I have a shiny new Android-based phone. I’d still rather have a MeeGo/Maemo one, but I got tired of waiting for something besides the expensive (though desirable) Nokia N900 to become available.
More to follow relatively soon, but I wanted to try out the beta-test version of the Android WordPress blog-thingie.
If you see this post, it works (at least well enough to get a basic post up-I still need to figure out how to do raw HTML from this thing…)
“Nero” here seems to be the only thing I can find growing in the stuff I put the Lyreleaf Sage flowers into. Maybe some kind of Brettanomyces yeast? I’m going to have to autodidact myself into a better understanding of yeast ecology. Not to mention yeast physiology – am I seeing two cells undergoing postconjugational sporulation there in the middle of the image?
I’m a bit puzzled that I don’t see anything that looks much like bacteria in here. “Everything is everywhere” right? And yet, I’m not seeing any obvious acetic-acid bacterial growth here. Kind of a bummer, since that’s REALLY what I’m after here overall, but that’s okay. I can play with Nero in the meantime. Anybody know if you can make (palatable) leavened dough with Brettanomyces yeasts?…
I still need to go try the same cultivation on some “Texas Bluebonnets” and “Indian Paintbrush” flowers, since those are blooming around here now too. I figure there’s bound to be some Gluconobacter floating around out there somewhere. I suppose in the worst case, I can try cultivating some off of fallen fruit later in the summer when stuff starts getting ripe.
This unassuming little flower just happened to be conveniently near here. As far as I can tell, it’s a “Lyreleaf Sage” (Salvia lyrata). I plucked a flowering section and dropped it into a container of my special selective media a couple of days ago. It’s starting to get a little flocculant and there’s a faint “fermenting yeast” smell, so there’s something going on in there. I didn’t see much yet last night when I took a closer look, but I did see these, which I assume to be pollen grains from my bioprospecting sample.
See?
I had to do a Fred Transplant last week. A grey fuzzy mold had taken up residence in on the sides of the jar above Fred’s liquid culture, so I set up a fresh container with fresh water and flour, and dipped a spoon down the center of Fred to the bottom, pulling up just a tiny amount of the stuff in there. Then I mixed it into the fresh stuff and covered it with plastic wrap (instead of a paper towel this time.)
Fred smells like Swiss Cheese Feet right now, but he’s obviously still growing, as you can see from last night’s “Gram Stain” microscopy. The slightly blurry light-red-brown lumps are, I believe, yeast cells, possibly Saccharomyces boulardii, since I dumped a capsule of supposedly-still-viable “probiotic” yeast of that species into Fred previously. I have no idea who the bacteria are in here at the moment. I did also see a small number of longer, thinner bacterial cells in there (presumably Lactobacillus) though most of them are the ones you see here.
Meanwhile, I’m about to dig out the still-unused Hillbilly Autoclave and try it out on the media I’m mixing up to try to obtain a culture of genuine wild “native flora” vinegar/kombucha yeast-and-bacteria to play with from the local wildflowers that are just now getting into full bloom.
My starting recipe goes something like this: I mix up about 2 Liters of distilled water with about 100g of glucose (“Dextrose”/”Corn Sugar”), 100g of sucrose, 500mg of L-Arginine, and enough phosphoric acid to drop the pH down to about 5.5 to 6.0. That is intended to be then poured into small “canning” jars in about 100ml amounts and pressure-cooked for at least 15 minutes to sufficiently sterilize and seal them. Meanwhile, a single generic-brand children’s chewable vitamin is crushed up and dumped into a 4-oz bottle of cheap vodka and well shaken.
Then when it comes time to go bioprospecting, I’ll pop open the jar of acidic sugar solution and add about 5ml of the cheap-vitamin-vodka to it to give me about 2% ethanol, and then go find some flowers to cut off and dump into the jars, which will be loosely covered with foil (to let air in but keep dust out) and put in a nice quiet cupboard to grow for a few days.
Hypothetically, the only things that are likely to grow in that will be microorganisms associated with vinegar-making. At some point I’ll also make up a batch of sweet black tea and see if I get a kombucha-like culture going in it, and make up some solid media to try to isolate individual microbes from it.
More to follow, but at least I think I’ve got thee blog software all updated and working properly again now.
I need to do some microbiology and cooking this weekend….
I got an unsolicited email asking for help boosting search-engine rank. Me! Complete with the particular phrase they wanted linked and everything. Normally, I’d be inclined to sneer and make mocking comments about marketers…except in this case it’s actually for something completely relevant…and kind of nifty, so I’m going to do it…
A company called ASPEX makes what they’re calling an “Affordable Desktop SEM”. Not having a gigantic corporate budget, government grants, or wealthy patron/matron backing me I’m having trouble thinking of ANY Scanning Electron Microscope (there’s that phrase and link…) as being “affordable”, but I’ve got to admit I want one now.
That’s not all, though – ASPEX (no, I don’t know why they capitalize the whole name) has a mind-blowingly cool offer going on right now as part of their promotional campaign. “Send Us Your Sample” – just like the name suggests, they’re soliciting samples to image and post. I know I’m planning to go for it. It’d be nice to have both old-school light-microscopy images AND Electron microscopy imagery of Fred (my sourdough culture in progress) to post.
I’m not sure what kind of magnification they can offer – The submission form is pretty simple but doesn’t say – but I’d be really interested to know if I’ve got any bacteriophages in my sourdough slowing down the lactic acid bacteria growth…
I would like to add that I’m getting no particular compensation for this post, but if anyone from ASPEX corporation wants to upgrade me to “paid shill”, I wouldn’t say “no” to an SEM of my own…
No? Dang.
Anyway, for anyone who hasn’t given up on my blog despite the slow updates lately, thanks. There will be more photos, along with other impending microbiological nerdity. And food – sadly, I have not managed to get time to actually make the first of the new pie that I’ve invented in time for Pi Day (“3.14″…March 14…”Pi day”. Insert joke about doing something at 1:59am and laugh track sound here…), but “pigsfly pie” will actually exist soon. Honestly.
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…
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…
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…
(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…
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