Relevant bibliographies by topics / Genomic comparisons

Academic literature on the topic 'Genomic comparisons'

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Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Genomic comparisons"

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Flanagan, Keith, Robert Stevens, Matthew Pocock, Pete Lee, and Anil Wipat. "Ontology for Genome Comparison and Genomic Rearrangements." Comparative and Functional Genomics 5, no. 6-7 (2004): 537–44. http://dx.doi.org/10.1002/cfg.436.

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We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation.
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Mrázek, Jan, Alfred M. Spormann, and Samuel Karlin. "Genomic comparisons among ?-proteobacteria." Environmental Microbiology 8, no. 2 (February 2006): 273–88. http://dx.doi.org/10.1111/j.1462-2920.2005.00894.x.

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Karlin, S., and I. Ladunga. "Comparisons of eukaryotic genomic sequences." Proceedings of the National Academy of Sciences 91, no. 26 (December 20, 1994): 12832–36. http://dx.doi.org/10.1073/pnas.91.26.12832.

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Tekaia, Fredj, Antonio Lazcano, and Bernard Dujon. "The Genomic Tree as Revealed from Whole Proteome Comparisons." Genome Research 9, no. 6 (June 1, 1999): 550–57. http://dx.doi.org/10.1101/gr.9.6.550.

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The availability of a number of complete cellular genome sequences allows the development of organisms’ classification, taking into account their genome content, the loss or acquisition of genes, and overall gene similarities as signatures of common ancestry. On the basis of correspondence analysis and hierarchical classification methods, a methodological framework is introduced here for the classification of the available 20 completely sequenced genomes and partial information for Schizosaccharomyces pombe, Homo sapiens, and Mus musculus. The outcome of such an analysis leads to a classification of genomes that we call a genomic tree. Although these trees are phenograms, they carry with them strong phylogenetic signatures and are remarkably similar to 16S-like rRNA-based phylogenies. Our results suggest that duplication and deletion events that took place through evolutionary time were globally similar in related organisms. The genomic trees presented here place the Archaea in the proximity of the Bacteria when the whole gene content of each organism is considered, and when ancestral gene duplications are eliminated. Genomic trees represent an additional approach for the understanding of evolution at the genomic level and may contribute to the proper assessment of the evolutionary relationships between extant species.
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Varki, Ajit, and David L. Nelson. "Genomic Comparisons of Humans and Chimpanzees." Annual Review of Anthropology 36, no. 1 (September 2007): 191–209. http://dx.doi.org/10.1146/annurev.anthro.36.081406.094339.

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Diaz-del-Pino, Sergio, Esteban Perez-Wohlfeil, and Oswaldo Trelles. "Unraveling Genome Evolution Throughout Visual Analysis: The XCout Portal." Bioinformatics and Biology Insights 15 (January 2021): 117793222110214. http://dx.doi.org/10.1177/11779322211021422.

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Due to major breakthroughs in sequencing technologies throughout the last decades, the time and cost per sequencing experiment have reduced drastically, overcoming the data generation barrier during the early genomic era. Such a shift has encouraged the scientific community to develop new computational methods that are able to compare large genomic sequences, thus enabling large-scale studies of genome evolution. The field of comparative genomics has proven itself invaluable for studying the evolutionary mechanisms and the forces driving genome evolution. In this line, a full genome comparison study between 2 species requires a quadratic number of comparisons in terms of the number of sequences (around 400 chromosome comparisons in the case of mammalian genomes); however, when studying conserved syntenies or evolutionary rearrangements, many sequence comparisons can be skipped for not all will contain significant signals. Subsequently, the scientific community has developed fast heuristics to perform multiple pairwise comparisons between large sequences to determine whether significant sets of conserved similarities exist. The data generation problem is no longer an issue, yet the limitations have shifted toward the analysis of such massive data. Therefore, we present XCout, a Web-based visual analytics application for multiple genome comparisons designed to improve the analysis of large-scale evolutionary studies using novel techniques in Web visualization. XCout enables to work on hundreds of comparisons at once, thus reducing the time of the analysis by identifying significant signals between chromosomes across multiple species. Among others, XCout introduces several techniques to aid in the analysis of large-scale genome rearrangements, particularly (1) an interactive heatmap interface to display comparisons using automatic color scales based on similarity thresholds to ease detection at first sight, (2) an overlay system to detect individual signal contributions between chromosomes, (3) a tracking tool to trace conserved blocks across different species to perform evolutionary studies, and (4) a search engine to search annotations throughout different species.
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Karlin, S., L. Brocchieri, A. Campbell, M. Cyert, and J. Mrazek. "Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes." Proceedings of the National Academy of Sciences 102, no. 20 (May 9, 2005): 7309–14. http://dx.doi.org/10.1073/pnas.0502314102.

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Welsh, Rory M., Elizabeth Misas, Kaitlin Forsberg, Meghan Lyman, and Nancy A. Chow. "Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines." Journal of Fungi 7, no. 3 (March 16, 2021): 214. http://dx.doi.org/10.3390/jof7030214.

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Candida auris is a multidrug-resistant pathogen that represents a serious public health threat due to its rapid global emergence, increasing incidence of healthcare-associated outbreaks, and high rates of antifungal resistance. Whole-genome sequencing and genomic surveillance have the potential to bolster C. auris surveillance networks moving forward. Laboratories conducting genomic surveillance need to be able to compare analyses from various national and international surveillance partners to ensure that results are mutually trusted and understood. Therefore, we established an empirical outbreak benchmark dataset consisting of 23 C. auris genomes to help validate comparisons of genomic analyses and facilitate communication among surveillance networks. Our outbreak benchmark dataset represents a polyclonal phylogeny with three subclades. The genomes in this dataset are from well-vetted studies that are supported by multiple lines of evidence, which demonstrate that the whole-genome sequencing data, phylogenetic tree, and epidemiological data are all in agreement. This C. auris benchmark set allows for standardized comparisons of phylogenomic pipelines, ultimately promoting effective C. auris collaborations.
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Cork, Douglas J., Steven Lembark, Sodsai Tovanabutra, Merlin L. Robb, and Jerome H. Kim. "W-Curve Alignments for HIV-1 Genomic Comparisons." PLoS ONE 5, no. 6 (June 1, 2010): e10829. http://dx.doi.org/10.1371/journal.pone.0010829.

