Relevant bibliographies by topics / Mammalian genomics

Academic literature on the topic 'Mammalian genomics'

Author: Grafiati
Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Mammalian genomics"

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Wayne, R. K., and E. A. Ostrander. "Mammalian genomics:." Heredity 92, no. 4 (March 24, 2004): 273–74. http://dx.doi.org/10.1038/sj.hdy.6800428.

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O'Brien, S. J. "GENOMICS: On Choosing Mammalian Genomes for Sequencing." Science 292, no. 5525 (June 22, 2001): 2264–66. http://dx.doi.org/10.1126/science.1059393.

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Jones, N. C., and P. A. Pevzner. "Comparative genomics reveals unusually long motifs in mammalian genomes." Bioinformatics 22, no. 14 (July 15, 2006): e236-e242. http://dx.doi.org/10.1093/bioinformatics/btl265.

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Wuest, Diane M., Sarah W. Harcum, and Kelvin H. Lee. "Genomics in mammalian cell culture bioprocessing." Biotechnology Advances 30, no. 3 (May 2012): 629–38. http://dx.doi.org/10.1016/j.biotechadv.2011.10.010.

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Wixon, Jo. "Meeting Highlights: Genome Sequencing and Biology 2001." Comparative and Functional Genomics 2, no. 4 (2001): 243–51. http://dx.doi.org/10.1002/cfg.97.

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We bring you a report from the CSHL Genome Sequencing and Biology Meeting, which has a long and prestigious history. This year there were sessions on large-scale sequencing and analysis, polymorphisms (covering discovery and technologies and mapping and analysis), comparative genomics of mammalian and model organism genomes, functional genomics and bioinformatics.
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Madende, Moses, and Gernot Osthoff. "Comparative genomics of casein genes." Journal of Dairy Research 86, no. 3 (July 24, 2019): 323–30. http://dx.doi.org/10.1017/s0022029919000414.

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AbstractThis research paper addresses the hypothesis that comparative genomics can give a new insight into the functionality of casein genes with respect to the casein micelle. Comparative genomics is a rapidly emerging field in computational biology whereby two or more genomes are compared in order to obtain a global view on genomes as well as assigning previously unknown functions for genes. Casein genes are among the most rapidly evolving mammalian genes, with the gene products mainly grouped into four types (αs1-, αs2-, β- and κ-casein). Functionally, casein genes are central to the casein micelle, the exact structure of which is still a subject of intense debate. Moreover, and adding to this complexity, some mammals lack some of the casein genes, although casein micelles have been observed in their milk. This observation has prompted an investigation into the distribution of casein genes across a host of mammalian species. It was apparent from this study that casein gene sequences are very diverse from each other and we confirmed that many mammalian species lack one or more of the casein genes. The genes encoding β- and κ-caseins are present in most mammals whereas α-casein encoding genes are less represented. This suggests different mechanisms for casein micelle formation in different species as well as the functions that are assigned to each individual casein.
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Rodriguez-Osorio, Nelida, Hongfeng Wang, Jennifer Rupinski, Susan M. Bridges, and Erdogan Memili. "Comparative functional genomics of mammalian DNA methyltransferases." Reproductive BioMedicine Online 20, no. 2 (February 2010): 243–55. http://dx.doi.org/10.1016/j.rbmo.2009.11.006.

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Holmes, Roger S., Laura A. Cox, and John L. VandeBerg. "Mammalian carboxylesterase 3: comparative genomics and proteomics." Genetica 138, no. 7 (April 28, 2010): 695–708. http://dx.doi.org/10.1007/s10709-010-9438-z.

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Holmes, Roger S., Laura A. Cox, and John L. VandeBerg. "Mammalian carboxylesterase 5: Comparative biochemistry and genomics." Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 3, no. 3 (September 2008): 195–204. http://dx.doi.org/10.1016/j.cbd.2008.05.002.

