Tuesday, September 13, 2011

Biophysics Seminar: Archaea

This week, we held our biophysics seminar early because I have to fly out to Santa Cruz on Wednesday to meet some potential open science collaborators--something I'm really excited about and will hopefully have good news to report on my other blog next week.  The two students in the course, Peter Relich and Godwin Amo-Kwao are excellent students and opted to hold the class early instead of postponing until next week.  I was really glad they chose to do so--it showed that they care about the class and are learning from our meetings.

We had decided last week to use this meeting to learn about Archaea by reading two items:
I spent about 3 hours myself re-reading these articles and venturing off to learn more about topics brought up in the articles.  I also read most of the article that Iddo was responding to: "The proportional lack of archaeal pathogens: Do viruses/phages hold the key?" Since hearing about Archaea ten or fifteen years ago, I've always found them fascinating, but never have learned much about them.  After just 3 hours of reading and our hour of discussion, I still don't know much, but am still in love with them.

I figured we'd have plenty to explore since none of the three of us knew very much coming in, and I was right.  I enjoy the format of our course--the students brought up what they found most interesting, and we'd Google & Wikipedia on the projector to find out more about what we were talking about.  Similar to what I'd do on my own "wasting time" learning about subjects not directly relevant to my research, but in this case, with an extra excuse that it counts as teaching :)

We also have an ongoing goal of making contributions publicly from our class, but it remains a challenge, since we don't have video recording and most of what we do is talk and browse articles online.  I've encouraged the students to individually leave comments on Iddo's blog, but at the time we couldn't find the commenting feature enabled.  So, for now, I'll just list a few fun things I learned and / or knowledge I was able to share with the students:

  • I didn't know before today that Archaea use as their primary membrane component a kind of lipid different from that used in Bacteria and Eukaryotes.  They use glycerol-ether lipids instead of glycerol-ester lipids.  This may make their membranes more resistant to extreme pH and temperatures, according to the wikipedia entry.
  • I learned that Archaea live in many parts of the human body, such as the gut.  Much of what is known about Archaea is about these methanogens, which are useful in industry for sewage treatment, biogas production and other purposes.  This is interesting to me for at least two reasons.  First, because I still hold the misconception that Archaea exist primarily in extreme environments.  This is what I first learned a decade or so ago, but it seems they exist everywhere and maybe most of them are not in extreme environments (though they certainly live there too--like hot springs, deep sea vents, highly salty water, etc.).  Second, it's interesting that Archaea thrive in our body but as Iddo and the research article talk about, we don't know of any pathogenic Archaea.
  • Peter pointed out in our discussion that the articles have good hypotheses for non-existence of pathogenic Archaea, but he's not thoroughly convinced.  Even though I know very little, I agree with him.  We wondered whether a place to look for pathogenic Archaea may be in more "extreme" or unusual human populations.  There wasn't any detailed reasoning for wondering this, aside from the fact that there are some amazing extremophiles in the Archaea domain.  If there are pathogenic Archaea, would they be more likely in more extreme environments?  For example, in Ramsar, Iran, where the natural background radiation is 200 times higher than the global average?  Like I said, there's no sound reasoning for wondering this, but it lead to fun discussion.
  • While thinking about environments and extremophiles, a question came up:  Currently, which domain of life has ventured farthest from Earth?  Archaea was our guess since they seem to be the extremest extremophiles.  We did a Google search for "archaea on the moon" and I was really surprised that there are zero hits.  We realize there is no atmosphere on the moon, but how preposterous is it that some Archaea from astronaut's boots were trampled into the soil and aren't yet dead?  "Archaea on the moon" should get at least one Google hit, right?  Well, more realistic is probably the possibility of Archaea on Mars.  As Peter pointed out, they seem to live everywhere, and we've possibly already contaminated Mars with the rover.  Since we can't culture the putative Archaea here on Earth, it will probably be tough to know where they came from if we do discover them on Mars. Like I pointed out above, our discussion group doesn't know much about the subject, but from what we know, it seems possible.
  • Our discussion was entertaining and educational.  It led us to discuss some topics more likely to come up in our own biophysics research such as RNA polymerase, DNA polymerase, and DNA damage repair.  We went about 20 minutes overtime and I could have gone on for hours.
For next week, we're going to read a couple papers about stochastic simulation--a more focused topic, and one definitely important for the research of all three of us. The papers are:
  • Gillespie, D. T. (2007). Stochastic simulation of chemical kinetics. Annual review of physical chemistry, 58, 35-55. doi:10.1146/annurev.physchem.58.032806.104637
  • Voter, A. F. (2005). Introduction to the Kinetic Monte Carlo Method. Radiation Effects.
I learned about these paper a few years ago when we began using stochastic simulation in our lab to study kinesin (see "A discrete-state model for kinesin-1 with neck linker tension").  I had been using stochastic simulation for years before that, as a very useful tool in the lab.  But I wasn't aware of the seminal work of Gillespie until I read an excellent paper on transcription out of the Kornberg lab, which pointed to Gillespie's 1977 paper: Gillespie, D. T. (1977). Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry, 81(25), 2340-2361. doi:10.1021/j100540a008

