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Use Of High Throughput Sequencing For The Characterization Of Extracellular Rna And To Study The Dynamics Of Bacterial Rna Modification
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Book Synopsis Use of High-throughput Sequencing for the Characterization of Extracellular RNA and to Study the Dynamics of Bacterial RNA Modification by : Adeline Galvanin
Download or read book Use of High-throughput Sequencing for the Characterization of Extracellular RNA and to Study the Dynamics of Bacterial RNA Modification written by Adeline Galvanin and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Genome-wide Studies of DNA and RNA with Modifications Through High-throughput Sequencing Analysis by : Blythe S. Moreland
Download or read book Genome-wide Studies of DNA and RNA with Modifications Through High-throughput Sequencing Analysis written by Blythe S. Moreland and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA/RNA-protein interactions are crucial to the maintenance, processing, and regulation of the genetic information contained within a cell. Sets of particular DNA/RNA-protein interactions can confer specificity to a protein's binding behavior, which makes the consideration of DNA and RNA with modifications interesting in how they alter the landscape of interactions. High-throughput sequencing (HTS) techniques of DNA and RNA can offer unmatched genome-wide characterizations of where and how proteins interact with DNA and RNA by generating libraries of millions of reads that can capture the whole distribution of these interaction events. In this dissertation we used HTS analysis techniques to probe the location and state of two nucleic acid modifications on a genome-wide scale: The methylation of Cytosines in the CpG dinucleotide (mCpG) in the human genome, and the nucleotide addition by 3'-5' polymerases to the 5'-ends of RNAs. In the case of DNA methylation, the sequencing data represents DNA fragments enriched in mCpGs by way of interaction with the methyl-CpG-binding domain (MBD) protein MBD2. In the case of 5'-end nucleotide addition, the sequencing data is a snapshot of non-coding RNAs whose 5'-ends may have been extended by a Thg1-like protein (TLP). In both sets of studies, the information about the modification in turn conveys information on the relevant DNA-protein and RNA-protein interactions, and what sequences or structures are preferred by the proteins reading or depositing the modifications. In Chapter 2, a deep sample of methylated genomic DNA allows us to characterize the sequence, spacing, and mCpG density biases introduced through MBD2 interaction during a protein pulldown experiment. In Chapter 3, we use the characterizations of those interactions -- the 3 bp minimum separation between mCpGs, the nonlinear relationship between mCpG number and pulldown efficiency -- to build a model to predict expected pulldown from a SssI Control sample, which is then used to increase the accuracy of methylation quantification from MBD pulldown data. We find that the use of our pulldown alignment model of an SssI Control data set is suitable for substitution for observed SssI Control data with use of the empirical Bayes' model BayMeth. In Chapter 4, we pivot to developing a HTS screen for unknown substrates of TLPs, BtTLP and DdiTLP4, by detecting changes in 5'-end composition under different TLP conditions. Importantly, we detect BtTLP's activity on tRNA-His, of U-1 addition, which sufficiently allows for the tRNA's essential recognition by Histidyl-tRNA synthetase (HisRS). HTS techniques and analysis will continue to improve our ability to differentiate the distributions of DNA/RNA-protein interactions between "background" and "modified" states of nucleic acids.
Book Synopsis Epitranscriptomics: The Novel RNA Frontier by : Giovanni Nigita
Download or read book Epitranscriptomics: The Novel RNA Frontier written by Giovanni Nigita and published by Frontiers Media SA. This book was released on 2019-01-31 with total page 127 pages. Available in PDF, EPUB and Kindle. Book excerpt: Following the formulation of the central dogma of molecular biology and the later discovery of classes of non-coding RNAs, the primary focus of Genetics was essentially on variation of DNA aiming at elucidating biological pathways perturbed in diseases. Recently, extensive attention has shifted towards the study of posttranscriptional RNA modifications occurring in both protein-coding as well as non-coding RNAs, revealing a novel and finer layer of complexity in gene regulation. This, in turn, has led to the birth of the novel field of ‘Epitranscriptomics’. The recent increase of applications of high-throughput sequencing technology (HTS) has allowed the unprecedented opportunity to identify on a transcriptome-wide scale, millions of RNA modifications in human genes, counting today more than 140 distinct types such as: methylation (e.g. m6A, m1A, m5C, hm5C, 2’OMe) methylation (e.g. m6A, m1A, m5C, hm5C, 2’OMe), pseudourylation (?), deamination (e.g. A-to-I RNA editing). The scope of this Research Topic was to collect both reviews and research articles addressing the wet lab approaches and bioinformatics methodologies necessary to aid in the identification of novel RNA modifications and characterization of their biological functions. Among the articles embracing the aim of the Research Topic, we have collected four original research and methods articles, five reviews, and a technology article.