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Li, W. H., J. Nadeau, E. Ostrander, B. Van Valkenburgh, and P. Waddell. "Comparative Genomics: Mammalian Radiations -- Genome Maps 10." Science 286, no. 5439 (October 15, 1999): 463–78. http://dx.doi.org/10.1126/science.286.5439.463.

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Dissertations / Theses on the topic "Mammalian genomics"

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Mikkelsen, Tarjei Sigurd 1978. "Mammalian comparative genomics and epigenomics." Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/52808.

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Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student submitted PDF version of thesis.
Includes bibliographical references.
The human genome sequence can be thought of as an instruction manual for our species, written and rewritten over more than a billion of years of evolution. Taking a complete inventory of our genome, dissecting its genes and their functional components, and elucidating how these genes are selectively used to establish and maintain cell types with markedly different behaviors, are key challenges of modern biology. In this thesis we present contributions to our understanding of the structure, function and evolution of the human genome. We rely on two complementary approaches. First, we study signatures of evolutionary processes that have acted on the genome using comparative sequence analysis. We generate high quality draft genome sequences of the chimpanzee, the dog and the opossum. These species share a last common ancestor with humans approximately 6 million, 80 million and 140 million years ago, respectively, and therefore provide distinct perspectives on our evolutionary history. We apply computational methods to explore the functional organization of the genome and to identify genes that contribute to shared and species-specific traits. Second, we study how the genome is bound by proteins and packaged into chromatin in distinct cell types. We develop new methods to map protein-DNA interactions and DNA methylation using single-molecule based sequencing technology. We apply these methods to identify new functional sequence elements based on characteristic chromatin signatures, and to explore the relationship between DNA sequence, chromatin and cellular state.
by Tarjei Sigurd Mikkelsen.
Ph.D.
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Kiritsy, Michael C. "Functional Genomics of Mammalian Innate Immunity." eScholarship@UMMS, 2020. https://escholarship.umassmed.edu/gsbs_diss/1102.

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The breadth of genetic diversity in the mammalian immune response stands out amongst the ubiquity of variation seen in the genome, evidence that microbial infections have been a major driver of evolution. As technology has facilitated an understanding of the etiology of immunological diversity, so too has it enabled the assessment of its varied functions. Functional genomics, with its ability to assess both cause and effect, has revolutionized our understanding of fundamental biological phenomena and recalibrated our hypotheses. We build upon the model of host immunity established by rare genetic variants that are causative of immunodeficiencies, but that incompletely consider the complexities of the genome. To expand our understanding, we performed a series of forward genetic screens to identify regulators of distinct functions of the innate immune system. Our studies discovered genes with novel functions in antigen presentation and immunoregulation, including several involved in central metabolism. Studies in macrophages and dendritic cells identified mitochondrial respiration as a positive regulator of the interferon-gamma response, and cells incapable of respiration failed to activate T cells. Notably, human mutations in several of these genes are responsible for immune dysfunction. In summary, this work uses new methods in genetic engineering to systematically assess the regulation of innate immunity. Our results suggest that variation in these regulatory pathways is likely to alter immunity in states of health and disease. Thus, our work validates a new approach to identify candidate genes relevant to immune dysfunction.
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Villanueva, Cañas José Luis 1984. "Insights into mammalian adaptive evolution through genomics data." Doctoral thesis, Universitat Pompeu Fabra, 2015. http://hdl.handle.net/10803/397756.

