Hillbilly Biotech – Page 3 – The Big Room (and the little things in it)

“They laughed at me! But I’ll show them all! AH, HAHAHAHA!”

Another T-shirt to add to my list of T-shirts I want.

I’m spending more hours shoveling my way through the books and papers and crap we’ve got up here at House v1.0, since if all goes well I’ll be making a brief run back down to Southeast Texas so we can sign the papers for House v2.0 down there, at which point we’ll be able to start actually moving. I sure hope this one goes through. Not only is it our third attempt to buy a house down there, but I’ve already identified a convenient location to build my “Intentional Food Microbiology” brewlab in it.

Since there’s no way I can afford to buy a -80�F freezer, I have an obvious interest in alternate means of preserving the yeast, mold, and bacterial cultures that I want to keep. To me, drying seems like the most desirable method when it’s feasible, since dried cultures should require the least amount of maintenance. After a several-month delay, I’ve finally gotten around to getting back in touch with the archivist at Brewer’s Digest to see about getting an old article on the viability of dried yeast cultures[1].

Speaking of old but useful scientific papers, there’s an extremely nifty challenge going on through the month of May (deadline: May 31st) over at “Skulls in the Stars” blog: find a classic scientific paper, read it, and blog about it.

“My �challenge�, for those sciencebloggers who choose to accept it, is this: read and research an old, classic scientific paper and write a blog post about it. I recommend choosing something pre- World War II, as that was the era of hand-crafted, �in your basement�-style science. There�s a lot to learn not only about the ingenuity of researchers in an era when materials were not readily available, but also about the problems and concerns of scientists of that era, often things we take for granted now!”

I think this is a brilliant idea – the classic papers often seem to be forgotten and often explain things that people seem to take for granted these days. I already mentioned my post about the Gram Stain (original paper published in 1884), though that post really talks more about what has happened with the Gram Stain over the last 125 years rather than only being about the original paper. There are a couple of other classic microbiology papers that I’m going to try to get to if I have time before the May 31st deadline arrives.

I also need to get some yeast activated and get my must processed – I’m hoping a brief boil will reduce the amount of a yeast-inhibiting substance in it. I’ll post more detail after I get it going.

[1] Wickerham LJ, AND Flickinger MH:”Viability of yeast preserved two years by
the lyophile process.” 1946; Brewers Digest, 21, 55-59; 65.

WANT: “Teamaker” hops

Just a brief “aw, crap, has it really been over two weeks since my last post?” post, really, but I thought this was interesting.

It would seem that there’s a variety of hops that’s been registered recently known as the “Teamaker” variety. It’s got all the magic bacteria-stopping power of a hops plant, but composed of almost entirely the non-bitter component. I’m not sure how hard it would be for me to get them to send me a plant or two to evaluate it’s usefulness for yeast cultivation (as an anti-firmicutes antibiotic) and for controlling the growth of bacteria in fermented foods and drinks…

House-hunting (“Yep, these are house droppings all right. Fresh ones too…” [everybody’s seen that Monty Python bit, right?]) in southeast Texas and the related travel (both in the area here and between here and the other abode in southeastern Idaho) is eating my life at the moment, but I’ll try not to neglect the blog so much.

More to follow.

Boosting fermentation with science

All right then – I’ve got five pounds of honey, a pound of frozen cherries, packets of a couple of different dried yeasts, miscellaneous other potential additives, two 2-gallon polyethylene terphthalate fermentation containers with screw-top lids and spigots, several feet of aquarium airline tubing and connectors, silicone sealant, and miscellaneous kitchen gadgets (including a hydrometer). Now it’s time to discuss what I’m about to do and fish for comments and criticisms before I jump into it.

My goal here with this brewing experiment is a quick primary fermentation. And to compare the results from two different yeast strains, uh, TWO goals, quick fermentation, yeast strain comparison, and fermentation container design. THREE goals. Quick fermentation, comparing yeast strains, fermentation container design, and to try to keep the yeast cultures from dying off too quickly during the fermentation. FOUR. Four goals…

In this post, I’ll stick to talking about what I’m putting into the brew and how I hypothesize my additives and process with speed the fermentation along and help keep a large portion of the yeast viable during the primary fermentation.

