Synthetic biology: A Methods for part, device characterization and chassis engineering
Gespeichert in:
Weitere Verfasser: | |
---|---|
Format: | Buch |
Sprache: | English |
Veröffentlicht: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2011
|
Ausgabe: | 1. ed. |
Schriftenreihe: | Methods in enzymology
497 |
Schlagworte: | |
Online-Zugang: | Inhaltsverzeichnis |
Beschreibung: | LII, 662 S. Ill., graph. Darst. |
ISBN: | 9780123850751 |
Internformat
MARC
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245 | 1 | 0 | |a Synthetic biology |n A |p Methods for part, device characterization and chassis engineering |c ed. by Christopher Voigt |
250 | |a 1. ed. | ||
264 | 1 | |a Amsterdam [u.a.] |b Elsevier, Acad. Press |c 2011 | |
300 | |a LII, 662 S. |b Ill., graph. Darst. | ||
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Datensatz im Suchindex
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---|---|
adam_text | Contents
Contributors
xiii
Preface
xxi
Volumes In Series xxiii
Section I. Measuring and Engineering
Central Dogma Processes
1
1.
Sequence-Specificity and Energy Landscapes of
DNA-Binding Molecules
3
Joshua R. Tietjen, Leslie J.
Donato, Devesh
Bhimisaria,
and Aseem Z. Ansari
1.
Introduction
4
2.
Array-Based Cognate Sequence Identification
. 6
3.
Solution-Based Cognate Sequence Identification
13
4.
Data Analysis and Visualization of Specificity, Binding Energy,
and Genomic-Association Landscapes
18
References
27
2.
Promoter Reliability in Modular Transcriptional Networks
31
Rajat Anand, Navneet
Rai,
and Mukund Thattai
1.
Results
33
2.
Conclusion
44
3.
Methods
45
Acknowledgments
47
References
47
3.
The Analysis of Ch I P-Seq Data
51
Wenxiu Ma and Wing Hung Wong
1.
Introduction
52
2.
Planning of ChlP-Seq Experiments
53
3.
Processing and Analyzing ChlP-Seq
Datasets
58
vj
Contents
4.
Discussion
68
Acknowledgment 70
References 71
4.
Using
DNA Microarrays
to Assay Part Function
75
Virgil A. Rhodius and Carol A. Gross
1.
Introduction
76
2.
Different Microarray Platforms
77
3.
Experimental Design
81
4.
Experimental Variation
82
5.
Sample Preparation
85
6.
Microarray Preprocessing
93
7.
Clustering
99
8.
Differential Expression Analysis
104
9.
Data Analysis: Understanding the Perturbation
106
10.
Closing Remarks
108
References
109
5.
Orthogonal Gene Expression in Escherichia
coli
115
Wenlin An and
Jason
W. Chin
1.
Introduction
116
2.
High-Throughput Screening for Orthogonal
17
Promoter
O-rbs System
119
3.
Integration of Orthogonal Pairs to Synthesize
Transcription-Translation FFL
122
4.
Engineering the FFL Delay via the Discovery of a Minimal O-rRNA
123
5.
Discussion
126
6.
Material and Methods
129
Acknowledgments
132
References
132
6.
Directed Evolution of Promoters and Tandem Gene Arrays for
Customizing
RNA
Synthesis Rates and Regulation
135
Keith E.
).
Tyo,
Elke Nevoigt,
and Gregory Stephanopoulos
1.
Introduction
136
2.
Promoter Modification by Error-Prone PCR
138
3.
Generating Stable Tandem Gene Arrays for Controlling
RNA
Synthesis Rate
150
4.
Concluding Remarks
153
References
154
Contents
vii
Section II. Device and System Design,
Optimization, and Debugging
157
7.
Design and Connection of Robust Genetic Circuits
159
Adrian Randall, Patrick Guye, Saurabh Gupta,
Xavier
Duportet,
and Ron Weiss
1.
Introduction
160
2.
Sources of Failure
161
3.
