Academic literature on the topic 'Genomics study'
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Journal articles on the topic "Genomics study"
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Parks, M., S. Subramanian, C. Baroni, M. C. Salvatore, G. Zhang, C. D. Millar, and D. M. Lambert. "Ancient population genomics and the study of evolution." Philosophical Transactions of the Royal Society B: Biological Sciences 370, no. 1660 (January 19, 2015): 20130381. http://dx.doi.org/10.1098/rstb.2013.0381.
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Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin ( Pygoscelis adeliae ). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution.
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Hien, Le Thi Thu, Nguyen Tuong Van, Kim Thi Phuong Oanh, Nguyen Dang Ton, Huynh Thi Thu Hue, Nguyen Thuy Duong, Pham Le Bich Hang, and Nguyen Hai Ha. "Genomics and big data: Research, development and applications." Vietnam Journal of Biotechnology 19, no. 3 (October 13, 2021): 393–410. http://dx.doi.org/10.15625/1811-4989/16158.
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Recent years, genomics and big data analytics have been widely applied and have significant impacts in various important areas of social life worldwide. The development of the next-generation sequencing (NGS) technologies, such as whole-genome sequencing (WGS), whole-exome sequencing (WES), transcriptome, and/or targeted sequencing, has enabled quickly generating the genomes of interested living organisms. Around the world many nations have invested in and promoted the development of genomics and big data analytics. A number of well-established projects on sequencing of human, animal, plant, and microorganism genomes to generate vast amounts of genomic data have been conducted independently or as collaborative efforts by national or international research networks of scientists specializing in different technical fields of genomics, bioinformatics, computational and statistical biology, automation, artificial intelligence, etc. Complicated and large genomic datasets have been effectively established, storage, managed, and used. Vietnam supports this new field of study through setting up governmental authorized institutions and conducting genomic research projects of human and other endemic organisms. In this paper, the research, development, and applications of genomic big data are reviewed with focusing on: (i) Available sequencing technologies for generating genomic datasets; (ii) Genomics and big data initiatives worldwide; (iii) Genomics and big data analytics in selected countries and Vietnam; (iv) Genomic data applications in key areas including medicine for human health care, agriculture - forestry, food safety, and environment.
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Taylor, Natalie, Stephanie Best, Melissa Martyn, Janet C. Long, Kathryn N. North, Jeffrey Braithwaite, and Clara Gaff. "A transformative translational change programme to introduce genomics into healthcare: a complexity and implementation science study protocol." BMJ Open 9, no. 3 (March 2019): e024681. http://dx.doi.org/10.1136/bmjopen-2018-024681.
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IntroductionTranslating scientific advances in genomic medicine into evidence-based clinical practice is challenging. Studying the natural translation of genomics into ‘early-adopting’ health system sectors is essential. We will (a) examine 29 health systems (Australian and Melbourne Genomics Health Alliance flagships) integrating genomics into practice and (b) combine this learning to co-design and test an evidence-based generalisable toolkit for translating genomics into healthcare.Methods and analysisTwenty-nine flagships integrating genomics into clinical settings are studied as complex adaptive systems to understand emergent and self-organising behaviours among inter-related actors and processes. The Effectiveness–Implementation Hybrid approach is applied to gather information on the delivery and potential for real-world implementation. Stages ‘1’ and ‘2a’ (representing hybrid model 1) are the focus of this protocol. The Translation Science to Population Impact (TSci Impact) framework is used to study policy decisions and service provision, and the Theoretical Domains Framework (TDF) is used to understand individual level behavioural change; both frameworks are applied across stages 1 and 2a. Stage 1 synthesises interview data from 32 participants involved in developing the genomics clinical practice systems and approaches across five ‘demonstration-phase’ (early adopter) flagships. In stage 2a, stakeholders are providing quantitative and qualitative data on process mapping, clinical audits, uptake and sustainability (TSci Impact), and psychosocial and environmental determinants of change (TDF). Findings will be synthesised before codesigning an intervention toolkit to facilitate implementation of genomic testing. Study methods to simultaneously test the comparative effectiveness of genomic testing and the implementation toolkit (stage 2b), and the refined implementation toolkit while simply observing the genomics intervention (stage 3) are summarised.Ethics and disseminationEthical approval has been granted. The results will be disseminated in academic forums and used to refine interventions to translate genomics evidence into healthcare. Non-traditional academic dissemination methods (eg, change in guidelines or government policy) will also be employed.
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Howard Sharp, Katianne M., Niki Jurbergs, Annastasia Ouma, Lynn Harrison, Elsie Gerhardt, Leslie Taylor, Kayla Hamilton, et al. "Factors Associated With Declining to Participate in a Pediatric Oncology Next-Generation Sequencing Study." JCO Precision Oncology, no. 4 (September 2020): 202–11. http://dx.doi.org/10.1200/po.19.00213.
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PURPOSE For the advances of pediatric oncology next-generation sequencing (NGS) research to equitably benefit all children, a diverse and representative sample of participants is needed. However, little is known about demographic and clinical characteristics that differentiate families who decline enrollment in pediatric oncology NGS research. METHODS Demographic and clinical data were retrospectively extracted for 363 pediatric patients (0-21 years) with cancer approached for enrollment in Genomes for Kids (G4K), a study examining the feasibility of comprehensive clinical genomic analysis of tumors and paired normal samples. Demographic and clinical factors that significantly differentiated which families declined were subsequently compared, for 348 families, with enrollment in Clinical Implementation of Pharmacogenetics (PG4KDS), a pharmacogenomics study with more explicit therapeutic benefit examining genes affecting drug responses and metabolism. RESULTS Fifty-three families (14.6%) declined enrollment in G4K. Race/ethnicity was the only variable that significantly differentiated study refusal according to multivariable logistic regression, with families of black children more likely to decline enrollment compared with families of non-Hispanic or Hispanic white children. Reasons for declining G4K were generally consistent with other pediatric genomics research: feeling overwhelmed and insurance discrimination fears were most frequently cited. Families of black children were also more likely to decline enrollment in PG4KDS. Thirteen (3.7%) of the 348 families approached for both studies declined PG4KDS. CONCLUSION Race/ethnicity differentiated study declination across two different pediatric oncology genomics studies, suggesting enrollment disparities in the context of pediatric oncology genomics research. Genomics research participant samples that do not fully represent racial and ethnic minorities risk further exacerbating health disparities. Additional work is needed to understand the nuances of parental decision making in genomic research and facilitate enrollment of diverse patient populations.
