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Languages : en
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The rapid development of large-scale genomic sequencing has dramatically changed the field of genetics, in part through the development of comparative genomics. Fungal comparative genomics is particularly powerful given the large number of genomes currently available, their compact architecture, and their relative ease of genetic manipulation. Fungal comparative genomics was employed in this work to address two related questions. First, it was used along with computational thermodynamic methods to predict non-coding RNA (ncRNA) in Saccharomyces cerevisiae. Sets of positive and negative control genes were evaluated to determine the effect of window sizes and step sizes on the sensitivity of ncRNA identification. The approach was then applied to predict ncRNA genes on chromosome 6 of S. cerevisiae and S. bayanus. Northern blot analysis, rapid amplification of cDNA ends (RACE), and publicly available cDNA library data were used to test the predictions. Strong experimental evidence was accumulated for four new ncRNA genes. Potential structural elements in the 5' and 3' untranslated regions (UTRs) of six annotated protein-coding genes were also identified. This work shows that thermodynamic approaches, coupled with comparative genomics, are powerful tools for predicting structural ncRNA. Second, comparative genomic approaches were employed to identify a non-reciprocal transfer event from Cryptococcus neoformans var. grubii to var. neoformans ~2 million years ago involving a 14 gene (~40 kb) region. The majority of clinical and environmental var. neoformans strains from around the world contain this sequence obtained from var. grubii. The introgression event likely occurred via an incomplete inter-varietal sexual cycle creating a hybrid intermediate where mobile elements common to both lineages mediated the exchange. The subsequent duplication in laboratory strains of a fragment of this same genomic region supports evolutionary theories that instabilities in subtelomeric.
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Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
The rapid development of large-scale genomic sequencing has dramatically changed the field of genetics, in part through the development of comparative genomics. Fungal comparative genomics is particularly powerful given the large number of genomes currently available, their compact architecture, and their relative ease of genetic manipulation. Fungal comparative genomics was employed in this work to address two related questions. First, it was used along with computational thermodynamic methods to predict non-coding RNA (ncRNA) in Saccharomyces cerevisiae. Sets of positive and negative control genes were evaluated to determine the effect of window sizes and step sizes on the sensitivity of ncRNA identification. The approach was then applied to predict ncRNA genes on chromosome 6 of S. cerevisiae and S. bayanus. Northern blot analysis, rapid amplification of cDNA ends (RACE), and publicly available cDNA library data were used to test the predictions. Strong experimental evidence was accumulated for four new ncRNA genes. Potential structural elements in the 5' and 3' untranslated regions (UTRs) of six annotated protein-coding genes were also identified. This work shows that thermodynamic approaches, coupled with comparative genomics, are powerful tools for predicting structural ncRNA. Second, comparative genomic approaches were employed to identify a non-reciprocal transfer event from Cryptococcus neoformans var. grubii to var. neoformans ~2 million years ago involving a 14 gene (~40 kb) region. The majority of clinical and environmental var. neoformans strains from around the world contain this sequence obtained from var. grubii. The introgression event likely occurred via an incomplete inter-varietal sexual cycle creating a hybrid intermediate where mobile elements common to both lineages mediated the exchange. The subsequent duplication in laboratory strains of a fragment of this same genomic region supports evolutionary theories that instabilities in subtelomeric.
Author: Laura Anne Kavanaugh
Publisher:
ISBN:
Category : Cryptococcus neoformans
Languages : en
Pages :
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Book Description
The rapid development of large-scale genomic sequencing has dramatically changed the field of genetics, in part through the development of comparative genomics. Fungal comparative genomics is particularly powerful given the large number of genomes currently available, their compact architecture, and their relative ease of genetic manipulation. Fungal comparative genomics was employed in this work to address two related questions. First, it was used along with computational thermodynamic methods to predict non-coding RNA (ncRNA) in Saccharomyces cerevisiae. Sets of positive and negative control genes were evaluated to determine the effect of window sizes and step sizes on the sensitivity of ncRNA identification. The approach was then applied to predict ncRNA genes on chromosome 6 of S. cerevisiae and S. bayanus. Northern blot analysis, rapid amplification of cDNA ends (RACE), and publicly available cDNA library data were used to test the predictions. Strong experimental evidence was accumulated for four new ncRNA genes. Potential structural elements in the 5' and 3' untranslated regions (UTRs) of six annotated protein-coding genes were also identified. This work shows that thermodynamic approaches, coupled with comparative genomics, are powerful tools for predicting structural ncRNA. Second, comparative genomic approaches were employed to identify a non-reciprocal transfer event from Cryptococcus neoformans var. grubii to var. neoformans ~2 million years ago involving a 14 gene (~40 kb) region. The majority of clinical and environmental var. neoformans strains from around the world contain this sequence obtained from var. grubii. The introgression event likely occurred via an incomplete inter-varietal sexual cycle creating a hybrid intermediate where mobile elements common to both lineages mediated the exchange. The subsequent duplication in laboratory strains of a fragment of this same genomic region supports evolutionary theories that instabilities in subtelomeric regions promote adaptive evolution through gene amplification and subsequent adaptation. These data indicate that DNA exchange between closely related sympatric varieties or species may be a recurrent theme in the evolution of fungal species. It further suggests that while evolutionary divergence is the primary force driving speciation, rare introgression events also play a potentially important role.
