Notable

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 seems to be very powerful in combination with some experimental data as illustrated in several examples in the paper. Implementation of mobility for the docking surfaces will be the essential next step, as pointed out by the authors." —Dorothee Kern, Brandeis University, US J. Buhler, "Efficient large-scale sequence comparison by locality-sensitive hashing," Bioinformatics, 17:419-28, May 2001. "The researchers describe a fast heuristic method for finding statistically significant similarities between long DNA sequences; in some situations the algorithm may be a substantial improvement over existing search methods. Current implementations of BLAST have a sizable probability of overlooking DNA alignments with a large percentage of mismatches, while the algorithm described here may be tuned to be highly sensitive, on average, without unduly increasing execution time. It is likely the method can be effectively extended to gapped alignments, but whether it can be effective for protein as well as DNA alignments awaits demonstration." —Stephen Altschul National Institutes of Health, US Proteomics E. Sprinzak, H. Margalit, "Correlated sequence-signatures as markers of protein-protein interaction," Journal of Molecular Biology, 311:681-92, Aug. 24, 2001. "Analyzing and understanding the protein interactions and networks taking place within cells and organisms is a crucial issue for the postgenomic era; the authors describe a novel technique using specific sequence signatures to analyze for preferential interacting protein combinations. Statistical evidence for preferential sequence-signature pairs is presented, and the potential for restricting search space and direct experimental design in Y2H experiments are discussed." —Klaus Mayer GSF - National Research Center for Environment and Health, Germany Genomes & Genetics S.W. Roy et al., "Footprints of primordial introns on the eukaryotic genome," Trends in Genetics, 17:496-501, September 2001. "This paper reports the very interesting finding that the bias of intron phases correlates with ages of gene sets: the older the genes, the stronger the bias is. This supports a conjecture of intron evolution that ancient introns evolved with later insertions of introns that would add random noise to the distribution of the phase." —Manyuan Long, University of Chicago, US Stem Cells M. Reyes et al., "Purification and ex vivo expansion of postnatal human marrow mesodermal progenitor cells," Blood, 98:2615-25, Nov. 1, 2001. "The authors identify protocols by which mesodermal progenitor cells can be cultured and differentiated into a variety of cell types including endothelial cells, osteoblasts, chondrocytes, adipocytes and skeletal myoblasts. The progenitor cells were isolated by depleting bone marrow mononuclear cells from CD45+ cells and then by carefully controlling the culture conditions these cells could be sent down differentiation pathways of choice. The significance of these results is that they open the way for the production (at least in theory) of large numbers of cells of specific differentiation types for clinical use in genetic or degenerative disease and take the field of stem cell biology that much closer to real clinical value." —Richard Vile, Mayo Clinic, US Designer Proteins L. Wang et al., "Adding L-3-(2-Naphthyl)alanine to the genetic code of E. coli," Journal of the American Chemical Society, 124:1836-7, Mar. 6, 2002. "These authors have moved one important step closer to the ability to co-opt the cell's native machinery to make a protein with unnatural amino acids. Here they report a specific tRNA synthetase that aminoacylates a specific tRNA that incorporates a non-native amino acid in response to a specific codon. They achieve fidelity approaching that of insertion of natural amino acids." —Mark Nelson, E.I. DuPont de Nemours & Co., US Immunology A.S. MacDonald et al., Cutting edge: Th2 response induction by dendritic cells: A role for CD40," Journal of Immunology, 168:537-40, Jan. 15, 2002. "This paper demonstrates, using a mouse model of schistosome infection, that CD40-CD154 interactions are required to induce Th2 but not Th1 responses. This interesting study examines how Th2 responses are initiated and shows that CD40 (-/-) dendritic cells are incapable of priming Th2 responses. Interestingly, CD40 (-/-) dendritic cells primed with Propionibacterium acnes, a Th1-driving stimulus, were fully capable of generating antigen specific Th1 responses, suggesting that CD40 expression is more important for the initiation of type 2 immune responses." —Thomas Wynn, National Institutes of Health, US Metabolomics B.H. ter Kuile, H.V. Westerhoff, "Transcriptome meets metabolome: Hierarchical and metabolic regulation of the glycolytic pathway," FEBS Letters, 500:169-71, July 6, 2001. "The authors show that in contrast to the generally held opinion, metabolic regulation is often more important than transcriptional regulation in the control of cell function. A method, based on metabolic control analysis, is developed to quantify the relative contribution of metabolic regulation and transcriptional regulation in the control of glycolysis in three parasitic protists. In steady-state chemostat cultures, enzyme activities were measured over a range of dilution rates and correlated to glucose consumption rates, after which a hierarchical and a metabolic regulation coefficient were calculated." —Jacky Snoep, University of Stellenbosch, South Africa

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