Category: Me, me, me

Personal blather about one of my favorite people – Me! (This should not be a common topic, actually…)

If I Win It…

One topic that I have hoped to emphasize much more on this blog is amateur science, and in particular (given my educational background) amateur Microbiology.

Don’t be dissuaded by my use of the word “amateur” here. I don’t mean “not really” science (i.e. the microbiological equivalent of the “baking soda volcano”). Rather, here I’m using “amateur” in its proper etymological sense – science done for the love of it. I don’t just mean my brief series of experiments on the toxicology of expired JellO®. I mean actual microbiology with potential practical application as well as educational value. Unfortunately, there are a few bits of equipment for this that I can’t reasonably cobble together out of spare parts or repurposed household appliances. A microscope, for instance. Or a dry-ice maker.

Being a full-time college student, I’m poor, and can’t afford a microscope. A decent ordinary “brightfield” microscope appears to cost about $400. Bonus materials like a “darkfield” condensor are extra, unless I think I can rig up an equivalent on my own. A nicer digital camera to take pictures with to share with you, my loyal reader(s) would add some more to the cost. Even in the case of equipment and supplies improvised from more ordinary and readily-available materials (pressure-cooker=”autoclave”), there is still a cost. Woe unto me, what shall I do?!?!?

For the moment, I shall revert to the time-honored traditions of “begging” and “hoping”…

You see, there appears to be a scholarship available for bloggers who are full-time college students. Why, what a coincidence! I blog…and I’m a full-time college student! What luck!

There appears to be a US$10,000 (that’s almost 10000 CANADIAN dollars!). It’s not explicitly stated but last year they also had $1,000 “runner-up” awards as well. Here, then, is my pledge to you all.

Should I be selected as a finalist for this scholarship competition, I will eat 2-year-old JellO! Furthermore, if I were to actually be selected to win a $1000 scholarship, I will buy a real microscope and be able to blog my microbiology experiments and studies much more vividly. I will also blog the design and construction of my own amateur microbiology lab, to the extent that I can afford. (Well, I was ALSO going to do this anyway, but with a scholarship I’d actually be able to start doing it…)

Were I to be selected to win the full $10,000 scholarship I propose to go absolutely Nucking Futs, with a microscope, a nice new digital camera, dry-ice maker and plenty of CO2, perhaps some dedicated hosting for this blog, and a complete collection of useful microbiology equipment (mostly improvised still, but that’s half of the education right there…). Furthermore, should my readers demand it, I might even be persuaded to drink a cup of fresh Lysogeny Broth!

Come on, who needs this money and attention more – me, or some wealthy (compared to me) graduate student over on scienceblogs.com? I bet none of them would eat 2-year-old JellO or drink E.coli Chow for it, would they?

10 Finalists are to be announced October 7th, from what I understand…wish me [good] luck…
UPDATE: I made the finals, though my fame doesn’t seem to be carrying along a rose-petal-strewn path to victory yet…

Why I blog, and the Office of Technology Assessment

Via a post over on the Aetiology blog (and Retrospectacle) I happened upon a survey being taking about science blogging. It got me thinking a bit about why I’m doing this – aside from the masses of screaming groupies I have.

Aside from just being fun (I like to write), I set up this particular blog as a platform to practice communicating scientific topics. It’s a skill that really isn’t emphasized much in science education as far as I can tell, and regardless of where my career may go post-graduation I’m sure the ability to articulate scientific and technical topics will be beneficial to me.

In fact, I can see two different ways I could go with a career either during or after graduate school. Obviously, I could end up employed in a capacity where I’m officially “doing” science, which could be anything from “brewmeister” to curating a culture collection to academic research to being a lab grunt. I could also see myself pursuing a policy or science communication angle as well, though. This could be anything from Public Relations for a scientific or technical company to science writing to scientific advising…which brings me to the Office of Technology Assessment.

