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E-raamat: Functional Genomics: Methods and Protocols

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In the last decade the life sciences have evolved at a startling rate, culminating in today’s high-throughput methods in biochemistry laboratories. In this book, expert researchers focus on dynamic aspects of the transcriptome, proteome and metabolome.

Over the last decade Life Science has undergone an accelerated evolution, culminating in the -omics era characterized by the development of a multitude of high throughput methods that are becoming more routinely applied in biochemistry labs. In Functional Genomics: Methods and Protocols, Second Edition expert researchers in the field detail many of the methods which are now commonly used for studies in the life sciences focusing on the dynamic aspects of the transcriptome, proteome and metabolome, respectively.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.Authoritative and practical, Functional Genomics: Methods and Protocols, Second Edition seeks to aid scientists in establishing  or extending technologies and techniques in their laboratories.
Preface v
Contributors xi
PART I BIOINFORMATICS
1 Prediction of Protein Tertiary Structures Using MUFOLD
3(12)
Jingfen Zhang
Zhiquan He
Qingguo Wang
Bogdan Barz
Ioan Kosztin
Yi Shang
Dong Xu
2 Prediction of Protein Functions
15(10)
Roy D. Sleator
3 Genome-Wide Screens for Expressed Hypothetical Proteins
25(14)
Claus Desler
Jon Ambak Durhuus
Lene Juel Rasmussen
4 Self-Custom-Made SFP Arrays for Nonmodel Organisms
39(12)
Ron Ophir
Amir Sherman
PART II DNA ANALYSIS
5 Construction and Analysis of Full-Length and Normalized cDNA Libraries from Citrus
51(16)
M. Carmen Marques
Miguel A. Perez-Amador
6 Assembling Linear DNA Templates for In Vitro Transcription and Translation
67(12)
Viktor Stein
Miriam Kaltenbach
Florian Hollfelder
7 Automated Computational Analysis of Genome-Wide DNA Methylation Profiling Data from HELP-Tagging Assays
79(12)
Qiang Jing
Andrew McLellan
John M. Greally
Masako Suzuki
PART III RNA ANALYSIS
8 Detection of RNA Editing Events in Human Cells Using High-Throughput Sequencing
91(12)
Iouri Chepelev
9 Comparative Study of Differential Gene Expression in Closely Related Bacterial Species by Comparative Hybridization
103(18)
Ruisheng An
Parwinder S. Grewal
10 Whole-Genome RT-qPCR MicroRNA Expression Profiling
121(10)
Pieter Mestdagh
Stefaan Derveaux
Jo Vandesompele
11 Using Quantitative Real-Time Reverse Transcriptase Polymerase Chain Reaction to Validate Gene Regulation by PTTG
131(16)
Siva Kumar Panguluri
Sham S. Kakar
12 FRET-Based Real-Time DNA Microarrays
147(16)
Arjang Hassibi
Haris Vikalo
Jose Luis Riechmann
Babak Hassibi
PART IV PROTEIN ANALYSIS I: QUANTIFICATION AND IDENTIFICATION
13 2-D Gel Electrophoresis: Constructing 2D-Gel Proteome Reference Maps
163(12)
Maria Paola Simula
Agata Notarpietro
Giuseppe Toffoli
Valli De Re
14 The Use of Antigen Microarrays in Antibody Profiling
175(12)
Krisztian Papp
Jozsef Prechl
15 Limited Proteolysis in Proteomics Using Protease-Immobilized Microreactors
187(12)
Hiroshi Yamaguchi
Masaya Miyazaki
Hideaki Maeda
16 Mass Spectrometry for Protein Quantification in Biomarker Discovery
199(30)
Mu Wang
Jinsam You
PART V PROTEIN ANALYSIS II: FUNCTIONAL CHARACTERIZATION
17 High-Throughput Microtitre Plate-Based Assay for DNA Topoisomerases
229(12)
James A. Taylor
Nicolas P. Burton
Anthony Maxwell
18 Microscale Thermophoresis as a Sensitive Method to Quantify Protein: Nucleic Acid Interactions in Solution
241(12)
Karina Zillner
Moran Jerabek-Willemsen
Stefan Duhr
Dieter Braun
Gernot Langst
Philipp Baaske
19 Bioluminescence Resonance Energy Transfer: An Emerging Tool for the Detection of Protein--Protein Interaction in Living Cells
253(12)
Søren W. Gersting
Amelie S. Lotz-Havla
Ania C. Muntau
20 LuMPIS: Luciferase-Based MBP-Pull-Down Protein Interaction Screening System
265(12)
Maria G. Vizoso Pinto
Armin Baiker
21 Yeast Two-Hybrid Screens: Improvement of Array-Based Screening Results by N- and C-terminally Tagged Fusion Proteins
277(12)
Thorsten Stellberger
Roman Hauser
Peter Uetz
Albrecht von Brunn
22 Inducible microRNA-Mediated Knockdown of the Endogenous Human Lamin A/C Gene
289(18)
Ina Weidenfeld
23 Multiple-Gene Silencing Using Antisense RNAs in Escherichia coli
307(14)
Nobutaka Nakashima
Shan Goh
Liam Good
Tomohiro Tamura
24 Functional Screen of Zebrafish Deubiquitylating Enzymes by Morpholino Knockdown and In Situ Hybridization
321(12)
William Ka Fai Tse
Yun-Jin Jiang
25 Silencing of Gene Expression by Gymnotic Delivery of Antisense Oligonucleotides
333(14)
Harris S. Soifer
Troels Koch
Johnathan Lai
Bo Hansen
Anja Hoeg
Henrik Oerum
C.A. Stein
26 Polycistronic Expression of Interfering RNAs from RNA Polymerase III Promoters
347(16)
Laura F. Steel
Viraj R. Sanghvi
PART VI METABOLITE ANALYSIS
27 Metabolite Analysis of Cannabis sativa L. by NMR Spectroscopy
363(14)
Isvett Josefina Flores-Sanchez
Young Hae Choi
Robert Verpoorte
28 Metabolome Analysis of Gram-Positive Bacteria such as Staphylococcus aureus by GC-MS and LC-MS
377(22)
Manuel Liebeke
Kirsten Dorries
Hanna Meyer
Michael Lalk
29 Metabolic Fingerprinting Using Comprehensive Two-Dimensional Gas Chromatography -- Time-of-Flight Mass Spectrometry
399(14)
Martin F. Almstetter
Peter J. Oefner
Katja Dettmer
Index 413