Showing posts with label C. elegans. Show all posts
Showing posts with label C. elegans. Show all posts

Saturday, July 25, 2009

I'm Trapped in the Network.

Chantilly, Virginia.
2009 host of the Leadership Alliance National Symposium.
Here I sit in the lobby of my hotel: The Marriott. It's one of the nicest hotels I've ever been in, except for one fault. There isn't any free internet in the rooms....it costs at least $16 to get the internet in the rooms. But there is free internet in the lobby. No poor college student is going to pay that fee when then can just walk out to the lobby and be inconvenienced. None that I know at any rate. So the conference has been going well enough. We left Hanover around 6ish on Friday. I was riding in AB's car with R. I attempted to do some GRE studying on the way, but I'm not sure if I got very far. I'm a little terrified that I'm not going to be ready. There is no possible way that I can memorize the other 125 words that I've got left to go for vocab or do over 100 pages of practice problems. I really really would have preferred to get more practice in. Ugh.

We got to the airport right on time, and got through to security without any problems. So apparently I don't pay attention to the rules about what things are allowed on planes. I should have just checked my suitcase, but I thought maybe it'd be easier to just use O's carry-on. I should have thought about the things that I put in said carry-on. Then I wouldn't have had to have my bag searched and a bottle of anti-static cling confiscated. As if I knew that wasn't allowed on the plane. *shrug* Oh well. It only cost me $1.45 of something. I'm not worried, but the guy looked at me as if I was gonna try to blow up the plane. We took off with no problems, flew with no problems, and then landed going too fast. It was actually kind of scary because it was like the plane had to slam on the brakes harder than normal, but that only lasted about 20 seconds before we were totally stopped on the tarmac. We got lost in the airport trying to find our contact and our bus. We finally got all that figured out and we got to the hotel. We checked in. Everyone was rooming with someone else from the program except for me. I don't know how it works out that I'm always the one getting left out from everything group oriented. Actually, my roommate is kind of great. She's doing summer research at Cornell, and she's really really nice. I'm glad that I got to meet her, but it still would have been nice to actually be on the inside for once. I signed in for the conference and got my free stuff!!!! We got these really nice portfolios and sticky notes and the program made us a couple of sheets of business cards to hand out as we network. We went to lunch at the hotel tavern. My sandwich was so small for the cost; it was ridiculous. Luckily, the program is going to reimburse me. We had this random orientation/starting networking thing in the afternoon. We had to give a 30-45 second elevator speech about ourselves. Obviously the elevator I was in got stuck somewhere on the way to the ground from the 8th floor because Ethan and I chatted for a good fifteen minutes about pretty much anything. So I made my first contact and he was quite nice.

After this session, I went back to the room for a bit to take a nap. Getting up at 5am is not exactly my idea of fun. I slept like a rock. I was totally out. When my alarm went off at 6:30 telling me that it was time for dinner, I was not pleased. Dinner was actually really good. N and I sat at a table with some new people and AB came to join us. I've got this really nice coin that I'm supposed to put on the table that signifies that I get the vegetarian meal. So I had a salad, some alfredo and cheesecake for dessert. It was delicious. During the end of dinner, they had the opening remarks and had this little exercise to get us involved. They read through all of our home institutions and we had to cheer when ours, or the school of a friend, was called. Let's just say that there were only 4 Ohio schools called and 1 Indiana school called. I cheered pretty loudly for me, but I was not crazy like some of the other people that were there. After dinner, they had this panel that was supposed to talk to us about grad school and get us to make informed decisions about our futures and whatnot. Three people, 2 professors and a woman who works for the FDA, talked to us about their research and what they can do with a Ph.D. in their field. It was kind of interesting, but I think it ran too long. After the panel, I sat out in the lobby for a bit using the free wireless with my friends and I went to bed pretty early. I didn't fall asleep right away, but when I did I was totally out.

