Relevant bibliographies by topics / Text genetics

Contents

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

Academic literature on the topic 'Text genetics'

Author: Grafiati
Published: 7 July 2024

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Journal articles on the topic "Text genetics"

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HUDSON, RICHARD R. "Population genetics text." Journal of Heredity 77, no. 2 (March 1986): 141–42. http://dx.doi.org/10.1093/oxfordjournals.jhered.a110199.

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Morrison, Patrick J. "A classic genetic text about classic genetic texts." European Journal of Human Genetics 13, no. 7 (June 23, 2005): 892. http://dx.doi.org/10.1038/sj.ejhg.5201417.

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Gibson, Greg, and David B. Goldstein. "Human Genetics: The Hidden Text of Genome-wide Associations." Current Biology 17, no. 21 (November 2007): R929—R932. http://dx.doi.org/10.1016/j.cub.2007.08.044.

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Cameron, Vicki L. "Teaching Advanced Genetics Without Lectures." Genetics 165, no. 3 (November 1, 2003): 945–50. http://dx.doi.org/10.1093/genetics/165.3.945.

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Abstract In an effort to increase student engagement and therefore student learning, an advanced genetics course was developed in which traditional lectures were eliminated. Instead, students were required to complete reading assignments before each class meeting, and those readings were then the topic of group discussion. Assigned readings alternated between text assignments and articles from the primary literature. Students were made accountable for their own preparation by the administration of a quiz at the start of each class. Group discussion of the topics engaged students in the learning process and readministration of the quiz at the end of class allowed them to benefit from the group interaction and understanding. Interspersing text readings and primary literature led to student understanding of how genetic knowledge is acquired and interpreted and how experimental detail leads to the construction of general models.
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Vazquez, M., P. Carmona-Saez, R. Nogales-Cadenas, M. Chagoyen, F. Tirado, J. M. Carazo, and A. Pascual-Montano. "SENT: semantic features in text." Nucleic Acids Research 37, Web Server (May 20, 2009): W153—W159. http://dx.doi.org/10.1093/nar/gkp392.

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Hooper, Stephen R. "The Genetics of Neurobehavioral Manifestation: Linkages and Prospects." Journal of the International Neuropsychological Society 8, no. 1 (January 2002): 140–41. http://dx.doi.org/10.1017/s1355617702251140.

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While genetic linkages to a variety of disorders have been suspected for decades, it has only been relatively recently that these linkages have come to be understood to a greater degree. The search for the genetic basis of some neurodevelopmental disorders, such as learning disabilities, has been elusive and fraught with complex hurdles, the genetic basis of other neurodevelopmental disorders, such as Down syndrome, has been much more clear. Other childhood disorders, such as Turner syndrome and fragile X syndrome, also documented clearly defined genotypes. Even when a clear genetic contribution is known (i.e., the genotype), the exact neurobehavioral manifestations (i.e., the phenotypes) remain unclear or poorly documented for many disorders. This edited volume addresses this quest and, perhaps, provides one of the most comprehensive descriptions of the available literature in the interface between genetics and behavior in childhood. As noted by the editors, one of the major objectives of this text is to provide students, clinicians, and researchers with a working knowledge base of behavioral genetics. In this regard, the editors wanted to provide a comprehensive text that was “organized in a framework that is understandable and immediately useful in clinical practice” (p. 6).
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Armstrong, Graeme. "Conservation and the Genetics of Populations." Pacific Conservation Biology 14, no. 2 (2008): 146. http://dx.doi.org/10.1071/pc080146.

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I am sure many readers have experienced the excruciating situation of being involved in a conservation project that makes no effort to include a genetic component in the methodology. This is often due to a lack of understanding by managers compounded by an inability of biologists to remedy this situation by demonstrating the importance of genetics to the desired conservation outcome. The authors of Conservation and the Genetics of Populations have aimed their text at ?broadly trained biologists? to enable an understanding and application of genetic principles to conservation problems. If successful this would go a long way to alleviating this problem.
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Islamaj, Rezarta, Dongseop Kwon, Sun Kim, and Zhiyong Lu. "TeamTat: a collaborative text annotation tool." Nucleic Acids Research 48, W1 (May 8, 2020): W5—W11. http://dx.doi.org/10.1093/nar/gkaa333.

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Abstract Manually annotated data is key to developing text-mining and information-extraction algorithms. However, human annotation requires considerable time, effort and expertise. Given the rapid growth of biomedical literature, it is paramount to build tools that facilitate speed and maintain expert quality. While existing text annotation tools may provide user-friendly interfaces to domain experts, limited support is available for figure display, project management, and multi-user team annotation. In response, we developed TeamTat (https://www.teamtat.org), a web-based annotation tool (local setup available), equipped to manage team annotation projects engagingly and efficiently. TeamTat is a novel tool for managing multi-user, multi-label document annotation, reflecting the entire production life cycle. Project managers can specify annotation schema for entities and relations and select annotator(s) and distribute documents anonymously to prevent bias. Document input format can be plain text, PDF or BioC (uploaded locally or automatically retrieved from PubMed/PMC), and output format is BioC with inline annotations. TeamTat displays figures from the full text for the annotator's convenience. Multiple users can work on the same document independently in their workspaces, and the team manager can track task completion. TeamTat provides corpus quality assessment via inter-annotator agreement statistics, and a user-friendly interface convenient for annotation review and inter-annotator disagreement resolution to improve corpus quality.
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Ravine, D. "Molecular Medicine. An Introductory Text for Students." Journal of Medical Genetics 32, no. 2 (February 1, 1995): 160. http://dx.doi.org/10.1136/jmg.32.2.160.

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Zeng, Z. B., and C. C. Cockerham. "Variance of neutral genetic variances within and between populations for a quantitative character." Genetics 129, no. 2 (October 1, 1991): 535–53. http://dx.doi.org/10.1093/genetics/129.2.535.

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Abstract The variances of genetic variances within and between finite populations were systematically studied using a general multiple allele model with mutation in terms of identity by descent measures. We partitioned the genetic variances into components corresponding to genetic variances and covariances within and between loci. We also analyzed the sampling variance. Both transient and equilibrium results were derived exactly and the results can be used in diverse applications. For the genetic variance within populations, sigma 2 omega, the coefficient of variation can be very well approximated as [formula: see text] for a normal distribution of allelic effects, ignoring recurrent mutation in the absence of linkage, where m is the number of loci, N is the effective population size, theta 1(0) is the initial identity by descent measure of two genes within populations and t is the generation number. The first term is due to genic variance, the second due to linkage disequilibrium, and third due to sampling. In the short term, the variation is predominantly due to linkage disequilibrium and sampling; but in the long term it can be largely due to genic variance. At equilibrium with mutation [formula: see text] where u is the mutation rate. The genetic variance between populations is a parameter. Variance arises only among sample estimates due to finite sampling of populations and individuals. The coefficient of variation for sample gentic variance between populations, sigma 2b, can be generally approximated as [formula: see text] when the number of loci is large where S is the number of sampling populations.
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Dissertations / Theses on the topic "Text genetics"

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Moreau, William Edgar. "David Thompson's writing of his Travels, the genetics of an emerging exploration text." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ45823.pdf.

