BAC vector sequence was almost perfectly excisable from the genome of the reconstituted virus CHV/BAC by co-infection with CHV/BAC and a recombinant adenovirus that expressed the Cre recombinase; and (iv) a recombinant virus in which the glycoprotein C gene was deleted was generated by lambda recombination followed by Flp recombination, which resulted in a reduction in viral titer compared with that of the wild-type virus. The infectious clone pCHV/BAC is useful for the modification of the CHV genome using bacterial genetics, and CHV/BAC should have multiple applications in the rapid generation of genetically engineered CHV recombinants and the development of CHV vectors for vaccination and gene therapy in domestic animals. PMID:16515874

  9. Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes.

    Science.gov (United States)

    Beier, Sebastian; Himmelbach, Axel; Schmutzer, Thomas; Felder, Marius; Taudien, Stefan; Mayer, Klaus F X; Platzer, Matthias; Stein, Nils; Scholz, Uwe; Mascher, Martin

    2016-07-01

    Hierarchical shotgun sequencing remains the method of choice for assembling high-quality reference sequences of complex plant genomes. The efficient exploitation of current high-throughput technologies and powerful computational facilities for large-insert clone sequencing necessitates the sequencing and assembly of a large number of clones in parallel. We developed a multiplexed pipeline for shotgun sequencing and assembling individual bacterial artificial chromosomes (BACs) using the Illumina sequencing platform. We illustrate our approach by sequencing 668 barley BACs (Hordeum vulgare L.) in a single Illumina HiSeq 2000 lane. Using a newly designed parallelized computational pipeline, we obtained sequence assemblies of individual BACs that consist, on average, of eight sequence scaffolds and represent >98% of the genomic inserts. Our BAC assemblies are clearly superior to a whole-genome shotgun assembly regarding contiguity, completeness and the representation of the gene space. Our methods may be employed to rapidly obtain high-quality assemblies of a large number of clones to assemble map-based reference sequences of plant and animal species with complex genomes by sequencing along a minimum tiling path. PMID:26801048

  10. Construction and Characterization of an Infectious Murine Gammaherpesivrus-68 Bacterial Artificial Chromosome

    Directory of Open Access Journals (Sweden)

    Ting-Ting Wu

    2011-01-01

    Full Text Available Here we describe the cloning of a sequenced WUMS isolate of murine gammaherpesvirus-68 (MHV-68, γHV-68, also known as MuHV-4 as a bacterial artificial chromosome (BAC. We engineered the insertion of the BAC sequence flanked by loxP sites into the left end of the viral genome before the M1 open reading frame. The infectious viruses were reconstituted following transfection of the MHV-68 BAC DNA into cells. The MHV-68 BAC-derived virus replicated indistinguishably from the wild-type virus in cultured cells. Excision of the BAC insert was efficiently achieved by coexpressing the Cre recombinase. Although the BAC insertion did not significantly affect acute productive infection in the lung, it severely compromised the ability of MHV-68 to establish splenic latency. Removal of the BAC sequence restored the wild-type level of latency. Site-specific mutagenesis was carried out by RecA-mediated recombination to demonstrate that this infectious BAC clone can be used for genetic studies of MHV-68.

  11. A novel method for increasing the transformation efficiency of Escherichia coli-application forbacterial artificial chromosome library construction.

    OpenAIRE

    Zhu, H; Dean, R.A.

    1999-01-01

    Bacterial artificial chromosome (BAC) libraries play a pivotal role in genomics studies. A crucial step in BAC library construction is the transformation of Escherichia coli by electroporation. Absolute efficiency (cfu/microgram DNA) is affected by a number of factors including the topological form and treatment of DNA samples. Here we report a simple new protocol using tRNA assisted precipitation that increased transformation efficiency by 70-fold for BAC ligations and up to 400-fold for pla...

  12. Visualization of lymphatic vessels by Prox1-promoter directed GFP reporter in a bacterial artificial chromosome-based transgenic mouse

    OpenAIRE

    Choi, Inho; Chung, Hee Kyoung; Ramu, Swapnika; Lee, Ha Neul; Kim, Kyu Eui; Lee, Sunju; Yoo, Jaehyuk; Choi, Dongwon; Lee, Yong Suk; Aguilar, Berenice; Hong, Young-Kwon

    2011-01-01

    Although the blood vessel-specific fluorescent transgenic mouse has been an excellent tool to study vasculogenesis and angiogenesis, a lymphatic-specific fluorescent mouse model has not been established to date. Here we report a transgenic animal model that expresses the green fluorescent protein under the promoter of Prox1, a master control gene in lymphatic development. Generated using an approximately 200-kb-long bacterial artificial chromosome harboring the entire Prox1 gene, this Prox1-g...

  13. Highly Efficient Modification of Bacterial Artificial Chromosomes (BACs) Using Novel Shuttle Vectors Containing the R6Kγ Origin of Replication

    OpenAIRE

    Gong, Shiaoching; Yang, Xiangdong William; Li, Chenjian; Heintz, Nathaniel

    2002-01-01

    Bacterial artificial chromosome (BAC) mediated transgenesis has proven to be a highly reliable way to obtain accurate transgene expression for in vivo studies of gene expression and function. A rate-limiting step in use of this technology to characterize large numbers of genes has been the process with which BACs can be modified by homologous recombination in Escherichia coli. We report here a highly efficient method for modifying BACs by using a novel set of shuttle vectors that contain the ...

  14. Incorporation of a lambda phage recombination system and EGFP detection to simplify mutagenesis of Herpes simplex virus bacterial artificial chromosomes

    OpenAIRE

    Weir Jerry P; Schmeisser Falko

    2007-01-01

    Abstract Background Targeted mutagenesis of the herpesvirus genomes has been facilitated by the use of bacterial artificial chromosome (BAC) technology. Such modified genomes have potential uses in understanding viral pathogenesis, gene identification and characterization, and the development of new viral vectors and vaccines. We have previously described the construction of a herpes simplex virus 2 (HSV-2) BAC and the use of an allele replacement strategy to construct HSV-2 recombinants. Whi...

  15. Complete Genome Sequence of Cell Culture-Attenuated Guinea Pig Cytomegalovirus Cloned as an Infectious Bacterial Artificial Chromosome

    OpenAIRE

    Yang, Dongmei; Alam, Zohaib; Cui, Xiaohong; Chen, Michael; Sherrod, Carly J.; McVoy, Michael A.; Schleiss, Mark R.; Dittmer, Dirk P

    2014-01-01

    The complete genome sequence of attenuated guinea pig cytomegalovirus cloned as bacterial artificial chromosome N13R10 was determined. Comparison to pathogenic salivary gland-derived virus revealed 13 differences, 1 of which disrupted overlapping open reading frames encoding GP129 and GP130. Attenuation of N13R10 may arise from an inability to express GP129 and/or GP130.

  16. Use of Recombination-Mediated Genetic Engineering for Construction of Rescue Human Cytomegalovirus Bacterial Artificial Chromosome Clones

    OpenAIRE

    Kalpana Dulal; Benjamin Silver; Hua Zhu

    2012-01-01

    Bacterial artificial chromosome (BAC) technology has contributed immensely to manipulation of larger genomes in many organisms including large DNA viruses like human cytomegalovirus (HCMV). The HCMV BAC clone propagated and maintained inside E. coli allows for accurate recombinant virus generation. Using this system, we have generated a panel of HCMV deletion mutants and their rescue clones. In this paper, we describe the construction of HCMV BAC mutants using a homologous recombination syste...

  17. Cloning human herpes virus 6A genome into bacterial artificial chromosomes and study of DNA replication intermediates

    OpenAIRE

    Borenstein, Ronen; Frenkel, Niza

    2009-01-01

    Cloning of large viral genomes into bacterial artificial chromosomes (BACs) facilitates analyses of viral functions and molecular mutagenesis. Previous derivations of viral BACs involved laborious recombinations within infected cells. We describe a single-step production of viral BACs by direct cloning of unit length genomes, derived from circular or head-to-tail concatemeric DNA replication intermediates. The BAC cloning is independent of intracellular recombinations and DNA packaging constr...

  18. Natural - synthetic - artificial!

    DEFF Research Database (Denmark)

    Nielsen, Peter E

    2010-01-01

    The terms "natural," "synthetic" and "artificial" are discussed in relation to synthetic and artificial chromosomes and genomes, synthetic and artificial cells and artificial life.......The terms "natural," "synthetic" and "artificial" are discussed in relation to synthetic and artificial chromosomes and genomes, synthetic and artificial cells and artificial life....

  19. CHARACTERIZATION AND CHROMOSOMAL ASSIGNMENT OF YEAST ARTIFICIAL CHROMOSOMES CONTAINING HUMAN 3P13-P21-SPECIFIC SEQUENCE-TAGGED SITES

    NARCIS (Netherlands)

    MICHAELIS, SC; BARDENHEUER, W; LUX, A; SCHRAMM, A; GOCKEL, A; SIEBERT, R; WILLERS, C; SCHMIDTKE, K; TODT, B; VANDERHOUT, AH; BUYS, CHCM; HEPPELLPARTON, AC; RABBITTS, PH; UNGAR, S; SMITH, D; LEPASLIER, D; COHEN, D; OPALKA, B; SCHUTTE, J

    1995-01-01

    Human chromosomal region 3p12-p23 is proposed to harbor at least three tumor suppressor genes involved in the development of lung cancer, renal cell carcinoma, and other neoplasias. In order to identify one of these genes we defined sequence tagged sites (STSs) specific for 3p13-p24.2 by analyzing a

  20. Quality control of the sheep bacterial artificial chromosome library, CHORI-243

    Directory of Open Access Journals (Sweden)

    Kirkness Ewen F

    2010-12-01

    Full Text Available Abstract Background The sheep CHORI-243 bacterial artificial chromosome (BAC library is being used in the construction of the virtual sheep genome, the sequencing and construction of the actual sheep genome assembly and as a source of DNA for regions of the genome of biological interest. The objective of our study is to assess the integrity of the clones and plates which make up the CHORI-243 library using the virtual sheep genome. Findings A series of analyses were undertaken based on the mapping the sheep BAC-end sequences (BESs to the virtual sheep genome. Overall, very few plate specific biases were identified, with only three of the 528 plates in the library significantly affected. The analysis of the number of tail-to-tail (concordant BACs on the plates identified a number of plates with lower than average numbers of such BACs. For plates 198 and 213 a partial swap of the BESs determined with one of the two primers appear to have occurred. A third plate, 341, also with a significant deficit in tail-to-tail BACs, appeared to contain a substantial number of sequences determined from contaminating eubacterial 16 S rRNA DNA. Additionally a small number of eubacterial 16 S rRNA DNA sequences were present on two other plates, 111 and 338, in the library. Conclusions The comparative genomic approach can be used to assess BAC library integrity in the absence of fingerprinting. The sequences of the sheep CHORI-243 library BACs have high integrity, especially with the corrections detailed above. The library represents a high quality resource for use by the sheep genomics community.

  1. Construction and characterization of the transformation-competent artificial chromosome(TAC)libraries of Leymus multicaulis

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Transformation-competent artificial chromosome system is able to clone and transfer genes efficiently in plants.In order to clone genes highly tolerant to barley yellow dwarf virus(BYDV),Aphids,drought and salt from Leymus multicaulis,the two TAC genomic libraries I and II were constructed in vector pYLTAC17 and pYLTAC747H/sacB,which contain about 165000 and 236000 recombinant clones sepa-rately.The genome coverage of the two libraries was totally estimated to be about 3―5 haploid genome equivalents,as size selection of genomic DNA fragments was approximately from 9 to 300 kb.Clones of the genomic libraries were collected as bulked pools each containing 500 clones or so,stored in twelve 96-deep-well plates and then were gridding in triplicate onto a high-density colony hybridization filter with a 3×3 pattern using a GeneTAC?G3 arraying robot after being transferred manually into three 384-well plates.Meanwhile 2501 and 2890 clones of Library in pYLTAC17 and in pYLTAC747H/sacB were stored individually in fourteen 384-well plates and then were automatically gridding in duplicate onto a high-density colony hybridization filter with a 6×6 pattern after a replication of plates.Nineteen positive clones were detected by using the probe glutahione reductase gene of L.multicaulis.TAC libraries constructed here can be used to isolate genomic clones containing target genes,and to carry out genome walking for positional cloning.Once the target TAC clones were isolated,they could be immediately transferred into plant genomes with the Agrobacterium system.

  2. Rapid construction of a Bacterial Artificial Chromosomal (BAC) expression vector using designer DNA fragments.

    Science.gov (United States)

    Chen, Chao; Zhao, Xinqing; Jin, Yingyu; Zhao, Zongbao Kent; Suh, Joo-Won

    2014-11-01

    Bacterial artificial chromosomal (BAC) vectors are increasingly being used in cloning large DNA fragments containing complex biosynthetic pathways to facilitate heterologous production of microbial metabolites for drug development. To express inserted genes using Streptomyces species as the production hosts, an integration expression cassette is required to be inserted into the BAC vector, which includes genetic elements encoding a phage-specific attachment site, an integrase, an origin of transfer, a selection marker and a promoter. Due to the large sizes of DNA inserted into the BAC vectors, it is normally inefficient and time-consuming to assemble these fragments by routine PCR amplifications and restriction-ligations. Here we present a rapid method to insert fragments to construct BAC-based expression vectors. A DNA fragment of about 130 bp was designed, which contains upstream and downstream homologous sequences of both BAC vector and pIB139 plasmid carrying the whole integration expression cassette. In-Fusion cloning was performed using the designer DNA fragment to modify pIB139, followed by λ-RED-mediated recombination to obtain the BAC-based expression vector. We demonstrated the effectiveness of this method by rapid construction of a BAC-based expression vector with an insert of about 120 kb that contains the entire gene cluster for biosynthesis of immunosuppressant FK506. The empty BAC-based expression vector constructed in this study can be conveniently used for construction of BAC libraries using either microbial pure culture or environmental DNA, and the selected BAC clones can be directly used for heterologous expression. Alternatively, if a BAC library has already been constructed using a commercial BAC vector, the selected BAC vectors can be manipulated using the method described here to get the BAC-based expression vectors with desired gene clusters for heterologous expression. The rapid construction of a BAC-based expression vector facilitates

  3. The development and characterisation of a bacterial artificial chromosome library for Fragaria vesca

    Directory of Open Access Journals (Sweden)

    Abbott Albert G

    2009-09-01

    Full Text Available Abstract Background The cultivated strawberry Fragaria ×ananassa is one of the most economically-important soft-fruit species. Few structural genomic resources have been reported for Fragaria and there exists an urgent need for the development of physical mapping resources for the genus. The first stage in the development of a physical map for Fragaria is the construction and characterisation of a high molecular weight bacterial artificial chromosome (BAC library. Methods A BAC library, consisting of 18,432 clones was constructed from Fragaria vesca f. semperflorens accession 'Ali Baba'. BAC DNA from individual library clones was pooled to create a PCR-based screening assay for the library, whereby individual clones could be identified with just 34 PCR reactions. These pools were used to screen the BAC library and anchor individual clones to the diploid Fragaria reference map (FV×FN. Findings Clones from the BAC library developed contained an average insert size of 85 kb, representing over seven genome equivalents. The pools and superpools developed were used to identify a set of BAC clones containing 70 molecular markers previously mapped to the diploid Fragaria FV×FN reference map. The number of positive colonies identified for each marker suggests the library represents between 4× and 10× coverage of the diploid Fragaria genome, which is in accordance with the estimate of library coverage based on average insert size. Conclusion This BAC library will be used for the construction of a physical map for F. vesca and the superpools will permit physical anchoring of molecular markers using PCR.

  4. Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses.

    Science.gov (United States)

    Yun, Sang-Im; Song, Byung-Hak; Kim, Jin-Kyoung; Lee, Young-Min

    2015-01-01

    Reverse genetics, an approach to rescue infectious virus entirely from a cloned cDNA, has revolutionized the field of positive-strand RNA viruses, whose genomes have the same polarity as cellular mRNA. The cDNA-based reverse genetics system is a seminal method that enables direct manipulation of the viral genomic RNA, thereby generating recombinant viruses for molecular and genetic studies of both viral RNA elements and gene products in viral replication and pathogenesis. It also provides a valuable platform that allows the development of genetically defined vaccines and viral vectors for the delivery of foreign genes. For many positive-strand RNA viruses such as Japanese encephalitis virus (JEV), however, the cloned cDNAs are unstable, posing a major obstacle to the construction and propagation of the functional cDNA. Here, the present report describes the strategic considerations in creating and amplifying a genetically stable full-length infectious JEV cDNA as a bacterial artificial chromosome (BAC) using the following general experimental procedures: viral RNA isolation, cDNA synthesis, cDNA subcloning and modification, assembly of a full-length cDNA, cDNA linearization, in vitro RNA synthesis, and virus recovery. This protocol provides a general methodology applicable to cloning full-length cDNA for a range of positive-strand RNA viruses, particularly those with a genome of >10 kb in length, into a BAC vector, from which infectious RNAs can be transcribed in vitro with a bacteriophage RNA polymerase. PMID:26780115

  5. Dysregulation of gene expression in the artificial human trisomy cells of chromosome 8 associated with transformed cell phenotypes.

    Directory of Open Access Journals (Sweden)

    Hisakatsu Nawata

    Full Text Available A change in chromosome number, known as aneuploidy, is a common characteristic of cancer. Aneuploidy disrupts gene expression in human cancer cells and immortalized human epithelial cells, but not in normal human cells. However, the relationship between aneuploidy and cancer remains unclear. To study the effects of aneuploidy in normal human cells, we generated artificial cells of human primary fibroblast having three chromosome 8 (trisomy 8 cells by using microcell-mediated chromosome transfer technique. In addition to decreased proliferation, the trisomy 8 cells lost contact inhibition and reproliferated after exhibiting senescence-like characteristics that are typical of transformed cells. Furthermore, the trisomy 8 cells exhibited chromosome instability, and the overall gene expression profile based on microarray analyses was significantly different from that of diploid human primary fibroblasts. Our data suggest that aneuploidy, even a single chromosome gain, can be introduced into normal human cells and causes, in some cases, a partial cancer phenotype due to a disruption in overall gene expression.

  6. Recovery of infectious virus from full-length cowpox virus (CPXV) DNA cloned as a bacterial artificial chromosome (BAC)

    OpenAIRE

    Roth Swaantje J; Höper Dirk; Beer Martin; Feineis Silke; Tischer B Karsten; Osterrieder Nikolaus

    2011-01-01

    Abstract Transmission from pet rats and cats to humans as well as severe infection in felids and other animal species have recently drawn increasing attention to cowpox virus (CPXV). We report the cloning of the entire genome of cowpox virus strain Brighton Red (BR) as a bacterial artificial chromosome (BAC) in Escherichia coli and the recovery of infectious virus from cloned DNA. Generation of a full-length CPXV DNA clone was achieved by first introducing a mini-F vector, which allows mainte...

  7. Repetitive genome elements in a European corn borer, Ostrinia nubilalis, bacterial artificial chromosome library were indicated by bacterial artificial chromosome end sequencing and development of sequence tag site markers: implications for lepidopteran genomic research.

    Science.gov (United States)

    Coates, Brad S; Sumerford, Douglas V; Hellmich, Richard L; Lewis, Leslie C

    2009-01-01

    The European corn borer, Ostrinia nubilalis, is a serious pest of food, fiber, and biofuel crops in Europe, North America, and Asia and a model system for insect olfaction and speciation. A bacterial artificial chromosome library constructed for O. nubilalis contains 36 864 clones with an estimated average insert size of >or=120 kb and genome coverage of 8.8-fold. Screening OnB1 clones comprising approximately 2.76 genome equivalents determined the physical position of 24 sequence tag site markers, including markers linked to ecologically important and Bacillus thuringiensis toxin resistance traits. OnB1 bacterial artificial chromosome end sequence reads (GenBank dbGSS accessions ET217010 to ET217273) showed homology to annotated genes or expressed sequence tags and identified repetitive genome elements, O. nubilalis miniature subterminal inverted repeat transposable elements (OnMITE01 and OnMITE02), and ezi-like long interspersed nuclear elements. Mobility of OnMITE01 was demonstrated by the presence or absence in O. nubilalis of introns at two different loci. A (GTCT)n tetranucleotide repeat at the 5' ends of OnMITE01 and OnMITE02 are evidence for transposon-mediated movement of lepidopteran microsatellite loci. The number of repetitive elements in lepidopteran genomes will affect genome assembly and marker development. Single-locus sequence tag site markers described here have downstream application for integration within linkage maps and comparative genomic studies. PMID:19132072

  8. A YAC contig in 6p23 based on sequence tagged sites

    Energy Technology Data Exchange (ETDEWEB)

    Nemani, M.; Cherif, D.; Chesne, H. [Foundation Jean Dausset, Paris (France)] [and others

    1994-07-15

    A yeast artificial chromosome (YAC) contig located in 6p23 and spanning roughly 2.5 Mb has been constructed from the content of 10 sequence tagged sites (STSs) for YAC clones in 66 yeast colonies. Nine of the STSs have been genetically mapped in CEPH families. The order of STSs mapped with the contig is consistent with that of the genetic map. The order of loci that did not recombine with each other on the genetic map was inferred from the contig. Various regions of the contig are covered by multiple YAC clones that complement observed STS deletions. The STS for the CAG repeat sequence contained in the gene for spinal cerebellar ataxia 1 (gene symbol SCA1) is localized in the contig. It is likely that this gene is located in 6p23. The frequency of chimeric YAC clones in this contig is 35%. Eleven yeast colonies were found to carry two or more YACs. YAC subclones from some of these colonies showed size variation, and for several subclones, evidence consistent with deletion of a sequence tagged site. 27 refs., 2 figs., 2 tabs.

  9. Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A

    OpenAIRE

    Poursarebani, N.; Nussbaumer, T.; Šimková, H. (Hana); Šafář, J.; Witsenboer, H.; van Oeveren, J.; Doležel, J. (Jaroslav); Mayer, K. F. X.; N. Stein; Schnurbusch, T.

    2014-01-01

    Bread wheat (Triticum aestivum L.) is the most important staple food crop for 35% of the world's population. International efforts are underway to facilitate an increase in wheat production, of which the International Wheat Genome Sequencing Consortium (IWGSC) plays an important role. As part of this effort, we have developed a sequence-based physical map of wheat chromosome 6A using whole-genome profiling (WGP (TM)). The bacterial artificial chromosome (BAC) contig assembly tools FINGERPRINT...

  10. Identification and Preliminary Analysis of Several Centromere-associated Bacterial Artificial Chromosome Clones from a Diploid Wheat Library

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Although the centromeres of some plants have been investigated previously, our knowledge of the wheat centromere is still very limited. To understand the structure and function of the wheat centromere, we used two centromeric repeats (RCS1 and CCS1-5ab) to obtain some centromere-associated bacterial artificial chromosome (BAC) clones in 32 RCS1-related BAC clones that had been screened out from a diploid wheat (Triticum boeoticum Boiss.; 2n=2x=14) BAC library. Southern hybridization results indicated that, of the 32 candidates,there were 28 RCS1-positive clones. Based on gel blot patterns, the frequency of RCS1 was approximately one copy every 69.4 kb in these 28 RCS1-positive BAC clones. More bands were detected when the same filter was probed with CCS1-5ab. Furthermore, the CCS1 bands covered all the bands detected by RCS1, which suggests that some CCS1 repeats were distributed together with RCS1. The frequency of CCS1 families was once every 35.8 kb, nearly twice that of RCS1. Fluorescence in situ hybridization (FISH) analysis indicated that the five BAC clones containing RCS1 and CCS1 sequences all detected signals at the centromeric regions in hexaploid wheat, but the signal intensities on the A-genome chromosomes were stronger than those on the B- and/or D-genome chromosomes. The FISH analysis among nine Triticeae cereals indicated that there were A-genomespecific (or rich) sequences dispersing on chromosome arms in the BAC clone TbBAC5. In addition, at the interphase cells, the centromeres of diploid species usually clustered at one pole and formed a ring-like allocation in the period before metaphase.

  11. Dicty_cDB: Contig-U08265-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available s vinifera contig VV78X097443.2, whole genome... 38 3.8 2 ( DW089917 ) CLPY13974.b1_L13.ab1 CLP(XYZ) lettuce peren...um 3D7 chromo... 77 1e-12 AM270145_16( AM270145 |pid:none) Aspergillus niger contig An07c028... 70 2e-10 DQ8...AACTCCATGAATATCCTCAACTAAATAAATAAATAAA TAAATAAATAAATAAATA Gap no gap Contig length 1268 Chromosome number (1..6, M) 4 Chromosome len...Contig-U08265-1 no gap 1268 4 2635072 2633797 MINUS 4 4 U08265 2 0 0 0 0 0 1 0 0 0 1 0 0 0 Show Contig...-U08265-1 Contig ID Contig-U08265-1 Contig update 2002. 9.13 Contig sequence >Contig-U08265-1 (Contig

  12. Construction of an Americn mink Bacterial Artificial Chromosome (BAC) library and sequencing candidate genes important for the fur industry

    DEFF Research Database (Denmark)

    Anistoroaei, Razvan Marian; Hallers, Boudewijn ten; Nefedov, Michael;

    2011-01-01

    consisting of 18,432 clones spotted in duplicate, have been produced for hybridization screening and are publicly available. Overgo probes derived from expressed sequence tags (ESTs), representing 21 candidate genes for traits important for the mink industry, were used to screen the BAC library......BACKGROUND: Bacterial artificial chromosome (BAC) libraries continue to be invaluable tools for the genomic analysis of complex organisms. Complemented by the newly and fast growing deep sequencing technologies, they provide an excellent source of information in genomics projects. RESULTS: Here, we...... report the construction and characterization of the CHORI-231 BAC library constructed from a Danish-farmed, male American mink (Neovison vison). The library contains approximately 165,888 clones with an average insert size of 170 kb, representing approximately 10-fold coverage. High-density filters, each...

  13. Use of Recombination-Mediated Genetic Engineering for Construction of Rescue Human Cytomegalovirus Bacterial Artificial Chromosome Clones

    Directory of Open Access Journals (Sweden)

    Kalpana Dulal

    2012-01-01

    Full Text Available Bacterial artificial chromosome (BAC technology has contributed immensely to manipulation of larger genomes in many organisms including large DNA viruses like human cytomegalovirus (HCMV. The HCMV BAC clone propagated and maintained inside E. coli allows for accurate recombinant virus generation. Using this system, we have generated a panel of HCMV deletion mutants and their rescue clones. In this paper, we describe the construction of HCMV BAC mutants using a homologous recombination system. A gene capture method, or gap repair cloning, to seize large fragments of DNA from the virus BAC in order to generate rescue viruses, is described in detail. Construction of rescue clones using gap repair cloning is highly efficient and provides a novel use of the homologous recombination-based method in E. coli for molecular cloning, known colloquially as recombineering, when rescuing large BAC deletions. This method of excising large fragments of DNA provides important prospects for in vitro homologous recombination for genetic cloning.

  14. Construction and Preliminary Characterization Analysis of Wuzhishan Miniature Pig Bacterial Artificial Chromosome Library with Approximately 8-Fold Genome Equivalent Coverage

    Directory of Open Access Journals (Sweden)

    Changqing Liu

    2013-01-01

    Full Text Available Bacterial artificial chromosome (BAC libraries have been invaluable tools for the genome-wide genetic dissection of complex organisms. Here, we report the construction and characterization of a high-redundancy BAC library from a very valuable pig breed in China, Wuzhishan miniature pig (Sus scrofa, using its blood cells and fibroblasts, respectively. The library contains approximately 153,600 clones ordered in 40 superpools of 10 × 384-deep well microplates. The average insert size of BAC clones was estimated to be 152.3 kb, representing approximately 7.68 genome equivalents of the porcine haploid genome and a 99.93% statistical probability of obtaining at least one clone containing a unique DNA sequence in the library. 19 pairs of microsatellite marker primers covering porcine chromosomes were used for screening the BAC library, which showed that each of these markers was positive in the library; the positive clone number was 2 to 9, and the average number was 7.89, which was consistent with 7.68-fold coverage of the porcine genome. And there were no significant differences of genomic BAC library from blood cells and fibroblast cells. Therefore, we identified 19 microsatellite markers that could potentially be used as genetic markers. As a result, this BAC library will serve as a valuable resource for gene identification, physical mapping, and comparative genomics and large-scale genome sequencing in the porcine.

  15. Dicty_cDB: Contig-U03792-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available am... 38 0.40 2 ( AM439697 ) Vitis vinifera contig VV79X002320.2, whole genome... 48 0.54 1 ( AX346056 ) Sequen...lis ATCC 29413, complete genome. Length = 256 Score = 35.0 bits (79), Expect = 3.1 Identities = 16/40 (40%), Positi... gap Contig length 833 Chromosome number (1..6, M) 1 Chromosome length 4919822 Start point 1341596 End point...Contig-U03792-1 no gap 833 1 1341596 1341957 PLUS 1 1 U03792 0 0 0 0 0 1 0 0 0 0 0 0 0 0 Show Contig...-U03792-1 Contig ID Contig-U03792-1 Contig update 2001. 8.29 Contig sequence >Contig-U03792-1 (Contig

  16. Gata3 Hypomorphic Mutant Mice Rescued with a Yeast Artificial Chromosome Transgene Suffer a Glomerular Mesangial Cell Defect.

    Science.gov (United States)

    Moriguchi, Takashi; Yu, Lei; Otsuki, Akihito; Ainoya, Keiko; Lim, Kim-Chew; Yamamoto, Masayuki; Engel, James Douglas

    2016-09-01

    GATA3 is a zinc finger transcription factor that plays a crucial role in embryonic kidney development, while its precise functions in the adult kidney remain largely unexplored. Here, we demonstrate that GATA3 is specifically expressed in glomerular mesangial cells and plays a critical role in the maintenance of renal glomerular function. Newly generated Gata3 hypomorphic mutant mice exhibited neonatal lethality associated with severe renal hypoplasia. Normal kidney size was restored by breeding the hypomorphic mutant with a rescuing transgenic mouse line bearing a 662-kb Gata3 yeast artificial chromosome (YAC), and these animals (termed G3YR mice) survived to adulthood. However, most of the G3YR mice showed degenerative changes in glomerular mesangial cells, which deteriorated progressively during postnatal development. Consequently, the G3YR adult mice suffered severe renal failure. We found that the 662-kb Gata3 YAC transgene recapitulated Gata3 expression in the renal tubules but failed to direct sufficient GATA3 activity to mesangial cells. Renal glomeruli of the G3YR mice had significantly reduced amounts of platelet-derived growth factor receptor (PDGFR), which is known to participate in the development and maintenance of glomerular mesangial cells. These results demonstrate a critical role for GATA3 in the maintenance of mesangial cells and its absolute requirement for prevention of glomerular disease. PMID:27296697

  17. Incorporation of a lambda phage recombination system and EGFP detection to simplify mutagenesis of Herpes simplex virus bacterial artificial chromosomes

    Directory of Open Access Journals (Sweden)

    Weir Jerry P

    2007-05-01

    Full Text Available Abstract Background Targeted mutagenesis of the herpesvirus genomes has been facilitated by the use of bacterial artificial chromosome (BAC technology. Such modified genomes have potential uses in understanding viral pathogenesis, gene identification and characterization, and the development of new viral vectors and vaccines. We have previously described the construction of a herpes simplex virus 2 (HSV-2 BAC and the use of an allele replacement strategy to construct HSV-2 recombinants. While the BAC mutagenesis procedure is a powerful method to generate HSV-2 recombinants, particularly in the absence of selective marker in eukaryotic culture, the mutagenesis procedure is still difficult and cumbersome. Results Here we describe the incorporation of a phage lambda recombination system into an allele replacement vector. This strategy enables any DNA fragment containing the phage attL recombination sites to be efficiently inserted into the attR sites of the allele replacement vector using phage lambda clonase. We also describe how the incorporation of EGFP into the allele replacement vector can facilitate the selection of the desired cross-over recombinant BACs when the allele replacement reaction is a viral gene deletion. Finally, we incorporate the lambda phage recombination sites directly into an HSV-2 BAC vector for direct recombination of gene cassettes using the phage lambda clonase-driven recombination reaction. Conclusion Together, these improvements to the techniques of HSV BAC mutagenesis will facilitate the construction of recombinant herpes simplex viruses and viral vectors.

  18. Construction and characterization of a bacterial artificial chromosome library of thermo-sensitive genic male-sterile rice 5460S

    Institute of Scientific and Technical Information of China (English)

    邱芳; 金德敏; 伏健民; 张超良; 谢纬武; 王斌; 杨仁崔; 张洪斌

    1999-01-01

    In order to develop a detailed physical map of the thermo-sensitive genie male-sterile (TGMS) gene-encompassing region and finally clone the TGMS gene, a high-quality rice bacterial artificial chromosome (BAC) library from TGMS rice 5460S was constructed. The method of constructing BAC library was examined and optimized. The 5460S library consists of 19 584 BAC clones with an average insert size of 110 kb, which represents about 5 times rice haploid genome equivalents. Rice inserts of up to 140 kb and 250 kb were isolated and appeared stable after 100 generations of serial growth. Hybridization of BAC clones with mitochondrial and chloroplastic genes as probes demonstrated that this library has no organellar contamination. The 5460S library was screened with 3 molecular markers linked to tmsl gene as probes and at least 1 BAC clone was identified with each probe. The insert ends of positive clones were successfully isolated using thermal asymmetric interlaced PCR (TAIL-PCR) technique.

  19. Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics

    Directory of Open Access Journals (Sweden)

    Chapple Clint

    2005-06-01

    Full Text Available Abstract Background The lycophytes are an ancient lineage of vascular plants that diverged from the seed plant lineage about 400 Myr ago. Although the lycophytes occupy an important phylogenetic position for understanding the evolution of plants and their genomes, no genomic resources exist for this group of plants. Results Here we describe the construction of a large-insert bacterial artificial chromosome (BAC library from the lycophyte Selaginella moellendorffii. Based on cell flow cytometry, this species has the smallest genome size among the different lycophytes tested, including Huperzia lucidula, Diphaiastrum digita, Isoetes engelmanii and S. kraussiana. The arrayed BAC library consists of 9126 clones; the average insert size is estimated to be 122 kb. Inserts of chloroplast origin account for 2.3% of the clones. The BAC library contains an estimated ten genome-equivalents based on DNA hybridizations using five single-copy and two duplicated S. moellendorffii genes as probes. Conclusion The S. moellenforffii BAC library, the first to be constructed from a lycophyte, will be useful to the scientific community as a resource for comparative plant genomics and evolution.

  20. Visualization of lymphatic vessels by Prox1-promoter directed GFP reporter in a bacterial artificial chromosome-based transgenic mouse

    Science.gov (United States)

    Choi, Inho; Chung, Hee Kyoung; Ramu, Swapnika; Lee, Ha Neul; Kim, Kyu Eui; Lee, Sunju; Yoo, Jaehyuk; Choi, Dongwon; Lee, Yong Suk; Aguilar, Berenice

    2011-01-01

    Although the blood vessel-specific fluorescent transgenic mouse has been an excellent tool to study vasculogenesis and angiogenesis, a lymphatic-specific fluorescent mouse model has not been established to date. Here we report a transgenic animal model that expresses the green fluorescent protein under the promoter of Prox1, a master control gene in lymphatic development. Generated using an approximately 200-kb-long bacterial artificial chromosome harboring the entire Prox1 gene, this Prox1-green fluorescent protein mouse was found to faithfully recapitulate the expression pattern of the Prox1 gene in lymphatic endothelial cells and other Prox1-expressing organs, and enabled us to conveniently visualize detailed structure and morphology of lymphatic vessels and networks throughout development. Our data demonstrate that this novel transgenic mouse can be extremely useful for detection, imaging, and isolation of lymphatic vessels and monitoring wound-associated lymphangiogenesis. Together, this Prox1-green fluorescent protein transgenic mouse will be a great tool for the lymphatic research. PMID:20962325

  1. Functional characterization of Kaposi's sarcoma-associated herpesvirus small capsid protein by bacterial artificial chromosome-based mutagenesis

    International Nuclear Information System (INIS)

    A systematic investigation of interactions amongst KSHV capsid proteins was undertaken in this study to comprehend lesser known KSHV capsid assembly mechanisms. Interestingly the interaction patterns of the KSHV small capsid protein, ORF65 suggested its plausible role in viral capsid assembly pathways. Towards further understanding this, ORF65-null recombinant mutants (BAC-Δ65 and BAC-stop65) employing a bacterial artificial chromosome (BAC) system were generated. No significant difference was found in both overall viral gene expression and lytic DNA replication between stable monolayers of 293T-BAC36 (wild-type) and 293T-BAC-ORF65-null upon induction with 12-O-tetradecanoylphorbol-13-acetate, though the latter released 30-fold fewer virions to the medium than 293T-BAC36 cells. Sedimentation profiles of capsid proteins of ORF65-null recombinant mutants were non-reflective of their organization into the KSHV capsids and were also undetectable in cytoplasmic extracts compared to noticeable levels in nuclear extracts. These observations collectively suggested the pivotal role of ORF65 in the KSHV capsid assembly processes.

  2. A Self-Excisable Infectious Bacterial Artificial Chromosome Clone of Varicella-Zoster Virus Allows Analysis of the Essential Tegument Protein Encoded by ORF9▿

    OpenAIRE

    Tischer, B. Karsten; Kaufer, Benedikt B; Sommer, Marvin; Wussow, Felix; Ann M Arvin; Osterrieder, Nikolaus

    2007-01-01

    In order to facilitate the generation of mutant viruses of varicella-zoster virus (VZV), the agent causing varicella (chicken pox) and herpes zoster (shingles), we generated a full-length infectious bacterial artificial chromosome (BAC) clone of the P-Oka strain. First, mini-F sequences were inserted into a preexisting VZV cosmid, and the SuperCos replicon was removed. Subsequently, mini-F-containing recombinant virus was generated from overlapping cosmid clones, and full-length VZV DNA recov...

  3. Autoexcision of Bacterial Artificial Chromosome Facilitated by Terminal Repeat-Mediated Homologous Recombination: a Novel Approach for Generating Traceless Genetic Mutants of Herpesviruses ▿

    OpenAIRE

    Zhou, Fuchun; Li, Qiuhua; Wong, Scott W.; Gao, Shou-jiang

    2010-01-01

    Infectious bacterial artificial chromosomes (BACs) of herpesviruses are powerful tools for genetic manipulation. However, the presence of BAC vector sequence in the viral genomes often causes genetic and phenotypic alterations. While the excision of the BAC vector cassette can be achieved by homologous recombination between extra duplicate viral sequences or loxP site-mediated recombination, these methods either are inefficient or leave a loxP site mark in the viral genome. Here we describe t...

  4. Highly selective isolation of human DNAs from rodent–human hybrid cells as circular yeast artificial chromosomes by transformation-associated recombination cloning

    OpenAIRE

    Larionov, Vladimir; Kouprina, Natalya; Graves, Joan; Resnick, Michael A.

    1996-01-01

    Transformation-associated recombination (TAR) can be exploited in yeast to clone human DNAs. TAR cloning was previously accomplished using one or two telomere-containing vectors with a common human repeat(s) that could recombine with human DNA during transformation to generate yeast artificial chromosomes (YACs). On basis of the proposal that broken DNA ends are more recombinogenic than internal sequences, we have investigated if TAR cloning could be applied to the...

  5. Cloning of the Full-Length Rhesus Cytomegalovirus Genome as an Infectious and Self-Excisable Bacterial Artificial Chromosome for Analysis of Viral Pathogenesis

    OpenAIRE

    Chang, W. L. William; Peter A Barry

    2003-01-01

    Rigorous investigation of many functions encoded by cytomegaloviruses (CMVs) requires analysis in the context of virus-host interactions. To facilitate the construction of rhesus CMV (RhCMV) mutants for in vivo studies, a bacterial artificial chromosome (BAC) containing an enhanced green fluorescent protein (EGFP) cassette was engineered into the intergenic region between unique short 1 (US1) and US2 of the full-length viral genome by Cre/lox-mediated recombination. Infectious virions were re...

  6. A high-coverage artificial chromosome library for the genome-wide screening of drug-resistance genes in malaria parasites

    OpenAIRE

    Iwanaga, Shiroh; Kaneko, Izumi; Yuda, Masao

    2012-01-01

    The global spread of drug-resistant parasites is a serious problem for the treatment of malaria. Although identifying drug-resistance genes is crucial for the efforts against resistant parasites, an effective approach has not yet been developed. Here, we report a robust method for identifying resistance genes from parasites by using a Plasmodium artificial chromosome (PAC). Large genomic DNA fragments (10–50 kb) from the drug-resistant rodent malaria parasite Plasmodium berghei were ligated i...

  7. Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics

    OpenAIRE

    Chapple Clint; Carlson John; Arumuganathan K; Mueller Christopher; Kudrna Dave; Weng Jing-Ke; Kim Hye Ran; Sisneros Nicholas; Luo Meizhong; Tanurdzic Milos; Wang Wenming; de Pamphilis Claude; Mandoli Dina; Tomkins Jeff; Wing Rod A

    2005-01-01

    Abstract Background The lycophytes are an ancient lineage of vascular plants that diverged from the seed plant lineage about 400 Myr ago. Although the lycophytes occupy an important phylogenetic position for understanding the evolution of plants and their genomes, no genomic resources exist for this group of plants. Results Here we describe the construction of a large-insert bacterial artificial chromosome (BAC) library from the lycophyte Selaginella moellendorffii. Based on cell flow cytomet...

  8. Production of High-Titer Epstein-Barr Virus Recombinants Derived from Akata Cells by Using a Bacterial Artificial Chromosome System

    OpenAIRE

    Kanda, Teru; Yajima, Misako; Ahsan, Nazmul; Tanaka, Mika; Takada, Kenzo

    2004-01-01

    An Epstein-Barr virus (EBV) genome in Burkitt's lymphoma-derived cell line Akata was cloned into a bacterial artificial chromosome (BAC) vector. The BAC clone, designated AK-BAC, was rapidly and precisely modified by means of efficient homologous recombination in Escherichia coli. This system was used to produce recombinant EBVs with transgenes. An expression cassette of green fluorescent protein (GFP) was inserted into AK-BAC, and the resultant BAC clone, AK-BAC-GFP, was transfected into Aka...

  9. Dicty_cDB: Contig-U12257-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available eftftcfliefmefll*nndfnld wsilventgf*nwd**stivlnd*rftritihhtrpnlvsesnlnl*elflsifni*nhl vdhfstithccypthflndrye...T GTGC Gap gap included Contig length 1694 Chromosome number (1..6, M) - Chromosome length - Start point - E...257-1 (Contig-U12257-1Q) /CSM_Contig/Contig-U12257-1Q.Seq.d Length = 1704 Score = 2083 bits (1051), Expect =...tig/Contig-U14366-1Q.Seq.d Length = 931 Score = 99.6 bits (50), Expect = 1e-20 Id...gtaaataaactgta 413 >Contig-U11698-1 (Contig-U11698-1Q) /CSM_Contig/Contig-U11698-1Q.Seq.d Length = 1510 Scor

  10. Dicty_cDB: Contig-U14702-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available *n**n*kf*ni*iiflkkiknlnykweiikkkk k own update 2004. 6.10 Homology vs CSM-cDNA Query= Contig-U14702-1 (Contig-U14702-1Q) /CSM_Contig....20 AM270352_17( AM270352 |pid:none) Aspergillus niger contig An15c025... 38 0.20 AC084319_4( AC084319 |pid:...AATAAAAAAAAAAAAAAAAAA Gap no gap Contig length 547 Chromosome number (1..6, M) 5 Chromosome length 5062330 Start...09. 7.12 Homology vs Protein Query= Contig-U14702-1 (Contig-U14702-1Q) /CSM_Contig/Contig-U14702-1Q.Seq.d (547 letter...hosiphon pisum ACYPI002634 mRNA, clone: 609I11, complete cds, full-insert cDNA sequence based on the ESTs (

  11. Yeast artificial chromosomes employed for random assembly of biosynthetic pathways and production of diverse compounds in Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Mitra Partha P

    2009-08-01

    Full Text Available Abstract Background Natural products are an important source of drugs and other commercially interesting compounds, however their isolation and production is often difficult. Metabolic engineering, mainly in bacteria and yeast, has sought to circumvent some of the associated problems but also this approach is impeded by technical limitations. Here we describe a novel strategy for production of diverse natural products, comprising the expression of an unprecedented large number of biosynthetic genes in a heterologous host. Results As an example, genes from different sources, representing enzymes of a seven step flavonoid pathway, were individually cloned into yeast expression cassettes, which were then randomly combined on Yeast Artificial Chromosomes and used, in a single transformation of yeast, to create a variety of flavonoid producing pathways. Randomly picked clones were analysed, and approximately half of them showed production of the flavanone naringenin, and a third of them produced the flavonol kaempferol in various amounts. This reflected the assembly of 5–7 step multi-species pathways converting the yeast metabolites phenylalanine and/or tyrosine into flavonoids, normally only produced by plants. Other flavonoids were also produced that were either direct intermediates or derivatives thereof. Feeding natural and unnatural, halogenated precursors to these recombinant clones demonstrated the potential to further diversify the type of molecules that can be produced with this technology. Conclusion The technology has many potential uses but is particularly suited for generating high numbers of structurally diverse compounds, some of which may not be amenable to chemical synthesis, thus greatly facilitating access to a huge chemical space in the search for new commercially interesting compounds

  12. Human Bacterial Artificial Chromosome (BAC) Transgenesis Fully Rescues Noradrenergic Function in Dopamine β-Hydroxylase Knockout Mice

    Science.gov (United States)

    Cubells, Joseph F.; Schroeder, Jason P.; Barrie, Elizabeth S.; Manvich, Daniel F.; Sadee, Wolfgang; Berg, Tiina; Mercer, Kristina; Stowe, Taylor A.; Liles, L. Cameron; Squires, Katherine E.; Mezher, Andrew; Curtin, Patrick; Perdomo, Dannie L.; Szot, Patricia; Weinshenker, David

    2016-01-01

    Dopamine β-hydroxylase (DBH) converts dopamine (DA) to norepinephrine (NE) in noradrenergic/adrenergic cells. DBH deficiency prevents NE production and causes sympathetic failure, hypotension and ptosis in humans and mice; DBH knockout (Dbh -/-) mice reveal other NE deficiency phenotypes including embryonic lethality, delayed growth, and behavioral defects. Furthermore, a single nucleotide polymorphism (SNP) in the human DBH gene promoter (-970C>T; rs1611115) is associated with variation in serum DBH activity and with several neurological- and neuropsychiatric-related disorders, although its impact on DBH expression is controversial. Phenotypes associated with DBH deficiency are typically treated with L-3,4-dihydroxyphenylserine (DOPS), which can be converted to NE by aromatic acid decarboxylase (AADC) in the absence of DBH. In this study, we generated transgenic mice carrying a human bacterial artificial chromosome (BAC) encompassing the DBH coding locus as well as ~45 kb of upstream and ~107 kb of downstream sequence to address two issues. First, we characterized the neuroanatomical, neurochemical, physiological, and behavioral transgenic rescue of DBH deficiency by crossing the BAC onto a Dbh -/- background. Second, we compared human DBH mRNA abundance between transgenic lines carrying either a “C” or a “T” at position -970. The BAC transgene drove human DBH mRNA expression in a pattern indistinguishable from the endogenous gene, restored normal catecholamine levels to the peripheral organs and brain of Dbh -/- mice, and fully rescued embryonic lethality, delayed growth, ptosis, reduced exploratory activity, and seizure susceptibility. In some cases, transgenic rescue was superior to DOPS. However, allelic variation at the rs1611115 SNP had no impact on mRNA levels in any tissue. These results indicate that the human BAC contains all of the genetic information required for tissue-specific, functional expression of DBH and can rescue all measured Dbh

  13. A method for producing transgenic cells using a multi-integrase system on a human artificial chromosome vector.

    Directory of Open Access Journals (Sweden)

    Shigeyuki Yamaguchi

    Full Text Available The production of cells capable of expressing gene(s of interest is important for a variety of applications in biomedicine and biotechnology, including gene therapy and animal transgenesis. The ability to insert transgenes at a precise location in the genome, using site-specific recombinases such as Cre, FLP, and ΦC31, has major benefits for the efficiency of transgenesis. Recent work on integrases from ΦC31, R4, TP901-1 and Bxb1 phages demonstrated that these recombinases catalyze site-specific recombination in mammalian cells. In the present study, we examined the activities of integrases on site-specific recombination and gene expression in mammalian cells. We designed a human artificial chromosome (HAC vector containing five recombination sites (ΦC31 attP, R4 attP, TP901-1 attP, Bxb1 attP and FRT; multi-integrase HAC vector and de novo mammalian codon-optimized integrases. The multi-integrase HAC vector has several functions, including gene integration in a precise locus and avoiding genomic position effects; therefore, it was used as a platform to investigate integrase activities. Integrases carried out site-specific recombination at frequencies ranging from 39.3-96.8%. Additionally, we observed homogenous gene expression in 77.3-87.5% of colonies obtained using the multi-integrase HAC vector. This vector is also transferable to another cell line, and is capable of accepting genes of interest in this environment. These data suggest that integrases have high DNA recombination efficiencies in mammalian cells. The multi-integrase HAC vector enables us to produce transgene-expressing cells efficiently and create platform cell lines for gene expression.

  14. Construction and Identification of Bacterial Artificial Chromosome Library for 0-613-2R in Upland Cotton

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A bacterial artificial chromosome (BAC) library containing a large genomic DNA insert is an important tool for genome physical mapping, map-based cloning, and genome sequencing. To isolate genes via a map-based cloning strategy and to perform physical mapping of the cotton genome, a high-quality BAC library containing large cotton DNA inserts is needed. We have developed a BAC library of the restoring line 0-613-2R for isolating the fertility restorer (Rf1) gene and genomic research in cotton (Gossypium hirsutum L.). The BAC library contains 97 825 clones stored in 255 pieces of a 384-well microtiter plate. Random samples of BACs digested with the Notl enzyme indicated that the average insert size is approximately 130 kb, with a range of 80-275 kb,and 95.7% of the BAC clones in the library have an average insert size larger than 100 kb. Based on a cotton genome size of 2 250 Mb, library coverage is 5.7 x haploid genome equivalents. Four clones were selected randomly from the library to determine the stability of the BAC clones. There were no different fingerprints for 0 and 100 generations of each clone digested with Notl and Hindlll enzymes. Thus, the stability of a single BAC clone can be sustained at least for 100 generations. Eight simple sequence repeat (SSR) markers flanking the Rf1 gene were chosen to screen the BAC library by pool using PCR method and 25 positive clones were identified with 3.1 positive clones per SSR marker.

