Tuesday, August 11, 2009

Going Door to Door for Science

In one of my most recent (and frequent) brainstorms, I came up with a really great idea. Koch and I were hiking on the La Luz Trail:

View La Luz Trail to North Tramway Trail in a larger map
At some point on the trail, we came really close to some really nice houses. That's when it hit me...

...We should go door-to-door discussing our research requesting donations to help our lab. At first I was kidding, and perhaps I still am, but just think about it. Having a private investor could be a lot of fun. You have a more personal interaction level with your funding source. First you are actively discussing a topic you are passionate about with a potential investor. Sure you can do that when writing grants, but there is structure and order to that which may be unnecessary. In this manner, you can get back to basics and prove your love of your research.

I also discussed how we could host a bunch of lab visits to let the investor check in. Let them see what there money is going to. There can be tons of other organized meetings. Various lunches and dinners would allow for an even more personal interaction and may even spark a new friendship. Of course your funding source would be invited to talks you give, which would allow them to learn about any advances you make, while also seeing the big picture.

The best aspect of this is that a rich person probably has more rich friends and if your philanthropist likes your research enough, he will tell his friends and maybe they would like to donate as well. Maybe he/she will host an event to support your cause and try to get all his friends to donate. All in the name of science.

Just think about what the wonders of having a financial backer could bring. The possibilities are endless. And if you are worried about getting rejected while going door-to-door then say to yourself, "It's no different than when I submit a proposal!"

Tuesday, June 30, 2009

Lab Recap: Anthony's Work

I haven't updated people in a very long while as to what I have been doing in the KochLab. Technically I haven't been doing anything in there at all. From January to June I have been working with a collaborator in their lab... the Osley Lab. Koch sent me over there to learn basic level molecular biology and to begin the process of shotgun cloning.

You can follow all of my notes at OpenWetWare, but I will sum it up for you here. To make a long story short, I digested the ENTIRE yeast genome (Saccharomyces cerevisiae) with both XhoI and EcoRI. I then ligated the resulting fragments to an unzipping construct designed by Koch. Now we are ready to unzip. Of course there is still a little bit to work out, and even more to follow up on, but theoretically I have unzippable DNA fragments. We won't find out till we try.


I have shared a presentation I made for the first ever KochLab Symposium (posted on SlideShare), basically because I am too lazy to upload any of the pictures I have made and this talk contains everything.

As I mentioned you start with genomic yeast DNA. I digested the DNA with the restriction enzymes mentioned. I also digested pBluescript with the same RE's. I ligated the resulting fragments into the plasmid. From here I was able to make clones of whatever fragments managed to find their way into the plasmid, using E. coli. Using the color selection of pBluescript, I selected about 20 clones which would be used for sequencing and unzipping preparation.

After extra the cloned plasmid DNA I digested each sample with SapI and NotI. From there I picked about 5 samples that looked different from each other. Even though there is a low chance that the same sequence of DNA would be 2 separate clones, it was best not to take the chance. After selection and digestion, we sent a small portion of the samples off for sequencing.

The remaining sample was ligated to an unzipping construct. The SapI digested fragments were ligated to a specially designed oligo with a SapI overhang. The NotI fragments, likewise, were ligated to an oligo with a NotI overhang. There were other differences, but they don't need to be discussed here. The oligos are special because they contain a digitylated site, a nick, and a biotinylated site respectively. This means that I can attach the DNA to glass using anti-dig, attach a microsphere (streptavidin coated) to the biotin, and unzip utilizing the nick between the two. Sweet isn't it?

Once the tweezers are completed and calibrated we will test my work to make sure everything is peachy. We are almost there and I'll update at the end of the summer to report our progress until that point. Hopefully by then I should officially be a Ph.D. candidate!

Tuesday, June 16, 2009

Designs of Sorts

I have been into graphic design for 2 years now and I am getting quite good (if I do say so myself). I started because nobody in the lab (out of Koch, Larry, and I) had any experience and I had wanted to get into web design type stuff. Then Koch and I determined that any future successful lab needs a brand. What was once the Koch Lab became KochLab (very different, I know) and I commenced work on an official logo.

