Intentional food microbiology:
UNintentional food microbiology:
I still don’t feel like I got nearly enough productive stuff done this weekend, but I did manage to do a bit of microscopy – plus demonstrating to myself that I still remember how to do a “Gram stain”. Real Post with explanation and more pictures to follow Real Soon Now…
Brew; Eat it; Food Science; Me, me, me; Microbiology; Pretty Pictures @ 18 Jan 2010 08:55 pm by Epicanis
People usually assume soap gets rid of funky microbes that might grow on things, so I was very amused several months ago when I spotted something growing on top of the soap in one of the household hand-soap dispensers. As of today, it looks as pictured at left. That lumpy yellow and brown mass atop the the soap looked to me like some sort of soap-sodden mold, and have been saving the dispenser specifically in the hopes that someday I’d have a microscope and could take a look at it. Meanwhile, the mass spread, and slowly started releasing some kind of yellow pigment into the soap.
Incidentally, I kind of doubt this indicates some sort of failure on the part of the manufacturer of the soap. I don’t recall for certain, but I think I may have opened the dispenser at one point to transfer some of the soap to another nearly-empty dispenser. When the mass started growing originally, it was a single spot, which suggests a single spore or speck of dust floating in and landing on the surface. Hey, it happens. Anyway, I’ve therefore blanked out the name of the manufacturer since I don’t think they really have anything to do with this.
This mysterious growth upon my soap remained mysterious until today. Thanks to the Minister of Domestic Affairs and VWR (who managed to find me a really good deal), I finally got to actually get a close look at that lumpy mass. Meet my new friend Minnie (pictured at right). I could gaze into those eyes for hours. I couldn’t afford a darkfield condenser, and I sure as heck couldn’t afford to upgrade to phase-contrast gear, but I can add either one later if the opportunity presents itself. I also can’t afford the overpriced proprietary digital camera attachments either, though working around that is a whole other project. Until I identify an affordable model that plays well with Linux or work out how to modify a webcam into an ocular attachment,
I’ll have to settle for a trick…
It turns out if you take a digital camera and set it for close-up photos, you can actually stick the camera lens right up to the eyepiece and often get a serviceable picture.. Now, I had to subject the pictures I got today to moderately heavy processing to bring out the detail a bit better, but at least part of that is just me working on learning how to optimize the camera settings for this kind of use.
Equipped with some surplus slides and cover-slips donated by a kind professor who had some extra packages, I opened up the soap container and smeared a little of the yellow crud on a couple of them. One I just slapped a coverslip on for direct observation – the other I smeared over a slide and let dry with the intention of staining using the tiny, previously-unused vial of methylene blue left over from a very old plastic toy microscope. While the latter dried, I took a look at the wet mount hoping to finally see the mold mycelia that I had been expecting…
There wasn’t enough contrast to bother trying to get a photo, but it was obvious at 400x that what I was looking at was bacteria, not mold. Nerdly joy at learning something by looking in the microscope that I wouldn’t have otherwise known ensued, along with happiness as I realized this meant I had a perfect excuse to dig out my recent shipment from the Maker Shed – materials for doing a “Gram Stain”. Incidentally, the “Maker Shed” had the supplies on the way to me within hours of my ordering it, and they have lots and lots of cool stuff. I highly recommend it. Anyway, I got to do a “Gram Stain” for the first time in a couple of years (and the first time ever outside of a school lab). Want to see?
Here it is – the nasty yellow goo that infected my bottle of hand-soap. My staining technique was a little off since I’m out of practice – the way I interpret the results is that what I’ve got here is neither a member of the Firmicutes (i.e. “Gram positive”) nor – probably – Actinobacteria. I really can’t guess at more than that, though. I think the few “Gram-positive”-looking cells there are artifacts of insufficient decolorization. I know I still had a surplus of the purple “Crystal Violet” stain still on the slide at the end. (How did I know? I’ll show you at the end…). The irregular bluish bits towards the bottom are, I believe, just bits of stuff from the soap itself.