Actually, the health of the yeast populations and the speed of fermentation are overlapping goals; more cells remaining alive and healthy means more cells simultaneously chewing up sugars and spitting out ethanol for me, resulting (hypothetically) in faster primary fermentation. In this experiment, I’m going to be focussing on nutrients and spices that are reported to benefit yeast activity. Here’s the process I am currently planning to follow, focussing primarily on the fermentation-boosting parts:

I’ll boil the 5 pounds of honey with enough tap-water to make about 2 gallons of must, adding the frozen cherries sometime after the boil gets underway.

Fermentation boost: we have water so hard that you have to wear a helmet to take a shower. (Joke stolen from my Environnmental Chemistry instructor, so you can blame Dr. Rosentreter for that one). It’s loaded with Mg²⁺ and Ca²⁺, which seem to be able to help the yeast to produce ethanol faster and survive higher ethanol concentrations better[1][2] as well as just being general nutrients[4].

Two approximately �-liter amounts of the must will be put into clean glass quart bottles and used to develop the initial yeast culture for pitching (each one for a different strain of yeast).

Fermentation Boost: Growing up a large population of yeast from the dried yeast packets before pitching will give me a faster start. In addition, the large headspace and the use of cloth rather than plastic or rubber covering of the top will allow oxygen to get into the starter culture, helping it to develop more quickly and in a more healthy fashion (i.e. a larger proportion of healthy, viable cells).

Nitrogen supplementation: Capsules of arginine picked up cheap at a certain big-box store will be added to the yeast starter.

Fermentation Boost: “Free Amino Nitrogen” is perhaps the most important bulk nutrient for yeast, and arginine seems to be the preferred amino acid source[3][4], presumably because it contains the most reduced nitrogen per molecule of the amino acids. I actually want to try to develop a process for using dry milk powder instead, but achieving sufficient hydrolysis of the milk proteins looks like it’s going to take some development on my part. For now I’ll “cheat” and use arginine instead.

Vitamin supplementation: A single well-crushed children’s “chewable vitamin” (“Flintstones�” or generic equivalent) will be added to each starter culture as well.

Fermentation Boost: Pantothenic Acid (Vitamin B5), Inositol, trace minerals, and small amounts of additional potassium and phosphate to supply vital nutrients to the yeast culture.[4]

Fermentation-enhancing spices: I will be adding ground ginger and cinnamon (actually cassia) to the must near the end of the boil.

Fermentation Boost: In addition to providing what I think will be excellent complementary flavors to the final product, it appears that even fairly large amounts of these two spices – among others – provide a boost to fermentation rate[5] (via Shirley O. Corriher’s “Cookwise”[6]) of Saccharomyces cerevisiae cultures. If I’m doing the conversions appropriately, the peak fermentation boost for ginger works out to something like 3 tbsp of ground ginger per liter, or something like (very roughly) 10 tablespoons per gallon. I don’t plan to add quite so much, but a couple of tablespoons of each spice in the two-gallon batch ought to provide some nice flavor while still hopefully providing a boost to the fermentation rate as well.

“Cinnamon”: In the US, the rust-colored stuff labelled “Cinnamon” is not, actually, cinnamon. True cinnamon (Cinnamomum zeylanicum)is actually tan in color. What you get in the US when you buy a bottle of “Ground Cinnamon” actually comes from Cassia (Cinnamomum aromaticum), a closely related plant. Realistically, as far as I have been able to find out so far, there’s not likely to be a huge difference in the active components or flavor. While I haven’t yet gotten my hands on a copy of the old article from Cereal Chemistry[5] mentioned above, I’d give good odds that the “cinnamon” used in the study was also actually cassia anyway.