I knew I wanted the theme to be cooking. Why? Mostly because nobody could say Koch's (pronounced cook) last name properly. Also because cooking is awesome. I then started work on the frying pan logo that has swept various presentations and OWW by storm. Next I got to work on a thumbnail version of the logo, which evolved into a chef hat. To add some final punch we incorporated merchandise this past Christmas.

Now we are beginning a new project and I thought I would make a new logo for this project. Previously Andy and I collaborated on a fun logo that got named Kiney. That was fun to make, but I wanted a vector graphics image and this is what I came up with:

If you want to see all the KochLab logos and their progression check this out.

Sunday, March 8, 2009

What's cooking and what's been koching?

I have two goals with this post: (a) to answer a question "why don't we have unzipping data yet" and (b) to explain some interesting simulation data we having related to an alternative splicing application of our shotgun DNA mapping technology.

What's been koching?

I have been getting asked the question a lot recently, in various forms and in various levels of directness: "how come you've had your new lab for two and a half years and you still don't have optical tweezers data?" This question comes about because of my mid-probationary tenure review, grant applications, collaborations, and just general behind-the-back chitter chatter. I have to stress that I find this question perfectly reasonable and totally valid. Most new professors get their lab up and running much more quickly than I have. Even I expected to be "up and running" sooner--but I am not disappointed. Rather, I am quite happy with where we are at, because my plan was to have the students involved in every aspect of our lab start-up, and to fundamentally understand optical tweezers, why we're building them, and what our impact is going to be. I've spent (or reserved) the majority of my start-up funds ($200K) on students. Those students are now poised to have a really great optical tweezers and a deep understanding of how we are going to make biological discoveries with this tool.

During my first two plus years as an assistant professor, I have failed at expressing my lab mentorship vision to my colleagues at UNM. I do think I've succeeded in privately communicating my vision to my department chair, mostly via my written annual updates and goals. But I've not communicated my plan to the vast majority of people who care about me, or at least care about me bringing in money. One of my graduate students, Andy, helped me realize yesterday this problem and I'm really happy that I now see it. Further discussion of this non-talent, I think I'll save for my other blog. My main point here is to just acknowledge that it's been my own failure to engage and communicate that has created this minor issue (only a major issue if I don't get my contract renewed, which is unlikely I think). My goal will be to much more aggressively communicate my vision to people when this issue comes up in face-to-face conversations. Maybe something like this:

"I know! I'm itching for the data to start coming out too. We've been much slower than average because my philosophy is that one of the missions of my lab is to mentor students. The students need to learn and need to be involved in the management of the construction of our instrumentation, the designing of our experiments, and even our grant writing. Because of that, we're not as far along in terms of data and publications as many people would have expected. On the other hand we are only a few weeks away from having a kick-ass optical tweezers system that the students have designed and constructed. And these students have a very solid understanding of what we're trying to achieve, and a self-driven motivation to achieve from this point onward. So, many good things are going to happen for us this year, and our rate of achievement over the next few years is going to be much, much higher than it would have been if I had simply built optical tweezers and commanded students to acquire data. Furthermore, because of their intense participation in our lab start-up, these students are going to be very strong in the next stages of their careers--particularly if they have to start-up their own lab."
I need to rehearse that. Sort of like my "30 seconds in the elevator with the CEO" kind of speech. Furthermore, when I'm asked this question by certain people, such as those that support all the extra BS and hoops that our graduate students have to jump through, I plan on going further to explain how those hoops and BS substantially impacted the progress of our research. What I have in mind here are the IGERT programs we have with ridiculous non-research requirements (including 4 extra courses) and our physics department's fixation on testing and retesting and retraining our graduate students on undergraduate quantum, classical, stat mech, and E&M.

The last thing I want to present in this section is a very clear example of the success of my student mentoring strategy: Andy, Larry, and Anthony (our three grad students) all applied for and were awarded individual research grants recently. These equipment grants were for $3,000 each, from UNM's graduate student association. Each of them drew up their own budget and individual research plan, and obviously they all succeeded in bringing in external funding for their research. They even went against my advice of combining their efforts to go for a single $3,000 award! I love that they proved me wrong, and I love even more that they have succeeded in getting their research funded at such an early stage in their careers. Each of them are purchasing specialized parts to make our optical tweezers better and they have thus succeeded in a major part of research: getting the funding so you can do the things you know you need to do. I'll end this section with a big congratulations to our grad students!