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Sahl, Jason W., Hans Steinsland, Julia C. Redman, Samuel V. Angiuoli, James P. Nataro, Halvor Sommerfelt, and David A. Rasko. "A Comparative Genomic Analysis of Diverse Clonal Types of EnterotoxigenicEscherichia coliReveals Pathovar-Specific Conservation." Infection and Immunity 79, no. 2 (November 15, 2010): 950–60. http://dx.doi.org/10.1128/iai.00932-10.

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ABSTRACTEnterotoxigenicEscherichia coli(ETEC) is a major cause of diarrheal illness in children less than 5 years of age in low- and middle-income nations, whereas it is an emerging enteric pathogen in industrialized nations. Despite being an important cause of diarrhea, little is known about the genomic composition of ETEC. To address this, we sequenced the genomes of five ETEC isolates obtained from children in Guinea-Bissau with diarrhea. These five isolates represent distinct and globally dominant ETEC clonal groups. Comparative genomic analyses utilizing a gene-independent whole-genome alignment method demonstrated that sequenced ETEC strains share approximately 2.7 million bases of genomic sequence. Phylogenetic analysis of this “core genome” confirmed the diverse history of the ETEC pathovar and provides a finer resolution of theE. colirelationships than multilocus sequence typing. No identified genomic regions were conserved exclusively in all ETEC genomes; however, we identified more genomic content conserved among ETEC genomes than among non-ETECE. coligenomes, suggesting that ETEC isolates share a genomic core. Comparisons of known virulence and of surface-exposed and colonization factor genes across all sequenced ETEC genomes not only identified variability but also indicated that some antigens are restricted to the ETEC pathovar. Overall, the generation of these five genome sequences, in addition to the two previously generated ETEC genomes, highlights the genomic diversity of ETEC. These studies increase our understanding of ETEC evolution, as well as provide insight into virulence factors and conserved proteins, which may be targets for vaccine development.
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Dissertations / Theses on the topic "Genomic comparisons"

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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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Li, Alice Hoy Lam. "Identification of virulence determinants of Mycobacterium tuberculosis via genetic comparisons of a virulent and an attenuated strain of Mycobacterium tuberculosis." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/596.

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Candidate virulence genes were sought through the genetic analyses of two strains of Mycobacterium tuberculosis, one virulent, H37Rv, one attenuated, H37Ra. Derived from the same parent, H37, genomic differences between strains were first examined via two-dimensional DNA technologies: two-dimensional bacterial genome display, and bacterial comparative genomic hybridisation. The two-dimensional technologies were optimised for mycobacterial use, but failed to yield reproducible genomic differences between the two strains. Expression differences between strains during their infection of murine bone-marrow-derived macrophages were then assessed using Bacterial Artificial Chromosome Fingerprint Arrays. This technique successfully identified expression differences between intracellular M. tuberculosis H37Ra and H37Rv, and six candidate genes were confirmed via quantitative real-time PCR for their differential expression at 168 hours post-infection. Genes identified to be upregulated in the attenuated H37Ra were frdB, frdC, and frdD. Genes upregulated in the virulent H37Rv were pks2, aceE, and Rv1571. Further qPCR analysis of these genes at 4 and 96h post-infection revealed that the frd operon (encoding for the fumarate reductase enzyme complex or FRD) was expressed at higher levels in the virulent H37Rv at earlier time points while the expression of aceE and pks2 was higher in the virulent strain throughout the course of infection. Assessment of frd transcripts in oxygen-limited cultures of M. tuberculosis H37Ra and H37Rv showed that the attenuated strain displayed a lag in frdA and frdB expression at the onset of culture when compared to microaerophilic cultures of H37Rv and aerated cultures of H37Ra. Furthermore, inhibition of the fumarate reductase complex in intracellular bacteria resulted in a significant reduction of intracellular growth. Microarray technology was also applied in the expression analysis of intracellular bacteria at 168h post-infection. Forty-eight genes were revealed to be differentially expressed between the H37Ra and H37Rv strains, and a subset were further analysed via qPCR to confirm and validate the microarray data. phoP was expressed at a lower level in the attenuated M. tuberculosis H37Ra, whereas members of the phoPR regulon were up-regulated in the virulent H37Rv. Additionally, a group of genes (Rv3616c-Rv3613c) that may associate with the region of difference 1 were also up-regulated in the virulent H37Rv.
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Batzoglou, Serafim. "Computational genomics : mapping, comparison, and annotation of genomes." Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/8629.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2000.
Includes bibliographical references (leaves 180-191).
The field of genomics provides many challenges to computer scientists and mathematicians. The area of computational genomics has been expanding recently, and the timely application of computer science in this field is proving to be an essential component of the large international effort in genomics. In this thesis we address key issues in the different stages of genome research: planning of a genome sequencing project, obtaining and assembling sequence information, and ultimately study, cross-species comparison, and annotation of finished genomic sequence. We present applications of computational techniques to the above areas: (1) In relation to the early stages of a genome project, we address physical mapping, and we present results on the theoretical problem of finding minimum superstrings of hypergraphs, a combinatorial problem motivated by physical mapping. We also present a statistical and simulation study of "walking with clone-end sequences", an important method for sequencing a large genome.
(cont.) (2) Turning to the problem of obtaining the finished genomic sequence, we present ARACHNE, a prototype software system for assembling sequence data that are derived from sequencing a genome with the "shotgun" method. (3) Finally, we turn to the computational analysis of finished genomic sequence. We present GLASS, a software system for obtaining global pairwise alignments of orthologous finished sequences. We finally use GLASS to perform a comparative structure and sequence analysis of orthologous human and mouse genomic regions, and develop ROSETTA, the first cross-species comparison-based system for the prediction of protein coding regions in genomic sequences.
by Serafin Batzoglou.
Ph.D.
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Dousseaud, Peggy Marie Madeleine. "A comparative genomic analysis of hydrocarbon synthesis in Desulfovibrio sp." Thesis, University of Exeter, 2018. http://hdl.handle.net/10871/34379.

