Bench Marks

Means to an End: Apoptosis and Other Cell Death Mechanisms is the new book from Douglas Green, a clear and comprehensive view of apoptosis and other death mechanisms. He examines the enzymes that perform the execution (caspases) and the molecular machinery that links their activation to signals that cause cell death, emphasizing the importance of BCL-2 proteins and cytochrome c released from mitochondria. Green also outlines the roles of cell death in embryogenesis, neuronal selection, and the development of self-tolerance in the immune system, explains how cell death defends the body against cancer, and traces the evolutionary origins of the apoptosis machinery back over a billion years.

There’s also an online companion resource that’s rapidly growing. Be sure not to miss Cell Death: The Movie.

If you’ve visited Cold Spring Harbor Protocols in the last 12 hours or so, you may have noticed that things look a little different. Welcome to Phase 1 of our re-design.

CSH Protocols was originally designed as a database, but over time, our readers and authors made it clear to us that their needs would be better served if it became more journal-like. For an author, publishing a peer-reviewed, PubMed indexed paper offers better rewards than contributing to a database. For readers who are used to digging information out of the published literature, a journal offers better findability. And so, we’ve redesigned the site to bring it into line with Cold Spring Harbor Laboratory Press’ other journal offerings.

The site still offers the same functionality, but now the navigation is greatly improved. The new design also allows us to start experimenting with widgets, adding further functionality. The next step will be migrating to our host, Highwire Press’ new H2O platform, which will allow for even further functionality to be built in (coming in the near future).

So take a look around, maybe you’ll find some things you haven’t found before. And stay tuned for future developments.

A cell devotes a significant amount of effort to maintaining the stability of its genome, preventing the sorts of chromosomal rearrangements characteristic of many cancers. Assays that measure the rate of gross chromosomal rearrangements (GCRs) are needed in order to understand the individual genes and the different pathways that suppress genomic instability. In the September issue of Cold Spring Harbor Protocols, Richard Kolodner and colleagues from the University of California, San Diego’s Ludwig Institute for Cancer Research present Determination of Gross Chromosomal Rearrangement Rates, a genetic assay to quantitatively measure the rate at which GCRs occur in yeast cells. The assay measures the rate of simultaneous inactivation of two markers placed on a nonessential end of a yeast chromosome. This simple protocol for determining GCR mutation rates in a variety of genetic backgrounds coupled with a diversity of modified GCR assays has provided tremendous insight into the large numbers of pathways that suppress genomic instability in yeast and appear to be relevant to cancer suppression pathways in humans. As one of September’s featured articles, the full text protocol is freely available to subscribers and nonsubscribers alike.

The Drosophila neuromuscular junction (NMJ) provides a superb model system for investigating the cellular and molecular mechanisms of synaptic transmission. The NMJ is large, easily accessed and its genetics are well-characterized. It shares many structural and functional similarities to synapses in other animals, including humans. In the September issue of Cold Spring Harbor Protocols, Bing Zhang and Bryan Stewart present an essential set of primers for electrophysiological recording from the Drosophila NMJ. The issue contains a detailed explanation of the Equipment Setup necessary, as well as instructions for Fabrication of Microelectrodes, Suction Electrodes, and Focal Electrodes. Protocols for Electrophysiological Recording from a ‘Model’ Cell, Electrophysiological Recording from Drosophila Larval Body-Wall Muscles, Voltage-Clamp Analysis of Synaptic Transmission at the Drosophila Larval Neuromuscular Junction, and Focal Recording of Synaptic Currents from Single Boutons at the Drosophila Neuromuscular Junction are also included. These protocols are adapted from Drosophila Neurobiology: A Laboratory Manual. Based on Cold Spring Harbor Laboratory’s long-running course, this manual has rapidly become an important resource for any neuroscience lab.

Large segments of DNA can vary in copy number between individuals. Such copy number variations (CNVs) contribute greatly to genetic diversity and are also thought to be associated with susceptibility or resistance to some diseases, including cancer. Simple Copy Number Determination with Reference Query Pyrosequencing (RQPS), featured in the September issue of Cold Spring Harbor Protocols, provides an assay for determining the copy number of any allele in the genome. The method, from Raphael Kopan and colleagues at Washington University, takes advantage of the fact that pyrosequencing can accurately measure the ratio of DNA fragments in a mixture that differ by a single nucleotide. A reference allele with a known copy number and a query allele with an unknown copy number are engineered with single nucleotide variations, and the ratio seen between these probes and genomic DNA reflects the copy number. RQPS can be used to measure copy number of any transgene, differentiate homozygotes from heterozygotes, detect the CNV of endogenous genes, and screen embryonic stem cells targeted with bacterial artificial chromosome (BAC) vectors. RQPS is rapid, inexpensive, sensitive, and adaptable to high-throughput approaches. As one of our featured articles, the protocol is freely available to subscribers and non-subscribers alike.