We had to get up pretty early on Saturday. Breakfast started at 7:30 and that's when everyone started putting up their posters. Before the poster session had even started, I'd already fielded a question by a non-science major. They asked what C. elegans was and this was an easy question. I hadn't been nervous about the whole conference until about 10 Friday night. This totally put my mind at ease. I could do it. I knew more about asymmetric cell division and apoptosis than any of the other undergraduates here. What could possibly go wrong. I was actually presenting at the second session, so I walked around the first session. I listened to one poster, but the guy wasn't clear at all so I didn't stick around. Then I moved to another poster. I picked people that didn't have anyone around. I wanted to be super supportive of everyone else. This guy was K. He's an undergraduate at Cornell and was also doing his research there. His poster was about Golgi tubulation and I didn't know anything about it, but he was really friendly and answered all of my questions. We chatted for at least 20 minutes. I gave him my card, but he didn't have his because he's not as cool as me. He promised to stop by my poster and listen to my spiel since I was pretty much the only one at his poster. I figured I'd better get moving if I wanted to finish walking around before my presentation at 9:45. Let's just say that I got really into the next poster. This was E. She's doing her summer research at Harvard, but she's originally from George Mason. Her poster was all about tuberculosis and this genetic screen that she's doing. We chatted about everything for about half an hour. We exchanged cards and I had to go get ready to present.

When I got to my poster, this group of people were standing in front of my poster. I didn't know what to do. I didn't want to butt in and be like get the heck out of my way. AB saved me by asking me to walk her through my poster and then asking the people to please move. After she left, the first person came up to my poster. This guy was a real talker. I think he really got into what I was doing because he asked a bunch of questions as I went and I think he really wanted to understand what I was doing. In the end, he finally introduced himself to me. Apparently he works at St. Jude's Children's Research Hospital and he totally tried to recruit me. He wants me to consider the University of Tennessee for graduate school because then I could come work at the hospital. And he told me that even if I choose to go somewhere else for grad school that I should consider the hospital for my post-doc. I about peed my pants. I couldn't believe that he was serious. We exchanged cards and I think I'll either stop by his table at the recruitment fair tomorrow or send him an quick e-mail thanking him for his interest in my work. Next I talked to one of the graduate students at the conference. He's from the University of Maryland at Baltimore. I think. He let me walk through the poster and he asked a bunch of questions, but I'm not really sure he was grasping the whole idea of what I was doing. I really had to keep trying new ways to explain the suppressor screen. Sandy came up and asked me to go through my poster with her, so I did. I actually think she probably got the best explaination of everyone because I knew she didn't have as strong a science background. As I was talking to her K came up and listened to my poster. After I answered all of Sandy's questions, she bailed so I could chat with him. He'd heard most of my presentation, so he didn't ask me to go through it again. He asked a few questions and I gave a little bit more explaination and then we parted ways. I saw two more people during the hour. Another graduate student came up and asked me what my project was about. I gave her two sentences and then she worked her own way through my poster. She asked one question and then moved on. At the very end of the hour another girl came up to my poster. They were trying to force us out of the room so she got the quick down-and-dirty version. I was really really surprised when she told me that I was the best presenter she had seen. I really wanted to ask her if I was the *only* one she had seen. But she said that I had been very clear and really emphasized the key points. So I'm going to take that super well. :)
After the poster session ended I came back up to the room for a nap. I had a killer migraine and my shoes had really pinched my toes. I feel bad because I skipped the entire first session of orals, but I did go to one every other session after that. Lunch came next. The food was significantly less interesting. I'm not even sure what I ate. I had vegetarian soup. It was actually really good, but a tad on the salty side. Then I had this really weird vegetable rice pastry. I was so confused about what it was, but I ate it anyway. They had this really pretty white cake with strawberries for dessert.

After lunch I went to the oral sessions to see some talks. It's actually breakfast time now so I'll have to finish my update later, probably when I am back in Hanover. Today (Sunday) is the networking fair and I am more than pumped. Hopefully my network will expand to more than 5 people. haha. talk to you later!

Wednesday, July 15, 2009

A spoonful of E. coli makes it so you can't keep anything down....I think I'll try sugar next time.

I've had the hardest time staying awake lately. I come home at the end of the day and barely make it to 11, which is now my bedtime. My sleep schedule is significantly different from before. I can't even begin to fathom staying up until 2am without a little (meaning a lot) of help from my good friend caffeine. I don't know why I'm so tired. And it's not like I'm not getting 8 hours of sleep most nights. I actually had a dream last night...maybe that's why I'm so tired now. Hmmm.