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Although the genome sequencing revolution is still in its infancy, we must acknowledge it as the major driver of biology since the beginning of the 21st century. The availability of a large collection of complete mammalian genomes due to high-throughput sequencing technologies allows us to begin the exploration of how the evolutionary diversification of gene content reflects the ecological adaptations of different taxa. Novelty arises in evolution through the transformation or combination of existing systems and, as shown recently, also from scratch. This thesis is centered around these different mechanisms of evolutionary innovation. It includes a common methodological part in which we propose a simple method to optimize multiple alignments and examine its effect in positive selection analyses, the exploration of the origin and evolution of mammalian-specific genes, and the study of gene regulation in mammalian adaptations (e.g. hibernation) using high-throughput technologies.
Tot i que la denominada era de la genòmica es troba encara a la seva infància, ha estat un dels principals impulsors de la biologia des del començament del segle 21. L’accés a una creixent col•lecció de genomes complets de mamífers, gràcies a les tècniques de seqüenciació massiva, ens permet explorar com la diversificació evolutiva dels gens es tradueix en les diferents adaptacions ecològiques dels diferents tàxons. La innovació apareix a l’evolució a través de la transformació o la combinació de sistemes preexistents, fins i tot, nous gens poden aparèixer a partir de regions prèviament no codificants, com s’ha demostrat recentment. Aquesta tesi s’articula al voltant d’aquests mecanismes d’innovació evolutiva. Inclou una part metodològica comuna on es proposa un mètode simple per optimitzar alineaments múltiples i avaluar-ne l’efecte en anàlisis de selecció positiva, l’exploració de l’origen i evolució de gens específics de mamífers i l’estudi de la regulació gènica en una adaptació pròpia dels mamífers (hibernació) mitjançant tècniques de seqüenciació massiva.
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Cheung, Hiu Tung (Tom). "Understanding mammalian transcriptional regulation using comparative and functional genomics." Diss., Connect to online resource, 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3207751.

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Jordan, Gregory. "Analysis of alignment error and sitewise constraint in mammalian comparative genomics." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610693.

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Siepel, Adam C. "Comparative mammalian genomics : models of evolution and detection of functional elements /." Diss., Digital Dissertations Database. Restricted to UC campuses, 2005. http://uclibs.org/PID/11984.

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Ratcliffe, Sarah. "Identification of a silicon-responsive gene in the mammalian genome." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610011.

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Hsiao, Albert. "Comparative functional genomics of energy metabolism and insulin resistance in mammalian systems." Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2005. http://wwwlib.umi.com/cr/ucsd/fullcit?p3165076.

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Thesis (Ph.D.)--University of California, San Diego, 2005.
Title from p. 1 of PDF file (viewed October 21, 2005) Vita. Includes bibliographical references (p. 170-175 ). Available online via UMI ProQuest Digital Dissertations.
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Saini, Harleen. "Intron and Small RNA Localization in Mammalian Neurons." eScholarship@UMMS, 2019. https://escholarship.umassmed.edu/gsbs_diss/1044.

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RNA molecules are diverse in form and function. They include messenger RNAs (mRNAs) that are templates for proteins, splice products such as introns that can generate functional noncoding RNAs, and a slew of smaller RNAs such as transfer RNAs (tRNAs) that help decode mRNAs into proteins. RNAs can show distinct patterns of subcellular localization that play an important role in protein localization. However, RNA distribution in cells is incompletely understood, with prior studies focusing primarily on RNAs that are long (>200 nucleotides), fully processed, and polyadenylated. We examined the distribution of RNAs in neurons. Neuronal compartments can be separated by long distances and play distinct roles, raising the possibility that RNA localization is especially overt and functionally meaningful in these cells. In our exploration, we physically dissected projections from cell bodies of neurons from the rat brain and sequenced total RNA. We describe two main findings. First, we identified excised introns that are enriched in neuronal projections and confirmed their localization by single- molecule fluorescence in situ hybridization. These are a previously unknown set of circular RNAs in neuronal projections: tailless lariats that possess a non- canonical C branchpoint. Second, we observed a highly abundant population of small (20-150 nucleotide) RNAs in neuronal projections, most of which are tRNAs. For both circular introns and tRNAs, we did not observe known RNA localization signals. Thus, many types of RNA, if sufficiently stable, appear free to diffuse to distant locations, their localization perhaps aided by the movement of large organelles in the confines of neuronal projections. Our survey of RNA molecules across subcellular compartments provides a foundation for investigating the function of these molecules and the mechanisms that localize them.
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Endo, Yoshinori. "Comparative study of mammalian evolution by genomic analyses and pluripotent stem cell technology." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263514.

