Category: Microbiology

Posts that are Microbiological in nature

I has a books.

I also has a bad grammar (curse you, internet!)

The front cover: 'Wine Microbiology - Practical Applications and Procedures'It’s slow going trying to get the mess up here in Idaho organized in preparation for the move to Texas, but I did manage to sacrifice a large number of my old books that I no longer need. Trading them in at the local representative of the “Hastings” bookstore chain got me a decent amount of store credit, and I was able to special-order this wine microbiology book I’ve been lusting after for months. It showed up a couple of days ago.

Very interesting so far, but I’m only a little ways into it. I’m still in the theory sections, so I can’t say if it covers yeast-mating or not (see previous two posts on this blog…)

Front cover: Wildbrews: Beer Beyond the Influence of Brewer's YeastPrior to that, I picked up a book I found at the local brewing-supply place in The Woodlands, Texas. It’s an entire book on the subject of Belgian and “Belgian-style” beers (like Lambic) fermented with “wild” yeasts and bacteria. It’s an excellent mix of history, science, travelogue, and “how-to”. I highly recommend it.

I noted with particularly nerdly glee that there are several breweries here in the U.S. doing non-traditional brewing cultures. At least one was brewing entirely with Brettanomyces yeasts! (Most traditional brewers and vintners shriek in horror at the thought of Brettanomyces in their brew instead of the standard Saccharomyces yeasts, blaming Brettanomyces for – you guessed it – “off-flavors“.)

That is so amazingly spiffy I can hardly stand it. I note that one of them appears to be only a few hours from the area we’re moving to. And two of them are in Colorado, more or less on the road between Idaho and Texas, so on my next trip down which is likely to be as early as next week, I may have to try to arrange to visit at least one of them and see if I can get a tour.

YEAST HERPES!

After my previous post, there are bound to be a few wiseguys/wisegals with dirty minds who couldn’t resist chuckling and wondering “yeah, well if yeast have sex, they must get STDs too, right? Ha ha!”

Yeah, well, very funny.

Of course they do.

In fact, that bottle of hefeweizen you may have consumed at one time or another was almost certainly full of Yeast Herpes!.

Alert readers will be wondering how I can have said “there don’t seem to be any viruses of yeast” in the last post and now be telling you you’ve been eating and drinking yeast-herpes all your life.

Here’s the deal: Generally when we think of viruses we’re thinking of little protein-wrapped packages of genetic material floating around freely, which can ultimately attach to and infect some cell, forcing the cell to make more copies of the virus which are released one way or another to continue the cycle.

Fungi, including yeasts, don’t seem to have any viruses that infect their cells from outside. They do, however, have “virus-like particles”, which seem like they were probably once more traditional types of virus, whose populations have lost whatever genes were necessary to be released from and infect into yeast cells. Without this ability, there’s only one good way for the virus to spread from an infected cell to an uninfected one: sex.

It would seem that there is so much yeast-sex going on that it ends up being a much more efficient way for the viral particles to spread. As a result, despite the fact that only the cell fusion of yeast-sex can spread the particles, there are very few known yeast strains that don’t carry double-stranded RNA virus particles (“L-A”, “L-BC”, “M1“, “M2“, and possibly some others), and there don’t seem to be any known yeast strains that aren’t infected with yeast-herpes.

It’s not actually “herpes” of course, but just like herpes, it is a retrovirus, which is actually merged into the yeast’s own DNA strands, and which is then transcribed into RNA to make virus particles.  These in turn get converted back to DNA by reverse transcriptase and integrated into the infected cell’s genome. The review I found whence I got all of this information[1] mentions three versions of these “retrotransposons designated “Ty1”, “Ty2”, and “Ty3”. (I assume that’s “Transposon, yeast”.).

If anyone stares at you when you yell “Yeast herpes! NOOOOO!!!!” and run screaming from the room next time someone offers you a beer, feel free to point them to this post for an explanation.

