Can I go to sleep yet?

Don't be at all surprised if this post is completely unintelligible. I've been up all night working in the lab again and I'm 29 hours into a 30 hour experiment. I feel like many parts of me are made of rubber. Like neurons, for instance. And they're about to snap back at any moment. But I must remain alert for another hour and a half before I can walk home (in the bracing cold, which I'm sure will wake me right up and then I won't be able to sleep -- argh), so I decided to write a little something.

I finished my second Seraphina shawl, which is a good thing because it gets cold in my apartment! It's the only thing about living in a tall building with lots and lots of windows that I don't like. I have afghans to wrap up in, but they're just so bulky. This will be much nicer when I'm curling up with a knitting project or thesis reference. I love this colorway so much -- I wish I could find more of it. I took dozens of pictures of it in all kinds of light (that were available) and I just can't get a good representation. It's such a rich chocolate brown and bright, cheery sky blue (Carolina blue!) but the picture is a little dull. And you can't really see the poofiness of the boucle yarn, either. It's very, very yummy.

Seraphina's Shawl by Doni
Joann Sensations Rainbow Boucle in blue/brown
Size US I hook

So now I have only one project that I'm seriously working on, but I'm getting ready to start another. Both are for Gator, so I'm not showing anything until he gets them. I may have to start something else too, just so I have something to blog about!

Although I wouldn't be surprised if I need to rant sometimes about my new TA assaignment...

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Warning! Boring! (it's what I do)

I spent all of Friday night in the lab. Yep, I'm just that kind o' party girl. As part of my "35-hour-experiment-from-hell" (well, it's actually much long than that, but the truly hellish part is only about 35 hours), I had a little slumber party with a bunch of ciliates. Oh, the fun! And, anyway, I got it into my head that some sick, bored person out there might like to see what kind of things make up long, drawn-out science-y things on the cutting edge of cell and molecular biology! (Actually, this is on the cutting edge like Kansas is on the ocean. But I digress.)

In short, feel free to skip this post.

It all starts on Friday morning, 5:00 am. I mix cells so they will mate and shake them around for a half an hour so they'll all mate pretty much at the same time (yes, that's really how we do that). Then I monitor the cells for several hours. Most of the late morning and early afternoon is spent making control slides and continuing to monitor the mating. I get to go home at 5:00 pm for a bit of a nap. Then the real fun begins.

Picture it: Friday night, 9:00 pm. I open the incubator and am confronted with the solutions of mating cells I prepared eeeaaarrrllly that morning:


I add growth medium to one of the flasks:


Then I start taking samples from both flasks:


And put them in little tubes.


I put the tubes in the centrifuge and spin them so all the cells go down into the bottom:


Then I suck off all the fluid leaving a little ball of cells at the bottom of the tube.


Then I wash the cells with 3 different washes of methanol (mix up the cells in methanol, let them sit, spin the cells down and suck off the methanol, repeat, repeat):


And then I finally drop some concentrated cells onto slides which I will stain, photograph and digitally analyze later.


Repeat every two hours for eleventy million hours. (Oh, okay. Fourteen.) Then repeat every twelve hours for a week. Because this is how many slides I'm making:



I don't know right now. A lot.

And now I have to go make some more. Ta!!

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Survival

Hi! Still not dead! In fact, feeling fairly jaunty for the moment. How are you?

In order to accomplish everything I needed to towards the end of this semester, I had to just put the hammer down and remove myself from the blogosphere entirely. So I haven't posted, and I haven't read any blogs since before Thanksgiving. So I have no idea what's up with y'all. It'll take forever for me to catch up. But I'll get there!

But I have officially made it through the semester, taken all my finals, written all my papers, and graded all the exams for the class I TA. I'm free! Well, except for all that research, but I'm actually looking forward to being able to focus on that alone for about a month. It will be great, in fact. And fairly normal feeling -- I'll spend a lot of time in the lab, I'm sure, but I get to actually leave at some point, and then I don't have to study or grade or prepare for discussions, etc, etc, etc. How novel! That means I get to knit and crochet some! Awesome! I've been jonesing.

The first thing I did was finish a little project I had started over Thanksgiving. See, every year the Biological Sciences department has a Christmas party that includes a potluck and a white elephant gift exchange. Last year I decided that this year I would make something for the gift exchange. So I whipped up a little something and I just finished it -- happy dance!

Oh, what is it, you ask?

Well, what would you make for a white elephant gift exchange?

I thought it was a no-brainer, actually...