Robustness Principles and Examples in Natural Systems
163
4.
Methods for Obtaining Robust Synthetic Circuits
165
5.
Robustness Trade-Offs
181
6.
Conclusion
182
References
182
8.
Engineering RNAi Circuits
187
Yaakov
Benenson
1.
Introduction
188
2.
Constructing a Computational Logic Core for the
RNAi-Based DNF Circuit
189
3.
Constructing a Computational Logic Core for the
RNAi-Based CNF Circuit
200
4.
Transition from siRNA to miRNA
202
Acknowledgments
204
References
204
9.
From SELEX to Cell: Dual Selections for Synthetic Riboswitches
207
Joy Sinha, Shana
Topp,
and Justin P.
Gallivan
1.
Introduction
207
2.
General Precautions
208
3.
In Vitro Selection
208
4.
In Vivo Selection
212
References
219
10.
Using Noisy Gene Expression Mediated by Engineered
Adenovirus to Probe Signaling Dynamics in Mammalian Cells
221
Jeffrey V. Wong, Guang Yao, Joseph R. Nevins, and Lingchong You
1.
Introduction
222
2.
Design and Construction
224
3.
Measurement
230
4.
Broader Applications
234
References
234
v¡¡¡
Contents
11.
De novo
Design and Construction of an Inducible
Gene Expression System in Mammalian Cells
239
Maria
Karlsson,
Wilfried
Weber, and Martin Fussenegger
1.
Introduction
240
2.
Selection of a Conditional DNA-Binding Protein
243
3.
Establishment of the Inducible Expression System
244
4.
Optimization of the Expression System
248
5.
Summary
250
Acknowledgments
251
References
251
12.
BioBuilding: Using Banana-Scented Bacteria to
Teach Synthetic Biology
255
James Dixon and Natalie Kuldell
1.
Introduction
256
2.
Eau
d eoli
257
3.
Eau
That Smell Teaching Lab Using the MIT ¡GEM
Team s
Eau
d eoli
Cells
259
4.
Teaching Labs Modified for Resource-Stretched Settings
267
5.
Summary
269
Acknowledgments
270
References
270
Section III. Device Measurement,
Optimization, and Debugging
273
13.
Use of Fluorescence Microscopy to Analyze
Genetic Circuit Dynamics
275
Giirol Sue!
1.
Fluorescent Reporters
276
2.
Constructing and Using Genetic Fluorescent Reporters
277
3.
Fluorescent Time-Lapse Microscopy
281
4.
Measuring and Interpreting Dynamics
284
5.
Applications for Measurement of Circuit Dynamics
286
References
292
14.
Microfluidics for Synthetic Biology: From Design to Execution
295
M. S. Ferry, I. A. Razinkov, and
).
Hasty
1.
Part I: Introduction
296
2.
Part II: Fabrication
338
Contents
їх
3.
Part III: Experiments
358
Acknowledgments
371
References
371
15.
Plate-Based Assays for Light-Regulated
Gene Expression Systems
373
Jeffrey J. Tabor
1.
Bacterial Photography Protocol
374
2.
Bacterial Edge Detection Protocol
379
3.
Setting up a Projector-Incubator
381
4.
The
ß-Galactosidase/S-Gal
Reporter System
384
5.
Quantifying Signal Intensity on the Plates
385
6.
Microscopic Imaging of
Agarose
Slabs
385
7.
Properties of Relevant Strains
386
8.
Properties of Relevant Plasmids
387
References
390
16.
Spatiotemporal
Control of Small GTPases with
Light Using the
LOV
Domain
393
Yi I. Wu, Xiaobo Wang, Li He,
Denise
Moriteli,
and Klaus M.
Hahn
1.
Introduction
394
2.
The
LOV
Domain as a Tool for Protein Caging
395
3.
Design and Structure Optimization of PA-Rac
395
4.
Activation of
ΡΑ
-Rac
in Living Cells
397
5.