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Lamichhaney, Sangeet, Daren C. Card, Phil Grayson, João F. R. Tonini, Gustavo A. Bravo, Kathrin Näpflin, Flavia Termignoni-Garcia, et al. "Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution." Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1777 (June 3, 2019): 20180248. http://dx.doi.org/10.1098/rstb.2018.0248.
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Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current ‘genomics gold rush’ in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep ‘vertical’, natural history knowledge with ‘horizontal’ knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
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Alam, Intikhab, Mike Cornell, Darren M. Soanes, Cornelia Hedeler, Han Min Wong, Magnus Rattray, Simon J. Hubbard, Nicholas J. Talbot, Stephen G. Oliver, and Norman W. Paton. "A Methodology for Comparative Functional Genomics." Journal of Integrative Bioinformatics 4, no. 3 (December 1, 2007): 112–22. http://dx.doi.org/10.1515/jib-2007-69.
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Abstract The continuing and rapid increase in the number of fully sequenced genomes is creating new opportunities for comparative studies. However, although many genomic databases store data from multiple organisms, for the most part they provide limited support for comparative genomics. We argue that refocusing genomic data management to provide more direct support for comparative studies enables systematic identification of important relationships between species, thereby increasing the value that can be obtained from sequenced genomes. The principal result of the paper is a methodology, in which comparative analyses are constructed over a foundation based on sequence clusters and evolutionary relationships. This methodology has been applied in a systematic study of the fungi, and we describe how comparative analyses have been implemented as an analysis library over the e-Fungi data warehouse.
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Blaškovičová, Jana, and Ján Labuda. "Analytical methods in herpesvirus genomics." Acta Chimica Slovaca 7, no. 2 (October 1, 2014): 109–18. http://dx.doi.org/10.2478/acs-2014-0019.
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Abstract Genomics is a branch of bioanalytical chemistry characterized as the study of the genome structure and function. Genome represents the complete set of chromosomal and extrachromosomal genes of an organism, a cell, an organelle or a virus. There are at least five from eight species of herpesviruses commonly widespread among humans, Herpes simplex virus type 1 and 2, Varicella zoster virus, Epstein-Barr virus and Cytomegalovirus. Human gammaherpesviruses can cause serious diseases including B-cell lymphoma and Kaposi’s sarcoma. Diagnostics and study of the herpesviruses is directly dependent on the development of modern analytical methods able to detect and determine the presence and evolution of herpesviral particles/ genomes. Diagnostics and genomic characterization of human herpesvirus species is based on bioanalytical methods such as polymerase chain reaction (PCR), DNA sequencing, gel electrophoresis, blotting and others. The progress in analytical approaches in the herpesvirus genomics is reviewed in this article.
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Lucas, Joseph E., Carlos M. Carvalho, Julia Ling-Yu Chen, Jen-Tsan Chi, and Mike West. "Cross-Study Projections of Genomic Biomarkers: An Evaluation in Cancer Genomics." PLoS ONE 4, no. 2 (February 19, 2009): e4523. http://dx.doi.org/10.1371/journal.pone.0004523.
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Vadlamudi, Lata, Carmen Maree Bennett, Melanie Tom, Ghusoon Abdulrasool, Kristian Brion, Ben Lundie, Hnin Aung, et al. "A Multi-Disciplinary Team Approach to Genomic Testing for Drug-Resistant Epilepsy Patients—The GENIE Study." Journal of Clinical Medicine 11, no. 14 (July 21, 2022): 4238. http://dx.doi.org/10.3390/jcm11144238.
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Background. The genomic era has led to enormous progress in clinical care and a multi-disciplinary team (MDT) approach is imperative for integration of genomics into epilepsy patient care. Methods. The MDT approach involved patient selection, genomic testing choice, variant discussions and return of results. Genomics analysis included cytogenomic testing and whole exome sequencing (WES). Neurologist surveys were undertaken at baseline and after genomic testing to determine if genomic diagnoses would alter their management, and if there was a change in confidence in genomic testing and neurologist perceptions of the MDT approach. Results. The total diagnostic yield from all genomic testing was 17% (11/66), with four diagnoses from cytogenomic analyses. All chromosomal microarray (CMA) diagnoses were in patients seen by adult neurologists. Diagnostic yield for WES was 11% (7/62). The most common gene with pathogenic variants was DCX, reported in three patients, of which two were mosaic. The genomic diagnosis impacted management in 82% (9/11). There was increased confidence with integrating genomics into clinical care (Pearson chi square = 83, p = 0.004) and qualitative comments were highly supportive of the MDT approach. Conclusions. We demonstrated diagnostic yield from genomic testing, and the impact on management in a cohort with drug-resistant epilepsy. The MDT approach increased confidence in genomic testing and neurologists valued the input from this approach. The utility of CMA was demonstrated in epilepsy patients seen by adult neurologists as was the importance of considering mosaicism for previously undiagnosed patients.
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Goldenberg, Aaron J., Roselle Ponsaran, Amy Gaviglio, Dalton Simancek, and Beth A. Tarini. "Genomics and Newborn Screening: Perspectives of Public Health Programs." International Journal of Neonatal Screening 8, no. 1 (January 28, 2022): 11. http://dx.doi.org/10.3390/ijns8010011.
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This study assesses the benefits and challenges of using genomics in Newborn Screening Programs (NBS) from the perspectives of State program officials. This project aims to help programs develop policies that will aid in the integration of genomic technology. Discussion groups were conducted with the NBS Program and Laboratory Directors in the seven HRSA Regional Genomics Collaboratives (August 2014–March 2016). The discussion groups addressed expected uses of genomics, potential benefits, and challenges of integrating genomic technology, and educational needs for parents and other NBS stakeholders: Twelve focus groups were conducted, which included participants from over 40 state programs. Benefits of incorporating genomics included improving screening modalities, supporting diagnostic procedures, and screening for a wider spectrum of disorders. Challenges included the costs of genomics, the ability to educate parents and health care providers about results, and the potential negative psychosocial impact of genomic information. Attempts to address the challenges of integrating genomics must focus on preserving the child welfare goals of NBS programs. Health departments will need to explore how genomics could be used to enhance programs while maintaining universal access to screening.
Dissertations / Theses on the topic "Genomics study"
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Pang, See-Tong. "A functional genomics approach to study prostate disorders /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-640-5/.
