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Posts Tagged ‘C. elegans’

Contamination

July 8, 2010 5 comments

I came to lab today to find that all of my C. elegans plates are contaminated again.  Woo. To give you a sense of what that means I took some pictures.

C. elegans is a small roundworm. It’s adult size is about 1 millimeter so it is treated in most respects as a microorganism.  This lab raises the worms on Nematode Growth Medium plates which are an agar plate with certain salt concentrations that make it an ideal place for worms to live.  These NGM plates also happen to be great places for other things to live. Things like fungus and bacteria. Unfortunately when you want to do controlled studies on worms you can’t have these other things living with the worms because they could be secreting toxins or otherwise making the worms not the same as the worms on the next plate over. This means that when your plates get contaminated you need to toss them or isolate clean worms from them.

This is an NGM plate with OP50, a strain of E. coli that the nematodes feed on. This plate is good. No colonies of other stuff is growing. These bacteria are added to the plate before the nematodes.

This is a picture of some more NGM plates with OP50, but without nematodes. These plates, however have colonies of some other organism growing and will eventually become covered by this invading contaminant species.

This plate has nematodes on it that are contaminated with some fungus or other junk. The yellowish cloudy stuff is what you don't want.

In short, it’s hard to keep junk from growing on your plates where you want nematodes and only nematodes. I go to great lengths to keep them clean, wearing a mask and gloves, working in the clean hood (sterilized with UV light), spraying everything with ethanol before using it, and minimizing the amount of time the plates spend with their lids off.  I must be doing something wrong, though because this keeps happening.

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Summer Days

July 8, 2010 1 comment

Each day I try to keep a fairly reasonable account of what happened so I’ll be able to remember this whole experience pretty well.  I often find myself writing in details and generally making these journal entries into blog-style posts.  So here are the journal/blog entries for the past several days, made more presentable than they would otherwise be.

7-2-2010

  • Woke up at 5 am (couldn’t sleep any more probably due to all the napping the past 2 days).
  • Went for a long run and ate breakfast at 7 am.
  • Dropped off laundry and went to lab.
  • Read stuff online for a while and determined that the internet in lab is really fast.
  • Planned out tests to do with cellulose and whatnot.
  • Picked up laundry and went to our group lunch.
  • After lunch I went to lab and carried out my tests.
  • Met/chatted with a couple of the undergrads in my lab.

I went back to the hotel and met up with Taylor.  We hung out In her room and watched V TV (it’s MTV in China and features both Chinese pop music as well as some American stuff) for a bit, played some apple-scrabble.  I was going to go bike around with Yun to take pictures but it was hot and I was getting tired (I woke up at 5, remember?).  So I hung out with Taylor.  We waited for Yun to come back before we ate dinner.  Anya showed up and eventually ate with us as well.  Nick and Matt came to dinner also.  We went to the blue place (bao zi) (so good).  After this we tried wrangling people together for soccer but more or less failed.  We did kick a soccer ball around a bit but not that much, we may have been yelled at to leave the field again. We left the field thinking that this was the case, in any case.  I then played some basketball with matt and Sarah, which was fun.  By this point my legs were/are really tired.  Now it’s bedtime.  I also managed to read a few pages of blue mars today.

7-3-2010: Woke up at 8:25 or so, ate breakfast, then went out shopping with Taylor, Sarah, Lily, Susan, and Veronica.  We went to a clothing area (visited 2 separate market buildings) near the zoo.  It was fun to give my commentary on clothes, provide my expert opinion as a male, and look at some guys clothes when it could be found.  Then we went to a more general market and got some trinket things.  We then headed back to the hotel and took a rest for an hour and a half.  I finished blue mars, took a short nap, got a blizzard from DQ and then had dinner at 5:30 at a restaurant near the courtyard.  I didn’t like it.  They made you pay for opening your chopsticks, but that was the only option (which isn’t a big deal, but it’s annoying).  They didn’t give us bowls for our soup except for when we asked and we had to ask a couple times to get spoons.  The chicken dish we got was weird.  We think it was chicken hearts?? Not sure…

So after that we went to wangfujing street.  We first went to the bookstore.  They had a big selection of dvds so I got Moon, Anya got Avatar.  Yun asked us to get her Fahrenheit 451 so I grabbed that for her, too.  We then headed to the snack street.  I ended up eating lots of sugary fruit and some grasshoppers.  The grasshoppers tasted like any little meat that was deliciously greasy due to being fried in grease.  I also got a satchel of candy from a candy store there.  I’ve liked what I’ve had pretty well so far.  We then headed back and watched the end of the world cup game.  Now sleep.

