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Sample records for aestivum bac genomic

  1. New approaches for genome characterization: genomic and chromosome-specific BAC libraries from hexaploid wheat

    Czech Academy of Sciences Publication Activity Database

    Chalhoub, B.; Šafář, Jan; Lefévre, A.; Rouault, P.; Pateyron, S.; Bellec, A.; Janda, Jaroslav; Faivre-Rampant, P.; Doležel, Jaroslav; Caboche, M.

    Califoria, 2003. s. -. [Plant and Animal Genome /11./. 11.01.2003-15.01.2003, San Diego] Institutional research plan: CEZ:AV0Z5038910 Keywords : Triticum aestivum L. * BAC librares * flow-assisted chromosome sorting Subject RIV: EB - Genetics ; Molecular Biology

  2. Towards isolating the durable stem rust resistance gene Sr2 from hexaploid wheat (Triticum aestivum L.)

    Czech Academy of Sciences Publication Activity Database

    Kota, R.; Spielmeyer, R.; Doležel, Jaroslav; Šafář, Jan; Paux, E.; McIntosh, R.A.; Lagudah, E.S.

    2006. p. 181. [International Conference “Plant and Animal Genome XIV”. 14.01.2006-18.01.2006, San Diego] Keywords : Triticum aestivum L. * flow-sorted chromosomes * BAC libraries Subject RIV: EB - Genetics ; Molecular Biology

  3. BAC-Pool Sequencing and Assembly of 19 Mb of the Complex Sugarcane Genome

    Science.gov (United States)

    Okura, Vagner Katsumi; de Souza, Rafael S. C.; de Siqueira Tada, Susely F.; Arruda, Paulo

    2016-01-01

    Sequencing plant genomes are often challenging because of their complex architecture and high content of repetitive sequences. Sugarcane has one of the most complex genomes. It is highly polyploid, preserves intact homeologous chromosomes from its parental species and contains >55% repetitive sequences. Although bacterial artificial chromosome (BAC) libraries have emerged as an alternative for accessing the sugarcane genome, sequencing individual clones is laborious and expensive. Here, we present a strategy for sequencing and assembly reads produced from the DNA of pooled BAC clones. A set of 178 BAC clones, randomly sampled from the SP80-3280 sugarcane BAC library, was pooled and sequenced using the Illumina HiSeq2000 and PacBio platforms. A hybrid assembly strategy was used to generate 2,451 scaffolds comprising 19.2 MB of assembled genome sequence. Scaffolds of ≥20 Kb corresponded to 80% of the assembled sequences, and the full sequences of forty BACs were recovered in one or two contigs. Alignment of the BAC scaffolds with the chromosome sequences of sorghum showed a high degree of collinearity and gene order. The alignment of the BAC scaffolds to the 10 sorghum chromosomes suggests that the genome of the SP80-3280 sugarcane variety is ∼19% contracted in relation to the sorghum genome. In conclusion, our data show that sequencing pools composed of high numbers of BAC clones may help to construct a reference scaffold map of the sugarcane genome. PMID:27047520

  4. The infectious BAC genomic DNA expression library: a high capacity vector system for functional genomics.

    Science.gov (United States)

    Lufino, Michele M P; Edser, Pauline A H; Quail, Michael A; Rice, Stephen; Adams, David J; Wade-Martins, Richard

    2016-01-01

    Gene dosage plays a critical role in a range of cellular phenotypes, yet most cellular expression systems use heterologous cDNA-based vectors which express proteins well above physiological levels. In contrast, genomic DNA expression vectors generate physiologically-relevant levels of gene expression by carrying the whole genomic DNA locus of a gene including its regulatory elements. Here we describe the first genomic DNA expression library generated using the high-capacity herpes simplex virus-1 amplicon technology to deliver bacterial artificial chromosomes (BACs) into cells by viral transduction. The infectious BAC (iBAC) library contains 184,320 clones with an average insert size of 134.5 kb. We show in a Chinese hamster ovary (CHO) disease model cell line and mouse embryonic stem (ES) cells that this library can be used for genetic rescue studies in a range of contexts including the physiological restoration of Ldlr deficiency, and viral receptor expression. The iBAC library represents an important new genetic analysis tool openly available to the research community. PMID:27353647

  5. Fishing for function: zebrafish BAC transgenics for functional genomics

    OpenAIRE

    Chatterjee, Sumantra; Lufkin, Thomas

    2011-01-01

    Transgenics using bacterial artificial chromosomes (BACs) offers a great opportunity to look at gene regulation in a developing embryo. The modified BAC containing a reporter inserted just before the translational start site of the gene of interest allows for the visualization of spatio-temporal gene expression. Though this method has been used in the mouse model extensively, its utility in zebrafish studies is relatively new. This review aims to look at the utility of making BAC transgenics ...

  6. An integrated BAC/BIBAC-based physical and genetic map of the cotton genome

    Science.gov (United States)

    Integrated genome-wide genetic and physical maps are crucial to many aspects of cotton genome research. We report a genome-wide BAC/BIBAC-based physical and genetic map of the upland cotton genome using a high-resolution and high-throughput capillary-based fingerprinting method. The map was constr...

  7. Distribution of Genes and Repetitive Elements in the Diabrotica virgifera virgifera Genome Estimated Using BAC Sequencing

    Directory of Open Access Journals (Sweden)

    Brad S. Coates

    2012-01-01

    Full Text Available Feeding damage caused by the western corn rootworm, Diabrotica virgifera virgifera, is destructive to corn plants in North America and Europe where control remains challenging due to evolution of resistance to chemical and transgenic toxins. A BAC library, DvvBAC1, containing 109,486 clones with 104±34.5 kb inserts was created, which has an ~4.56X genome coverage based upon a 2.58 Gb (2.80 pg flow cytometry-estimated haploid genome size. Paired end sequencing of 1037 BAC inserts produced 1.17 Mb of data (~0.05% genome coverage and indicated ~9.4 and 16.0% of reads encode, respectively, endogenous genes and transposable elements (TEs. Sequencing genes within BAC full inserts demonstrated that TE densities are high within intergenic and intron regions and contribute to the increased gene size. Comparison of homologous genome regions cloned within different BAC clones indicated that TE movement may cause haplotype variation within the inbred strain. The data presented here indicate that the D. virgifera virgifera genome is large in size and contains a high proportion of repetitive sequence. These BAC sequencing methods that are applicable for characterization of genomes prior to sequencing may likely be valuable resources for genome annotation as well as scaffolding.

  8. Development of the BAC Physical Maps of Wheat Chromosome 6B for Its Genomic Sequencing

    Czech Academy of Sciences Publication Activity Database

    Kobayashi, A.; Katagiri, S.; Karasawa, W.; Takumi, S.; Doležel, Jaroslav; Ogihara, Y.; Handa, H.

    Verlag : Springer, 2015 - (Handa, H.), s. 101-107 ISBN 978-4-431-55674-9 Institutional support: RVO:61389030 Keywords : genome sequencing * wheat * BAC chromosomes Subject RIV: EB - Genetics ; Molecular Biology

  9. Development of the BAC Physical Maps of Wheat Chromosome 6B for Its Genomic Sequencing

    Czech Academy of Sciences Publication Activity Database

    Kobayashi, A.; Katagiri, S.; Karasawa, W.; Takumi, S.; Doležel, Jaroslav; Ogihara, Y.; Handa, H.

    Verlag: Springer, 2015 - (Handa, H.), s. 101-107 ISBN 978-4-431-55674-9 Institutional support: RVO:61389030 Keywords : genome sequencing * wheat * BAC chromosomes Subject RIV: EB - Genetics ; Molecular Biology

  10. A complete mitochondrial genome of wheat (Triticum aestivum cv. Chinese Yumai), and fast evolving mitochondrial genes in higher plants

    Indian Academy of Sciences (India)

    Peng Cui; Huitao Liu; Qiang Lin; Feng Ding; Guoyin Zhuo; Songnian Hu; Dongcheng Liu; Wenlong Yang; Kehui Zhan; Aimin Zhang; Jun Yu

    2009-12-01

    Plant mitochondrial genomes, encoding necessary proteins involved in the system of energy production, play an important role in the development and reproduction of the plant. They occupy a specific evolutionary pattern relative to their nuclear counterparts. Here, we determined the winter wheat (Triticum aestivum cv. Chinese Yumai) mitochondrial genome in a length of 452 and 526 bp by shotgun sequencing its BAC library. It contains 202 genes, including 35 known protein-coding genes, three rRNA and 17 tRNA genes, as well as 149 open reading frames (ORFs; greater than 300 bp in length). The sequence is almost identical to the previously reported sequence of the spring wheat (T. aestivum cv. Chinese Spring); we only identified seven SNPs (three transitions and four transversions) and 10 indels (insertions and deletions) between the two independently acquired sequences, and all variations were found in non-coding regions. This result confirmed the accuracy of the previously reported mitochondrial sequence of the Chinese Spring wheat. The nucleotide frequency and codon usage of wheat are common among the lineage of higher plant with a high AT-content of 58%. Molecular evolutionary analysis demonstrated that plant mitochondrial genomes evolved at different rates, which may correlate with substantial variations in metabolic rate and generation time among plant lineages. In addition, through the estimation of the ratio of non-synonymous to synonymous substitution rates between orthologous mitochondrion-encoded genes of higher plants, we found an accelerated evolutionary rate that seems to be the result of relaxed selection.

  11. A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome

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    de Boer Jan M

    2011-12-01

    Full Text Available Abstract Background Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH. Results First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map. Conclusions The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and

  12. 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

  13. Toward an Integrated BAC Library Resource for Genome Sequencing and Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Simon, M. I.; Kim, U.-J.

    2002-02-26

    We developed a great deal of expertise in building large BAC libraries from a variety of DNA sources including humans, mice, corn, microorganisms, worms, and Arabidopsis. We greatly improved the technology for screening these libraries rapidly and for selecting appropriate BACs and mapping BACs to develop large overlapping contigs. We became involved in supplying BACs and BAC contigs to a variety of sequencing and mapping projects and we began to collaborate with Drs. Adams and Venter at TIGR and with Dr. Leroy Hood and his group at University of Washington to provide BACs for end sequencing and for mapping and sequencing of large fragments of chromosome 16. Together with Dr. Ian Dunham and his co-workers at the Sanger Center we completed the mapping and they completed the sequencing of the first human chromosome, chromosome 22. This was published in Nature in 1999 and our BAC contigs made a major contribution to this sequencing effort. Drs. Shizuya and Ding invented an automated highly accurate BAC mapping technique. We also developed long-term collaborations with Dr. Uli Weier at UCSF in the design of BAC probes for characterization of human tumors and specific chromosome deletions and breakpoints. Finally the contribution of our work to the human genome project has been recognized in the publication both by the international consortium and the NIH of a draft sequence of the human genome in Nature last year. Dr. Shizuya was acknowledged in the authorship of that landmark paper. Dr. Simon was also an author on the Venter/Adams Celera project sequencing the human genome that was published in Science last year.

  14. Toward an Integrated BAC Library Resource for Genome Sequencing and Analysis; FINAL

    International Nuclear Information System (INIS)

    We developed a great deal of expertise in building large BAC libraries from a variety of DNA sources including humans, mice, corn, microorganisms, worms, and Arabidopsis. We greatly improved the technology for screening these libraries rapidly and for selecting appropriate BACs and mapping BACs to develop large overlapping contigs. We became involved in supplying BACs and BAC contigs to a variety of sequencing and mapping projects and we began to collaborate with Drs. Adams and Venter at TIGR and with Dr. Leroy Hood and his group at University of Washington to provide BACs for end sequencing and for mapping and sequencing of large fragments of chromosome 16. Together with Dr. Ian Dunham and his co-workers at the Sanger Center we completed the mapping and they completed the sequencing of the first human chromosome, chromosome 22. This was published in Nature in 1999 and our BAC contigs made a major contribution to this sequencing effort. Drs. Shizuya and Ding invented an automated highly accurate BAC mapping technique. We also developed long-term collaborations with Dr. Uli Weier at UCSF in the design of BAC probes for characterization of human tumors and specific chromosome deletions and breakpoints. Finally the contribution of our work to the human genome project has been recognized in the publication both by the international consortium and the NIH of a draft sequence of the human genome in Nature last year. Dr. Shizuya was acknowledged in the authorship of that landmark paper. Dr. Simon was also an author on the Venter/Adams Celera project sequencing the human genome that was published in Science last year

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

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    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. Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries

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    Kudrna David

    2011-03-01

    Full Text Available Abstract Background Eucalyptus species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing. Results We describe the construction and characterization of two deep-coverage BAC libraries EG_Ba and EG_Bb obtained from nuclear DNA fragments of E. grandis (clone BRASUZ1 digested with HindIII and BstYI, respectively. Genome coverages of 17 and 15 haploid genome equivalents were estimated for EG_Ba and EG_Bb, respectively. Both libraries contained large inserts, with average sizes ranging from 135 Kb (Eg_Bb to 157 Kb (Eg_Ba, very low extra-nuclear genome contamination providing a probability of finding a single copy gene ≥ 99.99%. Libraries were screened for the presence of several genes of interest via hybridizations to high-density BAC filters followed by PCR validation. Five selected BAC clones were sequenced and assembled using the Roche GS FLX technology providing the whole sequence of the E. grandis chloroplast genome, and complete genomic sequences of important lignin biosynthesis genes. Conclusions The two E. grandis BAC libraries described in this study represent an important milestone for the advancement of Eucalyptus genomics and forest tree research. These BAC resources have a highly redundant genome coverage (> 15×, contain large average inserts and have a very low percentage of clones with organellar DNA or empty vectors. These publicly available BAC libraries are thus suitable for a broad range of applications in genetic and genomic research in Eucalyptus and possibly in related species of Myrtaceae

  17. The complexity of Rhipicephalus (Boophilus microplus genome characterised through detailed analysis of two BAC clones

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    Valle Manuel

    2011-07-01

    Full Text Available Abstract Background Rhipicephalus (Boophilus microplus (Rmi a major cattle ectoparasite and tick borne disease vector, impacts on animal welfare and industry productivity. In arthropod research there is an absence of a complete Chelicerate genome, which includes ticks, mites, spiders, scorpions and crustaceans. Model arthropod genomes such as Drosophila and Anopheles are too taxonomically distant for a reference in tick genomic sequence analysis. This study focuses on the de-novo assembly of two R. microplus BAC sequences from the understudied R microplus genome. Based on available R. microplus sequenced resources and comparative analysis, tick genomic structure and functional predictions identify complex gene structures and genomic targets expressed during tick-cattle interaction. Results In our BAC analyses we have assembled, using the correct positioning of BAC end sequences and transcript sequences, two challenging genomic regions. Cot DNA fractions compared to the BAC sequences confirmed a highly repetitive BAC sequence BM-012-E08 and a low repetitive BAC sequence BM-005-G14 which was gene rich and contained short interspersed elements (SINEs. Based directly on the BAC and Cot data comparisons, the genome wide frequency of the SINE Ruka element was estimated. Using a conservative approach to the assembly of the highly repetitive BM-012-E08, the sequence was de-convoluted into three repeat units, each unit containing an 18S, 5.8S and 28S ribosomal RNA (rRNA encoding gene sequence (rDNA, related internal transcribed spacer and complex intergenic region. In the low repetitive BM-005-G14, a novel gene complex was found between to 2 genes on the same strand. Nested in the second intron of a large 9 Kb papilin gene was a helicase gene. This helicase overlapped in two exonic regions with the papilin. Both these genes were shown expressed in different tick life stage important in ectoparasite interaction with the host. Tick specific sequence

  18. Genomic tools development for Aquilegia: construction of a BAC-based physical map

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    Hodges Scott A

    2010-11-01

    Full Text Available Abstract Background The genus Aquilegia, consisting of approximately 70 taxa, is a member of the basal eudicot lineage, Ranuculales, which is evolutionarily intermediate between monocots and core eudicots, and represents a relatively unstudied clade in the angiosperm phylogenetic tree that bridges the gap between these two major plant groups. Aquilegia species are closely related and their distribution covers highly diverse habitats. These provide rich resources to better understand the genetic basis of adaptation to different pollinators and habitats that in turn leads to rapid speciation. To gain insights into the genome structure and facilitate gene identification, comparative genomics and whole-genome shotgun sequencing assembly, BAC-based genomics resources are of crucial importance. Results BAC-based genomic resources, including two BAC libraries, a physical map with anchored markers and BAC end sequences, were established from A. formosa. The physical map was composed of a total of 50,155 BAC clones in 832 contigs and 3939 singletons, covering 21X genome equivalents. These contigs spanned a physical length of 689.8 Mb (~2.3X of the genome suggesting the complex heterozygosity of the genome. A set of 197 markers was developed from ESTs induced by drought-stress, or involved in anthocyanin biosynthesis or floral development, and was integrated into the physical map. Among these were 87 genetically mapped markers that anchored 54 contigs, spanning 76.4 Mb (25.5% across the genome. Analysis of a selection of 12,086 BAC end sequences (BESs from the minimal tiling path (MTP allowed a preview of the Aquilegia genome organization, including identification of transposable elements, simple sequence repeats and gene content. Common repetitive elements previously reported in both monocots and core eudicots were identified in Aquilegia suggesting the value of this genome in connecting the two major plant clades. Comparison with sequenced plant genomes

  19. 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...

  20. BAC-pool 454-sequencing: A rapid and efficient approach to sequence complex tetraploid cotton genomes

    Science.gov (United States)

    New and emerging next generation sequencing technologies have been promising in reducing sequencing costs, but not significantly for complex polyploid plant genomes such as cotton. Large and highly repetitive genome of G. hirsutum (~2.5GB) is less amenable and cost-intensive with traditional BAC-by...

  1. Comparative analysis of catfish BAC end sequences with the zebrafish genome

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    Abernathy Jason

    2009-12-01

    Full Text Available Abstract Background Comparative mapping is a powerful tool to transfer genomic information from sequenced genomes to closely related species for which whole genome sequence data are not yet available. However, such an approach is still very limited in catfish, the most important aquaculture species in the United States. This project was initiated to generate additional BAC end sequences and demonstrate their applications in comparative mapping in catfish. Results We reported the generation of 43,000 BAC end sequences and their applications for comparative genome analysis in catfish. Using these and the additional 20,000 existing BAC end sequences as a resource along with linkage mapping and existing physical map, conserved syntenic regions were identified between the catfish and zebrafish genomes. A total of 10,943 catfish BAC end sequences (17.3% had significant BLAST hits to the zebrafish genome (cutoff value ≤ e-5, of which 3,221 were unique gene hits, providing a platform for comparative mapping based on locations of these genes in catfish and zebrafish. Genetic linkage mapping of microsatellites associated with contigs allowed identification of large conserved genomic segments and construction of super scaffolds. Conclusion BAC end sequences and their associated polymorphic markers are great resources for comparative genome analysis in catfish. Highly conserved chromosomal regions were identified to exist between catfish and zebrafish. However, it appears that the level of conservation at local genomic regions are high while a high level of chromosomal shuffling and rearrangements exist between catfish and zebrafish genomes. Orthologous regions established through comparative analysis should facilitate both structural and functional genome analysis in catfish.

  2. An efficient approach to BAC based assembly of complex genomes

    Czech Academy of Sciences Publication Activity Database

    Visendi, P.; Berkman, P.J.; Hayashi, S.; Golicz, A.A.; Bayer, P.E.; Ruperao, P.; Hurgobin, B.; Montenegro, J.; Chan, C.K.K.; Staňková, Helena; Batley, J.; Šimková, Hana; Doležel, Jaroslav; Edwards, D.

    2016-01-01

    Roč. 12, JAN 20 (2016), s. 2. ISSN 1746-4811 R&D Projects: GA MŠk(CZ) LO1204; GA ČR(CZ) GAP501/12/2554 Institutional support: RVO:61389030 Keywords : Next-generation sequencing * SASSY * BAC Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.102, year: 2014

  3. Genomic insight into the common carp (Cyprinus carpio genome by sequencing analysis of BAC-end sequences

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    Wang Jintu

    2011-04-01

    Full Text Available Abstract Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio, a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3

  4. Comparative analysis of catfish BAC end sequences with the zebrafish genome

    OpenAIRE

    Abernathy Jason; Xu Peng; Somridhivej Benjaporn; Ninwichian Parichart; Wang Shaolin; Jiang Yanliang; Liu Hong; Kucuktas Huseyin; Liu Zhanjiang

    2009-01-01

    Abstract Background Comparative mapping is a powerful tool to transfer genomic information from sequenced genomes to closely related species for which whole genome sequence data are not yet available. However, such an approach is still very limited in catfish, the most important aquaculture species in the United States. This project was initiated to generate additional BAC end sequences and demonstrate their applications in comparative mapping in catfish. Results We reported the generation of...

  5. Comparative analysis of catfish BAC end sequences with the zebrafish genome

    OpenAIRE

    Liu, Hong; Jiang, Yanliang; Wang, Shaolin; Ninwichian, Parichart; Somridhivej, Benjaporn; Xu, Peng(Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190, Beijing, China); Abernathy, Jason; Kucuktas, Huseyin; Liu, Zhanjiang

    2009-01-01

    Background Comparative mapping is a powerful tool to transfer genomic information from sequenced genomes to closely related species for which whole genome sequence data are not yet available. However, such an approach is still very limited in catfish, the most important aquaculture species in the United States. This project was initiated to generate additional BAC end sequences and demonstrate their applications in comparative mapping in catfish. Results We reported the generation of 43,000 B...

  6. Development of the BAC Physical Maps of Wheat Chromosome 6B for Its Genomic Sequencing

    OpenAIRE

    Kobayashi, A.; Katagiri, S.; Karasawa, W.; Takumi, S.; Doležel, J. (Jaroslav); Ogihara, Y.; Handa, H.

    2015-01-01

    For a purpose of better understanding the genome structure of wheat and accelerating the development of DNA markers for gene isolations and breeding, the Japanese research group, as a member of The International Wheat Genome Sequencing Consortium, is now conducting the physical mapping and genomic sequencing of wheat chromosome 6B of ‘Chinese Spring’ (CS). BAC libraries were constructed respectively using the short and long arm-specific DNAs extracted from the flow-sorted chromosome 6BS and 6...

  7. Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy

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    Garcia-Mas Jordi

    2010-11-01

    Full Text Available Abstract Background Cucumis melo (melon belongs to the Cucurbitaceae family, whose economic importance among horticulture crops is second only to Solanaceae. Melon has a high intra-specific genetic variation, morphologic diversity and a small genome size (454 Mb, which make it suitable for a great variety of molecular and genetic studies. A number of genetic and genomic resources have already been developed, such as several genetic maps, BAC genomic libraries, a BAC-based physical map and EST collections. Sequence information would be invaluable to complete the picture of the melon genomic landscape, furthering our understanding of this species' evolution from its relatives and providing an important genetic tool. However, to this day there is little sequence data available, only a few melon genes and genomic regions are deposited in public databases. The development of massively parallel sequencing methods allows envisaging new strategies to obtain long fragments of genomic sequence at higher speed and lower cost than previous Sanger-based methods. Results In order to gain insight into the structure of a significant portion of the melon genome we set out to perform massive sequencing of pools of BAC clones. For this, a set of 57 BAC clones from a double haploid line was sequenced in two pools with the 454 system using both shotgun and paired-end approaches. The final assembly consists of an estimated 95% of the actual size of the melon BAC clones, with most likely complete sequences for 50 of the BACs, and a total sequence coverage of 39x. The accuracy of the assembly was assessed by comparing the previously available Sanger sequence of one of the BACs against its 454 sequence, and the polymorphisms found involved only 1.7 differences every 10,000 bp that were localized in 15 homopolymeric regions and two dinucleotide tandem repeats. Overall, the study provides approximately 6.7 Mb or 1.5% of the melon genome. The analysis of this new data has

  8. A BAC-based physical map of the Drosophila buzzatii genome

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, Josefa; Nefedov, Michael; Bosdet, Ian; Casals, Ferran; Calvete, Oriol; Delprat, Alejandra; Shin, Heesun; Chiu, Readman; Mathewson, Carrie; Wye, Natasja; Hoskins, Roger A.; Schein, JacquelineE.; de Jong, Pieter; Ruiz, Alfredo

    2005-03-18

    Large-insert genomic libraries facilitate cloning of large genomic regions, allow the construction of clone-based physical maps and provide useful resources for sequencing entire genomes. Drosophilabuzzatii is a representative species of the repleta group in the Drosophila subgenus, which is being widely used as a model in studies of genome evolution, ecological adaptation and speciation. We constructed a Bacterial Artificial Chromosome (BAC) genomic library of D. buzzatii using the shuttle vector pTARBAC2.1. The library comprises 18,353 clones with an average insert size of 152 kb and a {approx}18X expected representation of the D. buzzatii euchromatic genome. We screened the entire library with six euchromatic gene probes and estimated the actual genome representation to be {approx}23X. In addition, we fingerprinted by restriction digestion and agarose gel electrophoresis a sample of 9,555 clones, and assembled them using Finger Printed Contigs (FPC) software and manual editing into 345 contigs (mean of 26 clones per contig) and 670singletons. Finally, we anchored 181 large contigs (containing 7,788clones) to the D. buzzatii salivary gland polytene chromosomes by in situ hybridization of 427 representative clones. The BAC library and a database with all the information regarding the high coverage BAC-based physical map described in this paper are available to the research community.

  9. A comprehensive BAC resource

    OpenAIRE

    Zhao, Shaying

    2001-01-01

    The Human Genome Project has generated extensive map and sequence data for a large number of Bacterial Artificial Chromosome (BAC) clones. In order to maximize the efficient use of the data and to minimize the redundant work for the research community, The Institute for Genomic Research (TIGR) comprehensive BAC resource (cBACr) (http://www.tigr.org/tdb/BacResource/BAC_resource_intro.html) was built as an expansion of the TIGR human BAC ends database. This resource coll...

  10. Development of genomic resources for Citrus clementina: Characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences

    Directory of Open Access Journals (Sweden)

    Talon Manuel

    2008-09-01

    Full Text Available Abstract Background Citrus species constitute one of the major tree fruit crops of the subtropical regions with great economic importance. However, their peculiar reproductive characteristics, low genetic diversity and the long-term nature of tree breeding mostly impair citrus variety improvement. In woody plants, genomic science holds promise of improvements and in the Citrus genera the development of genomic tools may be crucial for further crop improvements. In this work we report the characterization of three BAC libraries from Clementine (Citrus clementina, one of the most relevant citrus fresh fruit market cultivars, and the analyses of 46.000 BAC end sequences. Clementine is a diploid plant with an estimated haploid genome size of 367 Mb and 2n = 18 chromosomes, which makes feasible the use of genomics tools to boost genetic improvement. Results Three genomic BAC libraries of Citrus clementina were constructed through EcoRI, MboI and HindIII digestions and 56,000 clones, representing an estimated genomic coverage of 19.5 haploid genome-equivalents, were picked. BAC end sequencing (BES of 28,000 clones produced 28.1 Mb of genomic sequence that allowed the identification of the repetitive fraction (12.5% of the genome and estimation of gene content (31,000 genes of this species. BES analyses identified 3,800 SSRs and 6,617 putative SNPs. Comparative genomic studies showed that citrus gene homology and microsyntheny with Populus trichocarpa was rather higher than with Arabidopsis thaliana, a species phylogenetically closer to citrus. Conclusion In this work, we report the characterization of three BAC libraries from C. clementina, and a new set of genomic resources that may be useful for isolation of genes underlying economically important traits, physical mapping and eventually crop improvement in Citrus species. In addition, BAC end sequencing has provided a first insight on the basic structure and organization of the citrus genome and has

  11. Study on the Mitochondrial Genome of Sea Island Cotton (Gossypium barbadense) by BAC Library Screening

    Institute of Scientific and Technical Information of China (English)

    SU Ai-guo; LI Shuang-shuang; LIU Guo-zheng; LEI Bin-bin; KANG Ding-ming; LI Zhao-hu; MA Zhi-ying; HUA Jin-ping

    2014-01-01

    The plant mitochondrial genome displays complex features, particularly in terms of cytoplasmic male sterility (CMS). Therefore, research on the cotton mitochondrial genome may provide important information for analyzing genome evolution and exploring the molecular mechanism of CMS. In this paper, we present a preliminary study on the mitochondrial genome of sea island cotton (Gossypium barbadense) based on positive clones from the bacterial artiifcial chromosome (BAC) library. Thirty-ifve primers designed with the conserved sequences of functional genes and exons of mitochondria were used to screen positive clones in the genome library of the sea island cotton variety called Pima 90-53. Ten BAC clones were obtained and veriifed for further study. A contig was obtained based on six overlapping clones and subsequently laid out primarily on the mitochondrial genome. One BAC clone, clone 6 harbored with the inserter of approximate 115 kb mtDNA sequence, in which more than 10 primers fragments could be ampliifed, was sequenced and assembled using the Solexa strategy. Fifteen mitochondrial functional genes were revealed in clone 6 by gene annotation. The characteristics of the syntenic gene/exon of the sequences and RNA editing were preliminarily predicted.

  12. Enhancing genome investigations in the mosquito Culex quinquefasciatus via BAC library construction and characterization

    Directory of Open Access Journals (Sweden)

    Saski Christopher A

    2011-09-01

    Full Text Available Abstract Background Culex quinquefasciatus (Say is a major species in the Culex pipiens complex and an important vector for several human pathogens including West Nile virus and parasitic filarial nematodes causing lymphatic filariasis. It is common throughout tropical and subtropical regions and is among the most geographically widespread mosquito species. Although the complete genome sequence is now available, additional genomic tools are needed to improve the sequence assembly. Findings We constructed a bacterial artificial chromosome (BAC library using the pIndigoBAC536 vector and HindIII partially digested DNA isolated from Cx. quinquefasciatus pupae, Johannesburg strain (NDJ. Insert size was estimated by NotI digestion and pulsed-field gel electrophoresis of 82 randomly selected clones. To estimate genome coverage, each 384-well plate was pooled for screening with 29 simple sequence repeat (SSR and five gene markers. The NDJ library consists of 55,296 clones arrayed in 144 384-well microplates. Fragment insert size ranged from 50 to 190 kb in length (mean = 106 kb. Based on a mean insert size of 106 kb and a genome size of 579 Mbp, the BAC library provides ~10.1-fold coverage of the Cx. quinquefasciatus genome. PCR screening of BAC DNA plate pools for SSR loci from the genetic linkage map and for four genes associated with reproductive diapause in Culex pipiens resulted in a mean of 9.0 positive plate pools per locus. Conclusion The NDJ library represents an excellent resource for genome assembly enhancement and characterization in Culex pipiens complex mosquitoes.

  13. Genetic stability of pestivirus genomes cloned into BACs

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Reimann, Ilona; Uttenthal, Åse;

    pestivirus strains. In a collaborative research project, between DTU Vet and FLI, on the establishment of genetically modified pestiviruses engineered specifically for the DIVA principle, we cloned a series of complete pestivirus genomes, obtained by full-length RT-PCR, directly into the bacterial artificial......Infectious cDNA clones are a prerequisite for directed genetic manipulations of pestivirus genomes to obtain attenuated pestiviruses designed as new modified live DIVA vaccine candidates against classical swine fever. However, the construction of new infectious pestivirus cDNA clones has been...... hampered due to the large size of the pestivirus genome and due to genetic instability of the cloned cDNA, which in combination with plasmid vectors tend to be unstable and deleterious in the bacterial host. Therefore, new strategies are needed to facilitate construction of stable infectious cDNA clones of...

  14. The first insight into the salvia (lamiaceae) genome via bac library construction and high-throughput sequencing of target bac clones

    International Nuclear Information System (INIS)

    Salvia is a representative genus of Lamiaceae, a eudicot family with significant species diversity and population adaptibility. One of the key goals of Salvia genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of medicinal plants to increase their health and productivity. Large-insert genomic libraries are a fundamental tool for achieving this purpose. We report herein the construction, characterization and screening of a gridded BAC library for Salvia officinalis (sage). The S. officinalis BAC library consists of 17,764 clones and the average insert size is 107 Kb, corresponding to 3 haploid genome equivalents. Seventeen positive clones (average insert size 115 Kb) containing five terpene synthase (TPS) genes were screened out by PCR and 12 of them were subject to Illumina HiSeq 2000 sequencing, which yielded 28,097,480 90-bp raw reads (2.53 Gb). Scaffolds containing sabinene synthase (Sab), a Sab homolog, TPS3 (kaurene synthase-like 2), copalyl diphosphate synthase 2 and one cytochrome P450 gene were retrieved via de novo assembly and annotation, which also have flanking noncoding sequences, including predicted promoters and repeat sequences. Among 2,638 repeat sequences, there are 330 amplifiable microsatellites. This BAC library provides a new resource for Lamiaceae genomic studies, including microsatellite marker development, physical mapping, comparative genomics and genome sequencing. Characterization of positive clones provided insights into the structure of the Salvia genome. These sequences will be used in the assembly of a future genome sequence for S. officinalis. (author)

  15. A first generation BAC-based physical map of the rainbow trout genome

    Directory of Open Access Journals (Sweden)

    Thorgaard Gary H

    2009-10-01

    Full Text Available Abstract Background Rainbow trout (Oncorhynchus mykiss are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. Coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. Many quantitative trait loci (QTL have been identified for production and life-history traits in rainbow trout. A bacterial artificial chromosome (BAC physical map is needed to facilitate fine mapping of QTL and the selection of positional candidate genes for incorporation in marker-assisted selection (MAS for improving rainbow trout aquaculture production. This resource will also facilitate efforts to obtain and assemble a whole-genome reference sequence for this species. Results The physical map was constructed from DNA fingerprinting of 192,096 BAC clones using the 4-color high-information content fingerprinting (HICF method. The clones were assembled into physical map contigs using the finger-printing contig (FPC program. The map is composed of 4,173 contigs and 9,379 singletons. The total number of unique fingerprinting fragments (consensus bands in contigs is 1,185,157, which corresponds to an estimated physical length of 2.0 Gb. The map assembly was validated by 1 comparison with probe hybridization results and agarose gel fingerprinting contigs; and 2 anchoring large contigs to the microsatellite-based genetic linkage map. Conclusion The production and validation of the first BAC physical map of the rainbow trout genome is described in this paper. We are currently integrating this map with the NCCCWA genetic map using more than 200 microsatellites isolated from BAC end sequences and by identifying BACs that harbor more than 300 previously mapped markers. The availability of an integrated physical and genetic map will enable detailed comparative genome

  16. Human BAC Ends

    OpenAIRE

    Zhao, Shaying

    2000-01-01

    The Human BAC Ends database includes all non-redundant human BAC end sequences (BESs) generated by The Institute for Genomic Research (TIGR), the University of Washington (UW) and California Institute of Technology (CalTech). It incorporates the available BAC mapping data from different genome centers and the annotation results of each end sequence for the contents of repeats, ESTs and STS markers. For each BAC end the database integrates the sequence, the phred quality scores, the map and th...

  17. 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.

  18. Wheat chromosomes sorting: dividing a komplex genome into sub-genomic specific BAC libraries

    Czech Academy of Sciences Publication Activity Database

    Lucretti, S.; Doležel, Jaroslav

    2005. P. 2.11. [Italian Society of Agricultural Genetics Annual Congress . 12.09.2005-15.09.2005, Potenza] Keywords : Wheat * flow-sorted chromosomes * BAC library Subject RIV: EB - Genetics ; Molecular Biology

  19. An overview of the Phalaenopsis orchid genome through BAC end sequence analysis

    Directory of Open Access Journals (Sweden)

    Hsiao Yu-Yun

    2011-01-01

    Full Text Available Abstract Background Phalaenopsis orchids are popular floral crops, and development of new cultivars is economically important to floricultural industries worldwide. Analysis of orchid genes could facilitate orchid improvement. Bacterial artificial chromosome (BAC end sequences (BESs can provide the first glimpses into the sequence composition of a novel genome and can yield molecular markers for use in genetic mapping and breeding. Results We used two BAC libraries (constructed using the BamHI and HindIII restriction enzymes of Phalaenopsis equestris to generate pair-end sequences from 2,920 BAC clones (71.4% and 28.6% from the BamHI and HindIII libraries, respectively, at a success rate of 95.7%. A total of 5,535 BESs were generated, representing 4.5 Mb, or about 0.3% of the Phalaenopsis genome. The trimmed sequences ranged from 123 to 1,397 base pairs (bp in size, with an average edited read length of 821 bp. When these BESs were subjected to sequence homology searches, it was found that 641 (11.6% were predicted to represent protein-encoding regions, whereas 1,272 (23.0% contained repetitive DNA. Most of the repetitive DNA sequences were gypsy- and copia-like retrotransposons (41.9% and 12.8%, respectively, whereas only 10.8% were DNA transposons. Further, 950 potential simple sequence repeats (SSRs were discovered. Dinucleotides were the most abundant repeat motifs; AT/TA dimer repeats were the most frequent SSRs, representing 253 (26.6% of all identified SSRs. Microsynteny analysis revealed that more BESs mapped to the whole-genome sequences of poplar than to those of grape or Arabidopsis, and even fewer mapped to the rice genome. This work will facilitate analysis of the Phalaenopsis genome, and will help clarify similarities and differences in genome composition between orchids and other plant species. Conclusion Using BES analysis, we obtained an overview of the Phalaenopsis genome in terms of gene abundance, the presence of repetitive

  20. 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

  1. Construction and characterization of a Lipotes vexillifer genomic DNA BAC library.

    Science.gov (United States)

    Du, Bo; Zhang, Xian-Feng; Fang, Sheng-Guo; Wang, Ding

    2007-04-01

    We constructed a genomic DNA library for Lipotes vexillifer (L. vexillifer), the Baiji or Yangtze River dolphin, one of the most endangered mammals in the world. The library consists of 149,000 BAC clones, with an average insert size of 83 kb, representing approximately 3.4 haploid genome equivalents. PCR amplification of four known L. vexillifer genes yielded two to four positive clones each. To demonstrate the utility of this library, we isolated and sequenced the L. vexillifer alpha lactalbumin gene, which is a gene specific to mammals and one which has been widely used as molecular tool in phylogenetic analysis. We also end-sequenced 20 randomly selected clones, resulting in the identification of at least five new L. vexillifer genes, five SSR loci, and one SINE locus. These results suggest that this library is a valuable resource for candidate gene cloning, physical mapping, and genome sequencing of this important and threatened species. PMID:17867838

  2. A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps

    Directory of Open Access Journals (Sweden)

    Fang Zheiwei

    2007-02-01

    Full Text Available Abstract Background Molecular markers serve three important functions in physical map assembly. First, they provide anchor points to genetic maps facilitating functional genomic studies. Second, they reduce the overlap required for BAC contig assembly from 80 to 50 percent. Finally, they validate assemblies based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy in combination with a high-throughput PCR-based screening method to anchor the maize genetic and physical maps. Results A total of 110,592 maize BAC clones (~ 6x haploid genome equivalents were pooled into six different matrices, each containing 48 pools of BAC DNA. The quality of the BAC DNA pools and their utility for identifying BACs containing target genomic sequences was tested using 254 PCR-based STS markers. Five types of PCR-based STS markers were screened to assess potential uses for the BAC pools. An average of 4.68 BAC clones were identified per marker analyzed. These results were integrated with BAC fingerprint data generated by the Arizona Genomics Institute (AGI and the Arizona Genomics Computational Laboratory (AGCoL to assemble the BAC contigs using the FingerPrinted Contigs (FPC software and contribute to the construction and anchoring of the physical map. A total of 234 markers (92.5% anchored BAC contigs to their genetic map positions. The results can be viewed on the integrated map of maize 12. Conclusion This BAC pooling strategy is a rapid, cost effective method for genome assembly and anchoring. The requirement for six replicate positive amplifications makes this a robust method for use in large genomes with high amounts of repetitive DNA such as maize. This strategy can be used to physically map duplicate loci, provide order information for loci in a small genetic interval or with no genetic recombination, and loci with conflicting hybridization-based information.

  3. Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

    OpenAIRE

    Xu, Jinsong; Qian, Xiaoju; Wang, Xiaofeng; Li, Ruiyuan; Cheng, Xiaomao; Yang, Yuan; Fu, Jie; Zhang, Shunchang; King, Graham J; Wu, Jiangsheng; Liu, Kede

    2010-01-01

    Background The Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola). Results In this study, we identified over 23,000 simple sequence repeats ...

  4. Completely Distinguishing Individual A-genome Chromosomes and Their Karyotyping Analysis by Multiple BAC-FISH

    Institute of Scientific and Technical Information of China (English)

    WANG Kai; GUO Wang-zhen; ZHANG Tian-zhen

    2008-01-01

    @@ Multiple BAC-FISH is a powerful tool for modern cytogenetic researching in both animals and plants.But in cotton,this technique is unavailable due to the high percentage of repetitive sequences.Here,we identified twenty BACs from more than fifty BACs,and successfully demonstrated the use of multiple BAC-FISH for cytogenetie research in a diploid cotton species,G.arboreum.The karyotyping should be a basic application of this technique,but the potential usage such as high-resolution physical mapping construction,assisting BAC-by-BAC sequencing will be invaluable.

  5. BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp

    Science.gov (United States)

    Zhao, Cui; Zhang, Xiaojun; Liu, Chengzhang; Huan, Pin; Li, Fuhua; Xiang, Jianhai; Huang, Chao

    2012-05-01

    Little is known about the genome of Pacific white shrimp ( Litopenaeus vannamei). To address this, we conducted BAC (bacterial artificial chromosome) end sequencing of L. vannamei. We selected and sequenced 7 812 BAC clones from the BAC library LvHE from the two ends of the inserts by Sanger sequencing. After trimming and quality filtering, 11 279 BAC end sequences (BESs) including 4 609 pairedends BESs were obtained. The total length of the BESs was 4 340 753 bp, representing 0.18% of the L. vannamei haploid genome. The lengths of the BESs ranged from 100 bp to 660 bp with an average length of 385 bp. Analysis of the BESs indicated that the L. vannamei genome is AT-rich and that the primary repeats patterns were simple sequence repeats (SSRs) and low complexity sequences. Dinucleotide and hexanucleotide repeats were the most common SSR types in the BESs. The most abundant transposable element was gypsy, which may contribute to the generation of the large genome size of L. vannamei. We successfully annotated 4 519 BESs by BLAST searching, including genes involved in immunity and sex determination. Our results provide an important resource for functional gene studies, map construction and integration, and complete genome assembly for this species.

  6. Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

    Directory of Open Access Journals (Sweden)

    King Graham J

    2010-10-01

    Full Text Available Abstract Background The Multinational Brassica rapa Genome Sequencing Project (BrGSP has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola. Results In this study, we identified over 23,000 simple sequence repeats (SSRs from 536 sequenced BACs. 890 SSR markers (designated as BrGMS were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH. Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs, 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus. Conclusion The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species.

  7. A first generation BAC-based physical map of the channel catfish genome

    Directory of Open Access Journals (Sweden)

    Waldbieser Geoffrey C

    2007-02-01

    Full Text Available Abstract Background Channel catfish, Ictalurus punctatus, is the leading species in North American aquaculture. Genetic improvement of catfish is performed through selective breeding, and genomic tools will help improve selection efficiency. A physical map is needed to integrate the genetic map with the karyotype and to support fine mapping of phenotypic trait alleles such as Quantitative Trait Loci (QTL and the effective positional cloning of genes. Results A genome-wide physical map of the channel catfish was constructed by High-Information-Content Fingerprinting (HICF of 46,548 Bacterial Artificial Chromosomes (BAC clones using the SNaPshot technique. The clones were assembled into contigs with FPC software. The resulting assembly contained 1,782 contigs and covered an estimated physical length of 0.93 Gb. The validity of the assembly was demonstrated by 1 anchoring 19 of the largest contigs to the microsatellite linkage map 2 comparing the assembly of a multi-gene family to Restriction Fragment Length Polymorphism (RFLP patterns seen in Southern blots, and 3 contig sequencing. Conclusion This is the first physical map for channel catfish. The HICF technique allowed the project to be finished with a limited amount of human resource in a high throughput manner. This physical map will greatly facilitate the detailed study of many different genomic regions in channel catfish, and the positional cloning of genes controlling economically important production traits.

  8. A Bac Library and Paired-PCR Approach to Mapping and Completing the Genome Sequence of Sulfolobus Solfataricus P2

    DEFF Research Database (Denmark)

    She, Qunxin; Confalonieri, F.; Zivanovic, Y.;

    2000-01-01

    The original strategy used in the Sulfolobus solfatnricus genome project was to sequence non overlapping, or minimally overlapping, cosmid or lambda inserts without constructing a physical map. However, after only about two thirds of the genome sequence was completed, this approach became counter...... selected for walking over small gaps and preparing template libraries for larger ones. It is concluded that an optimal strategy for sequencing microorganism genomes involves construction of a high-resolution physical map by BAC end analyses, PCR screening and paired-PCR chromosome walking after about half...... the genome sequence has been accumulated....

  9. Chimeric piggyBac transposases for genomic targeting in human cells.

    Science.gov (United States)

    Owens, Jesse B; Urschitz, Johann; Stoytchev, Ilko; Dang, Nong C; Stoytcheva, Zoia; Belcaid, Mahdi; Maragathavally, Kommineni J; Coates, Craig J; Segal, David J; Moisyadi, Stefan

    2012-08-01

    Integrating vectors such as viruses and transposons insert transgenes semi-randomly and can potentially disrupt or deregulate genes. For these techniques to be of therapeutic value, a method for controlling the precise location of insertion is required. The piggyBac (PB) transposase is an efficient gene transfer vector active in a variety of cell types and proven to be amenable to modification. Here we present the design and validation of chimeric PB proteins fused to the Gal4 DNA binding domain with the ability to target transgenes to pre-determined sites. Upstream activating sequence (UAS) Gal4 recognition sites harbored on recipient plasmids were preferentially targeted by the chimeric Gal4-PB transposase in human cells. To analyze the ability of these PB fusion proteins to target chromosomal locations, UAS sites were randomly integrated throughout the genome using the Sleeping Beauty transposon. Both N- and C-terminal Gal4-PB fusion proteins but not native PB were capable of targeting transposition nearby these introduced sites. A genome-wide integration analysis revealed the ability of our fusion constructs to bias 24% of integrations near endogenous Gal4 recognition sequences. This work provides a powerful approach to enhance the properties of the PB system for applications such as genetic engineering and gene therapy. PMID:22492708

  10. A whole-genome, radiation hybrid map of wheat

    Science.gov (United States)

    Generating a reference sequence of bread wheat (Triticum aestivum L.) is a challenging task because of its large, highly repetitive and allopolyploid genome. Ordering of BAC- and NGS-based contigs in ongoing wheat genome-sequencing projects primarily uses recombination and comparative genomics-base...

  11. Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae)

    OpenAIRE

    Gonthier Lucy; Bellec Arnaud; Blassiau Christelle; Prat Elisa; Helmstetter Nicolas; Rambaud Caroline; Huss Brigitte; Hendriks Theo; Bergès Hélène; Quillet Marie-Christine

    2010-01-01

    Abstract Background The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries ...

  12. Comparative BAC-based mapping in the white-throated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization

    Directory of Open Access Journals (Sweden)

    Gonser Rusty A

    2011-06-01

    Full Text Available Abstract Background The genomics era has produced an arsenal of resources from sequenced organisms allowing researchers to target species that do not have comparable mapping and sequence information. These new "non-model" organisms offer unique opportunities to examine environmental effects on genomic patterns and processes. Here we use comparative mapping as a first step in characterizing the genome organization of a novel animal model, the white-throated sparrow (Zonotrichia albicollis, which occurs as white or tan morphs that exhibit alternative behaviors and physiology. Morph is determined by the presence or absence of a complex chromosomal rearrangement. This species is an ideal model for behavioral genomics because the association between genotype and phenotype is absolute, making it possible to identify the genomic bases of phenotypic variation. Findings We initiated a genomic study in this species by characterizing the white-throated sparrow BAC library via filter hybridization with overgo probes designed for the chicken, turkey, and zebra finch. Cross-species hybridization resulted in 640 positive sparrow BACs assigned to 77 chicken loci across almost all macro-and microchromosomes, with a focus on the chromosomes associated with morph. Out of 216 overgos, 36% of the probes hybridized successfully, with an average number of 3.0 positive sparrow BACs per overgo. Conclusions These data will be utilized for determining chromosomal architecture and for fine-scale mapping of candidate genes associated with phenotypic differences. Our research confirms the utility of interspecies hybridization for developing comparative maps in other non-model organisms.

  13. Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

    Directory of Open Access Journals (Sweden)

    Blackmon Barbara P

    2011-07-01

    Full Text Available Abstract Background BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. Results This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. Conclusions Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed.

  14. Radiation hybrid maps of D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes

    Science.gov (United States)

    The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high-resolution genome maps saturated with ordered markers to assist in anchoring and orienting BAC contigs/ sequence scaffolds for whole genome sequence assembly. Radiation hybrid (RH) mapping has proven to be an e...

  15. Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L. genome

    Directory of Open Access Journals (Sweden)

    Cloutier Sylvie

    2011-05-01

    Full Text Available Abstract Background Flax (Linum usitatissimum L. is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES from 43,776 clones, providing initial insights into the genome. Results The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb. The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%, followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. Conclusion The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable

  16. Transposon Invasion of the Paramecium Germline Genome Countered by a Domesticated PiggyBac Transposase and the NHEJ Pathway

    Directory of Open Access Journals (Sweden)

    Emeline Dubois

    2012-01-01

    Full Text Available Sequences related to transposons constitute a large fraction of extant genomes, but insertions within coding sequences have generally not been tolerated during evolution. Thanks to their unique nuclear dimorphism and to their original mechanism of programmed DNA elimination from their somatic nucleus (macronucleus, ciliates are emerging model organisms for the study of the impact of transposable elements on genomes. The germline genome of the ciliate Paramecium, located in its micronucleus, contains thousands of short intervening sequences, the IESs, which interrupt 47% of genes. Recent data provided support to the hypothesis that an evolutionary link exists between Paramecium IESs and Tc1/mariner transposons. During development of the macronucleus, IESs are excised precisely thanks to the coordinated action of PiggyMac, a domesticated piggyBac transposase, and of the NHEJ double-strand break repair pathway. A PiggyMac homolog is also required for developmentally programmed DNA elimination in another ciliate, Tetrahymena. Here, we present an overview of the life cycle of these unicellular eukaryotes and of the developmentally programmed genome rearrangements that take place at each sexual cycle. We discuss how ancient domestication of a piggyBac transposase might have allowed Tc1/mariner elements to spread throughout the germline genome of Paramecium, without strong counterselection against insertion within genes.

  17. Analysis of the allohexaploid bread wheat genome (Triticum aestivum) using comparative whole genome shotgun sequencing

    Science.gov (United States)

    The large 17 Gb allopolyploid genome of bread wheat is a major challenge for genome analysis because it is composed of three closely- related and independently maintained genomes, with genes dispersed as small “islands” separated by vast tracts of repetitive DNA. We used a novel comparative genomi...

  18. Development of genomic resources for the prairie vole (Microtus ochrogaster: construction of a BAC library and vole-mouse comparative cytogenetic map

    Directory of Open Access Journals (Sweden)

    Young Larry J

    2010-01-01

    Full Text Available Abstract Background The prairie vole (Microtus ochrogaster is a premier animal model for understanding the genetic and neurological basis of social behaviors. Unlike other biomedical models, prairie voles display a rich repertoire of social behaviors including the formation of long-term pair bonds and biparental care. However, due to a lack of genomic resources for this species, studies have been limited to a handful of candidate genes. To provide a substrate for future development of genomic resources for this unique model organism, we report the construction and characterization of a bacterial artificial chromosome (BAC library from a single male prairie vole and a prairie vole-mouse (Mus musculus comparative cytogenetic map. Results We constructed a prairie vole BAC library (CHORI-232 consisting of 194,267 recombinant clones with an average insert size of 139 kb. Hybridization-based screening of the gridded library at 19 loci established that the library has an average depth of coverage of ~10×. To obtain a small-scale sampling of the prairie vole genome, we generated 3884 BAC end-sequences totaling ~2.8 Mb. One-third of these BAC-end sequences could be mapped to unique locations in the mouse genome, thereby anchoring 1003 prairie vole BAC clones to an orthologous position in the mouse genome. Fluorescence in situ hybridization (FISH mapping of 62 prairie vole clones with BAC-end sequences mapping to orthologous positions in the mouse genome was used to develop a first-generation genome-wide prairie vole-mouse comparative cytogenetic map. While conserved synteny was observed between this pair of rodent genomes, rearrangements between the prairie vole and mouse genomes were detected, including a minimum of five inversions and 16 inter-chromosomal rearrangements. Conclusions The construction of the prairie vole BAC library and the vole-mouse comparative cytogenetic map represent the first genome-wide modern genomic resources developed for this

  19. Chromosome arm-specific BAC end sequences permit comparative analysis of homoeologous chromosomes and genomes of polyploid wheat

    Directory of Open Access Journals (Sweden)

    Sehgal Sunish K

    2012-05-01

    Full Text Available Abstract Background Bread wheat, one of the world’s staple food crops, has the largest, highly repetitive and polyploid genome among the cereal crops. The wheat genome holds the key to crop genetic improvement against challenges such as climate change, environmental degradation, and water scarcity. To unravel the complex wheat genome, the International Wheat Genome Sequencing Consortium (IWGSC is pursuing a chromosome- and chromosome arm-based approach to physical mapping and sequencing. Here we report on the use of a BAC library made from flow-sorted telosomic chromosome 3A short arm (t3AS for marker development and analysis of sequence composition and comparative evolution of homoeologous genomes of hexaploid wheat. Results The end-sequencing of 9,984 random BACs from a chromosome arm 3AS-specific library (TaaCsp3AShA generated 11,014,359 bp of high quality sequence from 17,591 BAC-ends with an average length of 626 bp. The sequence represents 3.2% of t3AS with an average DNA sequence read every 19 kb. Overall, 79% of the sequence consisted of repetitive elements, 1.38% as coding regions (estimated 2,850 genes and another 19% of unknown origin. Comparative sequence analysis suggested that 70-77% of the genes present in both 3A and 3B were syntenic with model species. Among the transposable elements, gypsy/sabrina (12.4% was the most abundant repeat and was significantly more frequent in 3A compared to homoeologous chromosome 3B. Twenty novel repetitive sequences were also identified using de novo repeat identification. BESs were screened to identify simple sequence repeats (SSR and transposable element junctions. A total of 1,057 SSRs were identified with a density of one per 10.4 kb, and 7,928 junctions between transposable elements (TE and other sequences were identified with a density of one per 1.39 kb. With the objective of enhancing the marker density of chromosome 3AS, oligonucleotide primers were successfully designed from

  20. Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

    OpenAIRE

    King Graham J; Zhang Shunchang; Fu Jie, .; Yang Yuan; Cheng Xiaomao; Li Ruiyuan; Wang Xiaofeng; Qian Xiaoju; Xu Jinsong; Wu Jiangsheng; Liu Kede

    2010-01-01

    Abstract Background The Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola). Results In this study, we identified over 23,000 simple sequence...

  1. Development of Chromosome-Specific BAC Resources for Genomics of Bread Wheat

    Czech Academy of Sciences Publication Activity Database

    Šafář, Jan; Šimková, Hana; Kubaláková, Marie; Čihalíková, Jarmila; Suchánková, Pavla; Bartoš, Jan; Doležel, Jaroslav

    2010-01-01

    Roč. 129, 1-3 (2010), s. 211-223. ISSN 1424-8581 R&D Projects: GA ČR GA521/07/1573; GA MŠk(CZ) LC06004 Grant ostatní: European Community’s Seventh Framework Programme(XE) FP7/2007–2013 Institutional research plan: CEZ:AV0Z50380511 Keywords : BAC library * Chromosome * DNA markers Subject RIV: GE - Plant Breeding Impact factor: 1.783, year: 2010

  2. BAC ends library generation for Illumina sequencing

    OpenAIRE

    sprotocols

    2015-01-01

    Bacterial artificial chromosome (BAC) libraries are still a valuable tool for de novo assembly of complex genomes, such as many plants genomes. Shotgun sequencing of BACs, individually or by pools, produces first assemblies which usually need further improvement towards finished quality. We developed a new approach to obtain BAC ends libraries for Illumina sequencing (BES), overcoming the expensive and time consuming BAC ends Sanger sequencing. This new method could be useful for improving de...

  3. BAC CLONES GENERATED FROM SHEARED DNA

    OpenAIRE

    Osoegawa, Kazutoyo; Vessere, Gery M.; Shu, Chung Li; Hoskins, Roger A.; Abad, José P.; de Pablos, Beatriz; Villasante, Alfredo; de Jong, Pieter J.

    2006-01-01

    BAC libraries generated from restriction-digested genomic DNA display representational bias and lack some sequences. To facilitate completion of genome projects, procedures have been developed to create BACs from DNA physically sheared to create fragments extending up to 200 kb. The DNA fragments were repaired to create blunt ends and ligated to a new BAC vector. This approach has been tested by generating BAC libraries from Drosophila DNA, with average insert lengths between 50 – 150 kb. The...

  4. Chromosome sorting and its applications in common wheat (Triticum aestivum) genome sequencing

    Czech Academy of Sciences Publication Activity Database

    Wu, S.W.; Xiao, Y.; Zheng, X.; Cai, Y.F.; Doležel, Jaroslav; Liu, B.H.; Yang, L.; Song, M.F.; Zhou, P.; Zhou, Y.; Meng, F.H.; Wang, S.H.; Liu, H.W.; Zhai, H.Q.; Yang, J.P.