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Winslow, Hayley R. "Pre- and Post-Test Parent Perceptions of Genetic Testing for Children with Autism Spectrum Disorder (ASD)." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1492505122437373.

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Smith, Nichole. "Consumer Preferences for the Reporting of Genetic Variants of Uncertain Significance." University of Cincinnati / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1337352216.

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Bitencourt, Jossiane Boyen. "A constituição da coletividade na web : um estudo das ações no editor de texto coletivo ETC." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2007. http://hdl.handle.net/10183/13265.

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Esta dissertação trata de um estudo sobre as ações dos sujeitos para a constituição da coletividade em um Ambiente Virtual de Escrita Coletiva. Como recurso foi utilizado o Editor de Texto Coletivo - o ETC, desenvolvido pelo NUTED (Núcleo de Tecnologia Digital da Faculdade de Educação, da Universidade Federal do Rio Grande do Sul - UFRGS) que serviu de base para a coleta e análise dos dados. Os sujeitos da pesquisa foram estudantes de graduação e pós-graduação da Universidade Federal do Rio Grande do Sul (UFRGS) de disciplinas da área de informática na educação. Como fundamentação teórica utilizou-se a Epistemologia Genética de Jean Piaget que serviu como referencial para o desenvolvimento deste estudo. Para tanto, a coleta de dados foi realizada através de entrevistas semiestruturadas individuais e em grupo, buscando a fala do aluno. Também foram realizadas observações no ETC e analisadas a escrita e a ação dos sujeitos, no decorrer do processo de trabalho. Os resultados de tais observações foram capturados nos registros dos textos, comentários e no histórico do editor. Além disso, foi utilizado como complemento o Ambiente Virtual de Aprendizagem ROODA, através de extratos retirados das ferramentas fórum, diário, bate-papos e webfólio. As conclusões indicam um mapeamento das ações dos sujeitos para a constituição da coletividade na Web, a partir do conhecimento e da organização do grupo apoiada na identificação dos conflitos sócio-cognitivos, coordenação de ações/idéias e a construção de uma escala comum de valores entre os participantes. Entretanto foi necessário criar estratégias pedagógicas de utilização do ETC que propiciassem a interação entre os participantes, bem como verificar quais ferramentas potencializam a constituição da coletividade na Web.
This dissertation deals with the subject’s actions to derive a collective writing virtual environment. The Editor de Texto Coletivo [Collective Text Editor, ETC] was used as main resource – ETC, developed by NUTED (Núcleo de Tecnologia Digital da Faculdade de Educação, da Universidade Federal do Rio Grande do Sul - UFRGS) [Digital Technology Nucleolus of the School of Education of UFRGS [Federal University of Rio Grande do Sul] was used to collect and analyze data. Subjects were undergraduate and graduate students of the schools of Information Technology and Education. The background theory employed in this study is the Genetic Epistemology by Jean Piaget. Data were collected by structured and semi-structured interviews in order to get the student´s speech. ETC was also used to analyze the subjects’ writings and actions during the workshop. Results of these observations were stored from the texts, comments, and the editor’s records. Also ROODA [Virtual Learning Environment] was used as a tool for the forum summaries, chats, and the web foils. Conclusions indicate a mapping of the subjects’ actions to build a web community starting with the knowledge the group’s organization, its socio-cognitive conflicts, the group’s actions and ideas, as well as the group building of a common values scale. However, the use of pedagogical tools and the use of ETC were key allow the participant’s interaction and to detect the tools that enhance web community establishment.
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Parrott, Ashley. "Media Coverage of Direct-to-Consumer Genetic Testing." University of Cincinnati / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1276977244.

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Olsson, Elin. "Deriving Genetic Networks Using Text Mining." Thesis, University of Skövde, Department of Computer Science, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-708.

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On the Internet an enormous amount of information is available that is represented in an unstructured form. The purpose with a text mining tool is to collect this information and present it in a more structured form. In this report text mining is used to create an algorithm that searches abstracts available from PubMed and finds specific relationships between genes that can be used to create a network. The algorithm can also be used to find information about a specific gene. The network created by Mendoza et al. (1999) was verified in all the connections but one using the algorithm. This connection contained implicit information. The results suggest that the algorithm is better at extracting information about specific genes than finding connections between genes. One advantage with the algorithm is that it can also find connections between genes and proteins and genes and other chemical substances.

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HOLMGREN, LISA MICHELLE. "THE IMPACT OF TEST OUTCOME CERTAINTY ON INTEREST IN GENETIC TESTING AMONG COLLEGE WOMEN." University of Cincinnati / OhioLINK, 2001. http://rave.ohiolink.edu/etdc/view?acc_num=ucin994694629.

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Menke, Chelsea A. "Non-Genetics Pediatric Providers' Understanding and Interpretation of a VUS Result." University of Cincinnati / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1552398848715174.

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Girardi, Laura. "Development and Validation of Innovative Technologies for Highly Accurate and Cost-Effective Preimplantation Genetic Testing: Technical and Clinical Perspectives." Doctoral thesis, Università degli studi di Padova, 2019. http://hdl.handle.net/11577/3425772.

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Testing preimplantation embryos, obtained during in vitro fertilization treatments, using preimplantation genetic tests have been introduced into clinical practice in recent years. First applications involved the possibility of detecting embryos affected by monogenic disorders (PGT-M) inherited from parents. Subsequently, preimplantation genetic testing for aneuploidy (PGT-A) was introduced to improve IVF transfer outcomes. Indeed, identification of aneuploid and transfer of euploid embryos has demonstrated improved rates for implantation, pregnancy and live birth per transfer and reduced implantation failures. Developments in genomic technologies for PGT have revolutionized the ability to detect genetic abnormalities of various kinds, starting from a small number of cells biopsied from the embryo. The increased sensitivity and resolution of these methods has allowed to identify not only the gain or loss of entire chromosome but also partial or segmental aneuploidies and chromosomal mosaicism, introducing novel diagnostic categories with greater difficult management and interpretation. Of note the knowledge of the biology of these alterations and the outcomes is incomplete and still evolving. In recent years the demand for PGT has increased considerably. At the same time, the novel technologies adapted for preimplantation genetic diagnosis have allowed to increase the number of samples simultaneously analyzed, reducing the costs and time associated with analyses this allowed a greater diffusion and accessibility of PGT to a greater number of patients. Moreover, partial automation of procedures, increased analytical flexibility and simplified data analysis, provided by recent technologies, have significantly improved laboratory workflow and clinical management. The central theme of this thesis is the evolution of technologies and analytical methods employed in our laboratory for preimplantation genetic diagnosis. In this project the main application of PGT, chromosomal aneuploidies and monogenic disease, are presented separately. Since the beginning of my PhD training, I’ve been involved in the development and validation of new molecular genetics methodologies: the new Ion Reproseq protocol on Ion Torrent platform was validated and introduced into clinical practice for aneuploidy screening. Later Karyomapping approach was validated for monogenic disorders but didn’t replace the technology already in use. During the last year I focused my activity on the characterization of segmental aneuploidies: a considerable proportion was found to be mosaic in origin, reducing their diagnostic predictive value compared to whole chromosome aneuploidies.
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Sætre, Rune. "GeneTUC: Natural Language Understanding in Medical Text." Doctoral thesis, Norwegian University of Science and Technology, Department of Computer and Information Science, 2006. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-545.

