The course is turning out to be excellent background. So far I’ve learned about hydrology, mass budgets, reactor design, and risk assessment. I’ve also re-learned chemical equilibrium, but in the context of environmental chemistry.

I’ve figured out what I’ve got to do each week to keep on top of the material. I’m rather proud that the list is pretty different and more comprehensive than what I would’ve come up with in my early undergrad days. I’m taking it as more proof that a lot of my problem back then was more about attitude than aptitude.

The biggest downside has turned out to be time. While engineering courses require about the same amount of things to study as other courses, each ‘thing’ takes much longer.  Compare going through a 10 card flash deck with a 10-20 min example problem. I’m not spending every waking moment on the course or anything like that, but if I don’t spend a significant amount of time each day on it, I quickly fall behind my schedule.

Just a few weeks until I get to visit the wastewater treatment plant. Is it weird that I’m looking forward to that?

One of the issues I’m dealing with in picking out a graduate program is if I want to lean more towards science or engineering. I’ve got strong urges to both learn and create. I won’t be happy building yet another bog-standard anaerobic digester, but I also won’t be happy determining the ratio of micronutrients that triple nitrate reduction if it is never used in the real world. There are plenty of programs that offer opportunities for both, but they are generally lopsided in their mix. This course will help me figure out which side I’d rather have emphasized.

I do have a little anxiety. I am fine with math, and agree with Lord Kelvin that if you can’t measure something, you can’t improve it. However, this is the first course I’ve taken since graduation that flexes my mathematical, rather than conceptual, reasoning abilities.

As a bonus, we actually got to use E-Tubes and API-20 kits (aka watercolors of pipetting hell) for enteric identification. We can’t use them for the unknown ID final exam, but they’re still way cool to play with.

Got a microscope in the mail, but not the one I ordered. Ugh.

Things are looking a little up, I’m working things out with the scope supplier and lab promises to be interesting tonight. We inoculated some Pseudomonas aeruginosa last week on media that induces their characteristic blue-green pigment. I’ve been wanting to see this ever since I found of P. aeruginosa makes it;, the specific epithet even means ‘copper rust’. We’ve been using that bug all semester, but it doesn’t seem to want to express the pigment on TSA, so I’m looking forward to the pretty colors tonight.

I’m also going to see if I can get a whiff of the distinct odor (previous plates shared space with less-than-pleasant smelling bugs) and maybe even get use of the UV lamp to look for fluorescein.

I’ve realized that since my 30th birthday, I’ve had many more days where I’m growing bugs than days where I’m not. It may be silly, but this makes me pretty happy.

Edit: Blame it on stress during an exam.  The skin swabs went on MSA, not BA, which we’ll be using for throat swabs. All this makes sense, given the environments of skin and MSA. My beard came back with a higher than normal, but not super high bacterial count. Very nicely defined mannitol acid zones. No really scary bugs, just the usual Staphylococcus spp. suspects. Waiting on a trehalose test to narrow one down.

It’s a neat little bug that nestles next to members of Chromatium, forms a cytopathic bridge, and sucks out all their yummy cytoplasm. You generally hear about it as an example epibiont when people discuss bacteria-on-bacteria predation. It also comes up in microbiology classes around this time of year. Otherwise, there’s not a lot to be said about it. I’ll try to fix that.

Let’s say you see Vampirococcus spp. floating towards you, what are you going to do? Would treating it like a regular vampire work?

Regular vampires are known to be averse to garlic, sunlight, decapitation, holy water, silver (at least in recent movies), and, of course, wooden stakes.

Garlic would almost certainly work. It produces a compound called allicin which may be as effective as ciproflaxin(pdf). Just make sure you crush it first; crushing releases the enzyme alliinase which converts the amino acid alliin into allicin. You’ll know when it’s ready because allicin is also what makes garlic smell like, well, garlic.

Recent lore not only says regular vampires hate sunlight, but that it’s the UV which is specifically vampiricidal. This is also true for bacteria. However, they’ve spent a few billion years coming up with ways to cope, and since our bug preys on a photoautotroph, you can bet it knows how to deal with a little sun.

As for decapitation, it’s isn’t a stalked bacteria, so you tell me where the neck is. If you want to get metaphoric, you could go ahead and remove the genetic content. The problem there is that you’re now close enough to the bug for him to be sucking your sweet, sweet cytoplasm.