Meanwhile, this pretty much satisfies my curiousity about the Mystery Soap-Infecting Microbe. There’s certainly a lot more I could investigate, but my developing Hillbilly Biotech lab is really intended to support my interest in intentional food microbiology and perhaps evenutally some small-scale non-food industrial microbiology. I have some remaining curiousity about the yellow pigment and whether or not it might be useful for something, but I’m doubting there is any food or beverage I might want to grow this stuff in and therefore don’t have much use for it. Still, I’ll keep the bottle around for a while before I throw it out in case I think of something fun to do with it. If I end up being really interested in the identity of the bug growing on it, I should be able to find a liquid that I can grow a big mess of it in, then run it through a simple DNA extraction process. Then all I need to do is find someone who can supply PCR primers, a thermocycler, and sequencing services cheap. It might sound like I’m being facetious, but I wouldn’t be surprised these days if I manage to find somewhere that’d do it for $20/sample or less. I may eventually do this will the Mystery Soap Bug anyway, since I hope to be running through this process with cultures of sourdough, yogurt, cheese, vinegar, and brewing microbes that I develop myself. For now, though, it’s just nice to be playing with microbiology equipment again. And now fully independently! Wheeeeeeee!!!!!!
Yes, I’m a nerd. And proud of it!
Now that I finally have a microscope, I no longer have any excuse for not getting to work on the rest of my Hillbilly Biotech lab. Just this weekend I was pricing out Hillbilly Autoclaves. I picked up a cheap air pump and air stone
for potentially building an aerobic bubble-column fermenter (for quick growth of yeast starters or a working model of a “Fring’s Acetator®”-style vinegar generator. I still want to build an ozone generator for sanitization and to get a pH meter. I’d like to also get my hands on some wheat, barley, and rye seeds to sanitize, sprout, and grow here as the first stage of developing a truly local sourdough culture, plus arrange to have several pounds of plain flour irradiated to sterilize it.
I’m also like summer to be over. Yes, I’m writing this in Winter, but it’s not until later in the summer to autumn that locally-grown fruits will start becoming available, and locally grown fruits ought to be an ideal source of local brewing and baking yeasts and bacteria. Finally, I’d like to find a wealthy patron (or matron, I’m no sexist…) who would sponsor me so I could just pursue food-microbe bioprospecting and research full-time…
Oh, yes, and I need to get around to finishing Episode 4 of my little podcast project, especially since episode 4’s topic is a fundamental microbiology technique.
Comments welcome below – thanks for reading!
Oh, and as a reward for getting all the way to the end, here’s a picture that I thought was pretty – crystals of “Crystal Violet” and iodine. I told you I had too much left on the slide…
Double-Ewe Tea Eff (WTF); Food Science; Hillbilly Biotech; Me, me, me; Microbiology; Netcasts; Pretty Pictures; WANT; What I learned in school today @ 10 Jan 2010 10:06 pm by Epicanis
I’ve got two blog posts that I want to get done this weekend. This is one of them.
I’m something of a fan of MAKE magazine and its related websites and such, being a frustrated “Maker” and all. “Frustrated” because although I have a strong urge to make things, I seem to have a gross oversupply of chores and issues constantly popping up to keep me from getting much done. Still, I try, despite the efforts of the Dog and five (insert mild profanity here) cats (I seem to have been declared the household “Stuff that goes into and comes out of nonhuman mammal companions technician”), and living space that thinks it’s necessary to demonstrate how entropy works on a constant basis. MAKE’s slogan is “If you can’t open it, you don’t own it”, which I so passionately agree with that I wish they were a political party so I could vote for them.
Anyway…MAKE magazine recently posted a poll asking for opinions on the magazine, the website, and so on. The way the poll was structured didn’t really let me address what I really like and dislike about the site, so I thought I’d post it here in case anyone besides me is interested.
But first, some praise: part of the poll was asking about the online store they run – The Maker Shed. I filled in the poll just a day or so before I went and ordered something from it, so I couldn’t give any opinion of it at the time. Having now gotten what I ordered, I have to say the store seems to be moderately awesome.
One of my complaints about the MAKE franchise is that it often seems to be made entirely of Arduino™ electronics, Arts-and-crafts (e.g. knitted things), and baking-soda-volcano sorts of projects for children. In truth it’s not that bad, but I would personally like to see “less Arduino™, more ‘Bioreactor’” – they actually published a “Bio-hacking“-themed issue a while back, so there’s hope. I bring this up because what they had at the Maker Shed that I bought was microbiological staining supplies (not actually the kit pictured above, but they didn’t have pictures of individual bottles of what I got). I put in my order online expecting it to be shipped the next business day, and was pleasantly surprised to find an “okay, you’re order’s been shipped” notice in my email within an hour or two. The stuff even arrived by that weekend (i.e. today), hopefully leaving me time to use it for my planned second blog post of the weekend. So, definitely fast service at the Maker Shed.