  15. Recovery of infectious virus from full-length cowpox virus (CPXV DNA cloned as a bacterial artificial chromosome (BAC

    Directory of Open Access Journals (Sweden)

    Roth Swaantje J

    2011-01-01

    Full Text Available Abstract Transmission from pet rats and cats to humans as well as severe infection in felids and other animal species have recently drawn increasing attention to cowpox virus (CPXV. We report the cloning of the entire genome of cowpox virus strain Brighton Red (BR as a bacterial artificial chromosome (BAC in Escherichia coli and the recovery of infectious virus from cloned DNA. Generation of a full-length CPXV DNA clone was achieved by first introducing a mini-F vector, which allows maintenance of large circular DNA in E. coli, into the thymidine kinase locus of CPXV by homologous recombination. Circular replication intermediates were then electroporated into E. coli DH10B cells. Upon successful establishment of the infectious BR clone, we modified the full-length clone such that recombination-mediated excision of bacterial sequences can occur upon transfection in eukaryotic cells. This self-excision of the bacterial replicon is made possible by a sequence duplication within mini-F sequences and allows recovery of recombinant virus progeny without remaining marker or vector sequences. The in vitro growth properties of viruses derived from both BAC clones were determined and found to be virtually indistinguishable from those of parental, wild-type BR. Finally, the complete genomic sequence of the infectious clone was determined and the cloned viral genome was shown to be identical to that of the parental virus. In summary, the generated infectious clone will greatly facilitate studies on individual genes and pathogenesis of CPXV. Moreover, the vector potential of CPXV can now be more systematically explored using this newly generated tool.

  16. Construction of a nurse shark (Ginglymostoma cirratum bacterial artificial chromosome (BAC library and a preliminary genome survey

    Directory of Open Access Journals (Sweden)

    Inoko Hidetoshi

    2006-05-01

    Full Text Available Abstract Background Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. Aims In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC library for the nurse shark, Ginglymostoma cirratum. Results The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 × 1010 bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6–28 primary positive clones per probe of which 50–90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. Conclusion We have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome.

  17. Human Bacterial Artificial Chromosome (BAC) Transgenesis Fully Rescues Noradrenergic Function in Dopamine β-Hydroxylase Knockout Mice.

    Science.gov (United States)

    Cubells, Joseph F; Schroeder, Jason P; Barrie, Elizabeth S; Manvich, Daniel F; Sadee, Wolfgang; Berg, Tiina; Mercer, Kristina; Stowe, Taylor A; Liles, L Cameron; Squires, Katherine E; Mezher, Andrew; Curtin, Patrick; Perdomo, Dannie L; Szot, Patricia; Weinshenker, David

    2016-01-01

    Dopamine β-hydroxylase (DBH) converts dopamine (DA) to norepinephrine (NE) in noradrenergic/adrenergic cells. DBH deficiency prevents NE production and causes sympathetic failure, hypotension and ptosis in humans and mice; DBH knockout (Dbh -/-) mice reveal other NE deficiency phenotypes including embryonic lethality, delayed growth, and behavioral defects. Furthermore, a single nucleotide polymorphism (SNP) in the human DBH gene promoter (-970C>T; rs1611115) is associated with variation in serum DBH activity and with several neurological- and neuropsychiatric-related disorders, although its impact on DBH expression is controversial. Phenotypes associated with DBH deficiency are typically treated with L-3,4-dihydroxyphenylserine (DOPS), which can be converted to NE by aromatic acid decarboxylase (AADC) in the absence of DBH. In this study, we generated transgenic mice carrying a human bacterial artificial chromosome (BAC) encompassing the DBH coding locus as well as ~45 kb of upstream and ~107 kb of downstream sequence to address two issues. First, we characterized the neuroanatomical, neurochemical, physiological, and behavioral transgenic rescue of DBH deficiency by crossing the BAC onto a Dbh -/- background. Second, we compared human DBH mRNA abundance between transgenic lines carrying either a "C" or a "T" at position -970. The BAC transgene drove human DBH mRNA expression in a pattern indistinguishable from the endogenous gene, restored normal catecholamine levels to the peripheral organs and brain of Dbh -/- mice, and fully rescued embryonic lethality, delayed growth, ptosis, reduced exploratory activity, and seizure susceptibility. In some cases, transgenic rescue was superior to DOPS. However, allelic variation at the rs1611115 SNP had no impact on mRNA levels in any tissue. These results indicate that the human BAC contains all of the genetic information required for tissue-specific, functional expression of DBH and can rescue all measured Dbh deficiency

  18. Dicty_cDB: Contig-U08836-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available TTACAATTCATAAATCAGAAGGNAAGGTGGAAGGTA Gap gap included Contig length 731 Chromosome number (1..6, M) 4 Chromosome length 5430582 Start...) /CSM_Contig/Contig-U08836-1Q.Seq.d (741 letters) Database: CSM 6905 sequences; 5,674,871 total letters Sco...,845,959 sequences; 95,242,211,685 total letters Searching........................../CSM_Contig/Contig-U08836-1Q.Seq.d (741 letters) Database: nrp_A 3,204,285 sequences; 1,040,966,779 total...uences producing significant alignments: (bits) Value CR380955_381( CR380955 |pid:none) Candida glabrata str

  19. First Birth after Sperm Selection through Discontinuous Gradient Centrifugation and Artificial Insemination from a Chromosomal Translocation Carrier

    OpenAIRE

    Alexandre Rouen; Capucine Hyon; Richard Balet; Nicole Joyé; Nino Guy Cassuto; Jean-Pierre Siffroi

    2014-01-01

    Introduction. Balanced chromosomal carriers, though usually healthy, are confronted with recurrent spontaneous abortions and malformations in the offspring. Those are related to the transmission of an abnormal, chromosomally unbalanced genotype. We evidenced that the proportion of unbalanced spermatozoa can be significantly decreased through a sperm preparation process called discontinuous gradient centrifugation (DGC). We therefore started offering intrauterine inseminations with this proced...

  20. Dicty_cDB: Contig-U12110-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ne) Aspergillus niger contig An01c0130... 46 0.002 AC137988_20( AC137988 |pid:none) Trypanosoma cruzi strain Bren..._Ba0021O07, *** SEQUEN... 50 0.16 1 ( AE017226 ) Treponema denticola ATCC 35405, complete genome. 50 0.16 1 ( AC025313 ) Homo sapien...ne) Hydrogenobaculum sp. Y04AAS1, c... 34 6.7 AM486621_1( AM486621 |pid:none) Vitis vinifera contig...TGTGTAAATAATTTCAAAAAATAAATAAACAAA AAATAAATAATNAATAAATAAATAA Gap gap included Contig length 965 Chromosome number (1..6, M) 3 Chromos...-U12110-1 Contig ID Contig-U12110-1 Contig update 2002.12.18 Contig sequence >Contig-U12110-1 (Contig

  1. Dicty_cDB: Contig-U14165-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available qiknhkftf*qiiidlslklnqlkmn*knyilnqinfh*qviyigvfgqlfkl*i lksilii*nmvkhvlidimkletnf*isikfkyyylnackmnk...irgy**tnnanmyr qrdctmaln*daykkesitlannkemgsfgtrrlsstrke*vlsiyqckend*rg*nvga kigsi...ces; 5,674,871 total letters Score E Sequences producing significant alignments: (bits) Value Contig-U14165-1 (Contig...TAATCCGCAAAAATAAAAAAA TAATTTTAA Gap no gap Contig length 1059 Chromosome number (1..6, M) 2 Chromosome len...tters Searching..................................................done Score E Sequences producing significant alignment

  2. Cloning of human centromeres by transformation-associated recombination in yeast and generation of functional human artificial chromosomes

    OpenAIRE

    Kouprina, N.; Ebersole, T.; Koriabine, M.; Pak, E; Rogozin, I. B.; Katoh, M; Oshimura, M; Ogi, K; Peredelchuk, M.; Solomon, G; Brown, W.; Barrett, J. C.; Larionov, V

    2003-01-01

    Human centromeres remain poorly characterized regions of the human genome despite their importance for the maintenance of chromosomes. In part this is due to the difficulty of cloning of highly repetitive DNA fragments and distinguishing chromosome-specific clones in a genomic library. In this work we report the highly selective isolation of human centromeric DNA using transformation-associated recombination (TAR) cloning. A TAR vector with alphoid DNA monomers as targeting sequences was used...

  3. Construction of Oryza Sativa genome contigs by fingerprint strategy

    Institute of Scientific and Technical Information of China (English)

    TAOQUAZHOU; GUOFANHONG; 等

    1995-01-01

    We described the construction of BAC contigs of the genome of a indica variety of Oryza sativa.Guang Lu Ai 4. An entire representative(Sixfold coverage of rice chromosomes)and genetically stable BAC library of rice genome constructed in this lab has been systematically analysed by restriction enzyme fragmentation and polyacrylamide gel electrophoresis.And all the images thus obtained were subject to image-processing,which consisted of preliminary location of bands,cooperative tracking of lanes by correlation of adjacent bads.a precise densitometric pass,alignment at the marker bands with the standard,optional interactive editing,and normalization of the accepted bands.The contigs were generated based on the Computer Software specially designed for genome mapping.The number of contigs with 600 kb in length on average was 464.of contigs with 1000kb in length on average was 107; of contigs with 1500 kb in length on average was Construction of Oryza Sativa genome contigs.23.Therefor,all the contigs we have obtained ampunted up to 420 megabases in length.Considering the size of rice genome(430 megabased),the contigs generated in this lab have covered nearly 98% of the rice genome.We are now in the process of mapping the contigs to chromosomes.

  4. Dicty_cDB: Contig-U12781-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available |pid:none) Pseudomonas aeruginosa plasmid Rms... 37 0.50 AM270257_15( AM270257 |pid:none) Aspergillus niger contig...Homo sapiens mRNA for KIAA1801 pro... 33 9.4 AM270256_3( AM270256 |pid:none) Aspergillus niger contig... An11c0390... 33 9.4 CP000642_1( CP000642 |pid:none) Shigella sonnei Ss046 plasmid pSS0....TTGGTTTAGCTTCA Gap no gap Contig length 646 Chromosome number (1..6, M) 5 Chromosome length 5062330 Start...n update 2009. 7. 4 Homology vs Protein Query= Contig-U12781-1 (Contig-U12781-1Q) /CSM_Contig/Contig

  5. Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis.

    Science.gov (United States)

    Paux, Etienne; Legeai, Fabrice; Guilhot, Nicolas; Adam-Blondon, Anne-Françoise; Alaux, Michaël; Salse, Jérôme; Sourdille, Pierre; Leroy, Philippe; Feuillet, Catherine

    2008-02-01

    Anchored physical maps represent essential frameworks for map-based cloning, comparative genomics studies, and genome sequencing projects. High throughput anchoring can be achieved by polymerase chain reaction (PCR) screening of bacterial artificial chromosome (BAC) library pools with molecular markers. However, for large genomes such as wheat, the development of high dimension pools and the number of reactions that need to be performed can be extremely large making the screening laborious and costly. To improve the cost efficiency of anchoring in such large genomes, we have developed a new software named Elephant (electronic physical map anchoring tool) that combines BAC contig information generated by FingerPrinted Contig with results of BAC library pools screening to identify BAC addresses with a minimal amount of PCR reactions. Elephant was evaluated during the construction of a physical map of chromosome 3B of hexaploid wheat. Results show that a one dimensional pool screening can be sufficient to anchor a BAC contig while reducing the number of PCR by 384-fold thereby demonstrating that Elephant is an efficient and cost-effective tool to support physical mapping in large genomes. PMID:18038165

  6. Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Risager, Peter Christian; Fahnøe, Ulrik;

    2013-01-01

    Background Infectious cDNA clones are a prerequisite for directed genetic manipulation of RNA viruses. Here, a strategy to facilitate manipulation and rescue of classical swine fever viruses (CSFVs) from full-length cDNAs present within bacterial artificial chromosomes (BACs) is described. This...... strategy allows manipulation of viral cDNA by targeted recombination-mediated mutagenesis within bacteria. Results A new CSFV-BAC (pBeloR26) derived from the Riems vaccine strain has been constructed and subsequently modified in the E2 coding sequence, using the targeted recombination strategy to enable...... rescue of chimeric pestiviruses (vR26_E2gif and vR26_TAV) with potential as new marker vaccine candidates. Sequencing of the BACs revealed a high genetic stability during passages within bacteria. The complete genome sequences of rescued viruses, after extensive passages in mammalian cells showed that...

  7. The Selection and Use of Sorghum (Sorghum propinquum Bacterial Artificial Chromosomes as Cytogenetic FISH Probes for Maize (Zea mays L.

    Directory of Open Access Journals (Sweden)

    Debbie M. Figueroa

    2011-01-01

    Full Text Available The integration of genetic and physical maps of maize is progressing rapidly, but the cytogenetic maps lag behind, with the exception of the pachytene fluorescence in situ hybridization (FISH maps of maize chromosome 9. We sought to produce integrated FISH maps of other maize chromosomes using Core Bin Marker loci. Because these 1 Kb restriction fragment length polymorphism (RFLP probes are below the FISH detection limit, we used BACs from sorghum, a small-genome relative of maize, as surrogate clones for FISH mapping. We sequenced 151 maize RFLP probes and compared in silico BAC selection methods to that of library filter hybridization and found the latter to be the best. BAC library screening, clone verification, and single-clone selection criteria are presented along with an example of transgenomic BAC FISH mapping. This strategy has been used to facilitate the integration of RFLP and FISH maps in other large-genome species.

  8. The selection and use of sorghum (Sorghum propinquum) bacterial artificial chromosomes as cytogenetic FISH probes for maize (Zea mays L.).

    Science.gov (United States)

    Figueroa, Debbie M; Davis, James D; Strobel, Cornelia; Conejo, Maria S; Beckham, Katherine D; Ring, Brian C; Bass, Hank W

    2011-01-01

    The integration of genetic and physical maps of maize is progressing rapidly, but the cytogenetic maps lag behind, with the exception of the pachytene fluorescence in situ hybridization (FISH) maps of maize chromosome 9. We sought to produce integrated FISH maps of other maize chromosomes using Core Bin Marker loci. Because these 1 Kb restriction fragment length polymorphism (RFLP) probes are below the FISH detection limit, we used BACs from sorghum, a small-genome relative of maize, as surrogate clones for FISH mapping. We sequenced 151 maize RFLP probes and compared in silico BAC selection methods to that of library filter hybridization and found the latter to be the best. BAC library screening, clone verification, and single-clone selection criteria are presented along with an example of transgenomic BAC FISH mapping. This strategy has been used to facilitate the integration of RFLP and FISH maps in other large-genome species. PMID:21234422

  9. Polymorphisms in folate-metabolizing genes, chromosome damage, and risk of Down syndrome in Italian women: identification of key factors using artificial neural networks

    Directory of Open Access Journals (Sweden)

    Migheli Francesca

    2010-09-01

    Full Text Available Abstract Background Studies in mothers of Down syndrome individuals (MDS point to a role for polymorphisms in folate metabolic genes in increasing chromosome damage and maternal risk for a Down syndrome (DS pregnancy, suggesting complex gene-gene interactions. This study aimed to analyze a dataset of genetic and cytogenetic data in an Italian group of MDS and mothers of healthy children (control mothers to assess the predictive capacity of artificial neural networks assembled in TWIST system in distinguish consistently these two different conditions and to identify the variables expressing the maximal amount of relevant information to the condition of being mother of a DS child. The dataset consisted of the following variables: the frequency of chromosome damage in peripheral lymphocytes (BNMN frequency and the genotype for 7 common polymorphisms in folate metabolic genes (MTHFR 677C>T and 1298A>C, MTRR 66A>G, MTR 2756A>G, RFC1 80G>A and TYMS 28bp repeats and 1494 6bp deletion. Data were analysed using TWIST system in combination with supervised artificial neural networks, and a semantic connectivity map. Results TWIST system selected 6 variables (BNMN frequency, MTHFR 677TT, RFC1 80AA, TYMS 1494 6bp +/+, TYMS 28bp 3R/3R and MTR 2756AA genotypes that were subsequently used to discriminate between MDS and control mothers with 90% accuracy. The semantic connectivity map provided important information on the complex biological connections between the studied variables and the two conditions (being MDS or control mother. Conclusions Overall, the study suggests a link between polymorphisms in folate metabolic genes and DS risk in Italian women.

  10. 棉花细菌人工染色体文库构建方法探讨%Studies on Construction Method of Cotton Bacterial Artificial Chromosome Library

    Institute of Scientific and Technical Information of China (English)

    高海燕; 王省芬; 刘方; 彭仁海; 张艳; 马峙英; 王坤波

    2013-01-01

    细菌人工染色体(Bacterial artificial chromosome,BAC)文库是开展基因组测序、基因图位克隆、分子标记、物理作图等研究的重要基因组资源.本文在构建了二倍体野生棉阿非利加棉(Gossypium herbaceum var.africanum)BAC文库的基础上,就棉花细菌人工染色体基因组文库构建过程中高分子量基因组DNA的提取、部分酶切片段选择、DNA的回收、连接转化以及BAC文库的保存等过程中一些细节和注意事项进行了比较详细的分析比较,希望能为棉花BAC文库的构建提供一些可供借鉴的经验.%Bacterial artificial chromosome (BAC) library is an important genome resources to such research as genome sequencing, map-based cloning, molecular markers, and physical mapping. On the base of the construction of BAC library for Gossypi-um herbaceum var. africanum, this paper presents an exhaustive analysis on details and notices of the BAC library construction process. It includes extraction of high molecular weight (HMW) nuclear DNA, determination of the optimized enzyme for partial digestion of HMW DNA, two rounds of size fractionation, recovery of large fragments DNA, ligation and transformation of large fragments of DNA and storage of BAC library. Thus being able to supply an experience for constructing high efficiency cotton BAC library.

  11. Dicty_cDB: Contig-U09747-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available CCGAAATTAAATATGCACCAGAATTAC CATCA Gap gap included Contig length 1245 Chromosome number (1..6, M) - Chromosome length - Start point...iffi*k***f*wcyik******** vlyinyq**********skcnnntninsnknyrinrinrinii*sk*irrwn**nt*n*f rrf*tcigsrdgtnyritiiy*slfkstspfniitmvsdctsi...tters Score E Sequences producing significant alignments: (bits) Value Contig-U09747-1 (Contig-U09747-1Q) /CSM_Contig...tters Searching..................................................done Score E Sequences producing significant alignment...scoideum cDNA clone:ddv26l13, 3' end, single read. Length = 611 Score = 1098 bits (554), Expect = 0.0 Ident

  12. De novo assembly and identification of unique contigs in the bovine oviduct from animals with high and low circulating estradiol concentrations during timed artificial insemination

    Science.gov (United States)

    Reproductive efficiency is a large concern for many cattle producers and understanding the mechanisms responsible for biological variation in reproduction is key to improving reproductive efficiency. Timed artificial insemination of beef cows with high circulating estradiol concentrations at time o...

  13. First Birth after Sperm Selection through Discontinuous Gradient Centrifugation and Artificial Insemination from a Chromosomal Translocation Carrier

    Directory of Open Access Journals (Sweden)

    Alexandre Rouen

    2014-01-01

    Full Text Available Introduction. Balanced chromosomal carriers, though usually healthy, are confronted with recurrent spontaneous abortions and malformations in the offspring. Those are related to the transmission of an abnormal, chromosomally unbalanced genotype. We evidenced that the proportion of unbalanced spermatozoa can be significantly decreased through a sperm preparation process called discontinuous gradient centrifugation (DGC. We therefore started offering intrauterine inseminations with this procedure to couples with a male translocation carriers. Case Presentation. We report the case of a 37-year-old man carrying a t(3;10(q25;p13 reciprocal translocation. He and his partner had had trouble conceiving for ten years and had four spontaneous abortions. DGC in this patient decreased the proportion of unbalanced spermatozoa from 63.6% to 52.3%. They were therefore offered intrauterine insemination with DGC, which eventually led to the birth of a healthy female child carrying the paternal translocation. Conclusion. We showed that translocation carriers could be offered intrauterine inseminations with DGC. Before this, the only two options were natural conception with prenatal diagnosis and termination of chromosomally unbalanced fetuses or preimplantation genetic diagnosis, which is a much heavier and costly procedure. We are currently offering this option through a multicentric program in France, and this is the first birth originating from it.

  14. First Birth after Sperm Selection through Discontinuous Gradient Centrifugation and Artificial Insemination from a Chromosomal Translocation Carrier.

    Science.gov (United States)

    Rouen, Alexandre; Hyon, Capucine; Balet, Richard; Joyé, Nicole; Cassuto, Nino Guy; Siffroi, Jean-Pierre

    2014-01-01

    Introduction. Balanced chromosomal carriers, though usually healthy, are confronted with recurrent spontaneous abortions and malformations in the offspring. Those are related to the transmission of an abnormal, chromosomally unbalanced genotype. We evidenced that the proportion of unbalanced spermatozoa can be significantly decreased through a sperm preparation process called discontinuous gradient centrifugation (DGC). We therefore started offering intrauterine inseminations with this procedure to couples with a male translocation carriers. Case Presentation. We report the case of a 37-year-old man carrying a t(3;10)(q25;p13) reciprocal translocation. He and his partner had had trouble conceiving for ten years and had four spontaneous abortions. DGC in this patient decreased the proportion of unbalanced spermatozoa from 63.6% to 52.3%. They were therefore offered intrauterine insemination with DGC, which eventually led to the birth of a healthy female child carrying the paternal translocation. Conclusion. We showed that translocation carriers could be offered intrauterine inseminations with DGC. Before this, the only two options were natural conception with prenatal diagnosis and termination of chromosomally unbalanced fetuses or preimplantation genetic diagnosis, which is a much heavier and costly procedure. We are currently offering this option through a multicentric program in France, and this is the first birth originating from it. PMID:24587925

  15. Dicty_cDB: Contig-U13752-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available SEQUENCIN... 34 1.7 7 ( AM466122 ) Vitis vinifera contig VV78X156573.4, whole genome... 42 1.8 2 ( AC060230 ) Homo sapiens chromos... KBrH019G05,... 36 2.4 5 ( AM424734 ) Vitis vinifera contig VV78X103090.3, whole genome... 34 2.4 2 ( AC230760 ) Bos...us (Silura... 38 0.36 2 ( AM462900 ) Vitis vinifera contig VV78X056435.6, whole geno...CTGTTATAAAACAACCAACATTATATNNNN NNNNN Gap no gap Contig length 455 Chromosome number (1..6, M) 4 Chromosome len...Contig-U13752-1 no gap 455 4 4982581 4982135 MINUS 1 1 U13752 0 1 0 0 0 0 0 0 0 0 0 0 0 0 Show Contig

  16. Plant Artificial Chromosome:The Vector for the Next Generation of Genetic Engineering%植物人工染色体:下一代基因工程的载体

    Institute of Scientific and Technical Information of China (English)

    李晨; 闫晓红; 杨洁; 杨清; 魏文辉

    2011-01-01

    The simultaneous expression of multiple genes and genetically modified (GM) food security research have been considered as the research focus for genetic engineering in plants presently. Unlike conventional gene transformation technologies,plant artificial chromosomes provide one solution to the stable expression of multiple transgenes. As plant artificial chromosome segregation is independent of host chromosomes, they provide a platform for accelerating plant breeding and for studying the specific chromatin domains inserted into them. The generation of artificial plant chromosomes and their applications were reviewed in this article.%植物基因工程技术中的多基因转化及转基因安全已经成为其研究的2个重要方面.植物人工染色体可以在一条不含标记基因的附加染色体上提供稳定的多基因表达,是新一代的转基因载体.由于植物人工染色体独立于宿主染色体,为植物育种提供了便利,同时,也为研究染色质特殊区域的结构与功能提供了平台.本文就植物人工染色体的产生、研究现状及其应用前景等进行了综述和讨论.

  17. Dicty_cDB: Contig-U13963-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Contig-U13963-1 no gap 1697 - - - - 7 12 U13963 1 0 0 0 1 2 1 0 1 0 1 0 0 0 Show Contig-U13963-1 ... RP23-182N4 on chromosome X Contains a prohibitin (Phb ) pseudogene, the Cstf2 gene for cleavage stimulati ...

  18. Rapid and efficient introduction of a foreign gene into bacterial artificial chromosome-cloned varicella vaccine by Tn7-mediated site-specific transposition

    International Nuclear Information System (INIS)

    Using a rapid and reliable system based on Tn7-mediated site-specific transposition, we have successfully constructed a recombinant Oka varicella vaccine (vOka) expressing the mumps virus (MuV) fusion protein (F). The backbone of the vector was our previously reported vOka-BAC (bacterial artificial chromosome) genome. We inserted the transposon Tn7 attachment sequence, LacZα-mini-attTn7, into the region between ORF12 and ORF13 to generate a vOka-BAC-Tn genome. The MuV-F expressing cassette was transposed into the vOka-BAC genome at the mini-attTn7 transposition site. MuV-F protein was expressed in recombinant virus, rvOka-F infected cells. In addition, the MuV-F protein was cleaved in the rvOka-F infected cells as in MuV-infected cells. The growth of rvOka-F was similar to that of the original recombinant vOka without the F gene. Thus, we show that Tn7-mediated transposition is an efficient method for introducing a foreign gene expression cassette into the vOka-BAC genome as a live virus vector.

  19. A novel system for simultaneous or sequential integration of multiple gene-loading vectors into a defined site of a human artificial chromosome.

    Directory of Open Access Journals (Sweden)

    Teruhiko Suzuki

    Full Text Available Human artificial chromosomes (HACs are gene-delivery vectors suitable for introducing large DNA fragments into mammalian cells. Although a HAC theoretically incorporates multiple gene expression cassettes of unlimited DNA size, its application has been limited because the conventional gene-loading system accepts only one gene-loading vector (GLV into a HAC. We report a novel method for the simultaneous or sequential integration of multiple GLVs into a HAC vector (designated as the SIM system via combined usage of Cre, FLP, Bxb1, and φC31 recombinase/integrase. As a proof of principle, we first attempted simultaneous integration of three GLVs encoding EGFP, Venus, and TdTomato into a gene-loading site of a HAC in CHO cells. These cells successfully expressed all three fluorescent proteins. Furthermore, microcell-mediated transfer of HACs enabled the expression of those fluorescent proteins in recipient cells. We next demonstrated that GLVs could be introduced into a HAC one-by-one via reciprocal usage of recombinase/integrase. Lastly, we introduced a fourth GLV into a HAC after simultaneous integration of three GLVs by FLP-mediated DNA recombination. The SIM system expands the applicability of HAC vectors and is useful for various biomedical studies, including cell reprogramming.

  20. HIV gene expression from intact proviruses positioned in bacterial artificial chromosomes at integration sites previously identified in latently infected T cells

    International Nuclear Information System (INIS)

    HIV integration predominantly occurs in introns of transcriptionally active genes. To study the impact of the integration site on HIV gene expression, a complete HIV-1 provirus (with GFP as a fusion with Nef) was inserted into bacterial artificial chromosomes (BACs) at three sites previously identified in latent T cells of patients: topoisomerase II (Top2A), DNA methyltransferase 1 (DNMT1), or basic leucine transcription factor 2 (BACH2). Transfection of BAC-HIV into 293 T cells resulted in a fourfold difference in production of infectious HIV-1. Cell lines were established that contained BAC-Top2A, BAC-DNMT1, or BAC-BACH2, but only BAC-DNMT1 spontaneously produced virus, albeit at a low level. Stimulation with TNF-α resulted in virus production from four of five BAC-Top2A and all BAC-DNMT1 cell lines, but not from the BAC-BACH2 lines. The results of these studies highlight differences between integration sites identified in latent T cells to support virus production and reactivation from latency.

  1. Construction of an Excisable Bacterial Artificial Chromosome Containing a Full-Length Infectious Clone of Herpes Simplex Virus Type 1: Viruses Reconstituted from the Clone Exhibit Wild-Type Properties In Vitro and In Vivo

    OpenAIRE

    Tanaka, Michiko; Kagawa, Hiroyuki; Yamanashi, Yuji; Sata, Tetsutaro; Kawaguchi, Yasushi

    2003-01-01

    In recent years, several laboratories have reported on the cloning of herpes simplex virus type 1 (HSV-1) genomes as bacterial artificial chromosomes (BACs) in Escherichia coli and on procedures to manipulate these genomes by using the bacterial recombination machinery. However, the HSV-BACs reported so far are either replication incompetent or infectious, with a deletion of one or more viral genes due to the BAC vector insertion. For use as a multipurpose clone in research on HSV-1, we attem...

  2. Construction of a YAC contig and STS map spanning 2.5 Mbp in Xq25, the critical region for the X-linked lymphoproliferative (XLP) gene

    Energy Technology Data Exchange (ETDEWEB)

    Lanyi, A.; Li, B.F.; Li, S. [Univ. of Nebraska Medical Center, Omaha, NE (United States)] [and others

    1994-09-01

    X-linked lymphoproliferative disease (XLP) is characterized by a marked vulnerability in Epstein-Barr virus (EBV) infection. Infection of XLP patients with EBV invariably results in fatal mononucleosis, agammaglobulinemia or B-cell lymphoma. The XLP gene lies within a 10 cM region in Xq25 between DXS42 and DXS10. Initial chromosome studies revealed an interstitial, cytogenetically visible deletion in Xq25 in one XLP family (43-004). We estimated the size of the Xq25 deletion by dual laser flow karyotyping to involve 2% of the X chromosome, or approximately 3 Mbp of DNA sequences. To further delineate the deletion we performed a series of pulsed field gel electrophoresis (PFGE) analyses which showed that DXS6 and DXS100, two Xq25-specific markers, are missing from 45-004 DNA. Five yeast artificial chromosomes (YACs) from a chromosome X specific YAC library containing sequences deleted in patient`s 43-004 DNA were isolated. These five YACs did not overlap, and their end fragments were used to screen the CEPH MegaYAC library. Seven YACs were isolated from the CEPH MegaYAC library. They could be arranged into a contig which spans between DXS6 and DXS100. The contig contains a minimum of 2.5 Mbp of human DNA. A total of 12 YAC end clone, lambda subclones and STS probes have been used to order clones within the contig. These reagents were also used in Southern blot and patients showed interstitial deletions in Xq25. The size of these deletions range between 0.5 and 2.5 Mbp. The shortest deletion probably represents the critical region for the XLP gene.

  3. A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations

    Directory of Open Access Journals (Sweden)

    Giattina Emily

    2011-09-01

    Full Text Available Abstract Background Evolution of the Brassica species has been recursively affected by polyploidy events, and comparison to their relative, Arabidopsis thaliana, provides means to explore their genomic complexity. Results A genome-wide physical map of a rapid-cycling strain of B. oleracea was constructed by integrating high-information-content fingerprinting (HICF of Bacterial Artificial Chromosome (BAC clones with hybridization to sequence-tagged probes. Using 2907 contigs of two or more BACs, we performed several lines of comparative genomic analysis. Interspecific DNA synteny is much better preserved in euchromatin than heterochromatin, showing the qualitative difference in evolution of these respective genomic domains. About 67% of contigs can be aligned to the Arabidopsis genome, with 96.5% corresponding to euchromatic regions, and 3.5% (shown to contain repetitive sequences to pericentromeric regions. Overgo probe hybridization data showed that contigs aligned to Arabidopsis euchromatin contain ~80% of low-copy-number genes, while genes with high copy number are much more frequently associated with pericentromeric regions. We identified 39 interchromosomal breakpoints during the diversification of B. oleracea and Arabidopsis thaliana, a relatively high level of genomic change since their divergence. Comparison of the B. oleracea physical map with Arabidopsis and other available eudicot genomes showed appreciable 'shadowing' produced by more ancient polyploidies, resulting in a web of relatedness among contigs which increased genomic complexity. Conclusions A high-resolution genetically-anchored physical map sheds light on Brassica genome organization and advances positional cloning of specific genes, and may help to validate genome sequence assembly and alignment to chromosomes. All the physical mapping data is freely shared at a WebFPC site (http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/WebFPC/; Temporarily password-protected: account

  4. Dicty_cDB: Contig-U12504-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available *cgqrwsnwfkrciif*kfnvik* yfkrylaiirce*wifky*rffcsikisfigtngstsyfg*y*intsysttkik*yspik ...Contig-U12504-1 gap included 1907 5 138029 139945 PLUS 9 10 U12504 0 2 0 4 0 0 0 2 ...CA ATTAGCNAGGAACAAAA Gap gap included Contig length 1907 Chromosome number (1..6, M) 5 Chromosome length 5062330 Start poin...nkreldkrkfkln*tknynwkqs*nnnshknnnn*mrlgkm*kkrksnypl lkliinh*knkfqplesilnh*nhswnnnhhysekrvncltnkmkhsht*mmilkknnks ykrin...h*knkfqplesilnh*nhswnnnhhysekrvncltnkmkhsht*mmilkknnks ykrinnk

  5. Dicty_cDB: Contig-U12125-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available niitndficigsks*rkiniti lyiwitimvdigtnfnifl*eegilpiykikryhcingsiifilftlqhtffnvhfktil cggs...s) Database: CSM 6905 sequences; 5,674,871 total letters Score E Sequences producing significant alignments: (bits) Value Contig...A AAAAAAAAAAAAAAAAAAAAAAAAAAAAA Gap gap included Contig length 1519 Chromosome number (1..6, M) 4 Chromosome len...hing..................................................done Score E Sequences producing significant alig...gth adjustment: 24 Effective length of query: 1505 Effective length of database: 97,308,875

  6. YAC contig information - RGP physicalmap | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us RGP physical...ents YAC contigs on the rice chromosomes Data file File name: rgp_physicalmap_yac_contigs.zip File URL: ftp:...//ftp.biosciencedbc.jp/archive/rgp-physicalmap/LATEST/rgp_physicalmap_yac_contigs....zip File size: 1 KB Simple search URL http://togodb.biosciencedbc.jp/togodb/view/rgp_physicalmap_yac_contig...gion number Physical map image The file name of rice physical map First marker First DNA marker Distance of

  7. Dicty_cDB: Contig-U05006-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ... 34 2.9 AF205169_1( AF205169 |pid:none) Paratemnopteryx weinsteini Pwein1 ....70_1( AF205170 |pid:none) Paratemnopteryx weinsteini Pwein2 ... 34 2.9 AB005906_1...ATCCATAAATAAAAAAAAAAAAA AAAA Gap no gap Contig length 554 Chromosome number (1..6, M) 1 Chromosome length 4919822 Start...asmodium falciparum 3D7 chromosome 13. 36 0.30 10 ( M10129 ) Plasmodium falciparum (isolate FC27) S-antige...AC clone RP23-452P8 from chromosome... 46 1.5 1 ( AM466305 ) Vitis vinifera contig VV78X119936.4, whole geno

  8. Cloning of the Koi Herpesvirus Genome as an Infectious Bacterial Artificial Chromosome Demonstrates That Disruption of the Thymidine Kinase Locus Induces Partial Attenuation in Cyprinus carpio koi▿

    Science.gov (United States)

    Costes, B.; Fournier, G.; Michel, B.; Delforge, C.; Raj, V. Stalin; Dewals, B.; Gillet, L.; Drion, P.; Body, A.; Schynts, F.; Lieffrig, F.; Vanderplasschen, A.

    2008-01-01

    Koi herpesvirus (KHV) is the causative agent of a lethal disease in koi and common carp. In the present study, we describe the cloning of the KHV genome as a stable and infectious bacterial artificial chromosome (BAC) clone that can be used to produce KHV recombinant strains. This goal was achieved by the insertion of a loxP-flanked BAC cassette into the thymidine kinase (TK) locus. This insertion led to a BAC plasmid that was stably maintained in bacteria and was able to regenerate virions when permissive cells were transfected with the plasmid. Reconstituted virions free of the BAC cassette but carrying a disrupted TK locus (the FL BAC-excised strain) were produced by the transfection of Cre recombinase-expressing cells with the BAC. Similarly, virions with a wild-type revertant TK sequence (the FL BAC revertant strain) were produced by the cotransfection of cells with the BAC and a DNA fragment encoding the wild-type TK sequence. Reconstituted recombinant viruses were compared to the wild-type parental virus in vitro and in vivo. The FL BAC revertant strain and the FL BAC-excised strain replicated comparably to the parental FL strain. The FL BAC revertant strain induced KHV infection in koi carp that was indistinguishable from that induced by the parental strain, while the FL BAC-excised strain exhibited a partially attenuated phenotype. Finally, the usefulness of the KHV BAC for recombination studies was demonstrated by the production of an ORF16-deleted strain by using prokaryotic recombination technology. The availability of the KHV BAC is an important advance that will allow the study of viral genes involved in KHV pathogenesis, as well as the production of attenuated recombinant candidate vaccines. PMID:18337580

  9. Dicty_cDB: Contig-U02244-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ed Contig length 326 Chromosome number (1..6, M) - Chromosome length - Start point - End point - Strand...02244-1Q) /CSM_Contig/Contig-U02244-1Q.Seq.d Length = 336 Score = 91.7 bits (46), Expect = 5e-19 Identities = 46/46 (100%) Strand...tactctaaag 56 Score = 81.8 bits (41), Expect = 4e-16 Identities = 44/44 (100%) Strand = Plus / Plus Query: 1... 6e-06 Identities = 24/24 (100%) Strand = Plus / Plus Query: 312 tattttaatttactattttaccgg 335 ||||||||||||||...|||||||||| Sbjct: 312 tattttaatttactattttaccgg 335 Score = 40.1 bits (20), Expect = 0.001 Identities = 23/23 (100%) Strand

  10. Dicty_cDB: Contig-U13432-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available n... 65 6e-09 AM270374_9( AM270374 |pid:none) Aspergillus niger contig An16c0220... 64... 1e-08 AM270049_13( AM270049 |pid:none) Aspergillus niger contig An03c008... 64 1...Prosthecochloris aestuarii DSM ... 35 6.5 CP001117_63( CP001117 |pid:none) Deinococcus desert...AAAGAAGAAAATTATAAATAAAAGTATTTCCAAAA Gap no gap Contig length 1142 Chromosome number (1..6, M) 6 Chromosome length 3595308 Start...crilisvgfkfikwnpaliiivgfkwfgfh hihsfisigegsavksinivikvekl*kevfns*yfrpiywyfi*cyf*kptfrkwcnhc isniirs

  11. Dicty_cDB: Contig-U13162-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available WO0200928. 36 1.1 4 ( AM428650 ) Vitis vinifera contig VV78X026452.9, whole geno....9 1 ( CP000308 ) Yersinia pestis Antiqua, complete genome. 46 2.9 1 ( CP000305 ) Yersinia pestis Nepal516, complete geno...gth enric... 32 6.7 3 ( AM451575 ) Vitis vinifera contig VV78X027387.11, whole genom... ...AAAGATTCTAGACCATCAGCACCAAAGAAAC Gap no gap Contig length 1139 Chromosome number (1..6, M) 6 Chromosome length 3595308 Start point...) Yersinia pseudotuberculosis YPIII, complete genome. 46 2.9 1 ( CP000901 ) Yersinia pestis An

  12. Dicty_cDB: Contig-U15952-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available mic DNA c... 67 2e-09 AM270022_46( AM270022 |pid:none) Aspergillus niger contig An02...wlesi strain H chr... 38 0.76 AM270070_2( AM270070 |pid:none) Aspergillus niger contig An...GAATATTTAAAATAAAATAAAAAAAAAAAAAAAA Gap gap included Contig length 1125 Chromosome number (1..6, M) 5 Chromosome len...AE015450 ) Mycoplasma gallisepticum strain R complete genome. 40 1.1 17 ( AC201922 ) Mus musculus BAC clone RP24-140J4 from chromos...nments: (bits) Value AP002909_15( AP002909 |pid:none) Oryza sativa Japonica Group geno

  13. Dicty_cDB: Contig-U14991-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ......done Score E Sequences producing significant alignments: (bits) Value CP000099_1947( CP000099 |pid:none) Methanosarcina bar...GAAAA Gap no gap Contig length 637 Chromosome number (1..6, M) 2 Chromosome length 8467578 Start...g/Contig-U14991-1Q.Seq.d (637 letters) Database: CSM 8402 sequences; 8,075,542 total...1-1 (Contig-U14991-1Q) /CSM_Contig/Contig-U14991-1Q.Seq.d (637 letters) Database: ddbj_A 92,845,959 sequences; 95,242,211,685 total...ne... 40 0.004 2 ( AV171704 ) Mus musculus 17-day embryo head cDNA, partial seq... 40 0.30

  14. Dicty_cDB: Contig-U05231-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available -U05231-1Q) /CSM_Contig/Contig-U05231-1Q.Seq.d (716 letters) Database: nrp_A 3,268,448 sequences; 1,061,185,681 total letters Sear...AAAA Gap no gap Contig length 716 Chromosome number (1..6, M) 3 Chromosome length 6358359 Start point 557736...Q) /CSM_Contig/Contig-U05231-1Q.Seq.d (716 letters) Database: CSM 6905 sequences; 5,674,871 total letters Sc... sequences; 104,622,809,269 total letters Searching..................................................done Sc...ed DNA Entam... 38 0.51 3 ( EJ201977 ) 1092344308854 Global-Ocean-Sampling_GS-27-01-01-1.

  15. A BAC-based physical map of the Hessian fly genome anchored to polytene chromosomes

    Directory of Open Access Journals (Sweden)

    Fellers John P

    2009-07-01

    Full Text Available Abstract Background The Hessian fly (Mayetiola destructor is an important insect pest of wheat. It has tractable genetics, polytene chromosomes, and a small genome (158 Mb. Investigation of the Hessian fly presents excellent opportunities to study plant-insect interactions and the molecular mechanisms underlying genome imprinting and chromosome elimination. A physical map is needed to improve the ability to perform both positional cloning and comparative genomic analyses with the fully sequenced genomes of other dipteran species. Results An FPC-based genome wide physical map of the Hessian fly was constructed and anchored to the insect's polytene chromosomes. Bacterial artificial chromosome (BAC clones corresponding to 12-fold coverage of the Hessian fly genome were fingerprinted, using high information content fingerprinting (HIFC methodology, and end-sequenced. Fluorescence in situ hybridization (FISH co-localized two BAC clones from each of the 196 longest contigs on the polytene chromosomes. An additional 70 contigs were positioned using a single FISH probe. The 266 FISH mapped contigs were evenly distributed and covered 60% of the genome (95,668 kb. The ends of the fingerprinted BACs were then sequenced to develop the capacity to create sequenced tagged site (STS markers on the BACs in the map. Only 3.64% of the BAC-end sequence was composed of transposable elements, helicases, ribosomal repeats, simple sequence repeats, and sequences of low complexity. A relatively large fraction (14.27% of the BES was comprised of multi-copy gene sequences. Nearly 1% of the end sequence was composed of simple sequence repeats (SSRs. Conclusion This physical map provides the foundation for high-resolution genetic mapping, map-based cloning, and assembly of complete genome sequencing data. The results indicate that restriction fragment length heterogeneity in BAC libraries used to construct physical maps lower the length and the depth of the contigs, but is

  16. YAC and cosmid contigs encompassing the Fukuyama-type congenital muscular dystrophy (FCMD) candidate region on 9q31

    Energy Technology Data Exchange (ETDEWEB)

    Miyake, Masashi; Nakahori, Yutaka; Matsushita, Ikumi [Univ. of Tokyo (Japan)] [and others

    1997-03-01

    Fukuyama-type congenital muscular dystrophy (FCMD), the second most common form of childhood muscular dystrophy in Japan, is an autosomal recessive severe muscular dystrophy associated with an anomaly of the brain. We had mapped the FCMD gene to an approximately 5-cM interval between D9S127 and D9S2111 on 9q31-q33 and had also found evidence for linkage disequilibrium between FCMD and D9S306 in this candidate region. Through further analysis, we have defined another marker, D9S172, which showed stronger linkage disequilibrium than D9S306. A yeast artificial chromosome (YAC) contig spanning 3.5 Mb, which includes this D9S306-D9S172 interval on 9q31, has been constructed by a combination of sequence-tagged site, Alu-PCR, and restriction mapping. Also, cosmid clones subcloned from the YAC were assembled into three contigs, one of which contains D9S2107, which showed the strongest linkage disequilibrium with FCMD. These contigs also allowed us to order the markers as follows: cen-D9S127-({approximately}800 kb)-D9S306 (identical to D9S53)-({approximately}700 kb)-A107XF9-({approximately}500 kb)-D9S172-({approximately}30 kb)-D9S299 (identical to D9S774)-({approximately}120 kb)-WI2269-tel. Thus, we have constructed the first high-resolution physical map of the FCMD candidate region. The YAC and cosmid contigs established here will be a crucial resource for identification of the FCMD gene and other genes in this region. 37 refs., 7 figs., 2 tabs.

  17. Dicty_cDB: Contig-U11892-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available sapiens endogenous virus Human endogenous re... 44 8.9 1 ( AL163246 ) Homo sapiens chromosome 21 segm... sapiens rectosigmoid colon pr... 35 2.6 AF068897_1( AF068897 |pid:none) Homo...GTTTAAAATCTTTTAAAGACAGATGAGATGAAACACCAATT AAAAATTAAATTAAATAAAAAAAAATTAAATTAAATAATAAA Gap gap included Contig length 882 Chromos...ome number (1..6, M) 2 Chromosome length 8467578 Start point 3339714 End point 3340584 St...telium discoideum chromosome 2 map 2567470... 722 0.0 3 ( BJ383840 ) Dictyos

  18. Dicty_cDB: Contig-U10279-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available neage cell-specific prote... 39 0.094 BC167645_1( BC167645 |pid:none) Xenopus tropicalis cortactin, m...se: CSM 6905 sequences; 5,674,871 total letters Score E Sequences producing significant ali...AAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAA Gap no gap Contig length 563 Chromosome number (1..6, M) 5 Chromosome length 5062330 Start...-1 (Contig-U10279-1Q) /CSM_Contig/Contig-U10279-1Q.Seq.d (563 letters) Database: ddbj_A 92,845,959 sequences; 95,242,211,685 total...m clone CH211-107C24. 44 5.3 1 ( CR382133 ) Debaryomyces hansenii chromosome A of strain CBS7... 44 5.3 1 (

  19. High-resolution physical mapping and construction of a porcine contig spanning the intramuscular fat content QTL.

    Science.gov (United States)

    Sato, S; Hasebe, H; Sato, S; Asahi, Y; Hayashi, T; Kobayashi, E; Sugimoto, Y

    2006-04-01

    We previously mapped a locus for porcine intramuscular fat content (IMF) by linkage analysis to a 17.1-cM chromosome interval on Sus scrofa chromosome 7 (SSC7) flanked by microsatellite markers SW1083 and SW581. In this study, we identified 34 microsatellite markers and 14 STSs from the 17.1-cM IMF quantitative trait loci (QTL) region corresponding to HSA14q and aligned those loci using the INRA-University of Minnesota porcine radiation hybrid (IMpRH) panel. We then constructed a 5.2-Mb porcine bacterial artificial chromosome (BAC) contig of this region that was aligned using the RH panel. Finally, the IMF QTL was fine-mapped to 12.6 cM between SJ169 and MM70 at the 0.1% chromosome-wise significance level by genotyping the previously studied F2 resource family with 17 additional microsatellites. We also demonstrated that the SJ169-MM70 interval spans approximately 3.0 Mb and contains at least 12 genes: GALC, GPR65, KCNK10, SPATA7, PTPN21, FLJ11806, EML5, TTC8, CHES1, CAP2P1, CHORDC2P and C14orf143. PMID:16573525

  20. Comparative fluorescence in situ hybridization mapping of a 431-kb Arabidopsis thaliana bacterial artificial chromosome contig reveals the role of chromosomal duplications in the expansion of the Brassica rapa genome.

    OpenAIRE

    Jackson, S A; Cheng, Z; Wang, M L; Goodman, H M; Jiang, J

    2000-01-01

    Comparative genome studies are important contributors to our understanding of genome evolution. Most comparative genome studies in plants have been based on genetic mapping of homologous DNA loci in different genomes. Large-scale comparative physical mapping has been hindered by the lack of efficient and affordable techniques. We report here the adaptation of fluorescence in situ hybridization (FISH) techniques for comparative physical mapping between Arabidopsis thaliana and Brassica rapa. A...

  1. Three minimum tile paths from bacterial artificial chromosome libraries of the soybean (Glycine max cv. 'Forrest': tools for structural and functional genomics

    Directory of Open Access Journals (Sweden)

    Afzal AJ

    2006-05-01

    Full Text Available Abstract Background The creation of minimally redundant tile paths (hereafter MTP from contiguous sets of overlapping clones (hereafter contigs in physical maps is a critical step for structural and functional genomics. Build 4 of the physical map of soybean (Glycine max L. Merr. cv. 'Forrest' showed the 1 Gbp haploid genome was composed of 0.7 Gbp diploid, 0.1 Gbp tetraploid and 0.2 Gbp octoploid regions. Therefore, the size of the unique genome was about 0.8 Gbp. The aim here was to create MTP sub-libraries from the soybean cv. Forrest physical map builds 2 to 4. Results The first MTP, named MTP2, was 14,208 clones (of mean insert size 140 kbp picked from the 5,597 contigs of build 2. MTP2 was constructed from three BAC libraries (BamHI (B, HindIII (H and EcoRI (E inserts. MTP2 encompassed the contigs of build 3 that derived from build 2 by a series of contig merges. MTP2 encompassed 2 Gbp compared to the soybean haploid genome of 1 Gbp and does not distinguish regions by ploidy. The second and third MTPs, called MTP4BH and MTP4E, were each based on build 4. Each was semi-automatically selected from 2,854 contigs. MTP4BH was 4,608 B and H insert clones of mean size 173 kbp in the large (27.6 kbp T-DNA vector pCLD04541. MTP4BH was suitable for plant transformation and functional genomics. MTP4E was 4,608 BAC clones with large inserts (mean 175 kbp in the small (7.5 kbp pECBAC1 vector. MTP4E was suitable for DNA sequencing. MTP4BH and MTP4E clones each encompassed about 0.8 Gbp, the 0.7 Gbp diploid regions and 0.05 Gbp each from the tetraploid and octoploid regions. MTP2 and MTP4BH were used for BAC-end sequencing, EST integration, micro-satellite integration into the physical map and high information content fingerprinting. MTP4E will be used for genome sequence by pooled genomic clone index. Conclusion Each MTP and associated BES will be useful to deconvolute and ultimately finish the whole genome shotgun sequence of soybean.

