Oh, Canada!

I find myself this week in a strange and wonderful foreign land-- our mighty neighbor to the north: Canada. I am at the semi-(bi-?) annual North American edition of the yeast genetics and molecular biology meeting (the event that, two years ago, provided some wonderfully bloggable moments: click here or here or here and certainly here for some oldies but goodies).

Each day is packed with 20-30 speakers, and the evenings are filled with giant poster sessions (think: science fair for grown-ups) where the nations leading (and following) yeast research scientists gather to share ideas, debate hot button issues in yeast genetics and biochemistry (like this one), and conspire to collaborate on what they hope will be the next yeast-world-shaking fungal breakthrough. The scientists also get together at the much-anticipated conference-ending dance (which occurs tomorrow night). It is a week-long love-affair between man and Saccharomyces cerevisiae, a veritable cornucopia of yeastiality.

A highlight of my experience so far was being one of the first 20 participants to complete a yeast-themed crossword puzzle to win a baseball cap with the superhero budding yeast SuperBud, the microbial caped crusader. An eight letter word for "yeast food?" beginning beginning with V, ending with E? * A five-letter word for "Yeast cell form named after a comic strip character", second letter C? ** Here's a clever one: A ten-letter word for "GO:0005813"? *** My utmost thanks to the fine folks at the Saccharomyces Genome Database for the lovely hat. Without reservation, I recommend their site for all your yeast genetic informational needs.

Stay tuned for additional yeast meeting updates.







* VEGEMITE











** SCHMOO










*** CENTROSOME

Tell me, Brother, can you quantify?

Last night, Little Brother and I spoke on the phone to catch up with each other's impressions of the most recent installments of three of our mutual loves: Lost (the sci-fi drama about hapless plane-wreck survivors stranded on a desert island), Survivor (the reality series about hapless game show contestants stranded on a desert island), and Gilligan's Island (the TV Land comedy about hapless three-hour-tourists stranded on a desert island).

(OK, not Gilligan's Island.)

In order to demonstrate to each other that we are both still serious fans of Lost and Survivor, at some point during the course of these exchanges, the conversation inevitably degenerates into some semblance of the following dialogue (which has been abridged for readability):

Little Bro: Are you liking Lost?

Yajeev: I like it.

Little Bro: Do you love it?

Yajeev: Yeah, I love it.

Little Bro: How much do you love it?

Yajeev: I love it a lot.

Little Bro: Yeah, but how much?

Yajeev: How can I quantify it?

Little Bro: Well, who's your favorite character right now?

Yajeev: Sawyer's probably my favorite character, but Michael Emerson is my favorite actor on the show.

Little Bro: How much do you love Sawyer?

Yajeev: Yeah, he's great, Bro.

Little Bro: How great are the things he says?

Yajeev: They're the best. I loved when he warned Locke about harming "just one curly hair on Hurley's head."

Little Bro: That was the best! How much did you love that line?

Yajeev: I just told you: it was a great line.

Little Bro: Yeah, but how much did you love it?

Yajeev: A lot. I loved it a lot. How can I answer these questions?!

A few minutes later, the conversation turned to our favorite contestants on past seasons of Survivor.

Little Bro: How much did you love Frank in Survivor: Africa?

Yajeev: He was great.

Little Bro: Yeah, but how much did you love him?

Yajeev: Brother, I loved him a lot.

Little Bro: How much?

Yajeev (searching for some frame of reference): I love Frank as a Survivor contestant almost as much as I love Lost as a show.

Little Bro: Right. (pause) How much is that?

Yajeev: Uhhhh...

Little Bro: Wait--let me ask you this. How much did you love how he didn't know the meaning of the word "brunch"?

Little Bro proceeded to recount verbatim the conversations that took place during a Survivor episode he'd seen only once, on its original airdate in late 2001.

Yajeev: Yeah, that was great.

Little Bro: How great?

And so on.