A post over on the “Denialism Blog” at Scienceblogs.com started a stream of “Bring Back the Office of Technology Assessment” posts around the net. Now, there’s a dream job. I would personally love to have a job like that. Make an enjoyable and comfortable living from whatever talent I have at explaining scientific and technical topics, and directly and substantially benefit my country in the process? Sign me up! Of course, even when the OTA existed, it only had a small number of employees, and presumably they were all Ph.D.’s with backgrounds in science and public policy, so the odds of me getting hired there (specifically) would probably be comparatively slim. Still, I can dream, and perhaps if we luck out and my wife (a Ph.D. Geologist with a background in borehole geophysics, petroleum geology, nuclear technology, and a variety of other areas – anybody out on the East coast in the general vicinity of Washington D.C. need anybody like that?…) and I have the opportunity to move somewhere with a good “science and public policy” graduate program I may have a chance.

My personal desires aside, though, if there’s one thing the people who are supposed to be running the country seem to really need, it’s rational science and technology information. Since the disbanding of the OTA we’ve had the DMCA and the costly and predictable abuses it brought (such as DMCA lawsuits over printer ink refills and replacement garage door openers), minimally-rational ideological fights over things like stem cell research and global climate change, panic and “security theater” over technically improbable-to-impossible “terrorist” threats (like the possibility that a terrorist will blow up a plane with a “liquid bomb” made of 4 ounces of baby food and shampoo, or “blow up” the fuel depot at JFK airport) (Mayor Bloomberg’s “STFU and GBTW” style of response to the panic was a glimmer of hope to me that there was some rationality left among my fellow human beings). I will refrain from picking on Ted “Series of Tubes” Stevens other than bringing this up as another example of lack of good information for policy-setting congresspeople. All this disruptive fuss, largely over ignorance and misunderstanding, which seems to be what the Office of Technology Assessment was intended to address. I would definitely agree that the OTA or something like it appears to be an urgent need – either that or Congress should quit playing around and just formally declare a science-boosting ‘War on Science’.

There are one or two things I’d like to figure out before I start mailing letters to congresspeople and presidential candidates though. For one thing – what would be the difference between the Congressional Research Service’s Resources, Science, and Industry division? Would one group be more focussed on specific policy implications while the other deals with “just the facts”? Also, the one legitimate-sounding complaint that I’ve seen in some of the newspaper articles on the subject is that it would often take longer to come out with a report on a subject than congress had (that is, congress would end up having to assemble a law and vote on it before the reports were completed). Should whatever takes the place of the OTA be re-designed to focus more on getting quicker answers? Like, maybe, hiring a bunch more people? Including, say, eager and capable grad-students…Okay, I’ll stop begging…

More to follow on this and related topics. Oh, and advice on successfully pursuing this type of career would be welcome.

Expired JellO®! Flee! FLEE FOR YOUR LIVES!!!!

Expired JellO®! Deadly Poison, or Merely Debilitating? Can a human being withstand the toxic load of an *entire box* of it? Would he suffer embarassingly loud and messy gastrointestinal distress, or would immediate organ failure set in before this could take place? STAY TUNED TO FIND OUT!…

Yes, loyal readers, as I type this I have subjected my own body to unthinkable risks to answer these very questions. That, dear readers, is how much I care about your health and welfare. You can thank me later…

…If I survive!

What does it mean to be an “Applied Empirical Naturalist”, anyway? As a naturalist, I look for natural explanations for natural observations. If I survive this ordeal, I will not explain it as being due to protection by supernatural forces, and conversely if I end up confined to an intensive care unit, my body ravaged by Expired-Gelatin-Syndrome, I will not seek to explain it as divine punishment for violating Kosher. As an Empirical naturalist, I investigate things by actual observation and direct testing wherever possible, rather than purely philosophical means. And – particularly important to me – Applied Empirical Naturalism is intended to convey that I am primarily interested in investigations with practical uses. Discovering the “Pineapple-Upside-Down Quark” with an umpty-brazillion-dollar particle accelerator and six months of supercomputer time to crunch the data wouldn’t do me, personally, much good. Knowing whether expired JellO® is safe to eat or not, however, has obvious practical application. Especially considering that I seem to have about 5 more boxes of the stuff in the pantry.

