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Post Archive
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August (1)

Wednesday Micro Hits
Wednesday, August 17, 2011
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Is it worth getting an education?
Thursday, July 7, 2011
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Miscellany
Tuesday, June 28, 2011

It Gets Better
Thursday, June 2, 2011
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Wednesday Micro Hits
Wednesday, May 11, 2011

My first experience with science writing (Part 1 of 2)
Tuesday, May 10, 2011

This is why we get vaccinated
Thursday, May 5, 2011

Monday Morning Jam
Monday, May 2, 2011
April (2)

Saturday Morning Serenade
Saturday, April 23, 2011

So long, farewell ...
Friday, April 1, 2011
March (10)

Stay Tuned ...
Thursday, March 31, 2011

From the Union of Concerned Scientists
Tuesday, March 15, 2011

Week 23 - Hockey Pool
Monday, March 14, 2011

March Madness
Monday, March 14, 2011

Saturday Morning Serenade
Saturday, March 12, 2011

What a bargain!
Wednesday, March 9, 2011

Wednesday Micro Hits
Wednesday, March 9, 2011

Technique Overload
Monday, March 7, 2011

Saturday Morning Serenade
Saturday, March 5, 2011

Et tu FDA?
Wednesday, March 2, 2011
February (10)

Saturday Morning Serenade - A Hip Edition
Saturday, February 26, 2011

Saturday Morning Serenade
Saturday, February 19, 2011

Wednesday Micro Hits (on Thursday!)
Thursday, February 17, 2011

HR1
Wednesday, February 16, 2011

Happy Valentine's Day
Monday, February 14, 2011

Saturday Morning Serenade
Saturday, February 12, 2011

The GOP War on Science
Wednesday, February 9, 2011

Wednesday Micro Hits
Wednesday, February 9, 2011

People, how about some ...
Tuesday, February 8, 2011

Saturday Morning Serenade
Saturday, February 5, 2011
January (21)

Saturday Morning Serenade
Saturday, January 29, 2011

Sacrifice
Friday, January 28, 2011

Are you married to your reagents?
Thursday, January 27, 2011

Wednesday Micro Hits
Wednesday, January 26, 2011

Common Sense Tip #1
Tuesday, January 25, 2011

Saturday Morning Serenade
Saturday, January 22, 2011

From the Baby Boomers, a Big "Screw You"
Friday, January 21, 2011

Student Worker - More Student or More Worker?
Friday, January 21, 2011

Wednesday Micro Hits
Wednesday, January 19, 2011

Saturday Morning Serenade
Saturday, January 15, 2011

Holy moly!
Friday, January 14, 2011

Thursday Pondering
Thursday, January 13, 2011

The Electronic Office
Thursday, January 13, 2011

Wednesday Micro Hits
Wednesday, January 12, 2011

Saturday Morning Serenade
Saturday, January 8, 2011

The Plug - January Edition
Friday, January 7, 2011

Bits 'N Pieces
Thursday, January 6, 2011

Latest Manuscript Review
Wednesday, January 5, 2011

The $4 gallon of gas
Wednesday, January 5, 2011

Our slowly shrinking (and dying) planet
Tuesday, January 4, 2011

It's 2011 already? For reals?
Monday, January 3, 2011
2010 (46)
December (9)

Saturday Morning Serenade
Saturday, December 11, 2010

The State of Microbiology
Thursday, December 9, 2010

Wednesday Micro Hits
Wednesday, December 8, 2010

2010 blogging meme
Tuesday, December 7, 2010

The Environmental Impact of the Christmas Season
Tuesday, December 7, 2010

Music Snobbery
Thursday, December 2, 2010

Phantom Power
Thursday, December 2, 2010

What's Your Name?
Wednesday, December 1, 2010

Wednesday Micro Hits
Wednesday, December 1, 2010
November (8)

Saturday Morning Serenade
Saturday, November 27, 2010

Awakening from the food coma ...
Friday, November 26, 2010

Wednesday Micro Hits
Wednesday, November 24, 2010

Donor's Choose Final Followup (Recipes #3 and #4)
Tuesday, November 23, 2010

A Monday Mess
Monday, November 22, 2010

Saturday Morning Serenade
Saturday, November 6, 2010

Wednesday Micro Hits (Peer-Review Edition)
Wednesday, November 3, 2010

Day 2 of the ASA-CSSA-SSSA Meeting (#ACSMtg)
Wednesday, November 3, 2010
October (29)

ASA-CSSA-SSSA Meeting - Day 1
Sunday, October 31, 2010

Stayin' Alive
Sunday, October 31, 2010

Saturday Morning Serenade
Saturday, October 30, 2010

Wednesday Micro Hits (Vol. 4)
Wednesday, October 27, 2010

ASA-CSSA-SSSA Early Career Program
Monday, October 25, 2010

Saturday Morning Serenade
Saturday, October 23, 2010

Wednesday Micro Hits (Vol. 3)
Wednesday, October 20, 2010

Donor's Choose - Family Recipe Number 1
Sunday, October 17, 2010

Making Good on Donor's Choose Bribe - Comfort Food Recipe 1
Saturday, October 16, 2010