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Books on the topic "Mammalian genomics"

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Ruvinsky, A., and J. A. Marshall Graves, eds. Mammalian genomics. Wallingford: CABI, 2005. http://dx.doi.org/10.1079/9780851999104.0000.

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Organisation for Economic Co-operation and Development., ed. Mammalian embryo genomics. Paris: Organisation for Economic Co-operation and Development, 2003.

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Hu, Wei Shou, and An-Ping Zeng, eds. Genomics and Systems Biology of Mammalian Cell Culture. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-28350-5.

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An-Ping, Zeng, and SpringerLink (Online service), eds. Genomics and Systems Biology of Mammalian Cell Culture. 2nd ed. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012.

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Foreign DNA in mammalian systems. Weinheim: Wiley-VCH, 2000.

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Manocha, Marcus M. S. Isolation and characterization of genomic DNA sequences that enhance the stability of plasmid DNA in mammalian cells. St. Catharines, Ont: Brock University, Centre for Biotechnology, 2005.

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Mammalian Embryo Genomics. OECD, 2003. http://dx.doi.org/10.1787/9789264104273-en.

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(Editor), A. Ruvinsky, and J. A. Marshall Graves (Editor), eds. Mammalian Genomics (Cabi Publishing). CABI, 2005.

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Genomics And Systems Biology Of Mammalian Cell Culture. Springer, 2012.

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Zeng, An-Ping, and Wei Shou Hu. Genomics and Systems Biology of Mammalian Cell Culture. Springer, 2012.

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Book chapters on the topic "Mammalian genomics"

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Recillas-Targa, Félix, Georgina Guerrero, Martín Escamilla-del-Arenal, and Héctor Rincón-Arano. "Gene Expression in Mammalian Cells." In Genomics, 155–72. Chichester, UK: John Wiley & Sons, Ltd, 2010. http://dx.doi.org/10.1002/9780470711675.ch7.

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Goodstadt, Leo, and Chris P. Ponting. "Mammalian Genes and Evolutionary Genomics." In The Proteomics Protocols Handbook, 543–53. Totowa, NJ: Humana Press, 2005. http://dx.doi.org/10.1385/1-59259-890-0:543.

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Alekseyev, Max A., and Pavel A. Pevzner. "Limited Lifespan of Fragile Regions in Mammalian Evolution." In Comparative Genomics, 198–215. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-16181-0_17.

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Wienberg, J., L. Frönicke, and R. Stanyon. "Insights into Mammalian Genome Organization and Evolution by Molecular Cytogenetics." In Comparative Genomics, 207–44. Boston, MA: Springer US, 2000. http://dx.doi.org/10.1007/978-1-4615-4657-3_8.

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Delbridge, Margaret L. "Gene Content of the Mammalian X Chromosome." In Marsupial Genetics and Genomics, 173–85. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-9023-2_9.

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Ryvkin, Paul, Jin Jun, Edward Hemphill, and Craig Nelson. "Duplication Mechanism and Disruptions in Flanking Regions Influence the Fate of Mammalian Gene Duplicates." In Comparative Genomics, 26–39. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-87989-3_3.

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Banerjee, Nilanjana, and Andrea Califano. "Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment-Independent Conservation Maps." In Comparative Genomics, 200–214. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11864127_16.

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Jun, Jin, Paul Ryvkin, Edward Hemphill, Ion Măndoiu, and Craig Nelson. "Estimating the Relative Contributions of New Genes from Retrotransposition and Segmental Duplication Events during Mammalian Evolution." In Comparative Genomics, 40–54. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-87989-3_4.

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Matsuzawa, Shu-ichi, and John C. Reed. "Yeast and Mammalian Two-Hybrid Systems for Studying Protein-Protein Interactions." In Cancer Genomics and Proteomics, 215–25. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-335-6_14.

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Al Nadaf, Shafagh, Paul D. Waters, Janine E. Deakin, and Jennifer A. Marshall Graves. "Marsupial Genetics Reveals Insights into Evolution of Mammalian X Chromosome Inactivation." In Marsupial Genetics and Genomics, 259–80. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-9023-2_13.