Author: Thao Thanh Thi Tran
Publisher:
ISBN:
Category : Data mining
Languages : en
Pages :
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Book Description
The objective of this research is to develop a novel computational prediction algorithm for non-coding RNA (ncRNA) genes using features computable for any genomic sequence without the need for comparative analysis. Existing comparative-based methods require the knowledge of closely related organisms in order to search for sequence and structural similarities. This approach imposes constraints on the type of ncRNAs, the organism, and the regions where the ncRNAs can be found. We have developed a novel approach for ncRNA gene prediction without the limitations of current comparative-based methods. Our work has established a ncRNA database required for subsequent feature and genomic analysis. Furthermore, we have identified significant features from folding-, structural-, and ensemble-based statistics for use in ncRNA prediction. We have also examined higher-order gene structures, namely operons, to discover potential insights into how ncRNAs are transcribed. Being able to automatically identify ncRNAs on a genome-wide scale is immensely powerful for incorporating it into a pipeline for large-scale genome annotation. This work will contribute to a more comprehensive annotation of ncRNA genes in microbial genomes to meet the demands of functional and regulatory genomic studies.
Author:
Publisher:
ISBN:
Category : Dissertations, Academic
Languages : en
Pages : 868
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Book Description
Author: Nils Stein
Publisher: Springer
ISBN: 3319925288
Category : Science
Languages : en
Pages : 394
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Book Description
This book presents an overview of the state-of-the-art in barley genome analysis, covering all aspects of sequencing the genome and translating this important information into new knowledge in basic and applied crop plant biology and new tools for research and crop improvement. Unlimited access to a high-quality reference sequence is removing one of the major constraints in basic and applied research. This book summarizes the advanced knowledge of the composition of the barley genome, its genes and the much larger non-coding part of the genome, and how this information facilitates studying the specific characteristics of barley. One of the oldest domesticated crops, barley is the small grain cereal species that is best adapted to the highest altitudes and latitudes, and it exhibits the greatest tolerance to most abiotic stresses. With comprehensive access to the genome sequence, barley’s importance as a genetic model in comparative studies on crop species like wheat, rye, oats and even rice is likely to increase.
Author: National Academies of Sciences, Engineering, and Medicine
Publisher: National Academies Press
ISBN: 0309437385
Category : Science
Languages : en
Pages : 607
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Book Description
Genetically engineered (GE) crops were first introduced commercially in the 1990s. After two decades of production, some groups and individuals remain critical of the technology based on their concerns about possible adverse effects on human health, the environment, and ethical considerations. At the same time, others are concerned that the technology is not reaching its potential to improve human health and the environment because of stringent regulations and reduced public funding to develop products offering more benefits to society. While the debate about these and other questions related to the genetic engineering techniques of the first 20 years goes on, emerging genetic-engineering technologies are adding new complexities to the conversation. Genetically Engineered Crops builds on previous related Academies reports published between 1987 and 2010 by undertaking a retrospective examination of the purported positive and adverse effects of GE crops and to anticipate what emerging genetic-engineering technologies hold for the future. This report indicates where there are uncertainties about the economic, agronomic, health, safety, or other impacts of GE crops and food, and makes recommendations to fill gaps in safety assessments, increase regulatory clarity, and improve innovations in and access to GE technology.
