ACA 2011

I spent this last week in New Orleans at the American Crystallographic Association (ACA) conference. I was there with my awesome lab mate and new roommate, Christopher. This is the same conference that I went to in Chicago last year. The conference happened two months earlier this year due to the international crystallography conference that happens this summer. The ACA conference is meant to get scientist in the crystallography community together to share their research. This really is a prime way to learn what others are doing, develop ‘research relationships’, and bounce ideas off one another. I feel that these conferences are an essential component to scientific discovery.

Getting to New Orleans happened to be a bigger deal than one would have anticipated, but we had a few lucky breaks and got there only a few hours later than expected. When Jane, my PI, picked us up, it was raining very heavily, the kind of rain that simply doesn’t occur in Utah. Getting out to the car was enough to get my feet soaked wet. On the way to the airport we drove out of the storm and I thought we were going to be in the air soon enough. When we got situated at our gate another portion of the storm rolled in and set up camp over the airport. Pretty soon they had to delay all in-coming and out-going flights due to lightning. The airport was shutdown for about three hours. It quickly became apparent that we would miss our connection. The agents were very busy trying to help passengers sort out their missed connections so we had to wait quite a while to talk to sort out our connection. The agent

confirmed us on a flight from Atlanta to New Orleans in the morning and put us on stand-by for a flight later that night. She told us that Atlanta was already backed up from the same storm system and we’d likely have to spend the night at the Atlanta airport. Long story short, a very nice agent in Atlanta put us on priority stand-by and we made it onto the later flight. We were in New Orleans only a few hours later than scheduled.

I have to be honest; in my humble opinion New Orleans is not as cool as Chicago but pretty neat nonetheless. My biggest complaint was that the city seemed dirty to me. Christopher had a fair point when he mentioned that it was an old city and old cities generally looked dirtier. They had garbage bins on every curb, which I thought was odd. As I looked around though I realized how cramped the city was, especially in the French quarter, where else could they put the trash? The food was great. We went to Red Fish Grill on Bourbon Street, it was by far the best food we had there. We also went to Johnny’s Po Boys where I got the New Orleans original, the Muffaletta (See picture). Of course, we had gumbo and jambalaya.

Red Fish Grill

Johnny's Muffaletta

On the last night we were there we went to a Thai restaurant which was on the opposite side of the French Quarter from our Hotel. We walked down Royal Street all the way to the restaurant. My pineapple-fried rice was yummy. When we were done we decided to walk the entirety of Bourbon Street. By this time the sun was setting and things were getting started on Bourbon Street. Suffice it to say that two devout Christian men were educated. The live music in every bar was neat, live music is always pretty cool. Other then that I have nothing good to say about that street. I can say that women are prettier with cloths on and the adult superstore does NOT sell adults. I don’t plan on making that stroll ever again.

We spent most days in the conference listening to talks and interacting with other scientists and even a few legends in the field. Wednesday we decided to go to the local aquarium, right next to the Mississippi River. After going to look at the river and take a few pictures we went into the aquarium. It was a very neat attraction! I could go on about the variety of colorful fish, the sea otters or even the penguin exhibit. I’ll spare you and tell you my favorite creature there, the jellyfish! They were small but I think I like them best that way. They move so gracefully and are simply beautiful.

On Thursday I had to give a fifteen-minute talk. I talked mainly about recommendations made by a task force that Jane was on. It was on validation of crystallographic structures deposited in the PDB. I also talked about a new tool that I created called MolProbity Compare, which allows the user to compare two validation reports of two different models. Unfortunately my talk was in the afternoon on the last day, a lot of the participants are gone by that time. Further, there were other sessions that were happening simultaneously that I had to compete with. I frankly was surprised at the 10-15 people in the room who listened to my talk.

There you have it, New Orleans in a nutshell.