There’s one more thing that I hypothesize would help promote my goals that could be added: small amounts of oxygen[7] (say, less than 13% O₂, or very roughly speaking, around half of the normal atmospheric concentration or less). However, I’m still trying to work out an easy way to achieve this automatically and am not yet ready to try it. Besides, this is already pretty poorly-designed for a “real” scientific experiment as it is, considering the number of variables that are really contained in this brewing process. Really, my hypothesis here boils down to a relatively vague “This mixture and process will allow me to finish the primary fermentation within a day or two of pitching”. If I ever have opportunity to do serious experimentation on this, it’ll require setting up a large number of separate fermentation reactions to assess the effects varying each individual set of hypothetically-fermentation-boosting additives. Hopefully one of these days things will settle down enough to let me try it.

If anybody sees anything stupid (or just interesting) up there, please say something…

[1] Dombek KM, Ingram LO: “Magnesium limitation and its role in apparent toxicity of ethanol during yeast fermentation.”; Appl Environ Microbiol. 1986 Nov;52(5):975-81.
[2] Nabais RC, S�-Correia I, Viegas CA, Novais JM: “Influence of Calcium Ion on Ethanol Tolerance of Saccharomyces bayanus and Alcoholic Fermentation by Yeasts.”; Appl Environ Microbiol. 1988 Oct;54(10):2439-2446.
[3] Carter BL, Halvorson HO: “Periodic changes in rate of amino acid uptake during yeast cell cycle.”; J Cell Biol. 1973 Aug;58(2):401-9.
[4] Fugelsang KC, Edwards CG: “Wine Microbiology – Practical Applications and Procedures (2nd Ed.)”; 2007; Springer Science+Business Media LLC; pp 15-18
[5] Wright WJ, Bice CW, Fogelberg JM: “The Effect of Spices on Yeast Fermentation.”; Cereal Chemistry. 1954 Mar;Vol.31,100-112
[6] Corriher, SO: “Cookwise”; 1997; HarperCollins Publishers, inc; New York; pp 69-70
[7] Nagodawithana TW, Castellano C, Steinkraus KH: “Effect of dissolved oxygen, temperature, initial cell count, and sugar concentration on the viability of Saccharomyces cerevisiae in rapid fermentations.”; Appl Microbiol. 1974 Sep;28(3):383-91.

The care and feeding of Saccharomyces

Let me pause now for a moment to review what I’ve learned so far:

Yeast are filthy little jerks

No, seriously. I’ve previously reviewed their promiscuous sex lives,
their sexually-transmitted diseases, and their toiletry habits. Somehow, though I still want to do more brewing, so let’s continue.

Bag of 'Parodina Yeast Chow'. I am not affiliated with Purina Mills corporation! This image is PARODY!

Yeast need to be fed particular sugars

The three major elements needed by pretty much every living thing for “food” are Carbon, Nitrogen (as reduced “amino” nitrogen), and phosphorus (as oxidized phosphate) (Reduced sulfur is also needed in small amounts for proteins). Glucose (“dextrose” or “corn sugar”), fructose, or sucrose (“table sugar”, each molecule of which is made of a molecule of glucose attached to a molecule of fructose) are all used as carbon sources by Saccharomyces yeasts. Possibly also Galactose under certain conditions[1]. Saccharomyces yeasts don’t appear to be able to use lactose (“milk sugar”, each molecule of which is made of a molecule of glucose and a molecule of galactose), so some recipes include lactose in order to ensure there is some residual “sugar” in the mix at the end, for flavor and “body”.

Yeast need reduced nitrogen (amino nitrogen or ammonia…or urea)

Aside from sugars, this seems to be possibly the most important yeast nutrient. The most
“natural” source of this nutrient would seem to be amino acids or very short peptides (2-5 amino acids long). Apparently urea (carbamide) also makes a good yeast nutrient, but:

You don’t want TOO much nitrogen available to the yeast, or there’ll be excess urea dumped back into the brew

This could combine with the ethanol to make “ethyl carbamate”, which is considered
a probable carcinogen, at least if it’s present at a high enough level. Obviously if you use urea as a
yeast nutrient, that’s only going to increase the possibility of a problem.

Saccharomyces yeasts are effectively incapable of using proteins for nutrition.

