Notable

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 variability in spacing, and to assign scoring values to each parameter. Several examples of search descriptors and the results of the search are included to demonstrate the utility of the algorithm." —Tina Henkin, Ohio State University, US RNA Stability S.M. Elbashir et al., "Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate," EMBO Journal, 20:6877-88, Dec. 3, 2001. F1000 Recommendation: Must Read "Elbashir et al. get down to the hard work of dissecting how RNAi works at a molecular level. In this study they focus on the structural requirements of the siRNA template that mediates mRNA degradation. At the end of the paper they provide an "siRNA user guide" that should be of great help to anyone who wants to use RNAi as a technique. This work, however, also provides a good foundation for future studies to elucidate the mechanism of this fascinating process." —Jon Lorsch, Johns Hopkins University School of Medicine, US Transcription & Translation W.H. McClain, K. Gabriel, "Construction of an Escherichia coli knockout strain for functional analysis of tRNA(Asp)," Journal of Molecular Biology, 310:537-42, July 3, 2001. F1000 Recommendation: Recommended "The technique presented in this work allows the study, in the cell, of the effect of mutations in tRNAs for which suppressors cannot be designed because the native anticodon is required for recognition by the cognate synthetase (which is the most common case). Inactivation of tRNA genes is a challenge because there are generally multiple gene copies, deletion leaves no identifiable gene remnant to confirm the loss, and there is the possibility that flanking genes would be functionally disrupted. Application of this technique will refine our understanding of how identity determinants and antideterminants are balanced to target a set of isoaccepting tRNAs to one cognate synthetase." —Anne-Catherine Dock-Bregeon, Institut de Genetique et Biologie Moleculaire et Cellulaire, France Molecular Evolution J. Yin et al., "A comparative analysis of the immunological evolution of antibody 28B4,"Biochemistry, 40:10764-73, Sept. 11, 2001. F1000 Recommendation: Must Read "Through a combination of structural and mutagenesis studies, the details of antibody affinity enhancement throughout maturation of a catalytic antibody immune response is revealed. Structures of the germ-line antibody show induced-fit hapten binding, whereas the structure of the affinity matured antibody is better preorganized for binding, including a different orientation of bound hapten in the binding pocket. The emerging hypothesis, relevant to immunology as well as protein engineering, is that germ-line antibodies have more flexible binding sites capable of greater cross-reactivity, and these are enhanced by somatic mutations that sequentially increase pre-organized complementarity to antigen." —Brent Iverson, University of Texas, US Plant Genetics M. Lengerova, B. Vyskot, "Sex chromatin and nucleolar analyses in Rumex acetosa L," Protoplasma, 217:147-53, 2001. F1000 Recommendation: Exceptional "The relationship between chromatin packaging/organization and function is being seen as increasingly important; here, the authors show peripheral condensed bodies, observed exclusively in male (XY) nuclei of Rumex acetosa, a dioecious plant with sex chromosomes, represent constitutive hetero -chromatin of Y chromosomes. These condensed bodies are characterized by underacetylation of their histone H4, often a modification associated with reduced expression. Hypermethylation of the large domains of the heterochromatic Y chromosomes, compared to autosomes, is not observed in male cells, although inactive rRNA genes display prominent methylation." —JS Heslop-Harrison, University of Leicester, UK Cell Signaling D. Chilov et al., "Hypoxia affects expression of circadian genes PER1 and CLOCK in mouse brain," Federation of American Societies for Experimental Biology, 15:2613-22, December 2001. F1000 Recommendation: Recommended "This paper reports evidence that the basic helix-loop-helix PAS domain transcription factors PER1 and CLOCK are regulated not only by circadian signalling mechanisms but also by hypoxia, suggesting crosstalk between the circadian clockwork and oxygen homeostasis pathways. In addition, this paper presents evidence that PER1 interacts directly with the alpha subunit of hypoxia-inducible transcription factors, providing a potential molecular basis for the observed interaction between the circadian and hypoxic signalling pathways." —Ronald Conaway, Stowers Institute for Medical Research, US Microfluidics J.R. Webster et al., "Monolithic capillary electrophoresis device with integrated fluorescence detector," Analytical Chemistry, 73:1622-6, April 1, 2001. F1000 Recommendation: Recommended "In this paper, the successful integration of microfluidic, optical, and electronic devices into a monolithic chip is demonstrated for capillary electrophoresis. Fluorescence detection is made possible by combining integrated silicon photodiodes with a thin-film optical filter. With these technical advances, portable DNA detection devices are practical." —Deirdre Meldrum, University of Washington, US Genomics G.K. Wong et al., "Most of the human genome is transcribed," Genome Research, 11:1975-7, December 2001. F1000 Recommendation: Must Read "The paper points out that very large genes exist in the human genome, and that these are likely to be missed by existing annotation approaches, and even by studies of cDNA sequences. Using a sub-set of contigs that excludes small ones, an estimate of gene size is derived, assuming a total gene number between 30 and 40 thousand, and it is suggested that the mean value could be as high as 60kb or higher, implying that intergenic sequences may represent only a small fraction of the total human DNA." —Deborah Charlesworth, University of Edinburgh, UK

Notable

RNA Stability

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