Microbial Genomics Conference (Last Update)

I promised in a previous post to add more details about the Microbial Genomics conference in Lake Arrowhead. However, my wife went into pre-term labour, and is now on bed rest so I am a little short on time. I did give a conference review at a recent lab meeting so I thought I would post that as a quick substitute.

Microbial Genomics 2008 Conference Review

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Review of Arrowhead Conference

I was hoping to write this during the conference, but every talk I went to was really interesting and I ended up not using that time for blogging. However, there is at least one talk that I wanted to mention before I forgot to much.

I thought the most interesting talk was from Kim Lewis, who describes "persistor cells" as those bacteria that lay dormant in a population. These persistors are resistant to antibiotics because they are essentially shut down and passivly allow antibiotics to simply wash over them as opposed to normal bacteria cells that actively block or pump out antibiotics. Lewis also showed that late samples taken from cystic fibrosis patients had high levels of persistor cells. Kim then discussed unculturable bacteria (of which 99% of bacteria are) and suggested that when plated on media that these are actually dormant and not dead. To support this Kim showed that by innoculating an unculturable sample with E.coli caused growth of an unculturable strain around the E.coli spot. He later found a mutant that did not cause the effect and identified the key gene to be a sideophore. Lewis ends with this little tidbit, "Dormancy is the default mode of bacterial life". I find this really interesting because it suggests that most bacteria depend on a few bacteria to signal when their surrondings are optimal for growth.

There are a couple of more talks that I hope to blog about in the next day or two.

Microbial Genomics

I have been at Lake Arrowhead since Sunday for the 16th International Microbial Genomes Conference and I have to admit I am quite impressed. I think this conference has solidified in my mind that large conferences can't compete with smaller conferences. Let me list the reasons why in order of importance:

1. Food - in almost all cases the larger the group of people the worse the food will be. Now you may think I am slightly joking around saying that this is the most important, but I am quite serious. There is nothing worse than having to eat some cafeteria style food and then have to sit through 2-4 hours of talks with a cramping/rumbling/starving belly. Also, I find meals are the best place to meet and have discussions with other scientists.
   
2. Meeting people. You get a chance to meet almost everyone you want to without having to hunt them down like a gazelle. I really detest pouncing on a speaker as soon as they are done a talk. It is much nicer to see them at a break or at a meal (see above) and introduce yourself and ask a question then.
3. Better science. I find at smaller conferences the talks have been hand selected and tend to have a better line up of speakers
   
4. Location, location, location. Smaller conferences tend to have their meetings at nicer locations.
5. Beer & Wine - From my experience alcohol tends to be cheaper (or free) at smaller conferences which always makes everyone happy and tends to get scientists to loosen up some.
   

Mygazines

I recently found out about Mygazines.com, a website that allows users to upload and share scanned copies of magazines. This new form of digital piracy is getting the copyrights enforcers attention. I figured the site would be fairly lame with barely readable faded copies of old obscure magazines, but after checking out the site I was quite impressed. The images are clear and the website design is as good as any new social website. Over my lunch break I checked out the September issue of Discover and read a great article about personal DNA testing (p35). Personally, I don't see that many people cancelling their subscriptions, since most people still prefer to read from real paper. However, I was curious to see if any scientific journals were on the site. I figured some of the big ones such as Nature or Science might be, but ater a quick search it seems there are not that many scientists uploading yet. Of course I have access to all the science journals I need through my university, but I wonder if scientistis that don't have access would use such a source for information?

Evaluation of genomic island predictors using a comparative genomics approach

Well after a long hiatus from blogging I thought would start again with announcing my recently accepted paper, "Evaluation of genomic island predictors using a comparative genomics approach" in BMC Bioinformatics.

Quick Summary
This research provides a comparison of several previously published tools that are used to predict genomic islands (large regions of HGT in bacteria).These tools use various methods of identifying abnormal sequence composition, such as GC percent, to predict regions of HGT. The predicitons made by these tools were compared to reference datasets of genomic islands (GIs) and non-GIs (very conserved regions) that were constructed using whole genome alignments. One of the novel and cool (well I like to think so) things about this comparative genomics method, called IslandPick, is that it automatically selects appropriate genomes for comparison given a query genome. Normally in most compartive genomics studies the user/scientist has to pick which genomes are relavant and should be used in the comparison. This works well until you have to do it for ~1000 different genomes. If you want more information on how this works read the paper!

Publishing
This was my first experience with a very tough and stubborn reviewer. This would have been published almost 6 months ago if it wasn't for one reviewer that kept insisting that our method was flawed even after we clearly defended and addressed their concerns. After much correspondence and waiting, a fresh group of reviewers accepted the research after some minor revisions. *Sigh* Makes me wonder how much of publishing is just a crapshoot?

Master of the universe

I watch quite a bit of TV and that often includes special episodes or series based on science. Quite often when I get flustered with my own research, these shows will renew my passion and interest for science and remind me of why I am working on a PhD.

I get many of the shows I miss through the internet via multiple methods including web feeds (YouTube), download sites (bit torrent) , and live streaming (p2ptv). Disclaimer: Some of these methods may be illegal based on your location or the tv show provider so check out your laws first. :)

The first show I want to highlight is Stephen Hawking: Master of the Universe. This was a nicely balanced hour long segment that included just enough science along with a history of Hawking's debilitating illness. I remember my uncle giving me Hawking's book, "A Brief History of Time" when I was very young ( I am guessing around ~12 years old). I think I may dig it out and reread it with my much more educated brain.

Science and Beer

As always, I am looking for ways to improve my publishing and would consider pretty much trying anything. As pointed out in a recent NYTimes article a study showed that drinking less beer correlates with improved publishing.

Personally, I would suggest that the amount of beer consumed is a measure of the scientist's social life and as I think most agree better science often requires less social life. Sadly, I guess I will have to try to be the exception to the rule, since I am not quite ready to part with my bottle of suds.