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Conference papers on the topic "Mammalian genomics"

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Bhatkar, Anup, and J. L. Rana. "Notice of Violation of IEEE Publication Principles - Estimating neutral divergence amongst Mammals for Comparative Genomics with Mammalian scope." In 2006 9th International Conference on Information Technology. IEEE, 2006. http://dx.doi.org/10.1109/icit.2006.52.

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Faryabi, Babak, Golnaz Vahedi, Jean-Francois Chamberland, Aniruddha Datta, and Edward R. Dougherty. "Constrained intervention in a cancerous mammalian cell cycle network." In 2008 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). IEEE, 2008. http://dx.doi.org/10.1109/gensips.2008.4555669.

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Haussler, David. "Computational analysis of the human and other mammalian genomes." In the seventh annual international conference. New York, New York, USA: ACM Press, 2003. http://dx.doi.org/10.1145/640075.640093.

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Tsang, Hiu-Gwen, Emily L. Clark, Stephen J. Bush, David A. Hume, Brendan M. Corcoran, Vicky E. MacRae, and Kim M. Summers. "8 Generating a genomic-wide transcriptomic atlas of the mammalian cardiovascular system." In 20th Scottish Cardiovascular, Forum Abstracts, February 4th 2017, University of Glasgow, UK. BMJ Publishing Group Ltd and British Cardiovascular Society, 1997. http://dx.doi.org/10.1136/heartjnl-2017-311433.8.

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Vanoli, Fabio, Shuhei Ito, Richard L. Frock, Frederick W. Alt, Mary Ellen Moynahan, and Maria Jasin. "Abstract B37: PARP inhibitor olaparib induces genomic instability in normal mammalian cells." In Abstracts: AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; November 2-5, 2016; Montreal, QC, Canada. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1557-3125.dnarepair16-b37.

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Li, G., S. S. Nair, S. J. Lees, and F. W. Booth. "Regulation of G2/M Transition in Mammalian Cells by Oxidative Stress." In ASME 2005 International Mechanical Engineering Congress and Exposition. ASMEDC, 2005. http://dx.doi.org/10.1115/imece2005-82349.

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The regulation of the G2/M transition for the mammalian cell cycle has been modeled using 19 states to investigate the G2 checkpoint dynamics in response to oxidative stress. A detailed network model of G2/M regulation is presented and then a “core” subsystem is extracted from the full network. An existing model of Mitosis control is extended by adding two important pathways regulating G2/M transition in response to DNA damage induced by oxidative stress. Model predictions indicate that the p53 dependent pathway is not required for initial G2 arrest as the Chk1/Cdc25C pathway can arrest the cell in G2 right after DNA damage. However, p53 and p21 expression is important for a more sustained G2 arrest by inhibiting the Thr161 phosphorylation by CAK. By eliminating the phosphorylation effect of Chk1 on p53, two completely independent pathways are obtained and it is shown that it does not affect the G2 arrest much. So the p53/p21 pathway makes an important, independent contribution to G2 arrest in response to oxidative stress, and any defect in this pathway may lead to genomic instability and predisposition to cancer. Such strict control mechanisms probably provide protection for survival in the face of various environmental changes. The controversial issue related to the mechanism of inactivation of Cdc2 by p21 is addressed and simulation predictions indicate that G2 arrest would not be affected much by considering the direct binding of p21 to Cdc2/Cyclin B given that the inhibition of CAK by p21 is already present if the binding efficiency is within a certain range. Lastly, we show that the G2 arrest time in response to oxidative stress is sensitive to the p53 synthesis rate.
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Collins, Corolyn J., Richard B. Levene, Christina P. Ravera, Marker J. Dombalagian, David M. Livingston, and Dennis C. Lynch. "MOLECULAR CLONING OF THE HUMAN GENE FOR VON WILLEBRAND FACTOR AND IDENTIFICATION OF THE TRANSCRIPTION INITIATION SITE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642830.