    2010-01-01

    Roč. 55, č. 15 (2010), s. 1463-1468. ISSN 1001-6538 Institutional research plan: CEZ:AV0Z50380511 Keywords : Triticum aestivum * flow cytogenetics * chromosome sorting Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.087, year: 2010

  5. Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly

    Directory of Open Access Journals (Sweden)

    Shultz Jeffry

    2008-07-01

    Full Text Available Abstract Background Many of the world's most important food crops have either polyploid genomes or homeologous regions derived from segmental shuffling following polyploid formation. The soybean (Glycine max genome has been shown to be composed of approximately four thousand short interspersed homeologous regions with 1, 2 or 4 copies per haploid genome by RFLP analysis, microsatellite anchors to BACs and by contigs formed from BAC fingerprints. Despite these similar regions,, the genome has been sequenced by whole genome shotgun sequence (WGS. Here the aim was to use BAC end sequences (BES derived from three minimum tile paths (MTP to examine the extent and homogeneity of polyploid-like regions within contigs and the extent of correlation between the polyploid-like regions inferred from fingerprinting and the polyploid-like sequences inferred from WGS matches. Results Results show that when sequence divergence was 1–10%, the copy number of homeologous regions could be identified from sequence variation in WGS reads overlapping BES. Homeolog sequence variants (HSVs were single nucleotide polymorphisms (SNPs; 89% and single nucleotide indels (SNIs 10%. Larger indels were rare but present (1%. Simulations that had predicted fingerprints of homeologous regions could be separated when divergence exceeded 2% were shown to be false. We show that a 5–10% sequence divergence is necessary to separate homeologs by fingerprinting. BES compared to WGS traces showed polyploid-like regions with less than 1% sequence divergence exist at 2.3% of the locations assayed. Conclusion The use of HSVs like SNPs and SNIs to characterize BACs wil improve contig building methods. The implications for bioinformatic and functional annotation of polyploid and paleopolyploid genomes show that a combined approach of BAC fingerprint based physical maps, WGS sequence and HSV-based partitioning of BAC clones from homeologous regions to separate contigs will allow reliable de

  6. BAC CGH-array identified specific small-scale genomic imbalances in diploid DMBA-induced rat mammary tumors

    Directory of Open Access Journals (Sweden)

    Samuelson Emma

    2012-08-01

    Full Text Available Abstract Background Development of breast cancer is a multistage process influenced by hormonal and environmental factors as well as by genetic background. The search for genes underlying this malignancy has recently been highly productive, but the etiology behind this complex disease is still not understood. In studies using animal cancer models, heterogeneity of the genetic background and environmental factors is reduced and thus analysis and identification of genetic aberrations in tumors may become easier. To identify chromosomal regions potentially involved in the initiation and progression of mammary cancer, in the present work we subjected a subset of experimental mammary tumors to cytogenetic and molecular genetic analysis. Methods Mammary tumors were induced with DMBA (7,12-dimethylbenz[a]anthrazene in female rats from the susceptible SPRD-Cu3 strain and from crosses and backcrosses between this strain and the resistant WKY strain. We first produced a general overview of chromosomal aberrations in the tumors using conventional kartyotyping (G-banding and Comparative Genome Hybridization (CGH analyses. Particular chromosomal changes were then analyzed in more details using an in-house developed BAC (bacterial artificial chromosome CGH-array platform. Results Tumors appeared to be diploid by conventional karyotyping, however several sub-microscopic chromosome gains or losses in the tumor material were identified by BAC CGH-array analysis. An oncogenetic tree analysis based on the BAC CGH-array data suggested gain of rat chromosome (RNO band 12q11, loss of RNO5q32 or RNO6q21 as the earliest events in the development of these mammary tumors. Conclusions Some of the identified changes appear to be more specific for DMBA-induced mammary tumors and some are similar to those previously reported in ACI rat model for estradiol-induced mammary tumors. The later group of changes is more interesting, since they may represent anomalies that involve

  7. BAC CGH-array identified specific small-scale genomic imbalances in diploid DMBA-induced rat mammary tumors

    International Nuclear Information System (INIS)

    Development of breast cancer is a multistage process influenced by hormonal and environmental factors as well as by genetic background. The search for genes underlying this malignancy has recently been highly productive, but the etiology behind this complex disease is still not understood. In studies using animal cancer models, heterogeneity of the genetic background and environmental factors is reduced and thus analysis and identification of genetic aberrations in tumors may become easier. To identify chromosomal regions potentially involved in the initiation and progression of mammary cancer, in the present work we subjected a subset of experimental mammary tumors to cytogenetic and molecular genetic analysis. Mammary tumors were induced with DMBA (7,12-dimethylbenz[a]anthrazene) in female rats from the susceptible SPRD-Cu3 strain and from crosses and backcrosses between this strain and the resistant WKY strain. We first produced a general overview of chromosomal aberrations in the tumors using conventional kartyotyping (G-banding) and Comparative Genome Hybridization (CGH) analyses. Particular chromosomal changes were then analyzed in more details using an in-house developed BAC (bacterial artificial chromosome) CGH-array platform. Tumors appeared to be diploid by conventional karyotyping, however several sub-microscopic chromosome gains or losses in the tumor material were identified by BAC CGH-array analysis. An oncogenetic tree analysis based on the BAC CGH-array data suggested gain of rat chromosome (RNO) band 12q11, loss of RNO5q32 or RNO6q21 as the earliest events in the development of these mammary tumors. Some of the identified changes appear to be more specific for DMBA-induced mammary tumors and some are similar to those previously reported in ACI rat model for estradiol-induced mammary tumors. The later group of changes is more interesting, since they may represent anomalies that involve genes with a critical role in mammary tumor development. Genetic

  8. Physical mapping of black spot disease resistance/susceptibility-related genome regions in Japanese pear (Pyrus pyrifolia) by BAC-FISH.

    Science.gov (United States)

    Yamamoto, Masashi; Terakami, Shingo; Takada, Norio; Yamamoto, Toshiya

    2016-06-01

    Black spot disease, caused by Alternaria alternata Japanese pear pathotype, is one of the most harmful diseases in Japanese pear cultivation. In the present study, the locations of black spot disease resistance/susceptibility-related genome regions were studied by fluorescence in situ hybridization using BAC clone (BAC-FISH) on Japanese pear (Pyrus pyrifolia (Burm. f.) Nakai) chromosomes. Root tips of self-pollinated seedlings of 'Osa Gold' were used as materials. Chromosome samples were prepared by the enzymatic maceration and air-drying method. The BAC clone adjacent to the black spot disease-related gene was labeled as a probe for FISH analysis. Black spot disease-related genome regions were detected in telomeric positions of two medium size chromosomes. These two sites and six telomeric 18S-5.8S-25S rDNA sites were located on different chromosomes as determined from the results of multi-color FISH. The effectiveness of the physical mapping of useful genes on pear chromosomes achieved by the BAC-FISH method was unequivocally demonstrated. PMID:27436955

  9. Genome-wide target profiling of piggyBac and Tol2 in HEK 293: pros and cons for gene discovery and gene therapy

    OpenAIRE

    Meir, Yaa-Jyuhn J; Weirauch, Matthew T.; Yang, Herng-Shing; Chung, Pei-Cheng; Yu, Robert K.; Wu, Sareina C-Y

    2011-01-01

    Background DNA transposons have emerged as indispensible tools for manipulating vertebrate genomes with applications ranging from insertional mutagenesis and transgenesis to gene therapy. To fully explore the potential of two highly active DNA transposons, piggyBac and Tol2, as mammalian genetic tools, we have conducted a side-by-side comparison of the two transposon systems in the same setting to evaluate their advantages and disadvantages for use in gene therapy and gene discovery. Results ...

  10. PiggyBac transposon-based polyadenylation-signal trap for genome-wide mutagenesis in mice

    Science.gov (United States)

    Li, Limei; Liu, Peng; Sun, Liangliang; Bin Zhou; Fei, Jian

    2016-01-01

    We designed a new type of polyadenylation-signal (PAS) trap vector system in living mice, the piggyBac (PB) (PAS-trapping (EGFP)) gene trapping vector, which takes advantage of the efficient transposition ability of PB and efficient gene trap and insertional mutagenesis of PAS-trapping. The reporter gene of PB(PAS-trapping (EGFP)) is an EGFP gene with its own promoter, but lacking a poly(A) signal. Transgenic mouse lines carrying PB(PAS-trapping (EGFP)) and protamine 1 (Prm1) promoter-driven PB transposase transgenes (Prm1-PBase) were generated by microinjection. Male mice doubly positive for PB(PAS-trapping (EGFP)) and Prm1-PBase were crossed with WT females, generating offspring with various insertion mutations. We found that 44.8% (26/58) of pups were transposon-positive progenies. New transposon integrations comprised 26.9% (7/26) of the transposon-positive progenies. We found that 100% (5/5) of the EGFP fluorescence-positive mice had new trap insertions mediated by a PB transposon in transcriptional units. The direction of the EGFP gene in the vector was consistent with the direction of the endogenous gene reading frame. Furthermore, mice that were EGFP-PCR positive, but EGFP fluorescent negative, did not show successful gene trapping. Thus, the novel PB(PAS-trapping (EGFP)) system is an efficient genome-wide gene-trap mutagenesis in mice. PMID:27292714

  11. A First Generation Bac-Based Physical Map of the Channel Catfish Genome

    Science.gov (United States)

    Background: Channel catfish, Ictalurus punctatus, is the leading species in North American aquaculture. Genetic improvement of catfish is performed through selective breeding, and genomic tools will help improve selection efficiency. A physical map is needed to integrate the genetic map with the kar...

  12. Distribution of genes and repetitive elements in the Diabrotica virgifera virgifera genome estimated using BAC sequencing

    Science.gov (United States)

    Feeding damage caused by the corn rootworm, Diabrotica virgifera virgifera, is destructive to corn plants in North America and Europe where control remains challenging due to evolution of resistance traits that allow survival when exposed to chemical and transgenic toxins. Genome sequencing of an i...

  13. DaizuBase, an integrated soybean genome database including BAC-based physical maps

    OpenAIRE

    Katayose, Yuichi; Kanamori, Hiroyuki; Shimomura, Michihiko; Ohyanagi, Hajime; Ikawa, Hiroshi; Minami, Hiroshi; Shibata, Michie; Ito, Tomoko; Kurita, Kanako; Ito, Kazue; Tsubokura, Yasutaka; Kaga, Akito; Wu, Jianzhong; Matsumoto, Takashi; Harada, Kyuya

    2012-01-01

    Soybean [Glycine max (L) Merrill] is one of the most important leguminous crops and ranks fourth after to rice, wheat and maize in terms of world crop production. Soybean contains abundant protein and oil, which makes it a major source of nutritious food, livestock feed and industrial products. In Japan, soybean is also an important source of traditional staples such as tofu, natto, miso and soy sauce. The soybean genome was determined in 2010. With its enormous size, physical mapping and gen...

  14. SimBac: simulation of whole bacterial genomes with homologous recombination

    OpenAIRE

    Didelot, X.; De Maio, N.; Brown, T.; Wilson, DJ

    2015-01-01

    Bacteria can exchange genetic material, or acquire genes found in theenvironment. This process, generally known as bacterial recombination, can have a strong impact on the evolution and phenotype of bacteria, for example causing the spread of antibiotic resistance across clades and species, but can also disrupt phylogenetic and transmission inferences. With the increasing affordability of whole genome sequencing, the need has emerged for an efficient simulator of bacterial evolution to test a...

  15. Development of genomic resources for Citrus clementina: Characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences

    OpenAIRE

    Talon Manuel; Ollitrault Patrick; Naranjo M Angel; Terol Javier

    2008-01-01

    Abstract Background Citrus species constitute one of the major tree fruit crops of the subtropical regions with great economic importance. However, their peculiar reproductive characteristics, low genetic diversity and the long-term nature of tree breeding mostly impair citrus variety improvement. In woody plants, genomic science holds promise of improvements and in the Citrus genera the development of genomic tools may be crucial for further crop improvements. In this work we report the char...

  16. The first insight into the Salvia (Lamiaceae) genome via BAC library construction and high-throughput sequencing of target BAC clones

    OpenAIRE

    Vautrin, Sonia; Song, Chi; Zhu, Ying Jie; Berges, Hélène; Sun, Chao

    2015-01-01

    Salvia is a representative genus of Lamiaceae, a eudicot family with significant species diversity and population adaptibility. One of the key goals of Salvia genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of medicinal plants to increase their health and productivity. Large-insert genomic libraries are a fundamental tool for achieving this purpose. We report herein the cons...

  17. Transposon-mediated BAC transgenesis in zebrafish and mice

    OpenAIRE

    Sumiyama Kenta; Suster Maximiliano L; Kawakami Koichi

    2009-01-01

    Abstract Background Bacterial artificial chromosomes (BACs) are among the most widely used tools for studies of gene regulation and function in model vertebrates, yet methods for predictable delivery of BAC transgenes to the genome are currently limited. This is because BAC transgenes are usually microinjected as naked DNA into fertilized eggs and are known to integrate as multi-copy concatamers in the genome. Although conventional methods for BAC transgenesis have been very fruitful, complem...

  18. Toward Development of a Whole-genome, BAC/BIBAC-based IntegratedPhysical/Genetic Map of the Cotton Genome Using the Upland Cotton Genetic Standard TM-1: BAC Fingerprinting and Physical Map Contig Construction%利用BAC、BIBAC文库整合构建陆地棉遗传标准系TM 1全基因组的遗传、物理图谱:BAC文库的指纹分析及重叠群构建

    Institute of Scientific and Technical Information of China (English)

    Hong-bin ZHANG; Mi-Kyung LEE; John Z. YU; Russell J. KOHEL; David M. STELLY; Zhan-you XU; Lina COVALEDA; Ke-jiao DING; Liang-tao ZHANG; Cheng-cang WU

    2002-01-01

      We are developing a whole-genome, BAC/BIBAC-based integrated physical/genetic map of the cotton (Gossypium hirsutum L. ) genome using its genetic standard line TM-1 as the reference genotype. Whole-genome physical maps integrated with genetic maps will provide revolutionized tools and platforms for all kinds of genomics research, including large-scale gene mapping, cloning and target DNA marker development.……

  19. Sequencing of 15622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

    Czech Academy of Sciences Publication Activity Database

    Munoz-Amatriain, M.; Lonardi, S.; Luo, M.C.; Madishetty, K.; Svensson, J.T.; Moscou, M. J.; Wanamaker, S.; Kudrna, D.; Zheng, J.; Šimková, Hana; Doležel, Jaroslav; Grimwood, J.; Mammadov, J.; Close, T.J.

    2015-01-01

    Roč. 84, č. 1 (2015), s. 216-227. ISSN 0960-7412 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : Barley * Hordeum vulgare L * BAC sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.972, year: 2014

  20. Creation of a BAC resource to study the structure and evolution of the banana (Musa balbisiana) genome

    Czech Academy of Sciences Publication Activity Database

    Šafář, Jan; Noa-Carrazana, J. C.; Vrána, Jan; Bartoš, Jan; Alkhimova, Olena; Lheureux, F.; Šimková, Hana; Caruana, M. L.; Doležel, Jaroslav; Piffanelli, P.

    2004-01-01

    Roč. 47, - (2004), 1182ů1191. E-ISSN 1480-3321 R&D Projects: GA AV ČR IAA6038201 Grant ostatní: research contract IAEA(FR) 12230/RBF Institutional research plan: CEZ:AV0Z5038910 Keywords : bacterial artificial chromosome library * banana * BAC-FISH Subject RIV: EB - Genetics ; Molecular Biology

  1. Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae

    Directory of Open Access Journals (Sweden)

    Gonthier Lucy

    2010-08-01

    Full Text Available Abstract Background The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (Cichorium intybus L. constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae. Findings Two bacterial artificial chromosome (BAC libraries, CinS2S2 and CinS1S4, were constructed from HindIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and S2S2 for the S-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and S1S4. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers. Conclusions This

  2. BAC-end microsatellites from intra and inter-genic regions of the common bean genome and their correlation with cytogenetic features.

    Directory of Open Access Journals (Sweden)

    Matthew Wohlgemuth Blair

    Full Text Available Highly polymorphic markers such as simple sequence repeats (SSRs or microsatellites are very useful for genetic mapping. In this study novel SSRs were identified in BAC-end sequences (BES from non-contigged, non-overlapping bacterial artificial clones (BACs in common bean (Phaseolus vulgaris L.. These so called "singleton" BACs were from the G19833 Andean gene pool physical map and the new BES-SSR markers were used for the saturation of the inter-gene pool, DOR364×G19833 genetic map. A total of 899 SSR loci were found among the singleton BES, but only 346 loci corresponded to the single di- or tri-nucleotide motifs that were likely to be polymorphic (ATT or AG motifs, principally and useful for primer design and individual marker mapping. When these novel SSR markers were evaluated in the DOR364×G19833 population parents, 136 markers revealed polymorphism and 106 were mapped. Genetic mapping resulted in a map length of 2291 cM with an average distance between markers of 5.2 cM. The new genetic map was compared to the most recent cytogenetic analysis of common bean chromosomes. We found that the new singleton BES-SSR were helpful in filling peri-centromeric spaces on the cytogenetic map. Short genetic distances between some new singleton-derived BES-SSR markers was common showing suppressed recombination in these regions compared to other parts of the genome. The correlation of singleton-derived SSR marker distribution with other cytogenetic features of the bean genome is discussed.

  3. Whole genome association mapping of Fusarium head blight resistance in European winter wheat (Triticum aestivum L..

    Directory of Open Access Journals (Sweden)

    Sonja Kollers

    Full Text Available A total of 358 recent European winter wheat varieties plus 14 spring wheat varieties were evaluated for resistance to Fusarium head blight (FHB caused by Fusarium graminearum and Fusarium culmorum in four separate environments. The FHB scores based on FHB incidence (Type I resistance×FHB severity (Type II resistance indicated a wide phenotypic variation of the varieties with BLUE (best linear unbiased estimation values ranging from 0.07 to 33.67. Genotyping with 732 microsatellite markers resulted in 782 loci of which 620 were placed on the ITMI map. The resulting average marker distance of 6.8 cM allowed genome wide association mapping employing a mixed model. Though no clear population structure was discovered, a kinship matrix was used for stratification. A total of 794 significant (-log10(p-value≥3.0 associations between SSR-loci and environment-specific FHB scores or BLUE values were detected, which included 323 SSR alleles. For FHB incidence and FHB severity a total of 861 and 877 individual marker-trait associations (MTA were detected, respectively. Associations for both traits co-located with FHB score in most cases. Consistent associations detected in three or more environments were found on all chromosomes except chromosome 6B, and with the highest number of MTA on chromosome 5B. The dependence of the number of favourable and unfavourable alleles within a variety to the respective FHB scores indicated an additive effect of favourable and unfavourable alleles, i.e. genotypes with more favourable or less unfavourable alleles tended to show greater resistance to FHB. Assessment of a marker specific for the dwarfing gene Rht-D1 resulted in strong effects. The results provide a prerequisite for designing genome wide breeding strategies for FHB resistance.

  4. Generating resources for genomics of wheat homoeologous chromosome group 3: 3AS- and 3DS-specific BAC libraries

    Czech Academy of Sciences Publication Activity Database

    Šafář, Jan; Šimková, Hana; Kubaláková, Marie; Suchánková, Pavla; Čihalíková, Jarmila; Bartoš, Jan; Fiocchetti, F.; Roselli, M.; Gill, B. S.; Doležel, Jaroslav; Lucretti, S.

    2009-01-01

    Roč. 61, 1-2 (2009), s. 151-160. ISSN 0394-9257 R&D Projects: GA ČR GD521/05/H013; GA ČR GA521/06/1723; GA ČR GA521/07/1573; GA MŠk(CZ) LC06004; GA MŠk OC08025 Institutional research plan: CEZ:AV0Z50380511 Keywords : BAC library * Flow sorting * Homoeologous chromosomes Subject RIV: GE - Plant Breeding

  5. Whole genome association mapping of plant height in winter wheat (Triticum aestivum L..

    Directory of Open Access Journals (Sweden)

    Christine D Zanke

    Full Text Available The genetic architecture of plant height was investigated in a set of 358 recent European winter wheat varieties plus 14 spring wheat varieties based on field data in eight environments. Genotyping of diagnostic markers revealed the Rht-D1b mutant allele in 58% of the investigated varieties, while the Rht-B1b mutant was only present in 7% of the varieties. Rht-D1 was significantly associated with plant height by using a mixed linear model and employing a kinship matrix to correct for population stratification. Further genotyping data included 732 microsatellite markers, resulting in 770 loci, of which 635 markers were placed on the ITMI map plus a set of 7769 mapped SNP markers genotyped with the 90 k iSELECT chip. When Bonferroni correction was applied, a total of 153 significant marker-trait associations (MTAs were observed for plant height and the SSR markers (-log10 (P-value ≥ 4.82 and 280 (-log10 (P-value ≥ 5.89 for the SNPs. Linear regression between the most effective markers and the BLUEs for plant height indicated additive effects for the MTAs of different chromosomal regions. Analysis of syntenic regions in the rice genome revealed closely linked rice genes related to gibberellin acid (GA metabolism and perception, i.e. GA20 and GA2 oxidases orthologous to wheat chromosomes 1A, 2A, 3A, 3B, 5B, 5D and 7B, ent-kaurenoic acid oxidase orthologous to wheat chromosome 7A, ent-kaurene synthase on wheat chromosome 2B, as well as GA-receptors like DELLA genes orthologous to wheat chromosomes 4B, 4D and 7A and genes of the GID family orthologous to chromosomes 2B and 5B. The data indicated that besides the widely used GA-insensitive dwarfing genes Rht-B1 and Rht-D1 there is a wide spectrum of loci available that could be used for modulating plant height in variety development.

  6. Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas.

    Science.gov (United States)

    Mohapatra, Gayatry; Engler, David A; Starbuck, Kristen D; Kim, James C; Bernay, Derek C; Scangas, George A; Rousseau, Audrey; Batchelor, Tracy T; Betensky, Rebecca A; Louis, David N

    2011-04-01

    Array comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA). Because diffuse malignant gliomas are often sampled by small biopsies, formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis; FFPE tissues are also needed to study the intratumoral heterogeneity that characterizes these neoplasms. In this paper, we present a combination of evaluations and technical advances that provide strong support for the ready use of oligonucleotide aCGH on FFPE diffuse gliomas. We first compared aCGH using bacterial artificial chromosome (BAC) arrays in 45 paired frozen and FFPE gliomas, and demonstrate a high concordance rate between FFPE and frozen DNA in an individual clone-level analysis of sensitivity and specificity, assuring that under certain array conditions, frozen and FFPE DNA can perform nearly identically. However, because oligonucleotide arrays offer advantages to BAC arrays in genomic coverage and practical availability, we next developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. To demonstrate utility in FFPE tissues, we applied this approach to biphasic anaplastic oligoastrocytomas and demonstrate CNA differences between DNA obtained from the two components. Therefore, BAC and oligonucleotide aCGH can be sensitive and specific tools for detecting CNAs in FFPE DNA, and novel labeling techniques enable the routine use of oligonucleotide arrays for FFPE DNA. In combination, these advances should facilitate genome-wide analysis of rare, small and/or histologically heterogeneous gliomas from FFPE tissues. PMID:21080181

  7. Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome

    Directory of Open Access Journals (Sweden)

    Ritland Carol

    2009-08-01

    Full Text Available Abstract Background Conifers are a large group of gymnosperm trees which are separated from the angiosperms by more than 300 million years of independent evolution. Conifer genomes are extremely large and contain considerable amounts of repetitive DNA. Currently, conifer sequence resources exist predominantly as expressed sequence tags (ESTs and full-length (FLcDNAs. There is no genome sequence available for a conifer or any other gymnosperm. Conifer defence-related genes often group into large families with closely related members. The goals of this study are to assess the feasibility of targeted isolation and sequence assembly of conifer BAC clones containing specific genes from two large gene families, and to characterize large segments of genomic DNA sequence for the first time from a conifer. Results We used a PCR-based approach to identify BAC clones for two target genes, a terpene synthase (3-carene synthase; 3CAR and a cytochrome P450 (CYP720B4 from a non-arrayed genomic BAC library of white spruce (Picea glauca. Shotgun genomic fragments isolated from the BAC clones were sequenced to a depth of 15.6- and 16.0-fold coverage, respectively. Assembly and manual curation yielded sequence scaffolds of 172 kbp (3CAR and 94 kbp (CYP720B4 long. Inspection of the genomic sequences revealed the intron-exon structures, the putative promoter regions and putative cis-regulatory elements of these genes. Sequences related to transposable elements (TEs, high complexity repeats and simple repeats were prevalent and comprised approximately 40% of the sequenced genomic DNA. An in silico simulation of the effect of sequencing depth on the quality of the sequence assembly provides direction for future efforts of conifer genome sequencing. Conclusion We report the first targeted cloning, sequencing, assembly, and annotation of large segments of genomic DNA from a conifer. We demonstrate that genomic BAC clones for individual members of multi-member gene

  8. Herpesvirus BACs: Past, Present, and Future

    Directory of Open Access Journals (Sweden)

    Charles Warden

    2011-01-01

    Full Text Available The herpesviridae are a large family of DNA viruses with large and complicated genomes. Genetic manipulation and the generation of recombinant viruses have been extremely difficult. However, herpesvirus bacterial artificial chromosomes (BACs that were developed approximately 10 years ago have become useful and powerful genetic tools for generating recombinant viruses to study the biology and pathogenesis of herpesviruses. For example, BAC-directed deletion mutants are commonly used to determine the function and essentiality of viral genes. In this paper, we discuss the creation of herpesvirus BACs, functional analyses of herpesvirus mutants, and future applications for studies of herpesviruses. We describe commonly used methods to create and mutate herpesvirus BACs (such as site-directed mutagenesis and transposon mutagenesis. We also evaluate the potential future uses of viral BACs, including vaccine development and gene therapy.

  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. High throughput direct end sequencing of BAC clones.

    OpenAIRE

    Kelley, J M; Field, C E; Craven, M B; Bocskai, D; Kim, U J; Rounsley, S D; Adams, M D

    1999-01-01

    Libraries constructed in bacterial artificial chromosome (BAC) vectors have become the choice for clone sets in high throughput genomic sequencing projects primarily because of their high stability. BAC libraries have been proposed as a source for minimally over-lapping clones for sequencing large genomic regions, and the use of BAC end sequences (i.e. sequences adjoining the insert sites) has been proposed as a primary means for selecting minimally overlapping clones for sequencing large gen...

  11. Utilization of Super BAC Pools and Fluidigm Access Array Platform for High-Throughput BAC Clone Identification: Proof of Concept

    OpenAIRE

    Peter J Maughan; Smith, Scott M.; Joshua A. Raney

    2012-01-01

    Bacterial artificial chromosome (BAC) libraries are critical for identifying full-length genomic sequences, correlating genetic and physical maps, and comparative genomics. Here we describe the utilization of the Fluidigm access array genotyping system in conjunction with KASPar genotyping technology to identify individual BAC clones corresponding to specific single-nucleotide polymorphisms (SNPs) from an Amplicon Express seven-plate super pooled Amaranthus hypochondriacus BAC library. Ninety...

  12. Preliminary Study of BAC Library Construction in Black Tiger Shrimp, Penaeus monodon

    OpenAIRE

    Suwit WUTHISUTHIMETHAVEE; Aoki, Takashi; Hirono, Ikuo; Tassanakajon, Anchalee

    2009-01-01

    Availability of shrimp genome information is necessary for shrimp genetic studies and large-insert DNA clones, bacterial artificial chromosome (BACs) serve as valuable tools for obtaining genomic sequences. The construction of a BAC library was achieved from this preliminary study of P. monodon. High molecular weight (HMW) genomic DNA was isolated from abdominal muscle and the resulting hemocytes were of high quality and sufficient quantity for a BAC library construction. This BAC library was...

  13. Making the most of the hexaploid wheat (Triticum aestivum L.) Genome: Usage of gamma ray mutants for high throughput positional cloning

    International Nuclear Information System (INIS)

    The Triticum aestivum L. genome went through two polyploidisation events in the course of evolution. The result is a very complex structure that is limiting molecular based studies, making of wheat one of the last species for which a shift toward high throughput approaches has not yet been completed. We discuss here (i) how the wheat genome structure buffers the lethality associated with treatments at high dosage of gamma ray and (ii) how this high dosage generates an easy detectable binary polymorphism, at both phenotypic (1=M0 vs 0=KO mutant) and genotypic (1=Retention vs 0=Deletion) levels, (iii) how we exploited this 2 point difference to normalise for the genomic background influence when phenotyping early generations and (iv) to develop PCR based markers independent from allelic polymorphism. In particular, we are discussing the usage of a DARK Real Time marker design, free from needs of subgenome specificity, for direct genotyping of radiation mutants. A low resolution coretention map for the positioning of a boron toxicity tolerance gene, Bo1, on chromosome 7BL, is presented and the mapping resolution discussed in comparison with a genetic map. In conclusion, the usage of gamma ray mutagenesis represents a very expedient method to make the most of the very complex hexaploid wheat genome. (author)

  14. The tRNATyr multigene family of Triticum aestivum: genome organization, sequence analyses and maturation of intron-containing pre-tRNAs in wheat germ extract.

    Science.gov (United States)

    Arends, S; Kraus, J; Beier, H

    1996-04-22

    Southern analysis of Triticum DNA has revealed that nuclear tRNATyr genes are dispersed at a minimum of 16 loci in the genome. We have isolated six independent tRNATyr genes from a Triticum aestivum library in addition to three known members of the Triticum tRNATyr family. Four of the sequenced tRNATyr genes code for Triticum tRNA Tyr and two code for tRNA2Tyr. Three genes encode tRNAsTyr which carry one or two nucleotide substitutions as compared to the conventional genes. The nine Triticum tRNATyr genes possess highly conserved intron sequences ranging in size from 12 to 14 nucleotides. A common secondary intron structure with the 5' and 3' splice site loops separated by five base pairs can be formed by all pre-tRNAs Tyr which are efficiently spliced in the homologous wheat germ extract. PMID:8617358

  15. Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

    Science.gov (United States)

    Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework....

  16. Herpesvirus BACs: Past, Present, and Future

    OpenAIRE

    Charles Warden; Qiyi Tang; Hua Zhu

    2011-01-01

    The herpesviridae are a large family of DNA viruses with large and complicated genomes. Genetic manipulation and the generation of recombinant viruses have been extremely difficult. However, herpesvirus bacterial artificial chromosomes (BACs) that were developed approximately 10 years ago have become useful and powerful genetic tools for generating recombinant viruses to study the biology and pathogenesis of herpesviruses. For example, BAC-directed deletion mutants are commonly used to determ...

  17. Construction of a BAC library and mapping BAC clones to the linkage map of Barramundi, Lates calcarifer

    Directory of Open Access Journals (Sweden)

    Lin Grace

    2008-03-01

    Full Text Available Abstract Background Barramundi (Lates calcarifer is an important farmed marine food fish species. Its first generation linkage map has been applied to map QTL for growth traits. To identify genes located in QTL responsible for specific traits, genomic large insert libraries are of crucial importance. We reported herein a bacterial artificial chromosome (BAC library and the mapping of BAC clones to the linkage map. Results This BAC library consisted of 49,152 clones with an average insert size of 98 kb, representing 6.9-fold haploid genome coverage. Screening the library with 24 microsatellites and 15 ESTs/genes demonstrated that the library had good genome coverage. In addition, 62 novel microsatellites each isolated from 62 BAC clones were mapped onto the first generation linkage map. A total of 86 BAC clones were anchored on the linkage map with at least one BAC clone on each linkage group. Conclusion We have constructed the first BAC library for L. calcarifer and mapped 86 BAC clones to the first generation linkage map. This BAC library and the improved linkage map with 302 DNA markers not only supply an indispensable tool to the integration of physical and linkage maps, the fine mapping of QTL and map based cloning genes located in QTL of commercial importance, but also contribute to comparative genomic studies and eventually whole genome sequencing.

  18. BAC array CGH in patients with Velocardiofacial syndrome-like features reveals genomic aberrations on chromosome region 1q21.1

    Directory of Open Access Journals (Sweden)

    Estivill Xavier

    2009-12-01

    Full Text Available Abstract Background Microdeletion of the chromosome 22q11.2 region is the most common genetic aberration among patients with velocardiofacial syndrome (VCFS but a subset of subjects do not show alterations of this chromosome region. Methods We analyzed 18 patients with VCFS-like features by comparative genomic hybridisation (aCGH array and performed a face-to-face slide hybridization with two different arrays: a whole genome and a chromosome 22-specific BAC array. Putative rearrangements were confirmed by FISH and MLPA assays. Results One patient carried a combination of rearrangements on 1q21.1, consisting in a microduplication of 212 kb and a close microdeletion of 1.15 Mb, previously reported in patients with variable phenotypes, including mental retardation, congenital heart defects (CHD and schizophrenia. While 326 control samples were negative for both 1q21.1 rearrangements, one of 73 patients carried the same 212-kb microduplication, reciprocal to TAR microdeletion syndrome. Also, we detected four copy number variants (CNVs inherited from one parent (a 744-kb duplication on 10q11.22; a 160 kb duplication and deletion on 22q11.21 in two cases; and a gain of 140 kb on 22q13.2, not present in control subjects, raising the potential role of these CNVs in the VCFS-like phenotype. Conclusions Our results confirmed aCGH as a successful strategy in order to characterize additional submicroscopic aberrations in patients with VCF-like features that fail to show alterations in 22q11.2 region. We report a 212-kb microduplication on 1q21.1, detected in two patients, which may contribute to CHD.

  19. Advanced resources for plant genomics: BAC library specific for the short arm of wheat chromosome 1B

    Czech Academy of Sciences Publication Activity Database

    Janda, Jaroslav; Šafář, Jan; Kubaláková, Marie; Bartoš, Jan; Kovářová, Pavlína; Suchánková, Pavla; Pateyron, S.; Čihalíková, Jarmila; Sourdille, P.; Šimková, Hana; Faivre-Rampant, P.; Hřibová, Eva; Bernard, M.; Lukaszewski, A.; Doležel, Jaroslav; Chalhoub, B.

    2006-01-01

    Roč. 47, - (2006), s. 977-986. ISSN 0960-7412 R&D Projects: GA ČR GA521/04/0607; GA ČR GP521/05/P257; GA ČR GD521/05/H013; GA MŠk LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : wheat * genomics * chromosome sorting Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.565, year: 2006

  20. Construction of a BAC library and mapping BAC clones to the linkage map of Barramundi, Lates calcarifer

    OpenAIRE

    Lin Grace; Zhu Ze; Li Jian; Gong Ping; Feng Felicia; Lo Loong; Wang Chun; Yue Gen

    2008-01-01

    Abstract Background Barramundi (Lates calcarifer) is an important farmed marine food fish species. Its first generation linkage map has been applied to map QTL for growth traits. To identify genes located in QTL responsible for specific traits, genomic large insert libraries are of crucial importance. We reported herein a bacterial artificial chromosome (BAC) library and the mapping of BAC clones to the linkage map. Results This BAC library consisted of 49,152 clones with an average insert si...

  1. Construction of the Bac-to-Bac System of Bombyx mori Nucleopolyhedroviru

    Institute of Scientific and Technical Information of China (English)

    Jin-shan HUANG; Bi-fang HAO; Xiu-lian SUN; Fei DENG; Hua-lin WANG; Zhi-hong HU

    2007-01-01

    To construct the Bac-to-Bac expression system of Bombyx mori nucleopolyhedrovirus (BmNPV), a transfer vector was constructed which contained an Escherichia coli (E. coli) mini-F replicon and a lacZ: attTN7: lacZ cassette within the upstream and downstream regions of the BmNPV polyhedrin gene. B. mori larvae were cotransfected with wild-type BmNPV genomic DNA and the transfer vector through subcutaneous injection to generate recombinant viruses by homologous recombination in vivo. The genomic DNA of budded viruses extracted from the hemolymph of the transfected larvae was used to transform E. coli DH10B. Recombinant bacmids were screened by kanamycin resistance, PCR and restriction enzyme (REN) digestion. One of the bacmid colonies, BmBacJS13, which had similar REN profiles to that of wild-type BmNPV, was selected for further research. To investigate the infectivity of BmBacJS13, the polyhedrin gene was introduced into the bacmid and the resultant recombinant (BmBacJS13-ph) was transfected to BmN cells. The budded viruses were collected from the supernatant of the transfected cells and used for infecting BmN cells. Growth curve analysis indicated that BmBacJS13-ph had a similar growth curve to that of wild-type BmNPV. Bio-assays indicated that BmBacJS13-ph was also infectious to B. mori larvae.

  2. 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

  3. BacMet

    DEFF Research Database (Denmark)

    Pal, Chandan; Bengtsson-Palme, Johan; Rensing, Christopher Günther T;

    2014-01-01

    scientific literature. The BacMet database contains 470 experimentally verified resistance genes. In addition, the database also contains 25 477 potential resistance genes collected from public sequence repositories. All resistance genes in the BacMet database have been organized according to their molecular...

  4. BAC Library of T. pallidum DNA in E. coli

    OpenAIRE

    Šmajs, David; McKevitt, Matthew; Wang, Ling; Howell, Jerrilyn K.; Norris, Steven J; Palzkill, Timothy; Weinstock, George M.

    2002-01-01

    Treponema pallidum subspecies pallidum (Nichols) chromosomal DNA was used to construct a large insert bacterial artificial chromosome (BAC) library in Escherichia coli DH10B using the pBeloBAC11 cloning vector; 678 individual insert termini of 339 BAC clones (13.9 x coverage) were sequenced and the cloned chromosomal region in each clone was determined by comparison to the genomic sequence. A single 15.6-kb region of the T. pallidum chromosome was missing in the BAC library, between bp 248727...

  5. Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles

    Directory of Open Access Journals (Sweden)

    Boussaha Mekki

    2006-05-01

    Full Text Available Abstract Background The Fragile Histidine Triad gene (FHIT is an oncosuppressor implicated in many human cancers, including vesical tumors. FHIT is frequently hit by deletions caused by fragility at FRA3B, the most active of human common fragile sites, where FHIT lays. Vesical tumors affect also cattle, including animals grazing in the wild on bracken fern; compounds released by the fern are known to induce chromosome fragility and may trigger cancer with the interplay of latent Papilloma virus. Results The bovine FHIT was characterized by assembling a contig of 78 BACs. Sequence tags were designed on human exons and introns and used directly to select bovine BACs, or compared with sequence data in the bovine genome database or in the trace archive of the bovine genome sequencing project, and adapted before use. FHIT is split in ten exons like in man, with exons 5 to 9 coding for a 149 amino acids protein. VISTA global alignments between bovine genomic contigs retrieved from the bovine genome database and the human FHIT region were performed. Conservation was extremely high over a 2 Mb region spanning the whole FHIT locus, including the size of introns. Thus, the bovine FHIT covers about 1.6 Mb compared to 1.5 Mb in man. Expression was analyzed by RT-PCR and Northern blot, and was found to be ubiquitous. Four cDNA isoforms were isolated and sequenced, that originate from an alternative usage of three variants of exon 4, revealing a size very close to the major human FHIT cDNAs. Conclusion A comparative genomic approach allowed to assemble a contig of 78 BACs and to completely annotate a 1.6 Mb region spanning the bovine FHIT gene. The findings confirmed the very high level of conservation between human and bovine genomes and the importance of comparative mapping to speed the annotation process of the recently sequenced bovine genome. The detailed knowledge of the genomic FHIT region will allow to study the role of FHIT in bovine cancerogenesis

  6. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.).

    Science.gov (United States)

    Han, Bin; Wang, Changbiao; Tang, Zhaohui; Ren, Yongkang; Li, Yali; Zhang, Dayong; Dong, Yanhui; Zhao, Xinghua

    2015-01-01

    Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to

  7. Genome-wide association mapping of fusarium head blight resistance in wheat (Triticum aestivum L.) using genotyping by sequencing

    Science.gov (United States)

    Fusarium head blight (FHB) is one of the most important wheat diseases worldwide and host resistance displays complex genetic control. A genome-wide association study (GWAS) was performed on 273 winter wheat breeding lines from the mid-western and eastern regions of the US to identify chromosomal re...

  8. Hiro Hirai's BAC-FISH Protocol

    OpenAIRE

    sprotocols

    2014-01-01

    Author: Schistosoma Genome Network ### Overview This protocol is a modification of the standard FISH protocol published by Hiro Hirai and Phil LoVerde in Parasitology Today (1995, 11(8) p 310-314) that has been optimised for use with BAC probes and should be read in conjunction with the published protocol. This protocol uses the BIOPRIME reaction kit from GibcoBRL to prepare biotin-labelled BAC DNA which is detected using FITC-Avidin (Vector Labs, DCS grade). Reagents from other ...

  9. Chromosomal location of genomic SSR markers associated with yellow rust resistance in Turkish bread wheat (Triticum aestivum L.)

    Indian Academy of Sciences (India)

    F. Senturk Akfirat; F. Ertugrul; S. Hasancebi; Y. Aydin; K. Akan; Z. Mert; M. Cakir; A. Altinkut Uncuoglu

    2013-08-01

    We have previously reported Xgwm382 as a diagnostic marker for disease resistance against yellow rust in Izgi2001 × ES14 F2 population. Among the same earlier tested 230 primers, one SSR marker (Xgwm311) also amplified a fragment which is present in the resistant parent and in the resistant bulks, but absent in the susceptible parent and in the susceptible bulks. To understand the chromosome group location of these diagnostic markers, Xgwm382 and Xgwm311, in the same population, we selected 16 SSR markers mapped only in one genome of chromosome group 2 around 1–21 cM distance to these diagnostic markers based on the SSR consensus map of wheat. Out of 16 SSRs, Xwmc658 identified resistant F2 individuals as a diagnostic marker for yellow rust disease and provided the location of Xgwm382 and Xgwm311 on chromosome 2AL in our plant material.

  10. Analysis of main effect QTL for thousand grain weight in European winter wheat (Triticum aestivum L. by genome-wide association mapping

    Directory of Open Access Journals (Sweden)

    Christine Désirée Zanke

    2015-09-01

    Full Text Available Grain weight, an essential yield component, is under strong genetic control and at the same time markedly influenced by the environment. Genetic analysis of the thousand grain weight (TGW by genome-wide association study (GWAS was performed with a panel of 358 European winter wheat (Triticum aestivum L. varieties and 14 spring wheat varieties using phenotypic data of field tests in eight environments. Wide phenotypic variations were indicated for the TGW with BLUEs (best linear unbiased estimations values ranging from 35.9 g to 58.2 g with a mean value of 45.4 g and a heritability of H2=0.89. A total of 12 candidate genes for plant height, photoperiodism and grain weight were genotyped on all varieties. Only three candidates, the photoperiodism gene Ppd-D1, dwarfing gene Rht-B1and the TaGW-6A gene were significant explaining up to 14.4%, 2.3% and 3.4% of phenotypic variation, respectively. For a comprehensive genome-wide analysis of TGW-QTL genotyping data from 732 microsatellite markers and a set of 7769 mapped SNP markers genotyped with the 90k iSELECT array were analyzed. In total, 342 significant (-log10 (P-value > 3.0 marker trait associations (MTAs were detected for SSR markers and 1195 MTAs (-log10P-value > 3.0 for SNP markers in all single environments plus the BLUEs. After Bonferroni correction, 28 MTAs remained significant for SSR markers (-log10 (P-value > 4.82 and 58 MTAs for SNP markers (-log10 (P value > 5.89. Apart from chromosomes 4B and 6B for SSR markers and chromosomes 4D and 5D for SNP markers, MTAs were detected on all chromosomes. The highest number of significant SNP markers was found on chromosomes 3B and 1B, while for the SSRs most markers were significant on chromosomes 6D and 3D. Overall, TGW was determined by many markers with small effects. Only three SNP-markers had R2 values above 6%.

  11. Gram negative shuttle BAC vector for heterologous expression of metagenomic libraries

    OpenAIRE

    Kakirde, Kavita S.; Wild, Jadwiga; Godiska, Ronald; Mead, David A.; Wiggins, Andrew G.; Goodman, Robert M.; Szybalski, Waclaw; Liles, Mark R.

    2010-01-01

    Bacterial artificial chromosome (BAC) vectors enable stable cloning of large DNA fragments from single genomes or microbial assemblages. A novel shuttle BAC vector was constructed that permits replication of BAC clones in diverse Gram-negative species. The “Gram-negative shuttle BAC” vector (pGNS-BAC) uses the F replicon for stable single-copy replication in E. coli and the broad-host-range RK2 mini-replicon for high-copy replication in diverse Gram-negative bacteria. As with other BAC vector...

  12. SmartOrBAC

    Directory of Open Access Journals (Sweden)

    Imane BOUIJ-PASQUIER

    2015-11-01

    Full Text Available The emergence of the Internet of Things (IoT paradigm, provides a huge scope for more streamlined living through an increase of smart services but this coincides with an increase in security and privacy concerns, therefore access control has been an important factor in the development of IoT. This work proposes an authorization access model called SmartOrBAC built around a set of security and performance requirements. This model enhances the existing OrBAC (Organization-based Access Control model and adapts it to IoT environments. SmartOrBAC separates the problem into different functional layers and then distributes processing costs between constrained devices and less constrained ones and at the same time addresses the collaborative aspect with a specific solution. This paper also presents the application of SmartOrBAC on a real example of IoT and gives a complexity study demonstrating that even though this model is extensive, it does not add additional complexity regarding traditional access control models.

  13. Construction and characterization of a deep-coverage carrot (Daucus carota L.) BAC library

    Science.gov (United States)

    The first carrot (Daucus carota L.) BAC library was constructed using imbred line B8503, which is nematode-resistant and accumulates carotenes in its roots. The BAC library consists of 92,160 clones comprising 22.4 haploid genome equivalents based on a genome size of 473 Mb/1C. Upon the analysis of ...

  14. Utilization of Super BAC Pools and Fluidigm Access Array Platform for High-Throughput BAC Clone Identification: Proof of Concept

    Directory of Open Access Journals (Sweden)

    Peter J. Maughan

    2012-01-01

    Full Text Available Bacterial artificial chromosome (BAC libraries are critical for identifying full-length genomic sequences, correlating genetic and physical maps, and comparative genomics. Here we describe the utilization of the Fluidigm access array genotyping system in conjunction with KASPar genotyping technology to identify individual BAC clones corresponding to specific single-nucleotide polymorphisms (SNPs from an Amplicon Express seven-plate super pooled Amaranthus hypochondriacus BAC library. Ninety-six SNP loci, spanning the length of A. hypochondriacus linkage groups 1, 2, and 15, were simultaneously tested for clone identification from four BAC super pools, corresponding to 28 384-well plates, using a single Fluidigm integrated fluidic chip (IFC. Forty-six percent of the SNPs were associated with a single unambiguous identified BAC clone. PCR amplification and next-generation sequencing of individual BAC clones confirmed the IFC clone identification. Utilization of the Fluidigm Dynamic array platform allowed for the simultaneous PCR screening of 10,752 BAC pools for 96 SNP tag sites in less than three hours at a cost of ~$0.05 per reaction.

  15. A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS)

    Czech Academy of Sciences Publication Activity Database

    Šimková, Hana; Šafář, Jan; Suchánková, Pavla; Kovářová, Pavlína; Bartoš, Jan; Kubaláková, Marie; Janda, Jaroslav; Čihalíková, Jarmila; Mago, R.; Lelley, T.; Doležel, Jaroslav

    2008-01-01

    Roč. 9, č. 237 (2008), s. 101-109. ISSN 1471-2164 R&D Projects: GA ČR GA521/04/0607; GA ČR GP521/05/P257; GA ČR GD521/05/H013; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : flow cytometry * flow-sorted chromosomes * BAC library Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.926, year: 2008

  16. A BAC clone of MDV strain GX0101 with REV-LTR integration retained its pathogenicity

    Institute of Scientific and Technical Information of China (English)

    SUN AiJun; LAWRENCE Petherbridge; ZHAO YuGuang; LI YanPeng; NAIR Venugopal K; CUI ZhiZhong

    2009-01-01

    The complete genome of Marek's disease virus (MDV) strain GX0101,which was integrated with the LTR sequences of REV,was cloned in Escherichia coli as a bacterial artificial chromosome (BAC).BAC vector sequences were introduced into the US2 locus of the MDV genome by homologous recombination.The viral DNA containing the BAC vector was used to transform Escherichia coli strain of DH10B.Then the recombinant virus was successfully rescued by transfection of the recombinant BAC DNA into primary chicken embryo fibroblast (CEF).This BAC viral clone was named bac-GX0101.When the reconstituted virus was inoculated into 1-day-old birds,visceral tumors could be detected as early as 62 d post infection.There was no difference in growth ability and pathogenicity to birds between the BAC derived virus and its parental virus.The BAC derived virus maintained its oncogenicity and immunosuppressive effects.In conclusion,the complete genome of GX0101 strain was successfully cloned into BAC and the infectious clone was rescued.With the powerful BAC manipulation system,the infectious clone will provide a useful tool for further understanding the functional roles of the inserted REV-LTR sequence in the GX0101 strain of MDV.

  17. 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...

  18. GenMapDB: a database of mapped human BAC clones

    OpenAIRE

    Morley, Michael; Arcaro, Melissa; Burdick, Joshua; Yonescu, Raluca; Reid, Thomas; Kirsch, Ilan R.; Cheung, Vivian G.

    2001-01-01

    GenMapDB (http://genomics.med.upenn.edu/genmapdb) is a repository of human bacterial artificial chromosome (BAC) clones mapped by our laboratory to sequence-tagged site markers. Currently, GenMapDB contains over 3000 mapped clones that span 19 chromosomes, chromosomes 2, 4, 5, 9–22, X and Y. This database provides positional information about human BAC clones from the RPCI-11 human male BAC library. It also contains restriction fragment analysis data and end sequen...

  19. piggyBac can bypass DNA synthesis during cut and paste transposition

    OpenAIRE

    Mitra, Rupak; Fain-Thornton, Jennifer; Craig, Nancy L.

    2008-01-01

    DNA synthesis is considered a defining feature in the movement of transposable elements. In determining the mechanism of piggyBac transposition, an insect transposon that is being increasingly used for genome manipulation in a variety of systems including mammalian cells, we have found that DNA synthesis can be avoided during piggyBac transposition, both at the donor site following transposon excision and at the insertion site following transposon integration. We demonstrate that piggyBac tra...

  20. Genome-wide Profiling Reveals Remarkable Parallels Between Insertion Site Selection Properties of the MLV Retrovirus and the piggyBac Transposon in Primary Human CD4(+) T Cells.

    Science.gov (United States)

    Gogol-Döring, Andreas; Ammar, Ismahen; Gupta, Saumyashree; Bunse, Mario; Miskey, Csaba; Chen, Wei; Uckert, Wolfgang; Schulz, Thomas F; Izsvák, Zsuzsanna; Ivics, Zoltán

    2016-03-01

    The inherent risks associated with vector insertion in gene therapy need to be carefully assessed. We analyzed the genome-wide distributions of Sleeping Beauty (SB) and piggyBac (PB) transposon insertions as well as MLV retrovirus and HIV lentivirus insertions in human CD4(+) T cells with respect to a panel of 40 chromatin states. The distribution of SB transposon insertions displayed the least deviation from random, while the PB transposon and the MLV retrovirus showed unexpected parallels across all chromatin states. Both MLV and PB insertions are enriched at transcriptional start sites (TSSs) and co-localize with BRD4-associated sites. We demonstrate physical interaction between the PB transposase and bromodomain and extraterminal domain proteins (including BRD4), suggesting convergent evolution of a tethering mechanism that directs integrating genetic elements into TSSs. We detect unequal biases across the four systems with respect to targeting genes whose deregulation has been previously linked to serious adverse events in gene therapy clinical trials. The SB transposon has the highest theoretical chance of targeting a safe harbor locus in the human genome. The data underscore the significance of vector choice to reduce the mutagenic load on cells in clinical applications. PMID:26755332

  1. Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome

    OpenAIRE

    Cloutier Sylvie; Rathinavelu Rajkumar; Ragupathy Raja

    2011-01-01

    Abstract Background Flax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report ...

  2. A Comparative BAC Map for the Gilthead Sea Bream (Sparus aurata L.

    Directory of Open Access Journals (Sweden)

    Heiner Kuhl

    2011-01-01

    Full Text Available This study presents the first comparative BAC map of the gilthead sea bream (Sparus aurata, a highly valuated marine aquaculture fish species in the Mediterranean. High-throughput end sequencing of a BAC library yielded 92,468 reads (60.6 Mbp. Comparative mapping was achieved by anchoring BAC end sequences to the three-spined stickleback (Gasterosteus aculeatus genome. BACs that were consistently ordered along the stickleback chromosomes accounted for 14,265 clones. A fraction of 5,249 BACs constituted a minimal tiling path that covers 73.5% of the stickleback chromosomes and 70.2% of the genes that have been annotated. The N50 size of 1,485 “BACtigs” consisting of redundant BACs is 337,253 bp. The largest BACtig covers 2.15 Mbp in the stickleback genome. According to the insert size distribution of mapped BACs the sea bream genome is 1.71-fold larger than the stickleback genome. These results represent a valuable tool to researchers in the field and may support future projects to elucidate the whole sea bream genome.

  3. 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

  4. Technological exploration of BAC-FISH on mitotic chromosomes of maize

    Institute of Scientific and Technical Information of China (English)

    Yongsheng TAO; Zuxin ZHANG; Yonglin CHEN; Lijia LI; Yonglian ZHENG

    2008-01-01

    The rice BAC-DNA was used as probes and fluorescence in situ hybridization (FISH) was applied to the interphase and metaphase mitotic chromosomes of maize. To optimize the BAC-FISH technique, we respect-ively assayed the effect of several factors, including maize or rice genomic Cot DNA used as blocking reagent of DNA, washing temperatures and FAD concentration in the washing buffer and in the hybrid solution. The results show that Cot DNA of maize genome blocked the repet-itive sequence of the rice BAC-DNA when the Cot value was below 50. Meanwhile, it was necessary to adjust the Cot value according to the different probes and their ratios. Decreasing the concentration of FAD in the hybridization mixtures, adjusting the washing rate after hybridization, and most especially, blocking the rice-specific repetitive sequences of BAC-DNA could improve the positive signals of BAC-FISH.

  5. Genome-Wide Sequence Comparison of Centromeric Regions and BAC-Landing on Chromosomes Provide New Insights into Centromere Evolution Among Wheat, Brachypodium, and Rice

    Science.gov (United States)

    As an emerging model system, the nearly finished sequence of Brachypodium distachyon will provide new insights into comparative and functional genomics of grass species. However, centromeres of B. distachyon are unlikely to be sequenced and assembled precisely similar to many other sequenced organis...

  6. Studium syntenie chromosomu Z obaleče jablečného (Cydia pomonella) (L.) metodou BAC-FISH.

    OpenAIRE

    Nguyen, Petr

    2009-01-01

    In this study, the codling moth (Cydia pomonella) partial sequences orthologous to genes that are Z-linked in other lepidopteran species were isolated and used as probes for screening of the codling moth BAC library. Selected BAC clones were labelled and mapped by fluorescence in situ hybridization (the so-called BAC-FISH) to codling moth chromosomes. Where BAC clones were unavailable, Z-linkage was confirmed by Southern hybridization with male and female genomic DNAs. The results revealed co...

  7. Development of genome-specific primers for homoeologous genes in allopolyploid species: the waxy and starch synthase II genes in allohexaploid wheat (Triticum aestivum L. as examples

    Directory of Open Access Journals (Sweden)

    Brûlé-Babel Anita

    2010-05-01

    Full Text Available Abstract Background In allopolypoid crops, homoeologous genes in different genomes exhibit a very high sequence similarity, especially in the coding regions of genes. This makes it difficult to design genome-specific primers to amplify individual genes from different genomes. Development of genome-specific primers for agronomically important genes in allopolypoid crops is very important and useful not only for the study of sequence diversity and association mapping of genes in natural populations, but also for the development of gene-based functional markers for marker-assisted breeding. Here we report on a useful approach for the development of genome-specific primers in allohexaploid wheat. Findings In the present study, three genome-specific primer sets for the waxy (Wx genes and four genome-specific primer sets for the starch synthase II (SSII genes were developed mainly from single nucleotide polymorphisms (SNPs and/or insertions or deletions (Indels in introns and intron-exon junctions. The size of a single PCR product ranged from 750 bp to 1657 bp. The total length of amplified PCR products by these genome-specific primer sets accounted for 72.6%-87.0% of the Wx genes and 59.5%-61.6% of the SSII genes. Five genome-specific primer sets for the Wx genes (one for Wx-7A, three for Wx-4A and one for Wx-7D could distinguish the wild type wheat and partial waxy wheat lines. These genome-specific primer sets for the Wx and SSII genes produced amplifications in hexaploid wheat, cultivated durum wheat, and Aegilops tauschii accessions, but failed to generate amplification in the majority of wild diploid and tetraploid accessions. Conclusions For the first time, we report on the development of genome-specific primers from three homoeologous Wx and SSII genes covering the majority of the genes in allohexaploid wheat. These genome-specific primers are being used for the study of sequence diversity and association mapping of the three homoeologous Wx

  8. Library Resources for Bac End Sequencing. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Pieter J. de Jong

    2000-10-01

    Studies directed towards the specific aims outlined for this research award are summarized. The RPCI II Human Bac Library has been expanded by the addition of 6.9-fold genomic coverage. This segment has been generated from a MBOI partial digest of the same anonymous donor DNA used for the rest of the library. A new cloning vector, pTARBAC1, has been constructed and used in the construction of RPCI-II segment 5. This new cloning vector provides a new strategy in identifying targeted genomic regions and will greatly facilitate a large-scale analysis for positional cloning. A new maleCS7BC/6J mouse BAC library has been constructed. RPCI-23 contain 576 plates (approx 210,000 clones) and represents approximately 11-fold coverage of the mouse genome.

  9. Back to BAC: The Use of Infectious Clone Technologies for Viral Mutagenesis

    Directory of Open Access Journals (Sweden)

    Robyn N. Hall

    2012-02-01

    Full Text Available Bacterial artificial chromosome (BAC vectors were first developed to facilitate the propagation and manipulation of large DNA fragments in molecular biology studies for uses such as genome sequencing projects and genetic disease models. To facilitate these studies, methodologies have been developed to introduce specific mutations that can be directly applied to the mutagenesis of infectious clones (icBAC using BAC technologies. This has resulted in rapid identification of gene function and expression at unprecedented rates. Here we review the major developments in BAC mutagenesis in vitro. This review summarises the technologies used to construct and introduce mutations into herpesvirus icBAC. It also explores developing technologies likely to provide the next leap in understanding these important viruses.

  10. Effects of Blood-Alcohol Concentration (BAC) Feedback on BAC Estimates Over Time

    Science.gov (United States)

    Bullers, Susan; Ennis, Melissa

    2006-01-01

    This study examines the effects of self-tested blood alcohol concentration (BAC) feedback, from personal hand-held breathalyzers, on the accuracy of BAC estimation. Using an e-mail prompted web-based questionnaire, 19 participants were asked to report both BAC estimates and subsequently measured BAC levels over the course of 27 days. Results from…

  11. Molecular characterization and genomic mapping of the pathogenesis-related protein 1 (PR-1) gene family in hexaploid wheat (Triticum aestivum L.)

    Science.gov (United States)

    The group 1 pathogenesis-related (PR-1) proteins, known as hallmarks of defense pathways, are encoded by multigene families in plants as evidenced by the presence of 22 and 32 PR-1 genes in the finished Arabidopsis and rice genomes, respectively. Here, we report the initial characterization and mapp...

  12. BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.

    Directory of Open Access Journals (Sweden)

    Wu Cheng-Cang

    2011-05-01

    Full Text Available Background Although second generation sequencing (2GS technologies allow re-sequencing of previously gold-standard-sequenced genomes, whole genome shotgun sequencing and de novo assembly of large and complex eukaryotic genomes is still difficult. Availability of a genome-wide physical map is therefore still a prerequisite for whole genome sequencing for genomes like barley. To start such an endeavor, large insert genomic libraries, i.e. Bacterial Artificial Chromosome (BAC libraries, which are unbiased and representing deep haploid genome coverage, need to be ready in place. Result Five new BAC libraries were constructed for barley (Hordeum vulgare L. cultivar Morex. These libraries were constructed in different cloning sites (HindIII, EcoRI, MboI and BstXI of the respective vectors. In order to enhance unbiased genome representation and to minimize the number of gaps between BAC contigs, which are often due to uneven distribution of restriction sites, a mechanically sheared library was also generated. The new BAC libraries were fully characterized in depth by scrutinizing the major quality parameters such as average insert size, degree of contamination (plate wide, neighboring, and chloroplast, empty wells and off-scale clones (clones with 250 fragments. Additionally a set of gene-based probes were hybridized to high density BAC filters and showed that genome coverage of each library is between 2.4 and 6.6 X. Conclusion BAC libraries representing >20 haploid genomes are available as a new resource to the barley research community. Systematic utilization of these libraries in high-throughput BAC fingerprinting should allow developing a genome-wide physical map for the barley genome, which will be instrumental for map-based gene isolation and genome sequencing.

  13. Insertional Mutagenesis by a Hybrid PiggyBac and Sleeping Beauty Transposon in the Rat

    OpenAIRE

    Furushima, Kenryo; Jang, Chuan-Wei; Chen, Diane W.; Xiao, Ningna; Overbeek, Paul A.; Behringer, Richard R.

    2012-01-01

    A hybrid piggyBac/Sleeping Beauty transposon-based insertional mutagenesis system that can be mobilized by simple breeding was established in the rat. These transposons were engineered to include gene trap sequences and a tyrosinase (Tyr) pigmentation reporter to rescue the albinism of the genetic background used in the mutagenesis strategy. Single-copy transposon insertions were transposed into the rat genome by co-injection of plasmids carrying the transposon and RNA encoding piggyBac trans...

  14. The piggyBac transposon displays local and distant reintegration preferences and can cause mutations at noncanonical integration sites.

    Science.gov (United States)

    Li, Meng Amy; Pettitt, Stephen J; Eckert, Sabine; Ning, Zemin; Rice, Stephen; Cadiñanos, Juan; Yusa, Kosuke; Conte, Nathalie; Bradley, Allan

    2013-04-01

    The DNA transposon piggyBac is widely used as a tool in mammalian experimental systems for transgenesis, mutagenesis, and genome engineering. We have characterized genome-wide insertion site preferences of piggyBac by sequencing a large set of integration sites arising from transposition from two separate genomic loci and a plasmid donor in mouse embryonic stem cells. We found that piggyBac preferentially integrates locally to the excision site when mobilized from a chromosomal location and identified other nonlocal regions of the genome with elevated insertion frequencies. piggyBac insertions were associated with expressed genes and markers of open chromatin structure and were excluded from heterochromatin. At the nucleotide level, piggyBac prefers to insert into TA-rich regions within a broader GC-rich context. We also found that piggyBac can insert into sites other than its known TTAA insertion site at a low frequency (2%). Such insertions introduce mismatches that are repaired with signatures of host cell repair pathways. Transposons could be mobilized from plasmids with the observed noncanonical flanking regions, indicating that piggyBac could generate point mutations in the genome. PMID:23358416

  15. Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas

    OpenAIRE

    Mohapatra, Gayatry; Engler, David A.; Starbuck, Kristen D.; Kim, James C.; Bernay, Derek C.; Scangas, George A.; Rousseau, Audrey; Batchelor, Tracy T.; Betensky, Rebecca A.; Louis, David N.

    2010-01-01

    Molecular genetic analysis of cancer is rapidly evolving as a result of improvement in genomic technologies and the growing applicability of such analyses to clinical oncology. Array based comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA), particularly in solid tumors, and has been applied to the study of malignant gliomas. In the clinical setting, however, gliomas are often sampled by small biopsies and thus formalin-fixed paraffin-em...

  16. Developemnt of BAC resources for targeted analysis of the short arm of chromosome 1R (1RS)

    Czech Academy of Sciences Publication Activity Database

    Kovářová, Pavlína; Šafář, Jan; Šimková, Hana; Suchánková, Pavla; Bartoš, Jan; Janda, Jaroslav; Doleželová, Marie; Čihalíková, Jarmila; Lelley, T.; Doležel, Jaroslav

    2006. p. 81. [2nd Congress of the International Cytogenetics and Genome Society. 25.06.2006-29.06.2006, University of Kent, Canterbury] Keywords : BAC library * rye * chromosome 1R (1RS) Subject RIV: EB - Genetics ; Molecular Biology

  17. A dense genetic linkage map for common carp and its integration with a BAC-based physical map.

    Directory of Open Access Journals (Sweden)

    Lan Zhao

    Full Text Available BACKGROUND: Common carp (Cyprinus carpio is one of the most important aquaculture species with an annual global production of 3.4 million metric tons. It is also an important ornamental species as well as an important model species for aquaculture research. To improve the economically important traits of this fish, a number of genomic resources and genetic tools have been developed, including several genetic maps and a bacterial artificial chromosome (BAC-based physical map. However, integrated genetic and physical maps are not available to study quantitative trait loci (QTL and assist with fine mapping, positional cloning and whole genome sequencing and assembly. The objective of this study was to integrate the currently available BAC-based physical and genetic maps. RESULTS: The genetic map was updated with 592 novel markers, including 312 BAC-anchored microsatellites and 130 SNP markers, and contained 1,209 genetic markers on 50 linkage groups, spanning 3,565.9 cM in the common carp genome. An integrated genetic and physical map of the common carp genome was then constructed, which was composed of 463 physical map contigs and 88 single BACs. Combined lengths of the contigs and single BACs covered a physical length of 498.75 Mb, or around 30% of the common carp genome. Comparative analysis between common carp and zebrafish genomes was performed based on the integrated map, providing more insights into the common carp specific whole genome duplication and segmental rearrangements in the genome. CONCLUSION: We integrated a BAC-based physical map to a genetic linkage map of common carp by anchoring BAC-associated genetic markers. The density of the genetic linkage map was significantly increased. The integrated map provides a tool for both genetic and genomic studies of common carp, which will help us to understand the genomic architecture of common carp and facilitate fine mapping and positional cloning of economically important traits for

  18. Conversion of BAC clones into binary BAC (BIBAC) vectors and their delivery into basidiomycete fungal cells using Agrobacterium tumefaciens.

    Science.gov (United States)

    Ali, Shawkat; Bakkeren, Guus

    2015-01-01

    The genetic transformation of certain organisms, required for gene function analysis or complementation, is often not very efficient, especially when dealing with large gene constructs or genomic fragments. We have adapted the natural DNA transfer mechanism from the soil pathogenic bacterium Agrobacterium tumefaciens, to deliver intact large DNA constructs to basidiomycete fungi of the genus Ustilago where they stably integrated into their genome. To this end, Bacterial Artificial Chromosome (BAC) clones containing large fungal genomic DNA fragments were converted via a Lambda phage-based recombineering step to Agrobacterium transfer-competent binary vectors (BIBACs) with a Ustilago-specific selection marker. The fungal genomic DNA fragment was subsequently successfully delivered as T-DNA through Agrobacterium-mediated transformation into Ustilago species where an intact copy stably integrated into the genome. By modifying the recombineering vector, this method can theoretically be adapted for many different fungi. PMID:25239747

  19. Comparative sequence and genetic analyses of asparagus BACs reveal no microsynteny with onion or rice.

    Science.gov (United States)

    Jakse, Jernej; Telgmann, Alexa; Jung, Christian; Khar, Anil; Melgar, Sergio; Cheung, Foo; Town, Christopher D; Havey, Michael J

    2006-12-01

    The Poales (includes the grasses) and Asparagales [includes onion (Allium cepa L.) and asparagus (Asparagus officinalis L.)] are the two most economically important monocot orders. The Poales are a member of the commelinoid monocots, a group of orders sister to the Asparagales. Comparative genomic analyses have revealed a high degree of synteny among the grasses; however, it is not known if this synteny extends to other major monocot groups such as the Asparagales. Although we previously reported no evidence for synteny at the recombinational level between onion and rice, microsynteny may exist across shorter genomic regions in the grasses and Asparagales. We sequenced nine asparagus BACs to reveal physically linked genic-like sequences and determined their most similar positions in the onion and rice genomes. Four of the asparagus BACs were selected using molecular markers tightly linked to the sex-determining M locus on chromosome 5 of asparagus. These BACs possessed only two putative coding regions and had long tracts of degenerated retroviral elements and transposons. Five asparagus BACs were selected after hybridization of three onion cDNAs that mapped to three different onion chromosomes. Genic-like sequences that were physically linked on the cDNA-selected BACs or genetically linked on the M-linked BACs showed significant similarities (e asparagus and rice across these regions. Genic-like sequences that were linked in asparagus were used to identify highly similar (e asparagus and genetic linkages in onion. These results further indicate that synteny among grass genomes does not extend to a sister order in the monocots and that asparagus may not be an appropriate smaller genome model for plants in the Asparagales with enormous nuclear genomes. PMID:17016688

  20. Construction of a BAC library and identification of Dmrt1 gene of the rice field eel, Monopterus albus

    International Nuclear Information System (INIS)

    A bacterial artificial chromosome (BAC) library was constructed using nuclear DNA from the rice field eel (Monopterus albus). The BAC library consists of a total of 33,000 clones with an average insert size of 115 kb. Based on the rice field eel haploid genome size of 600 Mb, the BAC library is estimated to contain approximately 6.3 genome equivalents and represents 99.8% of the genome of the rice field eel. This is first BAC library constructed from this species. To estimate the possibility of isolating a specific clone, high-density colony hybridization-based library screening was performed using Dmrt1 cDNA of the rice field eel as a probe. Both library screening and PCR identification results revealed three positive BAC clones which were overlapped, and formed a contig covering the Dmrt1 gene of 195 kb. By sequence comparisons with the Dmrt1 cDNA and sequencing of first four intron-exon junctions, Dmrt1 gene of the rice field eel was predicted to contain four introns and five exons. The sizes of first and second intron are 1.5 and 2.6 kb, respectively, and the sizes of last two introns were predicted to be about 20 kb. The Dmrt1 gene structure was conserved in evolution. These results also indicate that the BAC library is a useful resource for BAC contig construction and molecular isolation of functional genes

  1. Inheritance and localisation of resistance to ¤Mycosphaerella graminicola¤ causing septoria tritici blotch and plant height in the wheat (¤Triticum aestivum¤ L.) genome with DNA markers

    DEFF Research Database (Denmark)

    Eriksen, L.; Borum, F.; Jahoor, A.

    2003-01-01

    Resistance to the disease septoria tritici blotch of wheat (Triticum aestivum L.), caused by the fungus Mycosphaerella graminicola (Fuckel.) J. Schrot in Cohn (anamorph Septoria tritici Roberge in Desmaz.) was investigated in a doubled-haploid (DH) population of a cross between the susceptible...

  2. BAC Library Construction and Physical Mapping of Bacillus anthracis A16R

    Institute of Scientific and Technical Information of China (English)

    Zhang Da; Zhu Houchu; Huang Liuyu

    2013-01-01

    Bacillus anthracis is an endospore-forming bacterium that causes severe inhalational anthrax, and bacillus anthracis A16R is an attenuated strain derived from Bacillus anthracis A16. The development of bacterial artificial chromosome (BAC) system has allowed the construction of large insert-size DNA libraries, and the bacterial artificial chromosomes (BACs) have become the preferred large insert cloning system for genomic analysis because such libraries are characteristically stable, high in ifdelity and easy to handle. To facilitate genome studies of this bacterium, a bacterial artiifcial chromosome library (BAC) has been established from genome DNA of Bacillus anthracis A16R. This library consisted of 9 600 clones randomly selected from more than 15 000 recombinant clones carrying inserts in the plindigoBAC-5 vectors. The mean insert size was 56 kbp, representing an approximate 12-fold genome coverage, while end sequences were obtained from 700 randomly selected clones. Sequences were compared with Bacillus anthracis Ames and Bacillus cereus ATCC 14579 Genome Project databases using the NCBI BLASTN search project. And most BLASTN results showed high identities and that the sequences’ sites could be used as STSs. To construct this physical map, Excel was used for the array of STSs and some gaps of the map were iflled up by PCR walking. Artemis-V4 was used in the construction of a genome-wide physical map with 93%genome coverage. The A16R BAC library proved to be a vital tool for the generation of a map that would not only allow the subsequent sequencing of defined areas of genome, but also provide immediate access to clones that were stable and convenient for functional genomic researches.

  3. BAC Library Construction and Physical Mapping of Bacillus anthracis A16R

    Directory of Open Access Journals (Sweden)

    Da Zhang

    2013-12-01

    Full Text Available Bacillus anthracis is an endospore-forming bacterium that causes severe inhalational anthrax, and bacillus anthracis A16R is an attenuated strain derived from Bacillus anthracis A16. The development of bacterial artificial chromosome (BAC system has allowed the construction of large insert-size DNA libraries, and the bacterial artificial chromosomes (BACs have become the preferred large insert cloning system for genomic analysis because such libraries are characteristically stable, high in fidelity and easy to handle. To facilitate genome studies of this bacterium, a bacterial artificial chromosome library (BAC has been established from genome DNA of Bacillus anthracis A16R. This library consisted of 9 600 clones randomly selected from more than 15 000 recombinant clones carrying inserts in the plindigoBAC-5 vectors. The mean insert size was 56 kbp, representing an approximate 12-fold genome coverage, while end sequences were obtained from 700 randomly selected clones. Sequences were compared with Bacillus anthracis Ames and Bacillus cereus ATCC 14579 Genome Project databases using the NCBI BLASTN search project. And most BLASTN results showed high identities and that the sequences’ sites could be used as STSs. To construct this physical map, Excel was used for the array of STSs and some gaps of the map were filled up by PCR walking. Artemis-V4 was used in the construction of a genome-wide physical map with 93% genome coverage. The A16R BAC library proved to be a vital tool for the generation of a map that would not only allow the subsequent sequencing of defined areas of genome, but also provide immediate access to clones that were stable and convenient for functional genomic researches.

  4. Suicidal Autointegration of Sleeping Beauty and piggyBac Transposons in Eukaryotic Cells

    OpenAIRE

    Yongming Wang; Jichang Wang; Anatharam Devaraj; Manvendra Singh; Ana Jimenez Orgaz; Jia-Xuan Chen; Matthias Selbach; Zoltán Ivics; Zsuzsanna Izsvák

    2014-01-01

    Transposons are discrete segments of DNA that have the distinctive ability to move and replicate within genomes across the tree of life. 'Cut and paste' DNA transposition involves excision from a donor locus and reintegration into a new locus in the genome. We studied molecular events following the excision steps of two eukaryotic DNA transposons, Sleeping Beauty (SB) and piggyBac (PB) that are widely used for genome manipulation in vertebrate species. SB originates from fish and PB from inse...

  5. A BAC-based physical map of Zhikong scallop (Chlamys farreri Jones et Preston.

    Directory of Open Access Journals (Sweden)

    Xiaojun Zhang

    Full Text Available Zhikong scallop (Chlamys farreri is one of the most economically important aquaculture species in China. Physical maps are crucial tools for genome sequencing, gene mapping and cloning, genetic improvement and selective breeding. In this study, we have developed a genome-wide, BAC-based physical map for the species. A total of 81,408 clones from two BAC libraries of the scallop were fingerprinted using an ABI 3130xl Genetic Analyzer and a fingerprinting kit developed in our laboratory. After data processing, 63,641 (∼5.8× genome coverage fingerprints were validated and used in the physical map assembly. A total of 3,696 contigs were assembled for the physical map. Each contig contained an average of 10.0 clones, with an average physical size of 490 kb. The combined total physical size of all contigs was 1.81 Gb, equivalent to approximately 1.5 fold of the scallop haploid genome. A total of 10,587 BAC end sequences (BESs and 167 markers were integrated into the physical map. We evaluated the physical map by overgo hybridization, BAC-FISH (fluorescence in situ hybridization, contig BAC pool screening and source BAC library screening. The results have provided evidence of the high reliability of the contig physical map. This is the first physical map in mollusc; therefore, it provides an important platform for advanced research of genomics and genetics, and mapping of genes and QTL of economical importance, thus facilitating the genetic improvement and selective breeding of the scallop and other marine molluscs.

  6. DNA sequences and composition from 12 BAC clones-derived MUSB SSR markers mapped to cotton (Gossypium Hirsutum L. x G. Barbadense L.)chromosomes 11 and 21

    Science.gov (United States)

    To discover resistance (R) and/or pathogen-induced (PR) genes involved in disease response, 12 bacterial artificial chromosome (BAC) clones from cv. Acala Maxxa (G. hirsutum) were sequenced at the Clemson University, Genomics Institute, Clemson, SC. These BACs derived MUSB single sequence repeat (SS...

  7. The first generation of a BAC-based physical map of Brassica rapa

    OpenAIRE

    Lee Soo; Lim Myung-Ho; Kim Jin A; Jin Mina; Kim Jung; Baek Seunghoon; Choi Beom-Soon; Kim Hye-Sun; Yang Tae-Jin; Kwon Soo-Jin; Mun Jeong-Hwan; Kim Ho-Il; Kim Hyungtae; Lim Yong; Park Beom-Seok

    2008-01-01

    Abstract Background The genus Brassica includes the most extensively cultivated vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene function associated with polyploidy and genome hybridization. A physical map of the B. rapa genome is a fundamental tool for analysis of Brassica "A" genome structure. Integration of a physical map with an existing genetic map by linking genetic markers and BAC clones...

  8. Hybrid nonviral/viral vector systems for improved piggyBac DNA transposon in vivo delivery.

    Science.gov (United States)

    Cooney, Ashley L; Singh, Brajesh K; Sinn, Patrick L

    2015-04-01

    The DNA transposon piggyBac is a potential therapeutic agent for multiple genetic diseases such as cystic fibrosis (CF). Recombinant piggyBac transposon and transposase are typically codelivered by plasmid transfection; however, plasmid delivery is inefficient in somatic cells in vivo and is a barrier to the therapeutic application of transposon-based vector systems. Here, we investigate the potential for hybrid piggyBac/viral vectors to transduce cells and support transposase-mediated genomic integration of the transposon. We tested both adenovirus (Ad) and adeno-associated virus (AAV) as transposon delivery vehicles. An Ad vector expressing hyperactive insect piggyBac transposase (iPB7) was codelivered. We show transposase-dependent transposition activity and mapped integrations in mammalian cells in vitro and in vivo from each viral vector platform. We also demonstrate efficient and persistent transgene expression following nasal delivery of piggyBac/viral vectors to mice. Furthermore, using piggyBac/Ad expressing Cystic Fibrosis transmembrane Conductance Regulator (CFTR), we show persistent correction of chloride current in well-differentiated primary cultures of human airway epithelial cells derived from CF patients. Combining the emerging technologies of DNA transposon-based vectors with well-studied adenoviral and AAV delivery provides new tools for in vivo gene transfer and presents an exciting opportunity to increase the delivery efficiency for therapeutic genes such as CFTR. PMID:25557623

  9. The first generation of a BAC-based physical map of Brassica rapa

    Directory of Open Access Journals (Sweden)

    Lee Soo

    2008-06-01

    Full Text Available Abstract Background The genus Brassica includes the most extensively cultivated vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene function associated with polyploidy and genome hybridization. A physical map of the B. rapa genome is a fundamental tool for analysis of Brassica "A" genome structure. Integration of a physical map with an existing genetic map by linking genetic markers and BAC clones in the sequencing pipeline provides a crucial resource for the ongoing genome sequencing effort and assembly of whole genome sequences. Results A genome-wide physical map of the B. rapa genome was constructed by the capillary electrophoresis-based fingerprinting of 67,468 Bacterial Artificial Chromosome (BAC clones using the five restriction enzyme SNaPshot technique. The clones were assembled into contigs by means of FPC v8.5.3. After contig validation and manual editing, the resulting contig assembly consists of 1,428 contigs and is estimated to span 717 Mb in physical length. This map provides 242 anchored contigs on 10 linkage groups to be served as seed points from which to continue bidirectional chromosome extension for genome sequencing. Conclusion The map reported here is the first physical map for Brassica "A" genome based on the High Information Content Fingerprinting (HICF technique. This physical map will serve as a fundamental genomic resource for accelerating genome sequencing, assembly of BAC sequences, and comparative genomics between Brassica genomes. The current build of the B. rapa physical map is available at the B. rapa Genome Project website for the user community.

  10. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  11. The bacterial artificial chromosome (BAC) library of the narrow-leafed lupin (Lupinus angustifolius L.)

    Czech Academy of Sciences Publication Activity Database

    Kasprzak, A.; Šafář, Jan; Janda, Jaroslav; Doležel, Jaroslav; Wolko, B.; Naganowska, B.

    2006-01-01

    Roč. 11, - (2006), s. 396-407. ISSN 1425-8153 R&D Projects: GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : BAC * genomic DNA library * Lupinus angustifolius L. Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.238, year: 2006

  12. A first generation BAC-based physical map of the Asian seabass (Lates calcarifer.

    Directory of Open Access Journals (Sweden)

    Jun Hong Xia

    Full Text Available BACKGROUND: The Asian seabass (Lates calcarifer is an important marine foodfish species in Southeast Asia and Australia. Genetic improvement of this species has been achieved to some extent through selective breeding programs since 1990s. Several genomic tools such as DNA markers, a linkage map, cDNA and BAC libraries have been developed to assist selective breeding. A physical map is still lacking, although it is essential for positional cloning of genes located in quantitative trait loci (QTL and assembly of whole genome sequences. METHODOLOGY/PRINCIPAL FINDINGS: A genome-wide physical map of the Asian seabass was constructed by restriction fingerprinting of 38,208 BAC clones with SNaPshot HICF FPC technique. A total of 30,454 were assembled into 2,865 contigs. The physical length of the assembled contigs summed up to 665 Mb. Analyses of some contigs using different methods demonstrated the reliability of the assembly. CONCLUSIONS/SIGNIFICANCE: The present physical map is the first physical map for Asian seabass. This physical map will facilitate the fine mapping of QTL for economically important traits and the positional cloning of genes located in QTL. It will also be useful for the whole genome sequencing and assembly. Detailed information about BAC-contigs and BAC clones are available upon request.

  13. BACTERIAL ARTIFICIAL CHROMOSOME(BAC)LIBRARIES CONSTRUCTED FROM THE GENETIC STANDARD OF UPLAND COTTON

    Science.gov (United States)

    Two BAC libraries and one plant transformation-competent BIBAC library were developed from the Gossypium hirsutum acc. TM-1 for the development of an integrative cotton physical and genetic map and other genomic applications. TM-1 is the most desirable choice for the physical map of Upland cotton be...

  14. GISH and BAC-FISH study of apomictic Beta M14

    Institute of Scientific and Technical Information of China (English)

    GE Yan; HE GuangChun; WANG ZhiWei; GUO DeDong; QIN Rui; LI RongTian

    2007-01-01

    Apomixis is a means of asexual reproduction by which plants produce embryos without fertilization and meiosis, therefore the embryo is of clonal and maternal origin. Interspecific hybrids between diploid B. vulgaris (2n=2x=18) and tetraploid B. corolliflora (2n=4x=36) were established, and then backcrossed with B. vulgaris. Among their offspring, monosomic addition line M14 (2n=2x=18+1) was selected because of the apomictic phenotype. We documented chromosome transmission from B. corolliflora into M14 by using genomic in situ hybridization (GISH). Suppression of cross-hybridization by blocking DNA was not necessary, indicating that the investigated Beta genome contains sufficient species-specific DNA, thus enabling the determination of genomic composition of the hybrids. We analyzed BAC microarrays of B. corolliflora chromosome 9 by using fluorescence-specific mRNA of B.vulgaris and Beta M14. BAC clones 16-M11 and 26-L15 were detected as fluorescence-specifics of BAC DNA of Beta M14. Then both BAC clones 16-M11 and 26-L15 were in situ hybridized to M14 chromosomes. The two hybridized BAC clones were located close to the telomere region of the long arm of a single chromosome 9, and showed hemizygosity. The results of BAC microarrays showed that these developments of embryo and endosperm have conservative expression patterns, indicating that sexual reproduction and apomixis have an interrelated pathway with common regulatory components and that the induction of a modified sexual reproduction program may enable the manifestation of apomixis in Beta species. It would be sufficient for the expression of apomixes with those apomictic-specific genes on chromosome 9 of B. corolliflora.

  15. Construction and sequence sampling of deep-coverage, large-insert BAC libraries for three model lepidopteran species

    Directory of Open Access Journals (Sweden)

    Zhao Shaying

    2009-06-01

    Full Text Available Abstract Background Manduca sexta, Heliothis virescens, and Heliconius erato represent three widely-used insect model species for genomic and fundamental studies in Lepidoptera. Large-insert BAC libraries of these insects are critical resources for many molecular studies, including physical mapping and genome sequencing, but not available to date. Results We report the construction and characterization of six large-insert BAC libraries for the three species and sampling sequence analysis of the genomes. The six BAC libraries were constructed with two restriction enzymes, two libraries for each species, and each has an average clone insert size ranging from 152–175 kb. We estimated that the genome coverage of each library ranged from 6–9 ×, with the two combined libraries of each species being equivalent to 13.0–16.3 × haploid genomes. The genome coverage, quality and utility of the libraries were further confirmed by library screening using 6~8 putative single-copy probes. To provide a first glimpse into these genomes, we sequenced and analyzed the BAC ends of ~200 clones randomly selected from the libraries of each species. The data revealed that the genomes are AT-rich, contain relatively small fractions of repeat elements with a majority belonging to the category of low complexity repeats, and are more abundant in retro-elements than DNA transposons. Among the species, the H. erato genome is somewhat more abundant in repeat elements and simple repeats than those of M. sexta and H. virescens. The BLAST analysis of the BAC end sequences suggested that the evolution of the three genomes is widely varied, with the genome of H. virescens being the most conserved as a typical lepidopteran, whereas both genomes of H. erato and M. sexta appear to have evolved significantly, resulting in a higher level of species- or evolutionary lineage-specific sequences. Conclusion The high-quality and large-insert BAC libraries of the insects, together

  16. A Domesticated PiggyBac Transposase Interacts with Heterochromatin and Catalyzes Reproducible DNA Elimination in Tetrahymena

    OpenAIRE

    Alexander Vogt; Kazufumi Mochizuki

    2013-01-01

    The somatic genome of the ciliated protist Tetrahymena undergoes DNA elimination of defined sequences called internal eliminated sequences (IESs), which account for ∼30% of the germline genome. During DNA elimination, IES regions are heterochromatinized and assembled into heterochromatin bodies in the developing somatic nucleus. The domesticated piggyBac transposase Tpb2p is essential for the formation of heterochromatin bodies and DNA elimination. In this study, we demonstrate that the activ...

  17. Versatile P(acman) BAC Libraries for Transgenesis Studies in Drosophila melanogaster

    Energy Technology Data Exchange (ETDEWEB)

    Venken, Koen J.T.; Carlson, Joseph W.; Schulze, Karen L.; Pan, Hongling; He, Yuchun; Spokony, Rebecca; Wan, Kenneth H.; Koriabine, Maxim; de Jong, Pieter J.; White, Kevin P.; Bellen, Hugo J.; Hoskins, Roger A.

    2009-04-21

    We constructed Drosophila melanogaster BAC libraries with 21-kb and 83-kb inserts in the P(acman) system. Clones representing 12-fold coverage and encompassing more than 95percent of annotated genes were mapped onto the reference genome. These clones can be integrated into predetermined attP sites in the genome using Phi C31 integrase to rescue mutations. They can be modified through recombineering, for example to incorporate protein tags and assess expression patterns.

  18. Extensive conserved synteny of genes between the karyotypes of Manduca sexta and Bombyx mori revealed by BAC-FISH mapping.

    Directory of Open Access Journals (Sweden)

    Yuji Yasukochi

    Full Text Available BACKGROUND: Genome sequencing projects have been completed for several species representing four highly diverged holometabolous insect orders, Diptera, Hymenoptera, Coleoptera, and Lepidoptera. The striking evolutionary diversity of insects argues a need for efficient methods to apply genome information from such models to genetically uncharacterized species. Constructing conserved synteny maps plays a crucial role in this task. Here, we demonstrate the use of fluorescence in situ hybridization with bacterial artificial chromosome probes as a powerful tool for physical mapping of genes and comparative genome analysis in Lepidoptera, which have numerous and morphologically uniform holokinetic chromosomes. METHODOLOGY/PRINCIPAL FINDINGS: We isolated 214 clones containing 159 orthologs of well conserved single-copy genes of a sequenced lepidopteran model, the silkworm, Bombyx mori, from a BAC library of a sphingid with an unexplored genome, the tobacco hornworm, Manduca sexta. We then constructed a BAC-FISH karyotype identifying all 28 chromosomes of M. sexta by mapping 124 loci using the corresponding BAC clones. BAC probes from three M. sexta chromosomes also generated clear signals on the corresponding chromosomes of the convolvulus hawk moth, Agrius convolvuli, which belongs to the same subfamily, Sphinginae, as M. sexta. CONCLUSIONS/SIGNIFICANCE: Comparison of the M. sexta BAC physical map with the linkage map and genome sequence of B. mori pointed to extensive conserved synteny including conserved gene order in most chromosomes. Only a few rearrangements, including three inversions, three translocations, and two fission/fusion events were estimated to have occurred after the divergence of Bombycidae and Sphingidae. These results add to accumulating evidence for the stability of lepidopteran genomes. Generating signals on A. convolvuli chromosomes using heterologous M. sexta probes demonstrated that BAC-FISH with orthologous sequences can be

  19. 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

  20. PiggyBac transposon mutagenesis: a tool for cancer gene discovery in mice.

    Science.gov (United States)

    Rad, Roland; Rad, Lena; Wang, Wei; Cadinanos, Juan; Vassiliou, George; Rice, Stephen; Campos, Lia S; Yusa, Kosuke; Banerjee, Ruby; Li, Meng Amy; de la Rosa, Jorge; Strong, Alexander; Lu, Dong; Ellis, Peter; Conte, Nathalie; Yang, Fang Tang; Liu, Pentao; Bradley, Allan

    2010-11-19

    Transposons are mobile DNA segments that can disrupt gene function by inserting in or near genes. Here, we show that insertional mutagenesis by the PiggyBac transposon can be used for cancer gene discovery in mice. PiggyBac transposition in genetically engineered transposon-transposase mice induced cancers whose type (hematopoietic versus solid) and latency were dependent on the regulatory elements introduced into transposons. Analysis of 63 hematopoietic tumors revealed that PiggyBac is capable of genome-wide mutagenesis. The PiggyBac screen uncovered many cancer genes not identified in previous retroviral or Sleeping Beauty transposon screens, including Spic, which encodes a PU.1-related transcription factor, and Hdac7, a histone deacetylase gene. PiggyBac and Sleeping Beauty have different integration preferences. To maximize the utility of the tool, we engineered 21 mouse lines to be compatible with both transposon systems in constitutive, tissue- or temporal-specific mutagenesis. Mice with different transposon types, copy numbers, and chromosomal locations support wide applicability. PMID:20947725

  1. Sequencing,annotation and comparative analysis of nine BACs of the giant panda(Ailuropoda melanoleuca)

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A 10-fold BAC library for the giant panda was constructed and nine BACs were selected to generate finish sequences.These BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of the giant panda newly generated by Illumina GA sequencing technology.Complete Sanger sequencing,assembly,annotation and comparative analysis were carried out on the selected BACs of a joint length 878 kb.Homologue search and de novo prediction methods were used to annotate genes and repeats.Twelve protein coding genes were predicted,seven of which could be functionally annotated.The seven genes have an average gene size of about 41 kb,an average coding size of about 1.2 kb and an average exon number of 6 per gene.Besides,seven tRNA genes were found.About 27 percent of the BAC sequence is composed of repeats.A phylogenetic tree was constructed using a neighbor-join algorithm across five species,including the giant panda,human,dog,cat and mouse,which reconfirms dog as the most closely related species to the giant panda.Our results provide detailed sequence and structure information for new genes and repeats of the giant panda,which will be helpful for further studies about the giant panda.

  2. 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.

  3. 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

  4. Experimental study on target treatment of nasopharyngeal carcinoma using 188Re-BAC5 combined with PYM-BAC5

    International Nuclear Information System (INIS)

    Objective: Combination of radiation and chemical agents was supposed to have better effect on nasopharyngeal cancer. This study compared the in vitro inhibiting effects of 188Re-monoclonal anti- body (BACs) with or without pingyangmycin conjugated BACs (PYM-BAC5) on nasopharyngeal carcinoma cells (CNE2). Methods: 188Re-BAC5 was prepared using 2-mereaptoethanol (ME), citric acid and tartaric acid as reducing and transchelation agents. Oxidized dextran T-40 (polyaldehyde dextran, PAD ) was used to conjugate PYM to BAC5. 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenylte-trazolium bromide (MTT) method was applied to assess anti-tumor effects of 188Re-BAC5 and PYM-BAC5 on CNE2 cells. Results: The labeling efficiency of 188Re-BACs was 92%-95% with a radioactive concentration of 5254 kBq/ml. The composition of PYM-BAC5 was m (PYM): m (BAC5)=1: 0.526, or n (PYM): n(BAC5)=1:51. The inhibition effects of each treatment regime were in a dose dependent manner. The 50% inhibition doses (IC50) of 188Re-BAC5, 188Re-mIgG and 188ReO4- were 264, 1062 and 882 kBq/ml, respectively. The IC50 of the PYM-BAC5 and free PYM were 10.07 and 63.60 μg/ml, respectively. Combining 188Re-BAC5 and PYM-BACs reduced the IC50 of 1'88Re-BAC5 and PYM-BACs down to 32.1 kBq/ml and 1.70 μg/ml. Conclusions: It was proved that targeted therapy had better anti-tumor effect. The combination of targeted radiation and chemical agents (188Re-BAC5 + PYM-BAC5) obtained the best therapeutic effect on cultured CNE2 cells. (authors)

  5. 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

  6. A highly redundant BAC library of Atlantic salmon (Salmo salar: an important tool for salmon projects

    Directory of Open Access Journals (Sweden)

    Koop Ben F

    2005-04-01

    Full Text Available Abstract Background As farming of Atlantic salmon is growing as an aquaculture enterprise, the need to identify the genomic mechanisms for specific traits is becoming more important in breeding and management of the animal. Traits of importance might be related to growth, disease resistance, food conversion efficiency, color or taste. To identify genomic regions responsible for specific traits, genomic large insert libraries have previously proven to be of crucial importance. These large insert libraries can be screened using gene or genetic markers in order to identify and map regions of interest. Furthermore, large-scale mapping can utilize highly redundant libraries in genome projects, and hence provide valuable data on the genome structure. Results Here we report the construction and characterization of a highly redundant bacterial artificial chromosome (BAC library constructed from a Norwegian aquaculture strain male of Atlantic salmon (Salmo salar. The library consists of a total number of 305 557 clones, in which approximately 299 000 are recombinants. The average insert size of the library is 188 kbp, representing 18-fold genome coverage. High-density filters each consisting of 18 432 clones spotted in duplicates have been produced for hybridization screening, and are publicly available 1. To characterize the library, 15 expressed sequence tags (ESTs derived overgos and 12 oligo sequences derived from microsatellite markers were used in hybridization screening of the complete BAC library. Secondary hybridizations with individual probes were performed for the clones detected. The BACs positive for the EST probes were fingerprinted and mapped into contigs, yielding an average of 3 contigs for each probe. Clones identified using genomic probes were PCR verified using microsatellite specific primers. Conclusion Identification of genes and genomic regions of interest is greatly aided by the availability of the CHORI-214 Atlantic salmon BAC

  7. Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca) BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome

    OpenAIRE

    Ritland Carol; Keeling Christopher I; Hamberger Britta; Oddy Claire; Yuen Mack; Hall Dawn; Hamberger Björn; Ritland Kermit; Bohlmann Jörg

    2009-01-01

    Abstract Background Conifers are a large group of gymnosperm trees which are separated from the angiosperms by more than 300 million years of independent evolution. Conifer genomes are extremely large and contain considerable amounts of repetitive DNA. Currently, conifer sequence resources exist predominantly as expressed sequence tags (ESTs) and full-length (FL)cDNAs. There is no genome sequence available for a conifer or any other gymnosperm. Conifer defence-related genes often group into l...

  8. Remobilizing deleted piggyBac vector post-integration for transgene stability in silkworm.

    Science.gov (United States)

    Wang, Feng; Wang, Riyuan; Wang, Yuancheng; Xu, Hanfu; Yuan, Lin; Ding, Huan; Ma, Sanyuan; Zhou, You; Zhao, Ping; Xia, Qingyou

    2015-06-01

    Deletion of transposable elements post-genomic integration holds great promise for stability of the transgene in the host genome and has an essential role for the practical application of transgenic animals. In this study, a modified piggyBac vector that mediated deletion of the transposon sequence post-integration for transgene stability in the economically important silkworm Bombyx mori was constructed. The piggyBac vector architecture contains inversed terminal repeat sequences L1, L2 and R1, which can form L1/R1 and L2/R1 types of transposition cassettes. hsp70-PIG as the piggyBac transposase expression cassette for initial transposition, further remobilization and transgene stabilization test was transiently expressed in a helper vector or integrated into the modified vector to produce a transgenic silkworm. Shortening L2 increased the transformation frequency of L1/R1 into the silkworm genome compared to L2/R1. After the integration of L1/R1 into the genome, the remobilization of L2/R1 impaired the transposon structure and the resulting transgene linked with an impaired transposon was stable in the genome even in the presence of exogenously introduced transposase, whereas those flanked by the intact transposon were highly mobile in the genome. Our results demonstrated the feasibility of post-integration deletion of transposable elements to guarantee true transgene stabilization in silkworm. We suggest that the modified vector will be a useful resource for studies of transgenic silkworms and other piggyBac-transformed organisms. PMID:25589404

  9. A PiggyBac-mediated approach for muscle gene transfer or cell therapy

    Directory of Open Access Journals (Sweden)

    Déborah Ley

    2014-11-01

    Full Text Available An emerging therapeutic approach for Duchenne muscular dystrophy is the transplantation of autologous myogenic progenitor cells genetically modified to express dystrophin. The use of this approach is challenged by the difficulty in maintaining these cells ex vivo while keeping their myogenic potential, and ensuring sufficient transgene expression following their transplantation and myogenic differentiation in vivo. We investigated the use of the piggyBac transposon system to achieve stable gene expression when transferred to cultured mesoangioblasts and into murine muscles. Without selection, up to 8% of the mesoangioblasts expressed the transgene from 1 to 2 genomic copies of the piggyBac vector. Integration occurred mostly in intergenic genomic DNA and transgene expression was stable in vitro. Intramuscular transplantation of mouse Tibialis anterior muscles with mesoangioblasts containing the transposon led to sustained myofiber GFP expression in vivo. In contrast, the direct electroporation of the transposon-donor plasmids in the mouse Tibialis muscles in vivo did not lead to sustained transgene expression despite molecular evidence of piggyBac transposition in vivo. Together these findings provide a proof-of-principle that piggyBac transposon may be considered for mesoangioblast cell-based therapies of muscular dystrophies.

  10. A PiggyBac-mediated approach for muscle gene transfer or cell therapy.

    Science.gov (United States)

    Ley, Déborah; Van Zwieten, Ruthger; Puttini, Stefania; Iyer, Pavithra; Cochard, Alessia; Mermod, Nicolas

    2014-11-01

    An emerging therapeutic approach for Duchenne muscular dystrophy is the transplantation of autologous myogenic progenitor cells genetically modified to express dystrophin. The use of this approach is challenged by the difficulty in maintaining these cells ex vivo while keeping their myogenic potential, and ensuring sufficient transgene expression following their transplantation and myogenic differentiation in vivo. We investigated the use of the piggyBac transposon system to achieve stable gene expression when transferred to cultured mesoangioblasts and into murine muscles. Without selection, up to 8% of the mesoangioblasts expressed the transgene from 1 to 2 genomic copies of the piggyBac vector. Integration occurred mostly in intergenic genomic DNA and transgene expression was stable in vitro. Intramuscular transplantation of mouse Tibialis anterior muscles with mesoangioblasts containing the transposon led to sustained myofiber GFP expression in vivo. In contrast, the direct electroporation of the transposon-donor plasmids in the mouse Tibialis muscles in vivo did not lead to sustained transgene expression despite molecular evidence of piggyBac transposition in vivo. Together these findings provide a proof-of-principle that piggyBac transposon may be considered for mesoangioblast cell-based therapies of muscular dystrophies. PMID:25310255

  11. Isolation and sequence analysis of the wheat B genome subtelomeric DNA

    Directory of Open Access Journals (Sweden)

    Huneau Cecile

    2009-09-01

    Full Text Available Abstract Background Telomeric and subtelomeric regions are essential for genome stability and regular chromosome replication. In this work, we have characterized the wheat BAC (bacterial artificial chromosome clones containing Spelt1 and Spelt52 sequences, which belong to the subtelomeric repeats of the B/G genomes of wheats and Aegilops species from the section Sitopsis. Results The BAC library from Triticum aestivum cv. Renan was screened using Spelt1 and Spelt52 as probes. Nine positive clones were isolated; of them, clone 2050O8 was localized mainly to the distal parts of wheat chromosomes by in situ hybridization. The distribution of the other clones indicated the presence of different types of repetitive sequences in BACs. Use of different approaches allowed us to prove that seven of the nine isolated clones belonged to the subtelomeric chromosomal regions. Clone 2050O8 was sequenced and its sequence of 119 737 bp was annotated. It is composed of 33% transposable elements (TEs, 8.2% Spelt52 (namely, the subfamily Spelt52.2 and five non-TE-related genes. DNA transposons are predominant, making up 24.6% of the entire BAC clone, whereas retroelements account for 8.4% of the clone length. The full-length CACTA transposon Caspar covers 11 666 bp, encoding a transposase and CTG-2 proteins, and this transposon accounts for 40% of the DNA transposons. The in situ hybridization data for 2050O8 derived subclones in combination with the BLAST search against wheat mapped ESTs (expressed sequence tags suggest that clone 2050O8 is located in the terminal bin 4BL-10 (0.95-1.0. Additionally, four of the predicted 2050O8 genes showed significant homology to four putative orthologous rice genes in the distal part of rice chromosome 3S and confirm the synteny to wheat 4BL. Conclusion Satellite DNA sequences from the subtelomeric regions of diploid wheat progenitor can be used for selecting the BAC clones from the corresponding regions of hexaploid wheat

  12. 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...

  13. BAC library development, and clone characterization for dormancy-responsive DREB4A, DAM, and FT from leafy spurge (Euphorbia esula L.) identifies differential splicing and conserved promoter motifs

    Science.gov (United States)

    We developed two leafy spurge BAC libraries that together represent approximately 5X coverage of the leafy spurge genome. The BAC libraries have an average insert size of approximately 143 kb, and copies of the library and filters for hybridization-based screening are publicly available through the ...

  14. A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat

    Science.gov (United States)

    The wheat high molecular weight (HMW)-glutenins are important seed storage proteins that determine bread-making quality in hexaploid wheat (Triticum aestivum). In this study, detailed comparative sequence analyses of large orthologous HMW-glutenin genomic regions from eight grass species, represent...

  15. End Sequencing and Finger Printing of Human & Mouse BAC Libraries

    Energy Technology Data Exchange (ETDEWEB)

    Fraser, C

    2005-09-27

    This project provided for continued end sequencing of existing and new BAC libraries constructed to support human sequencing as well as to initiate BAC end sequencing from the mouse BAC libraries constructed to support mouse sequencing. The clones, the sequences, and the fingerprints are now an available resource for the community at large. Research and development of new metaodologies for BAC end sequencing have reduced costs and increase throughput.

  16. 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...

  17. IMPROVING WHEAT TRITICUM AESTIVUM L. BY INTERSPECIFIC AND INTERGENERIC HYBRIDIZATION WITH POACEAE FAMILY SPECIES

    Directory of Open Access Journals (Sweden)

    Czaplicki A.Z.

    2012-08-01

    Full Text Available The related species of the family Poaceae (Triticeae are the source of unprecedented new genes that allow the extension of genetic variation of common wheat Triticum aestivum L. These species have similar homoeologous chromosomes and rDNA sequences very similar to T. aestivum L. [1-3]. This allows the introgression of alien genes and their incorporation into the genomes A, B and D of wheat, where they can function permanently in the wheat genetic systems. Many of them have already been transferred to the varieties of T. aestivum L. [4].The experimental material consisted of 28 lines of winter wheat obtained using the interspecific and intergeneric hybridization of T. aestivum L. with alien species T. durum Desf., T. timopheevii Zhuk., Lolium perenne L. and Aegilops speltoides Taush. Among them, 15 lines were developed from the cross-combination with tetraploid species (AABB T. durum Desf., 4 lines from the combination with other tetraploid species of different genome composition (AAGG T. timopheevii Zhuk., 4 lines from cross with L. perenne L. and 5 lines were the double hybrids (three-generic derived with two related species, T. durum Desf. (AABB and Ae. speltoides Taush (BB.The anther culture method was used for obtaining DH lines from these interspecific and intergeneric hybrids. In in vitro culture 124 green plants were regenerated. The method of cluster analysis grouped hybrids in terms of comprehensive general similarity of the studied traits.

  18. Immunotoxin BAC5-CT treated nasopharyngeal carcinoma

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    In this study, immunotoxin (IT) was prepared by conjugating BAC5 and CT with SPDP. The effects of IT on NPC and its mechanisms were explored using double labeled with radioactive nuclides, immunography and electron microscope technique in vivo and in vitro. The specific concentration of BAC5 in the tumor area showed. The radioactivity rate of tumor/nontumor (T/NT) was up to 10.26. IT had cytotoxic effects both on the cultured CNE-2 cell line and tumor multicell spheroides. In vivo, the preliminary result indicated that IT also had a inhibitory action on the nude mice models bearing human NPC (Reported in another article). Under electron microscope, the necrosis and apoptosis of tumor cells were found. The membranes of most tumor cells were found intacted not or corrosined, some of them had the character of apoptosis, including reduce of tumor cells membrane villi, condensation of cytoplasm and pyknosis or cleavage of nuclear. There were many of apoptosis bodies, which were occasionally phagocytosed by tumor cells. The infiltration of immunocytoes in tumor tissue could be seen. The results indicated that BAC5 can specifically combine with NPC cells and BAC5-CT has the inhibitory effect on NPC in vitro and in vivo, mechanism of which may be related to the effects that ‘warhead' CT dissolute the membrane of tumor cells directly, or/and IT promote the infiltration of immunocytoes so as to induce the apoptosis of tumor cell.

  19. Annotation and BAC/PAC localization of nonredundant ESTs from drought-stressed seedlings of an indica rice

    Indian Academy of Sciences (India)

    P. Ravindra Babu; A. Chandra Sekhar; Nagabhushana Ithal; G. Markandeya; Arjula R. Reddy

    2002-04-01

    To decipher the genes associated with drought stress response and to identify novel genes in rice, we utilized 1540 high-quality expressed sequence tags (ESTs) for functional annotation and mapping to rice genomic sequences. These ESTs were generated earlier by 3′-end single-pass sequencing of 2000 cDNA clones from normalized cDNA libraries constructed from drought-stressed seedlings of an indica rice. A rice UniGene set of 1025 transcripts was constructed from this collection through the BLASTN algorithm. Putative functions of 559 nonredundant ESTs were identified by BLAST similarity search against public databases. Putative functions were assigned at a stringency E value of 10-6 in BLASTN and BLASTX algorithms. To understand the gene structure and function further, we have utilized the publicly available finished and unfinished rice BAC/PAC (BAC, bacterial artificial chromosome; PAC, P1 artificial chromosome) sequences for similarity search using the BLASTN algorithm. Further, 603 nonredundant ESTs have been mapped to BAC/PAC clones. BAC clones were assigned by a homology of above 95% identity along 90% of EST sequence length in the aligned region. In all, 700 ESTs showed rice EST hits in GenBank. Of the 325 novel ESTs, 128 were localized to BAC clones. In addition, 127 ESTs with identified putative functions but with no homology in IRGSP (International Rice Genome Sequencing Program) BAC/PAC sequences were mapped to the Chinese WGS (whole genome shotgun contigs) draft sequence of the rice genome. Functional annotation uncovered about a hundred candidate ESTs associated with abiotic stress in rice and Arabidopsis that were previously reported based on microarray analysis and other studies. This study is a major effort in identifying genes associated with drought stress response and will serve as a resource to rice geneticists and molecular biologists.

  20. Toward a Molecular Cytogenetic Map for Cultivated Sunflower (Helianthus annuus L.) by Landed BAC/BIBAC Clones

    Science.gov (United States)

    Feng, Jiuhuan; Liu, Zhao; Cai, Xiwen; Jan, Chao-Chien

    2013-01-01

    Conventional karyotypes and various genetic linkage maps have been established in sunflower (Helianthus annuus L., 2n = 34). However, the relationship between linkage groups and individual chromosomes of sunflower remains unknown and has considerable relevance for the sunflower research community. Recently, a set of linkage group-specific bacterial /binary bacterial artificial chromosome (BAC/BIBAC) clones was identified from two complementary BAC and BIBAC libraries constructed for cultivated sunflower cv. HA89. In the present study, we used these linkage group-specific clones (∼100 kb in size) as probes to in situ hybridize to HA89 mitotic chromosomes at metaphase using the BAC- fluorescence in situ hybridization (FISH) technique. Because a characteristic of the sunflower genome is the abundance of repetitive DNA sequences, a high ratio of blocking DNA to probe DNA was applied to hybridization reactions to minimize the background noise. As a result, all sunflower chromosomes were anchored by one or two BAC/BIBAC clones with specific FISH signals. FISH analysis based on tandem repetitive sequences, such as rRNA genes, has been previously reported; however, the BAC-FISH technique developed here using restriction fragment length polymorphism (RFLP)−derived BAC/BIBAC clones as probes to apply genome-wide analysis is new for sunflower. As chromosome-specific cytogenetic markers, the selected BAC/BIBAC clones that encompass the 17 linkage groups provide a valuable tool for identifying sunflower cytogenetic stocks (such as trisomics) and tracking alien chromosomes in interspecific crosses. This work also demonstrates the potential of using a large-insert DNA library for the development of molecular cytogenetic resources. PMID:23316437

  1. Evolution of sex chromosomes ZW of Schistosoma mansoni inferred from chromosome paint and BAC mapping analyses.

    Science.gov (United States)

    Hirai, Hirohisa; Hirai, Yuriko; LoVerde, Philip T

    2012-12-01

    Chromosomes of schistosome parasites among digenetic flukes have a unique evolution because they exhibit the sex chromosomes ZW, which are not found in the other groups of flukes that are hermaphrodites. We conducted molecular cytogenetic analyses for investigating the sex chromosome evolution using chromosome paint analysis and BAC clones mapping. To carry this out, we developed a technique for making paint probes of genomic DNA from a single scraped chromosome segment using a chromosome microdissection system, and a FISH mapping technique for BAC clones. Paint probes clearly identified each of the 8 pairs of chromosomes by a different fluorochrome color. Combination analysis of chromosome paint analysis with Z/W probes and chromosome mapping with 93 BAC clones revealed that the W chromosome of Schistosoma mansoni has evolved by at least four inversion events and heterochromatinization. Nine of 93 BAC clones hybridized with both the Z and W chromosomes, but the locations were different between Z and W chromosomes. The homologous regions were estimated to have moved from the original Z chromosome to the differentiated W chromosome by three inversions events that occurred before W heterohcromatinization. An inversion that was observed in the heterochromatic region of the W chromosome likely occurred after W heterochromatinization. These inversions and heterochromatinization are hypothesized to be the key factors that promoted the evolution of the W chromosome of S. mansoni. PMID:22831897

  2. Chromosome evolution in Solanum traced by cross-species BAC-FISH.

    Science.gov (United States)

    Szinay, Dóra; Wijnker, Erik; van den Berg, Ronald; Visser, Richard G F; de Jong, Hans; Bai, Yuling

    2012-08-01

    Chromosomal rearrangements are relatively rare evolutionary events and can be used as markers to study karyotype evolution. This research aims to use such rearrangements to study chromosome evolution in Solanum. Chromosomal rearrangements between Solanum crops and several related wild species were investigated using tomato and potato bacterial artificial chromosomes (BACs) in a multicolour fluorescent in situ hybridization (FISH). The BACs selected are evenly distributed over seven chromosomal arms containing inversions described in previous studies. The presence/absence of these inversions among the studied Solanum species were determined and the order of the BAC-FISH signals was used to construct phylogenetic trees.Compared with earlier studies, data from this study provide support for the current grouping of species into different sections within Solanum; however, there are a few notable exceptions, such as the tree positions of S. etuberosum (closer to the tomato group than to the potato group) and S. lycopersicoides (sister to S. pennellii). These apparent contradictions might be explained by interspecific hybridization events and/or incomplete lineage sorting. This cross-species BAC painting technique provides unique information on genome organization, evolution and phylogenetic relationships in a wide variety of species. Such information is very helpful for introgressive breeding. PMID:22686400

  3. Reevaluation of the Coding Potential and Proteomic Analysis of the BAC Derived Rhesus Cytomegalovirus Strain 68-1

    Energy Technology Data Exchange (ETDEWEB)

    Malouli, Daniel; Nakayasu, Ernesto S.; Viswanathan, Kasinath; Camp, David G.; Chang, W. L.; Barry, Peter A.; Smith, Richard D.; Fruh, Klaus

    2012-09-01

    Cytomegaloviruses are highly host restricted resulting in co-speciation with their hosts. As a natural pathogen of rhesus macaques (RM), Rhesus Cytomegalovirus (RhCMV) has therefore emerged as a highly relevant experimental model for pathogenesis and vaccine development due to its close evolutionary relationship to human CMV (HCMV). To date, most in vivo experiments performed with RhCMV employed strain 68-1 cloned as bacterial artificial chromosome (BAC). However, the complete genome sequence of the 68-1 BAC has not been determined. Furthermore, the gene content of the RhCMV genome is unknown and previous open reading frame (ORF) predictions relied solely on uninterrupted ORFs with an arbitrary cutoff of 300bp. To obtain a more precise picture of the actual proteins encoded by the most commonly used molecular clone of RhCMV we re-evaluated the RhCMV 68-1 BAC-genome by whole genome shotgun sequencing and determined the protein content of the resulting RhCMV virions by proteomics. By additionally comparing the RhCMV genome to that of several closely related Old World Monkey (OWM) CMVs we were able to filter out many unlikely ORFs and obtain a simplified map of the RhCMV genome. This comparative genomics analysis eliminated many genes previously characterized as RhCMV-specific while consolidating a high conservation of ORFs among OWM-CMVs and between RhCMV and HCMV. Moreover, virion proteomics independently validated the revised ORF predictions since only proteins encoded by predicted ORFs could be detected. Taken together these data suggest a much higher conservation of genome and virion structure between CMVs of humans, apes and OWMs than previously assumed. Remarkably, BAC-derived RhCMV is able to establish and maintain persistent infection despite the lack of multiple genes homologous to HCMV genes involved in tissue tropism.

  4. BAC-pool sequencing and analysis of large segments of A12 and D12 homoeologous chromosomes in upland cotton.

    Directory of Open Access Journals (Sweden)

    Ramesh Buyyarapu

    Full Text Available Although new and emerging next-generation sequencing (NGS technologies have reduced sequencing costs significantly, much work remains to implement them for de novo sequencing of complex and highly repetitive genomes such as the tetraploid genome of Upland cotton (Gossypium hirsutum L.. Herein we report the results from implementing a novel, hybrid Sanger/454-based BAC-pool sequencing strategy using minimum tiling path (MTP BACs from Ctg-3301 and Ctg-465, two large genomic segments in A12 and D12 homoeologous chromosomes (Ctg. To enable generation of longer contig sequences in assembly, we implemented a hybrid assembly method to process ~35x data from 454 technology and 2.8-3x data from Sanger method. Hybrid assemblies offered higher sequence coverage and better sequence assemblies. Homology studies revealed the presence of retrotransposon regions like Copia and Gypsy elements in these contigs and also helped in identifying new genomic SSRs. Unigenes were anchored to the sequences in Ctg-3301 and Ctg-465 to support the physical map. Gene density, gene structure and protein sequence information derived from protein prediction programs were used to obtain the functional annotation of these genes. Comparative analysis of both contigs with Arabidopsis genome exhibited synteny and microcollinearity with a conserved gene order in both genomes. This study provides insight about use of MTP-based BAC-pool sequencing approach for sequencing complex polyploid genomes with limited constraints in generating better sequence assemblies to build reference scaffold sequences. Combining the utilities of MTP-based BAC-pool sequencing with current longer and short read NGS technologies in multiplexed format would provide a new direction to cost-effectively and precisely sequence complex plant genomes.

  5. Combining ability for Fusarium head blight resistance in wheat (Triticum aestivum L.

    Directory of Open Access Journals (Sweden)

    Subas Malla

    2010-12-01

    Full Text Available Fusarium head blight (FHB caused by Fusarium graminearum reduces wheat (Triticum aestivum L. em. Thell grain yield and end-use quality worldwide. Three each of FHB susceptible (‘Nekota’, ‘2137’, and ‘Harding’ and resistant (‘Ning 7840’, ‘ND2710’ and ‘BacUp’ parents were included in a partial diallel mating design (Griffing’s Method 4, Model 1. The F4:5 progeny was evaluated for healthy index, undamaged kernels, and deoxynivalenol (DON content following artificial inoculation and mist-irrigation in 2006 and 2007. General combining ability (GCA was highly significant (P < 0.01 for healthy index; whereas specific combining ability (SCA and GCA-by-year interaction were not significant. The combining ability ratio and narrow-sense heritability were 0.95 and 0.83, respectively. The Genotype, Genotype-by-Environment (GGE biplot analysis showed that the ND2710/BacUp combination had the best healthy index and undamaged kernels; whereas Ning 7840 contributed resistance to DON accumulation. The results indicated additive gene effects mainly control that healthy index. Thus, genetic gain in developing resistance in wheat can be achieved through selection.

  6. Construction of a BAC library and a physical map of a major QTL for CBB resistance of common bean (Phaseolus vulgaris L.).

    Science.gov (United States)

    Liu, S Y; Yu, K; Huffner, M; Park, S J; Banik, M; Pauls, K P; Crosby, W

    2010-07-01

    A major quantitative trait loci (QTL) conditioning common bacterial blight (CBB) resistance in common bean (Phaseolus vulgaris L.) lines HR45 and HR67 was derived from XAN159, a resistant line obtained from an interspecific cross between common bean lines and the tepary bean (P. acutifolius L.) line PI319443. This source of CBB resistance is widely used in bean breeding. Several other CBB resistance QTL have been identified but none of them have been physically mapped. Four molecular markers tightly linked to this QTL have been identified suitable for marker assisted selection and physical mapping of the resistance gene. A bacterial artificial chromosome (BAC) library was constructed from high molecular weight DNA of HR45 and is composed of 33,024 clones. The size of individual BAC clone inserts ranges from 30 kb to 280 kb with an average size of 107 kb. The library is estimated to represent approximately sixfold genome coverage. The BAC library was screened as BAC pools using four PCR-based molecular markers. Two to seven BAC clones were identified by each marker. Two clones were found to have both markers PV-tttc001 and STS183. One preliminary contig was assembled based on DNA finger printing of those positive BAC clones. The minimum tiling path of the contig contains 6 BAC clones spanning an estimated size of 750 kb covering the QTL region. PMID:20419470

  7. Transcriptional regulation of mouse alpha A-crystallin gene in a 148kb Cryaa BAC and its derivates

    Directory of Open Access Journals (Sweden)

    Yang Ying

    2008-09-01

    Full Text Available Abstract Background αA-crystallin is highly expressed in the embryonic, neonatal and adult mouse lens. Previously, we identified two novel distal control regions, DCR1 and DCR3. DCR1 was required for transgenic expression of enhanced green fluorescent protein, EGFP, in lens epithelium, whereas DCR3 was active during "late" stages of lens primary fiber cell differentiation. However, the onset of transgenic EGFP expression was delayed by 12–24 hours, compared to the expression of the endogenous Cryaa gene. Results Here, we used bacterial artificial chromosome (BAC and standard transgenic approaches to examine temporal and spatial regulation of the mouse Cryaa gene. Two BAC transgenes, with EGFP insertions into the third coding exon of Cryaa gene, were created: the intact αA-crystallin 148 kb BAC (αA-BAC and αA-BAC(ΔDCR3, which lacks approximately 1.0 kb of genomic DNA including DCR3. Expression of EGFP in the majority of both BAC transgenics nearly recapitulated the endogenous expression pattern of the Cryaa gene in lens, but not outside of the lens. The number of cells expressing αA-crystallin in the lens pit was higher compared to the number of cells expressing EGFP. Next, we generated additional lines using a 15 kb fragment of αA-crystallin locus derived from αA-BAC(ΔDCR3, 15 kb Cryaa/EGFP. A 15 kb region of Cryaa/EGFP supported the expression pattern of EGFP also in the lens pit. However, co-localization studies of αA-crystallin and EGFP indicated that the number of cells that showed transgenic expression was higher compared to cells expressing αA-crystallin in the lens pit. Conclusion We conclude that a 148 kb αA-BAC likely contains all of the regulatory regions required for αA-crystallin expression in the lens, but not in retina, spleen and thymus. In addition, while the 15 kb Cryaa/EGFP region also supported the expression of EGFP in the lens pit, expression in regions such as the hindbrain, indicate that additional genomic

  8. Comparison of BAC FISH with specific telomeres and centromere probes and chromosome painting on detection of chromosome translocation induced by irradiation

    International Nuclear Information System (INIS)

    Objective: To compare the efficiency of BAC FISH established in our lab and conventional chromosome painting (PAINT) on detection of radiation-induced chromosome translocation. Methods: Healthy human peripheral blood samples were irradiated with 0-5.0 Gy 60Co γ-rays. Then chromosome translocations in these samples were detected with BAC FISH and PAINT using chromosomes 1, 2 and 4. The genome translocation rates were calculated with observed chromosome translocation rates, and the dose-response curve of two methods were established. Results: The genome translocation rates induced by 0-5.0 Gy 60Co γ-rays detected by BAC FISH and PAINT were increased with absorbed doses. The observed translocation rates with BAC FISH were higher than that with PAINT at each dose level. The dose-response curve were Y=0.043D2 + 0.0008 D + 0.0048 for BAC FISH and Y=0.043 D2 + 0.006 D + 0.0027 for PAINT. Conclusions: The translocation rate detected by BAC FISH was higher than that by PAINT, and the parameters β in dose-response curve equation were same by two methods. (authors)

  9. The genome of the sea urchin Strongylocentrotus purpuratus.

    OpenAIRE

    SEA URCHIN GENOME SEQUENCING CONSORTIUM; SODERGREN E; WEINSTOCK GM; DAVIDSON EH; CAMERON RA; GIBBS RA; ANGERER RC; ANGERER LM; ARNONE MI; BURGESS DR; BURKE RD; COFFMAN JA; Dean, M.; ELPHICK MR; ETTENSOHN CA

    2006-01-01

    We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or ...

  10. RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.)

    OpenAIRE

    Pont, Caroline; Murat, Florent; Confolent, Carole; Balzergue, Sandrine; Salse, Jérôme

    2011-01-01

    Background Whole genome duplication is a common evolutionary event in plants. Bread wheat (Triticum aestivum L.) is a good model to investigate the impact of paleo- and neoduplications on the organization and function of modern plant genomes. Results We performed an RNA sequencing-based inference of the grain filling gene network in bread wheat and identified a set of 37,695 non-redundant sequence clusters, which is an unprecedented resolution corresponding to an estimated half of the wheat g...

  11. A hyperactive piggyBac transposase for mammalian applications

    OpenAIRE

    Yusa, K; Zhou, L.; Li, M. A.; Bradley, A; Craig, N. L.

    2011-01-01

    DNA transposons have been widely used for transgenesis and insertional mutagenesis in various organisms. Among the transposons active in mammalian cells, the moth-derived transposon piggyBac is most promising with its highly efficient transposition, large cargo capacity, and precise repair of the donor site. Here we report the generation of a hyperactive piggyBac transposase. The active transposition of piggyBac in multiple organisms allowed us to screen a transposase mutant library in yeast ...

  12. piggyBac-based insertional mutagenesis in the presence of stably integrated P elements in Drosophila.

    Science.gov (United States)

    Hacker, Udo; Nystedt, Sverker; Barmchi, Mojgan Padash; Horn, Carsten; Wimmer, Ernst A

    2003-06-24

    P element-mediated mutagenesis has been used to disrupt an estimated 25% of genes essential for Drosophila adult viability. Mutation of all genes in the fly genome, however, poses a problem, because P elements show significant hotspots of integration. In addition, advanced screening scenarios often require the use of P element-based tools like the generation of germ-line mosaics using FLP recombinase-mediated recombination or gene misexpression using the UAS/Gal4 system. These techniques are P element-based and can therefore not be combined with the use of P elements as mutagenic agents. To circumvent these limitations, we have developed an insertional mutagenesis system using non-P element transposons. An enhanced yellow fluorescent protein-marked piggyBac-based mutator element was mobilized by a piggyBac specific transposase source expressed from a Hermes-based jump-starter transposon marked with enhanced cyan fluorescent protein. In a pilot screen, we have generated 798 piggyBac insertions on FRT bearing third chromosomes of which 9% have sustained a putatively piggyBac-related lethal hit. The FRTs present on the target chromosome remained stably integrated during the screen and could subsequently be used to generate germ-line clones associated with maternal and zygotic phenotypes. PCR-based analysis of insertion loci shows that 57% of the insertions are in genes for which no P element insertions have been reported. Our data demonstrate the potential of this technique to facilitate the quest for saturation mutagenesis of the Drosophila genome. The system is Drosophila nonspecific and potentially applicable in a broad spectrum of nonmodel organisms. PMID:12802016

  13. Generation of BAC transgenic epithelial organoids.

    Directory of Open Access Journals (Sweden)

    Gerald Schwank

    Full Text Available Under previously developed culture conditions, mouse and human intestinal epithelia can be cultured and expanded over long periods. These so-called organoids recapitulate the three-dimensional architecture of the gut epithelium, and consist of all major intestinal cell types. One key advantage of these ex vivo cultures is their accessibility to live imaging. So far the establishment of transgenic fluorescent reporter organoids has required the generation of transgenic mice, a laborious and time-consuming process, which cannot be extended to human cultures. Here we present a transfection protocol that enables the generation of recombinant mouse and human reporter organoids using BAC (bacterial artificial chromosome technology.

  14. Olefin Isomerization Regiochemistries during Tandem Action of BacA and BacB on Prephenate in Bacilysin Biosynthesis†

    OpenAIRE

    Parker, Jared B.; Walsh, Christopher T.

    2012-01-01

    BacA and BacB, the first two enzymes of the bacilysin pathway, convert prephenate to an exocylic regioisomer of dihydrohydroxyphenylpyruvate (ex-H2HPP) on the way to the epoxycyclohexanone warhead in the dipeptide antibiotic, bacilysin. BacA decarboxylates prephenate without aromatization, converting the 1,4-diene in prephenate to the endocyclic 1,3 diene in Δ4Δ8-dihydrohydroxyphenylpyruvate (en-H2HPP). BacB then performs an allylic isomerization to bring the diene into conjugation with the 2...

  15. Molecular Characterization and Global Expression Analysis of Lectin Receptor Kinases in Bread Wheat (Triticum aestivum)

    Science.gov (United States)

    Pandey, Ajay K.; Singh, Kashmir; Upadhyay, Santosh Kumar

    2016-01-01

    Lectin receptor kinases (LRKs) play a critical role in plants during development and stress conditions, but a comprehensive analysis at genome level is still not carried out in Triticum aestivum. Herein, we performed the genome wide identification, characterization and expression analysis of these genes in T. aestivum (TaLRK). In-total 263 TaLRK genes were identified, which were further classified into three groups based on the nature of lectin domain. We identified, two TaLRKs consisted of calcium-dependent lectin (C-LRK), while 84 legume-lectin (L-LRK) and 177 bulb-lectin (B-LRK) domains. The L-LRK and B-LRK genes were distributed throughout the genome of T. aestivum. Most of the TaLRKs were clustered as homologs, which were distributed either in proximity on same chromosome or on homoeologous chromosomes of A, B and D sub-genomes. A total of 9 and 58 duplication events were also predicted in L-LRK and B-LRK, respectively. Phylogenetic analysis indicated conserved evolutionary relationship of homologous and orthologous genes from multiple plant species. Gene ontology analysis indicated TaLRKs role in binding, signaling and receptor activities. Most of the TaLRKs consisted of a trans-membrane domain and predicted to be localized in the plasma-membrane. A diverse expression pattern of TaLRK genes was found in various developmental stages and stress conditions. Some TaLRKs were found to be highly affected during a particular stress, which indicated a specialized role of each LRK gene in a specific stress condition. These results described various characteristic feature and expression pattern of TaLRK genes, which will pave the way for functional characterization in wheat. PMID:27111449

  16. Comparison of BAC FISH with specific telomeres and centromere probes and chromosome painting on detection of chromosome translocation induced by irradiation%BAC FISH与PAINT法检测辐射诱发染色体易位的比较

    Institute of Scientific and Technical Information of China (English)

    刘青杰; 陆雪; 封江彬; 王晓维; 陈德清

    2008-01-01

    Objective To compare the efficiency of BAC FISH established in our lab and conventional chromosome painting(PAINT)on detection of radiation-induced chromosome translocation.Methods Healthy human peripheral blood samples were irradiated with 0~5.0 Gy 60Co γ-rays.Then chromosome translocations in these samples were detected with BAC FISH and PAINT using chromosomes 1.2 and 4.The genome translocation rates were calculated with observed chromosome translocation rates,and the dose-response curve of two methods were established.Results The genome translocation rates induced by 0~5.0 Gy 60Co γ-rays detected by BAC FISH and PAINT were increased with absorbed doses.The observed translocation rates with BAC FISH were higher than that with PAINT at each dose level.The dose-response curve were Y=0.043 D2+0.0008D+0.0048 for BAC FISH and Y=0.043D2+0.006D+0.0027 for PAINT.Conclusions The translocation rate detected by BAC FISH was higher than that by PAINT,and the parameters β in dose-response curve equation were same by two methods.%目的 比较自行建立的BAC FISH方法和常规染色体涂染(PAINT)方法分析辐射诱发染色体易位有效性的不同.方法 对正常人外周血照射不同剂量(0~5.0 Gy)的60Co γ射线,用1、2和4号染色体特异性端粒和着丝粒探针BAC FISH及PAINT分析染色体易位,将观察到的染色体易位率换算为全基因组易位率,并建立两种方法分析辐射诱发的染色体易位率剂量-效应曲线.结果 用两种方法分析0~5.0 Gy 60Coγ射线诱发的全基因组易位率均随着吸收剂量的增加而增高;在相同的剂量点,BAC FISH染色体易位检出率高于PAINT方法.两种方法分析吸收剂量和全基因组易位率之间的剂量-效应曲线均为二次方程模式,分别为Y=0.043D2+0.0008D+0.0048(BAC FISH)和Y=0.043D2+0.006D+0.0027(PAINT).结论 自行建立的BAC FISH方法分析辐射诱发染色体易位检出率高于常规染色体涂染方法,两种方法建立的

  17. A New Normalizing Algorithm for BAC CGH Arrays with Quality Control Metrics

    Directory of Open Access Journals (Sweden)

    Jeffrey C. Miecznikowski

    2011-01-01

    Full Text Available The main focus in pin-tip (or print-tip microarray analysis is determining which probes, genes, or oligonucleotides are differentially expressed. Specifically in array comparative genomic hybridization (aCGH experiments, researchers search for chromosomal imbalances in the genome. To model this data, scientists apply statistical methods to the structure of the experiment and assume that the data consist of the signal plus random noise. In this paper we propose “SmoothArray”, a new method to preprocess comparative genomic hybridization (CGH bacterial artificial chromosome (BAC arrays and we show the effects on a cancer dataset. As part of our R software package “aCGHplus,” this freely available algorithm removes the variation due to the intensity effects, pin/print-tip, the spatial location on the microarray chip, and the relative location from the well plate. removal of this variation improves the downstream analysis and subsequent inferences made on the data. Further, we present measures to evaluate the quality of the dataset according to the arrayer pins, 384-well plates, plate rows, and plate columns. We compare our method against competing methods using several metrics to measure the biological signal. With this novel normalization algorithm and quality control measures, the user can improve their inferences on datasets and pinpoint problems that may arise in their BAC aCGH technology.

  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. PiggyBac:A flexible and highly active transposon as compared to Sleeping Beauty, Tol2, and Mos1 in mammalian cells

    Science.gov (United States)

    A non-viral vector for highly efficient site-specific integration would be desirable for many applications in transgenesis, including gene therapy. In this study, we directly compared the genomic integration efficiencies of piggyBac, hyperactive Sleeping Beauty(SB11), Tol2, and Mos1 in four mammalia...

  20. 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

  1. A nucleolus-predominant piggyBac transposase, NP-mPB, mediates elevated transposition efficiency in mammalian cells.

    Directory of Open Access Journals (Sweden)

    Jin-Bon Hong

    Full Text Available PiggyBac is a prevalent transposon system used to deliver transgenes and functionally explore the mammalian untouched genomic territory. The important features of piggyBac transposon are the relatively low insertion site preference and the ability of seamless removal from genome, which allow its potential uses in functional genomics and regenerative medicine. Efforts to increase its transposition efficiency in mammals were made through engineering the corresponding transposase (PBase codon usage to enhance its expression level and through screening for mutant PBase variants with increased enzyme activity. To improve the safety for its potential use in regenerative medicine applications, site-specific transposition was achieved by using engineered zinc finger- and Gal4-fused PBases. An excision-prone PBase variant has also been successfully developed. Here we describe the construction of a nucleolus-predominant PBase, NP-mPB, by adding a nucleolus-predominant (NP signal peptide from HIV-1 TAT protein to a mammalian codon-optimized PBase (mPB. Although there is a predominant fraction of the NP-mPB-tGFP fusion proteins concentrated in the nucleoli, an insertion site preference toward nucleolar organizer regions is not detected. Instead a 3-4 fold increase in piggyBac transposition efficiency is reproducibly observed in mouse and human cells.

  2. A Highly Efficient Protocol of Generating and Analyzing VZV ORF Deletion Mutants Based on a Newly Developed Luciferase VZV BAC System

    OpenAIRE

    Zhang, Zhen; Huang, Ying; Zhu, Hua

    2008-01-01

    Varicella Zoster Virus (VZV) is the causative agent for both varicella (chicken pox) and herpes zoster (shingles). As a member of the human herpesvirus family, VZV contains a large DNA genome, encoding 70 unique open reading frames (ORFs). The functions of the majority of these ORFs remain unknown. Recently, the full-length VZV (P-Oka strain) genome was cloned as a VZV bacteria artificial chromosome (BAC) and additionally a firefly luciferase cassette was inserted to generate a novel lucifera...

  3. Construction and characterization of a BAC library from a gynogenetic channel catfish Ictalurus punctatus

    Directory of Open Access Journals (Sweden)

    Wilson Melanie

    2003-11-01

    Full Text Available Abstract A bacterial artificial chromosome (BAC library was constructed by cloning HindIII-digested high molecular weight DNA from a gynogenetic channel catfish, Ictalurus punctatus, into the vector pBeloBAC11. Approximately 53 500 clones were arrayed in 384-well plates and stored at -80°C (CCBL1, while clones from a smaller insert size fraction were stored at -80°C without arraying (CCBL2. Pulsed-field gel electrophoresis of 100 clones after NotI digestion revealed an average insert size of 165 kb for CCBL1 and 113 kb for CCBL2. Further characterization of CCBL1 demonstrated that 10% of the clones did not contain an insert. CCBL1 provides a 7.2-fold coverage of the channel catfish haploid genome. PCR-based screening demonstrated that 68 out of 74 unique loci were present in the library. This represents a 92% chance to find a unique sequence. These libraries will be useful for physical mapping of the channel catfish genome, and identification of genes controlling major traits in this economically important species.

  4. Functional and genetic analysis of haplotypic sequence variation at the nicastrin genomic locus

    OpenAIRE

    Hamilton, Gillian; Killick, Richard; Lambert, Jean-Charles; Amouyel, Philippe; Carrasquillo, Minerva M.; Pankratz, V. Shane; Neill R Graff-Radford; Dickson, Dennis W.; Petersen, Ronald C.; Younkin, Steven G.; Powell, John F.; Wade-Martins, Richard

    2012-01-01

    Nicastrin (NCSTN) is a component of the γ-secretase complex and therefore potentially a candidate risk gene for Alzheimer's disease. Here, we have developed a novel functional genomics methodology to express common locus haplotypes to assess functional differences. DNA recombination was used to engineer 5 bacterial artificial chromosomes (BACs) to each express a different haplotype of the NCSTN locus. Each NCSTN-BAC was delivered to knockout nicastrin (Ncstn−/−) cells and clonal NCSTN-BAC+/Nc...

  5. L’italiano alla prova del Bac

    Directory of Open Access Journals (Sweden)

    Giulia Massignan

    2013-07-01

    Full Text Available Il lavoro propone alcune attività didattiche di preparazione dell’esame orale di italiano previsto dal Baccalauréat del liceo francese. Tale prova d’esame è stata recentemente oggetto di una riforma ministeriale volta a dare maggior peso alla pratica orale. Dopo uno studio delle nuove modalità della prove d’esame e dei suoi contenuti, ci si concentrerà sull’analisi delle abilità orali necessarie al suo superamento e sugli elementi linguistici e comunicativi su cui porre l’attenzione. Sulla base di queste premesse teoriche e metodologiche, si presentano alcuni interventi didattici di preparazione all’esame: due attività per la prova di comprensione orale e due per la prova di produzione e interazione orale; in entrambi i casi, si insiste sull’importanza di proporre strategie d’ascolto e di parlato insegnabili, che diventino consuetudini attive e parte integrante del bagaglio comunicativo del discente. The italian exam in the FrenchBacThe paper proposes some educational activities to prepare for the oral Italian examination as part of the French Baccalauréat. This exam has recently been the subject of a ministerial reform aimed at giving more weight to the oral practice. After illustrating new examination methods and content, we will focus on the analysis of oral skills necessary for passing the exam and aspects of language and communication on which to focus. Based on these theoretical and methodological premises, some educational exam preparation activities will be presented. Two activities test listening comprehension and two focus on production and oral interaction. The stress is on the importance of proposing teach able listening and speaking strategies, so that they become active habits and integral parts of the communicative learner’s baggage.

  6. "Cre/loxP plus BAC": a strategy for direct cloning of large DNA fragment and its applications in Photorhabdus luminescens and Agrobacterium tumefaciens.

    Science.gov (United States)

    Hu, Shengbiao; Liu, Zhengqiang; Zhang, Xu; Zhang, Guoyong; Xie, Yali; Ding, Xuezhi; Mo, Xiangtao; Stewart, A Francis; Fu, Jun; Zhang, Youming; Xia, Liqiu

    2016-01-01

    Heterologous expression has been proven to be a valid strategy for elucidating the natural products produced by gene clusters uncovered by genome sequencing projects. Efforts have been made to efficiently clone gene clusters directly from genomic DNA and several approaches have been developed. Here, we present an alternative strategy based on the site-specific recombinase system Cre/loxP for direct cloning gene clusters. A type three secretion system (T3SS) gene cluster (~32 kb) from Photorhabdus luminescens TT01 and DNA fragment (~78 kb) containing the siderophore biosynthetic gene cluster from Agrobacterium tumefaciens C58 have been successfully cloned into pBeloBAC11 with "Cre/loxP plus BAC" strategy. Based on the fact that Cre/loxP system has successfully used for genomic engineering in a wide range of organisms, we believe that this strategy could be widely used for direct cloning of large DNA fragment. PMID:27364376

  7. The genome of the sea urchin Strongylocentrotus purpuratus.

    Science.gov (United States)

    Sodergren, Erica; Weinstock, George M; Davidson, Eric H; Cameron, R Andrew; Gibbs, Richard A; Angerer, Robert C; Angerer, Lynne M; Arnone, Maria Ina; Burgess, David R; Burke, Robert D; Coffman, James A; Dean, Michael; Elphick, Maurice R; Ettensohn, Charles A; Foltz, Kathy R; Hamdoun, Amro; Hynes, Richard O; Klein, William H; Marzluff, William; McClay, David R; Morris, Robert L; Mushegian, Arcady; Rast, Jonathan P; Smith, L Courtney; Thorndyke, Michael C; Vacquier, Victor D; Wessel, Gary M; Wray, Greg; Zhang, Lan; Elsik, Christine G; Ermolaeva, Olga; Hlavina, Wratko; Hofmann, Gretchen; Kitts, Paul; Landrum, Melissa J; Mackey, Aaron J; Maglott, Donna; Panopoulou, Georgia; Poustka, Albert J; Pruitt, Kim; Sapojnikov, Victor; Song, Xingzhi; Souvorov, Alexandre; Solovyev, Victor; Wei, Zheng; Whittaker, Charles A; Worley, Kim; Durbin, K James; Shen, Yufeng; Fedrigo, Olivier; Garfield, David; Haygood, Ralph; Primus, Alexander; Satija, Rahul; Severson, Tonya; Gonzalez-Garay, Manuel L; Jackson, Andrew R; Milosavljevic, Aleksandar; Tong, Mark; Killian, Christopher E; Livingston, Brian T; Wilt, Fred H; Adams, Nikki; Bellé, Robert; Carbonneau, Seth; Cheung, Rocky; Cormier, Patrick; Cosson, Bertrand; Croce, Jenifer; Fernandez-Guerra, Antonio; Genevière, Anne-Marie; Goel, Manisha; Kelkar, Hemant; Morales, Julia; Mulner-Lorillon, Odile; Robertson, Anthony J; Goldstone, Jared V; Cole, Bryan; Epel, David; Gold, Bert; Hahn, Mark E; Howard-Ashby, Meredith; Scally, Mark; Stegeman, John J; Allgood, Erin L; Cool, Jonah; Judkins, Kyle M; McCafferty, Shawn S; Musante, Ashlan M; Obar, Robert A; Rawson, Amanda P; Rossetti, Blair J; Gibbons, Ian R; Hoffman, Matthew P; Leone, Andrew; Istrail, Sorin; Materna, Stefan C; Samanta, Manoj P; Stolc, Viktor; Tongprasit, Waraporn; Tu, Qiang; Bergeron, Karl-Frederik; Brandhorst, Bruce P; Whittle, James; Berney, Kevin; Bottjer, David J; Calestani, Cristina; Peterson, Kevin; Chow, Elly; Yuan, Qiu Autumn; Elhaik, Eran; Graur, Dan; Reese, Justin T; Bosdet, Ian; Heesun, Shin; Marra, Marco A; Schein, Jacqueline; Anderson, Michele K; Brockton, Virginia; Buckley, Katherine M; Cohen, Avis H; Fugmann, Sebastian D; Hibino, Taku; Loza-Coll, Mariano; Majeske, Audrey J; Messier, Cynthia; Nair, Sham V; Pancer, Zeev; Terwilliger, David P; Agca, Cavit; Arboleda, Enrique; Chen, Nansheng; Churcher, Allison M; Hallböök, F; Humphrey, Glen W; Idris, Mohammed M; Kiyama, Takae; Liang, Shuguang; Mellott, Dan; Mu, Xiuqian; Murray, Greg; Olinski, Robert P; Raible, Florian; Rowe, Matthew; Taylor, John S; Tessmar-Raible, Kristin; Wang, D; Wilson, Karen H; Yaguchi, Shunsuke; Gaasterland, Terry; Galindo, Blanca E; Gunaratne, Herath J; Juliano, Celina; Kinukawa, Masashi; Moy, Gary W; Neill, Anna T; Nomura, Mamoru; Raisch, Michael; Reade, Anna; Roux, Michelle M; Song, Jia L; Su, Yi-Hsien; Townley, Ian K; Voronina, Ekaterina; Wong, Julian L; Amore, Gabriele; Branno, Margherita; Brown, Euan R; Cavalieri, Vincenzo; Duboc, Véronique; Duloquin, Louise; Flytzanis, Constantin; Gache, Christian; Lapraz, François; Lepage, Thierry; Locascio, Annamaria; Martinez, Pedro; Matassi, Giorgio; Matranga, Valeria; Range, Ryan; Rizzo, Francesca; Röttinger, Eric; Beane, Wendy; Bradham, Cynthia; Byrum, Christine; Glenn, Tom; Hussain, Sofia; Manning, Gerard; Miranda, Esther; Thomason, Rebecca; Walton, Katherine; Wikramanayke, Athula; Wu, Shu-Yu; Xu, Ronghui; Brown, C Titus; Chen, Lili; Gray, Rachel F; Lee, Pei Yun; Nam, Jongmin; Oliveri, Paola; Smith, Joel; Muzny, Donna; Bell, Stephanie; Chacko, Joseph; Cree, Andrew; Curry, Stacey; Davis, Clay; Dinh, Huyen; Dugan-Rocha, Shannon; Fowler, Jerry; Gill, Rachel; Hamilton, Cerrissa; Hernandez, Judith; Hines, Sandra; Hume, Jennifer; Jackson, Laronda; Jolivet, Angela; Kovar, Christie; Lee, Sandra; Lewis, Lora; Miner, George; Morgan, Margaret; Nazareth, Lynne V; Okwuonu, Geoffrey; Parker, David; Pu, Ling-Ling; Thorn, Rachel; Wright, Rita

    2006-11-10

    We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes. PMID:17095691

  8. Isolation of bacteria from ectomycorrhizae of Tuber aestivum Vittad

    Directory of Open Access Journals (Sweden)

    Milana Gryndler

    2013-12-01

    Full Text Available Fifteen different cultivation media were used to isolate bacteria with the idea to obtain taxa specifically associated with ectomycorrhizae of Tuber aestivum. Ectomycorrhizae were collected at the sampling points previously analyzed for bacterial molecular diversity. We isolated 183 bacterial strains and identified them on the basis of the partial sequence of 16S rDNA. Out of these isolates, only 4 corresponded to operational taxonomic units significantly associated with T. aestivum ectomycorrhizae in previous molecular study. Preliminary study of the effect of 12 selected isolates on growth of T. aestivum mycelium showed no stimulation and one isolate induced the damage of hyphae. Different isolation strategy has to be developed to increase the probability of cultivation of potentially important components of T. aestivum mycorrhizosphere.

  9. Whole genome linkage disequilibrium maps in cattle

    Science.gov (United States)

    Bovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine genome organization which will allow the design of studies to associate genetic variation with economically important traits and also provides bac...

  10. Sequence composition of BAC clones and SSR markers mapped to Upland cotton chromosomes 11 and 21 targeting resistance to soil-borne pathogens

    Science.gov (United States)

    Wang, Congli; Ulloa, Mauricio; Shi, Xinyi; Yuan, Xiaohui; Saski, Christopher; Yu, John Z.; Roberts, Philip A.

    2015-01-01

    Genetic and physical framework mapping in cotton (Gossypium spp.) were used to discover putative gene sequences involved in resistance to common soil-borne pathogens. Chromosome (Chr) 11 and its homoeologous Chr 21 of Upland cotton (G. hirsutum) are foci for discovery of resistance (R) or pathogen-induced R (PR) genes underlying QTLs involved in response to root-knot nematode (Meloidogyne incognita), reniform nematode (Rotylenchulus reniformis), Fusarium wilt (Fusarium oxysporum f.sp. vasinfectum), Verticillium wilt (Verticillium dahliae), and black root rot (Thielaviopsis basicola). Simple sequence repeat (SSR) markers and bacterial artificial chromosome (BAC) clones from a BAC library developed from the Upland cotton Acala Maxxa were mapped on Chr 11 and Chr 21. DNA sequence through Gene Ontology (GO) of 99 of 256 Chr 11 and 109 of 239 Chr 21 previously mapped SSRs revealed response elements to internal and external stimulus, stress, signaling process, and cell death. The reconciliation between genetic and physical mapping of gene annotations from new DNA sequences of 20 BAC clones revealed 467 (Chr 11) and 285 (Chr 21) G. hirsutum putative coding sequences, plus 146 (Chr 11) and 98 (Chr 21) predicted genes. GO functional profiling of Unigenes uncovered genes involved in different metabolic functions and stress response elements (SRE). Our results revealed that Chrs 11 and 21 harbor resistance gene rich genomic regions. Sequence comparisons with the ancestral diploid D5 (G. raimondii), A2 (G. arboreum) and domesticated tetraploid TM-1 AD1 (G. hirsutum) genomes revealed abundance of transposable elements and confirmed the richness of resistance gene motifs in these chromosomes. The sequence information of SSR markers and BAC clones and the genetic mapping of BAC clones provide enhanced genetic and physical frameworks of resistance gene-rich regions of the cotton genome, thereby aiding discovery of R and PR genes and breeding for resistance to cotton diseases. PMID

  11. BacHbpred: Support Vector Machine Methods for the Prediction of Bacterial Hemoglobin-Like Proteins.

    Science.gov (United States)

    Selvaraj, MuthuKrishnan; Puri, Munish; Dikshit, Kanak L; Lefevre, Christophe

    2016-01-01

    The recent upsurge in microbial genome data has revealed that hemoglobin-like (HbL) proteins may be widely distributed among bacteria and that some organisms may carry more than one HbL encoding gene. However, the discovery of HbL proteins has been limited to a small number of bacteria only. This study describes the prediction of HbL proteins and their domain classification using a machine learning approach. Support vector machine (SVM) models were developed for predicting HbL proteins based upon amino acid composition (AC), dipeptide composition (DC), hybrid method (AC + DC), and position specific scoring matrix (PSSM). In addition, we introduce for the first time a new prediction method based on max to min amino acid residue (MM) profiles. The average accuracy, standard deviation (SD), false positive rate (FPR), confusion matrix, and receiver operating characteristic (ROC) were analyzed. We also compared the performance of our proposed models in homology detection databases. The performance of the different approaches was estimated using fivefold cross-validation techniques. Prediction accuracy was further investigated through confusion matrix and ROC curve analysis. All experimental results indicate that the proposed BacHbpred can be a perspective predictor for determination of HbL related proteins. BacHbpred, a web tool, has been developed for HbL prediction. PMID:27034664

  12. Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum lines

    Directory of Open Access Journals (Sweden)

    Qi Bao

    2012-01-01

    Full Text Available Abstract Background Alteration in gene expression resulting from allopolyploidization is a prominent feature in plants, but its spectrum and extent are not fully known. Common wheat (Triticum aestivum was formed via allohexaploidization about 10,000 years ago, and became the most important crop plant. To gain further insights into the genome-wide transcriptional dynamics associated with the onset of common wheat formation, we conducted microarray-based genome-wide gene expression analysis on two newly synthesized allohexaploid wheat lines with chromosomal stability and a genome constitution analogous to that of the present-day common wheat. Results Multi-color GISH (genomic in situ hybridization was used to identify individual plants from two nascent allohexaploid wheat lines between Triticum turgidum (2n = 4x = 28; genome BBAA and Aegilops tauschii (2n = 2x = 14; genome DD, which had a stable chromosomal constitution analogous to that of common wheat (2n = 6x = 42; genome BBAADD. Genome-wide analysis of gene expression was performed for these allohexaploid lines along with their parental plants from T. turgidum and Ae. tauschii, using the Affymetrix Gene Chip Wheat Genome-Array. Comparison with the parental plants coupled with inclusion of empirical mid-parent values (MPVs revealed that whereas the great majority of genes showed the expected parental additivity, two major patterns of alteration in gene expression in the allohexaploid lines were identified: parental dominance expression and non-additive expression. Genes involved in each of the two altered expression patterns could be classified into three distinct groups, stochastic, heritable and persistent, based on their transgenerational heritability and inter-line conservation. Strikingly, whereas both altered patterns of gene expression showed a propensity of inheritance, identity of the involved genes was highly stochastic, consistent with the involvement of diverse Gene Ontology (GO

  13. As Blood Alcohol Content (BAC) Increases, So Does Impairment | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... on. Feature: Rethinking Drinking As Blood Alcohol Content (BAC) Increases, So Does Impairment Past Issues / Spring 2014 ... For purposes of law enforcement, blood alcohol content (BAC) is used to define intoxication and provides a ...

  14. Microbial Genomics Research in China

    Institute of Scientific and Technical Information of China (English)

    ZHAOGuo-ping

    2004-01-01

    Microorganisms, including phage/virus, were initial targets and tools for developing DNA sequencing technology. Microbial genomic study was started as a model system for the Human Genome Project (HGP) and it did successfully supported the HGP, particularly with respect to BAC contig construction and large-scale shotgun sequencing and assembly. Microbial genomics study has become the fastest developed genomics discipline along with HGP, taking the advantage of the organisms' highly diversified physiology, extremely long history of evolution, close relationship with human/environment,as well as relatively small genome sizes and simple systems for functional analysis.

  15. Microbial Genomics Research in China

    Institute of Scientific and Technical Information of China (English)

    ZHAO Guo-ping

    2004-01-01

    @@ Microorganisms, including phage/virus, were initial targets and tools for developing DNA sequencing technology. Microbial genomic study was started as a model system for the Human Genome Project (HGP) and it did successfully supported the HGP, particularly with respect to BAC contig construction and large-scale shotgun sequencing and assembly. Microbial genomics study has become the fastest developed genomics discipline along with HGP, taking the advantage of the organisms' highly diversified physiology, extremely long history of evolution, close relationship with human/environment,as well as relatively small genome sizes and simple systems for functional analysis.

  16. Genome annotations - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ated to rice genomes in GenBank blastn/blastx results. Related to rice genomes is defined as follows: The word... Oryza sativa or rice is included in the definition of the entry and the word BAC, PAC, chromosome Genomic

  17. Red-Mediated Transposition and Final Release of the Mini-F Vector of a Cloned Infectious Herpesvirus Genome

    OpenAIRE

    Wussow, Felix; Fickenscher, Helmut; Tischer, B Karsten

    2009-01-01

    Bacterial artificial chromosomes (BACs) are well-established cloning vehicles for functional genomics and for constructing targeting vectors and infectious viral DNA clones. Red-recombination-based mutagenesis techniques have enabled the manipulation of BACs in Escherichia coli without any remaining operational sequences. Here, we describe that the F-factor-derived vector sequences can be inserted into a novel position and seamlessly removed from the present location of the BAC-cloned DNA via...

  18. Efficient conditional knockout targeting vector construction using co-selection BAC recombineering (CoSBR)

    OpenAIRE

    Robert J. Newman; Roose-Girma, Merone; Warming, Søren

    2015-01-01

    A simple and efficient strategy for Bacterial Artificial Chromosome (BAC) recombineering based on co-selection is described. We show that it is possible to efficiently modify two positions of a BAC simultaneously by co-transformation of a single-stranded DNA oligo and a double-stranded selection cassette. The use of co-selection BAC recombineering reduces the DNA manipulation needed to make a conditional knockout gene targeting vector to only two steps: a single round of BAC modification foll...

  19. 76 FR 44055 - BAC Home Loans Servicing, LP, et al.; Notice of Application and Temporary Order

    Science.gov (United States)

    2011-07-22

    ... COMMISSION BAC Home Loans Servicing, LP, et al.; Notice of Application and Temporary Order July 18, 2011... Act, with respect to an injunction entered against BAC Home Loans Servicing, LP (``HLS'') on May 31... (``BAC''). HLS is an entity that services mortgage loans and provides mortgage services,...

  20. A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block

    Directory of Open Access Journals (Sweden)

    Ma Wujun

    2010-05-01

    Full Text Available Abstract Background The complexity of the wheat genome has resulted from waves of retrotransposable element insertions. Gene deletions and disruptions generated by the fast replacement of repetitive elements in wheat have resulted in disruption of colinearity at a micro (sub-megabase level among the cereals. In view of genomic changes that are possible within a given time span, conservation of genes between species tends to imply an important functional or regional constraint that does not permit a change in genomic structure. The ctg1034 contig completed in this paper was initially studied because it was assigned to the Sr2 resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features. Results BAC shotgun sequencing of the hexaploid wheat (Triticum aestivum cv. Chinese Spring genome has been used to assemble a group of 15 wheat BACs from the chromosome 3B physical map FPC contig ctg1034 into a 783,553 bp genomic sequence. This ctg1034 sequence was annotated for biological features such as genes and transposable elements. A three-gene island was identified among >80% repetitive DNA sequence. Using bioinformatics analysis there were no observable similarity in their gene functions. The ctg1034 gene island also displayed complete conservation of gene order and orientation with syntenic gene islands found in publicly available genome sequences of Brachypodium distachyon, Oryza sativa, Sorghum bicolor and Zea mays, even though the intergenic space and introns were divergent. Conclusion We propose that ctg1034 is located within the heterochromatic C-band region of deletion bin 3BL7 based on the identification of heterochromatic tandem repeats and presence of significant matches to chromodomain-containing gypsy LTR retrotransposable elements. We also speculate that this location, among other highly repetitive sequences, may account for the relative stability in gene order and

  1. The Korea Brassica Genome Project: a Glimpse of the Brassica Genome Based on Comparative Genome Analysis With Arabidopsis

    Directory of Open Access Journals (Sweden)

    Beom-Seok Park

    2006-04-01

    Full Text Available A complete genome sequence provides unlimited information in the sequenced organism as well as in related taxa. According to the guidance of the Multinational Brassica Genome Project (MBGP, the Korea Brassica Genome Project (KBGP is sequencing chromosome 1 (cytogenetically oriented chromosome #1 of Brassica rapa. We have selected 48 seed BACs on chromosome 1 using EST genetic markers and FISH analyses. Among them, 30 BAC clones have been sequenced and 18 are on the way. Comparative genome analyses of the EST sequences and sequenced BAC clones from Brassica chromosome 1 revealed their homeologous partner regions on the Arabidopsis genome and a syntenic comparative map between Brassica chromosome 1 and Arabidopsis chromosomes. In silico chromosome walking and clone validation have been successfully applied to extending sequence contigs based on the comparative map and BAC end sequences. In addition, we have defined the (pericentromeric heterochromatin blocks with centromeric tandem repeats, rDNA and centromeric retrotransposons. In-depth sequence analyses of five homeologous BAC clones and an Arabidopsis chromosomal region reveal overall co-linearity, with 82% sequence similarity. The data indicate that the Brassica genome has undergone triplication and subsequent gene losses after the divergence of Arabidopsis and Brassica. Based on in-depth comparative genome analyses, we propose a comparative genomics approach for conquering the Brassica genome. In 2005 we intend to construct an integrated physical map, including sequence information from 500 BAC clones and integration of fingerprinting data and end sequence data of more than 100 000 BAC clones. The sequences have been submitted to GenBank with accession numbers: 10 204 BAC ends of the KBrH library (CW978640–CW988843; KBrH138P04, AC155338; KBrH117N09, AC155337; KBrH097M21, AC155348; KBrH093K03, AC155347; KBrH081N08, AC155346; KBrH080L24, AC155345; KBrH077A05, AC155343; KBrH020D15

  2. Thermochemical study of the molecule BaC2

    International Nuclear Information System (INIS)

    The enthalpy of the reaction Ba(g)+2C(graph.) = BaC2(g) has been determined by Knudsen effusion mass spectrometry over a barium alloy with noble metals contained in a graphite cell. The value ΔH/sup circle-open/0 = 252.5 +- 11.5kJ mol-1 has been obtained from second- and third-law evaluations of the equilibrium vapor in the temperature range 1778--2286 K. This reaction enthalpy has been combined with ancillary literature data to derive the following thermodynamic properties in kJ mol-1 of gaseous BaC2: the atomization energy, Δ/sub at/H/sup circle-open/0 , 1180.9 +- 12.2; the standard heat of formation, Δ/sub f/H/sup circle-open/298 , 437.1 +- 14.2; the enthalpy of sublimation of BaC2(s), Δ/sub sub/H/sup circle-open/298 , 511.2 +- 17.1; and the bond dissociation energy, D/sup circle-open/0 (Ba--C2), 581.7 +- 14.8. The results are discussed with regard to their possible significance in reactor technology

  3. Genome Improvement at JGI-HAGSC

    Energy Technology Data Exchange (ETDEWEB)

    Grimwood, Jane; Schmutz, Jeremy J.; Myers, Richard M.

    2012-03-03

    Since the completion of the sequencing of the human genome, the Joint Genome Institute (JGI) has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.

  4. Tissue-specific and neural activity-regulated expression of human BDNF gene in BAC transgenic mice

    Directory of Open Access Journals (Sweden)

    Palm Kaia

    2009-06-01

    Full Text Available Abstract Background Brain-derived neurotrophic factor (BDNF is a small secreted protein that has important roles in the developing and adult nervous system. Altered expression or changes in the regulation of the BDNF gene have been implicated in a variety of human nervous system disorders. Although regulation of the rodent BDNF gene has been extensively investigated, in vivo studies regarding the human BDNF gene are largely limited to postmortem analysis. Bacterial artificial chromosome (BAC transgenic mice harboring the human BDNF gene and its regulatory flanking sequences constitute a useful tool for studying human BDNF gene regulation and for identification of therapeutic compounds modulating BDNF expression. Results In this study we have generated and analyzed BAC transgenic mice carrying 168 kb of the human BDNF locus modified such that BDNF coding sequence was replaced with the sequence of a fusion protein consisting of N-terminal BDNF and the enhanced green fluorescent protein (EGFP. The human BDNF-BAC construct containing all BDNF 5' exons preceded by different promoters recapitulated the expression of endogenous BDNF mRNA in the brain and several non-neural tissues of transgenic mice. All different 5' exon-specific BDNF-EGFP alternative transcripts were expressed from the transgenic human BDNF-BAC construct, resembling the expression of endogenous BDNF. Furthermore, BDNF-EGFP mRNA was induced upon treatment with kainic acid in a promotor-specific manner, similarly to that of the endogenous mouse BDNF mRNA. Conclusion Genomic region covering 67 kb of human BDNF gene, 84 kb of upstream and 17 kb of downstream sequences is sufficient to drive tissue-specific and kainic acid-induced expression of the reporter gene in transgenic mice. The pattern of expression of the transgene is highly similar to BDNF gene expression in mouse and human. This is the first study to show that human BDNF gene is regulated by neural activity.

  5. [Cytogenetic analysis of alloplasmic recombinant lines (H. vulgare)-T. aestivum with unstable fertility and viability].

    Science.gov (United States)

    Badaeva, E D; Pershina, L A; Bil'danova, L L

    2006-02-01

    Comparative cytogenetic analysis was performed with four alloplasmic recombinant (Hordeum vulgare)-Triticum aestivum lines differing in morphological traits, number of seeds per spike, and seed plumpness. None of the lines displayed introgression of the barley genetic material: the karyotypes included only common wheat chromosomes. Two lines, 79(B) and 79(D), were cytogenetically stable. Plants of lines 79(A) and 79(C) displayed a high frequency of unbalanced chromosome aberrations, including dicentric and polycentric chromosomes, terminal deletions varying in size, acentric fragments, and multiple unidentifiable translocations. Previous studies of the mitochondrial genome showed that the two cytologically unstable lines, which were also unstable in fertility and viability, are characterized by heteroplasmy at the mitochondrial 18S-5S locus (simultaneous presence of barley and wheat fragments). Stable lines 79(B) and 79(D) with normal fertility contained only wheat mitochondrial markers. It was assumed that the substantial instability of the nuclear genome in lines 79(C) and 79(A) was a result of nuclear-cytoplasmic incompatibility and was associated with heteroplasmy, while elimination or considerable reduction of barley material in the mitochondrial genome stabilized the nuclear genome of lines 79(B) and 79(D). In turn, the instability of the nuclear genome was responsible for a decrease in viability and fertility of plants. PMID:16583704

  6. 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

  7. A BAC-bacterial recombination method to generate physically linked multiple gene reporter DNA constructs

    Directory of Open Access Journals (Sweden)

    Gong Shiaochin

    2009-03-01

    Full Text Available Abstract Background Reporter gene mice are valuable animal models for biological research providing a gene expression readout that can contribute to cellular characterization within the context of a developmental process. With the advancement of bacterial recombination techniques to engineer reporter gene constructs from BAC genomic clones and the generation of optically distinguishable fluorescent protein reporter genes, there is an unprecedented capability to engineer more informative transgenic reporter mouse models relative to what has been traditionally available. Results We demonstrate here our first effort on the development of a three stage bacterial recombination strategy to physically link multiple genes together with their respective fluorescent protein (FP reporters in one DNA fragment. This strategy uses bacterial recombination techniques to: (1 subclone genes of interest into BAC linking vectors, (2 insert desired reporter genes into respective genes and (3 link different gene-reporters together. As proof of concept, we have generated a single DNA fragment containing the genes Trap, Dmp1, and Ibsp driving the expression of ECFP, mCherry, and Topaz FP reporter genes, respectively. Using this DNA construct, we have successfully generated transgenic reporter mice that retain two to three gene readouts. Conclusion The three stage methodology to link multiple genes with their respective fluorescent protein reporter works with reasonable efficiency. Moreover, gene linkage allows for their common chromosomal integration into a single locus. However, the testing of this multi-reporter DNA construct by transgenesis does suggest that the linkage of two different genes together, despite their large size, can still create a positional effect. We believe that gene choice, genomic DNA fragment size and the presence of endogenous insulator elements are critical variables.

  8. Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa

    OpenAIRE

    Park Beom-Seok; Jin Mina; Van Nguyen Dan; Hossain Md; Lee Seo; Hong Chang; Bae Jina; Choi Su; Kim HyeRan; Bang Jea-Wook; Bancroft Ian; Lim Yong

    2009-01-01

    Abstract Background In view of the immense value of Brassica rapa in the fields of agriculture and molecular biology, the multinational Brassica rapa Genome Sequencing Project (BrGSP) was launched in 2003 by five countries. The developing BrGSP has valuable resources for the community, including a reference genetic map and seed BAC sequences. Although the initial B. rapa linkage map served as a reference for the BrGSP, there was ambiguity in reconciling the linkage groups with the ten chromos...

  9. 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...

  10. Theobroma cacao: A genetically integrated physical map and genome-scale comparative synteny analysis

    Science.gov (United States)

    A comprehensive integrated genomic framework is considered a centerpiece of genomic research. In collaboration with the USDA-ARS (SHRS) and Mars Inc., the Clemson University Genomics Institute (CUGI) has developed a genetically anchored physical map of the T. cacao genome. Three BAC libraries contai...

  11. A Domesticated piggyBac Transposase Plays Key Roles in Heterochromatin Dynamics and DNA Cleavage during Programmed DNA Deletion in Tetrahymena thermophila

    OpenAIRE

    Cheng CY; Vogt A; Mochizuki K.; Yao MC

    2010-01-01

    Transposons comprise large fractions of eukaryotic genomes and provide genetic reservoirs for the evolution of new cellular functions. We identified TPB2, a homolog of the piggyBac transposase gene that is required for programmed DNA deletion in Tetrahymena. TPB2 was expressed exclusively during the time of DNA excision, and its encoded protein Tpb2p was localized in DNA elimination heterochromatin structures. Notably, silencing of TPB2 by RNAi disrupts the final assembly of these heterochrom...

  12. Action and Timing of BacC and BacD in the Late Stages of Biosynthesis of the Dipeptide Antibiotic Bacilysin

    OpenAIRE

    Parker, Jared B.; Walsh, Christopher T.

    2013-01-01

    Biosynthesis of the dipeptide antibiotic bacilysin, encoded by the seven B. subtilis genes bacA-G, involves diversion of flux from prephenate to the noncognate amino acid anticapsin. The anticapsin warhead is then ligated to the C-terminus of l-alanine to produce mature bacilysin. We have previously noted the formation of two diastereomers of tetrahydrotyrosine (4S- and 4R-H4Tyr) by tandem action of the four purified enzymes BacABGF. BacC (oxidase) and BacD (ligase) have been hypothesized to ...

  13. Comparison of the BacT/Alert PF Pediatric FAN Blood Culture Bottle with the Standard Pediatric Blood Culture Bottle, the Pedi-BacT

    OpenAIRE

    Krisher, Karen K.; Gibb, Patrick; Corbett, Sandra; Church, Deidre

    2001-01-01

    The performance of the BacT/Alert PF (Organon-Teknika Corp., Durham, N.C.), a new nonvented pediatric FAN blood culture bottle, was compared to that of the original pediatric bottle, the Pedi-BacT, with matched aerobic cultures obtained from two separate facilities. A total of 244 clinically significant isolates were recovered from 4,015 compliant pairs. Among the positive cultures, 170 (70%) isolates were detected in both the BacT/Alert PF and the Pedi-BacT bottles, while 47 (19%) isolates w...

  14. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

    Directory of Open Access Journals (Sweden)

    Yandell Mark

    2010-07-01

    Full Text Available Abstract Background In today's age of genomic discovery, no attempt has been made to comprehensively sequence a gymnosperm genome. The largest genus in the coniferous family Pinaceae is Pinus, whose 110-120 species have extremely large genomes (c. 20-40 Gb, 2N = 24. The size and complexity of these genomes have prompted much speculation as to the feasibility of completing a conifer genome sequence. Conifer genomes are reputed to be highly repetitive, but there is little information available on the nature and identity of repetitive units in gymnosperms. The pines have extensive genetic resources, with approximately 329000 ESTs from eleven species and genetic maps in eight species, including a dense genetic map of the twelve linkage groups in Pinus taeda. Results We present here the Sanger sequence and annotation of ten P. taeda BAC clones and Genome Analyzer II whole genome shotgun (WGS sequences representing 7.5% of the genome. Computational annotation of ten BACs predicts three putative protein-coding genes and at least fifteen likely pseudogenes in nearly one megabase of sequence. We found three conifer-specific LTR retroelements in the BACs, and tentatively identified at least 15 others based on evidence from the distantly related angiosperms. Alignment of WGS sequences to the BACs indicates that 80% of BAC sequences have similar copies (≥ 75% nucleotide identity elsewhere in the genome, but only 23% have identical copies (99% identity. The three most common repetitive elements in the genome were identified and, when combined, represent less than 5% of the genome. Conclusions This study indicates that the majority of repeats in the P. taeda genome are 'novel' and will therefore require additional BAC or genomic sequencing for accurate characterization. The pine genome contains a very large number of diverged and probably defunct repetitive elements. This study also provides new evidence that sequencing a pine genome using a WGS approach is

  15. PiggyBac as a novel vector in cancer gene therapy: current perspective.

    Science.gov (United States)

    Mirzaei, H; Sahebkar, A; Jaafari, M R; Hadjati, J; Javanmard, S H; Mirzaei, H R; Salehi, R

    2016-02-01

    Selection of suitable delivery system is one of the crucial aspects in gene therapy that determines the efficiency of gene therapy. The past two decades have witnessed extensive efforts for finding safe and efficient vectors to overcome the limitations of viral vectors. The utilization of DNA transposon-based vectors for gene therapy has emerged as a promising non-viral alternative. DNA 'cut-and-paste' is one of the main mechanisms of genome engineering by transposon elements. However, the lack of an efficient transposition system has limited the utilization of transposon vectors in mice and mammalian systems. PiggyBac (PB) is known as a highly efficient DNA transposon originally isolated from Trichoplusia ni as an alternative to Sleeping Beauty (SB). It has been shown that PB can be functional in various species including mammalian systems. This vector could overcome some limitations of other vectors in cancer gene therapy. Some advantages of PB include the capacity for integration into the genome and providing a stable expression, capacity to harbor 10 and 9.1 kb of foreign DNA into the host genome, without a significant reduction in their transposition activity and display non-overlapping targeting preferences. However, to advance PB to clinical applications, some obstacles still require to be overcome to improve its safety and efficiency. Hence, it seems that this vector could open new horizons in gene and cancer therapy. PMID:26742580

  16. Analysis of the bread wheat genome using whole-genome shotgun sequencing

    OpenAIRE

    Brenchley R.; Brenchley, Rachel; Spannagl M.; Spannagl, Manuel; Pfeifer M; Pfeifer, Matthias; Barker, Gary L. A.; Barker G.L.A.; D'Amore R.; D'Amore, Rosalinda; Allen A.M.; Allen, Alexandra M.; McKenzie, Neil; McKenzie N.; Kramer, Melissa

    2012-01-01

    Summary Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20% of the calories consumed by mankind. We sequenced its large and challenging 17 Gb hexaploid genome using 454 pyrosequencing and compared this with the sequences of diploid ancestral and progenitor genomes. Between 94,000-96,000 genes were identified, and two-thirds were assigned to the A, B and D genomes. High-resolution synteny maps identified many small disruptions to conserved gene order. We show the h...

  17. Physical map-assisted whole-genome shotgun sequence assemblies

    OpenAIRE

    Warren, René L.; Varabei, Dmitry; Platt, Darren; Huang, Xiaoqiu; Messina, David; Yang, Shiaw-Pyng; Kronstad, James W.; Krzywinski, Martin; Warren, Wesley C; Wallis, John W.; Hillier, LaDeana W.; Chinwalla, Asif T.; Schein, Jacqueline E.; Siddiqui, Asim S.; Marra, Marco A.

    2006-01-01

    We describe a targeted approach to improve the contiguity of whole-genome shotgun sequence (WGS) assemblies at run-time, using information from Bacterial Artificial Chromosome (BAC)-based physical maps. Clone sizes and overlaps derived from clone fingerprints are used for the calculation of length constraints between any two BAC neighbors sharing 40% of their size. These constraints are used to promote the linkage and guide the arrangement of sequence contigs within a sequence scaffold at the...

  18. Intermediate fertile Triticum aestivum (+) Agropyron elongatum somatic hybrids are generated by low doses of UV irradiation

    Institute of Scientific and Technical Information of China (English)

    Ai Xia CHENG; Guang Min XIA; Da Ying ZHI; Hui Min CHEN

    2004-01-01

    We report the production and characterization of somatic hybrids between Triticum aestivum L. and Agropyron elongatum (Host) Nevishi (the synonym is Thinopyrum ponticum). Asymmetric protoplast fusion was performed between Agropyron elongatum protoplasts irradiated with a low UV dose and protoplasts of wheat taken from nonregenerable suspension cultures. More than 40 green plantlets were obtained from 15 regenerated clones and one of them produced seeds. The phenotypes of the hybrid plants and seeds were intermediate between wheat and Agropyron elongatum. All of the regenerated calli and plants were verified as intergeneric hybrids on the basis of morphological observation and analysis of isozyme,cytological,5SrDNA spacer sequences and random amplified polymorphic DNA (RAPD). RFLP analysis of the mitochondrial genome revealed evidence of random segregation and recombination of mtDNA.

  19. BacMet: antibacterial biocide and metal resistance genes database

    OpenAIRE

    Pal, Chandan; Bengtsson-Palme, Johan; Rensing, Christopher; Kristiansson, Erik; Larsson, D.G. Joakim

    2013-01-01

    Antibiotic resistance has become a major human health concern due to widespread use, misuse and overuse of antibiotics. In addition to antibiotics, antibacterial biocides and metals can contribute to the development and maintenance of antibiotic resistance in bacterial communities through co-selection. Information on metal and biocide resistance genes, including their sequences and molecular functions, is, however, scattered. Here, we introduce BacMet (http://bacmet.biomedicine.gu.se)—a manua...

  20. Effect of DNA damaging agents on Bac. stearothermophilus

    International Nuclear Information System (INIS)

    A thermophilic micro-organism Bac. stearothermophilus showes a high resistance to the effect of such DNA damaging agents as NMM, UV- and γ-radiation. Due to adaptation to high temperatures, at which intensive depurinization and depyrimidinization of DNA take place, thermophilic micro-organisms are suggested to acquire evolutionary a powerful system of repair of DNA damages, particularly, of apurine and apyrimidine sites

  1. Experimental study of 188Re-BAC5 radioimmunotherapy on nasopharyngeal carcinoma

    International Nuclear Information System (INIS)

    The feasibility of radioimmunotherapy for NPC with 188Re-BAC5, a kind of monoclonal antibody to NPC, was investigated. The 188Re-BAC5 was prepared by direct labeling method and its biological activity was determined. The MTT method was used to determine the inhibition effect of the 188Re-BAC5 on CNE-2 cell line culture, and the destruction effect on CNE-2 multicellular spheroids model was also observed. The control group were 188Re-BSA and 188ReO4-. The biological activity of BAC5 was 1:780000 after purification. The labeling yield of 188Re-BAC5 was above 80%. The immuno-activity of 188Re-BAC5 was 61% ± 15%. The results of MTT showed that the inhibition effect of 188Re-BAC5 group was much stronger than the control group (P188Re-BAC5 had a obvious destruction effect on spheroids, and there was a significant difference between 188Re-BAC5 and the control group. In conclusion, 188Re-BAC5 may serve a possible way in the treatment of NPC in the near future

  2. Inducible Transgene Expression in Human iPS Cells Using Versatile All-in-One piggyBac Transposons.

    Science.gov (United States)

    Kim, Shin-Il; Oceguera-Yanez, Fabian; Sakurai, Chiho; Nakagawa, Masato; Yamanaka, Shinya; Woltjen, Knut

    2016-01-01

    Transgenics is a mainstay of functional genomics. Conditionally overexpressing genes of interest (GOIs) helps to reveal their roles in the control of complex biological processes. Complemented by findings in classic animal model systems, recent advances in human embryonic stem cell (hESC) and patient-specific induced pluripotent stem cell (hiPSC) differentiation have led to sophisticated in vitro models of human development and disease. Yet, as transgenic elements encoding inducible systems must be introduced de novo into each genetically unique human stem cell line, robust and straightforward solutions to gene delivery are required. Transposons are a family of mobile DNA elements that have been adapted as experimental tools for stable genomic integration of transgenes. The piggyBac (PB) transposon from Trichoplusia ni presents a number of benefits over classic viral or BAC transgenesis: ease of application, simple integration-site mapping, and the unique capacity for traceless excision. Moreover, their large capacity permits the consolidation of multiple transgene components in a single vector system. In this chapter, we outline the features of a panel of "All-in-One" PB transposons designed for drug-inducible gene expression and provide guidelines to establish and validate populations or clones of transgenic hiPSCs. PMID:26025620

  3. Tuber aestivum association with non-host roots

    Czech Academy of Sciences Publication Activity Database

    Gryndler, Milan; Černá, Lucie; Bukovská, Petra; Hršelová, Hana; Jansa, Jan

    2014-01-01

    Roč. 24, č. 8 (2014), s. 603-610. ISSN 0940-6360 R&D Projects: GA ČR(CZ) P504/10/0382 Institutional support: RVO:61388971 Keywords : Tuber aestivum * ectomycorrhiza * soil Subject RIV: EE - Microbiology, Virology Impact factor: 3.459, year: 2014

  4. 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

  5. Performance of BAC process for treatment of micro-polluted water

    Institute of Scientific and Technical Information of China (English)

    WANG Chen; MA Fang; SHAN Dan; YANG Ji-xian; Chang Chein-chi

    2008-01-01

    Biological activated carbon (BAC) has been developed on the granular activated carbon by immobi-lization of selected and acclimated species of bacteria to treat the micro-polluted water. The BAC removal effi-ciencies for nitrobenzene, permanganate index, turbidity and ammonia were investigated. Effects of shock load-ing and SEM (Scanning Electron Microscope) observation on BAC were studied. Baekwashing and its intensity of BAC were also discussed. The results showed that BAC took short time to start up and recover to the normal condition after shock loading. The shock loading studies showed that the removal efficiency of BAC was not completely inhibited even at high concentration of nitrobenzene. Backwashing performed once every 10- 20 d,or an average of 15 d. Backwashing intensity was 12-14 L/( s·m2) with air and 3-4 L/( s·m2) with water.

  6. Toward Elucidating the Structure of Tetraploid Cotton Genome

    Institute of Scientific and Technical Information of China (English)

    GUO Wang-zhen

    2008-01-01

    @@ Upland cotton has the highest yield,and accounts for >95% of world cotton production.Decoding upland cotton genomes will undoubtedly provide the ultimate reference and resource for structural,functional,and evolutionary studies of the species.Here,we employed GeneTrek and BAC tagging information approaches to predict the general composition and structure of the allotetraploid cotton genome.

  7. Suicidal autointegration of sleeping beauty and piggyBac transposons in eukaryotic cells.

    Directory of Open Access Journals (Sweden)

    Yongming Wang

    2014-03-01

    Full Text Available Transposons are discrete segments of DNA that have the distinctive ability to move and replicate within genomes across the tree of life. 'Cut and paste' DNA transposition involves excision from a donor locus and reintegration into a new locus in the genome. We studied molecular events following the excision steps of two eukaryotic DNA transposons, Sleeping Beauty (SB and piggyBac (PB that are widely used for genome manipulation in vertebrate species. SB originates from fish and PB from insects; thus, by introducing these transposons to human cells we aimed to monitor the process of establishing a transposon-host relationship in a naïve cellular environment. Similarly to retroviruses, neither SB nor PB is capable of self-avoidance because a significant portion of the excised transposons integrated back into its own genome in a suicidal process called autointegration. Barrier-to-autointegration factor (BANF1, a cellular co-factor of certain retroviruses, inhibited transposon autointegration, and was detected in higher-order protein complexes containing the SB transposase. Increasing size sensitized transposition for autointegration, consistent with elevated vulnerability of larger transposons. Both SB and PB were affected similarly by the size of the transposon in three different assays: excision, autointegration and productive transposition. Prior to reintegration, SB is completely separated from the donor molecule and followed an unbiased autointegration pattern, not associated with local hopping. Self-disruptive autointegration occurred at similar frequency for both transposons, while aberrant, pseudo-transposition events were more frequently observed for PB.

  8. New Hybrids with D Genome Wheat Relatives

    OpenAIRE

    Zhao, Y H; Kimber, G.

    1984-01-01

    The cytology of nine new D genome hybrids involving Triticum syriacum, Triticum ventricosum, Triticum cyclindricum, Triticum juvenale, Triticum crassum, Triticum tauschii and Triticum aestivum is described. The calculation of numerical values of the relative affinity and the patterns of chromosome pairing indicate that the D genome in T. syriacum and T. juvenale may have been substantially modified and that of T. crassum somewhat modified from that of the diploid progenitor, T. tauschii.

  9. The Physical Location of Gm-2 and Gm-6 in O.officinalis with BAC-FISH Based on Comparative RFLP Map of Wild Rice and Cultivated Rice

    Institute of Scientific and Technical Information of China (English)

    QIN Rui; WEI Wen-hui; NING Shun-bin; JIN Wei-wei; HE Guang-cun; SONG Yun-chun

    2002-01-01

    Rice BAC library is used widely in rice genome research due to its distinctive advantages over other library systems. In this study, two rice BAC clones closely linked to rice gall midge resistance, Gm-2 and Gm-6, were in situ hybridized to Oryza officinalis chromosomes. They were located on the long arm of chromosome 4 with FL 72.33% and 77.10% respectively and their FL was consistent with the selective marker of rice, RG214 and RZ569. The frequency of signal detection was 61.2% and 59.5% respectively.Our study was based on comparative RFLP map of wild rice, O. officinalis, and cultivated rice, O. sativa.

  10. 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.

  11. Widespread distribution of the piggyBac transposon in various bactrocera species

    International Nuclear Information System (INIS)

    Full text: The piggyBac transposable element from the Lepidopteran species Trichoplusia ni is currently the most widely used vector for insect transgenesis. Consequently, the presence of piggyBac-like sequences has been investigated, by PCR and Southern analysis, in different species of target genera such as Ceratitis, Bactrocera and Anastrepha, along with Tirhitromina and Rhagoletis. PiggyBac-like sequences were detected in several Bactrocera species. The evolution of the piggyBac-like sequences is discussed with respect to the phylogenies of the hosts. (author)

  12. Ammonia, nitrite and nitrate nitrogen removal from polluted source water with ozonation and BAC processes

    International Nuclear Information System (INIS)

    Studies on the removal of ammonia-, nitrite-, and nitrate nitrogen with ozonation (O3), sand filtration (SF), biological activated carbon (BAC), SF-BAC, and/or O3-BAC processes were carried out in two pilot plants and a full scale plant, respectively. The results showed that all of the tested processes exhibited certain nitrogen removal efficiencies, of which both the O3-SF-BAC and O3-BAC processes were most effective and efficient in removing ammonia nitrogen, with mean removal efficiencies of some 90 and 80 percent, respectively. Ozonation was found able to oxidize some organic nitrogen into ammonia, and nitrite ion into nitrate ion. It was also found out, with interest, that the O3-BAC process can carry the nitrification process to the end under sufficient DO content, as well as more hydrocarbon substrates through ozonation that are more easily assimilated by some strains of nitrobacter that can multiply heterotrophically in its carbon beds. In the BAC process, both the DO and easily assimilated substrate contents were too low in its carbon beds due to no ozonation to sustain nitrobacter growth; but the nitrite conversion bacteria, like nitrosomas, can survive under such conditions. As a result, nitrite or nitrate ion content increased multiply in the effluents from BAC or O3-BAC processes over their influents, respectively. The removal mechanisms of various processes for the three forms of nitrogen were studied and discussed, and the optimum design parameters were determined as well

  13. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

    Science.gov (United States)

    As a major step toward understanding the biology and evolution of ruminants, the cattle genome was sequenced to ~7x coverage using a combined whole genome shotgun and BAC skim approach. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs found in seven mammalian...

  14. Breeding of T. aestivum-Ag. intermedium translocation lines with T. timopheevii cytoplasm and characterization by GISH

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A male-sterile T. aestivum-Ag. intermedium partial amphiploid with cytoplasm of T. timopheevii as a female parent was crossed to common wheat. The hybrid was backcrossed to the male parent several times continually and self-crossed at last. Two stable lines with common wheat phenotype, H96269-2 and H96278, have been obtained. The chromosome numbers of the two lines are all 2n = 42 in somatic cells. By inoculation test, the two lines show a high level of resistance to yellow rust. Through genomic in situ hybridization (GISH) with Ag. intermedium total genomic DNA as a probe, it is demonstrated that the two stable lines are all small segmental translocation lines, and the translocated chromosome segments from Ag. intermedium are located on the short arm terminals of wheat chromosomes. Genetics analysis suggests that the yellow rust resistance gene(s) are probably located on the translocated chromosome segments of Ag. intermedium.

  15. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA

    OpenAIRE

    Barrett, Michael T; Scheffer, Alicia; Ben-Dor, Amir; Sampas, Nick; Lipson, Doron; Kincaid, Robert; Tsang, Peter; Curry, Bo; Baird, Kristin; Meltzer, Paul S.; Yakhini, Zohar; Bruhn, Laurakay; Laderman, Stephen

    2004-01-01

    Array-based comparative genomic hybridization (CGH) measures copy-number variations at multiple loci simultaneously, providing an important tool for studying cancer and developmental disorders and for developing diagnostic and therapeutic targets. Arrays for CGH based on PCR products representing assemblies of BAC or cDNA clones typically require maintenance, propagation, replication, and verification of large clone sets. Furthermore, it is difficult to control the specificity of the hybridiz...

  16. A genome-wide survey of switchgrass genome structure and organization.

    Directory of Open Access Journals (Sweden)

    Manoj K Sharma

    Full Text Available The perennial grass, switchgrass (Panicum virgatum L., is a promising bioenergy crop and the target of whole genome sequencing. We constructed two bacterial artificial chromosome (BAC libraries from the AP13 clone of switchgrass to gain insight into the genome structure and organization, initiate functional and comparative genomic studies, and assist with genome assembly. Together representing 16 haploid genome equivalents of switchgrass, each library comprises 101,376 clones with average insert sizes of 144 (HindIII-generated and 110 kb (BstYI-generated. A total of 330,297 high quality BAC-end sequences (BES were generated, accounting for 263.2 Mbp (16.4% of the switchgrass genome. Analysis of the BES identified 279,099 known repetitive elements, >50,000 SSRs, and 2,528 novel repeat elements, named switchgrass repetitive elements (SREs. Comparative mapping of 47 full-length BAC sequences and 330K BES revealed high levels of synteny with the grass genomes sorghum, rice, maize, and Brachypodium. Our data indicate that the sorghum genome has retained larger microsyntenous regions with switchgrass besides high gene order conservation with rice. The resources generated in this effort will be useful for a broad range of applications.

  17. 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.

  18. Effects of nitrogen ion irradiation on endoglucanase activity and gene mutation of Bacillus subtilis Bac01

    International Nuclear Information System (INIS)

    Bacillus subtilis Bac01 was mutated by 15 keV N+ ions of 1.5xl016 cm-2. The mutant strain Bac11 with high yield of endoglucanase was isolated using carboxymethylcellulose sodium and congo red indicative plates. It exhibited higher endoglucanase activity (381.89IU) than the original strain Bac01 (93.33IU). Two 1,500 bp endoglucanase gene fragments were obtained with PCR amplification from B. subtilis Bac01 and mutant strain Bac11. BLAST comparison result indicated that 10 nucleotides mutated. Bioinformatics methods were used to analyze the two predicted amino acid sequences, and it was found that 5 amino acid residues changed, being all in the cellulose-binding domain of endoglucanase. (authors)

  19. Analysis and location of a rice BAC clone containing telomeric DNA sequences

    Institute of Scientific and Technical Information of China (English)

    翟文学; 陈浩; 颜辉煌; 严长杰; 王国梁; 朱立煌

    1999-01-01

    BAC2, a rice BAC clone containing (TTTAGGG)n homologous sequences, was analyzed by Southern hybridization and DNA sequencing of its subclones. It was disclosed that there were many tandem repeated satellite DNA sequences, called TA352, as well as simple tandem repeats consisting of TTTAGGG or its variant within the BAC2 insert. A 0. 8 kb (TTTAGGG) n-containing fragment in BAC2 was mapped in the telomere regions of at least 5 pairs of rice chromosomes by using fluorescence in situ hybridization (FISH). By RFLP analysis of low copy sequences the BAC2 clone was localized in one terminal region of chromosome 6. All the results strongly suggest that the telomeric DNA sequences of rice are TTTAGGG or its variant, and the linked satellite DNA TA352 sequences belong to telomere-associated sequences.

  20. Cloning and expression of human UDP-glucuronosyltransferase 1A4 in Bac-to-Bac system

    International Nuclear Information System (INIS)

    UDP-glucuronosyltransferases (UGTs) catalyze the transfer of glucuronic acid from uridine diphosphate-glucuronic acid (UDP-GA) to compounds with amine, hydroxyl, and carboxylic acid moieties. N-glucuronidation is an important pathway for elimination of many tertiary amine therapeutic agents used in humans. UGT1A4 has been reported to be specific for glucuronidating primary, secondary, and tertiary amines, forming N-glucuronides. To further investigate the drugs metabolized by UGT1A4, the Bac-to-Bac expression system was used to express the recombinant UGT1A4 with His-tag on the C-terminal. The His-tagged recombinant UGT1A4 expressed in Spodoptera frugiperda (Sf9) cells were detected using anti-His antibody and the molecular weight of the recombinant protein was approximately 55 kDa. The enzyme activity towards imipramine in cell homogenate protein was found to be 83.14 ± 15 pmol/min/mg protein (n=3) with 0.5 mM imipramine by HPLC, but was not detectable in blank Sf9 cells. It paved the way for the further studies for drug glucuronidation by UGT1A4. The purification of the UGT1A4 can be done by Ni-resin. This is helpful to do research on the structure of the UFT1A4

  1. piggyBac转座子及其在转基因昆虫中的应用%Advances on piggyBac transposon and its applications in insect transgenesis

    Institute of Scientific and Technical Information of China (English)

    王建军; 王常春; 韩召军

    2009-01-01

    piggyBac是一种从粉纹夜蛾Trichoplusia ni.中分离到的、具有TTAA插入位点特异性的DNA转座子.piggyBac可在昆虫基因组中准确切离,转化频率较高,并且不受宿主因子的限制,是目前转基因昆虫研究中应用最广的转座子载体.近年来的研究发现,piggyBac类转座子广泛分布于昆虫和其他生物基因组中.文章从piggyBac的结构、转座特性、在转基因昆虫中的应用以及piggyBac类转座子的分布等几个方面综述了piggyBac的研究进展.%The piggyBac element is a TTAA-insertion site specific DNA transposon and was originally discovered in Trichoplusia ni. The piggyBac element is capable of precise excision and shows high frequency of transformation in insect genome, and its activity is less restricted by host factors. These characteristics make piggyBac the most widely used gene vector in insect transgenesis. Recent studies revealed that piggyBac-like element is distributed in a wide variety of insect and other organisms. In this review, we introduced the structure and transposition characteristics of piggyBac and its application in insect transgenesis, and the distribution of piggyBac-like elements was also described.

  2. Effects of combined 131I- and CT-BAC5 immunotherapy on NPC CNE-2 multicellular spheroids

    International Nuclear Information System (INIS)

    Objective: To develop a new specific therapeutic method for treating nasopharyngeal carcinoma (NPC) and to evaluate its effects on an in vitro tumor spheroid model. Methods: The human NPC cell line CNE-2 spheroids were grown in culture medium, on a thin layer of 0.75% agarose. The average volume of the spheroids was estimated by 1/2 (short dimension)2 x (long dimension). Anti-NPC BAC5 MAb was labelled with 131I using chloramine-T method. Cytotoxin from Chinese cobra (CT) was conjugated with BAC5 by hetero bifunctional cross-linking reagent (SPDP). The spheroids were treated with either 131I-BAC5 or CT-BAC5 separately or with both of them together by incubating in culture medium. Results: The conjugated rate of BAC5 and CT was 32.4%. CT-BAC5 significantly inhibited the growth of CNE-2 multicellular spheroids comparing with control agent (normal saline) (P 131I-BAC5 did more than CT-BAC5 (P131I-BAC5 with CT-BAC5 treatment showed even stronger destructive effect on the spheroids (vs. normal saline, P 131I-BAC5 with CT-BAC5 is better than either of them working separately

  3. Potentially toxic elements in foodcrops: Triticum aestivum L., Zea mays L.

    Science.gov (United States)

    Bini, Claudio; Fontana, Silvia; Squizzato, Stefania; Minello, Fabiola; Fornasier, Flavio; Wahsha, Mohammad

    2013-04-01

    Soil is the basis of the ecosystems and of our system of food production. Crops can uptake heavy metals and potentially toxic elements from the soil and store them in the roots or translocate them to the aerial parts. Excessive content of these elements in edible parts can produce toxic effects and, through the food chain and food consumption, result in a potential hazard for human health. In this study soils and plants (spring wheat, Triticum aestivum L. and maize, Zea mays L.) from a tannery district in North-East Italy were analyzed to determine pedological characters, soil microbial indicators and the content of some major and micro-nutrients and potentially toxic elements (Al, Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Ni, P, Pb, S, Zn, V). The soils of the area are moderately polluted; Cr is the most important inorganic contaminant, followed by Ni, Cu and V. Factor analysis evidenced that the contaminants are in part anthropogenic and in part geogenic. Major anthropogenic origin was detected for Cr, Ni (from industrial activities), Zn, Cu, Cd (from agriculture practices). Biological Absorption Coefficient (BAC) from soil to plant roots and Translocation factor (TF) within the plant were calculated; major nutrients (K, P, S) and some micronutrients (Cu, Zn, Mg, Mn) are easily absorbed and translocated, whilst other nutrients (Ca, Fe) and potentially toxic elements or micronutrients (Al, Cd, Cr, Ni, Pb, V) are not accumulated in the seeds of the two considered species. However, the two edible species proved differently able to absorb and translocate elements, and this suggests to consider separately every species as potential PHEs transporter to the food chain and to humans. Cr concentrations in seeds and other aerial parts (stem and leaves) of the examined plants are higher than the values found for the same species and for other cereals grown on unpolluted soils. Comparing the Cr levels in edible parts with recommended dietary intake, besides other possible Cr sources

  4. Efficient Production of Fluorescent Transgenic Rats using the piggyBac Transposon.

    Science.gov (United States)

    Li, Tianda; Shuai, Ling; Mao, Junjie; Wang, Xuepeng; Wang, Mei; Zhang, Xinxin; Wang, Leyun; Li, Yanni; Li, Wei; Zhou, Qi

    2016-01-01

    Rats with fluorescent markers are of great value for studies that trace lineage-specific development, particularly those assessing the differentiation potential of embryonic stem cells (ESCs). The piggyBac (PB) transposon is widely used for the efficient introduction of genetic modifications into genomes, and has already been successfully used to produce transgenic mice and rats. Here, we generated transgenic rats carrying either the desRed fluorescent protein (RFP) gene or the enhanced green fluorescent protein (eGFP) gene by injecting pronuclei with PB plasmids. We showed that the transgenic rats expressed the RFP or eGFP gene in many organs and had the capability to transmit the marker gene to the next generation through germline integration. In addition, rat embryonic stem cells (ESCs) carrying an RFP reporter gene can be derived from the blastocysts of the transgenic rats. Moreover, the RFP gene can be detected in chimeras derived from RFP ESCs via blastocyst injection. This work suggests that PB-mediated transgenesis is a powerful tool to generate transgenic rats expressing fluorescent proteins with high efficiency, and this technique can be used to derive rat ESCs expressing a reporter protein. PMID:27624004

  5. Evaluation of chronic lymphocytic leukemia by BAC-based microarray analysis

    Directory of Open Access Journals (Sweden)

    McDaniel Lisa D

    2011-02-01

    Full Text Available Abstract Background Chronic lymphocytic leukemia (CLL is a highly variable disease with life expectancies ranging from months to decades. Cytogenetic findings play an integral role in defining the prognostic significance and treatment for individual patients. Results We have evaluated 25 clinical cases from a tertiary cancer center that have an established diagnosis of CLL and for which there was prior cytogenetic and/or fluorescence in situ hybridization (FISH data. We performed microarray-based comparative genomic hybridization (aCGH using a bacterial artificial chromosome (BAC-based microarray designed for the detection of known constitutional genetic syndromes. In 15 of the 25 cases, aCGH detected all copy number imbalances identified by prior cytogenetic and/or FISH studies. For the majority of those not detected, the aberrations were present at low levels of mosaicism. Furthermore, for 15 of the 25 cases, additional abnormalities were detected. Four of those cases had deletions that mapped to intervals implicated in inherited predisposition to CLL. For most cases, aCGH was able to detect abnormalities present in as few as 10% of cells. Although changes in ploidy are not easily discernable by aCGH, results for two cases illustrate the detection of additional copy gains and losses present within a mosaic tetraploid cell population. Conclusions Our results illustrate the successful evaluation of CLL using a microarray optimized for the interrogation of inherited disorders and the identification of alterations with possible relevance to CLL susceptibility.

  6. Construction of random sheared fosmid library from Chinese cabbage and its use for Brassica rapa genome sequencing project

    Institute of Scientific and Technical Information of China (English)

    Tae-Ho Park; Beom-Seok Park; Jin-A Kim; Joon Ki Hong; Mina Jin; Young-Joo Seol; Jeong-Hwan Mun

    2011-01-01

    As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome (BAC) by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones.Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa.

  7. Red-mediated transposition and final release of the mini-F vector of a cloned infectious herpesvirus genome.

    Directory of Open Access Journals (Sweden)

    Felix Wussow

    Full Text Available Bacterial artificial chromosomes (BACs are well-established cloning vehicles for functional genomics and for constructing targeting vectors and infectious viral DNA clones. Red-recombination-based mutagenesis techniques have enabled the manipulation of BACs in Escherichia coli without any remaining operational sequences. Here, we describe that the F-factor-derived vector sequences can be inserted into a novel position and seamlessly removed from the present location of the BAC-cloned DNA via synchronous Red-recombination in E. coli in an en passant mutagenesis-based procedure. Using this technique, the mini-F elements of a cloned infectious varicella zoster virus (VZV genome were specifically transposed into novel positions distributed over the viral DNA to generate six different BAC variants. In comparison to the other constructs, a BAC variant with mini-F sequences directly inserted into the junction of the genomic termini resulted in highly efficient viral DNA replication-mediated spontaneous vector excision upon virus reconstitution in transfected VZV-permissive eukaryotic cells. Moreover, the derived vector-free recombinant progeny exhibited virtually indistinguishable genome properties and replication kinetics to the wild-type virus. Thus, a sequence-independent, efficient, and easy-to-apply mini-F vector transposition procedure eliminates the last hurdle to perform virtually any kind of imaginable targeted BAC modifications in E. coli. The herpesviral terminal genomic junction was identified as an optimal mini-F vector integration site for the construction of an infectious BAC, which allows the rapid generation of mutant virus without any unwanted secondary genome alterations. The novel mini-F transposition technique can be a valuable tool to optimize, repair or restructure other established BACs as well and may facilitate the development of gene therapy or vaccine vectors.

  8. Identification of an extensive gene cluster among a family of PPOs in Trifolium pratense L. (red clover using a large insert BAC library

    Directory of Open Access Journals (Sweden)

    Thomas Ann

    2009-07-01

    Full Text Available Abstract Background Polyphenol oxidase (PPO activity in plants is a trait with potential economic, agricultural and environmental impact. In relation to the food industry, PPO-induced browning causes unacceptable discolouration in fruit and vegetables: from an agriculture perspective, PPO can protect plants against pathogens and environmental stress, improve ruminant growth by increasing nitrogen absorption and decreasing nitrogen loss to the environment through the animal's urine. The high PPO legume, red clover, has a significant economic and environmental role in sustaining low-input organic and conventional farms. Molecular markers for a range of important agricultural traits are being developed for red clover and improved knowledge of PPO genes and their structure will facilitate molecular breeding. Results A bacterial artificial chromosome (BAC library comprising 26,016 BAC clones with an average 135 Kb insert size, was constructed from Trifolium pratense L. (red clover, a diploid legume with a haploid genome size of 440–637 Mb. Library coverage of 6–8 genome equivalents ensured good representation of genes: the library was screened for polyphenol oxidase (PPO genes. Two single copy PPO genes, PPO4 and PPO5, were identified to add to a family of three, previously reported, paralogous genes (PPO1–PPO3. Multiple PPO1 copies were identified and characterised revealing a subfamily comprising three variants PPO1/2, PPO1/4 and PPO1/5. Six PPO genes clustered within the genome: four separate BAC clones could be assembled onto a predicted 190–510 Kb single BAC contig. Conclusion A PPO gene family in red clover resides as a cluster of at least 6 genes. Three of these genes have high homology, suggesting a more recent evolutionary event. This PPO cluster covers a longer region of the genome than clusters detected in rice or previously reported in tomato. Full-length coding sequences from PPO4, PPO5, PPO1/5 and PPO1/4 will facilitate

  9. Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat

    Science.gov (United States)

    Cycles of whole genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied...

  10. BacPP: a web-based tool for Gram-negative bacterial promoter prediction.

    Science.gov (United States)

    de Avila E Silva, S; Notari, D L; Neis, F A; Ribeiro, H G; Echeverrigaray, S

    2016-01-01

    Bacterial Promoter Prediction (BacPP) is a tool used to predict given sequences as promoters of Gram-negative bacteria according to the σ factor that recognizes it. The first version of BacPP was implemented in Python language in a desktop version without a friendly interface. For this reason, a web version of BacPP is now available with the purpose of improving its usability and availability. The present paper describes the implementation of the web version of this tool, focusing on its software architecture and user functionalities. The software is available at www.bacpp.bioinfoucs.com/home. PMID:27173187

  11. BAC: A computer program for calculating shielding in buildings against initial radiation

    Science.gov (United States)

    Danielson, G.

    1980-10-01

    Calculation methodology and transmission data for BAC in the event of a nuclear explosion are considered. The shielding factor is the rate between the radiation dose at one point in the building and the dose in open air. It is separately calculated for neutrons, gamma rays from fission products, and secondary gamma rays. For this calculation, BAC uses data for radiation transmission in concrete. This program is utilized for fallout shelters and other buildings where walls and floors/roofs are mostly made of concrete and bricks. Instructions for the program are given, and BAC results and values are in certain cases compared with those obtained with the Monte Carlo method.

  12. Role of Bacillus subtilis BacB in the Synthesis of Bacilysin

    OpenAIRE

    Rajavel, Malligarjunan; Mitra, Ashima; Gopal, Balasubramanian

    2009-01-01

    Bacilysin is a non-ribosomally synthesized dipeptide antibiotic that is active against a wide range of bacteria and some fungi. Synthesis of bacilysin (L-alanine-[2,3-epoxycyclohexano-4]-L-alanine) is achieved by proteins in the bac operon, also referred to as the bacABCDE (ywfBCDEF) gene cluster in B. subtilis. Extensive genetic analysis from several strains of B. subtilis suggests that the bacABC gene cluster encodes all the proteins that synthesize the epoxyhexanone ring of L-anticapsin...

  13. Genetic Relationships Among Five Basic Genomes St, E, A, B and D in Triticeae Revealed by Genomic Southern and in situ Hybridization

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The St and E are two important basic genomes in the perennial tribe Triticeae (Poaceae). They exist in many perennial species and are very closely related to the A, B and D genomes of bread wheat (Triticum aestivum L.). Genomic Southern hybridization and genomic in situ hybridization (GISH) were used to analyze the genomic relationships between the two genomes (St and E) and the three basic genomes (A, B and D) of T. aestivum. The semi-quantitative analysis of the Southern hybridization suggested that both St and E genomes are most closely related to the D genome, then the A genome, and relatively distant to the B genome. GISH analysis using St and E genomic DNA as probes further confirmed the conclusion.St and E are the two basic genomes of Thinopyrum ponticum (StStEeEbEx) and Th. intermedium (StEeEb), two perennial species successfully used in wheat improvement. Therefore, this paper provides a possible answer as to why most of the spontaneous wheat- Thinopyrum translocations and substitutions usually happen in the D genome, some in the A genome and rarely in the B genome. This would develop further use of alien species for wheat improvement, especially those containing St or E in their genome components.

  14. Chicken genome mapping - Constructing part of a road map for mining this bird's DNA

    NARCIS (Netherlands)

    Aerts, J.

    2005-01-01

    The aim of the research presented in this thesis was to aid in the international chicken genome mapping effort. To this purpose, a significant contribution was made to the construction of the chicken whole-genome BAC-based physical map (presented in Chapter A). An important aspect of this constructi

  15. BAC-Dkk3-EGFP Transgenic Mouse: An In Vivo Analytical Tool for Dkk3 Expression

    Directory of Open Access Journals (Sweden)

    Yuki Muranishi

    2012-01-01

    Full Text Available Dickkopf (DKK family proteins are secreted modulators of the Wnt signaling pathway and are capable of regulating the development of many organs and tissues. We previously identified Dkk3 to be a molecule predominantly expressed in the mouse embryonic retina. However, which cell expresses Dkk3 in the developing and mature mouse retina remains to be elucidated. To examine the precise expression of the Dkk3 protein, we generated BAC-Dkk3-EGFP transgenic mice that express EGFP integrated into the Dkk3 gene in a BAC plasmid. Expression analysis using the BAC-Dkk3-EGFP transgenic mice revealed that Dkk3 is expressed in retinal progenitor cells (RPCs at embryonic stages and in Müller glial cells in the adult retina. Since Müller glial cells may play a potential role in retinal regeneration, BAC-Dkk3-EGFP mice could be useful for retinal regeneration studies.

  16. Proportional counters as monitoring detectors of BAC chambers at the ZEUS experiment

    International Nuclear Information System (INIS)

    The aim of the investigations presented is the elaboration of the system monitoring working conditions of BAC chambers. The backing calorimeter (BAC) at the ZEUS detector of the HERA accelerator consisting of 5000 proportional chambers of a total volume of 60 m3 is supplied with a gas mixture of Ar+10% CO2 by an open gas system. Flow proportional counters with a 55Fe source are used as gas system monitoring detectors. These counters and sources were designed and made exclusively for that application. The ageing effect of the Ar+CO2 mixture has also been studied. Monitoring measurements of the pulse height distribution enable us to follow the changes of gas pressure and composition in BAC proportional chambers. The results of these measurements will be used for off-line corrections of BAC data. (orig.)

  17. Development and Identification of Triticum aestivum L.-Thinopyrum bessarabicum L(o)ve Chromosome Translocations

    Institute of Scientific and Technical Information of China (English)

    ZHUANG Li-fang; QI Zeng-jun; CHEN Pei-du; FENG Yi-gao; LIU Da-jun

    2004-01-01

    With ass7istance of chromosome C-banding and genomic in situ hybridization(GISH)combined with meiotic analysis,five germplasms with homozygous wheat-Th. Bessarabicum chromosome translocations were developed and identified among BC1F5 progenies of the cross between T. Aestivum cv. Chinese Spring and Chinese Spring-Th. Bessarabicum amphiploid. These lines included Tj01 and Tj02(2n=44)containing a pair of wheat-Th. Bessarabicum translocation chromosomes besides a pair of added Th. Bessarabicum chromosomes,Tj03(2n=44)with a pair of added interspecific translocation chromosomes,Tj04(2n=44)containing a pair of interspecific translocation chromosomes besides an added pair of Th. Bessarabicum chromosome arms and Tj05(2n=46)containing a pair of interspecific translocation chromosomes besides two pairs of added intact alien chromosomes. The breakpoints of all the translocations were found to be not around centromere. Meanwhile,all the lines showed normal plant growth,development and fertility,while the translocation chromosomes transmitted regularly. The obtained translocations might be of use for transferring elite genes from Th. Bessarabicum into wheat.

  18. Comparative Analysis of Codon Usage Patterns Among Mitochondrion, Chloroplast and Nuclear Genes in Triticum aestivum L.

    Institute of Scientific and Technical Information of China (English)

    Wen-Juan Zhang; Jie Zhou; Zuo-Feng Li; Li Wang; Xun Gu; Yang Zhong

    2007-01-01

    In many organisms, the difference in codon usage patterns among genes reflects variation in local base compositional biases and the intensity of natural selection. In this study, a comparative analysis was performed to investigate the characteristics of codon bias and factors in shaping the codon usage patterns among mitochondrion,chloroplast and nuclear genes in common wheat (Triticum aestivum L.). GC contents in nuclear genes were higher than that in mitochondrion and chloroplast genes. The neutrality and correspondence analyses indicated that the codon usage in nuclear genes would be a result of relative strong mutational bias, while the codon usage patterns of rnitochondrion and chloroplast genes were more conserved in GC content and influenced by translation level.The Parity Rule 2 (PR2) plot analysis showed that pyrimidines were used more frequently than purines at the third codon position in the three genomes. In addition, using a new alterative strategy, 11, 12, and 24 triplets were defined as preferred codons in the mitochondrion, chloroplast and nuclear genes, respectively. These findings suggested that the mitochondrion, chloroplast and nuclear genes shared particularly different features of codon usage and evolutionary constraints.

  19. DNA shuttling between plasmid vectors and a genome vector: systematic conversion and preservation of DNA libraries using the Bacillus subtilis genome (BGM) vector.

    Science.gov (United States)

    Kaneko, Shinya; Akioka, Manami; Tsuge, Kenji; Itaya, Mitsuhiro

    2005-06-24

    The combined use of the contemporary vector systems, the bacterial artificial chromosome (BAC) vector and the Bacillus subtilis genome (BGM) vector, makes possible the handling of giant-length DNA (above 100 kb). Our newly constructed BGM vector efficiently integrated DNA prepared in the BAC vector. A BAC library comprised of 18 independent clones prepared from mitochondrial DNA (mtDNA) of Arabidopsis thaliana was converted to a parallel BGM library using the new BGM vector. The effectiveness of the combined use of the vector systems was confirmed by the stable recovery of all 18 DNAs as BAC clones from the respective BGM clones. We show that DNA in BGM was stably preserved at room temperature after spore formation of the host B.subtilis. Rapid and stable shuttling between Escherichiacoli and the B. subtilis host, combined with spore-mediated DNA storage, may facilitate the long-term and low-cost preservation and the transportation of DNA resources. PMID:15913652

  20. PiggyBac Transposon Mutagenesis: A Tool for Cancer Gene Discovery in Mice

    OpenAIRE

    Rad, Roland; Rad, Lena; Wang, Wei; Cadinanos, Juan; Vassiliou, George; Rice, Stephen; Campos, Lia S.; Yusa, Kosuke; Banerjee, Ruby; Li, Meng Amy; de la Rosa, Jorge; Strong, Alexander; Lu, Dong; Ellis, Peter; Conte, Nathalie

    2010-01-01

    Transposons are mobile DNA segments that can disrupt gene function by inserting in or near genes. Here we show that insertional mutagenesis by the PiggyBac transposon can be used for cancer gene discovery in mice. PiggyBac transposition in genetically engineered transposon/transposase mice induced cancers whose type (hematopoietic versus solid) and latency were dependent on the regulatory elements introduced into transposons. Analysis of 63 hematopoietic tumors revealed the unique qualities o...

  1. Recombineering strategies for developing next generation BAC transgenic tools for optogenetics and beyond

    OpenAIRE

    Ting, Jonathan T; Guoping Feng

    2014-01-01

    The development and application of diverse BAC transgenic rodent lines has enabled rapid progress for precise molecular targeting of genetically-defined cell types in the mammalian central nervous system. These transgenic tools have played a central role in the optogenetic revolution in neuroscience. Indeed, an overwhelming proportion of studies in this field have made use of BAC transgenic cre driver lines to achieve targeted expression of optogenetic probes in the brain. In addition, sev...

  2. Effect of mea on DNA degradation in permeable irradiated Bac. stearothermophilus cells

    International Nuclear Information System (INIS)

    It was shown that DNA-degrading activity of permeable, intact and γ-irradiated cells of Bac. stearothermophilus decreased under the effect of β-mercaptoethylamine (MEA). MEA decreased also a DNAase activity, in a crude acellular extract of Bac. stearothermophilus, and activities of S1-nuclease and DNAase. I. The data obtained prompt an assumption that MEA has an inhibitory action on the activity of endonucleases irrespective of their substrate specificity

  3. 23 CFR 1225.4 - Adoption of 0.08 BAC per se law.

    Science.gov (United States)

    2010-04-01

    ... 23 Highways 1 2010-04-01 2010-04-01 false Adoption of 0.08 BAC per se law. 1225.4 Section 1225.4... TRANSPORTATION GUIDELINES OPERATION OF MOTOR VEHICLES BY INTOXICATED PERSONS § 1225.4 Adoption of 0.08 BAC per se... is enforcing a law that provides that any person with a blood or breath alcohol concentration...

  4. Measurement Properties of the Low Back Activity Confidence Scale (LoBACS).

    Science.gov (United States)

    Davenport, Todd E; Cleland, Joshua A; Yamada, Kimiko A; Kulig, Kornelia

    2016-06-01

    The purpose of this study was to determine the measurement properties of the Low Back Activity Confidence Scale (LoBACS) in individuals with post-acute low back pain (LBP) receiving nonsurgical intervention, including construct validity, factorial validity, and internal consistency reliability. Data were analyzed from an existing randomized clinical trial involving 112 patients with LBP. Evidence for convergent validity was observed through significant correlations between LoBACS subscale scores and other function, pain, and psychobehavioral measures. LoBACS subscales accounted for 36% of the unique variance in dependent variable measurements, suggesting a satisfactory level of statistical divergence between the LoBACS and other psychobehavioral measurements in this study. Cronbach's α ranged from .88 to .92 for LoBACS subscales, and item-total correlations exceeded .6, indicating high internal consistency reliability. Principal axis factoring confirmed the hypothesized three-subscale structure by correctly classifying 14 of the 15 items. These findings indicate the LoBACS is valid and internally consistent to measure domain-specific self-efficacy beliefs. PMID:24686745

  5. Toward Elucidating the Structure of Tetraploid Cotton Genome

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Upland cotton has the highest yield,and accounts for >95% of world cotton production.Decoding upland cotton genomes will undoubtedly provide the ultimate reference and resource for structural,functional,and evolutionary studies of the species.Here,we employed GeneTrek and BAC

  6. Construction of infectious cDNA clone derived from a classical swine fever virus field isolate in BAC vector using in vitro overlap extension PCR and recombination.

    Science.gov (United States)

    Kamboj, Aman; Saini, Mohini; Rajan, Lekshmi S; Patel, Chhabi Lal; Chaturvedi, V K; Gupta, Praveen K

    2015-12-15

    To develop reverse genetics system of RNA viruses, cloning of full-length viral genome is required which is often challenging due to many steps involved. In this study, we report cloning of full-length cDNA from an Indian field isolate (CSFV/IVRI/VB-131) of classical swine fever virus (CSFV) using in vitro overlap extension PCR and recombination which drastically reduced the number of cloning steps. The genome of CSFV was amplified in six overlapping cDNA fragments, linked by overlap extension PCR and cloned in a bacterial artificial chromosome (BAC) vector using in vitro recombination method to generate full-length cDNA clone. The full-length CSFV cDNA clone was found stable in E. coli Stellar and DH10B cells. The full-length RNA was transcribed in vitro using T7 RNA polymerase and transfected in PK15 cells using Neon-tip electroporator to rescue infectious CSFV. The progeny CSFV was propagated in PK15 cells and found indistinguishable from the parent virus. The expression of CSFV proteins were detected in cytoplasm of PK15 cells infected with progeny CSFV at 72 h post-infection. We concluded that the in vitro overlap extension PCR and recombination method is useful to construct stable full-length cDNA clone of RNA virus in BAC vector. PMID:26478540

  7. Uncertainty of Blood Alcohol Concentration (BAC Results as Related to Instrumental Conditions: Optimization and Robustness of BAC Analysis Headspace Parameters

    Directory of Open Access Journals (Sweden)

    Haleigh A. Boswell

    2015-12-01

    Full Text Available Analysis of blood alcohol concentration is a routine analysis performed in many forensic laboratories. This analysis commonly utilizes static headspace sampling, followed by gas chromatography combined with flame ionization detection (GC-FID. Studies have shown several “optimal” methods for instrumental operating conditions, which are intended to yield accurate and precise data. Given that different instruments, sampling methods, application specific columns and parameters are often utilized, it is much less common to find information on the robustness of these reported conditions. A major problem can arise when these “optimal” conditions may not also be robust, thus producing data with higher than desired uncertainty or potentially inaccurate results. The goal of this research was to incorporate the principles of quality by design (QBD in the adjustment and determination of BAC (blood alcohol concentration instrumental headspace parameters, thereby ensuring that minor instrumental variations, which occur as a matter of normal work, do not appreciably affect the final results of this analysis. This study discusses both the QBD principles as well as the results of the experiments, which allow for determination of more favorable instrumental headspace conditions. Additionally, method detection limits will also be reported in order to determine a reporting threshold and the degree of uncertainty at the common threshold value of 0.08 g/dL. Furthermore, the comparison of two internal standards, n-propanol and t-butanol, will be investigated. The study showed that an altered parameter of 85 °C headspace oven temperature and 15 psi headspace vial pressurization produces the lowest percent relative standard deviation of 1.3% when t-butanol is implemented as an internal standard, at least for one very common platform. The study also showed that an altered parameter of 100 °C headspace oven temperature and 15-psi headspace vial pressurization

  8. Ataxin-2 regulates RGS8 translation in a new BAC-SCA2 transgenic mouse model.

    Directory of Open Access Journals (Sweden)

    Warunee Dansithong

    2015-04-01

    Full Text Available Spinocerebellar ataxia type 2 (SCA2 is an autosomal dominant disorder with progressive degeneration of cerebellar Purkinje cells (PCs and other neurons caused by expansion of a glutamine (Q tract in the ATXN2 protein. We generated BAC transgenic lines in which the full-length human ATXN2 gene was transcribed using its endogenous regulatory machinery. Mice with the ATXN2 BAC transgene with an expanded CAG repeat (BAC-Q72 developed a progressive cellular and motor phenotype, whereas BAC mice expressing wild-type human ATXN2 (BAC-Q22 were indistinguishable from control mice. Expression analysis of laser-capture microdissected (LCM fractions and regional expression confirmed that the BAC transgene was expressed in PCs and in other neuronal groups such as granule cells (GCs and neurons in deep cerebellar nuclei as well as in spinal cord. Transcriptome analysis by deep RNA-sequencing revealed that BAC-Q72 mice had progressive changes in steady-state levels of specific mRNAs including Rgs8, one of the earliest down-regulated transcripts in the Pcp2-ATXN2[Q127] mouse line. Consistent with LCM analysis, transcriptome changes analyzed by deep RNA-sequencing were not restricted to PCs, but were also seen in transcripts enriched in GCs such as Neurod1. BAC-Q72, but not BAC-Q22 mice had reduced Rgs8 mRNA levels and even more severely reduced steady-state protein levels. Using RNA immunoprecipitation we showed that ATXN2 interacted selectively with RGS8 mRNA. This interaction was impaired when ATXN2 harbored an expanded polyglutamine. Mutant ATXN2 also reduced RGS8 expression in an in vitro coupled translation assay when compared with equal expression of wild-type ATXN2-Q22. Reduced abundance of Rgs8 in Pcp2-ATXN2[Q127] and BAC-Q72 mice supports our observations of a hyper-excitable mGluR1-ITPR1 signaling axis in SCA2, as RGS proteins are linked to attenuating mGluR1 signaling.

  9. Determination of flavonoids in Triticum aestivum L. treated with ampicillin

    Science.gov (United States)

    Soran, M. L.; Opriş, O.; Copaciu, F.; Varodi, C.

    2012-02-01

    Pharmaceutical residues in the environment, and their potential toxic effects, have been recognized as one of the emerging research area in the environmental chemistry. Antibiotics can reach plants from treated soil or due to irrigation. The flavonoids extraction from Triticum aestivum L. treated with ampicillin and separation of flavonoids are presented in this study. There were used classical and modern extraction techniques (maceration, microwave assisted solvents, etc). The efficiency of extraction process was spectrophotometricaly evaluated by determining the total flavonoids content and by HPTLC on silica gel plates using the mixture: carbon tetrachloride - acetone - formic acid (35:11:3, v/v) as mobile phase. The developed plates were inspected both in ultraviolet and visible after visualization with NTS reagent (diphenylboryloxyethylamin). The chromatographic plates were compared in respect to determine the changes in extract composition due to the different extraction techniques. Depending on the concentration of ampicillin administered to plants, comparative studies on flavonoids content were performed.

  10. The piggyBac-Based Gene Delivery System Can Confer Successful Production of Cloned Porcine Blastocysts with Multigene Constructs.

    Science.gov (United States)

    Sato, Masahiro; Maeda, Kosuke; Koriyama, Miyu; Inada, Emi; Saitoh, Issei; Miura, Hiromi; Ohtsuka, Masato; Nakamura, Shingo; Sakurai, Takayuki; Watanabe, Satoshi; Miyoshi, Kazuchika

    2016-01-01

    The introduction of multigene constructs into single cells is important for improving the performance of domestic animals, as well as understanding basic biological processes. In particular, multigene constructs allow the engineering and integration of multiple genes related to xenotransplantation into the porcine genome. The piggyBac (PB) transposon system allows multiple genes to be stably integrated into target genomes through a single transfection event. However, to our knowledge, no attempt to introduce multiple genes into a porcine genome has been made using this system. In this study, we simultaneously introduced seven transposons into a single porcine embryonic fibroblast (PEF). PEFs were transfected with seven transposons containing genes for five drug resistance proteins and two (red and green) fluorescent proteins, together with a PB transposase expression vector, pTrans (experimental group). The above seven transposons (without pTrans) were transfected concomitantly (control group). Selection of these transfected cells in the presence of multiple selection drugs resulted in the survival of several clones derived from the experimental group, but not from the control. PCR analysis demonstrated that approximately 90% (12/13 tested) of the surviving clones possessed all of the introduced transposons. Splinkerette PCR demonstrated that the transposons were inserted through the TTAA target sites of PB. Somatic cell nuclear transfer (SCNT) using a PEF clone with multigene constructs demonstrated successful production of cloned blastocysts expressing both red and green fluorescence. These results indicate the feasibility of this PB-mediated method for simultaneous transfer of multigene constructs into the porcine cell genome, which is useful for production of cloned transgenic pigs expressing multiple transgenes. PMID:27589724

  11. 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 ...

  12. Genomic instability of human aberrant crypt foci measured by inter-(simple sequence repeat) PCR and array-CGH.

    Science.gov (United States)

    Alrawi, Sadir J; Carroll, Robert E; Hill, Hank C; Gibbs, John F; Tan, Dongfeng; Brenner, Bruce M; Nowak, Norma J; Swede, Helen; Stoler, Daniel L; Anderson, Garth R

    2006-10-10

    Aberrant crypt foci (ACF) are the earliest identifiable neoplastic lesions in the colon. Thirty-two ACFs were examined for genomic instability in forms detectable either by inter-(simple sequence repeat) PCR or by array comparative genomic hybridization [array-CGH]. One-fourth of ACFs revealed moderate instability by inter-(simple sequence repeat) PCR; none showed amplifications or deletions on array-CGH. The absence of genomic events detectible by BAC array-CGH indicates early events in colorectal tumor progression are typically smaller than the approximate 150 kb size of a BAC clone insert. PMID:16806294

  13. Substitution of the α-lactalbumin transcription unit by a CAT cDNA within a BAC clone silenced the locus in transgenic mice without affecting the physically linked Cyclin T1 gene

    Directory of Open Access Journals (Sweden)

    Jean-Luc Vilotte

    2003-03-01

    Full Text Available Abstract We recently reported that a goat bacterial artificial chromosome (BAC clone conferred site-independent expression in transgenic mice of the two loci present within its insert, the ubiquitously expressed Cyclin T1 and the mammary specific β-lactalbumin (αlac genes. To assess if this vector could target mammary-restricted expression of cDNA, the CAT ORF was introduced by homologous recombination in Escherichia coli in place of the αlac transcription unit. The insert of this modified BAC was injected into mice and three transgenic lines were derived. None of these lines expressed the CAT gene suggesting that the use of long genomic inserts is not sufficient to support the expression of intron-less transgenes. The physically linked goat Cyclin T1 locus was found to be active in all three lines. This observation reinforced the hypothesis that the two loci are localised in two separate chromatin domains.

  14. The Chimp Genome Reveals a Retroviral Invasion in Primate Evolution

    OpenAIRE

    Chris T Yohn; Zhaoshi Jiang; McGrath, Sean D.; Hayden, Karen E.; Philipp Khaitovich; Matthew E. Johnson; Eichler, Marla Y.; McPherson, John D.; Shaying Zhao; Svante Pääbo; Eichler, Evan E.

    2005-01-01

    Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been proposed, but little evidence exists for such events in the human/great ape lineage of evolution. Based on analysis of finished BAC chimpanzee genome sequence, we characterize a retroviral element (Pan troglodytes endogenous retrovirus 1 [PTERV1]) that has become integrated in the germline of Africa...

  15. Phytochemical analysis and estimation of major bioactive compounds from Triticum aestivum L. grass with antimicrobial potential.

    Science.gov (United States)

    Rajoria, Anand; Mehta, Archana; Mehta, Pradeep; Ahirwal, Laxmi; Shukla, Shruti

    2015-11-01

    The aim of the present study was to investigate phytochemical analysis, and qualitative and quantitative determination of major bioactive compound present in various organic extracts of T. aestivum L. grass. Soxhlet apparatus was used for the extraction purpose using hexane, chloroform, methanol and distilled water as a solvent system. All the extracts derived from T. aestivum showed qualitative presence of major phytochemicals including alkaloids, steroids and cardiac glycosides tannins, flavonoids carbohydrates. Further, HPLC analysis revealed the presence of major bioactive compounds such as rutin, chlorogenic acid, tocopherol, chlorogenic acid, and gallic acid in various organic extracts responsible for the reported maximum antimicrobial activity of T. aestivum grass against pathogenic bacteria including Salmonella typhi, Staphylococcus aureus and Vibrio cholerae. These findings confirm that T. aestivum grass containing medicinally important bioactive compounds may have significant potential to be used in traditional medicine system for the treatment of various diseases caused by pathogenic microorganisms. PMID:26687741

  16. Effect of fresh Triticum aestivum grass juice on lipid profile of normal rats

    Directory of Open Access Journals (Sweden)

    Kothari Saroj

    2008-01-01

    Full Text Available Objective: To study the hypolipidemic activity of fresh grass juice of Triticum aestivum in normal rats. Materials and Methods: Freshly prepared Triticum aestivum grass juice was administered to normal rats at the dose of 5 ml/kg and 10 ml/kg orally once daily for 21 days. Blood samples were collected after 24 hours of last administration and used for estimation of lipid profile. Fresh grass juice was also subjected to preliminary phytochemical screening. Results: Fresh grass juice administration produced dose related significant (P < 0.05 reduction in total chloesterol,triglycerides,low density lipoprotein-cholesterol and very low density lipoprotein-cholesterol levels in normal rats as compared to control.Preliminary phytochemical screening revealed presence of alkaloids,tannins, saponins and sterols in Triticum aestivum grass. Conclusion: The results of the present study lndicate hypolipidemic activity of fresh Triticum aestivum grass juice.

  17. BacM, an N-terminally processed bactofilin of Myxococcus xanthus, is crucial for proper cell shape

    OpenAIRE

    Koch, Matthias K.; McHugh, Colleen A; Hoiczyk, Egbert

    2011-01-01

    Bactofilins are fibre-forming bacterial cytoskeletal proteins. Here, we report the structural and biochemical characterization of MXAN_7475 (BacM), one of the four bactofilins of Myxococcus xanthus. Absence of BacM leads to a characteristic ‘crooked’ cell morphology and an increased sensitivity to antibiotics targeting cell wall biosynthesis. The absence of the other three bactofilins MXAN_4637–4635 (BacN-P) has no obvious phenotype. In M. xanthus, BacM exists as a 150-amino-acid full-length ...

  18. Stereochemical Outcome at Four Stereogenic Centers During Conversion of Prephenate to Tetrahydrotyrosine by BacABGF in the Bacilysin Pathway†

    OpenAIRE

    Parker, Jared B.; Walsh, Christopher T.

    2012-01-01

    The first four enzymes of the bacilysin antibiotic pathway, BacABGF, convert prephenate to a tetrahydrotyrosine (H4Tyr) diastereomer on the way to the anticapsin warhead of the dipeptide antibiotic. BacB takes the BacA product endocyclic-Δ4,Δ8-7R-dihydrohydroxyphenylpyruvate (en-H2HPP) and generates a mixture of 3E- and 3Z-olefins of the exocyclic-Δ3,Δ5-dihydrohydroxyphenylpyruvate (ex-H2HPP). The NADH-utilizing BacG then catalyzes a conjugate reduction, adding a pro-S hydride equivalent to C...

  19. Deficiency of a Sinorhizobium meliloti bacA Mutant in Alfalfa Symbiosis Correlates with Alteration of the Cell Envelope

    OpenAIRE

    Ferguson, Gail P.; Roop II, R. Martin; Walker, Graham C.

    2002-01-01

    The BacA protein is essential for the long-term survival of Sinorhizobium meliloti and Brucella abortus within acidic compartments in plant and animal cells, respectively. Since both the S. meliloti and B. abortus bacA mutants have an increased resistance to bleomycin, it was hypothesized that BacA was a transporter of bleomycin and bleomycin-like compounds into the bacterial cell. However, our finding that the S. meliloti bacA mutant also has an increased sensitivity to detergents, a hydroph...

  20. Computational analysis of ordering in non-liquid crystalline versus liquid crystalline materials with special reference to nBAC

    International Nuclear Information System (INIS)

    A computational analysis of ordering in non-liquid crystalline p-n-alkyl benzoic acid, having 1 (1BAC), 2 (2BAC) and 3(3BAC) carbon atoms in the alkyl chain has been carried out with respect to translatory and orientational motions, but detailed results are reported only for 3BAC. The evaluation of net atomic charges and dipole moments at each atomic center has been carried out using complete neglect differential overlap (CNDO/2) method. The modified Rayleigh-Schrodinger perturbation theory along with the multicentered-multipole expansion method has been employed to evaluate long-range interactions, while a '6-exp' potential function has been assumed for short-range interactions. On the basis of stacking, in-plane and terminal interaction energy calculations, all possible arrangements of a molecular pair have been considered. A comparative picture of molecular parameters, such as total energy, binding energy, and total dipole moment of 3BAC with higher homologous series liquid crystalline compounds having 4(4BAC), 5(5BAC), and 6(6BAC) alkyl chain carbon atoms, has been given. It is found that, if a suitable functional group is attached to 3BAC, so that the length to breadth ratio is increased, the molecule will show a change in the long-range order, the phase transition temperature and other liquid crystalline properties.

  1. Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing

    Directory of Open Access Journals (Sweden)

    Nelson Rex T

    2007-09-01

    Full Text Available Abstract Background Soybean, Glycine max (L. Merr., is a well documented paleopolyploid. What remains relatively under characterized is the level of sequence identity in retained homeologous regions of the genome. Recently, the Department of Energy Joint Genome Institute and United States Department of Agriculture jointly announced the sequencing of the soybean genome. One of the initial concerns is to what extent sequence identity in homeologous regions would have on whole genome shotgun sequence assembly. Results Seventeen BACs representing ~2.03 Mb were sequenced as representative potential homeologous regions from the soybean genome. Genetic mapping of each BAC shows that 11 of the 20 chromosomes are represented. Sequence comparisons between homeologous BACs shows that the soybean genome is a mosaic of retained paleopolyploid regions. Some regions appear to be highly conserved while other regions have diverged significantly. Large-scale "batch" reassembly of all 17 BACs combined showed that even the most homeologous BACs with upwards of 95% sequence identity resolve into their respective homeologous sequences. Potential assembly errors were generated by tandemly duplicated pentatricopeptide repeat containing genes and long simple sequence repeats. Analysis of a whole-genome shotgun assembly of 80,000 randomly chosen JGI-DOE sequence traces reveals some new soybean-specific repeat sequences. Conclusion This analysis investigated both the structure of the paleopolyploid soybean genome and the potential effects retained homeology will have on assembling the whole genome shotgun sequence. Based upon these results, homeologous regions similar to those characterized here will not cause major assembly issues.

  2. ANTICANCER AND CYTOTOXIC POTENTIAL OF TRITICUM AESTIVUM EXTRACT ON HELA CELL LINE

    OpenAIRE

    Patel Janki B.; Patel Piyush M.

    2013-01-01

    The objective of the study was to analyze the anticancer property of the leaves of Triticum aestivum on HeLa cells. The Indian medicinal plant Triticum aestivum that is used in traditional medicine for cancer and non cancerous diseases was collected. The crude methanolic extract was prepared by using standard protocols. The antiproliferative effect the methanolic extract was evaluated in vitro by employing MTT assay. The potency of each plant extract concentration was calculated in terms of p...

  3. Ectomycorrhizal communities in a productive Tuber aestivum Vittad. orchard: composition, host influence and species replacement

    OpenAIRE

    Benucci, Gian Maria Niccolò; Raggi, Lorenzo; Albertini, Emidio; Grebenc, Tine; Bencivenga, Mattia; Falcinelli, Mario; Di Massimo, Gabriella

    2011-01-01

    Truffles (Tuber spp.) and other ectomycorrhizal species form species-rich assemblages in the wild as well as in cultivated ecosystems. We aimed to investigate the ectomycorrhizal communities of hazels and hornbeams that are growing in a 24-year-old Tuber aestivum orchard. We demonstrated that the ectomycorrhizal communities included numerous species and were phylogenetically diverse. Twenty-nine ectomycorrhizal taxa were identified. Tuber aestivum ectomycorrhizae were abundant (9.3%), only th...

  4. Effect of fresh Triticum aestivum grass juice on lipid profile of normal rats

    OpenAIRE

    Kothari, Saroj; Jain, Anand K.; Mehta, Swaroop C.; Tonpay, Shrinivas D.

    2008-01-01

    Objective: To study the hypolipidemic activity of fresh grass juice of Triticum aestivum in normal rats. Materials and Methods: Freshly prepared Triticum aestivum grass juice was administered to normal rats at the dose of 5 ml/kg and 10 ml/kg orally once daily for 21 days. Blood samples were collected after 24 hours of last administration and used for estimation of lipid profile. Fresh grass juice was also subjected to preliminary phytochemical screening. Results: Fresh grass juice administra...

  5. Effect of fresh Triticum aestivum grass juice on lipid profile of normal rats

    OpenAIRE

    Kothari Saroj; Jain Anand; Mehta Swaroop; Tonpay Shrinivas

    2008-01-01

    Objective: To study the hypolipidemic activity of fresh grass juice of Triticum aestivum in normal rats. Materials and Methods: Freshly prepared Triticum aestivum grass juice was administered to normal rats at the dose of 5 ml/kg and 10 ml/kg orally once daily for 21 days. Blood samples were collected after 24 hours of last administration and used for estimation of lipid profile. Fresh grass juice was also subjected to preliminary phytochemical screening. Results: Fresh grass juice admi...

  6. Competition increases sensitivity of wheat (Triticum aestivum to biotic plant-soil feedback.

    Directory of Open Access Journals (Sweden)

    W H Gera Hol

    Full Text Available Plant-soil feedback (PSF and plant competition play an important role in structuring vegetation composition, but their interaction remains unclear. Recent studies suggest that competing plants could dilute pathogenic effects, whereas the standing view is that competition may increase the sensitivity of the focal plant to PSF. In agro-ecosystems each of these two options would yield contrasting outcomes: reduced versus enhanced effects of weeds on crop biomass production. To test the effect of competition on sensitivity to PSF, we grew Triticum aestivum (Common wheat with and without competition from a weed community composed of Vicia villosa, Chenopodium album and Myosotis arvensis. Plants were grown in sterilized soil, with or without living field inoculum from 4 farms in the UK. In the conditioning phase, field inocula had both positive and negative effects on T. aestivum shoot biomass, depending on farm. In the feedback phase the differences between shoot biomass in T. aestivum monoculture on non-inoculated and inoculated soils had mostly disappeared. However, T. aestivum plants growing in mixtures in the feedback phase were larger on non-inoculated soil than on inoculated soil. Hence, T. aestivum was more sensitive to competition when the field soil biota was present. This was supported by the statistically significant negative correlation between shoot biomass of weeds and T. aestivum, which was absent on sterilized soil. In conclusion, competition in cereal crop-weed systems appears to increase cereal crop sensitivity to soil biota.

  7. Competition increases sensitivity of wheat (Triticum aestivum) to biotic plant-soil feedback.

    Science.gov (United States)

    Hol, W H Gera; de Boer, Wietse; ten Hooven, Freddy; van der Putten, Wim H

    2013-01-01

    Plant-soil feedback (PSF) and plant competition play an important role in structuring vegetation composition, but their interaction remains unclear. Recent studies suggest that competing plants could dilute pathogenic effects, whereas the standing view is that competition may increase the sensitivity of the focal plant to PSF. In agro-ecosystems each of these two options would yield contrasting outcomes: reduced versus enhanced effects of weeds on crop biomass production. To test the effect of competition on sensitivity to PSF, we grew Triticum aestivum (Common wheat) with and without competition from a weed community composed of Vicia villosa, Chenopodium album and Myosotis arvensis. Plants were grown in sterilized soil, with or without living field inoculum from 4 farms in the UK. In the conditioning phase, field inocula had both positive and negative effects on T. aestivum shoot biomass, depending on farm. In the feedback phase the differences between shoot biomass in T. aestivum monoculture on non-inoculated and inoculated soils had mostly disappeared. However, T. aestivum plants growing in mixtures in the feedback phase were larger on non-inoculated soil than on inoculated soil. Hence, T. aestivum was more sensitive to competition when the field soil biota was present. This was supported by the statistically significant negative correlation between shoot biomass of weeds and T. aestivum, which was absent on sterilized soil. In conclusion, competition in cereal crop-weed systems appears to increase cereal crop sensitivity to soil biota. PMID:23776610

  8. Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome

    OpenAIRE

    Navdeep Gill; Matteo Buti; Nolan Kane; Arnaud Bellec; Nicolas Helmstetter; Hélène Berges; Rieseberg, Loren H.

    2014-01-01

    Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the g...

  9. Genic regions of a large salamander genome contain long introns and novel genes

    Directory of Open Access Journals (Sweden)

    Bryant Susan V

    2009-01-01

    Full Text Available Abstract Background The basis of genome size variation remains an outstanding question because DNA sequence data are lacking for organisms with large genomes. Sixteen BAC clones from the Mexican axolotl (Ambystoma mexicanum: c-value = 32 × 109 bp were isolated and sequenced to characterize the structure of genic regions. Results Annotation of genes within BACs showed that axolotl introns are on average 10× longer than orthologous vertebrate introns and they are predicted to contain more functional elements, including miRNAs and snoRNAs. Loci were discovered within BACs for two novel EST transcripts that are differentially expressed during spinal cord regeneration and skin metamorphosis. Unexpectedly, a third novel gene was also discovered while manually annotating BACs. Analysis of human-axolotl protein-coding sequences suggests there are 2% more lineage specific genes in the axolotl genome than the human genome, but the great majority (86% of genes between axolotl and human are predicted to be 1:1 orthologs. Considering that axolotl genes are on average 5× larger than human genes, the genic component of the salamander genome is estimated to be incredibly large, approximately 2.8 gigabases! Conclusion This study shows that a large salamander genome has a correspondingly large genic component, primarily because genes have incredibly long introns. These intronic sequences may harbor novel coding and non-coding sequences that regulate biological processes that are unique to salamanders.