Saturday Morning Serenade
Saturday, October 16, 2010

Friday Wrap-Up and Random Thoughts (Vol. 2)
Friday, October 15, 2010

First I Begged, Now I Bribe
Thursday, October 14, 2010

Finding Out Things The Hard Way(TM)
Wednesday, October 13, 2010

Wednesday Micro Hits (Vol 2)
Wednesday, October 13, 2010

Here's where I start begging ...
Tuesday, October 12, 2010

#UnK3rn3d: Life Outside the Lab?
Tuesday, October 12, 2010

First fleas, now frogs?
Tuesday, October 12, 2010

No Fleas Please
Monday, October 11, 2010

My next Research Blogging article has been chosen ...
Sunday, October 10, 2010

Saturday Morning Serenade
Saturday, October 9, 2010

Donor's Choose
Friday, October 8, 2010

Friday Wrap-up and Random Thoughts
Friday, October 8, 2010

RB: Waste Not, Want Not.
Thursday, October 7, 2010

Research Blogging
Wednesday, October 6, 2010

Wednesday Micro Hits
Wednesday, October 6, 2010

What if I were not a microbiologist ...
Tuesday, October 5, 2010

TJ's Tips on Manuscript Review
Monday, October 4, 2010

Chinese plagiarism and the death of English-language journals
Friday, October 1, 2010

Allow Me a Formal Introduction
Friday, October 1, 2010
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Thomas Joseph

It's a Micro World after all is a blog dedicated to discussing pretty much whatever I feel like. When I delve into scientific matters it will primarily be discussing microbiology (agricultural, bioenergy, and environmental focus). Otherwise, I'll probably ramble on about sports and life.

My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

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Awesome Stuff
Wednesday, November 3, 2010

So I lost my original post. I had about 80% of what I had wanted to write on my update from the ASA-CSSA-SSSA tri-societal meeting and my stupid touch-pad sent me back a page. Doing so left me with nothing, and if I can't get Brian to institute an autosave feature *nudge nudge* I'm going to be supremely bummed ... and will start writing all my blog entries in Word. ;)

Anywho ... Comic-Con ended on Sunday so there was no temptation to spend the day hanging out with Stan Lee rather than attending symposia, which I guess is a good thing. I never did make it to the Keynote Address Sunday night, though from what I heard it was quite the talk. The tri-societies have made a conscious effort to bring in well-known speakers who interface with our mission, and this year they did a great job in getting Thomas Friedman, Pulitzer Prize winner, and author of The World is Flat and Hot, Flat and, Crowded. I wound up not attending because I had an obligation to participate in another meeting/workshop. As a matter of fact there were several meetings running concurrently with the Keynote Address, which I view as a bit of a problem. Since the tri-society is making a strong effort to bring in excellent speakers, these "side meetings" are going to see diminished numbers, or they are going to have disgruntled participants. This was my first year attending this particular meeting,  I opted out of the Keynote Address to network, but I can say I was not thrilled to be missing the talk. This needs to be rectified, though since most of these meetings are not directly society-related they have little control over this (and I don't think they should worry about it). Fortunately, this issue was addressed at our meeting, so we'll see what happens in the future.

Part of what I love about traveling is the food, so I'll blog about as much as my meals on trips as I will the science. After the meeting I wound up having beers with a couple of collaborator/friends of mine at the Rockbottom Brewery. Their Cyclone Pale Ale was really good, and their bacon burger was pretty nice as well. Standard bar-food fare, but it definitely hit the spot. It's a stone's throw from the convention center which was also nice. Other than getting yelled at by the police for crossing the street early (hey, no one was coming in one direction so I went halfway ... it's what we do on the Right Coast) the rest of the evening was fairly uneventful.

Day Two of the meeting is/was going to be the most exciting/busy/packed. SSSA's S03, S06, and S01 Divisions were sponsoring a metagenomics session (presided over by Dave Myrold and Tom Moorman), and I really wanted to attend those. Since I'm looking at a variety of deep 16S sequencing and future metagenomic projects, I really wanted to see what the field was doing. I will note at this point that I am twittering the meeting (or at least the talks I am attending), so if you want to follow along with me, you can do so essentially in real time. I'll try to fill in details in these blog entries but you can get the main points before I ever reach for my laptop.

