[metagenomics-jclub] Next meeting, Nov 16, noon, PSB271, Vital versus transcriptomes

[Adina Chuang Howe]

Next metagenomics journal club will be next week, Nov 16, noon,
PSB271.  Marius (Tiedje lab) will be presenting the attached paper.
Marius is an entertaining and great presenter, hope you can join!

-adina

----------------
Transcript amplification from single bacterium
for transcriptome analysis

Kang et al.

Total transcript amplification (TTA) from single eukaryotic cells for
transcriptome analysis is established, but TTA from
a single prokaryotic cell presents additional challenges with much
less starting material, the lack of poly(A)-tails, and the
fact that the messages can be polycistronic. Here, we describe a novel
method for single-bacterium TTA using a model
organism, Burkholderia thailandensis, exposed to a subinhibitory
concentration of the antibacterial agent, glyphosate. Utilizing a B.
thailandensis microarray to assess the TTA method showed low
fold-change bias (less than twofold difference and
Pearson correlation coefficient R ! 0.87–0.89) and drop-outs (4%–6% of
2842 detectable genes), compared with data
obtained from the larger-scale nonamplified RNA samples. Further
analysis of the microarray data suggests that
B. thailandensis, when exposed to the aromatic amino acid biosynthesis
inhibitor glyphosate, induces (or represses) genes to
possibly recuperate and balance the intracellular amino acid pool. We
validated our single-cell microarray data at the
multi-cell and single-cell levels with lacZ and gfp reporter-gene
fusions, respectively. Sanger sequencing of 192 clones
generated from the TTA product of a single cell, with and without
enrichment by elimination of rRNA and tRNA,
detected only B. thailandensis sequence

---------- Forwarded message ----------
From: Marius Vital <vitalm at msu.edu>
Date: Wed, Nov 9, 2011 at 1:38 PM
Subject: paper journal club
To: Adina Chuang Howe <adina.chuang at gmail.com>


Hi Adina,

Attached the paper for the journal club. Also, for the lazy guys, a
one page summary (opinion) on the paper.

Marius
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Kangetal_2011_GenomeRes.pdf
Type: application/octet-stream
Size: 2101027 bytes
Desc: not available
URL: <http://lists.idyll.org/pipermail/metagenomics-jclub/attachments/20111109/df58a754/attachment-0002.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Expressions of individuality.pdf
Type: application/octet-stream
Size: 107234 bytes
Desc: not available
URL: <http://lists.idyll.org/pipermail/metagenomics-jclub/attachments/20111109/df58a754/attachment-0003.obj>