So Sunday wasn't too terribly exciting. I got up at my normal sleep in time and sat around for a while. At 3:30, B, AH and I walked to the gym. They went to play tennis, but I decided that I'd rather just go do my workout. So I ran a mile and a half. One mile forwards, half a mile backwards and decided that I was done with my cardio. hahah. I really should probably be adding more time to my cardio, but oh well. Then I went and got on the biking machine, turned the tv on to HGTV and biked for nearly 40 minutes. I suppose the machines are accurate enough, but I don't know if I really biked 11 miles or not. I wish the bike did cardio work, but it is really only legs, which means I can ride for longer, but I'm not working out as hard as I would like. After the gym, we came back to mid-mass and cleaned up because R's sister L was taking us out to dinner. We went to Salt Hill Pub in Lebanon, NH. I had yet another veggie burger, but it was good enough. I had the best black and white cheesecake for dessert. It was so delicious. I'd thought about having the Guinness float, but decided that I really wasn't *that* brave. hahah. We got back around 9ish, and I decided to do nothing for the rest of the day. It was kind of wonderful, except that I didn't fall asleep real well when I went to bed. But N was still home for the weekend, so at least she wasn't keeping me up.

Monday morning and N *still* wasn't back from her birthday weekend. I got up and headed into work. Monday was a really great day of work. We had lab meeting at 10 again. Someone had brought in muffins for the meeting, which was great. I really liked this lab meeting as compared to the last one. We went around the table and everyone said what they had been working on thesse past few weeks and what their plans for the next week were and everyone gave suggestions and it was really interesting. I gave my short spiel. I've been absorbing everything and trying to keep my mind from exploading from all the imputs. I wrote an abstract and this week I have to make a poster. Then BC went into a little bit of detail about what actual work I'm doing. haha. She sort of explained the suppressor screen and such before moving on to the next person. After the meeting was lunch and after lunch I came back and started some real work. My first mutagenesis plates were ready, so I got to work with them for a bit. I'd seeded about 200 small plates on Friday, so away I went picking worms. One worm to a plate. 186 worms total. It took forever. Absolutely forever. Half of the worms went back in the 20 degree incubator and half went into the 15 degree incubator. This took me several hours, so I checked my e-mail and saw that BC had e-mailed me back a new abstract.

"Hi Beth,
You did a great job on your first ever abstract!!!! You definitely got the overall idea right. To get this idea across a bit better, I did some rearranging and added a few things like a description of the ces-1(gf)phenotype. See what you think.
B."

Oh my word. I was beyond pumped. I'd really spent most of the weekend thinking about what kind of criticisms I would get....and I suppose I didn't get any. She really did change my abstract around and add some stuff, but there are definitely traces of what I'd written originally. *grin* I was so pleased. So, if you'd like a nice and short summary about what I'm doing and why it's important, read here:
The nematode C. elegans has proven to be a good model for studying programmed cell death or apoptosis, a process that is important for development and cellular homeostasis in all multi-cellular organisms, including humans. Of the 131 cells that undergo programmed cell death during C. elegans development, the cells of interest arise from the neurosecretory motoneuron (NSM) neuroblast. Due to the activity of the gene ces-1, which encodes a zinc finger-containing transcription factor, the NSM neuroblast divides asymmetrically and gives rise to a large cell, the NSM, which develops into a neuron, and a small cell, the NSM sister cell, which undergoes apoptosis. How ces-1 acts in asymmetric cell division is currently unknown. To identify targets of ces-1 function, I will perform a ces-1(n703gf) suppressor screen using a reporter that tags the NSMs and ‘undead’ NSM sister cells with green fluorescence protein (GFP). Specifically, in animals that carry the ces-1 gain-of-function mutation n703gf, the NSM neuroblast divides symmetrically to give rise to two daughter cells of similar sizes both of which survive. Therefore, rather than one GFP-positive cell per side of the animal, two GFP-positive cells, the NSM and undead NSM sister cell, can be detected. As some mutations are temperature sensitive, mutagenized ces-1(n703gf) ‘P0’ animals will be incubated at a variety of temperatures. Their F2 generation will be screened for animals in which only one GFP-positive cell per side is detected. Potential suppressors will be identified, characterized and the penetrance of their phenotypes determined. The mammalian homologue of C. elegans ces-1 has previously been implicated in apoptosis regulation as well. In addition, ces-1-like genes have recently been shown to function in stem cells, which, like the NSM neuroblast of C. elegans, divide asymmetrically. Homologues of ces-1 targets identified in C. elegans may therefore function in apoptosis regulation and stem cells in mammals as well.

