Numerous potentially functional but non-genic conserved sequences on human chromosome 21

The use of comparative genomics to infer genome function relies on the understanding of how different components of the genome change over evolutionary time. The aim of such comparative analysis is to identify conserved, functionally transcribed sequences such as protein-coding genes and non-coding RNA genes, and other functional sequences such as regulatory regions, as well as other genomic features. Here, we have compared the entire human chromosome 21 with syntenic regions of the mouse genome, and have identified a large number of conserved blocks of unknown function. Although previous studies have made similar observations, it is unknown whether these conserved sequences are genes or not. Here we present an extensive experimental and computational analysis of human chromosome 21 in an effort to assign function to sequences conserved between human chromosome 21 (ref. 8) and the syntenic mouse regions. Our data support the presence of a large number of potentially functional non-genic sequences, probably regulatory and structural. The integration of the properties of the conserved components of human chromosome 21 to the rapidly accumulating functional data for this chromosome will improve considerably our understanding of the role of sequence conservation in mammalian genomes.     

Long-term in vivo imaging of experience-dependent synaptic plasticity in adult cortex

Do new synapses form in the adult cortex to support experience-dependent plasticity? To address this question, we repeatedly imaged individual pyramidal neurons in the mouse barrel cortex over periods of weeks. We found that, although dendritic structure is stable, some spines appear and disappear. Spine lifetimes vary greatly: stable spines, about 50% of the population, persist for at least a month, whereas the remainder are present for a few days or less. Serial-section electron microscopy of imaged dendritic segments revealed retrospectively that spine sprouting and retraction are associated with synapse formation and elimination. Experience-dependent plasticity of cortical receptive fields was accompanied by increased synapse turnover. Our measurements suggest that sensory experience drives the formation and elimination of synapses and that these changes might underlie adaptive remodelling of neural circuits.     

Tumorigenesis: RAF/RAS oncogenes and mismatch-repair status

Genes of the RAF family encode kinases that are regulated by Ras and mediate cellular responses to growth signals. Activating mutations in one RAF gene, BRAF, have been found in a high proportion of melanomas and in a small fraction of other cancers. Here we show that BRAF mutations in colorectal cancers occur only in tumours that do not carry mutations in a RAS gene known as KRAS, and that BRAF mutation is linked to the proficiency of these tumours in repairing mismatched bases in DNA. Our results not only provide genetic support for the idea that mutations in BRAF and KRAS exert equivalent effects in tumorigenesis, but also emphasize the role of repair processes in establishing the mutation spectra that underpin human cancer.     

Study on molecular interaction between NifA and NifL of Pseudomonas stutzeri A1501 by using the yeast two-hybrid system

Pseudomonas stutzeri AI501 (formerly Alcaligenes faecalis A1501), which was isolated from rice paddies in South China in 1980, can colonize tightly on rhizoplane of the host plants or invade the roots of plants for growth and nitrogen fixation. But A1501 can fix nitrogen only under the micro-aerobic and nitrogen-free conditions. The oxygen concentration and the availability of fixed nitrogen are therefore important factors in the regulation of nitrogenase biosynthesis of associative nitrogen-fixing bacteria.     

Mass march of termites into the deadly trap.

Carnivorous pitcher plants of the genus Nepenthes are not usually very selective about their prey, catching anything that is careless enough to walk on their slippery peristome, but Nepenthes albomarginata is an exception. We show here that this plant uses a fringe of edible white hairs to lure and then trap its prey, which consists exclusively of termites in enormous numbers. This singular feature accounts for the specialization of N. albomarginata for one prey taxon, unique so far among carnivorous plants.     

Indicators of δ13C and δ18O of gas hydrate-associated sediments

The analyses of δ13C and δ18O of gas hydrate-associated sediments from two cores on Hydrate Ridge in Cascadia convergent margin offshore Oregon, eastern North Pacific show the values of d 13C from -29.81‰ to -48.28‰ (PDB) and d 18O from 2.56‰ to 4.28‰ (PDB), which could be plotted into a group called typical carbonate minerals influenced by the methane in cold venting. Moreover, the values of d 13C and d 18O show a consistent trend in both cores from top to bottom with increasing of d 13C and decreasing of d 18O. This trend could be explained as an effect caused by the anaerobic oxidation of methane (AOM) in depth and the oxygen fraction during the formation of gas hydrate in depth together. These characteristics of d 13C and d 18O indicate that the gas hydrate-associated sediments are significantly different from the normal marine carbonates, and they are deeply influenced by the formation and evolution of gas hydrate. So, the distinct characteristics of d 13C and d 18O of gas hydrate-associated sediments could be undoubtedly believed as one of parameters to determine the presence of gas hydrates in other unknown marine sediment cores.