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Most patients with von Willebrand's disease appear to have a defect affecting the level of expression of the von Willebrand factor (vWf) gene. Thus, an understanding of the pathogenesis of von Willebrand's disease will require an analysis of the structure and function of the vWf gene in normals and in patients. To begin such analyses, we have screened a human genomic cosmid library with probes obtained from vWf cDNA and isolated a colinear segment spanning ≈175 kb in five overlapping clones. This segment extends ≈25 kb upstream and ≈5 kb downstream of the transcription start and stop sites for vWf mRNA, implying the vWf gene has a length of ≈150 kb. Within one of these clones, the vWf transcription initiation sites have been mapped. A portion of the promoter region has been sequenced, revealing a typical TATA box, a downstream CCAAT box, and a perfect downstream repeat of the 8 base pairs containing the major transcription start site. Primer extension analysis suggests that sequences contained within the downstream repeat of the transcription start site may be used as minor initiation sites in endothelial cells. Transfection studies are underway to evaluate the role of sequences within this promoter region in gene regulatory activity. Comparative restriction analyses of cloned and chromosomal DNA segments strongly suggests that no major alterations ocurred during cloning and that there is only one complete copy of the vWf gene in the human haploid genome. Similar analyses of DNA from vWf-expressing endothelial cells and non-expressing white blood cells suggests that no major rearrangements are associated with vWf gene expression. Finally, cross hybridization patterns among seven mammalian species suggests a strong conservation of genomic sequences encoding the plasma portion of vWf, but a lower degree of conservation of sequences encoding the N terminal region of provWf.
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"Detailed analysis of distribution of repetitive sequences across genomes of Martes (Mustelidae, Carnivora, Mammalia)." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-072.

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Reports on the topic "Mammalian genomics"

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Sadot, Einat, Christopher Staiger, and Zvi Kam Weizmann. functional genomic screen for new plant cytoskeletal proteins and the determination of their role in actin mediated functions and guard cells regulation. United States Department of Agriculture, January 2003. http://dx.doi.org/10.32747/2003.7587725.bard.

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The original objectives of the approved proposal were: 1. To construct a YFP fused Arabidopsis cDNA library in a mammalian expression vector. 2. To infect the library into a host fibroblast cell line and to screen for new cytoskeletal associated proteins using an automated microscope. 3. Isolate the new genes. 4. Characterize their role in plants. The project was approved as a feasibility study to allow proof of concept that would entail building the YFP library and picking up a couple of positive clones using the fluorescent screen. We report here on the construction of the YFP library, the development of the automatic microscope, the establishment of the screen and the isolation of positive clones that are plant cDNAs encoding cytoskeleton associated proteins. The rational underling a screen of plant library in fibroblasts is based on the high conservation of the cytoskeleton building blocks, actin and tubulin, between the two kingdoms (80-90% homology at the level of amino acids sequence). In addition, several publications demonstrated the recognition of mammalian cytoskeleton by plant cytoskeletal binding proteins and vice versa. The major achievements described here are: 1. The development of an automated microscope equipped with fast laser auto-focusing for high magnification and a software controlling 6 dimensions; X, Y position, auto focus, time, color, and the distribution and density of the fields acquired. This system is essential for the high throughput screen. 2. The construction of an extremely competent YFP library efficiently cloned (tens of thousands of clones collected, no empty vectors detected) with all inserts oriented 5't03'. These parameters render it well representative of the whole transcriptome and efficient in "in-frame" fusion to YFP. 3. The strategy developed for the screen allowing the isolation of individual positive cDNA clones following three rounds of microscopic scans. The major conclusion accomplished from the work described here is that the concept of using mammalian host cells for fishing new plant cytoskeletal proteins is feasible and that screening system developed is complete for addressing one of the major bottlenecks of the plant cytoskeleton field: the need for high throughput identification of functionally active cytoskeletal proteins. The new identified plant cytoskeletal proteins isolated in the pilot screen and additional new proteins which will be isolated in a comprehensive screen will shed light on cytoskeletal mediated processes playing a major role in cellular activities such as cell division, morphogenesis, and functioning such as chloroplast positioning, pollen tube and root hair elongation and the movement of guard cells. Therefore, in the long run the screen described here has clear agricultural implications.
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Seroussi, Eyal, and George Liu. Genome-Wide Association Study of Copy Number Variation and QTL for Economic Traits in Holstein Cattle. United States Department of Agriculture, September 2010. http://dx.doi.org/10.32747/2010.7593397.bard.