POSTSCRIPT: My previous post made it sound like yeast cells were normally haploid. The review paper I’m citing in this post makes an interesting assertion though: it states that in the wild, yeast cells are usually diploid, and haploid cells normally only show up as a result of environmental stresses. This is somewhat at odds with, for example, a more recent Genetics textbook[2] that I have in my possession, which explicitly describes that once the two haploid mating cells merge to form a diploid cell, it “promptly undergoes meiosis to produce four haploid ascospores”. This may perhaps be a case of a difference between growth in laboratory conditions versus normal environmental conditions. Perhaps in the natural environment which has not been carefully formulated to specifically promote yeast growth, diploid yeast cells persist until particular conditions induce meiosis. Hopefully the spiffy new book I have on order will show up one of these days and will hopefully have some discussion of the topic.

[1] Wickner RB: “Yeast virology.” FASEB J. 1989 Sep;3(11):2257-65.
[2] Snustad DP, Simmons MJ: “Principles of Genetics (3rd Edition)”; 2003; John Wiley & Sons, Hoboken NJ [ISBN: 0471441805], pp 42-43

Hot a on α action!

I’m busily house-hunting, but here’s a short science post anyway (even if for some reason I don’t appear to be showing up on the main “Just Science 2008” feed…)

Yeast have sex.

Of course, it’s a bit different from the way we multicellular organisms handle the process. For one thing, instead of “male” and “female”, they have “a” and “?”. No, I don’t know who came up with this bizarre naming scheme and yes, I also think whoever came up with it ought to be slapped, or at least forced to explain him- or herself in public.

Like humans, yeast cells have multiple chromosomes. Unlike humans, yeast are normally haploid (humans are diploid). [UPDATE: The review paper I cite in the next post suggests this statement may not be quite so clear-cut.]

Yeast spend most of their time reproducing asexually by “budding” – they make a copy of each of their chromosomes, then shove them all into a little “bud” of cell wall material along with enough enzymes to get started, and the bud then detaches and starts its life as a an independent cell. A clone of its parent cell, but independent anyway.

Yeast can also reproduce sexually, however. Both “a” and “?” cells excrete very tiny proteins referred to as “mating factors” – one type for “a” and one type for “?”. These factors inhibit DNA copying and budding in cells of the opposite “sex”, and instead helps trigger a process whereby cells of opposite “sexes” literally merge to form a single diploid cell. In athe same process of similar to meiosis by which reproductive cells of animals are made, this diploid cell can then make copies of each chromosome (giving a total of four copies of each chromosome – two copies of one parent cell’s chromosomes and two of the other). The parent cell then splits itself into four spores, each containing one more or less randomly-chosen copy of each chromosome. This little trick allows yeasts to reshuffle chromosomes around the population, helping to find and maintain the most advantageous combination of versions of each gene in the cell for the environment in which the population is living.

A practical side-effect of this is that you can effectively breed yeasts, by combining cultures with different characteristics. Hypothetically, many of the yeasts from each culture will end up “mating” with yeasts from the other culture, and if you have a good way of selecting cells that have the combined traits of both strains that you want you can easily make your own new naturally-recombinant strain.

This also seems to relate to why there don’t seem to be any viruses of yeasts…but I’ll save that for another post.

Grossly Oversimplified Science: Obtaining Pure Yeast Cultures

Various yeasts of the genus Saccharomyces (particularly the “Baker’s Yeast” Saccharomyces cerevisiae) represent quite possibly the most important bit of intentional microbiology that we have. We eat and drink the little critters and their byproducts in more or less every human culture that I know of, and are now getting more seriously into burning them, too.

As I’ve mentioned before, gluttony is my second most favorite deadly sin, so bread and booze microbiology is naturally of interest to me. It seemed worthwhile to look into developing my own yeast (and bacteria…but that’s for another post) stocks to brew, vint, and bake with, so I did some poking around. I dug out my copy of Rog Leistad’s “Yeast Culturing for the Homebrewer”, Peter Duncan and Bryan Acton’s “Progressive Winemaking”, a number of internet sources, and finally some scientific papers. I know, I’m a nerd.

I have so far not found much of anything about isolating yeasts from scratch – virtually everything seems to assume that you will “buy” your yeast from somewhere else, and aside from scientific papers most assume that you’re only bothering to culture your own yeast to save money by stretching the sample you bought to brew several batches before buying more yeast from “the professionals” again. This annoys me.

