Large numbers of protein-protein interactions have been mapped for yeast and worms, and now in the January 11 Nature, Rain et al. present the first large set of interactions for a prokaryote (Nature 2001, 409:211-215). The two-hybrid screen of 261 proteins from the gastric pathogen Heliobacter pylori against a library of genome-encoded polypeptides revealed 1,200 putative interactions. Screening against a library allows the identification of interacting domains, and reduces the rate of false ne

Pre-biotic evolution created something almost infinitely unlikely to have arisen by chance: reproducing entities whose many parts interact in a way that is vastly more complex and interdependent than the disorganized interactions of the inanimate objects in the surrounding environment. And yet this creation of primitive organisms was all achieved in perhaps a few hundred million years. In the January 16 Proceedings of the National Academy of Sciences, Jain and Krishna use mathematical modeling t

Mass spectrometry and pooled DNA samples allow for rapid genotyping of SNPs.

The same duplication event arises in multiple lines of bacteria as they adapt to heat.

Many cancers become resistant to chemotherapeutic drugs thanks to loss of the p53 protein, which promotes cell cycle arrest and apoptosis in response to certain drugs. Metastatic melanomas are unusual in that, despite their chemoresistance, they retain functional p53. In the January 11 Nature, Soengas et al. find that these melanomas still lose the p53 pathway thanks to deletion and methylation of the p53 effector Apaf-1 (Nature 2001, 409:207-211). The Apaf-1 locus shows over 40% loss of heteroz

In the January Nature Biotechnology, Raamsdonk et al. find that, even when mutation of a gene causes no obvious phenotype, metabolite profiling can still give clues to gene function (Nat Biotechnol 2001, 19:45-50). Their test case involves two yeast strains deleted for either one of the two redundant genes for 6-phosphofructo-2-kinase (6-PF-2-K). These deletion strains fail to show a growth defect, even in chemostat competition experiments, but an analysis of specific metabolites clearly sets th

Yeast is unusual in that its transcriptional activators cannot work over long distances. But in the 4 January Nature, de Bruin et al. report that the looping of heterochromatic-like telomere regions corrects this shortcoming (Nature 2001, 409:109-113). They place a binding site for the activator Gal4 downstream of a reporter gene. The site is inactive when the reporter is at an internal chromosomal locus, but active when the gene cassette is placed, in either orientation, near the telomere. Only

Approximately 1.6 million single nucleotide polymorphisms (SNPs) have been identified and deposited in public databases, but more are always needed for studies of other species and identification of mutations in candidate disease genes. In the January Nature Biotechnology, Nakatani et al. outline a new method for SNP identification using capture by a mismatch-specific ligand followed by surface plasmon resonance (SPR; Nat Biotechnol 2001, 19:51-55). The ligand, a dimeric naphthyridine, intercala

Duplication, deletion and mutation have created a new gene, denoted Sdic, that encodes a fly sperm axoneme protein. Sdic is present in the fly Drosophila melanogaster, but not in its close relative Drosophila simulans. In the 5 January Science, Nurminsky et al. find evidence for a selective sweep around Sdic in D. melanogaster (Science 2001, 291:128-130). D. melanogaster DNA has a significant depression in the level of synonymous polymorphism around Sdic, and an increase in the occurrence of rar

Array analysis of dividing cells has been tackled for yeast, but in the January Nature Genetics Cho et al. present the first large-scale analysis in human cells (Nat Genet 2001, 27:48-54). They identify 731 of 40,000 human genes and expressed sequence tags (ESTs) as being cell cycle regulated in primary fibroblasts, and use a functional classification system to identify coordinate regulation of pathways. Notable surprises include upregulation of motility-related genes in G2 (perhaps to prepare d

In the 22 December Science Ren et al. combine chromatin immunoprecipitation with DNA microarrays to identify all binding sites for two budding yeast transcription activators (Science 2000, 290:2306-2309). They start by breaking open cells, cross-linking bound protein to DNA, sonicating, and immunoprecipitating with an antibody against a particular transcription factor. The isolated DNA is amplified, and the abundance of the amplified fragments is compared with a whole genome amplification using

After comparing the genomic sequences of the two yeast species Saccharomyces cerevisiae and Candida albicans, Seoighe et al. report in the December 19 Proceedings of the National Academy of Sciences that gene adjacencies have been broken as frequently by small inversions as by translocations or long-distance transpositions (Proc Natl Acad Sci USA 2000, 97:14433-14437). Only 9% of gene pairs that are adjacent in one species are conserved as adjacent in the other, and the number of orientation cha

In the December 19 Proceedings of the National Academy of Sciences, Kawashima et al. compare their sequence of Thermoplasma volcanium with existing genomic sequences of seven other archaeons, and find that thermophiles adapt to increasing heat by clustering purines and pyrimidines, and by making more basic proteins (Proc Natl Acad Sci USA 2000, 97:14257-14262). The frequency of purine or pyrimidine dinucleotides in the genomic sequences rises with increasing optimum growth temperature (OGT), as

Immunization with amyloid-beta peptide reduces the learning deficits seen in mouse models of Alzheimer's disease.

In the 15 December Science, Laub et al. find that a full 19% of the genome of the bacterium Caulobacter crescentus is subject to cell-cycle-specific regulation (Science 2000, 290:2144-2148). A surprising number of genes are induced, as in yeast, just before they are needed. Other genes, such as those directing the construction of the flagella and pilus, are induced in transcriptional cascades, with the order of induction reflecting the order of assembly of the respective apparatus. Laub et al. a