Concepts and techniques in genomics and proteomics
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| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Oxford [u.a.]
Woodhead Publ.
2012
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| Schriftenreihe: | Woodhead publishing series in biomedicine
5 |
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| 020 | |a 9781907568107 |c hbk. |9 978-1-907568-10-7 | ||
| 020 | |a 1907568107 |c hbk. |9 1-907568-10-7 | ||
| 035 | |a (OCoLC)811762607 | ||
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| 100 | 1 | |a Saraswathy, Nachimuthu |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Concepts and techniques in genomics and proteomics |c Nachimuthu Saraswathy and Ponnusamy Ramalingam |
| 264 | 1 | |a Oxford [u.a.] |b Woodhead Publ. |c 2012 | |
| 300 | |a XXVI, 242 S. |b graph. Darst. |c 24 cm | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 1 | |a Woodhead publishing series in biomedicine |v 5 | |
| 500 | |a First published in 2011 by Biohealthcare Publishing (Oxford) Ltd. - Republished in 2012 by Woodhead Publishing Ltd. | ||
| 500 | |a Includes bibliographical references and index | ||
| 650 | 4 | |a Genomics | |
| 650 | 4 | |a Proteomics | |
| 650 | 4 | |a Proteomics |x Methodology | |
| 650 | 4 | |a Genomics |x Methodology | |
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| 830 | 0 | |a Woodhead publishing series in biomedicine |v 5 |w (DE-604)BV040675553 |9 5 | |
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| 943 | 1 | |a oai:aleph.bib-bvb.de:BVB01-025502153 | |
Datensatz im Suchindex
| _version_ | 1819718384374251520 |
|---|---|
| adam_text | Contents
List of
figures
xvii
List of tables
xix
Preface
xxi
Acknowledgements
xxiii
List of abbreviations
, xxv
About the authors
xxvii
1
Introduction to genes and genomes 1
1.1
Introduction
2
1.2
The cell
2
1.3
Mendel s contributions
4
1.4
The chromosomal theory of inheritance
4
1.5
The chemical nature of genetic material
5
1.6
Composition and structure of
DNA 7
1.7
The central dogma of life l
8
1.8
Genomes of prokaryotes and eukaryotes
9
1.9
The molecular structure of the gene
11
1.10
Conclusion
12
Review questions and answers
12
Recommended reading
13
2
The human genome project
15
2.1
The history of the HGP
16
2.2
The budget for the HGP
18
2.3
Goals of the HGP
18
2.4
Laboratories and investigators involved in the HGP
19
2.5
The Human Genome Organization (HUGO)
20
Published by Woodhead Publishing Limited
Concepts and Techniques in Genomics and Proteomics
2.6
Salient findings of the HGP
20
2.7
Potential applications of the HGP
22
2.8
Post-HGP challenges
23
2.9
Ethical, legal, social issues (ELSI) related to the HGP
23
2.10
The international HapMap Project
25
Review questions and answers
26
Recommended reading
27
3
Genomes of model organisms
29
3.1
Introduction
29
3.2
The viral genome
30
3.3
Bacterial genomes
31
3.3.1
Escherichia
coli
genome
32
3.4
Fungal genomes
33
3.4.1
Yeast: Saccharomyces cerevisiae
33
3.4.2
Neurospora
crassa
35
3.5
Worm genome: Caenorhabditis
elegans
36
3.6
Fruit fly:
Drosophila melanogaster
38
3.7
Plant genome
39
3.7.1
Mouse-ear cress: Arabidopsis thaliana
39
3.7.2
Rice genome: Oryza
sativa
41
3.8
Animal genome
42
3.8.1
Puffer fish:
Fugu rubripes
42
3.8.2
Mouse:
Mus musculus
43
3.8.3
Rat: Rattus rattus
44
3.9
The Microbial Genome Project
45
Review questions and answers
45
Recommended reading
47
4
High capacity vectors
49
4.1
Introduction
49
4.2
Cosmid vectors
50
4.3
Fosmid vectors
51
4.4
Bacteriophage P1 derived vector
52
4.5
PI derived artificial chromosome
(PAC)
53
4.6
Bacterial artificial chromosomes
(ВАС)
54
4.7
Yeast artificial chromosome
(YAC)
54
Review questions and answers
55
Recommended reading
56
Published by Woodhead Publishing Limited
Contents
v
xi
5 DNA
sequencing methods
-* 57
5.1
The history of
DNA
sequencing
■ 58
5.2
Steps in
DNA
sequencing
■ 59
5.3
Chemical degradation method of
DNA
sequencing
60
5.4
The chain termination method of
DNA
sequencing
64
5.4.1
Steps involved in the chain termination method
66
5.5
Advances in
DNA
sequencing methods
67
5.5.1
Fluorescent dye-labelled terminator
·■■ 68
5.5.2
Cycle sequencing
· ■ 69
5.5.3
Capillary electrophoresis °-
69
5.6
New sequencing methods
70
5.6.1