So after spending $6.75 for a chocolate chip muffin and diet coke (I finally found a 7-11 which will make life relatively less expensive for the remainder of my stay) I settled into the early talks. They started off fast and furious with Eric Triplett from UFlorida presenting data from his lab's soil metagenomic projects. What was particularly interesting about Eric's work is that during their soil metagenomics analysis, a low number of reads matched reference genomes (approximately 74K out of 206 million total) . Similarly, their 16S reads also showed a low number of those reads matching reference 16S sequences. Eric pointed out, and rightly so, that there is a paucity of reference strains for soil organisms in GenBank, and that funding organizations (USDA-NIFA) need to focus on getting more of these reference strains sequenced and publically available (why NIFA didn't do this in their current round of funding is anyone's guess).  When you look at the data, 0.03% of all metagenomic bases match to known genomes. Of course this presents a problem when trying to attempt to understand the microbial biochemistry of those samples. In addition, since archaea do make up a significant portion of the soil microbial community, analysis is hampered by the lack of arachael sequences in GenBank. Translation: soil metagenomics reveals a huge black box.

The matter of whole genome amplification (WGA) also came up, and it was revealed that it can introduce enormous biases in the resulting data. Heck, just switching DNA extraction kits can also introduce enormous bias in the relative abundances of particular phyla! Eric looked to see if some of this bias was the result of chimeras (an issue I've blogged about before), but they were able to demonstrate that it is probably secondary structure and a resulting lack of amplification.

Two additional metagenomic talks were given that morning, one by Rachel Mackelprang of JGI/LBNL, and Cheryl Kuske of LANL. Rachel reported on the metagenomics of permafrost soils, while Cheryl talked about soil fungal community metagenomics. Rachel's work looked at the differences between the active and permafrost layers of at least two sites, while also measuring carbon dioxide and methane at these sites and layers, prior to sequencing. She asked a number of questions such as hypothesizing that long term freezing of the permafrost layer would select for certain organisms, and whether or not organisms in permafrost soils would respond with increased activity to thawing temperatures. She was able to identify that bacteria (not archaea) were responsible for methane consumption in permafrost soils, as well as showing that community composition of these soils were high in Actinobacteria, Chloroflexi, and Proteobacteria. She used Illumina sequencing (after DNA extraction and WGA), and was able to monitor the microbial biochemistry of the soils before and after thaw, demonstrating changes in N-cycling after thaw. Additionally, she was able to identify an ~1.7 MB nitrogen fixing methanogen using Illumina sequencing!

Cheryl was focused on doing comparative as opposed to descriptive metagenomics. It was an impressive but complex project considering the high level of fungal diversity in soils. She was looking at elevated carbon dioxide levels on soil fungal communities, and had elevated vs. ambient carbon dioxide level samples from several sites across the United States. The samples were very diverse, and she demonstrated high spatial variability, even within sites! She even discussed the measurement of fungal gene expression (transcriptomics), which is infinitely easier in fungi than bacteria (which makes me supremely jealous as primarily a bacteriologist) thanks to the poly-A tail which is found at the end of eukaryotic  mRNA.

If I had not gone to another talk for the entirety of this meeting, these three talks would have made the trip worth it. All excellent presentations, all of which gave me any number of ideas for my own research. I did however attend more meetings, but since I'm already at two full typed pages (tl;dr), I'm going to stop this post here and follow it up with another in which I'll discuss the early career talk I attended. Stay tuned!

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Thomas Joseph
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When I get to a desktop, I'll add links to this page. Doing it from my laptop is a pain in the tookus. :)



Suzy
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Thanks for the update Tom. I wanted to attend those talks on Monday but I had a visiting scientist from New Zealand at the office and couldn't make it.


I helped Eric Triplett with some of their work. The WGA results are a problem for everyone doing metagenomics.


Did you see Janet Jansson's talk?



Thomas Joseph
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Jade, no I did not. I hope that a lot of the presenters allowed their talks to be recorded. Just too much to see. Do you helped Eric out? You and I need to talk, like for reals if you're up for it ... I'm starting to get heavily involved in metagenomics and could really stand to be pointed in the right direction. Everyone has an opinion on what you should do and/or get away with ... I need to sit down with someone I can trust and really plot out these experiments.



Suzy
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I helped Eric's lab with some of the experiments and I tried to help them find a WGA product that would work better than the standard kits. But every experiment is so expensive with next gen that they really couldn't try more than a couple.


It looks like WGA for microbial samples is really not a great idea. Just too much bias introduced. People don't want to hear that. So then it really becomes a problem when your paper goes for review and who is reviewing it.


Might be better to scale up and try to get enough DNA from a single sample. If you get enough DNA from your soil (~3-5 ug) you don't need to worry about it. Permafrost is usually very low in biomass.


I'll message you to discuss off line.



Evie
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Hah, funny, Ive always ended up at the Rockbottom Brewery when traveling for work too..



Thomas Joseph
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It was pretty good, but by far my two favorite eateries while I was here were L'Opera and Gaucho Grill.


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