As I was finishing up my first journal article post, I realized that I'll be using quite a lot of abbreviations for common things in the field. I'll start a list of them behind the cut. I'll also keep a list of term explanations, if needed. If you are reading these posts and don't know what something means, please comment here with the term and I'll add the definition as requested.

Oh and hey, what do you know, this becomes a portion of my thesis... [boggle]

( Abbreviations and Definitions )

They just need to ask me, please just ask me.

Title: Structural Mechanism for Rifampicin Inhibition of Bacterial RNA Polymerase
Authors: Elizabeth Campbell, Nataliya Korzheva, Arkady Mustaev, Katsuhiko Murakami, Satish Nair, Alex Goldfarb, Seth Darst

Brief Synopsis: RNA polymerase crystal structure has been known for quite a while but what hasn't been explored is the nature of the binding and structure with the antibiotic rifampicin. Rifampicin is an inhibitor of RNAP and the mechanism by which this works is revealed through Xray crystallography.
( Full review and notes )


Citation: Campbell et. al. 2001. Structural Mechanism for Rifampicin Inhibition of Bacterial RNA Polymerase. Cell 104: 901-912.

On a Masters track now, which is fine. Life gets in the way and you make these decisions. Doing a thesis option which means that having these journal entries will still be useful, just over a shorter time period.

More to follow as I'm writing my thesis ... like.. now. And I've identified target knowledge areas that I need to fill in ASAP.

A bit of background:
I've been working out details of a project lately where we want to compare gene expression of two identical populations under low pressure (25 mbar) versus 'Earth' pressure (~1010 mbar). My boss and I plan on using Agilent DNA microarrays but Agilent doesn't carry standard B. subtilis arrays. So we have to design our own array.

I have never done anything like this before. I'm wondering, what is involved in designing a microarray? Is there any literature I can read up on before jumping in? How much of the design is work we do versus sending out to a company with specification (like we would for primers)?

I'd like to know what I'm getting myself into with this project. Hopefully, if it works, it'll be the crowning glory of my thesis....


Edit... dammit, forgot to publish to the community, sorry Friends List!

Diversity and Desiccation Resistance of Bacteria from Arid Lands

( Fred Rainey LSU )

Germinable Endospores in Hyperarid Atacama Desert Soils
( Adrian Ponce - JPL )

"Pompeii" in the Mojave Desert
( Henry Sun - Desert Research Institute )

The Effect of Soil Moisture on Soil Microbial Communities in the Mojave Desert
( Elaine Bryant - San Jose State University )

I should mention I'm only writing about those that interest me from the sessions I attend so this in no way is every talk.

Okay, so yeah I haven't done quite what I intended, but there's been a change in plans. Anyway, I'm watching SG:1 so it's funny quote time!


Carter: It's trying to survive.
O'Neil: So do bacteria.
Carter: It's trying to communicate, sir.
O'Neil: So do bac.... oh.


I LOL'd


<3 <3 <3 all my seasons of Stargate.

Title: Survival and germinability of Bacillus subtilis spores exposed to simulated Mars solar radiation: Implications for life detection and planetary protection

Authors: Courtney Tauscher, Andrew C. Schuerger, Wayne L Nicholson

Brief Synopsis: Spores retain the ability to initiate molecular events long past they are deemed nonviable, thus still posing a risk as a false positive in life detection experiments on Mars.

( Full review and notes )


Citation: Tauscher C, Schuerger AC, Nicholson WL. 2006. Survival and germinability of Bacillus subtilis spores exposed to simulated Mars solar radiation: Implications for life detection and planetary protection. Astrobiology 6(4): 592-605.