Relevant bibliographies by topics / Genome

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Genome'

Author: Grafiati
Published: 4 June 2021
Last updated: 12 April 2025

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Journal articles on the topic "Genome"

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Barazandeh, A., M. R. Mohammadabadi, M. Ghaderi-Zefrehei, and H. Nezamabadi-pour. "Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features." Czech Journal of Animal Science 61, No. 11 (November 17, 2016): 487–95. http://dx.doi.org/10.17221/78/2015-cjas.

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Sakharkar, Kishore Ramaji, Iti Chaturvedi, Vincent T. K. Chow, Chee Keong Kwoh, Pandjassarame Kangueane, and Meena Kishore Sakharkar. "u-Genome: A Database on Genome Design in Unicellular Genomes." In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation 5, no. 5-6 (January 2005): 611–15. https://doi.org/10.3233/isb-00215.

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Unicellular eukaryotes were among the first ones to be selected for complete genome sequencing because of the small size of their genomes and their interactions with humans and a broad range of animals and plants. Currently, ten completely sequenced unicellular genome sequences have been publicly released and as the number of available unicellular genomes increases, comparative genomics analysis within this group of organisms becomes more and more instructive. However, such an analysis is difficult to carry out without a suitable platform gathering not only the original annotations but also relevant information available in public databases or obtained by applying common bioinformatics methods. With the aim of solving these difficulties, we have developed a web-accessible database named u-Genome, the unicellular genome design database. The database is unique in featuring three datasets namely (1) orthologous proteins (2) paralogous proteins and (3) statistical distributions on exons, introns, intergenic DNA and correlations between them. A tool, Uniview, designed to visualize the gene structures for individual genes in the genome is also integrated. This database is of importance in understanding unicellular genome design and architecture and evolution related studies. The database is available through a web interface at http://sege.ntu.edu.sg/wester/ugenome.
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Zhang, Hui, Yao Xiong, Wenhai Xiao, and Yi Wu. "Investigation of Genome Biology by Synthetic Genome Engineering." Bioengineering 10, no. 2 (February 20, 2023): 271. http://dx.doi.org/10.3390/bioengineering10020271.

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Synthetic genomes were designed based on an understanding of natural genomic information, offering an opportunity to engineer and investigate biological systems on a genome-wide scale. Currently, the designer version of the M. mycoides genome and the E. coli genome, as well as most of the S. cerevisiae genome, have been synthesized, and through the cycles of design–build–test and the following engineering of synthetic genomes, many fundamental questions of genome biology have been investigated. In this review, we summarize the use of synthetic genome engineering to explore the structure and function of genomes, and highlight the unique values of synthetic genomics.
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Beck, Stephan. "Genome acrobatics: understanding complex genomes." Drug Discovery Today 6, no. 23 (December 2001): 1181–82. http://dx.doi.org/10.1016/s1359-6446(01)02036-0.

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Wei, Jun-Zhi, and Richard R. C. Wang. "Genome- and species-specific markers and genome relationships of diploid perennial species in Triticeae based on RAPD analyses." Genome 38, no. 6 (December 1, 1995): 1230–36. http://dx.doi.org/10.1139/g95-161.

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Eight different genomes (E, H, I, P, R, St, W, and Ns) represented by 22 diploid species of the tribe Triticeae were analyzed using the random amplified polymorphic DNA (RAPD) technique. The genome relationships were obtained based on 371 RAPD fragments produced with 30 primers. The four species of the genus Psathyrostachys (having various Ns genomes) were closely related. The genomes Ee and Eb had a similarly close relationship and were distinct from all other genomes analyzed. Genomes P, R, and St were grouped in one cluster and genomes H and I in another. Genome W had a distant relationship with all other genomes. These results agree with the conclusions from studies of chromosome pairing and isozyme and DNA sequence analyses. Twenty-nine and 11 RAPD fragments are considered to be genome- and species-specific markers, respectively. One to six genome-specific markers were identified for each genome. These RAPD markers are useful in studies of genome evolution, analysis of genome composition, and genome identification.Key words: Triticeae, perennial, diploid, genome, RAPD, genome-specific markers.
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Sung, Bong Hyun, Donghui Choe, Sun Chang Kim, and Byung-Kwan Cho. "Construction of a minimal genome as a chassis for synthetic biology." Essays in Biochemistry 60, no. 4 (November 30, 2016): 337–46. http://dx.doi.org/10.1042/ebc20160024.

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Microbial diversity and complexity pose challenges in understanding the voluminous genetic information produced from whole-genome sequences, bioinformatics and high-throughput ‘-omics’ research. These challenges can be overcome by a core blueprint of a genome drawn with a minimal gene set, which is essential for life. Systems biology and large-scale gene inactivation studies have estimated the number of essential genes to be ∼300–500 in many microbial genomes. On the basis of the essential gene set information, minimal-genome strains have been generated using sophisticated genome engineering techniques, such as genome reduction and chemical genome synthesis. Current size-reduced genomes are not perfect minimal genomes, but chemically synthesized genomes have just been constructed. Some minimal genomes provide various desirable functions for bioindustry, such as improved genome stability, increased transformation efficacy and improved production of biomaterials. The minimal genome as a chassis genome for synthetic biology can be used to construct custom-designed genomes for various practical and industrial applications.
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Bernardi, Giorgio. "Questions About Genomes and Genome Projects." Nature Biotechnology 12, no. 8 (August 1994): 840. http://dx.doi.org/10.1038/nbt0894-840.