So, here I sit, perhaps writing my very last words ever before Expired-Gelatin-Shock causes my brains to swell up and explode messily and fatally from my ears like the popping of two superintelligent zits, in the service of Science. Here, then, is my story.

I begin by building my dire experiment around the following excessively-formal Valid Argument:

Upon expiration, JellO® becomes a deadly poison which causes great harm to those who dare ingest it
I prepare and consume an entire box of expired JellO®
Therefore, I suffer great harm due to its ingestion.

Last night, I plucked from the depths of my pantry an expired-2½-years-ago box of sugarless orange-flavored gelatin with which to begin this investigation. I blew the layer of dust off of the box, and carefully opened it, half-expecting to find some strange mutant gelatin-beast had developed in it over the years since expiration. One hand poised to protect myself should the creature leap from the box to eat my face in anger of being disturbed, I was both relieved and slightly disappointed to find nothing more than a foil packet containing what sounded like perfectly ordinary gelatin-powder. The packet proved to be intact, and the happy orange powder poured into a freshly-cleaned dish in a manner perfectly imitating that of wholesome non-expired gelatin. I dismissed the faint demonic snickering sound I seemed to hear as a figment of my fevered imagination and prepared the gelatin powder in the usual manner.

I took up my electric kettle, containing distilled water, and threw the switch. Seconds passed into minutes. Minutes passed into more minutes. Then, the water began boiling vigorously, and I applied one cup (8 fluid ounces) of this to the dish of powder, stirring it with a tablespoon. It seemed to take at least two minutes of continuous stirring, but the deceptively innocent-looking powder finally dissolved without the slightest scent of brimstone. As prescribed by the instructions on the box, I added a further 8 fluid ounces of cold water (from the tap of my kitchen sink), stirred briefly to mix, and placed the dish in the refrigerator to gel overnight.

I lay awake in bed for hours, wondering if I was doing the right thing. Was I insane? Did I not remember the tales of Jeckyll and Hyde? Of Doctor Frankenstein? Of Pons and Fleischman? What horrible fate was I setting myself up for? Finally, I dropped into a fitful slumber, disturbed only by dreams of amorphous orange demons stalking me to feast upon my soul…

Day broke, and this very afternoon I took the now solidified mass from the refrigerator. This was it. My last chance to avoid whatever hellish abuses this disturbingly orange substance had planned for me. But no…it was far too late to turn back now. I took up my spoon, and devoured every last bit of happy orange jiggliness.

This was approximately seven hours ago. In the intervening time, I have experienced the following symptoms: Occasional thirst, mild generalized anxiety about the near future, hunger, and an urge to write this blog post in a hyperbolic language more suited to an H.P. Lovecraft story than a scientific report. In other words…I appear to have been entirely unaffected, despite consuming an entire box of expired gelatin.

I’ve been taught that when hypothesis-testing, one considers the “null hypothesis”. That is, the hypothesis that would falsify the one that I’m starting with. In this case, it would be something to the effect of “I will suffer no harm whatsoever from eating expired JellO®”. Given the results in this experiment I must – in the tortured language of philosophical science – “fail to reject the null hypothesis”, because my results show no evidence whatsoever that I have suffered harm from eating expired gelatin. In other words, I cannot rationally cling to my original hypothesis as written, and must confess that perhaps expired instant gelatin still in intact packaging may, in fact, be harmless.

Ah, but I know what happens now. “Cad!”, you cry! “Fraud! Sham! This experiment is, like, totally bogus! This is not normal JellO® but a sugar-free impostor! And furthermore, this isn’t even JellO®-brand gelatin, but a cheap knock-off brand! How dare you, sir, feed us this crap, which proves nothing!”