Proteins can be a source of amino nitrogen (and carbon and sulfur), but like all real microbes, yeast cells cannot just “eat” chunks of protein. They have to be broken down into very small chains of amino acids or even as individual amino acid molecules before the yeast can suck them up and use them. Saccharomyces yeasts do not appear to normally excrete protein-digesting enzymes, so by themselves they cannot make any use of protein for nutrition[3].

Yeast need oxygen

Oxygen is necessary for making certain components of the cell membrane, in addition to it’s more obvious role in respiration. Without a way to replace used up membrane components, the yeast stop reproducing and eventually fall apart and die. There seems to be some suggestion that to a certain extent one can substitute some raw membrane material for oxygen here (either as “yeast hulls” or possibly even certain of the natural waxes on some fruits).

If you give yeast oxygen, though, they consume the sugars entirely instead of making alcohol…

…or do they? Between the “Crabtree effect” (when there are high concentrations of glucose, alcohol production continues even in the presence of oxygen) and indications in scientific papers[2], it seems SMALL amounts of oxygen may not be a problem, and might very well be beneficial.

Yeast need vitamins and minerals

B1 (“Thiamine”) is commonly mentioned, though apparently the need for it varies from strain to strain. Also potentially important are Pantothenic Acid (B5), Niacin (Nicotinic Acid, Vitamin B3), Biotin, Inositol, as well as Potassium, Magnesium, and trace amounts of calcium and a few other minerals[4].

Unhealthy yeasts are more prone to make (EEK!) Off-Flavors and Off-Odors (EEK again!)

For one thing, it seems to be a general rule that you don’t want your brew sitting on the corpses of dead yeast (the “lees” of wine, or “trub” of beer), because that is a potential source of (insert dramatic music and crash of thunder here)Off-Flavors and Off-Odors. Yeast dying and falling apart is also a major source of urea being dumped into the brew, too. Some strains of yeast under certain conditions, such as insufficient pantothenic acid, may be prone to producing nasty-smelling sulfides as well.

So, in most cases what we want to do when brewing is keep our yeast as alive and happy as possible, and get them to hurry up and finish our primary fermentation before they start dying off. Coming up: My (as yet untested) plot for accomplishing this – without specialized scientific equipment or materials.

[1] Wilkinson JF: “The pathway of adaptive fermentation of galactose by yeast” Biochem J. 1949; 44(4): 460�467
[2] Nagodawithana TW, Castellano C, Steinkraus KH: “Effect of dissolved oxygen, temperature, initial cell count, and sugar concentration on the viability of Saccharomyces cerevisiae in rapid fermentations.” Appl Microbiol. 1974 Sep;28(3):383-91.
[3] Bilinski CA, Russell I, Stewart GG: “Applicability of Yeast Extracellular Proteinases in Brewing: Physiological and Biochemical Aspects.” Appl Environ Microbiol. 1987 Mar;53(3):495-499.
[4] Fugelsang KG, Edwards CG: “Wine Microbiology: Practical Applications and Procedures” 2007; Springer Science+Business Media LLC, New York; pg 17

Do Not Want: Celestron LDM

Back in Idaho for the moment. The trip was somewhat exhausting, but I thought a followup to The previous post on the Celestron LDM microscope was in order, as I finally got a reply back after almost two weeks.

(20080329:Quick update. I am surprised to see this post is getting more interest that I’d anticipated. I’ve added a brief summary to the end of the post to help clarify my opinion since it seems people may be interested.)

I had asked them if it was possible to replace the objective lenses (so as to be able to use an oil-immersion lens to get 1000X magnification – pretty much a neccessity for decent bacteriological work – such as examining yogurt cultures) and whether the camera could be swapped for a regular eyepiece. Larger yeast cells used in brewing might be okay in 400X, but even there it’d be nice to be able to zoom in adequately to get better detail – like watching conjugation or budding of yeast cells.

The answer:

“The answer is ‘no’ to both because of the sizes, etc. are specific to this unit.”
Email ID: ZZR-372549
Department: Technical Support
Priority:
Status: Closed

I guess there’s no point in asking about getting a darkfield condenser for it. On the plus side, they did actually give me a reply at least.