New Orleans

At the end of this month I will be venturing to New Orleans to attend the American Crystallographic Association conference. This is a research conference that happens every year; last year that I attended the same conference in Chicago. The main goal of these kinds of conferences is to disseminate knowledge gained through research. This dissemination is usually done through two kinds of presentations, oral presentations and poster presentations. Just about every student that goes presents a poster. If the research that you propose to present is good and of general interest they will pick you to give a talk.

So, how does one propose a research presentation? That is done by submitting an abstract, which is a short synopsis of your research. My lab mate and I submitted our abstracts a few months back. The conference organizers will typically tell you well in advance that your abstract has been accepted and what kind of presentation you’d be giving, which is a poster presentation 95% of the time. It occurred to me last week that the conference was right around the corner and I had yet to hear from the conference. I got worried when someone informed me that they had tried to email me but it had not gone through. Was I sent an email from the conference but didn’t get it? So I sent an email to the conference organizers explaining my predicament.

While I was waiting for a reply, I went to the conference website and noticed that they had published the conference program. If my abstract had been accepted my name would appear in my program. The list of posters was quite extensive, as such, I searched for my name using the browser’s find function. My name came up not under posters but rather under talks. That’s right, I have been assigned to give a talk.
The talk will be 15 minutes long and I will mostly be talking about work that my mentor did. She was on an international task force whose job was to recommend validation methodologies that will be incorporated into the Protein Data Bank (PDB). The PDB is where all published protein models have to be deposited. Everybody is interested in this topic as everybody wants to have a model that looks good and thus will p ass as a good structure using the new validation techniques. I will also be presenting some of my research.

So there you have it, my exciting news. As a side note, I will be in Utah from June 29 to July 19. I cannot wait to see everybody!

Die tree, die!!

The past month has been pretty quiet. I have been getting ready for my initial committee meeting. This meeting is deigned to introduce my committee to myself but more importantly my project. For those who are unfamiliar with the process of getting a PhD this committee is made up of faculty members who will follow me throughout my tenure as a graduate student. Their job is to ensure that I am doing the things that I need to receive a PhD. Finally, at my dissertation defense I ‘defend’ my research to them. To get ready for the initial meeting one must prepare a short summary on my the research that I propose doing and prepare a very short presentation. I have also, of course, been continuing with my research. As usual in research, it is going slowly but going nonetheless.

This week I had the opportunity to go see a performance put on by the Young Ambassadors of BYU. Their program included singing and dancing. The performance followed the ideal life; childhood, adolescence, marriage, adulthood and growing old. They were very good at what they did…suffice it to say it reminded me of Saturday’s Warriors.

Unfortunately, the only biking that I get in is my daily commute to and from lab. I’d like tpo do more but another activity has taken priority, working in the yard. Yesterday I started to take down a tree in the backyard. A vicious vine was overtaking this tree, it was a matter of time before the vine would kill the tree. It also was in the way any time that I wanted to take out the garbage or mow the lawn. I was only able to take down half of it as there was only so much room in our yard waste bins; I’ll do the rest next week.

That’s it for now.

SBB Seminar

This past week has been rather busy for me but also very exciting. Busy because I had to give the seminar talk in front of my whole program on Monday. That includes graduate students as well as faculty. Further, the seminar talks are usually 50+ minutes long; I had never given a presentation that long before. The problem was that although I have done a lot while I've been here, the stuff I have done isn't very presentable. I needed a concrete example of the use of a method for which I had made tools for. Its like I had made a sledge hammer, something brand new and never before seen, but I had yet to show it could tear down walls. Thus, the last week or so was not filled with antagonizing over what to say or how to present my work, rather it was doing the work so that I had something to show for it. Now I will explain what I actually did, so feel free to skip the next paragraph.