I also started a couple little projects that I can't show just yet... But when I can, I will. Ah, this project startin' and finishin' just feels so good!!

Hopefully, we're back to our regularly scheduled blogging...

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Long time, no see!

::crawling up from underneath a mountain of research papers and PowerPoint presenttions::

Hi! Wow, it's bright up here. Even though it's overcast all the time and the sun is only up for about 4.5 hours per day, it's still much brighter than my dark corner of studyallthetime-ness. But it has to be done. The only way I accomplish anything is to just remove myself from the innernets altogether. Otherwise, I start "checking my mail" and the next thing I know, three hours have gone by. But I know what Britney bought at the convenience store yestrday, by golly. And isn't that what's truly important? I think I'll be back among the living sometime before Christmas. At least until I start studying for qualifying exams...

Anyway! I promise not to bore you with my exciting stories of learning about paramutation or oxygen-hemoglobin binding kinetics. No, really, I promise! You should really just praise me all day for this.

I poked my head out of the jumble because I'm winding things down so I can enjoy four uninterrupted days of not studying -- I'm going to Missouri to see Gator for Thanksgiving!!! I'm so excited!! I leave very early tomorrow morning for Chicago, where I'm meeting my friend Amanda, who is driving to Columbia. Roadtrip with fun friend and a long weekend with Gator! AWESOME!!

But before that happens, my cool New Friend Veronica (it's been, like, a year. You'd think I'd stop calling her "New". Apparently not.) is taking me to see Debbie Harry tonight! How fun is that? I'm so ready to rock out to Rapture. And now I'm in the Man From Mars! Tee hee.

So, okay, yes. I do get study breaks. And I've even spent some of them crocheting. Cwazy, I know! So I finally (only a couple of months late) finished "Sister" Annette's wedding potholders! I hope she likes them! (Of course, I hope Mick likes them, too!)




Bright and cheerful and cool. I like them, anyway. :)

And last, but CERTAINLY not least, I got the best surprise in the mail yesterday (all the way from England)! A pressie from blog buddy Judy! It's a little crocheted turkey "butt" refrigerator magnet and it came with the most lovely card. Ain't it the cutest? (And don't I look tired?)


Thank you, thank you, thank you! I love making friends on this here Interblag!

And now, excuse me while I go eat guitars... Hee!

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Oh look, a Saturday Sky, knitting, and everything!

It's a gray, hazy, autumn day in Beer Town. I rather like it, actually.


I had two horrible exams this week, a lab meeting presentation, and tons of research both in the lab and for future papers and presentations. In short, busy. I think maybe I've caught up on some sleep and no longer feel like an overwhelmed mess. The second test this week went well, I think, but the first one did not. In fact, I may have failed it. Straight up. Not that, "oh, that test went so badly and I'm sure I failed" and then it turns out I got a high B kind of thing. More like, "I left about half the answers blank because I didn't even have a bullshit answer for them and then I ran out of time" kind of thing. Pretty brutal. I could go on and on about why this happened, but I'm not going to because a) I don't want to think about it anymore, b) it won't help anything, and c) you don't really care. At least I wouldn't if I were you. So, onward and upward to handwork content instead!

Gator's best friend's baby came last month (welcome baby Owen!!), which meant that I had to get off my lazy butt and finally put the zipper in the zodiac and get it sent off. I had thought I would embroider a design on the body, but I finally decided against it altogether and went with simplicity. Plus, the buttons are pretty cute and add just a sweet touch of interest. I think it's perfectly fine just as it is.


The baby socks I made this summer were also intended for baby Owen, and I think together they make a nice little baby gift:


I've also started a new project -- a wedding gift for best friend Missa's sister, whom I call "sister" too. The wedding was actually last week, but I get a year to present them with a gift, right? So I figure I'm okay. I'm making them a set of the Round Star Flower Potholder, like the one I made for Gator last year (yes, I made my husband a potholder, and he loves it. What of it?) but in blue and yellow. I got a good start on it during a mini S n' B at Veronica's on Thursday night.


I have a lot of work to do this weekend, but I'm going to take a little time to crochet, too. I just feel better when I get some handwork time in. Otherwise I'm not sure what the weekend will bring, but I'll let you know if it's anything cool!

Have an awesome weekend. :)

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Reasons

Why I'm not in the mood to blog:

• Classes and my TA assignment have started. I did get the assignment to TA Cell Biology, which is only going to involve leading discussion (recitation) sections, not teaching the entire class (they don't do that here), so it's not quite as bad as some of you may have thought, but it's still about 10 hours a week that I can't research, plus it breaks up my days in annoying ways so some research is even more difficult.
  