So there you have it. My first ever piece of real honest-to-goodness scientific writing. With a little help, of course...but still. A true masterpiece, in my "unbiased" opinion. *giggle*

Monday was also GRE class again. It went much better than the last time. Obviously N is a verbal kind of girl. She only made a mistake a couple of times. I got to tell her that BEVY is to QUAIL as STAND is to TREE. But I only got that one after she told us that a bevy is a group of quail. As if anyone would really know that one! But apparently no one but me knew that a stand is a group of trees. I think there was another one of these analogies or maybe an antonym where I was the only one who knew the answer and it was really funny because I got to make the comment "that's what a midwest education can get you" because it had something to do with farming or something else rural. It cracked me up.

Tuesday was a good day as well. I spent too much time in front of the scope, but I enjoyed it. I'd only enjoy it more if using the scope were more ergonomical. I hate stretching to see down the scope. So I unpicked all 186 worms from the day before. This just means that I took the F1 worms off all of the plates and then I flamed them. It's a good thing I'm not too squeamish about killing worms. Now if these were mice on the other hand and they wanted me to gas them, I'm not so sure I could do that. But I put the plates back in the incubator so the F2 generation could develop. The F1 worms had layed a bunch of eggs overnight, which is good. Then I clonally picked 196 more worms from the 15 degree plates to small plates. I incubated 96 of the plates at 20 degrees and incubated 100 plates at 15 degrees.

Last night we didn't have journal club because AB is in the Dominican Republic. I'm super jealous. N's friends Anna, Erika and Beth came up to visit. We went to dinner at Molly's and I had the greatest Tomato Basil Pasta. It was super good and the tomatoes were all fresh tomatoes and I loved it. Then we took a tour of Remsen and Vail. N and I both got to show off our labs and I enjoyed that a lot. I think I like being knowledgable. :) We went out for ice cream at Ice Cream Fore U. I love this place. I've been several times because the ice cream is pretty inexpensive. A small hard serve ice cream is $2.25 and it's HUGE. It's just too much ice cream for me. I really should order the baby size next time I go. That's only $1.50 and is really the perfect amount of ice cream. Then they headed back to Keene and I went to bed. haha. I'm such a party pooper. That's okay though. Sleep is well worth it.

Today has been a good day so far. I had a little bit of trouble waking up this morning, so it's a good thing B didn't want to go running. I stumbled into the lab at 9 and immediately started unpicking the worms from yesterday. That took most of the morning, but I still had some time before lunch so I seeded about 300 small plates. I'm actually a little worried that I've managed to give myself an E. coli infection because I've not been feeling so great lately, but I haven't seen the really diagnostic symptom. Let's hope that it never shows and that I'm just tired and haven't been eating well enough. *crosses fingers*.

My Amazon package came in today. I've got 3 new books. 1 is the last textbook for my philosophy class: On The Beach by Nevil Shute. It was pretty hard to get a copy of this book....I had to buy the hardback edition and I think there was only one left after I bought my copy. I hope everyone else in my class has already ordered their copy or they might not get one. I also bought Good Omens which is my favorite book. I love Neil Gaiman, of course. Stardust is one of my absolute favorites too. This book was written with Terry Pratchett. While I've never read anything he's written before, Good Omens is an amazing read. The third and final book I ordered is Lamb: The Gospel According to Biff, Christ's Childhood Pal. J recommended this one to me. I'd started reading his copy twice, but I never made it past the first 100 pages. So I thought I'd order it and then maybe pass it along when I finish, if I don't absolutely love it. It's really funny so far, but a little inappropriate. I think it's sort of funny that the two books I ordered "just because" are funny books about Christianity. Good Omens is about the apocalypse and the antichrist. It's really really funny.