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Shebe, Khadija Ahmed. "Genomics study of anti-tuberculosis drug-induced hypersensitivity reactions." Master's thesis, University of Cape Town, 2015. http://hdl.handle.net/11427/15679.
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Introduction: All first-line anti-tuberculosis drugs can be associated with all phenotypes of cutaneous adverse drug reactions (CADR). Second-line drugs are associated with much poorer outcomes. Thus, identifying the offending drug in poly-pharmacy is difficult. Re -challenge with the drug is the gold standard in identifying the offender, however poses unacceptably high risk of CADR recurrence. Population and drug-specific genomics help identify those susceptible to adverse reactions to a drug facilitating avoidance of the drug. Objective: To investigate the genomic susceptibility in patients with confirmed rifampicin and or isoniazid-associated hypersensitivity reactions using both genome- wide association studies and candidate gene approaches. Methods: A case control study using 14 patients with previous tuberculosis-associated CADR who were re-challenged with first-line anti-tuberculosis drugs and subsequently developed re-challenge reactions to either isoniazid or rifampicin as cases. These were compared with 30 controls who had tolerated rifampicin and isoniazid during the re- challenge process (12 patients, Group 1a) and consecutive patients who had been on TB treatment for at least 12 weeks without developing any adverse drug reaction (1 8 patients, Group 1b) and 200 black South Africans from the general population. HLA genotypes of the samples were determined by SeCore® HLA Sequence based typing (Invitrogen, Life technologies, USA), and potential ambiguities were resolved by sequencing-based typing. Results: We found HLA-B*58:02 (OR=3.6; 95% CI: 1.4-8.99) and HLA-DRB1*09:01 (OR=15.3; 95% CI: 2.1-113.1) to be significantly more prevalent in patients who developed rifampicin and isoniazid-associated CADR as compared to black South African general population. However, we found no significant associations between HLA genotype and rifampicin/isoniazid-associated CADR when we compared the cases to our study controls that had tolerated rifampicin and isoniazid. HLA-B *58.02 was not found to be statistically associated with HIV positive status (p=0.42) and DRESS phenotype ( p= 0.6279). The majority of our cases were black Africans. Approximately 80% of our cases and controls were HIV-infected. DRESS/DIHS was the prevalent phenotype of CADR, accounting for approximately 80% of cases and controls. Discussion: To our knowledge, this is the first study to show an association between HLA-B*58:02 and HLA-DRB1*09:01 alleles and severe cutaneous adverse drugs reactions secondary to rifampicin and isoniazid in an African population. We identify 2 candidate HLA alleles that need confirmation of their association in African patients who develop rifampicin or isoniazid-associated CADR in larger studies. The value of identifying candidate alleles could lead to CADR preventative screening prior to initiating anti-tuberculosis therapy in black South Africans. The HLA-B*58:02 noted in our cases and controls tolerant of the drugs might not be associated with CADR but could be a reflection of the HIV status and control in HIV-TB co-infected persons. Conclusion: HLA-B*58:02 and HLA-DRB1*09:01 may be associated with rifampicin and isoniazid-associated CADR. Alternately HLA-B*58:02 may be associated with HIV status rather than CADR. A sufficiently powered study is needed to confirm this association.
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Norman-Marzella, Nancy L. "Evidence-Based Practice Self-Study Education Program for Staff Nurses on Genomics." ScholarWorks, 2019. https://scholarworks.waldenu.edu/dissertations/7416.
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Nurses routinely obtain genomic data when collecting family health histories. However, they report low confidence in their knowledge and understanding of genomics and the genetically engineered medications prescribed for their patients. The purpose of this project was the development and implementation of an evidence-based online education program about genetics and genomics to increase the nurses' understanding and ability to provide competent care for their patients receiving treatments based on the science of genomics. Knowles's principles of adult learning theory guided the development and delivery of the online education project to 12 medical-surgical registered nurses employed in a hospital in the northeastern United States. The Johns Hopkins nursing evidence-based practice model provided a guideline for organizing and evaluating the level and quality of evidence. A 2-tailed paired t test showed that the nurses' knowledge and understanding about genetics and genomics increased after participating in the evidence-based education program. The increase in nurses' knowledge on genomics has the potential to provide nurses with the competence and confidence to collaborate with physicians and pharmacists regarding treatment plans incorporating genomics, resulting in effective team collaboration and a positive social change that could improve patient outcomes.
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Weirather, Jason Lee. "Computational approaches to the study of human trypanosomatid infections." Diss., University of Iowa, 2012. https://ir.uiowa.edu/etd/4976.
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Trypanosomatids cause human diseases such as leishmaniasis and African trypanosomiasis. Trypanosomatids are protists from the order Trypanosomatida and include species of the genera Trypanosoma and Leishmania, which occupy a similar ecological niche. Both have digenic life-stages, alternating between an insect vector and a range of mammalian hosts. However, the strategies used to subvert the host immune system differ greatly as do the clinical outcome of infections between species. The genomes of both the host and the parasite instruct us about strategies the pathogens use to subvert the human immune system, and adaptations by the human host allowing us to better survive infections.
We have applied unsupervised learning algorithms to aid visualization of amino acid sequence similarity and the potential for recombination events within Trypanosoma brucei's large repertoire of variant surface glycoproteins (VSGs). Methods developed here reveal five groups of VSGs within a single sequenced genome of T. brucei, indicating many likely recombination events occurring between VSGs of the same type, but not between those of different types. These tools and methods can be broadly applied to identify groups of non-coding regulatory sequences within other Trypanosomatid genomes.
To aid in the detection, quantification, and species identification of leishmania DNA isolated from environmental or clinical specimens, we developed a set of quantitative-PCR primers and probes targeting a taxonomically and geographically broad spectrum of Leishmania species. This assay has been applied to DNA extracted from both human and canine hosts as well as the sand fly vector, demonstrating its flexibility and utility in a variety of research applications.
Within the host genomes, fine mapping SNP analysis was performed to detect polymorphisms in a family study of subjects in a region of Northeast Brazil that is endemic for Leishmania infantum chagasi, the parasite causing visceral leishmaniasis. These studies identified associations between genetic loci and the development of visceral leishmaniasis, with a single polymorphism associated with an asymptomatic outcome after infection.
The methods and results presented here have capitalized on the large amount of genomics data becoming available that will improve our understanding of both parasite and host genetics and their role in human disease.
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Curreem, Oi-ting Shirly. "The study of environmental adaptability of laribacter hongkongensis by genomic and proteomic approach." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43931686.