7-4-2010: In the morning Lily and some people went on a trip within Beijing with Lily’s lab. I chose to take it easy and hang around. I ended up hanging out with Veronica and blogging until I was recruited to go to Yuanmingyuan park (a ruined place where the emperor used to party (surprisingly enough)) which is supposed to be pretty nice (though it’s ruinous instead of being in good repair). We actually went on a tour of the pretty Tsinghua campus (led by Lily and Ray). It was Hot.  The campus was pretty. We returned home to get ready to go our dinner reservations at Bellagio’s (which is a Chinese restaurant… for some reason with an Italian name)

The meal ended up being 7-9 dollars (USD) today, depending on what sort of snazzy drink you got for yourself.  We should really try to relax about the price of meals, especially when going out to dinners like this.  We’re constantly fretting about the cost since it’s a fancy place, and it sort of poisons the time spent ordering and we might order one fewer dish since it might become “too expensive” but in reality it just slightly lessens the meal because you’re not quite satisfied.  I liked the food quite well, but I wasn’t really in the greatest of moods so it wasn’t my favorite dinner ever.  After dinner we went over to CarreFour and got some groceries. I was looking to get some cereal and milk and cookies. I decided against the cereal but I did get a bag of German oatmeal/rice puff stuff which I intend to eat with some of the yoghurt that I got (Have I mentioned that yoghurt is EVERYWHERE in china?). I also got some peanut butter Oreos (delicious), and some chips ahoy cookies.  I was surprised to find that the chips ahoy weren’t nearly as crumbly and not as jagged as US chips ahoy. They were more flat, smooth, and firm.

At night as people were getting to bed I got started talking to Sarah and Ray about my lab stuff and it became apparent that I was really frustrated by the whole situation.  I feel like the whole lab ignores me and doesn’t make an effort to talk to me.  Nobody in the lab introduced themselves to me, excepting a couple of undergrads, the grad student I was originally working with (Anasha) and the grad student I’m now working with (Yan Tang).  I need supplies and don’t know how to get them and don’t really feel comfortable talking to people to ask.  Sarah and Ray were full of good advice and I was glad I talked with them about it.  [Update: I feel much better about the lab situation now, post-lab meeting.]

7-5-2010: In the morning I worked on my powerpoint to show to the lab what I’m working on this summer (automating/speeding up the worm processing stuff) until 2. At 2 we had the lab meeting. I feel like my powerpoint went over well and that people in my lab were impressed by how thorough it was. Last night I was feeling really discouraged and felt like my lab didn’t care about me at all. They didn’t talk to me and mainly ignored me and I didn’t know how to get the materials I wanted to do things that I wanted to do (wire, basic tools).  I think by talking at the lab meeting they learned that I do sort of exist and have something to say.  I spread some bacteria on some plates and generally did a little worm wrangling and called it a day.  In the evening we ate at a cafeteria where you put what you want in a basket and they then cook it in a delicious sauce for you. It was really good, but really hot. Really hot was probably not the best choice as this was a record high temperature (106 Fahrenheit) for the day.  In the evening we chatted and figured out the transportation situation for going to Hohhot. We resolved that we’d get train tickets tomorrow morning for most people, and a couple people would get plane tickets.

7-6-2010: In the morning I went to get train tickets with Taylor and Frank’s help. You can buy them on campus, which is quite convenient. What was less convenient was that there were no sleeper tickets left for this Friday, when we wanted to leave. There were also no sleeper tickets for Thursday, or Saturday, or next Thursday, or next Friday… We did learn that the tickets for next Saturday go on sale tomorrow morning, so throughout the day we made sure everyone was ok with shifting the trip thusly and planned to get the tickets tomorrow morning.  Since I was planning to buy train tickets and didn’t I was walking around with many thousands of RMB, which was an odd feeling.

In lab today an undergrad in our lab, LinXuan, asked me to eat lunch with him, which was nice.  I was glad to have someone showing some interest in me AND manifesting that interest by communicating with me, rather than chatting about me in Chinese, which is the usual modus operandum.  I learned that he was in the science Olympiad in China and did well enough in it that he didn’t have to take the college entrance tests because he was automatically admitted!