• My course meeting times (the courses I'm taking, as opposed to the one I'm TAing) have been changed so that one meets at 7:45 am and the other runs until 5:15 pm. Long-ass days.
  
• Sunday, when coming home from the grocery store on the bus, my grocery cart-thingy rolled into my heel while I was taking a step and sliced open the back of my heel. It bled A LOT, right there on the bus, and the only thing I had to staunch the flow was my receipt from the grocery store. It was gross, uncomfortable (all those people sneering at my for having the incredibly poor manners to BLEED all over the bus -- and I mean there was A LOT of blood -- and of course none of them were at all interested in helping me), and a challenge to get home from the bus stop with my groceries while BLEEDING PROFUSELY, so much so that it was spattering out of my sandal with every step. It took forever to stop bleeding and it now pops open regularly due to heel flexion when I walk. I'm sure it needed a couple of stitches, but it's not going to get them, so I deal. But I don't feel much like doing anything -- even knitting or crocheting.
  
• Four big readings assigned yesterday, due tomorrow for intense discussion. Argh.
  
• General grumpiness.

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Don't worry, I know what I'm doing

Classes start next week which, while I'm not really enthused about because it will take so much time from my research, is not really too stress-inducing. But I also start a teaching assistanceship, which I am a little freaked out about. I've never TA'd before and, in order to do it right, I'm sure it will take a lot of time. The thing is, no one in the department wants anyone to spend a lot of time on their assistanceship because the priority is research. Now, apart from the educational priorities in higher education debate this could start, I am, of course, more concerned about how this affects, well, me.

See, I'm a bit of a perfectionist. Those who know me well are now howling with laughter at the understatement. And if I can't always be 100% competent, I like to at least appear 100% competent virtually 100% of the time. Now, we don't have official TA assignments yet -- we should get them today (and don't even get me started on why they wait so long to let us know what we'll be teaching -- classes start Monday, for Goodness' sake), but I'm fairly certain that I will be TAing Cell Biology. This is all well and good -- it's an upper division class, populated by fewer students than the survey courses and only biology majors, so they should be more dedicated, but there's a reason that this strikes some fear into my heart. I took cell biology as an undergrad in 1989. Oh, I know the basics, plus anything that I use regularly in my research or that applies to classes I've taken more recently, but there are a lot of details I've forgotten. The professor of the class thinks that this means that TAing this class will be particularly good for me, as I need a refresher on this material and this is an excellent opportunity for that. She's absolutely right. However, my stress level has ratcheted up several notches at the prospect.

So much so that last night I had a nightmare about it. Granted, in true dream fashion, it was ridiculous, but it was definitely a manifestation of my current apprehension. In the dream, I met my class in the proper room, only to find that the proper room was an ice cream parlor and that I was to teach them how ice cream was made and sold at said parlor, except I had no idea how ice cream was made and sold at said parlor because I had just gotten the TA assignment previous to entering the room. So, while under the guise of waiting a bit for latecomers to arrive, I tried to surreptitiously quiz the employees about the material and considered just delegating the actual instruction to the employees. While I debated whether this plan was smart or just lazy and whether I would look more incompetent if I tried to bullshit my way something I knew nothing about, or if I handed off instruction to a high-school age part-time worker, one of the students announced that my friends had arrived. (Never mind how they knew they were my friends -- this is a dream, kids. Wherein I'm TAing Ice Cream Parlor 101.) Sure enough, my friends, Meredith, Liz, and Laura were walking down the hall. I excused myself and went to greet them. As I explained my predicament to them, they all just looked at me like I'd lost my mind and told me that, no matter what, I had to go back and teach the class. I was disappointed that they hadn't seemed more compassionate to my plight when it hit me: They are all teachers. And that if I didn't somehow pull this out of my ass and find a way to be successful, I was not only going to look like an incompetent loser in front of my students, but I would also seem that way to my friends.

And then I woke up.

Not that I have issues, or anything.

Nope, not at all.

I've got it completely under control.

I know exactly what I'm doing.

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I'm flaking again

Title sung to the tune of "It's Raining Again" by Supertramp.

Now that Gator's socks are done, I'm trying to get back into my routine and flake it up on a weekly basis. I'm afraid I've become disillusioned with the patterns from the SimplySnowflakes group, so I'm going back to my solitary ways (though I'm staying with the group, I'm just not going to participate in the sign-ups anymore). This pattern was a free Lion Brand pattern (Number 4) and it's okay. Not my favorite, but not too bad. I had to go back to size 10 thread (I had been using size 20) because the pattern is actually written for sport weight and the middle was killing me in such a small gauge. I'm so used to size 20, though, that this seems so bulky and inelegant. I'm sure it's a personal problem, so I'm going to ignore it.