I answer in two parts: Firstly, ladies and gentlemen who are my readers, I assure you that the contents of the less-famous brand and the official Kraft® Foods brand are essentially identical, and indeed, might conceivably have come from the same source. It’s common practice for one factory’s product to be shipped to multiple sellers who each offer it under their own label, as the wide variety of affected brands during the recent “salmonella peanut butter” scare demonstrated. And secondly: as it happens, I also have in my possession a box of JellO®-brand lime-flavored gelatin, WITH sugar, which although it lists no obvious “expiration date”, has a code stamped on the box indicating that it was originally packaged in late 2003, and therefore should have exceeded the expected 24-month shelf-life about the same time as today’s test subject did. I swear to you, dear readers, that I will repeat my experiment with this sample next.

Stay tuned: “Expired JellO II: Lime’s Revenge”, coming soon to a blog near you!

UPDATE: The Expired JellO® Saga continues here!

The Oldest Microbiology Book (that I own)

There’s this thing that some people do sometimes when they’ve been getting stressed out in one place for a while. I hadn’t done it in so long I can’t remember what it’s called. You know, where you Leave the area and then avoid it for a while. Oh, yes, that was it, a vacate-shun. Anyway, leaving the barren desert wastelands of the West, we headed east, and spent a few days admiring the area around the midpoint of the Appalachian Trail: Harpers Ferry, West Virginia. (Incidentally, I can recommend the “Angler’s Inn” Bed and Breakfast there, and the whole time there was incredibly delightful to me. I think I’d love to move to the area.).

I was delighted to note that there was an Old Book store in downtown Harpers Ferry. One thing about the Eastern US is that it’s been settled by book-using folks for somewhat longer than the West, so it would seem it’s easier to find really good Old Books. I found a publication of a 110-year-old microbiology book. In decent condition, for just over $20, no less! Not counting the (relatively modern) reprint of Micrographia that I picked up from a library sale, this makes it by far the oldest microbiology book I own now.

Oh, yes, did I mention I collect (casually) old books, especially old scientific and technical books?

The book in question, published in 1897, is “Story of Germ Life”, by Herbert William Conn. Not to be confused with Harold Joel Conn of “Conn’s Biological Stains” fame…who happens to be Herbert William Conn’s son. To be fair, the book *I* got was actually a republication from 1904, so only 103 years old…back when copyright was more rational (7 years, plus an OPTIONAL 7 more years. Thus explaining why my republication came out 7 years after the original.) It appears to have been part of a series called “Library of Valuable Knowledge”. The bookstore actually had another one of them, but I don’t remember what its topic was.

“Story of Germ Life” isn’t really a textbook so much as an overview of the subject of “Bacteriology” (as understood in 1897) for otherwise well-educated people – the kind of book I don’t think there are enough of these days. The Gutenbook project actually has a plain-text-only version of the book online here. Of course, then you miss out on the incredibly useful illustrations:

I always find it interesting to go back and see the earlier stages of scientific endeavors – especially as relates to my own interests. There always seem to be things that have since been forgotten, abandoned, or glossed over in them.

H.W. Conn seems to have been most interested in dairy microbiology, so there is a substantial amount of space devoted to it. I’ve heard of “blue milk” before (Yummy!….Pseudomonas?), but not Red or Yellow milk. He also devotes space to discussing the affect of “good” (and “bad”) bacterial cultures on butter, cream, and cheeses. I’m not even sure if butter is cultured these days, or if they just churn it up fresh and cold with minimal growth. Dangit, one of these days we’re just going to have to move somewhere we can keep a miniature dairy cow so I can do some experimentation with real unpasteurized fresh milk.

