Download or read book 3D Organization of Eukaryotic and Prokaryotic Genomes written by Andreas Hofmann and published by . This book was released on 2020* with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Unravelling Genome Structure and Function Through Experimentally Informed Polymer Models written by Tatyana Pichugina and published by . This book was released on 2015 with total page 172 pages. Available in PDF, EPUB and Kindle. Book excerpt: The genome is the primary information storage system of the cell. However, it is not fully established how eukaryotic and prokaryotic genomes are organized and function within cells. To fill this gap I used experimentally informed polymer models to reconstruct the 3D structures of the Schizosaccharomyces pombe and Escherichia coli genomes. I generated 3D models of the E. coli chromosome that were non-specifically compressed within cells. These models have shown that at the scales of several kb the E. coli chromosome organization cannot be described as random chromosome packing, while at scales starting from several tens of kb the E. coli chromosome is highly mixed and entangled. The polymer models of the S. pombe genome provided evidence that chromosomal interactions, detected by conformation capture experiments, play a structural role in S. pombe genome organization. I used ensembles of the S. pombe genome structures to construct 3D maps of genes, epigenetic marks, and replication origins. The 3D maps demonstrated that the S. pombe genome is highly compartmentalized. I found that highly transcribed genes and active epigenetic marks (H3K4me) are preferentially located toward the S. pombe nuclear interior, and inactive epigenetic mark (H3K9me) towards the nuclear periphery. The 3D maps of genetic elements that I generated represent a significant step towards the development of unified models for spatial gene regulation, DNA repair and replication.
Download or read book Bacterial Chromatin written by Remus T. Dame and published by Springer Nature. This book was released on with total page 654 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Organization of the Prokaryotic Genome written by Robert L. Charlebois and published by . This book was released on 1999 with total page 378 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The 3D structure of the Escherichia Coli Nucleoid Through One Division written by Rachel Bowden and published by . This book was released on 2014 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: The three-dimensional (3D) architecture of both eukaryotic and prokaryotic genomes acts to reflect its functional state, but also plays a role in its regulation in terms of replication, recombination, chromosome segregation, and cell division (Dame, Kalmykowa et al. 2011; Thanbichler, Wang et al. 2005). It has become increasingly evident that chromosomal interactions with both each other and other nucleoid components play a critical role within this dynamic relationship between nucleoid organization and genome function in bacteria (Thanbichler, Wang et al. 2005). In addition to its obvious role as a the container for the genetic and biochemical material essential for life, the question remains as to whether bacterial cell shape has a functional contribution in regards to cellular functions including growth, adaptation and division. Previous work achieved an unbiased change in Escherichia coli (E. coli) cell shape by confining single cells within microchambers and forcing them to grow into the corresponding shape of the chamber (Takeuchi, Diluzio et al. 2005). The aim of the original project was to produce both circular and rod shaped E. coli cells in the absence of any genetic mutation based on the method by Takeuchi et al (2005), and subsequently perform Genome Conformation Capture (GCC) and RNA isolation. This would have allowed isolation of the effects of cell shape and concentration effects on both nucleoid structure and genome function. However, unexpected negative results meant that the original aims of this project could not be achieved. Previous works used a mixture of synchronized and non-synchronized prokaryotic cells to study genome organization (Cagliero, Grand et al. 2013; Umbarger, Toro et al. 2011). They both identified linkages between structure and functional outcomes, in particular regarding replication and transcription. However, neither addressed the issue of how structural nucleoid changes are linked to temporal progression through growth stages. Therefore, the aim of the second project was to identify any changes in the global nucleoid structure of an E. coli cell during progression from stationary phase through to cell division, and if these changes relate to transcription. To address this question, a population of E. coli cells was synchronized by passage through stationary phase (adapted from Cutler and Evans 1966), and were subsequently allowed to grow through one generation time. I used GCC and RNA-sequencing to isolate network connectivity maps and the transcriptome of the nucleoid at fixed points; the initial point being when cells were in stationary phase and the final point being just prior to cell division. The results from this experiment provide an understanding of the nucleoid geometry at the micron scale, consistent with the view that the nucleoid has a linearly arranged sausage-shaped structure with a temporally-conserved 'well-selfattached core' (Viollier, Thanbichler et al. 2004; Toro and Shapiro 2010). Moreover, the detection of both long and short distance interactions is consistent with previous work involving empirical measures and modeling which indicated that intra-nucleoid interactions play an important role in the E. coli nucleoid structure (Wiggins, Cheveralls et al. 2010).
Download or read book Genomes 3 written by Terence A. Brown and published by Garland Science. This book was released on 2007 with total page 736 pages. Available in PDF, EPUB and Kindle. Book excerpt: The VitalBook e-book version of Genomes 3 is only available in the US and Canada at the present time. To purchase or rent please visit http://store.vitalsource.com/show/9780815341383 Covering molecular genetics from the basics through to genome expression and molecular phylogenetics, Genomes 3is the latest edition of this pioneering textbook. Updated to incorporate the recent major advances, Genomes 3 is an invaluable companion for any undergraduate throughout their studies in molecular genetics. Genomes 3 builds on the achievements of the previous two editions by putting genomes, rather than genes, at the centre of molecular genetics teaching. Recognizing that molecular biology research was being driven more by genome sequencing and functional analysis than by research into genes, this approach has gathered momentum in recent years.