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Natural Language Understanding (NLU) is a 50 years old research field, but its application to molecular biology literature (BioNLU) is a less than 10 years old field. After the complete human genome sequence was published by Human Genome Project and Celera in 2001, there has been an explosion of research, shifting the NLU focus from domains like news articles to the domain of molecular biology and medical literature. BioNLU is needed, since there are almost 2000 new articles published and indexed every day, and the biologists need to know about existing knowledge regarding their own research. So far, BioNLU results are not as good as in other NLU domains, so more research is needed to solve the challenges of creating useful NLU applications for the biologists.

The work in this PhD thesis is a “proof of concept”. It is the first to show that an existing Question Answering (QA) system can be successfully applied in the hard BioNLU domain, after the essential challenge of unknown entities is solved. The core contribution is a system that discovers and classifies unknown entities and relations between them automatically. The World Wide Web (through Google) is used as the main resource, and the performance is almost as good as other named entity extraction systems, but the advantage of this approach is that it is much simpler and requires less manual labor than any of the other comparable systems.

The first paper in this collection gives an overview of the field of NLU and shows how the Information Extraction (IE) problem can be formulated with Local Grammars. The second paper uses Machine Learning to automatically recognize protein name based on features from the GSearch Engine. In the third paper, GSearch is substituted with Google, and the task in this paper is to extract all unknown names belonging to one of 273 biomedical entity classes, like genes, proteins, processes etc. After getting promising results with Google, the fourth paper shows that this approach can also be used to retrieve interactions or relationships between the named entities. The fifth paper describes an online implementation of the system, and shows that the method scales well to a larger set of entities.

The final paper concludes the “proof of concept” research, and shows that the performance of the original GeneTUC NLU system has increased from handling 10% of the sentences in a large collection of abstracts in 2001, to 50% in 2006. This is still not good enough to create a commercial system, but it is believed that another 40% performance gain can be achieved by importing more verb templates into GeneTUC, just like nouns were imported during this work. Work has already begun on this, in the form of a local Masters Thesis.

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Books on the topic "Text genetics"

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Trent, R. J. Molecular medicine: An introductory text. 3rd ed. Amsterdam: Elsevier Academic Press, 2005.

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Biological inheritance: An introductory genetics text. Sussex, England: Book Guild, 1994.

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Molecular medicine: An introductory text for students. Edinburgh: Churchill Livingstone, 1993.

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J, Russell Peter, ed. Instructor's guide to text and media Essential iGenetics. San Francisco, Calif: Benjamin Cummings, 2003.

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Moreau, William Edgar. David Thompson's writing of his Travels: The genetics of an emerging exploration text. Ottawa: National Library of Canada = Bibliothèque nationale du Canada, 1997.

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Wolfgang, Raible. Sprachliche Texte - genetische Texte: Sprachwissenschaft und molekulare Genetik. Heidelberg: C. Winter, 1993.

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R, Lashley Felissa, ed. Clinical genetics in nursing practice. 2nd ed. New York: Springer, 1998.

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Institute of Medicine (U.S.). Roundtable on Translating Genomic-Based Research for Health, ed. Generating evidence for genomic diagnostic test development: Workshop summary. Washington, D.C: National Academies Press, 2011.

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Conti, Adelaide, and Ascanio Sirignano. I test genetici: Etica, deontologia, responsabilità. Milano: Giuffrè, 2007.

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Jed, Deppman, Ferrer Daniel, and Groden Michael, eds. Genetic criticism: Texts and avant-textes. Philadelphia: University of Pennsylvania Press, 2004.

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Book chapters on the topic "Text genetics"

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Libby, Andrew, and Jennifer Cullin. "Genetics, Eugenics, and the Text of Real-World Experience." In Victorian Culture and Experiential Learning, 161–71. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-93791-1_10.

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Shonkwiler, Ronald W., and James Herod. "Genetics." In Undergraduate Texts in Mathematics, 419–60. New York, NY: Springer New York, 2009. http://dx.doi.org/10.1007/978-0-387-70984-0_13.

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Bhojwani, Sant Saran, and Prem Kumar Dantu. "Genetic Engineering." In Plant Tissue Culture: An Introductory Text, 199–226. India: Springer India, 2013. http://dx.doi.org/10.1007/978-81-322-1026-9_15.

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Goswami, A., and B. V. Rao. "Basic Mathematical Genetics." In Texts and Readings in Mathematics, 97–128. Gurgaon: Hindustan Book Agency, 2006. http://dx.doi.org/10.1007/978-93-86279-31-6_3.

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Loo-Dinkins, J. "Field Test Design." In Handbook of Quantitative Forest Genetics, 96–139. Dordrecht: Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-015-7987-2_4.

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Adams, S. Annie, Daniel L. Van Dyke, Rhett P. Ketterling, Erik C. Thorland, Timothy Caulfield, Lorraine Sheremeta, E. Richard Gold, Jon F. Merz, and David Castle. "Test Samples and Laboratory Protocols." In Genetic Testing, 292–339. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2006. http://dx.doi.org/10.1002/0471748897.ch12.

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O'daniel, Julianne M., Allyn McConkie-Rosell, and Patricia T. Kelly. "Test Results: Communication and Counseling." In Genetic Testing, 355–97. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2006. http://dx.doi.org/10.1002/0471748897.ch14.

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Bovbel, Eugene I., and Dzmitry V. Tsishkou. "Belarussian Speech Recognition Using Genetic Algorithms." In Text, Speech and Dialogue, 301–6. Berlin, Heidelberg: Springer Berlin Heidelberg, 2000. http://dx.doi.org/10.1007/3-540-45323-7_51.

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Goswami, A., and B. V. Rao. "Markov Models in Genetics." In Texts and Readings in Mathematics, 129–70. Gurgaon: Hindustan Book Agency, 2006. http://dx.doi.org/10.1007/978-93-86279-31-6_4.