  2. A bacterial artificial chromosome library for the Australian saltwater crocodile (Crocodylus porosus) and its utilization in gene isolation and genome characterization

    Science.gov (United States)

    2009-01-01

    Background Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group that also includes birds, dinosaurs, and pterosaurs. Consequently, crocodilian genomes represent a gateway through which the molecular evolution of avian lineages can be explored. To facilitate comparative genomics within Crocodylia and between crocodilians and other archosaurs, we have constructed a bacterial artificial chromosome (BAC) library for the Australian saltwater crocodile, Crocodylus porosus. This is the first BAC library for a crocodile and only the second BAC resource for a crocodilian. Results The C. porosus BAC library consists of 101,760 individually archived clones stored in 384-well microtiter plates. NotI digestion of random clones indicates an average insert size of 102 kb. Based on a genome size estimate of 2778 Mb, the library affords 3.7 fold (3.7×) coverage of the C. porosus genome. To investigate the utility of the library in studying sequence distribution, probes derived from CR1a and CR1b, two crocodilian CR1-like retrotransposon subfamilies, were hybridized to C. porosus macroarrays. The results indicate that there are a minimum of 20,000 CR1a/b elements in C. porosus and that their distribution throughout the genome is decidedly non-random. To demonstrate the utility of the library in gene isolation, we probed the C. porosus macroarrays with an overgo designed from a C-mos (oocyte maturation factor) partial cDNA. A BAC containing C-mos was identified and the C-mos locus was sequenced. Nucleotide and amino acid sequence alignment of the C. porosus C-mos coding sequence with avian and reptilian C-mos orthologs reveals greater sequence similarity between C. porosus and birds (specifically chicken and zebra finch) than between C. porosus and squamates (green anole). Conclusion We have demonstrated the utility of the

  3. 染色体多态性对供精人工授精治疗结局的影响%Influence of chromosomal polymorphism on treatment outcome of artificial insemination by donors

    Institute of Scientific and Technical Information of China (English)

    伍园园; 郑立新; 祝小丽; 舒小妹; 郑炜炜

    2013-01-01

    Objective: To investigate the relationship between the female chromosome polymorphism and the pregnancy outcome of artificial insemination by donors. Methods; The peripheral blood of patients was cultured rountinely for karotype analysis. Clinical pregnancy rate, cumulative pregnancy rate and early obortion rate were observed by treated patients with chromosomal polymorphism as the research group, and patients with normal chromosome as control group. Results: There was no significant difference in the clinical cycle pregnancy rate ( 19. 80% vs 19. 66% ) , cumulative pregnancy rate (44. 82% vs 41. 77% ) , early abortion rate ( 14. 58% vsl2. 07% ) between the two groups ( P > 0. 05 ) . Conclusion: Chromosomal polymorphism carrier status has no impact on treatment outcome of the patients receiving artificial insemination by donors.%目的 探讨女性染色体多态性与供精人工授精妊娠结局的关系.方法 对接受供精人工授精患者常规抽血行染色体检查,将发现有染色体多态的患者作为研究对象,与染色体正常群体对照,观察临床妊娠率、累积妊娠率和早期流产率.结果 染色体多态性组与正常组比较,临床周期妊娠率(19.80% vs 19.66%),累积妊娠率(44.82%vs 41.77%),早期流产率(14.58% vs12.07%),均无统计学差异(P>0.05).结论 染色体多态性携带状态不影响供精人工授精患者的治疗结局.

  4. Cloning of the Epstein-Barr Virus-Related Rhesus Lymphocryptovirus as a Bacterial Artificial Chromosome: a Loss-of-Function Mutation of the rhBARF1 Immune Evasion Gene ▿ †

    OpenAIRE

    Ohashi, Makoto; Orlova, Nina; Quink, Carol; Wang, Fred

    2010-01-01

    Rhesus macaques are naturally infected with a gammaherpesvirus which is in the same lymphocryptovirus (LCV) genus as and closely related to Epstein-Barr virus (EBV). The rhesus macaque LCV (rhLCV) contains a repertoire of genes identical to that of EBV, and experimental rhLCV infection of naive rhesus macaques accurately models acute and persistent EBV infection of humans. We cloned the LCL8664 rhLCV strain as a bacterial artificial chromosome to create recombinant rhLCV for investigation in ...

  5. Dicty_cDB: Contig-U11007-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available FKFNFL IDTQNFPNGSNDISKAFFDNENQQMTVTSVIIAIQKSPKTPSQQPSTK*fffkkiiflfs infsiflfifflkqiiiikkkkkkqnsfsknkkkkk Tra...ic tikysstynhntn*sttssfigsttktilw*cl**fitrnqfficksiftkfytttilti *ttttltksnyifii*ylchcyyyh*tkchrkd*rif...kkiiflfs infsiflfifflkqiiiikkkkkkqnsfsknkkkkk Frame B: DTNINTINDNNNNNNNNNNNNNNSVNNNLL...hskfpkwf**yfksil***kstndchlcyycnskit*nsfsatinqiiff*knnffify qffyffiylffktnnnnkkkkkktkfff...AAAAAAAAAA Gap gap included Contig length 1790 Chromosome number (1..6, M) 3 Chromosome length 6358359 Start

  6. Dicty_cDB: Contig-U16140-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ... 38 0.92 19 ( AM180355 ) Clostridium difficile 630 complete genome. 40 0.93 19 ( AZ539725 ) ENTFS11TR Entamoeba histolytica Shear...ikf cfif*flffnqsiildkskiilk*cfknfkiiifffffspifflssflcfffcflcfyky qnnnnnnnnnnnnnnnnnnnnnnnn... Contig length 1974 Chromosome number (1..6, M) 1 Chromosome length 4919822 Start...lllamspflsekfws kveyldyiqeipgvldrsniisklpqsikdydkglletpevteqvvsgmdtlgkeylssf assfnffs...stnpsswtspk*f*nnvlkilk*sfsffffppsffspvffvfffvfsvfini kiiiiiiiiiiiiiiiiiiiiiiiiiiinmy*y*iihyt*ynt*ytylst*

  7. Dicty_cDB: Contig-U11260-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available qqqqqqqpidlip spsielvkvegddcfvdlnnnhivdnsvpivdertvvddsdlgdlvvaatqipnstfynl vcfssprilyavqllimdnrlklqrdaiekyfkkkdlkddkkeleeeksikqiefek...itt rldslvanskewvkfigdddfvkrtdylikketellnqieqlnekifklevn*...ATTTATAAATAATAAANATTAAAATAAATAA Gap gap included Contig length 1334 Chromosome nu...mber (1..6, M) 6 Chromosome length 3595308 Start point 3347372 End point 3348711 Strand (PLUS/MINUS) PLUS Nu...*kerfkr**kgirrrein*tn*i*knhn* irfiscklkrmgkihw***fc*knrlfn*krn*iiksn*tik*knl*trseldnl*iixi kin Translated Am

  8. Dicty_cDB: Contig-U09509-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available rfrk*tkeiy twhfy**kkdfnvfnw*wys**srcyw*w*ryd*istisifs*kiffnlslkkkkkklyi ylfiffffffyfffff*kleek...liqlikmdhll*htlimvirkl*hlikldhqldl*ny*qikhwnkkiftstrs nssdskifknftrg**rg*ktktkensfnqiyesfeks*rrr*tknssle...*lw*ygnfni**n*ttn*ifkiisksnigtkkylqapd qiqvipkslkilpedseevkkqkqkkihsiksmnrlkkveeegkqktqawkdfvnkpkks ipgtftdr...AAAAAAAAAAACTCTATATTTATTTATTTATTTTTTTTT TCTTTTTCTTTTATTTCTTTTTTTTTTTTTAAAAATTAGAGGAAAAAAAA AAAACA Gap gap included Contig le...ngth 896 Chromosome number (1..6, M) 6 Chromosome length 3595308 Start point 3178885 End poi

  9. Dicty_cDB: Contig-U03376-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Contig-U03376-1 no gap 214 2 6424590 6424376 MINUS 2 1 U03376 0 0 0 0 0 0 0 0 0 0 0...ngth 214 Chromosome number (1..6, M) 2 Chromosome length 8467578 Start point 6424590 End point 6424376 Stran

  10. Dicty_cDB: Contig-U15573-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available lllgqplgeytsisnvsiyffnpkditnpngnsryfqysnkpplymktfsganfisn snfiktsitfsptkdigsavfalqinrtaaltgpseisisikdmkftil...sryfqysnkpplymktfsganfisn snfiktsitfsptkdigsavfalqinrtaaltgpseisisikdmkftilpktitqptlli kdselvnlpkpstsfdpqdss...s... 48 1.3 1 ( U23477 ) Dictyostelium discoideum phosphatidylinositol-4,5-d... 42 1.4 3 ( AB084781 ) Mycoplasma mobile gen... AGCNTTAACNGGNAA Gap gap included Contig length 2005 Chromosome number (1..6, M) 4 Chromosome len...xxlfrsnxslxxxxxxsxnxx Frame C: s*afigstig*iyiylkrfhlfl*skryyqskw*fkifpilkqttiiyen

  11. Three minimum tile paths from bacterial artificial chromosome libraries of the soybean (Glycine max cv. 'Forrest'): tools for structural and functional genomics

    OpenAIRE

    Afzal AJ; Yaegashi S; Yesudas C; Shultz JL; Kazi S; Lightfoot DA

    2006-01-01

    Abstract Background The creation of minimally redundant tile paths (hereafter MTP) from contiguous sets of overlapping clones (hereafter contigs) in physical maps is a critical step for structural and functional genomics. Build 4 of the physical map of soybean (Glycine max L. Merr. cv. 'Forrest') showed the 1 Gbp haploid genome was composed of 0.7 Gbp diploid, 0.1 Gbp tetraploid and 0.2 Gbp octoploid regions. Therefore, the size of the unique genome was about 0.8 Gbp. The aim here was to crea...

  12. Dicty_cDB: Contig-U15884-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available P000089 |pid:none) Dechloromonas aromatica RCB, co... 36 3.5 CP000740_763( CP000740 |pid:none) Sinorhizobium med...is vinifera contig VV78X149785.4, whole genome... 46 3.3 1 ( AC147365 ) Medicago ...onas palustris HaA2, complete genome. Length = 174 Score = 98.6 bits (244), Expect = 4e-19 Iden... Contig length 1300 Chromosome number (1..6, M) 4 Chromosome length...... 38 0.29 2 ( DN080300 ) JGI_CABD12377.fwd NIH_XGC_tropLun1 Xenopus (Silur... 38 0.29 2 ( AC208397 ) Macaca mulatta chromosome

  13. Dicty_cDB: Contig-U13219-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available length 111 Chromosome number (1..6, M) 2 Chromosome length 8467578 Start point 5686662 End point 5686561 Strand...tig-U13219-1Q) /CSM_Contig/Contig-U13219-1Q.Seq.d Length = 111 Score = 58.0 bits (29), Expect = 2e-09 Identities = 32/32 (100%) Stran...U12594-1Q) /CSM_Contig/Contig-U12594-1Q.Seq.d Length = 977 Score = 36.2 bits (18), Expect = 0.007 Identities = 20/21 (95%) Strand...taaataaataagtaat 540 Score = 32.2 bits (16), Expect = 0.11 Identities = 16/16 (100%) Strand... = 32.2 bits (16), Expect = 0.11 Identities = 16/16 (100%) Strand = Plus / Plus Query: 1 ataaataaataaataa 16

  14. Dicty_cDB: Contig-U03664-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available log (S. cere... 70 2e-10 U78868_1( U78868 |pid:none) Arabidopsis thaliana putative aspartat... 67 2e-09 CR38...e corpora qu... 49 5e-04 U78869_1( U78869 |pid:none) Arabidopsis thaliana putative asparta... Chromosome number (1..6, M) 3 Chromosome length 6358359 Start point 1197631 End point 1196460 Strand (PLUS/...= Contig-U03664-1 (Contig-U03664-1Q) /CSM_Contig/Contig-U03664-1Q.Seq.d (1184 letters) Database: CSM 6905 sequences; 5,674,871 total...ontig-U03664-1Q.Seq.d (1184 letters) Database: ddbj_A 102,105,510 sequences; 101,790,757,118 total

  15. Dicty_cDB: Contig-U10406-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 2 ( DJ076765 ) Neisseria Meningitidis Antigens and Compositions. 32 4.0 2 ( DJ075813 ) Neisseria Meningitidis Antigens and Compos...chrom... 46 1.6 1 ( AM451406 ) Vitis vinifera contig VV78X169805.8, whole genome... 46 1.6 1 ( DU912804 ) 32...TACAAATAAGTAAAGTTG ATAAAGAACAT Gap no gap Contig length 661 Chromosome number (1..6, M) 4 Chromosome len...am... 44 6.3 1 ( ET074965 ) QM0AAB1CD11FM1 CCER1 Citrus clementina genomic cl... 44 6.3 1 ( ...Contig-U10406-1 no gap 661 4 1621526 1620875 MINUS 1 1 U10406 0 0 1 0 0 0 0 0 0 0 0 0 0 0 Show Contig

  16. Dicty_cDB: Contig-U06424-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available s BAC clone RP23-252B13 from chromosom... 36 3.2 5 ( AM469026 ) Vitis vinifera contig VV78X008936.5, whole geno...ome. 44 5.2 1 ( GC525025 ) Sequence 121 from patent US 7410647. 40 5.9 2 ( DD104373 ) Antigenic Polypepti...lasma citri GII3-3X chromosome, contig Cont... 42 6.2 4 ( EI334702 ) GM_WBc0076A09.r GM_WBc Glycine max geno...ce, co... 44 5.2 1 ( AM435200 ) Vitis vinifera contig VV78X231747.3, whole geno...5 AM270295_8( AM270295 |pid:none) Aspergillus niger contig An13c0010... 50 4e-05 CU640366_621( CU640366 |pid:none) Podos

  17. Dicty_cDB: Contig-U08227-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available letters Score E Sequences producing significant alignments: (bits) Value Contig-U08227-1 (Contig-U08227-1Q) /CSM_Contig/Cont...osiga brevicollis mitochondrion, complete genome. 36 0.009 8 ( AF250284 ) Amsacta moorei ent...e Score E Sequences producing significant alignments: (bits) Value AY392438_1( AY392438 |pid:none) Dictyosteli...e Score E Sequences producing significant alignments: (bits) Value N ( AY392443 ) Dictyostelium discoideum possible en...ce 3 from Patent WO03072812. 36 0.11 7 ( AE014848 ) Plasmodium falciparum 3D7 chromosome 12, section

  18. Construction of a bacterial artificial chromosome (BAC) library of Lycopersicon esculentum cv. Stevens and its application to physically map the Sw-5 locus

    NARCIS (Netherlands)

    Spassova, MI; Prins, M; Stevens, MR; Hille, J; Goldbach, RW; Spassova, Mariana I.; Stevens, Mikel R.; Goldbach, Rob W.

    1999-01-01

    The Sw-5 gene is a dominantly inherited resistance gene in tomato and functional against a number of tospovirus species. The gene has been mapped on chromosome 9, tightly linked to RFLP markers CT220 and SCAR421. To analyse the Sw-5 locus, a BAC genomic library was constructed of tomato cv. Stevens,

  19. Dicty_cDB: Contig-U08834-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ATACAAGCAACTTCAAATATAACAATAACAAT Gap gap included Contig length 1335 Chromosome number (1..6, M) 6 Chromos...member 11... 48 3e-09 4 ( AC116957 ) Dictyostelium discoideum chromosome 2 map 16...telium discoideum chromosome 2 map 1-12595... 34 6e-07 13 ( AE014845 ) Plasmodium falciparum 3D7 chromos...e-04 3 ( AC115598 ) Dictyostelium discoideum chromosome 2 map 581427-... 34 4e-04 12 ( AC116986 ) Dictyos...telium discoideum chromosome 2 map 2234041... 34 5e-04 15 ( AY354195 ) Tetrahymena thermo

  20. High-resolution physical map for chromosome 16q12.1-q13, the Blau syndrome locus

    Directory of Open Access Journals (Sweden)

    Bonavita Gina

    2002-08-01

    Full Text Available Abstract Background The Blau syndrome (MIM 186580, an autosomal dominant granulomatous disease, was previously mapped to chromosome 16p12-q21. However, inconsistent physical maps of the region and consequently an unknown order of microsatellite markers, hampered us from further refining the genetic locus for the Blau syndrome. To address this problem, we constructed our own high-resolution physical map for the Blau susceptibility region. Results We generated a high-resolution physical map that provides more than 90% coverage of a refined Blau susceptibility region. The map consists of four contigs of sequence tagged site-based bacterial artificial chromosomes with a total of 124 bacterial artificial chromosomes, and spans approximately 7.5 Mbp; however, three gaps still exist in this map with sizes of 425, 530 and 375 kbp, respectively, estimated from radiation hybrid mapping. Conclusions Our high-resolution map will assist genetic studies of loci in the interval from D16S3080, near D16S409, and D16S408 (16q12.1 to 16q13.

  1. Diagnosis and Prognostication of Ductal Adenocarcinomas of the Pancreas Based on Genome-Wide DNA Methylation Profiling by Bacterial Artificial Chromosome Array-Based Methylated CpG Island Amplification

    Directory of Open Access Journals (Sweden)

    Masahiro Gotoh

    2011-01-01

    Full Text Available To establish diagnostic criteria for ductal adenocarcinomas of the pancreas (PCs, bacterial artificial chromosome (BAC array-based methylated CpG island amplification was performed using 139 tissue samples. Twelve BAC clones, for which DNA methylation status was able to discriminate cancerous tissue (T from noncancerous pancreatic tissue in the learning cohort with a specificity of 100%, were identified. Using criteria that combined the 12 BAC clones, T-samples were diagnosed as cancers with 100% sensitivity and specificity in both the learning and validation cohorts. DNA methylation status on 11 of the BAC clones, which was able to discriminate patients showing early relapse from those with no relapse in the learning cohort with 100% specificity, was correlated with the recurrence-free and overall survival rates in the validation cohort and was an independent prognostic factor by multivariate analysis. Genome-wide DNA methylation profiling may provide optimal diagnostic markers and prognostic indicators for patients with PCs.

  2. Dicty_cDB: Contig-U11228-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ktrtccidsrfl*rc*cgykgmesesrri*ssfq*ny lfiwlw*srcftnvfrrcttyairilsrgsrgfrircikighlgi**sstitikclnq*s rieqkvtfr*siniltfir...Contig-U11228-1 gap included 1910 3 1890716 1892614 PLUS 15 23 U11228 1 0 0 3 0 0 0...AAATA AAATATATATTAAAAAAAAA Gap gap included Contig length 1910 Chromosome number (1..6, M) 3 Chromosome length 6358359 Start poin...**synskisfnnskf*tfnfs fflkicfkikfneyyst*yqksyilyflllcrifwsw*yrkyk*f*nfinl*iynhf*ti fngciiigkdfhsiiigsnfilfve*qfecsktw*flncncl...one IM... 46 1e-08 3 ( DQ976364 ) Rattus norvegicus phosphatidylinositol glycan cla... 60

  3. Dicty_cDB: Contig-U15442-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 2 sequences; 8,075,542 total letters Score E Sequences producing significant alignments: (bits) Value Contig-U15442-1 (Conti...AAAAAAAAAAAAAAAAAAAA Gap no gap Contig length 944 Chromosome number (1..6, M) 2 Chromosome length 8467578 Start point....done Score E Sequences producing significant alignments: (bits) Value N ( AF487784 ) Dictyostelium discoideum prenyl cystein.....................................................done Score E Sequences producing significant alignments: (bi...ved CD11c +ve... 174 4e-42 BC092830_1( BC092830 |pid:none) Danio rerio isoprenylcysteine

  4. Dicty_cDB: Contig-U15082-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 3 ( AJ831725 ) Zygaena ignifera mitochondrial tRNA-Leu (CUN) gen... 42 4.1 2 ( AJ831719 ) Zygaena arme...na armena mitochondrial tRNA-Leu (CUN... 42 4.1 2 ( AJ831729 ) Zygaena loti macedonica...tckyinkinqifkhlkk k Translated Amino Acid sequence (All Frames) Frame A: kkp*hfkkkkppyfl*iiinnlnsiik*hllkvfv...AACACTTAAAAAAAAAA Gap no gap Contig length 545 Chromosome number (1..6, M) 4 Chromosome length 5430582 Start...8,075,542 total letters Score E Sequences producing significant alignments: (bits) Value Contig-U15082-1 (Co

  5. Dicty_cDB: Contig-U06586-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available gth 400 Chromosome number (1..6, M) 2 Chromosome length 8467578 Start point 6706112 End point 6706465 Strand..._Contig/Contig-U06586-1Q.Seq.d Length = 400 Score = 93.7 bits (47), Expect = 1e-19 Identities = 47/47 (100%) Strand... 130 Score = 77.8 bits (39), Expect = 8e-15 Identities = 48/48 (100%) Strand = Plus / Plus Query: 294 cataat...t = 8e-09 Identities = 32/32 (100%) Strand = Plus / Plus Query: 162 actgcnccctttcaagttcacacactccctac 193 |||... = 1e-07 Identities = 27/27 (100%) Strand = Plus / Plus Query: 362 ccctttcaagttca

  6. Dicty_cDB: Contig-U15423-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ngth 400 Chromosome number (1..6, M) 3 Chromosome length 6358359 Start point 3471026 End point 3470623 Strand...) /CSM_Contig/Contig-U15423-1Q.Seq.d Length = 400 Score = 293 bits (148), Expect = 1e-79 Identities = 148/148 (100%) Strand... Expect = 2e-13 Identities = 37/37 (100%) Strand = Plus / Plus Query: 331 cttaaaaattcttaaatctcatttcttattaatt...cttattaattttt 367 Score = 65.9 bits (33), Expect = 4e-11 Identities = 33/33 (100%) Strand = Plus / Plus Quer...Q.Seq.d Length = 4897 Score = 236 bits (119), Expect = 2e-62 Identities = 119/119 (100%) Strand = Plus / Plu

  7. Dicty_cDB: Contig-U13270-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Contig length 223 Chromosome number (1..6, M) 1 Chromosome length 4919822 Start point 634553 End point 634331 Strand...= 0.015 Identities = 18/18 (100%) Strand = Plus / Plus Query: 141 taataattaataattaat 158 |||||||||||||||||| .../Contig-U12060-1Q.Seq.d Length = 1537 Score = 36.2 bits (18), Expect = 0.015 Identities = 18/18 (100%) Strand...re = 36.2 bits (18), Expect = 0.015 Identities = 18/18 (100%) Strand = Plus / Plus Query: 141 taataattaataat... (18), Expect = 0.015 Identities = 18/18 (100%) Strand = Plus / Plus Query: 141 taataattaataattaat 158 |||||

  8. Dicty_cDB: Contig-U14550-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ngth 124 Chromosome number (1..6, M) - Chromosome length - Start point - End point - Strand (PLUS/MINUS) - N...14550-1Q) /CSM_Contig/Contig-U14550-1Q.Seq.d Length = 124 Score = 75.8 bits (38), Expect = 9e-15 Identities = 38/38 (100%) Strand...04 Identities = 24/25 (96%) Strand = Plus / Plus Query: 1 atttttatttttttaattttcattt 25 |||||||||||||| ||||||...6 Identities = 13/13 (100%) Strand = Plus / Plus Query: 2 tttttattttttt 14 ||||||||||||| Sbjct: 158 tttttatt...ttttt 170 Score = 26.3 bits (13), Expect = 7.6 Identities = 13/13 (100%) Strand = Plus / Plus Query: 2 ttttt

  9. Dicty_cDB: Contig-U09503-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available th 683 Chromosome number (1..6, M) - Chromosome length - Start point - End point - Strand (PLUS/MINUS) - Num...1Q) /CSM_Contig/Contig-U09503-1Q.Seq.d Length = 693 Score = 103 bits (52), Expect = 2e-22 Identities = 52/52 (100%) Strand...acacacatcacatgatcac 52 Score = 83.8 bits (42), Expect = 2e-16 Identities = 42/42 (100%) Strand = Plus / Plus...t = 2e-16 Identities = 51/51 (100%) Strand = Plus / Plus Query: 340 tcttatntgcttgccnngtttttccacacttgacgggggg...ttgacggggggtggttcccccc 390 Score = 56.0 bits (28), Expect = 5e-08 Identities = 28/28 (100%) Strand

  10. Dicty_cDB: Contig-U15562-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available rykgcsfymdrlqdrdn**lstlywgensnatirrsisri gci*s*higrtkkewstcyncrsyr*weivtlkdtfslqcpirlstiic*frpwsrfnhh trhnfsstysksigyrggvswwdsig...vki*hhlsinn*tvi k*sl*ivrykgcsfymdrlqdrdn**lstlywgensnatirrsisrigci*s*higrtkk ewstcyncrsyr*wei...nsnatirrsisri gci*s*higrtkkewstcyncrsyr*weivtlkdtfslqcpirlstiic*frpwsrfnhh trhnfsstysksig...135_21( AM270135 |pid:none) Aspergillus niger contig An07c018... 43 0.052 CP000561_47( CP000561 |pid:none) P...AAATAATAACAATAAGAACA TGTATTTTAAAA Gap gap included Contig length 2102 Chromosome number (1..6, M) 4 Chromosome length 5430582 Start

  11. Dicty_cDB: Contig-U11874-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ne) Aspergillus niger contig An11c027... 57 8e-07 AP007171_26( AP007171 |pid:none) Aspergillus oryzae RIB40 geno...modium falciparum 3D7 chromosome 14 section 3... 38 0.17 13 ( AY653733 ) Acanthamoeba polyphaga mimivirus, complete geno...CAAGCCTATAATAAAATCAACATTCCATTACTCAGGTC ATCAACTATGTCACCTTTTATTAGNAAACATCNAGGTTCAT Gap gap included Contig length 881 Chromos...MRC20-573A12... 32 1.4 9 ( CP000102 ) Methanosphaera stadtmanae DSM 3091, complete geno...me. 38 1.4 19 ( AC115599 ) Dictyostelium discoideum chromosome 2 map 4229098... 32 1.4 8 ( AM438418 ) Vitis vinifera, whole gen

  12. Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS

    Directory of Open Access Journals (Sweden)

    You Frank M

    2010-06-01

    Full Text Available Abstract Background Physical maps employing libraries of bacterial artificial chromosome (BAC clones are essential for comparative genomics and sequencing of large and repetitive genomes such as those of the hexaploid bread wheat. The diploid ancestor of the D-genome of hexaploid wheat (Triticum aestivum, Aegilops tauschii, is used as a resource for wheat genomics. The barley diploid genome also provides a good model for the Triticeae and T. aestivum since it is only slightly larger than the ancestor wheat D genome. Gene co-linearity between the grasses can be exploited by extrapolating from rice and Brachypodium distachyon to Ae. tauschii or barley, and then to wheat. Results We report the use of Ae. tauschii for the construction of the physical map of a large distal region of chromosome arm 3DS. A physical map of 25.4 Mb was constructed by anchoring BAC clones of Ae. tauschii with 85 EST on the Ae. tauschii and barley genetic maps. The 24 contigs were aligned to the rice and B. distachyon genomic sequences and a high density SNP genetic map of barley. As expected, the mapped region is highly collinear to the orthologous chromosome 1 in rice, chromosome 2 in B. distachyon and chromosome 3H in barley. However, the chromosome scale of the comparative maps presented provides new insights into grass genome organization. The disruptions of the Ae. tauschii-rice and Ae. tauschii-Brachypodium syntenies were identical. We observed chromosomal rearrangements between Ae. tauschii and barley. The comparison of Ae. tauschii physical and genetic maps showed that the recombination rate across the region dropped from 2.19 cM/Mb in the distal region to 0.09 cM/Mb in the proximal region. The size of the gaps between contigs was evaluated by comparing the recombination rate along the map with the local recombination rates calculated on single contigs. Conclusions The physical map reported here is the first physical map using fingerprinting of a complete

  13. Dicty_cDB: Contig-U02967-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 6 1.2 4 ( BK006337 ) TPA_exp: Drosophila persimilis mitochondrion, com... 38 1.2 3 ( AL590346 ) Arabidopsis thaliana DNA chromosome... 44 0.21 4 ( AL161537 ) Arabidopsis thaliana DNA chromosome 4, contig fra... 36 0... 10 section 3... 40 0.26 8 ( AE014851 ) Plasmodium falciparum 3D7 chromosome 12, sectio...89 ) 1092955209046 Global-Ocean-Sampling_GS-31-01-01-1... 36 0.36 3 ( AB012241 ) Arabidopsis thaliana genomic DNA, chromosome...icago truncatula clone mth2-10g3, complete seq... 42 0.67 5 ( AE017308 ) Mycoplasma mobile 163K complete genome

  14. Dicty_cDB: Contig-U14237-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available GACATTTCACCAATC TTAAAAACNAGNAACAAAAA Gap no gap Contig length 670 Chromosome number (1..6, M) 3 Chromosome...al RNA gene,... 34 0.087 2 ( AC116960 ) Dictyostelium discoideum chromosome 2 map complem... 2 map 5515173... 48 0.10 8 ( AY502546 ) HIV-1 isolate woman_116 clone 10 from Cen...tral Afr... 50 0.11 1 ( AY502311 ) HIV-1 isolate woman_116 clone 5 from Central Afri... 50 0.11 1 (... AY502192 ) HIV-1 isolate woman_116 clone 8 from Central Afri... 50 0.11 1 ( AY502180 ) HIV-1 isolate woman_116 clone 13 from Cen

  15. Dicty_cDB: Contig-U12657-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 634_1375( CP001634 |pid:none) Kosmotoga olearia TBF 19.5.1, c... 39 0.48 ( Q57626....33 3 ( AC214103 ) Pongo abelii chromosome UNKNOWN clone CH276-238M1... 42 0.34 7 ( AC006280 ) Plasmodium falciparum chromos...TGGAAATAATTTAAATCAAATTAATAATCAAGATAAGAAAATAAT ATTAAAAGGAAACNATTTTAAATAAAAAATTTTTAAAATAATAATAATA Gap no gap Contig length 1199 Chromos...ome number (1..6, M) 2 Chromosome length 8467578 Start point 3887035 End point 3885...quences producing significant alignments: (bits) Value N ( AC116986 ) Dictyostelium discoideum chromosome 2

  16. Dicty_cDB: Contig-U16248-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 34_574( CP001634 |pid:none) Kosmotoga olearia TBF 19.5.1, co... 41 0.041 CP000350_53( CP000350 |pid:none) Leptos...oma brucei chromosome 3 clone RPCI93-27C5... 32 4.0 2 ( AE014834 ) Plasmo...telium discoideum chromosom... 155 4e-43 AY596296_161( AY596296 |pid:none) Haloarcula marismo... Gap no gap Contig length 815 Chromosome number (1..6, M) 2 Chromosome length 8467578 Start point 3690671 En...telium discoideum 3B gene for prespore-spe... 632 0.0 4 ( AC116984 ) Dictyostelium discoideum chromos

  17. Dicty_cDB: Contig-U15383-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available , mRNA (cDNA cl... 44 6.6 1 ( AP001708 ) Homo sapiens genomic DNA, chromosome 21q, sect...arch space: 5177603720 effective search space used: 5177603720 T: 0 A: 40 X1: 6 (11.9 bits) X2: 15 (29.7 bits...... 44 6.6 1 ( ER964772 ) SOOAC28JR LargeInsertSoybeanGenLibBuild4 Glycine ... 44 6.6 1 ( ER312256 ) 1092343...l*k*kllry*ik*m**kikfnfattirttttttttttrskqkptn r*f*nv*rnpretrkrmglescctsslfr*cslkilktin*inq*inq*iiiiiiikitn lnynssinnnsinntnfrtns...8 0.017 >Contig-U15383-1 (Contig-U15383-1Q) /CSM_Contig/Contig-U15383-1Q.Seq.d Length = 668 Score = 628 bits (317), Expect

  18. Dicty_cDB: Contig-U14167-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available g-U14167-1 (Contig-U14167-1Q) /CSM_Contig/Contig-U14167-1Q.Seq.d (1587 letters) Database: CSM 6905 seque...nces; 5,674,871 total letters Score E Sequences producing significant alignments: (bits) Value...plasma citri GII3-3X chromosome, contig Cont... 36 0.17 10 ( CP000728 ) Clostridium botulinum F str....cName: Full=Cyclic AMP receptor-like protein G; 44 0.013 EU797667_1( EU797667 |pid:none) Acytostelium subglobo...1 BC070135_1( BC070135 |pid:none) Homo sapiens transmembrane protein... 38 0.91 AL731801_4( AL731801 |pid:none) Mouse DNA seque

  19. Dicty_cDB: Contig-U14427-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available M) 6 Chromosome length 3595308 Start point 1680723 End point 1680896 Strand (PLUS/MINUS) PLUS Number of clo...M_Contig/Contig-U14427-1Q.Seq.d Length = 183 Score = 188 bits (95), Expect = 1e-48 Identities = 95/95 (100%) Strand..._Contig/Contig-U09104-1Q.Seq.d Length = 1120 Score = 42.1 bits (21), Expect = 2e-04 Identities = 21/21 (100%) Strand...ngth = 985 Score = 40.1 bits (20), Expect = 8e-04 Identities = 20/20 (100%) Strand = Plus / Minus Query: 38 ...ect = 2.9 Identities = 14/14 (100%) Strand = Plus / Minus Query: 38 attattattatta

  20. Dicty_cDB: Contig-U10495-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 02242_48( AM502242 |pid:none) Leishmania infantum chromosome 24. 49 1e-04 AJ006855_1( AJ006855 |pid:none) Rattu...ATAAAAACTAAATAT AAAAATAAATAATAAATAAATAAATAAATAAATAATNATTTGTGTGTGTG T Gap no gap Contig length 701 Chromos...s clone R3-1035N16, W... 44 7.0 1 ( AY760475 ) RP41-10j22 TJ Papio anubis genomic DNA Papio anub...lhqlvvsflklpf *lvqfsllln*l*niklq*linqlyln*iqfiktkyknk**ink*innxlcvc own update 2004. 6.10 Homology vs CSM-cDNA Query= Cont...ts) dna update 2008.11.20 Homology vs DNA Query= Contig-U10495-1 (Contig-U10495-1Q) /CSM_Contig/Cont

  1. Dicty_cDB: Contig-U12824-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available pid:none) Lawsonia intracellularis PHE/MN1... 38 0.099 AM270386_19( AM270386 |pid:none) Aspergillus niger contig...C... 37 0.29 AM270143_13( AM270143 |pid:none) Aspergillus niger contig An07c026... 37 0.29 AP007166_181( AP007166 |pid:none) Asper...... 33 4.2 AM270295_23( AM270295 |pid:none) Aspergillus niger contig An13c001... 33 4.2 CP001177_1757...gillus niger contig An08c025... 32 5.4 CP000500_641( CP000500 |...SEQUENCING CANCELLED *... 42 4.6 1 ( CR940347 ) Theileria annulata genomic DNA chromosome 1 part 1. 42 4.6 1

  2. Exploring function of conserved non-coding DNA in its chromosomal context

    Directory of Open Access Journals (Sweden)

    Delores J. Grant

    2015-11-01

    Full Text Available There is renewed interest in understanding expression of vertebrate genes in their chromosomal context because regulatory sequences that confer tissue-specific expression are often distributed over large distances along the DNA from the gene. One approach inserts a universal sensor/reporter-gene into the mouse or zebrafish genome to identify regulatory sequences in highly conserved non-coding DNA in the vicinity of the integrated reporter-gene. However detailed mechanisms of interaction of these regulatory elements among themselves and/or with the genes they influence remain elusive with the strategy. The inability to associate distant regulatory elements with the genes they regulate makes it difficult to examine the contribution of sequence changes in regulatory DNA to human disease. Such associations have been obtained in favorable circumstances by testing the regulatory potential of highly conserved non-coding DNA individually in small reporter-gene-containing plasmids. Alternative approaches use tiny fragments of chromosomes in Bacterial Artificial Chromosomes, BACs, where the gene of interest is tagged in vitro with a reporter/sensor gene and integrated into the germ-line of animals for expression. Mutational analysis of the BAC DNA identifies regulatory sequences. A recent approach inserts a sensor/reporter-gene into a BAC that is also truncated progressively from an end of genomic insert, and the end-deleted BAC carrying the sensor is then integrated into the genome of a developing animal for expression. The approach allows mechanisms of tissue-specific gene expression to be explored in much greater detail, although the chromosomal context of such mechanisms is limited to the length of the BAC. Here we discuss the relative strengths of the various approaches and explore how the integrated-sensor in the BACs method applied to a contig of BACs spanning a chromosomal region is likely to address mechanistic questions on interactions between

  3. [Chromosomal organization of the genomes of small-chromosome plants].

    Science.gov (United States)

    Muravenko, O V; Zelenin, A V

    2009-11-01

    An effective approach to study the chromosome organization in genomes of plants with small chromosomes and/or with low-informative C-banding patterns was developed in the course of investigation of the karyotypes of cotton plant, camomile, flax, and pea. To increase the resolving power of chromosome analysis, methods were worked out for revealing early replication patterns on chromosomes and for artificial impairment of mitotic chromosome condensation with the use of a DNA intercalator, 9-aminoacridine (9-AMA). To estimate polymorphism of the patterns of C-banding of small chromosomes on preparations obtained with the use of 9-AMA, it is necessary to choose a length interval that must not exceed three average sizes of metaphase chromosomes without the intercalator. The use of 9-AMA increases the resolution of differential C- and OR-banding and the precision of physical chromosome mapping by the FISH method. Of particular importance in studying small chromosomes is optimization of the computer-aided methods used to obtain and process chromosome images. The complex approach developed for analysis of the chromosome organization in plant genomes was used to study the karyotypes of 24 species of the genus Linum L. It permitted their chromosomes to be identified for the first time, and, in addition, B chromosomes were discovered and studied in the karyotypes of the species of the section Syllinum. By similarity of the karyotypes, the studied flax species were distributed in eight groups in agreement with the clusterization of these species according to the results of RAPD analysis performed in parallel. Systematic positions and phylogenetic relationships of the studied flax species were verified. Out results can serve as an important argument in favour of the proposal to develop a special program for sequencing the genome of cultivated flax (L. usitatissimum L.), which is a major representative of small-chromosome species. PMID:20058798

  4. Dicty_cDB: Contig-U01574-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available .. 32 9.1 (Q6NZW0) RecName: Full=Coiled-coil domain-containing protein 102... 32 9.1 AF355995_1( AF355995 |pid:none) Corta...p no gap Contig length 338 Chromosome number (1..6, M) 2 Chromosome length 8467578 Start...SM_Contig/Contig-U01574-1Q.Seq.d (338 letters) Database: CSM 8361 sequences; 7,895,291 total letters Score E...se: ddbj_A 102,105,510 sequences; 101,790,757,118 total letters Searching................2 2.3 3 ( ER606076 ) 1093016276365 Global-Ocean-Sampling_GS-36-01-01-2... 32 2.4 3 ( AL078579 ) Arabidopsis thali

  5. Dicty_cDB: Contig-U06213-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available P001083_2943( CP001083 |pid:none) Clostridium botulinum Ba4 str. ... 33 3.2 T18403( T18403 ) asparagine/aspartate rich protein - mal....9 1 ( DR689814 ) EST1079900 Normalized pine embryo library, Lib_D ... 44 4.9 1 ( CO490209 ) GQ026M14.T24_B0...ap no gap Contig length 525 Chromosome number (1..6, M) 3 Chromosome length 6358359 Start point 4973211 End ..._Contig/Contig-U06213-1Q.Seq.d (525 letters) Database: CSM 6905 sequences; 5,674,871 total letters Score E S...se: ddbj_A 92,845,959 sequences; 95,242,211,685 total letters Searchi

  6. Dicty_cDB: Contig-U10026-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available train UAB CTIP) complete ge... 38 0.41 14 ( ET089256 ) QM0AAA13CH10RM1 CCL1 Citrus clementina genomic cl... ... chromosome 15 clone RP11-205B5 map 1... 36 0.21 7 ( AC115368 ) Rattus norvegicus clone CH230-102L11, *** SE...olum subsp. capricolum ATCC 2734... 38 6e-05 20 ( AC116963 ) Dictyostelium discoideum chromosome 2 map 4657875... 36 1e-04 15 ( AC11...eum cDNA clone:dda45b14, 3' ... 34 0.62 3 ( AL158819 ) Human DNA sequence from clone RP11-382F24 on chro... ...26-1 (Contig-U10026-1Q) /CSM_Contig/Contig-U10026-1Q.Seq.d AGACGAAAATAAAAAAAGAGAATGAAAAGTGCTGATGTTAGTGCCAGTAC TCTAATAGCAACACCACC

  7. 454 sequencing of pooled BAC clones on chromosome 3H of barley

    Directory of Open Access Journals (Sweden)

    Yamaji Nami

    2011-05-01

    Full Text Available Abstract Background Genome sequencing of barley has been delayed due to its large genome size (ca. 5,000Mbp. Among the fast sequencing systems, 454 liquid phase pyrosequencing provides the longest reads and is the most promising method for BAC clones. Here we report the results of pooled sequencing of BAC clones selected with ESTs genetically mapped to chromosome 3H. Results We sequenced pooled barley BAC clones using a 454 parallel genome sequencer. A PCR screening system based on primer sets derived from genetically mapped ESTs on chromosome 3H was used for clone selection in a BAC library developed from cultivar "Haruna Nijo". The DNA samples of 10 or 20 BAC clones were pooled and used for shotgun library development. The homology between contig sequences generated in each pooled library and mapped EST sequences was studied. The number of contigs assigned on chromosome 3H was 372. Their lengths ranged from 1,230 bp to 58,322 bp with an average 14,891 bp. Of these contigs, 240 showed homology and colinearity with the genome sequence of rice chromosome 1. A contig annotation browser supplemented with query search by unique sequence or genetic map position was developed. The identified contigs can be annotated with barley cDNAs and reference sequences on the browser. Homology analysis of these contigs with rice genes indicated that 1,239 rice genes can be assigned to barley contigs by the simple comparison of sequence lengths in both species. Of these genes, 492 are assigned to rice chromosome 1. Conclusions We demonstrate the efficiency of sequencing gene rich regions from barley chromosome 3H, with special reference to syntenic relationships with rice chromosome 1.

  8. Dicty_cDB: Contig-U05086-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available s*i*arrircsit*y* stfkrittrnsskfpnyfknctktfkrrrrd*sfgrifsn...s*i*arrircsit*y* stfkrittrnsskfpnyfknctktfkrrrrd*sfgrifsnvn*fq...lini* Frame C: nflyflvlfffffyinikpykkffi*n*kkkkkkkrqnhklkyqnnpl*k*yiyntlkne tlw*tktktrysrnnw*t*inirya*kkaniftr*irkreqekakvfsta... no gap Contig length 1025 Chromosome number (1..6, M) 2 Chromosome length 8467578 Star...SK218Z ,220,901 est5= SSJ342Z ,253,899 est6= SSF178E ,437,1026 Translated Amino Acid sequence kiffif*fcff

  9. Dicty_cDB: Contig-U15215-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available hfy*iigikkrifnkkkkkvimyf ifff*kllkkkk Frame C: llaywsfnqsf*y**tk*tqvstpi*pnqllisskrisq...AKVNNNRKVNISYIYNTSNNTKFVLGWNVNTKNFKQGNTFGATVNLTL*ivnfylh f*kekkknkntp*kykkkiiivnnciifkfgkinffhfy*iigikkrif...hhhstlvpntksipp vssklkltttekltsltstilattlnsf*vgmsilktlnkaillvlllt*lfkl*tfiyi fkkkkkktkihhknikkk****tiv*fsnlvksiffif...e: Full=DNA-directed RNA polymerase subunit beta;... 35 6.3 CP000866_452( CP000866 |pid:none) Nitrosopumilus mari...AAAAAAAAA Gap no gap Contig length 1117 Chromosome number (1..6, M) 2 Chromosome length 8467578 Start point

  10. Dicty_cDB: Contig-U01856-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available kkkkkqtyskkli*i*ikikmtklyikqkvfsfgekynvydefknkkfycegsvf swgskikmfsqdtnqlifvirqkvkfsfykkyfiydgndnllatvkqkslfkpkleivln eneqytckgdffs...i*kn*li*n sncqerkkekkkkkkkli*tstivrnclkkk*n*n*l*friv--- ---fftrclpffsf*kffffgvpff..., plant... 32 7.3 2 ( EY839504 ) PT11-C9-005-015-G04-CT.F Poncirus trifoliata see...AAAAAAAAAAAAAAAAAAA Gap gap included Contig length 1110 Chromosome number (1..6, M) 2 Chromosome length 8467578 Star...vfqlevlqreyyhgvihicwiyqrisnhpsllqlllqlt ivfiektmdnsly*ffdplkslyeyknkiiiikinlk*sfkfinncihyfsfkkin*fri pivrkek

  11. Dicty_cDB: Contig-U11925-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available *svvn virsidccnlksapdstslristsidfisslsklstfltlpw**tapwaitifnrsrsil qrfn*kawisgffta...i*nrhqiqlhlefqhrlisyhrylnyqhf*lyhgsrlrlgqlpfsidhaqsc ngsieklgyldsllpmyysslqwyqsliillaneivmkilvddsllnn Frame C: lgvh*inleitkiiiiiff...0442_353( CP000442 |pid:none) Burkholderia ambifaria AMMD chro... 69 1e-10 AM9206... included Contig length 794 Chromosome number (1..6, M) 5 Chromosome length 5062330 Start point 4585223 End ...lnn Translated Amino Acid sequence (All Frames) Frame A: isvcik*i*k*qk****YFLKYYKIIFFFFXXLKKKXXX--- ---*ffsr

  12. Dicty_cDB: Contig-U14993-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available kdlkdnndnnnnsnsnsnnhhpnnsiqesiv idkvhtxryds Frame B: tvglleysfqfffskhthnkflylkthlfnsiinysieklnfkyqtfpskf**if...dium perfringens ATCC 13... 35 9.2 AM180355_2045( AM180355 |pid:none) Clostridium diff...TT ATTGATAAAGTACACACNNAAAGATACGACTCT Gap no gap Contig length 1833 Chromosome number (1..6, M) 1 Chromosome length 4919822 Star...rames) Frame A: hcwptgvfisifffktht**islfknssf*fnyqlfn*ktqfqipnlsf*iliniqqwgi viasiieiiieiiiiiitiiiiiitiiitii...rv*rtisigknsk ildtkfkvcfilctnti*fkyt*fi*ig*sylyety*sivfrmg*skrgfqmyfffsflf ts*wfkw*mykilffna*fp*til*rvintist

  13. Dicty_cDB: Contig-U14490-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available SSIGQSGNFGGAQTSNQITGN GVVAGSKKSASGVYYHHEESKSSTTFVSGSSSENEFVGAWGH*ni*fl*tltfm*kffkm *sylklilpyink*vkfffs Frame B: xxxkiif...imknqnhlphllvevllkmnllvhgdirifnfykllllcesflkc kvt*s*yyhi*ink*nfff Frame C: xxxk*yfkkkinkn*yykkknvnf*inyflisx...kicfkiinwpkwkfwrctnlkpnnwkw cccrfkkkc*wcllss*rikiiyhic*wkff*k*icwcmgtleylifinsyfyvkvf*nv klpkanitiyk*iskifff...Gap no gap Contig length 420 Chromosome number (1..6, M) 1 Chromosome length 4919822 Start point 4476883 End...RKMSIFKSITSLSVSKSVSKSSIGQSGNFGGAQTSNQITGN GVVAGSKKSASGVYYHHEESKSSTTFVSGSSSENEFVGAWGH*ni*fl*tltfm*kffkm *sylklilpyink*vkfffs

  14. Dicty_cDB: Contig-U12128-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available hnkkhyh*fqlhsminqikinhqilslklikiq*qnhhh lhqsy*hiisqqilvqkmlknkshtll*laikrffsvplvmakfqlqlvliihqlifqin qftmdfm...AAATTTTATAAATTAAATACTACAAAAAAAAAAAAAAA Gap gap included Contig length 2228 Chromosome number (1..6, M) - Chromosome length - Star...s*csiepin*ikntn**ridwfsi swswlllgtkr*rik*sifi*cfncqyh**lfitlsnlfrigciypr*tiiftihwsgsk *lke*nsysr*nsl...qr**ynixxyixk***--- ---syynititnrwrw*ss**wk*ifyrwmatw*tnfntsn**q*qwhssiw*gflftic fssttfinfwfk*ntvsfkyk**fk****qqy****l**ff...prfkyftwflss*l*mycyk*r*fhya snksiffnst*siwyfkwfhlysclknnnnnk*tlkfyklnttkkkk own update 2004. 6.10 Homology v

  15. Dicty_cDB: Contig-U05867-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available kklkvnfpfms Frame C: kneahll*itlyafyigrifyyhkqnlieknmkf*kklneiqfkfhffskkkfffffgkr ktnffkst*nkkylwyswlnknf*KI...yyhkqnlieknmkf*kklneiqfkfhffskkkfffffgkr ktnffkst*nkkylwyswlnknf*KIKKKKKSLINKKNNYKKYWSKFFGF...rames) Frame A: gkmrliyyr*lymlfi*vvsstttnki*lkki*nfkkn*mksnlnfifsqkknfffflar eklif...CCATTCATGAGTCT Gap no gap Contig length 540 Chromosome number (1..6, M) 5 Chromosome length 5062330 Start po... of EST 1 Link to clone list U05867 List of clone(s) est1= SSM367E ,1,541 Translated Amino Acid sequence kneahll*itlyafyigrif

  16. Dicty_cDB: Contig-U09336-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available l*idl*itkkkikykkkkdgtn**nrnts krififsngknkrgrniikvikii*kytktiprsmcswfichfnyfsflnvfinl*krfi k*kktt*ntk*ta...AATTATAATAAATTTTAAAC Gap gap included Contig length 716 Chromosome number (1..6, M) 5 Chromosome length 5062330 Star...PKVSSNK--- ---FFXLTLFGFXCFFFLKKKKKKKKKKKKKKKFSKYQYYD**yliiinfk Translated Amino Acid sequence (All Frames) Frame A: qq*likififf...er*kyy*shqdylkiyqnnttinv*lvylpfqlf*fp*cfh*slkkvh qikknnlkhkinskhqlnhqlnnnklqirnnklqinninklqtkiklqikiklqikiklq snhqrfhqin--- ---ffs...4 ) Cpl19059 Papaya Genomic DNA BAC Library Carica pa... 44 7.2 1 ( DE449872 ) Bombyx mori genomic DNA, Fosm

  17. Dicty_cDB: Contig-U01586-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available vshslhv vlnfmqlktikrlkimvtmkhlllslv*ilknqlv*lllllerqrifqvpmimlflmlqi lhll*nqls*i*fqlslfvflfhfyyckttiiftyficffff...iivkpq*sshisfvfffsgkkkkklnkik*ifnnkk kkkkkkkkkkkkkkk own update 2004. 6...AAAAAAAAAAAAAAAAAAAAAAAAAAAAA Gap gap included Contig length 1227 Chromosome number (1..6, M) 4 Chromosome length 5430582 Star...*fl*nwkfy**lynlhflwy*tkrkfpilcmw c*ilcn*kqskd*r*w*q*sicyfhwfky*rtnwfncccy*kdkeffkcl*lccf*cskf fiffkinflkfnssflylyfyfif...ective HSP length: 16 effective length of query: 1221 effective length of database: 7,761,515 effective sear

  18. Dicty_cDB: Contig-U09528-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available nvlftl* lgl*esldfwyecrqllenytry*rqlgqhalqpygtstnhlllgyrwfqrp*hddgwqw wyvqhrvrvtlflmvliecpthcrm*ld*y*srdiinfnsl*shc...fwyecrqllenytry*rqlgqhalqpygtstnhlllgyrwfqrp*hddgwqw wyvqhrvrvtlflmvliecpthcrm*ld*y*srdiinfnsl*shcn*srsirctr...:none) Zea mays full-length cDNA clone ZM... 176 5e-50 AL939104_273( AL939104 |pid:none) Streptomyces coelic...AATTTATGGACTCAAACAAATCTTGGAACTTTTACT GAATCTTAGAAAGNATTCTTTAATTCCACCACAGGTGTATTATGTTAACT TAACACCAACAA Gap gap included Contig length... 902 Chromosome number (1..6, M) 2F Chromosome length 193677 Start point 50076 End po

  19. Dicty_cDB: Contig-U05010-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ap Contig length 427 Chromosome number (1..6, M) - Chromosome length - Start point - End point - Strand (PLU...5 Identities = 119/119 (100%) Strand = Plus / Plus Query: 218 catcacttaatcantnntc... bits (49), Expect = 9e-21 Identities = 52/52 (100%) Strand = Plus / Plus Query: 45 aatatttttacaatatattctaaa... Identities = 44/44 (100%) Strand = Plus / Plus Query: 151 aaaattattantnttcnnattttagtaactttgaatcaatttcc 194 ...re = 60.0 bits (30), Expect = 2e-09 Identities = 30/30 (100%) Strand = Plus / Plu

  20. Dicty_cDB: Contig-U15064-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available llmilvwa*aigst*flilgsmvgrssstvllrpvqagatalltmp sitviilflr*lrmnhgafgsldnalpkisysisskiis...-1Q.Seq.d (1813 letters) Database: ddbj_A 92,845,959 sequences; 95,242,211,685 total letters Searching.........0952 ) 1095515505910 Global-Ocean-Sampling_GS-31-01-01-1... 46 4.7 1 ( AM638263 ) Entamoeba dispar...A AAAAAATAAAAAT Gap no gap Contig length 1813 Chromosome number (1..6, M) 1 Chromosome length 4919822 Start ...eplplyafvfsfqilrdssnpfsigvlispmiflrclltcs siaglicdiidslillmilvwa*aigst*flilgsmvgrssstvllrpvqagatalltmp sitviilflr*lrmnhgafgsldnal

  1. Dicty_cDB: Contig-U09144-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available --yhhyigyqlvviyy*mvqpfnikiey*n*fnhlmrkliifyqqmkmkikmk*kqpis lvinn*mi*ylkiyhnn*hqvklnlkiervkclvlkqvkimlnlv*leek...ssi*r*kg*nv*c*sk*rsc*iwcn*kkrtfnsikeks nyeikinwfqfnhftfkiin*fny**ckensfk*nsskyfki...TTCAAAGAGTCAAGATATAAATCAACAAGAAATAAA Gap gap included Contig length 1233 Chromosome number (1..6, M) 6 Chromosome le...es) Frame A: vllg**els*fyqviwrrfqchwmkrvnwlqd*hgmvsnqiqniiki*qleni*hnnslv mvywilm...kliivnikrl*in*lkdflhiqplvillsqvyqvsivqif*ishlkvypy*rm mqmkllks*nvmefqwik*epmhnyivnslmngyhyqqpiqkrnvmr*rkklvv

  2. Dicty_cDB: Contig-U11567-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available wlsnysyfn*kd gcknqyglg*ilvkdigeilfpmfrsktry*kqrydipskdntllivtrvfttr*mv*lf c*cgfptlr*s*refkrnqfrrykitcfcftlksvltkfkyhhkm*si..............................done Score E Sequences producing significant alignments: (bits) Value N ( BJ360944 ) Dictyostelium di...ATATAAACAAATAAAA AAAATA Gap gap included Contig length 1696 Chromosome number (1..6, M) 5 Chromosome length 5062330 Start point...f*fii tyytfksr*irisme*if*tl*ihykyi*tsg*cfncqckindtinxkssnvnnvsfn*i n*kergfqysislyqivvtcw*cig*ycrenvnlfnsigs...ynpmg*yfisfe nlygsigitl*ictrvs*kyafgne**wci*ttnr*rirr*yl*ttlgfnlgcy**il

  3. Assembly and sorting of homologous BAC contigs in allotetraploid cotton genomes

    Science.gov (United States)

    Upland cotton (G. hirsutum) is a diploidized allopolyploid species containing At and Dt sub-genomes that have partial homology. Assembly and sorting of homologous BAC contigs into their subgenomes and further to individual chromosomes are of both great interest and great challenge for genome-wide i...