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Herniou, Elisabeth Anne. "Use of comparative genomics and phylogenetics to study the evolution of the Baculoviridae." Thesis, Imperial College London, 2003. http://hdl.handle.net/10044/1/7698.
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Martinez-Hernandez, Francisco. "The power of one: Study of the marine virosphere using single-virus genomics." Doctoral thesis, Universidad de Alicante, 2019. http://hdl.handle.net/10045/118218.
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Aunque tradicionalmente las dificultades asociadas a su estudio han subestimado la importancia de los virus en los ecosistemas, hoy en día el desarrollo de nuevas metodologías nos ha hecho comprender que estos juegan un papel relevante a nivel global, sobre todo en los océanos. La secuenciación del genoma vírico de una muestra ambiental (la virómica) y su posterior reconstrucción (ensamblaje de genomas), ha permitido ampliar el número de virus marinos conocidos, sin embargo, también han puesto de manifiesto la enorme diversidad de genomas víricos que continúan sin ser reconstruidos. En esta tesis, la novedosa metodología de Single-virus genomics (SVGs), una técnica en la que se separan virus mediante sorting y se amplifica y secuencia su genoma de forma individual, fue aplicada con éxito sobre muestras marinas, desvelándose el genoma de virus marinos, previamente desconocidos, a pesar de ser altamente abundantes a lo largo de todos los océanos del planeta. El motivo por el que la virómica no ha podido reconstruir estos genomas fue analizado también en la tesis y se le atribuyó a la (micro-)diversidad de estas abundantes poblaciones víricas. Uno de estos virus obtenidos por SVG, el vSAG 37-F6, resultó ser el más abundante en los océanos. Diferentes métodos in silico, basados en análisis de k-mer, espaciadores CRISPR y búsqueda de ARNt, fueron empleados para tratar de identificar su huésped, sin embargo, no dieron resultado, por lo que se diseñó una aproximación experimental. Se diseñaron unos primers de PCR, específicos para el vSAG 37-F6 y se probaron en una colección de células sorteadas individualmente cuyo genoma había sido amplificado (SAGs). Tras comprobar la correcta amplificación (no inespecificidades) en uno de estos SAGs, se secuenció su genoma, mostrando que estaba relacionado con los Pelagibacteriales, por lo que el vSAG 37-F6 se identificó como un pelagifago. Corroborando este resultado 3 contigs diferentes, similares al vSAG 37-F6 fueron encontrados en otros 3 SAGs identificados también como Pelagibacter sp, obtenidos cada uno de ellos en diferentes localizaciones (Océanos Atlántico y Pacífico), y en tres experimentos y trabajos diferentes. Estos Pelagifagos similares al 37-F6 estaban poco relacionados con los obtenidos por técnicas dependientes de cultivo. La abundancia de los virus en muestras ambientales es tradicionalmente estimada de forma relativa mediante el reclutamiento de fragmentos virómicos. Sin embargo, la ausencia de marcadores específicos dificulta el empleo de métodos para calcular su abundancia de forma absoluta, como se hace con los procariotas. En el tercer capítulo de esta tesis, se muestra la aplicación de la técnica de droplet digital PCR (ddPCR) para calcular la abundancia absoluta de 2 pelagifagos, el vSAG 37-F6, y el HTVC010P. Además, son evaluados los pasos críticos de esta metodología, como es el diseño de primers específicos, o la correlación matemática para su cálculo. Las abundancias absolutas de ambos virus fueron calculadas en tres muestras ambientales diferentes, dos del Mar Mediterráneo, y una del Atlántico Norte, procedente del Golfo de Maine (Estados Unidos). La pareja de primers empleada con el vSAG 37-F6 fue diseñada siguiendo el procedimiento propuesto en este trabajo, mientras que para el HTVC010P se empleó una pareja de primers obtenida de la bibliografía. Los valores de abundancia obtenidos estuvieron comprendidos entre los valores de 1,270-14,400 virus mL-1 y de 360 a 8,510 virus mL-1 para el HTVC010P y el vSAG 37-F6 respectivamente. Sin embargo, la secuenciación de los amplicones obtenidos por PCR, mostró una sobreestimación del 6% para los primers del HTVC010P, pero no para los del vSAG 37-F6. Los dos últimos apartados de esta tesis se corresponden con dos trabajos que están actualmente siendo desarrollados por el doctorando. En el primero de ellos se analiza la (micro-)diversidad de las poblaciones del vSAG 37-F6 desde varios puntos de vista. Y para finalizar la técnica de SVGs es aplicada en muestras marinas de profundidad, de las que poco se conoce actualmente.La presente tesis ha sido financiada por el Ministerio de Economía y competitividad español (refs. CGL2013-40564-R and SAF2013-49267-EXP), por la Generalitat Valenciana (ref. ACOM/2015/133 and ACIF/2015/332), y por la Gordon and Betty Moore Foundation (ref. 5334).
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Lee, Yiu-fai. "Analysis for segmental sharing and linkage disequilibrium a genomewide association study on myopia /." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43912217.
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Heeger, Felix [Verfasser]. "Genomics Approaches to the Study of Diversity and Function of Aquatic Fungi / Felix Heeger." Berlin : Freie Universität Berlin, 2019. http://d-nb.info/1176634666/34.
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Rhode, Clint. "Signatures of selection in natural and cultured Abalone (Haliotis midae) : a population genomics study." Thesis, Stellenbosch : Stellenbosch University, 2013. http://hdl.handle.net/10019.1/79895.
