Notable

T. Sicheritz-Pontén, S.G. Andersson, "A phylogenomic approach to microbial evolution," Nucleic Acids Research, 29[2]:545-52, Jan. 15, 2001.

"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."

J.E. Barrick et al., "Large libraries reveal diverse solutions to an RNA recognition problem," Proceedings of the National Academy of Sciences (PNAS), 98[22]: 12374-8, Oct. 23, 2001.

"The development of tight-binding and highly selective small molecule ligands for RNA remains a very challenging problem, but this article demonstrates that combinatorial selection approaches such as the in vitro mRNA-peptide fusion systems offer promising possibilities for RNA recognition. Using a previously described in vitro mRNA-peptide fusion system, libraries of 150, 1600, and 9 trillion different peptide sequences were constructed based on the arginine-rich, RNA-binding domain of the lambda N protein. This sequence is known to recognize with high affinity the boxBR RNA hairpin containing a five-base RNA loop that adopts a tetraloop fold. In this work, several high affinity RNA-binding peptides were isolated (down to low nanomolar dissociation constants), demonstrating the usefulness of biological combinatorial libraries at targeting RNA."

Y. Timsit, "Convergent evolution of MutS and topoisomerase II for clamping DNA crossovers and stacked Holliday junctions," Journal of Biomolecular Structure and Dynamics, 19[2]:215-8, October 2001.

"This study provides structural and evolutionary evidence for convergence at the protein structural level (between a DNA repair protein and a topoisomerase). This finding has major implications for molecular evolutionary studies, since it has been generally assumed by most researchers that structural similarity must be the result of homology (common ancestry) rather than analogy (e.g., convergence)."

S.K. Rehen et al., "Chromosomal variation in neurons of the developing and adult mammalian nervous system," PNAS, 98[23]:13361-6, Nov. 6, 2001.

"The basic assumption that the normal mammalian nervous system contains neurons with identical genomes is challenged by this study, which suggests that the nervous system is a genetic mosaic. Multiple lines of evidence suggested that genomes of developing and adult neurons can be different at the level of whole chromosomes, i.e. neurons exhibit chromosomal aneuploidy. The biological consequences of neuronal aneuploidy might be similar to X-inactivation, imprinting or allelic inactivation. Aneuploid neurons with altered physiology might have significant consequences for establishment of neural networks."

C. Kooperberg, et al., "Sequence analysis using logic regression," Genetic Epidemiology, 21[Suppl. 1]:S626-31, 2001.

"The authors develop a new adaptive regression methodology, called Logic Regression, that attempts to construct predictors as Boolean combinations of (binary) covariates; this methodology should be useful for finding associations between many genetic/environmental factors and disease outcomes. This is an exciting new approach to finding the few important predictors out of large pools of possible predictors, while allowing for complex interactions between the underlying predictors. For more details on this exciting and promising new methodology, see the authors' technical report on their Web page (bear.fhcrc.org/~clk/ref.html)."

C. Klein et al., "NMR spectroscopy reveals the solution dimerization interface of p53 core domains bound to their consensus DNA," Journal of Biological Chemistry, 276[52]:49020-7, Dec. 28, 2001.

"The activation mechanism of the p53 tumor suppressor protein is still unclear - this paper adds experimental data to address this question, and derives a new model for the dimerization of p53 after DNA binding. In this model, the dimerization interface includes the short H1 helix, which contains "hot spots" for p53 mutations and comprises the binding site for a putative p53 inhibitor."

T. Sasada et al., "A naturally processed mitochondrial self-peptide in complex with thymic MHC molecules functions as a selecting ligand for a viral-specific T cell receptor," Journal of Experimental Medicine, 194[7]:883-92, Oct. 1, 2001.

"This interesting paper describes the identification of a naturally processed thymic peptide involved in positive selection of a viral antigen specific T cell repertoire. The authors guide the biochemical isolation of the natural peptide with a functional assay involving TCR transgenic thymocytes. The peptide turned out to be derived from the widely expressed mitochondrial NADH ubiquinone oxidoreductase. Importantly, the peptide has little sequence homology with the cognate antigenic peptide, it is a weak agonist for mature specific T cells but induces functional differentiation of TCR transgenic thymocytes. Thus, this is the first naturally occurring ligand directly recovered from thymus that can mediate positive selection of immature T cells."