  4. Dicty_cDB: Contig-U14830-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Contig-U14830-1 no gap 677 4 5021454 5020787 MINUS 1 1 U14830 0 1 0 0 0 0 0 0 0 0 0 0 0 0 Show C ... chromosome II. 44 6.7 1 ( DD041861 ) Light-driven energy ... generation using proteorhodop... 44 6.7 1 ( CU8557 ...

  5. Dicty_cDB: Contig-U16120-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available parum strain PAK1 from Pakistan C... 32 6.1 3 ( AC115598 ) Dictyostelium discoideum chromosome 2 map 581427-... 18 ( AM479077 ) Vitis vinifera contig VV78X034366.12, whole genom... 40 6.1 5 ( AF134695 ) Plasmodium falci

  6. Report of the Fourth International Workshop on human X chromosome mapping 1993

    Energy Technology Data Exchange (ETDEWEB)

    Schlessinger, D.; Mandel, J.L.; Monaco, A.P.; Nelson, D.L.; Willard, H.F. [eds.

    1993-12-31

    Vigorous interactive efforts by the X chromosome community have led to accelerated mapping in the last six months. Seventy-five participants from 12 countries around the globe contributed progress reports to the Fourth International X Chromosome Workshop, at St. Louis, MO, May 9-12, 1993. It became clear that well over half the chromosome is now covered by YAC contigs that are being extended, verified, and aligned by their content of STSs and other markers placed by cytogenetic or linkage mapping techniques. The major aim of the workshop was to assemble the consensus map that appears in this report, summarizing both consensus order and YAC contig information.

  7. International workshop of chromosome 19

    Energy Technology Data Exchange (ETDEWEB)

    Pericak-Vance, M.A. (Duke Univ. Medical Center, Durham, NC (United States). Div. of Neurology); Carrano, A.J. (Lawrence Livermore National Lab., CA (United States))

    1991-09-16

    This document summarizes the workshop on physical and genetic mapping of chromosome 19. The first session discussed the major disease loci found on the chromosome. The second session concentrated on reference families, markers and linkage maps. The third session concentrated on radiation hybrid mapping, somatic cell hybrid panels, macro restriction maps and YACs, followed by cDNA and long range physical maps. The fourth session concentrated on compiling consensus genetic and physical maps as well as discussing regions of conflict. The final session dealt with the LLNL cosmid contig database and comparative mapping of homologous regions of the human and mouse genomes, and ended with a discussion of resource sharing. 18 refs., 2 figs. (MHB)

  8. AcEST: CL2016Contig1 [AcEST

    Lifescience Database Archive (English)

    Full Text Available CL2016Contig1 715 2 Adiantum capillus-veneris contig: CL2016contig1 sequence. Link to clone list Show CL2016...Contig1 Contig ID CL2016Contig1 Length 715 Number of clones 2 Definition Adiantum c...apillus-veneris contig: CL2016contig1 sequence. Link to clone list Link to clone list Clone ID DK957912 DK95

  9. AcEST: CL3000Contig1 [AcEST

    Lifescience Database Archive (English)

    Full Text Available CL3000Contig1 615 2 Adiantum capillus-veneris contig: CL3000contig1 sequence. Link to clone list Show CL3000...Contig1 Contig ID CL3000Contig1 Length 615 Number of clones 2 Definition Adiantum c...apillus-veneris contig: CL3000contig1 sequence. Link to clone list Link to clone list Clone ID DK945747 DK94

  10. AcEST: CL2333Contig1 [AcEST

    Lifescience Database Archive (English)

    Full Text Available CL2333Contig1 424 2 Adiantum capillus-veneris contig: CL2333contig1 sequence. Link to clone list Show CL2333...Contig1 Contig ID CL2333Contig1 Length 424 Number of clones 2 Definition Adiantum c...apillus-veneris contig: CL2333contig1 sequence. Link to clone list Link to clone list Clone ID BP914560 BP91

  11. Dicty_cDB: Contig-U14811-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available NNNNNNNN Gap no gap Contig length 641 Chromosome number (1..6, M) 3 Chromosome length 6358359 Star...ig VV78X065733.5, whole genome... 46 1.5 1 ( AM466497 ) Vitis vinifera contig VV78X075550.1, whole genome...... 2.1 6 ( AF250284 ) Amsacta moorei entomopoxvirus, complete genome. 40 2.6 6 ( AL157402 ) Human DNA sequence from.... 42 3.0 2 ( L29497 ) Pneumocystis carinii major surface glycoprotein B g... 38 3...9. 44 6.1 1 ( AC225908 ) Oryza minuta clone OM__Ba0212C10, complete sequence. 44 6.1 1 ( AC115032 ) Mus musculus chromosome

  12. Dicty_cDB: Contig-U14628-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available CATATACCANNNNNNNNN Gap no gap Contig length 545 Chromosome number (1..6, M) 2 Chromosome length 8467578 Star...4 0.0 2 ( AC115592 ) Dictyostelium discoideum chromosome 2 map 1-12595... 694 0.0 3 ( AY484460 ) Dictyosteli...4002E9, WO... 48 0.33 1 ( AC116957 ) Dictyostelium discoideum chromosome 2 map 1685067... 46 1.3 1 ( AB102779 ) Dictyos...esin heavy chain 1 (KHC1) ... 44 5.1 1 ( AC007496 ) Homo sapiens chromosome 16 clone RP11-357N13, com... 44 ...5.1 1 ( AC212314 ) Solanum lycopersicum chromosome 11 clone C11HBa00... 44 5.1 1

  13. Dicty_cDB: Contig-U16017-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available smodium falciparum 3D7 chromosome 14 section 1... 34 0.25 10 ( FM248889 ) Caenorhabditis elegans EST, clone B12_ce4.trans...stelium discoideum chromosome 2 map 2097701... 34 0.013 12 ( AE014822 ) Plasmodium falciparum 3D7 chromosome 14 sect...01078 ) Clostridium botulinum E3 str. Alaska E43, complet... 36 0.025 18 ( AE014833 ) Plasmodium falciparum 3D7 chromosome 10 sect...m falciparum 3D7 chromosome 10 section 2... 38 0.053 8 ( AM469829 ) Vitis vinifera contig VV78X104896.13, wh...) Sequence 180 from Patent WO0246454. 34 0.074 6 ( AE014845 ) Plasmodium falciparum 3D7 chromosome 12, secti

  14. Dicty_cDB: Contig-U12742-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available AATAATGATAATAATAATAATGA TAATAATAACAATAATCAATATCAAGAAGAATCAAATCAATNNNNNNNNN Gap no gap Contig length 600 Chromos...ome number (1..6, M) 3 Chromosome length 6358359 Start point 4811062 End point... ) Mus musculus BAC clone RP23-356I2 from 18, comple... 52 0.023 1 ( AC113003 ) Mus musculus chromos...105 1e-21 CP000496_690( CP000496 |pid:none) Pichia stipitis CBS 6054 chromos... 1...05 1e-21 BX538351_91( BX538351 |pid:none) Cryptosporidium parvum chromosome... 104 2e-21 EU834288_1( EU83428

  15. Dicty_cDB: Contig-U15507-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 9554 ) 255457978 Pea aphid whole body normalized full le... 40 0.13 2 ( AE014825 ) Plasmodium falciparum 3D7 chromosome 14 sectio...s flavipes symbiont library ... 36 0.25 4 ( EV816549 ) BGBV-aae68c07.g1 Snail_EST_pSMART Biom...35 3 ( EG407461 ) SAAH-aac46e10.b1 Agen 0058 Schmidtea mediterranea... 32 0.35 4 ( AC117176 ) Dictyostelium discoideum chromosome...TAATGCACCACAAGAAA ATAGNAGNGGNATAAAAAGAGAG Gap gap included Contig length 3713 Chromosome...osome 2 map 4229098... 40 0.001 5 ( EY392550 ) CAXA9868.fwd CAXA Helobdella robusta Subtracted

  16. Dicty_cDB: Contig-U01710-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available p. pekinensis clone KBrH001D23,... 46 2.4 1 ( AL313612 ) Tetraodon nigroviridis genome survey sequence T3 ......2 8 ( AE014851 ) Plasmodium falciparum 3D7 chromosome 12, section ... 32 7.5 11 ( CR119757 ) Forward strand read from insert...m... 44 9.3 1 ( AL262333 ) Tetraodon nigroviridis genome survey sequence PUC... 44 9.3 1 ( DU058789 ) 90...sicles of secretory system 4.0 %: extracellular, including cell wall >> prediction for C...p included Contig length 900 Chromosome number (1..6, M) 4 Chromosome length 5430582 Start point 4647014 End point 4646115 Str

  17. Dicty_cDB: Contig-U07944-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available A Gap gap included Contig length 1092 Chromosome number (1..6, M) 2 Chromosome length 8467578 Start point 17...14429 Number of successful extensions: 6222644 Number of sequences better than 10.0: 295 Length of query: 1102 Length...lderia vietnamiensis G4 c... 130 6e-29 CP000529_889( CP000529 |pid:none) Polaromonas naphtha...e-28 AM260479_371( AM260479 |pid:none) Ralstonia eutropha H16 chromosom... 129 1e-28 CP000239_2744( CP000239...uyveromyces lactis strain NRRL... 125 2e-27 CP000924_162( CP000924 |pid:none) Thermoanaerobacter pseudethano

  18. Dicty_cDB: Contig-U00222-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available -rich adhesin for platelets; AltNam... 37 1.5 CP001634_1377( CP001634 |pid:none) Kosmo...s clone CH230-9N18, *** SEQUENCIN... 46 3.4 1 ( AL844506 ) Plasmodium falciparum chromosome 7. 46 3.4 1 ( AC223206 ) Bos...TCCTCCCGTTCCACATCATCTTCCTCTTCTATTTCATATTCTT ATAATAAACAAATAAAAAACTATCACAATAAAAAAA Gap gap included Contig length 1276 Chromos...ome number (1..6, M) 1 Chromosome length 4919822 Start point 1528...um cDNA clone:dda8g07, 3' e... 333 e-128 2 ( AC116986 ) Dictyostelium discoideum chromos

  19. Dicty_cDB: Contig-U04005-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 46 3.4 1 ( AC198005 ) Medicago truncatula chromosome 7 BAC clone mth2-1... 46 3.4 1 ( AC189464 ) Brassica rapa subsp. pekinensis... Score E Sequences producing significant alignments: (bits) Value Contig-U04005-1 (Contig-U04005-1Q) /CSM_Co.............................done Score E Sequences producing significant alignments...ni_7_11_H1 Volcani07 Citrus reticulata x Cit... 50 0.22 1 ( CR855320 ) Zebrafish DNA sequence fr..._UP_021_H08_14FEB2005_050 Brassica napus ... 48 0.86 1 ( AM547256 ) Paracentrotus lividus EST, clone MPMGp11

  20. Dicty_cDB: Contig-U03447-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available OGRESS... 36 4.3 3 ( AC212632 ) Solanum lycopersicum chromosome 7 clone C07HBa012... 32 4.4 4 ( BX927393 ) Zebrafis...71 total letters Score E Sequences producing significant alignments: (bits) Value Contig-U03447-1 (Contig-U0...rs Searching..................................................done Score E Sequences producing significant a...TS. 44 2.5 1 ( DL174135 ) Enzyme and SNP marker for disease. 44 2.5 1 ( DJ133248 ) Method for identifica...Ba054-M18TR CccABa Cajanus cajan genomic clon... 36 8.0 2 ( CT027824 ) Zebrafish DNA sequence from

  1. Dicty_cDB: Contig-U06182-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 6, M) 5 Chromosome length 5062330 Start point 3210801 End point 3210986 Strand (PLUS/MINUS) PLUS Number of c...-35 Identities = 72/72 (100%) Strand = Plus / Plus Query: 80 tttcgacaacaatccaaattggtaataaaaataatgatatagttact...||||| Sbjct: 140 taattaaataat 151 Score = 129 bits (65), Expect = 1e-30 Identities = 65/65 (100%) Strand = P... /CSM_Contig/Contig-U13650-1Q.Seq.d Length = 659 Score = 56.0 bits (28), Expect = 1e-08 Identities = 31/32 (96%) Strand...3 Identities = 22/23 (95%) Strand = Plus / Plus Query: 4 caccaacaacaacaaaaacaaca 26 ||||||||||||||| |||||||

  2. Dicty_cDB: Contig-U16510-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available (1..6, M) - Chromosome length - Start point - End point - Strand (PLUS/MINUS) - ...1Q) /CSM_Contig/Contig-U16510-1Q.Seq.d Length = 4601 Score = 890 bits (449), Expect = 0.0 Identities = 449/449 (100%) Strand... 0.0 Identities = 448/448 (100%) Strand = Plus / Plus Query: 1 tcaaccatcgcaggctcaaccatcgcttcaattgcttctactatt... tcatcaagctctgcccccatcttcatct 448 Score = 761 bits (384), Expect = 0.0 Identities = 384/384 (100%) Strand...||| Sbjct: 3112 aaaatttatattaaattttatttt 3135 Score = 442 bits (223), Expect = e-123 Identities = 223/223 (100%) Strand

  3. Dicty_cDB: Contig-U16575-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available umber (1..6, M) 1 Chromosome length 4919822 Start point 4570803 End point 4569342 Strand (PLUS/MINUS) MINUS ...6575-1Q) /CSM_Contig/Contig-U16575-1Q.Seq.d Length = 1462 Score = 329 bits (166), Expect = 7e-90 Identities = 166/166 (100%) Strand...atcaacttcattattatcagcacaagcaatttcagc 388 Score = 121 bits (61), Expect = 3e-27 Identities = 61/61 (100%) Strand...= 8e-25 Identities = 57/57 (100%) Strand = Plus / Plus Query: 663 gaattggctgataaattagagaaagaacgtcaagagaaagag... Identities = 52/54 (96%) Strand = Plus / Plus Query: 663 gaattggctgataaattagagaaagaacgtcaagagaaagagttggctga

  4. Dicty_cDB: Contig-U12216-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available base: CSM 6905 sequences; 5,674,871 total letters Score E Sequences producing significant ali...Pb cDNA #17, Tommaso Pace, Marta Ponzi, ... 46 4.0 1 ( BB971888 ) Plasmodium berghei strain ANKA cDNA clone:...2216-1Q) /CSM_Contig/Contig-U12216-1Q.Seq.d (1548 letters) Database: nrp_B 3,236,559 sequences; 1,051,180,864 total letters Sear...6, M) 4 Chromosome length 5430582 Start point 4302381 End point 4303921 Strand (P...se: ddbj_A 92,845,959 sequences; 95,242,211,685 total letters Sear

  5. Dicty_cDB: Contig-U05118-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available e DNA of symbiotic bacteria of aphid. 40 1.6 14 ( AR409405 ) Sequence 1 from patent US 66329..... 36 4.0 17 ( AC212432 ) Solanum lycopersicum chromosome 11 clone C11HBa00... 38 4.0 8 ( CP000263 ) Buchnera aphidicol...ts) S2: 22 (44.1 bits) protein update 2009. 8. 1 Homology vs Protein Query= Contig-U05118-1 ...skcskf*inkkvkqknkkkknikmkinnfvt own update 2004. 6.10 Homology vs CSM-cDNA Query=...ts) S2: 15 (30.2 bits) dna update 2009. 7.12 Homology vs DNA Query= Contig

  6. Dicty_cDB: Contig-U06291-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Full=Pantothenate synthetase; Short=P... 108 1e-22 AM270398_24( AM270398 |pid:none) Aspergillus niger contig..... 102 1e-20 CP001114_830( CP001114 |pid:none) Deinococcus deserti VCD115, comp.....none) Rhizobium sp. NGR234, complete ... 96 9e-19 AM747054_1( AM747054 |pid:none) Bacillus weihenstephanensis part... CP001087_468( CP001087 |pid:none) Desulfobacterium autotrophicum H... 95 2e-18 AM747059_1( AM747059 |pid:none) Bacillus wei...TTATAATAAAATAAAA Gap no gap Contig length 649 Chromosome number (1..6, M) 5 Chrom

  7. Isolation and characterization of bovine herpesvirus 4 (BoHV-4 from a cow affected by post partum metritis and cloning of the genome as a bacterial artificial chromosome

    Directory of Open Access Journals (Sweden)

    Cavirani Sandro

    2009-08-01

    Full Text Available Abstract Background Bovine herpesvirus 4 (BoHV-4 is a gammaherpesvirus with a Worldwide distribution in cattle and is often isolated from the uterus of animals with postpartum metritis or pelvic inflammatory disease. Virus strain adaptation to an organ, tissue or cell type is an important issue for the pathogenesis of disease. To explore the mechanistic role of viral strain variation for uterine disease, the present study aimed to develop a tool enabling precise genetic discrimination between strains of BoHV-4 and to easily manipulate the viral genome. Methods A strain of BoHV-4 was isolated from the uterus of a persistently infected cow and designated BoHV-4-U. The authenticity of the isolate was confirmed by RFLP-PCR and sequencing using the TK and IE2 loci as genetic marker regions for the BoHV-4 genome. The isolated genome was cloned as a Bacterial Artificial Chromosome (BAC and manipulated through recombineering technology Results The BoHV-4-U genome was successfully cloned as a BAC, and the stability of the pBAC-BoHV-4-U clone was confirmed over twenty passages, with viral growth similar to the wild type virus. The feasibility of using BoHV-4-U for mutagenesis was demonstrated using the BAC recombineering system. Conclusion The analysis of genome strain variation is a key method for investigating genes associated with disease. A resource for dissection of the interactions between BoHV-4 and host endometrial cells was generated by cloning the genome of BoHV-4 as a BAC.

  8. The DNA sequence, annotation and analysis of human chromosome 3

    DEFF Research Database (Denmark)

    Muzny, Donna M; Scherer, Steven E; Kaul, Rajinder;

    2006-01-01

    chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well...... as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric...

  9. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.

    Science.gov (United States)

    Salanoubat, M; Lemcke, K; Rieger, M; Ansorge, W; Unseld, M; Fartmann, B; Valle, G; Blöcker, H; Perez-Alonso, M; Obermaier, B; Delseny, M; Boutry, M; Grivell, L A; Mache, R; Puigdomènech, P; De Simone, V; Choisne, N; Artiguenave, F; Robert, C; Brottier, P; Wincker, P; Cattolico, L; Weissenbach, J; Saurin, W; Quétier, F; Schäfer, M; Müller-Auer, S; Gabel, C; Fuchs, M; Benes, V; Wurmbach, E; Drzonek, H; Erfle, H; Jordan, N; Bangert, S; Wiedelmann, R; Kranz, H; Voss, H; Holland, R; Brandt, P; Nyakatura, G; Vezzi, A; D'Angelo, M; Pallavicini, A; Toppo, S; Simionati, B; Conrad, A; Hornischer, K; Kauer, G; Löhnert, T H; Nordsiek, G; Reichelt, J; Scharfe, M; Schön, O; Bargues, M; Terol, J; Climent, J; Navarro, P; Collado, C; Perez-Perez, A; Ottenwälder, B; Duchemin, D; Cooke, R; Laudie, M; Berger-Llauro, C; Purnelle, B; Masuy, D; de Haan, M; Maarse, A C; Alcaraz, J P; Cottet, A; Casacuberta, E; Monfort, A; Argiriou, A; flores, M; Liguori, R; Vitale, D; Mannhaupt, G; Haase, D; Schoof, H; Rudd, S; Zaccaria, P; Mewes, H W; Mayer, K F; Kaul, S; Town, C D; Koo, H L; Tallon, L J; Jenkins, J; Rooney, T; Rizzo, M; Walts, A; Utterback, T; Fujii, C Y; Shea, T P; Creasy, T H; Haas, B; Maiti, R; Wu, D; Peterson, J; Van Aken, S; Pai, G; Militscher, J; Sellers, P; Gill, J E; Feldblyum, T V; Preuss, D; Lin, X; Nierman, W C; Salzberg, S L; White, O; Venter, J C; Fraser, C M; Kaneko, T; Nakamura, Y; Sato, S; Kato, T; Asamizu, E; Sasamoto, S; Kimura, T; Idesawa, K; Kawashima, K; Kishida, Y; Kiyokawa, C; Kohara, M; Matsumoto, M; Matsuno, A; Muraki, A; Nakayama, S; Nakazaki, N; Shinpo, S; Takeuchi, C; Wada, T; Watanabe, A; Yamada, M; Yasuda, M; Tabata, S

    2000-12-14

    Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes. PMID:11130713

  10. Artificial intelligence

    CERN Document Server

    Hunt, Earl B

    1975-01-01

    Artificial Intelligence provides information pertinent to the fundamental aspects of artificial intelligence. This book presents the basic mathematical and computational approaches to problems in the artificial intelligence field.Organized into four parts encompassing 16 chapters, this book begins with an overview of the various fields of artificial intelligence. This text then attempts to connect artificial intelligence problems to some of the notions of computability and abstract computing devices. Other chapters consider the general notion of computability, with focus on the interaction bet

  11. Rapid De Novo Evolution of X Chromosome Dosage Compensation in Silene latifolia, a Plant with Young Sex Chromosomes

    Science.gov (United States)

    Deschamps, Clothilde; Mousset, Sylvain; Widmer, Alex; Marais, Gabriel A. B.

    2012-01-01

    Silene latifolia is a dioecious plant with heteromorphic sex chromosomes that have originated only ∼10 million years ago and is a promising model organism to study sex chromosome evolution in plants. Previous work suggests that S. latifolia XY chromosomes have gradually stopped recombining and the Y chromosome is undergoing degeneration as in animal sex chromosomes. However, this work has been limited by the paucity of sex-linked genes available. Here, we used 35 Gb of RNA-seq data from multiple males (XY) and females (XX) of an S. latifolia inbred line to detect sex-linked SNPs and identified more than 1,700 sex-linked contigs (with X-linked and Y-linked alleles). Analyses using known sex-linked and autosomal genes, together with simulations indicate that these newly identified sex-linked contigs are reliable. Using read numbers, we then estimated expression levels of X-linked and Y-linked alleles in males and found an overall trend of reduced expression of Y-linked alleles, consistent with a widespread ongoing degeneration of the S. latifolia Y chromosome. By comparing expression intensities of X-linked alleles in males and females, we found that X-linked allele expression increases as Y-linked allele expression decreases in males, which makes expression of sex-linked contigs similar in both sexes. This phenomenon is known as dosage compensation and has so far only been observed in evolutionary old animal sex chromosome systems. Our results suggest that dosage compensation has evolved in plants and that it can quickly evolve de novo after the origin of sex chromosomes. PMID:22529744

  12. Dicty_cDB: Contig-U09427-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available leen cDNA... 53 2e-05 (Q75AH6) RecName: Full=Mitochondrial aspartate-glutamate tr...gicus Ab1-114 mRNA, co... 51 9e-05 AF340168_1( AF340168 |pid:none) Neocallimastix frontalis hydrogeno... 51 ...hromosome number (1..6, M) 5 Chromosome length 5062330 Start point 4273701 End point 4272539 Strand (PLUS/MI...-U09427-1 (Contig-U09427-1Q) /CSM_Contig/Contig-U09427-1Q.Seq.d (1170 letters) Database: CSM 6905 sequences; 5,674,871 total...se: ddbj_A 92,845,959 sequences; 95,242,211,685 total letters Searching..................

  13. Dicty_cDB: Contig-U03446-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available _1( AK176255 |pid:none) Arabidopsis thaliana mRNA for mito... 40 0.026 CR382135_706( CR382135 |pid:none) Debar...n,... 35 0.84 (Q75AH6) RecName: Full=Mitochondrial aspartate-glutamate transpo... 35 0.84 EF676580_1...7 |pid:none) Zea mays full-length cDNA clone ZM... 32 7.1 AF340168_1( AF340168 |pid:none) Neocallimastix frontali... number (1..6, M) 2 Chromosome length 8467578 Start point 112298 End point 111995...1 (Contig-U03446-1Q) /CSM_Contig/Contig-U03446-1Q.Seq.d (303 letters) Database: CSM 6905 sequences; 5,674,871 total

  14. Dicty_cDB: Contig-U06970-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available AM270285 |pid:none) Aspergillus niger contig An12c029... 32 0.16 Z81073_6( Z81073 |pid:none) Caenorhabditis... 46 1.4 1 ( CG816784 ) SOYAO04TV LargeInsertSoybeanGenLib Glycine max ge... 46 1.4 1 ( FF068469 ) G1045P340R... CP000903 |pid:none) Bacillus weihenstephanensis KBA... 40 0.045 BT080960_1( BT080960 |pid:none) Caligus cle...-01-1... 48 0.35 1 ( AM448152 ) Vitis vinifera contig VV78X178033.10, whole genom...117247 ) Mus musculus BAC clone RP24-323L24 from chromosom... 44 5.5 1 ( AM459786 ) Vitis vinifera contig VV78X113014.3, whole ge

  15. Dicty_cDB: Contig-U04364-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available rhabditis elegans cosmid F23F... 35 3.1 S41400( S41400 )aspartic proteinase (EC 3.4.23.-) - wild cabbage (... 35 3.1 T14446( T14...73-1 (Contig-U14073-1Q) /CSM_Contig/Contig-U14073-1Q.Seq.d Length = 619 Score = 42.1 bits (21)...AC Library Solanum lycopersi... 40 1.4 2 ( AE001402 ) Plasmodium falciparum 3D7 chromosome 2 section 39... 40...-Tagu L... 46 1.8 1 ( CN921782 ) 000409AELA002649HT (AELA) Royal Gala young expand... 46 1.8 1 ( CK302409 ) ...92818. 34 4.6 2 ( FB695323 ) Sequence 17559 from Patent WO2006069200. 34 4.6 2 ( DL215616 ) NUCLEIC ACIDS AN

  16. Dicty_cDB: Contig-U12563-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available o... 46 3.6 1 ( ET799073 ) CHO_OF674xp06f1.ab1 CHO_OF Nicotiana tabacum geno... 46 3.6 1 ( ET092357 ) QM0AAA18AH11FM1 CCL1...... 34 9.1 2 ( BM901858 ) rc49e05.y1 Meloidogyne hapla egg pAMP1 v1 Meloido... 34 9.2 2 ( AL110487 ) Caenorh...CP001323_444( CP001323 |pid:none) Micromonas sp. RCC299 chromosome... 39 0.35 AC116100_9( AC116100 |pid:none...g-U12563-1 (Contig-U12563-1Q) /CSM_Contig/Contig-U12563-1Q.Seq.d TTTACCTATGTAGTTTCCCAATAAATGTTGGTGCTAATAGAACAATCC...AA GTTACACTTGCAAACACTGCCAGATATACTTATAAATATTCATATTCTCT ACCATGGCTTTCCAAATTCTTAACTGCC

  17. Dicty_cDB: Contig-U06387-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ne RP24-165F16 from chromosom... 48 0.28 1 ( EI685660 ) SB_BBd22-F04.F SB_BBd Sorghum bicolor geno... ( CC565344 ) CH240_478G17.TARBAC13P2 CHORI-240 Bos taurus geno... 44 4.4 1 ( DW237330 ) GH_RTMF_11R_G04_InvR_30Aug04_020_R Root (fre...A000016_619( BA000016 |pid:none) Clostridium perfringens str. 13 ... 32 7.1 ( P39630 ) RecName: Full=Spore coat pol...k*knwllfsltiiyfynnsfiny*ifnf own update 2004. 6.10 Homology vs CSM-cDNA Query= Contig-U06387-1 (C...ts) S2: 14 (28.2 bits) dna update 2008.11. 8 Homology vs DNA Query= Contig-U06387-1 (Contig-U06387-1Q) /CSM_

  18. Chromosomal aberration

    International Nuclear Information System (INIS)

    Chromosomal aberrations are classified into two types, chromosome-type and chromatid-type. Chromosom-type aberrations include terminal deletion, dicentric, ring and interstitial deletion, and chromatid-type aberrations include achromatic lesion, chromatid deletion, isochromatid deletion and chromatid exchange. Clastogens which induce chromosomal aberration are divided into ''S-dependent'' agents and ''S-independent''. It might mean whether they can induce double strand breaks independent of the S phase or not. Double strand breaks may be the ultimate lesions to induce chromosomal aberrations. Caffeine added even in the G2 phase appeared to modify the frequency of chromatid aberrations induced by X-rays and mitomycin C. Those might suggest that the G2 phase involves in the chromatid aberration formation. The double strand breaks might be repaired by ''G2 repair system'', the error of which might yield breakage types of chromatid aberrations and the by-pass of which might yield chromatid exchanges. Chromosome-type aberrations might be formed in the G1 phase. (author)

  19. Original Research: Generation of non-deletional hereditary persistence of fetal hemoglobin β-globin locus yeast artificial chromosome transgenic mouse models: -175 Black HPFH and -195 Brazilian HPFH.

    Science.gov (United States)

    Braghini, Carolina A; Costa, Flavia C; Fedosyuk, Halyna; Neades, Renee Y; Novikova, Lesya V; Parker, Matthew P; Winefield, Robert D; Peterson, Kenneth R

    2016-04-01

    Fetal hemoglobin is a major genetic modifier of the phenotypic heterogeneity in patients with sickle cell disease and certain β-thalassemias. Normal levels of fetal hemoglobin postnatally are approximately 1% of total hemoglobin. Patients who have hereditary persistence of fetal hemoglobin, characterized by elevated synthesis of γ-globin in adulthood, show reduced disease pathophysiology. Hereditary persistence of fetal hemoglobin is caused by β-globin locus deletions (deletional hereditary persistence of fetal hemoglobin) or γ-globin gene promoter point mutations (non-deletional hereditary persistence of fetal hemoglobin). Current research has focused on elucidating the pathways involved in the maintenance/reactivation of γ-globin in adult life. To better understand these pathways, we generated new β-globin locus yeast artificial chromosome transgenic mice bearing the (A)γ-globin -175 T > C or -195 C > G hereditary persistence of fetal hemoglobin mutations to model naturally occurring hereditary persistence of fetal hemoglobin. Adult -175 and -195 mutant β-YAC mice displayed a hereditary persistence of fetal hemoglobin phenotype, as measured at the mRNA and protein levels. The molecular basis for these phenotypes was examined by chromatin immunoprecipitation of transcription factor/co-factor binding, including YY1, PAX1, TAL1, LMO2, and LDB1. In -175 HPFH versus wild-type samples, the occupancy of LMO2, TAL1 and LDB1 proteins was enriched in HPFH mice (5.8-fold, 5.2-fold and 2.7-fold, respectively), a result that concurs with a recent study in cell lines showing that these proteins form a complex with GATA-1 to mediate long-range interactions between the locus control region and the (A)γ-globin gene. Both hereditary persistence of fetal hemoglobin mutations result in a gain of (A)γ-globin activation, in contrast to other hereditary persistence of fetal hemoglobin mutations that result in a loss of repression. The mice provide additional tools to

  20. Generation of non-deletional hereditary persistence of fetal hemoglobin β-globin locus yeast artificial chromosome transgenic mouse models: −175 Black HPFH and −195 Brazilian HPFH

    Science.gov (United States)

    Braghini, Carolina A; Costa, Flavia C; Fedosyuk, Halyna; Neades, Renee Y; Novikova, Lesya V; Parker, Matthew P; Winefield, Robert D; Peterson, Kenneth R

    2016-01-01

    Fetal hemoglobin is a major genetic modifier of the phenotypic heterogeneity in patients with sickle cell disease and certain β-thalassemias. Normal levels of fetal hemoglobin postnatally are approximately 1% of total hemoglobin. Patients who have hereditary persistence of fetal hemoglobin, characterized by elevated synthesis of γ-globin in adulthood, show reduced disease pathophysiology. Hereditary persistence of fetal hemoglobin is caused by β-globin locus deletions (deletional hereditary persistence of fetal hemoglobin) or γ-globin gene promoter point mutations (non-deletional hereditary persistence of fetal hemoglobin). Current research has focused on elucidating the pathways involved in the maintenance/reactivation of γ-globin in adult life. To better understand these pathways, we generated new β-globin locus yeast artificial chromosome transgenic mice bearing the Aγ-globin −175 T >C or −195 C >G hereditary persistence of fetal hemoglobin mutations to model naturally occurring hereditary persistence of fetal hemoglobin. Adult −175 and −195 mutant β-YAC mice displayed a hereditary persistence of fetal hemoglobin phenotype, as measured at the mRNA and protein levels. The molecular basis for these phenotypes was examined by chromatin immunoprecipitation of transcription factor/co-factor binding, including YY1, PAX1, TAL1, LMO2, and LDB1. In −175 HPFH versus wild-type samples, the occupancy of LMO2, TAL1 and LDB1 proteins was enriched in HPFH mice (5.8-fold, 5.2-fold and 2.7-fold, respectively), a result that concurs with a recent study in cell lines showing that these proteins form a complex with GATA-1 to mediate long-range interactions between the locus control region and the Aγ-globin gene. Both hereditary persistence of fetal hemoglobin mutations result in a gain of Aγ-globin activation, in contrast to other hereditary persistence of fetal hemoglobin mutations that result in a loss of repression. The mice provide additional tools to study

  1. 大白菜细菌人工染色体文库的构建及鉴定%Construction and Characterization of a Bacterial Artificial Chromosome Library from Chinese Cabbage

    Institute of Scientific and Technical Information of China (English)

    冯大领; 石学萍; 杨煜; 王彦华; 轩淑欣; 赵建军; 申书兴

    2011-01-01

    以我国优良的大白菜自交系'85-1'为材料,利用 pIndigoBAC-5 为载体,通过对高分子量DNA 的制备、大片段 DNA 的选择、连接转化条件等几个方面的优化,构建了大白菜细菌人工染色体文库.该文库由 57 600个克隆组成,平均大小为98.4 kb,空载率为1.5%;覆盖大白菜基因组 10.3 倍;挑取 6 个克隆培养5 d 后,经HindⅢ完全酶切检测,其指纹图谱稳定一致.大白菜细菌人工染色体文库的构建为重要功能基因的克隆和定位及比较基因组研究奠定了基础.%A bacterial artificial chromosome library of Brassica campestris L. ssp. pekinensis ( Lour.)Olsson (Chinese cabbage) was constructed from inbred line‘ 85-1’ with the vector pIndigoBAC-5. The key processes of the construction, such as preparation of high molecular weight DNA, selection of digested fragments, condition of ligation and transformation, were studied. The library consists of 57 600 clones in which the average insert size is about 98.4 kb and the empty clones are about 1.5%. The library represents an equivalent of 10.3 fold size of Chinese cabbage genome. Six clones randomly picked from this library show no HindⅢ fingerprint changes after 5 days' successive culture, which indicates that the clones in the library are stable. The library will lay the foundation for gene clone, location and comparative genomics research of Brassica.

  2. Artificial Limbs

    Science.gov (United States)

    ... you are missing an arm or leg, an artificial limb can sometimes replace it. The device, which ... activities such as walking, eating, or dressing. Some artificial limbs let you function nearly as well as ...

  3. Dicty_cDB: Contig-U13495-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available phatase BSL2... 39 0.22 AJ437480_3( AJ437480 |pid:none) Paramecium tetraurelia partial npe... 39 0.22 AL929106_7( AL929106 |pid:none...ifera contig VV78X148195.... 34 4.2 AK175424_1( AK175424 |pid:none) Arabidopsis thaliana mRNA, partia...) Oryza sativa (japonica cultivar-... 34 4.2 AY513272_1( AY513272 |pid:none) Mus musculus endothelia...TCATTAAAAAGAAAATTATAAAAT Gap no gap Contig length 737 Chromosome number (1..6, M) 5 Chromosome length 5062330 Start poin...kkislylcn*ynvncswwpn*itiinnfn*ry*nd*s*tiih* kenyk Frame B: iiiiiteevtviaivifvsi*vmifiywimnpy

  4. Dicty_cDB: Contig-U04548-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ri GII3-3X chromosome, contig Cont... 32 2.0 9 ( CP000882 ) Hemiselmis andersenii chromosome 2, complete seq... 0.13 14 ( AM460039 ) Vitis vinifera contig VV78X040253.6, whole genome... 38 0.16 2 ( AL596026 ) Zebrafish DNA seq...rovar 3 str. ATCC 700970, com... 38 0.33 14 ( BX324186 ) Zebrafish DNA seq...whole genom... 48 0.39 3 ( AC232517 ) Brassica rapa subsp. pekinensis clone KBrB070K15,... 40 0.40 4 ( CR382285 ) Human DNA seq...uence *** SEQUENCING IN PROGRESS *** f... 38 0.97 5 ( U49940 ) Caenorhabditis elegans cosmid T24D11, complete seq

  5. Dicty_cDB: Contig-U13693-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available length 126 Chromosome number (1..6, M) - Chromosome length - Start point - End point - Strand (PLUS/MINUS) -...ig-U13693-1Q) /CSM_Contig/Contig-U13693-1Q.Seq.d Length = 126 Score = 42.1 bits (21), Expect = 1e-04 Identities = 21/21 (100%) Strand...50-1Q.Seq.d Length = 143 Score = 42.1 bits (21), Expect = 1e-04 Identities = 21/21 (100%) Strand = Plus / Mi...bits (13), Expect = 7.8 Identities = 13/13 (100%) Strand = Plus / Plus Query: 1 t...tttttttttttt 13 ||||||||||||| Sbjct: 57 ttttttttttttt 69 Score = 26.3 bits (13), Expect = 7.8 Identities = 13/13 (100%) Strand

  6. Dicty_cDB: Contig-U01610-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available h 121 Chromosome number (1..6, M) - Chromosome length - Start point - End point - Strand (PLUS/MINUS) - Numb...Q) /CSM_Contig/Contig-U01610-1Q.Seq.d Length = 121 Score = 81.8 bits (41), Expect = 2e-16 Identities = 41/41 (100%) Strand....1 bits (20), Expect = 7e-04 Identities = 20/20 (100%) Strand = Plus / Minus Query: 12 atttaaatttaaatttaaat ...31 |||||||||||||||||||| Sbjct: 31 atttaaatttaaatttaaat 12 Score = 36.2 bits (18), Expect = 0.011 Identities = 18/18 (100%) Strand...d Length = 687 Score = 50.1 bits (25), Expect = 7e-07 Identities = 31/33 (93%) Strand = Plus / Minus Query:

  7. Dicty_cDB: Contig-U15144-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available :none) Streptomyces purpurascens rhodomycin ... 54 2e-06 AM269991_16( AM269991 |pid:none) Aspergillus niger contig...000285_1812( CP000285 |pid:none) Chromohalobacter salexigens DSM... 86 7e-16 CP001615_229( CP001615 |pid:none) Exiguobacter... 1e-15 AE017355_3732( AE017355 |pid:none) Bacillus thuringiensis serovar ... 85 1e-15 CP000903_3758( CP000903 |pid:none) Bacillus wei...r CPRD12 prot... 54 2e-06 BT076081_1( BT076081 |pid:none) Caligus rogercresseyi clone crog-e... 54 2e-06 AK1...AAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAA Gap no gap Contig length 558 Chromosome number (1..6, M) 6 Chromosome length 3595308 Start

  8. Dicty_cDB: Contig-U08900-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ction 5... 36 0.18 13 ( DQ927304 ) Tetrahymena paravorax strain RP mitochondrion, co... 34 0.20 7 ( AC128626 ) Rattus norve... 38 0.50 2 ( AB301598 ) Cerataphis freycinetiae mitochondrial genes for s... 46 0.53 2 >( BJ360035 ) Dictyos...-1Q) /CSM_Contig/Contig-U08900-1Q.Seq.d (1362 letters) Database: nrp_A 3,204,285 sequences; 1,040,966,779 total letters Searchi... NRRL... 275 4e-72 FN392319_1526( FN392319 |pid:none) Pichia pastoris GS115 chromosom... 274 6e-72 AP008217_...... 268 4e-70 BX538353_6( BX538353 |pid:none) Cryptosporidium parvum chromosome ... 267 6e-70 CP000500_675( CP000500 |pid:none) Pichi

  9. Synthetic chromosomes.

    Science.gov (United States)

    Schindler, Daniel; Waldminghaus, Torsten

    2015-11-01

    What a living organism looks like and how it works and what are its components-all this is encoded on DNA, the genetic blueprint. Consequently, the way to change an organism is to change its genetic information. Since the first pieces of recombinant DNA have been used to transform cells in the 1970s, this approach has been enormously extended. Bigger and bigger parts of the genetic information have been exchanged or added over the years. Now we are at a point where the construction of entire chromosomes becomes a reachable goal and first examples appear. This development leads to fundamental new questions, for example, about what is possible and desirable to build or what construction rules one needs to follow when building synthetic chromosomes. Here we review the recent progress in the field, discuss current challenges and speculate on the appearance of future synthetic chromosomes. PMID:26111960

  10. Dicty_cDB: Contig-U13520-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Contig-U13520-1 no gap 782 6 147501 146719 MINUS 5 5 U13520 0 4 1 0 0 0 0 0 0 0 0 0 0 0 Show Con ... ome number (1..6, M) 6 Chromosome length 3595308 Start ... point 147501 End point 146719 Strand (PLUS/MINUS) ... EL396453 ) CFFM7728.b1_O11.ab1 CFF(LMS) safflower Cart hamus ... 34 1.6 3 ( AC114463 ) Rattus norvegicus c ...