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To fulfil global energy demand and to mitigate economical, geopolitical and ecological challenges associated with fossil fuel utilisation, the energy sector is moving towards greater use of sustainable and environmentally friendly energy sources, including biofuels. The ideal transport biofuel would be hydrocarbons that are identical to fossil petroleum. However, to date characterised hydrocarbon biosynthetic pathways include a decarbonylation or decarboxylation reaction, which involves the loss of one carbon resulting in odd-numbered carbon chain hydrocarbons. This carbon loss decreases carbon efficiency for alkane production, which reduces microbial fuel economic competitiveness. Therefore, it is key that new pathways for alkane production are identified. The sulphate-reducing bacteria genus Desulfovibrio was previously reported to synthesise even-numbered carbon chain alkanes, which suggests an alternative route for alkane production without carbon loss. This investigation aimed to verify Desulfovibrio alkane biosynthesis and characterise the possible synthetic pathway. Ten Desulfovibrio strains, representing seven species, were screened for alkane synthesis using isotopically labelled growth media. The ability to produce alkanes within the Desulfovibrio genus was confirmed and was shown to be strain-specific under a set of culture conditions. The biogenic alkanes detected were octadecane (C18), nonadecane (C19) and eicosane (C20), with a predominance of even-numbered carbon chain alkanes. Fatty acid analysis of Desulfovibrio strains showed an alkane biosynthetic pathway was unlikely to involve a decarbonylation or decarboxylation step. A novel hypothesis was therefore proposed that alkane biosynthesis by Desulfovibrio follows a metabolic route, which has not previously been characterised, involving a series of reduction reactions from the fatty acid pool. The characterisation of the putative Desulfovibrio hydrogenation pathway for alkane biosynthesis was undertaken via a target-directed genome mining approach. The genomic DNA of nine Desulfovibrio spp. was purified, sequenced, de novo assembled and annotated. Seven of these nine genomes are unpublished to date. No homologs of previously characterised alkane biosynthetic enzymes from bacteria were in silico identified in the genomes and proteomes of alkane producing Desulfovibrio spp., suggesting that Desulfovibrio alkane biosynthetic pathway is likely to be catalysed by currently uncharacterised enzymes. The 16S rRNA-based phylogeny of Desulfovibrio spp. supported the hypothesis that the Desulfovibrio alkane biosynthetic pathway was acquired by a common ancestral strain via horizontal gene transfer. The ability of Desulfovibrio to produce alkanes was therefore hypothesised to be due to the presence of recruited genes encoding enzymes involved in alkane synthesis. A comparative genomic analysis intersecting six-alkane producing and four non-alkane producing Desulfovibrio genomes resulted in the in silico identification of 33 hypothetical proteins considered with high confidence to be exclusive to alkane producing Desulfovibrio strains. A novel hypothetical Desulfovibrio alkane biosynthetic pathway was proposed involving a V-type ATPase, an uncharacterised protein, named as a putative reductase in this investigation, and a putative methyltransferase, which were predicted to be exclusive to alkane producing Desulfovibrio spp. The inorganic phosphates resulting from the ATP hydrolysis catalysed by the V-type ATPase would be involved in a reaction with fatty alcohols to form alkyl phosphates, which are putative activated intermediates required for the hydrogenation route from fatty alcohols to alkanes. The putative reductase and the methyltransferase, predicted to share similar structural features with known alkane-binding proteins, would subsequently reduce alkyl phosphates to alkanes and to iso-alkanes respectively. Empirical investigation of the candidate molecular basis function in Desulfovibrio alkane biosynthesis was undertaken. The Desulfovibrio alkane biosynthetic pathway remains to be fully characterised.
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Jain, Gaurav. "Genomic comparison of species based on metabolic pathway components." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 61 p, 2008. http://proquest.umi.com/pqdweb?did=1605156451&sid=3&Fmt=2&clientId=8331&RQT=309&VName=PQD.

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Thesis (M.S.)--University of Delaware, 2008.
Principal faculty advisors: Li Liao, Dept. of Computer & Information Sciences and E. Fidelma Boyd, Dept. of Biological Sciences. Includes bibliographical references.
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Sharma, Ruchira. "Isolation, Characterization, and Genomic Comparison of Bacteriophages of Enterobacteriales Order." BYU ScholarsArchive, 2019. https://scholarsarchive.byu.edu/etd/8577.