There are a few annoyances I have with the MAKE franchise, though:
I’d actually really like to have actual no-video-required audio shows that I could listen to on my 2½-hour daily commute. Not all of us want to (or can!) sit and stare at computer and/or “iPod®” video screens but still would like regular infusions of MAKE-related news and information.
This isn’t a major technical problem for me – Mplayer handles the files just fine. However, given that Apple’s preferred formats are all heavily patent-encumbered and proprietary and therefore not really legally usable for “making” video without special paid-for permission from Apple® corporation, it seems an odd choice for the “If you can’t open it you don’t own it” folks. Perhaps they’re just paranoid that Steve Jobs is lurking just on the other side of the bay, waiting for an excuse to come up there and kick their butts if they aren’t pro-Apple® enough? In any case, I’m kind of surprised they seem to have no interest at all in legally-free, amateur-multimedia-maker friendly formats like Vorbis and Theora.
Or so I believe, anyway. They already split the arts-and-crafts stuff off into its own CRAFT magazine. If they also split off the “make a paper plate toy” stuff to “Make: Kids” (Wait, “making kids” sounds like some kind of pornographic euphemism. Make that “Kids: Make”) there’d be more room for the more hardcore stuff (and a higher chance of more stuff I’m personally interested in).
This isn’t really MAKE’s fault, unless they’re part of the secret cabal that conspires to keep me from having enough wealth and leisure time to attend things like this.
Okay, this has nothing to do with MAKE, but it’s annoying me right now.
There – now I’ve gotten it out of my system and out here where if anybody actually cares they can see it. Just some stuff that there was no way to convey in the survey. Otherwise I highly recommend MAKE magazine and its associated online material. The world needs more Makers and they’re doing some spiffy stuff to help in Sebastopol these days.
Now then, if all goes well I should have another post tomorrow with some pretty pictures of soap. Stay tuned…
Computer Nerdity; Me, me, me; Netcasts; Rant; Teaching Science @ 09 Jan 2010 09:56 pm by Epicanis
(Oops, quick edit: the references on erythritol toxicity – or rather lack thereof – are now actually included…)
Crowds, Crass Commercialism, and Crappy Christmas Choruses give me a nasty case of Yule Poisoning, and I’m sure I’m not the only one.
I spent the afternoon/evening prepping for and performing some cookie experiments again, and I feel much better. Yes, my cookies are that good.
I had a request for Peanut Butter cookies, so I figured I’d do some experimenting with that tonight. In fact, while I was braving the Christmas Consumption Crowds to get my supplies, I happened upon an ingredient that I decided I had to try as a variant.
(The picture, incidentally, is someone ELSE’S peanut butter cookies – “diekatrin” on Flickr – click photo to go to the Flickr page – I still haven’t quite gotten the hang of getting decent photos of my own food yet.)
My initial peanut-butter cookie recipe came out too dry and not sweet enough, but I think adding 50-75g of honey should solve that. That’s not the most successful experiment of the evening though. That’s reserved for the following recipe for…Sunflowerseedbutter cookies.
(Suitably pompous name pending, as soon as I test version 2.0 of the recipe, which will substitute bread flour for the “all-purpose” flour)
Powdery stuff
“Wet” stuff and sugars:
The “dry” goods were mixed in one container, while in a separate container, the “wet” goods and the sugars were mixed in another. The dry material was then blended carefully into the wet material in a large steel mixing bowl using an electric hand-held mixer until completely homogenized.
Once homogenized, the dough was spread out in the bowl and chilled at ~18°C(O°F) for approximately five minutes to enhance firmness.
The dough was then measured onto a “non-stick” baking sheet in approximately 30ml roughly-hemispherical aliquots using a small disher, and then pressed down with a fork to approximately half their original height. A few shelled, roasted sunflower seeds were pressed into the surface of each to make distinguishing them from peanutbutter cookies easier.