Yesterday I went to the Brewers game, which was great until the ninth inning when we blew a big lead only to go into extra innings and lose 8-6 to the Phillies. It was still a fun day, but the outcome of the game was a bummer.

After the game, New Friend Veronica took me to JoAnn so I could get a zipper to finish the Zodiac. I've decided not to embroider anything on it, mostly because a) I can't find a design that seems just right, b) I can't find a 50% cotton / 50% acrylic yarn in a yellow that will match the buttons, which I'm not willing to change, and c) my duplicate stitches always look like crap, and why crap up a perfectly good sleep sack? So I've decided to just block it, put in the zipper, finish a pair of baby socks that marginally match it (they're made from leftovers from my First Socks -- hey, there's some orange in there!), and call it good. The more I look at the Zodiac without embroidery, the more I like it, anyway.

Tomorrow is my final exam for the radioisotope safety class. I'm very excited for it to be over. So much so that I'm going to the Wisconsin State Fair right after the final as a reward. I'll try so hard to remember to take pictures of the craft and needlework highlights. And food on a stick. Because, really, it's all about foods on sticks.

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Crafting through the journey

Well, next week is finals and my first year of graduate school is drawing to a close. In a way it seems like I just got here and in others it seems like I've been here for eons. I've worked through homesickness and dealing with Gator's illness long-distance, feeling unsure about my sense of belonging, both professionally and personally. I've come out on the other side content, fairly centered, and happy (though I still miss Gator like the dickens!).

Also, I've made some stuff. Handwork has been my constant -- a therapeutic exercise, and means to ends I could not otherwise afford or at least justify, my preferred method of procrastination. I suppose that will continue; I certainly don't see why it wouldn't.

This week, while not getting right on top of studying for finals, I've worked on my Parfait Purse (named for the color scheme), making the design up as I went, though I had a pretty good mental image of what I wanted when I set out.


I admit that it's not an exact rendition of my original vision, but my vision is pretty good at adapting to what it's presented with in reality. I still think it will be pretty cute, but I also admit that my mind has already starting to design what it would rather have, so I guess I'll be making another purse when I'm done with this one.


It still wants a lining and decorative embellishments. By this time next week I'll have a full-fledged purse FO. It will be fun to take it out for a spin! For a parfait, no doubt. ;)

While going through my fabric stash for suitable lining, I decided I just wanted to reorganize the crap out of everything. I realized that all my embroidery supplies (and embroidery WIPs) were scattered about here and there among my fabric and my yarn. I decided this was dumb and set about righting it. During my organization, I ran across a wee little piece of cross-stitch that had originally been part of a little magnet kit. The stitching was complete, but the rest of the kit was completely missing. Not that I was terribly surprised. Another thing I found was a little wood-grain plastic embroidery hoop with built in hanging hook. The tiny piece of stitching fit the hoop perfectly, so I decided to just give in to fate and add a little bit of happiness over my kitchen sink. It looks pretty cute.


Fair warning -- I'll have no flake tomorrow. I have a final Tuesday and one on Wednesday. Then I'll be free to flake out all I want! Well, after the purse is done, of course.

So, one down, one more of classes to go, then three or four of research and writing. The journey is officially underway with a vengance.

Loving where you are

It was bright and sunny and beautiful here... yesterday. Today, I have one more in a long line of dreary overcast days. I don't mind the weather at all (in fact I kind of like it like this), I just get tired of taking the same picture over and over. Oh well. Summer will be upon us soon enough and I'll have bitchin' of a different kind, I'm sure.


I've been having a really happy time at school lately. It's like something, somewhere finally clicked and I feel really at home. All week I was really appreciating my school and my department and all the people I spend so much time with. Our department is small and incredibly friendly and any professor will take time to help you with anything, whether they've ever had any dealings with you in the past or not. Whether you're in the same field or not. It just doesn't matter. Everyone helps. How could I ever wish for anything other than this?? So I thought all my feelings about my life here in Beer Town were warm and fuzzy. And I was so wrong. But I didn't realize it until last night.