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Redi, C. A., and E. Capanna. "Genome Size Evolution: Sizing Mammalian Genomes." Cytogenetic and Genome Research 137, no. 2-4 (2012): 97–112. http://dx.doi.org/10.1159/000338820.

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Lupski, J. R. "Genome Mosaicism--One Human, Multiple Genomes." Science 341, no. 6144 (July 25, 2013): 358–59. http://dx.doi.org/10.1126/science.1239503.

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Leitch, A. R., and I. J. Leitch. "Plant genomes. Genome dynamics vol. 4." Annals of Botany 104, no. 7 (September 3, 2009): viii. http://dx.doi.org/10.1093/aob/mcp221.

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Dissertations / Theses on the topic "Genome"

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Schwartz, Marín Ernesto. "Genomic sovereignty and "the Mexican genome"." Thesis, University of Exeter, 2011. http://hdl.handle.net/10036/3500.

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This PhD seeks to explore the development of a bio-molecular (i.e., genomic) map as a sovereign resource in Mexico. The basic analytical thread of the dissertation is related to the circulation of genomic variability through the policy/legal and scientific social worlds that compose the Mexican medical-population genomics arena. It follows the construction of the Mexican Institute of Genomic Medicine (INMEGEN), the notion of genomic sovereignty, and the Mexican Genome Diversity Project (MGDP).The key argument for the construction of the INMEGEN relied in a nationalist policy framing, which considered the Mexican genome as a sovereign resource, coupling Mexican “uniqueness” to the very nature of genomic science. Nevertheless, the notion of genomic sovereignty was nothing similar to a paradigm, and was not based on shared visions of causality, since the very “nature” of the policy object —Mexican Genome— was, and still is, a disputed reality. It was through the rhetoric upon independence, emancipation and biopiracy: i.e. experiences of dispossession “in archaeology, botany or zoology” (IFS 2001: 25) that the novelty of population genomics became amenable to be understood as a sovereign matter. Therefore, the strategic reification of Mexicanhood fuelled the whole policy and the legal agenda of the INMEGEN as well, which permitted cooperation without consensus and opened the process of policy innovation. Conversely, scientists considered genomic sovereignty an unfounded exaggeration, but anyhow they cooperated and even created a new policy and scientific enterprise. Genomic sovereignty exemplifies the process of cooperation without consensus on its most extreme version .So, as the notion circulated and gradually became a law to protect Mexican genomic patrimony, the initial coalition of scientists, lawyers and policy makers disaggregated. Many of the original members of the coalition now think of genomic sovereignty as a strategy of the INMEGEN to monopolise genomic research in the country. This dissertation additionally explores the way in which the MGDP is constructed in mass media, in INMEGEN´s communication and in the laboratory practices. These different dimensions of the MGDP depict the difficulties that emerge between the probabilistic, relative and multiple constructions of population genomics and the rhetorical strategies to continually assert the existence of the unique “Mexican Genome”. I argue that the Mexican case study provides an entry point to what I and others (Benjamin 2009; Schwartz-Marin 2011) have identified as a postcolonial biopolitics in which the nation state is reasserted rather than diluted. However the relation between sovereignty, race and nation is not mediated by the biological purification of the nation (Agamben 1998; Foucault 2007), or the active participation of citizens looking to increase their vitality (Rose 2008, Rose & Rabinow 2006), but on an awareness of subalternity in the genomic arena and a collective desire to compete in the biomedical global economy.
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Pfeifer, Bastian [Verfasser]. "Whole-genome population genomic analyses / Bastian Pfeifer." Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2015. http://d-nb.info/1065803222/34.

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Davenport, Colin. "Genomic and metagenomic application of microbial genome signatures." Hannover Bibliothek der Medizinischen Hochschule Hannover, 2010. http://d-nb.info/100117173X/34.

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Ozato, Junior Tadaiti. "Complementação do seqüenciamento do genoma do Southern bean mosaic virus, isolado São Paulo, expressão da porção C-terminal da polimerase e produção de anti-soro policlonal /." São José do Rio Preto : [s.n.], 2007. http://hdl.handle.net/11449/92490.