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"Text-Mining." In Encyclopedia of Genetics, Genomics, Proteomics and Informatics, 1955. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6754-9_16876.

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Conference papers on the topic "Text genetics"

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Calderon Torres, Claudia Marissa. "WEBSITE FOR ONLINE OR BLENDED TEACHING OF GENETICS FOR THE DEVELOPMENT OF KNOWLEDGE AND SKILLS IN BIOLOGY STUDENTS." In EduCon Tokyo –International Conference on Education, 17-18 January 2024. Global Research & Development Services, 2024. http://dx.doi.org/10.20319/ictel.2024.3537.

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Genetics is the science that studies the transmission and variation of the hereditary information of organisms stored in DNA. Currently, Genetics encompasses a strategic set of knowledge and skills that biology professionals must have, in such a way that those who do not have this knowledge, techniques and even theories, run the risk of not entering a job position. Objective. This work presents a web page developed to facilitate the learning of Genetics knowledge. This project brings together participants who have carried out scientific and professional work, have taught genetics courses and know the problems of teaching and learning genetics. Results. The developed website (www.genetica.abaco2.org) incorporates: 1) Educational texts for the development of knowledge, skills and competencies on specific topics; 2) Multiple choice questionnaires for self-assessment; 3) Hardy-Weinberg simulator; and 4) Evaluation of the understanding of educational texts through the application of quick questionnaires. The texts are focused on undergraduate students of careers in the biological-medical area. The effect on learning of the contents of the website with the topic of genetic recombination was evaluated by comparing the learning in two groups of students: group A (133 students) with prior reading of the educational text and group B (119 students) without reading of the educational text. Through statistical analysis with the Z test it was found that group A had higher percentage (75.6% vs. 55.8%; P<0.01) of correct answers when answering a test of 10 questions. Conclusions: The designed website is a resource that teachers and students can benefit from by facilitating the teaching-learning process of Genetics.
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"Plant virus genome studies using novel databases and bioinformatics tools for text compression and entropy." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-080.

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Islam, Mohammad, Abdul Wahid, and Pradeep Kumar. "Understanding Intellectual Disability and Genetics with AI Perspective: A Text Mining Approach." In 2023 IEEE International Conference on Machine Learning and Applied Network Technologies (ICMLANT). IEEE, 2023. http://dx.doi.org/10.1109/icmlant59547.2023.10372970.

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Gomes, Victor Hugo de Souza Silva, Klesia Adaynny Rodrigues, Isadora Soares Constantini de Andrade, Beatriz Fulador, Bianca Barbosa Araldi, Bruno Ludvig Vieira Schaeffler, and Heloise Helena Siqueira. "Use of free genetic screening methods in neurology outpatients in cuiaba: advantages and interpretation difficulties." In XIV Congresso Paulista de Neurologia. Zeppelini Editorial e Comunicação, 2023. http://dx.doi.org/10.5327/1516-3180.141s1.368.

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Introduction: Medical genetics is increasingly gaining in modern medicine, through panels that enable the screening and diagnosis of rare diseases, becoming an effective ally in determination of some pathologies. In 2021, Invitae provided of medical outpatient clinics with kits for collecting genetic material in order to assist the specialist in diagnosing unusual and difficult-to-recognize conditions. In Cuiabá, the residency in Neurology was chosen to host the use of these methods. Objectives and methods: List the genetic tests collected through oral swabs and quantify the diagnoses made, in addition to the difficulty in determining them due to the technical language used. Results: In 12 months, 61 samples were collected, however, only 50 were analyzed. 11 tests were excluded. The analysis identified 30 male, representing 60% of panels, the average age of total sample was 33.64 years (SD). Received results from 20 samples with negative results in search for pathogenic alleles, while 22 showed only uncertain variants, not being conclusive for any diagnosis, just implying reproductive risk. Total of exams analyzed, 8 samples (16%) were positive for pathogenic variants, confirming the diagnosis of rare diseases and enabling appropriate therapeutic measures, initiation of supportive therapies and familiar guidance. Through this method, two patients were diagnosed with Spinal Muscular Atrophy type III, 1 with Wilson’s disease and two others with Niemann-Pick disease type C. Conclusion: Project ended in mid-2022, with the completion of free access to diagnoses. We emphasize that in many cases, access to genetic panel was extremely relevant, helped in the diagnostic direction, making it possible to start therapies for some patients with potentially treatable diseases. However, we encountered some difficulties, mainly in the interpretation of results provided by laboratory, due to extremely technical language and the large amount of information grouped in text. Conclud that medical genetics is extremely important in assisting medicals in diagnosis of rare diseases. However, there is a need for greater access to geneticists as well as genetic tests available in Brazilian Unified Health System.
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Bezerra, Rebeka Ellen de Alencar, Agda Yasmim Ferreira Correia, Héryka Wanessa do Nascimento Rolim, Júlia Ondrusch de Moraes Costa, Maressa Ferreira de Alencar Rocha, Palloma Abreu Tavares, and Alinne Beserra de Lucena Marcolino. "Importance of individualized diagnosis and treatment in refractory epilepsy associated with intellectual disability." In XIII Congresso Paulista de Neurologia. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1516-3180.050.

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Background: Epilepsy is a complex neurological disorder, that affects 0.5 to 1% of the population, with a diversified etiology, but with emphasis on its relation with genetics. Despite there are several therapies to treat it, in some cases, this variety is still insuficiente, featuring refractory epilepsy, frequent in people with intelectual disabilities (ID). Objectives: To analyze the scientific production about refractory epilepsy and ID. Methods: Integrative literature review that searched for international articles in the Virtual Health Library (VHL), using the keywords “Intellectual disability” AND “Refractory epilepsy” with the filter: “full text”. Results: From the 27 articles found, 2 were excluded for escaping the theme, having 25 articles as a final corpus and 2 thematic axes identified: (I) Genetic aspects related to ID and refractory epilepsy and (II) Therapeutic interventions in these patients. According to studies, refractory epilepsy in people with ID is related to mutations in some genes, such as: PCDH19, FMR1, TDP2, GABRB2 and SLC9A6. As for therapies for these patients, drugs such as stiripentol, lacosamide and benzodiazepines have been used, in addition to other interventions such as vagus nerve therapies, responsive neural stimulation, ketogenic diet, immunotherapy and resection surgery. Conclusions: The ID association with refractory epilepsy is strongly linked to genetic mutations, being essencial the genetic diagnosid to individualize the treatment and overcome insuficiente therapies for this epilepsy, especially in patients with associated ID, who tend to have a reduced life quality, having as primary objective the improvement of it.
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Kavi, Deniz. "Towards Adversarial Genetic Text Generation." In 8th International Conference on Computer Science and Information Technology (CoSIT 2021). AIRCC Publishing Corporation, 2021. http://dx.doi.org/10.5121/csit.2021.110407.

