Download or read book Single Molecule Barcoding Towards Genomic Analysis written by Dalia M. Dhingra and published by . This book was released on 2007 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Single Molecule and Single Cell Sequencing written by Yutaka Suzuki and published by Springer. This book was released on 2019-04-09 with total page 150 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of the recent technologies in single molecule and single cell sequencing. These sequencing technologies are revolutionizing the way of the genomic studies and the understanding of complex biological systems. The PacBio sequencer has enabled extremely long-read sequencing and the MinION sequencer has made the sequencing possible in developing countries. New developments and technologies are constantly emerging, which will further expand sequencing applications. In parallel, single cell sequencing technologies are rapidly becoming a popular platform. This volume presents not only an updated overview of these technologies, but also of the related developments in bioinformatics. Without powerful bioinformatics software, where rapid progress is taking place, these new technologies will not realize their full potential. All the contributors to this volume have been involved in the development of these technologies and software and have also made significant progress on their applications. This book is intended to be of interest to a wide audience ranging from genome researchers to basic molecular biologists and clinicians.
Download or read book DNA barcoding a practical tool for fundamental and applied biodiversity research written by Zoltan T Nagy and published by PenSoft Publishers LTD. This book was released on 2013-12-30 with total page 419 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA barcoding has become a well-accepted and popular tool for the identification of species and the detection of cryptic taxonomic diversity. As such, it has a tremendous potential for a wide variety of applications in taxonomy, agronomy, conservation biology, forensics etc. Therefore, several countries, institutions and organizations have launched DNA barcoding projects in the context of the international ?Consortium for the Barcode of Life? (CBOL) initiative. Also Belgium has done so with the establishment of the FWO research community ?Belgian Network for DNA barcoding?. In 2012, this network organized the ?Third European Conference for the Barcode of Life? (ECBOL3) in Brussels. During this event a call was made to publish a collection of papers under the thematic title ?DNA barcoding: a practical tool for fundamental and applied biodiversity research?. With the financial support of the EC project ?ViBRANT? (Virtual Biodiversity Research and Access Network for Taxonomy), 21 papers were bundled to form this special ?ZooKeys? issue with the aim to present various applications, advantages and limitations of DNA barcoding. Hence, it is the editors? hope that this issue provides a modest, but timely, contribution to the already vast literature on DNA barcoding.
Download or read book DNA Barcoding and Molecular Phylogeny written by Subrata Trivedi and published by Springer Nature. This book was released on 2020-08-24 with total page 259 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a comprehensive overview of DNA barcoding and molecular phylogeny, along with a number of case studies. It discusses a number of areas where DNA barcoding can be applied, such as clinical microbiology, especially in relation to infection management; DNA database management; and plant -animal interactions, and also presents valuable information on the DNA barcoding and molecular phylogeny of microbes, algae, elasmobranchs, fishes, birds and ruminant mammals. Furthermore it features unique case studies describing DNA barcoding of reptiles dwelling in Saudi Arabian deserts, genetic variation studies in both wild and hatchery populations of Anabas testudineus, DNA barcoding and molecular phylogeny of Ichthyoplankton and juvenile fishes of Kuantan River in Malaysia, and barcoding and molecular phylogenetic analysis of indigenous bacteria from fishes dwelling in a tropical tidal river. Moreover, since prompt identification and management of invasive species is vital to prevent economic and ecological loss, the book includes a chapter on DNA barcoding of invasive species. Given its scope, this book will appeal not only to researchers, teachers and students around the globe, but also to general readers.