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Orientador: José Osmar Gaspar
Banca: Claudia Regina Bonini Domingos
Banca: Eliezer Rodrigues de Souto
Resumo: O presente trabalho consistiu no seqüenciamento e caracterização molecular das Cadeias Abertas de Leitura (Open Reading Frames - ORFs) 2 e 3 do genoma do isolado São Paulo do Southern bean mosaic virus (SBMV-SP), completando-se o seqüenciamento de todo o genoma desse isolado. A ORF 2 codifica uma poliproteína (serino protease - VPg - RNA polimerase RNA-dependente) e a ORF 3 um produto com função desconhecida. O seqüenciamento da ORF 2 apresentou 2889 nucleotídeos, incluindo-se o códon de terminação UGA, com 962 aminoácidos deduzidos e massa molecular estimada de aproximadamente 105 kDa. Dentro da ORF 2, localiza-se a ORF 3 contendo 398 nucleotídeos, incluindo-se o códon de terminação UAA, com 132 aminoácidos e massa molecular estimada de aproximadamente 15 KDa. A análise feita a partir das seqüências das ORFS 2 e 3 do genoma do SBMV-SP, quando comparadas com outras espécies do mesmo gênero e isolados do SBMV, depositadas no GenBank, mostrou que a ORF 2 apresenta maior identidade (91,4% na seqüência de nucleotídeos e 95,0% na seqüência de aminoácidos deduzidos) com o isolado de Arkansas. Resultado similar foi obtido em relação à ORF 3 com valores de identidade de 97,0% tanto para as seqüências de nucleotídeos e aminoácidos deduzidos. Dados de filogenia corroboram os dados de identidade. Regiões conservadas do gênero Sobemovirus também foram identificadas, tais como Sítio de Ligação à Capa Protéica (CBPS), a tríade catalítica da serino protease (H-D-S) e a seqüência de heptanucleotídeos (TTTAAAC). A expressão em Escherichia coli da porção C-terminal da RNA Polimerase RNA Dependente (RpRd) produziu uma proteína de fusão de aproximadamente 67 kDa no sistema pMAL c2-x e de 30 kDa no sistema pET 28a. Quando a proteína de fusão foi injetada em coelhos houve a produção de anti-soro específico para a proteína recombinante.
Abstract: The present work consisted of the sequencing and molecular characterization of the Open Reading Frames (ORFs) 2 and 3 from the São Paulo isolate genome of Southern bean mosaic virus (SBMV-SP), completing the sequencing of all the genome of this isolate. The ORF 2 encodes a polyprotein (serine protease - VPg - RNA dependent RNA polimarase) and the ORF 3 one product with unknown function. The sequencing of the ORF 2 reveals 2889 nucleotides, including the stop codon (UGA), with 962 deduced amino acids e and estimated molecular weight of approximately 105 kDa. Nested in the ORF 2 were found the ORF 3 with 398 nucleotides, including the stop codon (UAA), with 132 deduced amino acids and estimated molecular weight of approximately 15 kDa. The analysis made from the sequences of the ORFs 2 and 3 from the SBMV-SP genome, when compared with other species of the same gender and isolates of SBMV, deposited in the GenBank, showed that the ORF 2 presents higher identity (91,4% in the nucleotide sequence and 95,0% in the deduced amino acids sequence) with Arkansas isolate. Similar result was obtained in relation to the ORF 3 with identity values of 97,0% for the nucleotides and deduced amino acids sequences. Phylogeny data corroborate the identity data. Conserved regions of the Sobemovirus gender had also been identified such as Coat Protein Binding Site (CPBS), serine protease catalytic triad (H-D-S) and heptanucleotide sequence (TTTAAAC). The Expression in Escherichia coli of the C-terminal region of the RNA dependent RNA polimerase produced a fusion protein of approximately 67 kDa in pMAL c2-x system and a 30 kDa protein in pET 28a system. When the fusion protein ...(Complete abstract click electronic access below)
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Groet, Jurgen. "Physical mapping and identification of novel genes in human chromosome 21q11." Thesis, University College London (University of London), 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312003.

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Merkel, Angelika. "Microsatellite Evolution in The Yeast Genome - A Genomic Approach." Thesis, University of Canterbury. School of Biological Sciences, 2008. http://hdl.handle.net/10092/3327.

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Microsatellites are short (1-6bp long) highly polymorphic tandem repeats, found in all genomes analyzed so far. Popular genetic markers for many applications including population genetics, pedigree analysis, genetic mapping and linkage analysis, some microsatellites also can cause a variety of human neurodegenerative diseases and may act as agents of adaptive evolution through the regulation of gene expression. As a consequence of these diverse uses and functions, the mutational and evolutionary dynamics of microsatellite sequences have gained much attention in recent years. Mostly, the focus of studies investigating microsatellite evolution has been to develop more refined evolutionary models for estimating parameters such as genetic distance or linkage disequilibrium. However, there is an incentive in using our understanding of the evolutionary processes that affect these sequences to examine the functional implications of microsatellite evolution. What has emerged from nearly two decades of study are highly complex mutational dynamics, with mutation rates varying across species, loci and alleles, and a multitude of potential influences on these rates, most of which are not yet fully understood. The increasing availability of whole genome sequences has immensely extended the scope for studying microsatellite evolution. For example, where once it was common to examine single loci, it is now possible to examine microsatellites using genome wide approaches. In the first part of my dissertation I discuss approaches and issues associated with detecting microsatellites in genomic data. In Chapter 2 I undertook a meta-analysis of studies investigating the distribution of microsatellites in yeast and showed that studies comparing the distribution of microsatellites in genomic data can be fraught due to the application of different definitions for microsatellites by different investigators. In particular, I found that variation in how investigators choose the repeat unit size of a microsatellite, handle imperfections in the array and especially the choice of minimum array length used, leads to a large divergence in results and can distort the conclusions drawn from such studies, particularly where inter-specific comparisons are being made. In a review of the currently available suite of bioinformatics tools (Chapter 3), I further showed that this bias extends beyond a solely theoretical controversy into a methodological issue because most software tools not only incorporate different definitions for the key parameters used to define microsatellites, but also employ different strategies to search and filter for microsatellites in genomic data. In this chapter I provide an overview of the available tools and a practical guide to help other researchers choose the appropriate tool for their research purpose. In the second part of my thesis, I use the analytical framework developed from the previous chapters to explore the biological significance of microsatellites exploiting the well annotated genome of the model organism Saccharomyces cerevisiae (baker’s yeast). Several studies in different organisms have indicated spatial associations between microsatellites and individual genomic features, such as transposable elements, recombinational hotspots, GC-content or local substitution rate. In Chapter 4, I summarized these studies and tested some of the underlying hypotheses on microsatellite distribution in the yeast genome using Generalized Linear Models (GLM) and wavelet transformation. I found that microsatellite type and distribution within the genome is strongly governed by local sequence composition and negative selection in coding regions, and that microsatellite frequency is inversely correlated with SNP density reflecting the stabilizing effect point mutations have on microsatellites. Microsatellites may also be markers for recent genome modifications, due to their depletion in regions nearby LTR transposons, and elements of potential structural importance, since I found associations with features such as meiotic double strand breaks, regulatory sites and nucleosomes. Microsatellites are subject to local genomic influences, particularly on small (1-2kb) scales. Although, these local scale influences might not be as dominant as other factors on a genome-wide scale they are certainly of importance with respect to individual loci. Analysis of locus conservation across 40 related yeast strains (Chapter 5) showed no bias in the type of microsatellites conserved, only a negative influence of coding sequences, which supports again the idea that microsatellites evolve neutrally. Polymorphism was rare, and despite a positive correlation with array length, there was no relationship with either genomic fraction or repeat size. However, the analysis also revealed a non-random distribution of microsatellites in genes of functionally distinct groups. For example, conserved microsatellites (similar to general microsatellites in yeast) are mostly found in genes associated with the regulation of biological and cellular processes. Polymorphic loci show further an association with the organization and biogenesis of cellular components, morphogenesis, development of anatomical structures and pheromone response, which, is absent for monomorphic loci. Whether this distribution is an indication of functionality or simply neutral mutation (e.g. genetic hitch-hiking) is debatable since most conserved microsatellites, particularly variable loci, are located within genes that show low selective constraints. Overall, microsatellites appear as neutrally evolving sequences, but owing to the sheer number of loci within a single genome, individual loci may well acquire some functionality. More work is definitely needed in this area, particularly experimental studies, such as reporter-gene expression assays, to confirm phenotypic effects.
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Bradwell, Katie. "Genomic comparisons and genome architecture of divergent Trypanosoma species." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4598.