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Thesis (PhD)--Stellenbosch University, 2013.ENGLISH ABSTRACT: The South African abalone, Haliotis midae, commonly known as perlemoen, is an economically important gastropod mollusc. Historically, this species maintained a lucrative fisheries sector; however with increasingly lower landings there has now been a shift to aquaculture. Efforts to conserve natural populations and to improve abalone aquaculture production are thus running in parallel. Previous studies reported significant disparities in parental contributions in aquaculture populations that could explain the rapid divergence of commercial stocks from wild populations. Furthermore, subtle, but significant, population differentiation has also been reported for wild populations on the west-, south-, and east coast of the South African coastline. This study therefore aimed to investigate the evolutionary forces, in particularly selection, facilitating population divergence in wild and cultured H. midae populations using a population genomics approach. By using both microsatellite- and single nucleotide polymorphism (SNP) markers it was found that approximately 10% to 27% of the H. midae genome may be influenced by selection. When incorporating these loci into analyses of population differentiation (e.g. AMOVA, factorial correspondence analysis and estimates of genetic distance) there was a marked increase in genetic divergence between wild and cultured populations (especially when using microsatellite loci) and amongst populations from different geographic regions (particularly supported by the SNP loci). The differences in population clustering as highlighted by microsatellite- and SNP markers can most likely be attributed to the genomic distribution of the respective loci: The SNP markers were developed from EST sequences and therefore mostly represents protein structural variation; whereas the microsatellite markers, found to be putatively under selection, were mainly located in regulatory motifs. The results of this study therefore confirmed previous observations of divergence amongst wild- and cultured populations, but more importantly demonstrated that selection is an important factor driving this divergence. In wild populations selection probably facilitates adaptation to local environmental conditions, whilst amongst aquaculture population adaptation to captivity, husbandry practices and artificial selection may be important determinants. There is evidence for population bottlenecks in wild- and cultured populations; nonetheless long-term effective population sizes seem to be large. Amongst the wild populations, however, short-term population sizes appear to be small most likely due to differential spawning rates amongst reproductively active animals leading to temporal fluctuation in genetic diversity. The results indicate that contact between wild and cultured abalone should be minimised to prevent any adverse effects due to outbreeding depression. With regards to conservation, an emphasis on maintaining adaptive diversity of the wild stocks might be warranted. Continued genetic monitoring is advisable for both wild and cultured abalone populations as to optimally manage the abalone resource for both conservation and commercial viability and sustainability.
AFRIKAANSE OPSOMMING: Die Suid-Afrikaanse perlemoen, Haliotis midae, is 'n ekonomies belangrike buikpotige weekdier. Histories het hierdie spesie 'n winsgewende vissery gehandhaaf, maar met steeds dalende vangste is daar nou 'n verskuiwing na akwakultuur. Pogings om natuurlike populasies te bewaar en perlemoen te verbeter vir verhoogde akwakultuur produksie loop dus in parallel. Vorige studies het bevind dat beduidende verskille in ouerlike bydraes tot die nageslag, in akwakultuur populasies, kan verduidelik hoekom die populasies so vinnig divergeer van die wilde voorouers. Verder, is subtiele, maar betekenisvolle genetiese differensiasie tussen wilde populasies aan die wes-, suid-en ooskus van die land gevind. Hierdie studie is dus daarop gemik om ondersoek in te stel na die mate waartoe verskeie evolusionêre prosesse, in besonder seleksie, die populasie divergensie in beide wilde en gekweekte H. midae teweegbring deur gebruik te maak van ‘n populasie genomika benadering. Deur gebruik te maak van beide mikrosatelliet- en enkel nukleotied polimorfisme (ENP) merkers is dit bevind dat ongeveer 10% tot 27% van die H. midae genoom moontlik beïnvloed word deur seleksie. Met die gebruik van loki onder seleksie tydens die ontleding van populasie differensiasie (bv. AMOVA, faktoriaal korrespondensie analise en genetiese afstand ramings) was daar 'n merkbare toename in genetiese divergensie tussen wilde- en gekweekte populasies (veral wanneer mikrosatelliet loki gebruik is) en onder die populasies vanuit verskillende geografiese gebiede (veral ondersteun deur die ENP loki). Die verskille in die populasie groeperings soos uitgelig deur die mikrosatelliet- en ENP-merkers kan waarskynlik toegeskryf word aan die genomiese verspreiding van die onderskeie loki: Die ENP-merkers is ontwikkel vanaf uitgedrukte volgorde merker (UVM) volgordes en daarom verteenwoordig dit meestal proteïen strukturele veranderinge, terwyl mikrosatelliet merkers eerder in regulatoriese motiewe geleë is. Die resultate van hierdie studie steun dus vorige waarnemings, maar meer belangrik, het dit getoon dat seleksie ‘n betekenisvolle faktor in populasie divergensie in beide wilde en gekweekte populasies is. In wilde populasies fasiliteer seleksie waarskynlik die aanpassing tot plaaslike omgewingstoestande terwyl seleksie onder die gekweekte populasies teweeggebring kan word as gevolg van aanpassing tot aanhouding, boerdery praktyke en kunsmatige seleksie. Daar is bewyse vir populasie bottelnekke in wilde- en gekweekte populasies; tog blyk langtermyn effektiewe populasiegroottes om redelik groot te wees. Onder die wilde populasies is egter gevind dat kort-termyn populasiegroottes klein kan wees, waarskynlik as gevolg van differensiële broeikoerse onder reproduktiewe diere. Dit het tot gevolg dat daar beduidende fluktuasies is in temporale genetiese diversiteit. Die resultate dui daarop dat kontak tussen wilde en gekweekte perlemoen tot 'n minimum beperk moet word om enige nadelige effekte weens uitteling depressie te voorkom. Verder, met betrekking tot bewaring, is ‘n klem op die handhawing van aangepaste genetiese diversitiet dalk geregverdig. Voortgesette genetiese monitering word aanbeveel vir beide wilde- en gekweekte perlemoen populasies ter wille van die optimale bestuur van die perlemoen hulpbron vir beide bewaring en kommersiële lewensvatbaarheid en volhoubaarheid.
International Foundation for Science
National Research Foundation of South Africa
Stellenbosch University
Books on the topic "Genomics study"
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Auteur, Jones Elizabeth W., and Lozovsky Elena R. Auteur, eds. Study guide and solutions manual to accompany Essential genetics. 4th ed. Boston: Jones and Bartlett Publishers, 2006.
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Dent, David. The convention on biological diversity and product commercialisation in development assistance projects: A case study of LUBILOSA. Wallingford, Oxon, UK: New York, NY, 2001.
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Waltenbury, Danielle. The use of RAPD genomic fingerprinting to study relatedness in strains of Acidithiobacillus ferrooxidans. Sudbury, Ont: Laurentian University, School of Graduate Studies, 2003.
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Radiat︠s︡ionno-indut︠s︡irovannai︠a︡ nestabilʹnostʹ genoma u rasteniĭ i bakteriĭ. Baku: Élm, 2007.
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R, Lozovsky Elena, and Jones Elizabeth W, eds. Student solutions manual and supplemental problems to accompany Genetics: Analysis of genes and genomes seventh edition. Sudbury, Mass: Jones and Bartlett Publishers, 2009.
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Unit, Heriot-Watt University SCHOLAR, ed. SQA CfE Higher Biology: DNA and the Genome. Edinburgh: Heriot-Watt University SCHOLAR, 2014.