The cookies were than baked at 190°C (~375°F) for approximately 18 minutes, then slid onto a “non-stick” wire cooling rack at Standard Temperature and Pressure until equilibrated with the temperature of the kitchen.
The experimenter believes this batch of cookies emerged a bit too soft – actually sliding them off of the baking sheet to the rack distorted them, and they still appeared (in the words of the experimenter) “squishy”. Once equilibrated with room temperature, the cookies had a texture more in line with what would be expected from a normal “soft cookie”. The flavor was judged to be superb by the experimenter, who happens to like the flavor of sunflower seeds.
The use of erythritol makes this a “reduced calorie” and “reduced-sugar” recipe, though not entirely sugarless or “diabetic safe” necessarily, due to the use of honey. Erythritol is a sugar alcohol like sorbitol, mannitol, xylitol, or glycerol (”glycerine”), all of which are often used as low-glycemic substitutes for sucrose or other sugars. Sugar alcohols can often cause digestive discomfort, however, because they are poorly absorbed by human digestive tracts, leaving them to be digested by gas-producing gut microbes. Erythritol is unique in that it appears to be well-absorbed by humans, and yet is not metabolized by humans to any substantial degree and is safely filtered out by the kidneys and excreted in urine[1]. Being unmetabilized by humans, it is theoretically “zero calorie”, though the US FDA mandates a calculation of 0.2 calories per gram (compare to 4 calories per gram for sucrose). Unlike xylitol, erythritol is also safe for dogs[2] and ferrets[Sorry, can't find the citation for this one at the moment...], for whom xylitol can induce fatal insulin shock and/or liver damage. Erythritol, unlike glycerol or sucrose (”table sugar”), is not appreciably hygroscopic, though, so adjustments must be made to recipes using it to avoid an overly dry result.
Glycerol (sold as “Glycerine”, which can be found in cake-making supplies as an ingredient used to keep cake frosting moist) closely resembles erythritol in structure, being (to oversimplify) a one-carbon-shorter version of the same molecule. In addition to hopefully helping to prevent drying out of the cookies, this was included here in the hopes that it would also help the erythritol dissolve. Previous informal testing (unpublished results) appears to support this hypothesis.
Honey was used as a second sweetener so as to include a “real” sugar and to help counter-balance the lack of hygroscopicity of the erythritol. The experimenter also notes that he believes mixing sweeteners tends to provide a better-tasting sweetness than relying entirely on one sweetener, particularly when including less sweet “sugar substitutes” in the mix. Honey was also chosen to provide additional moisture, as a previous batch of peanut-butter cookies (the recipe from which this recipe for sunflower-seed butter is derived) using ordinary sugar and “brown sugar” had turned out excessively dry.
“Xanthan gum” is a polysaccharide (as are cornstarch and pectin, for example) produced by a natural fermentation process from the γ-Proteobacterium Xanthomonas campestris. Along with a wide variety of exotic industrial uses (such as oil-well drilling “mud”), Xanthan gum is also used as a safe food ingredient to help hold water and keep soft foods from being too runny. It helps protect ice-cream from becoming grainy during possibly partial thaw-and-refreeze cycles during shipping and storage. It’s also used to hold “gluten-free” doughs together, which is nice for people who may be allergic to gluten proteins but who still would like to eat bread…
As far as the potentially excessive softness of the cookie, the experimenter believes that substituting bread flour for “all-purpose” flour and baking for up to 20 minutes should solve the softness problem, resulting in a chewier texture which the experimenter believes will be more appropriate.
The experimenter also notes that a second batch of the same recipe, cooked for approximately 20 minutes at ~205°C (~400°F) were nearly burned, though they did come out firmer but drier in texture. The flavor was still judged superb, other than the slight burnt note. Subsequent versions of this recipe will revert back to the original 190°C cooking temperature.
Obviously, further research is needed to determine the correct modifications to achieve perfect texture, and of course, to broaden the sample size of of the taste-testing group, and the experimenter should be given a sizable grant and a nobel prize for this research. Well, a grant at least.
Or at least some praise or something. Or a cookie, except that the experimenter obviously already has some.