Author :National Academies of Sciences Engineering and Medicine Publisher : ISBN 13 :9780309706957 Total Pages :0 pages Book Rating :4.7/5 (69 download)
Book Synopsis Charting a Future for Sequencing RNA and Its Modifications by : National Academies of Sciences Engineering and Medicine
Download or read book Charting a Future for Sequencing RNA and Its Modifications written by National Academies of Sciences Engineering and Medicine and published by . This book was released on 2024-11-21 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Concerted efforts to deepen understanding of RNA modifications and their role in living systems hold the potential to advance human health, improve crop yields, and address other pressing societal challenges. RNA, which carries the information encoded by DNA to the places where it is needed, is amazingly diverse and dynamic. RNA is processed and modified through natural biological pathways, giving rise to hundreds, in some cases thousands, of distinct RNA molecules for each gene, thereby diversifying genetic information. RNA modifications are known to be pivotal players in nearly all biological processes, and their dysregulation has been implicated in a wide range of human diseases and disorders. Yet, our knowledge of RNA modifications remains incomplete, hindered by current technological limitations. Existing methods cannot discover all RNA modifications, let alone comprehensively sequence them on every RNA molecule. Nonetheless, what is known about RNA modifications has already been leveraged in the development of vaccines that helped saved millions of lives worldwide during the COVID-19 pandemic. RNA modifications also have applications beyond health, for example, enhancing agricultural productivity. Charting a Future for Sequencing RNA and Its Modifications: A New Era for Biology and Medicine calls for a focused, large-scale effort to accelerate technological innovation to harness the full potential of RNA modifications to address pressing societal challenges in health, agriculture, and beyond. This report assesses the scientific and technological breakthroughs, workforce, and infrastructure needs to sequence RNA and its modifications, and ultimately understand the roles RNA modifications play in biological processes and disease. It proposes a roadmap of innovation that will make it possible for any RNA from any biological system to be sequenced end-to-end with all of its modifications - a capability that could lead to more personalized and targeted treatments and instigate transformative changes across various sectors beyond health and medicine.
Book Synopsis RNA Modifications: Impact on Protein Binding, Co-transcriptional Regulation, and Sequencing Signatures by : Katherine Ismei Zhou
Download or read book RNA Modifications: Impact on Protein Binding, Co-transcriptional Regulation, and Sequencing Signatures written by Katherine Ismei Zhou and published by . This book was released on 2018 with total page 195 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene expression is controlled by a complex and interconnected regulatory system. In this thesis, I explore how RNA modifications impact protein binding, co-transcriptional regulation, and sequencing signatures. The cellular functions of the abundant messenger RNA (mRNA) modification N6-methyladenosine (m6A) are mediated by m6A reader proteins. Some m6A reader proteins selectively bind m6A-modified RNAs by recognizing motifs that become accessible upon an m6A-induced change in RNA structure. In Chapter 2, I use biophysical methods to examine how m6A modification alters the structure of an RNA hairpin to enhance binding of the protein heterogeneous nuclear ribonucleoprotein C (hnRNPC). In Chapter 3, I describe the discovery of another m6A reader protein, hnRNPG, which binds to a motif that becomes exposed upon m6A modification of an RNA hairpin. Unlike hnRNPC, hnRNPG binds to a motif that includes the m6A site. Moreover, hnRNPG uses Arg-Gly-Gly (RGG) repeats in a low-complexity region to selectively bind to m6A-modified RNA. In Chapter 4, I explore the cellular functions of hnRNPG binding to m6A-modified RNAs. The hnRNPG protein binds to the phosphorylated C-terminal domain of RNA polymerase II and to nascent m6A-modified RNA for co-transcriptional, m6A-dependent gene regulation. In Chapter 5, I build on existing sequencing methods for the detection of another RNA modification, pseudouridine (Psi). This work spans a variety of perspectives on the impact of RNA modifications, from a biophysical study of the effect of m6 A on RNA structure and protein binding, to an investigation of the cellular functions of m6A in gene regulation, to method development for the detection of pseudouridines in high-throughput sequencing data. Together, these diverse perspectives demonstrate the widespread impact of RNA modifications.
