Cecum II

It should be noted that, upon reflection, I have seen a bigger cecum than the one noted before, but it was in a mouse infected with cholera, and as such was mostly liquid anyway.

Cecum

It's like the murine equivalent of an appendix, only with a digestive function and not just as a reservoir for normal gut flora. The jejunum feeds it and the ileum drains it, but it's pretty much a big J-shaped sack that holds digesting food. I do not know what it's contents would look like in a wild mouse with a heterogeneous diet, but in lab animals with a homogeneous diet it is uniformly brown (think pre-poop).

I bring up the cecum because I dissected out possibly the biggest cecum I have ever seen the other day. It was from a Germ-free Swiss Webster mouse, about 18 months of age, who was suffering bloat from a downstream gut twist. Ceca tend to bloat anyway in germ-free mice, and the gut twist may have backed up materials as well (although it pooped on me anyway when I picked it up), but the mouse still had retained ~3g of cecal contents (mouse weighed maybe 25g). That's incredible!

If I had the same relative mass of undigested food in me, that'd be about 9kg!

(I have a morbid tendency to calculate things upward from mice to my own mass. For example, the LD50 of Stx-2 (Shiga-like-toxin-2, produced in very virulent O157:H7 E coli strains) in mice is about 1.3E-5g/kg [if I am remembering the paper on it correctly]. Which means that the LD50 for me would be only about 3mg!).

Cartoon

Guild

Just got out of the lab. Spent 3 hours in the flow hood plating serial dilutions of bacteria. Tedium. Tedium in which I must remain very accurate and precise with my measurements, which had to be done a couple hundred times (the same measurements).

Sometimes I look back to the craft guilds of the 17th century prior to the Industrial Revolution. They regulated all the craftsmen and their products and what was allowable and who could sell where and what and how and for how much. But they also trained young people as apprentices, then when they became competent let them be journeymen, and finally, after their masterpiece was complete, they were masters of their trade. In some ways, becoming a research scientist recapitulates that progression.

I very recently graduated with a Bachelor of Science in Cell and Molecular Biology. As an undergraduate, I worked in labs, and on my own project, kind of like an apprentice. I learned the practical basics that they can't teach in lecture halls, such as pipetting, cell culture, operating cantankerous equipment. Now I've graduated and am working in a lab as a technician. This is like the journeyman stage. Later, when graduate school happens, it will be as if the guild has granted me permission to continue to advance my craft as a journeyman. And in graduate school, I will have to research and defend a thesis, the academic equivalent to a masterpiece.

The only problem with this is that I feel like I should have my own tools. A good set of micropipettes, maybe a pH meter, a couple sheafs of protocols. Unfortunately, micropipettes are a lot more expensive than hammers.

Office Enterprise 2007

It can really suck sometimes.

I made this really cool Powerpoint presentation that I was going to post on here. It was all about enterohemorrhagic E. coli (EHEC) and the genetics of Shiga toxin expression (which are really cool!). But Office Enterprise 2007 isn't nice enough to allow me to do so. I tried converting it to an .html file, but then Office wouldn't let me access the actual code, only look at it through my default browser. Now, yes, I could have gone and coded it all by hand, but that would have taken up much more time that I was willing to spare for this (it's finals season for me!). So you all (maybe there's one of you, but we're going to pretend that you're plural, just like we're pretending like we're plural) will just have to imagine how cool the genetics of Shiga toxin in pathogenic strains of E. coli are.

It's probably better that way anyway.

Brain Extractions

Surprisingly sticky.

I managed to decapitate the mouse well enough (it was already dead at this point, decapitation was not the primary means of euthanasia [that occurred sometime between putting it to forever sleep and exsanguinating it by means of cardiac puncture]), but skinning its head was quite difficult. Mainly because it was very slippery. You have to sort of peel the skin back (like an orange) until you can see the eyes and then fold it into a handle for yourself to cut through bones. Next you cut across the bone between the eyes, then through the ears to the back of the skull. Then it pretty much pops open once you split the skull down the middle.

But the mouse brain itself? Pale and smooth. A bit larger than I had expected for such a small mammal. Also very dense, it didn't squish very easily (I wasn't trying to squish it into paste [and I didn't], but seeing how much give it had, just gently pinching it a little).