Bacterial phylogeny was so quaint back then. “Bacillus acidi lacti.” Ha! I love it. Interestingly, the term “Schizomycete” doesn’t appear anywhere in the text, though that may or may not be because it was considered unnecessarily technical for the intended audience. There’s actually very little about microbiological methods, too, which is the one major disappointment for me. Oh well, still interesting stuff. Conn actually mentions various “industrial” uses of bacteria including retting (soaking fibrous plants like flax or hemp so that bacteria eat the softer plant material to free the fibers), the roles of different bacterial cultures in curing tobacco, and even a fermentation in the production of opium (which Conn says is fungal rather than bacterial).

Also, much to my approval, the first 2/3 of the book is not about diseases. Only the last third of the book discusses “parasitic bacteria” and related topics. I leave you with this quote from the book’s 1897 Preface, which I think is still relevant today:

“Few people who read could be found to-day who have not some little idea of these organisms and their relation to disease. It is, however, unfortunately a fact that it is only their relation to disease which has been impressed upon the public. The very word bacteria, or microbe, conveys to most people an idea of evil. The last few years have above all things emphasized the importance of these organisms in many relations entirely independent of disease, but this side of the subject has not yet attracted very general attention, nor does it yet appeal to the reader with any special force. It is the purpose of the following pages to give a brief outline of our knowledge of bacteria and their importance in the world, including not only their well-known agency in causing disease, but their even greater importance as agents in other natural phenomena. It is hoped that the result may be to show that these organisms are to be regarded not primarily in the light of enemies, but as friends, and thus to correct some of the very general but erroneous idea concerning their relation to our life.” — April 1, 1897

Simplify, Simplify…

DNA seems to have two main threats to its well-being once it’s extracted and purified.

  • Nucleases
  • Spontaneous Hydrolysis by water

Nucleases are the big one that everyone seems to mention. The seem to be fairly sturdy enzymes, and they’re everywhere (including fingertips – hence the need to wear gloves whenever you get near DNA samples…), and they “eat” DNA rapidly. Theoretically, you can destroy the enzymes with enough heat, but you still need to worry about them getting in every time you pop open your sample to get some out.

Apparently, DNA even in pure water can tend to slowly fall apart spontaneously. It doesn’t happen very fast, but bit by bit, it can undo the links between the individual nucleotides.

A common way to try to deal with nucleases is to add EDTA to the solution. Nucleases need magnesium ions dissolved in the water to do their job, and EDTA tightly binds to magnesium (and calcium). The idea is to “use up” any stray magnesium ions in the solution so that even if nucleases get in, they’re inactive because they have no magnesium available. That’s why you see EDTA in the recipes for so many DNA-related solutions. Of course – EDTA doesn’t permanently bind up all the magnesium – there’s always a tiny fraction that stays in the solution. So, although EDTA can drastically slow down any nucleases, it won’t actually stop them.

There are also some interesting chemicals which can be added to destroy all proteins (including nuclease enzymes). Guanidine Thiocyanate is one rather nasty chemical that does this. 2-mercaptoethanol is another. Various other detergents like CTAB may also denature any proteins. Since they don’t harm the DNA in the process, you could keep the DNA sample dissolved in a solution with these chemicals…but then you can’t do PCR with the sample as it is, since the protein-denaturing chemicals will also destroy any enzymes that you WANT, like DNA Polymerase, when you try to mix it into your reaction.

I think the latter option will be great for collecting field samples (in fact, it’s papers specifically on the subject of preserving samples in the field with CTAB and Guanidine Thiocyanate based solutions that I’m adapting from), but isn’t going to be real useful once I’ve got my DNA relatively purified. What to do, what to do…

Actually, I think the answer’s simpler than I originally expected. I’ll just dry the purified DNA out. No water – no hydrolysis…and no nuclease activity, either.

