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Reconstructing And Profiling Extrachromosomal Dna
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Book Synopsis Reconstructing and Profiling Extrachromosomal DNA by : Jens-Christian Luebeck
Download or read book Reconstructing and Profiling Extrachromosomal DNA written by Jens-Christian Luebeck and published by . This book was released on 2021 with total page 217 pages. Available in PDF, EPUB and Kindle. Book excerpt: Circular extrachromosomal DNA (ecDNA) are a genomic lesion occurring in tumors, and represent a foundational, growing frontier in cancer biology. The discovery that focal amplifications exist in multiple topologies and arise by different mechanisms has enabled cancer researchers to study the consequences of different types of focal amplification--revealing that focal amplifications like ecDNA lead to worse patient survival. Consequently, there is an urgent need for bioinformatic methods and tools to study these focal amplifications, particularly ecDNA. This thesis describes novel tools and methods which can be used to study ecDNA, and other focal amplifications. It also demonstrates how those tools and methods can be used to profile focal amplifications across different cancer types, ultimately revealing novel biology about the structure, function and genesis of ecDNA in different contexts. I first present two methods, AmpliconReconstructor (AR) and FaNDOM, which incorporate optical mapping data to resolve the structures of ecDNA and other focal amplifications. AR incorporates both optical mapping and NGS data and builds upon a prior method for ecDNA detection with NGS data, AmpliconArchitect (AA). FaNDOM utilizes optical mapping solely and enables the rapid characterization of large structural variants using assembled OM contigs or individual OM molecules. I also describe the landscape of ecDNA in oropharyngeal squamous cell carcinoma, demonstrating that both human and hybrid human-viral ecDNA exist and are associated with distinct patterns of transcriptional splicing. Visualizations of the rearranged ecDNA structures and overlaid transcription-level data reveal the overexpression of genes carried on ecDNA. Lastly, I describe the genesis of ecDNA in Barrett's esophagus, the precursor tissue of esophageal adenocarcinoma. We utilized methods for profiling ecDNA, such as AmpliconClassifier, to demonstrate that ecDNA exist in pre-cancerous tissue, are associated with worse histology, that they are subsequently found again in cancer, and that they tend to undergo positive selection during the malignant transformation. These findings solidify ecDNA as a potent driver of cancer, and not an opportunistic passenger.
Book Synopsis Research in Computational Molecular Biology by : Jian Ma
Download or read book Research in Computational Molecular Biology written by Jian Ma and published by Springer Nature. This book was released on with total page 508 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Energy Research Abstracts written by and published by . This book was released on 1986 with total page 784 pages. Available in PDF, EPUB and Kindle. Book excerpt: Semiannual, with semiannual and annual indexes. References to all scientific and technical literature coming from DOE, its laboratories, energy centers, and contractors. Includes all works deriving from DOE, other related government-sponsored information, and foreign nonnuclear information. Arranged under 39 categories, e.g., Biomedical sciences, basic studies; Biomedical sciences, applied studies; Health and safety; and Fusion energy. Entry gives bibliographical information and abstract. Corporate, author, subject, report number indexes.
Book Synopsis The Cheating Cell by : Athena Aktipis
Download or read book The Cheating Cell written by Athena Aktipis and published by Princeton University Press. This book was released on 2020-03-24 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: A fundamental and groundbreaking reassessment of how we view and manage cancer When we think of the forces driving cancer, we don’t necessarily think of evolution. But evolution and cancer are closely linked because the historical processes that created life also created cancer. The Cheating Cell delves into this extraordinary relationship, and shows that by understanding cancer’s evolutionary origins, researchers can come up with more effective, revolutionary treatments. Athena Aktipis goes back billions of years to explore when unicellular forms became multicellular organisms. Within these bodies of cooperating cells, cheating ones arose, overusing resources and replicating out of control, giving rise to cancer. Aktipis illustrates how evolution has paved the way for cancer’s ubiquity, and why it will exist as long as multicellular life does. Even so, she argues, this doesn’t mean we should give up on treating cancer—in fact, evolutionary approaches offer new and promising options for the disease’s prevention and treatments that aim at long-term management rather than simple eradication. Looking across species—from sponges and cacti to dogs and elephants—we are discovering new mechanisms of tumor suppression and the many ways that multicellular life-forms have evolved to keep cancer under control. By accepting that cancer is a part of our biological past, present, and future—and that we cannot win a war against evolution—treatments can become smarter, more strategic, and more humane. Unifying the latest research from biology, ecology, medicine, and social science, The Cheating Cell challenges us to rethink cancer’s fundamental nature and our relationship to it.