Micro-electrophoresis
70
5.6.2
Array hybridization sequencing
· 71
5.7
Next generation sequencing methods
71
5.7.1 454
sequencing technologies
71
5.7.2
ABI-SOLiD sequencing technology
73
5.7.3
Illumina
sequencing technology
74
Review questions and answers
74
Recommended reading
, 76
6
Genome mapping
77
6.1
Introduction
: 78
6.2
Importance of genome mapping in the context
of genome sequencing
78
6.3
Genetic mapping
78
6.3.1
Genetic mapping using genes
79
6.3.2
Genetic mapping using molecular markers
80
6.3.3
Restriction fragment length polymorphism (RFLP)
80
6.4
Genetic mapping in humans
81
6.5
Physical mapping methods
82
6.5.1
Cytogenetic mapping
82
6.5.2
FISH in genome mapping
83
6.5.3
Restriction mapping :
·> : 85
6.5.4
STS
content mapping
87
6.5.5
Radiation hybrid mapping
, 88
Review questions and answers
. 90
Recommended reading
*-> 93
Published by Woodhead Publishing Limited:
xii
Concepts and Techniques in Genomics and Proteomics
7
Genome sequencing methods
95
7.1
Introduction
96
7.2
The clone-by-clone genome sequencing method
97
7.2.1
Preparation of the
ВАС
clone library
97
7.2.2
Preparation of the clone fingerprint
97
7.2.3
ВАС
clone sequencing
99
7.2.4
Sequence assembly
99
7.3
The whole genome shotgun sequencing method
100
7.4
Error control in genome sequencing
104
Review questions and answers
106
Recommended reading
106
8
Genome sequence assembly and annotation
109
8.1
Introduction
109
8.2
Clone contig assembly
110
8.3
Genome assembly program
113
8.3.1
PHRAP
113
8.3.2
CAP3
114
8.3.3
Overlap lay-out consensus
114
8.3.4
Eulerianpath
114
8.4
Gaps and gap closing methods
114
8.4.1
Gap closing methods
115
8.5
Draft and finished genome sequences
116
8.5.1
Draft genome sequence
116
8.5.2
Finished genome sequence
117
8.6
Genome annotation
118
8.7
Comparative genomics
118
Review questions and answers
120
Recommended reading
121
9
Functional genomics
123
9.1
Introduction
124
9.2
Northern blotting
125
9.3
Subtractive hybridization
128
9.3.1
Principles of subtractive hybridization
128
9.4
Differential Display Reverse Transcription
PCR (DDRT-PCR)
131
9.5
Representational Difference Analysis
(RDA)
134
Published by Woodhead Publishing Limited
Contents xiii
9.6
Serial
Analysis
Gene Expression (SAGE) ·. , r · 136
9.6.1
Principles of
SAGE 136
9.6.2 MicroS
AG E
139
9.7 Microarray
technology
140
9.7.1
Principles of
microarray
hybridization
140
Review questions and answers
143
Recommended reading
144
10
Introduction to proteomics
147
10.1
Introduction
■.·..·■-;=. · . 148
10.2
Traditional route of protein study
·.
:
148
10.2.1
Proteome and proteomics
.; ,,. , 148
10.3
Protein isolation methods
149
10.3.1
Extraction methods
150
10.3.2
Protein separation techniques
, 151
10.4
Branches of proteomics
.-.:
j;
153
10.4.1
Quantitative proteomics
154
10.4.2
Protein-protein interaction
155
10.5
Characteristics of proteomics
155
Review questions and answers
156
Recommended reading
157
11
Two-dimensional gel electrophoresis of proteins
159
11.1
Introduction
160
11.2
Principles of 2D-PAG
E
160
11.3
2D-PAG
E
apparatus
161
11.3.1
The IEF unit
161
11.3.2
The second dimensional unit
161
11.4
Sample preparation
162
11.5
First-dimensional separation by isoelectric focusing
163
11.5.1
Preparation of
pH
gradient for IEF
163
11.5.2
Sample loading
164
11.5.3
Isoelectric focusing
164
11.6
Equilibration
165
11.7
Second-dimensional separation by SDS-PAGE
165
11.8
Detection of
proteinson
2D-PAG
E
gels
166
11.9
Image analysis
167
11.10
Application of 2D-PAG
E
in proteomics
J
168
Review questions and answers
169
Recommended reading
170
Published by Woodhead Publishing Limited
xiv
Concepts and Techniques in Genomics and Proteomics
12
Mass
spectrometry for proteomics 171
12.1
Introduction
172
12.2
History of the mass spectrometer
172
12.3
Mass spectrometer
174
12.3.1
Basic MS instrumentation
174
12.3.2
lonization sources
175
12.3.3
Mass analyzers
177
12.3.4
Output of the mass spectrometer
178
12.3.5
Resolution of the mass spectrometer
179
12.4
Protein sample preparation for MS analysis
179
12.5
Applications of MS proteomics
180
Review questions and answers
181
Recommended reading
182
13
Protein Identification by
Peptide
Mass
Fingerprinting (PMF)
185
13.1
Introduction
185
13.2
Principles of
peptide
mass fingerprinting
186
