Friday, May 27, 2011

Making progress on The Danger Zone

From my neck to my knees, my entire body (still) hurts. I think David has recovered from our work on the garden on Wednesday night, but my body is still asking me why I thought that all of that garden work would be a better exercise plan than taking a spinning class! Last year we used two wheelbarrows full of compost for our entire plot, and while things grew pretty well last year, that was not the appropriate amount of compost. And so this year...I think we overcompensated. We used 24 wheelbarrows worth of compost, and spread it evenly all over our garden plot so that we could till all of it into the soil to make planting beds. And since I have to prove that my body is sore for a reason, let me just brag for a moment - I shoveled 18 of the 24 wheelbarrows! I think this is one normal step for most of mankind, but a huge step for people with noodle-arms!

Last year, as a result of not using enough compost, we also did not do a very good job of tilling the soil. After researching how much it would cost to rent a tiller, we decided just to purchase the above garden cultivator from Home Depot. I was super excited to try this out, but it turned out to be difficult to use this tool since the ground had a clay-like texture and was not easy to tear up. I was still able to use it somewhat (and save David a little of the really heavy duty work that involved manually tilling the soil with a hoe).

Our progress! We have made 7 of the 10 planting beds! This took about 3 1/2 hours. We will make the other 3 beds next week and plant our seeds/seedlings.

Last year we had to do A LOT of weeding, especially between planting beds. This year we are trying something a little different; we decided to put weed protectors between the beds so that we will (hopefully) only have to weed the beds themselves.

Last night (Thursday), we also made a door. We were going to continue to make the beds, but then...giant thunderstorms prevailed. I forgot to bring my camera though, so I will have to take a picture of that on our next visit when we finish our prep work.

Tuesday, May 24, 2011

What I do all day

I often get asked what it is I do, and I often fumble the question. Despite the fact that I have an English major under my belt in addition to all of the science training, it is hard for me to tell a story about the science that I do without getting people lost in the jargon. (David is much better at this than I am.) For scientists, talking about our jobs is like playing a game of Taboo - many of the words are (and should be) disallowed, because they won't allow people outside of science to fully understand. However, I have had some really great results in lab recently, so I thought I would try to talk about what it is I am working on so I can share my great results with all of you.

And so...a little background. (There will be pictures later, so feel free to skip to the bottom of the page.)

As a biochemist, I am interested in studying proteins. If you think of a cell as a giant city, proteins are all of the people inside of the city going to work every day. Each protein is made of up of the same types of building blocks, but how these building blocks come together to make each unique protein are a big part of what dictates what job a protein will perform in the cell (just as we all have traits and talents enabling us to do whatever it is that we do). My thesis project at Penn was spent learning about how proteins are built to do the jobs that they do. I studied the building blocks of proteins and applied that knowledge towards using those blocks to engineer new, designed (non-natural) proteins to perform specific, existing functions. At Cornell, I wanted to take my studies in a slightly different direction. Instead of studying the individual building blocks and how to put them together myself, I now want to know what natural proteins look like once they are fully assembled. What is their structure? And how does the way the protein is structured contribute to its ability to perform its job? And do we get information about the structure of proteins? There are many different techniques to do this, but the technique my laboratory uses is called x-ray crystallography. So what does that mean exactly?

Did you all ever have these kits as a child? Or perhaps you ate these? (I know I had an obsession with these rocks of sugary goodness for a stretch of time in elementary school.) Just as salt and sugar molecules can form crystals, so can protein molecules. Crystals are advantageous to study because they are ordered (what allows them to form). This basically means that when a crystal of protein forms, it is many protein molecules coming together in one solid, with each protein having its building blocks in the exact same arrangement. To relate this back to people, this would be the equivalent of having multiple copies of me in a room (that room would be LOUD) in the exact same position without moving! If one of my copies blinked, or scratched her head, the "Sarah crystal" would crack and the whole room would become disordered. This is what makes protein crystallography so difficult - proteins, like people (me in particular) are dynamic, which means their building blocks are always moving into slightly different positions. They aren't designed to "stay put" in one conformation (position) and most of the time, their jobs actually depend on them being dynamic. Finding a condition for them to crystallize and "stay put" is bit of scientific voodoo and a lot of luck, though there are sets of conditions that have been demonstrated to be better than others for crystallizing proteins. (As there are for salts and sugars, which is why there are kits and recipes for the examples above.)

