Category: Microbiology

Posts that are Microbiological in nature

Coming Soon to a Bigroom.org blog post near you!

I got a little money for Christmas, but I’m feeling quite guilty as I didn’t really have the time and money to reciprocate in advance. I also haven’t been able to figure out what to spend it on until now. Now, I have a solution for both problems.

Xanthomonas campestris growing in a petri dish and exuding slimeI intend to spend it all on fermentation-related food ingredients and do some experimentation with sweet-tasting foods. Initially, in addition to flavors (spices and whatnot), I need to track down bulk quantities of:

  • Erythritol, which is a virtually non-caloric sugar alcohol which unlike sorbitol and so forth is not normally prone to cause gastric distress, and unlike Xylitol is not hazardous for beloved household pets. Better still, it actually is very tasty unlike that nasty hippy “Stevia” crap (which isn’t produced by fermentation anyway, as far as I know).
  • Food-grade Glycerol (“Glycerine”), which I hypothesize is close enough to the structure of Erythritol to mix well with it and help the erythritol dissolve (and hopefully prevent crystallization, much the same way the “corn syrup” does with sucrose).
  • Xanthan Gum. MMmmmmm…edible bacteria-snot. (Okay, for all that this sounds disgusting, it’s really somewhat similar to pectin, which like xanthan gum is a polysaccharide. Pectin is just fruit-snot rather than bacteria snot. Dietarily, both count as “soluble fiber”.)

There are probably other ingredients I can come up with as well. For those of you out there who are owed gifts: Chewy candies, hard candies, baked goods, and/or beverages, what’s your preference for my initial experimentation? Assuming anyone’s interested, I will probably blog my results…

Meanwhile, I’ve also been thinking about geolocation, geotagging of audio and video media, and Asterisk again. I want to take the lessons learned from my playing with the “Where Was I?” prototype and turn it into a real geolocation system, integrating with Asterisk and Laconica (which turned out to be easier to set up than I’d feared – I’ve now got my own Laconica server at http://omniblab.dogphilosophy.net/laconica, though I need to sit down and activate the IM integration (Twitter may have abandoned IM, but it reportedly works fine in Laconica).

It also turns out that you can use Asterisk with cellphones(!), at least if they have bluetooth. That’s handy to know…

Argh – too much to do, not enough time!…

Obscure scientific papers, Mad Science, Travel, and other randomness

First – an amazingly astute observation that I’m ashamed to have not previously noticed myself (click image to go to it’s original site and see it full-size…):
Most 'Mad Scientists' are actually just 'mad engineers'...

I’m proud to say that I think testing Mad Hypotheses is great, and will continue to try to be a Mad Scientist. And a “Dirty Old Man” someday, but that’s a whole separate issue.

Second – I am really loving the perks of my new job – namely access to the college library system. I had previously mentioned (see last couple of paragraphs) a certain article that I wanted to get my hands on:

Greenberg LA:”The Definition of an Intoxicating Beverage”;Q J Stud Alcohol. 1955 Jun;16(2):316-25

Not only does the medical library have copies of a Czechoslovakian microbiology journal, the main library had a set of this old journal, too. I have my bedtime reading for tonight…

Thirdly – Another Giant’s Shoulders carnival has come and gone. I now believe that Eduard Buchner had hit upon not only a useful truth of living systems, but also a nifty alternative “mad scientist” hairstyle. Now I need to come up with one for next month. It’s been getting me thinking, though. That blog carnival is intended for “Classic” papers. Implied is that the papers are somehow important to the development of some scientific field or other. I’d like to see a variation on the “old papers” theme focussing on random old papers (where “old” might mean a few years or decades, depending on the subject) that people have found useful or interesting. Stuff that isn’t necessarily ground-breaking and has perhaps been forgotten or lost to obscurity but still has useful things to teach us. Naturally, I’m thinking especially Microbiology (and especially Microbiology other than Medicine) and Food Science. The Carnival could be called something like “Second Chance Science” or something of the sort. Just a thought.

Fourth – speaking of “Microbiology Other Than Medicine” and Food Science, apparently The National Academies of Science want to know what scientific topics people most want to read about. As usual, “microbiology” appears to have been relegated in their breakdown to merely a subset of either medicine/diseases, “biology”, and perhaps a small subset of “energy” and “Feeding the World” (no, seriously). The survey includes space to tell them what they’re missing – I heartily encourage anyone who cares to make sure you take the survey, and mention industrial and environmental microbiology and food science as subjects they shouldn’t continue to neglect.

And, finally – next week I need to make a very-long-overdue run back up to Idaho to grab some things from the old house and make sure it’s still standing, the water’s really turned off, nothing unnecessary is running, etc. 1600 miles of driving each way. Ugh. Anybody got any good recommendations for things to listen to on the trip? Other than having a chance to finally grab some things that I am missing, maybe I’ll at least have a chance to visit New Belgium Brewing Company again, since my route goes right past it. So long as I’m not driving by on Christmas day (when I assume they’ll be closed) I may have a chance.

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!

“Top Ten Favorite Microbes” proto-meme…

Dr. Joseph over on the “(It’s a…) Micro World (…after all)” blog posted a list of his ten favorite microbes. After showing up in the comments of his post and being a wiseass about E.coli and Gram staining, the least I can do is participate here. Besides, it’s a great idea. Therefore here are ten of my current favorite microbes:

Continue reading “Top Ten Favorite Microbes” proto-meme…

“On the lactic fermentation and its bearings on pathology.”