This conversation has made it clear that when it comes to how much I like something, I have no clear method of quantitation, which makes my descriptions of the degree of like/love I maintain for a given television show or character or Survivor contestant vague and devoid of real meaning.

By contrast, most important traits can be quantifiably determined and so communicated. The piquancy of a chicken wing drenched in Louisiana Lickers sauce (my poultry coating of choice) can be conveyed in Scoville Heat Units (SHU) (Louisiana Lickers wings are a zippy 1,220 SHU on a scale of 16,000,000). Likewise, when I visit the doctor tomorrow and step on the scales, I hope to weigh in at about a slug (not this kind of slug) less than I did four months ago. Similarly, when I wish to express to someone how much of the enzyme invertase a given yeast culture secretes under conditions of glucose scarcity, I can give a near exact value: 4o0 milli-units of invertase per 1 milliliter of cells at an optical density of 1.0 in light of 600 nanometer wavelength (mU/OD).

Towards the end of being able to specifically delineate the degree to which a person, place, or thing is liked, I hereby propose a new unit of fondness: The philiac.

Of course, before this term can be introduced to the public lexicon, the scale must be calibrated. In order for this new unit of fondness to be useful, we need to be clear on what a philiac is.

Below are a list of things and people that I like to varying degrees and their corresponding philiac values.

The wife: 1,000,000 philiacs = 1 megaphiliac (1 Mp)
Coffee: 50,000 philiacs = 50 kilophiliacs (50 kp)
Watson Steve: 10,000 philiacs = 1 kilophiliac (10 kp)
LOST: 1000 philiacs = 1 kilophiliac (1 kp)
Frank on Survivor: Africa: 950 philiacs (950 p)
Monte Cello's pepperoni pizza: 800 philiacs (800 p)
Pittsburgh Steelers: 700 philiacs (750 p)
Yeast genetics and biochemistry: 500 philiacs (100 p)
Minnesota Twins: 350 philiacs (350 p)
Tomato soup: 50 philiacs (50 p)
Mowing the lawn: 20 philiacs (20 p)
Clipping my fingernails: 1 philiac (1 p)
Walking uphill half a mile: 0.1 philiacs = 100 milliphiliacs (500 mp)
Removing splinters: 0.03 philiacs = 30 milliphiliacs (50 mp)
Gram staining bacterial isolates: 0.005 philiacs = 5 milliphiliacs (5 mp)
Preparing radioactive waste for removal: 0.00005 philiacs = 50 microphiliacs (50 μp)
Using gas station restrooms: 0.000001 philiacs = 1 microphiliac (1 μp)

I know that I am not the first to attempt to generate a numerical rating system. However, the advantage of the philiac is that, by virtue of its nearly limitless span, the philiac allows a far-greater range and much higher resolution than do the more commonly used five-star or two-thumb systems-- consider, for example, the trillion-fold difference in likedness of the wife (1 megaphiliac) with that of using gas station restrooms (1 microphiliac).

It is the hope of this bloggist that the philiac will facilitate and enhance communication among those who love to rate and rank.

(Mostly) civil defense

His first question was funny.

My advisor had slipped my father (a marketing consultant, not a biochemist) a piece of paper with a query that he should pose during the question period of my dissertation defense.

"Have you considered a possible role for the yeast 14-3-3 proteins as regulators of the phosphorylation event you've discussed today?" he asked, having no comprehension of the words that were coming out of his mouth.

"That's a very interesting question, Dad," I responded. "In fact, I have considered such a role for these proteins, as you might have known this had you been paying attention during the conclusion of my presentation." He had of course been paying attention--he'd videotaped my every word and gesture for posterity. The language barrier, however, for the uninitiated can be intense, as every other word in such a presentation tends unavoidably toward the jargonish. Phrases like "altered sensitivity to an adenine analog", "half-time of dephosphorylation in the absence of de novo phosphate addition" and "multimerization of heterotrimers into higher-order structures" can be overwhelming even to a scientist working in a different subfield.

