F13 lecture 24(2)

Used for light sensins related to animal opsins beja

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Unformatted text preview: rated poten6al for detec6on –  had low sensi6vity •  concluded that only genes from popula6ons contribu6ng >5% of “environmental genomes” can be detected with this method early studies •  Taroncher- Oldenburg et al 2003 –  microarray with probes of genes involved in nitrifica6on (ammonia - > nitrite, nitrate), nitrogen fixa6on (N2- > ammonia), and denitrifica6on –  samples from river sediment –  amplified samples with specific primers to these genes –  (see next page) phylogeny of nirS (cytochrome cdcontaining nitrite reductase) genes in two samples from sediments of Choptank River, Maryland; black = probes on microarray not found white on black = functinal mRNAs in cample confirmed by competitive DOWNSTREAM; microarray HIGH SALINITY hybridization) UPSTREAM; LOW SALINITY Interpretation: a wide diversity of nirS genes were found in both areas diversity lower downstream; parallels community biodiversity GeoChip (He et al. 2007) •  microarray with genes from 290 gene families (version 3.0) –  27,812 probes (50 nt each) –  genes involved with: carbon, nitrogen, phosphorus, and sulfur cycles, energy metabolism, an6bio6c resistance, metal resistance, contaminant degrada6on •  first study: found that soil where plant monoculture grew had fewer func6onal microbial genes in the soil than soil from plots growing 4, 9, or 16 plant species use of metagenomic methods to discover new func6onal biomolecules •  e.g. Proteorhodopsin –  rhodopsins are pigment proteins that span cell membranes and like other opsins bind to re6nal (a deriva6ve of vitamin A) to become sensi6ve to light in the first step of vision •  human rod cells have rhodopsin, cone cells have photopsin •  bacteria/archaea have a rhodopsin (bacteriorhodopsin) that acts in conver6ng light to energy –  func6onally very different from vertebrate rhodopsin –  analagous to but dis6nct from photosynthesis, which uses chlorophylls rhodopsins in archaea •  three groups –  halorhodopsins – use light energy to pump cholorine across cell membrane –  bacteriorhodopsins – use light energy to pump H+ (protons) across cell membrane –  sensory rhodopsins •  used for light sensins •  related to animal opsins Beja et al 2000 •  used pulsed- field gel electrophoresis to isolate and clone large DNA fragments from ocean water •  sequenced a 130 kb fragment –  16S rRNA from a previously uncultured member of marine gammaproteobacteria –  and, an open reading frame for a rhodopsin like protein,...
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This document was uploaded on 02/27/2014.

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