  10. Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat

    Czech Academy of Sciences Publication Activity Database

    Šafář, Jan; Bartoš, Jan; Janda, Jaroslav; Bellec, A.; Kubaláková, Marie; Valárik, Miroslav; Pateyron, S.; Weiserová, Jitka; Tušková, Radka; Čihalíková, Jarmila; Vrána, Jan; Šimková, Hana; Faivre-Rampant, P.; Sourdille, P.; Caboche, M.; Bernard, M.; Doležel, Jaroslav; Chalhoub, B.

    2004-01-01

    Roč. 39, - (2004), s. 960-968. ISSN 0960-7412 R&D Projects: GA ČR GA522/03/0354; GA ČR GA521/04/0607; GA MZe QC1336 Institutional research plan: CEZ:AV0Z5038910 Keywords : wheat * flow sorting * DNA library Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.367, year: 2004

  11. A first generation BAC-based physical map of the Rainbow trout genome

    Science.gov (United States)

    BACKGROUND: Rainbow trout (Oncorhynchus mykiss) are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. Coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production effici...

  12. A first generation integrated map of the rainbow trout genome

    Directory of Open Access Journals (Sweden)

    Tabet-Canale Kamila

    2011-04-01

    Full Text Available Abstract Background Rainbow trout (Oncorhynchus mykiss are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. Coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. Many quantitative trait loci (QTL have been identified for production and life-history traits in rainbow trout. An integrated physical and genetic map is needed to facilitate fine mapping of QTL and the selection of positional candidate genes for incorporation in marker-assisted selection (MAS programs for improving rainbow trout aquaculture production. Results The first generation integrated map of the rainbow trout genome is composed of 238 BAC contigs anchored to chromosomes of the genetic map. It covers more than 10% of the genome across segments from all 29 chromosomes. Anchoring of 203 contigs to chromosomes of the National Center for Cool and Cold Water Aquaculture (NCCCWA genetic map was achieved through mapping of 288 genetic markers derived from BAC end sequences (BES, screening of the BAC library with previously mapped markers and matching of SNPs with BES reads. In addition, 35 contigs were anchored to linkage groups of the INRA (French National Institute of Agricultural Research genetic map through markers that were not informative for linkage analysis in the NCCCWA mapping panel. The ratio of physical to genetic linkage distances varied substantially among chromosomes and BAC contigs with an average of 3,033 Kb/cM. Conclusions The integrated map described here provides a framework for a robust composite genome map for rainbow trout. This resource is needed for genomic analyses in this research model and economically important species and will facilitate comparative genome mapping with other salmonids and with model fish species. This resource will also

  13. Impact of the D genome and quantitative trait loci on quantitative traits in a spring durum by spring bread wheat cross

    Science.gov (United States)

    Desirable agronomic traits are similar for common hexaploid (6X) bread wheat (Triticum aestivum, 2n = 6x = 42, genome, AABBDD) and tetraploid (4X) durum wheat (Triticum turgidum durum, 2n = 4x = 28, genome, AABB). However, they are genetically isolated from each other due to an unequal number of ge...

  14. In vitro Studies of Iron Chelation Activity of Purified Active Ingredients Extracted from Triticum aestivum Linn. (Wheat Grass)

    OpenAIRE

    Das Priyabrata; Mukhopadhyay Ashis; Mandal Suvra; Pal Bikas Chandra; Mishra Raghwendra; Mukherjee Debarati; Mukhopadhyay Soma; Basak Jayasri; Kar Manoj

    2012-01-01

    Objective: Seven to eight days germinated plants of Triticum aestivum (wheat grass) are a rich source of vitamin A, C, calcium, magnesium, phosphorus, potassium, sodium, sulphur, cobalt, zinc and protein. Traditionally the aqueous extract of T. aestivum was reported to be used as a health tonic in folk and ayurvedic medicine. We previously reported that aqueous extract of T. aestivum was found to reduce the blood transfusion requirement in iron overloaded Thalassemia and Myelod...

  15. Whole genome comparative analysis of channel catfish (Ictalurus punctatus) with four model fish species

    OpenAIRE

    Jiang, Yanliang; Gao, Xiaoyu; Liu, Shikai; Zhang, Yu; Liu, Hong; Sun, Fanyue; Bao, Lisui; Waldbieser, Geoff; Liu, Zhanjiang

    2013-01-01

    Background Comparative mapping is a powerful tool to study evolution of genomes. It allows transfer of genome information from the well-studied model species to non-model species. Catfish is an economically important aquaculture species in United States. A large amount of genome resources have been developed from catfish including genetic linkage maps, physical maps, BAC end sequences (BES), integrated linkage and physical maps using BES-derived markers, physical map contig-specific sequences...

  16. 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...

  17. Estimating Driver Risk Using Alcohol Biomarkers, Interlock BAC Tests and Psychometric Assessments: Initial Descriptives

    Science.gov (United States)

    Marques, Paul; Tippetts, Scott; Allen, John; Javors, Martin; Alling, Christer; Yegles, Michel; Pragst, Fritz; Wurst, Friedrich

    2009-01-01

    Aim To identify alcohol biomarker and psychometric measures that relate to drivers’ blood alcohol concentration (BAC) patterns from ignition interlock devices (IIDs). Design, Setting, Participants, Measurements In Alberta, Canada, 534 drivers, convicted of driving under the influence of alcohol (DUI), installed IIDs and agreed to participate in a research study. IID BAC tests are an established proxy for predicting future DUI convictions. Three risk groups were defined by rates of failed BAC tests. Program entry and followup blood samples (n=302, 171) were used to measure phosphatidyl ethanol (PETH), carbohydrate deficient transferrin (%CDT), gamma glutamyltransferase (GGT) and other biomarkers. Program entry urine (n=130) was analyzed for ethyl glucuronide (ETG) and ethyl sulfate (ETS). Entry hair samples were tested for fatty acid ethyl esters (FAEE) (n=92) and ETG (n=146). Psychometric measures included the DSM-4 Diagnostic Interview Schedule Alcohol Module, Alcohol Use Disorders Identification Test (AUDIT), the Timeline Followback (TLFB), the Drinker Inventory of Consequences (DRINC), and the Temptation and Restraint Inventory (TRI). Findings Except for FAEE, all alcohol biomarkers were significantly related to the interlock BAC test profiles; higher marker levels predicted higher rates of interlock BAC test failures. PETH, the strongest with an overall ANOVA F ratio of 35.5, had significant correlations with all nine of the other alcohol biomarkers and with 16 of 19 psychometric variables. Urine ETG and ETS were strongly correlated with the IID BAC tests. Conclusions The findings suggest several alcohol biomarkers and assessments could play an important role in the prediction and control of driver alcohol risk when relicensing. PMID:19922520

  18. An abbreviated version of the brief assessment of cognition in schizophrenia (BACS

    Directory of Open Access Journals (Sweden)

    MD Yasuhiro Kaneda

    2015-06-01

    Full Text Available Background and Objectives: A short version of the Brief Assessment of Cognition in Schizophrenia (BACS was derived. Methods: We calculated the corrected item-total correlation (CITC for each test score relative to the composite score, and then computed the proportion of variance that each test shares with the global score excluding that test (Rt² = CITCt² and the variance explained per minute of administration time for each test (Rt²/mint. Results and Conclusions: The 3 tests with the highest Rt²/mint, Symbol Coding, Digit Sequencing, and Token Motor, were selected for the Abbreviated BACS.

  19. 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

  20. BAC Libraries from Wheat Chromosome 7D: Efficient Tool for Positional Cloning of Aphid Resistance Genes

    Czech Academy of Sciences Publication Activity Database

    Šimková, Hana; Šafář, Jan; Kubaláková, Marie; Suchánková, Pavla; Čihalíková, Jarmila; Robert-Quatre, Heda; Azhaguvel, P.; Weng, Y. Q.; Peng, J.; Lapitan, N. L. V.; Ma, Y. Q.; You, F. M.; Luo, M. C.; Bartoš, Jan; Doležel, Jaroslav

    -, č. 302543 (2011), s. 1-11. ISSN 1110-7243 R&D Projects: GA ČR GA521/07/1573; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : TRITICUM-AESTIVUM L. * HEXAPLOID WHEAT * BREAD WHEAT Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.436, year: 2011

  1. Definition of the zebrafish genome using flow cytometry and cytogenetic mapping

    Directory of Open Access Journals (Sweden)

    Zhou Yi

    2007-06-01

    Full Text Available Abstract Background The zebrafish (Danio rerio is an important vertebrate model organism system for biomedical research. The syntenic conservation between the zebrafish and human genome allows one to investigate the function of human genes using the zebrafish model. To facilitate analysis of the zebrafish genome, genetic maps have been constructed and sequence annotation of a reference zebrafish genome is ongoing. However, the duplicative nature of teleost genomes, including the zebrafish, complicates accurate assembly and annotation of a representative genome sequence. Cytogenetic approaches provide "anchors" that can be integrated with accumulating genomic data. Results Here, we cytogenetically define the zebrafish genome by first estimating the size of each linkage group (LG chromosome using flow cytometry, followed by the cytogenetic mapping of 575 bacterial artificial chromosome (BAC clones onto metaphase chromosomes. Of the 575 BAC clones, 544 clones localized to apparently unique chromosomal locations. 93.8% of these clones were assigned to a specific LG chromosome location using fluorescence in situ hybridization (FISH and compared to the LG chromosome assignment reported in the zebrafish genome databases. Thirty-one BAC clones localized to multiple chromosomal locations in several different hybridization patterns. From these data, a refined second generation probe panel for each LG chromosome was also constructed. Conclusion The chromosomal mapping of the 575 large-insert DNA clones allows for these clones to be integrated into existing zebrafish mapping data. An accurately annotated zebrafish reference genome serves as a valuable resource for investigating the molecular basis of human diseases using zebrafish mutant models.

  2. Estimates of genetic variability in mutated population of triticum aestivum

    International Nuclear Information System (INIS)

    M2 populations of four cultivars of Mexican origin (Mexipak-65, Nayab, Pak-70 and 6134 x C-271) and two locally bred cultivars (H-68 and C-591) of bread wheat, triticum aestivum (2n = 6x = AA BB DD) derived from six irradiation treatments (gamma rays 60sub(Co); 10, 15 and 20 kR and fast neutrons; 300, 600 and 900 RADS) were critically examined for spike length, spikelets per spike, grains per spike and grain yield. Genotypes varied significantly (p>=0.01) for all the characters. Irradiation treatment were instrumental in creating significant variability for all the characters, indicating that varieties did not perform uniformly across different gamma rays as well as fast neutron treatments. In the M2 generation there was a considerable increase in variance for all the four metrical traits. Comparisons were made between controls and treated populations. Mutagenic treatments shifted the mean values mostly towards the negative direction, but the shift was not unidirectional nor equally effective for all the characters. The differences in mean values and the nature of variability observed in M2 indicated a possible preference of selection M3 generation. In general, estimates of genetic variability and heritability (b.s) increased with increasing doses of gamma rays and fast neutrons. Genetic advance also exhibited similar trend. The observed variability can be utilized in the evolution of new varieties. (authors)

  3. FISH applications for genomics and plant breeding strategies in tomato and other solanaceous crops.

    Science.gov (United States)

    Szinay, D; Bai, Y; Visser, R; de Jong, H

    2010-07-01

    This paper describes the use of advanced fluorescence in situ hybridization (FISH) technologies for genomics and breeding of tomato and related Solanum species. The first part deals with the major determinants of FISH technology: (1) spatial resolution, which depends on the diffraction limit of the microscope and the type of chromosome, chromatin or isolated DNA fibres as target for the hybridisation; (2) the detection sensitivity, which is limited by the sensitivity and dynamic range of the CCD camera and the quality of the microscope, and the amplification system of the weak signals from tiny probe molecules; (3) simultaneous detection of multiple probes labelled directly or indirectly with up to 5 different fluorophores, whether or not in different combinations and/or mixed at different ratios. The power and usability of such multicolour FISH is indispensable when large numbers of bacterial artificial chromosomes (BACs) or other vectors with genomic DNA are available. Mapping of multiple BACs on chromosomes are powerful instruments confirming their assumed genetic position, whereas pooled BACs for a given chromosome arm will reveal the gaps between the BACs or derived contigs of their physical maps. Tandem and dispersed repeats, which are abundant in the genomes of most species, can be analysed in repeat bar coding FISH, showing the major blocks of repeats in heterochromatin and euchromatin areas. Repeat-rich areas of the chromosomes can also be demonstrated by hybridisation of probed Cot fractions of sheared genomic DNA; a powerful method to elucidate the heterochromatin domains for genomic studies. In addition, unlabelled Cot DNA, as blocking agent in BAC-FISH painting, suppresses repetitive sequences from the BACs to hybridise on the chromosomes. Cross-species BAC-FISH painting with labelled probes from tomato and potato BACs and hybridised on the chromosomes of related species, under appropriate conditions, is a powerful instrument to demonstrate chromosomal

  4. piggyBac transposon plus insulators overcome epigenetic silencing to provide for stable signaling pathway reporter cell lines.

    Science.gov (United States)

    Mossine, Valeri V; Waters, James K; Hannink, Mark; Mawhinney, Thomas P

    2013-01-01

    Genetically modified hematopoietic progenitors represent an important testing platform for a variety of cell-based therapies, pharmaceuticals, diagnostics and other applications. Stable expression of a transfected gene of interest in the cells is often obstructed by its silencing. DNA transposons offer an attractive non-viral alternative of transgene integration into the host genome, but their broad applicability to leukocytes and other "transgene unfriendly" cells has not been fully demonstrated. Here we assess stability of piggyBac transposon-based reporter expression in murine prostate adenocarcinoma TRAMP-C2, human monocyte THP-1 and erythroleukemia K562 cell lines, along with macrophages and dendritic cells (DCs) that have differentiated from the THP-1 transfects. The most efficient and stable reporter activity was observed for combinations of the transposon inverted terminal repeats and one 5'- or two cHS4 core insulators flanking a green fluorescent protein reporter construct, with no detectable silencing over 10 months of continuous cell culture in absence of any selective pressure. In monocytic THP-1 cells, the functional activity of luciferase reporters for NF-κB, Nrf2, or HIF-1α has not decreased over time and was retained following differentiation into macrophages and DCs, as well. These results imply pB as a versatile tool for gene integration in monocytic cells in general, and as a convenient access route to DC-based signaling pathway reporters suitable for high-throughput assays, in particular. PMID:24376882

  5. Antidiabetic and Antioxidant Properties of Triticum aestivum in Streptozotocin-Induced Diabetic Rats.

    Science.gov (United States)

    Mohan, Yogesha; Jesuthankaraj, Grace Nirmala; Ramasamy Thangavelu, Narendhirakannan

    2013-01-01

    The antidiabetic and antioxidant potential of Triticum aestivum were evaluated by using in vivo methods in normal and streptozotocin-induced diabetic rats. Diabetes was induced in the Wistar strain albino rats by injecting streptozotocin at a dose of 55 mg/kg body weight. Ethanolic extracts of Triticum aestivum at doses of 100 mg/kg body weight were administered orally for 30 days. Various parameters were studied and the treatment group with the extract showed a significant increase in the liver glycogen and a significant decrease in fasting blood glucose, glycosylated hemoglobin levels, and serum marker enzyme levels. The total cholesterol and serum triglycerides levels, low density lipoprotein, and very low density lipoprotein were also significantly reduced and the high density lipoprotein level was significantly increased upon treatment with the Triticum aestivum ethanol extract. A significant decrease in the levels of lipid peroxides, superoxide dismutase, and glutathione peroxidise and increase in the levels of vitamin E, catalase, and reduced glutathione were observed in Triticum aestivum treated diabetic rats. Thus, from this study we conclude that ethanolic extract of Triticum aestivum exhibited significant antihyperglycemic, hypolipidemic, and antioxidant activities in streptozotocin-induced diabetic rats. PMID:24416041

  6. Antidiabetic and Antioxidant Properties of Triticum aestivum in Streptozotocin-Induced Diabetic Rats

    Directory of Open Access Journals (Sweden)

    Yogesha Mohan

    2013-01-01

    Full Text Available The antidiabetic and antioxidant potential of Triticum aestivum were evaluated by using in vivo methods in normal and streptozotocin-induced diabetic rats. Diabetes was induced in the Wistar strain albino rats by injecting streptozotocin at a dose of 55 mg/kg body weight. Ethanolic extracts of Triticum aestivum at doses of 100 mg/kg body weight were administered orally for 30 days. Various parameters were studied and the treatment group with the extract showed a significant increase in the liver glycogen and a significant decrease in fasting blood glucose, glycosylated hemoglobin levels, and serum marker enzyme levels. The total cholesterol and serum triglycerides levels, low density lipoprotein, and very low density lipoprotein were also significantly reduced and the high density lipoprotein level was significantly increased upon treatment with the Triticum aestivum ethanol extract. A significant decrease in the levels of lipid peroxides, superoxide dismutase, and glutathione peroxidise and increase in the levels of vitamin E, catalase, and reduced glutathione were observed in Triticum aestivum treated diabetic rats. Thus, from this study we conclude that ethanolic extract of Triticum aestivum exhibited significant antihyperglycemic, hypolipidemic, and antioxidant activities in streptozotocin-induced diabetic rats.

  7. Insect transformation with piggyBac: getting the number of injections just right.

    Science.gov (United States)

    Gregory, M; Alphey, L; Morrison, N I; Shimeld, S M

    2016-06-01

    The insertion of exogenous genetic cargo into insects using transposable elements is a powerful research tool with potential applications in meeting food security and public health challenges facing humanity. piggyBac is the transposable element most commonly utilized for insect germline transformation. The described efficiency of this process is variable in the published literature, and a comprehensive review of transformation efficiency in insects is lacking. This study compared and contrasted all available published data with a comprehensive data set provided by a biotechnology group specializing in insect transformation. Based on analysis of these data, with particular focus on the more complete observational data from the biotechnology group, we designed a decision tool to aid researchers' decision-making when using piggyBac to transform insects by microinjection. A combination of statistical techniques was used to define appropriate summary statistics of piggyBac transformation efficiency by species and insect order. Publication bias was assessed by comparing the data sets. The bias was assessed using strategies co-opted from the medical literature. The work culminated in building the Goldilocks decision tool, a Markov-Chain Monte-Carlo simulation operated via a graphical interface and providing guidance on best practice for those seeking to transform insects using piggyBac. PMID:27027400

  8. Genetic Transformation of the Codling Moth, Cydia pomonella L., with piggyBac EGFP

    Science.gov (United States)

    Genetic transformation of the codling moth, Cydia pomonella, was accomplished through embryo microinjection with a plasmid-based piggyBac vector containing the enhanced green fluorescent protein (EGFP) gene. Sequencing of the flanking regions around the inserted construct results in identification o...

  9. 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)

  10. Comparison of Transformation Efficiency of piggyBac Transposon among Three Different Silkworm Bombyx mori Strains

    Institute of Scientific and Technical Information of China (English)

    Boxiong ZHONG; Jianying LI; Jin'e CHEN; Jian YE; Songdong YU

    2007-01-01

    The transformation rate of three different strains of silkworm Bombyx mori was compared after the introduction of enhanced green fluorescence protein (EGFP)-encoding genes into the silkworm eggs by microinjection of a mixture of piggyBac vector and helper plasmid containing a transposase-encoding sequence. Although there were no significant differences among the three strains in the percentages of fertile moths in microinjected eggs (P=0.1258), the percentages of Go transformed moths in fertile moths and injected eggs were both significantly different (P=0.01368 and P=0.02398, respectively). The transformation rate of the Nistari strain (Indian strain) was significantly higher than that of the other two strains, Golden-yellow-cocoon (Vietnamese strain) and Jiaqiu (Chinese strain), which had similar rate. These results indicate that the transformation efficiency of the piggyBac-based system might vary with silkworm strains with different genetic backgrounds. The presence of endogenous piggyBac-like elements might be an important factor influencing the transformation efficiency of introduced piggyBac-derived vectors, and the diverse amount and activation in different silkworm strains might account for the significant differences.

  11. Measuring brain activity cycling (BAC) in long term EEG monitoring of preterm babies

    International Nuclear Information System (INIS)

    Measuring fluctuation of vigilance states in early preterm infants undergoing long term intensive care holds promise for monitoring their neurological well-being. There is currently, however, neither objective nor quantitative methods available for this purpose in a research or clinical environment. The aim of this proof-of-concept study was, therefore, to develop quantitative measures of the fluctuation in vigilance states or brain activity cycling (BAC) in early preterm infants. The proposed measures of BAC were summary statistics computed on a frequency domain representation of the proportional duration of spontaneous activity transients (SAT%) calculated from electroencephalograph (EEG) recordings. Eighteen combinations of three statistics and six frequency domain representations were compared to a visual interpretation of cycling in the SAT% signal. Three high performing measures (band energy/periodogram: R = 0.809, relative band energy/nonstationary frequency marginal: R = 0.711, g-statistic/nonstationary frequency marginal: R = 0.638) were then compared to a grading of sleep wake cycling based on the visual interpretation of the amplitude-integrated EEG trend. These measures of BAC are conceptually straightforward, correlate well with the visual scores of BAC and sleep wake cycling, are robust enough to cope with the technically compromised monitoring data available in intensive care units, and are recommended for further validation in prospective studies. (paper)

  12. Differential CT features of infectious pneumonia versus bronchioloalveolar carcinoma (BAC) mimicking pneumonia

    International Nuclear Information System (INIS)

    The purpose of this study was to evaluate retrospectively the differential CT features of bronchioloalveolar carcinoma (BAC) mimicking pneumonia and infectious pneumonia at the lung periphery. CT images were reviewed in 47 patients with focal areas of parenchymal opacification at the lung periphery. We evaluated the presence of ground-glass attenuation, marginal conspicuity of the lesion, CT angiogram sign, air-bronchogram sign, a bubble-like low-attenuation area within the lesion, presence of pleural thickening and retraction associated with the lesion, presence of pleural effusion and extra-pleural fatty hypertrophy, presence of bronchial wall thickening proximal to the lesion, and air-trapping in the normal lung near the lesion. BAC (n=18) depicted the presence of a bubble-like low-attenuation area within the lesion, whereas infectious pneumonia (n=29) represented the pleural thickening associated with the lesion and bronchial wall thickening proximal to the lesion (P0.05). The focal areas of the parenchymal opacification on the CT images may suggest infectious pneumonia rather than BAC when they show bronchial wall thickening proximal to the lesion and pleural thickening associated with the lesion, whereas BAC is characterized as the presence of a bubble-like low attenuation area within the tumor. (orig.)

  13. C9ORF72-ALS/FTD: Transgenic Mice Make a Come-BAC.

    Science.gov (United States)

    Hayes, Lindsey R; Rothstein, Jeffrey D

    2016-05-01

    For five years, since the landmark discovery of the C9ORF72 hexanucleotide repeat expansion in ALS/FTD, a transgenic mouse model has remained elusive. Now, two laboratories (Liu et al., 2016; Jiang et al., 2016) report the development of BAC transgenic mice that recapitulate features of the human disease. PMID:27151634

  14. BAC and Beer: Operationalizing Drunk Driving Laws in a Research Methods Course Exercise.

    Science.gov (United States)

    Taylor, Ralph B.; McConnell, Patrick

    2001-01-01

    Focuses on an exercise utilized in a research methods class and based on social problems that invites student interest. Explains the exercise has students determine their blood alcohol level (BAC) by asking them to estimate the number of beers it would take to have them just reach driving under the influence (DUI) status. (CMK)

  15. Anode wire ageing in proportional detectors at the BAC calorimeter of the ZEUS experiment

    International Nuclear Information System (INIS)

    Experimental results of ageing effects in proportional counters are presented. The measurements were carried out for 158 ZEUS-BAC gas system monitoring counters. Deterioration of the pulse height distribution in azimuth and along the anode wire are presented. The influence of water admixture on counting gas is also described. (orig.)

  16. Genomics of banana and plantain (Musa spp.), major staple crops in the tropics

    International Nuclear Information System (INIS)

    This chapter on Musa (banana and plantain) genomics covers the latest information on activities and resources developed by the Global Musa Genomics Consortium. Section 4.1 describes the morphology of the plant, its socio-economical importance and usefulness as an experimental organism. Section 4.2 describes the complexity of Musa taxonomy and the importance of genetic diversity Section 4.3 details the genetic maps which have recently been developed and those that are currently being developed. Section 4.4 presents the five BAC libraries which are now publicly available from the Musa Genome Resource Centre and can be distributed in various forms under a material transfer agreement. Section 4.5 gives an overview of cytogenetics and genome organization, showing that the genus Musa has a quite high proportion of repetitive DNA; the discovery of the first pararetrovirus integrated in the genome makes it unique. Section 4.6 explains the first attempts to sequence the genome by BAC end sequencing, whole BAC sequencing, and reduced representation sequencing. Section 4.7 validation using gene trapping, mutation induction and tilling techniques, as well as genetic transformation. Section 4.8 draws overall conclusions. This chapter demonstrated that by organizing the Global Musa Genomics Consortium (currently comprising 33 member institutions from 23 countries), duplication of effort can be minimized and the results of Musa genomics research are rapidly made accessible to taxonomists, breeders and the biotechnology community. (author)

  17. Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish

    Directory of Open Access Journals (Sweden)

    Mazzuchelli Juliana

    2012-09-01

    Full Text Available Abstract Background The availability of a large number of recently sequenced vertebrate genomes opens new avenues to integrate cytogenetics and genomics in comparative and evolutionary studies. Cytogenetic mapping can offer alternative means to identify conserved synteny shared by distinct genomes and also to define genome regions that are still not fine characterized even after wide-ranging nucleotide sequence efforts. An efficient way to perform comparative cytogenetic mapping is based on BAC clones mapping by fluorescence in situ hybridization. In this report, to address the knowledge gap on the genome evolution in cichlid fishes, BAC clones of an Oreochromis niloticus library covering the linkage groups (LG 1, 3, 5, and 7 were mapped onto the chromosomes of 9 African cichlid species. The cytogenetic mapping data were also integrated with BAC-end sequences information of O. niloticus and comparatively analyzed against the genome of other fish species and vertebrates. Results The location of BACs from LG1, 3, 5, and 7 revealed a strong chromosomal conservation among the analyzed cichlid species genomes, which evidenced a synteny of the markers of each LG. Comparative in silico analysis also identified large genomic blocks that were conserved in distantly related fish groups and also in other vertebrates. Conclusions Although it has been suggested that fishes contain plastic genomes with high rates of chromosomal rearrangements and probably low rates of synteny conservation, our results evidence that large syntenic chromosome segments have been maintained conserved during evolution, at least for the considered markers. Additionally, our current cytogenetic mapping efforts integrated with genomic approaches conduct to a new perspective to address important questions involving chromosome evolution in fishes.

  18. Membrane Topology and Biochemical Characterization of the Escherichia coli BacA Undecaprenyl-Pyrophosphate Phosphatase.

    Directory of Open Access Journals (Sweden)

    Guillaume Manat

    Full Text Available Several integral membrane proteins exhibiting undecaprenyl-pyrophosphate (C55-PP phosphatase activity were previously identified in Escherichia coli that belonged to two distinct protein families: the BacA protein, which accounts for 75% of the C55-PP phosphatase activity detected in E. coli cell membranes, and three members of the PAP2 phosphatidic acid phosphatase family, namely PgpB, YbjG and LpxT. This dephosphorylation step is required to provide the C55-P carrier lipid which plays a central role in the biosynthesis of various cell wall polymers. We here report detailed investigations of the biochemical properties and membrane topology of the BacA protein. Optimal activity conditions were determined and a narrow-range substrate specificity with a clear preference for C55-PP was observed for this enzyme. Alignments of BacA protein sequences revealed two particularly well-conserved regions and several invariant residues whose role in enzyme activity was questioned by using a site-directed mutagenesis approach and complementary in vitro and in vivo activity assays. Three essential residues Glu21, Ser27, and Arg174 were identified, allowing us to propose a catalytic mechanism for this enzyme. The membrane topology of the BacA protein determined here experimentally did not validate previous program-based predicted models. It comprises seven transmembrane segments and contains in particular two large periplasmic loops carrying the highly-conserved active site residues. Our data thus provide evidence that all the different E. coli C55-PP phosphatases identified to date (BacA and PAP2 catalyze the dephosphorylation of C55-PP molecules on the same (outer side of the plasma membrane.

  19. The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes

    Directory of Open Access Journals (Sweden)

    Anderson Olin D

    2008-07-01

    Full Text Available Abstract Background Wheat, barley, and rye, of tribe Triticeae in the Poaceae, are among the most important crops worldwide but they present many challenges to genomics-aided crop improvement. Brachypodium distachyon, a close relative of those cereals has recently emerged as a model for grass functional genomics. Sequencing of the nuclear and organelle genomes of Brachypodium is one of the first steps towards making this species available as a tool for researchers interested in cereals biology. Findings The chloroplast genome of Brachypodium distachyon was sequenced by a combinational approach using BAC end and shotgun sequences derived from a selected BAC containing the entire chloroplast genome. Comparative analysis indicated that the chloroplast genome is conserved in gene number and organization with respect to those of other cereals. However, several Brachypodium genes evolve at a faster rate than those in other grasses. Sequence analysis reveals that rice and wheat have a ~2.1 kb deletion in their plastid genomes and this deletion must have occurred independently in both species. Conclusion We demonstrate that BAC libraries can be used to sequence plastid, and likely other organellar, genomes. As expected, the Brachypodium chloroplast genome is very similar to those of other sequenced grasses. The phylogenetic analyses and the pattern of insertions and deletions in the chloroplast genome confirmed that Brachypodium is a close relative of the tribe Triticeae. Nevertheless, we show that some large indels can arise multiple times and may confound phylogenetic reconstruction.

  20. Dispersion and domestication shaped the genome of bread wheat

    Czech Academy of Sciences Publication Activity Database

    Berkman, P.J.; Visendi, P.; Lee, H.C.; Stiller, J.; Šimková, Hana; Kubaláková, Marie; Song, W.N.; Doležel, Jaroslav; Edwards, D.

    2013-01-01

    Roč. 11, č. 5 (2013), s. 564-571. ISSN 1467-7644 R&D Projects: GA ČR(CZ) GAP501/12/2554 Grant ostatní: GA MŠk(CZ) ED0007/01/01 Institutional research plan: CEZ:AV0Z50380511 Keywords : Triticum aestivum * genome sequencing * evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.677, year: 2013

  1. Swine Genome Sequencing Consortium (SGSC: A Strategic Roadmap for Sequencing The Pig Genome

    Directory of Open Access Journals (Sweden)

    Kellye Eversole

    2006-04-01

    Full Text Available The Swine Genome Sequencing Consortium (SGSC was formed in September 2003 by academic, government and industry representatives to provide international coordination for sequencing the pig genome. The SGSC’s mission is to advance biomedical research for animal production and health by the development of DNAbased tools and products resulting from the sequencing of the swine genome. During the past 2 years, the SGSC has met bi-annually to develop a strategic roadmap for creating the required scientific resources, to integrate existing physical maps, and to create a sequencing strategy that captured international participation and a broad funding base. During the past year, SGSC members have integrated their respective physical mapping data with the goal of creating a minimal tiling path (MTP that will be used as the sequencing template. During the recent Plant and Animal Genome meeting (January 16, 2005 San Diego, CA, presentations demonstrated that a human–pig comparative map has been completed, BAC fingerprint contigs (FPC for each of the autosomes and X chromosome have been constructed and that BAC end-sequencing has permitted, through BLAST analysis and RH-mapping, anchoring of the contigs. Thus, significant progress has been made towards the creation of a MTP. In addition, whole-genome (WG shotgun libraries have been constructed and are currently being sequenced in various laboratories around the globe. Thus, a hybrid sequencing approach in which 3x coverage of BACs comprising the MTP and 3x of the WG-shotgun libraries will be used to develop a draft 6x coverage of the pig genome.

  2. Role of Triticum aestivum aqueous extract in glucocorticoid induced osteoporosis in rats.

    Science.gov (United States)

    Banji, David; Banji, Otilia J F; Chiluka, Vijaya Laxmi; Abbagoni, Saidulu

    2014-02-01

    Administration of aqueous extract of T. aestivum (200 and 400 mg/kg/day, po, for 30 days) and risedronate (20 microg/kg, sc, five times a week for 30 days) following methyl prednisolone sodium succinate (10 mg/kg, sc, thrice a week for 4 weeks) induced osteoporosis in Wistar rats showed an increase in the serum levels of bone mineral content markers, decrease in the serum and urinary levels of bone resorption markers. An incline in strength of femur and tibia was seen particularly with 400 mg/kg of T. aestivum. Maintenance of calcium homeostasis, formation of collagen and scavenging of free radicals can plausibly be the mode of action of aqueous extract of T. aestivum thereby combating osteoporosis induced by glucocorticoids. PMID:24597148

  3. Genomics of banana and plantain (Musa spp.), major staple crops in the tropics

    Czech Academy of Sciences Publication Activity Database

    Roux, N.; Baurens, F.C.; Doležel, Jaroslav; Hřibová, Eva; Heslop-Harrison, P.; Town, C.; Sasaki, T.; Matsumoto, T.; Aert, R.; Remy, S.; Souza, M.; Lagoda, P.

    New York : Springer, 2008 - (Moore, P.; Ming, R.), s. 83-111 ISBN 978-0-387-71218-5 R&D Projects: GA AV ČR IAA600380703 Institutional research plan: CEZ:AV0Z50380511 Keywords : Banana and plantain * genomics * BAC libraries Subject RIV: EB - Genetics ; Molecular Biology

  4. Complete Genome Sequence of Border Disease Virus Genotype 3 Strain Gifhorn

    DEFF Research Database (Denmark)

    Fahnøe, Ulrik; Höper, Dirk; Beer, Martin; Rasmussen, Thomas Bruun

    2014-01-01

    The complete genome sequence of the genotype 3 border disease virus strain Gifhorn has been determined; this strain was originally isolated from pigs. This represents the consensus sequence for the virus used to produce the bacterial artificial chromosome (BAC) cDNA clone pBeloGif3, which yields a...

  5. 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

  6. Analysis of genomic regions of Trichoderma harzianum IOC-3844 related to biomass degradation.

    Directory of Open Access Journals (Sweden)

    Aline Crucello

    Full Text Available Trichoderma harzianum IOC-3844 secretes high levels of cellulolytic-active enzymes and is therefore a promising strain for use in biotechnological applications in second-generation bioethanol production. However, the T. harzianum biomass degradation mechanism has not been well explored at the genetic level. The present work investigates six genomic regions (~150 kbp each in this fungus that are enriched with genes related to biomass conversion. A BAC library consisting of 5,760 clones was constructed, with an average insert length of 90 kbp. The assembled BAC sequences revealed 232 predicted genes, 31.5% of which were related to catabolic pathways, including those involved in biomass degradation. An expression profile analysis based on RNA-Seq data demonstrated that putative regulatory elements, such as membrane transport proteins and transcription factors, are located in the same genomic regions as genes related to carbohydrate metabolism and exhibit similar expression profiles. Thus, we demonstrate a rapid and efficient tool that focuses on specific genomic regions by combining a BAC library with transcriptomic data. This is the first BAC-based structural genomic study of the cellulolytic fungus T. harzianum, and its findings provide new perspectives regarding the use of this species in biomass degradation processes.

  7. Production of galanthamine by Leucojum aestivum shoots grown in different bioreactor systems.

    Science.gov (United States)

    Schumann, Anika; Berkov, Strahil; Claus, Diana; Gerth, André; Bastida, Jaume; Codina, Carles

    2012-08-01

    The production of galanthamine by shoots of Leucojum aestivum grown in different bioreactor systems (shaking and nonshaking batch culture, temporary immersion system, bubble bioreactor, continuous and discontinuous gassing bioreactor) under different culture conditions was studied. The influence of the nutrient medium, weight of inoculum, and size of bioreactor on both growth and galanthamine production was studied. The maximal yield of galanthamine (19.416 mg) was achieved by cultivating the L. aestivum shoots (10 g of fresh inoculum) in a temporary immersion system in a 1-L bioreactor vessel which was used as an airlift culture vessel, gassing 12 times per day (5 min). PMID:22639366

  8. Antidiabetic and Antioxidant Properties of Triticum aestivum in Streptozotocin-Induced Diabetic Rats

    OpenAIRE

    Yogesha Mohan; Grace Nirmala Jesuthankaraj; Narendhirakannan Ramasamy Thangavelu

    2013-01-01

    The antidiabetic and antioxidant potential of Triticum aestivum were evaluated by using in vivo methods in normal and streptozotocin-induced diabetic rats. Diabetes was induced in the Wistar strain albino rats by injecting streptozotocin at a dose of 55 mg/kg body weight. Ethanolic extracts of Triticum aestivum at doses of 100 mg/kg body weight were administered orally for 30 days. Various parameters were studied and the treatment group with the extract showed a significant increase in the li...

  9. Characterization of Aegilops kotschyi Boiss. x Triticum aestivum L. hybrid lines

    OpenAIRE

    Roman Prażak; Edyta Paczos-Grzęda

    2014-01-01

    A study of four F5 and one BC1F1 Aegilops kotschyi Boiss. x Triticum aestivum L. hybrid lines was conducted to determine their quantitative morphological and qualitative features as well as a molecular investigation was carried out. Observations of ten quantitative traits showed that the F5 hybrid lines exhibited intermediate values between Ae. kotschyi Boiss. and T. aestivum L., or had similar traits to one of the parents. These hybrid lines had a significantly lower number and weight of gra...

  10. Introduction of temperature-sensitive helper and donor plasmids into Bac-to-Bac baculovirus expression systems

    Institute of Scientific and Technical Information of China (English)

    Zhihong; Huang; Ao; Li; Mengjia; Pan; Wenbi; Wu; Meijin; Yuan; Kai; Yang

    2015-01-01

    In the baculovirus shuttle vector(bacmid) system, a helper plasmid and a donor plasmid are employed to insert heterologous genes into a cloned baculovirus genome via Tn7 transposition in Escherichia coli. The helper and donor plasmids are usually cotransfected with constructed bacmids into insect cells, which will lead to integration of these plasmids into the viral genome,and hence to the production of defective virions. In this study, to facilitate the preparation of plasmid-free recombinant bacmids, we modified a set of helper and donor plasmids by replacing their replication origins with that of a temperature-sensitive(ts) plasmid, p SIM6. Using the resulting ts helper plasmid p MON7124 ts and the ts donor plasmid p FB1ts-PH-GFP, a recombinant bacmid,b Ac WT-PG(-), was constructed, and the transposition efficiency was found to be 33.1%. The plasmids were then removed by culturing at 37 °C. For b Ac WT-PG(-), the infectious progeny virus titer and the protein expression level under the control of the polyhedrin promoter were similar to those of a bacmid constructed with unmodified helper and donor plasmids. These ts plasmids will be useful for obtaining plasmid-free bacmids for both heterologous protein production and fundamental studies of baculovirus biology.

  11. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

    Czech Academy of Sciences Publication Activity Database

    Mayer, K. F. X.; Rogers, J.; Doležel, Jaroslav; Pozniak, C.; Feuillet, C.; Lukaszewski, A.J.; Sourdille, P.; Kubaláková, Marie; Čihalíková, Jarmila; Dubská, Zdeňka; Vrána, Jan; Šperková, Romana; Šimková, Hana; Choulet, F.; Stein, N.; Praud, S.

    2014-01-01

    Roč. 345, č. 6194 (2014). ISSN 0036-8075 R&D Projects: GA ČR GBP501/12/G090; GA ČR(CZ) GAP501/12/2554; GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : GENE-EXPRESSION * POLYPLOID WHEAT * AEGILOPS-TAUSCHII Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 33.611, year: 2014 http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=CCC&DestLinkType=FullRecord&UT=000339400700040

  12. Genetic transformation of Drosophila willistoni using piggyBac transposon and GFP

    Directory of Open Access Journals (Sweden)

    Manuela Finokiet

    2007-01-01

    Full Text Available Studies were carried out on the use of piggyBac transposable element as vector and the green fluorescent protein (EGFP from the jellyfish, Aquorea victoria, as a genetic marker for the transformation of Drosophila willistoni. Preblastoderm embryos of D. willistoni white mutant were microinjected with a plasmid containing the EGFP marker and the piggyBac ITRs, together with a helper plasmid containing the piggyBac transposase placed under the control of the D. melanogaster hsp70 promoter. G0 adults transformants were recovered at a frequency of approximately 67%. Expression of EGFP in larvae, pupae and adults was observed up to the third generation, suggesting that this transposon was not stable in D. willistoni. Transformed individuals displayed high levels of EGFP expression during larvae and adult stages in the eye, abdomen, thorax and legs, suggesting a wide expression pattern in this species than reported to other species of Drosophilidae.Descrevemos neste trabalho a transformação genética de Drosophila willistoni empregando o elemento transponível piggyBac como vetor e o gene EGFP (green fluorescent protein retirado da água-viva Aquorea victoria, como marcador de transformação. Embriões de D. willistoni em estágio pré-blastoderme, mutantes para o gene white, foram microinjetados com plasmídio contendo o marcador EGFP e as regiões ITRs do transposon piggyBac concomitantemente com um plasmídio auxiliar possuindo o gene da transposase de piggyBac sobre o controle do promotor do gene hsp70 de Drosophila melanogaster. Adultos transformantes Go foram gerados em uma taxa de 67%. A expressão de GFP em larvas, pupas e adultos foi observada somente até a terceira geração, sugerindo que este transposon não é estável em D. willistoni. Os indivíduos transformados exigem um alto nível de expressão de EGFP durante os estágios de larva e, também em adultos o gene marcador é expresso nos olhos, abdome, tórax e patas, mostrando um

  13. Evaluation of assembly strategies using RNA-seq data associated with grain development of wheat (Triticum aestivum L.).

    Science.gov (United States)

    Li, Huai-Zhu; Gao, Xiang; Li, Xiao-Yan; Chen, Qi-Jiao; Dong, Jian; Zhao, Wan-Chun

    2013-01-01

    Wheat (Triticum aestivum L.) is one of the most important crops cultivated worldwide. Identifying the complete transcriptome of wheat grain could serve as foundation for further study of wheat seed development. However, the relatively large size and the polyploid complexity of the genome have been substantial barriers to molecular genetics and transcriptome analysis of wheat. Alternatively, RNA sequencing has provided some useful information about wheat genes. However, because of the large number of short reads generated by RNA sequencing, factors that are crucial to transcriptome assembly, including software, candidate parameters and assembly strategies, need to be optimized and evaluated for wheat data. In the present study, four cDNA libraries associated with wheat grain development were constructed and sequenced. A total of 14.17 Gb of high-quality reads were obtained and used to assess different assembly strategies. The most successful approach was to filter the reads with Q30 prior to de novo assembly using Trinity, merge the assembled contigs with genes available in wheat cDNA reference data sets, and combine the resulting assembly with an assembly from a reference-based strategy. Using this approach, a relatively accurate and nearly complete transcriptome associated with wheat grain development was obtained, suggesting that this is an effective strategy for generation of a high-quality transcriptome from RNA sequencing data. PMID:24349528

  14. 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.

  15. Ultraviolet-B-induced DNA lesions and their removal in wheat (Triticum aestivum L.) leaves

    International Nuclear Information System (INIS)

    Monoclonal antibodies were used in an enzyme-linked immunosorbent assay (ELISA) to detect the induction and removal of cyclobutane pyrimidine dimers (CPDs) and (6-4) photoproducts in DNA isolated from ultraviolet B (UV-B)-exposed primary wheat (Triticum aestivum L. cv. Chinese Spring) leaf tissue. The accumulation of lesions in the primary leaves of 6-d-old wheat seedlings was followed during the exposure of the leaf to an approximate dose of 3.6×10−1 W m−2 UV-B (Caldwell weighting). Significant increases in the levels of both CPDs and (6-4) photoproducts were detected in wheat leaves exposed to UV-B in the absence of other light However, only an increase in (6-4) photoproduct levels could be measured in wheat leaves exposed to the same UV-B source in the presence of supplemental white light. The removal of CPD antibody binding sites in the DNA after irradiation was rapid under conditions of high light intensity in contrast to the removal of (6-4) photoproduct antibody binding sites, which was significantly slower. The removal of CPDs appeared to be light dependent, this rate of removal decreasing with decreasing light fluences. The removal of (6-4) photoproducts also appeared light dependent, but to a lesser extent than the removal of CPDs, under the conditions studied here. Gene expression in the primary wheat leaf was measured and showed an up-regulation of chalcone synthase expression and a reduction in expression of chlorophyll a/b-binding protein (cab) in response to supplementary UV-B. No effect was seen on the expression of the other photosynthetic genes studied (the genes coding for the enzymes sedoheptu-lose 1,7-bisphosphatase and fructose 1,6-bisphosphatase). Measurement of the levels of DNA lesions in this same tissue showed that the observed changes in gene expression accompanied the appearance of UV-B induced lesions in the form of (6-4) photoproducts in the wheat leaf genome. (author)

  16. 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...

  17. Genome engineering and gene drive in the mosquito aedes aegypti

    OpenAIRE

    St John, Oliver Tudor Lockhart; Sinkins, Steven; Alphey, Luke

    2012-01-01

    Genetic control strategies are a novel method for reducing populations of pest insects such as the yellow fever mosquito Aedes aegypti, a major vector of several important arboviral diseases. This thesis describes efforts to develop new tools to engineer the Ae. aegypti genome and to better understand existing tools, and furthermore to use these to engineer a gene drive system in Ae. aegypti. The piggyBac transposon was found to be extremely stable in the germline of Ae. aegypti, and transpos...

  18. Heat stress in wheat (Triticum aestivum L.) : Effects on grain growth and quality traits

    NARCIS (Netherlands)

    Spiertz, J.H.J.; Hamer, R.J.; Xu, H.; Primo Martin, C.; Don, C.; Putten, van der P.E.L.

    2006-01-01

    Heat stress effects on grain dry mass and quality were studied in spring wheat genotypes (Triticum aestivum L.). Three cultivars were chosen with respect to heat tolerance: Lavett (genotype 1), selected for temperate growing conditions and two CIMMYT cultivars, Ciano-79 (genotype 2) and Attila (geno

  19. Heat stress in wheat (Triticum aestivum L.): Effects on grain growth and quality traits

    NARCIS (Netherlands)

    Spiertz, J.H.J.; Hamer, R.J.; Xu, H.; Primo-Martin, C.; Don, C.; Putten, P.E.L. van der

    2006-01-01

    Heat stress effects on grain dry mass and quality were studied in spring wheat genotypes (Triticum aestivum L.). Three cultivars were chosen with respect to heat tolerance: Lavett (genotype 1), selected for temperate growing conditions and two CIMMYT cultivars, Ciano-79 (genotype 2) and Attila (geno

  20. Inheritance of grain polyphenol oxidase (PPO) activity in multiple wheat (Triticum aestivum L.) genetic backgrounds

    Science.gov (United States)

    Grain polyphenol oxidase (PPO) activity can cause discoloration of wheat (Triticum aestivum L.) food products. Five crosses (PI 117635/Antelope; Fielder/NW03681; Fielder/Antelope; NW07OR1070/Antelope; NW07OR1066/OR2050272H) were selected to study the genetic inheritance of PPO activity. STS marker...

  1. Nitrogen and Water Stress Impacts Hard Red Spring Wheat (Triticum aestivum) Canopy Reflectance

    Science.gov (United States)

    Remote sensing offers a simple, time efficient method for making in-season nitrogen (N) recommendations for spring wheat (Triticum aestivum). However, spectral crop reflectance can be confounded by water and N stress that simultaneously impact protein content and yields. The objective of this stu...

  2. In vitro effect of wheat bran (Triticum aestivum) extract on calcium oxalate urolithiasis crystallization.

    Science.gov (United States)

    Sekkoum, Khaled; Cheriti, Abdelkrim; Taleb, Safia

    2011-10-01

    Urolithiasis can lead to the loss of renal function in some cases. In this study, we tested the inhibiting effect of wheat bran (Triticum aestivum L) extract on calcium oxalate crystallization in a turbidimetric model, by FTIR spectroscopy, and polarized microscopy. The results show that this plant extract has a major inhibitory effect on calcium oxalate crystallization. PMID:22164778

  3. Metabolic Pathways of the Wheat (Triticum aestivum)Endosperm Amyloplast Revealed by Proteomics

    Science.gov (United States)

    By definition, amyloplasts are plastids specialized for starch production. However, amyloplasts have a broader range of functions that are not widely recognized. A recent proteomic study of amyloplasts isolated from wheat (Triticum aestivum Butte 86) endosperm suggested that they share many of the ...

  4. Triticum aestivum L., 1753, pšenice setá

    Czech Academy of Sciences Publication Activity Database

    Mahelka, Václav

    Praha : ČSOP, 2006 - (Mlíkovský, J.; Stýblo, P.), s. 191-193 ISBN 80-86770-17-6 Grant ostatní: GA MŽP(CZ) SM/6/37/04 Institutional research plan: CEZ:AV0Z60050516 Keywords : Triticum aestivum * distribution * invasibility Subject RIV: EF - Botanics

  5. Flow Sorting of Mitotic Chromosomes in Common Wheat (Triticum aestivum L.)

    Czech Academy of Sciences Publication Activity Database

    Vrána, Jan; Doleželová, Marie; Šimková, Hana; Čihalíková, Jarmila; Lysák, Martin; Doležel, Jaroslav

    2000-01-01

    Roč. 156, - (2000), s. 2033-2041. ISSN 0016-6731 R&D Projects: GA ČR GV521/96/K117; GA MŠk ME 376 Institutional research plan: CEZ:AV0Z5038910 Keywords : Mitotic Chromosomes * Triticum aestivum L. Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.687, year: 2000

  6. Allelopathic effect of Ashwagandha against the germination and radicle growth of Cicer arietinum and Triticum aestivum

    Directory of Open Access Journals (Sweden)

    Sangita Chandra

    2012-01-01

    Full Text Available Background: Ashwagandha (Withania somnifera is an important medicinal plant in Indian traditional system of medicine and traditionally has been used for several medicinal purposes in the Indian subcontinent. Objective: The present study was aimed at the evaluation of allelopathic effect of hydroalcoholic extract of ashwagandha against germination and radicle growth of Cicer arietinum and Triticum aestivum seeds. Materials and Methods: The extract at different concentrations was incubated in controlled conditions with the surface sterilized seeds of C. arietinum and T. aestivum and observed periodically for seed germination and radicle growth to assess the allelopathic behavior. Results: The extract mainly at higher concentrations demonstrated promising allelopathic potential by significantly affecting seed germination and radicle elongation of both C. arietinum and T. aestivum in a concentration dependent manner. T. aestivum was found to be more sensitive than C. arietinum. Conclusion: The present study demonstrated remarkable allelopathic potential of ashwagandha against the test seeds. The effect was plausibly due to the alkaloid and withanolide contents of ashwagandha.

  7. Toward a Molecular Cytogenetic Map for Cultivated Sunflower (Helianthus annuus L.) by Landed BAC/BIBAC Clones

    OpenAIRE

    Feng, Jiuhuan; Liu, Zhao; Cai, Xiwen; Jan, Chao-Chien

    2013-01-01

    Conventional karyotypes and various genetic linkage maps have been established in sunflower (Helianthus annuus L., 2n = 34). However, the relationship between linkage groups and individual chromosomes of sunflower remains unknown and has considerable relevance for the sunflower research community. Recently, a set of linkage group-specific bacterial /binary bacterial artificial chromosome (BAC/BIBAC) clones was identified from two complementary BAC and BIBAC libraries constructed for cultivate...

  8. GENSAT BAC Cre-recombinase driver lines to study the functional organization of cerebral cortical and basal ganglia circuits

    OpenAIRE

    Gerfen, Charles R.; Paletzki, Ronald; Heintz, Nathaniel

    2013-01-01

    Recent development of molecular genetic techniques are rapidly advancing understanding of the functional role of brain circuits in behavior. Critical to this approach is the ability to target specific neuron populations and circuits. The collection of over 250 BAC Cre-recombinase driver lines produced by the GENSAT project provides a resource for such studies. Here we provide characterization of GENSAT BAC-Cre driver lines with expression in specific neuroanatomical pathways within the cerebr...

  9. Neutralization of endotoxin in vitro and in vivo by Bac7(1-35), a proline-rich antibacterial peptide.

    Science.gov (United States)

    Ghiselli, Roberto; Giacometti, Andrea; Cirioni, Oscar; Circo, Raffaella; Mocchegiani, Federico; Skerlavaj, Barbara; D'Amato, Giuseppina; Scalise, Giorgio; Zanetti, Margherita; Saba, Vittorio

    2003-06-01

    Lipopolysaccharides (LPS), or endotoxins, are structural components of gram-negative bacteria implicated in the pathogenesis of septic shock. In this study the antiendotoxin activity of Bac7(1-35), a synthetic peptide based on the sequence of a proline-rich antibacterial peptide from bovine neutrophils, was investigated in vitro and in an experimental rat model of gram-negative septic shock. The ability of Bac7(1-35) to bind LPS from Escherichia coli O111:B4 was determined using a sensitive Limulus chromogenic assay. In the in vivo study, adult male Wistar rats were given an intraperitoneal injection of 1 x 10(9) colony-forming units of E. coli ATCC 25922. All animals were randomized to receive intraperitoneally 1 mg/kg Bac7(1-35), or isotonic sodium chloride solution (control group C1), 60 mg/kg of piperacillin and 1 mg/kg polymyxin B, 1 mg/kg of polymyxin B plus 60 mg/kg of piperacillin, and 1 mg/kg of Bac7(1-35) plus 60 mg/kg of piperacillin. Each group included 15 animals. Bac7(1-35) was found to completely inhibit the LPS procoagulant activity at approximately 10 microM peptide concentration, as determined by in vitro LAL chromogenic assay. Treatment with Bac7(1-35) resulted in significant decrease in plasma endotoxin levels and lethality rates compared with saline injected control animals. No statistically significant differences were noted between Bac7(1-35) and polymyxin B in reducing all variables measured. These results provide evidence for the ability of Bac7(1-35) to effectively bind LPS and protect animals from lethal effects of this molecule, and point to its potential use for the treatment of endotoxin-induced septic shock. PMID:12785015

  10. Essential Role for the BacA Protein in the Uptake of a Truncated Eukaryotic Peptide in Sinorhizobium meliloti▿

    OpenAIRE

    Marlow, Victoria L.; Haag, Andreas F.; Kobayashi, Hajime; Fletcher, Vivien; Scocchi, Marco; Walker, Graham C.; Ferguson, Gail P.

    2008-01-01

    The inner membrane BacA protein is essential for the establishment of chronic intracellular infections by Sinorhizobium meliloti and Brucella abortus within plant and mammalian hosts, respectively. In their free-living state, S. meliloti and B. abortus mutants lacking BacA have reductions in their outer membrane lipid A very-long-chain fatty acid (VLCFA) contents and exhibit low-level resistance to the glycopeptide bleomycin in comparison to their respective parent strains. In this paper we i...

  11. A PiggyBac-mediated approach for muscle gene transfer or cell therapy

    OpenAIRE

    Déborah Ley; Ruthger Van Zwieten; Stefania Puttini; Pavithra Iyer; Alessia Cochard; Nicolas Mermod

    2014-01-01

    An emerging therapeutic approach for Duchenne muscular dystrophy is the transplantation of autologous myogenic progenitor cells genetically modified to express dystrophin. The use of this approach is challenged by the difficulty in maintaining these cells ex vivo while keeping their myogenic potential, and ensuring sufficient transgene expression following their transplantation and myogenic differentiation in vivo. We investigated the use of the piggyBac transposon system to achieve stable ge...

  12. Endoderm lineage labelling using BAC reporter constructs in ES cells and mouse embryos

    OpenAIRE

    Imhof, Sascha

    2009-01-01

    The endoderm is one of the three embryonic germ layers that gives rise to inner organs like lung, liver and pancreas. BAC recombineering was used to generate transgenic embryonic stem cells and mouse lines containing fluorescent reporters under the control of important endodermal genes like Foxa2, Sox17, Hhex, Nkx2.1 and Pdx1. This allowed the analysis of the specific expression patterns of those genes during endoderm and organ formation. In particular, the analysis of the Hhex reporter expre...

  13. Technology at Washington University School of Medicine Library: BACS, PHILSOM, and OCTANET.

    OpenAIRE

    Crawford, S; Johnson, M.F.; Kelly, E A

    1983-01-01

    A brief overview of the Bibliographic Access and Control System developed by the Washington University School of Medicine Library is presented. Because the system has been described in two previous reports, this paper focuses on its relationship to other automated programs (i.e., PHILSOM and OCTANET), education of users, evaluation of the system, and outreach to the medical center. In operation for more than two years, BACS represents the computerization of much of the managerial and operatio...

  14. A BAC-based transgenic mouse specifically expresses an inducible Cre in the urothelium.

    Directory of Open Access Journals (Sweden)

    Tian Huai Shen

    Full Text Available Cre-loxp mediated conditional knockout strategy has played critical roles for revealing functions of many genes essential for development, as well as the causal relationships between gene mutations and diseases in the postnatal adult mice. One key factor of this strategy is the availability of mice with tissue- or cell type-specific Cre expression. However, the success of the traditional molecular cloning approach to generate mice with tissue specific Cre expression often depends on luck. Here we provide a better alternative by using bacterial artificial chromosome (BAC-based recombineering to insert iCreERT2 cDNA at the ATG start of the Upk2 gene. The BAC-based transgenic mice express the inducible Cre specifically in the urothelium as demonstrated by mRNA expression and staining for LacZ expression after crossing with a Rosa26 reporter mouse. Taking into consideration the size of the gene of interest and neighboring genes included in a BAC, this method should be widely applicable for generation of mice with tissue specific gene expression or deletions in a more specific manner than previously reported.

  15. Controlling of crustacean zooplankton reproduction in biological activated carbon (BAC) filters by strengthen operation and management of conventional process

    Institute of Scientific and Technical Information of China (English)

    LIU Li-jun; ZHANG Jin-song; LI Xiao-wei; HE Jun-guo

    2010-01-01

    To counter the mass reproduction and penetration of crustacean zooplankton in Biological Activated Carbon (BAC) filters which may result in the presence of organisms in potable water and water pollution,this paper analyzed the factors affecting organisms' reproduction in BAC filters.A comparative study was performed on the density and composition of crustacean zooplankton of the concerned water treatment units of two advanced water plants (Plant A and B) which with the same raw water and the same treatment technique in southern China.The results obtained show that the crustaceans' density and composition was very different between the sand filtered water of Plant A and Plant B.which Harpacticoida bred sharply in the sediment tanks and penetrated sand filter into BAC falters was the primary reason of crustaceans reproduce in BAC filters of Plant A.For prevention of the organisms reproduction in BAC,some strengthen measures was taken including pre-chlorination,cleaning coagulation tanks and sediment tanks completely,increasing sludge disposal frequency to stop organisms enter BAC filters,and the finished water quality was improved and enhanced.