  11. LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes

    Directory of Open Access Journals (Sweden)

    Feuillet Catherine

    2010-11-01

    Full Text Available Abstract Background Physical maps are the substrate of genome sequencing and map-based cloning and their construction relies on the accurate assembly of BAC clones into large contigs that are then anchored to genetic maps with molecular markers. High Information Content Fingerprinting has become the method of choice for large and repetitive genomes such as those of maize, barley, and wheat. However, the high level of repeated DNA present in these genomes requires the application of very stringent criteria to ensure a reliable assembly with the FingerPrinted Contig (FPC software, which often results in short contig lengths (of 3-5 clones before merging as well as an unreliable assembly in some difficult regions. Difficulties can originate from a non-linear topological structure of clone overlaps, low power of clone ordering algorithms, and the absence of tools to identify sources of gaps in Minimal Tiling Paths (MTPs. Results To address these problems, we propose a novel approach that: (i reduces the rate of false connections and Q-clones by using a new cutoff calculation method; (ii obtains reliable clusters robust to the exclusion of single clone or clone overlap; (iii explores the topological contig structure by considering contigs as networks of clones connected by significant overlaps; (iv performs iterative clone clustering combined with ordering and order verification using re-sampling methods; and (v uses global optimization methods for clone ordering and Band Map construction. The elements of this new analytical framework called Linear Topological Contig (LTC were applied on datasets used previously for the construction of the physical map of wheat chromosome 3B with FPC. The performance of LTC vs. FPC was compared also on the simulated BAC libraries based on the known genome sequences for chromosome 1 of rice and chromosome 1 of maize. Conclusions The results show that compared to other methods, LTC enables the construction of highly

  12. Dicty_cDB: Contig-U04232-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available kkkqpthklfify*ihtnkyfikkkkkkklkifliliflilsfs ivlingdyleykrvhlvaqvslsngntiyifrgngp...e) Kluyveromyces thermotolerans str... 38 0.59 ( O94526 ) RecName: Full=Phosphatidylinositol-3,4,5-trisphosp...0 m3b: 0.00 m_ : 1.00 44.0 %: cytoplasmic 36.0 %: nuclear 8.0 %: vacuolar 4.0 %: mitochond...TATTATTTTACAAAAATAAAAAAAAAA AAAAA Gap no gap Contig length 955 Chromosome number (1..6, M) 4 Chromosome length 5430582 Start po...int 1259034 End point 1258079 Strand (PLUS/MINUS) MINUS Number of clon

  13. Dicty_cDB: Contig-U13948-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available nqrkilkiktkkivmtnhyqskwlswiskeskilnlqietkyfywli*krk*in Frame B: illllffylltdhqnvepykhylyyldfviffymfn*lffsk*tfs...*lllskcskkcckn cnvspikfrsqyfiiylprnsyfq*pc*klv**k*kf*ffgklklklifflffklhgfys sllflnddkfnwrkkyar... whole genome shotgu... 40 0.86 2 ( ED280205 ) AUAC-aax35c01.g1 Ascaris suum whole genome shotgu... 40 0.89 ...ATTTTTATTGGCTTATATAAAAAAGGAAATAAATAAA TAA Gap no gap Contig length 1253 Chromosome number (1..6, M) 4 Chromosome length 5430582 Star...Acid sequence (All Frames) Frame A: yiiiiiflfin*sskc*ai*tlfilfgfcyfflhv*laff**idi*litplqmfkkml*e l*cfsh*ipvsvfyhlssqe*lfs

  14. Dicty_cDB: Contig-U09459-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 248969_1( DQ248969 |pid:none) Lates calcarifer deleted in azoosp... 35 2.3 T16825( T16825 )hypothetical prot...AAAAAAAAAAAAAAAAAAAAAAAAAA Gap gap included Contig length 832 Chromosome number (1..6, M) 3 Chromosome length 6358359 Star...4 Translated Amino Acid sequence rfacyiinnnnns*ylkdrlidylhnflffsflkkninfkyinikklfl****hn*kkkk *nkkkk*kkqq**nff...stk*tkfkwl*f********qq****sk*f*ktsks***krsiqitf*yin*iykqq kkkkkkkkk Frame B: *vcllynkq*qq*lifer*idrlftqffiffff...NNFRKPQKVDNKKEASK*pfdt*ikyinnk kkkkkkkkk Frame C: rfacyiinnnnns*ylkdrlidylhnflffs

  15. Dicty_cDB: Contig-U13015-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available SFFRFFFFYYKXNWXXGFXIFFFFFKKXXX Frame B: knytniyiltsylyfflsfvfffsiikxigxxvfxffffflkkxxx Frame C: kiirifiy*hhififfflsffffll*kxlxxgff...ANNNNNNNNN Gap no gap Contig length 140 Chromosome number (1..6, M) 2 Chromosome length 8467578 Start point ...ective length of query: 125 effective length of database: 5,571,296 effective sear...-2. 42 4.6 1 ( EY162031 ) CBTN8751.b1_N04.ab1:P Triphysaria pusilla root ti... 42 4.6 1 ( AE017194 ) Bacillu...ective length of database: 93,199,600,587 Effective search space: 10997552869266 Effective search sp

  16. Dicty_cDB: Contig-U13712-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ence (All Frames) Frame A: td*KYHCKLSISKPNLFLVQKIKFFFFFIYFYPQKKKKKKKXPXKK Frame B: likniivnyqfpsqiyf*fkk*nfffslfif...ilkkkkkkkkxpxkk Frame C: *lkisl*iinfqakfifssknkiffflylflsskkkkkkkkxxxkk own...ANAAAAAAAA Gap no gap Contig length 140 Chromosome number (1..6, M) 1 Chromosome length 4919822 Start point ... length of query: 125 effective length of database: 5,571,296 effective search space: 696412000 effective sear...a glycines J2 pAMP1 v8 Chiape... 46 0.29 1 ( BB908206 ) Trifolium pratense cDNA c

  17. Dicty_cDB: Contig-U09307-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available qwlqihwvks--- ---mgdiwf*yvmdnrikipirgrnilgycsrfnsflnlktltkksiki**srnssnfir srsiirf*xsffsplltskslkskskskln*in...k**iil*ll*****llnk*nk*ikyff iffiffflcliikpkkkk Frame B: *ktiklfkrm*nikdisndwlfkeifkisgygyysddfwiytiyw*fcissctill*l*t ar...4 7.1 1 ( EY820106 ) PT11-C1-901-012-E05-CT.F Poncirus trifoliata leaf... 44 7.1 1 ( AC024106 ) Homo sapiens...AAAAAAA Gap gap included Contig length 703 Chromosome number (1..6, M) 1 Chromosome length 4919822 Start poi...GKE--- ---ggylvlvcygqpy*dshswaqyfgvllkvqqls*s*nsykein*nmiikklk*fy*v kinyqilkxfffttfnfkiikikikikt*lnk*iinniiviiiiiiiik*ik*inkiffy ff

  18. Dicty_cDB: Contig-U12809-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available *fffsnlii*liifilgfync letn*re*kt*hsv*yk*ysfn*********f*prr*rqirrtgy*********q**yrr k*ttrfksk********ri....4 1 ( DU275782 ) 1098448035744 CHORI-243 Ovis aries genomic clone ... 44 8.4 1 ( DE241979 ) Trifolium prate...knhqllliiiiiiii*iiiikiivkiiikiiiiklvnq*qr lk*vvldqikvlvfymidkikhgfqqlrin*yqhqvmlmq Frame B: iifyihnflyifffthftfylilfkyfqihffyyyflff...ACATCAGGTGATGTTAATGCAGT Gap no gap Contig length 841 Chromosome number (1..6, M) 4 Chromosome length 5430582 Star... est8= CHK307F ,169,734 Translated Amino Acid sequence *yfiftifyiyfflpilhsi*fylniskstsfiiifyffnfsfqi*lfn*sflfs

  19. Dicty_cDB: Contig-U07966-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available kik*kknk Translated Amino Acid sequence (All Frames) Frame A: vfvknlssqfkfffffffyftlffsiflff*ivlfyikvkennkink*inktk*nnrkn* kik**kkff... g... 46 5.0 1 ( EY819433 ) PT11-C1-901-008-B08-CT.F Poncirus trifoliata leaf... 46 5.0 1 ( AE016830 ) Enter...AATAAAATAAAATAAAATAAAAAAAAAATAAA Gap gap included Contig length 1931 Chromosome number (1..6, M) - Chromosome length - Star... SSF794Z ,1717,1914 Translated Amino Acid sequence lc*klivtiqvfffffflfhslffyffiflnssflykskrkq*nk*inkqnkvk*pqklk nkiikkiff...yns*y*k*k ik*nkikkk* Frame B: sllktyrhnssfffffffislsfflffyffk*fffi*k*kktik*ink*tkqskitakik k*nnkknfffkkfkklkklqq*qif

  20. Dicty_cDB: Contig-U12408-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available wl*llnfgilhlrlsppfttkvtllakqfmklll kqtkkernkknfn*xknsikic Frame B: qiyflknilkriffs...380Z ,319,876 est10= VHE391Z ,323,756 est11= VHE349Z ,373,885 Translated Amino Acid sequence qiyflknilkrif...kqtkkernkknfn*xknsikic Translated Amino Acid sequence (All Frames) Frame A: tnlffkkyikkdiffsncliklflyffi*k*fff... Contig length 890 Chromosome number (1..6, M) 3 Chromosome length 6358359 Start point 4093826 End point 409...enlsleqleeicpkfhkyqrgfgfsfsilgyci*dchrhsqrr*hy*qnnl*sfc* srqrrreirktlirxkiqskfv Frame C: kfif*kiy*kgyff

  1. Dicty_cDB: Contig-U07162-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available siqhfkn*nshikikcqdls vvkfgtqslifinv*ivklmiivqfvltvlrrinmldidid**lvlmavvivvilvrgkr rdvvqcmlnvkvkrkvmilr*snhcqrvqss**siff*pey*rif...inv*ivklmiivqfvltvlrrinmldidid**lvlmavvivvilvrgkr rdvvqcmlnvkvkrkvmilr*snhcqrvqss**siff*pey*rifqsidillqlshf*if...msfqflagmwvrngdpmknqianyfrvkdqnstvdlylmqyvslamepkiffsqfld rcelcsgfi*rsyfyxnki Frame B: kqnktxqs..._GS-28-01-01-1... 46 5.4 1 ( EI944303 ) akm3al56r Km3-3010m-Ionian Sea marine metagenome ... 46 5.4 1 ( ED72...GAGGTCATATTTTTATNAN AACAAAATCA Gap gap included Contig length 2100 Chromosome number (1..6, M) 6 Chromosome length 3595308 Star

  2. Dicty_cDB: Contig-U13654-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available LC Translated Amino Acid sequence (All Frames) Frame A: kiffsntqqtifiivllltgk****k***nvrfywfircr*l**y*rikwk*...... 33 8.7 AF542023_1( AF542023 |pid:none) Griffithsia japonica DnaJ-like pro... 33 8.7 ( P33892 ) RecName: ... no gap Contig length 628 Chromosome number (1..6, M) 3 Chromosome length 6358359 Star...ennsnksnnkmsdfiglsdadnydnieesngneyviddslp liekikkyvkselvlhtiicy*rif*fn*nsi*tsk*ninniyrgssnr**tsd*tsisr tnsin...ective length of database: 5,564,391 effective search space: 3405407292 effective sear

  3. Dicty_cDB: Contig-U03439-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available nubilalis tRNA-Leu gene, partial sequenc... 34 2.5 3 ( AC208278 ) Nomascus leucogenys leucogenys clone...sculus 11 days embryo head c... 39 0.51 D17546_1( D17546 |pid:none) Mus musculus mRNA for collagen, partia.....) Mus musculus Axin mRNA, partial cds. 35 5.7 T28708( T28708 )hypothetical protein T21D12.2 - Caenorhabditi...opus laevis hypothetical protei... 35 5.7 S53787( S53787 )collagen alpha chain - Paralvine...AAAAAAAAATAAGAAAAAAAGAACAATTTAAAAAA Gap no gap Contig length 1249 Chromosome number (1..6, M) 6 Chromosome length 3595308 Start poin

  4. Dicty_cDB: Contig-U03328-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available : PnFL2-103_B24, 5'end. 44 2.4 1 ( AU082707 ) Oryza sativa Japonica Group cDNA, part...) Plasmodium knowlesi strain H chro... 55 8e-07 CR382129_916( CR382129 |pid:none) Yarrowia lipolytica strain...TCTTTTTAAAGCAG CATGAG Gap no gap Contig length 256 Chromosome number (1..6, M) 2 Chromosome length 8467578 Start poin...yqi*nliliihfflkqhe Frame C: nww*limitn*ynsf*tstyiitititiiiaintnncitnfi*i*l*l*wykrfnirdls rffh**...6 0.62 1 ( Z67753 ) Odontella sinensis complete chloroplast genome. 46 0.62 1 ( X55026 ) Podospora anserina complete mitochondria

  5. Dicty_cDB: Contig-U16200-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available pt livqerdsklklmpsllklmlnkkprinkskktrrskpnsknternsanqkrprpknssl sknskqitreprkkllmnnnnvlllktisvntsvkshyskmplisynviti...cluded Contig length 3455 Chromosome number (1..6, M) 4 Chromosome length 5430582 Start point 4454867 End point...' ... 34 1.8 4 ( EX476109 ) EST_lsal_evj_796653 lsalevj mixed_tissue_mixed_st... 46 1.9 2 ( BW284033 ) Ciona intestin...... 99 7e-35 D89990_1( D89990 |pid:none) Cyprinus carpio mRNA for myosin heavy ... 102 7e-35...-9; AltName: Full=Myosin heavy chai... 132 4e-29 D89991_1( D89991 |pid:none) Cyprinus carpio mRNA for myosin

  6. Dicty_cDB: Contig-U14970-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available CP000562_1925( CP000562 |pid:none) Methanoculleus marisnigri JR1, ... 83 3e-14 AL...GACGAAGGTTTCATTTTACCT Gap no gap Contig length 1525 Chromosome number (1..6, M) 1 Chromosome length 4919822 Start...RP43-082A08.TJ. 52 0.063 1 ( X87631 ) P.falciparum putative plastid clpC gene (part...f successful extensions: 9903330 Number of sequences better than 10.0: 200 Length of query: 1525 Length of d...175542 |pid:none) Arabidopsis thaliana mRNA for puta... 383 e-105 AM456869_1( AM456869 |pid:none) Vitis vini

  7. Dicty_cDB: Contig-U06796-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 825_2361( AE016825 |pid:none) Chromobacterium violaceum ATCC ... 33 4.1 CP000529_902( CP000529 |pid:none) Polaromonas naphtha...T Gap no gap Contig length 357 Chromosome number (1..6, M) - Chromosome length - Start...er of extensions: 8353030 Number of successful extensions: 350045 Number of sequences better than 10.0: 18 Length of query: 357 Le...lenivorans CJ... 32 5.3 CP000091_208( CP000091 |pid:none) Ralstonia eutropha... JMP134 chromo... 32 5.3 AM260480_1943( AM260480 |pid:none) Ralstonia eutropha H16 chromoso... 3

  8. Dicty_cDB: Contig-U15917-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available AATAAATAAATAAATAAT Gap gap included Contig length 2208 Chromosome number (1..6, M) - Chromosome length - Start...od and nucleic acids for pharmacogenomic meth... 36 0.97 2 ( AX348470 ) Sequence 165... ) Lycopersicon esculentum 1-aminocyclopropane-1-car... 46 5.7 1 ( AC002411 ) Arabidopsis tha...sions: 13479111 Number of sequences better than 10.0: 603 Length of query: 2218 Length...id:none) Azotobacter vinelandii DJ, comp... 57 4e-06 BX950229_1526( BX950229 |pid:none) Methanococcus mar

  9. Dicty_cDB: Contig-U10340-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available AAAAAAAAAAAAAAAAAAA Gap no gap Contig length 1127 Chromosome number (1..6, M) 1 Chromosome length 4919822 Start... of extensions: 86282206 Number of successful extensions: 7429659 Number of sequences better than 10.0: 150 Length of query: 1127 Le...00609_88( CP000609 |pid:none) Methanococcus maripaludis C5, com... 46 0.003 CP001...AE005176_548( AE005176 |pid:none) Lactococcus lactis subsp. lactis... 40 0.20 CP000450_160( CP000450 |pid:none) Nitrosomonas eut...3073 |pid:none) Kuenenia stuttgartiensis genome ... 38 0.57 DQ498906_1( DQ498906 |pid:none) Staphylococcus x

  10. Dicty_cDB: Contig-U11305-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 4 0.015 CP000583_469( CP000583 |pid:none) Ostreococcus lucimarinus CCE9901... 44 ...240-130J22, WORKING DRAFT SEQU... 46 3.9 1 ( ER915386 ) AH_PBa0037B17.g1 AH_PBa Amaranthus hypochondriacu......from Patent WO0134809. 38 8.8 3 ( AR485378 ) Sequence 3464 from patent US 6703492. 38 8.8 3 ( AF269422 ) Staphylococc...B25), the sdha gene for succinate dehydrogenase complex, subunit A, flavoprotein (Fp), the gene for a novel ...p included Contig length 1496 Chromosome number (1..6, M) - Chromosome length - Start point - End point - St

  11. Dicty_cDB: Contig-U16574-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available luded Contig length 1873 Chromosome number (1..6, M) 1 Chromosome length 4919822 Start point 4567836 End point 4566121 Strand...tig-U16576-1Q.Seq.d Length = 2165 Score = 648 bits (327), Expect = 0.0 Identities = 327/327 (100%) Strand...caactactaaaaagaaaatt 1299 Score = 69.9 bits (35), Expect = 1e-11 Identities = 35/35 (100%) Strand = Plus / P...||||||||| Sbjct: 568 aagagaaacaagataaagaattggctgataagctt 602 Score = 61.9 bits (31), Expect = 3e-09 Identities = 31/31 (100%) Strand...Expect = 5e-08 Identities = 29/29 (100%) Strand = Plus / Plus Query: 504 cgtcaagagaaagaattggctgataaatt 532 |

  12. Dicty_cDB: Contig-U06679-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Contig length 345 Chromosome number (1..6, M) - Chromosome length - Start point - End point - Strand..., Expect = 1e-07 Identities = 42/42 (100%) Strand = Plus / Plus Query: 200 aaatnaaattaaattaaatnccaatttnntttt...aa 241 Score = 36.2 bits (18), Expect = 0.024 Identities = 18/18 (100%) Strand = ...0.37 Identities = 18/19 (94%) Strand = Plus / Plus Query: 200 aaatnaaattaaattaaat 218 |||| |||||||||||||| Sb...jct: 402 aaattaaattaaattaaat 420 Score = 28.2 bits (14), Expect = 5.8 Identities = 14/14 (100%) Strand

  13. Dicty_cDB: Contig-U16021-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available p included Contig length 897 Chromosome number (1..6, M) 2 Chromosome length 8467578 Start point 4464700 End point 4463885 Strand... = e-151 Identities = 268/268 (100%) Strand = Plus / Plus Query: 252 tgacagaaacatctactgctaaagttgccacaacaaaga...actgcttcagcttcttcatctgg 519 Score = 131 bits (66), Expect = 2e-30 Identities = 88/96 (91%) Strand = Plus / P...| Sbjct: 633 aaaatcattacagtttccattaattgtacatacatt 668 Score = 115 bits (58), Expect = 1e-25 Identities = 98/118 (83%) Strand...cattatcaataactcaaccaacc 233 Score = 67.9 bits (34), Expect = 3e-11 Identities = 34/34 (100%) Strand

  14. Dicty_cDB: Contig-U13720-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available AAAAGAAN NNNNNNNN Gap no gap Contig length 558 Chromosome number (1..6, M) - Chromosome length - Start point - End point - Strand...), Expect = 8e-25 Identities = 56/56 (100%) Strand = Plus / Plus Query: 244 ttggatgatcaagaatggaagagaaaggaaca...= 2e-19 Identities = 47/47 (100%) Strand = Plus / Plus Query: 158 agagagaacttgaaattcgtaaacaacaacaattggaacacc...aaattcgtaaacaacaacaattggaacaccaattg 204 Score = 87.7 bits (44), Expect = 1e-17 Identities = 44/44 (100%) Strand... bits (21), Expect = 6e-04 Identities = 21/21 (100%) Strand = Plus / Plus Query: 76 gttcaacaattattattaaaa 96

  15. Dicty_cDB: Contig-U09802-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ATTTTTT Gap gap included Contig length 427 Chromosome number (1..6, M) - Chromosome length - Start point - End point - Strand...9802-1Q.Seq.d Length = 437 Score = 46.1 bits (23), Expect = 3e-05 Identities = 23/23 (100%) Strand...tgtgtgttgaaacaaccc 40 Score = 42.1 bits (21), Expect = 5e-04 Identities = 24/24 (100%) Strand = Plus / Plus ...re = 40.1 bits (20), Expect = 0.002 Identities = 20/20 (100%) Strand = Plus / Plu...ts (19), Expect = 0.008 Identities = 22/22 (100%) Strand = Plus / Plus Query: 214 cccccnttttaaaaaaaaaaaa 235

  16. Dicty_cDB: Contig-U01743-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available AAAAA AAAAAAAAAAAAA Gap no gap Contig length 163 Chromosome number (1..6, M) - Chromosome length - Start point - End point - Strand...Identities = 28/28 (100%) Strand = Plus / Plus Query: 1 ttttaatatatatatatatatttaaccc 28 ||||||||||||||||||||...|||||||| Sbjct: 1 ttttaatatatatatatatatttaaccc 28 Score = 36.2 bits (18), Expect = 0.015 Identities = 18/18 (100%) Strand... 1102 Score = 52.0 bits (26), Expect = 2e-07 Identities = 26/26 (100%) Strand = Plus / Plus Query: 1 ttttaat...s (18), Expect = 0.015 Identities = 18/18 (100%) Strand = Plus / Minus Query: 5 a

  17. Dicty_cDB: Contig-U11362-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available se: CSM 6905 sequences; 5,674,871 total letters Score E Sequences producing significant alignments: (bits) Val...AAA Gap gap included Contig length 1201 Chromosome number (1..6, M) 3 Chromosome length 6358359 Start point ...se: ddbj_A 92,845,959 sequences; 95,242,211,685 total letters Searching................enome. 38 2.8 15 ( EJ363084 ) 1092963694809 Global-Ocean-Sampling_GS-28-01-01-1... 44 3.0 2 ( AE014820 ) Plasmodium falcipar...se: nrp_A 3,204,285 sequences; 1,040,966,779 total letters Searching.........................

  18. Dicty_cDB: Contig-U12765-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available of sequences better than 10.0: 409 length of query: 1256 length of database: 5,674,871 effective HSP length: 16 effe...ctive length of query: 1240 effective length of database: 5,564,391 effective search space: 6899844840 effe...11795 ) oeh48g11.g1 B.oleracea002 Brassica oleracea genom... 44 0.060 2 ( CP000102 ) Methanosphaera stadtman... ) Dictyostelium discoideum chromosome 2 map 126059-... 32 0.70 7 ( AM427875 ) Vitis vinifera contig VV78X10...ocaldococcus jannaschii DSM 2661, complete ge... 48 0.81 1 ( AC116551 ) Dictyostelium discoideum chromosome 2 ma

  19. Dicty_cDB: Contig-U15388-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ......................................done Score E Sequences producing significant alignments: (bits) Val...,559 sequences; 1,051,180,864 total letters Searching..................................................don...-07 CU633899_32( CU633899 |pid:none) Podospora anserina genomic DNA ch... 59 4e-07 CU928176_52( CU928176 |pid:none) Zygosaccharo...e) Wolbachia endosymbiont strain TR... 47 0.003 (Q9PE61) RecName: Full=50S ribosomal prot...GAAAAGA GAGAAAAAT Gap no gap Contig length 1709 Chromosome number (1..6, M) M Chromosome length 55569 Start point 43948 End point

  20. Dicty_cDB: Contig-U15763-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available **isvglrdhs cfgpntfplqrvygtfckygqrd*sgqsswskgtiaigrv*yssnhidgfedsl*ldlks tstigleif*tkq*snhfsnl*l*tcr*iqlyqrgenrfgsi...245848 ) pSB1423.2 S. bicolor BTx623 PstI-digested total g... 38 4.8 2 ( EH631649 ) EST2756 LK04 Laupala kohalensi...nveeaaavrsdkpalknffknaqiikdinnqifsilntycpppppsnmilsppate qaeqfivtttveeqsiqqqqqqqqqqqlqqstsnsgs...AAAAAAAAA AAAAAAAAAAAAAA Gap gap included Contig length 4054 Chromosome number (1..6, M) 5 Chromosome length 5062330 Start point...vpfnl*svghslsrftsrgtsniqrig*qfgiyesf gssyhsnr*l*lcqsctfpwyhsrdlerfrtih*gsnpsitivlsitkvgstlge*trgc qiftitq*ygckrmacr*ilssi

  1. Dicty_cDB: Contig-U02303-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 4 ( AC005139 ) Plasmodium falciparum chromosome 12, *** SEQUENCI... 36 0.012 11 ( DC218207 ) Plasmodium berg...5 1 ( EY366382 ) CAXA10700.fwd CAXA Helobdella robusta Subtracted ... 46 1.5 1 ( BX005275 ) Zebrafish DNA sequence fro...AATAAAAAAGATTTATATGTAGAA GCAATTGATTTAAGAAAAGATATACCATCAGAAGCATTTAATGCAAA Gap no gap Contig length 597 Chromosome number...CT511567 ) A BAC library has been constructed from cultivar ... 54 0.006 1 ( CT489372 ) A BAC library has been constructed fro...DH533769 ) Rattus norvegicus DNA, BAC clone: RNB1-035J21, 3'... 48 0.39 1 ( CR264572 ) Forward strand read from inser

  2. Dicty_cDB: Contig-U10979-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 97348 ) Plasmodium falciparum MAL3P1. 38 0.67 5 ( AM440723 ) Vitis vinifera contig...... 123 1e-26 AM270010_44( AM270010 |pid:none) Aspergillus niger contig An02c015... 123 1e-26 AM...-U10979-1 Contig ID Contig-U10979-1 Contig update 2002.12.18 Contig sequence >Contig-U10979-1 (Contig...ces producing significant alignments: (bits) Value Contig-U10979-1 (Contig...-U10979-1 (Contig-U10979-1Q) /CSM_Contig/Contig-U10979-1Q.Seq.d Len

  3. Dicty_cDB: Contig-U15132-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 46 2e-04 2 ( DN557308 ) Ls_af1_14e12_T7 Litomosoides sigmodontis adult fe... 58 7e-04 1 ( BM517910 ) ki84c0...Gap no gap Contig length 1107 Chromosome number (1..6, M) 1 Chromosome length 4919822 Start point 3202229 En...02 ) MDEST614 Hessian fly salivary gland cDNA Library ... 50 0.001 2 ( BX538350 ) Cryptosporidium parvum chromos...dium falciparum 3D7 chromosome 2 section 14... 42 0.025 3 ( CN761259 ) ID0AAA2DD04RM1 ApMS Acyrthos...2511 ) 256563403 Pea aphid whole body normalized full le... 48 0.047 2 ( AC016830 ) Homo sapiens chromosome

  4. Dicty_cDB: Contig-U14754-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ic DNA, chromosome 4, clone:... 44 5.4 1 ( AY445658 ) Antheraea pernyi diapause hormone-phermone bio...0.48 2 ( ES586711 ) Hm_pwAE2_31G04_M13rev Amplicon Express mixed pupa... 44 0.48 2 ( CX700726 ) Hm_L6w_05D11_T7seq Heliconius melpome...bacterium animalis subsp. lactis AD011, complete genome. Length = 511 Score = 45.8 bits (107), Expect = 8e-0...CCCATCTCCGATGTTTTATTAAT ATACTTAATTGTTAANGAAA Gap no gap Contig length 570 Chromosome number (1..6, M) 5 Chromosome... clone CH73-162A18 in ... 46 0.010 4 ( AC161223 ) Mus musculus chromosome 3, clone RP24-173A7, com

  5. Dicty_cDB: Contig-U05424-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 6040 ) AGN_PNL224af1_c3.trimmed.seq AGN_PNL Nicotiana ta... 38 0.18 2 ( DE187625 ) Bombyx mori genomic DNA, ...6 0.76 1 ( ES409972 ) HTAB-aaa11h06.b2 Heterorhabditis_bacteriophora_HT... 46 0.76 1 ( AC116982 ) Dictyostelium discoideum chromosome...001133_964( CP001133 |pid:none) Vibrio fischeri MJ11 chromosome ... 82 8e-15 AE016825_3230( AE016825 |pid:none) Chromobacterium vio...626_863( CP000626 |pid:none) Vibrio cholerae O395 chromosome ... 72 6e-12 CP000626_873( CP000626 |pid:none) Vibrio...TAATATTAATAATA AAAAGGATTAATCATTAATTTTTAATAATAATAATAATAAATAATATTAA Gap no gap Contig length 300 Chromosome number (1..6, M) 1 Chrom

  6. Dicty_cDB: Contig-U15970-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available s BAC clone RP11-466J24 from 4, comple... 36 7.2 5 ( AC136471 ) Solanum demissum chromosome 11 clone PGEC561, co...1097_1557( CP001097 |pid:none) Chlorobium limicola DSM 245, co... 35 2.6 AL035477...ntig VV78X060648.8, whole genome... 44 1.2 2 ( AC116984 ) Dictyostelium discoideum chromosome 2 ma... chromosome 6 clone XX-283K... 42 1.7 4 ( AC115581 ) Dictyostelium discoideum chromosome 2 map complem..., ... 38 2.6 2 ( AM441840 ) Vitis vinifera contig VV78X086203.8, whole genome... 44 2.6 2 ( AC116982 ) Dictyostelium discoide

  7. Dicty_cDB: Contig-U04414-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 75... 36 0.70 10 ( EK422054 ) 1095515517229 Global-Ocean-Sampling_GS-31-01-01-1... 34 0.74 4 ( AC138192 ) Mus musculus chromosome...242783 ) 1095333011098 Global-Ocean-Sampling_GS-27-01-01-1... 38 5.4 2 ( AC233380 ) Solanum tuberosum chromosome...285_1( BT077285 |pid:none) Caligus rogercresseyi clone crog-e... 70 1e-10 (A8XAD0) RecName: Full=GTP-binding protein Rheb homol...01-01-1... 30 6.4 4 ( EK434804 ) 1095521024236 Global-Ocean-Sampling_GS-31-01-01-1... 36 6.5 2 ( AC198230 ) Zea mays chromosome...ifera contig VV78X177359.2, whole genome... 38 0.21 3 ( AC116960 ) Dictyostelium discoideum chromosome 2 map com

  8. Dicty_cDB: Contig-U01717-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 6_15( CT005266 |pid:none) Leishmania major strain Friedlin,... 62 4e-08 (Q5R8G5) RecName: Full=Major facilitator superfamily dom...: Full=Major facilitator superfamily domain-cont... 62 2e-08 BC030542_1( BC030542 |pid:none) Hom...AAAAAAAAAAA Gap gap included Contig length 919 Chromosome number (1..6, M) 4 Chromosome length 5430582 Start...o sapiens chromosome 10 clone RP11-420L7, comp... 52 0.03... 15, clone RP24-343E7, com... 50 0.15 1 ( AC163011 ) Mus musculus chromosome 15 clone RP24-375G8 map

  9. Dicty_cDB: Contig-U14277-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available e uptake protein glcU; &AL009126_3... 36 2.5 CP001634_15( CP001634 |pid:none) Kosmotog... R3-3112M23, W... 44 0.033 7 ( AC004688 ) Plasmodium falciparum chromosome 12 clone 3D7, **... 32 0.037 10 ( AC115598 ) Dictyos...e SMART pGEM Me... 38 0.62 2 ( AL929355 ) Plasmodium falciparum strain 3D7, chromosome 9; s... 36 0.64 9 ( C...mpling_GS-28-01-01-1... 38 0.22 2 ( DE147205 ) Bombyx mori genomic DNA, Fosmid cl...TAAAATAAAACT Gap no gap Contig length 1224 Chromosome number (1..6, M) 3 Chromosome length 6358359 Start poi

  10. Towards sequencing the 1 Gb wheat chromosome 3B

    OpenAIRE

    Choulet, Frédéric; Paux, Etienne; Leroy, Philippe; Sourdille, Pierre; Schlub, Stéphane; Brunel, Dominique; Barbe, Valérie; Wincker, Patrick; Feuillet, Catherine

    2009-01-01

    * BACKGROUND: Wheat is the most widely grown crop worldwide but so far, the access to its genome sequence has been hampered by its size (17 Gb) and highly repetitive structure. We plan to sequence and annotate the largest bread wheat chromosome, 3B (1 Gb i.e. 2.5x the rice genome) using a hybrid approach combining Roche454 Titanium sequencing of BACs and Whole Chromosome Shotgun (WCS) with Illumina/Solexa GAII PE reads. In a pilot project, we sequenced and annotated 13 large contigs (18 Mb) ...

  11. Chromosome Microarray.

    Science.gov (United States)

    Anderson, Sharon

    2016-01-01

    Over the last half century, knowledge about genetics, genetic testing, and its complexity has flourished. Completion of the Human Genome Project provided a foundation upon which the accuracy of genetics, genomics, and integration of bioinformatics knowledge and testing has grown exponentially. What is lagging, however, are efforts to reach and engage nurses about this rapidly changing field. The purpose of this article is to familiarize nurses with several frequently ordered genetic tests including chromosomes and fluorescence in situ hybridization followed by a comprehensive review of chromosome microarray. It shares the complexity of microarray including how testing is performed and results analyzed. A case report demonstrates how this technology is applied in clinical practice and reveals benefits and limitations of this scientific and bioinformatics genetic technology. Clinical implications for maternal-child nurses across practice levels are discussed. PMID:27276104

  12. Association Between Pachytene Chromosomes and Linkage Groups in Carrot

    Science.gov (United States)

    The genome of carrot (Daucus carota L.) consists of ~ 480 Mb/1C organized in 9 chromosome pairs. The importance of carrots in human nutrition is triggering the development of genomic resources, including carrot linkage maps, a bacterial artificial chromosome (BAC) clone library and BAC end sequence...

  13. Artificial blood

    Directory of Open Access Journals (Sweden)

    Sarkar Suman

    2008-01-01

    Full Text Available Artificial blood is a product made to act as a substitute for red blood cells. While true blood serves many different functions, artificial blood is designed for the sole purpose of transporting oxygen and carbon dioxide throughout the body. Depending on the type of artificial blood, it can be produced in different ways using synthetic production, chemical isolation, or recombinant biochemical technology. Development of the first blood substitutes dates back to the early 1600s, and the search for the ideal blood substitute continues. Various manufacturers have products in clinical trials; however, no truly safe and effective artificial blood product is currently marketed. It is anticipated that when an artificial blood product is available, it will have annual sales of over $7.6 billion in the United States alone.

  14. Safe and complete contig assembly via omnitigs

    OpenAIRE

    Alexandru I. Tomescu; Medvedev, Paul

    2016-01-01

    Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs -- a set of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question was never solved: given a genome graph $G$ (e.g. a de Bruijn, or a string graph), what are all the strings that can be saf...

  15. A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B

    OpenAIRE

    Kobayashi, F; Wu, J. Z.; Kanamori, H; Tanaka, T.; Katagiri, S.; Karasawa, W.; Kaneko, S.; Watanabe, S; Sakaguchi, T; Šafář, J. (Jan); Šimková, H. (Hana); Mukai, Y.; M. Hamada; Saito, M; Hayakawa, K

    2015-01-01

    Background: A complete genome sequence is an essential tool for the genetic improvement of wheat. Because the wheat genome is large, highly repetitive and complex due to its allohexaploid nature, the International Wheat Genome Sequencing Consortium (IWGSC) chose a strategy that involves constructing bacterial artificial chromosome (BAC)-based physical maps of individual chromosomes and performing BAC-by-BAC sequencing. Here, we report the construction of a physical map of chromosome 6B with t...

  16. Artificial intelligence

    CERN Document Server

    Ennals, J R

    1987-01-01

    Artificial Intelligence: State of the Art Report is a two-part report consisting of the invited papers and the analysis. The editor first gives an introduction to the invited papers before presenting each paper and the analysis, and then concludes with the list of references related to the study. The invited papers explore the various aspects of artificial intelligence. The analysis part assesses the major advances in artificial intelligence and provides a balanced analysis of the state of the art in this field. The Bibliography compiles the most important published material on the subject of

  17. Artificial urushi.

    Science.gov (United States)

    Kobayashi, S; Uyama, H; Ikeda, R

    2001-11-19

    A new concept for the design and laccase-catalyzed preparation of "artificial urushi" from new urushiol analogues is described. The curing proceeded under mild reaction conditions to produce the very hard cross-linked film (artificial urushi) with a high gloss surface. A new cross-linkable polyphenol was synthesized by oxidative polymerization of cardanol, a phenol derivative from cashew-nut-shell liquid, by enzyme-related catalysts. The polyphenol was readily cured to produce the film (also artificial urushi) showing excellent dynamic viscoelasticity. PMID:11763444

  18. Artificial Reefs

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — An artificial reef is a human-made underwater structure, typically built to promote marine life in areas with a generally featureless bottom, control erosion, block...

  19. A YAC contig spanning the ataxia-telangiectasia locus (groups A and C) at 11q22-q23

    Energy Technology Data Exchange (ETDEWEB)

    Rotman, G.; Savitsky, K.; Ziv, Y. [Tel Aviv Univ. Ramat Aviv (Israel)] [and others

    1994-11-15

    Ataxia-telangiectasia (A-T) is an autosomal recessive disease involving cerebellar degeneration, immunodeficiency, cancer predisposition, chromosomal instability and radiosensitivity. A-T is heterogeneous, and the majority of A-T cases are associated with two complementation groups, A and C. The ATA and ATC loci are closely linked at chromosome 11q22-q23. Recombination mapping and linkage disequilibrium analysis have confined both loci between the markers D11S1817 and D11S927. Construction of this contig was expedited by prior generation of a region-specific ICRF sublibrary using Alu-PCR products derived from a radiation hybrid. The contig was expanded further by screening the libraries with Alu-PCR products derived from YAC clones and with STSs from YAC ends. YAC clones were aligned by fingerprinting with moderately repetitive probes. 56 refs., 5 figs., 1 tab.

  20. Dicty_cDB: Contig-U14091-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available map 3,... 44 9.9 1 ( AL844506 ) Plasmodium falciparum chromosome 7. 44 9.9 1 ( AC218886 ) Procavia capensis...chromosome 2 map 4101105... 36 9.2 6 ( BV439306 ) S237P6509RE1.T0 PortugueseWaterDog Canis familiar...AP008218 ) Oryza sativa (japonica cultivar-group) genomic DN... 44 9.9 1 ( AM453516 ) Vitis vinifera contig ...c_trunk Homo s... 44 0.76 2 ( AF028707 ) Phaseolus vulgaris ribulose 1,5-bisphosphate car...aenorhabditis elegans cDN... 46 2.5 1 ( CP000806 ) Cyanothece sp. ATCC 51142 circular chromosome, co... 46 2

  1. Dicty_cDB: Contig-U11755-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 1 ( AC130097 ) Rattus norvegicus clone CH230-177D14, *** SEQUENC... 48 0.89 1 ( AC225375 ) Nomascus leucogenys chromosome UNK clone...e... 38 1.0 5 ( AM285321 ) Spiroplasma citri GII3-3X chromosome, contig Cont... 36 1.0 5 ( AC189417 ) Brassica rapa subsp. pekinen...ces; 95,242,211,685 total letters Searching..................................................done Score E Sequences producin...L77117 ) Methanocaldococcus jannaschii DSM 2661, complete ge... 36 0.30 23 ( CP000939 ) Clostridium botulinu...dorffii mix... 34 0.64 2 ( AC116977 ) Dictyostelium discoideum chromosome 2 map 5515173... 38 0.69 11 ( CP000263 ) Buchnera aphi

  2. Dicty_cDB: Contig-U02029-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 39_1935( CP000539 |pid:none) Acidovorax sp. JS42, complete g... 50 2e-04 CP000738_2958( CP000738 |pid:none) Sinorhizobium med...trongyloides ratti whole genome... 60 1e-05 2 ( FC809434 ) Sr_pASP6_01a11_SP6 S. ratti mixed stage pAMP Stro...USDA 1... 37 0.95 CP000739_394( CP000739 |pid:none) Sinorhizobium medicae WSM419 pla... 37 0.95 CP000472_317... TATTTCC Gap gap included Contig length 1097 Chromosome number (1..6, M) 4 Chromosome length 5430582 Start p...belii BAC clone CH276-246K6 from chromosom... 42 9e-04 7 ( ES272476 ) BGBV-aac54c01.b1 Snail_EST_pSMART Biom

  3. Dicty_cDB: Contig-U15543-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available seae H(+)-ATPase (HA5) mRNA, complete cds. 52 0.11 1 ( AL161576 ) Arabidopsis thaliana DNA chromosome... 4, contig fra... 52 0.11 1 ( AL109796 ) Arabidopsis thaliana DNA chromosome 4, B... for Ca2+... 218 1e-54 AL050352_14( AL050352 |pid:none) Arabidopsis thaliana DNA chromoso... 218 1e-54 CP001...... 215 6e-54 AM494954_59( AM494954 |pid:none) Leishmania braziliensis chromosom... 215 6e-54 A9804... ( AL403413 ) T3 end of clone AT0AA008E05 of library AT0AA from... 56 0.007 1 ( AV554289 ) Arabidopsis

  4. Dicty_cDB: Contig-U14382-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available t US 7238100. 46 1.0 1 ( DD441737 ) Avian Transgenesis Using a Chicken Ovalbumin Gene... 46 1.0 1 ( DD420017 ) Gene cons...S SLNIXLKKGIXKKTKXSXESF Translated Amino Acid sequence (All Frames) Frame A: xxxxkicksivfss*i*xkft*inifrrkfi....34 3 ( AL929352 ) Plasmodium falciparum strain 3D7, chromosome 5, s... 34 0.38 9 ( AP009757 ) Lotus japonicus genomic...6249 ) Beta-1,3-galactosyltransferase and DNA encoding t... 46 1.0 1 ( AR613460 ) Sequence 3 from patent US ...ATTTT Gap no gap Contig length 425 Chromosome number (1..6, M) 5 Chromosome length 5062330 Start point 4958608 End point 4958193 Stra

  5. Dicty_cDB: Contig-U12868-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available te s... 48 0.80 1 ( AC009910 ) Drosophila melanogaster, chromosome 2L, region 25... 48 0.80 1 ( AC004721 ) Drosophila melanogas...8_2( AE014298 |pid:none) Drosophila melanogaster chromosome... 40 0.13 CP000675_1739( CP000675 |pid:none) Legio...a contig VV78X133858.3, whole genome... 48 0.80 1 ( AE014134 ) Drosophila melanogaster chromosome 2L, comple... norvegicus clone CH230-82A3, *** SEQUENCIN... 48 0.80 1 ( AC017455 ) Drosophila melanogaster, *** SEQUENCIN...38 ch... 37 1.5 AY121666_1( AY121666 |pid:none) Drosophila melanogaster RE10888 fu... 37 1.5 AF387518_1( AF3

  6. Dicty_cDB: Contig-U12512-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available S *** f... 36 4.0 12 ( AC116986 ) Dictyostelium discoideum chromosome 2 map 2234041... 34 4.1 14 ( AM285311 ) Spirop...m different de... 46 5.1 1 ( EY188489 ) LLAE0117C Spider Loxosceles laeta cDNA library Lo... 46 5.1 1 ( AC116551 ) Dictyost...8 1.7 18 ( AR550016 ) Sequence 5147 from patent US 6747137. 46 1.7 2 ( AM285302 ) Spiroplasma citri GII3-3X chromos..... 36 2.7 2 ( AM285318 ) Spiroplasma citri GII3-3X chromosome, contig Cont... 38 ...d:none) Xenopus tropicalis hypothetical pr... 35 7.7 AL590442_111( AL590442 |pid:none) chromosome II of st

  7. Dicty_cDB: Contig-U11835-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 0.43 CP001634_414( CP001634 |pid:none) Kosmotoga olearia TBF 19.5.1, co... 39 0.56 CP001129_1715( CP001129 |...ome 2 map 3108975... 36 0.10 8 ( AE014843 ) Plasmodium falciparum 3D7 chromosome 11 section 8... 3...f N... 40 0.13 2 ( AE014818 ) Plasmodium falciparum 3D7 chromosome 14 section 3... 36 0.15 12 ( AC116979 ) Dictyos...TATTAAAAAAAAAAATAATAAAAAAAAA Gap gap included Contig length 1638 Chromosome number (1..6, M) - Chromos... 1 ( EB326274 ) CNSN01-F-105027-501 Normalized CNS library (juven... 58 0.001 1 ( AC117070 ) Dictyostelium discoideum chromos

  8. Dicty_cDB: Contig-U02216-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available omal protein L17; &CP001185_121... 46 0.001 CP001634_1825( CP001634 |pid:none) Kosmo... 62 2e-08 AM910992_98( AM910992 |pid:none) Plasmodium knowlesi strain H chro... 62 2e-08 (Q6F1W6) RecName: Full=50S ribos... chr... 44 0.007 AE014187_287( AE014187 |pid:none) Plasmodium falciparum 3D7 chromo... 43 0.012 (Q7UIC4) RecName: Full=50S ribos...TAAGTTTTTTATTTTATTTTATTTTTTTTAAA Gap gap included Contig length 728 Chromosome number (1..6, M) 3 Chromosome... alignments: (bits) Value CP001324_319( CP001324 |pid:none) Micromonas sp. RCC299 chromosome... 100 4e-20 (Q

  9. Dicty_cDB: Contig-U04627-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available a*SFININFAVSAPIGIAIGVGVASSLNVNGPTYLIV QGVFDSVCAGILLYIGFSLMIKDFPEDMEELCRGKKYEYFLRAGLFIGLWVGAAMMAFIG KYL* own update 2004. 6.10 Homolog...bits) X2: 15 (29.7 bits) S1: 12 (24.3 bits) S2: 14 (28.2 bits) dna update 2009. 6.27 Homology vs DNA Query= ....8 bits) S2: 21 (42.1 bits) protein update 2009. 7.30 Homology vs Protein Query= Contig-U04627-1 (Contig-U04...coideum chromosome 2 map 3879572... 555 0.0 2 ( AU036936 ) Dictyostelium discoideum slug cDNA, clo...re E Sequences producing significant alignments: (bits) Value AC117072_46( AC117072 |pid:none) Dictyostelium discoideum chromo

  10. Dicty_cDB: Contig-U05449-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available om chromosom... 46 0.80 1 ( FM995165 ) Candida castellii complete mitochondrial g...-1Q) /CSM_Contig/Contig-U11298-1Q.Seq.d Length = 2244 Score = 42.1 bits (21), Expect = 4e-04 Identities = 24/25 (96%) Strand...g-U10389-1Q.Seq.d Length = 1028 Score = 40.1 bits (20), Expect = 0.001 Identities = 20/20 (100%) Strand = Pl...tataaaatataaaatata 1026 Score = 34.2 bits (17), Expect = 0.085 Identities = 17/17 (100%) Strand = Plus / Plu...is familiaris ST... 44 3.2 1 ( BV225547 ) S233P6430RD7.T0 LabradorRetriever Canis familiari... 4

  11. Dicty_cDB: Contig-U06933-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available tters) Database: ddbj_A 92,845,959 sequences; 95,242,211,685 total letters Searching.....la melanogaster RE27864 full insert cDNA. 46 1.3 1 ( AE013599 ) Drosophila melanogaster chromosome 2R, complete...9 4 ( BG226596 ) kp91c05.y1 TBN95TM-SSFH Strongyloides stercoralis... 34 4.8 2 ( AL772269 ) Mouse DNA sequence fro...3-1Q) /CSM_Contig/Contig-U06933-1Q.Seq.d (545 letters) Database: nrp_A 3,204,285 sequences; 1,040,966,779 total letters Searchi... s... 46 1.3 1 ( AC099030 ) Drosophila melanogaster, chromo

  12. Dicty_cDB: Contig-U01628-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available rus flaviplurus strain XP94-Colombia cytoch... 44 7.3 1 ( EU005474 ) Pedicia albivitta voucher O'Grady 20001...O0055325. 50 0.12 1 ( AR777056 ) Sequence 211 from patent US 6972197. 50 0.12 1 ( AC131128 ) Rattus norvegicus clo...ts) S2: 15 (30.2 bits) dna update 2009. 5. 3 Homology vs DNA Query= Contig-U01628-1 (Contig-U01628-1Q) /CSM_Co.... 44 7.3 1 ( BM627209 ) 17000687496537 A.Gam.ad.cDNA1 Anopheles gambiae c... 44 7.3 1 ( BM581988 ) 17000687275251 A.Gam.ad.cDNA.blo...5( AC006592 |pid:none) Arabidopsis thaliana chromosome 2 ... 52 2e-05 (Q6CLN2) RecName: Full=GPI ethanolamine phosphate tran

  13. Dicty_cDB: Contig-U04917-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ( GC697946 ) Sequence 13191 from patent US 6812339. 44 6.0 1 ( AX050037 ) Sequence 50 from Patent WO0071710... FJ753577_2( FJ753577 |pid:none) Glomerella lindemuthiana isolate L... 51 3e-05 BT043141_1( BT043141 |pid:no...721_1( AF047721 |pid:none) Arabidopsis thaliana ecotype Colum... 47 3e-04 DQ52229...ts) S2: 15 (30.2 bits) dna update 2009. 7. 5 Homology vs DNA Query= Contig-U04917-1 (Contig-U04917-1Q) /CSM_Co...ne) Zea mays full-length cDNA clone ZM... 50 4e-05 AC005623_8( AC005623 |pid:none) Arabidopsis thaliana chromosom

  14. Dicty_cDB: Contig-U06344-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available protei... 40 0.025 CP001140_94( CP001140 |pid:none) Desulfurococcus kamchatkensis 122... 40 0...179_66( CU928179 |pid:none) Zygosaccharomyces rouxii strain C... 37 0.16 BT048285_1( BT048285 |pid:none) Salmo salar clone ssal... 8.9 AC005278_7( AC005278 |pid:none) Arabidopsis thaliana chromosome 1 ... 32 8.9...344-1Q) /CSM_Contig/Contig-U06344-1Q.Seq.d (464 letters) Database: ddbj_A 92,845,959 sequences; 95,242,211,685 total letters Search...15l05_T7 S. ratti mixed stage pAMP Stro... 68 6e-12 2 ( CD524298 ) ku98d03.y1 Str

  15. Dicty_cDB: Contig-U05022-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ces producing significant alignments: (bits) Value CR382136_498( CR382136 |pid:none) Debaryomyces hansenii s...M_Contig/Contig-U05022-1Q.Seq.d (666 letters) Database: nrp_A 3,268,448 sequences; 1,061,185,681 total letters Sear...EU552421_3( EU552421 |pid:none) Starmerella bombicola putative F-b... 40 0.081 BC121621_1( BC121621 |pid:none) Xenopus tropicali... AK303646_1( AK303646 |pid:none) Homo sapiens cDNA FLJ61523 complet... 37 0.53 BC167645_1( BC167645 |pid:none) Xenopus tropicali...1..6, M) 4 Chromosome length 5430582 Start point 587231 End point 587897 Strand (PLUS/MINUS) PLUS Number of

  16. Dicty_cDB: Contig-U13486-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available e) Rattus norvegicus membrane-associa... 37 0.41 (Q8WXI2) RecName: Full=Connector enhancer of kinase suppressor...ig-U12931-1Q) /CSM_Contig/Contig-U12931-1Q.Seq.d Length = 655 Score = 44.1 bits (22), Expect = 2e-04 Identities...s: 16644 Number of successful extensions: 2014 Number of sequences better than 10.0: 257 length of qu... 0.75 2 ( AC114263 ) Dictyostelium discoideum chromosome 2 map 215673-... 32 0.76 8 ( AC160570 ) Pan troglodytes BAC clon...: 92845959 Number of Hits to DB: 839,620,352 Number of extensions: 53805075 Number of successful extension

  17. Dicty_cDB: Contig-U06595-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 50 2e-05 BT076158_1( BT076158 |pid:none) Caligus rogercresseyi clone crog-e... 50 3e-05 AM494957_319( AM494957 |pid:none) Lei...19, WORKING DRAFT SEQU... 36 8.4 6 ( AM437041 ) Vitis vinifera contig VV78X263242.7, whole genome... 38 9.1 2 ( BA000021 ) Wig...( P35418 ) RecName: Full=Paramyosin; AltName: Full=Antigen B; ... 32 9.1 Z46608_1( Z46608 |pid:none) Drosophila melanogaster...mic DNA, chromosome 1, clone:... 44 3.8 1 ( AM460427 ) Vitis vinifera contig VV78X219843.14, whole genom... ....4 3 ( DD148295 ) Method for testing of predisposition to hypertens... 40 4.4 3 (

  18. Dicty_cDB: Contig-U02004-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available iovorax paradoxus S110 chrom... 105 2e-21 AM270101_5( AM270101 |pid:none) Aspergillus niger contig An05c0010...oides vulgatus ATCC 8482,... 92 3e-17 AM269986_34( AM269986 |pid:none) Aspergillus niger contig...ichia coli SMS-3-5, compl... 154 8e-36 AE005674_2894( AE005674 |pid:none) Shigella flexneri 2a str. 301, .... 1e-35 CU928160_2940( CU928160 |pid:none) Escherichia coli IAI1 chromosom... 152 2e-35 CP000036_2857( CP000036 |pid:none) Shige...1( AM286415 |pid:none) Yersinia enterocolitica subsp. ... 150 9e-35 AF041033_1( AF041033 |pid:none) Shigella flexner

  19. Dicty_cDB: Contig-U05309-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 5 ( CU571403 ) Zebrafish DNA sequence from clone DKEY-96J1 in li... 38 2.0 4 ( DC219816 ) Plasmodium berghe....0 2 ( AX345916 ) Sequence 987 from Patent WO0200928. 30 1.1 6 ( EI379169 ) POTCG15TR Solanum tuberosum RHPO...contig VV78X035256.5, whole genome... 36 8.7 3 ( DC224280 ) Plasmodium berghei strain ANKA cDNA clone:MZ0087...AAAAAAAAAAAAAAAA Gap no gap Contig length 649 Chromosome number (1..6, M) 1 Chrom...m Sugano ... 38 0.13 3 ( FP016231 ) Zebrafish DNA sequence from clone CH73-231O20. 36 0.21 4 ( AM426622 ) Vitis vinifer

  20. Dicty_cDB: Contig-U01558-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available *f*iqknntkk*ykk ntkki own update 2004. 6. 7 Homology vs CSM-cDNA Query= Contig-U01558-1 (Contig-U01558-1Q) /....9 bits) X2: 15 (29.7 bits) S1: 12 (24.3 bits) S2: 15 (30.2 bits) dna update 2009. 5. 1 Homolog..._Ba0210I23.r OC__Ba Oryza coarctata genomic cl... 40 0.027 2 ( DE226514 ) Trifolium pratense DNA, clone:RCG1...... 50 0.13 1 ( DH464435 ) Monosiga ovata DNA, fosmid clone: MOF-005B13, gen... 50 0.13 1 ( CR165209 ) Forward strand re...2 ) Nicotiana plumbaginifolia 120 kDa pistil extensin... 46 2.0 1 ( AP010372 ) Lotus japonicus genomic DNA, chromosome 1, clo

  1. Artificial noses.

    Science.gov (United States)

    Stitzel, Shannon E; Aernecke, Matthew J; Walt, David R

    2011-08-15

    The mammalian olfactory system is able to detect many more odorants than the number of receptors it has by utilizing cross-reactive odorant receptors that generate unique response patterns for each odorant. Mimicking the mammalian system, artificial noses combine cross-reactive sensor arrays with pattern recognition algorithms to create robust odor-discrimination systems. The first artificial nose reported in 1982 utilized a tin-oxide sensor array. Since then, however, a wide range of sensor technologies have been developed and commercialized. This review highlights the most commonly employed sensor types in artificial noses: electrical, gravimetric, and optical sensors. The applications of nose systems are also reviewed, covering areas such as food and beverage quality control, chemical warfare agent detection, and medical diagnostics. A brief discussion of future trends for the technology is also provided. PMID:21417721

  2. Artificial intelligence

    International Nuclear Information System (INIS)

    A vivid example of the growing need for frontier physics experiments to make use of frontier technology is in the field of artificial intelligence and related themes. This was reflected in the second international workshop on 'Software Engineering, Artificial Intelligence and Expert Systems in High Energy and Nuclear Physics' which took place from 13-18 January at France Telecom's Agelonde site at La Londe des Maures, Provence. It was the second in a series, the first having been held at Lyon in 1990

  3. Artificial Intelligence

    CERN Document Server

    Warwick, Kevin

    2011-01-01

    if AI is outside your field, or you know something of the subject and would like to know more then Artificial Intelligence: The Basics is a brilliant primer.' - Nick Smith, Engineering and Technology Magazine November 2011 Artificial Intelligence: The Basics is a concise and cutting-edge introduction to the fast moving world of AI. The author Kevin Warwick, a pioneer in the field, examines issues of what it means to be man or machine and looks at advances in robotics which have blurred the boundaries. Topics covered include: how intelligence can be defined whether machines can 'think' sensory

  4. Caracterização citogenética, viabilidade de pólen e hibridação artificial em gérbera Chromosome number, pollen viability and gerbera hybridization

    Directory of Open Access Journals (Sweden)

    Raquel DL Cardoso

    2009-03-01

    Full Text Available Este trabalho foi conduzido com o objetivo de confirmar o número de cromossomos em cultivares de Gerbera hybrida Hort., determinar o número de cromossomos em acessos não comerciais de Gerbera sp., avaliar a viabilidade de pólen e a possibilidade de cruzamentos entre cultivares e acessos não comerciais. Foram coletados ápices de raízes e pólen de seis cultivares e de sete acessos não comerciais. O material coletado foi corado com carmim acético a 45%. A contagem dos cromossomos foi realizada em células metafásicas intactas e a estimativa de viabilidade de pólen realizada por meio da contagem do número de grãos de pólen viáveis e não viáveis. A possibilidade de cruzamento entre as cultivares e entre as cultivares e acessos não comerciais foi avaliada por meio da hibridação entre os genitores femininos, cv. Terra Fame e acesso A8, e masculinos, cvs. Cariba e Azteca. Todos os acessos contiveram cinqüenta cromossomos, indicando que a variação morfológica nos capítulos (simples, semidobrado e dobrado não é devida a mutações cromossômicas numéricas ou a poliploidia. A viabilidade do pólen variou de 87,67% a 99,27%. A formação de sementes foi de 4,46% nos cruzamentos entre cultivares, e de 50% entre o A8 e as cultivares. A compatibilidade genômica entre os acessos, a alta viabilidade do pólen e o sucesso na obtenção de sementes entre acessos comercias e não comerciais, revela a possibilidade de produção de híbridos com novas combinações alélicas e transferência de caracteres desejáveis dos acessos não comerciais para os comerciaisThis work was conducted to confirm the chromosomes number of Gerbera hybrida Hort. cultivars, to determine the chromosomes number in the non commercial accessions of Gerbera sp., and to estimate the pollen viability and the possibility of crossings among different accessions. Root-tip and pollen were collected from six cultivars and seven non commercial accessions. The collected

  5. Mitotic chromosome structure

    International Nuclear Information System (INIS)

    Mounting evidence is compiling linking the physical organizational structure of chromosomes and the nuclear structure to biological function. At the base of the physical organizational structure of both is the concept of loop formation. This implies that physical proximity within chromosomes is provided for otherwise distal genomic regions and thus hierarchically organizing the chromosomes. Together with entropy many experimental observations can be explained with these two concepts. Among the observations that can be explained are the measured physical extent of the chromosomes, their shape, mechanical behavior, the segregation into territories (chromosomal and territories within chromosomes), the results from chromosome conformation capture experiments, as well as linking gene expression to structural organization.