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According to CDC, every year at least 2 million people are affected and 23,000 dies as a result of antibiotic resistance in U.S. It is considered one of the biggest threats to global health. More and more bacterial infections are becoming harder to treat. One such infection is fire blight, one of the most destructive disease of apple and pear trees. It is caused by bacteria Erwinia amylovora and its outbreaks have been known to destroy entire orchards in a single season. The conventional method of treatments includes use of antibiotics like streptomycin and oxytetracycline but the incidences like presence of multi-drug resistant bacteria in the mammals grazing in the fields have raised concerns. Phage therapy is considered one of the few ways available to combat bacterial resistance and prevent fire blight. In this method, a cocktail of highly lytic bacteriophages is prepared and sprayed on the trees at different time intervals. Bacteriophages are an “intelligent” drug. They multiply at the site of the infection until there are no more bacteria and then they are excreted back into the nature. These phenomena make them more efficient than an antibiotic, which kills all kind of bacteria including good bacteria and can be maintained in the environment for long periods of time. These qualities of bacteriophage have resulted in many commercially available phage therapies. The initial part of this research focuses on isolation, characterization and genomic comparison of bacteriophages that infect a plant pathogen E.amylovora of Erwiniaceae family of Enterobacteriales order. In this study, 28 novel bacteriophages were isolated, fully sequenced, characterized and grouped into seven families based on phage homology. To take this further, we characterized a novel jumbo family of bacteriophages that has a small burst size of 4.6-4.9 and are most similar to bacteriophages that infect Pseudomonas and Ralstonia rather than Enterobacteriales bacteria by protein similarity. These bacteriophages are shown to infect Erwinia and Pantoea bacterial strains, but no infection of 9 other bacterial strains tested, was seen, under laboratory conditions. The results of this work provide an insight on special characteristics that makes bacteriophage so unique and adaptable. The final part of this research explores the enormous diversity of bacteriophages. In 2014 Grose and Casjens grouped 337 fully sequenced tailed phages into 56 diverse clusters (32 lytic and 24 temperate). We further expanded our current understanding of these clusters by performing the comprehensive analysis of genomes and proteomes of 1037 tailed bacteriophages, posted on GenBank. The results of this work provide insights into diversity and relatedness of bacteriophages and the data is posted on GenBank.
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Dong, Xin. "Comparative genomics of rickettsia species." Thesis, Aix-Marseille, 2012. http://www.theses.fr/2012AIXM5054/document.

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Le genre Rickettsia, sont des petites bactéries Gram-négatives et symbiotes intracellulaires obligatoires des eucaryotes. Les Rickettsia sont surtout connus pour leur pathogénicité et pour provoquer des maladies graves chez l'homme et les autres animaux. À ce jour, 26 espèces valides de Rickettsies ont été identifiées dans le monde entier, dont 20 sont des agents pathogènes éprouvées. Toutes les espèces de Rickettsies validées sont associées à des arthropodes. Les phylogénies basées sur divers marqueurs moléculaires ont présenté des topologies discordantes, avec seulement R. bellii et R. canadensis qui ne sont classées ni parmi la fièvre boutonneuse groupe rickettsies, ni parmi le typhus groupe rickettsies. En utilisant les méthodes avancées de séquençage de génomes entiers, nous avons obtenu et analysé quatre séquences génomiques de Rickettsies : R. helvetica, R. honei, R. australis et R. japonica. Via la phylogénomique qui constitue une nouvelle stratégie permettant de mieux comprendre leur évolution, l'on remarque que ces micro-organismes ont subi une évolution génomique réduite au cours de spécialisation en intracellulaire. Plusieurs caractéristiques évolutives, comme le réarrangement des gènes, la réduction génomique, le transfert horizontal de gènes et l'acquisition d'ADN égoïste, ont formé les génomes Rickettsia d'aujourd'hui. Ces processus peuvent jouer un rôle important pour équilibrer la taille du génome afin de l'adapter au mode de vie intracellulaire. En outre, la pathogénicité des rickettsies peut être associée à la réduction génomique
The Rickettsia genus is composed of small, Gram-negative, bacteria that are obligate intracellular eukaryotic symbionts. Members of the genus Rickettsia are best known for infecting and causing severe diseases in humans and other animals. To date, 26 valid Rickettsia species have been identified worldwide, including 20 that are proven pathogens. All validated Rickettsia species are associated to arthropods that act as vectors and/or reservoirs. The phylogenies based on various molecular markers have resulted in discrepant topologies, with R. bellii and R. canadensis being classified neither among spotted fever nor typhus group rickettsiae. In this thesis, using the advanced whole genomic sequencing methods, we have and analyzed the genomic sequences from four Rickettsia species, including R. helvetica, R. honei, R. australis and R. japonica. Phylogenomics constitute a new strategy to better understand their evolution. These microorganisms underwent a reductive genomic evolution during their specialization to their intracellular lifestyle. Several evolutive characteristics, such as gene rearrangement, reduction, horizontal gene transfer and aquisition of selfish DNA, have shaped Rickettsia genomes. These processes may play an important role in free-living bacteria for balancing the size of genome in order to adapt the intracellular life style. In addition, in contrast with the concept of bacteria becoming pathogens by acquisition of virulence factors, rickettsial pathogenecity may be linked to genomic reduction of metabolism and regulation pathways
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Wetterbom, Anna. "Genome and Transcriptome Comparisons between Human and Chimpanzee." Doctoral thesis, Uppsala universitet, Genomik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-112893.

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The chimpanzee is humankind’s closest living relative and the two species diverged ~6 million years ago. Comparative studies of the human and chimpanzee genomes and transcriptomes are of great interest to understand the molecular mechanisms of speciation and the development of species-specific traits. The aim of this thesis is to characterize differences between the two species with regard to their genome sequences and the resulting transcript profiles. The first two papers focus on indel divergence and in particular, indels causing premature termination codons (PTCs) in 8% of the chimpanzee genes. The density of PTC genes is correlated with both the distance to the telomere and the indel divergence. Many PTC genes have several associated transcripts and since not all are affected by the PTC we propose that PTCs may affect the pattern of expressed isoforms. In the third paper, we investigate the transcriptome divergence in cerebellum, heart and liver, using high-density exon arrays. The results show that gene expression differs more between tissues than between species. Approximately 15% of the genes are differentially expressed between species, and half of the genes show different splicing patterns. We identify 28 cassette exons which are only included in one of the species, often in a tissue-specific manner. In the fourth paper, we use massive parallel sequencing to study the chimpanzee transcriptome in frontal cortex and liver. We estimate gene expression and search for novel transcribed regions (TRs). The majority of TRs are located close to genes and possibly extend the annotations. A subset of TRs are not found in the human genome. The brain transcriptome differs substantially from that of the liver and we identify a subset of genes enriched with TRs in frontal cortex. In conclusion, this thesis provides evidence of extensive genomic and transcriptomic variability between human and chimpanzee. The findings provide a basis for further studies of the underlying differences affecting phenotypic divergence between human and chimpanzee.
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Dickens, Nicholas J. "Comparisons of proteins and genomes by integrating bioinformatics data." Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.496848.

