mRNA Processing, Yongsheng Shi

Автор: Shi, Yongsheng.
Название: MRNA processing :
ISBN: 1493972030 ISBN-13(EAN): 9781493972036
Издательство: Springer
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Описание: This detailed volume assembles a number of the most commonly used and state-of-the-art methodologies in the revolutionary field of mRNA processing in order to aid researchers in choosing the best method for their specific problems.

Автор: Robert E. Rhoads
Название: Synthetic mRNA
ISBN: 1493936239 ISBN-13(EAN): 9781493936236
Издательство: Springer
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Описание: This volumepresents detailed laboratory protocols for invitro synthesis of mRNA with favorable properties, its introduction intocells by a variety of techniques, and the measurement of physiological andclinical consequences such as protein replacement and cancer immunotherapy.

Автор: Klemens J. Hertel
Название: Spliceosomal Pre-mRNA Splicing
ISBN: 1627039791 ISBN-13(EAN): 9781627039796
Издательство: Springer
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Цена: 16769.00 р.
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Описание:

Part I: Introductory Chapters

1. The Pre-mRNA Splicing Reaction

Somsakul Wongpalee and Shalini Sharma

2. Diversity and Evolution of Spliceosomal Systems

Scott William Roy and Manuel Irimia

3. Mechanisms of Spliceosomal Assembly

Ni-ting Chiou and Kristen W. Lynch

4. Alternative Pre-mRNA Splicing

Stacey D. Wagner and J. Andrew Berglund

5. Regulation of Alternative Pre-mRNA Splicing

Miguel B. Coelho and Christopher W.J. Smith

6. Introduction to Co-Transcriptional RNA Splicing

Evan C. Merkhofer, Peter Hu, and Tracy L. Johnson

7. Chromatin and Splicing

Nazmul Haque and Shalini Oberdoerffer

Part II: Methods Chapters

8. Preparation of Splicing Competent Nuclear Extracts

Chiu-Ho T. Webb and Klemens J. Hertel

9. Preparation of Yeast Whole Cell Splicing Extract

Elizabeth A. Dunn and Stephen D. Rader

10. Efficient Splinted Ligation of Synthetic RNA Using RNA Ligase

Martha R. Stark and Stephen D. Rader

11. In Vitro Assay of Pre-mRNA Splicing in Mammalian Nuclear Extract

Maliheh Movassat, William F. Mueller, and Klemens J. Hertel

12. Kinetic Analysis of In Vitro Pre-mRNA Splicing in HeLa Nuclear Extract

William F. Mueller and Klemens J. Hertel

13. In Vitro Systems for Coupling RNAP II Transcription to Splicing and Polyadenylation

Eric G. Folco and Robin Reed

14. Isolation and Accumulation of Spliceosomal Assembly Intermediates

Janine O. Ilagan and Melissa S. Jurica

15. Complementation of U4 snRNA in S. cerevisiae Splicing Extracts for Biochemical Studies of snRNP Assembly and Function