Unfortunately, I’m still on the road and haven’t had time to directly embark on my culture project here. I’m also having a heck of a time tonight trying to come up with a way to make the process of isolating a pure culture sound interesting to anyone besides me. Here’s the extremely abbreviated version:

  • Take something that’s got (in this case) yeast in it (sourdough starter, unfiltered beer, whatever)
  • Make up some solidified yeast food: typically this is something like a mixture of sugar, predigested milk protein, and water, mixed with agar to solidify it, and with a small amount of acid added, since the acidity helps inhibit bacteria that might contaminate the yeast culture
  • Take a tiny bit of the original stuff-with-yeast-in-it, and smear it thinly over the top of the solid medium.
  • Cover the solid medium and put it somewhere warm for a while until you can see individual spots (“colonies”) of growth

    • (The idea is that if done right, at some point on the solid media the “smearing” will have spread out the yeast cells far enough that you can make out the mounds of offspring that an individual yeast cell has made. Each distinguishable round spot of growth is effectively made up of millions of clones of the original single cell that started the “colony”)

  • Take a bit of a single colony and put it in some sterile culture media.

If everything works correctly, this gives you a “pure” culture, isolated from any other kinds of cells that may have been in the original sample. In this example, this is hopefully a brewing or bread yeast culture that you can now use to make beer, wine, bread, or fuel ethanol (the latter assuming you have permission from the Bureau of Alcohol, Tobacco, and Firearms, since it requires distillation.)

Tomorrow: Fun facts about yeast cultures.

All this week: A topic important to secular and religious people alike

It’s not midnight here yet, I’m still on time!

Hello, “Just Science 2008” subscribers and everyone else. My life is insane at the moment but dagnabbit I’m going to do my best to get at least one post up on a scientific topic every day from today (Monday, February 4th) until Friday…

Today’s post is in the form of a gedanken experiment.

First, imagine the following:

  • Some “entities” existing somewhere

    • It doesn’t matter what “entities” you are imagining, whether they are products in a market setting, or data structures in a computer program, or topics of discussion on a news broadcast. All that matters is that there can be more than one of them.

  • A mechanism by which these “entities” are copied (and, optionally, also sometimes removed)

    • Products are manufactured or recalled, data structures can be copied or deleted, additional news anchors can be added to comment on a topic or conversely may shut up about them…

  • At least one mechanism by which changes can occur between or during copies

    • Product designs can be changed, a computer program may consult a “random number” generator and use it to make small changes in the data structure, scriptwriters may alter the news anchor’s teleprompter messages…

  • Some aspect of the “entities” that affects the rate at which they are copied (and/or, optionally, removed).

    • Demand by buyers in the market results in ramping-up of production, a computer program may perform some test or comparison of a data structure and use the result to determine how many copies of it to make (or whether or not to delete it), news topics that result in more people watching are repeated more often while those that people tune out from are dropped from the schedule…

What happens to this group of “entities” over time should be obvious. Taking the example of products in a market, producers introduce a variety of products (the group of “entities” in this example) and buyers examine their characteristics and, based on which ones they like, buy some of them. The producers observe which kinds of products are selling more and make more of those, while reducing or outright eliminating the production of those that aren’t selling well. Over time, a few of the kinds of products in this group which best fit the preferences of the buyers and the ability of the producers to make them. These products will dominate the market until the preferences of the buyers or the ability of the producers to produce them change [example: a shortage in the price of a particular material needed for a popular product].

You have most likely observed this process in the “news topic” context yourself, where it tends to happen much faster as “cheap and easy” news stories are happily picked up by news agencies to broadcast until people get sick of them and tune out.

This can all, hopefully, be understood as a purely logical outcome – a conclusion that universally and necessarily follows from the premises given. There should be nothing supernatural or even surprising here, is there?

So, now that you understand why and how evolution works (if you didn’t before), I can move on. (Incidentally, the part of the example above that describes a computerized system is actually referred to as a “genetic algorithm”.)

