Bench Marks

I’ve recently written two pieces on scientists and social networks over at my other blogging gig, and thought they might be of interest to readers here:

Scientists Still Not Joining Social Networks

and

NIH Funds a Social Network for Scientists–Is It Likely to Succeed?

Volume 2 of our Emerging Model Organisms series rolls on in the October issue of Cold Spring Harbor Protocols. This month brings a look at two emerging models, one all-time classic.

Neelima Sinha and colleagues present “The Mother of Thousands” (Kalanchoë daigremontiana), a plant which has the fascinating ability to regenerate and entire organism from somatic cells. The process of forming a somatic embryo outside of a seed environment provides an attractive model system for studying embryogenesis. Kalanchoë is also used in the study of Crassulacean acid metabolism (CAM), which is an important evolutionary adaptation of the photosynthetic carbon assimilation pathway to arid environments. In addition, natural compounds extracted from tissues of Kalanchoë have potential applicability in treating tumors and inflammatory and allergic diseases, and have been shown to have insecticidal properties. Protocols are provided for fixing and sectioning tissues, in situ hybridization, transformation using agrobacterium, DNA extraction and RNA extraction.

John Werren and colleagues provide The Parasitoid Wasp Nasonia: An Emerging Model System with Haploid Male Genetics. Nasonia is a genus consisting of four interfertile species. They’re particularly useful as a genetic tool for study because females are diploid and develop from fertilized eggs, and males are haploid and develop from unfertilized eggs. This allows geneticists to exploit many of the advantages of haploid genetics in an otherwise complex eukaryotic organism. Protocols are available for field collection, strain maintenance, rearing fly hosts, egg collection, virgin collection and crossing methods, larval RNAi and curing Wolbachia bacterial infections.

As for that “classic” system mentioned above, if you know genetics, then you know Barbara McClintock, and you know that Maize has been a keystone model system for nearly a century. Micheal Scanlon and colleagues have written up Maize (Zea mays): A Model Organism for Basic and Applied Research in Plant Biology, which gives an up-to-date discussion of the state of Maize research.

RNA molecules interact with proteins to drive many cellular activities, including post-transcriptional processing of RNA, regulation of translation, and transport of RNA to name but a few. These ribonucleoprotein complexes are isolated by coimmunoprecipitation (co-IP), where a protein-specific antibody is used to purify the protein of choice and its associated complex members. Analysis of RNA-Protein Complexes by RNA Coimmunoprecipitation and RT-PCR Analysis from Caenorhabditis elegans gives step-by-step instructions for RNA co-IP from C. elegans whole-worm extracts. The protocol, from Christian Eckmann and colleagues at the Max Planck Institute of Molecular Cell Biology and Genetics, starts with the large-scale growth of worms and describes the preparation of whole-worm extracts, RNA co-IP, isolation of the purified RNA, and identification of specific genes through RT-PCR. As one of our featured articles for October, the protocol is freely available to subscribers and non-subscribers alike. Eckmann and colleagues have also contributed an accompanying article describing Analysis of In Vivo Protein Complexes by Coimmunoprecipitation from Caenorhabditis elegans.

Light carries momentum, so an object that reflects or refracts a beam of light experiences a force. This force is very small, but still strong enough to manipulate objects, such as a polystyrene bead. Using light focused through a lens, beads can be “trapped” near the focus. These optical traps, or “optical tweezers” have become an important tool that allows researchers to manipulate individual molecules or molecular complexes. High-resolution optical trapping techniques can now detect movements on the scale of a single base pair of DNA, 3.4 angstroms. The October issue of Cold Spring Harbor Protocols includes a series of articles detailing the concepts behind optical trapping, the components of an optical trapping system and the single-molecule experiments in which they are used. Carlos Bustamante, Yann Chemla, and Jeffrey Moffitt provide an introduction to High Resolution Dual-Trap Optical Tweezers with Differential Detection, and subsequent articles on Managing Environmental Noise, Instrument Design, Data Collection and Instrument Calibration, Minimizing the Influence of Measurement Noise and Alignment of Instrument Components.

Some recent articles discussing computer software designed for use by biologists (I can’t personally vouch for any of these programs, but thought they might be of interest to readers of CSH Protocols):

Even Better Free Molecular Biology Software: Serial Cloner–the always valuable Bitesize Bio website has a review of Serial Cloner, a cross platform program for molecular biologists:

“It is very intuitive and is packed with features; from basics like constructing importing sequences, constructing plasmid maps and restriction mapping, through more complex things like sequence alignment, Gateway cloning and siRNA design.”

One of the commenters on the article also suggests PlasmaDNA.

iPhone apps every biologist needs: article from The Scientist, detailing 10 apps of interest. While many look useful, I’m not sure how many of them have added appeal on a mobile device (as opposed to use on a laptop or desktop computer). How often do you need to consult the periodic table while you’re on-the-go?

Also, I may be a luddite, but in my lab days, you wouldn’t even take a lab manual to the bench, you’d photocopy the protocol you were going to use because you didn’t want the expensive manual exposed to harsh chemicals and other contaminants. Are people really using expensive and fragile items like the iPhone at the lab bench? Do you set your iPhone down next to the phenol, just behind the HCl? Can you use it while wearing gloves? Wouldn’t you worry about all the E. coli contaminating your gloves from the plasmid preps you’re doing? Do you really want to smear that all over the device you’ll be holding next to your face?

9/12/09–Edited to add–Here’s another list, of 50 Useful iPhone Apps for Science Students & Teachers.

Congratulations go out to this year’s winners of the Nobel Prize for Medicine, Jack Szostak, Carol Greider and Elizabeth Blackburn for their pioneering work on telomeres. Cold Spring Harbor Laboratory Press is proud to be the publisher of Telomeres, a recent book on the subject co-edited by Blackburn.

Blackburn was interviewed by Joe Gall as part of the Genetics Society of America’s “Conversations in Genetics” oral history project. Some clips from the video conversation are available online:

Sequencing the first telomeres


Going to Cambridge

The whole conversation is available on DVD individually, or as part of a larger volume that includes Sydney Brenner, Charles Yanofsky, Victor McKusick, and Ray Owen.

The study of RNA has long been the tool of choice for understanding where and when genes are expressed in a cell, tissue, or organism during development or under specific physiological or environmental conditions. Recent discoveries have revolutionized our concept of RNA function; it is now known to be active in a much wider set of biological processes than was previously believed. Techniques for isolating RNA and for uncovering its interactions with proteins have taken on new importance as many laboratories define the roles of specific RNAs in the cell. The October issue of Cold Spring Harbor Protocols features articles detailing methods for RNA analysis.

Quantitative Real-Time RT-PCR (qRT-PCR) of Zebrafish Transcripts: Optimization of RNA Extraction, Quality Control Considerations and Data Analysis from Donald Love and colleagues at the University of Auckland presents an optimized method for RNA isolation from zebrafish, along with quality assessment and the use of reference genes. A protocol for quantitative real-time polymerase chain reaction (qRT-PCR) is also included. Like all of our featured articles, these protocols are freely available to subscribers and non-subscribers alike.