Martha R. Stark and Stephen D. Rader

16. Expression and Purification of Splicing Proteins from Mammalian Cells

Eric Allemand and Michelle L. Hastings

17. Single Molecule Approaches for Studying Spliceosome Assembly and Catalysis

Eric G. Anderson and Aaron A. Hoskins

18. Cell-Based Splicing of Minigenes

Sarah A. Smith and Kristen W. Lynch

19. Quantifying the Ratio of Spliceosome Components Assembled on Pre-mRNA

Noa Neufeld, Yehuda Brody, and Yaron Shav-Tal

20. Antisense Methods to Modulate Pre-mRNA Splicing

Joonbae Seo, Eric W. Ottesen, and Ravindra N. Singh

21. Using Yeast Genetics to Study Splicing Mechanisms

Munshi Azad Hossain and Tracy L. Johnson

22. Medium Throughput Analysis of Alternative Splicing by Fluorescently Labeled RT-PCR

Ryan Percifield, Daniel Murphy, and Peter Stoilov

23. Chromatin Immunoprecipitation Approaches to Determine Co-Transcriptional Nature of Splicing

Nicole I. Bieberstein, Korinna Straube, and Karla M. Neugebauer

24. Computational Approaches to Mine Publicly Available Databases

Rodger B. Voelker, William A. Cresko, and J. Andrew Berglund

25. Approaches to Link RNA Secondary Structures with Splicing Regulation

Mireya Plass and Eduardo Eyras

26. Methods to Study Splicing from High-Throughput RNA Sequencing Data

Gael P. Alamancos, Eneritz Agirre, and Eduardo Eyras

27. Global Protein-RNA Interaction Mapping at Single Nucleotide Resolution by iCLIP-Seq

Chengguo Yao, Lingjie Weng, and Yongsheng Shi

28. Predicting Alternative Splicing

Yoseph Barash and Jorge Vaquero Garcia

Автор: Yeo Gene W.
Название: RNA Processing: Disease and Genome-Wide Probing
ISBN: 3319804847 ISBN-13(EAN): 9783319804842
Издательство: Springer
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Цена: 20962.00 р.
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Описание: Ribonucleic acid (RNA) binding proteins currently number in the thousands and defects in their function are at the heart of diseases such as cancer and neurodegeneration. RNA binding proteins have become implicated in the intricate control of surprisingly diverse biological settings, such as circadian rhythm, stem cell self-renewal, oncogenesis and germ cell development. This book surveys a range of genome-wide and systems approaches to studying RNA binding proteins, the importance of RNA binding proteins in development, cancer and circadian rhythm.

Автор: Francisco M. Couto
Название: Data and Text Processing for Health and Life Sciences
ISBN: 3030138445 ISBN-13(EAN): 9783030138448
Издательство: Springer
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Цена: 19564.00 р.
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Описание: This open access book is a step-by-step introduction on how shell scripting can help solve many of the data processing tasks that Health and Life specialists face everyday with minimal software dependencies. The examples presented in the book show how simple command line tools can be used and combined to retrieve data and text from web resources, to filter and mine literature, and to explore the semantics encoded in biomedical ontologies. To store data this book relies on open standard text file formats, such as TSV, CSV, XML, and OWL, that can be open by any text editor or spreadsheet application. The first two chapters, Introduction and Resources, provide a brief introduction to the shell scripting and describe popular data resources in Health and Life Sciences. The third chapter, Data Retrieval, starts by introducing a common data processing task that involves multiple data resources. Then, this chapter explains how to automate each step of that task by introducing the required commands line tools one by one. The fourth chapter, Text Processing, shows how to filter and analyze text by using simple string matching techniques and regular expressions. The last chapter, Semantic Processing, shows how XPath queries and shell scripting is able to process complex data, such as the graphs used to specify ontologies. Besides being almost immutable for more than four decades and being available in most of our personal computers, shell scripting is relatively easy to learn by Health and Life specialists as a sequence of independent commands. Comprehending them is like conducting a new laboratory protocol by testing and understanding its procedural steps and variables, and combining their intermediate results. Thus, this book is particularly relevant to Health and Life specialists or students that want to easily learn how to process data and text, and which in return may facilitate and inspire them to acquire deeper bioinformatics skills in the future.

Автор: Klemens J. Hertel
Название: Spliceosomal Pre-mRNA Splicing
ISBN: 149396044X ISBN-13(EAN): 9781493960446
Издательство: Springer
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Цена: 16769.00 р.
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Описание:

Part I: Introductory Chapters

1. The Pre-mRNA Splicing Reaction

Somsakul Wongpalee and Shalini Sharma

2. Diversity and Evolution of Spliceosomal Systems

Scott William Roy and Manuel Irimia

3. Mechanisms of Spliceosomal Assembly

Ni-ting Chiou and Kristen W. Lynch

4. Alternative Pre-mRNA Splicing

Stacey D. Wagner and J. Andrew Berglund

5. Regulation of Alternative Pre-mRNA Splicing

Miguel B. Coelho and Christopher W.J. Smith

6. Introduction to Co-Transcriptional RNA Splicing

Evan C. Merkhofer, Peter Hu, and Tracy L. Johnson

7. Chromatin and Splicing

Nazmul Haque and Shalini Oberdoerffer

Part II: Methods Chapters

8. Preparation of Splicing Competent Nuclear Extracts

Chiu-Ho T. Webb and Klemens J. Hertel

9. Preparation of Yeast Whole Cell Splicing Extract

Elizabeth A. Dunn and Stephen D. Rader

10. Efficient Splinted Ligation of Synthetic RNA Using RNA Ligase

Martha R. Stark and Stephen D. Rader

11. In Vitro Assay of Pre-mRNA Splicing in Mammalian Nuclear Extract

Maliheh Movassat, William F. Mueller, and Klemens J. Hertel

12. Kinetic Analysis of In Vitro Pre-mRNA Splicing in HeLa Nuclear Extract

William F. Mueller and Klemens J. Hertel

13. In Vitro Systems for Coupling RNAP II Transcription to Splicing and Polyadenylation

Eric G. Folco and Robin Reed

14. Isolation and Accumulation of Spliceosomal Assembly Intermediates

Janine O. Ilagan and Melissa S. Jurica

15. Complementation of U4 snRNA in S. cerevisiae Splicing Extracts for Biochemical Studies of snRNP Assembly and Function

Martha R. Stark and Stephen D. Rader

16. Expression and Purification of Splicing Proteins from Mammalian Cells

Eric Allemand and Michelle L. Hastings

17. Single Molecule Approaches for Studying Spliceosome Assembly and Catalysis

Eric G. Anderson and Aaron A. Hoskins

18. Cell-Based Splicing of Minigenes

Sarah A. Smith and Kristen W. Lynch

19. Quantifying the Ratio of Spliceosome Components Assembled on Pre-mRNA

Noa Neufeld, Yehuda Brody, and Yaron Shav-Tal

20. Antisense Methods to Modulate Pre-mRNA Splicing

Joonbae Seo, Eric W. Ottesen, and Ravindra N. Singh

21. Using Yeast Genetics to Study Splicing Mechanisms

Munshi Azad Hossain and Tracy L. Johnson

22. Medium Throughput Analysis of Alternative Splicing by Fluorescently Labeled RT-PCR

Ryan Percifield, Daniel Murphy, and Peter Stoilov

23. Chromatin Immunoprecipitation Approaches to Determine Co-Transcriptional Nature of Splicing

Nicole I. Bieberstein, Korinna Straube, and Karla M. Neugebauer

24. Computational Approaches to Mine Publicly Available Databases

Rodger B. Voelker, William A. Cresko, and J. Andrew Berglund

25. Approaches to Link RNA Secondary Structures with Splicing Regulation

Mireya Plass and Eduardo Eyras

26. Methods to Study Splicing from High-Throughput RNA Sequencing Data

Gael P. Alamancos, Eneritz Agirre, and Eduardo Eyras

27. Global Protein-RNA Interaction Mapping at Single Nucleotide Resolution by iCLIP-Seq

Chengguo Yao, Lingjie Weng, and Yongsheng Shi

28. Predicting Alternative Splicing

Yoseph Barash and Jorge Vaquero Garcia

Автор: Shireen R. Lamand?
Название: mRNA Decay
ISBN: 1493975390 ISBN-13(EAN): 9781493975396
Издательство: Springer
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Описание: This detailed volume explores the latest methods that can be used to probe mRNA decay pathways and identify mRNA-binding protein targets as well as miRNA targets.