I work on methodologies to improve model accuracy given low-resolution crystallographic data. I am specifically focusing on proteins. Getting an accurate model with little error at low resolution is very difficult. In fact, there has yet to exist a mode with little error given low-resolution data. In order to get an accurate model one needs to have a good backbone. This is like saying, in order to have a sound building you must have a solid foundation. Current low-resolution structures don't even have good backbone. There are methods by which you can use hydrogen bond restraints that will keep certain regions of the backbone look like they are suppose to look. These are like extra support for the backbone. However, defining these restraints is fairly tedious. In fact, this process is simply not tractable for large molecules. My tool allows one to easily defining hydrogen bond restraints. After you do this you have to put your model through a process called refinement, luckily the computer does this step. The is where you can get backbone errors but hopefully the restraints keep the errors from occurring. So what I did was take a low-resolution model and refined it without and with several different restraints. The results were good, kind of. The backbone in regions where hydrogen bond restraints were defined looked great. However, other areas gained more errors. That means more research for me, YIPEEE!

Suffice it to say that the presentation went better than expected. I had practiced the talk the day before and got worried because I quickly got tired and my dysdtonic movements got worse making it even more difficult to talk. All though this worried me I was relatively calm going into the seminar. I decided to do something unorthodox that I had done before which is to sit rather than stand to give my presentation. It worked like a charm. I also believe that I did better live because I was getting feedback from the audience. I made them laugh, I could tell that at least some in the audience were engaged, and asking rhetorical question at the right time to further engage them. It was great. I got two similar comments, that I've actually received before, saying that my use of humor was great and actually added to the presentation. I am glad it is done now though!!

Now onto the exciting news. Las fall I had applied for two fellowships. One through the NSF and the other through the NIH. These fellowships pay for my stipend and one helps with tuition. This simply takes the burden off my PIs. I heard back from the NSF and I got the fellowship! After I had received the award letter I decided to check the status of my NIH fellowship... The status bar said that my application had been reviewed but I would nor receive word on wether or not I got funded til council meets in May. However, I was able to see the reviewers comments and the score that the gave me. The score I go was 10. OK...what does that mean? When I started reading the reviewers comments I knew 10 had to be good as there were very little criticisms. But I didn't learn what 10 meant, I went to the web for that. It turns out that what the reviewers do is score the application on different criteria on a 1-9 scale, 1 being the best. then all the reviewers come together, average their individual scores and time by ten to give you your overall score. That mens that the overall score ranges from 10-90. I was flabbergasted! Now I have to see if they'll fund me. I think they will. Now I have to see if I can take both or choose one. This is a dilemma that I don't mind having.

Lawrence Berkley Labratory

This last week I was in Berkeley California at the Phenix developer’s workshop. Phenix is a software package whose goal it is to advance the automation of macromolecular structure determination. The workshop was held on the grounds of Lawrence Berkeley National Laboratory, situated on the hillside right above the campus of UC Berkeley. I liked the area a lot. As I showed in my last post, the lab has its own resident turkeys. Further, black-tailed deer can be seen further up the hill. The mornings were awesome, they reminded me of mornings in Utah. I think it is because there was a large hill immediately to the east, thus the direct-sunlight wasn’t seen until later in the morning.

While at the workshop I had the opportunity to work with lots of cool people. I truly enjoyed working with my Phenix friends. My PI had a great idea for a research project that I could tackle to be part of my dissertation project. While there I told a colleague about the project and he suggested a way in which I might accomplish the project, he even had code that advanced my project by several steps! However, this has mad me keenly aware of the fact that I have a ton to learn!! It is good though as this gives me direction whereas before I feel I was lacking a clear direction.

The fight home was my first red-eye. Its very difficult to fly east with the time change. Anyway, we left San Francisco at midnight, Pacific Time, and landed in Durham around 9:30 AM, Eastern Time. I find it hard to sleep in a bed let alone on an airplane. Needless to say, I did not sleep on the plane, one of only a handful on the flight. By the time I got home I was, surprisingly, wide-awake. I didn’t go to bed until 11PM that night making 39 consecutive hours without sleep, a new record for me!

Anyway, it was a great trip and I am looking forward to the next Phenix workshop this fall here at Duke.