What's cooking?

Optical tweezers

We have a lot of things cooking right now, and like I said above, I think 2009 is going to be a really big year for our lab. Of course, optical tweezers construction has been a major focus. Anthony, Larry, and Linh have been working on this for over a year and achieved a number of milestones. Recently, Andy Maloney has brought his amazing optics and design skills to the project. He's also making a transition to open science, and has started publishing a lot of his work on OpenWetWare, Google 3D Warehouse, and elsewhere. Just one cool example is the current condenser / detection optics design, you can see a snapshot of Andy's sketchup design here.

Molecular biology and yeast genetics

In addition to constructing optical tweezers and control software, we've had a lot of things going on. One major area has been with our collaborator, Mary Ann Osley, working to create site-specific chromatin tethers and other biological constructs. Diego Ramallo Pardo (now at Stanford biophysics graduate school) initiated this work for us and made a lot of progress towards our goal of creating "unzippable" native chromatin fragments from a specific locus in yeast. Diego succeeded in transfecting yeast with a PHO5 plasmid having a unique I-SceI restriction site and he also succeeded in making dig/biotin DNA tethers. Further, he worked on our protocol for creating the versatile unzipping construct. This is a construct I designed during my graduate work. The beauty of this construct is that it allows for unzipping of virtually any DNA fragment that has a sticky end (see the figure). The versatility and power of this design has been demonstrated by students in the Wang lab who used the design to study helicase (Dan Johnson, preliminary work by Richard Yeh), mismatch repair protein (Lucy Bai), and mononucleosomes (Alla Shundrovsky, now Michael Hall), and of course my own work demonstrating the ability to map and probe protein-DNA interactions by unzipping.

Before he left for graduate school, Diego taught another student, Brandon Beck, what he had learned, and Brandon succeeded in creating unzipping constructs from an XhoI-digested plasmid DNA. The torch has now been passed to Anthony, who also has a strong natural talent for molecular biology. Furthermore, he's added an Open Notebook Science dimension to the project. You can find his notebook on openwetware. Anthony is focusing on creating shotgun clones from XhoI-digested DNA. We will use this to demonstrate shotgun DNA mapping of yeast genomic DNA--because we can sequence the clones to validate our single-molecule technique.

Alternative splicing: very promising simulation results


I want to update you on one specific result that Larry achieved recently: demonstrating that single-molecule analysis of splicing by unzipping looks very promising. Like all of the above fascinating unzipping studies, this too will be enabled by the versatile unzipping construct and the ability to unzip any DNA fragment with a known sticky end. We have been thinking that structural genome mapping would be a very cool application of our shotgun DNA mapping technology. (See our preprint on Nature Precedings.) Mary Ann Osley, our collaborator on our chromatin mapping project, suggested a couple months ago that we simulate an inversion mutation, since these are tricky to detect with ensemble methods, since they are "balanced" mutations. We asked around on friendfeed and got advice to check out "inv16" for acute myeloid leukemia. Unfortunately, Larry and I didn't know enough about genetics to figure out what exactly inv16 involved, and thus we couldn't easily simulate it. However, at that time, I remembered some very intersting material I had seen Scott Ness present, related to alternative splicing. It occured to me that unzipping would be perfect for analyzing splice variants, because large deletions, insertions, or rearrangements are easily detected by single-molecule unzipping. So, Larry found a recent paper from the Ness lab, about alternative splicing of c-Myb, which is the fascinating topic I'd heard Scott Ness talk about. Larry was able to find the sequence for a couple splice variants (8 and 8-b) on Pub Med, and put them into his unzipping simulation LabVIEW application. You can see the results of this simulation in the figure. Clearly, the difference between the two splice variants is one or more exons being missing in the black (variant 8) versus the red (variant 8b) curves.