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Study guide/solutions manual to accompany Genetics: From genes to genomes, third edition, Leland H. Hartwell, Ann E. Reynolds, Leroy Hood, Lee M. Silver, Michael L. Goldberg, Ruth C. Veres. New York: McGraw-Hill, 2008.
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Gloyn, Anna L., and Mark I. McCarthy. Genetics in diabetes: Type 2 diabetes and related traits. Basel: Karger, 2014.
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Weinmann, Hilmar, and Stefan Jaroch. Chemical Genomics: Small Molecule Probes to Study Cellular Function. Springer, 2016.
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Geeen, J. E. Genomic Approaches to the Study of Breast Cancer. IOS Press, 2004.
Find full textBook chapters on the topic "Genomics study"
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Gabaldón, Toni, and Marina Marcet-Houben. "3 Phylogenomics for the Study of Fungal Biology." In Fungal Genomics, 61–79. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-45218-5_3.
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Badescu, Dunarel, Abdoulaye Baniré Diallo, Mathieu Blanchette, and Vladimir Makarenkov. "An Evolutionary Study of the Human Papillomavirus Genomes." In Comparative Genomics, 128–42. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-87989-3_10.
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Anderson, Robyn, Cassandria Tay Fernandez, Yuxuan Yuan, Agnieszka A. Golicz, David Edwards, and Philipp E. Bayer. "Method for Genome-Wide Association Study: A Soybean Example." In Legume Genomics, 147–58. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0235-5_7.
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Qin, Haide, and Yin Yao. "From Family Study to Population Study: A History of Genetic Mapping for Nasopharyngeal Carcinoma (NPC)." In Applied Computational Genomics, 81–106. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-13-1071-3_7.
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Jorgensen, Timothy J., Hai-De Qin, and Yin Yao Shugart. "From Family Study to Population Study: A History of Genetic Mapping for Nasopharyngeal Carcinoma (NPC)." In Applied Computational Genomics, 35–60. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-5558-1_4.
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Li, Rong, Haifeng Chen, Songli Yuan, and Xinan Zhou. "Overview and Application of Soybean Genomics Study." In Oil Crop Genomics, 37–51. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-70420-9_2.
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Dias, Ulisses, Zanoni Dias, and João C. Setubal. "A Simulation Tool for the Study of Symmetric Inversions in Bacterial Genomes." In Comparative Genomics, 240–51. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-16181-0_20.
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Trail, Frances, and Donald M. Gardiner. "11 Application of Genomics to the Study of Pathogenicity and Development in Fusarium." In Fungal Genomics, 267–300. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-45218-5_11.
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Shelest, Ekaterina, and Kerstin Voigt. "2 Genomics to Study Basal Lineage Fungal Biology: Phylogenomics Suggests a Common Origin." In Fungal Genomics, 31–60. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-45218-5_2.
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Abhimanyu and Chakresh Kumar Jain. "Computational Interaction Study of Immunomodulatory Plant Derivatives Against SARS-Cov-2 Mpro Target." In Phytochemical Genomics, 681–98. Singapore: Springer Nature Singapore, 2022. http://dx.doi.org/10.1007/978-981-19-5779-6_29.
Full textConference papers on the topic "Genomics study"
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"Study of the introduction collection of the Miscanthus." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-076.
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"An integrated approach to study genetics of Triticum aestivum vegetation period." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-099.
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"Study of the leaf rust resistance gene Lr52 by targeted sequencing." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-033.
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"Study of genetic basis of the melanin biosynthesis in barley grain." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-062.
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"Study of the role of the MtWOX9-1 gene in somatic embryogenesis." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-015.
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"The allelic diversity study of regulatory genes involved in flavonoid biosynthesis in cotton." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-132.
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"Study of varieties of spring triticale for the presence of the wbm gene." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-102.
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"The study of state transitions in phyA and phyB mutants of Arabidopsis thaliana." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-026.
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"Genome-wide approaches in the study of common fig in the Nikita Botanical Gardens." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-136.
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"Testing safety of genetically modified products of rice: Case study on Sprague Dawley rats." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-112.
Full textReports on the topic "Genomics study"
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Ron, Eliora, and Eugene Eugene Nester. Global functional genomics of plant cell transformation by agrobacterium. United States Department of Agriculture, March 2009. http://dx.doi.org/10.32747/2009.7695860.bard.
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The aim of this study was to carry out a global functional genomics analysis of plant cell transformation by Agrobacterium in order to define and characterize the physiology of Agrobacterium in the acidic environment of a wounded plant. We planed to study the proteome and transcriptome of Agrobacterium in response to a change in pH, from 7.2 to 5.5 and identify genes and circuits directly involved in this change. Bacteria-plant interactions involve a large number of global regulatory systems, which are essential for protection against new stressful conditions. The interaction of bacteria with their hosts has been previously studied by genetic-physiological methods. We wanted to make use of the new capabilities to study these interactions on a global scale, using transcription analysis (transcriptomics, microarrays) and proteomics (2D gel electrophoresis and mass spectrometry). The results provided extensive data on the functional genomics under conditions that partially mimic plant infection and – in addition - revealed some surprising and significant data. Thus, we identified the genes whose expression is modulated when Agrobacterium is grown under the acidic conditions found in the rhizosphere (pH 5.5), an essential environmental factor in Agrobacterium – plant interactions essential for induction of the virulence program by plant signal molecules. Among the 45 genes whose expression was significantly elevated, of special interest is the two-component chromosomally encoded system, ChvG/I which is involved in regulating acid inducible genes. A second exciting system under acid and ChvG/Icontrol is a secretion system for proteins, T6SS, encoded by 14 genes which appears to be important for Rhizobium leguminosarum nodule formation and nitrogen fixation and for virulence of Agrobacterium. The proteome analysis revealed that gamma aminobutyric acid (GABA), a metabolite secreted by wounded plants, induces the synthesis of an Agrobacterium lactonase which degrades the quorum sensing signal, N-acyl homoserine lactone (AHL), resulting in attenuation of virulence. In addition, through a transcriptomic analysis of Agrobacterium growing at the pH of the rhizosphere (pH=5.5), we demonstrated that salicylic acid (SA) a well-studied plant signal molecule important in plant defense, attenuates Agrobacterium virulence in two distinct ways - by down regulating the synthesis of the virulence (vir) genes required for the processing and transfer of the T-DNA and by inducing the same lactonase, which in turn degrades the AHL. Thus, GABA and SA with different molecular structures, induce the expression of these same genes. The identification of genes whose expression is modulated by conditions that mimic plant infection, as well as the identification of regulatory molecules that help control the early stages of infection, advance our understanding of this complex bacterial-plant interaction and has immediate potential applications to modify it. We expect that the data generated by our research will be used to develop novel strategies for the control of crown gall disease. Moreover, these results will also provide the basis for future biotechnological approaches that will use genetic manipulations to improve bacterial-plant interactions, leading to more efficient DNA transfer to recalcitrant plants and robust symbiosis. These advances will, in turn, contribute to plant protection by introducing genes for resistance against other bacteria, pests and environmental stress.