Author: Supratim Choudhuri
Publisher: Elsevier
ISBN: 0124105106
Category : Science
Languages : en
Pages : 238
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Book Description
Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools provides a coherent and friendly treatment of bioinformatics for any student or scientist within biology who has not routinely performed bioinformatic analysis. The book discusses the relevant principles needed to understand the theoretical underpinnings of bioinformatic analysis and demonstrates, with examples, targeted analysis using freely available web-based software and publicly available databases. Eschewing non-essential information, the work focuses on principles and hands-on analysis, also pointing to further study options. Avoids non-essential coverage, yet fully describes the field for beginners Explains the molecular basis of evolution to place bioinformatic analysis in biological context Provides useful links to the vast resource of publicly available bioinformatic databases and analysis tools Contains over 100 figures that aid in concept discovery and illustration
Author:
Publisher: Academic Press
ISBN: 9780123694782
Category : Science
Languages : en
Pages : 730
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Book Description
Focusing on Saccharomyces cerevisiae, the second edition of Yeast Gene Analysis represents a major reworking of the original edition, with many completely new chapters and major revisions to all previous chapters. Originally published shortly after completion of the yeast genome sequence, the new edition covers many of the major genome-wide strategies that have been developed since then such as microarray analysis of transcription, synthetic gene array studies, protein microarrays and chemical genetic approaches. It represents a valuable resource for any research laboratory using budding yeast as their experimental system in which to identify new yeast gene functions. The chapters are written in a readable style with useful background information, technical tips and specific experimental protocols included as appropriate, enabling both the novice and the experienced yeast researcher to adopt new procedures with confidence. New chapters on: Strain construction; genome-wide two-hybrid approaches; use of microarrays for transcript analysis; real-time analysis of chromosome behaviour and FRET; synthetic gene array technology and protein arrays; chemical genomics and yeast prions; RNA gene analysis and mitochondrial gene function analysis; phylogenetic footprinting; discovering human gene function and predicting yeast gene function
Author: Charlotte Lindqvist
Publisher: Springer
ISBN: 3030047539
Category : Science
Languages : en
Pages : 427
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Book Description
Advances in genome-scale DNA sequencing technologies have revolutionized genetic research on ancient organisms, extinct species, and past environments. When it is recoverable after hundreds or thousands of years of unintended preservation, “ancient DNA” (or aDNA) is often highly degraded, necessitating specialized handling and analytical approaches. Paleogenomics defines the field of reconstructing and analyzing the genomes of historic or long-dead organisms, most often through comparison with modern representatives of the same or similar species. The opportunity to isolate and study paleogenomes has radically transformed many fields, spanning biology, anthropology, agriculture, and medicine. Examples include understanding evolutionary relationships of extinct species known only from fossils, the domestication of plants and animals, and the evolution and geographical spread of certain pathogens. This pioneering book presents a snapshot view of the history, current status, and future prospects of paleogenomics, taking a broad viewpoint that covers a range of topics and organisms to provide an up-to-date status of the applications, challenges, and promise of the field. This book is intended for a variety of readerships, including upper-level undergraduate and graduate students, professionals and experts in the field, as well as anyone excited by the extraordinary insights that paleogenomics offers.
Author: Thomas Liehr
Publisher: Academic Press
ISBN: 0128235802
Category : Science
Languages : en
Pages : 430
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Book Description
Cytogenomics demonstrates that chromosomes are crucial in understanding the human genome and that new high-throughput approaches are central to advancing cytogenetics in the 21st century. After an introduction to (molecular) cytogenetics, being the basic of all cytogenomic research, this book highlights the strengths and newfound advantages of cytogenomic research methods and technologies, enabling researchers to jump-start their own projects and more effectively gather and interpret chromosomal data. Methods discussed include banding and molecular cytogenetics, molecular combing, molecular karyotyping, next-generation sequencing, epigenetic study approaches, optical mapping/karyomapping, and CRISPR-cas9 applications for cytogenomics. The book’s second half demonstrates recent applications of cytogenomic techniques, such as characterizing 3D chromosome structure across different tissue types and insights into multilayer organization of chromosomes, role of repetitive elements and noncoding RNAs in human genome, studies in topologically associated domains, interchromosomal interactions, and chromoanagenesis. This book is an important reference source for researchers, students, basic and translational scientists, and clinicians in the areas of human genetics, genomics, reproductive medicine, gynecology, obstetrics, internal medicine, oncology, bioinformatics, medical genetics, and prenatal testing, as well as genetic counselors, clinical laboratory geneticists, bioethicists, and fertility specialists. Offers applied approaches empowering a new generation of cytogenomic research using a balanced combination of classical and advanced technologies Provides a framework for interpreting chromosome structure and how this affects the functioning of the genome in health and disease Features chapter contributions from international leaders in the field