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:
Book Synopsis Regulating with RNA in Bacteria and Archaea by : Gisela Storz
Download or read book Regulating with RNA in Bacteria and Archaea written by Gisela Storz and published by John Wiley & Sons. This book was released on 2018-11-01 with total page 1065 pages. Available in PDF, EPUB and Kindle. Book excerpt: Revealing the many roles of RNA in regulating gene expression For decades after the discoveries of messenger RNA, transfer RNA, and ribosomal RNA, it was largely assumed that the role of RNA in the cell was limited to shuttling the genomic message, chaperoning amino acids, and toiling in the ribosomes. Eventually, hints that RNA molecules might have regulatory roles began to appear. With the advent of genomics and bioinformatics, it became evident that numerous other RNA forms exist and have specific functions, including small RNAs (sRNA), RNA thermometers, and riboswitches to regulate core metabolic pathways, bacterial pathogenesis, iron homeostasis, quorum sensing, and biofilm formation. All of these functions, and more, are presented in Regulating with RNA in Bacteria and Archaea, written by RNA biologists from around the globe. Divided into eight sections-RNases and Helicases, Cis-Acting RNAs, Cis Encoded Base Pairing RNAs, Trans-Encoded Base Pairing RNAs, Protein Titration and Scaffolding, General Considerations, Emerging Topics, and Resources-this book serves as an excellent resource for established RNA biologists and for the many scientists who are studying regulated cellular systems. It is no longer a fair assumption that gene expression regulation is the provenance of proteins only or that control is exerted primarily at the level of transcription. This book makes clear that regulatory RNAs are key partners along with proteins in controlling the complex interactions and pathways found within prokaryotes.
Book Synopsis The New Science of Metagenomics by : National Research Council
Download or read book The New Science of Metagenomics written by National Research Council and published by National Academies Press. This book was released on 2007-06-24 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.
Book Synopsis Flow Cytometry by : Alice Longobardi Givan
Download or read book Flow Cytometry written by Alice Longobardi Givan and published by John Wiley & Sons. This book was released on 2013-04-10 with total page 309 pages. Available in PDF, EPUB and Kindle. Book excerpt: Flow cytometry continually amazes scientists with its ever-expanding utility. Advances in flow cytometry have opened new directions in theoretical science, clinical diagnosis, and medical practice. The new edition of Flow Cytometry: First Principles provides a thorough update of this now classic text, reflecting innovations in the field while outlining the fundamental elements of instrumentation, sample preparation, and data analysis. Flow Cytometry: First Principles, Second Edition explains the basic principles of flow cytometry, surveying its primary scientific and clinical applications and highlighting state-of-the-art techniques at the frontiers of research. This edition contains extensive revisions of all chapters, including new discussions on fluorochrome and laser options for multicolor analysis, an additionalsection on apoptosis in the chapter on DNA, and new chapters onintracellular protein staining and cell sorting, including high-speed sorting and alternative sorting methods, as well as traditional technology. This essential resource: Assumes no prior knowledge of flow cytometry Progresses with an informal, engaging lecture style from simpleto more complex concepts Offers a clear introduction to new vocabulary, principles of instrumentation, and strategies for data analysis Emphasizes the theory relevant to all flow cytometry, with examples from a variety of clinical and scientific fields Flow Cytometry: First Principles, Second Edition provides scientists, clinicians, technologists, and students with the knowledge necessary for beginning the practice of flow cytometry and for understanding related literature.