We showed this simulation to the lead author on the paper, "Johnny O" a postdoc in the Ness lab. Even without explaining what the hell we were doing, he immediately saw what we were talking about. (Man I wish he was reviewing our grants!) (Johnny O is an excellent scientist, and he even has that sweet nickname, so definitely he is destined for greatness.) Our plan is to wait until (a) we have our optical tweezers going and (b) Anthony has mastered the DNA ligation method for creating the unzipping construct. Once we get to that point, we're going to get in contact again with Johnny O and see if we can develop a collaboration with him and Ness to try some single-molecule typing of cDNA clones of splice variants (using variations of our shotgun DNA mapping algorithm). The fact that cDNA clones have known restriction sites should make this experiment quite easy to try out once we have (a) and (b) going. This will be yet another example of the versatility of the unzipping construct I developed. And the fact that splice variants have large structural changes makes it highly likely we can succeed in single-molecule typing of splice variants (supported by our simulation above). I'm in love with this idea so much that I'm thinking it should evolve into a specific aim for our upcoming R01 applications. I'll talk more about that on my research blog, which I tend to use more for discussion of funding and future research plans.

So, that's my update on what's cooking now -- hopefully I've conveyed enough for you to understand why I'm excited for our lab and for our students in the coming months!


Wednesday, March 4, 2009

The Fear of Scooping

All my hopes and dreams... gone in a flash. I wanted to be the first or at least be able to establish my thesis based on this line of work. Instead that hope has been reduced to nothing. What can I do now? How can I continue? I don't want to find a new research topic. I don't want to find a new field. I don't want to start all over again. I just don't want to...

These are the thoughts that went through my head as I glanced over a poster at the Biophysical Society Meeting. The poster described establishing a force profile of RNA Polymerase and studying how it affects nucleosome dissociation. The work was being done by a grad student in a competing lab. The lab was that of my PI's (Steve Koch) former graduate lab in Cornell, the Michelle Wang lab.

I decided to read the poster after Larry had pointed out that Dr. Wang had a student poster not too far from where I was standing. Larry didn't really care to read it. I walked over and glanced. I rapidly read the title. I don't remember gathering much information from the title, but after quickly scanning the poster an image of RNAP with the transcription bubble caught my eye and urged further reading. I walked closer and read a little more. I inched closer and read more. Each reading prodded me closer and to divulge further. Finally I decided to read the whole thing and ask the student questions.

The student (whose name escapes me as of this writing) was very friendly and nice. She discussed with me what they were doing and I told her that I would be doing the same thing (or so I thought). She was very interested in the technique I would apply and I told her it would be the same as hers. I then told her I worked for Koch and she immediately recognized the name. She shot me a smile as she realized that all her work was based on his prior work (the tweezers are courtesy of he and Richard Yeh, and their anchor construct is all Koch's doing).

In reality all the fears I had were premature. Sure they were warranted. A competing lab is working on the same topic and idea that we are. Turns out they are working with E. coli while KochLab is initially working with yeast (proof of principle stuff) and eventually will be upgrading to human genome studies.

As I gazed at every single section of the poster, I pondered in both wonder and fear. Wonder because the work done was very good and interesting. I was fearful because it was all the same work that I wanted to achieve. To feel like my project was being ripped out from right underneath me could quite possibly be the worst feeling in the world. I did have other endeavors I could follow, but the RNA Pol II studies are what I am most interested in, and I truly would like to be the first to carry out those experiments.

I have learned a very valuable lesson from that experience. The fear of scooping is a very real fear. Being an open scientist, I suppose now I could fear that even more, but I really don't have it in me. I want the whole world to know what I plan to do and share my experiences in real time instead of portraying the clean cut science at the very end of it with just a paper. I in fact would like to turn this experience into a positive. After seeing some of the work that my competitor is doing I would like to see if there is a way we could collaborate. Maybe that can never be, but at least by this offer I can put my fear aside and make it a strength.

Overview of the Biophysical Society Meeting: Boston, 2009

This is my second science conference ever with my first coming last year at the same meeting but in Long Beach, California (LBC). Last year was immensely fun both conference wise and extracurricularly. Outside the conference I had many adventures, and during there were so many talks I wanted to go to and posters I wanted to see that I couldn't keep my head on straight. I really had no chance of seeing it all.