[1] Munro IC, Berndt WO, Borzelleca JF, Flamm G, Lynch BS, Kennepohl E, Bär EA, Modderman J:”Erythritol: an interpretive summary of biochemical, metabolic, toxicological and clinical data.”;Food Chem Toxicol. 1998 Dec;36(12):1139-74.
[2]Dean I, Jackson F, Greenough RJ:”Chronic (1-year) oral toxicity study of erythritol in dogs.”;Regul Toxicol Pharmacol. 1996 Oct;24(2 Pt 2):S254-60.
Dangit, I’m out of time. I was going to try out some crazy ideas with my Ginger Cookie recipe, too, and see if I can develop a Kombucha culture from scratch. Guess that’ll have to wait, because it’s bedtime now. Back to work in the morning…
Brew; Eat it; Feedback Solicitation; Food Science; Hillbilly Biotech; Me, me, me; Microbiology; Play With It @ 06 Dec 2009 09:18 pm by Epicanis
“Kimz” left a comment over on the blog’s “About” page asking about geotagging of audio, so I thought that was a good excuse to bring the topic back up here.
Even less audio (and video, for that matter) seems to get geotagged than pictures, and even though more photographs online are getting geotagged automatically by GPS-enabled cellphones, I still usually find myself disappointed when running into an interesting photograph online and finding no geographical information in the image telling me where it was taken.
I have the same kind of interest in where and when other kinds of recordings where made. I’m obviously not the only one: the Freesound project also maintains geographical information for some of the sound recordings they have. Unfortunately, although they SAY the recordings are “geotagged”, they’re not.
Take this sound sample, for example. It’s an ambient sound recording from the lobby of an office building, and you can see there’s a link to a map showing where the recording was made. However…if you download the actual sound file, there is not geographical information associated with it at all. If the geographical information is not directly attached to the file, then I maintain that the file is not “geotagged”.
Let’s say I work in a very odd sort of specialty shop, and one day we get in a shipment of inflatable anatomically-correct life-sized Australian marsupials. “Price-tag these”, the boss says. The next day someone asks the boss how much the inflatable male platypodes are. “Isn’t it on the price tag?” “There is no price tag!” When the boss chews me out for not doing my job, do you think I’ll be forgiven when I explain that I DID “price-tag” the shipment…by writing down the prices in a little notebook that I keep with me, separate from the actual merchandise? No? Then keeping the geographical information in a little database that your server keeps separate from the files isn’t “geotagging”, either!
I suppose the bizarre and potentially incoherent nature of that example just serves to illustrate my over-busy and under-slept state. Anyway, the point is that I’d love to see more geographically-tagged media, and I open up this post for discussion of how, why, and what to geotag. (For “How”, I would offer up my “Geostrings” proposal as an option that ought to be feasible for virtually any kind of media…).
If they ever get around to publishing “Mapping Hacks, Volume 2″, what should the entry for geotagging media include?
Computer Nerdity; Feedback Solicitation; Methods; The Big Room; Where Was I?; neogeography @ 12 Nov 2009 09:30 pm by Epicanis
Looks like the truckloads of candy-seeking larvae are done finally. Wretched little urchins now get driven from block to block rather than walking the neighborhood like we did.
(It doesn’t actually bother me as much as that makes it sound, I just like having an excuse to say “wretched little urchins”…which reminds me – I have only about a month to get a cheerful flashing “Bah! Humbug!” sign built…)
The only thing that really annoyed me is the fact that having to be ready to be interrupted by another horde of costumed consumers meant I couldn’t really spend any of the evening getting into anything requiring any real attention…which means the 113g of CaCl2.2H2O I’ve got sitting here now to go with my Xanthan Gum has been left neglected, and I still don’t know if I can make Xanthan Gum gel into beads the way you can with sodium alginate. I figure it must be possible, given that both Xanthan gum and Alginate (among others) were all formed into little “bio-booger” beads using the same kind of process in the paper I discussed in Episode 2 of my little audio oggcast. Perhaps I’ll have time to find out tomorrow.
For now, it’s time for bed. Daylight Losings Time starts tonight, so if the critters allow me to actually sleep, I ought to be well rested to attempt some serious lake-spanking in the morning – there’s supposedly a resort on the shore of the lake that has a sushi bar, and the idea of being able to paddle out for sushi amuses me. It looks like it’s at least 9-10 miles away, though, so it’ll be a long trip if I attempt it. Hopefully I’ll have time left after that.