I’ve got to say I’m seriously disappointed that Celestron has evidently intentionally engineered this microscope product (and their other offerings as well, perhaps?) to Not Play Well With Others. Why else go to the trouble and additional expense of coming up with your own special specifications for the parts when standard parts are readily available?

This seems especially absurd in a product aimed at science enthusiasts, who strike me as very likely to be strongly aligned with the “Maker” attitude…at least if they’re any good at Science Enthusiasm. I think the “if you can’t open it, you don’t own it” concept meshes very well with the investigative attitude necessary for science. So, we want “internet”, and they give us “AOL” instead. A sad, sad fate for an otherwise great concept, and on this basis I must render a verdict of “Do Not Want”.

Find me a version of this product – from any vendor – which can accept standard oculars and objective lenses and I’ll sell blood plasma and beg on the street to raise money for it. (If nothing else, it’d give me an excuse to finally start up the “science begging” blog-post series I’ve been threatening for a while now…) Of course, it’d be nice to have an ordinary “real” microscope, too…this blog still doesn’t have enough pictures.
(P.S. Dear Celestron: although I doubt anybody at Celestron will ever even see my obscure blog, and in that respect my previous post’s comment about sending me one to review was just a joke. Despite this, I was sincere, so in the unlikely event that someone out there sees this post and has the authority and inclination to do so, feel free to send me one to review anyway. And a pony.)

SUMMARY (in my opinion):
Good:

VERY nice, highly desirable concept overall.
Self-contained, platform-neutral design, should work with anything that can support SD cards or USB Storage devices.
Potentially a nice field microscope? (Probably not hard to hack together a battery pack that could be used in place of the AC adapter)

Bad:

Does NOT appear suitable for bacteriological or similarly high-magnification applications
Non-standard components prevent upgrades.
Non-standard components mean vendor lock-in problems (if Celestron gets tired of making replacement parts and some kid scratches your objective lenses or cracks the viewscreen, you’re out of luck.)
Digital camera and viewscreen appear to be integral, so if the camera or viewscreen dies I’d guess the whole device becomes a useless lump.

My recommendations for Celestron or other microscope manufacturers (should any of them care about the opinion of some nerd on some obscure blog like this one):

Please, please use standard parts wherever possible – it makes your device a much safer bet for anyone thinking ahead towards possible upgrades or replacement parts.
Don’t ignore bacteriological applications.
Easily replaceable parts make for graceful failures. For example, if the camera on this model could be swapped for an ordinary ocular, the microscope would at least be usable while the camera portion was being sent in for repair or replacement.

WANT(?)

My parents, apparently comfortable with being microbiology “enablers“, ran into a digital microscope (pictured at right) that they pointed me to. It looks pretty nifty for the price, except for one issue: it only comes with three objectives, topping out at 40X. I can find marketing materials for this microscope, but no technical information beyond what’s on the company’s website (click image to reach that). Therefore, I can’t tell if the objectives are replaceable or not. If they are, the idea of picking up an inexpensive surplus 100X oil-immersion lens and ending up with a decent microscope with which to watch the Yeast Porn and such – on a nice digital screen, no less, rather than squinting into an eyepiece – has a certain appeal to it. The fact that the digital camera takes the pictures itself and only needs a computer connection to transfer files – and not even then if you use an SD card – means that I wouldn’t have to worry about ending up with something that requires Microsoft� Windows� just to look at some microbes (or post glamour shots of them to this blog).

However, I don’t think trying to view conjugating yeast cells or, say, Lactobacillus or Gluconobacter/Acetobacter bacterial cells at 400X would be very rewarding, so an oil-immersion lens is a necessity. And don’t let the “up to 1600 Power with Digital Zoom” thing fool you – it just makes the picture bigger and blockier, not actually more detailed.

So….do I WANT, or not? I sent off an email to Celestron asking about whether I could swap out objective lenses on this model or not. I got back the form “we got your email” email – we’ll see if I get a real reply from them or not. If so, I’ll update this post.