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Copy number variation (CNV) has been recently identified in human and other mammalian genomes and increasing awareness that CNV might be a major source for heritable variation in complex traits has emerged. Despite this, little has been published on CNVs in Holsteins. In order to fill this knowledge-gap, we proposed a genome-wide association study between quantitative trait loci (QTL) for economic traits and CNV in the Holstein cattle. The approved feasibility study was aimed at the genome-wide characterization of CNVs in Holstein cattle and at the demonstrating of their possible association with economic traits by performing the activities of preparation of DNA samples, Comparative Genomic Hybridization (CGH), initial association study between CNVs and production traits and characterization of CNVSNP associations. For both countries, 40 genomic DNA samples of bulls representing the extreme sub-populations for economically important traits were CGH analyzed using the same reference genome on a NimbleGen tiling array. We designed this array based on the latest build of the bovine genome (UMD3) with average probe spacing of 1150 bases (total number of probes was 2,166,672). Two CNV gene clusters, PLA2G2D on BTA2 and KIAA1683 on BTA7 revealed significant association with milk percentage and cow fertility, respectively, and were chosen for further characterization and verification in a larger sample using other methodologies including sequencing, tag SNPs and real time PCR (qPCR). Comparison between these four methods indicated that there is under estimation of the number of CNV loci in Holstein cattle and their complexity. The variation in sequence between different copies seemed to affect their functionality and thus the hybridization based methods were less informative than the methods that are based on sequencing. We thus conclude that large scale sequencing effort complemented by array CGH should be considered to better detect and characterize CNVs in order to effectively employ them in marker-assisted selection.
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3

Jander, Georg, Gad Galili, and Yair Shachar-Hill. Genetic, Genomic and Biochemical Analysis of Arabidopsis Threonine Aldolase and Associated Molecular and Metabolic Networks. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7696546.bard.

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Since the amino acids threonine and isoleucine can be limiting in mammalian diet and there is interest in increasing their abundance in certain crop plants. To meet this need, a BARD proposal was written with two main research objectives: (i) investigate new avenues for manipulating threonine and isoleucine content in plants and (ii) study the role of threonine aldolase in plant metabolism. Research conducted to meet these goals included analysis of the sub-cellular localization of threonine aldolase in the plant, analysis of metabolic flux in developing embryos, over- and under-expression of Arabidopsis threonine aldolases, and transcriptional and metabolic analysis of perturbations resulting from altered threonine aldolase expression. Additionally, the broader metabolic effects of increasing lysine biosynthesis were investigated. An interesting observation that came up in the course of the project is that threonine aldolase activity affects methionine gamma-lyase in Arabidopsis. Further research showed that threonine deaminase and methionine gamma-lyase both contribute to isoleucine biosynthesis in plants. Therefore, isoleucine content can be altered by manipulating the expression of either or both of these enzymes. Additionally, both enzymes contribute to the up to 100-fold increase in isoleucine that is observed in drought-stressed Arabidopsis. Toward the end of the project it was discovered that through different projects, both groups had been able to independently up-regulate phenylalanine accumulation by different mechanisms. The Galili lab transformed Arabidopsis with a feedbackinsensitive bacterial enzyme and the Jander lab found a feedback insensitive mutation in Arabidopsis arogenate dehydratase. Exchange of the respective plant lines has allowed a comparative analysis of the different methods for increasing phenylalanine content and the creation of double mutants. The research that was conducted as part of this BARD project has led to new insights into plant amino acid metabolism. Additionally, new approaches that were found to increase the accumulation of threonine, isoleucine, and phenylalanine in plants have potential practical applications. Increased threonine and isoleucine levels can increase the nutritional value of crop plants. Elevated isoleucine accumulation may increase the osmotic stress tolerance of plants. Up-regulation of phenylalanine biosynthesis can be used to increase the production of downstream higher-value plant metabolites of biofuel feed stocks.
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4