Application of
ΡΑ
-Rac
in
Drosophila
Ovarian Border Cell Migration
400
References
407
17.
Light Control of Plasma Membrane Recruitment
Using the Phy-PIF System
409
Jared E. Toettcher, Delquin Gong, Wendell
A. Lim,
and Orion D. Weiner
1.
Introduction
410
2.
Light-Controlled Phy-PIF Interaction
411
3.
Genetic Constructs Encoding Phy and
PIF
Components
412
4.
Purification of
PCB
from Spirulina
415
5.
Cell Culture Preparation for Phy-PIF
Translocation
418
6.
Imaging
PIF Translocation
Using Spinning Disk Confocal Microscopy
419
Acknowledgments
421
References
421
x
Contents
18.
Synthetic Physiology: Strategies for Adapting Tools from
Nature for Genetically Targeted Control of Fast Biological
Processes
425
Brian Y. Chow, Amy S. Chuong, Nathan
С
Klapoetke, and
Edward S. Boyden
1.
Introduction
426
2.
Molecular Design and Construction
429
3.
Transduction of Microbial Opsins into Cells for
Heterologous Expression
432
4.
Physiological Assays
435
5.
Conclusion
438
Acknowledgments
439
References
439
Section IV. Devices for Metabolic Engineering
445
19.
Metabolic Pathway Flux Enhancement by
Synthetic Protein Scaffolding
447
Weston R. Whitaker and John E. Dueber
1.
Introduction
448
2.
Method—How to Build Modular Protein
Scaffolded Systems for Metabolic Engineering Applications
454
3.
Systems that May Benefit from Scaffolding
465
4.
Concluding Remarks
465
Acknowledgments
466
References
466
20.
A Synthetic Iterative Pathway for Ketoacid Elongation
469
C. R.
Shen and
J. C
Liao
1.
Introduction
470
2.
Natural Pathways Involving Ketoacid Chain Elongations
Catalyzed by the LeuABCD-Dependent Mechanisms
471
3.
IPMS and Similar Enzymes
473
4.
Expansion to Nonnatural Pathways
475
5.
Transfer of Citramalate Pathway to
E. coli
for Ketoacid
Chain Elongation
478
6.
Conclusion Remarks
480
References
480
Contents
x¡
Section
V. Expanding Chassis
483
21.
Synthetic Biology in Streptomyces Bacteria
485
Marnix
H. Medema, Rainer
Breitling,
and
Eriko Takáno
1.
Synthetic Biology for Novel Compound Discovery in Streptomyces
486
2.
Practical Considerations for Synthetic Biology in Streptomyces
488
3.
Iterative
Reengineering
of Secondary Metabolite Gene Clusters
489
4.
The Molecular Toolbox for Streptomyces Synthetic Biology
491
5.
Transcriptional Control
492
6.
Translational Control
494
7.
Vectors
494
Acknowledgments
497
References
497
22.
Methods for Engineering
Sulfate
Reducing Bacteria
of the Genus Desulfovibrio
503
Kimberly L. Keller, Judy D. Wall, and Swapnil Chhabra
1.
Introduction
504
2.
Chromosomal Modifications Through Homologous Recombination
505
3.
Culturing Conditions and Antibiotic Selection
507
4. DNA
Transformation
510
5.
Screening Colonies for Proper Integration
513
6.
Complementing Gene Deletions
514
7.
Concluding Remarks
515
Acknowledgments
516
References
516
23.
Modification of the Genome of Rhodobacter
sphaeroides and Construction of Synthetic
Opérons
519
Paul R.
Jasenke,
Rafael G.
Saer, Stephan
Noll, and J. Thomas Beatty
1.
Introduction
520
2.
Gene Disruption and Deletion
522
3.
Construction of Synthetic
Opérons
527
4.
Future Directions
532
References
533
xii
fcontrnb
24.
Synthetic Biology in Cyanobacteria: Engineering and
Analyzing Novel Functions
539
Thorsten Heidorn, Daniel Camsund,
Hsin-Ho Huang,
Pia Lindberg,
Paulo
Oliveira,
Karin
Stensjp, and Peter
Lindblad
1.