Holy water might work. If you think of ‘holy’ as ‘pure’, you might be able to get some sort of osmotic lysis going on. More interesting is that the thing people sprinkle holy water with is called an aspergillium. The resemblance of some fungi to a liturgical super soaker is why their genus is named Aspergillus. And, interestingly enough, at least one species, Aspergillus clavatus produces an antibiotic. I’m not saying beating a bacteria with an aspergillium is going to work, but if you’ve got no other options, give it a whack.

Silver is actually pretty well known to kill bugs. Back before we had antibiotics, we used to drip silver nitrate solution into the eyes of newborn babies so they didn’t get ocular gonorrhea. Go ahead and pelt Vampirococcus with the good gravy boat.

Wooden stake lore is fascinating. Did you know that some legends are specific about what kind of wood you have to use? The most common suggestions are oak, ash, woodruff, and rose. Each of these have at least one species, local to the area which prefers it for slaying, whose essential oil exhibits bactericidal effects. The big problem is that most of the oils are extracted from leaves and berries, not good stake making material. Your best bet is to either go with ash, whose oils are in the bark(go for that rustic look), or oak, which is riddled with endophytic fungi that produce antibiotics.

On a serious note, I found out Vampirococcus didn’t have a Wikipedia page, so I actually had the pleasure of starting a new one and watching as people helped improve it. If you know me personally, you know how much I love Wikipedia and can guess how jazzed I am to have been able to contribute to it.

Happy Halloween!

(Artist’s interpretation of Vampirococcus modified from this vampire image)

I love learning, I like to sink deep into a topic, read my fill, and end up with even more things I want to learn about. The more resources available, the happier I am.

For reasons that’ll be clear a few posts from now, I was interested in the antimicrobial properties of various essential oils. I was able to gather some understanding from a few of abstracts, but far too many were of the form ‘We tested A, B, and C.  Some showed moderate activity.’  No hint of which ones showed the vaguely defined ‘moderate’ activity.  And hey, maybe I want to read the methods section (either to see if it’s bullshit, or to find out how to try it at home).  Open access lets amateurs(in the old for the love of it sense of of the word) like myself learn, so I support it.

I mean, come on, OA lets anyone who can get to a computer learn all they want about how T. rex may have been brought down by an ancestor of a chicken parasite.

He’d bring in the same whiskey he just used to wash out the bullet hole received while laying down the law.  I grabbed a small amount of my Jameson Irish Whiskey (40% alc by volume) and headed out to the lab.

To test it, we divided two petri dishes into five sections.  One dish was for Pseudomonas aeruginosa, the other for Staphylococcus aureus. The first section of each plate was labelled ‘0′ and streaked with an undiluted culture of the appropriate bug.

Next, we diluted 0.5 mL of each broth with 5 mL of Jameson Irish Whiskey. At 2.5, 5, 10, and 20 minutes after dilution, we streaked a section of each plate.  (I finally got to use a nifty mechanical pipette, rather than the ABCDE rubber valve, YAY!)

We left them incubating at 37 Celsius until this evening. Here are the results, growth is ranked relative to the initial streak on a scale of 0(no growth) to 4(about the same):

* There was a single colony. Multiple groups working with S. aureus had an unexplained ‘no growth’ at 2.5. Let me know if you have ideas. Also apologies for the unstyled table, I’ll make it pretty after I finish studying.

This is fairly effective. Indeed, it was much more effective than Lysol against Pseudomonas, which didn’t even make a dent.  If you think 10 minutes is a long time, double check the instructions on your household cleaners.  Yeah, you’re not supposed to mop it up as soon as you spray it.  This is why.

Now, remember that this data is really only good for disinfecting flat surfaces, not as an antiseptic for actual cowboy bullet wounds, which have a lot of complicating factors. I also make no guarantees about effectiveness vs spore-formers. Finally, Jameson costs more than most similarly effective disinfectants and tastes good enough that it would be a pity to regularly use it in this manner.

P.S. If/when I start plating from home, I’ll take pictures, rather than just feed y’all tables.

She often refers to enzymes as Oompa-loompas, I think this is a perfect way to think of them.