This year I expected nothing less. I made no plans as far as venturing the city and left it all to chance. I tend to be that way. I like to go with the flow and make it up as I go. Don't think that I'm not organized or have any motivations, because that is just not true. I just don't like to make plans unless I have to and I like to keep my schedule free. As far as talks and posters go I have some experience under my belt so it shouldn't have been as tough as last year. I also know a great deal about my own research and the overall focus of the lab so I can pick appropriate talks and posters easier.

My feelings this year is that nothing really blew me away. I remember learning so much last year, but this year I am not walking away with that same feeling. There were some talks that I was really looking forward to just to find out that the research being presented had very little to do with what I expected (from the title). I was also a little disappointed in the quality of some of the posters I looked at.

With that said, it wasn't a total bust and there were some very noteworthy things as can be found here.

Some highlights:
The Block Lab showed why they are the best at what they do yet again. This year they cleverly attached DNA handles to kinesin motor heads to study the mechanics of the step. By using DNA fragments shorter than the persistence length of DNA they were able to use the DNA to manipulate the heads to gather force intel and other information about the stroke.

There was a beautiful talk detailing the truth about S-phase DNA. The group used specifically binding proteins and fluorescent labels to attach to dsDNA and ssDNA to distinguish melted DNA from the mythical s-phase.

The Wang poster was pretty good (about RNA Polymerase unzipping) and actually gave me hope for my project. We can also use their data as fuel to the fire for my own proposed experiments.

Meeting Micah and viewing the Williams Lab was awesome. We had a great night and learned a lot about aligning tweezers and setting them up from him. I look forward to meeting him again in the future.

Being in a city with a great public transportation system and plenty of things to do was amazing. The food was great and everything will be greatly missed when I return to boring old ABQ.

Thursday, February 26, 2009

Some Science-y Images

I haven't really had much time lately for fun extraneous stuff (like blogging), but I figured I have some time before I go to Boston so I might as well show something.

Larry is presenting at Biophysical society so he called on yours truly to create a bunch of graphics to accurately represent our science. Below are a few figures from the poster for your pre-viewing pleasure.

This first image quickly details my aspect of KochLab. That is the molecular biology aspect of the lab. The green blobs are yeast chromosomes, and the cleaver is a restriction endonuclease.

This next image is used to diagram the different aspects involved in unzipping DNA, namely that one has to deal with base-pairing, single stranded DNA (ssDNA), and double stranded DNA (dsDNA).

I made the next image to demonstrate how the optical tweezers will function. As you can see, the DNA is attached to a microsphere in an optical trap. This interaction is through bonding between streptavidin (on the sphere) and biotin (embedded in the DNA). On the other end, the DNA is affixed to a glass surface because of the specific binding of dig (on the DNA) and anti-dig (on the glass). This setup is made possible by the use of Koch's anchor DNA. It is created from dsDNA with a nick. The dig is on one side of the nick and the biotin is on the other. This short segment of DNA (an oligo) is ligated (attached) to a fragment of DNA that a user would want to inspect, in our case yeast genomic DNA. And that is as good a quick description of the process as you are going to get.

If you are going to be at the Biophysical Society Meeting, come check out Larry's poster (Lawrence Herskowitz) and admire our very cool science (and my sweet images).

Monday, February 2, 2009

My First Bio Lab Experience

I feel like a boy on his first date. As the whirlwind of stuff that I must learn in the coming months is quickly explained to me I wonder to myself, "This is a nice place. I can envision a continuing collaboration with these folk. I can't wait to settle down and become a more permanent fixture. I don't want to meet her dad though..." Whoops wrong side of the analogy.

I don't want to start making assumptions (I may end up hating biology), but the atmosphere is very nice. I think I just need to take it slow.

First things first, keep everything clean! This is going to be the hardest part for me to get used to. That and not dropping everything. Despite my pretty good hand-eye coordination, I am pretty clumsy. I am also forgetful which makes the sanitizing part difficult. I am organized though so that should be pretty useful.

I do have minimal experience in a wet lab setting. At KochLab, we will perform minor bio-prep for experimentation on the microscope and that I have done many times. The procedure we follow is called tethering and the protocols we employ can be found on the wiki (too lazy to link). Everything that I am currently embarking, however, is completely new. I am going to have to learn to run in this lab. It is a good thing that Kelly has decided to mentor me in the techniques needed for this project.