I started my electrotaxis experiments in a rudimentary way as well.  I dug around the lab and found some electrodes which I plugged into an electrophoresis machine, I put some worms in a plate of salt water and stuck in the electrodes and turned that bad boy on (rudimentary, remember?).  To my dismay, a cloud of precipitate rapidly formed around the cathode.  We puzzled at this because the stuff in solution shouldn’t be forming precipitates.  As I was about to check whether the water we were using was contaminated Mr. Wang, a graduate student in our lab came over with an old electrophoresis box and pulled the platinum electrodes off of it and tied them around my electrodes. I now had platinum wires to use as electrodes! This solved the precipitate issue which I assume was the steel reacting with stuff in solution. I spent the next few hours trying to rig up my electrodes to a plate with worms on it, putting buffer on  top of the agar plate, and zapping worms in a buffer suspension. My conclusions from the day were: It seems like the worms sort of move toward the cathode, like they’re supposed to. I have more in the works for the future. In the evening I ate dinner with Sarah, which was nice. Afterward I taught Sarah and Taylor cribbage. We broke for a fruit party and watching Phantom of the Opera online.  Watermelon in China continues to be amazing.  Asian pears, or “papples” (pear-apples) as Taylor, and all of us, have taken to calling them are plentiful and we like them well enough.  Phantom of the Opera is hilarious with commentary from friends about how creepy the whole situation is in a sort of “I have candy, get in the van” sort of creepy.

7-7-2010: This morning I woke up and checked for a line at the train ticket place. It was clear so I went back and ate breakfast and returned to the ticket place with Ray. We had to return at 9 when the tickets we wanted to buy actually went on sale (we’d forgotten what time they did, exactly) .  [PRO TIP: Train tickets go on sale 10 days in advance of the departure. Get them when they first go on sale if you want to be confident in having seats you want (read: soft sleepers). This is for you, next year’s UM PKU REU students]  Tickets purchased we returned to the hotel to put them somewhere safe. I never really made it back out of the hotel…

I wanted to have a clear plan for what I was going to do before I went back in to lab. I didn’t succeed in making this plan until like, 5, and even now it’s not super-clear, but it’s at least translucent.  I spent the day instead reading about awesome things like zombifying parasites , and listening to NPR’s science Friday.  I cannot stress enough how much I love hearing about Cool Stuff that is in the world.  Lunch was tasty cafeteria food with Veronica, Chanan, and Megan who weren’t working because they were recovering from illness ( 😦 ), letting a reaction run, and the machine she’d be using is broken and her graduate student is working on a paper.  I had dinner with Anya and Veronica at the place where you throw stuff in a basket which they then cook (it’s still super delicious).  After dinner we went for a walk to a park nearby and talked and saw some crazy Chinese outdoor exercise equipment. THEN, played some docile basketball with Sarah and Taylor and Nick and Yun. THEN, we returned to Taylor, Sarah, and Yun’s room to watch the rest of Phantom of the Opera, which was pretty swell.

Life in China is crazy, not so much because it is in China, but because we are here together and we have become friends and we can constantly have a good time with each other.

Science! An introduction to worms

June 22, 2010 8 comments

Though my blog thus far may have led you to believe otherwise, the NSF is not paying for us to be in China just to have an all-around good time. They also want us to do some science and gain some valuable research experience while we’re here. As such we all chose a few top picks for which lab we’d work in and depending on various factors were placed into one of those labs.  The lab I’m in is that of Dr. Zengyi Chang. I was interested in his work because his site and biography said that they studied proteins related to the aging process, a topic that I think is fairly interesting because I’d like to do my best to prevent aging.  Andrew Bernier is in the same lab as me this summer. Most of the students with our group have their own labs but Andrew and I and another pair, Taylor Carlson and Lester Sabo, are both in the same lab.

When Andrew and I first met Dr. Chang he asked a bit about the program and was very inviting but a bit disconcertingly unprepared in terms of what we would do.   He asked us what we wanted to do in the lab, we said we didn’t know what was going on in his lab and he proceeded to sit thinking for a few minutes. Eventually he called in one of his students and conferred with her. The decision was that we would help her, Anastasia Ngozi (who is from Nigeria, originally), with working on dauer formation in C. elegans.  And now, a brief introduction to C. elegans.

Caenorhabditis elegans is a species of roundworm.  It is a common, well-studied model organism.  It is harmless (as far as I am aware) to those working with it, it feeds on E. coli bacteria, another model organism that is easily cultured in the lab, the developmental fate of every cell in its body has been determined, it’s life-cycle is rapid (3 days from egg to reproducing adult under good conditions), it is a eukaryote so it is evolutionarily slightly similar to humans, and it grows to about 1mm in length, so it is visible to the naked eye.

