It’s going to be a good season, I can tell already. It’s finals week, so I’ll still have an abrupt pile of grading to do on Thursday, but otherwise, my teaching obligations are done for the semester. Now I’m trapped, trapped I tell you, in Morris for almost (I do have two quick trips to Europe planned) the entire summer with a collection of administrative responsibilities, but the good part of that is that I have ambitious plans for what I’ll be doing in the lab. I’m also going to be living the good life.
So this morning I slept in to 7:00. I know, it’s slothful of me, but I have the freedom to indulge myself a little bit now and then. After I got up, I took a nice brisk walk downtown, did some shopping, stocked up on some fresh vegetables, and once I got home, chopped them up and set them to soak in a tasty marinade. I’ll roast them up for dinner tonight.
Then I started reading up an accumulated mass of papers that’ll give me some implementation ideas for the work I have planned.
I’ll have a student working with me, and we’ve got a couple of projects in the works.
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There’s some boring scut work to be done: lab cleanup, clearing out old reagents from the refrigerator, making up new stock solutions. Don’t be disillusioned, but part of the research life is janitorial…so much dishwashing.
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My grand plan requires an expansion of my fish colony to include multiple genetic strains, so we’re going to be scrubbing tanks, sterilizing surfaces, setting up new tanks with boring feeder fish to get the nitrogen cycle going and condition the water, getting the brine shrimp hatchery (live fish food!) thriving, all that sort of stuff that qualifies you to be a clerk in a pet store.
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Once all the tanks are bubbling away happily, we’re getting some new strains from the zebrafish stock center. Then it’s a few months of nursing them along, collecting eggs, propagating new generations and raising them to adulthood to get the whole colony self-sustaining, and to prepare for crosses to produce hybrid strains. After all this, my student will be well-trained to be a hobbyist aquarist.
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Concurrently, we’ll be doing some real science on the embryos we get, analyzing their behavior quantitatively to identify consistent differences between strains, and also in response to different environmental stresses. This is going to require a bit of computer work and — oh, no! — basic math to develop image analysis protocols. That’s what I’ve been reading about; I’ve done some of this in the past on an obsolete software system, so I’m going to have to piece together some custom bits to make it all work. I’ve been reading about Fourier analysis and power spectra all morning, and I’m kinda jazzed. Math! Computers! Embryos! Science!
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The dream is that once we’ve found some subtle differences between different strains, we can start doing crosses to dissect out and isolate the genetic components, if any, of the behavior. That’s going to take a couple of generations of crosses, which means that if I’m lucky we’ll get those results next year, or at worst, the year after. Behavioral Genetics! Yay! Long generation times! Boo!
It’s step #4 that’ll give us some quick quantitative results, I hope, and maybe something presentable at a meeting or even publishable. It’s all going to be preliminary and descriptive, but that’s what you need to do to establish a foundation for experiments.
Unfortunately for you, I won’t be blogging about any of the details of the work this summer — I’ve been scooped before when I foolishly posted protocols on the web, and especially when you have a very small lab with limited humanpower to throw at a problem, that costs. But I might just occasionally say a few general things about the kinds of analyses we’re doing.
Or I could talk about the moldy stuff we throw out of the refrigerator. That’s probably safe.
Don’t throw out the yoghurt, it might still be good…
And if it’s not, you can always convince someone else that it is…
Throw it OUT? Remember Alex Fleming!
Good lord. That sounds exhausting. I’m so glad the stuff I work with is already dead.
My personal record for out-of-date lab stuff (reagent kits mostly) was a T7 RNA kit that was 12 years out of date. Fairly sure that enzyme had had it… Thankfully got to pass the rest of the crap onto the boss to sort out, anything that looked vaguely important I passed on to him to judge whether or not to keep. He’s the only person who was in the lab when that work was being done 10+ years ago anyway!
I’d recommend ImageJ for your image analysis work, simplest program I’ve ever used (we have some proprietary stuff for confocal, but it’s much more complicated to use). If it’s highly repetitive analysis work the macros in ImageJ are wonderful, once you’ve got the protocol set it’s a simple keyboard shortcut to run the analysis on any given image. Of course, that’s no guarantee that the experiment will work {grumbles about trying to measure pH using ratiometric dyes/GFP in live cells, whole bluddy year on that without producing meaningful data}
Yeah, ImageJ is probably going to be it — it’s not as simple as the custom software I wrote years ago (and which now only runs on grossly obsolete hardware), but there are add-ons I can use. I do not want to get trapped in an endless cycle of software tweaking, though, and will settle for something that works.
