Run and Tumble

All water is poo water.  Unless you want your guts eaten, your brain eaten, or cysts in your tissues, don’t swim and stick to beer.

Tonight we’re going to be using Bergey’s Manual to identify some unknowns.   It’s basically the book for bacterial identification and classification. I’ve been wanting to get a look at Bergey’s since the first time I read about it, so I’m super jazzed for lab!

(edit: This was written last Saturday, but I accidentally saved it as a draft, rather than publishing it.)

We were assigned an extra credit project, make an 8 to 15 slide presentation deck on a microbiology topic of our choice.

I’m doing mine on microbial bioremediation, of course. I’m amused that my biggest problem is figuring out how to keep it short enough.

Small Things Considered is running a great article wherein Ted Park recalls uncovering the way way penicillin works.

I find articles like this fascinating. It would be nice if there were more written experiences of “I didn’t know, but I had some hunches, so I tried this, this and this.  A colleague mentioned such-and-such and that gave me a context to relate a,b, and c, which I’d studied earlier.” There’s a sweet spot somewhere between popular science and academic papers that gives a real feel for the investigative thought process.

Test #2 is slated for tomorrow. I’m all studied up. I don’t have any problems with the material. A few of the practice questions had subtly different answers where one was ‘kind of right’ and the other was ‘just a little righter’. If anything besides brainfarts or rushing trips me up, it’ll be that.

In the meantime I’m looking forward to seeing the results of the biochem tubes we inoculated last week.

Last night’s lab was spent learning about and inoculating more selective and differential media. We were mainly differentiating based on carbohydrate catabolism using fermentation tubes, MRVP broth, starch agar, OF-glucose media, and Simmon’s citrate. We’ll see the results on Tuesday.

We’re building up a toolbox of techniques we can use to work through a d-key and identify bugs in an unknown culture.

There’s three things I take away from all this.

It’s just incredibly awesome to see how flexible bacteria are when it comes to metabolism. Heck, some of the tests are time sensitive because a bug will rewire itself to take better advantage of the changing biochemical landscape. No more glucose? Ok, let me just turn on my lactose fermentation machinery.  It’s a pain in the ass for diagnostics, but really neat.  If it can be nommed, there’s a bug out there that can do it. Seriously, Pseudomonas aeruginosa can eat phenol. Not just degrade, but actually use it as the sole carbon source.  We usually use phenol to kill bugs, not feed them.

The manner of thinking used to create these tests and to work through a d-key is strikingly similar to that which I use when debugging code, it’s very comfortable and feels ‘right’.

I love that half the stuff is named So-and-so’s something; it feels like I’m acquiring old school D&D spells. Nerd. Quick, which is in the lab and which is in the AD&D Player’s Handbook ?  Tenser’s floating disc, Masson’s trichrome

Remember the lab practical I was worried about?  I still think I should practice the areas I pointed out, but we got our grades back, and I did very well. So, that’s one less thing to worry about.

On studying for the staining portion of a lab practical, “How do they cram all that Gram?”

Finished lab practical #1 last night. I think I did ok, but I did mess up a bit. Here’s where I’m predicting I lost points, and subsequently, what I’ve got to focus on.

• Ran out of time before finishing 3rd streak on my streak plate. I’ve got to learn to work a little more quickly, but still carefully. Mainly, I’ve got to be quicker with probe heating/cooling.
• I caught myself writing down a few brainfart mistakes. I’m hoping that I caught all the ones I made. I’ve got to stop tensing up over stuff I know.
• I can easily rattle off all sorts of terms for colony morphologies and cell morphology/arrangement. Unfortunately, I’ve been practicing with diagrams or picture-perfect textbook micrographs. In the real world, things can have a mostly entire margin, but be edging into undulate territory. Or, you’ll see definite cocci on a slide, but have to make a judgment call on whether they’re tetrads that occasionally broke apart into diplococci or diplococci that occasionally glommed together into tetrads. I should look at a bunch of non-ideal examples, make those judgement calls, and then compare them to commonly accepted answer.

I’m not too worried about my grade, and I’m all about making mistakes and moving on, but it would’ve been nice to continue batting 1000.

Oh, one part that gave me no trouble was using the scope to find bacteria on a slide I prepped. So, that’s a victory.

I started two Winogradsky columns this past weekend.

They’re really simple to set up and were invented by Sergei  Winogradsky, one of the founding fathers of soil microbiology. The basic concept is that you get some mud and water, put it all in a semi-sealed tube exposed to light, and watch as bugs set up shop.

The tube quickly forms zones containing different microenvironments; the bottom becomes anaerobic, the top stays aerobic, and other minerals form a gradient within the mud. The zones attract different bugs and often end up forming different colored layers.

There’s a rich interplay where one zone’s trash becomes another zone’s treasure; you end up with the major biogeochemical cycles in a can. The elegance of those cycles deeply appeals to me and is one the major reasons I’m gravitating towards environmental microbiology and bioremediation. I’ve wanted to make my own columns for some time.

As a bonus, the columns generate a mild but measurable electrochemical gradient. It’s not going to charge a laptop, but it is nifty.

I  loosely followed the procedure here. I took my samples from a nearby bayside park. Since the bay is saline and the local area was covered in acidic pine straw, I opted to use water from the site, rather than top off the columns at home. Why shock the bugs more than necessary? The mud had a nice black layer*, so I’m hoping for some ready-to-go sulfur reducers.

I used shredded newspaper for a cellulose source. For sulfur and calcium carbonate, I just boiled some eggs and crumbled the shells and yolks. I was all set to make a joke about albumin disposal via Carnivorous Albumin-digesting Trypsin Sacks, but it turns out neither of my cats like boiled egg whites.  Traitors.

I used some old speaker wire for the electric leads. Next time, I’ll use something stiffer.  Getting them to play nice with a multimeter’s probes was a pita. I did manage to make life easier by taping the wires in place before filling the column.  I’ll be taking measurements periodically and then posting the data in a few weeks.

The first column is a nice, cheap glass cylinder I got, at the awesome wife’s suggestion, from a craft store. It was in the ‘hollow glass things you can fill with beads and sand’ section. The second column is just a large plastic container that used to contain a ridiculous amount of biscotti. I’m planning on figuring out a way to puncture and re-seal the plastic so that I can get at the various layers. Bonus points if I end up using duct tape. Here are the columns, minutes after I finished inserting a lead into the mud-water interface and semi-sealing the tops.*

* photos forthcoming, as soon as my camera’s dongle turns up