I mentioned earlier that the lab is studying dauer formation, and to understand that statement I need to bring in a handy-dandy chart of the C. elegans life cycle.

The C. elegans life cycle
The normal life cycle for C. elegans takes about 3 days (for an egg to become a sexually mature adult worm).  The worms proceed through 4 larval stages which are characterized by different physiological markers before becoming adults.  They go through this normal life cycle when living in a place with plenty of food, enough space, at a nice temperature, and away from any chemical dangers.  In the face of unfavorable circumstances such as a lack of food, overcrowding, high temperature, or toxic environment developing worms have the capability to enter a dormant state called “dauer” from L1 instead of proceeding on to L2.  (Dauer is pronounced dow (as in dow chemical)-err (as in “err… what?”) and is simply the name for the dormant state of C. elegans.) If a worm enters dauer it stops pharyngeal pumping (it stops eating), forms plugs at both ends of its digestive tract (it’s not eating anyway, right?), and only moves if it needs to actively escape from danger (such as a scientist poking it with a platinum wire).
So I’m working with C. elegans for the next couple of months and I’ll do my best to keep you informed on the why’s what’s and how’s of the whole shebang.  Hopefully you’ll get to hear from some of my fellow Americans about what they’re researching too(I’ll try to force them to write guest posts).

Introductions

June 8, 2010 1 comment

I would like to apologize for not keeping this updated but rest assured that I have intentions of posting retroactively about the many interesting things we’ve done this past week.

Today was more relaxed that most have been so far.  In the morning I went with Ray to get laundry done.  The way it works here is you can drop off bags of laundry with detergent, they wash stuff at some time you tell them, and you can then pick it up after that.  It’s 25 kuai for a card which allows you to do 8 loads.

Language class was really good today.  We learned about directions (Stop! Keep going. Left, Right) and more with food.  I now have a tiny notebook in which I’m writing useful phrases and characters so I have them handy when I need to say something.  Tomorrow we’ll be doing little skits using the Chinese we’ve learned so far. Veronica and I have been reviewing and preparing our skit this evening.  Anya and Sarah asked our teacher Liu Nian about how we could keep learning Chinese after tomorrow, which is the last day of language class scheduled by our program and she suggested finding a language buddy/group at a cafe on campus as those are fairly common and they’d be informal and free.  That seems like a good idea and I’ll look into it.

For lunch many of us got snacky stuff on the campus of 北大(bei3 da4 = Peking University) as we had to get back to the hotel to get our passport numbers because they were needed to get us our food cards.  We’re going to be getting cards that start with 20 RMB and can be loaded with money to be used at campus dining halls/ campus associated restaurants (I think).

In culture class today we talked about marriage, divorce, relationships, and family in China. A main thing I’ve found interesting is the distinction between paternal and maternal sides of the family.  Our teacher showed us a list of people who take care of kids when one or both parents move away to work, which is a fairly common occurrence in China.  On that list being left “alone” (probably only for older kids) was more common than being left with the parents of a child’s mother.  Maternal grandparents tend to not live with their children’s families while paternal grandparents do.  The importance of family structure and the traditional heirarchies are clear in the number of words there are in Chinese for different family relations.  For example: In English we have one word for cousin, and 1 word for uncle whereas in Chinese there are 10 or more for cousin and at least 3 for uncle.  There is a separate word for males and females who are the children of a maternal uncle, a maternal aunt, a paternal aunt, a paternal uncle who is older than your father, and a paternal uncle who is younger than your father.

After culture class Andrew and I went to visit our lab and meet our professor, Zengyi Chang,  and the grad student we’ll be working with, Anastasia.  They both seemed nice and said they’d train us to do what we will be doing in the lab.  It sounds like we’ll be working with C. elegans and trying to figure out what causes the changes in dauer (dormancy frequency) phenotypes that were observed by a post doc in the lab. In short, when you stress out C. elegans they go into a dormancy in which their metabolic rate decreases.  The frequency of this dormancy changes with certain mutations. So I still have some trepidation about working in the lab such as learning everything in a timely fashion, but it sounds like my graduate student will be helpful and understanding.

For dinner I went searching with some people and we found out that there’s a sort of courtyard area right across the street from our hotel with tons of restaurants and outdoor tables. It was really nice.

Tomorrow is our last day of language class and culture class and our “last” group dinner and on Thursday we start working in labs.  Stay tuned. Science is coming! (and fun stories)