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Virulent Trypanosoma cruzi, and the non-pathogenic Trypanosoma conorhini and Trypanosoma rangeli are protozoan parasites with divergent lifestyles. T. cruzi and T. rangeli are endemic to Latin America, whereas T. conorhini is tropicopolitan. Reduviid bug vectors spread these parasites to mammalian hosts, within which T. rangeli and T. conorhini replicate extracellularly, while T. cruzi has intracellular stages. Firstly, this work compares the genomes of these parasites to understand their differing phenotypes. Secondly, genome architecture of T. cruzi is examined to address the effect of a complex hybridization history, polycistronic transcription, and genome plasticity on this organism, and study its highly repetitive nature and cryptic genome organization. Whole genome sequencing, assembly and comparison, as well as chromosome-scale genome mapping were employed. This study presents the first comprehensive whole-genome maps of Trypanosoma, and the first T. conorhini strain ever sequenced. Original contributions vii to knowledge include the ~21-25 Mbp assembled genomes of the less virulent T. cruzi G, T. rangeli AM80, and T. conorhini 025E, containing ~10,000 to 13,000 genes, and the ~36 Mbp genome assembly of highly virulent T. cruzi CL with ~24,000 genes. The T. cruzi strains exhibited ~74% identity to proteins of T. rangeli or T. conorhini. T. rangeli and T. conorhini displayed greater complex carbohydrate metabolic capabilities, and contained fewer retrotransposons and multigene family copies, e.g. mucins, DGF-1, and MASP, compared to T. cruzi. Although all four genomes appear highly syntenic, T. rangeli and T. conorhini exhibited greater karyotype conservation. T. cruzi genome architecture studies revealed 66 maps varying from 0.13 to 2.4 Mbp. At least 2.6% of the genome comprises highly repetitive repeat regions, and 7.4% exhibits repetitive regions barren of labels. The 66 putative chromosomes identified are likely diploid. However, 20 of these maps contained regions of up to 1.25 Mbp of homology to at least one other map, suggestive of widespread segmental duplication or an ancient hybridization event that resulted in a genome with significant redundancy. Assembled genomes of these parasites closely reflect their phylogenetic relationships and give a greater context for understanding their divergent lifestyles. Genome mapping provides insight on the genomic evolution of these parasites.
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Rumrill, Deborah. "Initiating international collaboration : a study of the human genome organization /." Thesis, This resource online, 1993. http://scholar.lib.vt.edu/theses/available/etd-09122009-040530/.

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Boardman, Anelda Philine. "Assessment of genome visualization tools relevant to HIV genome research: development of a genome browser prototype." Thesis, University of the Western Cape, 2004. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_3632_1185446929.

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Over the past two decades of HIV research, effective vaccine candidates have been elusive. Traditionally viral research has been characterized by a gene -by-gene approach, but in the light of the availability of complete genome sequences and the tractable size of the HIV genome, a genomic approach may improve insight into the biology and epidemiology of this virus. A genomic approach to finding HIV vaccine candidates can be facilitated by the use of genome sequence visualization. Genome browsers have been used extensively by various groups to shed light on the biology and evolution of several organisms including human, mouse, rat, Drosophila and C.elegans. Application of a genome browser to HIV genomes and related annotations can yield insight into forces that drive evolution, identify highly conserved regions as well as regions that yields a strong immune response in patients, and track mutations that appear over the course of infection. Access to graphical representations of such information is bound to support the search for effective HIV vaccine candidates. This study aimed to answer the question of whether a tool or application exists that can be modified to be used as a platform for development of an HIV visualization application and to assess the viability of such an implementation. Existing applications can only be assessed for their suitability as a basis for development of an HIV genome browser once a well-defined set of assessment criteria has been compiled.

