Notable

Volume 16 | Issue 13 | 29 | Jun. 24, 2002 Previous | Next New & Notable Selected articles from faculty member reviews | Compiled by Jeffrey M. Perkel The Faculty of 1000 is aWeb-based literature awareness tool published by BioMed Central. For more information visit www.facultyof1000.com. RIBOZYME DESIGN D.H. Burke et al., "Allosteric Hammerhead Ribozyme TRAPs," Biochemistry, 41:6588-94, May 28, 2002. "Hammerhead ribozyme activity has been upregulated allosterically more than 250-fold with "activator" DNA oligonucleotides that bind not to the ribozyme core, but to an "attenuator" region appended to the ribozyme. The upregulation of single-turnover activity could be increased even further by inclusion of 'antiattenuator' sequence on the activating oligo. Several features of the work offer interesting potential for more general application: (1) The assembly order of the ribozyme, substrate, and activating oligonucleotide affects the final activity level; (2) Neither the activator nor the attenuator sequences need to interact directly with the ribozyme core nucleotides; (3) Substantial knowledge of ribozyme structure or chemistry should not be needed to apply this to other systems." --Scott K. Silverman, University of Illinois, US MITOCHONDRIAL INDEPENDENCE T.J. Collins et al., "Mitochondria are morphologically and functionally heterogeneous within cells," EMBO Journal, 21:1616-27, April 1, 2002. "This paper uses several optical techniques to demonstrate, in a variety of cell types, that the different mitochondria in a single cell function autonomously. Mitochondria defined morphologically and shown not to be lumenally connected, using fluorescence recovery after photobleaching, respond independently to irradiation, histamine and tert-butyl hydroperoxide. Although hints of this kind of behavior have been reported previously, this paper dramatically illustrates that membrane potential, calcium entry and transmembrane potential are all regulated independently by the different mitochondria in a single cell." --David Andrews, McMaster University, Canada ADVANCING NMR A. Grishaev, M. Llinas, "CLOUDS, a protocol for deriving a molecular proton density via NMR," Proceedings of the National Academy of Sciences, 99:6707-12, May 14, 2002. "The authors describe in a series of two papers (see below) a novel approach to determining 3-dimensional structures of proteins from nuclear magnetic resonance (NMR) data. The beauty of the approach is that the traditional bottleneck of assigning chemical shift to the component atoms is circumvented. Rather, a 'cloud' of unassigned protons is obtained from a set of NOE [nuclear Overhauser effects] crosspeak intensities, via a molecular dynamics simulated annealing approach. Subsequently, the primary sequence of the protein is threaded onto the family of clouds via a Bayesian approach that identifies backbone and side-chain atoms. The process is thus analogous to chain-tracing a protein to measure electron density from X-ray diffraction experiments, and represents a departure from traditional NMR approaches. (See also: A. Grishaev, M. Llinas, "Protein structure elucidation from NMR proton densities," PNAS, 99:6713-18, May 14, 2002)." --Tracy Handel, University of California, Berkeley, US C.A. Rohl, D. Baker, "De novo determination of protein backbone structure from residual dipolar couplings using Rosetta," Journal of the American Chemical Society, 124:2723-9, March 20, 2002. "This manuscript describes combined use of the Rosetta algorithm and residual dipolar coupling solution nuclear magnetic resonance (NMR) data for de novo determination of small protein structures. The combined algorithm produces impressively accurate initial folds, which may be used as a basis for functional studies. The initial folds may also be used to expedite assignment of NMR NOESY [nuclear Overhauser effect spectroscopy] data, which are used for high-resolution structure determination." --Kristina Downing, University of Oxford, UK CHROMATIN IN VITRO H.B. Landsverk et al., "Reprogrammed gene expression in a somatic cell-free extract," EMBO Reports, 3:384-9, April 2002. "This study reports on development of a simple cell-free system that remodels chromatin and activates gene expression in heterologous differentiated nuclei. The reprogramming of nuclei may have broad applications in the research of transcriptional control and for manipulating the cell program." --Rivka Dikstein, Weizmann Institute of Science, Israel MICROBIAL IDENTIFICATION K.H. Wilson et al., "High-density micro-array of small-subunit ribosomal DNA probes," Applied Environmental Micro-biology, 68:2535-41, May 2002. "Wilson and colleagues describe the development and evaluation of a first-generation rDNA oligonucleotide microarray. A microarray that provides highly parallel, reliable and efficient analysis of large numbers of different rDNA sequences will dramatically advance the study of complex microbial communities. This first generation tool functioned well in identifying a number of specific bacteria when they were present alone in a simple experimental context, and it performed reasonably well in characterizing a complex mixture, but improvements in coverage, discrimination, and pattern recognition will be needed." --David Relman, Stanford University, US PROMOTER DESIGN R.P. Bandwar et al., "Kinetic and thermodynamic basis of promoter strength: multiple steps of transcription initiation by T7 RNA polymerase are modulated by the promoter sequence," Biochemistry, 41:3586-95, March 19, 2002. "The authors provide a framework for thinking about how different promoters may be exploited for differential gene expression in metabolic engineering. The binding of T7 RNA polymerase to promoters of varying strength is analyzed in thermodynamic terms and in terms of the specific bases in the promoters. This kind of approach should allow for design or discovery of different-strength promoters that will allow fine-tuning of expression of proteins in engineered metabolic pathways." --Mark Nelson, E.I. DuPont de Nemours & Co., US ©2002, The Scientist Inc. Comment E-mail article

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