And so, for the past year, it has been my goal to crystallize a specific protein (that has a specific job that I find cool and exciting) and determine its structure. No one has ever determined the structure of this protein before, so it would be a big advancement to my field to know how the arrangement of this protein's building blocks contribute to why and how it functions. The great result I would like to share with all of you is that after a VERY frustrating year, I have finally made progress!

Above is a photo of my protein crystals, clustered together. (Sorry, the image is not great, because I am still learning how to use the camera attached to our microscope.) These crystals are not ideal because they grew together rather than separately, but I was able to break them apart without damaging them (luck rather than skill). These crystals are 100 microns big, which translates to being 0.1 mm, or 0.003 inches. Working with them is challenging for me because I have to use a microscope just to see them, and when I am looking through the microscope, I cannot watch what my hands are doing at the same time. These crystals are made of many copies of just a small part of my entire protein. Some proteins are very large assemblies of building blocks (mine is), and it can be easier to isolate and study the structure of many small pieces individually rather than going for the whole thing all at once. (Imagine studying just the arm of a Mr. Potato Head doll, and then the nose, and then the leg, and so forth, and then using what you learned to put together the whole toy.) Obtaining my protein (and its pieces) was not an easy task, and I spent almost my entire first year working on just that part.

Once I obtained protein crystals, I needed to do an experiment to help me determine how all of its building blocks are arranged (structure). We mount the crystal and expose it to a beam (narrow stream) of x-rays (electromagnetic radiation, just like the x-rays used in medicine, but much more focused). Just like getting an x-ray of your arm produces a 2-D image of your "structure," we get a 2-D image of our protein structure too.

My 2-D image looks like the picture above, and this is called a diffraction pattern. Basically, the x-rays bounce off the surface of the crystal (this is called diffraction) onto a detector. The pattern above is the read-out of all of the diffraction spots (each dot) that occurred from the crystal at a single angle. We then change the angle of the beam by 1 degree and measure this pattern again, and do this for all 360 angles (or one full rotation). The further the spots are spread out from the center of the beam (the cross in the white spot in the center of the image), the more data we have, and the more detailed our structure can be. We can combine the 2-D diffraction data collected at all 360 angles into one data set, and then mathematically convert that into 3-D coordinates (to over-simplify it a bit). This is the stage that I am at right now. I will eventually use what we know about other protein structures and the known 3-D coordinates for each type of building block to build up the 3-D structure of my protein.

Cornell has one of six facilities in the United States to collect high resolution x-ray diffraction data (called synchrotrons), and it is called CHESS - Cornell High Energy Synchrotron Source. Working at CHESS is like what I imagine it would be like to work on a submarine. There are so many switches and lights and monitors! I keep waiting to push the button that shuts the whole place down by mistake, but so far, I have not caused any major disasters while collecting data. Also, there are many safety protocols in place to ensure that none of us get exposed to massive amounts of x-rays while we are collecting data, and many of them involve loud alarms that sound until doors and switches are locked securely. It is amazing how difficult it is to turn a key and close a door when a giant alarm is sounding all around you! I still get stressed out just from the noise.

This lighted sign tells us that everything is running and we are able to collect data.

And so, that is a bit about what I have been up to over the past few weeks! Hopefully some of this made some sense. I will post what my protein structure looks like once it is solved.

Monday, May 23, 2011

Trip to MA #1 - Boston Pops with Elliot

Over the eight weeks of May and June, I have four scheduled visits to the state of Massachusetts! It would be ridiculous, except I happen to love both the state of Massachusetts and the people that reside in it, and welcome any (and every) opportunity to visit.