  16. Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

    Directory of Open Access Journals (Sweden)

    Phillips Ruth B

    2010-10-01

    Full Text Available Abstract Background The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent model organisms for studying comparative genomics, evolutionary processes, fates of duplicated genes and the genetic and physiological processes associated with complex behavioral phenotypes. The evolution of the tetrapod hemoglobin genes is well studied; however, little is known about the genomic organization and evolution of teleost hemoglobin genes, particularly those of salmonids. The Atlantic salmon serves as a representative salmonid species for genomics studies. Given the well documented role of hemoglobin in adaptation to varied environmental conditions as well as its use as a model protein for evolutionary analyses, an understanding of the genomic structure and organization of the Atlantic salmon α and β hemoglobin genes is of great interest. Results We identified four bacterial artificial chromosomes (BACs comprising two hemoglobin gene clusters spanning the entire α and β hemoglobin gene repertoire of the Atlantic salmon genome. Their chromosomal locations were established using fluorescence in situ hybridization (FISH analysis and linkage mapping, demonstrating that the two clusters are located on separate chromosomes. The BACs were sequenced and assembled into scaffolds, which were annotated for putatively functional and pseudogenized hemoglobin-like genes. This revealed that the tail-to-tail organization and alternating pattern of the α and β hemoglobin genes are well conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobin genes, including non-Bohr β globin genes, than the genomes of other teleosts that have been sequenced. Conclusions We suggest that the most parsimonious evolutionary path leading to the present organization of the Atlantic salmon

  17. Dynamics of rhizosphere properties and antioxidative responses in wheat (Triticum aestivum L.) under cadmium stress.

    Science.gov (United States)

    Li, Yonghua; Wang, Li; Yang, Linsheng; Li, Hairong

    2014-04-01

    In this study, we performed a rhizobox experiment to examine the dynamic changes in the rhizosphere properties and antioxidant enzyme responses of Triticum aestivum L. under three levels of cadmium stress. A set of micro-techniques (i.e., Rhizobox and Rhizon SMS) were applied for the dynamically non-destructive collection of the rhizosphere soil solution to enable the observation at a high temporal resolution. The dynamics of soluble cadmium and dissolved organic carbon (DOC) in the rhizosphere soil solutions of the Triticum aestivum L. were characterised by the sequence week 0 after sowing (WAS0)soil solution pH was found to follow an opposite distribution pattern. Systematically, both superoxide dismutase (SOD) and catalase (CAT) activities in the leaves of the Triticum aestivum L. increased concomitantly with increasing cadmium levels (p>0.05) and growth duration (pstress with a decrease at high cadmium stress (p>0.05). These results suggested the enhancement of DOC production and the greater antioxidant enzyme activities were two important protective mechanisms of Triticum aestivum L. under cadmium stress, whereas rhizosphere acidification might be an important mechanism for the mobilisation of soil cadmium. The results also revealed that plant-soil interactions strongly influence the soil solution chemistry in the rhizosphere of Triticum aestivum L., that, in turn, can stimulate chemical and biochemical responses in the plants. In most cases, these responses to cadmium stress were sensitive and might allow us to develop strategies for reducing the risks of the cadmium contamination to crop production. PMID:24580822

  18. SSR-based identification of genetic groups within European populations of Tuber aestivum Vittad.

    Science.gov (United States)

    Molinier, Virginie; Murat, Claude; Peter, Martina; Gollotte, Armelle; De la Varga, Herminia; Meier, Barbara; Egli, Simon; Belfiori, Beatrice; Paolocci, Francesco; Wipf, Daniel

    2016-02-01

    Tuber species are ectomycorrhizal ascomycetes establishing relationships with different host trees and forming hypogeous fruiting bodies known as truffles. Among Tuber species, Tuber aestivum Vittad. has a wide distributional range being found naturally all over Europe. Here, we performed large-scale population genetic analyses in T. aestivum to (i) investigate its genetic diversity at the European scale, (ii) characterize its genetic structure and test for the presence of ecotypes and (iii) shed light into its demographic history. To reach these goals, 230 ascocarps from different populations were genotyped using 15 polymorphic simple sequence repeat markers. We identified 181 multilocus genotypes and four genetic groups which did not show a clear geographical separation; although, one of them was present exclusively in Southeast France, Italy and Spain. Fixation index values between pairs of genetic groups were generally high and ranged from 0.29 to 0.45. A significant deficit of heterozygosity indicated a population expansion instead of a recent population bottleneck, suggesting that T. aestivum is not endangered in Europe, not even in Mediterranean regions. Our study based on a large-scale population genetic analysis suggests that genetically distinct populations and likely ecotypes within T. aestivum are present. In turn, this study paves the way to future investigations aimed at addressing the biological and/or ecological factors that have concurred in shaping the population genetic structure of this species. Present results should also have implications for the truffle market since defining genetic markers are now possible at least for some specific T. aestivum genetic groups. PMID:26070448

  19. Construction and characterization of new piggyBac vectors for constitutive or inducible expression of heterologous gene pairs and the identification of a previously unrecognized activator sequence in piggyBac

    Directory of Open Access Journals (Sweden)

    Hollister Jason R

    2007-01-01

    Full Text Available Abstract Background We constructed and characterized several new piggyBac vectors to provide transposition of constitutively- or inducibly-expressible heterologous gene pairs. The dual constitutive control element consists of back-to-back copies of a baculovirus immediate early (ie1 promoter separated by a baculovirus enhancer (hr5. The dual inducible control element consists of back-to-back copies of a minimal cytomegalovirus (CMVmin promoter separated by a synthetic operator (TetO7, which drives transcription in the presence of a mutant transcriptional repressor plus tetracycline. Results Characterization of these vectors revealed an unexpected position effect, in which heterologous genes adjacent to the 3'- terminal region ("rightward" genes were consistently expressed at higher levels than those adjacent to the 5'-terminal region ("leftward" genes of the piggyBac element. This position effect was observed with all six heterologous genes examined and with both transcriptional control elements. Further analysis demonstrated that this position effect resulted from stimulation of rightward gene expression by the internal domain sequence of the 3'-terminal region of piggyBac. Inserting a copy of this sequence into the 5'- terminal repeat region of our new piggyBac vectors in either orientation stimulated leftward gene expression. Representative piggyBac vectors designed for constitutive or inducible expression of heterologous gene pairs were shown to be functional as insect transformation vectors. Conclusion This study is significant because (a it demonstrates the utility of a strategy for the construction of piggyBac vectors that can provide constitutive or inducible heterologous gene pair expression and (b it reveals the presence of a previously unrecognized transcriptional activator in piggyBac, which is an important and increasingly utilized transposable element.

  20. The Varicella-Zoster Virus Genome

    OpenAIRE

    Cohen, Jeffrey I.

    2010-01-01

    The varicella-zoster virus (VZV) genome contains at least 70 genes, and all but 6 have homologs in herpes simplex virus. Cosmids and BACs corresponding to the VZV parental Oka and vaccine Oka viruses have been used to “knock-out” 34 VZV genes. Seven VZV genes (ORF4, 5, 9, 21, 29, 62, and 68) have been shown to be required for growth in vitro. Recombinant viruses expressing several markers (e.g. beta-galactosidase, green fluorescence protein, luciferase) and several foreign viral genes (from h...

  1. Endosperm Tolerance of Paternal Aneuploidy Allows Radiation Hybrid Mapping of the Wheat D-Genome and a Measure of γ Ray-Induced Chromosome Breaks

    OpenAIRE

    Tiwari, Vijay K; Oscar Riera-Lizarazu; Hilary L Gunn; Kasandra Lopez; M Javed Iqbal; Kianian, Shahryar F; Leonard, Jeffrey M.

    2012-01-01

    Physical mapping and genome sequencing are underway for the ≈17 Gb wheat genome. Physical mapping methods independent of meiotic recombination, such as radiation hybrid (RH) mapping, will aid precise anchoring of BAC contigs in the large regions of suppressed recombination in Triticeae genomes. Reports of endosperm development following pollination with irradiated pollen at dosages that cause embryo abortion prompted us to investigate endosperm as a potential source of RH mapping germplasm. H...

  2. EFFECTS OF SIMULATED ACIDIC RAIN ON YIELDS OF 'RAPHANUS SATIVUS', 'LACTUCA SATIVA', 'TRITICUM AESTIVUM' AND 'MEDICAGO SATIVA'

    Science.gov (United States)

    Experiments were performed to determine effects of simulated acidic rain on radishes (Raphanus sativus), wheat(Triticum aestivum) and alfalfa (Medicago sativa) grown under greenhouse conditions. Experimental designs allowed the detection of statistically significant differences a...

  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. 23 CFR Appendix A to Part 1225 - Effects of the 0.08 BAC Sanction Program on Non-Complying States

    Science.gov (United States)

    2010-04-01

    ... 23 Highways 1 2010-04-01 2010-04-01 false Effects of the 0.08 BAC Sanction Program on Non... INTOXICATED PERSONS Pt. 1225, App. A Appendix A to Part 1225—Effects of the 0.08 BAC Sanction Program on Non-Complying States Effects of the 0.08 BAC Sanction Program on Non-Complying States Fiscalyear Withhold...

  5. Relevance of BAC transgene copy number in mice: transgene copy number variation across multiple transgenic lines and correlations with transgene integrity and expression

    OpenAIRE

    Chandler, Kelly J.; Chandler, Ronald L.; Broeckelmann, Eva M.; HOU, YUE; Southard-Smith, E. Michelle; Mortlock, Douglas P.

    2007-01-01

    Bacterial artificial chromosomes (BACs) are excellent tools for manipulating large DNA fragments and, as a result, are increasingly utilized to engineer transgenic mice by pronuclear injection. The demand for BAC transgenic mice underscores the need for careful inspection of BAC integrity and fidelity following transgenesis, which may be crucial for interpreting transgene function. Thus, it is imperative that reliable methods for assessing these parameters are available. However, there are li...

  6. Heavy metal uptake, translocation, and bioaccumulation studies of Triticum aestivum cultivated in contaminated dredged materials.

    Science.gov (United States)

    Shumaker, Ketia L; Begonia, Gregorio

    2005-08-01

    Phytoremediation is a technology that uses vegetation to remediate contaminants from water, soil, and sediments. Unlike traditional remediation techniques such as soil washing or vitrification, phytoremediation offers a technology that is solar-driven, aesthetically pleasing, and cost effective. Recent studies indicate that winter wheat (Triticum aestivum L.) is a potential accumulator for heavy metals such as lead (Pb) and cadmium (Cd) in hydroponic systems. Based on these findings, a laboratory study was conducted with the primary objective of determining the phytoaccumulation capability of this plant species for heavy metals from contaminated dredged materials (DMs) originating from two confined disposal facilities (CDF). The United States Army Corps of Engineers (USACE) manages several hundred million cubic meters of DMs each year, and 5 to 10 % of these DMs require special handling because they are contaminated with hazardous substances that can move from the substrates into food webs causing unacceptable risk outside CDFs. Phytoremediation may offer an alternative to decrease this risk. Chemical analyses by USACE personnel identified 17 metals in various DMs, but in this present study, only zinc (Zn) and Cd were investigated. Pre-germinated seeds of the test plants were planted under laboratory conditions in pots containing the various DMs and reference soil. Four weeks after planting, plants were harvested and separated into roots and shoots for biomass production and tissue metal concentrations analyses. Results showed that T. aestivum plants have the capacity to tolerate and grow in multiple-metal contaminated DMs with the potential of accumulating various amounts of Zn and Cd. Root and shoot biomass of T. aestivum were not significantly affected by the DMs on which the plants were grown suggesting that this plant species can grow just as well on DMs contaminated by various metals as in the reference soil. No significant differences in the Zn tissue

  7. Heavy Metal Uptake, Translocation, and Bioaccumulation Studies of Triticum aestivum Cultivated in Contaminated Dredged Materials

    Directory of Open Access Journals (Sweden)

    Gregorio Begonia

    2005-08-01

    Full Text Available Phytoremediation is a technology that uses vegetation to remediate contaminants from water, soil, and sediments. Unlike traditional remediation techniques such as soil washing or vitrification, phytoremediation offers a technology that is solar-driven, aesthetically pleasing, and cost effective. Recent studies indicate that winter wheat (Triticum aestivum L. is a potential accumulator for heavy metals such as lead (Pb and cadmium (Cd in hydroponic systems. Based on these findings, a laboratory study was conducted with the primary objective of determining the phytoaccumulation capability of this plant species for heavy metals from contaminated dredged materials (DMs originating from two confined disposal facilities (CDF. The United States Army Corps of Engineers (USACE manages several hundred million cubic meters of DMs each year, and 5 to 10 % of these DMs require special handling because they are contaminated with hazardous substances that can move from the substrates into food webs causing unacceptable risk outside CDFs. Phytoremediation may offer an alternative to decrease this risk. Chemical analyses by USACE personnel identified 17 metals in various DMs, but in this present study, only zinc (Zn and Cd were investigated. Pre-germinated seeds of the test plants were planted under laboratory conditions in pots containing the various DMs and reference soil. Four weeks after planting, plants were harvested and separated into roots and shoots for biomass production and tissue metal concentrations analyses. Results showed that T. aestivum plants have the capacity to tolerate and grow in multiple-metal contaminated DMs with the potential of accumulating various amounts of Zn and Cd. Root and shoot biomass of T. aestivum were not significantly affected by the DMs on which the plants were grown suggesting that this plant species can grow just as well on DMs contaminated by various metals as in the reference soil. No significant differences in the Zn

  8. Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L. Genome

    Directory of Open Access Journals (Sweden)

    Navdeep Gill

    2014-04-01

    Full Text Available Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are “novel” to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence.

  9. Protein Level and Heavy Metals (Pb, Cr, and Cd) Concentrations in Wheat (Triticum aestivum) and in Oat (Avena sativa) Plants

    OpenAIRE

    Syed Noor Ul Abideen; Syed Ainul Abideen

    2013-01-01

    The aim of the study was to investigate heavy metal accumulation in wheat (Triticum aestivum) and oat (Avena sativa), and other physiological and biochemical parameters affected by these heavy metals. The data revealed that maximum plant fresh weight and plant dry weight was recorded for oat and minimum plant fresh weight and plant dry weight was noted for wheat (Triticum aestivum). The data also indicated that higher concentration of proline and DNA concentration was noted in wheat (Triticum...

  10. STUDY OF THE ANTIHYPERLIPIDEMIC, ANTIOXIDATIVE AND ANTIATHEROGENIC ACTIVITY OF TRITICUM AESTIVUM LINN. IN RABBIT RECEIVING HIGH FAT DIET

    OpenAIRE

    Das Swarnamoni; Hakim Abdul; Mittal Ajay

    2012-01-01

    The aim was to study of the antihyperlipidemic, antioxidative and antiatherogenic activity of Triticum aestivum Linn. in rabbit receiving high fat diet. Twenty rabbits of either sex were taken and divided into four groups five in each as - Normal Control- received normal diet, Hyperlipidemic control- received high fat diet, Test drug group - received high fat diet plus ethanolic extract of Triticum aestivum 500 mg/Kg /day orally and Standard Drug group- received high fat diet plus Atorvastati...

  11. A Study of the Protective Effect of Triticum aestivum L. in an Experimental Animal Model of Chronic Fatigue Syndrome

    OpenAIRE

    Mukundam Borah; Phulen Sarma; Swarnamoni Das

    2014-01-01

    Background: Oxidative stress plays a major role in the pathogenesis of chronic fatigue syndrome (CFS). Keeping in view the proven antioxidant activity of Triticum aestivum L., this study has been undertaken to explore the potential therapeutic benefit of this plant in the treatment of CFS. Objective: To study the protective effect of the ethanolic extract of the leaves of Triticum aestivum (EETA) in an experimental mice model of CFS. Materials and Methods: Five groups of albino mice (20-25 g)...

  12. BacT/ALERT 3 D系统在结核性脑膜炎诊断中的应用%Value of BacT/ALERT 3 D microbial detection system in rapid diagnosis of tuberculosis men-ingitis

    Institute of Scientific and Technical Information of China (English)

    张继萍; 任丽娟; 李永利; 叶迎宾; 黄秀香; 郑立恒

    2015-01-01

    目的:评价BacT/ALERT 3D系统在诊断结核性脑膜炎中的应用价值。方法:收集2009年1月~2014年6月间200例结核性脑膜炎患者早期脑脊液标本480份,每份标本分别用离心涂片法、罗氏培养法和BacT/ALERT 3D系统培养法检测,对其结果进行分析,总结3种方法对确诊结核性脑膜炎之间的差异。结果:480份脑脊液标本中,离心涂片法、罗氏培养法、BacT/ALERT 3D系统培养法的结核杆菌阳性检出率分别为3.13%、5.42%、10.63%,BacT/ALERT 3D系统培养法结核杆菌初代分离时间短于罗氏培养法。结论:BacT/ALERT 3D系统有较高的检出率、较快的检出时间,有助于提高结核性脑膜炎的发现率,值得临床推广应用。%Objective:To evaluate the application value of BacT/ALERT 3D microbial detection system in rapid diagnosis of tuberculosis meningitis . Methods:480 specimens in cerebrospinsl fluid ( CSF) of 200 patients diagnosed with tuberculosis meningitis were collected from January 2009 to June 2014.These specimens were processed for detection of the mycobacterium tuberculosis by centrifugal smear acid-fast stain ( Ziehl-Neelsen staining) and Lowenstein-Jensen cultivation,as well as the BacT/ALERT 3D system.The above results were analyzed and compared regarding the positive rates in order to evaluate the value in diagnosing tuberculosis meningitis .Results:The positive rates of the centrifugal smear acid-fast smear,Lowenstein-Jensen cultiva-tion and BacT/ALERT 3D system cultivation were 3.13%,5.42% and 10.63% respectively.Conclusion: BacT/Alert 3D microbial detection system may lead to higher sensitivity and shortened detection time ,which is worthy of wider clinical recommendation .

  13. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome.

    Science.gov (United States)

    Chapman, Jarrod A; Mascher, Martin; Buluç, Aydın; Barry, Kerrie; Georganas, Evangelos; Session, Adam; Strnadova, Veronika; Jenkins, Jerry; Sehgal, Sunish; Oliker, Leonid; Schmutz, Jeremy; Yelick, Katherine A; Scholz, Uwe; Waugh, Robbie; Poland, Jesse A; Muehlbauer, Gary J; Stein, Nils; Rokhsar, Daniel S

    2015-01-01

    Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population. PMID:25637298

  14. 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.

  15. ANTICANCER AND CYTOTOXIC POTENTIAL OF TRITICUM AESTIVUM EXTRACT ON HELA CELL LINE

    Directory of Open Access Journals (Sweden)

    Patel Janki B.

    2013-01-01

    Full Text Available The objective of the study was to analyze the anticancer property of the leaves of Triticum aestivum on HeLa cells. The Indian medicinal plant Triticum aestivum that is used in traditional medicine for cancer and non cancerous diseases was collected. The crude methanolic extract was prepared by using standard protocols. The antiproliferative effect the methanolic extract was evaluated in vitro by employing MTT assay. The potency of each plant extract concentration was calculated in terms of percent decrease in viable HeLa cells as compared to the control value. The extract showed dose dependent antitumor activity. The MTT assay showed an anti proliferative activity (IC50 at 156 μg/ml of crude extract.

  16. Physical location of rice Gm-6,Pi-5(t) genes in O. officinalis with BAC-FISH

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A fluorescence in situ hybridization (FISH) procedure was adoptedto physically map two rice BAC clones 24E21 and 4F22 linked to Gm-6 and Pi-5(t) in O. officinalis. FISH results showed that the two BAC clones were located at 4L. The percentage distance from the centromere to the hybridization sites was 72±2.62 for 24E21 and 54±5.43 for 4F22, the detection rates were 52.70% and 61.2%. The results obtained from the BAC and plasmid clones, RG214 and RZ565 of cultivated rice and O. officinalis were the same. This suggested that the markers, RG214 and RZ565 of cultivated rice and O. officinalis were in the same BAC clones. The homologous sequences of Gm-6 and Pi-5(t) in O. officinalis were positions that signals existed on the 4L. Many signals were observed when no Cot-1 DNA blocked. This also showed that repetitive sequences were some homolgous between cultivated rice and O. officinalis. The identification of chromosome 4 of O. officinalis is based on Jena et al. (1994). In our study, we discussed the possibility of physical map in O. officinalis with rice BAC clones.

  17. Computational analysis of ordering in higher homologous series of nBAC: The effect of a dielectric medium

    International Nuclear Information System (INIS)

    A computational analysis of ordering in higher homologous series of p-n-alkylbenzoic acids (nBAC) that have 7 (7BAC) and 9 (9BAC) carbon atoms in the alkyl chain has been carried out on the basis of quantum mechanics and intermolecular forces. The molecular geometry of 7BAC and 9BAC has been constructed on the basis of published crystallographic data with the standard values of bond lengths and bond angles. The evaluation of atomic charge and dipole moment at each atomic center has been carried out through the complete neglect differential overlap (CNDO/2) method. The configurational energy has been computed via the Rayleigh-Schroedinger perturbation method. The total interaction energy values obtained through these computations were used to calculate the probability of each configuration in a dielectric medium at the nematic-isotropic-transition temperature through the use of the Maxwell-Boltzmann formula. It has been observed that there is a considerable rise in the probability of interactions, although the order of preference remains the same. The present article offers theoretical support to the experimental observations. In addition, this provides a new way of looking at the liquid-crystalline molecules in a dielectric medium

  18. Diversification of Lrk/Tak Kinase Gene Clusters is Associated with Subfunctionalization and Cultivar-specific Transcript Accumulation in Barley

    Science.gov (United States)

    Lrk (Lr10 receptor-like kinase) and Tak (Triticum aestivum kinase) belong to the receptor-like kinase (RLK) super-gene family in higher plants. Three Lrk/Tak gene regions spanning greater than 600 kb were identified via a genome-wide survey of barley gene-rich BAC (Bacterial Artificial Chromosome) ...

  19. Expression of Human CAR Splicing Variants in BAC-Transgenic Mice

    OpenAIRE

    Zhang, Yu-Kun Jennifer; LU, Hong; Klaassen, Curtis D.

    2012-01-01

    The nuclear receptor constitutive androstane receptor (CAR) is a key regulator for drug metabolism in liver. Human CAR (hCAR) transcripts are subjected to alternative splicing. Some hCAR splicing variants (SVs) have been shown to encode functional proteins by reporter assays. However, in vivo research on the activity of these hCAR SVs has been impeded by the absence of a valid model. This study engineered an hCAR-BAC-transgenic (hCAR-TG) mouse model by integrating the 8.5-kbp hCAR gene as wel...

  20. Germline transformation of Aedes fluviatilis (Diptera:Culicidae) with the piggyBac transposable element.

    Science.gov (United States)

    Rodrigues, Flávia Guimarães; Oliveira, Sabrina Barbosa; Rocha, Bruno Coelho; Moreira, Luciano Andrade

    2006-11-01

    The technique to generate transgenic mosquitoes requires adaptation for each target species because of aspects related to species biology, sensitivity to manipulation and rearing conditions. Here we tested different parameters on the microinjection procedure in order to obtain a transgenic Neotropical mosquito species. By using a transposon-based strategy we were able to successfully transform Aedes fluviatilis (Lutz), which can be used as an avian malaria model. These results demonstrate the usefulness of the piggyBac transposable element as a transformation vector for Neotropical mosquito species and opens up new research frontiers for South American mosquito vectors. PMID:17160283

  1. Germline transformation of Aedes fluviatilis (Diptera:Culicidae with the piggyBac transposable element

    Directory of Open Access Journals (Sweden)

    Flávia Guimarães Rodrigues

    2006-11-01

    Full Text Available The technique to generate transgenic mosquitoes requires adaptation for each target species because of aspects related to species biology, sensitivity to manipulation and rearing conditions. Here we tested different parameters on the microinjection procedure in order to obtain a transgenic Neotropical mosquito species. By using a transposon-based strategy we were able to successfully transform Aedes fluviatilis (Lutz, which can be used as an avian malaria model. These results demonstrate the usefulness of the piggyBac transposable element as a transformation vector for Neotropical mosquito species and opens up new research frontiers for South American mosquito vectors.

  2. Reframing Nationality through Local and Regional Social Practices – Europe Direct Bacău Relay

    Directory of Open Access Journals (Sweden)

    Camelia Cmeciu

    2009-06-01

    Full Text Available Paraphrasing the famous European syntagm “unity in diversity”, we will introduce anothersyntagm, namely “nationality in diversity”, thus laying an emphasis on the strategies (social practicesadopted by each of the thirty one Europe Direct relays in Romania in order to achieve their goals.Having as theoretical background the four semiotic systems (represented participants, interactiveparticipants, composition, modality of social semiotics (van Leeuwen, Kress, 2001, 2005, we willinterpret the 2009 campaign promoted by Europe Direct Bacău as an alternative interweaving ofcognitive, affective and behavioural effects.

  3. Optimization of WDM lightwave systems (BAC) design using error control coding

    Science.gov (United States)

    Mruthyunjaya, H. S.; Umesh, G.; Sathish Kumar, M.

    2007-04-01

    In a binary asymmetric channel (BAC) it may be necessary to correct only those errors which result from incorrect transmission of one of the two code elements. In optical fiber multichannel systems, the optical amplifiers are critical components and amplified spontaneous emission noise in the optical amplifiers is the major source of noise in it. The property of erbium doped fiber amplifier is nearly ideal for application in lightwave long haul transmission. We investigate performance of error correcting codes in such systems in presence of stimulated Raman scattering and amplified spontaneous emission noise with asymmetric channel statistics. Performance of some best known concatenated coding schemes is reported.

  4. Main varieties of bread (Triticum aestivum L.) and durum (Triticum durum Desf.) wheat.

    OpenAIRE

    Чебаков, М. П.

    2008-01-01

    Results of systematization and morphological characteristics of two wheat species-bread (Triticum aestivum L.) and hard (Triticum durum Desf.) are given. Detail descriptions of 55 main varieties of bread wheat and 32 varieties of hard wheat arep- resented in table version. In practical application these result enable plant breeders, seed producers and variety testers to determine wheat varieties easily sinse it is method for morphological systematics of wheat.

  5. Synthesis of Silver Nanoparticles Using Triticum aestivum and Its Effect on Peroxide Catalytic Activity and Toxicology

    OpenAIRE

    Sharada Dagade; Pooja Chavan; Shobha Waghmode; Vidya Kalyankar

    2013-01-01

    The synthesis of stable silver nanoparticles using bioreduction method was investigated. Biological synthesis of silver nanoparticles using Triticum aestivum (khapali ghahu) extract was investigated. The effect of a specific variety of plants and how it affects the growth of silver nanoparticles was investigated in our work and it was polydispersed. UV-visible spectroscopy was used to monitor the formation of silver nanoparticles within 15 minutes. The peaks in XRD pattern are in good agreeme...

  6. Anticancer Effect of Rutin Isolated from the Methanolic Extract of Triticum aestivum Straw in Mice

    OpenAIRE

    Savita Dixit

    2014-01-01

    Rutin is the bioactive flavanoid isolated from the straw part of Triticum aestivum and possess various pharmacological applications. The aim of this study is to evaluate the chemopreventive potential of rutin in an experimental skin carcinogenesis mice model system. Skin tumor was induced by topical application of 7,12-dimethyl benz(a) anthracene (DMBA) and promoted by croton oil in Swiss albino mice. To assess the chemopreventive potential of rutin, it was orally administered at a concentrat...

  7. Heavy Metal Uptake, Translocation, and Bioaccumulation Studies of Triticum aestivum Cultivated in Contaminated Dredged Materials

    OpenAIRE

    Gregorio Begonia; Shumaker, Ketia L.

    2005-01-01

    Phytoremediation is a technology that uses vegetation to remediate contaminants from water, soil, and sediments. Unlike traditional remediation techniques such as soil washing or vitrification, phytoremediation offers a technology that is solar-driven, aesthetically pleasing, and cost effective. Recent studies indicate that winter wheat (Triticum aestivum L.) is a potential accumulator for heavy metals such as lead (Pb) and cadmium (Cd) in hydroponic systems. Based on these findings, a labora...

  8. Contaminants in organically and conventionally produced winter wheat (Triticum aestivum) in Belgium

    OpenAIRE

    Pussemier, Luc; Harcz, Peter; De Temmerman, Ludwig; De Voghel, Simon; Waegeneers, Nadia; Wilmart, Olivier; Vromman, Valérie; Schmit, Jean-François; Moons, Emmanuelle; Van Peteghem, Carlos; De Saeger, Sarah; Schneider, Yves Jacques; Larondelle, Yvan

    2007-01-01

    Abstract A database has been compiled with the levels of important contaminants (mycotoxins, heavy metals and pesticides) measured from 2002 to 2005 in winter wheat (Triticum aestivum) grown in Belgium according to the organic and conventional farming systems. Assuming no further change in contaminant levels during cereal processing and during the preparation of foodstuffs, conservative intakes are estimated for the consumers of cereal based products such as flour, bread, breakfast...

  9. The stem structure of Triticum aestivum L. under different mineral nutrition

    Directory of Open Access Journals (Sweden)

    Olga I. Zhuk

    2014-04-01

    Full Text Available The effect of supplying of winter wheat (Triticum aestivum L. plants by nitrogen, phosphorus and potassium on the main stem structure and plant productivity was studied for cultivars ‘Mironivska 808’ and ‘Smuglyanka’. It was shown that increased mineral nutrition causes increasing stem and central xylem vessels diameter on average of 1 mm. Increased plant productivity was supported by increasing grains quantity per ear and mass of 1000 grains.

  10. Genetic and ecological aspects of gene flow from wheat (Triticum aestivum L.) to Aegilops L. species

    OpenAIRE

    Schoenenberger, Nicola; Küpfer, Philippe

    2006-01-01

    Genetic and ecological aspects of gene flow from wheat (Triticum aestivum L.) to Aegilops L. species Hybridisation and introgression from crops to wild relatives is a key issue in risk assessment. In the present study, hybridisation and introgression dynamics from hexaploid wheat (2n=42) to tetraploid Aegilops species (2n=28) were investigated by experiments in natural conditions or in the greenhouse, and by genetic analyses. In order to study crop-weed hybridisation as a function of distance...

  11. Water movement into dormant and non-dormant wheat (Triticum aestivum L.) grains

    OpenAIRE

    Rathjen, Judith R.; Strounina, Ekaterina V.; Mares, Daryl J.

    2009-01-01

    The movement of water into harvest-ripe grains of dormant and non-dormant genotypes of wheat (Triticum aestivum L.) was investigated using Magnetic Resonance Micro-Imaging (MRMI). Images of virtual sections, both longitudinal and transverse, throughout the grain were collected at intervals after the start of imbibition and used to reconstruct a picture of water location within the different grain tissues and changes over time. The observations were supplemented by the weighing measurements of...

  12. Proteomic Analysis Reveals Key Proteins and Phosphoproteins upon Seed Germination of Wheat (Triticum aestivum L.)

    OpenAIRE

    Dong, Kun; Zhen, Shoumin; Cheng, Zhiwei; Cao, Hui; Ge, Pei; Yan, Yueming

    2015-01-01

    Wheat (Triticum aestivum L.) is one of the oldest cultivated crops and the second most important food crop in the world. Seed germination is the key developmental process in plant growth and development, and poor germination directly affects plant growth and subsequent grain yield. In this study, we performed the first dynamic proteome analysis of wheat seed germination using a two-dimensional differential gel electrophoresis (2D-DIGE)-based proteomic approach. A total of 166 differentially e...

  13. Allelopathic effect of Ashwagandha against the germination and radicle growth of Cicer arietinum and Triticum aestivum

    OpenAIRE

    Sangita Chandra; Priyanka Chatterjee; Protapaditya Dey; Sanjib Bhattacharya

    2012-01-01

    Background: Ashwagandha (Withania somnifera) is an important medicinal plant in Indian traditional system of medicine and traditionally has been used for several medicinal purposes in the Indian subcontinent. Objective: The present study was aimed at the evaluation of allelopathic effect of hydroalcoholic extract of ashwagandha against germination and radicle growth of Cicer arietinum and Triticum aestivum seeds. Materials and Methods: The extract at different concentrations was incubated in ...

  14. Evaluation of seedling characteristics of wheat (triticum aestivum L.) through canonical correlation analysis

    OpenAIRE

    Erayman, Mustafa; Abeyo, Bekele Geleta; Baenziger, P. Stephen; Budak, Hikmet; Eskridge, Kent M

    2006-01-01

    To examine the seedling characteristics of nine different bread wheat (Triticum aestivum L.) varieties, several variables regarding seedling size and germination characteristics were analyzed using canonical correlation analysis. Significantly correlated first canonical variate pairs indicated that the variables within each set such as coleoptile length, shoot length and fresh weight within size set, and emergence rate index and germination percentage can be regarded as main factors for vigor...

  15. EVALUATING THE DROUGHT STRESS TOLERANCE EFFICIENCY OF WHEAT ( TRITICUM AESTIVUM L.) CULTIVARS

    OpenAIRE

    SAMMAR RAZA M.A.; Saleem, M. F.; Khan, I H; M. Jamil; Ijaz, M.; Khan, M. A.

    2012-01-01

    The study was conducted at the Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan to evaluate the drought stress tolerance efficiency of wheat cultivars. Eight wheat (Triticum aestivum L.) genotypes namely (Pasban-90, Inqalab-91, Auqab-2000, AS-2002, Sahar-2006, Shafaq-2006, Lasani-2008, and FSD-2008) were used for screening in laboratory. Three techniques were used for the screening. These techniques are (I) seed germination at -0.6 MPa external water potential (PEG-6...

  16. In vivo evaluation of wheat (Triticum aestivum L.) cultivars for moisture stress

    OpenAIRE

    S. Tamiru

    2014-01-01

    In Ethiopia, wheat productivity is constrained by water stress especially at germination and seedling stage. The objective of this research was to determine the effect of moisture stress on bread wheat (Triticum aestivum) cultivars. Four wheat cultivars (Danda’a, Kubsa, Huluka and Local) were treated with six levels of water stress (0, 50, 100, 150, 200 and 250 g L-1) using PEG-6000. The experiment was arranged factorally in completely randomized design with three replications. Data on germin...

  17. Genetic analysis of preharvest sprouting tolerance in bread wheat (Triticum aestivum L. emend. Thell.)

    OpenAIRE

    Yücel, Cemal; BALOCH, Faheem Shehzad; HATİPOĞLU, RÜŞTÜ; Özkan, Hakan

    2011-01-01

    Rains during grain ripening in wheat (Triticum aestivum L.) can cause preharvest sprouting (PHS), which drastically affects the grain yield and the baking quality of flour. In the present study, to screen 7 cultivars and 4 lines of spring bread wheat for PHS, germination tests were conducted with seeds obtained from wet spikes harvested immediately after natural rainfall. Germination tests were carried out as 3 different treatments: 1) seeds immediately germinated after hand-threshing on samp...

  18. Glycinebetaine applied under drought improved the physiological efficiency of wheat (Triticum aestivum L.) plant

    OpenAIRE

    Muhammad Aown Sammar Raza, Muhammad Farrukh Saleem; Muhammad Yasin Ashraf; Asghar Ali; Hafiz Naeem Asghar

    2012-01-01

    Study to find out the response of wheat (Triticum aestivum L.) cultivars to exogenous application of 100 mM glycinebetaine (GB) at different growth stages (vegetative, flowering and grain filling) was carried out under water limited environment, at the Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad during 2008-09, to find out the best GB application stage for improvement in drought tolerance potential. The wire house experiment was laid out in completely randomized design. D...

  19. Evaluation of drought tolerance in several genotypes of spelt (Triticum aestivum Var. Spelta)

    OpenAIRE

    Silva, João Miguel Borges Branco da

    2014-01-01

    Domestication of plants and plant breeding have dramatically eroded the allelic variations of crop species which led to an increasing susceptibility of crop plants to environmental stresses, diseases and pests. Drought is a major environmental stress factor that affects the growth and development of plants so the selection of tolerant genotypes becomes increasingly important with respect to the predicted effects of global warming. In this study, several genotypes of Spelt (Triticum aestivum v...

  20. Molecular markers validation to drought resistance in wheat meal (Triticum aestivum L.) under greenhouse conditions

    OpenAIRE

    Gabriel Julio; Veramendi Silene; España Pablo

    2013-01-01

    With the aim to study the genetic resistance to drought and validate molecular markers co-localized with genes/QTLs for this factor, 16 varieties were evaluated as well as advanced lines of wheat meal (Triticum aestivum) in two stages of crop development. Physiological parameters were considered: amount of chlorophyll (clo), wilting or severity degree (SEV) and recovery (reco), morphological parameters: foliage dry matter (FDM) and root dry matter (RDM), the integrated resistance mechanisms:...

  1. ANTHOCYANIN PIGMENTATION IN TRITICUM AESTIVUM L.: GENETIC BASIS AND ROLE UNDER ABIOTIC STRESS CONDITIONS

    OpenAIRE

    Tereshchenko O.Yu.; E.I. Gordeeva; V.S. Arbuzova; E.K. Khlestkina

    2012-01-01

    Anthocyanins are secondary metabolites of plants. They have a wide range of biological activity such as antioxidant, photoprotection, osmoregulation, heavy metal ions chelation, antimicrobial and antifungal activities, which help plants to survive under different stress conditions. Bread wheat (T. aestivum L.) can have purple pigmentation provided by anthocyanin compounds in different organs, such as grain pericarp, coleoptile, culm, leaf blades, leaf sheaths, glumes and anthers. However, the...

  2. The role of pH in Tuber aestivum syn. uncinatum mycorrhiza development within commercial orchards

    Directory of Open Access Journals (Sweden)

    Paul W. Thomas

    2013-12-01

    Full Text Available The accepted advice when establishing a plantation of Tuber aestivum syn. uncinatum is that young inoculated trees should be planted on calcareous soils with a naturally high pH level. When a site is employed that has a naturally low pH level, lime is often applied to raise the pH to a considered ideal level of c.7.5. However, this may not be the correct approach. Here we present data from 33 data points taken from commercial truffle orchards in England, UK. Soil pH is correlated to Tuber aestivum syn. uncinatum mycorrhiza survivorship and development. The optimal observed pH was 7.51 but the actual optimal pH for cultivation may be higher. Sub optimal pH levels lead to a reduction of Tuber aestivum syn. uncinatum mycorrhiza. This reduction is not permanent and mycorrhization levels may be improved within a 12 month period by amending the soil pH. The importance of understanding the interaction of pH with other variables and the results in relation truffle cultivation are discussed.

  3. Ecological characteristics of a Hungarian summer truffle (Tuber aestivum Vittad. producing area

    Directory of Open Access Journals (Sweden)

    Csorbai A. Gógán

    2013-12-01

    Full Text Available Hungary has outstanding environment for natural truffle production in some regions including plain and hilly areas. The most famous of all the natural summer truffle (Tuber aestivum Vittad. habitats is the commonly called Jászság region. This area is situated in the middle of Hungary, between river Danube and Tisza. The flatland area is basically covered by river alluviums with main soils of chernozems, fluvisols, solonchaks and arenosols. Climate of the region is typically continental: warm and dry summers and cold winters vary. The area is traditionally of agricultural use, although strong afforestation was made in the late 1950’s. The English oak (Quercus robur L. populations planted at that time gave a basis for current excellent truffle production. Nowadays the region has proved to be the best natural summer truffle (T. aestivum producing area of Hungary with early season opening (June and high quality truffles as early as August. In the research the best truffle producing forest blocks were selected for ecological investigation. Results of the detailed site description showed uniform climate characteristics and dominance of English oak (Q. robur or mixed English oak-Turkey oak (Quercus cerris L. forests. Soil types revealed differences from earlier findings: dominance of gleysols and water affected chernozems was declared. Soil chemical parameters are in accordance with literature data: pH, organic matter and active carbonate content of the examined soils fall within the range indicated as the requirement of T. aestivum.

  4. Ectomycorrhizal communities above and below ground and truffle productivity in a Tuber aestivum orchard

    Directory of Open Access Journals (Sweden)

    Elena Salerni

    2014-08-01

    Full Text Available Aim of study: The diversity of ectomycorrhizal fungal communities (EM above (EMFb and below (EMMt ground associated with Quercus cerris L., Q. pubescens Willd., and Pinus nigra J.F.Arnold was analyzed.Area of study: A 20 year-old orchard that produces Tuber aestivum truffles, located a few kilometers from Chiusi della Verna (latitude 43° 41’ 53’’; longitude 11° 56’ 9’’ in Tuscany (central Italy was observed.Material and Methods: This investigation combined analyses of EMFb, EMMt, T. aestivum productivity, different host trees, and statistical data on community ecology.Main results: The EM communities showed high species richness and differed slightly in relation to both the host tree and their location above or below ground, providing frequent findings of Tricholoma and Tomentella, respectively. Positive correlations were found between the number of truffles and host trees, and between the weight and number of truffles and EMFb.Research highlights: Mycorrhizal fungi and truffle production are not in competition.Key words: Fungal communities; fruiting bodies; morphotypes; Tuber aestivum; competition; Italy.

  5. Cadmium toxicity on seed germination and seedling growth of wheat Triticum aestivum

    Directory of Open Access Journals (Sweden)

    Maria de Fátima Souza Guilherme

    2015-11-01

    Full Text Available Cadmium toxicity in seed germination and seedling growth of wheat (Triticum aestivum, var. IAC-370 is assessed. The ecotoxicological effects of six experimental concentrations of cadmium (0.03; 0.06; 0.12; 0.6; 1.2; 2.4; 4.8 mM, and control were evaluated. All assays were performed in quadruplicates with 25 seeds per replication in Petri dishes. Responses for toxic effect comprised the variables germination percentage, index of velocity of germination (IVG, length of aerial section and root of the seedlings, green and dry mass of the seedlings. Results showed that T. aestivum seeds exposed to cadmium decreased their normal germination percentage as from 0.03 mM concentration, with a 31% reduction of germination percentage and a 20% decrease in IVG. Cadmium´s inhibition effect on initial growth of seedlings influenced growth of roots and aerial part as from concentration 0.12 mM and reduced the production of green and dry mass of seedlings as from 0.06 mM. The presence and accumulation of cadmium in the soil cultivated with T. aestivum may trigger liabilities in productivity and/or viability caused by its toxicity as from 0.03mM concentrations absorbed by the plant roots.

  6. Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies

    Directory of Open Access Journals (Sweden)

    Halder Georg

    2008-07-01

    Full Text Available Abstract Background With over 20 parapatric races differing in their warningly colored wing patterns, the butterfly Heliconius erato provides a fascinating example of an adaptive radiation. Together with matching races of its co-mimic Heliconius melpomene, H. erato also represents a textbook case of Müllerian mimicry, a phenomenon where common warning signals are shared amongst noxious organisms. It is of great interest to identify the specific genes that control the mimetic wing patterns of H. erato and H. melpomene. To this end we have undertaken comparative mapping and targeted genomic sequencing in both species. This paper reports on a comparative analysis of genomic sequences linked to color pattern mimicry genes in Heliconius. Results Scoring AFLP polymorphisms in H. erato broods allowed us to survey loci at approximately 362 kb intervals across the genome. With this strategy we were able to identify markers tightly linked to two color pattern genes: D and Cr, which were then used to screen H. erato BAC libraries in order to identify clones for sequencing. Gene density across 600 kb of BAC sequences appeared relatively low, although the number of predicted open reading frames was typical for an insect. We focused analyses on the D- and Cr-linked H. erato BAC sequences and on the Yb-linked H. melpomene BAC sequence. A comparative analysis between homologous regions of H. erato (Cr-linked BAC and H. melpomene (Yb-linked BAC revealed high levels of sequence conservation and microsynteny between the two species. We found that repeated elements constitute 26% and 20% of BAC sequences from H. erato and H. melpomene respectively. The majority of these repetitive sequences appear to be novel, as they showed no significant similarity to any other available insect sequences. We also observed signs of fine scale conservation of gene order between Heliconius and the moth Bombyx mori, suggesting that lepidopteran genome architecture may be conserved

  7. Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus microplus

    Directory of Open Access Journals (Sweden)

    Bellgard Matthew

    2010-06-01

    Full Text Available Abstract Background The size and repetitive nature of the Rhipicephalus microplus genome makes obtaining a full genome sequence fiscally and technically problematic. To selectively obtain gene-enriched regions of this tick's genome, Cot filtration was performed, and Cot-filtered DNA was sequenced via 454 FLX pyrosequencing. Results The sequenced Cot-filtered genomic DNA was assembled with an EST-based gene index of 14,586 unique entries where each EST served as a potential "seed" for scaffold formation. The new sequence assembly extended the lengths of 3,913 of the 14,586 gene index entries. Over half of the extensions corresponded to extensions of over 30 amino acids. To survey the repetitive elements in the tick genome, the complete sequences of five BAC clones were determined. Both Class I and II transposable elements were found. Comparison of the BAC and Cot filtration data indicates that Cot filtration was highly successful in filtering repetitive DNA out of the genomic DNA used in 454 sequencing. Conclusion Cot filtration is a very useful strategy to incorporate into genome sequencing projects on organisms with large genome sizes and which contain high percentages of repetitive, difficult to assemble, genomic DNA. Combining the Cot selection approach with 454 sequencing and assembly with a pre-existing EST database as seeds resulted in extensions of 27% of the members of the EST database.

  8. Effect of mercaptoethylamine on DNA degradation in thermophilic bacteria Bac. stearothermophilus exposed to γ-, UV-radiation or methylnitrosourea

    International Nuclear Information System (INIS)

    The effect of mercaptoethylamine (MEA) on degradation of DNA in thermophilic bacteria Bac. stear. exposed to γ-, UV-rays or methylnitrosourea (MNU) was studied. Using centrifugation on alkaline and neutral sucrose gradients, it was shown that MEA inhibits the accumulation of breaks in the DNA of Bac. stear. It also lowers the level of DNA degradation in toluene-treated cells of Bac. stear. under the action of the intrinsic nuclease, reduces the activity of the endonuclease specific for apurinic DNA, as well as that of S1-nuclease and DNase-I in vitro. The inhibition in the accumulation of DNA breaks is assumed to be due to a decrease of the endonuclease activity in the cells of thermophilic bacteria. (orig.)

  9. Comparative genomics of chondrichthyan Hoxa clusters

    Directory of Open Access Journals (Sweden)

    Zhong Ying-Fu

    2009-09-01

    Full Text Available Abstract Background The chondrichthyan or cartilaginous fish (chimeras, sharks, skates and rays occupy an important phylogenetic position as the sister group to all other jawed vertebrates and as an early lineage to diverge from the vertebrate lineage following two whole genome duplication events in vertebrate evolution. There have been few comparative genomic analyses incorporating data from chondrichthyan fish and none comparing genomic information from within the group. We have sequenced the complete Hoxa cluster of the Little Skate (Leucoraja erinacea and compared to the published Hoxa cluster of the Horn Shark (Heterodontus francisci and to available data from the Elephant Shark (Callorhinchus milii genome project. Results A BAC clone containing the full Little Skate Hoxa cluster was fully sequenced and assembled. Analyses of coding sequences and conserved non-coding elements reveal a strikingly high level of conservation across the cartilaginous fish, with twenty ultraconserved elements (100%,100 bp found between Skate and Horn Shark, compared to three between human and marsupials. We have also identified novel potential non-coding RNAs in the Skate BAC clone, some of which are conserved to other species. Conclusion We find that the Little Skate Hoxa cluster is remarkably similar to the previously published Horn Shark Hoxa cluster with respect to sequence identity, gene size and intergenic distance despite over 180 million years of separation between the two lineages. We suggest that the genomes of cartilaginous fish are more highly conserved than those of tetrapods or teleost fish and so are more likely to have retained ancestral non-coding elements. While useful for isolating homologous DNA, this complicates bioinformatic approaches to identify chondrichthyan-specific non-coding DNA elements

  10. Genomic analysis of a 1 Mb region near the telomere of Hessian fly chromosome X2 and avirulence gene vH13

    Directory of Open Access Journals (Sweden)

    Chen Ming-Shun

    2006-01-01

    Full Text Available Abstract Background To have an insight into the Mayetiola destructor (Hessian fly genome, we performed an in silico comparative genomic analysis utilizing genetic mapping, genomic sequence and EST sequence data along with data available from public databases. Results Chromosome walking and FISH were utilized to identify a contig of 50 BAC clones near the telomere of the short arm of Hessian fly chromosome X2 and near the avirulence gene vH13. These clones enabled us to correlate physical and genetic distance in this region of the Hessian fly genome. Sequence data from these BAC ends encompassing a 760 kb region, and a fully sequenced and assembled 42.6 kb BAC clone, was utilized to perform a comparative genomic study. In silico gene prediction combined with BLAST analyses was used to determine putative orthology to the sequenced dipteran genomes of the fruit fly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae, and to infer evolutionary relationships. Conclusion This initial effort enables us to advance our understanding of the structure, composition and evolution of the genome of this important agricultural pest and is an invaluable tool for a whole genome sequencing effort.

  11. An Innovative Process to Improve Turbidity and Organics Removal by BAC Filters

    Institute of Scientific and Technical Information of China (English)

    MIAO Jia; ZHAO Qingliang; WANG Baozhen; LI Ji; ZHANG Jinsong

    2006-01-01

    The turbidity criterion for the product water of a WTP according to the State Project ‘863' on the safeguard technology of drinking water in the southern areas of China is 0.1 NTU. The turbidity removal in the activated carbon filter was analyzed in a pilot-scale test and an innovative technology to improve the turbidity removal in a biologically activated carbon (BAC) filter was put forward in order to meet the criterion. Experimental results showed that the enhanced filtration by adding polymerized aluminium chloride (PAC) into the BAC filter was quite effective in turbidity control. The effluent turbidity was kept at a stable level (mean) of 0.033 NTU with a high removal of about 80% for influent turbidity of 0.110 -0240 NTU with an addition of PAC at 0.05 mg L-1, meeting the requirement for filtrate turbidity equal to or less than 0.1NTUC totally. In addition, the larger the PAC dosage was, the lower the effluent turbidity was. However, further improvement of turbidity removal was not obvious for PAC dosages beyond 0.10 mg L- 1, and an optimal PAC dosage in the range of 0.05 - 0.10 mg L- 1 was proposed.

  12. Motor coordination deficits in Alpk1 mutant mice with the inserted piggyBac transposon

    Directory of Open Access Journals (Sweden)

    Xu Rener

    2011-01-01

    Full Text Available Abstract Background ALPK1 (α-kinase 1 is a member of an unconventional alpha-kinase family, and its biological function remains largely unknown. Here we report the phenotypic characterization of one mutant line, in which the piggyBac (PB transposon is inserted into the Alpk1 gene. Results The piggyBac(PB insertion site in mutants was mapped to the first intron of the Alpk1 gene, resulting in the effective disruption of the intact Alpk1 transcript expression. The transposon-inserted Alpk1 homozygous mutants (Alpk1PB/PB displayed severe defects in motor coordination in a series of behavioral analysis, including dowel test, hanging wire test, rotarod analysis and footprint analysis. However, the cerebellar architecture, Purkinje cell morphology and electrophysiology of the Purkinje cells appeared normal in mutants. The motor coordination deficits in the Alpk1PB/PB mice were rescued by transgenic mice expressing the full-length Alpk1-coding sequence under the control of the ubiquitous expression promoter. Conclusions Our results indicate that ALPK1 plays an important role in the regulation of motor coordination. Alpk1PB/PB mice would be a useful model to provide a clue to the better understanding of the cellular and molecular mechanisms of ALPK1 in the control of fine motor activities.

  13. An innovative process to improve turbidity and Organics Removal by BAC filters

    Science.gov (United States)

    Miao, Jia; Zhao, Qingliang; Wang, Baozhen; Li, Ji; Zhang, Jinsong

    2006-10-01

    The turbidity criterion for the product water of a WTP according to the State Project ‘863’ on the safeguard technology of drinking water in the southern areas of China is 0.1 NTU. The turbidity removal in the activated carbon filter was analyzed in a pilot-scale test and an innovative technology to improve the turbidity removal in a biologically activated carbon (BAC) filter was put forward in order to meet the criterion. Experimental results showed that the enhanced filtration by adding polymerized aluminium chloride (PAC) into the BAC filter was quite effective in turbidity control. The effluent turbidity was kept at a stable level (mean) of 0.033 NTU with a high removal of about 80% for influent turbidity of 0.110 0240 NTU with an addition of PAC at 0.05 mg L-1, meeting the requirement for filtrate turbidity equal to or less than 0.1 NTUC totally. In addition, the larger the PAC dosage was, the lower the effluent turbidity was. However, further improvement of turbidity removal was not obvious for PAC dosages beyond 0.l0 mg L-, and an optimal PAC dosage in the range of 0.05 0.10 mg L- was proposed.

  14. Cytogenetical anchoring of sheep linkage map and syntenic groups using a sheep BAC library

    Directory of Open Access Journals (Sweden)

    Cribiu Edmond-Paul

    2000-07-01

    Full Text Available Abstract In order to simultaneously integrate linkage and syntenic groups to the ovine chromosomal map, a sheep bacterial artificial chromosome (BAC library was screened with previously assigned microsatellites using a sheep-hamster hybrid panel and genetic linkage. Thirty-three BACs were obtained, fluorescently labelled and hybridised on sheep-goat hybrid metaphases (2n = 57. This study allowed us, (i, to anchor all linkage groups on sheep chromosomes, (ii, to give information on the probable position of the centromere on the linkage map for the centromeric chromosomes, (iii, to contradict the previous orientation of the ovine × linkage group by the mapping of BMS1008 on OARXq38. Concerning our somatic cell hybrid panel, this study resulted in the assignment of all the previously unassigned groups to ovine chromosomes and a complete characterisation of the hybrid panel. In addition, since hybridisations were performed on a sheep-goat hybrid, new marker/anchoring points were added to the caprine cytogenetic map.

  15. 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

  16. Structural and enzymatic characterization of BacD, an l-amino acid dipeptide ligase from Bacillus subtilis

    OpenAIRE

    Shomura, Yasuhito; Hinokuchi, Emi; Ikeda, Hajime; Senoo, Akihiro; Takahashi, Yuichi; Saito, Jun-ichi; Komori, Hirofumi; Shibata,Naoki; Yonetani, Yoshiyuki; Higuchi, Yoshiki

    2012-01-01

    BacD is an ATP-dependent dipeptide ligase responsible for the biosynthesis of l-alanyl-l-anticapsin, a precursor of an antibiotic produced by Bacillus spp. In contrast to the well-studied and phylogenetically related d-alanine: d-alanine ligase (Ddl), BacD synthesizes dipeptides using l-amino acids as substrates and has a low substrate specificity in vitro. The enzyme is of great interest because of its potential application in industrial protein engineering for the environmentally friendly b...

  17. Intra- and interchromosomal rearrangements between cowpea [Vigna unguiculata (L.) Walp.] and common bean (Phaseolus vulgaris L.) revealed by BAC-FISH.

    Science.gov (United States)

    Vasconcelos, Emanuelle Varão; de Andrade Fonsêca, Artur Fellipe; Pedrosa-Harand, Andrea; de Andrade Bortoleti, Kyria Cilene; Benko-Iseppon, Ana Maria; da Costa, Antônio Félix; Brasileiro-Vidal, Ana Christina

    2015-06-01

    Cowpea (Vigna unguiculata) is an annual legume grown in tropical and subtropical regions, which is economically relevant due to high protein content in dried beans, green pods, and leaves. In this work, a comparative cytogenetic study between V. unguiculata and Phaseolus vulgaris (common bean) was conducted using BAC-FISH. Sequences previously mapped in P. vulgaris chromosomes (Pv) were used as probes in V. unguiculata chromosomes (Vu), contributing to the analysis of macrosynteny between both legumes. Thirty-seven clones from P. vulgaris 'BAT93' BAC library, corresponding to its 11 linkage groups, were hybridized in situ. Several chromosomal rearrangements were identified, such as translocations (between BACs from Pv1 and Pv8; Pv2 and Pv3; as well as Pv2 and Pv11), duplications (BAC from Pv3), as well as paracentric and pericentric inversions (BACs from Pv3, and Pv4, respectively). Two BACs (from Pv2 and Pv7), which hybridized at terminal regions in almost all P. vulgaris chromosomes, showed single-copy signal in Vu. Additionally, 17 BACs showed no signal in V. unguiculata chromosomes. The present results demonstrate the feasibility of using BAC libraries in comparative chromosomal mapping and karyotype evolution studies between Phaseolus and Vigna species, and revealed several macrosynteny and collinearity breaks among both legumes. PMID:25634499

  18. Efficacy of a BAC clone of a recombinant strain of Marek’s disease virus containing reticuloendotheliosis virus LTR following in ovo Vaccination at 18 days of embryonation

    Science.gov (United States)

    We have previously reported on the pathogenicity of various passage levels of a bacterial artificial chromosome (BAC) clone of a recombinant Marek’s disease virus (MDV) strain rMd5 containing reticuloendotheliosis virus (REV) long terminal repeat (LTR) termed rMd5 REV LTR BAC. In this study, we eval...

  19. Effect of 2,4-D on Seedling Physiology and Cytogenetical Studies in Triticum aestivum and Phalaris minor ( Gramineae )%Effect of 2,4-D on Seedling Physiology and Cytogenetical Studies in Triticum aestivum and Phalaris minor (Gramineae)

    Institute of Scientific and Technical Information of China (English)

    Muhammad Rashid Khan; Khawaja Muhammad Aslam

    2006-01-01

    Effects of 2,4-D on seedling growth and chromosomal abnormalities were studied in Triticum aestivum and Phalaris minor. Seeds were soaked at different concentrations of 2,4 -D (0.01%, 0.1%, 1.0% ) for 4, 8, 12 and 16 hours. 2,4-D suppressed the germination more severely in P. minor than in T. aestivum. Shoot and root length was retarded with the increase of concentration and time of treatment in both species. Generally radical was more negatively affected than coleoptile and emergence of radical was not observed at 1.0% concentration at 8, 12, and 16 hours of treatment in T. aestivum while in P. minor there was a total lack of radical emergence at 1.0% concentration for all durations of treatment. Stiff and curled roots and undifferentiated callus like scutellar tissues were observed in T. aestivum, while in P. minor the coleoptile obtained was lean, pale green in colour and was lying flat on filter paper. Mitotic index decreased, while chromosomal abnormalities, bridges and laggards were increased with the increase of concentration and soaking time however, laggards were not observed in T. aestivum. Clumping and chain formation of chromosomes at metaphase was also noticed in P. minor.

  20. Quantitative Traits of Ion Beam Induced Mutagenesis in Triticum aestivum

    Institute of Scientific and Technical Information of China (English)

    Huan FANG; Zhen JIAO

    2012-01-01

    [Objective] The aim of this study was to elucidate the quantitative traits of plants mutagenized by ion beam. [Method] The particular variation phenotypes, a- gronomic traits, and protein and wet gluten contents of progenies derived from the same ion beam induced mutant were investigated. [Result] Morphological polymor- phism existed in some individuals. Plant height, spike length and protein content were significantly influenced by ion beam, and effective tiller number and wet gluten content were moderately influenced. Multiple comparisons of all the indices within groups indicated genomic instability among these groups. Coefficient of variation im- plied the differences within group were very low. [Conclusion] Ion beam irradiation displayed characteristics of multi-directivity and non-directiveness. It aroused multiple variations in the same mutant. Instability among progeny indicates cells had different fate even in the same irradiated tissue. It may take several generations for mutants to stabilize particular phenotypes. The effects of ion beam irradiation may be the in- terrelated direct irradiation damage, indirect irradiation damage and late effect, such as bystander effect and adaptive response.