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Dörr, Daniel [Verfasser]. "Gene family-free genome comparison / Daniel Dörr." Bielefeld : Universitätsbibliothek Bielefeld, 2016. http://d-nb.info/1096457229/34.

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Books on the topic "Genomic comparisons"

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Straalen, Nico, and Dick Roelofs. Human Evolution and Development. NL Amsterdam: Amsterdam University Press, 2019. http://dx.doi.org/10.5117/9789463729208.

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Our understanding of human evolution is proceeding at an unprecedented rate over the last years due to spectacular fossil finds, reconstructions based on genome comparison, ancient DNA sequencing and new insights into developmental genetics. This book takes an integrative approach in which the development of the human embryo, the evolutionary history of our body, the structure of human populations, their dispersal over the world and their cultures are examined by integrating paleoanthropology, developmental biology, comparative zoology, population genetics and phylogenetic reconstruction. The authors discuss questions like: - What do we know about ancient humans? - What happens in the development of an embryo? - How did we manage to walk upright and why did we lose our hair? - What is the relationship between language, migration and evolution? - How does our body respond to the challenges of modern society? In addition to being a core text for the study of the life sciences, Human Evolution and Development is an easy-to-read overview for the interested layperson.
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Gunnels, John A. A comparison of simulated annealing and genetic algorithms for the genome mapping problems. 1993.

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Rayner, Arthur Graham *. The comparison of unidentified open reading frames in the liverwort, tobacco, and "Vicia faba" chloroplast genomes. 1988.

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Ayala, Francisco J., and Camilo J. Cela-Conde. Neanderthals and modern humans. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198739906.003.0011.

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This chapter deals with the similarities and differences between Homo neanderthalensis and Homo sapiens, by considering genetic, brain, and cognitive evidence. The genetic differentiation emerges from fossil genetic evidence obtained first from mtDNA and later from nuclear DNA. With high throughput whole genome sequencing, sequences have been obtained from the Denisova Cave (Siberia) fossils. Nuclear DNA of a third species (“Denisovans”) has been obtained from the same cave and used to define the phylogenetic relationships among the three species during the Upper Palaeolithic. Archaeological comparisons make it possible to advance a four-mode model of the evolution of symbolism. Neanderthals and modern humans would share a “modern mind” as defined up to Symbolic Mode 3. Whether the Neanderthals reached symbolic Mode 4 remains unsettled.
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Epstein-Levi, Rebecca J. Intertextually Modified Organisms. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780190456023.003.0011.

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The chapter examines genetic engineering through analogy with the Torah: if Judaism permits rabbis, in some very specific circumstances, to alter the text of the sacred Torah, might it not also permit alteration of the “sacred text” of a plant’s genome? The chapter carefully plots these specific circumstances and their plant-based analogues to argue, with a comparison of genetic and scriptural languages, for respectful “dialogical engagement” to promote human and nonhuman flourishing. While not offering a clear answer to a challenging issue, the purpose is to establish the beginning of a religiously and textually attentive ethical framework with which to evaluate genetic technology.
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Cattran, Daniel C., and Heather N. Reich. Membranous glomerulonephritis. Edited by Neil Turner. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780199592548.003.0064_update_001.

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It has been clear for several decades from comparison with the rodent model disease Heymann nephritis that membranous glomerulonephritis (MGN) is an immune condition in which antibodies, usually autoantibodies, bind to targets on the surface of podocytes. However, the antigen in Heymann nephritis, megalin, is not present on human podocytes. The first potential antigen was identified by studying rare examples of maternal alloimmunization, leading to congenital membranous nephropathy in the infant caused by antibodies to neutral endopeptidase. More recently, the target of autoantibody formation in most patients with primary MGN has been identified to be the phospholipase A2 receptor, PLA2R. Genome-wide association studies identify predisposing genetic loci at HLADQ and at the locus encoding the autoantigen itself. So antibodies to at least two different molecular targets can cause MGN, and it seems likely that there may be other targets in secondary types of MGN, and possibly haptenized or otherwise modified molecules are implicated in drug- and toxin-induced MGN. Once antibodies are fixed, animal models and human observations suggest that complement is involved in mediating tissue damage. However, immunoglobulin G4, not thought to fix complement, is the predominant isotype in human MGN, and the mechanisms are not fully unravelled. Podocyte injury is known to cause proteinuria. In MGN, antibody fixation or cell damage may stimulate production of extracellular matrix to account for the increased GBM thickness with ‘podocyte type’ basement membrane collagen isoforms, and ultimately cell death and glomerulosclerosis.
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Book chapters on the topic "Genomic comparisons"

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Brown, Gord, Duane Martindale, Michael D. Wilson, and Ben F. Koop. "Human and Mouse DNA Sequence Comparisons: Further Evidence for a Mosaic Model of Genomic Evolution." In Comparative Genomics, 59–69. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4309-7_7.

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Höög, Jan-Olov. "Mammalian Class II Alcohol Dehydrogenase: Species and Class Comparisons at Genomic and Protein Levels." In Enzymology and Molecular Biology of Carbonyl Metabolism 3, 285–92. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4684-5901-2_31.

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Doerr, Daniel, Pedro Feijão, and Jens Stoye. "Family-Free Genome Comparison." In Comparative Genomics, 331–42. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7463-4_12.

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Bergeron, Anne, Marie-Jean Meurs, Romy Valiquette-Labonté, and Krister M. Swenson. "On the Comparison of Bacteriophage Populations." In Comparative Genomics, 3–20. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-06220-9_1.

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Paten, Benedict, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard Suh, and David Haussler. "Cactus Graphs for Genome Comparisons." In Lecture Notes in Computer Science, 410–25. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-12683-3_27.

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Karlin, Samuel, and Jan Mrázek. "Prokaryotic Genome-Wide Comparisons and Evolutionary Implications." In Bacterial Genomes, 196–212. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4615-6369-3_19.