My first trip was a trip to Boston with Elliot. He had never been to Boston, and I was very happy to show him around my favorite city. We booked our trip around seeing Linda Eder sing the Judy Garland songbook with the Boston Pops. (Side note for all of my friends in Boston: we discovered when buying these tickets that the Pops offer $25 best seat available tickets to anyone that is under 40!! This is too good of a deal to pass up, and I plan to see the Pops again during at least one more of my visits this summer.) We were obsessed with Linda Eder when we were little, and I was particularly obsessed her version of this song. The concert did not disappoint. The first act was the Pops performing modern classics (including a SOUND OF MUSIC SING-A-LONG!!!) and the second act was Linda and the Pops. Linda was even more amazing live than I have ever seen her on video. I swear that woman does not need to breathe while singing! The only funny thing about her performance was her shyness, which manifested itself between songs. It was a strange contrast to hear her amazing singing voice fill the room over an entire orchestra, only to then struggle to hear her speaking voice as she mumbled with her head down between songs.

After the concert, we got dressed up and went out on the town. This photo was taken as I put on what I was calling Elliot's "Screech Powers" sunglasses and acted like a diva. ("Sarah, go 'head girl...")

The next day, we put our weekend T pass to good use and went all around the town sightseeing and eating. We kicked the day off by meeting Anna and Jen for pizza at The Upper Crust. It was so nice to see both of them, though we missed Kim! :) The photo above was taken at The Salty Dog Cafe after consuming massive quantities of fried clams. We were happy people! (Those clams are so delicious.) We also had thai food at Brown Sugar Cafe, clam chowder at Legal Seafoods, and ice cream at JP Licks.

Trip #2 to MA will happen this weekend, when we head to Westborough to see Brian and Jane. I am heading into this trip with a bit of guilt, because I made a crazy list of demands for Brian and Jane to carry out upon our arrival (I was kidding about everything except Brian making tacos). Regardless of whether they meet all of my demands, I am really looking forward to visiting them. It seems like it has been forever since we saw them last over Christmas break.

Preparing The Danger Zone for planting

After weeks of waiting, the community land where we have our farm plot has been plowed...and it is time to get our farm on! David and I have been very excited to started. Now that we have the experience of last summer behind us, I think we will be able to "farm" much more effectively this year.

However, Ithaca is currently a soggy, swampy mess due to the unusual amount of rainfall (which is why it took so long to plow the land in the first place) and so we did not make as much progress last weekend as we would have liked to. Above is the river that is currently running through one side of our plot.

We did manage to put up our fence and set aside some compost for future planting. David was in charge of putting the posts in to hold up our fence, and he did an awesome job despite the mud. It was really not an easy task, because David was sinking into the ground as he was trying to stabilize the posts!

Here are David's shoes after he was finished putting the fence in!

And here are mine after securing all of the zip ties needed to attach the fence to the post!

David is standing next to our beautiful metal fence. You will notice that we upgraded the orange hazard fencing from last year to something more sturdy this year. We are still trying to figure out what to use for a door though, so perhaps the orange fencing may resurface in some capacity. The plot next to ours (with the yellow yarn on top) belongs to two of David's friends, Jon and Lexi. It is nice to have some company on the farm this year!

My manual labor contribution to Saturday's farming activities was shoveling compost into a wheelbarrow that David then took back to our plot. (We did not trust that I would be able to transport the compost without spilling it all over the place, as I am too uncoordinated to avoid falling in the mud.) I shoveled this entire pile that I am standing next to, which is quite a feat for someone with arms as noodle-like as mine are!

We are hoping that the rain will hold off over the next few days so that we can begin planting!

Tuesday, May 3, 2011

Benjamin Michael Hoertz

I just returned from visiting the Hoertzes, and Amanda and Paul really have an adorable baby son. I am so excited that I am Ben's godmother.

Look at that face! What a heartbreaker in the making.

Lovely Amanda with Ben on the couch. I am very glad she let me take this picture, because photos have been limited to only her "camera ready" moments so far. (I can relate though - I do not encourage photos of me when I am not "camera ready" either.)

Amanda, Paul, and Ben. I think this photo would make a very cute Christmas card. (Amanda and Paul did have a professional photographer come to take photos of them with Ben, so I am sure the photographer did a better job!)

Be on the lookouts for updates about this cute fella as we anticipate this summer's christening event!