The audience laughed at our little exchange, certainly not a typical Ph.D. defense Q & A. I prepared to take other (legitimate) questions, but he continued with a new line of interrogation, this time of his own invention, asking about the naming conventions of yeast genes: "Why are your words sometimes in capitals and other times in lower case?"

I laughed politely and asked, "Are there any other questions?" I asked, attempting to restore some semblance of post-presentation normalcy.

"And, sometimes, you have them in italics!" he added, enthusiastically, to scattered chuckles in the audience. It was clear from his exuberance that my dad was in fact proud of me. It was also clear that he'd never been to a biochemistry dissertation defense before (most haven't).

Fortunately, my dissertation committee was (nearly) as supportive as my father. In the closed-door portion of the exam (no proud fathers allowed), the committee members asked a few obligatory questions to ensure that I was capable of sustaining scientific conversation. Four of the five members were willing to accept my dissertation without revision. The fifth member I had run into at a Pittsburgh Pirates baseball game two nights prior.

"Shouldn't you be studying?" she had asked me at the home plate entrance to PNC Park in front of the Honus Wagner statue.

"Shouldn't you be reading my dissertation?" I retorted, feigning confidence. Touché.

"It's on my things-to-do list--I'll read it by Monday," she promised.

She lived up to her word--and then some. In fact, she read the document more thoroughly than the other committee members and was equipped with a list of questions and concerns. "Why didn't you include a discussion of the connection between XYZ enzyme and the subject of your work?" she asked.

"Well," I began, attempting to craft a careful response, "There was one paper written that connects these two in the manner to which you elude. It was written by a research group in Wisconsin, but as far as I know, there hasn't been any additional significant work corroborating this linkage."

"There is one other paper," she responded.

"I'm not aware of it," I replied.

"I wrote it."

My advisor and I responded, simultaneously: "You did?!"

She did.

Fortunately, despite my oversight, she and the other committee members were willing to sign off on my magnum opus, asking for minimal adjustments (two to three additional paragraphs). Forms were signed and handshakes exchanged, and the deed was done: I had passed my final exam.




Bonus feature for today's blog entry:

Pictured at left is one artist's rendering (mine) of the heterotrimeric enzyme that is the subject of my dissertation research. For the sake of the pseudoanonymity I manage to maintain on the blog, I have replaced the protein names with their generic designations: alpha, beta, and gamma.

Poll Results: Science, alcohol favorites among Land of Yajeev readers

Thanks to all who took part in the survey on this site. This time, you were asked: "What is your favorite aspect of the yeast Saccharomyces cerevisiae?"

Perhaps the most significant result is that votership was up nearly 70% from the last survey (n=10).

40% of respondents reported their favorite aspect is the service of yeast as a model genetic organism, allowing researchers to unravel the mysteries of eukaryotic biochemistry at the level of the single cell. Scientific discoveries originally made in yeast have contributed to our understanding and, in some cases, the treatment of complex human conditions like diabetes, cancer, aging, and Alzheimer's disease.

An equal lot selected yeast's ability to ferment sugar to alcohol as their favorite.

That these two options were tied for first among those surveyed shouldn't surprise me. I've never seen as much science discussed or alcohol imbibed as when I attended the yeast genetics and biochemistry meeting last summer. Not nearly as much bread was consumed as beer at the convention, and this is consistent with half as many selecting how yeast "makes bread rise" as their favorite aspect of the multi-talented unicellular organism.

Scientists often refer to "TAPOYG": The Awesome Power Of Yeast Genetics. Based on these survey results, I'd like to amend the acronym to: "TAPOYGAFASMBR": The Awesome Power Of Yeast Genetics And Fermentation And Sometimes Making Bread Rise.

In any event, for a good time, BYOY: Bring Your Own Yeast.

In the strain 2000...

I had no idea that fame and glory were on the line.

As you have almost certainly gathered from previous entries, I work in a yeast genetics lab. It’s very fascinating; I’m sure you can imagine. One of the things we do on a routine basis is generate new mutant yeast strains… strains with mutations in genes we hope to study and understand (the former is easy, the latter rarely occurs).