My purpose in starting with this is because it really and truly is fundamental to the topic that I expect to spend most of this week posting about, and which has been of vital importance to human culture and intellectual development for thousands of years. This most important subject involves such notable figures as Charles Darwin,St. Thomas Aquinas, Noted American Science-guy Benjamin Franklin, New England Puritan Cotton Mather and Quaker William Penn ,Hardcore Catholics like Pope John Paul II, Hardcore Athiests like PZ Myers, even famous religious figures like Jesus.

I refer, of course, to wine (and beer and other examples of ethanol production).

Okay, here’s the background: I just graduated with my B.S. in Microbiology, and I’ve got this whole “Hillbilly Biotech”/”Do-it-yourself”/”Practical Science” kind of thing going on in my interests. That being the case, I wondered what it would take to isolate, culture, and maintain my own yeast (and bacteria – more on that later) stocks from the environment rather than buying “canned” cultures – or at least play with the “canned” yeasts to create my own stocks. As I was poking around, though, I kept running into the same attitudes – namely that it’s “too hard” to do this, and although there are a number of people who advocate re-culturing canned commercial yeasts for a short time to save money, none of them think it’s feasible to do this for more than a couple of generations, at which point we are assured that you have to go buy it again or else “mutations” will inevitably appear and scary and mysterious “off-flavors” will result and the brewing police will come and throw you in jail for deviating from the archetype of whatever pre-defined style of wine or beer you’re trying to make. Or something like that. In any case, it’s because of this fear of “mutations” that I am starting out with this “evolution”-related post: in biological evolution, various forms of alterations in the genetic material are the “changes before or during copying” in the gedanken experiment above.

I didn’t buy it when people were telling me that it was “too hard” to learn how my computer works so that I could run Linux and should instead leave deciding what my computer should do to the “professionals”, and I’m not buying the same argument about commercial yeasts, either. If I felt that way, I might as well leave the rest of the complex technology of brewing to the “professionals” too, and consign myself to “Lite Beer” and “Thunderbird” for the rest of my life.

I’ve been spending much of the last few weeks perusing books, online articles, and scientific papers on subjects related to brewing in general and brewing yeasts in particular, and this should form the bulk of this week’s post topics, of not well beyond this week. Tomorrow I intend to start in on the actual process of culturing yeasts. Meanwhile, feel free to correct my no doubt horribly over-simplified explanation of evolutionary processes in the comments.

I should be getting more done…

Im Name des Nudelmonster! It’s been over a week since my last post!

“Someone” seems to have located a replacement original disk of a game I had many years ago (but lost when I loaned it to someone) and bought it for me. Now, in addition to a variety of issues I need to deal with related to moving over the next few months, I have this delightfully surreal old computer game beckoning at me. ARGH! MAKE IT STOP!

Meanwhile, I’ve been trying to put together topics for next week’s “Just Science 2008”. We’ll find out who, besides me, is interested in fermentation once it starts. I think I’ll have to start off the series with a post on evolution, however, since it really does play a fundamental role when it comes to yeast culture. I also think I may be able to work JellO® into at least one of the posts, too…

Internet connection will be spotty the rest of this week as we travel towards the area that is to be our New Home, but I should have posts assembled in time for next week.

If I get a chance, there will hopefully be at least one more Geostrings post, possibly with a sample mp3 and/or Ogg/Vorbis audio file.

“Hooray for me!” or “About Friggin’ Time!”, take your pick.

Still traveling, and don’t currently have an especially good internet connection at the moment. More substantial posts to follow soon, honest, but in the meantime:

The college doesn’t wipe out my login for another week or so, so I was able to get logged into my registration information page. It still lists me as a “Senior”. However, when I have it generate an “Unofficial Transcript” for me, it now has the following before the class listings:

Degree: ASSOCIATE OF SCIENCE CORE CERTIFIED Date: 12/21/07
Major: CHEMISTRY
Degree: BACHELOR OF SCIENCE Date: 12/21/07
Major: MICROBIOLOGY

They don’t send out the actual pieces of paper until March, I’m told, so this is the first direct confirmation I’ve seen that indeed I can not continue to use “but I’m just an undergrad” as a disclaimer in my posts.