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Fornace, Jr, A J. A functional genomics approach using radiation-induced changes in gene expression to study low dose radiation effects in vitro and in vivo. Office of Scientific and Technical Information (OSTI), March 2007. http://dx.doi.org/10.2172/900232.
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Bloch, Guy, Gene E. Robinson, and Mark Band. Functional genomics of reproduction and division of labor in a key non-Apis pollinator. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7699867.bard.
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i. List the original objectives, as defined in the approved proposal, and any revisions made at the beginning or during the course of project. Our objectives were: 1) develop state-of-the-art functional genomics tools for B. terrestris. These resources will be then used to: 2) characterize genes and molecular pathways that are associated with reproduction, 3) characterize genes and molecular pathways associated with specialization in foraging or nursing activities, and 4) determine the extent to which juvenile hormone (JH) is involved in the regulation of reproduction and division of labor. 5) Use RNA interference to down regulate genes associated with reproductive physiology, division of labor, or both. A decrease in the cost of RNA sequencing enabled us to further use the BARD support to extend our research to three additional related projects: A) The regulation of body size which is crucial for understanding both reproduction (castedetermination) and (size based) division of labor in bumblebees. B) Analyze RNA editing in our RNA sequencing data which improves the molecular understanding of the systems we study. C) The influence of JH on the fat body in addition to the brain on which we focused in our proposal. The fat body is a key tissue regulating insect reproduction and health. ii. Background to the topic. Bees are by far the most important pollinators in agricultural and natural ecosystems. The recent collapse of honey bee populations, together with declines in wild bee (including bumble bee) populations, puts their vital pollination services under severe threat. A promising strategy for circumventing this risk is the domestication and mass-rearing of non-Apis bees. This approach has been successfully implemented for several bumble bees including Bombusterrestris in Israel, and B. impatiens in the US, which are mass-reared in captivity. In spite of their critical economic and environmental value, little is known about the physiology and molecular biology of bumble bees. In this collaborative project we developed functional genomics tools for the bumble bee B. terrestris and use these tools for a first thorough study on the physiology and molecular biology of reproduction, dominance, and division of labor in a bumble bee. iii. Major conclusions, solutions. The valuable molecular data of this project together with the functional tools and molecular information generated in this BARD funded project significantly advanced the understanding of bumblebee biology which is essential for maintaining their vital pollination services for US and Israel agriculture.
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Lers, Amnon, and Gan Susheng. Study of the regulatory mechanism involved in dark-induced Postharvest leaf senescence. United States Department of Agriculture, January 2009. http://dx.doi.org/10.32747/2009.7591734.bard.
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Postharvest leaf senescence contributes to quality losses in flowers and leafy vegetables. The general goal of this research project was to investigate the regulatory mechanisms involved in dark-induced leaf senescence. The regulatory system involved in senescence induction and control is highly complex and possibly involves a network of senescence promoting pathways responsible for activation of the senescence-associated genes. Pathways involving different internal signals and environmental factors may have distinctive importance in different leaf senescence systems. Darkness is known to have a role in enhancement of postharvest leaf senescence and for getting an insight into its regulatory mechanism/s we have applied molecular genetics and functional genomics approaches. The original objectives were: 1. Identification of dark-induced SAGs in Arabidopsis using enhancer/promoter trap lines and microarray approaches; 2. Molecular and functional characterization of the identified genes by analyzing their expression and examining the phenotypes in related knockout mutant plants; 3. Initial studies of promoter sequences for selected early dark-induced SAGs. Since genomic studies of senescence, with emphasis on dark-induced senescence, were early-on published which included information on potential regulatory genes we decided to use this new information. This is instead of using the uncharacterized enhancer/promoter trap lines as originally planned. We have also focused on specific relevant genes identified in the two laboratories. Based on the available genomic analyses of leaf senescence 10 candidate genes hypothesized to have a regulatory role in dark-induced senescence were subjected to both expression as well as functional analyses. For most of these genes senescence-specific regulation was confirmed, however, functional analyses using knock-out mutants indicated no consequence to senescence progression. The transcription factor WARK75 was found to be specifically expressed during natural and dark-induced leaf senescence. Functional analysis demonstrated that in detached leaves senescence under darkness was significantly delayed while no phenotypic consequences could be observed on growth and development, including no effect on natural leaf senescence,. Thus, WARKY75 is suggested to have a role in dark-induced senescence, but not in natural senescence. Another regulatory gene identified to have a role in senescence is MKK9 encoding for a Mitogen-Activated Protein Kinase Kinase 9 which is upregulated during senescence in harvested leaves as well as in naturally senescing leaves. MKK9 can specifically phosphorylate another kinase, MPK6. Both knockouts of MKK9 and MPK6 displayed a significantly senescence delay in harvested leaves and possibly function as a phosphorelay that regulates senescence. To our knowledge, this is the first report that clearly demonstrates the involvement of a MAP kinase pathway in senescence. This research not only revealed a new signal transduction pathway, but more important provided significant insights into the regulatory mechanisms underlying senescence in harvested leaves. In an additional line of research we have employed the promoter of the senescence-induced BFN1 gene as a handle for identifying components of the regulatory mechanism. This gene was shown to be activated during darkinduced senescence of detached leaves, as well as natural senescence. This was shown by following protein accumulation and promoter activity which demonstrated that this promoter is activated during dark-induced senescence. Analysis of the promoter established that, at least some of the regulatory sequences reside in an 80 bps long fragment of the promoter. Overall, progress was made in identification of components with a role in dark-induced senescence in this project. Further studies should be done in order to better understand the function of these components and develop approaches for modulating the progress of senescence in crop plants for the benefit of agriculture.