Lunchtime – time to get this posted…(Let me know if this page is loading way too slowly…)

For this month’s “Giant’s Shoulders” I offer you mouthwash and yogurt.

Indirectly, at least.
Continue reading “On the lactic fermentation and its bearings on pathology.”

Stir-Fried Random Ep 02:Sex, Violence, and Cinnamon Bears, y’all!

Only about five more days until the next “Giant’s Shoulders” blog carnival. I still need to pick a paper. ARGH!
(UPDATE 20081126: I’ve removed the embedded flash player – it seems to ignore me when I explicitly tell it NOT to automatically start playing rather than waiting until you intentionally hit “play”. Sorry for anyone annoyed by the autoplay. The embedded player will not return until I solve this.)

Meanwhile, here’s this week’s episode of “Stir-Fried Random”, weighing in at a MASSIVE 12 WHOLE MINUTES or so. As before, there’s an “<audio>” tag pointing directly at the Ogg Vorbis audio for those of you running a beta of the Firefox 3.1 series, a recent version of Opera, or (I believe) the current Safari on a system with the Ogg Vorbis Quicktime component installed. There is also the usual embedded Flash®-based mp3 player and direct download links for both versions.

Somebody please let me know if I’m making a fool of myself here… Anyway, here are the show notes:
Continue reading Stir-Fried Random Ep 02:Sex, Violence, and Cinnamon Bears, y’all!

Stir-Fried Random: Alferbeetagama!

(Update 20081104T1050: added a minimal embedded flash-based player at the bottom of the post, if you’re willing to settle for mp3 quality and want to listen from your web browser…)
(Update again 20081126: I wish I had realized before that the stupid thing was autoplaying despite explicitly including “autoplay=false” in the parameters. I’ve removed the embedded player again until I find a way to prevent autoplaying. Sorry about anyone that was annoyed by this.)

I was going to post this last night, but there appears to have been another bout of database connection errors again at my ISP (“host blocked due to too many connection errors”). I’m guessing either someone is DOS’ing the database server or one of the other users had some very badly behaved custom code running. They’ve got it fixed now, so here we go…

After staying up too (insert profanity here) late again despite having to get up extra-early this morning to vote before work…here’s the first real episode of Stir-Fried Random. Still only about 10 minutes long – I’d like to make it longer, but it’ll still probably take a few episodes of building up to it. An actual shiny new <audio> tag is included for those with bleeding-edge browsers that support it (let me know if it works – hypothetically the 3.1 Beeta[sic] version of Firefox and I believe the most recent Opera support this.). Otherwise, direct-download is available below the show notes:
Continue reading Stir-Fried Random: Alferbeetagama!

Phylogenetic structure of the prokaryotic domain: the primary kingdoms.

Ike’s comin’ right for us, so I don’t know when the my power and internet access will die, and if so how long it’ll be before it comes back. However, while I’m still connected I wanted to contribute something again to this month’s The Giant’s Shoulders blog carnival. Since it’s in three days and there’s a chance our power might be out when the deadline passes, I figured I’d better hurry. Because of the hurry there are no fancy graphics nor even too much explanatory text here, but I’ll do what I can. Fortunately, the basics of today’s post isn’t too complex.

Depending on how rigorous your biology education was, there are a variety of ways that you might tend to categorize the fundamental types of living things. You might vaguely recall something about “five kingdoms”, which as I recall were “Animals, Plants, Fungi, Protozoa [e.g. amoeba], and Bacteria”. You might just segregate everything into either “animal” or “plant”. If your memory of biology education is a bit stronger, you might remember that “bacteria” are a separate group from the true plants and animals. A step more precise and you may split living things into the two domains of “prokaryote” and “eukaryote”.

The “plant” and “animal” distinction is pretty classic – until comparatively recently, bacteria were assumed to be “plants”, just as fungi (“plants” that lacked chlorophyll) were. Non-photosynthetic bacteria were referred to as “schizomycetes” (literally “fission” [splitting in two] fungi, because they reproduce by splitting from one cell into two rather than forming spores), while bacteria with chlorophyll (cyanobacteria or “blue-green” algae, and possibly the “green sulfur bacteria”) were designated “schizophyta” (“fission plants”).

Within the last fifty years or so, though, it’s become obvious that bacteria were a different type of life from fungi, chlorophyll-containing plants, or animals. The latter critters have cells that in turn contain “organelles”, which are more or less very specialized “mini-cells” within themselves. The nucleus, for example, is a compartment within the cell where the cell’s DNA is kept and processed. Bacteria, it turned out, don’t have any of these organelles (in fact there’s good evidence that at least some if not all organelles used to be bacteria, but this post’s long enough already so I won’t go into that), and life was re-organized into the bacterial “prokaryotes” (“before nucleus”) and the “eukaryotes” (having a “true nucleus” – i.e. everything that isn’t bacteria).

Then, along comes Carl Woese, who spoils this nice simple dichotomy. In 1977, he published (along with G.E. Fox) the subject of today’s post:
Continue reading Phylogenetic structure of the prokaryotic domain: the primary kingdoms.