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Text generation is the task of generating natural language, and producing outputs similar to or better than human texts. Due to deep learning’s recent success in the field of natural language processing, computer generated text has come closer to becoming indistinguishable to human writing. Genetic Algorithms have not been as popular in the field of text generation. We propose a genetic algorithm combined with text classification and clustering models which automatically grade the texts generated by the genetic algorithm. The genetic algorithm is given poorly generated texts from a Markov chain, these texts are then graded by a text classifier and a text clustering model. We then apply crossover to pairs of texts, with emphasis on those that received higher grades. Changes to the grading system and further improvements to the genetic algorithm are to be the focus of future research.
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Ge, Yong-Feng, Yue-Jiao Gong, Wei-Jie Yu, Xiao-Min Hu, and Jun Zhang. "Reconstructing Cross-Cut Shredded Text Documents." In GECCO '15: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2015. http://dx.doi.org/10.1145/2739480.2754677.

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Gomez, Juan Carlos, Stijn Hoskens, and Marie-Francine Moens. "Evolutionary learning of meta-rules for text classification." In GECCO '17: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2017. http://dx.doi.org/10.1145/3067695.3075601.

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Andersen, Hayden, Xiaoying Gao, Bing Xue, and Mengjie Zhang. "Evolving network structures for text classification using genetic algorithms." In GECCO '20: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2020. http://dx.doi.org/10.1145/3377929.3390068.

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Nadai, Pamela Cristina Ferreira de, MATEUS ROSSETTO VIDAL, LUCAS FORTINO LASMAR, CLAUDIO OLIVEIRA, and FAUSTO FORESTI. "ANÁLISE DE PRESENÇA E ATIVIDADE DO GENE TERT DA TELOMERASE EM CROMOSSOMOS B DE PSALIDODON PARANAE (TELEOSTEI, CHARACIDAE)." In I Congresso Nacional de Pesquisas e Estudos Genéticos On-line. Revista Multidisciplinar em Saúde, 2022. http://dx.doi.org/10.51161/geneticon/9129.

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Introdução: Diversos organismos eucariotos possuem elementos genômicos extras, conhecidos como cromossomo B. Esses elementos são em geral heterocromáticos e compostos principalmente por sequências repetitivas de DNA, além de também possuírem genes ativamente transcritos. Os telômeros são estruturas cuja a função é manter a integridade estrutural dos cromossomos, e são constituídos por sequências não codificantes e repetitivas de DNA (TTAGGG). Neste sentido, a enzima telomerase, codificada pelo gene tert (telomerase RNA reverse transcriptase), desempenha um papel importante, atuando diretamente no elongamento dos telômeros. Considerando que os cromossomos B são elementos extras no genoma, pode-se supor que, por um mecanismo de compensação, uma maior atividade do gene tert seja induzida pela presença destes cromossomos. Objetivo: Deste modo, nosso objetivo foi analisar a presença do gene tert em cromossomo B de indivíduos Psalidodon paranae, tal como analisar se há expressão diferencial desse gene associado a presença do cromossomo B entre indivíduos 0B e B+. Metodologia: Para isso, foram coletados espécimes de P. paranae do ribeirão Cascatinha em Botucatu-SP (22°53’30”S 48°28’36”W), sendo 3 indivíduos B+ e 3 indivíduos 0B. Para análise da presença e da expressão do gene tert nesses indivíduos, foram utilizadas leituras curtas de alto rendimento de bibliotecas de DNA e RNA, obtidas através do sequenciamento Illumina. Em seguida, foi realizado o mapeamento das leituras usando o software SSAHA2 tendo a sequência codificadora do gene tert como referência. Foram usados scripts customizados para contabilizar o número de leituras mapeados e gerar os gráficos de cobertura. As análises bioinformáticas em bibliotecas de DNA e RNA não apresentaram diferença de cobertura entre as bibliotecas B+ e 0B, indicando ausência do gene tert no cromossomo B e ausência de expressão diferencial. Resultados: Nossos resultados indicam que os cromossomos B não exercem nenhuma influência na maquinaria de regulação telomérica. Pode-se especular, portanto, que estes elementos poderiam levar, em longo prazo, a efeitos deletérios. No entanto, para melhor elucidação desta hipótese estudos futuros comparando expressão gênica entre adultos e juvenis são necessários. Conclusão: Ainda, considerando que P. paranae possui no máximo dois cromossomos B, em um cenário similar estes efeitos poderiam ser intensificados em organismos com maiores números de cromossomos B.
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Reports on the topic "Text genetics"

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Sherman, Amir, Rebecca Grumet, Ron Ophir, Nurit Katzir, and Yiqun Weng. Whole genome approach for genetic analysis in cucumber: Fruit size as a test case. United States Department of Agriculture, December 2013. http://dx.doi.org/10.32747/2013.7594399.bard.

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The Cucurbitaceae family includes a broad array of economically and nutritionally important crop species that are consumed as vegetables, staple starches and desserts. Fruit of these species, and types within species, exhibit extensive diversity as evidenced by variation in size, shape, color, flavor, and others. Fruit size and shape are critical quality determinants that delineate uses and market classes and are key traits under selection in breeding programs. However, the underlying genetic bases for variation in fruit size remain to be determined. A few species the Cucurbitaceae family were sequenced during the time of this project (cucumber was already sequenced when the project started watermelon and melon sequence became available during the project) but functional genomic tools are still missing. This research program had three major goals: 1. Develop whole genome cucumber and melon SNP arrays. 2. Develop and characterize cucumber populations segregating for fruit size. 3. Combine genomic tools, segregating populations, and phenotypic characterization to identify loci associated with fruit size. As suggested by the reviewers the work concentrated mostly in cucumber and not both in cucumber and melon. In order to develop a SNP (single nucleotide polymorphism) array for cucumber, available and newly generated sequence from two cucumber cultivars with extreme differences in shape and size, pickling GY14 and Chinese long 9930, were analyzed for variation (SNPs). A large set of high quality SNPs was discovered between the two parents of the RILs population (GY14 and 9930) and used to design a custom SNP array with 35000 SNPs using Agilent technology. The array was validated using 9930, Gy14 and F1 progeny of the two parents. Several mapping populations were developed for linkage mapping of quantitative trait loci (QTL) for fruit size These includes 145 F3 families and 150 recombinant inbred line (RILs F7 or F8 (Gy14 X 9930) and third population contained 450 F2 plants from a cross between Gy14 and a wild plant from India. The main population that was used in this study is the RILs population of Gy14 X 9930. Phenotypic and morphological analyses of 9930, Gy14, and their segregating F2 and RIL progeny indicated that several, likely independent, factors influence cucumber fruit size and shape, including factors that act both pre-anthesis and post-pollination. These include: amount, rate, duration, and plane of cell division pre- and post-anthesis and orientation of cell expansion. Analysis of F2 and RIL progeny indicated that factors influencing fruit length were largely determined pre-anthesis, while fruit diameter was more strongly influenced by environment and growth factors post-anthesis. These results suggest involvement of multiple genetically segregating factors expected to map independently onto the cucumber genome. Using the SNP array and the phenotypic data two major QTLs for fruit size of cucumber were mapped in very high accuracy (around 300 Kb) with large set of markers that should facilitate identification and cloning of major genes that contribute to fruit size in cucumber. In addition, a highly accurate haplotype map of all RILS was created to allow fine mapping of other traits segregating in this population. A detailed cucumber genetic map with 6000 markers was also established (currently the most detailed genetic map of cucumber). The integration of genetics physiology and genomic approaches in this project yielded new major infrastructure tools that can be used for understanding fruit size and many other traits of importance in cucumber. The SNP array and genetic population with an ultra-fine map can be used for future breeding efforts, high resolution mapping and cloning of traits of interest that segregate in this population. The genetic map that was developed can be used for other breeding efforts in other populations. The study of fruit development that was done during this project will be important in dissecting function of genes that that contribute to the fruit size QTLs. The SNP array can be used as tool for mapping different traits in cucumber. The development of the tools and knowledge will thus promote genetic improvement of cucumber and related cucurbits.
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Cawley, John, Euna Han, Jiyoon Kim, and Edward Norton. Sibling Correlation in Educational Attainment: A Test of Genetic Nurture. Cambridge, MA: National Bureau of Economic Research, June 2020. http://dx.doi.org/10.3386/w27336.