Download or read book Optical Mapping and Targeted Sequence Capture written by and published by . This book was released on 2013 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in DNA sequencing technology has led to the study of the nucleotide content of genomes on an unprecedented scale. However, DNA sequence in isolation provides an incomplete description of a genome. The context and connectivity of a given sequence is just as important as the nucleotide content in determining its functional effect. Genomic analysis starting from high molecular weight DNA recovers this long-range structure and is essential for understanding the architecture of complex genomes. In this thesis, we describe the development and application of research platforms that utilize large DNA molecules for genomic analysis. First, the Optical Mapping System is used to explore the complex and disperse mutational spectrum of solid tumor oligodendroglioma. Optical Mapping creates high-resolution physical maps of genomes through the analysis of ensembles of single molecule ordered restriction maps. Over a thousand structural variants have been identified in each tumor sample, ranging in size from single base changes to loss of entire chromosomes and comprise insertions, deletions, inversions and compound events. These findings were then validated by comprehensive comparisons to variants reported in external and internal databases, and by selected experimental corroborations. The structure of each alteration has been elucidated at sub-genic resolution, while retaining the long-range context of the event. 94 somatic mutations, including 24 genes, were identified. These novel candidate cancer genes provide focused, testable hypotheses for follow-up functional investigation. Next, we present a novel method for targeted capture of large, contiguous segments of DNA from genomes. Our approach is based on the creation of single stranded flaps of known sequence using nicking endonucleases, in conjunction with DNA polymerases that are capable of strand displacement. Biotinylated capture oligonucleotides are then incorporated by ligation to the flap, and targets are purified using streptavidin coated magnetic beads. We demonstrate proof-of-principle by capture of kilobase sized plasmid and phage genomes as intact DNA molecules, and develop protocols for flap mediated capture from more complex genomes.
Download or read book DNA Barcoding written by Robert DeSalle and published by Springer Nature. This book was released on with total page 577 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Single Molecule Systems written by Sang Alex Lim and published by . This book was released on 2004 with total page 218 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Chromosome Architecture written by Mark C. Leake and published by Humana. This book was released on 2016-06-10 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details a valuable collection of protocols and reviews, such as emerging experimental and theoretical approaches. These approaches have resulted in a substantial improvement in the understanding of chromosome architecture. Chromosome Architecture: Methods and Protocols guides readers through cutting-edge interdisciplinary methods which allow for an understanding of architecture of chromosomes with exceptionally enhanced resolution, both in terms of space and time. Written in the highly successful Methods in Molecular Biology series format, 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 cutting-edge, Chromosome Architecture: Methods and Protocols aims to ensure successful results in the further study of this vital field.
Download or read book A Nanoconfinement System for Genome Analysis written by Kristy Leigh Kounovsky-Shafer and published by . This book was released on 2013 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The high-throughput analysis of individual DNA molecules is altering the pace and scope of biological investigation. In this regard, the Optical Mapping System was developed as a single molecule platform for construction of physical maps that span entire genomes. This platform effectively discovers genomic structural alterations including insertions, deletions, etc.; however, a system with greater throughput enables not only the characterization of individuals but entire human populations. For this purpose, we developed new ways to synergistically load and present very high densities of arrayed DNA molecules using nanoconfinement through the development of new fluidic devices with nanoslit and molecular cup features. In addition, we leverage entropic differences between the microchannel and nanoslit dimensions and electrostatic repulsion, from decreasing the overall ionic strength, to further elongate DNA molecules in "spacious" nanoslits. Furthermore, genomic DNA molecules are "barcoded" by the sequence-specific incorporation of fluorochrome labels prior to loading within nanoslits for presentation and optical detection. As such, a major goal was to design and fabricate nanoslit devices for the efficient loading of barcoded molecules. Part of this effort was centered on the characterization and leveraging of novel molecular confinement phenomena that enhanced the resolution of detectable barcode features. Finally, the first genome to be mapped under nanoconfinement, Mesoplasma florum, allowed convincing demonstration of a highly integrated system for genome analysis, which will supplant the Optical Mapping System for many applications
Download or read book Next Generation Genome Sequencing written by Michal Janitz and published by John Wiley & Sons. This book was released on 2011-08-24 with total page 281 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by leading experts from industry and academia, this first single comprehensive resource addresses recent developments in next generation DNA sequencing technology and their impact on genome research, drug discovery and health care. As such, it presents a detailed comparative analysis of commercially available platforms as well as insights into alternative, emerging sequencing techniques. In addition, the book not only covers the principles of DNA sequencing techniques but also social, ethical and commercial aspects, the concept of personalized medicine and a five-year perspective of DNA sequencing.
