Dunn:Education/Biophysics Research Blog

= 2/10/10: Nerding out over hair cells = Sorry about the delay in updates, but everyone in lab has been quite busy with lab work and classes. Next week we go to the Biophys. Conference, so we're trying to run our final experiments before then since we won't have many chances to perform them during that week.

Today I wanted to post about some material from a class that I am currently taking called "Biology by the Numbers" (BIOC236). One thing that drew me to biophysics as an undergrad was the curiosity and wonder that overtook me whenever I saw something like this cochlear hair cell in action:

   

In case you have never learned about how hearing works in humans, here is a very general explanation. Sound consists of vibrations that travel through some medium (like air), and when these sound waves run into a barrier, they are able to apply some pressure on it. In our case, the barrier is the very elegant auditory system which then transduces and amplifies the pressure as waves from the eardrum all the way to the cochlea. Here the pressure waves stimulate hair cells that respond to this mechanical stimulus by "firing" to generate an electric signal that propagates to other neurons in your brain. Thus, a conversion of mechanical energy to electrical energy occurs thanks to these hair cells.

You can learn more about the system on wikipedia if you want, but the video above focuses on these little guys called outer hair cells that sit at the end of the system. Unlike other hair cells this cell is able to take electrical energy (notice the electrode that is poking it and providing the electrical stimulus in the video?) and convert it back to chemical energy while changing its length in the process. Anyways, when Professor Theriot showed this to us in class, I had a good chuckle and thought that it would be perfect for the blog.

As someone who likes to dance, it is good to know that everyone has some part of themselves dancing when the music is playing. This video has given me ideas for ways to encourage others to learn to dance. None of which involve tasing a person of course. --Ramalldf 00:57, 11 February 2010 (EST)

=1/22/10: One month until Biophysical Society Meeting = There's less than a month to go before this year's meeting and the Dunn lab is very excited about attending. I've only gone once (Long Beach) when I was working in the Koch lab, but I had such a great time that it made me want to return every year. Though the poster presentations were very interesting, it was great to be able to meet student scientists from all over the world that were interested in your work. Since you don't often find people that are experts on your topic within your own campus, it is refreshing to meet another(s) that understands your frustration what papers you are referring to and who may give you insight about how the system studied may work (one may also get good tips about a problem or find a collaborator while networking). This year the meeting is in San Francisco, so luckily it will be cheap for us to attend since it is only a 45 min ride from the Stanford campus. Professor Dunn will be giving a talk about his work on myosin V so you should check it out if you find yourself at the meeting. The program (Abstract list) is now available online and is fairly simple to use to search for talks or poster presentations.

This year, the National Lecture will be given by Roger Tsien, winner of last year's Nobel Prize in Chemistry. You've probably seen his work somewhere (hint: fluorescent proteins). If not, here's a good intro into it:

   

Lastly, if you want a chance to see thousands of drunk nerds dancing, the conference gives you that option too (party during one of the last few days). --Ramalldf 06:16, 23 January 2010 (EST)

= 1/15/10: Stretching λ DNA with flow =

This is by no means a new achievement, but here's the Dunn lab's go at stretching tethered DNA molecules with flow courtesy of Arjun:



You can learn a lot of great stuff about Bacteriophage λ from its wikipedia page, but the relevant piece of information is that it possesses very long DNA. When stained with a fluorescent dye, single-molecules of it can easily be seen with epifluorescence microscopy. Here, Arjun tethered the molecules to the surface of a glass slide in a microfluidic chamber and recorded what he observed once fluid passed through the chamber.

If you are interested, the Koch lab has a good protocol for tethering single-molecules of DNA in a microfluidic chamber and observing the attached microspheres. The Green lab also has some great movies of "DNA curtains" being stretched. --Ramalldf 01:30, 16 January 2010 (EST)
 * Steve Koch 00:16, 20 January 2010 (EST)Awesome! And thanks for the KochLab shoutout!  Seeing this here, I realize that wiki is not ideal for a blog.  I feel guilty leaving this comment here and screwing up your blog.  Are you going to switch to something better?  I'm on blogger, but wish I were on wordpress.  Others I talked to, though, think Blogger is fine, so maybe it's a grass is greener thing.  As for lambda DNA stretching, it is so fun to watch with your own eyes.  We have a cool protocol that makes it very easy to see what you showed using HIV reverse transcriptase.  I stumbled upon this in grad school, and Pat Jurney repeated it here a couple years ago.  I'm not sure the utility, except that it's easy to do on untreated glass (RT sticks to ends preferentially...just mix RT with lambda DNA & dye and flow onto glass).  How did you make your tethers?

Ramalldf 05:35, 20 January 2010 (EST):Hey! Our first reader! :) I think that you're right for the most part. I follow a couple of blogs and one of the most common trends that I see is that an entry will often continue "after the fold" in its own page (this makes the main page easier to read if you have lengthy entries, particularly if readers' comments are allowed for each entry). Though possible to do this by just creating a new page for each entry, I could see it getting ugly as the blog increases in size. That being said, I like the fact that I have the OWW navigation bar along with the lab's mini menu all on the same screen. Since I'm the only one using the blog at the moment, I think that I'll keep the blog here for now to encourage our members to use OWW if/when they want to make contributions (in an ideal world I'd hope to have a design like the Molecular modeling blog for our blog). As far as the tethering goes, your approach is very clever. I don't think we have any RT at the moment but I imagine that we could do the same with a restriction enzyme that doesn't have any free metal ions floating around right? I think that what Arjun did was to just ligate a biotinylated oligo to λ DNA and add it to some neutravidin that had been flowed into the cell right before the passivation step.

=1/14/10: Using Mediawiki for a blog=

Although OWW has an option for blogging, I thought that we should start by using one of the pages on the main site to see how well it works as a blogging tool first. I know that we have the ability to tag pages. However, I am not sure how well the entries can be categorized if they're on the same page. Anyways I'll give it a shot, and if it doesn't work I'll just transfer the blog over to an OWW blog or use blogger or wordpress. I'll start by posting some things that you would normally see on a somewhat entertaining blog:

Pictures:



Embedded videos:

   

Slide shows:

<iframe src="http://docs.google.com/present/embed?id=dfbjvmrb_400gf38qzff" frameborder="0" width="410" height="342">

So, does it look good or does it look good? I like it, I'll have to try a few more things with it in the next couple of weeks, but for now I'm happy. --Ramalldf 04:54, 14 January 2010 (EST)

=1/13/10: We're officially blogging now=

Warning: As far as I know, noone in this lab has started their own blog before. If you're looking for top-notch writing, this may not be the first place to look......yet. Our goal is to educate our readers (novices and experts) about our scientific field and to show that biophysics, and science in general, has tremendously exciting topics going on today. Since we are amateurs at this, we ask you to be patient with any choppy writing, but to please feel free to correct us if we make any mistakes. The point is to educate you about our field, not mislead you with inaccurate mumbo jumbo. Finally, although we hope to be able to include as many topics in biophysics as possible, there will be some preference for the areas of single-molecule methods and force-dependent biological systems (sorry crystallographers). Lastly (really), most of these entries will be contributions from the grad students in Professor Dunn's lab so don't blame him for any problems that you may have with the contents of our entries. I think that is all, enjoy. --Ramalldf 04:19, 14 January 2010 (EST)