Also, the developer of the libdmtx datamatrix barcode encoder and decoder software posted a recent comment on my previous post about the software and its potential uses – looks like some interesting projects going on there, including one intended to generate ID cards that only legitimate authorities could read (so as to prevent identity theft).
P.S. Anybody know how to build a really good (but simple) ozone generator for sanitization purposes? Or the effective pore sizes of commonly available materials like plastic wrap? Or if a corporate entity can be a shareholder/partner in a Limited Liability Company?
Computer Nerdity; Eat it; Feedback Solicitation; Food Science; Hillbilly Biotech; Me, me, me; Methods; Microbiology; Netcasts; People are Lazy; Play With It; biochemistry @ 31 Oct 2009 08:10 pm by Epicanis
Yes, I’m still here – though I don’t know if any of YOU are.
The pay at my job is somewhat low for the skillset it requires, but makes up for that by having a very reasonable workload, a pleasant work environment, and certain perks – like access to the electronic journals that my employer subscribes to. I added an RSS feed from pubmed intended to cover my main interests – basically edible and industrial microbiology and biotechnology. Every day, a list of 300-600 or so new scientific articles pops up in my feedreader and I scan through the titles looking for anything interesting to me. Unintentionally, my selection appears to also result in quite a bit of diabetes, obesity, and sports medicine research. Lately I’ve taken a moderate interest in our own most blatantly bacterial components, the mitochondria.
Mitochondria are kind of like a nearly 2-billion-year-long case of typhus (or Rocky Mountain Spotted Fever, if you prefer). After infecting our ancestors (and now us) for so long, they’ve been reduced to dependency on living in our cells. Perhaps a bit like the progression from wolves to Chinese Crested dogs. On the other hand, having thoroughly domesticated them, we get a lot of use out of them, and couldn’t live without them. Their ability to harness the electron-sucking power of oxygen means we get almost 20 times more energy out of our food than we otherwise would, which is a good thing since biologically speaking, keeping the hideously complicated mess of biochemistry that makes up a human body takes a ridiculous amount of biochemical energy compared to that of normal organisms (i.e. prokaryotes).
Lately in the stream of new publications I’ve been seeing a number of papers suggesting that a lack of proper mitochondrial activity might be related to obesity and related problems (e.g. “metabolic syndrome”, type 2 diabetes and insulin resistance, obesity-related “inflammation”, and so on) and even some age-related problems, both physical and mental. There is some seriously interesting research going on into treatments to potentially stimulate mitochondrial activity and whether this might help solve a number of health problems.
So…take good care of your mitochondria. For the past couple of weeks I’ve been trying to pay special attention to properly feeding my mitochondria and making sure I take them for regular walks (and paddling trips and so on). It could, of course, be purely psychosomatic, but right now I feel better than James Brown…
There’s a fair amount of rational skepticism over using drugs or nutritional supplements to stimulate mitochondria, but here’s a tip that I suspect everyone’s doctor would accept: make sure you take your mitochondria for regular walks. Frequent exercise (particularly endurance exercise) seems to be a scientifically well-accepted way to induce production of more mitochondria.
But now I have to go to bed. My main complaint with work these days is that it eats up essentially my entire day, leaving me with just enough time for some household chores between getting up in the morning and going to bed in the evening. Not their fault I live almost and hour and a half from work, though (and at least the commute is through relatively low-traffic and scenic terrain.). Still, it makes it hard to get blog posts and podcasts done (episode 4, on the subject of “heat-fixing” of bacteria for microscopy – particularly Mycobacterium tuberculosis – will be out as soon as I can manage. Still pondering the subject of Episode 5. I’m saving the “Two Mass Spectrometers, High Performance Liquid Chromatography, and a Female Donkey” episode for later when I manage to surpass the “nearly 3″ listeners that I seem to be stuck at…)
Eat it; Food Science; Freakish Eukaryotes; Grossly Oversimplified Science; Me, me, me; Microbiology; Netcasts; People are Lazy; Thinking is Work; Why Does It Work?; biochemistry @ 11 Oct 2009 08:41 pm by Epicanis
FINALLY – with this vowel movement I am finally over this recent bout of podstipation. Episode 3 of “Stir-Fried Stochasticity” is finally up. Today’s paper is:
Bowden G, Thatcher W, Stein RS, Hudnut KW, Peltzer G:”Tectonic Contraction across Los Angeles after Removal of Groundwater Pumping Effects”; Nature; 2001; vol412; pp812-815
You can download the audio or (if you are using a modern-enough web browser) listen to this episode directly here.