As new strains are created, they are given systematic names: MAYxxx, where the prefix MAY is constant and the xxx represents the strain number, increasing by one with each new strain. Permanent stocks of the yeast strains are stored at -80°C until they are needed for future analysis, and the pertinent information is entered into a central lab database. When I joined the lab in 2004, the group was up to about MAY800.

In the past few weeks, I had noticed that we were approaching MAY1000. It turns out, in fact, that Daksha happened to be the one to create MAY1000. Could’ve been any of us: me, Rhonda, Annie… even Pavol. But, fate smiled on Daksha. Oh, I thought, how nice: the thousandth strain of the lab. It was a nice yeast name, a nice round number, but that was all. Not thinking much of it, I carried on with my western blot.

A few days later, at a lab lunch, my advisor revealed an “official” certificate he had manufactured with a gift card to Panera Bread. He announced, “We have reached an important milestone in the lab: our thousandth strain. And, Daksha, bless her heart, is the genetic engineer responsible for MAY1000. I now present her with this certificate acknowledging her achievement and this gift card to Panera Bread in recognition of what she has done for the lab.”

I was floored. I had no idea that there was official recognition or a prize up for grabs. Had I known, I would have toiled at the bench day and night, generating new mutant strains like gangbusters.

Outwardly, I was calm, serene, even congratulatory. But on the inside I was fuming, insanely jealous. It was at this moment that I committed never to be scooped like this again. I committed in my heart that I would be the Frankenstein to MAY2000. I would be the object of lab-wide adulation. I would have the points.

Here’s the catch. The lab has been in operation for over a decade and a half. I’ve been in the lab for about three years, and, if all goes as planned, I will be gone in less than a year. At the present rate of strain creation, MAY2000 will be created and maintained at -80°C in suspended animation by the year 2015. Give or take. By that time, I (and likely the other current lab members) will have moved on to better (or at least different) places, and a whole new complement of minions will be about my advisor’s business.

Thus, I hatched a plan and executed it today. In a recent burst of baby strain making, I had four new yeasts to add to the collection, which were named (in order): MAY1009, MAY1010, MAY2000, and MAY1011. Did you catch it? Read the list again, slowly. That’s right; now you see it. I have engaged in preemptive straining. I don’t anticipate this subtle tactic to be detected any time in the near future. However, in a dozen or so years, as the lab nears the creation of its 2000th strain, my advisor will almost certainly make a startling discovery: I’d already made the 2000th strain. Right after I made the 1010th. He’ll find MAY2000 in the database and will finally be forced to give me the respect I deserve (or at least crave).

I can’t wait. I will be in my late thirties when I eventually get the call. He will tell me that he is near retirement and has hit a landmark event that he couldn’t have reached (or at least didn’t reach) without my contribution: the 2000th strain. He’ll invite me to the lab lunch. I’ll graciously accept the offer (I’ll request that we eat at Spice Island Tea House). Over pad thai, he’ll give the speech about my accomplishment, this important milestone. He’ll reach across the table, shake my hand, and present to me the certificate and gift card. I will give some small speech, overcome with surprise and humility, just as Daksha was after she’d made MAY1000. I might also be heard uttering to the then current crew of jealous lab underlings: “Scoreboard!”

In the game of life, how many points is the 2000th strain? I’d say at least ten, since that is how many years this sort of accomplishment typically takes. I just took the accelerated course.

Awkward moment at TGI Fridays

We recently went out to eat with my parents at TGI Fridays (I ate a Dippable Cheesy Bacon Burger). My parents are routinely asking me about my work in graduate school, which, as my readers know, concerns yeast genetics.

They inquired about what I would like to do next, and I mentioned, somewhat flippantly, that I'd probably end up working on a sexier research project, at which point my mom began singing (with feeling), "He's too sexy for his yeast."

I'm not sure if she knows that's not how the song goes.


Originally Posted: Tuesday, December 3, 2006
(Then) Curent Mood: weird
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