I hope all goes well and I do become a more permanent fixture of this lab (Osley). More to come.

Saturday, January 31, 2009

Our (open) contributions to science the past week

I want to make a short post to point out the contributions to science members of my lab made last week. Our activities have really been ramping up, so I don't think we can keep up these kinds of updates, which is good! Here are the things I wanted to note:

  • Anthony started doing open notebook science. His notebook is on openwetware. Actually he started this a couple weeks ago, but I was so used to using our private wiki that I didn't notice until this week. I think Anthony has the perfect demeanor for open notebook science, so I'm thinking this is going to work out really well. There are still problems ahead, though, especially since he's going to be working in a collaborator's lab, on totally new science to him. So there will be technical (it's tough to do wet lab and wiki at same time) as well as procedural issues (some people may not be comfortable with openness).
  • Andy began posting much of the work he's done w/ Google Sketchup in his "3D warehouse." He's very talented with this application, and he's built a whole bunch of models of optical components (mostly from Thor Labs). I think these modules will be useful to others around the globe who are using Sketchup for designing optical systems. You can see one of his full designs on this youtube video. A very interesting point about that video is that he found a Sketchup model of an Olympus IX-81 microscope that another user had generously shared. Since it's pretty much the same as the IX-71 we have, it saved Andy a bunch of time--and is a perfect example of how sharing these kinds of things can speed research progress.
  • Caleb also began open notebook research. His notebook is on OpenWetWare. He's only been using the notebook for the past couple days, and he's been adding notebook features daily. For example, today he implemented a feature so he can link to differences in the code he's writing. I thought that was pretty cool. Caleb has many amazing talents with computers, networking, and that kind of stuff (I don't know the correct terminology). He set up our incredibly useful and stable lab network, which includes a windows server, exchange server, VPN, MediaWiki server, ... and I don't know how many other things that I don't even know about, but which make our research so much easier. This semester, he's leveraging those talents for the purpose of creating new tools to make open science easier for us and others who use MediaWiki. For example, he's currently working on an extension to make it easy and transparent to recover any notebook data lost due to wiki problems. Another thing we're thinking about is implementing an "email to wiki" feature, which I think would be very helpful for lab workers.

Tuesday, January 27, 2009

My First Grant Application

This is for a small student grant. The award is $3500 or so and I wrote on some cancer related research in the field of telomeres. You can find my application (written back in October) on Scribd:

http://www.scribd.com/doc/11446505/GRD-Application

Open Science

I guess I'm officially the guinea pig of the KochLab (I don't know why Koch puts a space there... it's not like it's his lab or anything). Well Koch is the real pioneer because he is the one who initiated the whole open science thing 2 years ago. If I have to guess, I would say I am the most open person to the idea. This could stem from the fact that I really have no clue how most scientists behave when it comes to research. I always envisioned a world where everyone shares what they study. In a sense that is true, but I never imagined that there would be underhandedness like scooping. Wikipedia and other internet media have fueled my ideas, but then Koch showed me the real world.

Anyways, as Koch mentioned in another post (on another blog) we've been a part of OpenWetWare (KochLab)for two years now. While a part of them for so long, we have not performed much open research. We have had our own little community on a private wiki they supplied us. That experience has been amazing. On there I have the freedom to do anything. I mean anything. I keep a lot of personal information there (which can be viewed on my personal blog). The private wiki allows me to enjoy science a little more and the fun things I do there have really helped me learn wiki-ing a lot. Some of those things I don't feel I could/should do in the public eye because it isn't of the utmost professionalism. Maybe in time I will loosen on that stance.

I started on the public wiki around the time I first joined the lab (same time I started using the private wiki). Koch warned us of some dangers of going open, and since I've kept my exposure at a minimum. I'm not saying Koch is holding me back, that's far from the truth. I just felt that since there are more reputations than my own at stake, I should be a team player and do what I think is best for us all.