Now I just need to decide whether to go to grad school or just become a wealthy industrialist…

More on geotagging

Some good comments came up in the last post on georeferencing. I thought a followup post was
merited.

The itch I’m trying to scratch here is that I want to be able to georeference just about any kind of data,
and I want to be able to embed the georeference information directly in the data file, whether it’s a
graphic, or audio, or video, or gene sequence data, or anything else. I want to have a standard form for tagging any of these files. And I don’t want to store the location metadata in a separate file.

What I think I need, then, is a standard, simple way of making geographic notations in a terse, concise format that is both easily parsed by and readily recognizeable to a computer, is reasonably human readable, and can be made to fit just about anywhere that arbitrary text is allowed.

Right now, there are only two types of files that have some way of embedding geographic information into them that I know of. The obvious one is that EXIF data in JPEG files can contain “GPS” tags. For hardcore GIS people, GeoTIFF is the other one. Both are for photographs or other still-image data only. What about the rest?

A variation of one of the current geotagging XML formats like the W3C (“<geo:lat>41.4354840</geo:lat><geo:lon>-112.6660845</geo:lon>”) or GeoRSS is an obvious possibility. XML has two potential problems though, as I see it. First, it’s not very terse – the markup substantially increases the amount of space the information takes up. I think in most cases that wouldn’t necessarily be a problem, but I suspect there are a few file formats out there with only comparatively small spaces set aside for a “comment” or “description” field.

The second potential “problem” is something odd that occurred to me today: it’s hard to pronounce out loud. There are some popular audio formats (e.g. “.wav”) that as far as I know have no space whatsoever for arbitrary text…but if my little standard was something that could be distinctly spoken, someone making a recording could literally speak the metadata in a format that a speech-to-text engine (like Sphinx) might be able to recognize and convert to a compatible string of text which could be parsed just like data from anywhere else. This is something of a corner case, I admit, but I think it’s at least worth considering.

Another good point that came up was what you do if your data extends beyond a single point. For example, if I want to georeference an audio recording I might make while narrating what I’m seeing out the window of a speeding train, it makes good sense to at least try to store line segments rather than just a point. That way, if someone wants to find the spot within a several-mile stretch where I suddenly exclaim “Hey, wow, look at that!” they can. The ability to define areas with a polygon or a point-and-radius seems like it would be handy, too, though obviously much more optional.

So, let’s see, I’m looking for a format with minimal markup, but which is easily recognized, is made of plain text which could be crammed into, say, a PNG tEXt chunk, an mp3 comment frame, a Genbank “Source” field, or any other field which allows arbitrary text. I want a form that’s minimally objectionable to anyone else who might be willing to use it. And I think I want it to be able handle points consisting of at least latitude, longitude, optional elevation, optional timestamp, and possibly even an optional heading and angle, and can handle more than one point per file (for the case of lines). Am I forgetting anything?

Besides “going to bed before 3am”?

’tis the season to be greedy

Members of my immediate family start asking around this time of year about what kinds of things I’d like for Christmas presents this year.

This strikes me as a good way to break the week-long bout of blogstipation I’ve been having. Here, then, is what I want for Christmas, Xmas, Hannukah, Kwanzaa, Cephalopodmas, or whatever gift-giving winter holiday you prefer (each category is sorted roughly in order of desire at the moment):

Ridiculously Expensive Stuff

Which I only list on the off-chance that someone wins the lottery or happens to find an amazing bargain on “e-bay®” or something.

Relatively Expensive Books

Other kinda-expensive-but-maybe-you-can-find-it-at-reasonable-price stuff

Relatively Cheap Stuff (but still spiffy)

I know there was more, but my brain seems to have gone on break right now…

“Does beer and ice cream make gas?”

I get some odd Google searches hitting this site. Once in a while, however, I see one asking a question of vital importance and great usefulness to the general public. Today’s brief topic is this query: “Does beer and ice cream make gas?”.

I’m assuming the searcher did not mean gasoline. Biodiesel is all well and good, but who the heck would waste perfectly good beer and ice cream on such a thing? No, I assume the searcher wanted to know if eating these two fine foods together would expose one to the risk of increased flatulence.

