Category: Methods

“How To Do Stuff”

Fred Transplant: Success!

A Gram-stained view of yeasts and bacteria in a sourdough culture named 'Fred'.

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.

Even Scanning Electron Microscope manufacturers have marketers…

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 tiny Scanning Electron Microscope manufactured by ASPEX 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.

Audio Geotagging

“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?

YOU DANG KIDS GET OFFA MY LAWN!

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?

Yummy mold!

Fuzzy mold growing in a petri dishYes, I mean “mold” as in “fuzzy fungus”, not as in “something you put JellO® in to harden into a funny shape”. I’m not even talking about “Blue Cheese”, though blue cheese is pretty good too. I’m actually referring to Fusarium venenatum.

Okay, the picture linked here is actually F. oxysporum, one of several Fusarium species that are crop diseases (mmmmm, rotted moldy potatoes…), but I haven’t found a picture of a F. venenatum culture yet. Anyway, before going to bed I just wanted to mention that I’ve run into the first genuinely good “meat substitute” that I’ve tasted so far, and it’s made of mold.

They evidently grow it in vats, dry it into mats, mix it with some egg white to hold it together, and then make meat-like food product out of it. “They” being Astra-Zeneca, who appear to be the owners of the “Quorn®” trademark.

The chicken-like food product (“Chik’n”) patties they make are actually passable imitations of chicken, and actually taste good. They make a breaded Gruyere-“Chik’n” patty thing that I will probably go out and buy more of, of my own free will – which will be a first for “vegetarian” food for me.

Makes me wonder what I’d get if I subjected another known edible mold like Penicillium roquefortii (Mmmmmm…Blue Cheese) to the same process. Would I get blue “meat”?…

And, no, I’m not actually a paid shill for Astra-Zeneca or Marlowe Foods (who distribute the “Quorn®” products), though as I mentioned a while back to the dairy industry in my “Margarine makes you stupid” post, if anyone wants to HIRE me as a paid shill independent advocate, I could sure (yes, still) use a good microscope. Come on, Astra-Zeneca! A fancy biotech company such as yourselves must surely have dozens of surplus microscopes laying around!…

“Improvements in the Fermentation and Maturation of Beers”

Judging by my webserver’s logs, almost nobody actually bothers to click through the blog-carnival host’s site to read my Giant’s Shoulders” posts. This could be due to a secret conspiracy involving famous bloggers and several shadowy government agencies. I suppose, though, that there’s a chance that simply nobody but me is that interested in non-medical microbiology. Well…today’s post is an attempt to disprove that concept, for what aspect of non-medical microbiology could be more universally appealing than beer?

Unfortunately, in the middle of trying to assemble this posting, I see the February host has decided to put the carnival up a day early, undercutting my experiment. See, I told you it was a conspiracy! I suspect the Secret Cabal of Popular Bloggers was getting pressure from the Trilateral Comission, the NSA, and Pepsico® to silence me, so they had to do it. At least being forced to miss one, I am now free from the “I’ve been posting to these since the beginning, I can’t miss one now!” treadmill.

That means, loyal readers, that you get to see this post a month before everyone else! Hooray! Stick it to The Man™! Comically paranoid rantings aside, it also means I can split this up into more than one post, which may be more readable considering how much ground the article in question actually covers. Today’s Classic Scientific Paper is:

Nathan, L:”Improvements in the fermentation and maturation of beers.”; 1930; J. Inst. Brewing; 36; pp538-550

I ran across this reference recently while working my way through an industrial microbiology text[1] that I checked out of the campus library. According to the author of this text, “The use of cylindro-conical vessels in the brewing of lager was first proposed by Nathan (1930)[…]”, referring to the now-ubiquitous style of metal fermenter seen in small brewpubs and “MegaBladderwashCo” large-scale industrial breweries alike. Based on this I had expected the reference to be a digression on the design, construction, and testing of the fermenter. When inter-library loan managed to get me a copy of the paper, I found something much more involved.