  6. Artificial sweeteners

    DEFF Research Database (Denmark)

    Raben, Anne Birgitte; Richelsen, Bjørn

    2012-01-01

    Artificial sweeteners can be a helpful tool to reduce energy intake and body weight and thereby risk for diabetes and cardiovascular diseases (CVD). Considering the prevailing diabesity (obesity and diabetes) epidemic, this can, therefore, be an important alternative to natural, calorie-containin...

  7. Artificial photosynthesis

    OpenAIRE

    Andrew C. Benniston; Anthony Harriman

    2008-01-01

    We raise here a series of critical issues regarding artificial photosynthesis with the intention of increasing awareness about what needs to be done to bring about a working prototype. Factors under consideration include energy and electron transfers, coupled redox reactions, repair mechanisms, and integrated photosystems.

  8. Fetal chromosome analysis: screening for chromosome disease?

    DEFF Research Database (Denmark)

    Philip, J; Tabor, Ann; Bang, J;

    1983-01-01

    A + B). Pregnant women 35 years of age, women who previously had a chromosomally abnormal child, families with translocation carriers or other heritable chromosomal disease, families where the father was 50 years or more and women in families with a history of Down's syndrome (group A), were...... unbalanced chromosome abnormality in group A (women with elevated risk) is significantly higher than in group B + C (women without elevated risk) (relative risk 2.4). Women with a known familial translocation and women 40 years or more have a relative risk of 5.7 of having an unbalanced chromosome......The aim of the study was to investigate the rationale of the current indications for fetal chromosome analysis. 5372 women had 5423 amniocentesis performed, this group constituting a consecutive sample at the chromosome laboratory, Rigshospitalet, Copenhagen from March 1973 to September 1980 (Group...

  9. Chromatin structure and ionizing-radiation-induced chromosome aberrations

    International Nuclear Information System (INIS)

    The possible influence of chromatic structure or activity on chromosomal radiosensitivity was studied. A cell line was isolated which contained some 105 copies of an amplified plasmid in a single large mosquito artificial chromosome (MAC). This chromosome was hypersensitive to DNase I. Its radiosensitivity was some three fold greater than normal mosquito chromosomes in the same cell. In cultured human cells irradiated during G0, the initial breakage frequency in chromosome 4, 19 and the euchromatic and heterochromatic portions of the Y chromosome were measured over a wide range of doses by inducing Premature Chromosome Condensation (PCC) immediately after irradiation with Cs-137 gamma rays. No evidence was seen that Y heterochromatin or large fragments of it remained unbroken. The only significant deviation from the expected initial breakage frequency per Gy per unit length of chromosome was that observed for the euchromatic portion of the Y chromosome, with breakage nearly twice that expected. The development of aberrations involving X and Y chromosomes at the first mitosis after irradation was also studied. Normal female cells sustained about twice the frequency of aberrations involving X chromosomes for a dose of 7.3 Gy than the corresponding male cells. Fibroblasts from individuals with supernumerary X chromosomes did not show any further increase in X aberrations for this dos. The frequency of aberrations involving the heterochromatic portion of the long arm of the Y chromosome was about what would be expected for a similar length of autosome, but the euchromatic portion of the Y was about 3 times more radiosensitive per unit length. 5-Azacytidine treatment of cultured human female fibroblasts or fibroblasts from a 49,XXXXY individual, reduced the methylation of cytosine residues in DNA, and resulted in an increased chromosomal radiosensitivity in general, but it did not increase the frequency of aberrations involving the X chromosomes

  10. Dicty_cDB: Contig-U12705-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ne) Leishmania infantum chromosome 32. 228 4e-58 EU365390_1( EU365390 |pid:none) Euplotes octocarina...AL161545_37( AL161545 |pid:none) Arabidopsis thaliana DNA chromoso... 236 1e-60 EF144593_1( EF144593 |pid:none) Populus trichoc...ne) Thalassiosira pseudonana CCMP133... 175 2e-42 AM484190_1( AM484190 |pid:none) Vitis vinifera contig VV7... = 2e-14 Identities = 53/60 (88%) Strand = Plus / Plus Query: 955 cataaattaataataatatacnnnnnnnactattaacaaacaatatattattact...ne) Drosophila melanogaster LD29476 fu... 293 8e-78 BT076415_1( BT076415 |pid:none) Ca

  11. Dicty_cDB: Contig-U06590-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available lverleaf sunflower... 34 4.1 2 ( EB265894 ) MCCN20-F-133114-501 Normalized MCC Neurons Aplysi... 32 4.1 2 ( ...920435_310( AM920435 |pid:none) Penicillium chrysogenum Wisconsin 54-1255 complete genome, contig Pc00c20. L...70170 ) 1092960031664 Global-Ocean-Sampling_GS-29-01-01-1... 40 3.7 2 ( AC083977 ) Homo sapiens chromosome 8, clon...ucing significant alignments: (bits) Value AM920435_310( AM920435 |pid:none) Penicillium chrysogenum Wiscons...e) Rattus norvegicus nipsnap homolog ... 66 8e-10 FN318477_1( FN318477 |pid:none) Schistosoma japonicum iso

  12. Dicty_cDB: Contig-U01765-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available tis aeruginosa PCC 7806 g... 33 4.0 AP009256_715( AP009256 |pid:none) Bifidobacterium adolescent...tters Searching..................................................done Score E Sequences producing significant alignments: (bits................................done Score E Sequences producing significant alignments: (bits...tters Score E Sequences producing significant alignments: (bits) Value Contig-U01765-1 (Cont...deum chromosome 2 map 3108975-3191114 strain AX4, complete sequence. Length = 220 Score = 179 bits (454), Expect = 3e-44 Identities

  13. Dicty_cDB: Contig-U07284-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Contig-U07284-1 gap included 1390 3 4957912 4956520 MINUS 3 5 U07284 2 0 1 0 0 0 0 0 0 0 0 0 0 0 ... 0.051 3 ( CU469464 ) Candidatus Phytoplasma mali strain ... AT complete ch... 36 0.064 18 ( AC152639 ) Bos tau ... 1, comple... 48 0.91 1 ( AC084287 ) Mus Musculus S train ... C57BL6/J chromosome 1 BAC, ... 48 0.91 1 ( AC10721 ...

  14. Dicty_cDB: Contig-U04897-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available PV_GBa0087M02.f PV_GBa Phaseolus vulgaris genomic... 30 6.0 3 ( CU469537 ) Zebrafi... contig VV78X127380.2, whole genome... 34 3.2 2 ( AC187009 ) Canis lupus familiaris chromosome 20 clon...pona bicolor mitochondrial genome, partial se... 28 9.6 5 ( DB728844 ) Apis mellifera head cDNA, RIKEN full...cilaria changii cDNA library Gracilari... 40 0.002 3 ( AM469388 ) Vitis vinifera cont...DRAFT SEQU... 44 0.11 5 ( CU104722 ) Zebrafish DNA sequence *** SEQUENCING IN PRO

  15. Dicty_cDB: Contig-U09598-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available lksldr*wshiqqlnskrhqtippkil*tlqhitvfhiwlxsv qp--- ---xx*xilviml*mdwvqqrvimkmqmmvkls*vqr*siqkqri*nwnirdwilipl...WO2007089584. 48 0.46 1 ( Z49154 ) Human DNA sequence from clone LA04NC01-1C2 on chrom... 48 0.46 1 ( AL390059 ) Human... ( AL161492 ) Arabidopsis thaliana DNA chromosome 4, contig fra... 44 7.2 1 ( AF069300 ) Arabidopsis thaliana...ys full-length cDNA clone ZM... 54 6e-06 AE017343_104( AE017343 |pid:none) Cryptococcus neoformans var. n...eo... 52 1e-05 CP000595_142( CP000595 |pid:none) Ostreococcus lucimarinus CCE9901

  16. Dicty_cDB: Contig-U02999-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available mosome 7 c... 39 0.41 ( O94383 ) RecName: Full=Structural maintenance of chromosomes pro...91 AK047190_1( AK047190 |pid:none) Mus musculus 10 days neonate cereb... 37 1.2 Z69666_1( Z69666 |pid:none) Human DNA sequence fro...s Score E Sequences producing significant alignments: (bits)...s; 101,790,757,118 total letters Searching..................................................done Score E Sequences producin...... 34 8.4 7 ( AM448435 ) Vitis vinifera contig VV78X199971.8, whole genome... 36 8.5 5 ( AC151436 ) Carollia perspicill

  17. Dicty_cDB: Contig-U01876-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available d Phytophthora infe... 36 9.6 3 ( EF640401 ) Libellula saturata 12S ri...mena thermophila strain SB210 mitochondrio... 36 0.45 9 ( AY217738 ) Eimeria tenella apicoplast, compl... 0.66 20 ( AM443874 ) Vitis vinifera contig VV78X089951.4, whole genome... 44 0.69 2 ( CP000049 ) Borrelia turicatae 91E135, compl... 1.2 2 ( CU633648 ) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 46 1.3 5 ( CP000770 ) Candidatus Sulcia muelleri...ium discoideum chromosome 2 map 4158743... 32 2.3 6 ( DQ158857 ) Bigelowiell

  18. Dicty_cDB: Contig-U07116-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Contig-U07116-1 no gap 264 1 1167130 1167394 PLUS 1 2 U07116 1 0 0 0 0 0 0 0 0 0 0 0 0 0 Show Co ... 2 from Patent WO2007020617. 44 2.4 1 ( BD265942 ) Schizophrenia ... associated genes, proteins and bial... 44 2.4 1 ( ... 4 2.4 1 ( AE014306 ) Homo sapiens chromosome 13q34 schizophrenia ... regio... 44 2.4 1 ( AC007052 ) Homo sapiens chromo ...

  19. Dicty_cDB: Contig-U12609-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available yces cerevisiae clon... 56 2e-16 5 ( EA397242 ) Sequence 46066 from patent US 7314974...contig VV78X015564.9, whole genome... 88 4e-15 4 ( EA681515 ) Sequence 60394 from patent...merase II... 80 2e-12 2 ( DQ017097 ) Coriaria sarmentosa RNA polymerase II second larg... 58 3e-12 4 ( AL035527 ) Arabidopsis thalian...a DNA chromosome 4, BAC clone ... 68 3e-12 5 ( DQ408114 ) Phallus hadriani isolate AFTOL-ID 683 RNA pol...s isolate AFTOL-ID 979 RNA... 68 6e-11 2 ( EF014406 ) Coelomomyces stegomyiae RNA polyme

  20. Dicty_cDB: Contig-U02820-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ces; 5,674,871 total letters Score E Sequences producing significant alignments: (bits) Value Contig-U02820-1 (Cont...ces producing significant alignments: (bits) Value N ( BJ344428 ) Dictyostelium discoideum cDNA clon...e Score E Sequences producing significant alignments: (bits) Value BC081036_1( BC081036 |pid:none) Xen...ce 28 from Patent WO0246454. 36 1.6 4 ( AE014849 ) Plasmodium falciparum 3D7 chromosome 12, section... 44 6.2 1 ( BW404170 ) Ciona intestinalis cDNA, clone:ciem844j10, 3'end,... 44 6.2 1 ( BW106515 ) Cion

  1. Dicty_cDB: Contig-U10030-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Contig-U10030-1 no gap 899 4 2174711 2173812 MINUS 5 5 U10030 1 0 1 0 1 0 2 0 0 0 0 0 0 0 Show C ... osome number (1..6, M) 4 Chromosome length 5430582 Star t point 2174711 End point 2173812 Strand (PLUS/MINU ... , mRNA (cDNA ... 56 1e-06 ( Q92502 ) RecName: Full=StAR -related lipid transfer protein 8; Al... 56 2e-06 C ...

  2. Dicty_cDB: Contig-U14599-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Contig-U14599-1 no gap 604 5 1222900 1222306 MINUS 1 1 U14599 0 0 0 0 0 0 0 1 0 0 0 0 0 0 Show C ... osome number (1..6, M) 5 Chromosome length 5062330 Star t point 1222900 End point 1222306 Strand (PLUS/MINU ... 0.065 BC027830_1( BC027830 |pid:none) Mus musculus StAR -related lipid tr... 40 0.065 AK136202_1( AK136202 ...

  3. Dicty_cDB: Contig-U13684-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Contig-U13684-1 no gap 713 4 3118184 3117481 MINUS 1 1 U13684 0 1 0 0 0 0 0 0 0 0 0 0 0 0 Show C ... osome number (1..6, M) 4 Chromosome length 5430582 Star t point 3118184 End point 3117481 Strand (PLUS/MINU ... some 13 Rho GTP... 49 2e-04 (Q86XT1) RecName: Full=StAR -related lipid transfer protein 13; A... 49 2e-04 B ...

  4. Dicty_cDB: Contig-U01148-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ,895,291 total letters Score E Sequences producing significant alignments: (bits) Value Contig-U01148-1 (Con...rching..................................................done Score E Sequences producing significant alignme...2 0.036 1 ( FM992690 ) Candida dubliniensis CD36 chromosome 3, complete ... 52 0.036 1 ( AP008214 ) Oryza sativa (japonica.......................done Score E Sequences producing significant alignments: (bit...2 2 ( CT347042 ) Sus scrofa genomic clone CH242-42E9, genomic surv... 44 0.002 2 ( CT737255 ) Zebrafish DNA

  5. Dicty_cDB: Contig-U14235-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available tyostelium discoideum chromosome 2 map 2567470... 52 0.020 1 ( EX931469 ) li56d03.g7 Ginkgo female leaf (NYBG) Gin...:none) Vitis vinifera contig VV78X086495.... 32 7.2 AB005237_20( AB005237 |pid:none) Arabidopsis thaliana genomic...A129Z ,1,508 Translated Amino Acid sequence XXXXRRKTGSRRNTLWTTEDDEKFAEAYNKYGKSWKTIHSHLPDKTREQVQSHGQYLIRI GKL...QDLHKDGRRTRHIKPDLGLGNNNNNSNSNSNNNNNNNNNNSGGGNNHHHSSHHNHHS PSHHNDNKHHHHHNNNNNNNNNNNNHNNNLNILNNLTNNNHNNNNNYXYDSP Translated Amino Acid...026 AP005823_19( AP005823 |pid:none) Oryza sativa Japonica Group genom... 40 0.026 DQ822984_1( DQ822984 |pid:none) Glycin

  6. Dicty_cDB: Contig-U12872-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available strain ... 39 0.13 CP001140_681( CP001140 |pid:none) Desulfurococcus kamchatkensi... US 6747137. 34 3.1 2 ( AM467689 ) Vitis vinifera contig VV78X207576.2, whole genome... 44 7.4 1 ( AZ927243 ) 476.dis73b08.s1 Saccha..... 132 1e-29 AC007258_14( AC007258 |pid:none) Arabidopsis thaliana chromosome I.....28170 |pid:none) Kluyveromyces thermotolerans str... 93 8e-18 CU928173_311( CU928173 |pid:none) Zygosaccharo...baudi chabaudi calci... 39 0.13 CU928179_647( CU928179 |pid:none) Zygosaccharomyces rouxii

  7. Dicty_cDB: Contig-U11319-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available kx*kr*kcfch*yffixexnwld***tic*xf*tsfttittttsiisnsnnnnnini isttttiatikyinyynynn*rrcf*kti*tnittttxstttnstipttttttttttti...KTIDPKYNQ NQTNIFISSTIQPGNSKKAGNEINMFYGNNIVXXX--- ---xxxrfst**r*kcslyxtksndvnnr*kttnfstriinslftnstinftivfirfn* *st..............................done Score E Sequences producing significant alignments: (bits) Value N ( AC116982 ) Dictyost...... 36 0.55 2 ( AC154632 ) Mus musculus BAC clone RP23-292P17 from chromosom... 34 0.78 7 ( AM482385 ) Vitis vinifera conti...GS-30-02-01-1... 40 1.2 2 ( AA757129 ) ah54g07.s1 Soares_testis_NHT Homo sapiens cDNA cl... 38 1.9 2 ( AC188114 ) Pongo

  8. Dicty_cDB: Contig-U14442-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available e) Chlamydomonas incerta microtubule-... 167 3e-40 EF148151_1( EF148151 |pid:non...n 8; AltName: Ful... 160 3e-38 U93506_1( U93506 |pid:none) Laccaria bicolor symbios...02237_66( AM502237 |pid:none) Leishmania infantum chromosome 19. 55 3e-06 AM502237_68( AM502237 |pid:none) Leishmania infantu...e) Leishmania braziliensis chromoso... 49 1e-04 BC045759_1( BC045759 |pid:none) Homo sapiens microtubule...AAACANAAATAACTTTTCTATTGTTTTTTTTTTTTATAC ATAAAAAAAAAAAAAAAACAAAAAAAAAAAAAATAAACAAA Gap no gap Contig length 791 Chromos

  9. Dicty_cDB: Contig-U08199-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 2351 ) Medicago truncatula chromosome 8 clone mth2-75b20... 46 3.2 1 ( DD321750 ) Method for improving organism's environ...tory system 4.0 %: cytoplasmic >> prediction for Contig-U08199-1 is...0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences...; 5,674,871 total letters Score E Sequences producing significant alignments: (bits) Value Con...tence: 5, Extension: 2 Number of Hits to DB: 22,851 Number of Sequences: 6905 Number of extension

  10. Dicty_cDB: Contig-U05667-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available y: 434 length of database: 5,674,871 effective HSP length: 16 effective length of query: 418 effe...ctive length of database: 5,564,391 effective search space: 2325915438 effective search space used: 23...... 44 4.0 1 ( AM485409 ) Vitis vinifera contig VV78X054646.1, whole genome... 44 4.0 1 ( AB012243 ) Arabidopsis thalian...y: 434 Length of database: 95,242,211,685 Length adjustment: 23 Effective length of query: 411 Effective l... baumannii AB307-0... 32 9.0 >AC116920_8( AC116920 |pid:none) Dictyostelium discoideum chromosome 2 ma

  11. Dicty_cDB: Contig-U01498-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Contig-U01498-1 gap included 922 6 1471136 1472059 PLUS 3 5 U01498 0 0 0 0 0 0 3 0 0 0 0 0 0 0 S ... from Patent EP1865317. 38 9.4 6 ( AP008211 ) Oryza sat iva (japonica cultivar-group) genomic DN... 44 9.5 ... 1 ( AC124141 ) Oryza sat iva Japonica Group chromosome 5 clone OS... 44 9.5 ... 426893_1( AB426893 |pid:none) Kluyveromyces lactis SAT ... gene for ... 35 3.6 AB439526_1( AB439526 |pid:none ...

  12. Dicty_cDB: Contig-U15272-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available CP000514_2356( CP000514 |pid:none) Marinobacter aquaeolei VT8, com... 40 0.15 CP000038_4051( CP000038 |pid:none) Shigella sonnei... lovleyi SZ, complete ... 39 0.26 AM270165_115( AM270165 |pid:none) Aspergillus niger contig An08c01......hpivkqiqi*fkhqyhkllllqqf*iivtttttttttttttt ttttlhhhhyhhqqhqnqqhqlqyqhhlqlqhqlqyqpqqhhhqlliiisiiernslrd* myl*rnl*iillslqkmige...mpling_GS-32-01-01-1... 50 0.19 1 ( CR940347 ) Theileria annulata genomic DNA chromosome 1 part... Ss046, complete... 40 0.15 D11024_2( D11024 |pid:none) Shigella flexneri vacB ge

  13. Dicty_cDB: Contig-U07012-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Contig-U07012-1 no gap 130 2 5760852 5760750 MINUS 1 1 U07012 1 0 0 0 0 0 0 0 0 0 0 0 0 0 Show C ... ne:VS... 159 3e-35 1 ( FK814934 ) PRAG-aac86e11.g1 Sand _fly_EST_Normalized Phleboto... 48 0.068 1 ( AL9538 ... 32 6.8 CP000882_111( CP000882 |pid:none) Hemiselmis and ersenii chromosome... 32 6.8 U97010_6( U97010 |pid ...

  14. Dicty_cDB: Contig-U15584-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 2 ( AY894732 ) Campylopus savannarum AtpB (atpB) gene, partial c... 36 1.7 2 ( AM628161 ) Entamoeba dispar G...S... 38 1.4 7 ( CU326391 ) Medicago truncatula chromosome 5 clone mth2-182c4... 38 1.4 7 ( AY894733 ) Campylopus savan...6 2 ( AY159920 ) Bryohumbertia flavicoma isolate BfatpB atpB-rbcL ... 36 2.6 2 ( AY159909 ) Campylopus savan...tters Score E Sequences producing significant alignments: (bits) Value Contig-U15584-1 (Cont..............done Score E Sequences producing significant alignments: (bits) Value N ( BJ415438 ) Dictyosteliu

  15. Artificial Intelligence.

    Science.gov (United States)

    Lawrence, David R; Palacios-González, César; Harris, John

    2016-04-01

    It seems natural to think that the same prudential and ethical reasons for mutual respect and tolerance that one has vis-à-vis other human persons would hold toward newly encountered paradigmatic but nonhuman biological persons. One also tends to think that they would have similar reasons for treating we humans as creatures that count morally in our own right. This line of thought transcends biological boundaries-namely, with regard to artificially (super)intelligent persons-but is this a safe assumption? The issue concerns ultimate moral significance: the significance possessed by human persons, persons from other planets, and hypothetical nonorganic persons in the form of artificial intelligence (AI). This article investigates why our possible relations to AI persons could be more complicated than they first might appear, given that they might possess a radically different nature to us, to the point that civilized or peaceful coexistence in a determinate geographical space could be impossible to achieve. PMID:26957450

  16. Artificial intelligence

    OpenAIRE

    Duda, Antonín

    2009-01-01

    Abstract : Issue of this work is to acquaint the reader with the history of artificial inteligence, esspecialy branch of chess computing. Main attention is given to progress from fifties to the present. The work also deals with fighting chess programs against each other, and against human opponents. The greatest attention is focused on 1997 and duel Garry Kasparov against chess program Deep Blue. The work is divided into chapters according to chronological order.

  17. Report on sequencing the wheat chromosome 3B

    OpenAIRE

    Choulet, Frédéric; Wincker, Patrick; Quesneville, Hadi; Brunel, Dominique; Gill, Bikram S; Appels, Rudi; Keller, Beat; Feuillet, Catherine

    2011-01-01

    Because of its 17 Gb hexaploid genome, wheat genomics has been lagging behind the one of the other major crops. Two years after the establishment of the first physical map of the biggest wheat chromosome, the 3B, which represents 1 Gb, its complete sequencing is now underway (ANR project 3BSEQ). In order to prepare for its complete sequencing and analysis, we performed a pilot project on 18 Mb of large BAC contigs which allowed us to improve our understanding of the wheat genome composition a...

  18. Analysis of 5S rDNA Arrays in Arabidopsis thaliana: Physical Mapping and Chromosome-Specific Polymorphisms

    OpenAIRE

    Cloix, C.; Tutois, S; O. Mathieu; Cuvillier, C.; Espagnol, M C; G. Picard; Tourmente, S

    2000-01-01

    A physical map of a pericentromeric region of chromosome 5 containing a 5S rDNA locus and spanning ∼1000 kb was established using the CIC YAC clones. Three 5S rDNA arrays were resolved in this YAC contig by PFGE analysis and we have mapped different types of sequences between these three blocks. 5S rDNA units from each of these three arrays of chromosome 5, and from chromosomes 3 and 4, were isolated by PCR. A total of 38 new DNA sequences were obtained. Two types of 5S rDNA repeated units ex...

  19. AcEST: CL4178Contig1 [AcEST

    Lifescience Database Archive (English)

    Full Text Available CL4178Contig1 663 2 Adiantum capillus-veneris contig: CL4178contig1 sequence. Link to clone list ... ne ID BP919660 DK963003 Sequence GGATCATCTTGCAAAGGCTCC ATTTCTTCGGCAGGCTGTTTCTTTGCCATGAGACCTTTG CTGCCTTTCAA ... TTTCC GTGTTACTACTTCATCTACAGCATGCAGCGCAGACAAGCACTTT CC ATCA ... CCCTCTGCTTCTAAAGGAAGTCC AAATGCTAAAGTAAAAAGATCCTCCTCC TCA TTGGAAAGGACAGTAGAAA ... TAGCTGTCC GAATCATACTACAAACTGCTCGAACAGTTCTA CAATAAGAATATAACAAA ...

  20. AcEST: CL498Contig1 [AcEST

    Lifescience Database Archive (English)

    Full Text Available CL498Contig1 664 5 Adiantum capillus-veneris contig: CL498contig1 sequence. Link to clone list S ... 955909 DK953831 Sequence GACCAGCAAAAGCACTCAAGACACCGTCC TTCGTATGAAAGATTGATACAAATGACCACT TAGGAATCAAAATAGTCAA ... AAACCTAATATCC TGTCTAAGGAATTCAACATTGAAATCC C CGGTTAAAACTTCAGGCTGACT ... TGG TACATCACAAATGTTTTCTGCTCTCAATAAAAAAACCCAAGGACTTTTCC ACCCACATTC TTCC TTCGTGCTTCATCATGATCC ATGATTCC AGCTGATG ... TTGTCAACACAATATGGCCA AACTGTCTTGAAGGAAGAAGGCGTGCTGTCC AAGCCTCTAGCTCACCAACTGCTACATCA TAACGAGGACTAATCACTCC A ...

  1. Chromosome painting in plants.

    NARCIS (Netherlands)

    Schubert, I.; Fransz, P.F.; Fuchs, J.; Jong, de J.H.

    2001-01-01

    The current 'state-of-art' as to chromosome painting in plants is reviewed. We define different situations described as painting so far: i) Genomic in situ hybridisation (GISH) with total genomic DNA to distinguish alien chromosomes on the basis of divergent dispersed repeats, ii) 'Chromosomal in si

  2. Dicty_cDB: Contig-U04877-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available n 5'HPRT inserti... 46 0.87 1 ( CD575412 ) UCRPT01_04ac01_b1 Poncirus trifoliata CTV-challen... 46 0.87 1 ( ...quence from clone CH1073-130M24 i... 36 2.4 2 ( CO830196 ) LM_GB5_010522 Locusta migratoria gregari...c... 44 3.4 1 ( CX546414 ) UCRPT01_5_028_G07_T3 Poncirus trifoliata CTV-chal... 44 3.4 1 ( CX306531 ) C18...AATGATTAA A Gap no gap Contig length 351 Chromosome number (1..6, M) 2 Chromosome length 8467578 Star... EST 1 Link to clone list U04877 List of clone(s) est1= SSD569Z ,1,352 Translated Amino Acid sequence ifffqq

  3. Dicty_cDB: Contig-U06660-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available NA clone:VS... 900 0.0 1 ( AC225673 ) Procavia capensis clone CH280-104B22, WORKING DRA... 38 0.013 2 ( AM451422 ) Vitis vi...s... 37 0.37 AF065168_1( AF065168 |pid:none) Giardia intestinalis variant-speci... 36 0.48 EF538805_1( EF538...%: cytoplasmic 4.0 %: cytoskeletal 4.0 %: vacuolar 4.0 %: mitochondrial 4.0 %: ve...Contig length 516 Chromosome number (1..6, M) 1 Chromosome length 4919822 Start point 403647 End point 40322...NNPNQYSSQYVCL*kkkkkkkkinq*nkiqi*ni Translated Amino Acid sequence (All Frames) Frame A: mhvilvmflhvemmvklymicmkdiivmvq*clvw*lrmmfvi

  4. Dicty_cDB: Contig-U08806-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 8X011041.... 39 0.38 AJ298992_1( AJ298992 |pid:none) Fagus sylvatica partial mRNA for p... 39 0.38 AY064216_1( AY064216 |pid:none...ase 1; ... 38 0.64 AJ577132_1( AJ577132 |pid:none) Yarrowia lipolytica partia...2-10... 36 2.4 AP008209_1380( AP008209 |pid:none) Oryza sativa (japonica cultivar... 36 2.4 FJ795037_1( FJ795037 |pid:none) Glycine...AAAAATTAAATTATTTAAA Gap gap included Contig length 1217 Chromosome number (1..6, M) 3 Chromosome length 6358359 Start poin...3( A38903 ;A36474) protein kinase 1 - fission yeast (Schizosa... 36 3.2 CR382139_422( CR382139 |pid:none) Debaryomyces hansen

  5. Dicty_cDB: Contig-U02567-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ococcus citri cytochrome b (cytb) gene, parti... 34 9.4 3 ( AQ897728 ) HS_3135_A2_C10_T7C CIT Approved Human Gen...AATATTCC TTTTATAATTGCTGGTGATATAAATCATAATAGAA Gap no gap Contig length 585 Chromosome number (1..6, M) - Chromosome length - Start... seq... 36 0.82 2 ( FG664257 ) G1142P322FO10.T0 Anolis carolinensis pooled norma... 34 0.88 3 ( AC234734 ) B....5 1 ( EJ210176 ) 1092345450015 Global-Ocean-Sampling_GS-27-01-01-1... 46 1.5 1 ( CR347576 ) mte1-81B17FM1 BAC end, cultivar...ifera, whole genome shotgun sequence, co... 34 5.1 4 ( AY325300 ) Paramecium primaurelia strain

  6. Dicty_cDB: Contig-U14805-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available omo sapiens c... 46 0.002 AF398469_1( AF398469 |pid:none) Muntiacus reevesi GTP binding prot... 46 0.002 L21...... 49 2e-04 D38625( D38625 )GTP-binding protein o-rab1 - electric ray (Discopy... 49 3e-04 GM977163_1( G...) RecName: Full=Ras-like GTP-binding protein YPT1; &JC53... 43 0.018 CP000587_71( CP000587 |pid:none) Ostreococcus lucimarin...h space used: 154454907530 Neighboring words threshold: 12 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bi...TTGTAGATAAGATAAAAAAAAA Gap no gap Contig length 1126 Chromosome number (1..6, M) 2 Chromosome length 8467578 Start point

  7. Dicty_cDB: Contig-U05123-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available plete ... 40 1.8 3 ( BH148936 ) ENTPH42TF Entamoeba histolytica Sheared DNA Entam... 38 1.8 2 ( EF104895 ) Phytoliriomyza me...0 4e-05 1 ( AM465516 ) Vitis vinifera contig VV78X130101.4, whole genome... 42 4e-04 3 ( CT733056 ) Danio rerio...394571 ) Zebrafish DNA sequence from clone CH211-180M12 in... 38 0.090 2 ( EG404537 ) SAAH-aab87a06.b1 Agen 0058 Schmidtea med... clone DKEY-22H13 in l... 36 0.23 4 ( AC172741 ) Medicago truncatula chromosome...8.rev CAWZ Helobdella robusta Primary Late... 36 0.44 2 ( AC021639 ) Drosophila melanogaster, chromosome X, regio

  8. Dicty_cDB: Contig-U01505-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 0 5 ( AL161502 ) Arabidopsis thaliana DNA chromosome 4, contig fra... 44 0.52 2 ( AM477924 ) Vitis vinifera,...lete se... 46 1.4 1 ( AC002332 ) Arabidopsis thaliana chromosome 2 clone F4P9 map...) OGAHG10TC ZM2_0.7_1.5_KB Zea mays genomic clone Z... 46 1.4 1 ( BH850378 ) SALK_071199.55.50.x Arabidopsis thaliana... ) saq56g01.y1 Gm-c1076 Glycine max cDNA clone SOYBE... 46 1.4 1 ( BP808035 ) Arabidopsis thaliana cDNA clon...pus Cold acclimation - light B... 44 5.4 1 ( EV200974 ) 0102127 Brassica napus Cold acclima

  9. Dicty_cDB: Contig-U05111-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available mosome 2 clone T13P21 ma... 46 1.4 1 ( DD392022 ) Method and nucleic acids for the improved treatme... ...NCING IN PROGRESS... 38 0.58 5 ( CR047337 ) Forward strand read from insert in 3'HPRT inserti... 38 0.58 2 ( AC197661 ) Sper...endoplasmic reticulum 20.0 %: mitochondrial 12.0 %: plasma membrane 8.0 %: extracellular, including cell wal...ap Contig length 518 Chromosome number (1..6, M) 3 Chromosome length 6358359 Start point 2841596 End point 2842114 Str... -3 Gap Penalties: Existence: 5, Extension: 2 Number of Hits to DB: 22,514 Number of Sequences: 6905 Number of ext

  10. Dicty_cDB: Contig-U10149-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available AATAAAAAAAAAATAACTTTTTTT Gap no gap Contig length 1131 Chromosome number (1..6, M) 4 Chromosome length 5430582 Start...65 Number of sequences better than 10.0: 139 Length of query: 1131 Length of database: 95,242,211,685 Le...iones unguiculatus akr-L6 mRNA ... 76 5e-40 AK227354_1( AK227354 |pid:none) Arabidopsis thaliana mRNA for put.... 77 1e-33 AB045829_1( AB045829 |pid:none) Homo sapiens mRNA for 3alpha-hydro... 70 1e-33 AB264706_1( AB2647...( AE016877 |pid:none) Bacillus cereus ATCC 14579, com... 88 1e-32 ( P26690 ) RecName: Full=NAD(P)H-dependent 6'-deoxychalcone syntha

  11. Dicty_cDB: Contig-U16503-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ( O83080 ) RecName: Full=D-lactate dehydrogenase; Short=D... 92 1e-17 BX950229_1588( BX950229 |pid:none) Methanococcus mar...CAAGATCACAATGGTT Gap gap included Contig length 711 Chromosome number (1..6, M) 3 Chromosome length 6358359 Start...983659 Number of successful extensions: 2112242 Number of sequences better than 10.0: 94 Length of query: 721 Length...21 |pid:none) Shewanella sediminis HAW-EB3, co... 157 2e-37 CP000450_1261( CP000450 |pid:none) Nitrosomonas eutropha... AY313608 |pid:none) Mastigamoeba balamuthi putative D-... 137 3e-31 CP000388_2073( CP000388 |pid:none) Pseu

  12. Dicty_cDB: Contig-U14871-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available P001014_170( CP001014 |pid:none) Thermoproteus neutrophilus V24St... 130 5e-29 CP001562_647( CP001562 |pid:none) Bartonella graha...' ... 1289 0.0 1 ( BJ426186 ) Dictyostelium discoideum cDNA clone:ddv58n02, 5' ... 900 0.0 1 ( DQ332680 ) Synthetic construct Sacchar...928181 |pid:none) Zygosaccharomyces rouxii strain C... 167 3e-40 CP000099_3062( CP000099 |pid:none) Metha...TTTAAAAAAAA Gap no gap Contig length 828 Chromosome number (1..6, M) 2 Chromosome length 8467578 Start point...liana clone 3116 mR... 154 3e-36 CP000300_706( CP000300 |pid:none) Methanococcoides burt

  13. Dicty_cDB: Contig-U00879-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available U928165_129( CU928165 |pid:none) Kluyveromyces thermotolerans str... 35 2.3 AE017349_346( AE017349 |pid:none) Cryptococcus neoform...34 4.0 CU928169_605( CU928169 |pid:none) Kluyveromyces thermotolerans str... 34 4.0 (Q8CDM1) RecName: Full=A...TPase family AAA domain-containing prote... 34 4.0 CU928180_17( CU928180 |pid:none) Kluyveromyces thermo...2 0.41 14 ( ET300977 ) S0015D22_T7 CHORI-214 Salmo salar genomic clone S... 36 0.44 3 ( AF141214 ) Rhabdomys pumilio country South...GAAGAAGATGT Gap no gap Contig length 723 Chromosome number (1..6, M) 1 Chromosome length 4919822 Start point

  14. Dicty_cDB: Contig-U15845-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 6.7 1 ( AC212437 ) Solanum lycopersicum chromosome 11 clone C11HBa01... 44 6.7 1 ( AC185959 ) Glycine max clone gmw1-58k3, co... of extensions: 32743 Number of successful extensions: 3654 Number of sequences better...5 4 ( AC221587 ) Bos taurus clone CH240-391M15, WORKING DRAFT SEQU... 40 0.40 5 ( AP009410 ) Solanum lycopersicum...V78X098896.3, whole genome... 44 6.7 1 ( AM437243 ) Vitis vinifera contig VV78X069574.5, whole genome... 44 ...Park Can... 44 6.7 1 ( AC006275 ) Homo sapiens chromosome 19, cosmid R32203, comple... 44 6.7 1 ( AC156786 ) Rhinolophus ferrume

  15. Dicty_cDB: Contig-U03273-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available pid:none) Candidatus Methanosphaerula pal... 50 3e-05 CP001140_1084( CP001140 |pid:none) Desulfurococcus kamcha...N3 in l... 46 1.5 1 ( X79279 ) A.thaliana AtK-1 gene. 46 1.5 1 ( AM455935 ) Vitis vinifera contig VV78X206236.3, whole...clone CH240-413G23, WORKING DRAFT SEQU... 40 6.6 2 ( AL161543 ) Arabidopsis thaliana DNA chromosome 4, conti...42141 m... 95 2e-18 AK176351_1( AK176351 |pid:none) Arabidopsis thaliana mRNA, complet... 95 2e-18 AC006585_...8( AC006585 |pid:none) Arabidopsis thaliana chromosome 2 ... 95 2e-18 AE014296_21

  16. Dicty_cDB: Contig-U13364-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available se: CSM 6905 sequences; 5,674,871 total letters Score E Sequences producing significant alignments: (bits) Val...ntig/Contig-U13364-1Q.Seq.d (313 letters) Database: ddbj_A 92,845,959 sequences; 95,242,211,685 total letters Sear...tig-U13364-1Q.Seq.d (313 letters) Database: nrp_B 3,236,559 sequences; 1,051,180,864 total letters Searching... Chromosome number (1..6, M) 5 Chromosome length 5062330 Start point 2995935 End ...|pid:none) Mus musculus mRNA for mKIAA1728 pr... 37 0.17 AM904787_1( AM904787 |pid:none) Ministeria vibrans partial

  17. Dicty_cDB: Contig-U09061-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available n) mRNA... 43 0.033 AC096673_18( AC096673 |pid:none) Trypanosoma brucei chromosom...ne) Dictyostelium discoideum chromosom... 37 1.8 AF008227_1( AF008227 |pid:none) Drosophila melano...35 5.2 AE014134_2530( AE014134 |pid:none) Drosophila melanogaster chromos... 35 5.2 AK176188_1( AK176188 |pid:none) Arabidopsis...kkm*ir*wklvypifivlmdqlylnmlilmysihliinl*ktiqivl ymlllsfhkrhpiiqfqwvhiqfn*ismsmifvyqfqkvdshlglsl*lssfhqsle*ls...A9, WO... 42 0.42 7 ( AM426746 ) Vitis vinifera contig VV78X267462.3, whole genome... 34 0.53 2 ( AE014306 ) Homo sapiens chromo

  18. Dicty_cDB: Contig-U09386-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available e UNK clone CH250-50H12, ... 44 8.2 1 ( AF001339 ) Hydnophytum formicarum ribosomal protein S16 (rps... 44 8..... 38 0.40 2 ( AC186278 ) Spermophilus tridecemlineatus clone VMRC20-243P12... 42 0.44 5 ( EC825719 ) SME00003353 esmbsro2 Sawyeri...s blakesleeanus NRRL15... 38 1.2 2 ( EX857898 ) CBNF4222.fwd CBNF Phycomyces blakesleeanus NRRL15... 38 1.2 ...2 ( DQ274179 ) Solanum tuberosum patatin-rich BAC 14K07, complet... 34 1.9 6 ( Z9...cluded Contig length 812 Chromosome number (1..6, M) 6 Chromosome length 3595308 Start point 821563 End poin

  19. Dicty_cDB: Contig-U06466-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available nome. 68 3e-14 2 ( CP000903 ) Bacillus weihenstephanensis KBAB4, complete ge...... 80 2e-14 (B6YUN0) RecName: Full=Methionyl-tRNA synthetase; EC=6.... 64 2e-09 CP001117_321( CP001117 |pid:none) Deinococcus desert...25( CP000034 |pid:none) Shigella dysenteriae Sd197, com... 45 0.001 (A5UBS8) RecName: Full=Methionyl-tRNA sy...000721 |pid:none) Clostridium beijerinckii NCIMB 80... 38 0.12 CP001114_1020( CP001114 |pid:none) Deinococcus desert...TAATTATAAAATAAAATTAAAAATATTAAA AAAAAA Gap no gap Contig length 456 Chromosome number (1..6, M) 6 Chromosome length 3595308 Start

  20. Dicty_cDB: Contig-U06395-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available K061837_1( AK061837 |pid:none) Oryza sativa Japonica Group cDNA c... 49 7e-05 AM270218_55( AM270218 |pid:none) Aspergillus niger...osome ... 57 2e-07 CP001114_2492( CP001114 |pid:none) Deinococcus deserti VCD115, com... 57 2e-07 AE013598_4...AAATGTCCAAAAAAAAA Gap no gap Contig length 440 Chromosome number (1..6, M) 5 Chromosome length 5062330 Start...ylivf*fkd*etlilklvavfifqiklqikhtkl s*lklaledvlpmvllhhs*rkvivfylmnlhlekksl*mvlnvkfslkmkf*vlweikk k*nkikink*in...215( CP000359 |pid:none) Deinococcus geothermalis DSM 11... 62 6e-09 (Q0C0T1) RecName: Full=10 kDa chaper

  1. Dicty_cDB: Contig-U13709-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available F395110 |pid:none) Naegleria gruberi RNA polymerase I... 82 2e-14 CP000504_695( CP000504 |pid:none) Pyrob... 3e-04 EU153422_1( EU153422 |pid:none) Pelodera teres strain EM437 RNA po... 48 3e-04 EU153441_1( EU153441 |pid:none) Acrobe...ase subu... 49 2e-04 AM712239_99( AM712239 |pid:none) African swine fever virus Benin 9... 49 2e-04 (P0C988) RecName: Full=Prob...TAAT Gap no gap Contig length 822 Chromosome number (1..6, M) 2 Chromosome length 8467578 Start point 578514...mantle Lot... 46 2.1 1 ( FC565667 ) CAWF6148.fwd CAWF Lottia gigantea from mantle (H)... 46 2.1 1 ( EK275252 ) 1095462274096 Glob

  2. Dicty_cDB: Contig-U12912-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ( BX530721 |pid:none) Zebrafish DNA sequence from clone ... 75 2e-12 ( P31751 ) RecName: Full=RAC-be...BC171344_1( BC171344 |pid:none) Danio rerio LATS, large tumor supp... 75 3e-12 FB811462_1( FB811462 |pid:none) Sequence 30735 fro...2_5( BX004962 |pid:none) Zebrafish DNA sequence from clone ... 72 1e-11 (Q7TT50) RecName: Full=Serine/threonine-pro...AAAAAATCAAAAA Gap no gap Contig length 725 Chromosome number (1..6, M) 5 Chromosome length 5062330 Start poi...B084130 ) hq10c11.b1 Hedyotis centranthoides flower - Stage... 50 0.12 1 ( EY373181 ) CAXA14420.fwd CAXA Helobdella rob

  3. Dicty_cDB: Contig-U15021-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available e-51 EF419256_1( EF419256 |pid:none) Drosophila melanogaster isolate T4... 161 2e-51 CS038992_1( CS038992 |p.... 131 6e-29 DQ363495_1( DQ363495 |pid:none) Ictalurus punctatus isolate SOOH01... 98 5e-27 AY297429_1( AY297...e-15 CP001139_979( CP001139 |pid:none) Vibrio fischeri MJ11 chromosome ... 55 2e-12 FM954973_73( FM954973 |pid:none) Vibrio splendi...nuclear 16.0 %: mitochondrial 4.0 %: vacuolar 4.0 %: peroxisomal >> prediction for Contig-U15021-1 is cyt VS...cago truncatula chromosome 7 BAC clone mth4-4... 42 0.18 4 ( EC571128 ) 057432_0369_0337 LNCAP + R1881 synthetic And

  4. Dicty_cDB: Contig-U14142-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 4.9 1 ( FG798507 ) G1148P318FB3.T0 Anolis carolinensis pooled normal... 44 4.9 1 ( EV480875 ) Fc_nor_65A12_M13F Folsomia candi...p Contig length 516 Chromosome number (1..6, M) 4 Chromosome length 5430582 Start point 5227120 End point 5226614 Strand.................done Score E Sequences producing significant alignments: (bits) Value N ( BJ338269 ) Dictyostelium dis..._A11 GQ041 - Shoot tip - Dormant (Norma... 30 5.3 3 ( C91275 ) Dictyostelium discoideum slug cDNA, clone SSJ..._C21 GQ025: Annual flush SHOOTS diurnal ... 30 6.8 3 ( EC973956 ) WIN1017.C21_F11 Muscat Hamburg post-veraiso

  5. Restriction mapping of a YAC contig in the hemochromatosis gene region

    Energy Technology Data Exchange (ETDEWEB)

    Burt, M.J.; Smit, D.J.; Pyper, W.R. [Univ. of Queensland, Brisbane (Australia)

    1994-09-01

    Hemochromatosis is a common inherited disorder of iron metabolism that can lead to cirrhosis, hepatocellular carcinoma, cardiomyopathy, diabetes and anthropathy. We have mapped the hemochromatosis gene to within 1 cM of HLA-A and the microsatellite D6S105, and our allele association studies have shown that D6S105 is the marker most closely associated with the hemochromatosis gene. We are currently constructing a YAC contig and restriction map of this region as part of a positional cloning strategy to identify the hemochromatosis gene. YACs containing HLA-A or D6S105 were selected, and fluorescent-in-situ-hybridization (FISH) was performed to confirm chromosomal location and exclude chimerism. YAC DNA was digested with a panel of rare cutters, separated by pulsed field gel electrophoresis, Southern blotted and probed with the vector arms to create restriction maps. YAC insert terminal ends were isolated using vectorette methodology. A contig extending 600 kb centromeric and 350 kb telomeric of HLA-A has been established. HLA-A, HLA-F and the microsatellite D6S265 have been positioned on this map. The contig does not yet overlap any D6S105 positive YACs but the telomeric end of the contig has been sequenced and is being used to identify additional YACs to bridge this interval. Restriction mapping of three D6S105 YACs has shown the presence of several CpG islands in this region. As these CpG islands are in close proximity to D6S105, they are being used to isolate coding sequences to determine whether any of these mark the position of the hemochromatosis gene.

  6. Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A

    Czech Academy of Sciences Publication Activity Database

    Poursarebani, N.; Nussbaumer, T.; Šimková, Hana; Šafář, Jan; Witsenboer, H.; van Oeveren, J.; Doležel, Jaroslav; Mayer, K. F. X.; Stein, N.; Schnurbusch, T.

    2014-01-01

    Roč. 79, č. 2 (2014), s. 334-347. ISSN 0960-7412 Institutional support: RVO:61389030 Keywords : bread wheat chromosome 6A * whole -genome profiling * LINEAR TOPOLOGICAL CONTIGS Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.972, year: 2014

  7. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    Science.gov (United States)

    de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

  8. Chromosome-specific DNA Repeat Probes

    Energy Technology Data Exchange (ETDEWEB)

    Baumgartner, Adolf; Weier, Jingly Fung; Weier, Heinz-Ulrich G.

    2006-03-16

    In research as well as in clinical applications, fluorescence in situ hybridization (FISH) has gained increasing popularity as a highly sensitive technique to study cytogenetic changes. Today, hundreds of commercially available DNA probes serve the basic needs of the biomedical research community. Widespread applications, however, are often limited by the lack of appropriately labeled, specific nucleic acid probes. We describe two approaches for an expeditious preparation of chromosome-specific DNAs and the subsequent probe labeling with reporter molecules of choice. The described techniques allow the preparation of highly specific DNA repeat probes suitable for enumeration of chromosomes in interphase cell nuclei or tissue sections. In addition, there is no need for chromosome enrichment by flow cytometry and sorting or molecular cloning. Our PCR-based method uses either bacterial artificial chromosomes or human genomic DNA as templates with {alpha}-satellite-specific primers. Here we demonstrate the production of fluorochrome-labeled DNA repeat probes specific for human chromosomes 17 and 18 in just a few days without the need for highly specialized equipment and without the limitation to only a few fluorochrome labels.

  9. Chimpanzee chromosome 12 is homologous to human chromosome 2q

    Energy Technology Data Exchange (ETDEWEB)

    Sun, N. C.; Sun, C. R.Y.; Ho, T.

