Cold Spring Harbor Protocols, Table of Contents
Volume 2009, Issue 7

July 2009

Cover Illustration: A worker (top) and queen (bottom) of Pseudomyrmex pallidus twig ants. The queen has scar tissue from where her wings were attached. These ants are known for their elongate bodies and large eyes, likely adaptations to their arboreal habitat. These were collected living in the hollowed shoots of dead Smilax sp. in the Apalachicola National Forest near Tallahassee, Florida. (Image courtesy of Adrian A. Smith.) For more information on the use of ants as model experimental systems, see Ants (Formicidae): Models for Social Complexity (doi:10.1101/pdb.emo125).

Emerging Model Organisms

The Painted Turtle, Chrysemys picta: A Model System for Vertebrate Evolution, Ecology, and Human Health
Nicole Valenzuela
CSH Protocols; 2009; doi:10.1101/pdb.emo124
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Ants (Formicidae): Models for Social Complexity
Chris R. Smith, Adam Dolezal, Dorit Eliyahu, C. Tate Holbrook, and Jürgen Gadau
CSH Protocols; 2009; doi:10.1101/pdb.emo125
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Topic Introductions

Using Hidden Markov Models to Align Multiple Sequences
David W. Mount
CSH Protocols; 2009; doi:10.1101/pdb.top41
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Using Progressive Methods for Global Multiple Sequence Alignment
David W. Mount
CSH Protocols; 2009; doi:10.1101/pdb.top43
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Using Iterative Methods for Global Multiple Sequence Alignment
David W. Mount
CSH Protocols; 2009; doi:10.1101/pdb.top44
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Using Multiple Sequence Alignment Editors and Formatters
David W. Mount
CSH Protocols; 2009; doi:10.1101/pdb.top45
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Indicators Based on Fluorescence Resonance Energy Transfer (FRET)
Roger Y. Tsien
CSH Protocols; 2009; doi:10.1101/pdb.top57
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Information Panel

Comparing Programs and Methods to Use for Global Multiple Sequence Alignment
David W. Mount
CSH Protocols; 2009; doi:10.1101/pdb.ip61
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Protocols

Phenotypic Analysis of Arabidopsis Mutants: Bacterial Pathogens
Detlef Weigel and Jane Glazebrook
CSH Protocols; 2009; doi:10.1101/pdb.prot4983
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Egg Incubation and Collection of Painted Turtle Embryos
Nicole Valenzuela
CSH Protocols; 2009; doi:10.1101/pdb.prot5238
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Collecting Live Ant Specimens (Colony Sampling)
Chris R. Smith and Walter R. Tschinkel
CSH Protocols; 2009; doi:10.1101/pdb.prot5239
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Marking Individual Ants for Behavioral Sampling in a Laboratory Colony
C. Tate Holbrook
CSH Protocols; 2009; doi:10.1101/pdb.prot5240
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Ecological Sampling of Ants: Competition and Biodiversity
Chris R. Smith
CSH Protocols; 2009; doi:10.1101/pdb.prot5241
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Stable Isotope and Elemental Analysis in Ants
Chris R. Smith and Chadwick V. Tillberg
CSH Protocols; 2009; doi:10.1101/pdb.prot5242
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Ant Fat Extraction with a Soxhlet Extractor
Chris R. Smith and Walter R. Tschinkel
CSH Protocols; 2009; doi:10.1101/pdb.prot5243
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General Dissection of Female Ant Reproductive System and Brain
Adam Dolezal and Colin Brent
CSH Protocols; 2009; doi:10.1101/pdb.prot5244
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DNA Isolation from Ants
Jürgen Gadau
CSH Protocols; 2009; doi:10.1101/pdb.prot5245
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Juvenile Hormone Extraction, Purification, and Quantification in Ants
Colin Brent and Adam Dolezal
CSH Protocols; 2009; doi:10.1101/pdb.prot5246
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Ant Ecdysteroid Extraction and Radioimmunoassay
Colin Brent and Adam Dolezal
CSH Protocols; 2009; doi:10.1101/pdb.prot5247
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Radiochemical Assay of Juvenile Hormone Biosynthesis Rate in Ants
Colin Brent and Adam Dolezal
CSH Protocols; 2009; doi:10.1101/pdb.prot5248
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GC-MS for Characterization and Identification of Ant Semiochemicals
Dorit Eliyahu
CSH Protocols; 2009; doi:10.1101/pdb.prot5249
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In Situ Hybridization on Ant Ovaries and Embryos
Abderrahman Khila and Ehab Abouheif
CSH Protocols; 2009; doi:10.1101/pdb.prot5250
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Phase-Unknown Linkage Mapping in Ants
Jürgen Gadau
CSH Protocols; 2009; doi:10.1101/pdb.prot5251
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Nested Patch PCR for Highly Multiplexed Amplification of Genomic Loci
Katherine E. Varley and Robi D. Mitra
CSH Protocols; 2009; doi:10.1101/pdb.prot5252
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Use of Fluorescence In Situ Hybridization and the daime Image Analysis Program for the Cultivation-Independent Quantification of Microorganisms in Environmental and Medical Samples
Holger Daims
CSH Protocols; 2009; doi:10.1101/pdb.prot5253
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Preparation of High-Molecular-Weight DNA from Drosophila Embryos
Gary H. Karpen
CSH Protocols; 2009; doi:10.1101/pdb.prot5254
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