I could actually just leave it as a dried pellet in the bottom of a microcentrifuge tube, but that leaves the problem of taking only a little bit of it for processing rather than taking the whole thing, and I want to avoid reconstituting it and re-drying it repeatedly. I think a variation of the “dry the DNA on a piece of paper” process will be in order – then I can just cut off a small strip of the paper to get a portion of the DNA. It appears that you can actually dunk the DNA-impregnated bit of paper right into whatever solution you’re using (like a buffered polymerase-and-primers solution for PCR) and go for it.

Among the several references I found on this, here are two:
Kawai J, Hayashizaki Y: “DNA Book”; Genome Res. 2003 13: 1488-1495
Burgoyne LA: U.S. Patent #5496562 “Solid medium and method for DNA storage” (1996); U.S. Patent and Trademark Office, Washington D.C.

Okay then…

My summer classes are finally over. Got an “A” in immunology (go, me). Now I just need to make sure everything’s done next semester. I’ve already signed up for the last two Underwater-Basket-Weaving-type “General education” classes required at this college: Intro to Philosophy and “History of Western Art”. I also went ahead and signed up for Environmental Chemistry, too – it’s not required, but it’s one of the last “not required but useful if I have time for it” classes on my list.

Meanwhile – is it just me, or is DNA some obnoxiously fragile stuff when you don’t want it to be? Sure, leave a few flakes of skin or hair follicles at a crime scene and they’ll nail you weeks or months later, but try to “gel purify” some DNA and it just falls apart…

The samples from my last post, about the colony PCR of my Lactic Acid beer-bacteria, I cut the bright bands of presumably-16s rDNA out of the gel and ran them through one of those canned “gel purification kit” processes. Then I froze them until I had a chance to finish my classes and play with them.

Yes, I was wearing gloves. No, I didn’t lick the gel. I think I must have looked at them too closely or something and they just disintegrated out of spite. In any case, my attempt at a restriction enzyme digest turned up NOTHING (other than the “ladder” lanes) on the gel.

I’m beginning to really distrust canned kits. On the upside, that means I get to learn some more in the process of developing my own replacement protocols.

I will probably try re-amplifying DNA from the frozen samples and see if there’s anything at all left in there that can be saved. Otherwise, I’ll also check and see if the plates I made a few days ago still grew okay.

In other news – I’m toying with the idea of literally begging for my own microscope and home-microbiology lab equipment. As in, actually putting on a lab coat, taking an old hat, and sitting outside of scientific meetings and such with a cardboard sign saying “want my own microscope – please help”. Of course, I’d have to report any donations as “income” for tax purposes – I doubt they’d let me form a 501(c)(3) corporation dedicated to just buying me toystools for my own microbiological amusement.

I haven’t decided, but it’s under active consideration. It’d make for some interesting blogging (and I promise in return that I’d account on the blog for any money donated, and blog all uses of the equipment under Creative Commons terms so everyone can use it). It’d presumably take a while for this to get anywhere if it ever did – it seems it’ll cost about $400-$500 just for a (good) basic light microscope, plus another few hundred for a darkfield condenser and related upgrades. Plus, of course, me wanting to build some LED-based lighting for fluorescence microscopy ($500 canned commercial upgrade? Bah!). Incidentally, it seems Green Fluorescent Protein fluoresces best right around the wavelength of a typical, inexpensive, off-the-shelf ultraviolet LED…

And then of course I need a pressure cooker and one or more incubator setups and some petri dishes and trips to the grocery store for growth media and staining supplies and slides and… well, anyway, as much stuff as I can arrange to get. But the microscope is the one component that is unavoidably expensive.

Oh, yeah, and some space to keep cheese and beer culture organisms and such for later use…

Comments, anyone? Suggestions?

Short Low-content (but relevant) post

Mainly to remind myself, but in case anyone’s interested:

I’m going to have to do another “Searches that led to pages on this blog” post soon – there are some interesting ones.