Book Synopsis RNA-RNA Interactions by : Frank J. Schmidt
Download or read book RNA-RNA Interactions written by Frank J. Schmidt and published by Humana Press. This book was released on 2014-10-29 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this volume expert researchers in the field detail many of the methods which are now commonly used to study RNA. These methods are presented as a guidebook to scientists who are experienced with RNA research and want to brush up on a new technique. 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 key tips on troubleshooting and avoiding known pitfalls. Thorough and intuitive, RNA-RNA Interactions: Methods and Protocols guides scientists investigating biological systems and studying RNA.
Book Synopsis RNA Infrastructure and Networks by : Lesley J. Collins
Download or read book RNA Infrastructure and Networks written by Lesley J. Collins and published by Springer Science & Business Media. This book was released on 2011-09-15 with total page 297 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNAs form complexes with proteins and other RNAs. The RNA‐infrastructure represents the spatiotemporal interaction of these proteins and RNAs in a cell‐wide network. RNA Infrastructure and Networks brings together these ideas to illustrate the scope of RNA‐based biology, and how connecting RNA mechanisms is a powerful tool to investigate regulatory pathways. This book is but a taste of the wide range of RNA‐based mechanisms that connect in the RNA infrastructure.
Download or read book Bacteriophages written by David R. Harper and published by Springer Nature. This book was released on 2021-01-30 with total page 1376 pages. Available in PDF, EPUB and Kindle. Book excerpt: This first major reference work dedicated to the mannifold industrial and medical applications of bacteriophages provides both theoretical and practical insights into the emerging field of bacteriophage biotechnology. The book introduces to bacteriophage biology, ecology and history and reviews the latest technologies and tools in bacteriophage detection, strain optimization and nanotechnology. Usage of bacteriophages in food safety, agriculture, and different therapeutic areas is discussed in detail. This book serves as essential guide for researchers in applied microbiology, biotechnology and medicine coming from both academia and industry.
Book Synopsis Virulence Mechanisms of Bacterial Pathogens by : Indira T. Kudva
Download or read book Virulence Mechanisms of Bacterial Pathogens written by Indira T. Kudva and published by John Wiley & Sons. This book was released on 2020-07-10 with total page 871 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ground-breaking overview of an enduring topic Despite the use of antibiotics, bacterial diseases continue to be a critical issue in public health, and bacterial pathogenesis remains a tantalizing problem for research microbiologists. This new edition of Virulence Mechanisms of Bacterial Pathogens broadly covers the knowledge base surrounding this topic and presents recently unraveled bacterial virulence strategies and cutting-edge therapies. A team of editors, led by USDA scientist Indira Kudva, compiled perspectives from experts to explain the wide variety of mechanisms through which bacterial pathogens cause disease: the host interface, host cell enslavement, and bacterial communication, secretion, defenses, and persistence. A collection of reviews on targeted therapies rounds out the seven sections of this unique book. The new edition provides insights into some of the most recent advances in the area of bacterial pathogenesis, including how metabolism shapes the host-pathogen interface interactions across species and genera mechanisms of the secretion systems evasion, survival, and persistence mechanisms new therapies targeting various adaptive and virulence mechanisms of bacterial pathogens Written to promote discussion, extrapolation, exploration, and multidimensional thinking, Virulence Mechanisms of Bacterial Pathogens serves as a textbook for graduate courses on bacterial pathogenesis and a resource for specialists in bacterial pathogenicity, such as molecular biologists, physician scientists, infectious disease clinicians, dental scientists, veterinarians, molecular biologists, industry researchers, and technicians.
