SEQanswers

Go Back   SEQanswers > Applications Forums > Metagenomics



Similar Threads
Thread Thread Starter Forum Replies Last Post
PubMed: Quantifying microbial communities with 454 pyrosequencing: does read abundanc Newsbot! Literature Watch 0 11-06-2010 07:40 AM
PubMed: Systematic artifacts in metagenomes from complex microbial communities. Newsbot! Literature Watch 0 07-10-2009 05:00 AM
PubMed: Characterization of airborne microbial communities at a high elevation site a Newsbot! Literature Watch 0 06-09-2009 05:00 AM
PubMed: Bias in assessments of marine microbial biodiversity in fosmid libraries as e Newsbot! Literature Watch 0 04-03-2009 05:01 AM
PubMed: Comparative day/night metatranscriptomic analysis of microbial communities in Newsbot! Metagenomics 0 02-12-2009 05:01 AM

Reply
 
Thread Tools
Old 02-21-2009, 05:03 AM   #1
Newsbot!
RSS Posting Maniac
 

Join Date: Feb 2008
Posts: 1,443
Default PubMed: Analyzing Gene Expression from Marine Microbial Communities using Environment

Syndicated from PubMed RSS Feeds

Related Articles Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics.

J Vis Exp. 2009;(24):

Authors: Poretsky RS, Gifford S, Rinta-Kanto J, Vila-Costa M, Moran MA

Analogous to metagenomics, environmental transcriptomics (metatranscriptomics) retrieves and sequences environmental mRNAs from a microbial assemblage without prior knowledge of what genes the community might be expressing. Thus it provides the most unbiased perspective on community gene expression in situ. Environmental transcriptomics protocols are technically difficult since prokaryotic mRNAs generally lack the poly(A) tails that make isolation of eukaryotic messages relatively straightforward (1) and because of the relatively short half lives of mRNAs (2). In addition, mRNAs are much less abundant than rRNAs in total RNA extracts, thus an rRNA background often overwhelms mRNA signals. However, techniques for overcoming some of these difficulties have recently been developed. A procedure for analyzing environmental transcriptomes by creating clone libraries using random primers to reverse-transcribe and amplify environmental mRNAs was recently described was successful in two different natural environments, but results were biased by selection of the random primers used to initiate cDNA synthesis (3). Advances in linear amplification of mRNA obviate the need for random primers in the amplification step and make it possible to use less starting material decreasing the collection and processing time of samples and thereby minimizing RNA degradation (4). In vitro transcription methods for amplifying mRNA involve polyadenylating the mRNA and incorporating a T7 promoter onto the 3' end of the transcript. Amplified RNA (aRNA) can then be converted to double stranded cDNA using random hexamers and directly sequenced by pyrosequencing (5). A first use of this method at Station ALOHA demonstrated its utility for characterizing microbial community gene expression (6).

PMID: 19229184 [PubMed - in process]



More...
Newsbot! is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:36 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO