Nonmammalian Genomes Analysis : A Practical Guide

by Bruce W. Birren; Eric Lai

• ISBN13: 9780121012854
• ISBN10: 0121012859
• Format: Paperback
• Copyright: 1996-07-01
• Publisher: Academic Pr

Summary

Offering detailed protocols for those needing to construct a variety of maps and isolate genes, this unique book is intended to popularize the new techniques of genome analysis derived from the Human Genome Project. The power of these new methods is often most striking when applied to problems outside of human genetics, particularly the nonmammalian systems on which many researchers focus. Many of these organisms are economically important and biologically rich. Nonmammalian Genomic Analysis: A Practical Guide covers the "how to" aspects of preparation, handling, cloning, and analysis of large DNA and the creation of chromosome and genome maps. This lab manual facilitates the transfer of these technologies to small "low tech" environments and allows them to be used by those with no background in genome mapping or large-fragment cloning. Like having a local expert, this collection provides procedures for anyone, anywhere, and allows the replication of others' success. Key Features * Includes detailed and clearly-written step-by-step protocols * Evinces expected results and offers trouble shooting advice * Provides techniques appropriate for small laboratories as well as those with limited resources * Covers a broad variety of cloning systems, including single copy vectors * Discusses a diverse range of organisms, from prokaryotes to eukaryotes, from single-celled organisms to highly complex organisms

Table of Contents

Contributors	ix	(4)
Preface	xiii
1 Introduction to Pulsed-Field Gels and Preparation and Analysis of Large DNA	1	(24)
Jennifer S. Lee
Bruce Birren
Eric Lai
I. Pulsed-Field Gel Electrophoresis (PFGE)	1	(10)
II. Materials	11	(2)
III. Preparation of Nonmammalian Chromosomes	13	(5)
IV. Enzymatic Reactions Using DNA-Agarose Plugs	18	(1)
V. Southern Blotting of Pulsed-Field Gels	19	(3)
VI. Troubleshooting Pulsed-Field Gels	22	(1)
References	23	(2)
2 Electrophoretic Karyotyping in Fungi	25	(36)
Ken Dewar
Louis Bernier
Roger C. Leavesque
I. Introduction	25	(4)
II. Choice of Sample Material	29	(1)
III. Sample Preparation	30	(8)
IV. Constructing Electrophoretic Karyotypes	38	(9)
V. Applications of Electrophoretic Karyotyping	47	(5)
VI. Conclusion	52	(1)
References	53	(8)
3 Isolation and Analysis of High-Molecular-Weight DNA from Plants	61	(14)
Martin Ganal
I. Introduction	61	(1)
II. Materials	62	(1)
III. Procedures	63	(3)
IV. Pitfalls	66	(6)
References	72	(3)
4 Generating and Using DNA Markers in Plants	75	(60)
J. Antoni Rafalski
Julie M. Vogel
Michele Morgante
Wayne Powell
Chaz Andre
Scott V. Tingey
I. Introduction	75	(1)
II. Comparison of DNA Marker Systems	76	(3)
III. Materials	79	(1)
IV. Restrictive Fragment Length Polymorphism Markers	80	(7)
V. Cleavable Amplified Polymorphic Sequences	87	(1)
VI. Random Amplified Polymorphic DNA	88	(8)
VII. Microsatellite Markers (Simple Sequence Repeats, SSR)	96	(12)
VIII. Sequence-Based Polymorphism Assays	108	(2)
IX. Higher Multiplex Ratio Assays: Amplified Fragment Length Polymorphism and Interrepeat Amplification	110	(17)
X. Choosing Appropriate Technology	127	(2)
References	129	(6)
Genome Mapping of Protozoan Parasites by Linking Clones	135	(30)
S. P. Morzaria
I. Introduction	135	(1)
II. Strategy	136	(2)
III. Materials	138	(3)
IV. Procedures	141	(20)
V. General Remarks and Conclusions	161	(1)
References	162	(3)
Macrorestriction Mapping and Analysis of Bacterial Genomes	165	(32)
Ute Romling
Rainer Fislage
Burkhard Tummler
I. Introduction	165	(1)
II. Materials	165	(4)
III. Topology of Bacterial Genomes	169	(4)
IV. Construction of Macrorestriction Maps	173	(21)
References	194	(3)
7 Cosmid Cloning with Small Genomes	197	(26)
Rainer Wenzel
Richard Herrmann
I. Introduction	197	(1)
II. General Considerations	198	(1)
III. Choice of Vector	199	(3)
IV. Construction of the Library	202	(8)
V. Sorting the Library	210	(7)
VI. Mapping Problems	217	(2)
VII. Summary	219	(1)
VIII. References	220	(3)
8 Construction of P1 Artificial Chromosome (PAC) Libraries from Lower Vertebrates	223	(34)
Chris T. Amemiya
Tatsuya Ota
Gary W. Litman
I. Introduction	223	(3)
II. Materials	226	(3)
III. Protocols	229	(23)
IV. Summary	252	(1)
References	253	(4)
9 The Selection of Chromosome-Specific DNA Clones from African Trypanosome Genomic Libraries	257	(36)
Sara E. Melville
Nancy S. Shepherd
Caroline S. Gerrard
Richard W. F. Le Page
I. Introduction	257	(1)
II. Materials	258	(3)
III. Procedures	261	(25)
IV. Notes and Pitfalls	286	(3)
References	289	(4)
10 Analysis of the Dictyostelium discoidenum Genome	293	(26)
Adam Kuspa
William F. Loomis
I. Introduction	293	(2)
II. Materials	295	(3)
III. Preparation and Restriction Analysis of Genomic DNA	298	(2)
IV. The Use of YACs in Genome Analysis	300	(7)
V. Restriction Enzyme-Mediated Integration (REMI)-RFLP Analysis	307	(6)
VI. Random Insertional Mutagenesis Using REMI	313	(3)
References	316	(3)
11 Integrated Genome Mapping by Hybridization Techniques	319	(28)
Jorg D. Hoheisel
Elmar Maier
Richard Mott
Hans Lehrach
I. Introduction	319	(2)
II. Materials	321	(2)
III. Procedures	323	(20)
IV. Conclusions	343	(1)
References	344	(3)
Index	347