Ehrlich, Marcelo, John S. Parker, and Terence S. Dermody. Development of a Plasmid-Based Reverse Genetics System for the Bluetongue and Epizootic Hemorrhagic Disease Viruses to Allow a Comparative Characterization of the Function of the NS3 Viroporin in Viral Egress. United States Department of Agriculture, September 2013. http://dx.doi.org/10.32747/2013.7699840.bard.

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Project Title: "Development of a plasmid-based reverse genetics system for the Bluetongue and Epizootic Hemorrhagic Disease viruses to allow comparative characterization of the function of the NS3 viroporin in viral egress". Project details: No - IS-4192-09; Participants – Ehrlich M. (Tel Aviv University), Parker J.S. (Cornell University), DermodyT.S. (Vanderbilt University); Period - 2009-2013. Orbiviruses are insect-borne infectious agents of ruminants that cause diseases with considerable economical impact in Israel and the United States. The recent outbreaks of BTV in Europe and of Epizootic Hemorrhagic Disease Virus (EHDV) in Israel, underscore the need for: (i) a better comprehension of the infection process of orbiviruses, (ii) the identification of unique vs. common traits among different orbiviruses, (iii) the development of novel diagnosis and treatment techniques and approaches; all aimed at the achievement of more effective control and treatment measures. It is the context of these broad goals that the present project was carried out. To fulfill our long-term goal of identifying specific viral determinants of virulence, growth, and transmission of the orbiviruses, we proposed to: (i) develop reverse genetics systems for BTV and EHDV2-Ibaraki; and (ii) identify the molecular determinants of the NS3 nonstructural protein related to viroporin/viral egress activities. The first objective was pursued with a two-pronged approach: (i) development of a plasmid-based reverse genetics system for BTV-17, and (ii) development of an "in-vitro" transcription-based reverse genetics system for EHDV2-Ibaraki. Both approaches encountered technical problems that hampered their achievement. However, dissection of the possible causes of the failure to achieve viral spread of EHDV2-Ibaraki, following the transfection of in-vitro transcribed genomic segments of the virus, revealed a novel characteristic of EHDV2-Ibaraki infection: an uncharacteristically low fold increase in titer upon infection of different cell models. To address the function and regulation of NS3 we employed the following approaches: (i) development (together with Anima Cell Metrology) of a novel technique (based on the transfection of fluorescently-labeledtRNAs) that allows for the detection of the levels of synthesis of individual viral proteins (i.e. NS3) in single cells; (ii) development of a siRNA-mediated knockdown approach for the reduction in levels of expression of NS3 in EHDV2-Ibaraki infected cells; (iii) biochemical and microscopy-based analysis of the localization, levels and post-translational modifications of NS3 in infected cells. In addition, we identified the altered regulation and spatial compartmentalization of protein synthesis in cells infected with EHDV2-Ibaraki or the mammalian reovirus. In EHDV2-Ibaraki-infected cells such altered regulation in protein synthesis occurs in the context of a cell stress reponse that includes the induction of apoptosis, autophagy and activation of the stressrelated kinase c-Jun N-terminal Kinase (JNK). Interestingly, inhibition of such stress-related cellular processes diminishes the production of infectious virions, suggesting that EHDV usurps these responses for the benefit of efficient infection. Taken together, while the present project fell short of the generation of novel reverse genetics systems for orbiviruses, the development of novel experimental approaches and techniques, and their employment in the analysis of EHDV-infected cells, yielded novel insights in the interactions of orbiviruses with mammalian cells.
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