The paper is a presentation made by Dr. Leopold Nathan in 1930 to the Scottish section of the Institute of Brewing. The topic was not simply a fermenter design but the entire “Nathan System” of brewing which appears to be the basis of modern large-scale brewing, especially for Lager-type beers. At this point, Dr. Nathan had apparently already been developing this system for about thirty years (apparently starting with a German patent in 1908, which I’ve yet to find a copy of), so as you might guess it was not just a single invention but a whole collection of them. Compared to the more rustic techniques frequently in use at the time, the “Nathan System” of brewing promised to provide faster production, more consistent results, and a better final product. It does this mainly by improving the removal of “trub” (the cloudy bits of protein and such that settle out of the malt-water – the “wort” – after you boil it), preventing infection of the beer with undesirable organisms during the cooling, hops-infusion, and aeration, and by eliminating the need to “age” the brew to make it palatable. The most important improvement in the “Nathan Process” seems to be how he treats the wort between boiling and “pitching”.

—
For anyone unfamiliar with the brewing process, here’s a Grossly Oversimplified review of the steps:

  • Boil some malt-sugar dissolved in water to sterilize it and to help coagulate the “trub” proteins so they’ll settle out of the liquid.
  • Cool the malt solution and aerate it so that the yeast will grow in it.
  • “Pitch” your yeast into the now-cooled-and-aerated malt-water, in a container that will keep air out while letting out the carbon dioxide bubbles that the yeast will give of during the fermentation
  • Wait until the yeast get done fermenting, then put the resulting liquid into bottles/kegs/casks/whatever.

—

Diagram showing the containment vessel, cooling system, and sterile-air generator for the 'Nathan method' of brewing
I’ve added a couple of labels to that image from the paper, which I’m guessing was itself copied from a contemporary patent of Dr. Nathan’s. There are two purposes to this part of the Nathan Process – To cool and aerate the wort quickly without exposing it to risk of contamination, and to move trub and volatile sulfur compounds that would otherwise make the brew taste and smell funny. The hot boiled wort is pumped directly into an insulated vat (labelled “A” in the diagram) from the boiling kettle. At this stage the wort is hot enough to prevent anything from landing in it and growing. Then, the hot wort is pumped from the top of this vat into a clean-room containing a cooling device that the wort is poured on, cooling and aerating it as it flows through. Infection is prevented here by the fact that the room has a continuous stream of “sterilized” (or at least well-filtered) air, which is exhausted through the vent in the ceiling. The cooled, aerated wort is then pumped back out of the room and into the bottom of the insulated container below the still-hot wort.

Because of the large open cooling room with its constant stream of clean air, the cooling and aeration step also allows the volatile sulfurous compounds of “jungbukett” (The “Bouquet of Youth”; the unpleasant smells and tastes of immature beer, described in this paper as ‘onion-like’) to evaporate off and be carried away. Since waiting for these compounds to break down was apparently a primary reason for having to “age” lager before selling it, this not only improves the quality but eliminates the need to store the beer for months after fermentation.

The now-chilled wort then rests back in vat “A” and the trub settles out onto horizontal plates inside the vat, where it stays behind when the clarified wort is pumped out to the fermenters.

I did some poking around, and this appears to be what is described in US Patent# 1,581,194 (application filed in August of 1921), in case you are bored and want to look that up. If not, or if you don’t want to deal with the frustrating hassle of trying to view TIFF files in your browser, I intend to provide a followup post with some more details of the process and some interesting bits I found in it, and I’ll include a pdf of the patents, assuming anyone wants them.

Oh, one last thing – I’ve had no luck getting any biographical information about Dr. Leopold Nathan. Unfortunately when you search for “Leopold Nathan”, the results are clogged with references to a murdering smartass named “Nathan Leopold” instead. Doesn’t Google™ realize that brewmeisters are far more important than obscure murderers? No pictures of him, either, so I can’t even say whether his hairstyle is cooler than Eduard Buchner’s or not.

[1] Stanbury PF, Whitaker A, Hall SJ:”Principles of Fermentation Technology (2nd edition)”; 1995; Elsevier Science, Ltd; Tarrytown NY

I have a shocking confession to make.

I think I may be a nerd.

No, no, don’t try to deny it. I think it pretty much has to be true for someone who reads a 10-page scientific paper (hover or click here to see the reference) in order to learn that bacteria-snot is slimy. Yes, I am a nerd. And for that I am deeply, deeply….

Oh, who am I kidding? I like being a nerd.

Stainless Steel fermenters at a breweryFor one thing, being a nerd allows me to fully enjoy one of the perks that my job gives me – namely access to a lot of scientific papers that I otherwise wouldn’t be able to afford to obtain access to from the greedy [insert your favority profanity here] who insist on charging $30 for permission to look at a decades-old articles for a day. I should add that this perk includes Inter-Library Loan for articles that I can’t get online, and the service on campus is great so far. Same day delivery of a classic article from 1930 in what I’m guessing most people would probably consider an obscure journal.