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Perl, Avichai, Bruce I. Reisch, and Ofra Lotan. Transgenic Endochitinase Producing Grapevine for the Improvement of Resistance to Powdery Mildew (Uncinula necator). United States Department of Agriculture, January 1994. http://dx.doi.org/10.32747/1994.7568766.bard.

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The original objectives are listed below: 1. Design vectors for constitutive expression of endochitinase from Trichoderma harzianum strain P1. Design vectors with signal peptides to target gene expression. 2. Extend transformation/regeneration technology to other cultivars of importance in the U.S. and Israel. 3. Transform cultivars with the endochitinase constructs developed as part of objective 1. A. Characterize foliar powdery mildew resistance in transgenic plants. Background of the topic Conventional breeding of grapevines is a slow and imprecise process. The long generation cycle, large space requirements and poor understanding of grapevine genetics prevent rapid progress. There remains great need to improve existing important cultivars without the loss of identity that follows from hybridization. Powdery mildew (Uncinula necator) is the most important fungal pathogen of grapevines, causing economic losses around the world. Genetic control of powdery mildew would reduce the requirement for chemical or cultural control of the disease. Yet, since the trait is under polygenic control, it is difficult to manipulate through hybridization and breeding. Also, because grapevines are heterozygous and vegetatively propagated cultivar identity is lost in the breeding process. Therefore, there is great need for techniques to produce transgenic versions of established cultivars with heterologous genes conferring disease resistance. Such a gene is now available for control of powdery mildew of grapevines. The protein coded by the Endochitinase gene, derived from Trichoderma harzianum, is very effective in suppressing U. necator growth. The goal of this proposal is to develop transgenic grapevines with this antifungal gene, and to test the effect of this gene on resistance to powdery mildew. Conclusions, achievements and implications Gene transfer technology for grape was developed using commercial cultivars for both wine and table grapes. It paved the way for a new tool in grapevine genetic studies enabling the alteration of specific important traits while maintaining the essential features of existing elite cultivars. Regeneration and transformation technologies were developed and are currently at an advanced stage for USA wine and Israeli seedless cultivars, representing the cutting edge of grape genetic engineering studies worldwide. Transgenic plants produced are tested for powdery mildew resistance in greenhouse and field experiments at both locations. It is our ultimate goal to develop transgenic grapes which will be more efficient and economical for growers to produce, while also providing consumers with familiar products grown with reduced chemical inputs.
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Van Haverbeke, David F. Genetic variation in ponderosa pine: A 15-year test of provenances in the Great Plains. Ft. Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Forest and Range Experiment Station, 1986. http://dx.doi.org/10.2737/rm-rp-265.

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Paterson, Andrew H., Yehoshua Saranga, and Dan Yakir. Improving Productivity of Cotton (Gossypsum spp.) in Arid Region Agriculture: An Integrated Physiological/Genetic Approach. United States Department of Agriculture, December 1999. http://dx.doi.org/10.32747/1999.7573066.bard.

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Objectives: We seek to establish the basis for improving cotton productivity under arid conditions, by studying the water use efficiency - evaporative cooling interrelationship. Specifically, we will test the hypothesis that cotton productivity under arid conditions can be improved by combining high seasonal WUE with efficient evaporative cooling, evaluate whether high WUE and/or evaporative cooling are based on specific physiological factors such as diurnal flexibility in stomatal conductance, stomatal density, photosynthetic capacity, chlorophyll fluorescence, and plant water status. Genes influencing both WUE and evaporative cooling, as well as other parameters such as economic products (lint yield, quality, harvest index) of cotton will also be mapped, in order to evaluate influences of water relations on these parameters. Approach: Carbon isotope ratio will be used to evaluate WUE, accompanied by additional parameters to elucidate the relationship between WUE, evaporative cooling, and cotton productivity. A detailed RFLP map will be used to determine the number, location, and phenotypic effects of genes underlying genetic variation in WUE between cultivated cottons, as well as test associations of these genes with traits of economic importance such as harvest index, lint yield, and lint quality. Major Conclusions: Productivity and quality of cotton grown under well-watered versus water-limited conditions was shown to be partly accounted for by different quantitative trait loci (QTLs). Among a suite of physiological traits often found to differ between genotypes adapted to arid versus well-watered conditions, genetic mapping implicated only reduced plant osmotic potential in improved cotton productivity under arid conditions. Our findings clearly implicate OP as a major component of cotton adaptation to arid conditions. However, testing of further physiological hypotheses is clearly needed to account for additional QTL alleles conferring higher seed-cotton yield under arid conditions, such as three of the five we found. Near-isogenic lines being made for QTLs discovered herein will offer a powerful new tool useful toward identification of the underlying gene(s) by using fine-scale mapping approaches (Paterson et al 1990). Implications: Adaptation to both arid and favorable conditions can be combined into the same genotype. We have identified diagnostic DNA markers that are being applied to creation of such desirable genotypes. Simultaneous improvement of productivity (and/or quality) for both arid and irrigated conditions will require more extensive field testing and the manipulation of larger numbers of genes, reducing the expected rate of genetic gain These difficulties may be at least partly ameliorated by efficiencies gained through identification and use of diagnostic DNA markers. Genomic tools and approaches may expedite adaptation of crops to arid cultivation, help to test roles of additional physiological factors, and guide the isolation of the underlying genes that protect crop performance under arid conditions.
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Figueredo, Luisa, Liliana Martinez, and Joao Paulo Almeida. Current role of Endoscopic Endonasal Approach for Craniopharyngiomas. A 10-year Systematic review and Meta-Analysis Comparison with the Open Transcranial Approach. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, January 2023. http://dx.doi.org/10.37766/inplasy2023.1.0045.

