No, this posting isn’t an Aesopian fable, it’s a note on our Emerging Model Organisms featured in July’s issue of Cold Spring Harbor Protocols. This month we’re covering Ants (Formicidae) and the The Painted Turtle, Chrysemys picta.

Painted Turtles have been the subject of study in many areas, including their buoyancy system, the trade-offs between offspring size and number, the ability to “overwinter”, the reptilian lymphatic system, and as an example of temperature dependent sex determination. Nicole Valenzuela from Iowa State University provides The Painted Turtle, Chrysemys picta: A Model System for Vertebrate Evolution, Ecology, and Human Health, along with a protocol for Egg Incubation and Collection of Painted Turtle Embryos.

Like many other organisms included in this series, it’s probably a misnomer to refer to ants as an “emerging model organism” as they’ve long been a key species for studying ecology, evolution, behavior, and development. Chris Smith and colleagues provide Ants (Formicidae): Models for Social Complexity, which gives an overview of ants as a model system. Protocols are available for colony sampling, marking individual ants, ecological sampling, stable isotope and elemental analysis, fat extraction, dissection, DNA isolation, hormone extraction, ecdysteroid extraction and radioimmunoassay, assay of hormone biosynthesis, GC-MS for characterization of semiochemicals, in situ hybridization, and phase-unknown linkage mapping. They’ve also supplied this month’s cover, and we made an extra effort to make sure we used an appropriate species.

Nested Patch PCR is a method designed to identify SNPs and mutations across many targeted loci for many samples in parallel. In the July issue of Cold Spring Harbor Protocols, Robi Mitra and colleagues from Washington University present Nested Patch PCR for Highly Multiplexed Amplification of Genomic Loci, a method where a large number (greater than 90) of targeted loci from genomic DNA are simultaneously amplified in the same reaction. These amplified loci can then be sequenced on a second-generation sequencing machine to detect single nucleotide polymorphisms (SNPs) and mutations.

Methods that employ mulitplexing during PCR reactions are often hampered by increased interprimer interactions that inhibit uniform amplification and increased formation of mispriming products. The protocol presented here was designed to reduce these two problems and results in a high specificity, with 90% of sequencing reads mapping to targeted loci. Nested Patch PCR is well-suited for the amplification of an intermediate number (100-1000) of targeted regions across a large number of samples and it offers a simple workflow that is compatible with 96-well plates and sample-specific DNA barcodes.

Microbial populations have traditionally been studied in carefully controlled, laboratory-grown cultures. New metagenomic approaches are being developed to study these organisms in environmental or medical samples. The July issue of Cold Spring Harbor Protocols presents a method developed by Holger Daims from the University of Vienna for quantifying populations of microorganisms in a variety of naturally occurring conditions such as plankton samples or biofilms. Use of Fluorescence In Situ Hybridization and the daime Image Analysis Program for the Cultivation-Independent Quantification of Microorganisms in Environmental and Medical Samples combines fluorescent in situ hybridization using rRNA-targeted probes with digital image analysis. The results show an organism’s “biovolume fraction” in a given sample; this indicates the share of biochemical reaction space occupied by the quantified population and can be more relevant ecologically than absolute cell numbers. Like all of our featured articles, this protocol is freely available to subscribers and non-subscribers alike.

Micropatterning methods are rapidly becoming standard approaches for investigating cellular behaviors such as growth and migration. Adhesive Micropatterns for Cells: A Microcontact Printing Protocol from Matthieu Piel and colleagues at the Institut Curie offers a simple, fast, and efficient method for generating micropatterns for cellular studies. Employing an elastomeric stamp to print proteins on the substrate of choice, this technique does not require much of the expensive equipment and technical expertise needed for most micropatterning methods, making it easier to implement in biology laboratories. The authors have provided a movie that illustrates the technique step-by-step as part of the protocol. The article is a featured protocol for July, and like all our featured articles, it is freely available to subscribers and non-subscribers alike.