Author :National Academies of Sciences, Engineering, and Medicine Publisher :National Academies Press ISBN 13 :0309465184 Total Pages :189 pages Book Rating :4.3/5 (94 download)
Book Synopsis Biodefense in the Age of Synthetic Biology by : National Academies of Sciences, Engineering, and Medicine
Download or read book Biodefense in the Age of Synthetic Biology written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2019-01-05 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientific advances over the past several decades have accelerated the ability to engineer existing organisms and to potentially create novel ones not found in nature. Synthetic biology, which collectively refers to concepts, approaches, and tools that enable the modification or creation of biological organisms, is being pursued overwhelmingly for beneficial purposes ranging from reducing the burden of disease to improving agricultural yields to remediating pollution. Although the contributions synthetic biology can make in these and other areas hold great promise, it is also possible to imagine malicious uses that could threaten U.S. citizens and military personnel. Making informed decisions about how to address such concerns requires a realistic assessment of the capabilities that could be misused. Biodefense in the Age of Synthetic Biology explores and envisions potential misuses of synthetic biology. This report develops a framework to guide an assessment of the security concerns related to advances in synthetic biology, assesses the levels of concern warranted for such advances, and identifies options that could help mitigate those concerns.
Book Synopsis Barrett's Esophagus and Esophageal Adenocarcinoma by : Prateek Sharma
Download or read book Barrett's Esophagus and Esophageal Adenocarcinoma written by Prateek Sharma and published by John Wiley & Sons. This book was released on 2008-04-15 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: The leading reference text entirely devoted to this increasinglysignificant condition This text is dedicated to Barrett’s esophagus and providesrecent evidence and current approaches to patient management. Ithas been completely revised, updated and extended to include thelatest research findings and describes how these affect day-to-dayclinical practice. It includes seven new chapters and even more color images thanthe last edition. Each chapter, written by the leadinginternational experts in the field, provides clear, didacticguidance on diagnosis, treatment and management of thiscondition. Barrett’s Espohagus gives an extensive overviewcovering epidemiology, screening, pathology, gastroenterology andsurgery. It looks at the precursor lesions leading to thedevelopment of Barrett’s epithelium, the uniquecharacteristics of Barrett’s esophagus, and the consequencesof malignant degeneration. All aspects of diagnosis, secondaryprevention, multimodality, and medical and surgical treatment areclearly explained. This is a complete guide on the latest thinking on diagnosis andtreatment of Barrett’s esophagus which can be referred toover and over again.
Book Synopsis Microbial Megaplasmids by : Edward Schwartz
Download or read book Microbial Megaplasmids written by Edward Schwartz and published by Springer Science & Business Media. This book was released on 2009-01-29 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: Megaplasmids are extrachromosomal genetic elements in the size range of 100 kb and larger. They are found in physiologically and phylogenetically diverse groups of bacteria and archaea. By definition, megaplasmids are not essential for the viability of their hosts under all growth conditions, but paradoxically many megaplasmids carry the genetic information for the defining and characteristic traits of the organism in which they reside. Microbial Megaplasmids reviews our knowledge of the extensively studied representatives, such as the catabolic plasmids of the pseudomonads, the rhizobial Sym plasmids, the Ti plasmids of the genus Agrobacterium and the giant enterobacterial virulence plasmids. It also presents snapshots of more recently discovered megaplasmids. The contribution of megaplasmids to the biology of their hosts is described, highlighting the interactions between megaplasmid and chromosomal genes.
Book Synopsis Drug Resistance in Cancer Therapy by : Robert F Ozols
Download or read book Drug Resistance in Cancer Therapy written by Robert F Ozols and published by . This book was released on 1989-08-31 with total page 228 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The Biology of Plasmids by : David Summers
Download or read book The Biology of Plasmids written by David Summers and published by John Wiley & Sons. This book was released on 2009-07-17 with total page 169 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plasmids are closed, circular pieces of DNA that are able to self-replicate and are carried by many bacteria. They provide unique functions for bacteria by allowing them to sexually replicate and to pass on genetic material between each other. Plasmids are also responsible for the genetic factors that give resistance to antibiotics, and provide the enzymes needed to break down poorly metabolised food resources. The author has provided an updated treatment of the structure, function and application of plasmids suitable for undergraduates and medical students. Employing an original teaching perspective--examining plasmids as living organisms with either a symbiotic or parasitic mode of survival--this text provides an important framework for understanding the structure and function of plasmids in an evolutionary context. The most up to date text on plasmids An innovative teaching perspective makes for easy student understanding Contains crucial chapters on the importance of plasmids for clinical and biological research
Book Synopsis CRISPR-Cas Systems by : Rodolphe Barrangou
Download or read book CRISPR-Cas Systems written by Rodolphe Barrangou and published by Springer Science & Business Media. This book was released on 2012-12-13 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: CRISPR/Cas is a recently described defense system that protects bacteria and archaea against invasion by mobile genetic elements such as viruses and plasmids. A wide spectrum of distinct CRISPR/Cas systems has been identified in at least half of the available prokaryotic genomes. On-going structural and functional analyses have resulted in a far greater insight into the functions and possible applications of these systems, although many secrets remain to be discovered. In this book, experts summarize the state of the art in this exciting field.
