We’re getting toward the end of the second volume of our Emerging Model Organisms series in Cold Spring Harbor Protocols, and November’s issue brings us a look at the Hawaiian Bobtail Squid and the genus Dioscorea, or True Yams.

Euprymna scolopes, the Hawaiian Bobtail Squid (our cover model this month, see below) is a cephalopod that’s well-suited for study in the laboratory. E. scolopes is primarily studied in three contexts:
1) as a model for cephalopod development–the embryos and protective chorions are clear, making it amenable for the observations and manipulations common in other studied model systems
2) as a model of animal-bacteria symbioses with the luminous marine bacterium Vibrio fischeri
3) as a system for studying the interaction of tissues with light, as the squid features a specialized light organ.

Heinz Gert de Couet and colleagues supply an overview of the Hawaiian Bobtail Squid as a model system, along with protocols for Preparation of Genomic DNA, Confocal Immunocytochemistry, Whole-Mount In Situ Hybridization (parts 1 and 2), and Culture and Observation.

Dioscorea is a large genus of plants that are monocots but that look like dicots, and are closely related to the phylogenetically derived group containing the grasses. It’s interesting evolutionarily because of the position it occupies, as a link between the eudicots and grasses–groups that contain all the model flowering plant species. The true yam is also important as a food crop. R. Geeta and colleagues provide an overview of the genus, and protocols for husbandry, culturing tissues, management of plantlets, controlled crosses, and DNA extraction.

CSH Protocols November Cover

The tandem affinity purification (TAP) procedure was pioneered in yeast for the purpose of purifying and characterizing protein complexes and has since been adapted for use in many organisms, including mammalian systems. The TAP procedure involves two sequential affinity purification steps to avoid non-specific protein interactions, a common problem in identifying proteins in complexes. Bimolecular Affinity Purification (BAP): Tandem Affinity Purification Using Two Protein Baits, from Ezra Burstein and colleagues, presents a variation on the TAP procedure in which the affinity moieties are placed on two different proteins of a molecular complex to isolate or detect components present in the complex. This variation, called bimolecular affinity purification (BAP), is suited for the identification of specific molecular complexes marked by the presence of two known components. The article is featured in the November issue of Cold Spring Harbor Protocols and like all our featured articles, is freely available to subscribers and non-subscribers alike.

Glutathione-S-transferase (GST) fusion proteins are used in a wide variety of applications in the lab. GST was originally selected as a fusion moiety because it’s not sequestered in inclusion bodies when expressed in bacteria and it can be affinity-purified without denaturation. Purification is fairly straightforward process, and GST fusion proteins are routinely used for antibody generation and purification, protein-protein interaction studies, and biochemical analysis.

Protocols describing the use of GST fusion proteins are among our most popular, and November’s issue of Cold Spring Harbor Protocols brings two new sets of instructions, covering Preparation of Soluble GST Fusion Proteins and Preparation of Insoluble GST Fusion Proteins. These articles complement our already extensive coverage, which includes the previously featured (and still freely available) article Preparation of GST Fusion Proteins. Our readers also frequently access Identification of Protein-Protein Interactions with Glutathione-S-Transferase (GST) Fusion Proteins, GST Pull-down, Detection of Protein-Protein Interactions Using the GST Fusion Protein Pulldown Technique, Detection of Protein-Protein Interactions Using Far Western with GST Fusion Proteins, Far Western: Labeling GST Fusion Proteins, and Far Western: Probing Membranes.

The National Library of Medicine (NLM) has informed us that Cold Spring Harbor Protocols has been selected to be indexed and included in MEDLINE, and that our articles will now be included and searchable using PubMed. We’re very pleased to share this announcement as it should make it easier for readers to find the high quality protocols our authors have contributed since the journal’s inception. I’m not sure how long the indexing process takes, but look for us to start turning up in your search results in the near future.

Inclusion in PubMed is another great reason to publish your methods papers with us. As a reminder to all, CSH Protocols is a peer-reviewed journal with no page charges, and we offer authors a royalty based on the usage of their articles. A high level of editorial support is available for authors and we’re happy to work with you to turn your innovative laboratory procedures into a useful community resource. Instructions for authors can be found here.

The introduction of high-throughput laboratory methods has greatly increased the pace of research into the genetics of complex diseases. Instead of focusing only on one or a few coding variants in a small sample of individuals, the ability to accurately and efficiently genotype many individuals and to cover more of the variation within individual genes has resulted in genetic studies with greater statistical power. Laboratory Methods for High-Throughput Genotyping, from Howard Edenberg and Yunlong Liu at the University of Indiana, presents an overview of the commonly used methods for high-throughput single-nucleotide polymorphism (SNP) genotyping for different stages of genetic studies and briefly reviews some of the high-throughput sequencing methods just coming into use. The authors also discuss recent developments in “next-generation” sequencing that will enable other kinds of studies. The article is excerpted from the recently published Genetics of Complex Human Diseases laboratory manual. It is featured in the November issue of Cold Spring Harbor Protocols, and like all our featured articles, is freely available to subscribers and non-subscribers alike.