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Shaw, Daniel 1993. "Streamlining minimal bacterial genomes : Analysis of the pan bacterial essential genome, and a novel strategy for random genome deletions in Mycoplasma pneumoniae." Doctoral thesis, Universitat Pompeu Fabra, 2019. http://hdl.handle.net/10803/668244.

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Understanding what constitutes a true Minimal Cell is a key challenge in synthetic biology. In this work, we present two new tools to aid in this endeavour. i) A novel methodology for minimising the Mycoplasma pneumoniae genome via random deletions of genetic material. This protocol utilises the Cre Lox system coupled with random transposon mutagenesis to create a population with random lox sites dispersed around the genome. This allows for a population of cells containing a high variability of large and small-scale deletions ranging from 50bp to 25Kb within M. pneumoniae. ii) The first large scale analysis of the essentiality of genes from multiple bacterial species, and how the composition and function of the essential genome of a bacterium changes based on the genome’s complexity.
Discernir cuales son los componentes que podrían constituir una célula mínima es un desafío clave para la Biología Sintética. En esta tesis, se presentan dos nuevas herramientas para facilitar esta tarea. (i) Una nueva metodología para minimizar el genoma de Mycoplasma pneumoniae mediante la deleción aleatoria de material genético. Esta técnica combina el sistema Cre/lox con la mutagénesis aleatoria mediada por transposones para generar poblaciones bacterianas en las que los sitios lox están distribuidos de manera aleatoria a lo largo de su genoma. Esto permite la generación de poblaciones bacterianas en las que el tamaño de las deleciones efectuadas varia desde 50 pb hasta 25 kb. (ii) El primer análisis a gran escala de la esencialidad genética en múltiples especies bacterianas, y cómo la composición y función del grupo de genes esenciales de una bacteria cambia en función de la complejidad de su genoma.
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Books on the topic "Genome"

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Kimura, Akira. Genomu biseibutsugaku: Microbiology of genome. Tōkyō: Maruzen Shuppan, 2012.

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Olshevsky and Church George M, eds. Understanding the genome. New York, NY: Warner Books, 2002.

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Brown, T. A. Genomes. 2nd ed. Oxford: BIOS, 2002.

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Kuldell, Natalie, and Neal Lerner. Genome Refactoring. Cham: Springer International Publishing, 2009. http://dx.doi.org/10.1007/978-3-031-02569-3.

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Kondrashov, Alexey S. Crumbling Genome. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2017. http://dx.doi.org/10.1002/9781118952146.

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Bolshoy, Alexander, Zeev (Vladimir) Volkovich, Valery Kirzhner, and Zeev Barzily. Genome Clustering. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-12952-0.

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Turksen, Kursad, ed. Genome Editing. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-34148-4.

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Cathomen, Toni, Matthew Hirsch, and Matthew Porteus, eds. Genome Editing. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3509-3.

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Gustafson, J. Perry, Randy Shoemaker, and John W. Snape, eds. Genome Exploitation. Boston, MA: Springer US, 2005. http://dx.doi.org/10.1007/b104751.

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Lankenau, Dirk-Henner, ed. Genome Integrity. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/b104871.

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Book chapters on the topic "Genome"

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Jespersen, Nathan, Leonardo Monrroy, and Jonas Barandun. "Impact of Genome Reduction in Microsporidia." In Experientia Supplementum, 1–42. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-93306-7_1.

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AbstractMicrosporidia represent an evolutionary outlier in the tree of life and occupy the extreme edge of the eukaryotic domain with some of their biological features. Many of these unicellular fungi-like organisms have reduced their genomic content to potentially the lowest limit. With some of the most compacted eukaryotic genomes, microsporidia are excellent model organisms to study reductive evolution and its functional consequences. While the growing number of sequenced microsporidian genomes have elucidated genome composition and organization, a recent increase in complementary post-genomic studies has started to shed light on the impacts of genome reduction in these unique pathogens. This chapter will discuss the biological framework enabling genome minimization and will use one of the most ancient and essential macromolecular complexes, the ribosome, to illustrate the effects of extreme genome reduction on a structural, molecular, and cellular level. We outline how reductive evolution in microsporidia has shaped DNA organization, the composition and function of the ribosome, and the complexity of the ribosome biogenesis process. Studying compacted mechanisms, processes, or macromolecular machines in microsporidia illuminates their unique lifestyle and provides valuable insights for comparative eukaryotic structural biology.
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Wu, Shan, Mercy Kitavi, John P. Hamilton, C. Robin Buell, and Zhangjun Fei. "US Efforts in Sweetpotato Genome Sequencing: Advances in the Development of Reference Genomes to Facilitate Research and Breeding of a Key Food Security Crop." In Compendium of Plant Genomes, 11–17. Cham: Springer International Publishing, 2024. http://dx.doi.org/10.1007/978-3-031-65003-1_2.