    1977-01-01

    Most of the 46 human chromosomes find their counterparts in the 48 chimpanzee chromosomes except for chromosome 2 which has been hypothesized to have been derived from a centric fusion of two chimpanzee acrocentric chromosomes. These two chromosomes correspond to the human chromosomes 2p and 2g. This conclusion is based primarily on chromosome banding techniques, and the somatic cell hybridization technique has also been used. (HLW)

  10. Construction of two YAC contigs in human xp11.23-p11.22, one encompassing the loci OATL1, GATA, TFE3, and SYP, the other linking DXS255 to DXS146

    Energy Technology Data Exchange (ETDEWEB)

    Fisher, S.E.; Hatchwell, E.; Chand, A.; Ockenden, N.; Craig, I.W. [Univ. of Oxford, Oxford (United Kingdom)] [and others

    1995-09-20

    We have constructed two YAC contigs in the Xp11.23-p11.22 interval of the human X chromosome, a region that was previously poorly characterized. One contig, of at least 1.4 Mb, links the pseudogene OATL1 to the genes GATA1, TFE3, and SYP and also contains loci implicated in Wiskott-Aldrich syndrome and synovial sarcoma. A second contig, mapping proximal to the first, is estimated to be over 2.1 Mb and links the hypervariable locus DXS255 to DXS146, and also contains a chloride channel gene that is responsible for hereditary nephrolithiasis. We have used plasmid rescue, inverse PCR, and Alu-PCR to generate 20 novel markers from this region, 1 of which is polymorphic, and have positioned these relative to one another on the basis of YAC analysis. The order of previously known markers within our contigs, Xpter-OATL1-GATA-TFE3-SYP-DXS255-DXS146-Xcen, agrees with genomic pulsed-field maps of the region. In addition, we have constructed a rare-cutter restriction map for a 710-kb region of the DXS255-DXS146 contig and have identified three CpG islands. These contigs and new markers will provide a useful resource for more detailed analysis of Xp11.23-p11.22, a region implicated in several genetic diseases. 32 refs., 2 figs., 2 tabs.

  11. Evolution of Chromosome 6 of Solanum Species Revealed by Comparative Fluorescence in Situ Hybridization Mapping

    Science.gov (United States)

    Comparative genome mapping is an important tool in evolutionary research. Here we demonstrate a comparative fluorescent in situ hybridization (FISH) mapping strategy. A set of 13 bacterial artificial chromosome (BAC) clones derived from potato chromosome 6 was used for FISH mapping in seven differen...

  12. Physical Map and Organization of Chromosome 7 in the Rice Blast Fungus, Magnaporthe grisea

    OpenAIRE

    Zhu, Heng; Blackmon, Barbara P.; Sasinowski, Maciek; Dean, Ralph A.

    1999-01-01

    The rice blast fungus Magnaporthe grisea is a highly destructive plant pathogen and one of the most important for studying various aspects of host-plant interactions. It has been widely adopted as a model organism because it is ideally suited for genetic and biological studies. To facilitate map-based cloning, chromosome walking, and genome organization studies of M. grisea, a complete physical map of chromosome 7 was constructed using a large-insert (130 kb) bacterial artificial chromosome (...

  13. Dicty_cDB: Contig-U01283-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available nase D; EC=2.... 98 4e-19 AL731614_16( AL731614 |pid:none) Oryza sativa genomic DNA, chromos...-U01283-1 Contig ID Contig-U01283-1 Contig update 2001. 8.29 Contig sequence >Contig-U01283-1 (Contig...TTCAAATTTCATTAATTCAAAATTATAAATTA AAAAGAAAATAAAAAATATATAAAAATATGTGTAATACCCAAAAAAAAAA AAAAAAAAAAAAAAAAAAA Gap gap included Contig len...-U01283-1Q) /CSM_Contig/Contig-U01283-1Q.Seq.d Length = 1019 Score = 15...-U01283-1 (Contig-U01283-1Q) /CSM_Contig/Contig-U01283-1Q.Seq.d (1019 letters) Database: ddbj_A 102,105,510 sequen

  14. Artificial Economy

    Directory of Open Access Journals (Sweden)

    Alexandru JIVAN

    2011-08-01

    Full Text Available This paper proposes to eliminate, a routine in the economic thinking, claimed to be responsible for the negative essence of economic developments, from the point of view, of the ecological implications (employment in the planetary ecosystem. The methodological foundations start from the natural origins of the functionality of the human economic society according to the originary physiocrat liberalism, and from specific natural characteristics of the humankind. This paper begins with a comment-analysis of the difference between natural and artificial within the economy, and then explains some of the most serious diversions from the natural essence of economic liberalism. It shall be explained the original (heterodox interpretation of the Classical political economy (economics, by making calls to the Romanian economic thinking from aggravating past century. Highlighting the destructive impact of the economy - which, under the invoked doctrines, we call unnatural - allows an intuitive presentation of a logical extension of Marshall's market price, based on previous research. Besides the doctrinal arguments presented, the economic realities inventoried along the way (major deficiencies and effects, determined demonstrate the validity of the hypothesis of the unnatural character and therefore necessarily to be corrected, of the concept and of the mechanisms of the current economy.The results of this paper consist of original heterodox methodspresented, intuitive or developed that can be found conclusively within the key proposals for education and regulation.

  15. Plant sex chromosome evolution.

    Science.gov (United States)

    Charlesworth, Deborah

    2013-01-01

    It is now well established that plants have an important place in studies of sex chromosome evolution because of the repeated independent evolution of separate sexes and sex chromosomes. There has been considerable recent progress in studying plant sex chromosomes. In this review, I focus on how these recent studies have helped clarify or answer several important questions about sex chromosome evolution, and I shall also try to clarify some common misconceptions. I also outline future work that will be needed to make further progress, including testing some important ideas by genetic, molecular, and developmental approaches. Systems with different ages can clearly help show the time course of events during changes from an ancestral co-sexual state (hermaphroditism or monoecy), and I will also explain how different questions can be studied in lineages whose dioecy or sex chromosomes evolved at different times in the past. PMID:23125359

  16. Vibrio chromosomes share common history

    OpenAIRE

    Gevers Dirk; Chang Sarah; Chang LeeAnn; Kirkup Benjamin C; Polz Martin F

    2010-01-01

    Abstract Background While most gamma proteobacteria have a single circular chromosome, Vibrionales have two circular chromosomes. Horizontal gene transfer is common among Vibrios, and in light of this genetic mobility, it is an open question to what extent the two chromosomes themselves share a common history since their formation. Results Single copy genes from each chromosome (142 genes from chromosome I and 42 genes from chromosome II) were identified from 19 sequenced Vibrionales genomes ...

  17. BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.

    Science.gov (United States)

    Staňková, Helena; Hastie, Alex R; Chan, Saki; Vrána, Jan; Tulpová, Zuzana; Kubaláková, Marie; Visendi, Paul; Hayashi, Satomi; Luo, Mingcheng; Batley, Jacqueline; Edwards, David; Doležel, Jaroslav; Šimková, Hana

    2016-07-01

    The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules. PMID:26801360

  18. Sequential cloning of chromosomes

    Energy Technology Data Exchange (ETDEWEB)

    Lacks, S.A.

    1991-12-31

    A method for sequential cloning of chromosomal DNA and chromosomal DNA cloned by this method are disclosed. The method includes the selection of a target organism having a segment of chromosomal DNA to be sequentially cloned. A first DNA segment, having a first restriction enzyme site on either side. homologous to the chromosomal DNA to be sequentially cloned is isolated. A first vector product is formed by ligating the homologous segment into a suitably designed vector. The first vector product is circularly integrated into the target organism`s chromosomal DNA. The resulting integrated chromosomal DNA segment includes the homologous DNA segment at either end of the integrated vector segment. The integrated chromosomal DNA is cleaved with a second restriction enzyme and ligated to form a vector-containing plasmid, which is replicated in a host organism. The replicated plasmid is then cleaved with the first restriction enzyme. Next, a DNA segment containing the vector and a segment of DNA homologous to a distal portion of the previously isolated DNA segment is isolated. This segment is then ligated to form a plasmid which is replicated within a suitable host. This plasmid is then circularly integrated into the target chromosomal DNA. The chromosomal DNA containing the circularly integrated vector is treated with a third, retrorestriction enzyme. The cleaved DNA is ligated to give a plasmid that is used to transform a host permissive for replication of its vector. The sequential cloning process continues by repeated cycles of circular integration and excision. The excision is carried out alternately with the second and third enzymes.

  19. A new chromosome was born: comparative chromosome painting in Boechera.

    Science.gov (United States)

    Koch, Marcus A

    2015-09-01

    Comparative chromosome painting is a powerful tool to study the evolution of chromosomes and genomes. Analyzing karyotype evolution in cruciferous plants highlights the origin of aberrant chromosomes in apomictic Boechera and further establishes the cruciferous plants as important model system for our understanding of plant chromosome and genome evolution. PMID:26228436

  20. Evolutionary Design of Rule Changing Artificial Society Using Genetic Algorithms

    Science.gov (United States)

    Wu, Yun; Kanoh, Hitoshi

    Socioeconomic phenomena, cultural progress and political organization have recently been studied by creating artificial societies consisting of simulated agents. In this paper we propose a new method to design action rules of agents in artificial society that can realize given requests using genetic algorithms (GAs). In this paper we propose an efficient method for designing the action rules of agents that will constitute an artificial society that meets a specified demand by using a GAs. In the proposed method, each chromosome in the GA population represents a candidate set of action rules and the number of rule iterations. While a conventional method applies distinct rules in order of precedence, the present method applies a set of rules repeatedly for a certain period. The present method is aiming at both firm evolution of agent population and continuous action by that. Experimental results using the artificial society proved that the present method can generate artificial society which fills a demand in high probability.

  1. High-resolution fluorescence mapping of 46 DNA markers to the short arm of human chromosome 1

    Energy Technology Data Exchange (ETDEWEB)

    Van Roy, N.; Speleman, F.; Laureys, G. (University Hospital, Gent (Belgium)); Versteeg, R. (Academic Medical Center, Amsterdam (Netherlands)); Opdenakker, G. (Univ. of Leuven (Belgium))

    1993-10-01

    The authors describe a high-resolution cytogenetic map for 46 DNA markers previously assigned to the short arm of human chromosome 1. Using fluorescence in situ hybridization on simultaneously R-banded prometaphase chromosomes, a refined map position was found for 45 probes. For 6 of these probes, additional hybridization sites were observed and for another 7 probes, conflicting results were found with regard to previous localizations. For some probes with overlapping map positions, probe order could be determined by dual-color hybridization on elongated chromosomes. The present high-resolution map can be used to refine the previously published composite map and also provides additional landmarks for the construction of a contig map of the short arm of chromosome 1. 56 refs., 2 figs., 2 tabs.

  2. Dicty_cDB: Contig-U12668-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available s / Plus Query: 13 aaaaagggacttgngagtntgntgatttngatccnaaaccnnnnnnnngnaaaantgntg 72 |||||||||||||||||||||||||...|||||||||||||||| || |||||||||||| Sbjct: 13 aaaaagggacttgngagtntgntgatttngatccnaaaccnttnntttgnaaaantgntg 72 Q...aaaggntntgnntnctggaaancnagncaaggngnttcaa 192 Query: 193 nggccccntnaaangccnatcccctt 218 |||||||||||||||||||||...||||| Sbjct: 193 nggccccntnaaangccnatcccctt 218 >Contig-U11508-1 (Contig-U11508-1Q) /CSM_Contig/Contig-U1150...us Query: 13 aaaaagggacttgngagtntgntgatttngatccnaaaccnnnnnnnngnaaaantgntg 72 ||||

  3. Dicty_cDB: Contig-U12850-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available tcncttnattantttcgtttaaaaatttgtnnnaaacatgntnttgga 133 Query: 134 atcgccnaacntta 14...7 |||||||||||||| Sbjct: 134 atcgccnaacntta 147 >Contig-U13258-1 (Contig-U13258-1Q) /CSM_Contig/Contig-U13258...ttgtnnnaaacatgntnttgga 27 Query: 134 atcgccnaacntta 147 |||||||||||||| Sbjct: 26 atcgccnaacntta 13 Lambda K

  4. Chimpanzee chromosome 13 is homologous to human chromosome 2p

    Energy Technology Data Exchange (ETDEWEB)

    Sun, N. C.; Sun, C. R.Y.; Ho, T.

    1977-01-01

    Similarities between human and chimpanzee chromosomes are shown by chromosome banding techniques and somatic cell hybridization techniques. Cell hybrids were obtained from the chimpanzee lymphocyte LE-7, and the Chinese hamster mutant cell, Gal-2. Experiments showed that the ACPL, MDHs, and Gal-Act genes could be assigned to chimpanzee chromosome 13, and since these genes have been assigned to human chromosme 2p, it is suggested that chimpanzee chromosome 13 is homologous to human chromosome 2p. (HLW)

  5. Chromosome condensation and segmentation

    International Nuclear Information System (INIS)

    Some aspects of chromosome condensation in mammalians -humans especially- were studied by means of cytogenetic techniques of chromosome banding. Two further approaches were adopted: a study of normal condensation as early as prophase, and an analysis of chromosome segmentation induced by physical (temperature and γ-rays) or chemical agents (base analogues, antibiotics, ...) in order to show out the factors liable to affect condensation. Here 'segmentation' means an abnormal chromosome condensation appearing systematically and being reproducible. The study of normal condensation was made possible by the development of a technique based on cell synchronization by thymidine and giving prophasic and prometaphasic cells. Besides, the possibility of inducing R-banding segmentations on these cells by BrdU (5-bromodeoxyuridine) allowed a much finer analysis of karyotypes. Another technique was developed using 5-ACR (5-azacytidine), it allowed to induce a segmentation similar to the one obtained using BrdU and identify heterochromatic areas rich in G-C bases pairs

  6. Chromosomal abnormalities and autism

    Directory of Open Access Journals (Sweden)

    Farida El-Baz

    2016-01-01

    Conclusion: Chromosomal abnormalities were not detected in the studied autistic children, and so the relation between the genetics and autism still needs further work up with different study methods and techniques.

  7. Chromosome numbers in Bromeliaceae

    OpenAIRE

    2000-01-01

    The present study reports chromosome numbers of 17 species of Bromeliaceae, belonging to the genera Encholirium, Bromelia, Orthophytum, Hohenbergia, Billbergia, Neoglaziovia, Aechmea, Cryptanthus and Ananas. Most species present 2n = 50, however, Bromelia laciniosa, Orthophytum burle-marxii and O. maracasense are polyploids with 2n = 150, 2n = 100 and 2n = 150, respectively, while for Cryptanthus bahianus, 2n = 34 + 1-4B. B chromosomes were observed in Bromelia plumieri and Hohenbergia aff. u...

  8. Micromechanics of human mitotic chromosomes

    International Nuclear Information System (INIS)

    Eukaryote cells dramatically reorganize their long chromosomal DNAs to facilitate their physical segregation during mitosis. The internal organization of folded mitotic chromosomes remains a basic mystery of cell biology; its understanding would likely shed light on how chromosomes are separated from one another as well as into chromosome structure between cell divisions. We report biophysical experiments on single mitotic chromosomes from human cells, where we combine micromanipulation, nano-Newton-scale force measurement and biochemical treatments to study chromosome connectivity and topology. Results are in accord with previous experiments on amphibian chromosomes and support the 'chromatin network' model of mitotic chromosome structure. Prospects for studies of chromosome-organizing proteins using siRNA expression knockdowns, as well as for differential studies of chromosomes with and without mutations associated with genetic diseases, are also discussed

  9. Vibrio chromosomes share common history

    Directory of Open Access Journals (Sweden)

    Gevers Dirk

    2010-05-01

    Full Text Available Abstract Background While most gamma proteobacteria have a single circular chromosome, Vibrionales have two circular chromosomes. Horizontal gene transfer is common among Vibrios, and in light of this genetic mobility, it is an open question to what extent the two chromosomes themselves share a common history since their formation. Results Single copy genes from each chromosome (142 genes from chromosome I and 42 genes from chromosome II were identified from 19 sequenced Vibrionales genomes and their phylogenetic comparison suggests consistent phylogenies for each chromosome. Additionally, study of the gene organization and phylogeny of the respective origins of replication confirmed the shared history. Conclusions Thus, while elements within the chromosomes may have experienced significant genetic mobility, the backbones share a common history. This allows conclusions based on multilocus sequence analysis (MLSA for one chromosome to be applied equally to both chromosomes.

  10. Dicty_cDB: Contig-U07107-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ... 32 6.9 (Q54QK4) RecName: Full=COMM domain-containing protein 3; 32 6.9 ( P62371 ) RecName: Full=Histidyl-tRNA synthetase...0 0 0 Show Contig-U07107-1 Contig ID Contig-U07107-1 Contig update 2001. 8.30 Contig sequence >Contig-U07107...t of clone(s) est1= VSK428Z ,1,427 est2= VSK428F ,12,310 Translated Amino Acid seq...ikkk*k*k***yineikkitlg ltkelicfne*kngrcdrvefn Translated Amino Acid sequence (All Frames) Frame A: PRXRLNDMD...uery= Contig-U07107-1 (Contig-U07107-1Q) /CSM_Contig/Contig-U07107-1Q.Seq.d (426 letters) Database: CSM 6905 seq

  11. Dicty_cDB: Contig-U05758-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available taurus clone CH240-307J2, WORKING DRAFT SEQUE... 46 0.19 2 ( AM464344 ) Vitis vinifera contig VV78X137023.6, whole geno...ne) Kluyveromyces thermotolerans str... 36 0.47 AM270008_6( AM270008 |pid:none) Aspergillus niger contig An...AA4CH11RM1 CitNFL Citrus clementina cDNA 5', ... 36 1.2 2 ( AF250284 ) Amsacta moorei entomopoxvirus, complete geno...Contig-U05758-1 no gap 350 3 900580 900230 MINUS 1 2 U05758 0 0 0 0 0 0 1 0 0 0 0 0 0 0 Show Contig...-U05758-1 Contig ID Contig-U05758-1 Contig update 2002. 9.13 Contig sequence >Contig-U05758-1 (Contig

  12. Artificial Inteligence and Law

    OpenAIRE

    Fuková, Kateřina

    2012-01-01

    Submitted diploma work Artificial Intelligence and Law deals with the rule of law and its position in the process of new advanced technologies in computer cybernetics and further scientific disciplines related with artificial intelligence and its creation. The first part of the work introduces the history of the first imagines about artificial intelligence and concerns with its birth. This chapter presents main theoretical knowledge and hypotheses defined artificial intelligence and progre...

  13. Artificial Skin in Robotics

    OpenAIRE

    Strohmayr, Michael

    2012-01-01

    Artificial Skin - A comprehensive interface for system-environment interaction - This thesis investigates a multifunctional artificial skin as touch sensitive whole-body cover for robotic systems. To further the evolution from tactile sensors to an implementable artificial skin a general concept for the design process is derived. A standard test procedure is proposed to evaluate the performance. The artificial skin contributes to a safe and intuitive physical human robot interaction.

  14. Dicty_cDB: Contig-U04794-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available nuclear 16.0 %: mitochondrial 4.0 %: cytoskeletal >> prediction for Contig-U04794-1 is cyt VS (DIR, S) 0 VH...train 3D7, chromosome 9; s... 36 0.16 10 ( AP006628 ) Onion yellows phytoplasma OY-M DNA, complete genome. 3....4 4 ( CP001078 ) Clostridium botulinum E3 str. Alaska E43, complet... 40 1.4 14 ( FP102340 ) H.melpomene DN...e RP21-509E24 on chro... 34 6.8 4 ( AL035476 ) Plasmodium falciparum MAL4P3. 40 6.9 7 ( CP000061 ) Aster yell... SALK_089472.55.40.n Arabidopsis thaliana TDNA ins... 34 0.80 2 ( DT957227 ) CFW150-B03.x1d-t SHGC-CFW Gaste

  15. Dicty_cDB: Contig-U13867-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 0 (Q0SM54) RecName: Full=DNA mismatch repair protein mutS; &CP000... 35 4.0 T22894( T22894 ) hypothetical prote... of onion Allium... 46 3.1 1 ( AE014831 ) Plasmodium falciparum 3D7 chromosome 10 section 3... 40 3.3 11 ( FD453731 ) EGGAP49TR Haema...* fl*wlfkllc*rn**k*rktsqemgilyk*iiypahtk own update 2004. 6.10 Homology vs CSM-cDNA Query= Contig-U13867-1 (Conti...abase: 6905 Lambda K H 1.37 0.711 1.31 Gapped Lambda K H 1.37 0.711 1.31 Matrix: blastn matrix:1 -3 Gap Penalties: Existe...tobia irritans eggs Haematobia irr... 30 3.4 4 ( AE01485

  16. Dicty_cDB: Contig-U12340-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 8 2.7 5 ( AP007663 ) Lotus japonicus genomic DNA, chromosome 1, clone:... 32 2.8 8 ( AC215389 ) Solanum lycopersicum chro.... 34 3.0 7 ( AM437780 ) Vitis vinifera contig VV78X043497.20, whole genom... 42 3.2 2 ( AC121216 ) Rattus norvegi...*** SEQUENCIN... 40 6.5 7 ( EJ195879 ) 1092344237116 Global-Ocean-Sampling_GS-27-01-01-1... 36 6.5 2 ( AC133755 ) Rattus norvegi...200928. 30 8.0 4 ( CR855313 ) Zebrafish DNA sequence from clone CH211-198C17 in... 44 8.1 1 ( AC145790 ) Xenopus trop...us E33L, complete genome. 44 8.1 1 ( AE017355 ) Bacillus thuringiensis serovar ko

  17. Dicty_cDB: Contig-U16438-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available s sp. CC9902, compl... 37 7.1 ( P32864 ) RecName: Full=Rab proteins geranylgeranyltransferase co... 36 9.2 X70339_2( X70339 |pid:non...psis thaliana 26S proteasom... 442 e-151 AC003974_14( AC003974 |pid:none) Arabidopsis thaliana chromosome... 2... 442 e-151 AY242527_1( AY242527 |pid:none) Arabidopsis thaliana 26S proteasom... 440 e-151 AM458338_1( AM458338 |pid:non...orted] - ... 60 8e-07 AY230829_1( AY230829 |pid:none) Arabidopsis thaliana 26S proteasom... 59 1e-06 BT058758_1( BT058758 |pid:non...e) Vitis vinifera contig VV78X165900.... 441 e-151 BC014013_1( BC014013 |pid:none) Homo sapiens proteasome (proso

  18. Dicty_cDB: Contig-U06695-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Contig-U06695-1 no gap 782 5 1146712 1147499 PLUS 1 1 U06695 1 0 0 0 0 0 0 0 0 0 0 0 0 0 Show Co ... ry gland RCB-052... 37 0.92 (Q3UMB5) RecName: Full=Smith -Magenis syndrome chromosomal region... 37 0.92 BC0 ... 85095_1( BC085095 |pid:none) Mus musculus Smith -Magenis syndrom... 37 0.92 ( P47460 ) RecName: Ful ... 5 2.7 AF467440_1( AF467440 |pid:none) Homo sapiens Smith -Magenis syndrom... 35 3.5 (Q9UWW9) RecName: Full=V ... 000678_524( CP000678 |pid:none) Methanobrevibacter smith ii ATCC ... 35 3.5 CP000500_417( CP000500 |pid:none ...

  19. Dicty_cDB: Contig-U09024-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available : 5,564,391 effective search space: 4857713343 effective search space used: 4857713343 T: 0 A: 40 X1: 6 (11.9 bits...rovar 3 str. ATCC 700970 sect... 38 0.65 3 ( AM451152 ) Vitis vinifera contig VV78X013054.24... Rattus norvegicus DNA, BAC clone: RNB1-065G09, 3'... 34 2.0 3 ( AE014836 ) Plasmodium falciparum 3D7 chromosome 11 sect... 1 ( ER966253 ) SOOAU08JR LargeInsertSoybeanGenLibBuild4 Glycine ... 44 8.9 1 ( ER966076 ) SOOAO83JR LargeInse...rtSoybeanGenLibBuild4 Glycine ... 44 8.9 1 ( ER965865 ) SOOAP03JR LargeInsertSoybeanGenLibBuild4 Glycine .

  20. Dicty_cDB: Contig-U09438-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available e) Trypanosoma brucei chaperone (DNAJ... 45 0.008 (Q6MTJ6) RecName: Full=GTP-binding pro...SS *** f... 36 0.94 9 ( AP009597 ) Solanum lycopersicum DNA, chromosome 8, clone: C0... 36 1.1 9 ( CZ706610 ...732527_1( AL732527 |pid:none) Mouse DNA sequence from clone RP23... 107 2e-21 EU621369_1( EU621369 |pid:none) Solanum lycoper...e) Oryza sativa Japonica Group genom... 67 2e-09 BT075006_1( BT075006 |pid:none) Osmerus mordax clone...e) Aspergillus niger contig An05c001... 49 5e-04 (B0K5N4) R

  1. Dicty_cDB: Contig-U04657-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 04002 ) Sequence 68317 from patent US 7214786. 38 0.17 2 ( BJ236677 ) Triticum aestivum cDNA clone:whe22k05,...5135... 32 8.4 7 ( AX392734 ) Sequence 24 from Patent WO0212526. 32 8.4 5 ( AR707081 ) Sequence 24 from patent...ne RP24-95H13 from chromosome... 40 2.2 2 ( X77854 ) P.falciparum (FCBR-Columbia...SS *** f... 34 2.4 6 ( BX572083 ) Zebrafish DNA sequence from clone DKEY-232J4 in l... 40 2.4 5 ( AL049658 ) Arabidopsis thalian...670974928920 X1: 11 (21.8 bits) S2: 22 (44.1 bits) protein update 2009. 7.30 Homology vs Protein Query= Contig-U04657-1 (Co

  2. Dicty_cDB: Contig-U05501-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available c0... 40 1.0 2 ( GC696613 ) Sequence 11857 from patent US 6812339. 46 1.1 1 ( AL357127 ) Human...e GM_WBc0028K1... 30 9.4 6 ( GC700442 ) Sequence 15687 from patent US 6812339. 38 9.5 3 ( AC226709 ) Oryza minuta clo...e... 44 4.2 1 ( EA690864 ) Sequence 69743 from patent US 7365185. 44 4.2 1 ( EA625507 ) Sequence 4386 from patent...ts) S1: 12 (24.3 bits) S2: 14 (28.2 bits) dna update 2009. 7.28 Homology vs DNA Query= Contig-U05501-1 (Co...9( CP001324 |pid:none) Micromonas sp. RCC299 chromosome... 52 5e-06 BT003919_1( BT003919 |pid:none) Arabidopsis thaliana clo

  3. Dicty_cDB: Contig-U14001-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available one) Debaryomyces hansenii strain CBS7... 41 0.016 FN392320_967( FN392320 |pid:none) Pichia pastoris GS115 chromo...e complete mitochondrial g... 36 0.061 7 ( AE014840 ) Plasmodium falciparum 3D7 chromosome 11 ...05 CP000499_475( CP000499 |pid:none) Pichia stipitis CBS 6054 chromos... 42 3e-04 AP007162_308( AP007162 |pi...cff*ihlylhhh*llhflhqipniptyiyxxy Frame B: ylellphvt*lilplniiigsglaelvk*ylnifingvlil*fisliisliassndgins fgeeixrpdnf*lksvk*siltsi*ch...ntig/Contig-U14001-1Q.Seq.d (478 letters) Database: ddbj_A 92,845,959 sequences; 95,242,211,685 total letters Searchi

  4. Dicty_cDB: Contig-U15444-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available panosoma cruzi ribosomal protei... 159 2e-37 FN392319_525( FN392319 |pid:none) Pichia pastoris GS115 chromos...tellanii snu13p-li... 52 3e-05 FN392321_1070( FN392321 |pid:none) Pichia pastoris GS115 chromosom... 52 3e-... 5e-06 BT082604_1( BT082604 |pid:none) Anoplopoma fimbria clone afim-evh-... 55 5e-06 CP000502_181( CP000502 |pid:none) Pichia...m3b: 0.00 m_ : 1.00 72.0 %: cytoplasmic 28.0 %: mitochondrial >> prediction for Contig-U15444-1 is cyt VS (D...( FE250526 ) CAPH2905.rev CAPH Naegleria gruberi amoeba stage ... 42 0.011 2 ( BJ010249 ) Oryzias

  5. Dicty_cDB: Contig-U13177-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ... 47 9e-04 CR940353_474( CR940353 |pid:none) Theileria annulata strain Ankara... 39 0.14 CR925677_106( CR925677 |pid:none) Ehrlichi...5 2.0 FN357468_4( FN357468 |pid:none) Schistosoma mansoni genome sequenc... 35 2.6 AE014187_477( AE014187 |pid:none) Plasmo...30C14, WORK... 38 2.6 5 ( AP002894 ) Homo sapiens genomic DNA, chromosome 18q11.2, clo... 42 3.1 3 ( AE017245 ) Mycoplasma synovia...Contig-U13177-1Q.Seq.d (762 letters) Database: nrp_B 3,236,559 sequences; 1,051,180,864 total letters Searchi...r curvus 525.92, co... 37 0.52 BX248583_293( BX248583 |pid:none) Blochmannia flor

  6. Dicty_cDB: Contig-U10171-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available AM425875_2( AM425875 |pid:none) Vitis vinifera contig VV79X000674.... 46 0.002 AM180355_2015( AM180355 |pid:none) Clostridium diffici...3 CP000882_106( CP000882 |pid:none) Hemiselmis andersenii chromosome... 181 3e-56 CP000582_297( CP000582 |pid...:none) Neurospora crassa DNA linkage grou... 86 3e-15 AM920431_439( AM920431 |pid:none) Penici...71 List of clone(s) est1= SFJ447F ,1,598 est2= VFI696E ,1,1196 est3= VFJ806E ,4,1196 est4= SFJ447Z ,552,1197 Translated Amino Acid...vhxifxss Translated Amino Acid sequence (All Frames) Frame A: nkfqnnenernhcnlnynnknnr

  7. Dicty_cDB: Contig-U02687-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available osome number (1..6, M) - Chromosome length - Start point - End point - Strand (PLUS/MINUS) - Number of clone...ig/Contig-U02687-1Q.Seq.d Length = 110 Score = 50.1 bits (25), Expect = 5e-07 Identities = 28/28 (100%) Strand...-1Q.Seq.d Length = 192 Score = 36.2 bits (18), Expect = 0.007 Identities = 18/18 (100%) Strand = Plus / Plus...xpect = 0.027 Identities = 17/17 (100%) Strand = Plus / Plus Query: 1 ccccccccccc...cccccg 17 ||||||||||||||||| Sbjct: 27 ccccccccccccccccg 43 Score = 32.2 bits (16), Expect = 0.11 Identities = 16/16 (100%) Strand

  8. Dicty_cDB: Contig-U12581-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available .20 FM992688_643( FM992688 |pid:none) Candida dubliniensis CD36 chromo... 40 0.20 AB052049_1( AB052049 |pid:none) Astragalus curvi...0... 36 0.001 17 ( CR548612 ) Paramecium tetraurelia macronuclear largest chrom... 40 0.002 20 ( CP000942 ) Ureaplasma parvum sero... 1005175... 36 0.042 17 ( AE002120 ) Ureaplasma parvum serovar 3 str. ATCC 700970 sect... 34 0.048 6 ( AC116330 ) Dictyost...s maripaludis C6, co... 37 1.3 AB052056_1( AB052056 |pid:none) Astragalus subsecundus chloroplast... Patent WO0200932. 34 0.49 13 ( AM285307 ) Spiroplasma citri GII3-3X chromosome, contig Cont... 32 0.51 8 ( CP000939 ) Clostr

  9. Dicty_cDB: Contig-U04356-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available iparum 3D7 chromo... 35 3.9 AJ224982_1( AJ224982 |pid:none) Arabidopsis thaliana MAP3K epsilo...lus weihenstephanensis KBAB... 35 3.9 CP001634_186( CP001634 |pid:none) Kosmotoga olearia TBF 19.5...ne SSH186. 170 1e-49 2 ( AG370890 ) Mus musculus molossinus DNA, clone:MSMg01-176B09.... 54 0.010 1 ( AM437...ome 4, contig fra... 46 2.5 1 ( AL022373 ) Arabidopsis thaliana DNA chromosome 4, BAC clone ... ... full length cDNA. 46 2.5 1 ( DL211775 ) Full length cDNA. 46 2.5 1 ( DL178705 ) Novel full length cDNA. 46

  10. Dicty_cDB: Contig-U01541-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ula chromosome 7 BAC clone mth2-7... 36 3.7 5 ( FG283242 ) 1108457714276 New World Screwworm Egg 9261 ESTs C...1-1... 40 3.8 2 ( AM448784 ) Vitis vinifera contig VV78X077229.13, whole genom... 40 3.8 5 ( FG299281 ) 1108793334783 New World...malized cDNA li... 34 3.8 3 ( FG298782 ) 1108793320683 New World Screwworm Larvae 9387 EST... 40 3.8 2 ( AC2...) Populus trichocarpa clone POP011-A24, complete se... 38 3.9 5 ( FG298363 ) 1108793311332 New World Screwwo...rm Larvae 9387 EST... 40 3.9 2 ( AE017263 ) Mesoplasma florum L1 complete genome. 34 3.9 11 ( FG290177 ) 1108793315292 New World

  11. Dicty_cDB: Contig-U09615-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available m Patent WO0200932. 38 3.3 11 ( AF209182 ) Homo sapiens Xp-probe P20 sequence. 44 3.4 2 .... 36 8.4 2 ( AY044868 ) Campylobacter jejuni heptosyltransferase I (waaC)... 36 8.4 2 ( GC474820 ) Sequence 1 fro...138258. 36 8.4 2 ( CS299359 ) Sequence 1 from Patent EP1652927. 36 8.4 2 ( BD249790 ) Campylobacter glycolsyltransfer... domain containi... 38 0.76 AY438272_1( AY438272 |pid:none) Plasmodium berghei UOS7/S20 gene, ... 38 0.76 AY...TGCAAGATTAGAAAGATTAGAAAAAGATGCTATGCTAAAAATA Gap gap included Contig length 1134 Chromosome number (1..6, M) 3 Chro

  12. Dicty_cDB: Contig-U14906-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 0.89 2 ( AM438236 ) Vitis vinifera contig VV78X141747.12, whole genom... 36 0.98 2 ( BC059806 ) Danio reri...o G protein-coupled receptor 143, mRNA ... 32 1.0 2 ( CD754949 ) AGENCOURT_14627365 NCI_CGAP_ZEmb2 Danio...s brain cDNA clone: QmoA-11183,... 46 1.5 1 ( CU638744 ) Podospora anserina genomic DNA chromosome 6, supe...-06 FN357541_15( FN357541 |pid:none) Schistosoma mansoni genome sequen... 52 1e-05 AF204783_1( AF204783 |pid:none) Lycopersico...AY373584_1( AY373584 |pid:none) Emericella nidulans diploid state ... 34 4.0 AJ938182_419( AJ938182 |pid:none) Staphyloco

  13. Dicty_cDB: Contig-U10800-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ica Group genomi... 35 8.9 L80071_1( L80071 |pid:none) Paramecium tetraurelia immobilization ... 35 ...46 1.4 4 ( AM439248 ) Vitis vinifera contig VV79X007207.11, whole genom... 34 1.4 6 ( EK294420 ) 1095462342281 Global-Ocean-Sampli... IIa - blue crab 36 3.1 S25111( S25111 ;S32554) alpha-2-macroglobulin receptor precursor -... 36 3.1 AC024830_9( AC024830 |pid:non...e) Danio rerio coagulation factor VII... 35 8.9 AP005419_8( AP005419 |pid:none) Oryza sativa Japon...AP000247 ) Homo sapiens genomic DNA, chromosome 21q, clone:R... 46 3.7 1 >( AF318287 ) Dictyostelium discoideum putative calmoduli

  14. Dicty_cDB: Contig-U14894-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available P001634_1671( CP001634 |pid:none) Kosmotoga olearia TBF 19.5.1, c... 38 0.30 (Q6MKR6) RecName: Full=Glutamyl...5( CP001229 |pid:none) Sulfurihydrogenibium azorense Az... 52 2e-05 CP001634_1902( CP001634 |pid:none) Kos...AATTAAAATGAAACA AAAAGTTTGGA Gap no gap Contig length 661 Chromosome number (1..6, M) 2 Chromos...telium discoideum vegetative cDNA clone:VS... 268 e-130 2 ( AC116925 ) Dictyostelium discoideum chromos...7 1 ( AC161462 ) Gallus gallus BAC clone CH261-174G12 from chromos... 50 0.10 1 ( AC224135 ) Bos taurus clon

  15. Dicty_cDB: Contig-U12617-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available plete g... 32 8.7 2 ( EI347844 ) GM_WBc0094G22.f GM_WBc Glycine max genomic clone ... 34 9.6 2 >( BJ366788 ) Dict... assembly factor 1 subunit B; ... 154 1e-36 (Q9D0N7) RecName: Full=Chromatin assembly facto...) Leishmania infantum chromosome 24. 52 1e-05 (Q8C092) RecName: Full=Transcription initiation facto...ifera contig VV78X154848.... 50 7e-05 >(Q5R1S9) RecName: Full=Chromatin assembly factor 1 subunit...atin assembly factor 1 subunit B; ... 160 3e-38 AJ719705_1( AJ719705 |pid:none) Gallu

  16. Development of a novel HAC-based "gain of signal" quantitative assay for measuring chromosome instability (CIN) in cancer cells

    OpenAIRE

    Kim, Jung Hyun; Lee, Hee Sheung; Lee, Nicholas C.O.; Goncharov, Nikolay V.; Kumeiko, Vadim; Masumoto, Hiroshi; Earnshaw, William C.; Kouprina, Natalay; Larionov, Vladimir

    2016-01-01

    Accumulating data indicates that chromosome instability (CIN) common to cancer cells can be used as a target for cancer therapy. At present the rate of chromosome mis-segregation is quantified by laborious techniques such as coupling clonal cell analysis with karyotyping or fluorescence in situ hybridization (FISH). Recently, a novel assay was developed based on the loss of a non-essential human artificial chromosome (HAC) carrying a constitutively expressed EGFP transgene ("loss of signal" a...

  17. Sequencing and association analysis of the type 1 diabetes – linked region on chromosome 10p12-q11

    Directory of Open Access Journals (Sweden)

    Barratt Bryan J

    2007-05-01

    Full Text Available Abstract Background In an effort to locate susceptibility genes for type 1 diabetes (T1D several genome-wide linkage scans have been undertaken. A chromosomal region designated IDDM10 retained genome-wide significance in a combined analysis of the main linkage scans. Here, we studied sequence polymorphisms in 23 Mb on chromosome 10p12-q11, including the putative IDDM10 region, to identify genes associated with T1D. Results Initially, we resequenced the functional candidate genes, CREM and SDF1, located in this region, genotyped 13 tag single nucleotide polymorphisms (SNPs and found no association with T1D. We then undertook analysis of the whole 23 Mb region. We constructed and sequenced a contig tile path from two bacterial artificial clone libraries. By comparison with a clone library from an unrelated person used in the Human Genome Project, we identified 12,058 SNPs. We genotyped 303 SNPs and 25 polymorphic microsatellite markers in 765 multiplex T1D families and followed up 22 associated polymorphisms in up to 2,857 families. We found nominal evidence of association in six loci (P = 0.05 – 0.0026, located near the PAPD1 gene. Therefore, we resequenced 38.8 kb in this region, found 147 SNPs and genotyped 84 of them in the T1D families. We also tested 13 polymorphisms in the PAPD1 gene and in five other loci in 1,612 T1D patients and 1,828 controls from the UK. Overall, only the D10S193 microsatellite marker located 28 kb downstream of PAPD1 showed nominal evidence of association in both T1D families and in the case-control sample (P = 0.037 and 0.03, respectively. Conclusion We conclude that polymorphisms in the CREM and SDF1 genes have no major effect on T1D. The weak T1D association that we detected in the association scan near the PAPD1 gene may be either false or due to a small genuine effect, and cannot explain linkage at the IDDM10 region.

  18. Chromosome duplication in Lolium multiflorum Lam.

    Directory of Open Access Journals (Sweden)

    Roselaine Cristina Pereira

    2014-11-01

    Full Text Available Artificial chromosome duplication of diploid genotypes of Lolium multiflorum (2n=2x=14 is worthy to breeding, and aims to increase the expression of traits with agronomic interest. The purpose of this study was to obtain polyploid plants of L. multiflorum from local diploid populations in order to exploit adaptation and future verification of the effects of polyploidy in agronomic traits. Seedlings were immersed in different colchicine solutions for an exposure time of 3h and 24h. Ploidy determination was made by the DNA content and certified by chromosomes counts. The plants confirmed as tetraploids were placed in a greenhouse, and, at flowering, pollen viability was evaluated, and seeds were harvested to assess the stability of the progenies. The percentage of polyploids obtained was 20%. Pollen viability of the tetraploids generated ranged from 58% to 69%. The tetraploid plants obtained in the experiment generated 164 progenies, of which 109 presented DNA content compatible with the tetraploid level, showing stability of chromosome duplication in the filial generation.

  19. Sex determination by chromosome manipulation in fish

    International Nuclear Information System (INIS)

    Since it is impossible to artificially remove only sex chromosomes in sperm, gamma- or UV-irradiation has been used in destroying all chromosomes without loss of abilities of sperm movement and egg activation. It has been shown that a dose of gamma rays required for this purpose is 105 rad in any species of fish. For UV-irradiation, a 15 W lamp is used and irradiation for 60 to 120 seconds is required. With such an irradiation technique, gynogenetic haploid embryogenesis is induced. In developing normal diploid embryos of eggs inseminated with irradiated sperm (gynogenetic diploid embryogenesis with XX type), it is furthermore necessary to use physical procedures, such as low or high temperature and hydrostatic pressure. Irradiated sperm of different species of fish has also been used in inducing gynogenesis. As the most desirable technique, it is proposed to physiologically convert the sex of gynogenetic diploid embryos into males and to use sperm from those physiological males with XX chromosomes. Theoretical possibility of developing androgenetic haploid embryogenesis has been suggested. (Namekawa, K.)

  20. Chromosome numbers in Bromeliaceae

    Directory of Open Access Journals (Sweden)

    Cotias-de-Oliveira Ana Lúcia Pires

    2000-01-01

    Full Text Available The present study reports chromosome numbers of 17 species of Bromeliaceae, belonging to the genera Encholirium, Bromelia, Orthophytum, Hohenbergia, Billbergia, Neoglaziovia, Aechmea, Cryptanthus and Ananas. Most species present 2n = 50, however, Bromelia laciniosa, Orthophytum burle-marxii and O. maracasense are polyploids with 2n = 150, 2n = 100 and 2n = 150, respectively, while for Cryptanthus bahianus, 2n = 34 + 1-4B. B chromosomes were observed in Bromelia plumieri and Hohenbergia aff. utriculosa. The chromosome number of all species was determined for the first time, except for Billbergia chlorosticta and Cryptanthus bahianus. Our data supports the hypothesis of a basic number of x = 25 for the Bromeliaceae family and decreasing aneuploidy in the genus Cryptanthus.

  1. Those amazing dinoflagellate chromosomes

    Institute of Scientific and Technical Information of China (English)

    PETER J RIZZO

    2003-01-01

    Dinoflagellates are a very large and diverse group of eukaryotic algae that play a major role in aquatic food webs of both fresh water and marine habitats. Moreover, the toxic members of this group pose a health threat in the form of red tides. Finally, dinoflagellates are of great evolutionary importance,because of their taxonomic position, and their unusual chromosome structure and composition. While the cytoplasm of dinoflagellates is typically eukaryotic, the nucleus is unique when compared to the nucleus of other eukaryotes. More specifically, while the chromosomes of all other eukaryotes contain histones,dinoflagellate chromosomes lack histones completely. There are no known exceptions to this observation: all dinoflagellates lack histones, and all other eukaryotes contain histones. Nevertheless, dinoflagellates remain a relatively unstudied group of eukaryotes.

  2. A panel of sequence tagged sites for chromosome band 11q23

    Energy Technology Data Exchange (ETDEWEB)

    Tunnacliffe, A.; Perry, H. (Univ. of Cambridge (United Kingdom)); Radice, P. (Univ. of Cambridge (United Kingdom) Istituto Nazionale Tumori, Milan (Italy)); Budarf, M.L.; Emanuel, B.S. (Univ. of Pennsylvania School of Medicine, Philadelphia, PA (United States))

    1993-09-01

    A panel of sequence tagged sites (STSs) representing 30 markers previously assigned to human chromosome band 11q23 has been assembled. Eleven STSs represent cloned genes, and the remainder are from anonymous DNA segments. The STSs have been used in PCR experiments to localize their cognate sequences further with respect to five translocation breakpoints that define three intervals in 11q23. Two of these translocation breakpoints have been mapped more precisely by the STS assignments. The STS panel will form a useful starting point for the generation of a genomic contig of band 11q23. 32 refs., 1 fig., 1 tab.

  3. The testis and ovary transcriptomes of the rock bream (Oplegnathus fasciatus: A bony fish with a unique neo Y chromosome

    Directory of Open Access Journals (Sweden)

    Dongdong Xu

    2016-03-01

    Full Text Available The rock bream (Oplegnathus fasciatus is considerably one of the most economically important marine fish in East Asia and has a unique neo-Y chromosome system that is a good model to study the sex determination and differentiation in fish. In the present study, we used Illumina sequencing technology (HiSeq2000 to sequence, assemble and annotate the transcriptome of the testis and ovary tissues of rock bream. A total of 40,004,378 (NCBI SRA database SRX1406649 and 53,108,992 (NCBI SRA database SRX1406648 high quality reads were obtained from testis and ovary RNA sequencing, respectively, and 60,421 contigs (with average length of 1301 bp were obtained after de novo assembling with Trinity software. Digital gene expression analysis reveals 14,036 contigs that show gender-enriched expressional profile with either testis-enriched (237 contigs or ovary-enriched (581 contigs with RPKM >100. There are 237 male- and 582 female-abundant expressed genes that show sex dimorphic expression. We hope that the gonad transcriptome and those gender-enriched transcripts of rock bream can provide some insight into the understanding of genome-wide transcriptome profile of teleost gonad tissue and give useful information in fish gonad development.

  4. Chromosomal rearrangements in cattle and pigs revealed by chromosome microdissection and chromosome painting

    Directory of Open Access Journals (Sweden)

    Yerle Martine

    2003-11-01

    Full Text Available Abstract A pericentric inversion of chromosome 4 in a boar, as well as a case of (2q-;5p+ translocation mosaicism in a bull were analysed by chromosome painting using probes generated by conventional microdissection. For the porcine inversion, probes specific for p arms and q arms were produced and hybridised simultaneously on metaphases of a heterozygote carrier. In the case of the bovine translocation, two whole chromosome probes (chromosome 5, and derived chromosome 5 were elaborated and hybridised independently on chromosomal preparations of the bull who was a carrier of the mosaic translocation. The impossibility of differentiating chromosomes 2 and der(2 from other chromosomes of the metaphases did not allow the production of painting probes for these chromosomes. For all experiments, the quality of painting was comparable to that usually observed with probes obtained from flow-sorted chromosomes. The results obtained allowed confirmation of the interpretations proposed with G-banding karyotype analyses. In the bovine case, however, the reciprocity of the translocation could not be proven. The results presented in this paper show the usefulness of the microdissection technique for characterising chromosomal rearrangements in species for which commercial probes are not available. They also confirmed that the main limiting factor of the technique is the quality of the chromosomal preparations, which does not allow the identification of target chromosomes or chromosome fragments in all cases.

  5. Speeding up chromosome evolution in Phaseolus: multiple rearrangements associated with a one-step descending dysploidy.

    Science.gov (United States)

    Fonsêca, Artur; Ferraz, Maria Eduarda; Pedrosa-Harand, Andrea

    2016-06-01

    The genus Phaseolus L. has been subject of extensive cytogenetic studies due to its global economic importance. It is considered karyotypically stable, with most of its ca. 75 species having 2n = 22 chromosomes, and only three species (Phaseolus leptostachyus, Phaseolus macvaughii, and Phaseolus micranthus), which form the Leptostachyus clade, having 2n = 20. To test whether a simple chromosomal fusion was the cause of this descending dysploidy, mitotic chromosomes of P. leptostachyus (2n = 20) were comparatively mapped by fluorescent in situ hybridization (FISH) using bacterial artificial chromosomes (BACs) and ribosomal DNA (rDNA) probes. Our results corroborated the conservation of the 5S and 45S rDNA sites on ancestral chromosomes 10 and 6, respectively. The reduction from x = 11 to x = 10 was the result of the insertion of chromosome 10 into the centromeric region of chromosome 11, supporting a nested chromosome fusion (NCF) as the main cause of this dysploidy. Additionally, the terminal region of the long arm of chromosome 6 was translocated to this larger chromosome. Surprisingly, the NCF was accompanied by several additional translocations and inversions previously unknown for the genus, suggesting that the dysploidy may have been associated to a burst of genome reorganization in this otherwise stable, diploid plant genus. PMID:26490170

  6. Identification of Chromosomes from Multiple Rice Genomes Using a Universal Molecular Cytogenetic Marker System

    Institute of Scientific and Technical Information of China (English)

    Xiaomin Tang; Weidong Bao; Wenli Zhang; Zhukuan Cheng

    2007-01-01

    To develop reliable techniques for chromosome identification is critical for cytogenetic research, especially for genomes with a large number and smaller-sized chromosomes. An efficient approach using bacterial artificial chromosome (BAG) clones as molecular cytological markers has been developed for many organisms. Herein, we present a set of chromosomal arm-specific molecular cytological markers derived from the gene-enriched regions of the sequenced rice genome. All these markers are able to generate very strong signals on the pachytene chromosomes of Oryza satlva L. (AA genome) when used as fluorescence in situ hybridization (FISH) probes. We further probed those markers to the pachytene chromosomes of O. punctata (BB genome) and O. officinalis (CC genome) and also got very strong signals on the relevant pachytene chromosomes. The signal position of each marker on the related chromosomes from the three different rice genomes was pretty much stable, which enabled us to identify different chromosomes among various rice genomes. We also constructed the karyotype for both O. punctata and O. officinalis with the BB and CC genomes, respectively, by analysis of 10 pachytene cells anchored by these chromosomal arm-specific markers.

  7. Construction of BAC Libraries from Flow-Sorted Chromosomes.

    Science.gov (United States)

    Šafář, Jan; Šimková, Hana; Doležel, Jaroslav

    2016-01-01

    Cloned DNA libraries in bacterial artificial chromosome (BAC) are the most widely used form of large-insert DNA libraries. BAC libraries are typically represented by ordered clones derived from genomic DNA of a particular organism. In the case of large eukaryotic genomes, whole-genome libraries consist of a hundred thousand to a million clones, which make their handling and screening a daunting task. The labor and cost of working with whole-genome libraries can be greatly reduced by constructing a library derived from a smaller part of the genome. Here we describe construction of BAC libraries from mitotic chromosomes purified by flow cytometric sorting. Chromosome-specific BAC libraries facilitate positional gene cloning, physical mapping, and sequencing in complex plant genomes. PMID:27511172

  8. Linked genetic variants on chromosome 10 control ear morphology and body mass among dog breeds

    OpenAIRE

    Webster, Matthew T.; Kamgari, Nona; Perloski, Michele; Höppner, Marc P.; Axelsson, Erik; Hedhammar, Ake; Pielberg, Gerli; Lindblad-Toh, Kerstin

    2015-01-01

    Background The domestic dog is a rich resource for mapping the genetic components of phenotypic variation due to its unique population history involving strong artificial selection. Genome-wide association studies have revealed a number of chromosomal regions where genetic variation associates with morphological characters that typify dog breeds. A region on chromosome 10 is among those with the highest levels of genetic differentiation between dog breeds and is associated with body mass and ...