Speaking of which – still no reply from Bristol Brewing Company. Guess they’re either just not “nerd-friendly”, or the person who handles email queries is on vacation or something.

P.S. Dear Celestron – if you were to send me an evaluation model, I’d be happy to review it here on my blog for the ~~thousands~~ ~~hundreds~~ ~~dozens~~ pairs of people who read my ~~elegant prose~~ incoherent babbling…

Drugs make you stupid. And so does fear.

Ignorance breeds fear. Fear breeds terrorism. Terrorism breeds interruption of homebrewing. There was a disturbing article that came up today. Evidently, someone’s burglar alarm went off, so the security company drove by to check it out. They opened the garage (where I guess the alarm indicated an attempted break-in or something) and thought they saw a “still”. Naturally, anything that looks science-y with copper tubes or whatever can only be for one thing: drugs, right?

A bunch of police officers in both marked and unmarked cars AND the fire department later, somebody finally finds out it’s just somebody’s (completely legal!) homebrewing setup. Of course, officials describe the panic as “an appropriate response”. You might think this was in notoriously over-reacting Boston, but no – it was Hamilton, New Zealand.

My first thought was that it probably wasn’t even a “still”, which due to unrepealed prohibition-era laws is still treated pretty much the same that meth-lab equipment would be in terms of legality here in the US. I kind of assumed it was probably just the owner’s fermentation container, or possibly a wort-chiller (see image – click for context). Without some apparently-rather-expensive permits, it’s extremely illegal to have distillation equipment in the US, and I’m under the impression that most places around the world still criminalize home distillation. It’s worse, though – apparently New Zealand repealed the ban on home distillation for personal use over a decade ago. Even if what the panicky security guys saw really WAS a “still”, it’s STILL a completely legal piece of equipment there. And yet, surrounding the guy’s house with marked and unmarked police cars and firefighting equipment was “appropriate response.” Because somebody said “drugs”. The original article may be found here.

In fairness to the public officials, it sounds like once the police and fire department showed up, they actually talked to someone at the house (no tasing or teargas required) and had no trouble figuring out that nothing illegal was actually going on, so the damage was pretty much limited to the time wasted by the police and fire-department in responding. What I want to know is why the “security” company gets a free pass on causing all this fuss by reporting a completely legal piece of vaguely science-like equipment as a “clandestine drug lab”? At the very least, I’d expect people to want to know which “security” company is supposed to be protecting their houses but cannot tell the difference between legal homebrewing equipment and real criminal activity.

As a fairly hardcore nerd with an interest in intentional food microbiology (brewing, cheese, etc.) this kind of thing worries me. I intend to build myself a fairly decent science-lab setup for doing food microbiology. I’m already planning to label everything as though it were part of a public museum exhibit, just in case some idiot happens to see it and assume it’s some kind of terrorist drug lab or something.

Here in the US, I consider “amateur” science and technology to be part of the very foundation of my country’s greatness. Think Thomas Edison. Nikolai Tesla [yes, he was a naturalized American citizen]. Benjamin Franklin. And no doubt many, many others who are less famous but nonetheless made major contributions to the advancement of their country. When we set about attacking that, we’re harming our country – yes, you people outside the US, this applies to you, too.

The moral of the story is this: Please, people – science and technology are fun. Yes, there are many of us out here who quite happily set up “science-lab stuff” to play with food, or rocks, or plants, or electronic circuits or whatever else in a completely safe and legal manner. Sure, it’s a good thing when good police-work closes down some drug-crazed freak’s meth-production setup – I don’t want some idiot blowing up my neighborhood with unsafe chemical activity nor attracting violent criminals anywhere near where I live. All I’m asking is, will people please stop panicking and screaming “drugs!” or “terrorism!” every time you see some glass tubes or blinking lights? Please? Thank you.

This Public Service Announcement has been brought to you by the popular drug 1,3,7-trimethylxanthine. We now return you to your regularly scheduled (and, it should be emphasized, completely legal) nerdity.

I has a books.

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

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…)

Prior 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.

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.