13.3
Protein preparation for PMF
187
13.4
Mass spectrometric analysis of
peptide
fragments
188
13.5
Data analysis and identification of protein
188
13.5.1
ALDENTE
peptide
mass fingerprinting tool
189
Review question and answer
189
Recommended reading
191
14
Protein sequencing techniques
193
14.1
Introduction
194
14.2
Preparation of protein sample for sequencing
195
14.3
Steps in protein sequencing
195
14.3.1
Determination of
amino
acid composition
195
14.3.2
N-terminal
amino
acid determination
196
14.3.3
C-terminal
sequencing
196
14.3.4
Disulfide bond breakage
196
14.3.5
Proteolytic cleavage of the proteins
196
14.4
Protein sequencing by
Edman
degradation
197
14.5
De novo
protein sequencing by mass spectrometry
198
Review questions and answers
200
Recommended reading
201
Published by Woodhead Publishing Limited
Contents xv
15 Phosphoproteomics 203
15.1 Post-translational
modifications
of proteins
204
15.2 Phosphoproteomics 204
15.2.1
Effect of phosphorylation on proteins
205
15.3
Phosphoproteins enrichment methods
206
15.3.1
SDS-PAG
E
separation of phosphoproteins
206
15.3.2
Immunoprecipitation
206
15.3.3
Immobilized metal affinity chromatography
207
15.3.4
Strong cation exchange chromatography
207
15.4
Mass spectrometry for phosphoprotein identification
208
Review questions and answers
210
Recommended reading
210
16
Glycoproteomics
213
16.1
Glycoproteins
213
16.1.1
Glycoprotein synthesis
215
16.1.2
Functions of glycoproteins
; 215
16.2
Glycoprotein enrichment methods
215
16.3
Mass spectrometric analysis of glycoproteins
216
16.4
Importance of glycoproteins in human diseases
216
Review questions and answers
217
Recommended reading
218
Conclusion
219
Glossary
221
Index
237
Published by Woodhead Publishing Limited
|
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| author | Saraswathy, Nachimuthu Ramalingam, Ponnusamy |
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| id | DE-604.BV040675678 |
| illustrated | Illustrated |
| indexdate | 2024-12-24T03:00:53Z |
| institution | BVB |
| isbn | 9781907568107 1907568107 |
| language | English |
| lccn | 2011293054 |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-025502153 |
| oclc_num | 811762607 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR |
| owner_facet | DE-355 DE-BY-UBR |
| physical | XXVI, 242 S. graph. Darst. 24 cm |
| publishDate | 2012 |
| publishDateSearch | 2012 |
| publishDateSort | 2012 |
| publisher | Woodhead Publ. |
| record_format | marc |
| series | Woodhead publishing series in biomedicine |
| series2 | Woodhead publishing series in biomedicine |
| spellingShingle | Saraswathy, Nachimuthu Ramalingam, Ponnusamy Concepts and techniques in genomics and proteomics Woodhead publishing series in biomedicine Genomics Proteomics Proteomics Methodology Genomics Methodology Methode (DE-588)4038971-6 gnd Genomik (DE-588)4776397-8 gnd Proteomanalyse (DE-588)4596545-6 gnd |
| subject_GND | (DE-588)4038971-6 (DE-588)4776397-8 (DE-588)4596545-6 |
| title | Concepts and techniques in genomics and proteomics |
| title_auth | Concepts and techniques in genomics and proteomics |
| title_exact_search | Concepts and techniques in genomics and proteomics |
| title_full | Concepts and techniques in genomics and proteomics Nachimuthu Saraswathy and Ponnusamy Ramalingam |
| title_fullStr | Concepts and techniques in genomics and proteomics Nachimuthu Saraswathy and Ponnusamy Ramalingam |
| title_full_unstemmed | Concepts and techniques in genomics and proteomics Nachimuthu Saraswathy and Ponnusamy Ramalingam |
| title_short | Concepts and techniques in genomics and proteomics |
| title_sort | concepts and techniques in genomics and proteomics |
| topic | Genomics Proteomics Proteomics Methodology Genomics Methodology Methode (DE-588)4038971-6 gnd Genomik (DE-588)4776397-8 gnd Proteomanalyse (DE-588)4596545-6 gnd |
| topic_facet | Genomics Proteomics Proteomics Methodology Genomics Methodology Methode Genomik Proteomanalyse |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025502153&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV040675553 |
| work_keys_str_mv | AT saraswathynachimuthu conceptsandtechniquesingenomicsandproteomics AT ramalingamponnusamy conceptsandtechniquesingenomicsandproteomics |