Book Synopsis Bioinformatics of Genome Regulation and Systems Biology by : Yuriy L. Orlov
Download or read book Bioinformatics of Genome Regulation and Systems Biology written by Yuriy L. Orlov and published by Frontiers Media SA. This book was released on 2020-09-17 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
Book Synopsis Genetics and Biotechnology by : Ulrich Kück
Download or read book Genetics and Biotechnology written by Ulrich Kück and published by Springer Science & Business Media. This book was released on 2013-03-09 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mycology, the study of fungi, originated as a subdiscipline of botany and was a descriptive discipline, largely neglected as an experimental science until the early years of this century. A seminal paper by Blakeslee in 1904 provided evidence for self incompatibility, termed "heterothallism", and stimulated interest in studies related to the control of sexual reproduction in fungi by mating-type specificities. Soon to follow was the demonstration that sexually reproducing fungi exhibit Mendelian inheritance and that it was possible to conduct formal genetic analysis with fungi. The names Burgeff, Kniep and Lindegren are all associated with this early period of fungal genetics research. These studies and the discovery of penicillin by Fleming, who shared a Nobel Prize in 1945, provided further impetus for experimental research with fungi. Thus began a period of interest in mutation induction and analysis of mutants for bio chemical traits. Such fundamental research, conducted largely with Neurospora crassa, led to the one gene: one enzyme hypothesis and to a second Nobel Prize for fungal research awarded to Beadle and Tatum in 1958. Fundamental research in biochemical genetics was extended to other fungi, especially to Saccharomyces cere visiae, and by the mid-1960s fungal systems were much favored for studies in eukaryotic molecular biology and were soon able to compete with bacterial systems in the molecular arena.
Book Synopsis Studies in Viral Ecology, Volume 1 by : Christon J. Hurst
Download or read book Studies in Viral Ecology, Volume 1 written by Christon J. Hurst and published by John Wiley & Sons. This book was released on 2011-06-20 with total page 389 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explains the ecology of viruses by examining their interactive dynamics with their hosting species (in this volume, in microbes and plants), including the types of transmission cycles that viruses have evolved encompassing principal and alternate hosts, vehicles, and vectoring species. Examining virology from an organismal biology approach and focusing on the concept that viral infections represent areas of overlap in the ecologies of the involved species, Viral Ecology is essential for students and professionals who either may be non-virologists or virologists whose previous familiarity has been very specialized.
Book Synopsis Cancer Genomics by : Graham Dellaire
Download or read book Cancer Genomics written by Graham Dellaire and published by Academic Press. This book was released on 2013-11-21 with total page 511 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cancer Genomics addresses how recent technological advances in genomics are shaping how we diagnose and treat cancer. Built on the historical context of cancer genetics over the past 30 years, the book provides a snapshot of the current issues and state-of-the-art technologies used in cancer genomics. Subsequent chapters highlight how these approaches have informed our understanding of hereditary cancer syndromes and the diagnosis, treatment and outcome in a variety of adult and pediatric solid tumors and hematologic malignancies. The dramatic increase in cancer genomics research and ever-increasing availability of genomic testing are not without significant ethical issues, which are addressed in the context of the return of research results and the legal considerations underlying the commercialization of genomic discoveries. Finally, the book concludes with "Future Directions", examining the next great challenges to face the field of cancer genomics, namely the contribution of non-coding RNAs to disease pathogenesis and the interaction of the human genome with the environment. Tools such as sidebars, key concept summaries, a glossary, and acronym and abbreviation definitions make this book highly accessible to researchers from several fields associated with cancer genomics. Contributions from thought leaders provide valuable historical perspective to relate the advances in the field to current technologies and literature.
Book Synopsis Chromothripsis by : Franck Pellestor
Download or read book Chromothripsis written by Franck Pellestor and published by Humana Press. This book was released on 2018-03-21 with total page 367 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed book presents an up-to-date view on methods and experimental approaches developed to identify and explore the chromothripsis phenomenon. Beginning with a section exploring the genesis and impact of chromothripsis, the collection continues by covering the identification of chromothripsis, the causal mechanisms of chromothripsis, the bioinformatics tools for chromothripsis analysis, and experimental systems recently developed for the in vitro investigation of chromothripsis. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Chromothripsis: Methods and Protocols serves as a vital resource for cell biologists, molecular biologists, cytogeneticists, and geneticists investigating chromothripsis, but also for students and researchers new to the field of chromothripsis and genomic instability.
Download or read book C. Elegans Atlas written by David H. Hall and published by CSHL Press. This book was released on 2008 with total page 353 pages. Available in PDF, EPUB and Kindle. Book excerpt: Derived from the acclaimed online “WormAtlas,†C. elegansAtlas is a large-format, full-color atlas of the hermaphroditic form of the model organism C. elegans, known affectionately as “the worm†by workers in the field. Prepared by the editors of the WormAtlas Consortium, David H. Hall and Zeynep F. Altun, this book combines explanatory text with copious, labeled, color illustrations and electron micrographs of the major body systems of C. elegans. Also included are electron microscopy cross sections of the worm. This laboratory reference is essential for the working worm biologist, at the bench and at the microscope, and provides a superb companion to the C. elegansII monograph. It is also a valuable tool for investigators in the fields of developmental biology, neurobiology, reproductive biology, gene expression, and molecular biology.
Download or read book Index Medicus written by and published by . This book was released on 2003 with total page 1748 pages. Available in PDF, EPUB and Kindle. Book excerpt: Vols. for 1963- include as pt. 2 of the Jan. issue: Medical subject headings.