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Review question / Objective: To identify and review studies published in the last ten years, presenting the efficacy and outcomes of EEA and TCA for patients with cranio-pharyngiomas. Eligibility criteria: Studies meeting the following criteria were included: (a) retrospective and prospective studies and (b) observational studies (i.e., cross-sectional, case-control, case-series). The outcomes included visual outcomes (improvement, no changes, worsening), endocrinological outcomes (permanent diabetes insipidus and hypopituitarism), operatory site infection, meningitis, cerebrospinal fluid leak, stroke, hemorrhage, and mortality. Studies were excluded if they were determined to be: (a) case-report studies, (b) studies testing genetic disorders, (c) poster presentation abstracts without full-text availability, (d) systematic reviews, and (e) metanalyses.
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Gothilf, Yoav, Roger Cone, Berta Levavi-Sivan, and Sheenan Harpaz. Genetic manipulations of MC4R for increased growth and feed efficiency in fish. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7600043.bard.

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The hypothalamic melanocortin system plays a central role in the regulation of food consumption and energy homeostasis in mammals. Accordingly, our working hypothesis in this project was that genetic editing of the mc4r gene, encoding Melanocortin Receptor 4 (MC4R), will enhance food consumption, feed efficiency and growth in fish. To test this hypothesis and to assess the utility of mc4r editing for the enhancement of feed efficiency and growth in fish, the following objectives were set: Test the effect of the mc4r-null allele on feeding behavior, growth, metabolism and survival in zebrafish. Generate mc4r-null alleles in tilapia and examine the consequences for growth and survival, feed efficiency and body composition. Generate and examine the effect of naturally-occurring mc4r alleles found in swordfish on feeding behavior, growth and survival in zebrafish. Define the MC4R-mediated and MC4R-independent effects of AgRP by crossing mc4r- null strains with fish lacking AgRP neurons or the agrpgene. Our results in zebrafish did not support our hypothesis. While knockout of the agrpgene or genetic ablation of hypothalamic AgRP neurons led to reduced food intake in zebrafish larvae, knockout (KO) of the mc4r gene not only did not increase the rate of food intake but even reduced it. Since Melanocortin Receptor 3 (MC3R) has also been proposed to be involved in hypothalamic control of food intake, we also tested the effectofmc3r gene KO. Again, contrary to our hypothesis, the rate of food intake decreased. The next step was to generate a double mutant lucking both functional MC3R and MC4R. Again, the double KO exhibited reduced food intake. Thus, the only manipulation within the melanocortin system that affected food intake in consistent with the expected role of the system was seen in zebrafish larvae upon agrpKO. Interestingly, despite the apparent reduced food intake in the larval stage, these fish grow to be of the same size as wildtype fish at the adult stage. Altogether, it seems that there is a compensatory mechanism that overrides the effect of genetic manipulations of the melanocortin system in zebrafish. Under Aim 3, we introduced the Xna1, XnB1l, and XnB2A mutations from the Xiphophorus MC4R alleles into the zebrafish MC4R gene. We hypothesized that these MC4R mutations would act as dominant negative alleles to increase growth by suppressing endogenous MC4R activity. When we examined the activity of the three mutant alleles, we were unable to document any inhibition of a co-transfected wild type MC4R allele, hence we did not introduce these alleles into zebrafish. Since teleost fish possess two agrpgenes we also tested the effect of KO of the agrp2 gene and ablation of the AgRP2 cells. We found that the AgRP2 system does not affect food consumption but may rather be involved in modulating the stress response. To try to apply genetic editing in farmed fish species we turned to tilapia. Injection of exogenous AgRP in adult tilapia induced significant changes in the expression of pituitary hormones. Genetic editing in tilapia is far more complicated than in zebrafish. Nevertheless, we managed to generate one mutant fish carrying a mutation in mc4r. That individual died before reaching sexual maturity. Thus, our attempt to generate an mc4r-mutant tilapia line was almost successful and indicate out non-obvious capability to generate mutant tilapia.
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Sadka, Avi, Mikeal L. Roose, and Yair Erner. Molecular Genetic Analysis of Citric Acid Accumulation in Citrus Fruit. United States Department of Agriculture, March 2001. http://dx.doi.org/10.32747/2001.7573071.bard.

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The acid content of the juice sac cells is a major determinant of maturity and fruit quality in citrus. Many citrus varieties accumulate acid in concentrations that exceed market desires, reducing grower income and consumer satisfaction. Pulp acidity is thought to be dependent on two mechanisms: the accumulation of citric acid in the vacuoles of the juice sac cells, and acidification of the vacuole. The major aim of the project was to direct effort toward understanding the mechanism of citric acid accumulation in the fruit. The following objectives were suggested: Measure the activity of enzymes likely to be involved in acid accumulation and follow their pattern of expression in developing fruit (Sadka, Erner). Identify and clone genes which are associated with high and low acid phenotypes and with elevated acid level (Roose, Sadka, Erner). Convert RAPD markers that map near a gene that causes low acid phenotype to specific co dominant markers (Roose). Use genetic co segregation to test whether specific gene products are responsible for low acid phenotype (Roose and Sadka). Objective 1 was fully achieved. Most of the enzymes of organic acid metabolism were cloned from lemon pulp. Their expression was studied during fruit development in low and high acid varieties. The activity and expression of citrate synthase, aconitase and NADP-isocitrate dehydrogenase (IDH) were studied in detail. The role that each enzyme plays in acid accumulation and decline was evaluated. As a result, a better understanding of the metabolic changes that contribute to acid accumulation was achieved. It was found that the activity of the mitochondrial aconitase is greatly reduced early in high-acid fruits, but not in acidless ones, suggesting that this enzyme plays an important role in acid accumulation. In addition, it was demonstrated that increases in the cytosolic forms of aconitase and NADP-IDH towards fruit maturation play probably a major role in acid decline. Our studies also demonstrated that the two mechanisms that contribute to fruit acidity, vacuolar acidification and citric acid accumulation, are independent, although they are tightly co-regulated. Additional, we demonstrated that sodium arsenite, which reduce fruit acidity, causes a transient inhibition in the activity of citrate synthase, but an induction in the gene expression. This part of the work has resulted in 4 papers. Objective 3 was also fully achieved. Using bulked segregant analysis, three random amplified polymorphic DNA (RAPD) markers were identified as linked to acitric, a gene controlling the acidless phenotype of pummelo 2240. One of them, which mapped 1.2 cM from acitric was converted into sequence characterized amplified region (SCAR marker, and into co dominant restriction length polymorphism (RFLP) marker. These markers were highly polymorphic among 59 citrus accessions, and therefore, they should be useful for selecting seedling progeny heterozygous for acitric in nearly all crosses between pummelo 2240 and other citrus genotypes. This part of the project resulted in one paper. Objective 4 was also fully achieved. Clones isolated by the Israeli group were sent to the American laboratory for co segregation analysis. However, none of them seemed to co segregate with the low acid phenotype. Both laboratories invested much effort in achieving the goals of Objective 2, namely the isolation of genes that are elevated in expression in low and high acid phenotypes, and in tissue cultures treated with arsenite (a treatment which reduces fruit acidity). However, conventional differential display and restriction fragment differential display analyses could not identify any differentially expressed genes. The isolation of such genes was the major aim of a continuation project, which was recently submitted.
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Gur, Amit, Edward Buckler, Joseph Burger, Yaakov Tadmor, and Iftach Klapp. Characterization of genetic variation and yield heterosis in Cucumis melo. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7600047.bard.