It doesn’t have quite the same thing in it that I expected from the source that pointed me to it, but I think it can still be considered “classic”. I need to re-read it more carefully to make a final decision on this, but I think I have my next “The Giant’s Shoulders” article in time for this month’s upcoming issue. And, yes, the picture attached to this post is a hint (and, no, it’s not directly related to the bacteria-snot article mentioned above in any way…)

Über alkoholische Gärung ohne Hefezellen

In my last submission to “The Giants’ Shoulders” blog carnival, we saw how the famous surgeon Dr. Joseph Lister deftly demonstrated definitively that fermentation processes were caused by live microbes rather than some sort of mysterious soluble substance that just happened to be associated with microbes. In today’s episode, we will see how Eduard Buchner definitely demonstrated that fermentation was caused by a soluble substance that was associated with microbes, and no microbes are actually needed.

Better still…they’re both right. “Wait…what?” Read on, O Seeker of Microbiological Knowledge, and be enlightened by this month’s entry: Continue reading Über alkoholische Gärung ohne Hefezellen

Saccharomyces cerevisiae – Shameless Libertine!

I’ve been wondering about starting my own little yeast-breeding operation. I haven’t yet figured out where you can by the necessary teeny, tiny yeast-sized versions of the Implements of Extremely Impolite Probing that breeders of other species use, but even before that, I need to understand yeast reproduction better in the first place.

I had gotten an impression from some of the stuff that I’d read in a Genetics textbook and online that yeasts were normally haploid, and only became diploid briefly during mating (you see, when an “?” haploid yeast cell and an “a” haploid yeast cell fall in love, sometimes they’ll…). On the other hand, while reading a review of yeast virology[1], the author explicitly wrote that yeast cells are normally diploid. How to resolve this issue? Plus, I was wondering how, if I happened to have a pure culture of a haploid yeast, how could I tell if it was “a” or “?”?

I recently realized that there was one Dr. Bryk in the department where I work who specifically researches yeast chromosomes…so I asked her…

Continue reading Saccharomyces cerevisiae – Shameless Libertine!

Nerd Reading Spasm!

Did I mention the place I work has some amazingly spiffy perks for a nerd like me?

Last night, I was poking around pubmed looking for references to yeast and erythritol (namely, do yeast interact with it, and will they metabolize it?) I found precisely one relevant reference. From 1975. In a Czechoslavokian microbiology journal. A no-longer-existent Czechoslovakian microbiology journal. Even though it was a journal published in English, I didn’t figure I’d be able to find the article I was looking for. It did turn out that the greedy (insert long string of profanity here) anti-open-access “SpringerLink®” Netherlands organization has an electronic copy of the article…which I can get limited access to for a short time for a mere $34.00. Not going to happen, obviously.

Just in case the college had a subscription that would let me get to the article at no extra cost, I checked. No such luck. But…

…The campus medical science library just two buildings over from where I work has dead-tree editions of essentially the entire journal! Im name des Nudelmonster! Instead of paying $34.00, I got a photocopy of the article for about $0.50. Bonus: As I had hoped, the article[1] reports that erythritol is not metabolized by yeasts, although it is taken up to a small extent. That means I can add erythritol (or xylitol or sorbitol or whatever) to must or wort, and it’ll still be there when the yeast finish, leaving the resulting beverage still sweet. Hooray!

Plus, I was also able to get access to an electronic copy of a review of the uses of poly-?-glutamate[2], which I was bemoaning not having access to over on an interesting Small Things Considered post recently.

Speaking of reading, one thing I really could use are any worthwhile books on the general subject of applied/industrial microbiology, bioprocess engineering, fermentation, and so on. “Worthwhile” here means practical texts that are A)primarily about microbiological processes (as opposed to, say, bioengineering of plants) B)Reasonably technical, and C)Either “not very old” or “very old indeed” (I collect old science books).

I’m not a fan of Amazon.com’s abuses of the patent system, but I’m in a hurry since it’s past my bedtime already. Therefore, purely as a sampling of the kinds of books that sounded interesting to me, here is a selection in more or less random order of books that came up in a quick search on amazon.com. Anybody out there have any other suggestions?

Continue reading Nerd Reading Spasm!