My initial work involved some minor changes to the OWW logo and some random other things. I stole the userbox template from Wikipedia and added that to OWW. The Wiki-ing and the OWW logo allowed me to rediscover a passion in a new media - graphic design. After messing with the OWW logo I embarked on a mission to create the ultimate KochLab logo (hopefully soon to be added to this page). I do other graphic design too (also on my blog), but that has been put aside so that I can focus on developing my own projects. I will post descriptions of these in more detail eventually on the public site.

Koch realized that I have some talents in the biological aspects of our course of study (we all have been physics trained), and now I am joining (part time) a biology lab in the cancer research section of campus. I will publish everything I do in my notebook on OWW, and hope to bring a little open science to our friends over at UNM Cancer Research (sorry, I'm just tired of adding links). You can follow everything I do (almost daily) research wise in my notebook and I encourage you to follow our lab on OWW as well. Also check out other things that I do on my user page.

Times are changing and I'm proud I get to be one of the pioneers of it all.

Saturday, January 24, 2009

Build your own laser diode control system

Andy hasn't started blogging yet, so I wanted to put up a quick note. Andy designed and built a laser diode system using OEM parts from Thor Labs and elsewhere. Anthony and Larry helped him assemble it, and I think Linh helped with some of the latter parts too. We're going to use it with a 1 watt 690 nm laser diode for our optical tweezers (OT). The idea for doing this came from both Andy and Mark Williams, who visited us and told us that they really like using laser diodes for OT, because when the diode is shot, it's only $500 or less to replace it. The reason I'm posting now is because Andy has posted on OpenWetWare his detailed instructions for how to do build the setup. I've been encouraging him to do so, because I think his instructions could really help out a bunch of people around the globe who would like to assemble the same system. My over / under is six months before someone emails Andy to say, "Thank you / one more question:". If you take a look at the page, I think you will agree with my conclusion that two things kick ass:
  • The laser diode system that he built
  • Andy for writing up and illustrating such amazing instructions

Thank you, Andy!

Monday, January 19, 2009

Draft of our first paper: Shotgun DNA Mapping!


Today, Larry, Anthony, Linh, and I hunkered down and created a draft of our first paper that will come out of our lab. We had been really struggling to write this paper collaboratively in bits and pieces on the wiki, and so we decided to just block off a bunch of time and try to write it together using Word, an overhead projector, and a whiteboard. This took us about 9 hours and worked fantastically. Pats on the back for all of us.

You can find a draft of our paper on Scribd. We welcome any comments or criticisms on this draft!

The work we are describing was done by Larry at the end of last year (2008, August and on) and we believe it presents really promising evidence that shotgun DNA mapping (SMD) by unzipping single DNA molecules will work in a variety of applications. We've been discussing the idea for over a year, particularly during Diego Ramallo Pardo's work towards single-molecule chromatin mapping in collaboration with the Osley laboratory. We had been thinking that SDM would enable single-molecule mapping of native chromatin molecules (we'll call that "shotgun chromatin mapping"), but we now envision other areas of high impact. One area would be in structural genome mapping. We cite the paper by Kidd et al. (2008) which described the amount of structural genome variation between 8 human individuals. Due to the nature of this kind of variation, it would be very well suited for detection by single-molecule DNA unzipping. Furthermore, we envision in the future shotgun DNA mapping of DNA from tumor cells, which (if someone made the method suitably high-throughput) could be a way of typing tumors based on structural genome variety. Another possibility is a genome could be scanned for protein binding sites by shotgun DNA mapping in the presence of purified protein (e.g. finding new binding sites for a newly purified protein of interest).

We're currently planning on submitting our paper to Biophysical Journal. This is a very good journal that we often read. However, we're still wondering whether we may be able to publish in a higher impact journal and reach more biologists if we can better explain the potential applications of our work. We're hoping our biologist friends will have some suggestions about this after reading our draft. And please do let us know your opinion!

(You can read more of Steve's comments about the writing process on his research blog.)

Tuesday, January 13, 2009

Early Days of Grad School

I have been in the lab for about 1.5 years and a graduate student for 2.5 years. Seems like a long time for me (maybe not so much for some grad students), and even though I am where I am now... it hasn't always been the easiest path. In fact it has been quite the opposite.