Download or read book CELL GEOMETRY written by G. V. SHIVASHANKAR and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Genomes 4 written by T. A. Brown and published by Garland Science. This book was released on 2018-12-07 with total page 520 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomes 4 has been completely revised and updated. It is a thoroughly modern textbook about genomes and how they are investigated. As with Genomes 3, techniques come first, then genome anatomies, followed by genome function, and finally genome evolution. The genomes of all types of organism are covered: viruses, bacteria, fungi, plants, and animals including humans and other hominids. Genome sequencing and assembly methods have been thoroughly revised including a survey of four genome projects: human, Neanderthal, giant panda, and barley. Coverage of genome annotation emphasizes genome-wide RNA mapping, with CRISPR-Cas 9 and GWAS methods of determining gene function covered. The knowledge gained from these techniques forms the basis of the three chapters that describe the three main types of genomes: eukaryotic, prokaryotic (including eukaryotic organelles), and viral (including mobile genetic elements). Coverage of genome expression and replication is truly genomic, concentrating on the genome-wide implications of DNA packaging, epigenome modifications, DNA-binding proteins, non-coding RNAs, regulatory genome sequences, and protein-protein interactions. Also included are applications of transcriptome analysis, metabolomics, and systems biology. The final chapter is on genome evolution, focusing on the evolution of the epigenome, using genomics to study human evolution, and using population genomics to advance plant breeding. Established methods of molecular biology are included if they are still relevant today and there is always an explanation as to why the method is still important. Each chapter has a set of short-answer questions, in-depth problems, and annotated further reading. There is also an extensive glossary. Genomes 4 is the ideal text for upper level courses focused on genomes and genomics.
Download or read book The Kiwifruit Genome written by Raffaele Testolin and published by Springer. This book was released on 2016-05-02 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the basic botanical features of kiwifruit and its wild relatives, reports on the steps that led to its genome sequencing, and discusses the results obtained with the assembly and annotation. The core chapters provide essential insights into the main gene families that characterize this species as a crop, including the genes controlling sugar and starch metabolism, pigment biosynthesis and degradation, the ascorbic-acid pathway, fruit softening and postharvest metabolism, allergens, and resistance to pests and diseases. The book offers a valuable reference guide for taxonomists, geneticists and horticulturists. Further, since information gained from the genome sequence is extraordinarily useful in assessing the breeding value of individuals based on whole-genome scans, it will especially benefit plant breeders. Accordingly, chapters are included that focus on gene introgression from wild relatives and genome-based breeding.
Download or read book Chemical Biology of the Genome written by Siddhartha Roy and published by Academic Press. This book was released on 2021-05-14 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical Biology of the Genome provides a comprehensive overview of essential concepts and principles of genomic and epigenomics dynamics as explored through the lens of chemical biology. Key examples and case studies illustrate chemical biology methods for study and analysis of the genome and epigenome, with an emphasis on relevance to physiological and pathophysiological processes and drug discovery. Authors and international leaders in biochemical studies of the genome, Drs. Siddhartha Roy and Tapas Kundu, adopt an integrated, interdisciplinary approach throughout, demonstrating how fast evolving chemical and mass-scale sequencing tools are increasingly used to interpret biochemical processes of the genome. Later sections discuss chemical modifications of the genome, DNA sequence recognition by proteins and gene regulation, GWAS and EpiGWAS studies, 3D architecture of the genome, and functional genome architecture. In-depth, discovery focused chapters examine intervention in gene networks using SiRNA/ShRNA, miRNA, and anti-miR, small molecule modulation of iPS, drug resistance pathways altered DNA methylation as drug targets, anti-miR as therapeutics, and nanodelivery of drugs. - Offers an interdisciplinary discussion of the chemical biology of the genome and epigenome, employing illustrative case studies in both physiological and pathophysiological contexts - Supports researchers in employing chemical and mass-scale sequencing approaches to interpret genomic and epigenomic dynamics - Highlights innovative pathways and molecular targets for new disease study and drug discovery
Download or read book Chromosome Structure and Aberrations written by Tariq Ahmad Bhat and published by Springer. This book was released on 2017-02-08 with total page 377 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a compilation of various chapters contributed by a group of leading researchers from different countries and covering up to date information based on published reports and personal experience of authors in the field of cytogenetics. Beginning with the introduction of chromosome, the subsequent chapters on organization of genetic material, karyotype evolution, structural and numerical variations in chromosomes, B-chromosomes and chromosomal aberrations provide an in-depth knowledge and easy understanding of the subject matter. A special feature of the book is the inclusion of a series of chapters on various types of chromosomal aberrations and their impact on breeding behaviour and crop improvement. The possible mechanism, their consequences and role in genetic analysis has been emphasized in these chapters. A few chapters have also been dedicated on various techniques routinely used in the laboratory by students and researchers. Each chapter ends with an extensive bibliography so that the students and researchers may find it relevant to consult more literature on the subject than a book of this size can offer. The book is intended to fulfill the needs of undergraduate and post graduate students of botany, zoology and agriculture besides, teachers and researchers engaged in the field of genetics, cytogenetics, and molecular genetics. In general the readers will find each chapter of the book informative and easy to understand.