I would appreciate any constructive or at least mildly witty feedback – please post in the comments below…
Uncategorized @ 07 Sep 2009 07:43 pm by Epicanis
Episode 3 of Stir-Fried Stochasticity should be recorded and posted soon. I had intended to already have it done, but there have been…delays.
Most recently, I had to drop everything to take care of the Minister of Chew Toys here at the Asylum for the Sufficiently Nerdy. Cornelia (our dog) came down with her yearly sudden, extremely messy and foul diarrhea problem. After getting everything cleaned up, and a minimally-sleepful night of getting up every few hours to let the dog out to emit foul-smelling material and disgusting noises, I got her to the vet this morning and came home with the usual prescription for Metronidazole and special food. If previous years are any indication, the symptoms should be over by tomorrow.
But, even as I cleaned up the foul mess that greeted me when I got home, I found myself wondering if the slimy material was being produced by the dog or by whatever bug was causing the problem. (Despite Episode 2 of Stir-Fried Stochasticity, I did NOT consider whether it could be turned into a food additive. Even I have my limits…) And, despite not wanting to be anywhere near the mess I was cleaning up, I found myself wishing I had a microscope.
And today, after the veterinarian took a look at a sample under the microscope (and let me look, too), and tentatively suggested infection by a Clostridium species, I found myself wondering if I could culture it, obtain a phage that infects the bacteria, generate and purify a huge sample of the phage, and then save it for next year and try to treat next year’s infection with it. And then I thought “Hey, if I also culture up the bacteria to produce a lot of that slimy stuff and purify it, I could make phage-containing bio-boogers (go back and listen to Episode 2 if you don’t know what I mean), which might be more effective!” on the assumption that the bacteria in question might also secrete enzymes to break down the slime that I’m assuming it produces, thus releasing the phage particles around the active bacteria…
And then I realized that if I had the equipment, supplies, and time right now (and was willing to deal with regulatory hassles involved in playing with Potentially Pathogenic Prokaryotes), I would probably actually follow through and try it…though I’d probably stop short of actually testing the treatment on my dog without some sort of approval and supervision by a real veterinarian. Even now I’m resisting a slight urge to save a small dried “sample” (which would be full of long-lasting spores that I would probably be able to culture later). Don’t worry, it’s not hard to resist…the point is just that the temptation is actually there.
I still insist I have very little interest in medical microbiology. Really.
At least I know that between potential digestive-tract phage therapy and probiotics, if we end up having to move back to where we came from for financial reasons, I might at least find a place for some graduate work in the “poop group” (sic) at my previous college institution if nothing else.
Meanwhile – Episode 3 is coming, honest! It’s a rather small but dense paper that explains how it’s hard to monitor the tectonic activity in the Los Angeles area because Los Angeles sucks. I’m hoping to get that recorded this weekend, along with the other mass of stuff I need to do.
Any words of encouragement and/or threats (or other useful or allegedly witty comments) may be posted below in the meantime.
Uncategorized @ 22 Aug 2009 10:23 am by Epicanis
After getting rave reviews from nearly four people for the pilot episode, I’m hopeful that Episode Two will be even better. (Seriously – I don’t think more than a handful of people even know this project is going on, but the few people who’ve listened and commented to me have been very encouraging so far.)
You can listen to and/or download the audio directly in either they shiny new spiffy Ogg Vorbis format or old-school .mp3 by clicking right here. As always, I’d very much appreciate comments, suggestions, questions, amusing limericks on the subject of the paper, etc. – feel free to post below, or you can email me at the usual location: epicanis+sf at bigroom.org.
This episode’s paper: Ding WK,Shah NP:”Effect of Various Encapsulating Materials on the Stability of Probiotic Bacteria”;2009;J. Food Sci.;vol.74 #2; pp M100-M107. Enjoy!
Uncategorized @ 09 Aug 2009 09:08 pm by Epicanis
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