Last night, New Friend Veronica and I planned to crochet. Really, we did. But we got a hankerin' for Roly Poly, which is all the way in Brookfield, and while we were there we shopped (God, how can you not in that total commercial immersion experience?), then we just drove around. I love doing this. I get to see parts of the city I ordinarily never go like the East Side and, in the case of last night, suburbs such as Bayshore. It's fun and cool, even though we usually do it at night, when it's hard to see most of the sights. At one point, we turned around and drove along the lakeshore back towards the city. I was newly enthralled with my city. I love our water tower (beautifully illuminated, along with its fountain, at night),

the Milwaukee Art Museum is super cool,

and I just got chills as we drove towards the heart of downtown. I wish I'd had my camera because I can't find a picture on the 'net that does the view justice. But it was like seeing an old friend. "Oh, you!! I really like you!!!

It was one of the moments when you realize, as much as you like the life you've made for yourself, you've allowed it to narrow to the immediate surroundings: Work in lab, sleep in apartment, shop, eat, and drink in establishments between the two, and that's about it. I'd forgotten how much I love the city that's basically just across the street from me in the other direction. I suppose winter and being busy do that.

So I'm newly in love again with my new city and I feel at home in my department and my lab. Life is good. This summer is going to be great. I can't wait.

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I made a snowflake this week, it's just that with the exam and everything, I didn't get it posted. Well, okay, I didn't even get it blocked, but I suppose that's minor. So here, utterly unblocked and perched on my awesome lime cutting board (Target Dollar Spot, baby!), is this week's flake, one day late:



Ah yes, the exam. Well, it's over! Not the best exam I've ever taken, but not the worst either. We'll see what the grading is like. Everything else is going really well this semester. Even if I do poorly on this one exam, it certainly won't be the end of the world.

Totally off topic: Have you had your Cadbury Creme Egg yet this year?? I have a long-held tradition of having one every year before Easter (I guess I just can't wait until Easter, once I see them on the shelves). One. Because one is about all I can stand in a year's time. They're good but, egads, are they sweet. Do they make anyone else's teeth hurt?

Mmmmm... Sugary fondant fake egg yolk...

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On the mend

My cold is getting much better. I went to school yesterday and didn't cough very much in the morning. Then I had a seminar class in which a friend was presenting. Of course, that was when I had a horrible coughing fit. And when I excused myself to have my coughing fit out in the hall, I twisted my ankle and slammed into the wall. Yes, I'm grace personified. The rest of the day I was fine. Of course.


It is hazy and foggy today. It's burned off a bit since I took this photo and the forecast is 59 F and sunny. We'll see. I have a huge exam on Monday that I must study for, so I won't get to enjoy the weather much. This school stuff is really cramping my weather enjoyment and handcrafting style. Galdarnit anyway.

In other school-related news -- even though there is another week left of my rotation, I have gone ahead and joined Dr. Karrer's lab. So, be prepared for five years of Tetrahymena updates. You'll feel so smart by the end, you'll want a doctorate, too.

Must study -- but first, Whad'ya Know?, coffee, and crochet. Then study.

Knit and basketball

I attend a "basketball school". Marquette has put itself on the map due to its inclusion in the NCAA men's basketball tournament over the past several years, and the subsequent success of Dwayne Wade in the NBA. So, when Marquette plays in the NCAA tournament, they throw a big party at the Union Annex. And because I want to get the most out of my Marquette experience, last night I attended this party.

We played Michigan State in the first round of the tournament and, how to put this delicately, we stunk it up big time. Michigan State whomped us. Although, I think we established the title of only team to ever score all of their first half baskets from the 3-point range. I think we only had about a half dozen two-pointers in the whole game. It was crazy. That, and we didn't score at all in the first 8 1/2 minutes. It was brutal. But! I got free pom poms out of the deal! There's always gotta be a bright side.

On an unrelated topic (yet sort of related, purely by chance), I have to rant for a bit about a certain type of fellow knitter. You see, I took knitting with me to the party. Just a plain cotton dishcloth, the kind I can knit without looking at it at all; the kind I always knit while watching sporting events or award shows. While we were waiting for our food, an older woman came around asking if we'd like our faces painted. When she saw me knitting, she immediately said, "Oh, you throw". Now, to the non-knitters out there, "throwing", also called "American" technique, means you knit by controlling the yarn with your right hand, and actively wrap the yarn around the needle during each stitch. It's the way most Americans learn to knit. The other main technique is called "Continental" and means that you control the yarn with your left hand and basically use the needle itself to wrap the yarn around for each stitch. There's a little waggling of the index finger for purling, but you get the general idea. Now, it may just be me, but it seems that many times it is implied that only novice dumbasses "throw", and experienced, or "real", knitters knit Continental. The face-painter was one of these. She went on and on about how Continental was so much better and I would never want to throw again once I learned it. I tried to be gracious while trying to get her to shut up -- I wasn't in the mood for a knitting lecture and tried to inform her that I just wanted to knit as I could without looking -- the whole point of bringing the dishcloth to knit while watching the game -- and that I could knit Continental, just not without looking. She finally gave up and moved on. But I was rankled.