There were moments where I thought I was going to fail out of grad school. Classes were so hard. In undergrad I was used to putting in a total of 5 hours (max) a week for all my classes. Coming to UNM, Larry (the other grad student) and I realized we needed to do far more. For our first couple of semesters (Fall 06 - Spring 07) we needed to work at least 20-30 hours a week on homework. We were taking half as many classes and putting in 5 times the effort.

We even saw a decrease in our GPA. We went from being 4.0 students to getting B-'s (2.66 roughly) in ALL of our classes. Passing at UNM is a 3.0 for graduate students. Needless to say, I felt very defeated and I didn't believe that I belonged at UNM. I was recruited by Koch with the aid of Larry to join his new startup lab. This was the first turning point of my career.

That summer (2007) Larry and I did a lot of work in the lab, and had a really good time doing it all. My confidence was returned. Thanks to our awesome PI. He had so much faith and confidence in our abilities that I believed that I could survive grad school and attain my Ph. D.

The end of my first summer in the lab came the prelim exams. I had just returned from a trip to Hawaii, and Larry and I began studying at least 10 hours a day for a week for these tests. After all that work I had failed both exams I took (there are a total of four with each being in a different branch of Physics) and Larry had passed both (we studied for two). I was again feeling down. The upcoming semester brought more hardships through classes which we did slightly better in (now achieving B's and B+'s). But I still wasn't getting above the level required for staying at UNM.

Winter 08 brought my next try at the prelims. I had to pass 2 exams in order to stay here. Larry and I took the tests we hadn't taken over the summer. Larry passed them both and I felt like I did horrible. I even took a third test to improve my chances. That test I didn't study for though. Surprisingly I managed to pass one of the exams I studied for and the one I didn't. I was here to stay for at least another semester and the summer.

Spring 08 helped me by a mile. This time we did well in our classes and met the requirements (although barely). The summer came and research continued. It was full of productivity and ingenuity and all those other appropriate words that describe a lab kicking ass (sorry for the vulgarity). I had to derail myself though because I had to pass two more prelim exams.

Koch and I set up a competition to help me study. He would run 1 mile for every hour I studied. I managed to rack up a lot of hours (each week was on the order of 30 hours) and he managed to get in good shape. The prelims came. Those tests can really knock the wind out of your sails. I went in feeling really confident and left thinking that I was on the verge of a dropout. When all was said and done though, I had passed both exams and I was set to stay in grad school. My stresses (for the time being) were over!

Now I am here contributing to several places (this blog and openwetware.org to name a few) and more importantly a firm member of the KochLab.

If I can offer one piece of advice to any aspiring Grad Student it will be: Do what you can in undergrad to make sure you understand everything. Grad School will be a pain in the ass and very difficult, but once you are past the obstacles you are free to embark on the career path of your choosing. Enjoy it while it lasts because not everything is fun and games!

Monday, January 12, 2009

Hi from New Mexico!

My name is Anthony and I am one of the first grad student members of the KochLab. I will come with news of all sorts for everyone to read. I will describe what it is like to be a graduate student and what it is that I do here. I will also be telling you some funny stories from the lab.

I come from the internet age I suppose. What does this mean? Well in science right now there seems to be 2 groups. Science 1.0 and Open Science. Science 1.0 is the old way of doing things. 1.0ists will discuss science with others, but they certainly wouldn't broadcast it out there for the world. I would fit more in with the open science crowd.

What is open science? Just think of Wikipedia. Everything known, and hypothesized is published there and anyone can come and read it and others still can contribute to the general knowledge. The KochLab are members of OpenWetWare which is a community of open scientists that want to share their research with the world. We joined because the PI (Steve Koch) wanted to be able to join the "open" world while still being able to protect himself from unseen harms as a new PI with a new lab.

We call our research interface the Wiki because we can post and edit each other's work (on OpenWetWare) just like you could on Wikipedia. We have two aspects, one is a private wiki and the other is public. As of now most of the students (and Koch himself) make great use of the private, but not so much on the public site. This is all going to change real soon...

I am going to take the leap into open science by broadcasting all my work in the public light. You can follow our lab work on our page as well as follow along here. Other lab stuff include facebook groups, citeulike, a youtube channel, and soon to be many more. You can also follow my personal life (non science stuff) on my own blog.
 
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