Run and Tumble

Someone in the previous lab session threw out my plates, so no data on what’s in my kittie’s guts, and if their different diets affect what lives in them. Had to spend most of the lab sitting on my thumbs waiting for another group to finish so I could use their plate.

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.

You are the winning buyer for the item below. Thank you for your business!
Item title: 40X-1600X BIOLOGICAL BINOCULAR COMPOUND MICROSCOPE

I’ll make a bigger post when I actually have it and comment on the quality.

Next lab is on bacteria of the GI tract.  People with pets or babies were asked to volunteer to take fecal swabs. I’ve got two cats on different diets, so I’m excited to see if there’s any difference. Awesome wife isn’t phased by this, she even volunteered to be on poo patrol while I’m at work.

One of the stations at the lab practical last week had us streaking skin swabs onto blood agar. That was my first time using that medium, I’m looking forward to seeing what grew. I chose to swab my chin, since I’ve got a beard, most people don’t pick the chin area, and beards may be a minor hazard in micro lab (sorry, Movember friends).

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.

In the spirit of the holiday, I present to you a bit of information on members of the informal genus Vampirococcus.

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)

We’re halfway through the halfway point of Open Access Week 2009. The basic idea of open access is that we all benefit if results from research are published online for free.  The site does a good job of explaining why this is so, and I leave it to people who deal with journals on a daily basis to defend the major points. I want to talk about why it matters to me, right now.

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.

The most recent lab was spent testing antiseptics and disinfectants.  We were tasked with bringing in something from home.  I didn’t want to be student #1000 who brought in mouthwash or bleach, so I asked myself what would John Wayne do?

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.

My prof is big into metaphorical explanations.

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

Last week was spent putting the finishing touches on, tearing down, and re-finishing my slides on microbial bioremediation. It was pretty fun, and the first presentation I’ve prepared in a while. I was pleasantly surprised by how much I ended up learning about topic I felt pretty solid on (well, solid enough for a 15 slide deck). The next time I want to get a firm grip on a topic, I’m going to remember that helping someone else learn something is a great way to do so.

Since I still am learning, there may be mistakes here, so don’t take it as the gospel, and if you do catch me in an error, please, please let me know.

Microbial Bioremediation

(also available in pptx and a partially braindead ppt, if you need it)

Just a reminder that today is Global Handwashing Day.  And if you don’t think that’s important, zombie Holmes and Semmelweis would like to have a word with you.