I am kind of a solitary knitter and everything I know about it I have taught myself from books or articles on the internet and I like it that way. For the record, Continental does offer an economy of movement and speed over throwing, and I would like to become proficient at it, if only to have an alternate technique in my repertoire. But I'm not yet proficient at it, and I feel clumsy and awkward when I do it. Mastering it will require practice, and when I'm trying to watch a game while knitting is not the time for it. If I do master it, it may very well be that I prefer it to throwing. But as it is, I am a very proficient knitter and turn out some lovely items using my lowly little technique. And if I do switch to primarily knitting Continental and come across some other knitter who is throwing, I shall ask about her project, compliment her stitches, and generally have a nice chat with her (or him). I will not mention what technique she is using because who the F*** cares????? Knitting is a hobby, a form of relaxation, and a means to and end -- lovely handmade items to keep or give as gifts. It is not a competitive sport. I will not become a party to making it such.

Yarn snobs and technique snobs. I daresay the community would be better off without them. But then, I'm just a novice dumbass -- what would I know??

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Oh, baby baby!

Last night I decided a little change was in order. Isn't the new layout cute and festive? I like it. :) Mad props to Mela and her creative template skilz. I could probably make a cute layout myself if I learned just a little more CSS, but I'd rather spend that time crocheting and knitting, so I'm really thankful that people like Mela offer such great stuff to the masses for free. Yay! Spring-y! Yes, I'll admit, I was sorely tempted by the Hello Kitty layouts.

I also made the second pair of baby booties last night. Same pattern as the last ones, different yarn. I like the contrasting cuff on this pair.



So, two cute gifts done. Now I can get back (again) to my WIPs. I swear I'm going to say that for the rest of my life.

I'm trying desperately to get some results that I can present at the Midwest Protozoology Meeting in St. Louis at the end of this month. I'm afraid it's not going to happen. I shouldn't be too upset -- it's extremely rare to have a poster during a rotation, but I was really hoping that my project was straightforward enough and relevant to Tetrahymena researchers that I could pull it off. Oh well. I'll keep trying for the next week. Maybe I'll be surprised.

Now my blog has little bugs like my lab does! Different bugs, to be sure, but! Bugs! Yay!

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Never be afraid to ask

Yesterday Becky said:

I'm almost afraid to ask...What is a tetrahymena?

Well, maybe you should be afraid... Never ask a scientist about their research -- they'll totally tell you!!!


What I see with a light microscope (phase microscopy)

Tetrahymena thermophila (T. thermophila) is a protozoan, a unicellular ciliate that my lab uses as a model organism for genetic research. It has been used in some very important genetic discoveries, most notably the better understanding of the nature RNA interference and the discovery of telomerase. Here's a great little article about my cute little buddies:

What's Shaped Like a Pear and Has Two Genomes? Check The Pond


Fluorescently stained mating Tetrahymenae

If you could peer microscopically into the closest freshwater pond, you'd hesitate before dipping a toe. Amid the murky water, you'd probably notice an oddly furry, pear-shaped organism gliding along and gobbling up everything in its path. This tiny predator has a big name--Tetrahymena thermophila--and a big fan club among scientists, as a star organism for research into how cells work.


Scientists have now sequenced, assembled, and analyzed T. thermophila's macronuclear genome. Their work, reported in today's issue of Public Library of Science (PLoS) Biology, explains the organism's impressive versatility. Rather than dividing labor into several types of cells, as humans and other multicellular organisms do, T. thermophila divides its activities, either into different places inside a cell or by changing the cell over time. It is a master multi-tasker.

"This organism is a true generalist," says evolutionary biologist Jonathan A. Eisen, who led the Tetrahymena project while at The Institute for Genomic Research (TIGR) and is now at the University of California, Davis. "Whatever this unicell touches with its hairlike projections, it will try to eat. If it does not bump into anything, the organism will seek out food with diverse sensory systems. It can protect itself from radiation and other threats and also can fight back against competitors and predators. In short, versatility is its strength. Now, we can understand how this versatility works."

