Experimental investigation of the energy and depth dependence of flux peaking

The yield of helium ions backscattered from Yb implanted in silicon crystals has been studied as a function of the angle between the incident beam direction and various symmetry axes of the silicon crystal. The depth of the implanted Yb has been varied by using different implantation energies, and the analyzing beam energy has been varied from 0.5 to 2 MeV in an effort to obtain information about the energy and depth dependence of the flux-peaking phenomenon. The results are compared with those of Andersen and coworkers. We have observed the oscillation with depth of the flux in the center of a channel predicted by Van Vliet.     

In vivo enhancer analysis of human conserved non-coding sequences

Identifying the sequences that direct the spatial and temporal expression of genes and defining their function in vivo remains a significant challenge in the annotation of vertebrate genomes. One major obstacle is the lack of experimentally validated training sets. In this study, we made use of extreme evolutionary sequence conservation as a filter to identify putative gene regulatory elements, and characterized the in vivo enhancer activity of a large group of non-coding elements in the human genome that are conserved in human-pufferfish, Takifugu (Fugu) rubripes, or ultraconserved in human-mouse-rat. We tested 167 of these extremely conserved sequences in a transgenic mouse enhancer assay. Here we report that 45% of these sequences functioned reproducibly as tissue-specific enhancers of gene expression at embryonic day 11.5. While directing expression in a broad range of anatomical structures in the embryo, the majority of the 75 enhancers directed expression to various regions of the developing nervous system. We identified sequence signatures enriched in a subset of these elements that targeted forebrain expression, and used these features to rank all approximately 3,100 non-coding elements in the human genome that are conserved between human and Fugu. The testing of the top predictions in transgenic mice resulted in a threefold enrichment for sequences with forebrain enhancer activity. These data dramatically expand the catalogue of human gene enhancers that have been characterized in vivo, and illustrate the utility of such training sets for a variety of biological applications, including decoding the regulatory vocabulary of the human genome.     

Unsuspected diversity among marine aerobic anoxygenic phototrophs

Aerobic, anoxygenic, phototrophic bacteria containing bacteriochlorophyll a (Bchla) require oxygen for both growth and Bchla synthesis. Recent reports suggest that these bacteria are widely distributed in marine plankton, and that they may account for up to 5% of surface ocean photosynthetic electron transport and 11% of the total microbial community. Known planktonic anoxygenic phototrophs belong to only a few restricted groups within the Proteobacteria alpha-subclass. Here we report genomic analyses of the photosynthetic gene content and operon organization in naturally occurring marine bacteria. These photosynthetic gene clusters included some that most closely resembled those of Proteobacteria from the beta-subclass, which have never before been observed in marine environments. Furthermore, these photosynthetic genes were broadly distributed in marine plankton, and actively expressed in neritic bacterioplankton assemblages, indicating that the newly identified phototrophs were photosynthetically competent. Our data demonstrate that planktonic bacterial assemblages are not simply composed of one uniform, widespread class of anoxygenic phototrophs, as previously proposed; rather, these assemblages contain multiple, distantly related, photosynthetically active bacterial groups, including some unrelated to known and cultivated types.     

Capillary gas chromatography of monosubstituted cyclopentenes and cyclohexenes

Summary Regularities in the variation of retention indices (I) and index increments (δI/°C, H, ΔI) of monosubstituted cyclopentenes and cyclohexenes with molecular structure on various liquid phases are discussed. An equation for the linear dependence of I on the carbon number is given. Differences in gas chromatographic characteristics between 1- and 3-isomers are more pronounced in the n-alkylcyclopentene series. In the n-alkylcyclohexene series extension of the side chain and increase of column temperature lead to the inversion of the elution order of 1-and 3-isomers. The temperature increments of I for cyclenes are markedly greater than those for open chain hydrocarbons (n-alkenes, n-alkynes).