Introduction ci40
2.
Cyanobacterial Chassis
(Ш
3.
Biological Parts in Cyanobacteria
4M
4.
Genetic Engineering of Cyarmbaeteria
4%
5.
Molecular Analysis of Cyanobacteria S62
6.
Conclusion and Outlook %7i
Acknowledgments
572
References
$72
25.
Developing a Synthetic Signal Transduction System in Plants
581
Kevin J. Morey, Mauricio S.
Antunes,
Kirk D.
Albrecht,
Tessa A. Bowen,
jared F. Troupe, Keira L. Havens, and
lune
I.
Medförd
1.
Introduction
582
2.
Foundation for Developing a Molecular Testing Platform
for
Η Κ
Systems
586
3.
Technical Considerations in Developing a Eukaryotic Synthetic
Signal Transduction System Based on Bacterial TCS Components
589
4.
A Partial Synthetic Signal Transduction System Using Cytokinin Input
592
5.
A Eukaryotic Synthetic Signal Transduction Pathway
593
6.
Conclusions
$95
7.
Protocols B97
Acknowledgments
§99
References
26.
Lentiviral Vectors to Study Stochastic Noise in Gene Expression
603
Kate Franz, Abhyudai Singh, and Leor S. Weinberger
1.
Introduction
604
2.
The Lentivlral-Vector Approach
605
3.
Production of Lentiviral Vectors and Transduced Cell
Unes
609
4.
Procedure for Constructing a
CV2
Versus Mean Plot
616
5.
Inferring Promoter Regulatory Architecture from
CV2
Versus
Mean Analysis
616
6.
Conclusion
620
Acknowledgments
620
References
620
Author Index
$23
Subject Index
$ζΐ
|
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edition | 1. ed. |
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spelling | Synthetic biology A Methods for part, device characterization and chassis engineering ed. by Christopher Voigt 1. ed. Amsterdam [u.a.] Elsevier, Acad. Press 2011 LII, 662 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 497 Methods in enzymology ... Methode (DE-588)4038971-6 gnd rswk-swf Molekularbiologie (DE-588)4039983-7 gnd rswk-swf Biotechnologie (DE-588)4069491-4 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Biotechnologie (DE-588)4069491-4 s Molekularbiologie (DE-588)4039983-7 s Methode (DE-588)4038971-6 s b DE-604 Voigt, Christopher edt (DE-604)BV039160172 1 Methods in enzymology 497 (DE-604)BV000000938 497 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024177699&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
spellingShingle | Synthetic biology Methods in enzymology Methode (DE-588)4038971-6 gnd Molekularbiologie (DE-588)4039983-7 gnd Biotechnologie (DE-588)4069491-4 gnd |
subject_GND | (DE-588)4038971-6 (DE-588)4039983-7 (DE-588)4069491-4 (DE-588)4143413-4 |
title | Synthetic biology |
title_auth | Synthetic biology |
title_exact_search | Synthetic biology |
title_full | Synthetic biology A Methods for part, device characterization and chassis engineering ed. by Christopher Voigt |
title_fullStr | Synthetic biology A Methods for part, device characterization and chassis engineering ed. by Christopher Voigt |
title_full_unstemmed | Synthetic biology A Methods for part, device characterization and chassis engineering ed. by Christopher Voigt |
title_short | Synthetic biology |
title_sort | synthetic biology methods for part device characterization and chassis engineering |
topic | Methode (DE-588)4038971-6 gnd Molekularbiologie (DE-588)4039983-7 gnd Biotechnologie (DE-588)4069491-4 gnd |
topic_facet | Methode Molekularbiologie Biotechnologie Aufsatzsammlung |
url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024177699&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
volume_link | (DE-604)BV039160172 (DE-604)BV000000938 |
work_keys_str_mv | AT voigtchristopher syntheticbiologya |