Download or read book DNA Barcodes written by Ida Lopez and published by Humana Press. This book was released on 2012-06-12 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: A DNA barcode in its simplest definition is one or more short gene sequences taken from a standardized portion of the genome that is used to identify species through reference to DNA sequence libraries or databases. In DNA Barcodes: Methods and Protocols expert researchers in the field detail many of the methods which are now commonly used with DNA barcodes. These methods include the latest information on techniques for generating, applying, and analyzing DNA barcodes across the Tree of Life including animals, fungi, protists, algae, and plants. Written in the highly successful Methods in Molecular BiologyTM series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, DNA Barcodes: Methods and Protocols aids scientists in continuing to study methods from wet-lab protocols, statistical, and ecological analyses along with guides to future, large-scale collections campaigns.
Download or read book Plant DNA Fingerprinting and Barcoding written by Nikolaus J. Sucher and published by Humana Press. This book was released on 2016-08-23 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular cloning and DNA-based analysis have become part of every molecular life science laboratory. The rapid adoption of DNA-based techniques has been facilitated by the introduction of the polymerase chain reaction (PCR), which has made cloning and characterization of DNA quick and relatively simple. PCR is virtually part of every variation of the plethora of approaches used for DNA fingerprinting today. Plant DNA Fingerprinting: Methods and Protocols aims to bring together the different currently available genome-based techniques into one repository. This volume contains detailed protocols for the preparation of plant genomic DNA, fingerprinting of plants for the detection of intra-species variations, the use of DNA barcoding, as well as methods for the bioinformatic analysis of data. Also included are several discussions on the broader issues of genome-based approaches in order to provide a sound understanding of the principles of these methods. Written in the successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Plant DNA Fingerprinting: Methods and Protocols is tailored principally for those who seek to augment their current methods of plant analysis and quality control using genome-based approaches as well as for scientists and researchers in different plant sciences.
Download or read book New High Throughput Technologies for DNA Sequencing and Genomics written by Keith R. Mitchelson and published by Elsevier. This book was released on 2011-09-22 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the independent invention of DNA sequencing by Sanger and by Gilbert 30 years ago, it has grown from a small scale technique capable of reading several kilobase-pair of sequence per day into today's multibillion dollar industry. This growth has spurred the development of new sequencing technologies that do not involve either electrophoresis or Sanger sequencing chemistries. Sequencing by Synthesis (SBS) involves multiple parallel micro-sequencing addition events occurring on a surface, where data from each round is detected by imaging. New High Throughput Technologies for DNA Sequencing and Genomics is the second volume in the Perspectives in Bioanalysis series, which looks at the electroanalytical chemistry of nucleic acids and proteins, development of electrochemical sensors and their application in biomedicine and in the new fields of genomics and proteomics. The authors have expertly formatted the information for a wide variety of readers, including new developments that will inspire students and young scientists to create new tools for science and medicine in the 21st century.Reviews of complementary developments in Sanger and SBS sequencing chemistries, capillary electrophoresis and microdevice integration, MS sequencing and applications set the framework for the book.* 'Hot Topic' with DNA sequencing continuing as a major research activity in many areas of life science and medicine.* Bringing together new developments in DNA sequencing technology* Reviewing issues relevant to the new applications used
Download or read book Barcoding Nature written by Claire Waterton and published by Routledge. This book was released on 2017-07-05 with total page 225 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA Barcoding has been promoted since 2003 as a new, fast, digital genomics-based means of identifying natural species based on the idea that a small standard fragment of any organism's genome (a so-called "micro-genome") can faithfully identify and help to classify every species on the planet. The fear that species are becoming extinct before they have ever been known fuels barcoders, and the speed, scope, economy and "user-friendliness" claimed for DNA barcoding, as part of the larger ferment around the "genomics revolution", has also encouraged promises that it could inspire humanity to reverse its biodiversity-destructive habits. This book is based on six years of ethnographic research on changing practices in the identification and classification of natural species. Informed both by Science and Technology Studies (STS) and the anthropology of science, the authors analyse DNA barcoding in the context of a sense of crisis concerning global biodiversity loss, but also the felt inadequacy of taxonomic science to address such loss. The authors chart the specific changes that this innovation is propelling in the collecting, organizing, analyzing, and archiving of biological specimens and biodiversity data. As they do so they highlight the many questions, ambiguities and contradictions that accompany the quest to create a genomics-based environmental technoscience dedicated to biodiversity protection. They ask what it might mean to recognise ambiguity, contradiction, and excess more publicly as a constitutive part of this and other genomic technosciences. Barcoding Nature will be of interest to students and scholars of sociology of science, science and technology studies, politics of the environment, genomics and post-genomics, philosophy and history of biology, and the anthropology of science.