  9. Quo Vadis, Artificial Intelligence?

    OpenAIRE

    Alfons Schuster; Daniel Berrar; Naoyuki Sato

    2010-01-01

    Since its conception in the mid 1950s, artificial intelligence with its great ambition to understand and emulate intelligence in natural and artificial environments alike is now a truly multidisciplinary field that reaches out and is inspired by a great diversity of other fields. Rapid advances in research and technology in various fields have created environments into which artificial intelligence could embed itself naturally and comfortably. Neuroscience with its desire to understand nervou...

  10. Anticipatory Artificial Autopoiesis

    OpenAIRE

    DuBois, Daniel; Holmberg, Stig C.

    2010-01-01

    In examining relationships between autopoiesis and anticipation in artificial life (Alife) systems it is demonstrated that anticipation may increase efficiency and viability in artificial autopoietic living systems. This paper, firstly, gives a review of the Varela et al [1974] automata algorithm of an autopoietic living cell. Some problems in this algorithm must be corrected. Secondly, a new and original anticipatory artificial autopoiesis algorithm for automata is presented. ...

  11. Artificial cognition architectures

    CERN Document Server

    Crowder, James A; Friess, Shelli A

    2013-01-01

    The goal of this book is to establish the foundation, principles, theory, and concepts that are the backbone of real, autonomous Artificial Intelligence. Presented here are some basic human intelligence concepts framed for Artificial Intelligence systems. These include concepts like Metacognition and Metamemory, along with architectural constructs for Artificial Intelligence versions of human brain functions like the prefrontal cortex. Also presented are possible hardware and software architectures that lend themselves to learning, reasoning, and self-evolution

  12. Doped Colloidal Artificial Ice

    OpenAIRE

    Libal, A.; Reichhardt, C. J. Olson; Reichhardt, C.

    2015-01-01

    We examine square and kagome artificial spin ice for colloids confined in arrays of double-well traps. Unlike magnetic artificial spin ices, colloidal and vortex artificial spin ice realizations allow creation of doping sites through double occupation of individual traps. We find that doping square and kagome ice geometries produces opposite effects. For square ice, doping creates local excitations in the ground state configuration that produce a local melting effect as the temperature is rai...

  13. Inteligencia artificial en vehiculo

    OpenAIRE

    Amador Díaz, Pedro

    2012-01-01

    Desarrollo de un robot seguidor de líneas, en el que se implementan diversas soluciones de las áreas de sistemas embebidos e inteligencia artificial. Desenvolupament d'un robot seguidor de línies, en el qual s'implementen diverses solucions de les àrees de sistemes encastats i intel·ligència artificial. Follower robot development of lines, in which various solutions are implemented in the areas of artificial intelligence embedded systems.

  14. Ring chromosome 13

    DEFF Research Database (Denmark)

    Brandt, C A; Hertz, Jens Michael; Petersen, M B; Vogel, F; Noer, H; Mikkelsen, M

    1992-01-01

    A stillborn male child with anencephaly and multiple malformations was found to have the karyotype 46,XY,r(13) (p11q21.1). The breakpoint at 13q21.1, determined by high resolution banding, is the most proximal breakpoint ever reported in patients with ring chromosome 13. In situ hybridisation with...

  15. The Y Chromosome

    Science.gov (United States)

    Offner, Susan

    2010-01-01

    The Y chromosome is of great interest to students and can be used to teach about many important biological concepts in addition to sex determination. This paper discusses mutation, recombination, mammalian sex determination, sex determination in general, and the evolution of sex determination in mammals. It includes a student activity that…

  16. Chromosomes, cancer and radiosensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Samouhos, E.

    1983-08-01

    Some specific chromosomal abnormalities are associated with certain cancers. The earliest description of such a specific association is the one of the Philadelphia chromosome and myelogenous leukemia (1960). Other congenital karyotype abnormalities are associated with specific cancers. Examples of these are Down's syndrome with leukemia and Klinefelter's syndrome with male breast cancer. Genetic diseases of increased chromosome breakage, or of defective chromosome repair, are associated with greatly increased cancer incidence. Three such diseases have been recognized: 1) Fanconi's anemia, associated with leukemias and lymphomas, 2) Bloom's syndrome, associated with acute leukemias and lymphosarcoma, and 3) ataxia telangiectasia, associated with Hodgkin's disease, leukemia, and lymphosarcomas. Ten percent of individuals with ataxia telangiectasia will develop one of these neoplasms. Individuals with certain of these syndromes display an unusually high radiosensitivity. Radiation therapy for cancers has been fatal in patients who received as low as 3000 rad. This remarkable radiosensitivity has been quantitated in cell cultures from such cases. Evidence suggests that the apparent sensitivity may reflect subnormal ability to repair radiation damage. The rapid proliferation of information in this field stems from the interdigitation of many disciplines and specialties, including cytogenetics, cell biology, molecular biology, epidemiology, radiobiology, and several others. This paper is intended for clinicians; it presents a structured analytic scheme for correlating and classifying this multidisciplinary information as it becomes available.

  17. Chromosomes, cancer and radiosensitivity

    International Nuclear Information System (INIS)

    Some specific chromosomal abnormalities are associated with certain cancers. The earliest description of such a specific association is the one of the Philadelphia chromosome and myelogenous leukemia (1960). Other congenital karyotype abnormalities are associated with specific cancers. Examples of these are Down's syndrome with leukemia and Klinefelter's syndrome with male breast cancer. Genetic diseases of increased chromosome breakage, or of defective chromosome repair, are associated with greatly increased cancer incidence. Three such diseases have been recognized: 1) Fanconi's anemia, associated with leukemias and lymphomas, 2) Bloom's syndrome, associated with acute leukemias and lymphosarcoma, and 3) ataxia telangiectasia, associated with Hodgkin's disease, leukemia, and lymphosarcomas. Ten percent of individuals with ataxia telangiectasia will develop one of these neoplasms. Individuals with certain of these syndromes display an unusually high radiosensitivity. Radiation therapy for cancers has been fatal in patients who received as low as 3000 rad. This remarkable radiosensitivity has been quantitated in cell cultures from such cases. Evidence suggests that the apparent sensitivity may reflect subnormal ability to repair radiation damage. The rapid proliferation of information in this field stems from the interdigitation of many disciplines and specialties, including cytogenetics, cell biology, molecular biology, epidemiology, radiobiology, and several others. This paper is intended for clinicians; it presents a structured analytic scheme for correlating and classifying this multidisciplinary information as it becomes available

  18. Chromosome Morphology in Kniphofia.

    Directory of Open Access Journals (Sweden)

    J. M. J de Wet

    1960-12-01

    Full Text Available A number of species and varieties of the genus  Kniphofia (Liliaceae were studied cytologically. The somatic chromosome number is  2n = 12 in all the species. This is also true in  Notosceptrum natalense Baker.

  19. Genetic and physical mapping of the bovine X chromosome

    Energy Technology Data Exchange (ETDEWEB)

    Yeh, Chen Chen; Taylor, J.F.; Sanders, J. O. [Texas A& M Univ., College Station, TX (United States)] [and others

    1996-03-01

    Three hundred eighty reciprocal backcross and F{sub 2} full sib progeny from 33 families produced by embryo transfer from 77 Angus (Bos taurus), Brahman (Bos indicus), and F{sub 1} parents and grandparents were used to construct genetic maps of the bovine X and Y chromosomes. All individuals were scored for 15 microsatellite loci, with an average of 608 informative meioses per locus. The length of the bovine X chromosome genetic map was 118.7 cM (female only) and of the pseudoautosomal region was 13.0 cM (male only). The 15-marker framework map in Kosambi centimorgans is (BM6017-6.1-TGLA89-35.8-TEXAN13-3.4-TGLA128-1.3-BM2713-21.1-BM4604-2.4-BR215-12.9-TGLA68-10.0-BM4321-1.0-HEL14-4.9-TGLA15-2.3-INRA120-12.5-TGLA325-1.6-MAF45-3.2-INRA30), with an average interval of 7.91 cM. Clones containing pseudoautosomal or sex-linked microsatellites were isolated from a bovine bacterial artificial chromosome library and were physically mapped to bovine metaphase chromosomes by fluorescence in situ hybridization to orient the X and Y chromosome maps. BAC57, containing the pseudoautosomal microsatellite INRA30, mapped to the distal end of the long arm of the X chromosome at q42-ter and to the short arm of the Y chromosome at p13-ter. This confirms the published assignment of this region to Yp12-ter, but challenges the published assignment of Xp14-ter and thus reorients the X chromosome physical map. BAC204, containing the X-linked microsatellite BM4604, mapped to the middle of the long arm of the X chromosome at q26-q31. The position of the physically mapped to the middle of the long arm of the X chromosome at q26-q31. The position of the physically mapped markers indicates either a lack of microsatellite markers for a large (30 to 50 cM) region of the short arm of the X chromosome or heterogeneity of recombination along the X chromosome. 46 refs., 2 figs., 3 tabs.

  20. Telomere dysfunction and chromosome instability

    Energy Technology Data Exchange (ETDEWEB)

    Murnane, John P., E-mail: jmurnane@radonc.ucsf.edu [Department of Radiation Oncology, University of California San Francisco, 2340 Sutter Street, San Francisco, CA 94143-1331 (United States)

    2012-02-01

    The ends of chromosomes are composed of a short repeat sequence and associated proteins that together form a cap, called a telomere, that keeps the ends from appearing as double-strand breaks (DSBs) and prevents chromosome fusion. The loss of telomeric repeat sequences or deficiencies in telomeric proteins can result in chromosome fusion and lead to chromosome instability. The similarity between chromosome rearrangements resulting from telomere loss and those found in cancer cells implicates telomere loss as an important mechanism for the chromosome instability contributing to human cancer. Telomere loss in cancer cells can occur through gradual shortening due to insufficient telomerase, the protein that maintains telomeres. However, cancer cells often have a high rate of spontaneous telomere loss despite the expression of telomerase, which has been proposed to result from a combination of oncogene-mediated replication stress and a deficiency in DSB repair in telomeric regions. Chromosome fusion in mammalian cells primarily involves nonhomologous end joining (NHEJ), which is the major form of DSB repair. Chromosome fusion initiates chromosome instability involving breakage-fusion-bridge (B/F/B) cycles, in which dicentric chromosomes form bridges and break as the cell attempts to divide, repeating the process in subsequent cell cycles. Fusion between sister chromatids results in large inverted repeats on the end of the chromosome, which amplify further following additional B/F/B cycles. B/F/B cycles continue until the chromosome acquires a new telomere, most often by translocation of the end of another chromosome. The instability is not confined to a chromosome that loses its telomere, because the instability is transferred to the chromosome donating a translocation. Moreover, the amplified regions are unstable and form extrachromosomal DNA that can reintegrate at new locations. Knowledge concerning the factors promoting telomere loss and its consequences is

  1. Organization of the bacterial chromosome.

    OpenAIRE

    Krawiec, S.; Riley, M

    1990-01-01

    Recent progress in studies on the bacterial chromosome is summarized. Although the greatest amount of information comes from studies on Escherichia coli, reports on studies of many other bacteria are also included. A compilation of the sizes of chromosomal DNAs as determined by pulsed-field electrophoresis is given, as well as a discussion of factors that affect gene dosage, including redundancy of chromosomes on the one hand and inactivation of chromosomes on the other hand. The distinction ...

  2. Dicty_cDB: Contig-U15416-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available e 219 from Patent WO2005119262. 44 3.9 1 ( CS246279 ) Sequence 218 from Paten...t WO2005119262. 44 3.9 1 ( CS246278 ) Sequence 217 from Patent WO2005119262. 44 3.9 1 ( CS165019 ) Sequence 1207 from Pate...nt WO2005083125. 44 3.9 1 ( AX746180 ) Sequence 31 from Patent WO0208399. 44 3.9 1 ( AX166564 ) Sequenc... 0 0 0 Show Contig-U15416-1 Contig ID Contig-U15416-1 Contig update 2004. 6.11 Contig sequence >Contig-U1541...KGKGGEETPESPSEPSGSNYEDPSINDI ELGPDDPEASEEFMPEFYQEVGVLKTLMTSVKRSVRSIEDKYVLSLNSINVDQGSKYEDD IQQMLDGTNKSFSEL Translated Amino Aci

  3. Dicty_cDB: Contig-U10650-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available . 44 6.3 1 ( AL315319 ) Tetraodon nigroviridis genome survey sequence SP6... 44 6.3 1 ( DU084492 ) 280194 Tomato Hi...clones 1 Number of EST 1 Link to clone list U10650 List of clone(s) est1= VFM286F ,1,653 Translated Amino Acid seq...0 0 0 Show Contig-U10650-1 Contig ID Contig-U10650-1 Contig update 2002. 9.13 Contig sequence >Contig-U10650...NNSIS PFKQSRTSSQQTSPFKSIVSPLQISPPKTTLSQSQIQXXX Translated Amino Acid sequence (All Frames) Frame A: RSDDGGNS...: CSM 6905 sequences; 5,674,871 total letters Score E Sequences pro

  4. Dicty_cDB: Contig-U14678-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available TCEDLNCERKGLHCAMKTVP IDKENCCEKVPVCYSTNPLLDGGHGFI*rkkkkknitqnnn*lktnknnli*kkkkkk Frame B: knvasdpidhhhqkfvh*dah...qnmnvnlmimvknvv*rfivmkfvi*ivvevlnvkldmm vqnvvsvqkdhthhnmknvirdahqamnvklinmeknvallpidhhqnal*dvhqdmvkn vallpidhhqnah...AC139706_5( AC139706 |pid:none) Medicago truncatula clone mth2-28n... 36 1.0 AB430854_1( AB430854 |pid:none) Oryza sativa Ind...34 5.1 DQ158187_1( DQ158187 |pid:none) Nicotiana repanda trypsin proteina... 34 5...ig-U14678-1 Contig ID Contig-U14678-1 Contig update 2002.12.18 Contig sequence >Contig-U14678-1 (Contig-U146

  5. The B chromosomes of the African cichlid fish Haplochromis obliquidens harbour 18S rRNA gene copies

    Directory of Open Access Journals (Sweden)

    Martins Cesar

    2010-01-01

    Full Text Available Abstract Background Diverse plant and animal species have B chromosomes, also known as accessory, extra or supernumerary chromosomes. Despite being widely distributed among different taxa, the genomic nature and genetic behavior of B chromosomes are still poorly understood. Results In this study we describe the occurrence of B chromosomes in the African cichlid fish Haplochromis obliquidens. One or two large B chromosome(s occurring in 39.6% of the analyzed individuals (both male and female were identified. To better characterize the karyotype and assess the nature of the B chromosomes, fluorescence in situ hybridization (FISH was performed using probes for telomeric DNA repeats, 18S and 5S rRNA genes, SATA centromeric satellites, and bacterial artificial chromosomes (BACs enriched in repeated DNA sequences. The B chromosomes are enriched in repeated DNAs, especially non-active 18S rRNA gene-like sequences. Conclusion Our results suggest that the B chromosome could have originated from rDNA bearing subtelo/acrocentric A chromosomes through formation of an isochromosome, or by accumulation of repeated DNAs and rRNA gene-like sequences in a small proto-B chromosome derived from the A complement.

  6. Artificial life and life artificialization in Tron

    Directory of Open Access Journals (Sweden)

    Carolina Dantas Figueiredo

    2012-12-01

    Full Text Available Cinema constantly shows the struggle between the men and artificial intelligences. Fiction, and more specifically fiction films, lends itself to explore possibilities asking “what if?”. “What if”, in this case, is related to the eventual rebellion of artificial intelligences, theme explored in the movies Tron (1982 and Tron Legacy (2010 trat portray the conflict between programs and users. The present paper examines these films, observing particularly the possibility programs empowering. Finally, is briefly mentioned the concept of cyborg as a possibility of response to human concerns.

  7. Artificial insemination in poultry

    Science.gov (United States)

    Artificial insemination is a relative simple yet powerful tool geneticists can employ for the propagation of economically important traits in livestock and poultry. In this chapter, we address the fundamental methods of the artificial insemination of poultry, including semen collection, semen evalu...

  8. Chromosome 19 International Workshop

    Energy Technology Data Exchange (ETDEWEB)

    Pericak-Vance, M.A. (Duke Univ., Durham, NC (United States). Medical Center); Ropers, H.H. (Univ. Hospital Nijmegen, (The Netherlands). Dept. of Human Genetics); Carrano, A.J. (Lawrence Livermore National Lab., CA (United States))

    1993-01-04

    The Second International Workshop on Human Chromosome 19 was hosted on January 25 and 26, 1992, by the Department of Human Genetics, University Hospital Nijmegen, The Netherlands, at the 'Meerdal Conference Center'. The workshop was supported by a grant from the European Community obtained through HUGO, the Dutch Research Organization (NWO) and the Muscular Dystrophy Association (MDA). Travel support for American participants was provided by the Department of Energy. The goals of this workshop were to produce genetic, physical and integrated maps of chromosome 19, to identify inconsistencies and gaps, and to discuss and exchange resources and techniques available for the completion of these maps. The second day of the meeting was largely devoted to region or disease specific efforts. In particular, the meeting served as a platform for assessing and discussing the recent progress made into the molecular elucidation of myotonic dystrophy.

  9. Genetic and physical mapping of the bovine X chromosome.

    Science.gov (United States)

    Yeh, C C; Taylor, J F; Gallagher, D S; Sanders, J O; Turner, J W; Davis, S K

    1996-03-01

    Three hundred eighty reciprocal backcross and F(2) full sib progeny from 33 families produced by embryo transfer from 77 Angus (Bos taurus), Brahman (Bos indicus), and F1 parents and grandparents were used to construct genetic maps of the bovine X and Y chromosomes. Ml individuals were scored for 15 microsatellite loci, with an average of 608 informative meioses per locus. The length of the bovine X chromosome genetic map was 118.7 cM (female only) and of the pseudoautosomal region was 13.0 cM (male only). The 15-marker framework map in Kosambi centimorgans is [BM6017-6.1 -TGLA89-35.8-TEXAN13-3.4-TGLA128-1.3 -BM2713 -21.1 -BM4604-2.4-BR215 - 12.9-TGLA68-10.0-BM4321 - 1.0-HEL14-4.9-TGLA15-2.3-INRA12O- 12.5-TGLA325- 1.6-MAF45-3.2-INRA3O], with an average interval of 7.91 cM. Clones containing pseudoautosomal or sex-linked microsatellites were isolated from a bovine bacterial artificial chromosome library and were physically mapped to bovine metaphase chromosomes by fluorescence in situ hybridization to orient the X and Y chromosome maps. BAC57, containing the pseudoautosomal microsatellite INRA3O, mapped to the distal end of the long arm of the X chromosome at q42-ter and to the short arm of the Y chromosome at p13-ter. This confirms the published assignment of this region to Ypl2-ter, but challenges the published assignment of Xpl4-ter and thus reorients the X chromosome physical map. BAC2O4, containing the X-linked microsatellite BM4604, mapped to the middle of the long arm of the X chromosome at q26-q31. The position of the physically mapped markers indicates either a lack of microsatellite markers for a large (30 to 50 cM) region of the short arm of the X chromosome or heterogeneity of recombination along the X chromosome. PMID:8833151

  10. Chromosome numbers and meiotic analysis in the pre-breeding of Brachiaria decumbens (Poaceae)

    Indian Academy of Sciences (India)

    Gléia Cristina Laverde Ricci; Alice Maria De Souza-Kaneshima; Mariana Ferrari Felismino; Andrea Beatriz Mendes-Bonato; Maria Suely Pagliarini; Cacilda Borges Do Valle

    2011-08-01

    A total of 44 accessions of Brachiaria decumbens were analysed for chromosome count and meiotic behaviour in order to identify potential progenitors for crosses. Among them, 15 accessions presented $2n = 18$; 27 accessions, $2n = 36$; and 2 accessions, $2n = 45$ chromosomes. Among the diploid accessions, the rate of meiotic abnormalities was low, ranging from 0.82% to 7.93%. In the 27 tetraploid accessions, the rate of meiotic abnormalities ranged from 18.41% to 65.83%. The most common meiotic abnormalities were related to irregular chromosome segregation, but chromosome stickiness and abnormal cytokinesis were observed in low frequency. All abnormalities can compromise pollen viability by generating unbalanced gametes. Based on the chromosome number and meiotic stability, the present study indicates the apomictic tetraploid accessions that can act as male genitor to produce interspecific hybrids with B. ruziziensis or intraspecific hybrids with recently artificially tetraploidized accessions.

  11. Chromosome Evolution in African Cichlid Fish: Contributions from the Physical Mapping of Repeated DNAs

    Science.gov (United States)

    Ferreira, I.A.; Poletto, A.B.; Kocher, T.D.; Mota-Velasco, J.C.; Penman, D.J.; Martins, C.

    2010-01-01

    Cichlid fishes have been the subject of increasing scientific interest because of their rapid adaptive radiation that has led to extensive ecological diversity and because of their enormous importance to tropical and subtropical aquaculture. To further understanding of chromosome evolution among cichlid species, we have comparatively mapped the SATA satellite DNA, the transposable element ROn-1, and repeated sequences in the bacterial artificial chromosome clone BAC-C4E09 on the chromosomes of a range of African species of Cichlidae, using fluorescence in situ hybridization. The SATA satellite DNA was mapped in almost all the centromeres of all tilapiine and haplochromine species studied. The maintenance and centromeric distribution of the SATA satellite DNA in African cichlids suggest that this sequence plays an important role in the organization and function of the centromere in these species. Furthermore, analysis of SATA element distribution clarifies that chromosome fusions occurred independently in Oreochromis and Tilapia genera, and led to the reduced chromosome number detected in O. karongae and T. mariae. The comparative chromosome mapping of the ROn-1 SINE-like element and BAC-C4E09 shows that the repeated sequences have been maintained among tilapiine, haplochromine and hemichromine fishes and has demonstrated the homology of the largest chromosomes among these groups. Furthermore, the mapping of ROn-1 suggested that different chromosomal rearrangements could have occurred in the origin of the largest chromosome pairs of tilapiines and non-tilapiines. PMID:20606399

  12. Dicty_cDB: Contig-U00819-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available |||||||||||||||| Sbjct: 61 acaaaatnnacnagntnnacaaaatnnacnagntcnacaaaatnnacnagntcnacaaaa 120 Query: 121 tnnacnagnncaacaaaatccccna...||||||||||||| Sbjct: 121 tnnacnagnncaacaaaatccccnagntcnacnagntcnacaaaacc 167 >Contig-U16510-1 (Contig-U16510...aagctcaacaaaatcaacaagctcaacaaaatcaacaagctcaacaaa 2335 Query: 102 atnnacnagntcnacaaaatnnacnagnncaacaaaatccccna...uery: 102 atnnacnagntcnacaaaatnnacnagnncaacaaaatccccnagntcnacnagntcnac 161 || || || || ||||||| || || |||||||...173 acaaaatnnacnagntnnacaaaatnnacnagntcnacaaaatnnacnagntcnacaaaa 114 Query: 121 tnnacnagnncaacaaaatccccna

  13. Dicty_cDB: Contig-U14471-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available s vinifera contig VV78X028385.7, whole genome... 38 4.8 3 ( FG220631 ) Aaov03804 Ant...CELLED *** f... 40 7.7 6 ( AM458993 ) Vitis vinifera contig VV78X185503.4, whole genome... 36 7.8 4 ( BD460323 ) Diagnos... 32 5.5 10 ( AM427483 ) Vitis vinifera contig VV78X172617.3, whole genome... 36 5.7 3 ( AM477107 ) Vitis vinifera contig...s vinifera contig VV78X211100.7, whole genome... 44 8.6 1 ( AM447611 ) Vitis vinifera contig VV78X174034.1, whole geno...me... 44 8.6 1 ( AM434095 ) Vitis vinifera contig VV78X109527.29, whole genom... 44 8.6 1 ( AM432369 ) Viti

  14. A FISH-based chromosome map for the European corn borer yields insights into ancient chromosomal fusions in the silkworm.

    Science.gov (United States)

    Yasukochi, Y; Ohno, M; Shibata, F; Jouraku, A; Nakano, R; Ishikawa, Y; Sahara, K

    2016-01-01

    A significant feature of the genomes of Lepidoptera, butterflies and moths, is the high conservation of chromosome organization. Recent remarkable progress in genome sequencing of Lepidoptera has revealed that syntenic gene order is extensively conserved across phylogenetically distant species. The ancestral karyotype of Lepidoptera is thought to be n=31; however, that of the most well-studied moth, Bombyx mori, is n=28, and diverse studies suggest that three chromosomal fusion events occurred in this lineage. To identify the boundaries between predicted ancient fusions involving B. mori chromosomes 11, 23 and 24, we constructed fluorescence in situ hybridization (FISH)-based chromosome maps of the European corn borer, Ostrinia nubilalis (n=31). We first determined a 511 Mb genomic sequence of the Asian corn borer, O. furnacalis, a congener of O. nubilalis, and isolated bacterial artificial chromosomes and fosmid clones that were expected to localize in candidate regions for the boundaries using these sequences. Combined with FISH and genetic analysis, we narrowed down the candidate regions to 40 kb-1.5 Mb, in strong agreement with a previous estimate based on the genome of a butterfly, Melitaea cinxia. The significant difference in the lengths of the candidate regions where no functional genes were observed may reflect the evolutionary time after fusion events. PMID:26264548

  15. Artificial ecosystem selection.

    Science.gov (United States)

    Swenson, W; Wilson, D S; Elias, R

    2000-08-01

    Artificial selection has been practiced for centuries to shape the properties of individual organisms, providing Darwin with a powerful argument for his theory of natural selection. We show that the properties of whole ecosystems can also be shaped by artificial selection procedures. Ecosystems initiated in the laboratory vary phenotypically and a proportion of the variation is heritable, despite the fact that the ecosystems initially are composed of thousands of species and millions of individuals. Artificial ecosystem selection can be used for practical purposes, illustrates an important role for complex interactions in evolution, and challenges a widespread belief that selection is most effective at lower levels of the biological hierarchy. PMID:10890915

  16. Dicty_cDB: Contig-U14796-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 0.2 bits (15), Expect = 1.0 Identities = 21/21 (100%) Strand = Plus / Plus Query: 11 tcccnaaaanccccccccccc 3...1 ||||||||||||||||||||| Sbjct: 11 tcccnaaaanccccccccccc 31 >Contig-U13959-1 (Contig-U13959-1Q) /CSM_Contig/C...d = Plus / Minus Query: 11 tcccnaaaanccccccccccc 31 ||||||||||||||||||||| Sbjct: 239 tcccnaaaanccccccccccc 2

  17. Developing Creativity: Artificial Barriers in Artificial Intelligence

    OpenAIRE

    Jennings, Kyle E.

    2010-01-01

    The greatest rhetorical challenge to developers of creative artificial intelligence systems is convincingly arguing that their software is more than just an extension of their own creativity. This paper suggests that “creative autonomy,” which exists when a system not only evaluates creations on its own, but also changes its standards without explicit direction, is a necessary condition for making this argument. Rather than requiring that the system be hermetically sealed to avoid perceptions...

  18. Genetic and physical mapping of the Chediak-Higashi syndrome on chromosome 1q42-43

    Energy Technology Data Exchange (ETDEWEB)

    Barrat, F.J.; Auloge, L.; Pastural, E. [INSERM, Paris (France)] [and others

    1996-09-01

    The Chediak-Higashi syndrome (CHS) is a severe autosomal recessive condition, features of which are partial oculocutaneous albinism, increased susceptibility to infections, deficient natural killer cell activity, and the presence of large intracytoplasmic granulations in various cell types. Similar genetic disorders have been described in other species, including the beige mouse. On the basis of the hypothesis that the murine chromosome 13 region containing the beige locus was homologous to human chromosome 1, we have mapped the CHS locus to a 5-cM interval in chromosome segment 1q42.1-q42.2. The highest LOD score was obtained with the marker D1S235 (Z{sub max} = 5.38; {theta} = 0). Haplotype analysis enabled us to establish D1S2680 and D1S163, respectively, as the telomeric and the centromeric flanking markers. Multipoint linkage analysis confirms the localization of the CHS locus in this interval. Three YAC clones were found to cover the entire region in a contig established by YAC end-sequence characterization and sequence-tagged site mapping. The YAC contig contains all genetic markers that are nonrecombinant for the disease in the nine CHS families studied. This mapping confirms the previous hypothesis that the same gene defect causes CHS in human and beige phenotype in mice and provides a genetic framework for the identification of candidate genes. 36 refs., 4 figs., 1 tab.

  19. Molecular fundamentals of chromosomal mutagenesis

    International Nuclear Information System (INIS)

    Precise quantitative correlation between the yield of chromosome structure damages and the yield of DNA damages is shown when comparing data on molecular and cytogenetic investigations carried out in cultural Mammalia cells. As the chromosome structure damage is to be connected with the damage of its carcass structure, then it is natural that DNA damage in loop regions is not to affect considerably the structure, while DNA damage lying on the loop base and connected with the chromosome carcass is to play a determining role in chromosomal mutagenesis. This DNA constitutes 1-2% from the total quantity of nuclear DNA. If one accepts that damages of these regions of DNA are ''hot'' points of chromosomal mutagenesis, then it becomes clear why 1-2% of preparation damages in a cell are realized in chromosome structural damages

  20. Electochemical detection of chromosome translocation

    DEFF Research Database (Denmark)

    Kwasny, Dorota; Dimaki, Maria; Silahtaroglu, Asli;

    2014-01-01

    Cytogenetics is a study of the cell structure with a main focus on chromosomes content and their structure. Chromosome abnormalities, such as translocations may cause various genetic disorders and heametological malignancies. Chromosome translocations are structural rearrangements of two...... hybridization approach developed for label-free detection of the chromosome translocations. For specific translocation detection it is necessary to determine that the two DNA sequences forming a derivative chromosome are connected, which is achieved by two subsequent hybridization steps. The electrochemical...... impedance spectroscopy was selected as the sensing method on a microfabricated chip with array of 12 electrode sets. Two independent chips (Chip1 and Chip2) were used for targeting the chromosomal fragments involved in the translocation. Each chip was differentially functionalized with DNA probes matching...

  1. Assignment of genetic linkage maps to diploid Solanum tuberosum pachytene chromosomes by BAC-FISH technology

    NARCIS (Netherlands)

    Tang, X.; Boer, de J.M.; Eck, van H.J.; Bachem, C.W.B.; Visser, R.G.F.; Jong, de J.H.

    2009-01-01

    A cytogenetic map has been developed for diploid potato (Solanum tuberosum), in which the arms of the 12 potato bivalents can be identified in pachytene complements using multicolor fluorescence in situ hybridization (FISH) with a set of 60 genetically anchored bacterial artificial chromosome (BAC)

  2. Intraspecific chromosome variability

    Directory of Open Access Journals (Sweden)

    N Dubinin

    2010-12-01

    Full Text Available (Editorial preface. The publication is presented in order to remind us of one of dramatic pages of the history of genetics. It re-opens for the contemporary reader a comprehensive work marking the priority change from plant cytogenetics to animal cytogenetics led by wide population studies which were conducted on Drosophila polytene chromosomes. The year of the publication (1937 became the point of irretrievable branching between the directions of Old World and New World genetics connected with the problems of chromosome variability and its significance for the evolution of the species. The famous book of T. Dobzhansky (1937 was published by Columbia University in the US under the title “Genetics and the origin of species”, and in the shadow of this American ‘skybuilding’ all other works grew dim. It is remarkable that both Dobzhansky and Dubinin come to similar conclusions about the role of chromosomes in speciation. This is not surprising given that they both might be considered as representatives of the Russian genetic school, by their birth and education. Interestingly, Dobzhansky had never referred to the full paper of Dubinin et al. (1937, though a previous short communication in Nature (1936 was included together with all former papers on the related subject. In full, the volume of the original publication printed in the Biological Journal in Moscow comprised 47 pages, in that number 41 pages of the Russian text accompanied by 16 Figs, a table and reference list, and, above all, 6 pages of the English summary. This final part in English is now reproduced in the authors’ version with the only addition being the reference list in the originally printed form.

  3. Development and physical analysis of YAC contigs covering 7 Mb of Xp22.3-p22.2

    Energy Technology Data Exchange (ETDEWEB)

    Herrell, S.; Novo, F.J.; Charlton, R. [Univ. of Cambridge (United Kingdom)] [and others

    1995-01-20

    A total of YAC clones have been isolated from the region of Xp22.2-p22.3 extending from the amelogenin gene locus to DXS31. Restriction analysis of these clones in association with STS contenting and end clone analysis has facilitated the construction of 6 contigs covering a total of 7 Mb in which 20 potential CpG islands have been located. Thirty new STSs have been developed from probe and YAC end clone sequences, and these have been used in the analysis of patients suffering from different combinations of chondrodysplasia punctata, mental retardation, X-linked ichthyosis, and Kallmann syndrome. The results suggest that (1) the gene for chondrodysplasia punctata must lie between the X chromosome pseudoautosomal boundary (PABX) and DXS1145; (2) a gene for mental retardation lies between DXS1145 and the sequence tagged site GS1; and (3) the gene for ocular albinism type 1 lies proximal to the STS G13. The CpG islands within the YAC contigs constitute valuable markers for the potential positions of genes. Genes found associated with any of these potential CpG islands would be possible candidates for the disease genes mentioned above. 47 refs., 3 figs., 5 tabs.

  4. Reference-assisted chromosome assembly

    OpenAIRE

    Kim, Jaebum; Larkin, Denis M; Cai, Qingle; Asan,; Zhang, Yongfen; Ge, Ri-Li; Auvil, Loretta; Capitanu, Boris; Zhang, Guojie; Lewin, Harris A.; Ma, Jian

    2013-01-01

    One of the most difficult problems in modern genomics is the assembly of full-length chromosomes using next generation sequencing (NGS) data. To address this problem, we developed “reference-assisted chromosome assembly” (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads. Evaluation of results using simulated and real genome assemblies indicates that ou...

  5. Principles of artificial intelligence

    CERN Document Server

    Nilsson, Nils J

    1980-01-01

    A classic introduction to artificial intelligence intended to bridge the gap between theory and practice, Principles of Artificial Intelligence describes fundamental AI ideas that underlie applications such as natural language processing, automatic programming, robotics, machine vision, automatic theorem proving, and intelligent data retrieval. Rather than focusing on the subject matter of the applications, the book is organized around general computational concepts involving the kinds of data structures used, the types of operations performed on the data structures, and the properties of th

  6. Intelligence: Real or artificial?

    OpenAIRE

    Schlinger, Henry D

    1992-01-01

    Throughout the history of the artificial intelligence movement, researchers have strived to create computers that could simulate general human intelligence. This paper argues that workers in artificial intelligence have failed to achieve this goal because they adopted the wrong model of human behavior and intelligence, namely a cognitive essentialist model with origins in the traditional philosophies of natural intelligence. An analysis of the word “intelligence” suggests that it originally r...

  7. Artificial Personality and Disfluency

    OpenAIRE

    Wester, Mirjam; Aylett, Matthew; Tomalin, Marcus; Dall, Rasmus

    2015-01-01

    The focus of this paper is artificial voices with different personalities. Previous studies have shown links between an individual's use of disfluencies in their speech and their perceived personality. Here, filled pauses (uh and um) and discourse markers (like, you know, I mean) have been included in synthetic speech as a way of creating an artificial voice with different personalities. We discuss the automatic insertion of filled pauses and discourse markers (i.e., fillers) into otherwise f...

  8. The Artificial Anal Sphincter

    OpenAIRE

    Christiansen, John

    2000-01-01

    The artificial anal sphincter as treatment for end stage anal incontinence was first described in 1987. Published series concern a total of 42 patients, with a success rate of approximately 80%. Infection has been the most serious complication, but a number of technical complications related to the device have also occurred and required revisional procedures in 40% to 60% of the patients. The artificial anal sphincter may be used for the same indications as dynamic graciloplasty except in pat...

  9. Artificial skin. Jinko hifu

    Energy Technology Data Exchange (ETDEWEB)

    Kifune, K. (Unitika Ltd., Osaka (Japan))

    1993-06-15

    In order to restore the human skin wounds, the transplantation is only one measure. The transplantation can take only when own skin is used, and there is no successful example by using other person's skin. When the own skin is not sufficient due to the too vast damage, the artificial skin, which can be regenerated as it is, is required. The artificial skin is said to be the most difficult organ among the artificial organs, even though its function is quite simple. Although there are the pig skin, the collagen membrane and the synthetic materials such as the polyurethane and so forth, as the materials similar to the artificial skin, they cover the wounds just until the cuticle is formed. Recently there is a cultivated skin. Firstly the normal skin with a size of the stamp is cut off, and then the cuticle cells are taken to pieces and cultivated, and consequently it is possible to increase the area by several 10 times. In addition, there is also a trial to make the artificial skin synthetically. Its upper layer is composed of the silicon, and the lower layer is the collagen membrane with a sponge structure. The silicon, membrane can be said to be an ideal artificial skin, because it detaches naturally. The chitin, which has recently appeared as the wound protection material, is also the promising material. 3 figs.

  10. Physical and transcription map of a 25 Mb region on human chromosome 7 (region q21-q22)

    Energy Technology Data Exchange (ETDEWEB)

    Scherer, S. [Univ. of Toronto (Canada)]|[Hosptial for Sick Children, Toronto (Canada); Little, S.; Vandenberg, A. [Hospital for Sick Children, Toronto (Canada)] [and others

    1994-09-01

    We are interested in the q21-q22 region of chromosome 7 because of its implication in a number of diseases. This region of about 25 Mb appears to be involved in ectrodactyly/ectodermal dysplasia/cleft plate (EEC) and split hand/split foot deformity (SHFD1), as well as myelodysplastic syndrome and acute non-lymphocyte leukemia. In order to identify the genes responsible for these and other diseases, we have constructed a physical map of this region. The proximal and distal boundaries of the region were operationally defined by the microsatellite markers D7S660 and D7S692, which are about 35 cM apart. This region between these two markers could be divided into 13 intervals on the basis of chromosome breakpoints contained in somatic cell hybrids. The map positions for 43 additional microsatellite markers and 25 cloned genes were determined with respect to these intervals. A physical map based on contigs of over 250 YACs has also been assembled. While the contigs encompass all of the known genetic markers mapped to the region and almost cover the entire 25-Mb region, there are 3 gaps on the map. One of these gaps spans a set of DNA markers for which no corresponding YAC clones could be identified. To connect the two adjacent contigs we have initiated cosmid walking with a chromosome 7-specific library (Lawrence Livermore Laboratory). A tiling path of 60 contiguous YAC clones has been assembled and used for direct cDNA selection. Over 300 cDNA clones have been isolated and characterized. They are being grouped into transcription units by Northern blot analysis and screening of full-length cDNA libraries. Further, exon amplification and direct cDNA library screening with evolutionarily conserved sequences are being performed for a 1-Mb region spanning the SHFD1 locus to ensure detection of all transcribed sequences.

  11. Whole-Genome and Chromosome Evolution Associated with Host Adaptation and Speciation of the Wheat Pathogen Mycosphaerella graminicola

    Science.gov (United States)

    Stukenbrock, Eva H.; Jørgensen, Frank G.; Zala, Marcello; Hansen, Troels T.; McDonald, Bruce A.; Schierup, Mikkel H.

    2010-01-01

    The fungus Mycosphaerella graminicola has been a pathogen of wheat since host domestication 10,000–12,000 years ago in the Fertile Crescent. The wheat-infecting lineage emerged from closely related Mycosphaerella pathogens infecting wild grasses. We use a comparative genomics approach to assess how the process of host specialization affected the genome structure of M. graminicola since divergence from the closest known progenitor species named M. graminicola S1. The genome of S1 was obtained by Illumina sequencing resulting in a 35 Mb draft genome sequence of 32X. Assembled contigs were aligned to the previously sequenced M. graminicola genome. The alignment covered >90% of the non-repetitive portion of the M. graminicola genome with an average divergence of 7%. The sequenced M. graminicola strain is known to harbor thirteen essential chromosomes plus eight dispensable chromosomes. We found evidence that structural rearrangements significantly affected the dispensable chromosomes while the essential chromosomes were syntenic. At the nucleotide level, the essential and dispensable chromosomes have evolved differently. The average synonymous substitution rate in dispensable chromosomes is considerably lower than in essential chromosomes, whereas the average non-synonymous substitution rate is three times higher. Differences in molecular evolution can be related to different transmission and recombination patterns, as well as to differences in effective population sizes of essential and dispensable chromosomes. In order to identify genes potentially involved in host specialization or speciation, we calculated ratios of synonymous and non-synonymous substitution rates in the >9,500 aligned protein coding genes. The genes are generally under strong purifying selection. We identified 43 candidate genes showing evidence of positive selection, one encoding a potential pathogen effector protein. We conclude that divergence of these pathogens was accompanied by structural

  12. Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola.

    Directory of Open Access Journals (Sweden)

    Eva H Stukenbrock

    Full Text Available The fungus Mycosphaerella graminicola has been a pathogen of wheat since host domestication 10,000-12,000 years ago in the Fertile Crescent. The wheat-infecting lineage emerged from closely related Mycosphaerella pathogens infecting wild grasses. We use a comparative genomics approach to assess how the process of host specialization affected the genome structure of M. graminicola since divergence from the closest known progenitor species named M. graminicola S1. The genome of S1 was obtained by Illumina sequencing resulting in a 35 Mb draft genome sequence of 32X. Assembled contigs were aligned to the previously sequenced M. graminicola genome. The alignment covered >90% of the non-repetitive portion of the M. graminicola genome with an average divergence of 7%. The sequenced M. graminicola strain is known to harbor thirteen essential chromosomes plus eight dispensable chromosomes. We found evidence that structural rearrangements significantly affected the dispensable chromosomes while the essential chromosomes were syntenic. At the nucleotide level, the essential and dispensable chromosomes have evolved differently. The average synonymous substitution rate in dispensable chromosomes is considerably lower than in essential chromosomes, whereas the average non-synonymous substitution rate is three times higher. Differences in molecular evolution can be related to different transmission and recombination patterns, as well as to differences in effective population sizes of essential and dispensable chromosomes. In order to identify genes potentially involved in host specialization or speciation, we calculated ratios of synonymous and non-synonymous substitution rates in the >9,500 aligned protein coding genes. The genes are generally under strong purifying selection. We identified 43 candidate genes showing evidence of positive selection, one encoding a potential pathogen effector protein. We conclude that divergence of these pathogens was

  13. Chromosome Connections: Compelling Clues to Common Ancestry

    Science.gov (United States)

    Flammer, Larry

    2013-01-01

    Students compare banding patterns on hominid chromosomes and see striking evidence of their common ancestry. To test this, human chromosome no. 2 is matched with two shorter chimpanzee chromosomes, leading to the hypothesis that human chromosome 2 resulted from the fusion of the two shorter chromosomes. Students test that hypothesis by looking for…

  14. X-chromosome workshop.

    Science.gov (United States)

    Paterson, A D

    1998-01-01

    Researchers presented results of ongoing research to the X-chromosome workshop of the Fifth World Congress on Psychiatric Genetics, covering a wide range of disorders: X-linked infantile spasms; a complex phenotype associated with deletions of Xp11; male homosexuality; degree of handedness; bipolar affective disorder; schizophrenia; childhood onset psychosis; and autism. This report summarizes the presentations, as well as reviewing previous studies. The focus of this report is on linkage findings for schizophrenia and bipolar disorder from a number of groups. For schizophrenia, low positive lod scores were obtained for markers DXS991 and DXS993 from two studies, although the sharing of alleles was greatest from brother-brother pairs in one study, and sister-sister in the other. Data from the Irish schizophrenia study was also submitted, with no strong evidence for linkage on the X chromosome. For bipolar disease, following the report of a Finnish family linked to Xq24-q27, the Columbia group reported some positive results for this region from 57 families, however, another group found no evidence for linkage to this region. Of interest, is the clustering of low positive linkage results that point to regions for possible further study. PMID:9686435

  15. Chromosome analysis and sorting

    Czech Academy of Sciences Publication Activity Database

    Doležel, Jaroslav; Kubaláková, Marie; Suchánková, Pavla; Kovářová, Pavlína; Bartoš, Jan; Šimková, Hana

    Weinheim : Wiley-VCH, 2007 - (Doležel, J.; Greilhuber, J.; Suda, J.), s. 373-403 ISBN 978-3-527-31487-4 R&D Projects: GA ČR GA521/04/0607; GA ČR GP521/05/P257; GA ČR GD521/05/H013; GA MŠk(CZ) LC06004 Grant ostatní: Mendelova zemědělská a lesnická univerzita v Brně / Agronomická fakulta(CZ) ME 844 Institutional research plan: CEZ:AV0Z5038910 Source of funding: V - iné verejné zdroje ; V - iné verejné zdroje ; V - iné verejné zdroje ; V - iné verejné zdroje ; V - iné verejné zdroje Keywords : Plant flow cytometry * chromosome sorting * flow cytogenetics Subject RIV: EB - Genetics ; Molecular Biology http://books. google .com/books?id=3cwakORieqUC&pg=PA373&lpg=PA373&dq=Chromosome+analysis+and+sorting&source=web&ots=8IyvJlBQyq&sig=_NlXyQQgBCwpj1pTC9YITvvVZqU

  16. Report of the fifth international workshop on human X chromosome mapping

    Energy Technology Data Exchange (ETDEWEB)

    Willard, H.F.; Cremers, F.; Mandel, J.L.; Monaco, A.P.; Nelson, D.L.; Schlessinger, D.

    1994-12-31

    A high-quality integrated genetic and physical map of the X chromosome from telomere to telomere, based primarily on YACs formatted with probes and STSs, is increasingly close to reality. At the Fifth International X Chromosome Workshop, organized by A.M. Poustka and D. Schlessinger in Heidelberg, Germany, April 24--27, 1994, substantial progress was recorded on extension and refinement of the physical map, on the integration of genetic and cytogenetic data, on attempts to use the map to direct gene searches, and on nascent large-scale sequencing efforts. This report summarizes physical and genetic mapping information presented at the workshop and/or published since the reports of the fourth International X Chromosome Workshop. The principle aim of the workshop was to derive a consensus map of the chromosome, in terms of physical contigs emphasizing the location of genes and microsatellite markers. The resulting map is presented and updates previous versions. This report also updates the list of highly informative microsatellites. The text highlights the working state of the map, the genes known to reside on the X, and the progress toward integration of various types of data.

  17. Structural analysis and physical mapping of a pericentromeric region of chromosome 5 of Arabidopsis thaliana.

    Science.gov (United States)

    Tutois, S; Cloix, C; Cuvillier, C; Espagnol, M C; Lafleuriel, J; Picard, G; Tourmente, S

    1999-01-01

    The Arabidopsis thaliana CIC YAC 2D2, 510 kb long and containing a small block of 180 bp satellite units was subcloned after EcoR1 digestion in the pBluescript plasmid. One of these clones was mapped genetically in the pericentromeric region of chromosome 5. The analysis of 40 subclones of this YAC showed that they all contain repeated sequences with a high proportion of transposable elements. Three new retrotransposons, two Ty-3 Gypsy-like and one Ty-1 Copia, were identified in addition to two new tandem-repeat families. A physical map of the chromosome 5 pericentromeric region was established using CIC YAC clones, spanning around 1000 kb. This contig extends from the CIC YAC 9F5 and 7A2 positioned on the left arm of chromosome 5 to a 5S rDNA genes block localized by in-situ hybridization in the pericentromeric region. Hybridization of the subclones on the CIC YAC library showed that some of them are restricted to the pericentromeric region of chromosome 5 and represent specific markers of this region. PMID:10328626

  18. Dicty_cDB: Contig-U05922-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available gillus niger contig An15c0060... 32 5.2 AF402141_4( AF402...hvqvgm*lkkvipamiwpllvk lllinscvqinwitmlvnsskleenivvikcigilsd**nkkeweiyckiyryetfkf*f c*ffkkik*kynieqlf*yk Fra...nomic clone ... 46 0.99 1 ( CG815370 ) SOYAI73TH LargeInsert...date 2009. 6.20 Homology vs Protein Query= Contig-U05922-1 (Contig-U05922-1Q) /CSM_Contig/Contig-U05922-1Q.Seq.d (420 letter...tive length of database: 707,721,139 Effective search space: 25477961004 Effective search space used: 25477961004 Neig

  19. Dicty_cDB: Contig-U15615-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ... 46 4.8 1 ( ET207125 ) MUGQ_CH252P406K03T7_CP774_006 CHORI-252 Vervet Mo... 46 4.8 1 ( ET087319 ) QM0AAA10DG07FM1 CCL1...ne CH230-238F5, *** SEQUENCI... 46 4.8 1 ( AC096810 ) Rattus norvegicus clone CH230-29L11, *** SEQUENCI... 4...12 0 1 1 0 0 0 0 Show Contig-U15615-1 Contig ID Contig-U15615-1 Contig update 2004. 6.11 Contig sequence >Co...AGATAAATTTACAAGTGAAGATATA ATACAAATACCATTTGGTGCTAAATTATATTTTTCTGGAGATGTAGTATT TAATTATCCAGTTAATTTCAATTGTCAACCA...TCACTTAAAAAGGAATTAT CACGTTTTGTTTATGAAATTGATTGTCTTCAAGTTTTTTCCAATGGTACC ATCACCTATA

  20. Chromothripsis-like chromosomal rearrangements induced by ionizing radiation using proton microbeam irradiation system.

    Science.gov (United States)

    Morishita, Maki; Muramatsu, Tomoki; Suto, Yumiko; Hirai, Momoki; Konishi, Teruaki; Hayashi, Shin; Shigemizu, Daichi; Tsunoda, Tatsuhiko; Moriyama, Keiji; Inazawa, Johji

    2016-03-01

    Chromothripsis is the massive but highly localized chromosomal rearrangement in response to a one-step catastrophic event, rather than an accumulation of a series of subsequent and random alterations. Chromothripsis occurs commonly in various human cancers and is thought to be associated with increased malignancy and carcinogenesis. However, the causes and consequences of chromothripsis remain unclear. Therefore, to identify the mechanism underlying the generation of chromothripsis, we investigated whether chromothripsis could be artificially induced by ionizing radiation. We first elicited DNA double-strand breaks in an oral squamous cell carcinoma cell line HOC313-P and its highly metastatic subline HOC313-LM, using Single Particle Irradiation system to Cell (SPICE), a focused vertical microbeam system designed to irradiate a spot within the nuclei of adhesive cells, and then established irradiated monoclonal sublines from them, respectively. SNP array analysis detected a number of chromosomal copy number alterations (CNAs) in these sublines, and one HOC313-LM-derived monoclonal subline irradiated with 200 protons by the microbeam displayed multiple CNAs involved locally in chromosome 7. Multi-color FISH showed a complex translocation of chromosome 7 involving chromosomes 11 and 12. Furthermore, whole genome sequencing analysis revealed multiple de novo complex chromosomal rearrangements localized in chromosomes 2, 5, 7, and 20, resembling chromothripsis. These findings suggested that localized ionizing irradiation within the nucleus may induce chromothripsis-like complex chromosomal alterations via local DNA damage in the nucleus. PMID:26862731