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Breiman, Adina, Jan Dvorak, Abraham Korol, and Eduard Akhunov. Population Genomics and Association Mapping of Disease Resistance Genes in Israeli Populations of Wild Relatives of Wheat, Triticum dicoccoides and Aegilops speltoides. United States Department of Agriculture, December 2011. http://dx.doi.org/10.32747/2011.7697121.bard.
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Wheat is the most widely grown crop on earth, together with rice it is second to maize in total global tonnage. One of the emerging threats to wheat is stripe (yellow) rust, especially in North Africa, West and Central Asia and North America. The most efficient way to control plant diseases is to introduce disease resistant genes. However, the pathogens can overcome rapidly the effectiveness of these genes when they are wildly used. Therefore, there is a constant need to find new resistance genes to replace the non-effective genes. The resistance gene pool in the cultivated wheat is depleted and there is a need to find new genes in the wild relative of wheat. Wild emmer (Triticum dicoccoides) the progenitor of the cultivated wheat can serve as valuable gene pool for breeding for disease resistance. Transferring of novel genes into elite cultivars is highly facilitated by the availability of information of their chromosomal location. Therefore, our goals in this study was to find stripe rust resistant and susceptible genotypes in Israeli T. dicoccoides population, genotype them using state of the art genotyping methods and to find association between genetic markers and stripe rust resistance. We have screened 129 accessions from our collection of wild emmer wheat for resistance to three isolates of stripe rust. About 30% of the accessions were resistant to one or more isolates, 50% susceptible, and the rest displayed intermediate response. The accessions were genotyped with Illumina'sInfinium assay which consists of 9K single nucleotide polymorphism (SNP) markers. About 13% (1179) of the SNPs were polymorphic in the wild emmer population. Cluster analysis based on SNP diversity has shown that there are two main groups in the wild population. A big cluster probably belongs to the Horanum ssp. and a small cluster of the Judaicum ssp. In order to avoid population structure bias, the Judaicum spp. was removed from the association analysis. In the remaining group of genotypes, linkage disequilibrium (LD) measured along the chromosomes decayed rapidly within one centimorgan. This is the first time when such analysis is conducted on a genome wide level in wild emmer. Such a rapid decay in LD level, quite unexpected for a selfer, was not observed in cultivated wheat collection. It indicates that wild emmer populations are highly suitable for association studies yielding a better resolution than association studies in cultivated wheat or genetic mapping in bi-parental populations. Significant association was found between an SNP marker located in the distal region of chromosome arm 1BL and resistance to one of the isolates. This region is not known in the literature to bear a stripe rust resistance gene. Therefore, there may be a new stripe rust resistance gene in this locus. With the current fast increase of wheat genome sequence data, genome wide association analysis becomes a feasible task and efficient strategy for searching novel genes in wild emmer wheat. In this study, we have shown that the wild emmer gene pool is a valuable source for new stripe rust resistance genes that can protect the cultivated wheat.
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Patterson, Garth I. Genomic Study of Breast Cancer Genes. Fort Belvoir, VA: Defense Technical Information Center, August 2004. http://dx.doi.org/10.21236/ada443776.
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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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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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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.
Full textAbstract:
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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Joel, Daniel M., Steven J. Knapp, and Yaakov Tadmor. Genomic Approaches for Understanding Virulence and Resistance in the Sunflower-Orobanche Host-Parasite Interaction. United States Department of Agriculture, August 2011. http://dx.doi.org/10.32747/2011.7592655.bard.
Full textAbstract:
Oroginal Objectives: (i) identify DNA markers linked to the avirulence (Avr) locus and locate the Avr locus through genetic mapping with an inter-race Orobanche cumana population; (ii) develop high-throughput fingerprint DNA markers for genotypingO. cumana races; (iii) identify nucleotide binding domain leucine rich repeat (NB-LRR) genes encoding R proteins conferring resistance to O. cumana in sunflower; (iv) increase the resolution of the chromosomal segment harboring Or₅ and related R genes through genetic and physical mapping in previously and newly developed mapping populations of sunflower; and (v) develop high-throughput DNA markers for rapidly and efficiently identifying and transferring sunflower R genes through marker-assisted selection. Revisions made during the course of project: Following changes in O. cumana race distribution in Israel, the newly arrived virulent race H was chosen for further analysis. HA412-HO, which was primarily chosen as a susceptible sunflower cultivar, was more resistant to the new parasite populations than var. Shemesh, thus we shifted sunflower research into analyzing the resistance of HA412-HO. We exceeded the deliverables for Objectives #3-5 by securing funding for complete physical and high-density genetic mapping of the sunflower genome, in addition to producing a complete draft sequence of the sunflower genome. We discovered limited diversity between the parents of the O. cumana population developed for the mapping study. Hence, the developed DNA marker resources were insufficient to support genetic map construction. This objective was beyond the scale and scope of the funding. This objective is challenging enough to be the entire focus of follow up studies. Background to the topic: O. cumana, an obligate parasitic weed, is one of the most economically important and damaging diseases of sunflower, causes significant yield losses in susceptible genotypes, and threatens production in Israel and many other countries. Breeding for resistance has been crucial for protecting sunflower from O. cumana, and problematic because new races of the pathogen continually emerge, necessitating discovery and deployment of new R genes. The process is challenging because of the uncertainty in identifying races in a genetically diverse parasite. Major conclusions, solutions, achievements: We developed a small collection of SSR markers for genetic mapping in O. cumana and completed a diversity study to lay the ground for objective #1. Because DNA sequencing and SNPgenotyping technology dramatically advanced during the course of the study, we recommend shifting future work to SNP discovery and mapping using array-based approaches, instead of SSR markers. We completed a pilot study using a 96-SNP array, but it was not large enough to support genetic mapping in O.cumana. The development of further SNPs was beyond the scope of the grant. However, the collection of SSR markers was ideal for genetic diversity analysis, which indicated that O. cumanapopulations in Israel considerably differ frompopulations in other Mediterranean countries. We supplied physical and genetic mapping resources for identifying R-genes in sunflower responsible for resistance to O. cumana. Several thousand mapped SNP markers and a complete draft of the sunflower genome sequence are powerful tools for identifying additional candidate genes and understanding the genomic architecture of O. cumana-resistanceanddisease-resistance genes. Implications: The OrobancheSSR markers have utility in sunflower breeding and genetics programs, as well as a tool for understanding the heterogeneity of races in the field and for geographically mapping of pathotypes.The segregating populations of both Orobanche and sunflower hybrids are now available for QTL analyses.