It takes plenty of genes. In fact, T. thermophila has roughly 25,000 genes, nearly as many as humans do. Although the organism is single-celled, it contains a genetic repertoire of seemingly more complex organisms. It shares, with humans and other animals, many genes and processes typically absent in single-celled organisms. That means Tetrahymena may be an ideal model organism for studies of the processes these genes encode.

In the new study, genome analysis showed that one way that Tetrahymena adapts to diverse environments via gene duplication, a process that allows organisms to diversify pre-existing genes and adapt them for new functions. In the case of Tetrahymena, duplications appear to be concentrated in genes involved in sensing and responding to environment. From a small number of proteases (enzymes that degrade proteins), for instance, Tetrahymena has built an eating machine that allows it to digest nearly any protein it encounters.

Among its most quirky features, Tetrahymena has, inside each of its cells, two distinct nuclei, each with a different genome. Inside one nucleus, the "micronuclear" genome is reserved for sex and reproduction, remaining genetically silent during growth. Inside the second, working nucleus is the "macronuclear" genome, which expresses genes that govern behavior. The current study sequenced the macronuclear genome, an impressively packaged bunch of coding genes, free of so-called junk DNA (noncoding sequences and other extraneous genetic elements) that litter the genomes of many organisms.


Electron micrograph of Tetrahymena thermophila

"Publication of the Tetrahymena genome marks the culmination of a remarkable collaboration within the research community," said Anthony Carter, Ph.D., of the National Institute of General Medical Sciences (NIGMS), which co-funded the project with the National Science Foundation (NSF). "Tetrahymena has a long and eminent history in the world of cell biology, and publication of its genome is likely to lead to further fundamental insights into how cells work."

Throughout the project, Eisen says, collaboration between researchers has been critical, including work by co-author Eduardo Orias of the University of California-Santa Barbara. The team emphasized open access to data, providing the genome sequence data to outside researchers, without restriction, since the project began in 2003. As a result, Tetrahymena researchers have already published dozens of studies making use of the genomic data.

In addition to releasing the sequence data early on TIGR's website (http://www.tigr.org/tdb/e2k1/ttg/index.shtml) and via Genbank, the project also underwrote the creation of a major free community resource: The Tetrahymena Genome Database (TGD; http://ciliate.org/), headed by Mike Cherry at Stanford University. The publication in the open access journal PLoS Biology represents a commitment to free and open access to scientific literature as well. Now anyone, anywhere in the world, can read about the genome of this fascinating organism before taking a dip in the local pond.

Source: The Institute for Genomic Research

That may have been more than you wanted to know. But, you know, you asked.

_____

Exam blues

I spent six hours in the lab yesterday, but I didn't get any studying done for my exam tomorrow. The class with the eight papers per day. Yeah, that one. (Note to those who think that's a spiffy idea -- with this kind of volume, I'm learning next to nothing in this class. I'm just memorizing as much as I can until after the exam. When we focus more intently on less material, I learn tons. I'm just sayin'.) So guess what I'm doing today? Can't I just work in the lab more instead?? Oh well. I'm really honing my ability to procrastinate up here.

Since I didn't post a sky yesterday, here's a pic of dawn-ish from this morning.



There's really nothing else to say. Have a great Sunday!

You would think...

...that I would be a swirling fury of studying, what with the beginning of the semester and all. But my heart's just not in it. Not that too much has been expected of me so far. I love being in the lab, I love doing research -- I just hate the classes. Can I skip strait to quals and do my dissertation research, please? I really didn't ever think I'd be burned out on school in the classic sense, but boyo am I. This semester is going to be a trial, I fear. I know I have to take the classes in order to do the research. I know all the things I'm supposed to know about how this process works. I don't need plucky platitudes -- I know them all. But when one professor assigns eight (8) articles for one class, and you know he's not going to actually cover them all, or ask any questions, and pretty much tell you what he wants you to know about them, the motivation to actually read the freakin' mountain o' papers gets pretty low. So I crochet. It's just my way.

Oh, look! A snowflake!



Okay, I guess I'll go print the articles at least.

Oh, and I'm starting my new rotation today! Wohoo! (see? I'm totally excited about some aspects of this program!!)

Finishing up, moving on

It's my last week at my second lab rotation. This one has been a little weird. I like the work (I won't bore you with a description), but it turns out that if I want to continue with it permanently, I would actually be working in the lab in which I did my first rotation. And that, kids, ain't gonna happen. So if I can get my Western blot to turn out (the last two have been dismal failures), I'm done with this one. Then I move on to my third, at the lab of a woman I already admire greatly. I'm really hoping it works out well. So my life is pretty boring right now -- work, study, sleep, knit a couple of rows before bed but no real progress.