LBL

What, may you ask, is LBL? Well, I'm here to not only tell you but show you also. LBL stands for Lawrence Berkeley Laboratory. It is on the campus of the University of California, you know, the one in Berkeley. This happens to be where I am right now, for a collaboration workshop. This workshop, which is held every six months, rotates between here, Duke, and Cambridge. I may have more to say when all is said and done at the end of the week. Until then, enjoy these pictures I managed to get with my phone this morning.

Looking down onto the campus from LBL.

The LBL guest house.

Trees and the overcast sky.

Resident turkeys.

A resident.

A random building.

Look out on the bay.

Opposition in all Things

So, from my last post it looks like I promised to write a new post a few weeks ago. Obviously, this did not happen. I have been quite busy with life in general; taxes, research, class, TA duties, and yard work…you get the idea. Yup, you heard right, I said yard work. It has been warm as of late and I have been turning the soil over in my garden. I meant to get early crops in but time was not to be found. I have been really busy in the lab, learning a new programming language, Java. Programming is quite simple, all you are doing is telling the computer to take input from the user and if that input is some action, such as a right-click, then do thing A. There are really only a very few primitive commands that you need to make a program, quite amazing. I have been busy doing other school activities too, class and TA responsibilities (A.K.A. thermodynamics and grading).

You may ask then, what do I do when I am not in lab or doing the school thing? I do bike but not a lot. When I get done with the day I usually go home trying ever so hard to keep school and lab things behind. One thing I do not do when I get home is sit in front of the TV; I can’t stand TV. Instead I read. Since I am a great believer in opposition in all things, I have chosen to read Stephen Hawking’s ‘A brief History of Time.’ How does this introduce opposition? Quit simply really. You see, as a student of structural biology I am working in a world where measurements are made on the angstrom scale. An angstrom is a whole magnitude of order less than a nanometer! Certainly almost all have heard of a nanometer but that doesn’t mean that you have an intuition of how small that is. Let me try to instill some intuition about the nanometer and then the angstrom.

I will assume you are familiar with the length of a meter. One tenth of a meter is a decimeter (or 0.1 meter) and one tenth of a decimeter (or one one-hundredth of a meter if you’d like) is a centimeter (or 0.01 meter). Approximately 2.5 centimeters is the length of an inch (this will be the only reference I will give to the cockamamie U.S. convention of length measurement). So, a tenth of a tenth of a meter is a centimeter. Are you with me so far? Good. A tenth of a centimeter is a millimeter (or a tenth of a tenth of a tenth of a meter or 0.001 meter). Now think of a human hair, the average size of which is a tenth of a millimeter, pretty small!

This will be the last reference of anything observable to the human eye as anything smaller is fairly difficult, if not impossible, to see with the naked eye. We’ve come a long way but the millimeter is not even half way to the angstrom! Go down three orders of magnitude from a millimeter and you’ll arrive at the micrometer (or 0.000 001 meter). Lets jump down ANOTHER three orders of magnitude, we’ve now arrived at the nanometer (or 0.000 000 001 meter). Recap: three orders of magnitude below meter is millimeter, three more orders down is the micrometer, and three orders down still is the nanometer. Now we go just one order of magnitude below the nanometer and we finally arrive at the angstrom (1 angstrom = 0. 000 000 000 1meter). I hope you followed; my goal was simply to underscore the fact that I am constantly thinking in these small lengths within my research and schoolwork too.

I have yet to answer the question that brought on that rant, why does reading ‘A Brief History of Time’ introduce opposition at all into my life? Well, you see, being a theoretical astrophysicist and all Stephen Hawking tends to write about length scales that are, quite literally, astronomically big. It is nice to come home and peek into another world where people are always thinking about large distances rather than small distances, as I do.

Opposition is like taking a break from a grueling run. It does not only feels amazing but is essential for physical and mental health. Did I just compare my research to a grueling run? Yes, yes I did. I’m ok with that.