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AbstractGenomic information provides a fundamental tool for modern crop breeding. Sweetpotato [Ipomoea batatas (L.) Lam.] is a globally important crop. However, the genome of sweetpotato is understudied due to its highly heterozygous hexaploid nature, preventing straightforward access to its genomic landscape. Here, we summarize the previous and on-going efforts in the US in the development of reference genomes for sweetpotato. Genomeassemblies of diploid wild relatives, I. trifida and I. triloba, were first generated to serve as robust references for the hexaploid cultivated sweetpotato. Taking advantage of recently improved sequencing technologies and assembly algorithms, we have been generating phased genomeassemblies of hexaploidy sweetpotato. Chromosome-scale haplotype-resolved genomeassemblies, along with high-quality genome annotations of hexaploid sweetpotato, have been made available to the scientific and breeding communities. Multiple reference-grade phased hexaploid sweetpotato genomes set the foundation for construction of a pan-genome comprising intra- and inter-genome variations that will facilitate biological discovery and breeding of sweetpotato.
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Benabdellah, Karim, Simone Thomas, and Hinrich Abken. "Genetic Engineering of Autologous or Allogeneic Immune Effector Cells." In The EBMT/EHA CAR-T Cell Handbook, 7–10. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-94353-0_2.

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AbstractManufacturing immune effector cells (T or NK cells) with CAR-encoding DNA sequences requires efficient and safe genetic engineering procedures. For this purpose, an appropriate genetic vector is chosen according to numerous factors, including the vector genome packaging capacity, cellular tropism, genomic integration, immune toxicity, and other factors. In clinical trials, genomes integrating viral vectors, in particular vectors based on members of the Retroviridae family, such as retroviruses and lentiviruses, have been successfully used for more than 20 years. These vectors contain an RNA genome that when transcribed into double-stranded DNA by reverse transcriptase integrates into the genome of the transduced cell.
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Quirino, Betania Ferraz, Cristine Chaves Barreto, Georgios J. Pappas, Karsten Zengler, Konstantinos Krampis, and Ricardo H. Krüger. "Genomes and Post-genome Technology." In The Prokaryotes, 329–44. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-30194-0_15.

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Peck, Stewart B., Carol C. Mapes, Netta Dorchin, John B. Heppner, Eileen A. Buss, Gustavo Moya-Raygoza, Marjorie A. Hoy, et al. "Genome." In Encyclopedia of Entomology, 1600. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6359-6_1067.

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Nahler, Gerhard. "genome." In Dictionary of Pharmaceutical Medicine, 80. Vienna: Springer Vienna, 2009. http://dx.doi.org/10.1007/978-3-211-89836-9_599.

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Briones, Carlos. "Genome." In Encyclopedia of Astrobiology, 1–3. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-27833-4_634-3.

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Briones, Carlos. "Genome." In Encyclopedia of Astrobiology, 942–44. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-662-44185-5_634.

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Babiuk, Shawn. "Genome." In Lumpy Skin Disease, 29–35. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-92411-3_8.

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Wagner, Peter, Frank C. Mooren, Hidde J. Haisma, Stephen H. Day, Alun G. Williams, Julius Bogomolovas, Henk Granzier, et al. "Genome." In Encyclopedia of Exercise Medicine in Health and Disease, 363. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-540-29807-6_2434.

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Conference papers on the topic "Genome"

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Nareddy, Sahith Sai, Erik Westover, Kristina Hillesland, and Wooyoung Kim. "Genome dynamics in coevolved genomes." In BCB '14: ACM-BCB '14. New York, NY, USA: ACM, 2014. http://dx.doi.org/10.1145/2649387.2660810.

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Zaccaron, Alex. "Impact of genomic structural variations on virulence of the tomato pathogen Cladosporium fulvum." In IS-MPMI Congress. IS-MPMI, 2023. http://dx.doi.org/10.1094/ismpmi-2023-1.

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Cladosporium fulvum causes tomato leaf mold and has been extensively used in the past as a model species to study plant-microbe interactions. Although the first chromosome-scale reference genome of the fungus was released in 2022, still little is known about how its genome architecture and structural variations (SVs) thereof impact its virulence. In this study, we used PacBio HiFi to sequence the genomes of four additional C. fulvum isolates and further assembled them at chromosome level. Comparative genome analyses revealed high chromosomal synteny among the five isolates, and a set of 13 core and two dispensable chromosomes, one of which carries pseudogenized copies of effector genes and likely emerged by duplication of subtelomeric regions of core chromosome. Between 14906 and 14993 genes were predicted in each C. fulvum genome with an estimated completeness of >99%. A pangenome analysis of the five isolates revealed a low number of 331 accessory genes, indicating high conservation of gene content among isolates of the fungus. An analysis of SVs showed no enriched of effectors or of other pathogenicity-related genes in these regions. However, SVs in subtelomeric regions affected virulence by prompting the loss of effector genes residing in them, as we have found is the case for the Avr9 effector gene of C. fulvum. Collectively, these results provide new insights of how genomic SVs can contribute to virulence of fungal pathogens.
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Muntyan, Victoria S., Mariia E. Vladimirova, Alexey M. Afonin, Alexey N. Muntyan, and Marina L. Roumiantseva. "ANALYSIS OF SALT-SENSITIVE AND SALT-TOLERANT SINORHIZOBIUM MELILOTI STRAINS USING DNA MICROARRAY, PHENOTYPE MICROARRAY AND GENOME MINING TECHNIQUES." In 23rd SGEM International Multidisciplinary Scientific GeoConference 2023. STEF92 Technology, 2023. http://dx.doi.org/10.5593/sgem2023/6.1/s25.15.

