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
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.emo125
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Topic Introductions

Using Hidden Markov Models to Align Multiple Sequences
David W. Mount
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.top41
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Using Progressive Methods for Global Multiple Sequence Alignment
David W. Mount
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.top43
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Using Iterative Methods for Global Multiple Sequence Alignment
David W. Mount
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.top44
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Using Multiple Sequence Alignment Editors and Formatters
David W. Mount
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.top45
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Indicators Based on Fluorescence Resonance Energy Transfer (FRET)
Roger Y. Tsien
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.ip61
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Protocols

Phenotypic Analysis of Arabidopsis Mutants: Bacterial Pathogens
Detlef Weigel and Jane Glazebrook
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot4983
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Egg Incubation and Collection of Painted Turtle Embryos
Nicole Valenzuela
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5238
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Collecting Live Ant Specimens (Colony Sampling)
Chris R. Smith and Walter R. Tschinkel
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5239
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Marking Individual Ants for Behavioral Sampling in a Laboratory Colony
C. Tate Holbrook
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5240
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Ecological Sampling of Ants: Competition and Biodiversity
Chris R. Smith
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5241
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Stable Isotope and Elemental Analysis in Ants
Chris R. Smith and Chadwick V. Tillberg
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5242
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Ant Fat Extraction with a Soxhlet Extractor
Chris R. Smith and Walter R. Tschinkel
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5243
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General Dissection of Female Ant Reproductive System and Brain
Adam Dolezal and Colin Brent
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5244
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DNA Isolation from Ants
Jürgen Gadau
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5245
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Juvenile Hormone Extraction, Purification, and Quantification in Ants
Colin Brent and Adam Dolezal
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5246
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Ant Ecdysteroid Extraction and Radioimmunoassay
Colin Brent and Adam Dolezal
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5247
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Radiochemical Assay of Juvenile Hormone Biosynthesis Rate in Ants
Colin Brent and Adam Dolezal
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5248
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GC-MS for Characterization and Identification of Ant Semiochemicals
Dorit Eliyahu
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5249
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In Situ Hybridization on Ant Ovaries and Embryos
Abderrahman Khila and Ehab Abouheif
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5250
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Phase-Unknown Linkage Mapping in Ants
Jürgen Gadau
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 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
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5253
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Preparation of High-Molecular-Weight DNA from Drosophila Embryos
Gary H. Karpen
Cold Spring Harb Protoc; 2009; doi:10.1101/pdb.prot5254
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