Автор: Fabrice Lejeune
Название: Nonsense-Mediated mRNA Decay in Human Disease
ISBN: 0128044683 ISBN-13(EAN): 9780128044681
Издательство: Elsevier Science
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Цена: 11620.00 р.
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Описание: . Nonsense Mutation Correction in Human Diseases: An Approach for Targeted Medicine provides an introduction on genetic diseases, discusses the prevalence of nonsense mutations, the consequences of a nonsense mutation for the expression of the mutant gene, and the presentation of the nonsense-mediated mRNA decay (NMD). . It presents the mechanism of action and rationale associated with each strategy to correct nonsense mutations with the results of clinical trials to further support this basis. In addition, the book shows how it may be possible to combine several of these strategies to ultimately improve the efficiency of correction, also suggesting the future goals and objectives to improve treatment modalities in this evolving sphere of personalized medicine.

Автор: Thomas K?hler; Dirk La?ner; Anne-Katrin Rost; Barb
Название: Quantitation of mRNA by Polymerase Chain Reaction
ISBN: 3642797148 ISBN-13(EAN): 9783642797149
Издательство: Springer
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Цена: 16979.00 р.
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Описание: In this laboratory "cook-book", the authors provide a concise guide to PCR-based techniques to quantify nucleic acids in biological and clinical samples using exclusively nonradioactive detection methods, e.g.

Автор: Marlene Oeffinger; Daniel Zenklusen
Название: The Biology of mRNA: Structure and Function
ISBN: 3030314332 ISBN-13(EAN): 9783030314330
Издательство: Springer
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Описание:

Автор: Lu?sa Rom?o
Название: The mRNA Metabolism in Human Disease
ISBN: 3030199657 ISBN-13(EAN): 9783030199654
Издательство: Springer
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Цена: 19564.00 р.
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Описание: The eukaryotic gene expression pathway involves a number of interlinked steps, with messenger RNA (mRNA) being the key intermediate. The precursor mRNA is transcribed from DNA, processed by removal of introns and addition of the cap structure and the poly(A) tail. The mature mRNA is then exported to the cytoplasm where it is translated into protein and finally degraded. In this process, mRNA is associated with RNA-binding proteins forming ribonucleoprotein complexes, whose protein content evolves throughout the lifetime of the mRNA. While the complexity of eukaryotic gene expression allows the production of proteins to be controlled at many levels, it also makes the process vulnerable to errors. Although eukaryotic cells have evolved elaborate mRNA quality control mechanisms that ensure the fidelity of gene expression, some defects are not detected, thus affecting mRNA metabolism. This condition plays a fundamental role in the pathogenesis of several disease processes, such as neurodegeneration and oncogenesis. Besides, exciting recent data have shown that cellular RNAs can be modified post-transcriptionally via dynamic and reversible chemical modifications, the so-called epitranscriptome. These modifications can alter mRNA structure, being able to modulate different steps of the mRNA metabolism that can be associated with various human diseases, such as systemic lupus erythematosus and cancer. This book provides a collection of novel studies and hypotheses aimed to define the pathophysiological consequences of altered mRNA metabolism events in human cells, and is written for a wide spectrum of readers in the field of gene expression regulation. The last chapter highlights how the discovery of disease-causing defects (or modifications) in mRNA can provide a variety of therapeutic targets that can be used for the development of new RNA-based therapeutics. Hopefully, it may also contribute to inspire the drug-developing scientific community.

Автор: Shireen R. Lamand?
Название: mRNA Decay
ISBN: 1493985159 ISBN-13(EAN): 9781493985159
Издательство: Springer
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Цена: 15372.00 р.
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Описание: This detailed volume explores the latest methods that can be used to probe mRNA decay pathways and identify mRNA-binding protein targets as well as miRNA targets. Subjects include metabolic labelling and RNAseq methods for determining RNA decay rates, approaches for discovering RNA-binding protein targets, bioinformatics, miRNA targets and novel components of the miRNA-directed decay pathway, and recently developed approaches for studying nonsense-mediated mRNA decay, among other areas. Written for the highly popular 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.