But I don't know. It was sort of profound. There I was, sitting in the lab with another creature's brain in the palm of my hand. As if there was some kind of phylogenetic resonance recapitulating my evolution of my own brain from one similar to that in my hand. Like saying hello to a baby. I would even have to admit that it was kind of cute, so grayish pink, almost like a newborn mouse pup (but less wrinkly). I sat there and looked at it, thinking to myself: "So this is what propelled the little creatures in their cage to climb over each other and twitch their whiskers in alarm each time we manipulated their cage." It was cool.

Perhaps I'll post some sketches of the procedure if I ever remember to draw them.



Disclaimer:
Although it may appear otherwise, I am not a sick fuck. I respect the animals that we use in science and always feel regret when I am required to euthanize them. But in seeing how they are put together and how all of the organs and systems are connected to one another: that is undeniably cool. And while it is important to remember that laboratory mice are living things that must be treated as such, it is also important that we as scientists be able to speak of them frankly and with all the delighted curiosity that (hopefully) brought us to science in the first place.

Vampires

Gotta start remembering that I have one of these blog things. I got some new software (Propellerhead Reason) and I've been neglecting everything else just to play with it.

Although maybe it would be cool for me to speculate to the molecular biology of vampires, that's not what I'm doing. Instead, this is a short commentary on the morbid-ness of scientists. For example, one of the lab techs told me at lunch that now we were taking brain samples for histology and that it was gross. My immediate response was "Cool! How do we do that?", which led to an explanation of splitting the scalp open, rolling it down off the head, and then cracking the skull and peeling it like an orange. I must learn how to do this myself.

Or, as another example, I just sent an email to the germ-free animal manager asking if we had any uninfected mice that needed culling. Not because I want to go over and slaughter hapless mice, but because I could make good use of their serum for my project and I might as well get it anyway if they're slated to die.

Just saying.

Why Flow Cytometry Is Cool

It has lasers!

(insert awesome laser picture here)

And it shoots lasers at cells!

Cells and lasers are cool!

Therefore, flow cytometry is double-cool! Maybe even Gigacool!

And, furthermore, that the physics of how it works and its optics aren't too convoluted to understand! Woo! And it calls groups of different cells pots! Pots! How absurd is that? Would you like a pot of cells? Why yes, sir, thank you very much, but may I have some PE-A and CD3 with them? Ah yes, very tasty. Lasers!

Cart

So the cart in my lab is probably about as old as I am. It's made entirely of metal, made for a much shorter person than ever uses it, and rattles so much that you can't even hear your own footsteps when you're stomping. No, we don't have a nice new cart made of HDPE that doesn't rattle or anything. Ours is like an angry dinosaur in desperate need of new ball bearings.

Why do I mention the cart?

Because it occurs to me that I should stop running down the hallways with it, loaded with biohazard waste, before I knock one of the old tenured PIs over and have to wear a Crystal Violet "U" (for Unfit Scientist). But there are some PIs who'd be funny to chase...

Still Alive

Been in a quasi-hibernation in this quasi-kaamos.

So I'm trying to reconcile 2 statements the professor of my Microbial Genetics course made in class last Thursday.

1) There are approximately 100 bacteria to every 1 cell in the human body.

2) It is estimated that only 1% of bacteria in any given sample of anything can be cultured and identified.

Each statement could be taken as true in its own context, at least if you ignore questions as to how such statements were formulated*, but together they don't make a lot of sense. Yes, there are ~3kg of bacteria in the human digestive tract alone (thinking of this ensures that I never feel lonely--I've always got a couple trillion close friends at hand). Nonetheless, if only 1% of the bacteria, even in a gut lumen sample, can be cultured and quantified, then how do we know how many were there to begin with? And as such, then how can we know what the ratio of bacterial cells to human cells is?

And as for the first statement, how does that work spatially? Bacteria range in size from 0.5-5.0 micrometers, and eukaryotic cells (e.g., human cells) are 10X as large. If these figures can be taken as directly proportional to volume and not just length, then there should be at most 10 bacteria to each human cell, and even then the total size and mass of those bacterial cells would be the same as the size and mass of the human. But if they are not directly proportional, then maybe it could work, although I still have a hard time imaging those volumes working out.

*Seriously though, how the hell did they get this figure? Did they take a whole healthy human and fractionate the entire body into its cellular components, then centrifuge everything and run it through flow cytometry to get the ratios? Or did they just take a liver biopsy and count that? But that would be inaccurate...