Download or read book HiC Pro an Optimized and Flexible Pipeline for Hi C Data Processing written by Oldenburg Oldenburg Press and published by . This book was released on 2016-01-29 with total page 40 pages. Available in PDF, EPUB and Kindle. Book excerpt: HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant/HiC-Pro.
Download or read book Prokaryotic Cytoskeletons written by Jan Löwe and published by Springer. This book was released on 2017-05-11 with total page 457 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the structures and functions of active protein filaments, found in bacteria and archaea, and now known to perform crucial roles in cell division and intra-cellular motility, as well as being essential for controlling cell shape and growth. These roles are possible because the cytoskeletal and cytomotive filaments provide long range order from small subunits. Studies of these filaments are therefore of central importance to understanding prokaryotic cell biology. The wide variation in subunit and polymer structure and its relationship with the range of functions also provide important insights into cell evolution, including the emergence of eukaryotic cells. Individual chapters, written by leading researchers, review the great advances made in the past 20-25 years, and still ongoing, to discover the architectures, dynamics and roles of filaments found in relevant model organisms. Others describe one of the families of dynamic filaments found in many species. The most common types of filament are deeply related to eukaryotic cytoskeletal proteins, notably actin and tubulin that polymerise and depolymerise under the control of nucleotide hydrolysis. Related systems are found to perform a variety of roles, depending on the organisms. Surprisingly, prokaryotes all lack the molecular motors associated with eukaryotic F-actin and microtubules. Archaea, but not bacteria, also have active filaments related to the eukaryotic ESCRT system. Non-dynamic fibres, including intermediate filament-like structures, are known to occur in some bacteria.. Details of known filament structures are discussed and related to what has been established about their molecular mechanisms, including current controversies. The final chapter covers the use of some of these dynamic filaments in Systems Biology research. The level of information in all chapters is suitable both for active researchers and for advanced students in courses involving bacterial or archaeal physiology, molecular microbiology, structural cell biology, molecular motility or evolution. Chapter 3 of this book is open access under a CC BY 4.0 license.
Download or read book Sequence Evolution Function written by Eugene V. Koonin and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.
Download or read book DNA written by James D. Watson and published by Knopf. This book was released on 2009-01-21 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fifty years ago, James D. Watson, then just twentyfour, helped launch the greatest ongoing scientific quest of our time. Now, with unique authority and sweeping vision, he gives us the first full account of the genetic revolution—from Mendel’s garden to the double helix to the sequencing of the human genome and beyond. Watson’s lively, panoramic narrative begins with the fanciful speculations of the ancients as to why “like begets like” before skipping ahead to 1866, when an Austrian monk named Gregor Mendel first deduced the basic laws of inheritance. But genetics as we recognize it today—with its capacity, both thrilling and sobering, to manipulate the very essence of living things—came into being only with the rise of molecular investigations culminating in the breakthrough discovery of the structure of DNA, for which Watson shared a Nobel prize in 1962. In the DNA molecule’s graceful curves was the key to a whole new science. Having shown that the secret of life is chemical, modern genetics has set mankind off on a journey unimaginable just a few decades ago. Watson provides the general reader with clear explanations of molecular processes and emerging technologies. He shows us how DNA continues to alter our understanding of human origins, and of our identities as groups and as individuals. And with the insight of one who has remained close to every advance in research since the double helix, he reveals how genetics has unleashed a wealth of possibilities to alter the human condition—from genetically modified foods to genetically modified babies—and transformed itself from a domain of pure research into one of big business as well. It is a sometimes topsy-turvy world full of great minds and great egos, driven by ambitions to improve the human condition as well as to improve investment portfolios, a world vividly captured in these pages. Facing a future of choices and social and ethical implications of which we dare not remain uninformed, we could have no better guide than James Watson, who leads us with the same bravura storytelling that made The Double Helix one of the most successful books on science ever published. Infused with a scientist’s awe at nature’s marvels and a humanist’s profound sympathies, DNA is destined to become the classic telling of the defining scientific saga of our age.
Download or read book Long Range Control of Gene Expression written by Veronica van Heyningen and published by Academic Press. This book was released on 2011-09-02 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: Long-Range Control of Gene Expression covers the current progress in understanding the mechanisms for genomic control of gene expression, which has grown considerably in the last few years as insight into genome organization and chromatin regulation has advanced. Discusses the evolution of cis-regulatory sequences in drosophila Includes information on genomic imprinting and imprinting defects in humans Includes a chapter on epigenetic gene regulation in cancer