Download or read book Fruit Flies of Economic Significance written by Ian M. White and published by Cab International. This book was released on 1992 with total page 601 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents biosystematic information on fruit flies of the world that are of economic importance, and includes host data for about 250 species, as well as illustrated keys to adults, distribution data and recent references for over 100 of these species. In addition there is extensive coverage of larval stages, with the inclusion of keys separating the final instar larvae of over 60 species and detailed new descriptions of 34 of these species. As a whole, the book is a comprehensive identification guide to fruit fly pests across many temperate regions and will be invaluable to entomologists and pest control specialists.
Download or read book Biocode written by Dawn Field and published by OUP Oxford. This book was released on 2015-03-26 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: The living world runs on genomic software - what Dawn Field and Neil Davies call the 'biocode' - the sum of all DNA on Earth. In Biocode, they tell the story of a new age of scientific discovery: the growing global effort to read and map the biocode, and what that might mean for the future. The structure of DNA was identified in 1953, and the whole human genome was mapped by 2003. Since then the new field of genomics has mushroomed and is now operating on an industrial scale. Genomes can now be sequenced rapidly and increasingly cheaply. The genomes of large numbers of organisms from mammals to microbes, have been mapped. Getting your genome sequenced is becoming affordable for many. You too can check paternity, find out where your ancestors came from, or whether you are at risk of some diseases. Some check out the pedigree of their pets, while others turn genomes into art. A stray hair is enough to crudely reconstruct the face of the owner. From reading to constructing: the first steps to creating artificial life have already been taken. Some may find the rapidity of developments, and the potential for misuse, alarming. But they also open up unprecedented possibilities. The ability to read DNA has changed how we view ourselves and understand our place in nature. From the largest oceans, to the insides of our guts, we are able to explore the biosphere as never before, from the genome up. Sequencing technology has made the invisible world of microbes visible, and biodiversity genomics is revealing whole new worlds within us and without. The findings are transformational: we are all ecosystems now. Already the first efforts at 'barcoding' entire ecological communities and creating 'genomic observatories' have begun. The future, the authors argue, will involve biocoding the entire planet.
Download or read book Nonmammalian Genomic Analysis written by Bruce Birren and published by Academic Press. This book was released on 1996-09-25 with total page 369 pages. Available in PDF, EPUB and Kindle. Book excerpt: Offering detailed protocols for those needing to construct a variety of maps and isolate genes, this unique book is intended to popularize the new techniques of genome analysis derived from the Human Genome Project. The power of these new methods is often most striking when applied to problems outside of human genetics, particularly the nonmammalian systems on which many researchers focus. Many of these organisms are economically important and biologically rich.Nonmammalian Genomic Analysis: A Practical Guide covers the "how to" aspects of preparation, handling, cloning, and analysis of large DNA and the creation of chromosome and genome maps. This lab manual facilitates the transfer of these technologies to small "low tech" environments and allows them to be used by those with no background in genome mapping or large-fragment cloning. Like having a local expert, this collection provides procedures for anyone, anywhere, and allows the replication of others' success. - Includes detailed and clearly-written step-by-step protocols - Evinces expected results and offers trouble shooting advice - Provides techniques appropriate for small laboratories as well as those with limited resources - Covers a broad variety of cloning systems, including single copy vectors - Discusses a diverse range of organisms, from prokaryotes to eukaryotes, from single-celled organisms to highly complex organisms