If I have my way, I’ll also be in a position to do some posts on bacterial virology, yogurt, and the microbiology of Belgian Lambic ales. (For the Bacterial Virology lab, I’m going to see if I can play with temperate (“lysogenic“) phages in yogurt, and for the “food microbiology” portion of the Pathogenic Microbiology lab, I’m going to see if I can talk them into letting me try to isolate [normal] bacteria from Lambic [assuming there are any still living in there].)

Sorry about the recent case of blogstipation…

So, here I am blogging from the hospital…

What? Oh, no, I’m fine, it’s just right across the street from where all of my classes are this semester, and they have a fairly decent cheap cafeteria. Plus, if I get this particular table, I can just barely get enough of a signal with my laptop’s external antenna to connect to my college network account.

Last week was spring break. Although I probably SHOULD have spent it drunk and naked, according to common wisdom, I instead spent it trying to catch up on sleep and doing a bit of culturally and educationally enlightening travel.

Aside from yesterday’s trip to the Opera, we managed to get out to visit Lehman Caves. As one might guess, I was hoping I’d get to find out something about the microbiology of the cave (in addition to ogling the impressive mineral stuff.)

As far as the microbiology goes, I was quite disappointed. One of the small books in the visitor’s center mentioned the existence of chemolithoautotrophic bacteria. In one paragraph. The entire content of which I just summarized here. Not even an identification of what kind of bacteria they are. The guide for the cave tour only knew that the bacteria in the cave were “harmless” (well, yeah, I kind of imagined they would be). There were also cyanobacteria happily if slowly growing near the lights, which nobody seemed to know too much about either.

I did get the name of the person responsible for issuing research permits – I’m seriously considering trying to make the cave one of the sites for my Senior Thesis study.

I did some other things, too, but I’ve got to pack up and head for class now. In case anyone besides my immediate family is reading this regularly (please comment if you are!) I will try to post a lot more often now – the last couple of weeks have just been a major distraction.

I’ve got DNA! I’ve got DNA! I’ve got DNA!…

As you can see, I’ve got DNA. I’ve been trying to get this stuff successfully extracted and the 16s rDNA amplified for months (off and on) now. Looks like doing the whole-genome-amplification step first did the trick – this is from a set of mixed halophiles in a phlogisticated environment growing in approximately 18% salt solution, and they grow very slowly. It’s hard to get enough DNA extracted from such a small population to do useful work with.image of electrophoresis of 16s DNA amplicons

The gel “bands” you see to the right of the image are (or at least should be) made of copies of the DNA which codes for various “16s small-subunit ribosomal RNA” sequences for the one-or-more different kinds of prokaryotes living in my culture. The brighter the band, the more DNA is there.

Since all of the samples were processed exactly the same way, then, the brightness of the band should, at least indirectly, indicate how many bacteria were in each sample to begin with. This isn’t necessarily true – there can be variation in how many copies of the gene each kind of bacteria has, so if the populations are very different the results could be misleading. Still, it’s gratifying that my little ‘proof-of-concept’ experiment not only finally gave me some DNA but even shows exactly the kind of difference I originally hoped for. (The second “lane” from the top with the brightest band was SUPPOSED to be enriched for certain types of bacteria, according to my hypothesis. The first “lane” should have had less, and it does. The third lane is my “positive control”, growing without special influences, and the fourth lane with no DNA visible is my negative control, which I hoped would have little or no DNA (indicating little or no bacteria growing in it) – and that’s what I see.

It doesn’t prove anything at this point, but finally getting results and having them turn out to look the way I’d hoped is a good start. I wonder if I can get them into a clone library, separated, and sequenced before next weekend?

I’ll have to remember to thank last semester’s “Senior Seminar in Microbiology” instructor for assigning me that paper[1] – I thought some of the technology described in it sounded like it’d be useful to me personally.

Anybody else going to the Northwest Regional ASM meeting next weekend?…

[1] Wu L, Liu X, Schadt CW, Zhou J: “Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification.” Appl Environ Microbiol. 2006 Jul;72(7):4931-41.