I worked briefly in George Streisinger’s lab at the UO, at about the time he was building up his zebrafish work and searching for visual system mutants. In his refrigerator, he had ancient vials of stuff from his phage days…some of it was 20 years old or more.
Not only was it old, but it was the biggest leap I had ever encountered: from phage genetics to studying the nervous system in vertebrates. I was kind of impressed.
Yay indeed.
looking forward to seeing what you get.
Oh my goodness, I forgot how incredibly boring Morris is once school’s out. You have my condolences.
@ PZ
Ok, so I’ve installed ImageJ from the Ubuntu repositories. What do I do now???
Hey, I might be getting back into zebrafish again, oddly as developmental models for other fish, so I for one would love to see more zfish posts around these parts.
embryo behavior, you say?
what, wiggle-rate?
Always with the zebrafish. I used to room with a genetics grad student and I asked about why she was always on about zebrafish, and she said, “Dude, zebrafish are where it’s AT.”
That always amused.
Zebrafish are INDEED where it’s at.
Totally off topic question, but… how difficult is it to breed zebrafish? I’ve raised tetras, but never managed to get the conditions right for spawning. (Guppies, no problem, except that they all start to look the same after a couple of generations.)
Do you ever do selected lines of zebrafish based on behavior? My colleagues select lines of mice who, for example, drink a lot of alcohol and don’t drink much at all. After several generations of breeding high drinkers to high drinkers and low drinkers to low drinkers, they have lines of mice that binge drink and get their blood alcohol to 160 mg/dl and lines that avoid alcohol entirely. Then they look at genetic differences between the lines. Not at all sure what characteristic behaviors you can look at in zebrafish, but with several lines, you have the potential….
Long generation times? Cheer up, it could be worse. You could be a botanist, working on Agave americana or some such.
And BTW–You’ll not get away with taunting us with that ‘marinading of the vegies for later roasting’ bullshit without sharing the recipe……………….or it DOES NOT count towards your heart health at all!11Eleventy
Is there any particular reason you don’t do a fish-less cycle? As an amateur fish-keeper I was told by many more experienced people that ammonia cycling was the way to go.
I would be looking for any excuse possible to use this MIT algorithm for detecting minute changes in shit. Like zebra fish or whatever.
TL;DR version of post:
“What do you want to do this summer, Professor Brain?”
Same thing we do every summer, Student Pinky: Try To Take Over The World!!!”
What’s your behavioral assay? I have friends in Seattle who are looking at rheotaxis…….
I’m going to be trying to get some flies to express a viral protein this summer. Much fun.
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I thought the purpose of using the fishless cycle is to prevent causing stress to the fish being used to start the nitrogen cycle. However if you are using feeder fish they have a chance at changing their fate. If they can survive the cycling process they will have a longer life than being fed to an Arowana or some other predatory fish. If you had a choice of inhaling ammonia and maybe surviving or being ate by a tiger what would you choose?
Yeah, seems to me that some fishless cycling ought to be done in this system :)
We use cheap danios we get at local pet stores for cycling. The advantage is that while they’re pissing out nitrogen for us, they also lay eggs we can use for preliminary testing and training students.
Then they get moved to a tank we set up just to look pretty, rather than produce science. It’s also the retirement tank — I hate euthanizing fish, so when they get old and unproductive, they get shuffled off to the big tank with the lovely gravel bottom and interesting rocks and plants wafting about, where they can idle away their days until they die a natural death.
We also use the retirement tank for water testing, so it’s not all skittles and beer. Morris tap water is toxic, nasty stuff full of minerals that the fish don’t like. We use RO water with trace salts added, but…a few years ago we had a catastrophe when the idiots in the physical plant decided to do maintenance on the RO filter, pulled it out and let unfiltered water flow in. We did our routine water change one day, and watched in horror as all the fish in the tanks spasmed and died.
So now, before we add water to the main system or the working tanks, we do a preliminary water change on the retirement tank. Canaries in the coal mine, or fish in a hard water environment.
(I don’t think Morris tap water is usually instantly lethal — I think physical plant did something else horrible when they fucked up the filters, and let some other contaminant in.)
Sorry, Andy, I’m keeping mum about the specifics. It’s just me and one student trying to get some simple results, it’s nothing earthshaking or astonishing, but I’d like to get it out via a scientific presentation or paper first, rather than just burbling on the web. It’s really hard for a tiny underfunded lab to get something publishable without the big well-funded lab doing it first, ten times more thoroughly and in a quarter of the time.