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Galves, Miguel, and Zanoni Dias. "Comparison of Genomic DNA to cDNA Alignment Methods." In Advances in Bioinformatics and Computational Biology, 170–80. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11532323_18.

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Wassenaar, T. M., J. Bohlin, T. T. Binnewies, and D. W. Ussery. "Genome Comparison of Bacterial Pathogens." In Microbial Pathogenomics, 1–20. Basel: KARGER, 2009. http://dx.doi.org/10.1159/000235759.

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Gentles, Andrew J., and Samuel Karlin. "Genome Signature Comparisons of the Proteobacteria." In Evolutionary Theory and Processes: Modern Horizons, 195–206. Dordrecht: Springer Netherlands, 2004. http://dx.doi.org/10.1007/978-94-017-0443-4_11.

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Wassenaar, T. M., T. T. Binnewies, P. F. Hallin, and D. W. Ussery. "Tools for Comparison of Bacterial Genomes." In Handbook of Hydrocarbon and Lipid Microbiology, 4313–27. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-77587-4_337.

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Conference papers on the topic "Genomic comparisons"

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Teng, Mingxiang, Yadong Wang, Yunlong Liu, Seongho Kim, Curt Balch, Kenneth P. Nephew, and Lang Li. "Empirical bayes model comparisons for differential methylation analysis." In 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). IEEE, 2011. http://dx.doi.org/10.1109/gensips.2011.6169428.

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Wagner, Isabel. "Genomic Privacy Metrics: A Systematic Comparison." In 2015 IEEE Security and Privacy Workshops (SPW). IEEE, 2015. http://dx.doi.org/10.1109/spw.2015.15.

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Lippert, Ross A., Xiaoyue Zhao, Liliana Florea, Clark Mobarry, and Sorin Istrail. "Finding anchors for genomic sequence comparison." In the eighth annual international conference. New York, New York, USA: ACM Press, 2004. http://dx.doi.org/10.1145/974614.974645.

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Marfil, Juan Jose, and Daniel Mozos. "Optimizing Reconfigurable Hardware for Genomic Sequences Comparison." In 2008 4th Southern Conference on Programmable Logic (SPL). IEEE, 2008. http://dx.doi.org/10.1109/spl.2008.4547763.

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Liu, Jonathan H. W., Yang Washington Shao, Sam D. Molyneux, Rama Khokha, and Geoffrey A. Wood. "Abstract 398: Genome-wide comparison of matched canine osteosarcoma primary tumours and metastases by array comparative genomic hybridization." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-398.

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Heinzlreiter, Paul, Michael T. Krieger, and Iris Leitner. "Hadoop-Based Genome Comparisons." In 2012 International Conference on Cloud and Green Computing (CGC). IEEE, 2012. http://dx.doi.org/10.1109/cgc.2012.83.

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Needham, Rachel H. V., Arturo B. Ramirez, Iman Kishawi, Jackie L. Stilwell, and Eric P. Kaldjian. "Abstract 3615: Comparison of whole genome amplification methods on single and pooled cells for comparative genomic hybridization array analysis." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-3615.

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Martins, Wellington S., Juan del Cuvillo, Wenwu Cui, and Guang R. Gao. "Whole Genome Alignment using a Multithreaded Parallel Implementation." In Simpósio de Arquitetura de Computadores e Processamento de Alto Desempenho. Sociedade Brasileira de Computação, 2001. http://dx.doi.org/10.5753/sbac-pad.2001.22185.

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Alignment of long DNA sequences is a challenging task due to its high demands for computational power and memory. We have developed a multithreaded parallel implementation of a sequence alignment algorithm that is able to align whole genomes with reliable output and reasonable cost. The implementation is based on a fine-grain multithreaded execution model, the EARTH model, which effectively tolerates latency through the overlapping of computation and communication. Human and mice mitochondrial genomes, human and Drosophila mitochondrial genomes are aligned respectively to demonstrate that the implementation can be used to align both closely related as well as less similar genomes. Results from Mycoplasma genitalium and Mycoplasma pneumoniae genomes, which are much larger than the tested mitochondrial genomes, are also presented. From the output, the homologous regions can be easily detected. This tool should facilitate alignment of syntenic regions, strain to strain comparisons, identification of regulatory elements and evolutionary comparisons as well.
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Jain, Gaurav, Haozhu Wang, Li Liao, and E. Fidelma Boyd. "Genomic Comparison of Bacterial Species Based on Metabolic Characteristics." In 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing. IEEE, 2009. http://dx.doi.org/10.1109/ijcbs.2009.52.

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Blazadonakis, M. E., and M. E. Zervakis. "Comparison and unification of genomic signatures in breast cancer." In 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2009. http://dx.doi.org/10.1109/iembs.2009.5332633.

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Reports on the topic "Genomic comparisons"

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George M. Church. Genomic Sequence Comparisons, 1987-2003 Final Report. Office of Scientific and Technical Information (OSTI), July 2004. http://dx.doi.org/10.2172/827024.

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Katzir, Nurit, James Giovannoni, Marla Binzel, Efraim Lewinsohn, Joseph Burger, and Arthur Schaffer. Genomic Approach to the Improvement of Fruit Quality in Melon (Cucumis melo) and Related Cucurbit Crops II: Functional Genomics. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7592123.bard.