Friday, September 9, 2011

Biophysics Seminar Series

This semester, in addition to Junior Lab, I am leading a one-credit biophysics seminar.  There are two biophysics graduate students enrolled.  Peter Relich is a 2nd year biophysics student, working in the Keith Lidke lab on (I think) super-resolution microscopy and hyperspectral imaging of live cells (in collaboration with the Diane Lidke lab).  Godwin Amo-Kwao is finishing his maters thesis in Physics, working on quantum mechanical calculations of amino acids to be used as a basis set for the charge-transfer (CT) force field for molecular dynamics in the Susan Atlas lab.  He is also beginning as a Ph.D. student in UNM's Nanoscience and Microsystems (NSMS) program.

So far, the course has been a lot of fun.  I like the small group as we can easily have discussions with everyone participating.  Our general plan for the course is to learn some biophysics while also learning about open science and modern tools that researchers can use in their research.  A mindmap of our initial thoughts is here: http://www.mindmeister.com/106137967/2011-phyc-500

We want to carry out the course as openly as possible, but we don't have a great way of doing that.  Especially since our meetings are face to face and we are not setup for video recording or anything like that.  But when we do have a chance to contribute openly, we are going to.  For example, when we read PLoS papers, we intend to rate them and leave comments, either as a group or individually.

For this week, we read two classic papers by Gilbert Lewis about the effects of heavy water (D2O) on living organisms.  These papers are:

  • 1. Lewis, G. N. (1933). The biochemistry of water containing hydrogen isotope. Journal of the American Chemical Society55(8), 3503–3504. American Chemical Society. doi:10.1021/ja01335a509
  • 2. Lewis, G. N. (1934). THE BIOLOGY OF HEAVY WATER. Science (New York, N.Y.)79(2042), 151-153. doi:10.1126/science.79.2042.151
Both are easy read, fascinating, and in my opinion ground-breaking at the time.  We had a good time discussing the papers.  Much of the time we spent doing google searches for deuterium-depleted water, and wondering at the prevalence of companies selling deuterium-depleted water (DDW) as a cure for cancer and other health benefits.  I was really surprised that one company recommends that everyone should drink only DDW for two months out of every year!  Obviously there should be some fundamental research supporting this extreme recommendation.  In my own lab, we've begun DDW studies on  tobacco seeds, for the first time (that I know of) carrying out the research that Lewis proposed in the 1934 Science paper.  Our work is open notebook science and can be viewed on Anthony Salvagno's blog.  Certainly, basic research such as this is required to support any future therapies based on DDW.

In order to contribute a little bit publicly from our discussion, we used PaperCritic to leave feedback on the articles.  These entries are:
PaperCritic plugs into Mendeley, but has some significant bugs still.  For example, I cannot figure out how to edit the reviews after we submitted them.  So, on the second review linked above, I could not give credit to Peter and Godwin.

For next week, we are reading two items, to learn more about fascinating Archaea:

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