J.O. Korbel et al., "SHOT: A Web server for the construction of genome phylogenies," Trends in Genetics, 18[3]:158-62, March 1, 2002. "This paper reports the results of phylogenetic analysis using whole genome comparisons and introduces a new Web server (named "SHOT") for further analysis by gene-content and gene-order methods. Among the results, the gene-content method showed Homo sapiens to be more closely related to Drosophila melanogaster than Caenorhabditis elegans, and both methods showed

Foster City, Calif.-based Applied Biosystems (ABI) officially launched its entry into the proteomics market, the 4700 Proteomics Analyzer, in January. Based on the first commercially available, tandem time-of-flight (TOF/TOF™) mass spectrometer (MS) and offering a number of productivity-enhancing features, the 4700 is designed specifically to excel at proteomics applications, according to David Hicks, ABI's director of marketing for proteomics applications. The 4700 includes the matrix-a

Mass spectrometry (MS) is largely responsible for propelling the ongoing proteomics revolution,1 and the boom in MS applications has not gone unnoticed by instrument manufacturers. For the past few months Micromass, Thermo Finnigan, and Applied Biosystems have rolled out new instruments or offered new technologies to enhance existing hardware. The Scientist reviews three of these developments below. When researchers perform peptide mass fingerprinting on gel slices, they typically use matrix-as

S.B. Ficarro et al., "Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae," Nature Biotechnology, 20[3]:301-5, March 2002. "This is a long-awaited paper detailing more than 200 phosphorylation sites from Saccharomyces cerevisiae. The authors used immobilized metal affinity chromatography (IMAC) to selectively isolate phosphopeptides from nonphosphopeptides. The new advance is the selectivity of the IMAC column when utilized after methylation of aspartat

There's more to life than DNA, RNA, and proteins. Literally. Sugars are also in the mix. And the roles that carbohydrates play in biology are just as important as those of any member of the better-characterized trinity. These macromolecules affect cell-cell interactions, immune function, and protein regulation, and disruption of their biology results in disease. One magazine likened the study of carbohydrates, called glycobiology, to Cinderella—neglected stepsister to her two more glamoro

K. Rein et al., "The Drosophila standard brain," Current Biology, 12[3]:227-31, Feb. 5, 2002. "The authors present an approach to create a 3D image of the fly brain. This is a very useful resource tool that will make it possible to create an atlas of gene expression patterns and will be very useful for analyzing brain structure in mutant backgrounds." —Oliver Hobert, Columbia University College of Physicians and Surgeons, US X-Ray Crystallography F.J. Lopez-Jaramillo et al., "Crystalliz

A. Fahmy, G. Wagner, "TreeDock: A tool for protein docking based on minimizing van der Waals energies," Journal of the American Chemical Society, 124:1241-50, Feb. 20, 2002. "Current understanding of protein-protein and protein-ligand interactions is very limited. This paper describes a new algorithm that allows exploration of the interaction surface very fast and consequently at very fine resolution. The rationale behind the program is to keep the two molecules always in contact. This program

Ebersberg, Germany-based MWG-Biotech AG has officially entered the human genome microarray market. The company's Pan® Human Array, scheduled for release this month, consists of three slides containing a total of 30,000 known or described human genes; MWG began offering the first slide in the set last December. Santa Clara, Calif.-based Affymetrix Inc. also recently launched a human genome microarray product, the GeneChip® Human Genome U133 set.1 However, the two products differ in thr

M. Gray, S.M. Honigberg, "Effect of chromosomal locus, GC content and length of homology on PCR-mediated targeted gene replacement in Saccharomyces," Nucleic Acids Research, 29:5156-62, Dec. 15, 2001. F1000 Rating: Recommended "While gene knockouts or replacements are easily and commonly done in yeast, the targeting efficiency is quite variable. The authors have systematically evaluated key parameters and found that a GC content of at least 40% in the regions of homology improves targeting ef

J.S. Andersen et al., "Directed proteomic analysis of the human nucleolus," Current Biology, 12:1-11, Jan. 8, 2002. F1000 Recommendation: Must Read "This is a good paper showing the large scale analysis of a very large protein complex, the nucleolus. [Points of interest]: The size of the complex and that it is dynamic. The mass spectrometry methods used here were a combination of high throughput (matrix-assisted laser desorption ionization coupled to time of flight detection) and low throughpu

Nanotechnology hit the big time in July 1995, when it debuted on the television show, The Outer Limits. In an episode entitled "The New Breed," a scientist develops nanorobots capable of repairing damaged cells and correcting physical defects. But, like any good morality play, the experiment goes horribly wrong, turning a panacea into a nightmare. Clearly, nanotechnology makes for good science fiction, but scientists have been working to make it an interesting reality, too. Nanotechnology refers

M.B. Yaffe et al., "A motif-based profile scanning approach for genome-wide prediction of signaling pathways," Nature Biotechnology, 19:348-53, April 2001. F1000 Rating: Recommended "This paper describes a powerful fusion of experimental and computational methods to predict binding motifs in signal transduction pathways. Functional screens of degenerate peptide libraries are used to determine experimentally verified sequence preferences (motifs) that are the basis for a pattern matching approac