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Nodule bacteria increase the resistance of host plants to abiotic stress factors; however, the role of the genetic potential of rhizobia in the formation of productive salt-tolerant plant-microbial symbiosis remains underestimated. The aim of the study was to evaluate the pool of genes responsible for the salt tolerance of the alfalfa microsymbiont, Sinorhizobium meliloti, using the DNA microarray technique, phenotype microarray (PM), NGS and NNGS-technologies and genome mining (antismash 5.0). As a result of the analysis of the genomes of strains contrastingly different in salt tolerance, it was found that nucleotide changes in genes in salt-sensitive strains occurred significantly more often in genomic islands located on the chromosome. The genome of the salttolerant strain contained at least 25 genes involved in the DNA replication and repair and metabolism of nucleotides (1 KEGG group), amino acids (8 KEGG groups), lipids (2 KEGG groups), and carbohydrates (4 KEGG groups). Genomic analysis of the saltsensitive strain revealed 2 unique secondary metabolite biosynthesis gene clusters on pSymB (NAGGN) and on the cryptic plasmid (phosphonate and ectoine), while both gene clusters are involved in the synthesis of substances that involved in osmotic stress response. In the genomes of salt-tolerant phenotype strains, changes occurred in a smaller number of genes belonging to other KEGG groups. Two unique clusters of antibiotic synthesis, the class of macrolides (conglobactin) and aminoglycosides (2- deoxystreptamine), as well as an additional cluster of synthesis of thioamitide RiPPs, were identified on the chromosome of a salt-tolerant strain using genome mining. The use of the PM technique made it possible to show that the salt-tolerant strain is resistant to 10 beta-lactam antibiotics, 7 cephalosporins, 9 aminoglycoside antibiotics, 5 tetracyclines, polymyxin E, and 16 antibiotics that block the synthesis of DNA, RNA, enzymes and proteins, while the salt-sensitive strain grew up on alternative sources of organic sulfur and carbon. The revealed characteristics of strains that contrastingly differ in stress tolerance are promising for their use in agrobiotechnology.
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Sujeeun, Lakshmi, Shakuntala Baichoo, Zahra Mungloo-Dilmohamud, and Yasmina Jaufeerally-Fakim. "Detection of Genome Sequence Outliers Across Pan-Genomes." In 2019 Conference on Next Generation Computing Applications (NextComp). IEEE, 2019. http://dx.doi.org/10.1109/nextcomp.2019.8883624.

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Brown, Susan. "Genome maps to complement genome sequence." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.94582.

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Кучур, П. Д., С. Д. Афонникова, and А. С. Комиссаров. "IMPROVEMENT OF GINOFIP - ALGORITHM FOR IDENTIFICATION OF OPERONS OF INTEREST." In Биотехнология в растениеводстве, животноводстве и сельскохозяйственной микробиологии, 23. Crossref, 2021. http://dx.doi.org/10.48397/arriab.2021.21.xxi.008.

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Бактериальные геномы – один из наиболее распространенных видов данных секвенирования. По этой причине они всё чаще становятся объектами исследований. Фокус внимания исследователей постепенно смещается с анализа одной геномной сборки на сравнительный анализ нескольких геномов. Проводить его на уровне всего генома всё ещё не целесообразно, однако можно сконцентрироваться на сопоставлении отдельных его структур. Геном бактерий представлен оперонами – функциональными единицами, которые сочетают в себе несколько генов, контролирующих общий процесс. Bacterial genomes are one of the most common types of sequencing data. For this reason, they are increasingly becoming objects of research. The focus of attention of researchers is gradually shifting from the analysis of one genomic assembly to the comparative analysis of several genomes. It is still not advisable to conduct it at the level of the entire genome, but one can concentrate on comparing its individual structures. The genome of bacteria is represented by operons - functional units that combine several genes that control the overall process.
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Zaccaron, Alex. "The genomic architecture of the grape powdery mildew pathogen Erysiphe necator and its impact on the pathogen’s biology and virulence." In IS-MPMI Congress. IS-MPMI, 2023. http://dx.doi.org/10.1094/ismpmi-2023-2.

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Erysiphe necator causes grape powdery mildew, globally the most important fungal disease on grapevines. The current reference genome assembly of the pathogen is highly fragmented due to its repetitive DNA content, which prevents a detailed analysis of its genomic architecture. Here, we present an 81.1 Mb genome assembly for E. necator that is 98% complete and consists of 34 scaffolds, 11 of which represent complete chromosomes. Analysis of the chromosomes’ content showed that they all contain large centromeric-like regions that account for 15.8% of the genome. Repeats and transposable elements (TEs) represent 62.7% of their content and, while they are almost evenly interspersed outside centromeric and telomeric regions, they massively overlap with regions of annotated genes, indicating that they could have a significant impact on their evolution. Indeed, abundant gene duplicates were observed, particularly in genes encoding candidate secreted effector proteins (CSEPs) that could have been spawned by TE activity. Copies of duplicated CSEP-encoding genes were further found to be frequently clustered in the genome, suggesting recurrent events of local gene duplications and adaptive variation. Finally, in accordance with the obligate biotrophic nature of E. necator, abundant losses in genes needed to synthesize metabolites that can be obtained directly through the host environment were also observed. These and other genomic architectural features of E. necator will be discussed.
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Carvalho, GFS, LL Vieira, BM Wolff, YG Oliveira, VT Almeida, AM Nascimento, and LD Kulikowski. "EPIGENOMIC ANALYSIS REVEAL CRITICAL ASSOCIATION BETWEEN METHYLATION STATUS AND CLINICAL PHENOTYPE." In Resumos do 54º Congresso Brasileiro de Patologia Clínica/Medicina Laboratorial, 24–25. Zeppelini Editorial e Comunicação, 2022. http://dx.doi.org/10.5327/1516-3180.140s1.5803.