Sad to say, the answer is most likely “yes”.

Flatulence gas (from humans, at least) is made up mostly of carbon dioxide and hydrogen gas[1], and for some people (but apparently not all!) methane. It’s worth noting that none of these components have any odor. All of the offensive smell comes from comparatively tiny amounts of sulfur-containing chemicals – most notably plain old Hydrogen Sulfide, and maybe a few molecules of indole-type compounds such as skatole which can make the origin of the stench obvious.

These main gases come from two sources – swallowed gases (air and carbonated beverages) and microbial fermentation. Obviously this is one place beer comes in – the carbonation adds to the amount of gas entering the digestive tract. Secondly, the beer probably contains some amount of remaining malt which some intestinal bacteria, like the yeast that made the beer in the first place, can break down and eat, possibly generating more carbon dioxide in the process. Beer also has small amounts of sulfur compounds in it which give it some of its flavors. It’s possible that some of this sulfur can end up as smelly by-products of microbial action as well.

I tend to assume that problems one might have with ice cream are mainly related to the lactose from the cream. Lactose is actually a combination of two kinds of “simple” sugar molecules linked together in pairs – glucose and galactose. Many unfortunate human beings are cursed with a lack of production of lactase, which is an enzyme that breaks lactose into its two simple sugars which can be easily absorbed and digested. Many bacteria which can live in the human intestine, on the other hand, make their own lactase. If the human eating the ice cream doesn’t make their own lactase so as to absorb and use up the simple sugars, it all gets down to the intestines where the intestinal bacteria can turn it into a major feast. Many bacteria generate a lot of carbon dioxide when eating these sugars, too, and this adds to the gases that build up in the intestine. This is similar to the issue with beans[2] and similarly ‘indigestible’ substances which can appear in food[3] – humans don’t use them up, so the bacteria get it all and make a huge amount of gas in the process of eating it.

Milk also has at least some sulfur in it[4], like just about any protein-containing food, but I’m not sure if it’s enough to add to the smell problem.

So, yes, beer and ice cream probably do make gas.

Incidentally, it seems as though methane production in humans only happens in some people. Methane is only produced by certain kinds of archaea, and not all humans have them growing in their intestines along with the regular bacteria. Don’t quote me on this, but I would tend to suspect that this would actually reduce the amount of gas that actually results in the end. Methanogens actually make the methane out of the other two major flatulence gases: carbon dioxide and hydrogen. I haven’t looked up the biochemistry, but I suspect the other byproduct is water. Since the pressure of a particular bubble of gas (and therefore its volume when your container is stretchable, like an intestine) is dependent on the number of actual molecules of any kind of gas in it, if you have methanogenic archaea in your intestines they should be taking a molecule of carbon dioxide plus more than one molecule of hydrogen gas, and producing just one molecule of methane out of it (plus some liquid water), so where you once had three or more molecules of gas you end up with just one. I’m sure somebody somewhere has done some kind of study on this, maybe I’ll go dig for it at some point. While I’m at it, perhaps I should look at patenting the use of archaeal “natural flora” as a probiotic?…

The picture at the head of this post, incidentally, came from this blog post of odd signs – apparently this one’s from an advertisement for some kind of backache treatment. Still, I couldn’t pass up putting it here…

[1] Furne JK, Levitt MD: “Factors influencing frequency of flatus emission by healthy subjects.” Digestive Diseases and Sciences, 1996; 41:8; pp 1631-1635
[2] Rockland LB, Gardiner BL, Pieczarka D: “Stimulation of Gas Production and Growth of Clostridium perfringens Type A (No. 3624) by Legumes.” Journal of Food Science; 1996; 34 (5); pp 411–414.
[3] Cummings JH, Macfarlane GT, Englyst HN: “Prebiotic digestion and fermentation” American Journal of Clinical Nutrition; 2001; 73(2); pp 415-420
[4] Ramsdell GA, Whittier GO: “Composition of Casein in Milk” Journal of Biological Chemistry; 1944; 154; pp 413-419