Confocal microscopes and other related tools allow researchers to take optical sections through a sample to create a three-dimensional picture of that object. But most things worth looking at under a microscope are not static; they move and change shape over time. Coventry, England-based Improvision now offers a software product that allows researchers to study the structure of complex objects over time—that is, in 4D. Company literature describes Volocity as "the first true color 4D rende

T.J. Macke et al., "RNAMotif, an RNA secondary structure definition and search algorithm," Nucleic Acids Research, 29:4724-35, Nov. 15, 2001. F1000 Recommendation: Recommended "This paper describes a new computer program that allows searching of genomic sequence databases for complex RNA structural elements. RNAMotif represents a major technical advance over previously available tools in that it allows the user to specify multiple parameters, including non-canonical base-pairings and variabilit

T. Sicheritz-Pontén, S.G. Andersson, "A phylogenomic approach to microbial evolution," Nucleic Acids Research, 29[2]:545-52, Jan. 15, 2001. F1000 Rating: Must Read "The paper describes methods and computer programs for automated phylogenetic analysis of complete genome datasets, as well as useful visualization tools for the results. The tools should be useful to those looking for genes that may have unusual evolutionary histories relative to other genes in the same genome." —Jonath

Sometimes it pays to listen to your adviser. Hui Ge, a graduate student in Marc Vidal's lab at Harvard Medical School did, pursuing one of her adviser's pet projects, and was published in Nature Genetics for her trouble.1 Ge and second author Zhihua Liu were partners in genetics professor George Church's annual course, Genomics and Computational Biology. As part of that course, students must pick an individual project and run with it, says Church. "If the projects are good enough, then I continu

J.A. Camarero et al., "Peptide chemical ligation inside living cells: In vivo generation of a circular protein domain," Bioorganic and Medicinal Chemistry, 9[9]:2479-84, September 2001. F1000 Rating: Recommended "To investigate whether chemo-selective peptide ligations work in vivo, the authors demonstrate the in vivo head-to-tail cyclization of a bioactive SH3 domain using native chemical ligation. The protein precursor was constructed using a clever combination of an intein-fusion protein an

Few biological fields have benefited from technological advances as much as genomics. The field could not be where it is today without progress in automated sequencing methods and in software to interpret, annotate, and manage the voluminous data that these automated sequencers churn out. Without this latter development, researchers would be hard pressed to read and understand these gigabytes of data--the equivalent of having an encrypted encyclopedia without a deciphering key. (See related sto

Paradigms don't shift easily. But in a recent paper,1 researchers-nearly four years after their initial observation and one year after boarding the journal-submission carousel-are challenging one of modern biology's central tenets. For at least 25 years, biologists have believed that although transcription and translation are coupled in bacteria, they are separated in eukaryotic cells. However, new work from Peter Cook's laboratory at the University of Oxford, UK, which demonstrates translation

Atomic force microscopes can generate a highly detailed topological map of a specimen by moving a stylus coupled to a cantilever over the sample surface, using a laser to measure deflection of the cantilever.1 Now, researchers at the University of California at Berkeley have adopted this principle to create a system capable of quantifying intermolecular interactions, with potential applications for both clinicians and high-throughput proteomics researchers.2 In a research article published in

To determine whether a given transcription factor activity is present in a sample, you need look no farther than the standard electrophoretic mobility shift assay (EMSA). In an EMSA, researchers mix a radioactively labeled DNA probe with a protein extract and run the entire reaction on a nondenaturing polyacrylamide gel. Because the protein-bound probe will migrate more slowly than a free probe, the experiment is described as a "gel shift." Unfortunately, the gel shift is a cumbersome way to pro

The defining characteristic of diabetes is its failure to properly maintain blood glucose levels. Normally, the elevated glucose concentration that occurs after eating induces the release of the hormone insulin from pancreatic beta cells. Cells expressing the insulin receptor can bind insulin and respond to the signal, thereby maintaining glucose homeostasis through changes in gene expression patterns and cellular metabolism. Insulin-induced effects include enhanced glucose uptake and glycogen s

Researchers interested in gene expression studies adopt one of two approaches. They can either examine the expression of a given gene in a population of cells in aggregate, or they can study the gene on a cell-by-cell basis in situ. The advantage of the former approach is its simplicity: It is generally easy to prepare RNA or protein from a given tissue sample and to probe it for the gene or protein of interest. But there are several disadvantages associated with the population approach. First o

R2-D2 and C3PO would probably have enjoyed the scene. After all, the exhibit hall at the World Trade Center in Boston buzzed with robots, gadgets, widgets, and, of course, humans--lots of humans. More than 4,000 attendees and 300 exhibitors met Aug. 12-17 at the sixth annual Drug Discovery Technology (DDT) conference. Automated multichannel liquid dispensers, robotic arms, cell sorters, and computers whirred and hummed, while scientists poked and played, queried, and chatted. All this high-tech