So much to share!

Dear family and friends,

Happy July! My blogging time lately has been interrupted by busy days at lab. I am mentoring a summer undergraduate student until August, and my days are filled with keeping her busy (which keeps me busy). However, I have so many June adventures to share with you...like...

...TWO more trips to Massachusetts!

...Danger Zone updates!

...Pictures of the Crane Lab's new laboratory space! (TODAY IS MOVING DAY! We are moving to the third floor of this building.)

I promise to update you soon. Until then, let us all marvel over the fact that the Pirates are one game away from first place! Way to go, Buccos! I hope you continue to play like it's 1990-1991.

Happy 2nd anniversary :)

While I was visiting Boston last weekend (look out for upcoming posts about MA Trips #3 and #4 for more details about my trips), I went to see a late night showing of Conan O'Brien Can't Stop. I bought some popcorn and a glass of wine, and settled into my seat for a fantastic movie about the darker days of my favorite late night television host. After the movie, a cute guy sitting next to me struck up a conversation about the film and politely asked me if I wanted to go get a drink with him.

My undergraduate dream come true! When I was in college, this was my definition of a "fairy tale" romance. A chance meeting at the movie theater, which could then lead to a whirlwind courtship full of video rentals and dessert at Finale. A fateful meeting while in the checkout line of a grocery store could lead to sharing my recipes with a new boyfriend. (And in fact, I used to smile at every guy standing with me in the lines of the Commonwealth Avenue Shaw's grocer on the off chance it would inspire them to talk to me. Oh younger Sarah...you were so silly.)

Of course the irony is that I know now that this version of a fairy tale is really not a fairy tale at all. I know now that real fairy tale romances are not made of chance encounters with people who do not know you, but moments spent with the one person who knows you and loves you. I continue to be so glad (and slightly amazed) that this person is David.

So for all of our fairy tale moments, and those yet to come...happy, happy second anniversary David :)

Grandmom Trush

My great-grandmother Trush passed away on Wednesday, at the remarkable age of 98. Sophie Trush was a woman that truly sparkled - captivating us all with her sass, her stories, and her ridiculously good Polish food. Some of my favorite memories childhood memories are from our times together.

My family and I spent many summers and holidays on the Trush farm in Sassamansville, PA with my great-grandparents, and my grandmother lived there for several years even after my grandfather passed away. Part of the adventure of visiting them (as a little kid, anyway) was the six hour car ride on the PA Turnpike. One winter, it snowed so badly as we were driving that the Turnpike shut down and we were stranded on the side of the road for several hours! To combat the misery of spending six hours (or more) in the car, my sister and I would get to make toy boxes full of things from home to entertain us during the car ride. I recommend this trick to all parents traveling with small children! Having our toys with us was a nice thing for my parents I'm sure, but the best part about the boxes for us was getting to decorate them. My dad would bring home computer paper and computer paper boxes from work, and we would use the paper to cover the boxes and then color on the outside. My parents still have two of these boxes (one of my sister's and one of mine) in their attic somewhere.

My great-grandmother told the best stories, mainly involving what her life was like when she was younger. For many years, she worked as a waitress in a diner not far from the farm, and she had a lot of really entertaining stories about the people she served and the girls she worked with! She also told a lot of stories about surviving the Great Depression, and at times, I don't think she was convinced it was not still happening. She did not trust banks to store her money, and as a result, started storing her money under the mattresses of the beds in the house. When her oven was broken and my dad needed some money to buy a replacement part from the store, she told him to get it from between two mattresses. When he flipped the mattress over, he found tens of thousands of dollars in cash! My father then followed her around the house as she revealed all of her hiding spots (and then he promptly took her to the bank). Thank goodness no one had ever tried to rob her while she was living alone - they would have made off with her entire life savings!

I also loved her stories about her marriage to Stephen Trush, my great-grandfather. My great-grandparents were an example of a couple in love throughout their entire marriage. They were definitely the quintessential cute older couple that all of us younger married people aspire to be when we retire. After my great-grandfather died in 1995, she still always talked about "her honey" and what it was like to fall in love with him. I loved hearing those stories, because they kept his memory alive and brought the sparkle back to her eyes.

My sister and I had many adventures on their 40 acres of farm land. We learned how to shoot a coffee can with a shotgun and mow the lawn with a tractor. We played pretend, swung from the tire swing with the neighborhood kids, and picked blueberries. We would walk to the post office with my mom and dad sometimes to pick up Grandmom's mail (maybe this was the beginning of my absolute love for receiving mail?), and played a lot of games of hide and seek outside. Well...mostly outside anyway. During one game, Jenn and I cheated and hid indoors and then watched through the windows of the farmhouse as Mom searched for us outside. (Sorry Mom, this still makes me laugh every time I think about it.)

The trips to the farm also involved visiting the local sights of Sassamansville and Philadelphia. Sassamansville has some really great things going on (like this, and this), but I loved going into the city. I was convinced I was going to move to Philadelphia when I got older. It seems my 8 year old self was pretty insightful! My younger self had two goals for her life in Philadelphia: I wanted to have an apartment by the art museum (the ones I had picked out as a kid turned out to be out of my price range) and a membership to the zoo (this I did have for three years). Though I did not end up wanting to live in Philadelphia permanently, many of the things I love about the city are things I learned from my dad. (To name two - there is a great Italian ice place in South Philly on 12th and Shunk Streets, and a hole in the wall family-owned deli where you can buy Polish kielbasa.)