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Project objectives: 1) Characterization of variation for yield heterosis in melon using Half-Diallele (HDA) design. 2) Development and implementation of image-based yield phenotyping in melon. 3) Characterization of genetic, epigenetic and transcriptional variation across 25 founder lines and selected hybrids. The epigentic part of this objective was modified during the course of the project: instead of characterization of chromatin structure in a single melon line through genome-wide mapping of nucleosomes using MNase-seq approach, we took advantage of rapid advancements in single-molecule sequencing and shifted the focus to Nanoporelong-read sequencing of all 25 founder lines. This analysis provides invaluable information on genome-wide structural variation across our diversity 4) Integrated analyses and development of prediction models Agricultural heterosis relates to hybrids that outperform their inbred parents for yield. First generation (F1) hybrids are produced in many crop species and it is estimated that heterosis increases yield by 15-30% globally. Melon (Cucumismelo) is an economically important species of The Cucurbitaceae family and is among the most important fleshy fruits for fresh consumption Worldwide. The major goal of this project was to explore the patterns and magnitude of yield heterosis in melon and link it to whole genome sequence variation. A core subset of 25 diverse lines was selected from the Newe-Yaar melon diversity panel for whole-genome re-sequencing (WGS) and test-crosses, to produce structured half-diallele design of 300 F1 hybrids (MelHDA25). Yield variation was measured in replicated yield trials at the whole-plant and at the rootstock levels (through a common-scion grafted experiments), across the F1s and parental lines. As part of this project we also developed an algorithmic pipeline for detection and yield estimation of melons from aerial-images, towards future implementation of such high throughput, cost-effective method for remote yield evaluation in open-field melons. We found extensive, highly heritable root-derived yield variation across the diallele population that was characterized by prominent best-parent heterosis (BPH), where hybrids rootstocks outperformed their parents by 38% and 56 % under optimal irrigation and drought- stress, respectively. Through integration of the genotypic data (~4,000,000 SNPs) and yield analyses we show that root-derived hybrids yield is independent of parental genetic distance. However, we mapped novel root-derived yield QTLs through genome-wide association (GWA) analysis and a multi-QTLs model explained more than 45% of the hybrids yield variation, providing a potential route for marker-assisted hybrid rootstock breeding. Four selected hybrid rootstocks are further studied under multiple scion varieties and their validated positive effect on yield performance is now leading to ongoing evaluation of their commercial potential. On the genomic level, this project resulted in 3 layers of data: 1) whole-genome short-read Illumina sequencing (30X) of the 25 founder lines provided us with 25 genome alignments and high-density melon HapMap that is already shown to be an effective resource for QTL annotation and candidate gene analysis in melon. 2) fast advancements in long-read single-molecule sequencing allowed us to shift focus towards this technology and generate ~50X Nanoporesequencing of the 25 founders which in combination with the short-read data now enable de novo assembly of the 25 genomes that will soon lead to construction of the first melon pan-genome. 3) Transcriptomic (3' RNA-Seq) analysis of several selected hybrids and their parents provide preliminary information on differentially expressed genes that can be further used to explain the root-derived yield variation. Taken together, this project expanded our view on yield heterosis in melon with novel specific insights on root-derived yield heterosis. To our knowledge, thus far this is the largest systematic genetic analysis of rootstock effects on yield heterosis in cucurbits or any other crop plant, and our results are now translated into potential breeding applications. The genomic resources that were developed as part of this project are putting melon in the forefront of genomic research and will continue to be useful tool for the cucurbits community in years to come.
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Weil, Clifford F., Anne B. Britt, and Avraham Levy. Nonhomologous DNA End-Joining in Plants: Genes and Mechanisms. United States Department of Agriculture, July 2001. http://dx.doi.org/10.32747/2001.7585194.bard.

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Repair of DNA breaks is an essential function in plant cells as well as a crucial step in addition of modified DNA to plant cells. In addition, our inability to introduce modified DNA to its appropriate locus in the plant genome remains an important hurdle in genetically engineering crop species.We have taken a combined forward and reverse genetics approach to examining DNA double strand break repair in plants, focusing primarily on nonhomologous DNA end-joining. The forward approach utilizes a gamma-plantlet assay (miniature plants that are metabolically active but do not undergo cell division, due to cell cycle arrest) and has resulted in identification of five Arabidopsis mutants, including a new one defective in the homolog of the yeast RAD10 gene. The reverse genetics approach has identified knockouts of the Arabidopsis homologs for Ku80, DNA ligase 4 and Rad54 (one gene in what proves to be a gene family involved in DNA repair as well as chromatin remodeling and gene silencing)). All these mutants have phenotypic defects in DNA repair but are otherwise healthy and fertile. Additional PCR based screens are in progress to find knockouts of Ku70, Rad50, and Mre11, among others. Two DNA end-joining assays have been developed to further our screens and our ability to test candidate genes. One of these involves recovering linearized plasmids that have been added to and then rejoined in plant cells; plasmids are either recovered directly or transformed into E. coli and recovered. The products recovered from various mutant lines are then compared. The other assay involves using plant transposon excision to create DNA breaks in yeast cells and then uses the yeast cell as a system to examine those genes involved in the repair and to screen plant genes that might be involved as well. This award supported three graduate students, one in Israel and two in the U.S., as well as a technician in the U.S., and is ultimately expected to result directly in five publications and one Masters thesis.
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