  1. Genomic profiles of colorectal cancers differ based on patient smoking status.

    Science.gov (United States)

    Swede, Helen; Bartos, Jeremy D; Chen, Neng; Shaukat, Aasma; Dutt, Smitha S; McQuaid, Devin A; Natarajan, Nachimuthu; Rodriguez-Bigas, Miguel A; Nowak, Norma J; Wiseman, Sam M; Alrawi, Sadir; Brenner, Bruce M; Petrelli, Nicholas J; Cummings, K Michael; Stoler, Daniel L; Anderson, Garth R

    2006-07-15

    Human sporadic colorectal cancer is the result of a lengthy somatic evolutionary process facilitated by various forms of genomic instability. Such instability arises endogenously from mutations in genes whose role is to preserve genomic integrity, and exogenously from environmental agents that generate genomic damage. We have found that cigarette smoking shifts the genomic profiles and genomic instability patterns of colorectal carcinomas. The genomic profiles of 57 consecutive cancers were examined; 31 cases were current or former smokers and 26 were nonsmokers. Genome-wide allelotypes of 348 markers were examined, along with comparative genomic hybridization (CGH) on ordered BAC microarrays, microsatellite instability, and inter-(simple sequence repeat) polymerase chain reaction instability. Tumors from nonsmokers exhibited losses of heterozygosity, particularly on chromosomes 14 and 18, whereas tumors from smokers exhibited a more diffuse pattern of allelic losses. Tumors from smokers exhibited higher overall rates of loss of heterozygosity, but showed lower rates of background microsatellite instability (MSI-L). On BAC array CGH, higher levels of generalized amplifications and deletions were observed in tumors from smokers, differentially affecting male smokers. In the transforming growth factor-beta signaling pathway, MADH4 mutations were more common in tumors from smokers, whereas transforming growth factor-beta RII mutations were more common among nonsmokers. PMID:16843098

  2. Fractionation of Rare Earth Elements in Plants Ⅰ. Fractionation Patterns and Their Forming Mechanisms in Different Organs of Triticum Aestivum

    Institute of Scientific and Technical Information of China (English)

    Liang Tao; Ding Shiming; Zhang Chaosheng; Zhang Zili; Yan Juncai; Li Haitao

    2005-01-01

    Fractionations of rare earth elements (REEs) and the forming mechanisms in plants were studied using Triticum aestivum as plant material with application of exogenous REEs and hydroponic culture. REEs were significantly fractionated in different parts of Triticum aestivum. M-type tetrad effect could be observed in both root and shoot of Triticum aestivum, which might result from the different abilities of REEs to form phosphate precipitation. Middle REEs (MREEs), light REEs (LREEs) and heavy REEs (HREEs) were enriched in root, stem and leaf of Triticum aestivum, respectively. REE speciation calculations using VMINTEQ program show REEs in simulated xylem solution mainly exist as REE-EDTA- and RE3+, but only HREEs are enriched in REE-EDTA-, while LREEs are enriched in the other REE species. It is suggested that the fractionation between LREEs and HREEs might be caused by the uptake of REE-EDTA- in Triticum aestivum leaves, but might result from the uptake of the other REE species in their stems.

  3. 转座子PiggyBac在哺乳动物中的应用%PiggyBac Transposon for Mammalian Applications

    Institute of Scientific and Technical Information of China (English)

    马元武; 张连峰

    2012-01-01

    As a tool of genetic engineering, DNA transposons have been widely used for transgenesis and insertional mutagenesis in various organisms. Till now, transposons active in mammalian include; 1) hAT-like Tol2; 2) , two Te1-like transposons, Sleeping Beauty (SB) and Frog Prince ( FP) ; 3) PiggyBac family. Among those transposons, the moth-derived transposon piggybac appears to be the most promising genetic tool due to its higher efficient transposition and higher cargo capacity. Therefore, it can be used for transgenesis, discovery of cancer gene and tumor suppressor gene, and gene therapy. The traceless excision transposition property of the PB transposon can be used to generate transgene-free iPS cells while maintaining an unaltered genome. In this review we will discuss the application and the future of PB transposon in mammalian.%DNA转座子作为一种遗传工程工具已广泛应用于多物种的转基因及产生插入突变等研究.目前,在哺乳动物中有转座活性的转座子可分为三类:1)hAT样转座子;2)Tcl样转座子包括Sleeping Beauty和Frog Prince;3) PiggyBac转座子家族.其中甘蓝蠖度尺蛾(Cabbage looper moth Trichoplusia ni)来源的PiggyBac转座子是目前在哺乳动物中活性最高的转座子,并且可以携带十几kb的外源基因转座而不影响其效率,使其在哺乳动物的转基因、癌基因的发现、基因治疗研究方面具有巨大的应用潜力.此外,PB的无痕迹转座对于无转基因、无遗传物质改变的诱导多潜能干细胞(iPS)研究也具有非常重要的意义.本文主要对针对PB在哺乳动物中的应用现状及前景作一介绍.

  4. A transgenic Bm cell line of piggyBac transposon-derived targeting expression of humanized glycoproteins through N-glycosylation.

    Science.gov (United States)

    Hu, Jia-Biao; Zhang, Peng; Wang, Mei-Xian; Zhou, Fang; Niu, Yan-Shan; Miao, Yun-Gen

    2012-08-01

    Glycoproteins have been implicated in a wide variety of important biochemical and biological functions, including protein stability, immune function, enzymatic function, cellular adhesion and others. Unfortunately, there is no therapeutic protein produced in insect system to date, due to the expressed glycoproteins are paucimannosidic N-glycans, rather than the complex, terminally sialylated N-glycans in mammalian cells. In this paper, we cloned the necessary genes in glycosylation of mammalian cells, such as N-acetylglucosaminyltransferase II (Gn-TII), galactosyltransferases (Gal-Ts), 2,6-Sial-T (ST6 GalII)and 2,3-Sial-T (ST3GalIII), and transformed them to silkworm genome of BmN cell line through transgenesis to establish a transgenic Bm cell line of piggyBac transposon-derived targeting expression of humanized glycoproteins. The study supplied a new insect cell line which is practically to produce "bisected" complex N-glycans like in mammalian cells. PMID:22699878

  5. Advancing Eucalyptus Genomics: Cytogenomics Reveals Conservation of Eucalyptus Genomes

    Science.gov (United States)

    Ribeiro, Teresa; Barrela, Ricardo M.; Bergès, Hélène; Marques, Cristina; Loureiro, João; Morais-Cecílio, Leonor; Paiva, Jorge A. P.

    2016-01-01

    The genus Eucalyptus encloses several species with high ecological and economic value, being the subgenus Symphyomyrtus one of the most important. Species such as E. grandis and E. globulus are well characterized at the molecular level but knowledge regarding genome and chromosome organization is very scarce. Here we characterized and compared the karyotypes of three economically important species, E. grandis, E. globulus, and E. calmadulensis, and three with ecological relevance, E. pulverulenta, E. cornuta, and E. occidentalis, through an integrative approach including genome size estimation, fluorochrome banding, rDNA FISH, and BAC landing comprising genes involved in lignin biosynthesis. All karyotypes show a high degree of conservation with pericentromeric 35S and 5S rDNA loci in the first and third pairs, respectively. GC-rich heterochromatin was restricted to the 35S rDNA locus while the AT-rich heterochromatin pattern was species-specific. The slight differences in karyotype formulas and distribution of AT-rich heterochromatin, along with genome sizes estimations, support the idea of Eucalyptus genome evolution by local expansions of heterochromatin clusters. The unusual co-localization of both rDNA with AT-rich heterochromatin was attributed mainly to the presence of silent transposable elements in those loci. The cinnamoyl CoA reductase gene (CCR1) previously assessed to linkage group 10 (LG10) was clearly localized distally at the long arm of chromosome 9 establishing an unexpected correlation between the cytogenetic chromosome 9 and the LG10. Our work is novel and contributes to the understanding of Eucalyptus genome organization which is essential to develop successful advanced breeding strategies for this genus.

  6. Advancing Eucalyptus genomics: cytogenomics reveals conservation of Eucalyptus genomes

    Directory of Open Access Journals (Sweden)

    Teresa Mousinho Resina Ribeiro

    2016-04-01

    Full Text Available The genus Eucalyptus encloses several species with high ecological and economic value, being the subgenus Symphyomyrtus one of the most important. Species such as E. grandis and E. globulus are well characterized at the molecular level but knowledge regarding genome and chromosome organization is very scarce. Here we characterized and compared the karyotypes of three economically important species, E. grandis, E. globulus and E. calmadulensis, and three with ecological relevance, E. pulverulenta, E. cornuta and E. occidentalis, through an integrative approach including genome size estimation, fluorochrome banding, rDNA FISH and BAC landing comprising genes involved in lignin biosynthesis. All karyotypes show a high degree of conservation with pericentromeric 35S and 5S rDNA loci in the first and third pairs, respectively. GC-rich heterochromatin was restricted to the 35S locus while the AT-rich het pattern was species-specific. The slight differences in karyotype formulas and distribution of AT-rich het, along with genome sizes estimations, supports the idea of Eucalyptus genome evolution by local expansions of heterochromatin clusters. The unusual co-localization of both rDNA with AT-rich het was attributed mainly to the presence of silent transposable elements in those loci. The cinnamoyl CoA reductase gene (CCR1 previously assessed to linkage group 10 (LG10 was clearly localized distally at the long arm of chromosome 9 establishing an unexpected correlation between the cytogenetic chromosome 9 and the LG10. Our work is novel and contributes to the understanding of Eucalyptus genome organization which is essential to develop successful advanced breeding strategies for this genus.

  7. BacT/ALERT 3D检测系统在结核病诊治中的运用

    Institute of Scientific and Technical Information of China (English)

    刘子龙; 曹剑昆

    2010-01-01

    目的 评估BacT/ALERT 3D仪在结核病诊治中的运用价值.方法 采用BacT/ALERT 3D仪对432份临床标本进行分支杆菌快速检测,阳性者进行分支杆菌菌型鉴定和药敏试验,并与罗氏培养法进行比较.结果 BacT/ALERT 3D快速培养分支杆菌的阳性率为38.2%,明显高于罗氏法的28.0%(P<0.01);培养报告时间仅14.24 d,明显短于罗氏法的29.61 d;涂片阳性及阴性组快速培养的阳性率均高于罗氏法(P<0.01).结论 BacT/ALERT 3D快速培养检测系统有助于结核病的诊断和治疗,是一种快速、有效的检测方法.

  8. Characterization of Extracellular Penicilin G Acylase Produced by A New Local Strain of Bacillus subtilis BAC4

    Directory of Open Access Journals (Sweden)

    SUPARTONO

    2008-06-01

    Full Text Available Penicillin G acylase (PGA which catalyses penicillin G hydrolysis reaction is a key enzyme for the industrial production of penicilin G derivatives used in therapeutics. A new local strain of Bacillus subtilis BAC4 was found capable of producing extracellular PGA. However, characteristics of this extracellular PGA are not known. The goal of this research was to characterize the extracellular PGA produced by B. subtilis BAC4. Enzyme production was carried out by batch fermentation, followed by enzyme purification and characterization of the PGA. The PGA activity was determined by the Kornfeld method, with optimal activity for hydrolysing penicillin G observed at 43 oC and pH 8.5. The activation energy of penicillin G hydrolysis by the PGA of B. subtilis BAC4 was determined as 4.9 kcal.mol-1 and Vmax and Km values were found to be 0.7 µmole.min-1.mg-1 and 3.5 mM respectively. PGA catalytic activity was competitively inhibited by phenylacetic acid with an inhibition constant, Ki(PAA, of 347.2 mM. It was concluded that the extracellular PGA of B. subtilis BAC4 can hydrolyse penicillin G efficiently.

  9. Development of a Set of Chromosome-Specific Cytogenetic DNA Markers in Sunflower Using BAC-FISH

    Science.gov (United States)

    In diploid sunflower (2n=34), conventional karyotypes and various genetic linkage maps have been established. However, the relationship between genetic linkage groups and individual chromosomes of sunflower remains unknown. Recently, a set of linkage group-specific BAC and BIBAC clones were identifi...

  10. Development of Health Education Learning Module in Bac.TSE-LDPE Programme in TTI: Needs Analysis Study

    Science.gov (United States)

    Ujang, Alijah; Alias, Norlidah; Siraj, Saedah

    2015-01-01

    This study is to explore the need to develop learning modules of health education for trainee teachers in the Bachelor Of Teaching (Hons)(Special Education-Learning Disabilities For Primary Education) Programme (Bac.TSE-LDPE) in the Teacher Training Institute (TTI). The questionnaire uses the Likert scale with the close ended questions analysed by…

  11. Distribution and radioimmunoimaging of 131I labeled anti-NPC monoclonal antibody BAC5 in tumor bearing nude mice

    International Nuclear Information System (INIS)

    To provide an evidence for clinical applications, the distribution and radioimmunoimaging of 131I labeled anti nasopharyngeal carcinoma (NPC) monoclonal antibody BAC5 in tumor bearing nude mice were studied. McAb BAC5, against NPC, was labeled with 131I and injected into nude mice bearing NPC cell line CNE-2. The biodistribution of 131I-BAC5 and whole body ECT imaging were studied at various intervals after injection. The % ID/g were 6.38, 11.27 and 14.19 for tumor and 7.78, 3.48 and 2.59 for liver at 48, 96 and 144h postinjection respectively. The T/NT ratios were 0.82, 3.24 and 5.47 for liver at 48, 96 and 144h postinjection respectively. Tumor showed clearly at 3 days after injection. The quality of tumor images was relevant to the T/NT ratio. The results demonstrated that McAb BAC5 has specifically bind to NPC tissue and may also possess the capability of leading to human NPC

  12. Responses of alloplasmic (cytoplasm=Triticum timopheevii) and euplasmic wheats (Triticum aestivum) to photoperiod and vernalization.

    Science.gov (United States)

    Ward, R W; Heyne, E G; Paulsen, G M

    1983-07-01

    Studies were conducted to determine the influence of the male sterility-inducing cytoplasm of Triticum timopheevii (Zhuk.) Zhuk. on response of several common winter wheat (T. aestivum L.) nuclear genotypes to photoperiod and vernalization. Comparative studies of cytoplasmic substitution lines provide information on the role of the cytoplasmic genetic mechanism in growth and development. In the case of cytoplasmic male sterility-based hybrid production systems, ubiquity of sterility-inducing cytoplasm in derived hybrids warrants thorough characterization of its influence on plant phenotype. Factorial combinations of cytoplasm (T. timopheevii and T. aestivum), nuclear genotype, and photoperiod or vernalization treatments were evaluated under hydroponic conditions in controlled environment chambers. Interaction of cytoplasm, photoperiod, and nuclear genotype was significant in one or more experiments for days to anthesis and potential spikelet number, and interaction of cytoplasm, vernalization, and nuclear genotype was significant for days to spike emergence. Long day length was associated with increased percentage seed set in one study, but interactions of photoperiod and cytoplasm were not detected for percentage seed set. Interactions involving cytoplasm and photoperiod or vernalization were interpreted as evidence of the existence of genetic factors in cytoplsam of T. timopheevii which alter photoperiod or vernalization responses of alloplasmic plants relative to responses exhibited by euplasmic plants. Since photoperiod and vernalization responses are critical to adaptation, T. timopheevii cytoplasm can alter adaptability of T. aestivum. The specific effect would be nuclear genotype dependent, and does not appear to be of a magnitude greater than that induced by nuclear genetic variability at loci conditioning photoperiod or vernalization responses or other adaptation-determining characteristics. Normal multilocation/year testing of alloplasmic hybrids should

  13. Integration of Lupinus angustifolius L. (narrow-leafed lupin) genome maps and comparative mapping within legumes.

    Science.gov (United States)

    Wyrwa, Katarzyna; Książkiewicz, Michał; Szczepaniak, Anna; Susek, Karolina; Podkowiński, Jan; Naganowska, Barbara

    2016-09-01

    Narrow-leafed lupin (Lupinus angustifolius L.) has recently been considered a reference genome for the Lupinus genus. In the present work, genetic and cytogenetic maps of L. angustifolius were supplemented with 30 new molecular markers representing lupin genome regions, harboring genes involved in nitrogen fixation during the symbiotic interaction of legumes and soil bacteria (Rhizobiaceae). Our studies resulted in the precise localization of bacterial artificial chromosomes (BACs) carrying sequence variants for early nodulin 40, nodulin 26, nodulin 45, aspartate aminotransferase P2, asparagine synthetase, cytosolic glutamine synthetase, and phosphoenolpyruvate carboxylase. Together with previously mapped chromosomes, the integrated L. angustifolius map encompasses 73 chromosome markers, including 5S ribosomal DNA (rDNA) and 45S rDNA, and anchors 20 L. angustifolius linkage groups to corresponding chromosomes. Chromosomal identification using BAC fluorescence in situ hybridization identified two BAC clones as narrow-leafed lupin centromere-specific markers, which served as templates for preliminary studies of centromere composition within the genus. Bioinformatic analysis of these two BACs revealed that centromeric/pericentromeric regions of narrow-leafed lupin chromosomes consisted of simple sequence repeats ordered into tandem repeats containing the trinucleotide and pentanucleotide simple sequence repeats AGG and GATAC, structured into long arrays. Moreover, cross-genus microsynteny analysis revealed syntenic patterns of 31 single-locus BAC clones among several legume species. The gene and chromosome level findings provide evidence of ancient duplication events that must have occurred very early in the divergence of papilionoid lineages. This work provides a strong foundation for future comparative mapping among legumes and may facilitate understanding of mechanisms involved in shaping legume chromosomes. PMID:27168155

  14. Data quality management system (DQMS) for BAC detector in the ZEUS experiment at the HERA accelerator

    Science.gov (United States)

    Luszczak, Zbigniew; Jezynski, Tomasz; Romaniuk, Ryszard S.; Pozniak, Krzysztof T.; Kuthan, Marcin; Bigos, Grzegorz; Gierej, Artur

    2003-10-01

    The paper presents functional structure of database system of data measurement quality for BAC detector in ZEUS experiment. The system collects diagnostic and experimental data. Diagnostic data are: work parameters of the detector and electronics/photonics, tests of electronic/photonic blocks. These data are archived for certain period of time. The quality of current data collection process is estimated using these archived data. The result of such estimation is generated in a form of status map of the detector. Such maps, describing status of the hardware, are fundamental for elementary particle analysis by the calorimeter. The DAQ system, collecting data to the database, estimates data quality on-line during transmission and writing. This mechanism of fast on-line data quality management leads to early discoveries of detector work irregularities and faults.

  15. The effect of foliar fungicides on the mycoflora of seeds of Triticum aestivum

    Directory of Open Access Journals (Sweden)

    Janusz Błaszkowski

    2014-08-01

    Full Text Available The effect of three foliar fungicides. i.e., Bayloton 25 WP, Dithane M-45, and Funaben K. on the mycoflora associated with the seeds of spring Triticum aestivum cv. Kolibri cultivated in the field was investigated. The fungicide which highly reduced the number of both fungal colonies and species was Funaben K. Of the fungi most frequently occurring. Only Funaben K applied on the seeds reduced the proportion of seeds with Alternaria alternata, Cladosporium spp.. and Septoria nodorum. In contrast. seeds from plants traeted with Funaben K harboured significantly more colonies of non-sporulating fungi.

  16. DIVERSIDAD GENÉTICA DE GLUTENINAS Y GLIADINAS EN TRIGOS HARINEROS (Triticum aestivum L.) MEXICANOS

    OpenAIRE

    Eliel Martínez-Cruz; Eduardo Espitia-Rangel; Héctor E. Villaseñor-Mir; José D. Molina-Galán; Ignacio Benítez-Riquelme; Amalio Santacruz-Varela; Roberto J. Peña-Bautista

    2010-01-01

    Las gluteninas y las gliadinas del trigo harinero (Triticum aestivum L.) tienen una función fundamental en la definición de la calidad de panificación. Con el objetivo de caracterizar la composición de las subunidades de gluteninas de alto (G-APM) y bajo (G-BPM) peso molecular, y de las omega;-gliadinas, en 72 progenitores usados por el programa de fitomejoramiento de trigo harinero para temporal del Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (CEVAMEX-INIFAP) y en...

  17. Induced mutations and their genetic aspects in wheat (Triticum aestivum vulgare)

    International Nuclear Information System (INIS)

    The hexaploid nature of common wheat (Triticum aestivum vulgare) and triplication of the genes allow a great number of primary induced changes to be present and maintained through generations. Induced mutations have been obtained in the morphological characters of the wheat spike, grain character, plant height, disease resistance, and in many other quantitative characters. In some of our experiments these have been followed through 25 generations. The genetic aspects of these changes, their effect on the micro-evolutionary processes in the populations, and their applicability in plant breeding are discussed. (author). 56 refs

  18. Uptake and elimination of lanthanum by excised roots of Triticum aestivum

    International Nuclear Information System (INIS)

    In this paper, uptake and elimination of lanthanum by excised roots of Triticum aestivum L. in various conditions were studied. Lanthanum concentrations in the roots were determined by neutron activation analysis. Results showed that the uptake of La in the excised root was almost independent of vitality, and the bonding of La with the roots was tight, but could be removed by EDTA treatment. There was significant dose dependent accumulation of La in the excised roots within the experimental concentration (0-40 μmol/l). (author)

  19. Results of Utilization of Chernobyl Radio Mutant in Breeding Programmes of Triticum aestivum L

    International Nuclear Information System (INIS)

    A large spectrum of mutations was observed as a result of winter wheat T. aestivum L. irradiation for two consecutive vegetative seasons (during 1986-87) in the fields close to the ruined reactor of the Chernobyl Nuclear Power Station. Mutants taken from the different generations (L147/91, BC 47 square head, dwarf 20104/89) were used for development of the varieties Lybid, Yasochka and Tsarivna to utilize traits from the mutants such as hardiness, drought tolerance, disease and lodging resistance and bread quality. These varieties were included in the State Variety Register of Ukraine, while another one, Lisova Pisnya is included in the list of perspective varieties. (author)

  20. Ectomycorrhizal communities above and below ground and truffle productivity in a Tuber aestivum orchard

    OpenAIRE

    Elena Salerni; Maria D'Aguanno; Pamela Leonardi; Claudia Perini

    2014-01-01

    Aim of study: The diversity of ectomycorrhizal fungal communities (EM) above (EMFb) and below (EMMt) ground associated with Quercus cerris L., Q. pubescens Willd., and Pinus nigra J.F.Arnold was analyzed.Area of study: A 20 year-old orchard that produces Tuber aestivum truffles, located a few kilometers from Chiusi della Verna (latitude 43° 41’ 53’’; longitude 11° 56’ 9’’) in Tuscany (central Italy) was observed.Material and Methods: This investigation combined analyses of EMFb, EMMt, T. aest...

  1. Fuzzy clustering analysis for the varietal radiosensitivity of triticum aestivum L

    International Nuclear Information System (INIS)

    Fussy clustering classification to the varietal radiosensitivity of wheat (Triticum aestivum L.) was carried out. According to their response to the radiation of gamma rays, 49 wheat varieties were classified into five groups: higher resistant, resistant, intermediate response, sensitive, and higher sensitive. The research presents a new approach for the classification of the varietal radiosensitivity of a certain plant species, and the result was valuable for choosing the adequate irradiated materials and determining the optimal dosage so as to enhance the mutagenic efficiency in wheat radiation breeding. The reliability and advantage of the Fussy clustering classification for the plant varietal radiosensitivity were briefly discussed

  2. Effects of high temperature after anthesis on starch granules in grains of wheat (Triticum aestivum L.)

    OpenAIRE

    Liu, P.; Guo, W; Jiang, Z.; Pu, H.; Feng, C.; Zhu, X.; Peng, Y.; KUANG, A.; LITTLE, C. R.

    2010-01-01

    SUMMARY The effect of high temperatures (above 25°C) on starch concentration and the morphology of starch granules in the grains of wheat (Triticum aestivum L.) were studied. Wheat plants of cultivars Yangmai 9 (weak-gluten) and Yangmai 12 (medium-gluten) were treated with high temperatures for 3 days at different times after anthesis. The results showed that the starch concentration of grains given a heat-shock treatment above 30°C were lower than those developing at normal temperature in bo...

  3. Physiological processes associated with genetic progress in yield potential of wheat (Triticum aestivum L.)

    OpenAIRE

    Aisawi, Khaled A. Boulgasem

    2012-01-01

    Wheat (Triticum aestivum L.) is the most widely grown of any crop and provides one-fifth of the total calories of the world's population. Since the 1960s, increases in productivity have been achieved as a result of wide-scale adoption of Green Revolution technologies. However, in spite of growing demand, the challenges of increasing production to feed an estimated world population of 9 billion in 2050 are still considerable. Due to the increased demand, it is estimated that food production mu...

  4. Effect of Organic Contaminations on Seed Germination Studies in Tritium Aestivum (L.)

    OpenAIRE

    Smita Sureshrao Kharkale, Pratibha Sunil Agrawal, Lalitmohan Jainarayan Paliwal, Int J Cur Bio Med Sci.

    2011-01-01

    An attempt has been made for germination studies in Triticum Aestivum (L.) with1,2,4,5-trtrazin. It has a wide range of biological activity covering anticoagulant, bactericidal, fungicidal, neurotropopic. Such a vast uses of 1,2,4,5-Tetrazines, necessitate to concentrate on 1,2,4,5-Tetrazines for studying the germination pattern. The experimental data was used to calculate plant growth which in turn is decided on the basis of parameters such as percentage of germination survival, seedling hei...

  5. Hydrogen peroxide scavenging regulates germination ability during wheat (Triticum aestivum L.) seed maturation

    OpenAIRE

    Ishibashi, Yushi; Yamamoto, Kouhei; Tawaratsumida, Tomoya; Yuasa, Takashi; Iwaya-Inoue, Mari

    2008-01-01

    Hydrogen peroxide (H2O2) promotes seed germination of cereal plants and ascorbic acid which acts as antioxidant suppresses the germination of wheat seeds, but the role of H2O2 scavenging on germination during seed maturation has not been demonstrated. We investigated relationship of germination, ascorbate, H2O2 scavenging enzymes and sensitivity to ascorbic acid (AsA) maturing seeds of two typical wheat (Triticum aestivum L.) cultivars, cvs. Shirogane-Komugi and Norin61. Shirogane-Komugi had ...

  6. Cadmium toxicity on seed germination and seedling growth of wheat Triticum aestivum

    OpenAIRE

    Maria de Fátima Souza Guilherme; Habyhabanne Maia Oliveira; Edevaldo da Silva

    2015-01-01

    Cadmium toxicity in seed germination and seedling growth of wheat (Triticum aestivum, var. IAC-370) is assessed. The ecotoxicological effects of six experimental concentrations of cadmium (0.03; 0.06; 0.12; 0.6; 1.2; 2.4; 4.8 mM), and control were evaluated. All assays were performed in quadruplicates with 25 seeds per replication in Petri dishes. Responses for toxic effect comprised the variables germination percentage, index of velocity of germination (IVG), length of aerial section and roo...

  7. Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L..

    Directory of Open Access Journals (Sweden)

    Mahendar Thudi

    Full Text Available Chickpea (Cicer arietinum L. is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR markers from bacterial artificial chromosome (BAC-end sequences (BESs and diversity arrays technology (DArT markers, and to construct a high-density genetic map based on recombinant inbred line (RIL population ICC 4958 (C. arietinum×PI 489777 (C. reticulatum. A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/. The number of markers per linkage group ranged from 68 (LG 8 to 218 (LG 3 with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes.

  8. Tethering of the conserved piggyBac transposase fusion protein CSB-PGBD3 to chromosomal AP-1 proteins regulates expression of nearby genes in humans.

    Directory of Open Access Journals (Sweden)

    Lucas T Gray

    2012-09-01

    Full Text Available The CSB-PGBD3 fusion protein arose more than 43 million years ago when a 2.5-kb piggyBac 3 (PGBD3 transposon inserted into intron 5 of the Cockayne syndrome Group B (CSB gene in the common ancestor of all higher primates. As a result, full-length CSB is now coexpressed with an abundant CSB-PGBD3 fusion protein by alternative splicing of CSB exons 1-5 to the PGBD3 transposase. An internal deletion of the piggyBac transposase ORF also gave rise to 889 dispersed, 140-bp MER85 elements that were mobilized in trans by PGBD3 transposase. The CSB-PGBD3 fusion protein binds MER85s in vitro and induces a strong interferon-like innate antiviral immune response when expressed in CSB-null UVSS1KO cells. To explore the connection between DNA binding and gene expression changes induced by CSB-PGBD3, we investigated the genome-wide DNA binding profile of the fusion protein. CSB-PGBD3 binds to 363 MER85 elements in vivo, but these sites do not correlate with gene expression changes induced by the fusion protein. Instead, CSB-PGBD3 is enriched at AP-1, TEAD1, and CTCF motifs, presumably through protein-protein interactions with the cognate transcription factors; moreover, recruitment of CSB-PGBD3 to AP-1 and TEAD1 motifs correlates with nearby genes regulated by CSB-PGBD3 expression in UVSS1KO cells and downregulated by CSB rescue of mutant CS1AN cells. Consistent with these data, the N-terminal CSB domain of the CSB-PGBD3 fusion protein interacts with the AP-1 transcription factor c-Jun and with RNA polymerase II, and a chimeric CSB-LacI construct containing only the N-terminus of CSB upregulates many of the genes induced by CSB-PGBD3. We conclude that the CSB-PGBD3 fusion protein substantially reshapes the transcriptome in CS patient CS1AN and that continued expression of the CSB-PGBD3 fusion protein in the absence of functional CSB may affect the clinical presentation of CS patients by directly altering the transcriptional program.

  9. Konstrukce chromozómově specifické knihovny DNA klonované ve vektoru BAC pro chromozóm 3B pšenice (Triticum aestivum)

    Czech Academy of Sciences Publication Activity Database

    Šafář, Jan; Janda, Jaroslav; Bartoš, Jan; Doleželová, Marie; Čihalíková, Jarmila; Vrána, Jan; Bernard, M.; Chalhoub, B.; Doležel, Jaroslav

    Czech society for Analytical Cytology, 2003. s. 111 [Analytical cytometry /2./. 11.05.2003-14.05.2003, Brno] Institutional research plan: CEZ:AV0Z5038910 Keywords : chromosome specific libraries * flow cytometry * chromosome sorting Subject RIV: EB - Genetics ; Molecular Biology

  10. Insights into the Musa genome: Syntenic relationships to rice and between Musa species

    Directory of Open Access Journals (Sweden)

    Althoff Ryan

    2008-01-01

    Full Text Available Abstract Background Musa species (Zingiberaceae, Zingiberales including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of Musa genomic sequence have been conducted. This study compares genomic sequence in two Musa species with orthologous regions in the rice genome. Results We produced 1.4 Mb of Musa sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for Musa-Zingiber (Zingiberaceae, Zingiberales orthologs and paralogs provide strong evidence for a large-scale duplication event in the Musa lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from M. acuminata and M. balbisiana revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya. Conclusion These results point to the utility of comparative analyses between distantly-related monocot species such as rice and Musa for improving our understanding of monocot genome evolution. Sequencing the genome of M. acuminata would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated Musa polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic

  11. The alleviating effect of elevated CO2 on heat stress susceptibility of two wheat (Triticum aestivum L.) cultivars

    DEFF Research Database (Denmark)

    Kjær, Katrine Heinsvig; Ottosen, Carl-Otto; Rosenqvist, Eva S. K.;

    2013-01-01

    Title: The alleviating effect of elevated CO2 on heat stress susceptibility of two wheat (Triticum aestivum L.) cultivars Session: Plant response and adaptation to abiotic stress Sindhuja Shanmugam1, Katrine Heinsvig Kjaer2*, Carl-Otto Ottosen2, Eva Rosenqvist3, Dew Kumari Sharma3 and Bernd......Institute for Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark *Presenting author This study analysed the alleviating effect of elevated CO2 on stress-induced decreases in photosynthesis and changes in carbohydrate metabolism in two wheat cultivars (Triticum aestivum L.) of different...

  12. 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...

  13. Array comparative genomic hybridisation (aCGH) analysis of premenopausal breast cancers from a nuclear fallout area and matched cases from Western New York

    OpenAIRE

    Varma, G.; Varma, R.; Huang, H.; Pryshchepava, A; Groth, J.; Fleming, D; Nowak, N. J.; McQuaid, D; Conroy, J.; Mahoney, M; Moysich, K.; Falkner, K L; Geradts, J

    2005-01-01

    High-resolution array comparative genomic hybridisation (aCGH) analysis of DNA copy number aberrations (CNAs) was performed on breast carcinomas in premenopausal women from Western New York (WNY) and from Gomel, Belarus, an area exposed to fallout from the 1986 Chernobyl nuclear accident. Genomic DNA was isolated from 47 frozen tumour specimens from 42 patients and hybridised to arrays spotted with more than 3000 BAC clones. In all, 20 samples were from WNY and 27 were from Belarus. In total,...

  14. A one-megabase physical map provides insights on gene organization in the enormous mitochondrial genome of cucumber.

    Science.gov (United States)

    Bartoszewski, Grzegorz; Gawronski, Piotr; Szklarczyk, Marek; Verbakel, Henk; Havey, Michael J

    2009-04-01

    Cucumber (Cucumis sativus) has one of the largest mitochondrial genomes known among all eukaryotes, due in part to the accumulation of short 20 to 60 bp repetitive DNA motifs. Recombination among these repetitive DNAs produces rearrangements affecting organization and expression of mitochondrial genes. To more efficiently identify rearrangements in the cucumber mitochondrial DNA, we built two nonoverlapping 800 and 220 kb BAC contigs and assigned major mitochondrial genes to these BACs. Polymorphism carried on the largest BAC contig was used to confirm paternal transmission. Mitochondrial genes were distributed across BACs and physically distant, although occasional clustering was observed. Introns in the nad1, nad4, and nad7 genes were larger than those reported in other plants, due in part to accumulation of short repetitive DNAs and indicating that increased intron sizes contributed to mitochondrial genome expansion in cucumber. Mitochondrial genes atp6 and atp9 are physically close to each other and cotranscribed. These physical contigs will be useful for eventual sequencing of the cucumber mitochondrial DNA, which can be exploited to more efficiently screen for unique rearrangements affecting mitochondrial gene expression. PMID:19370086

  15. Využití BAC klonů při studiu pohlavního chromosomu W obaleče jablečného Cydia pomonella (Lepidoptera: Tortricidae)

    OpenAIRE

    Dalíková, Martina

    2009-01-01

    In the present study, the W sex-chromosome of the codling moth was studied by means of fluorescence in situ hybridization (FISH) with probes prepared from bacterial artificial chromosome (BAC), which were isolated from the codling moth BAC library. The BAC library was screened for clones derived from both the W and Z sex chromosomes using three sets of molecular markers of codling moth sex chromosomes. A total of 54 BAC clones have been obtained. In this work, only 3 W-derived BAC clones and ...

  16. Nicotine addiction phenotypes in a BAC transgenic mouse model overexpressing the CHRNA5/A3/B4 genomic cluster

    OpenAIRE

    Molas Casacuberta, Susanna, 1985-

    2012-01-01

    El cluster gen??mic CHRNA5/A3/B4 codifica per les subunitats alfa5, alfa3 i beta4dels receptors d???acetilcolina (nAChRs). Estudis de gen??tica humana han revelat quevariants en aquesta regi?? gen??mica estan significativament associats a la dependencia anicotina. Malauradament, els mecanismes pels quals la sobreexpressi?? d???aquestes tressubunitats influencia comportaments relacionats amb el consum de tabac no s??n del totconeguts. Per tal d???entendre els possibles mecanismes, hem utilitza...

  17. Chromosome arm-specific BAC end sequences permit comparative analysis of homoeologous chromosomes and genomes of polyploid wheat

    Czech Academy of Sciences Publication Activity Database

    Sehgal, S. K.; Li, W.; Rabinowicz, P. D.; Chan, A.; Šimková, Hana; Doležel, Jaroslav; Gill, B. S.

    2012-01-01

    Roč. 12, č. 64 (2012). ISSN 1471-2229 Grant ostatní: GA MŠk(CZ) ED0007/01/01 Institutional research plan: CEZ:AV0Z50380511 Keywords : BREAD WHEAT * BRACHYPODIUM-DISTACHYON * REPETITIVE ELEMENTS Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.354, year: 2012

  18. 普通小麦-簇毛麦易位系T6BS·6BL-2VS的选育%Identification of Triticum aestivum-Haynaldia villosa Translocation Line T6BS·6BL-2VS

    Institute of Scientific and Technical Information of China (English)

    陈全战; 张边江; 周峰; 吴梅; 李华春

    2008-01-01

    [Objective] The aim of experiment was to provide a new germplasm for wheat breeding by further using desirable genes in 2V chromosome of Haynaldia villosa.[Method] Through hybridization between common wheat(Triticum aestivum)-Haynaldia villosa disomic substitution line and common wheat Nonglin26-3C chromosome of Aegilops triuncialis disomic addition line, the analysis methods such as chromosome C-banding, genomic in situ hybridization and molecular marker technique were comprehensively applied and combined characters investigation.[Result] The wheat-Haynaldia villosa translocation line(T6BS·6BL-2VS) was selected from hybrid progenies to conduct characters investigation,which found some bristles on glume ridge of T6BS·6BL-2VS.[Conclusion] The translocation line induced by gametocidal chromosome was a small segment translocation line and the gene of bristle on glume ridge of Haynaldia villosa was located between the middle and the terminal of 2VS.

  19. Minimus: a fast, lightweight genome assembler

    Directory of Open Access Journals (Sweden)

    Salzberg Steven L

    2007-02-01

    Full Text Available Abstract Background Genome assemblers have grown very large and complex in response to the need for algorithms to handle the challenges of large whole-genome sequencing projects. Many of the most common uses of assemblers, however, are best served by a simpler type of assembler that requires fewer software components, uses less memory, and is far easier to install and run. Results We have developed the Minimus assembler to address these issues, and tested it on a range of assembly problems. We show that Minimus performs well on several small assembly tasks, including the assembly of viral genomes, individual genes, and BAC clones. In addition, we evaluate Minimus' performance in assembling bacterial genomes in order to assess its suitability as a component of a larger assembly pipeline. We show that, unlike other software currently used for these tasks, Minimus produces significantly fewer assembly errors, at the cost of generating a more fragmented assembly. Conclusion We find that for small genomes and other small assembly tasks, Minimus is faster and far more flexible than existing tools. Due to its small size and modular design Minimus is perfectly suited to be a component of complex assembly pipelines. Minimus is released as an open-source software project and the code is available as part of the AMOS project at Sourceforge.

  20. BACs-on-Beads:5所产前诊断实验室的前瞻性研究”点评

    Institute of Scientific and Technical Information of China (English)

    刘鹏飞; 王谢桐

    2012-01-01

    <正>1 原文摘要 Objective We previously reported on the validation of Prenatal BACs-on-Beads TM on retrospectively selected and prospective prenatal samples.This bead-based multiplex assay detects chromosome 13 , 18 , 21and X / Y aneuploidies and the nine most frequent microdeletion syndromes. We demonstrated that Prenatal BACs-on-Beads TM is a newgeneration , prenatal screening tool.Here , we describe the experience of five European prenatal diagnosis laboratories concerning the ongoing use of Prenatal BACs- on-Beads TM . Methods Some 1653samples were analyzed.

  1. Multiple endpoint analysis of BAC-preserved and unpreserved antiallergic eye drops on a 3D-reconstituted corneal epithelial model

    OpenAIRE

    Pauly, A; Brasnu, E.; Riancho, L.; Brignole-Baudouin, F.; Baudouin, C.

    2011-01-01

    Purpose To compare the effects of benzalkonium chloride (BAC)-preserved and unpreserved antiallergic eye drops on the human 3D-reconstituted corneal epithelial model (3D-HCE). Methods 3D-HCE were treated for 24 h followed or not by a 24 h post-incubation recovery period (24 h+24 h) with phosphate-buffered saline (PBS), 0.01% BAC, unpreserved formulations of ketotifen, N Acetyl-Aspartyl Glutamic Acid (NAAGA), cromoglycate, or BAC-preserved commercial formulations of ketotifen, olopatadine, epi...

  2. Genetic analysis of the Rhizobium meliloti bacA gene: functional interchangeability with the Escherichia coli sbmA gene and phenotypes of mutants.

    OpenAIRE

    Ichige, A; Walker, G C

    1997-01-01

    The Rhizobium meliloti bacA gene encodes a function that is essential for bacterial differentiation into bacteroids within plant cells in the symbiosis between R. meliloti and alfalfa. An Escherichia coli homolog of BacA, SbmA, is implicated in the uptake of microcin B17, microcin J25 (formerly microcin 25), and bleomycin. When expressed in E. coli with the lacZ promoter, the R. meliloti bacA gene was found to suppress all the known defects of E. coli sbmA mutants, namely, increased resistanc...

  3. Observing copepods through a genomic lens

    Directory of Open Access Journals (Sweden)

    Johnson Stewart C

    2011-09-01

    Full Text Available Abstract Background Copepods outnumber every other multicellular animal group. They are critical components of the world's freshwater and marine ecosystems, sensitive indicators of local and global climate change, key ecosystem service providers, parasites and predators of economically important aquatic animals and potential vectors of waterborne disease. Copepods sustain the world fisheries that nourish and support human populations. Although genomic tools have transformed many areas of biological and biomedical research, their power to elucidate aspects of the biology, behavior and ecology of copepods has only recently begun to be exploited. Discussion The extraordinary biological and ecological diversity of the subclass Copepoda provides both unique advantages for addressing key problems in aquatic systems and formidable challenges for developing a focused genomics strategy. This article provides an overview of genomic studies of copepods and discusses strategies for using genomics tools to address key questions at levels extending from individuals to ecosystems. Genomics can, for instance, help to decipher patterns of genome evolution such as those that occur during transitions from free living to symbiotic and parasitic lifestyles and can assist in the identification of genetic mechanisms and accompanying physiological changes associated with adaptation to new or physiologically challenging environments. The adaptive significance of the diversity in genome size and unique mechanisms of genome reorganization during development could similarly be explored. Genome-wide and EST studies of parasitic copepods of salmon and large EST studies of selected free-living copepods have demonstrated the potential utility of modern genomics approaches for the study of copepods and have generated resources such as EST libraries, shotgun genome sequences, BAC libraries, genome maps and inbred lines that will be invaluable in assisting further efforts to

  4. Biochemical analysis of whole wheat (triticum aestivum) flour of different wheat cultivars commonly grown in NWFP

    International Nuclear Information System (INIS)

    Whole wheat (Triticum aestivum) flour of six different NWFP wheat (Triticum aestivum) cultivars named as Ghaznavi-98, Auqab, Fakhr-e-sarhad Saleem-2000, Khyber-87 and Pirsabak-2005 were evaluated for Biochemical, Physical and Sensory characteristics in order to highlight their nutritional significance. The maximum level of Protein content (16.11%) was found in wheat cultivar Pirsabak-2005 where as minimum protein content was found in Auqab (11.73%). Crude fat content of whole-wheat flour was found lower in Khyber-87 (1.74%)and higher in Fakhr-e-sarhad (2.21%), Ghaznavi-98 was found to have maximum crude fiber value (0.74%) while Saleem-2000 was found to have minimum value (0.40%). Maximum ash content was found for Fakhr-e-sarhad (2.12%) and minimum was found for Saleem-2000 (1.05%). Wheat cultivars Ghaznavi-98 was found to have maximum moisture content (14%), while Pirsabak-2005 was found to have lower moisture content (13.11%). The wet gluten content was recorded in the range of 8.7 to 5.2% while dry gluten content was found in the ranged of 2.82 to 2.03% and The falling number was recorded in the range of 64 to 214 and significantly higher in saleem-2000 (214). For Sensory Evaluation, it is evidence that maximum overall acceptability were found both for Ghaznavi-98 and Pirsabak-2000 and Minimum for Saleem-2000 (6.4). (author)

  5. Effects of Radiofrequency Waves on the Catalase Content in Triticum Aestivum

    International Nuclear Information System (INIS)

    Full text: The aim of the present study is to investigate the possible effects on enzyme biosynthesis in Triticum aestivum cariopsydes due to exposure to traveling radiofrequency (RF) waves. Triticum cariopsydes have been exposed to traveling RF waves inside a transverse electromagnetic (TEM) cell fed by a RF Power Generator. The frequency of the exposure field was 400 MHz. The TEM cell was excited with 2W RF power in order to obtain a power density of about 1 mW/cm2. Four sets of Triticum aestivum samples were placed in four Petri dishes. For each set of Triticum cariopsydes there has been chosen a daily exposure duration of 1, 2, 4 and 8 hours respectively. Experimental exposure was carried out for five consecutive days. After the electromagnetic treatment cariopsydes were let to germinate in Petri dishes on porous filter paper support. A couple of days later the catalase assay was performed. In comparison to the control samples, exposed samples revealed modified catalase content, significantly over the error level (five replays of every sample were assayed in identical experimental conditions in order to provide a reliable statistic result). All exposed samples presented higher catalase levels in comparison to the control samples. However, the experimental data do not suggest an evident analytical dependence between the catalase content and the exposure time duration. We presume that exposure to traveling RF waves seems to be a stimulatory factor of the enzyme biosynthesis being able to improve Triticum capacity of enzyme biosynthesis in the described experimental conditions. (author)

  6. The physiological significance of HKT1, a Na+ - coupled high affinity K+ transporter in 'Triticum aestivum'

    International Nuclear Information System (INIS)

    Full text: Several mechanisms for high affinity K+ uptake by higher plants have been proposed:-an ATP-energised K:+ pump, a K+/H+ antiport and a H+coupled carrier. Recently, a Na+--coupled high affinity K+ transporter, HKT1, was isolated from wheat roots. Whilst Na+K+ symports have been described in charophyte algae, the cloning of HKT1 from wheat is the first, evidence that this type d transport mechanism may function in higher plants. Is the activity of HKT1 an important mechanism involved in K+ acquisition by wheat? The aim of this study was to assess the physiological significance of Na+- coupled high affinity K+ uptake in T. aestivum. To determine whether HKT1 plays a significant role in wheat growth, we measured the dry weights and ion content of plants grown in a range of [K+], with and without Na+. To directly assess the activity of Na+- coupled K+ transport, 86Rb+ and 22Na+ flux analyses were performed on the elongation zones and whole roots of intact seedlings, expressing a high affinity K+ uptake system. The results of these growth and tracer flux studies will be discussed in relation to the expression of the gene encoding HKT1 in T. aestivum

  7. Molecular verification of the integration of Tripsacum dactyloides DNA into wheat genome through wide hybridization

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    RAPD and RFLP analyses of double haploid lines which derived from hybridization between hexaploid wheat (Triticum aestivum L.2n=42) and eastern gamagrass (Tripsacum dactyloides L.2n=4x=72) are reported.Two of the 340 Operon primers have been screened,which stably amplified Tripsacum dactyloides (male parent) specific bands in the double haploid lines.These results confirm the fact that Tripsacum dactyloides DNA has been integrated into wheat genome by sexual hybridization at molecular level.This idea has been further testified by RFLP analysis.Application and potentials of transferring Tripsacum dactyloides DNA into wheat genome by sexual hybridization in wheat breeding are discussed.

  8. Molecular characterization of LMW-GS genes from a somatic hybrid introgression line Ⅱ-12 between Triticum aestivum and Agropyron elongatum in relation to quick evolution

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    In order to exploit the evolution and find novel low-molecular-weight glutenin subunit(LMW-GS)for improvement of common wheat quality,thirteen variants from a somatic hybrid introgression line Ⅱ-12 between Triticum aestivum cv.Jinan 177(JN177)and Agropyron elongatum were characterized via genomic PCR.Four clones were pseudogenes because they contained an internal stop codon.The remaining nine variants contained intact open reading frames(ORFs).Sequence alignment indicates that the proteins deduced from the nine ORFs have similar primary structure with LMW-GS cloned from its parents previously.However,they have some unique modifications in the structures.For example,EU292737 contains not only an extra Cys residue in the C-terminal domain but also a long repetitive domain.Both EU159511 and EU292738 start their first Cys residue in the N-terminal repetitive domain,but not in the N-conserved domain traditionally.These structural alterations may have positive contributions to wheat flour quality.The results of phylogeny showed that most LMW-GS variances from Ⅱ-12 were homologous to those from parent JN 177 and other wheat lines.The reason for quick evolution of LMW-GS in Ⅱ-12 was discussed.

  9. 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.

  10. STUDY OF THE ANTIHYPERLIPIDEMIC, ANTIOXIDATIVE AND ANTIATHEROGENIC ACTIVITY OF TRITICUM AESTIVUM LINN. IN RABBIT RECEIVING HIGH FAT DIET

    Directory of Open Access Journals (Sweden)

    Das Swarnamoni

    2012-10-01

    Full Text Available The aim was to study of the antihyperlipidemic, antioxidative and antiatherogenic activity of Triticum aestivum Linn. in rabbit receiving high fat diet. Twenty rabbits of either sex were taken and divided into four groups five in each as - Normal Control- received normal diet, Hyperlipidemic control- received high fat diet, Test drug group - received high fat diet plus ethanolic extract of Triticum aestivum 500 mg/Kg /day orally and Standard Drug group- received high fat diet plus Atorvastatin 2.1 mg/Kg/day orally for 12 weeks and then animals were sacrificed. Blood sample were collected and lipid profile, catalase, superoxide dismutase and malondialdehyde levels were measured. The antiatherogenic effect was examined by histopathology of aorta. Data were statistically analysed by one way ANOVA followed by Dunnett’s multiple comparison test. Triticum aestivum significantly decreased serum lipids towards normal levels. It also increases catalase and superoxide dismutase activity and decreases malondialdehyde level and histopathological examination revealed prevention of atherosclerosis. Triticum aestivum has antihyperlipidemic, antioxidant and anti atherogenic effects.

  11. Acute toxicity test of a natural iron chelator and an antioxidant, extracted from Triticum aestivum Linn. (wheat grass).

    Science.gov (United States)

    Das, Priyabrata; Mukhopadhyay, Soma; Mandal, Suvra; Chakraborty, Abhijit; Pal, Amartya; Sarkar, Nirmal Kumar; Mukhopadhyay, Ashis

    2014-01-01

    Triticum aestivum (wheat grass) is widely used in traditional medicine to treat various diseases. Previously the purified compounds and crude extract of T. aestivum were established to have iron chelation potency and antioxidant activity. So it is necessary to evaluate the toxic properties of any compound isolated from plant extract to prevent any untoward side effects. The aim of this study was to determine the acute oral toxicity level of our purified compounds, i.e. mugineic acids and methylpheophorbide a., and crude extract of T. aestivum, on Swiss albino mice at dosage of 2000 mg/kg for a period of 14 days using the organisation for economic co-operation and development guidelines 423. There was no mortality. No change in behavioural pattern, clinical signs, body weight and blood biochemistry profile were observed. Kidney and liver showed normal histo-pathological architecture. Hence, the oral administration of compounds and extract of T. aestivum did not produce any significant toxic effect on mice. Thus we may conclude that the extract can be utilised for pharmaceutical formulations as iron chelator and antioxidant agent for various diseases. PMID:24697628

  12. Studies on certain aspects of seed-borne fungi. VI. Fungi associated with different cultivars of wheat (Triticum aestivum L.)

    OpenAIRE

    Pandey, K. K.

    2014-01-01

    Fungi associated with eight cultivars of wheat have been investigated. Twenty seven species were isolated from external and internal surface of all the wheat (Triticum aestivum L.) cultivars respectively. Out of five dominant and subdominant fungi anly Aspergillus terreus and Alternaria tenuis were able to colonize internally. The culture filtrates of test fungi reduced the germination of all wheat varieties up to different degrees.

  13. TOXICITY OF METHYL-TERT BYTYL ETHER (MTBE) TO PLANTS (AVENA SATIVA, ZEA MAYS, TRITICUM AESTIVUM, AND LACTUCA SATIVA)

    Science.gov (United States)

    Effects of Methyl tert-butyl ether (MTBE) on the germination of seeds and growth of the plant were studied in some laboratory experiments. Test plants were wild oat (Avena sative), sweet corn (Zea mays), wheat (Triticum aestivum), and lettuce (Lactuca sativa). Seed germination,...

  14. The genome of chelonid herpesvirus 5 harbors atypical genes

    OpenAIRE

    Ackermann, Mathias; Koriabine, Maxim; Hartmann-Fritsch, Fabienne; de Jong, Pieter J; Lewis, Teresa D.; Schetle, Nelli; Work, Thierry M.; Dagenais, Julie; Balazs, George H.; Leong, Ann C

    2012-01-01

    The Chelonid fibropapilloma-associated herpesvirus (CFPHV; ChHV5) is believed to be the causative agent of fibropapillomatosis (FP), a neoplastic disease of marine turtles. While clinical signs and pathology of FP are well known, research on ChHV5 has been impeded because no cell culture system for its propagation exists. We have cloned a BAC containing ChHV5 in pTARBAC2.1 and determined its nucleotide sequence. Accordingly, ChHV5 has a type D genome and its predominant gene order is typical ...

  15. Natural production of Tuber aestivum in central Spain: Pinus spp. versus Quercus spp. brûlés

    Directory of Open Access Journals (Sweden)

    Luis G. Garcia-Montero

    2014-08-01

    Full Text Available Aim of study: Tuber aestivum is the most widespread edible truffle, with increasing commercial interest. This species can produce carpophores with conifer hosts, in contrast with the inability of Pinus spp. to induce fruiting in other truffle species such as Tuber melanosporum. Therefore the objective is to compare the characteristics and carpophore production of T. aestivum brûlés associated with Pinus spp. versus Quercus spp.Area of study: We studied the natural habitats of T. aestivum in the Alto Tajo Nature Reserve in central Spain.Material and methods: During 5 years, we monitored the production of carpophores and brûlé size of 145 T. aestivum brûlés associated with Pinus nigra subsp. salzmanni and P. sylvestris and Quercus ilex subsp. ballota and Q. faginea hosts. Statistical treatment was performed using the Statistica Program v. 6.Main Results: The size of brûlés associated with Pinus was significantly smaller than that of brûlés associated with Quercus. However, carpophore production per brûlé, and especially for brûlés of similar size, was greater when the host plant was a pine. After accounting for brûlé size, the production of brûlés associated with Pinus spp. was 2.23 (95% CI, between 1.35 and 3.69 and 1.61 (95% CI, between 1.02 and 2.54 times greater than the production of brûlés associated with Quercus faginea and Q. ilex subsp. ballota, respectively.Research highlights: The considerable ability of Pinus nigra subsp. salzmanni and P. sylvestris to form effective brûlés and to produce carpophores of Tuber aestivum in natural conditions was clearly demonstrated, and suggest that those species can be of use in the culture of T. aestivum.Key words: Summer truffle; Tuber aestivum; truffle culture; truffle ecology; Pinus spp.; Quercus spp.

  16. Primers for the Amplification of the Circular Chloroplast DNA from the A-genome Group of Cultivated Cotton

    Institute of Scientific and Technical Information of China (English)

    IBRAHIM Rashid Ismael Hag; AZUMA Jun-Ichi; SAKAMOTO Masahiro

    2008-01-01

    @@ The availability of the plastid genome sequences is one of the bases for comparative,functional,and structural genomic studies of plastid-containing living organisms,in addition to the application of plastid genetic engineering technology.The past efforts to sequence plastid genomes involve complicated preparation protocols.One procedure starts with the isolation of plastids,which was tiresome and time wasting that followed by a second step to extract plastid DNA from the isolated plastids,then finally the build up of plasmid or bacterial artificial chromosome (BAC) library.

  17. Thinopyrum ponticum chromatin-integrated wheat genome shows salt-tolerance at germination stage.

    Science.gov (United States)

    Yuan, Wen-Ye; Tomita, Motonori

    2015-01-01

    A wild wheatgrass, Thinopyrum ponticum (2n = 10x = 70), which exhibits substantially higher levels of salt tolerance than cultivated wheat, was employed to transfer its salt tolerance to common wheat by means of wide hybridization. A highly salt-tolerant wheat line S148 (2n = 42) was obtained from the BC3F2 progenies between Triticum aestivum (2n = 42) and Th. ponticum. In the cross of S148 × salt-sensitive wheat variety Chinese Spring, the BC4F2 seeds at germination stage segregated into a ratio of 3 salt tolerant to 1 salt sensitive, indicating that the salt tolerance was conferred by a dominant gene block. Genomic in situ hybridization analysis revealed that S148 had a single pair of Th. ponticum-T. aestivum translocated chromosomes bearing the salt-tolerance. This is an initial step of molecular breeding for salt-tolerant wheat. PMID:25809604

  18. Thinopyrum ponticum Chromatin-Integrated Wheat Genome Shows Salt-Tolerance at Germination Stage

    Directory of Open Access Journals (Sweden)

    Wen-Ye Yuan

    2015-02-01

    Full Text Available A wild wheatgrass, Thinopyrum ponticum (2n = 10x = 70, which exhibits substantially higher levels of salt tolerance than cultivated wheat, was employed to transfer its salt tolerance to common wheat by means of wide hybridization. A highly salt-tolerant wheat line S148 (2n = 42 was obtained from the BC3F2 progenies between Triticum aestivum (2n = 42 and Th. ponticum. In the cross of S148 × salt-sensitive wheat variety Chinese Spring, the BC4F2 seeds at germination stage segregated into a ratio of 3 salt tolerant to 1 salt sensitive, indicating that the salt tolerance was conferred by a dominant gene block. Genomic in situ hybridization analysis revealed that S148 had a single pair of Th. ponticum–T. aestivum translocated chromosomes bearing the salt-tolerance. This is an initial step of molecular breeding for salt-tolerant wheat.

  19. Sequencing of bovine herpesvirus 4 v.test strain reveals important genome features

    Directory of Open Access Journals (Sweden)

    Gillet Laurent

    2011-08-01

    Full Text Available Abstract Background Bovine herpesvirus 4 (BoHV-4 is a useful model for the human pathogenic gammaherpesviruses Epstein-Barr virus and Kaposi's Sarcoma-associated Herpesvirus. Although genome manipulations of this virus have been greatly facilitated by the cloning of the BoHV-4 V.test strain as a Bacterial Artificial Chromosome (BAC, the lack of a complete genome sequence for this strain limits its experimental use. Methods In this study, we have determined the complete sequence of BoHV-4 V.test strain by a pyrosequencing approach. Results The long unique coding region (LUR consists of 108,241 bp encoding at least 79 open reading frames and is flanked by several polyrepetitive DNA units (prDNA. As previously suggested, we showed that the prDNA unit located at the left prDNA-LUR junction (prDNA-G differs from the other prDNA units (prDNA-inner. Namely, the prDNA-G unit lacks the conserved pac-2 cleavage and packaging signal in its right terminal region. Based on the mechanisms of cleavage and packaging of herpesvirus genomes, this feature implies that only genomes bearing left and right end prDNA units are encapsulated into virions. Conclusions In this study, we have determined the complete genome sequence of the BAC-cloned BoHV-4 V.test strain and identified genome organization features that could be important in other herpesviruses.

  20. Impact of Low-Energy Ion Beam Implantation on the Expression of Ty1-copia-like Retrotransposons in Wheat (Triticum aestivum)

    International Nuclear Information System (INIS)

    Retrotransposon-like elements are major constituents of most eukaryotic genomes. For example, they account for roughly 90% of the wheat (Triticum aestivum) genome. Previous study on a wheat strain treated by low-energy N+ ions indicated the variations in AFLP (Amplified Fragment Length Polymorphism ) markers. One such variation was caused by the re-activation of Ty1-copia-like retrotransposons, implying that the mutagenic effects of low-energy ions might work through elevated activation of retrotransposons. In this paper an expression profile of Ty1-copia-like retrotransposons in wheat treated by low-energy N+ ions is reported. The reverse transcriptase (RT) domains of these retrotransposons were amplified by reverse-transcriptional polymerase chain reaction (RT-PCR) and sequentially cloned. 42 and 65 clones were obtained from the treated (CL) and control materials (CK), respectively. Sequence analysis of each clone was performed by software. Phylogeny and classification were calculated responding to the sequences of the RT domains. All the results show that there is much difference in the RT domain between the control sample and the treated sample. Especially, the RT domains from the treated group encode significantly more functional ORF (open reading frames) than those from the control sample. This observation suggests that the treated sample has higher activation of retrotransposons, possibly as a consequence of low-energy ion beam irradiation. It also suggests that retrotransposons in the two groups impact the host gene expression in two different ways and carry out different functions in wheat cells