I have some very funny memories of my grandmother, and many of them revolve around food. My grandmother was an incredible cook when it came to cooking Polish food (the food of her heritage), but when she cooked or served anything else, it was disastrous. If you say the words "farm", "Easter", and "ham" to anyone in my immediate family, all of us will immediately cringe at the memory. I am not sure what she did to that ham, but it was crazy horrible. Everyone at the table raved about how good it was as we all struggled to swallow it. She also had the worst orange juice I have ever tasted in my life (I am not sure if it was the brand of orange juice or the amount of time it lasted in her fridge), and she always wanted to serve it to Jenn and/or me at all times. Jenn and I used to both take the orange juice (usually because my mom or dad told us to be nice and drink some), and then take turns transferring our juice into the other's glass. (Or maybe I just did that.) She also loved when we took her out to eat at Bonanza steakhouse. That was a really big treat for her, and we had a lot of fun going there (even though that food was also not the finest food one could find in Sassamansville).

Perhaps one of the funniest things about Sophie Trush was her adoration for Jerry Springer. Grandmom Trush firmly (and not sarcastically) believed that Jerry Springer helped those people that came onto his show, and she never missed an episode. It was mind-boggling. My favorite part was that she would chant along with the studio audience when they were saying "Jerry, Jerry, Jerry" and encourage us all to chant too. She wanted to cheer him on, because she felt truly bad for these people caught up in "such a horrible mess." She also reminded Jenn and me that we should always date nice men, so that we wouldn't "end up like one of the girls on Jerry's show with their trampy dresses and hair all unwashed. They are not young ladies!"

I am truly grateful to have had such a delightful grandmother, and to have so many wonderful memories to remember her by. David and I will celebrate Grandmom Trush's life and our memories with her with the rest of my family at her funeral mass on Monday.

Trip to MA #2 - visiting Brian and Jane

Over Memorial Day weekend, we went to see Brian and Jane at their home in Westborough, MA. It was a really nice visit. Originally, Brian and Jane were supposed to come to Ithaca, but it ended up being much less complicated for us to go visit them. As a joke, I began composing a list of "demands" that would need to be met for us to come visit while David was on the phone with Jane: dinner at PF Changs, an Easter egg hunt (David made an Easter egg hunt when Jane and Brian came to visit us for Easter the year before), Brian making us a taco dinner (he makes homemade taco shells that are very delicious), and playing a game of Risk (this was David's demand that he added to the end of my list). I am happy to report that Brian and Jane met all of my diva demands and then some, and we had a fantastic visit. (I will note that we would have had a fantastic visit just seeing them, but the demands being met just made it over-the-top crazy fun.)

On Saturday morning we had our Memorial Day weekend egg hunt. Jane did such a good job with it! The only eggs left at CVS were incredibly cute - David's were sports-themed, and mine were shaped like animals. Though I am normally completely oblivious to my surroundings, I would like to state for public record that I found all of my eggs before David did! Here is a picture of us with our baskets at the end of the hunt. David is holding skis in this photo because Brian gave David his skis and David was very excited about them.

One thing that I did not demand beforehand but became a daily demand once I arrived in Westborough was going to Dairy Queen. I LOVE DQ. LOVE IT!! I used to go all the time when I lived in Butler, and it is still my favorite place to get ice cream. (Some people might even say I am slightly obsessed. My dad once asked if I come to Butler to see him, or to get a M&M Blizzard.) Ithaca does not have a DQ, and so whenever I travel to somewhere that has one, I feel compelled to take in as much DQ as I can eat. Jane and Brian live right down the street from a DQ, and we went every night. It was spoonfuls of happiness.

We will see Jane (and maybe Brian) when we visit Ken and Carol in Lenox, MA in two weeks (MA trip #3). We will finally get to see Ken and Carol's new house, and we will attend Kate and Chris's wedding at Mount Holyoke College. It will be a fun, but busy trip!

All planted!

After several long hours of work, we finally got everything planted in The Danger Zone.

Here is a photo of our door. We decided to use the metal fencing for the door because we did not have enough bright orange hazard fencing left. I think it is going to work out well - it is certainly much more sturdy!

We got up at 5:30 am on Tuesday and got to work. We first had to finish making the garden beds and secure our door, and then we started planting all of our seedlings (that were not in the best shape because we had to wait so long to plant them). You will notice in the picture above that David has covered his head and legs with dirt - the dirt was his makeshift bug shield. The mosquitos were out in full force that morning, and David was their meal of choice. While the bugs seemed more content to crawl into my eyes than to bite me, David was covered head to toe in bug bites (and still is)! We were also fighting off these tiny black bugs that were keen to eat the leaves off of our seedlings that we had just planted! (Apparently eggplant is their absolute favorite.) We lost a lot of our leafy crops to bugs last year, and so we promptly went to Agway and bought a small spray bottle of pesticide to protect our vegetables from being maimed by these tiny black destroyers. (Sorry Cornell, this garden will not be completely organic this year...)

Here is a list of what we planted in each row:

1 lettuce/carrots/black-tipped lettuce/microgreens

2 big bertha tomatoes/thai basil/grape tomatoes/basil/heritage tomatoes/oregano/celebrity (striped) tomatoes

3 Eggplant/thyme/cajun pepper/tarragon/bell pepper/rosemary

4 sugar snap peas/cucumbers/peas/pickling cucumbers/lavender

5 white swiss chard/broccoli/red swiss chard/sage

6 mustard greens/collard greens/bush beans/cilantro

7 onions/dill/brussel sprouts

top of 8/9 sunflower/corn

8 squash

9 pumpkin

Here is a picture of rows 2 and 3 (the rows that had the most seedlings, which makes for the best picture at this point).

Some of our plants came with fun names this year, like "Big Bertha", or my personal favorite, the "Mr. Stripey" heirloom tomato.

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.

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 so...how 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.