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Background: Genomics tools for enhancement of melon research, with an emphasis on fruit, were developed through a previous BARD project of the PIs (IS -333-02). These included the first public melon EST collection, a database to relay this information to the research community and a publicly available microarray. The current project (IS-3877- 06) aimed to apply these tools for identification of important genes for improvement of melon (Cucumis melo) fruit quality. Specifically, the research plans included expression analysis using the microarray and functional analyses of selected genes. The original project objectives, as they appeared in the approved project, were: Objective 1: Utilization of a public melon microarray developed under the existing project to characterize melon transcriptome activity during the ripening of normal melon fruit (cv. Galia) in order to provide a basis for both a general view of melon transcriptome activity during ripening and for comparison with existing transcriptome data of developing tomato and pepper fruit. Objective 2: Utilization of the same public melon microarray to characterize melon transcriptome activity in lines available in the collection of the Israeli group, focusing on sugar, organic acids and aroma metabolism, so as to identify potentially useful candidates for functional analysis and possible manipulation, through comparison with the general fruit development profile resulting from (1) above. Objective 3: Expansion of our existing melon EST database to include publicly available gene expression data and query tools, as the US group has done with tomato. Objective 4: Selection of 6-8 candidate genes for functional analysis and development of DNA constructs for repression or over-expression. Objective 5: Creation of transgenic melon lines, or transgenic heterologous systems (e.g. E. coli or tomato), to assess putative functions and potential as tools for molecular enhancement of melon fruit quality, using the candidate gene constructs from (4).
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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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Serres, Margrethe H. Functional Analysis of Shewanella, a cross genome comparison. Office of Scientific and Technical Information (OSTI), May 2009. http://dx.doi.org/10.2172/952450.

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Katzir, Nurit, James Giovannoni, and Joseph Burger. Genomic approach to the improvement of fruit quality in melon (Cucumis melo) and related cucurbit crops. United States Department of Agriculture, June 2006. http://dx.doi.org/10.32747/2006.7587224.bard.

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Fruit quality is determined by numerous genetic traits that affect taste, aroma, texture, pigmentation, nutritional value and duration of shelf-life. The molecular basis of many of these important traits is poorly understood and it’s understanding offers an excellent opportunity for adding value to agricultural products. Improvement of melon fruit quality was the primary goal of the project. The original objectives of the project were: The isolation of a minimum of 1000 fruit specific ESTs. The development of a microarray of melon fruit ESTs. The analysis of gene expression in melon using melon and tomato fruit enriched microarrays. A comprehensive study of fruit gene expression of the major cucurbit crops. In our current project we have focused on the development of genomics tools for the enhancement of melon research with an emphasis on fruit, specifically the first public melon EST collection. We have also developed a database to relay this information to the research community and developed a publicly available microarray. The release of this information was one of the catalysts for the establishment of the International Cucurbit Genomic Initiative (ICuGI, Barcelona, Spain, July 2005) aimed at collecting and generating up to 100,000 melon EST sequences in 2006, leveraging a significant expansion of melon genomic resources. A total of 1000 ESTs were promised under the original proposal (Objective 1). Non-subtracted mature fruit and young fruit flesh of a climacteric variety in addition to a non-climacteric variety resulted in the majority of additional EST sequences for a total of 4800 attempted reads. 3731 high quality sequences from independent ESTs were assembled, representing 2,467 melon unigenes (1,873 singletons, 594 contigs). In comparison, as of June 2004, a total of 170 melon mRNA sequences had been deposited in GENBANK. The current project has thus resulted in nearly five- fold the number of ESTs promised and ca. 15-fold increase in the depth of publicly available melon gene sequences. All of these sequences have been deposited in GENBANK and are also available and searchable via multiple approaches in the public database (http://melon.bti.cornell.edu). Our database was selected as the central location for presentation of public melon EST data of the International Cucurbit Genomic Initiative. With the available unigenes we recently constructed a microarray, which was successfully applied in hybridizations (planned public release by August 2006). Current gene expression analyses focus on fruit development and on comparative studies between climacteric and non-climacteric melons. Earlier, expression profiling was conducted using macroarrays developed at the preliminary stage of the project. This analysis replaced the study of tomato microarray following the recommendations of the reviewers and the panel of the original project. Comparative study between melon and other cucurbit crops have begun, mainly with watermelon, in collaboration with Dr. Amnon Levi (USDA-ARS). In conclusion, all four objectives have been addressed and achieved. In the continuation project that have been approved we plan to apply the genomic tools developed here to achieve detailed functional analyses of genes associated with major metabolic pathway.
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Timme, Ruth E., Jennifer V. Kuehl, Jeffrey L. Boore, and Robert K. Jansen. A Comparison of the First Two Sequenced Chloroplast Genomes in Asteraceae: Lettuce and Sunflower. Office of Scientific and Technical Information (OSTI), January 2006. http://dx.doi.org/10.2172/960402.

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Ahlgren, Per, Tobias Jeppsson, Esa Stenberg, and Erik Berg. A bibliometric analysis of battery research with the BATTERY 2030+ roadmap as point of departure. Uppsala universitet, 2022. http://dx.doi.org/10.33063/diva-473454.

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In this bibliometric study, we analyze the six battery research subfields identified in the BATTERY 2030+ roadmap: Battery Interface Genome, Materials Acceleration Platform, Recyclability, Smart functionalities: Self-healing, Smart functionalities: Sensing, and Manufacturability. In addition, we analyze the entire research field related to BATTERY 2030+ as a whole, using two operationalizations. We (a) evaluate the European standing in the subfields/the BATTERY 2030+ field in comparison to the rest of the world, and (b) identify strongholds of the subfields/the BATTERY 2030+ field across Europe. For each subfield and the field as a whole, we used seed articles, i.e. articles listed in the BATTERY 2030+ roadmap or cited by such articles, in order to generate additional, similar articles located in an algorithmically obtained classification system. The output of the analysis is publication volumes, field normalized citation impact values with comparisons between country/country aggregates and between organizations, co-publishing networks between countries and organizations, and keyword co-occurrence networks. For the results related to (a), the performance of EU & associated (countries) is similar to China and the aggregate Japan-South Korea-Singapore and well below North America regarding citation impact and with respect to the field as a whole. Exceptions are, however, the subfields Battery Interface Genome and Recyclability. For the results related to (b), there is a large variability in the EU & associated organizations regarding volume in the different subfields. For citation impact, examples of high-performing EU & associated organizations are ETH Zurich and Max Planck Society for the Advancement of Science.
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Palmer, Guy, Varda Shkap, Wendy Brown, and Thea Molad. Control of bovine anaplasmosis: cytokine enhancement of vaccine efficacy. United States Department of Agriculture, March 2007. http://dx.doi.org/10.32747/2007.7695879.bard.