But I have taken the time to surf while waiting for timers to go off, etc. and I present you with more innernets fun!

• Everything I Need To Know I Learned From Iron Maiden -- Heavy metal history class. Hilarious.
  
• Finally! The terrible void in representational jewelry has been filled (Ha! Pun!) by a company called Luna Parc. Yes, kids, you too can now own lovingly crafted enema bag pins and earrings! Life is now complete.
  
• Who knew that the most painful thing from the eighties was a Microsoft promo video?? This is the most freakish thing I've ever seen. It's 12 minutes long, and the first 5 minutes or so are boring, but then, according to the metadata, "the production is taken over by crack-smoking monkeys."
  
• You know those annoying porcelain figurines of French ladies in powdered wigs and huge gowns looking coquettish? An artist named Shary Boyle has a fabulous new take on them. I'm not sure how they would look on my end table, but I love the concept.
  
• I'm a big fan of the folks over at Make: magazine. Now they're delving into my end of the pool and I think it's hilarious. How to isolate amniotic stem cells from a placenta -- the home version. I read the protocol -- it's real. Now everyone can do it!
  

Now it's back to work. I hope this Western works. Cross you fingers for me, would you?

End of break

My snowflake today is in the Voodoo stage:


Snowflake #16 of 99 Snowflakes from Leisure Arts

Classes officially begin tomorrow, but I don't have any until Wednesday. On the one hand, I think I may be ready to start a new semester and see if I can't alter my expectations so that I enjoy the process more. On the other hand, I dont' feel rejuvenated by my break and I'm not ready for the franticness of the semester. I will still have my creative time, it will just be less spontaneous and more limited. I'm still trying to keep an open mind, but I'm trying to be a little more practical about it, too. I don't have to love every aspect of graduate school. I just have to love one or two. I just have to love my research. I have to love learning. I don't have to love all my classes. I am allowed to think some aspects of classwork are as crappy as I did in undergrad without feeling ungrateful for the opportunity to be here. I can dread required classes that are outside my field of interest. Otherwise, perhaps that would be my field of interest. I'm letting myself just get through the last couple of weeks of this useless rotation without going above and beyond. This puts a lot of pressure on my next rotation, but I have faith. I really, really do.

I just reread that last paragraph and parts of it don't even make sense to me. Don't feel bad if you got lost. But I'm leaving it because it's so much cheaper than therapy. Even though, technically, I could get that for free through the school. But I would have to walk to the offices and it's cold. So I guess it's just warmer than therapy. Whatever works.

I'm going to put away at least part of the Christmas decorations now. Are anyone else's sinuses completely and utterly pissed off these days? Oy vey.

Back among the living

Hi! I've survived my first semester of grad school! How are you?

Actually, I was done on Friday, but I needed a little recovery time before I could even blog. The funny thing is, I took the weekend off from life (well, I worked in the lab for five hours on Saturday, so that wasn't really off), and now I'm all busy again. Baked over 100 cookies last night (stupidly burned half my Sandies, grrrrr), getting ready for a little get-together tonight (the apartment is a disaster), Christmas party at the lab today, laundry, packing, etc. etc. I know, boo hoo.

I haven't quite yet processed how I feel about this first semester and the prospect of another 4 1/2 years of the same. Other than "roller coaster". I'm going to let it percolate in my brain and get back to you.

So, yes, "time off" = handwork, handwork, handwork!!!

Finished my tree skirt!



Worked on the braided cable scarf (even in a restaurant while watching a football game, using a toothpick as cable needle 'cause I forgot mine -- it works -- tee hee). And I did something I have wanted to do for some time. Yes, kids, Sus has started a sweater. It's nothing elaborate, but it's a sweater. It doesn't really look like it just yet...



It's the Country Contrasts pattern from Knitting the New Classics. They call for a looped mohair blend, but I'm knitting it in, Red Heart SS you say? Why, no! I'm moving up in the world! I'm using TLC heathers! LOL! (For those of you who aren't yarn savvy, that's just a different cheap, plastic yarn. But it was free, so hey.) I really have worked with good, natural fiber yarn, but I have such a huge RH stash!!! It's got to be used up, and now, while I'm getting my knitting feet under me, seems like a good time to do that. Plus, it's just what you use for things like tree skirts and tissue box covers. The yarn snobs can get over it. (Woohoo! Watch Sus defend herself to people who don't even read her blog! Yeah! Issues, anyone?)

Okay, that PCR ain't gonna run itself. I'm off. Ta!