Well, my lunch break is officially over five minutes ago, so I'm gonna go back to work. I've got to see if I can borrow 100 small plates from someone since mine aren't dry yet and then I have to go pick 100 more worms. *sigh* It's never-ending and I still suck at it. Oh well.

Thursday, July 9, 2009

I swear I'm twenty-one, honest to goodness.

Okay, so journal club went well. My presentation was by far the shortest and had the least amount of scientific information. The presentation was only supposed to be 2-3 minutes! Some people talked for like 10 minutes explaining their research in detail. It's not that I don't want to know that stuff, but that wasn't the point of the exercise. It was really just to make sure we all had projects of our own and that our summer had some direction. I felt like a total slacker in comparison to everyone else, but at least I know how to follow directions. *grin* Actually, most everyone's project seemed to be really cool. I wouldn't want to work on some of them, but that's okay. I'm quite happy right where I am.
After journal club a carload of us went to West Leb. to do some shopping. I got a bunch of fresh fruit and stuff to make pb&j sandwiches. I *finally* bought a pillow. Oh it felt so nice to sleep on a fat, extra firm pillow. I've been managing with this really thin, squishy pillow for the last two weeks and it's been awful. haha. On the way back it poured. I walked with N from Lot A back to Mid Mass and that's a 20 minute walk. It was pretty yucky. It seems to be raining in Hanover frequently. It's a bit ridiculous. haha. Then yesterday was an interesting day. I came right in and got to work. D had a few instructions from BC for me and so I did that job first. I had to look at my mutagenesis plate and pick out 150 healthy worms to 10 different plates. They mostly looked good, so I hope the mutagenesis actually worked. This took me about an hour and a half to do, but at the end I felt really accomplished. At the beginning, I was really sucking at picking worms. By the end, I was picking 3 worms at a time and not having to chase them around the plates. That's a huge accomplishment. Of course it helped that I wasn't having to pick them by age. Since I'd picked them all as L4s the day before, they were all young adults so it didn't matter.
When I was picking the worms, SR asked me if it was okay if he put music on. He said that he thought we didn't listen to music every day because BC didn't like us to. So he put on some Top40s-type song and the two of us and S were enjoying it when D marched right into the lab and demanded that we turn it off. She said we couldn't listen to music until after 5pm. We were all really dumbfounded. We weren't disrupting anyone and it wasn't affecting our work. She wasn't even in that lab, she works in the lab across the hall, so we were all really confused and not very happy. I was mostly sad because we'd been doing some real lab bonding at that point. Negative brownie points for D for that. :(
After lunch I started looking at my heat shock plates for males. Most of the progeny are too young to really see so I can't tell if the heat shocking worked or not. Perhaps it'll be easier tomorrow and I know I'll be able to tell by Monday. Then I looked at the plates for the other strain that I'm going to mutagenize. These are the bag-of-worms worms. They are super creepy. haha. While I was doing this, D came in to stand over my shoulder to make sure I'm not going to blow up the lab. I wasn't particularly pleased with this, but what can I do? I wasn't even using the ethanol burner at this point. Oh well. When I finished looking at the worms under the scope, I decided that it was time to do some more scoring, so I tried a couple ways to figure out how to get one of those bags of worms onto a slide and not rupture the cuticle. I finally figured it out and I headed for the small scope. I turned on the GFP filter and got up close to the worms. It was really disgusting. R was on the computer in the same room as the scope so she laughed at my reactions to the worms. It was actually really kind of cool though. I got to see all the worms wiggling around inside the cuticle, which was nice because they couldn't wiggle outside of my view, but I hadn't done anything to keep them from moving, so it was kind of hard to actually score them. sort of. Since these haven't been mutagenized yet, they all had 4 GFP positive cells, so it should have been easy.
When I tired of looking at those worms, I brought out my plate of double mutants, put them on ice and worked on scoring some of those worms. I'm getting significantly better on the small scope. I hit a few snags when I would lose the worm, but I was more than capable of seeing the GFP positive cells, even though the sample wasn't really magnified a great deal. I think I do better on the large scope, but I'm gonna try to use the small scope for the most part because I don't kill the worms on the small scope like I do on the big scope.