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Anaplasmosis an arthropod-born disease of cattle caused by the rickettsia Anaplasma marginale and is an impediment to efficient production of healthy livestock in both Israel and the United States. Currently the only effective vaccines are derived from the blood of infected cattle. The risk of widespread transmission of both known and newly emergent pathogens has prevented licensure of live blood-based vaccines in the U.S. and is a major concern for their continued use in Israel. Consequently development of a safe, effective vaccine is a high priority. In this collaborative project we focused on two approaches to vaccine development. The first focused o n improving antigen delivery to livestock and specifically examined how DNA vaccines could be improved to enhance priming and expansion of the immune response. This research resulted in development and testing of two novel vaccine delivery systems--one that targeted antigen spread among dendritic cells (the key cell in priming immune responses and a follow-on construct that also specifically targeted antigen to the endosomal-lysosomal compartment the processing organelle within the dendritic cell that directs vaccine antigen to the MHC class ll-CD4* T cell priming pathway). The optimized construct targeting vaccine antigen to the dendritic cell MHC class II pathway was tested for ability to prime A. marginale specific immune responses in outbred cattle. The results demonstrated both statistically significant effects of priming with a single immunization, continued expansion of the primary immune response including development of high affinity lgG antibodies and rapid recall of the memory response following antigen challenge. This portion of the study represented a significant advance in vaccine delivery for livestock. Importantly the impact of these studies is not limited to A. marginale a s the targeting motifs are optimized for cattle and can be adapted to other cattle vaccinations by inserting a relevant pathogen-specific antigen. The second approach (which represented an addition to the project for which approval was requested as part of the first annual report) was a comparative approach between A . marginale and the Israel A . centrale vaccines train. This addition was requested as studies on Major Surface Protein( MSP)- 2 have shown that this antigen is highly antigenically variable and presented solely as a "static vaccine" antigen does not give cross-strain immunity. In contrast A. . centrale is an effective vaccine which Kimron Veterinary institute has used in the field in Israel for over 50 years. Taking advantage of this expertise, a broad comparison of wild type A. marginale and vaccine strain was initiated. These studies revealed three primary findings: i) use of the vaccine is associated with superinfection, but absence of clinical disease upon superinfection with A. marginale; ii) the A. centrale vaccine strain is not only less virulent but transmission in competent in Dermacentor spp. ticks; and iii) some but not all MSPs are conserved in basic orthologous structure but there are significant polymorphisms among the strains. These studies clearly indicated that there are statistically significant differences in biology (virulence and transmission) and provide a clear path for mapping of biology with the genomes. Based on these findings, we initiated complete genome sequencing of the Israel vaccine strain (although not currently funded by BARD) and plant to proceed with a comparative genomics approach using already sequenced wild-type A. marginale. These findings and ongoing collaborative research tie together filed vaccine experience with new genomic data, providing a new approach to vaccine development against a complex pathogen.
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Heifetz, Yael, and Michael Bender. Success and failure in insect fertilization and reproduction - the role of the female accessory glands. United States Department of Agriculture, December 2006. http://dx.doi.org/10.32747/2006.7695586.bard.

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The research problem. Understanding of insect reproduction has been critical to the design of insect pest control strategies including disruptions of mate-finding, courtship and sperm transfer by male insects. It is well known that males transfer proteins to females during mating that profoundly affect female reproductive physiology, but little is known about the molecular basis of female mating response and no attempts have yet been made to interfere with female post-mating responses that directly bear on the efficacy of fertilization. The female reproductive tract provides a crucial environment for the events of fertilization yet thus far those events and the role of the female tract in influencing them are poorly understood. For this project, we have chosen to focus on the lower reproductive tract because it is the site of two processes critical to reproduction: sperm management (storage, maintenance, and release from storage) and fertilization. E,fforts during this project period centered on the elucidation of mating responses in the female lower reproductive tract The central goals of this project were: 1. To identify mating-responsive genes in the female lower reproductive tract using DNA microarray technology. 2. In parallel, to identify mating-responsive genes in these tissues using proteomic assays (2D gels and LC-MS/MS techniques). 3. To integrate proteomic and genomic analyses of reproductive tract gene expression to identify significant genes for functional analysis. Our main achievements were: 1. Identification of mating-responsive genes in the female lower reproductive tract. We identified 539 mating-responsive genes using genomic and proteomic approaches. This analysis revealed a shift from gene silencing to gene activation soon after mating and a peak in differential gene expression at 6 hours post-mating. In addition, comparison of the two datasets revealed an expression pattern consistent with the model that important reproductive proteins are pre-programmed for synthesis prior to mating. This work was published in Mack et al. (2006). Validation experiments using real-time PCR techniques suggest that microarray assays provide a conservativestimate of the true transcriptional activity in reproductive tissues. 2.lntegration of proteomics and genomics data sets. We compared the expression profiles from DNA microarray data with the proteins identified in our proteomic experiments. Although comparing the two data sets poses analyical challenges, it provides a more complete view of gene expression as well as insights into how specific genes may be regulated. This work was published in Mack et al. (2006). 3. Development of primary reproductive tract cell cultures. We developed primary cell cultures of dispersed reproductive tract cell types and determined conditions for organ culture of the entire reproductive tract. This work will allow us to rapidly screen mating-responsive genes for a variety of reproductive-tract specifi c functions. Scientific and agricultural significance. Together, these studies have defined the genetic response to mating in a part of the female reproductive tract that is critical for successful fertllization and have identified alarge set of mating-responsive genes. This work is the first to combine both genomic and proteomic approaches in determining female mating response in these tissues and has provided important insights into insect reproductive behavior.
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Wu, Liyou, T. Y. Yi, Joy Van Nostrand, and Jizhong Zhou. Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparison with Other Methods. Office of Scientific and Technical Information (OSTI), May 2010. http://dx.doi.org/10.2172/986917.

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