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Objective: Copy number variations (CNVs) are DNA fragments deleted or duplicated in relation to a reference genome. Some genome variants, classified as variants with uncertain significance (VUS), do not present a safe conclusion with clinical phenotypes, which makes the diagnostic conclusion difficult. We know that hypermethylation of gene promoter regions often leads to transcriptional silencing, in addition to DNA methylation changes in gene and/or intergenic regions can play a critical role in genomic regulation and stability. With epigenomic investigation, we can gain a more comprehensive understanding of the modulation in gene expression associated with genomic imbalance in different diseases and in different genomic variations. So, our objective is to understand the impact of methylation status associated with genomic imbalances in clinical phenotypes. Method: Our study evaluated, using the Infinium Methylation EPIC Bead Chip platform, 10 DNA samples from patients with intellectual disability and dysmorphic features with CNVs classified as VUS without a definitive clinical diagnosis, in addition to six control samples from participants without clinical conditions. Conclusion: Genomic methylation, associated with genomic structural imbalances, can play a critical role in clinical features and can be used as an important marker for patients with uncertain clinical diagnosis.
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"APPLICATION OF GENOME LINGUISTIC APPROACHES FOR IDENTIFICATION OF GENOMIC ISLAND IN BACTERIAL GENOMES AND TRACKING DOWN THEIR ORIGINS - Genome Linguistics to Visualize Horizontal Gene Exchange." In International Conference on Bioinformatics Models, Methods and Algorithms. SciTePress - Science and and Technology Publications, 2012. http://dx.doi.org/10.5220/0003704201180123.

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Galimova, A. A., E. A. Zaikina, and B. R. Kuluev. "SNP analysis of common wheat baking qualities." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.082.

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The allelic states of waxy genes in genomes A, B and D were studied by genome-specific primers in cultivars and lines of common wheat of the pre-Ural steppe. The studied cultivars and lines revealed differences in genotypes for genome A.
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Reports on the topic "Genome"

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Aroney, Sam, Rhys Newell, Gene Tyson, and Ben Woodcroft. Recovering novel genomes from the rare biosphere using Bin Chicken. Queensland University of Technology, October 2024. http://dx.doi.org/10.5204/rep.eprints.253145.

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Recovery of microbial genomes from metagenomic datasets has provided genomic representation for hundreds of thousands of species from diverse biomes. However, low abundance microorganisms are often missed due to insufficient genomic coverage. Here we present Bin Chicken, an algorithm which substantially improves genome recovery through automated, targeted selection of metagenomes for coassembly based on shared marker gene sequences derived from raw reads. Marker gene sequences that are divergent from known reference genomes can be further prioritised, providing an efficient means of recovering highly novel genomes. Applying Bin Chicken to public metagenomes and coassembling 800 sample-groups recovered 77,562 microbial genomes, including the first genomic representatives of 6 phyla, 41 classes, and 24,028 species. These genomes expand the genomic tree of life and uncover a wealth of novel microbial lineages for further research.
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Wentworth, Jonathan, and David Rapley. Genome edited animals. Parliamentary Office of Science and Technology, November 2022. http://dx.doi.org/10.58248/pb50.

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Genome editing, also known as gene editing, encompasses a broad range of techniques that allows targeted changes in the DNA of animals (and plants). The Genetic Technology (Precision Breeding) Bill 2022 -2023, due for Second Reading in the House of Lords on 21 November 2022, intends to change the regulatory definition of certain genome-edited animals.
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Block, S., J. Cornwall, F. Dyson, S. Koonin, N. Lewis, and R. Schwitters. Exploiting the genome. Office of Scientific and Technical Information (OSTI), September 1998. http://dx.doi.org/10.2172/1183980.

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Block, S., J. Cornwall, W. Dally, F. Dyson, N. Fortson, G. Joyce, H. J. Kimble, et al. Human Genome Project. Office of Scientific and Technical Information (OSTI), January 1998. http://dx.doi.org/10.2172/1184016.

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Carmell, Michelle A., and Gregory J. Hannon. Whole Genome Epigenetics. Fort Belvoir, VA: Defense Technical Information Center, May 2005. http://dx.doi.org/10.21236/ada446925.

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Carmell, Michelle A., and Gregory J. Hannon. Whole Genome Epigenetics. Fort Belvoir, VA: Defense Technical Information Center, May 2003. http://dx.doi.org/10.21236/ada417880.

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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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Su, Li-Kuo. BRCA2 and Genome Integrity. Fort Belvoir, VA: Defense Technical Information Center, July 2001. http://dx.doi.org/10.21236/ada396672.

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Gardner, Malcolm J. Malaria Genome Sequencing Project. Fort Belvoir, VA: Defense Technical Information Center, January 2002. http://dx.doi.org/10.21236/ada400972.

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Su, Li-Kuo. BRCA2 and Genome Integrity. Fort Belvoir, VA: Defense Technical Information Center, July 2002. http://dx.doi.org/10.21236/ada408131.

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