Book Synopsis Deep Learning for Cancer Diagnosis by : Utku Kose
Download or read book Deep Learning for Cancer Diagnosis written by Utku Kose and published by Springer Nature. This book was released on 2020-09-12 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explores various applications of deep learning to the diagnosis of cancer,while also outlining the future face of deep learning-assisted cancer diagnostics. As is commonly known, artificial intelligence has paved the way for countless new solutions in the field of medicine. In this context, deep learning is a recent and remarkable sub-field, which can effectively cope with huge amounts of data and deliver more accurate results. As a vital research area, medical diagnosis is among those in which deep learning-oriented solutions are often employed. Accordingly, the objective of this book is to highlight recent advanced applications of deep learning for diagnosing different types of cancer. The target audience includes scientists, experts, MSc and PhD students, postdocs, and anyone interested in the subjects discussed. The book can be used as a reference work to support courses on artificial intelligence, medical and biomedicaleducation.
Book Synopsis Encyclopedia of Bioinformatics and Computational Biology by :
Download or read book Encyclopedia of Bioinformatics and Computational Biology written by and published by Elsevier. This book was released on 2018-08-21 with total page 3421 pages. Available in PDF, EPUB and Kindle. Book excerpt: Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases
Book Synopsis Advanced Healthcare Materials by : Ashutosh Tiwari
Download or read book Advanced Healthcare Materials written by Ashutosh Tiwari and published by John Wiley & Sons. This book was released on 2014-05-09 with total page 421 pages. Available in PDF, EPUB and Kindle. Book excerpt: Offers a comprehensive and interdisciplinary view of cutting-edge research on advanced materials for healthcare technology and applications Advanced healthcare materials are attracting strong interest in fundamental as well as applied medical science and technology. This book summarizes the current state of knowledge in the field of advanced materials for functional therapeutics, point-of-care diagnostics, translational materials, and up-and-coming bioengineering devices. Advanced Healthcare Materials highlights the key features that enable the design of stimuli-responsive smart nanoparticles, novel biomaterials, and nano/micro devices for either diagnosis or therapy, or both, called theranostics. It also presents the latest advancements in healthcare materials and medical technology. The senior researchers from global knowledge centers have written topics including: State-of-the-art of biomaterials for human health Micro- and nanoparticles and their application in biosensors The role of immunoassays Stimuli-responsive smart nanoparticles Diagnosis and treatment of cancer Advanced materials for biomedical application and drug delivery Nanoparticles for diagnosis and/or treatment of Alzheimers disease Hierarchical modelling of elastic behavior of human dental tissue Biodegradable porous hydrogels Hydrogels in tissue engineering, drug delivery, and wound care Modified natural zeolites Supramolecular hydrogels based on cyclodextrin poly(pseudo)rotaxane Polyhydroxyalkanoate-based biomaterials Biomimetic molecularly imprinted polymers
Book Synopsis Mechanisms of antibiotic resistance by : Jun Lin
Download or read book Mechanisms of antibiotic resistance written by Jun Lin and published by Frontiers Media SA. This book was released on 2015-06-01 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: Antibiotics represent one of the most successful forms of therapy in medicine. But the efficiency of antibiotics is compromised by the growing number of antibiotic-resistant pathogens. Antibiotic resistance, which is implicated in elevated morbidity and mortality rates as well as in the increased treatment costs, is considered to be one of the major global public health threats (www.who.int/drugresistance/en/) and the magnitude of the problem recently prompted a number of international and national bodies to take actions to protect the public (http://ec.europa.eu/dgs/health_consumer/docs/road-map-amr_en.pdf: http://www.who.int/drugresistance/amr_global_action_plan/en/; http://www.whitehouse.gov/sites/default/files/docs/carb_national_strategy.pdf). Understanding the mechanisms by which bacteria successfully defend themselves against the antibiotic assault represent the main theme of this eBook published as a Research Topic in Frontiers in Microbiology, section of Antimicrobials, Resistance, and Chemotherapy. The articles in the eBook update the reader on various aspects and mechanisms of antibiotic resistance. A better understanding of these mechanisms should facilitate the development of means to potentiate the efficacy and increase the lifespan of antibiotics while minimizing the emergence of antibiotic resistance among pathogens.