When my eyes started to hurt from using the scopes, I put the worms away and read a little bit at my desk until I couldn't stand it anymore and went home. Dinner was in Thayer with most of the people from the program and then GRE class was after that. I was really excited about getting to take the Kaplan course, but our teacher totally bombed the first day. I actually felt bad for her, she tanked so hard. I don't know if it's her first class or what, but she didn't understand the math we were doing. I don't know how many times we had to correct her to tell her she told us the wrong answer. She was really nice though and next week she's bringing us pizza for dinner. I'm hoping that the next session will go better.....we did learn some really neat tricks about some of the problems, but for the most part it was a waste of time. I really want to know how my diagnostic exam went, but they haven't posted our scores online yet.
Today was an interesting day. B and I got up at 7 and went running in the sports center. It was a nice 40 minute workout. By the time I got to lab, I'd already been up for two hours and I was wide awake. I feel like I was a bit of a waste today. I got to lab around 9:15 and got all my stuff set up. Then I got my worms out and looked at a couple of my strains. The worms on my heat shock plates are too young to set up male plates, so I ignored them. Then I looked at my plates for the bag of worms mutants and those worms were too young for mutagenesis. So I started looking at corpses to see if they had larvae in them. So I was counting corpses today and that was really the highlight of my day. After this, I went back to work on my poster. I'd sort of started to get it set up yesterday, but I really started thinking about what I wanted on my poster. I set up a little outline and started making some notes about material to include. Right before lunch I went into BC's office to ask her for some help. I told her all about how I need a title and abstract ASAP and how I have to have a poster ready to print by next Tuesday because I'm presenting my poster to the journal club Tuesday night and then fly to Virginia that Friday. So I think I might ask S or R for some help making a poster. I don't know if SR has ever made a poster, so he might not be a good choice. I think that BC and I are gonna do my title and abstract tomorrow. So she gave me some pointers about how to think about doing my abstract and told me to work on it this afternoon. Then she showed me how to chunk my plates to transfer "starving" plates to fresh plates. We go through worms like crazy in this lab. I feel bad, but I don't at the same time. *shrug*
So from 1ish when I got back from lunch until 5ish when I left, I was working on my abstract. I read the Masters Thesis that I have again to really get more information about my methods. I also reread a couple pages of some of my papers to get a feel for the imporant things to include and I finally started writing. I managed about 150 words, but it's not finished and I'm not sure that it's good. hahaha. I'm really nervous about showing it to B tomorrow. Especially since I took so much time working on it. ugh. I wish I were more confident with my scientific writing...but I'm not. But I'm looking forward to tomorrow. More mutagenesis and abstract writing and who knows what other cool things. :D
I was so pumped to have time off this evening. These 12 hour days are really rough. We all went out to dinner tonight. N's 21st birthday is this weekend, so she said we were celebrating, but I think most of us just wanted actual food. I had a black bean burger with some really good broccoli. And we all split a thing of chips and salsa. I also had a frozen mango margarita. I really enjoyed the drink and it wasn't too strong like the one I had at applebees. I wasn't so sure I'd be served alcohol because our server must have thought we all had fake ids. She looked at them all and then said she had to take them back to the back. I don't know if she had them scanned or if she asked someone about them or if she had them photocopied or what, but she was gone forever. N wanted us all to get up and leave if they refuesed us service. But, as it was, she finally brought us our drinks...and they were cheap and that was wonderful. :)
Oh! I got my Amazon package today. So now I have a few books to read. I'm already 1/3 of the way through Never Let Me Go by Kazuo Ishiguro. I'm actually really enjoying it so far. I also got Of Mice and Men and Brave New World. Those are next on my list of things to read. I haven't read all that much this summer. Every year I reread the Song of Ice and Fire series by George R.R. Martin, but this summer I only had time to read A Game of Thrones before leaving for Pittsburgh. I also read probably two dozen YA books, but I can't remember one of them. I think the best thing I've read this summer is The Kite Runner. I'm glad I went to see the one man production in Ada this past year, and I loved the book. I didn't expect it to be quite so powerful. I know I just got some new things to read, but I already made my next purchase. I'll wait until those books come in to tell you about them though.
Well, it's time for me to head to bed....I've gotta get up early again to go running with B. We're gonna try to work out every morning for the next two weeks. We'll see how that goes....I am kind of a lazy bum and I really really like my sleep.
Until next time!