Friday's Discovery

As most of you know, my original project - the one I spent all semester in the writing seminar drafting a proposal for - was published before I got a chance to finish it. In fact, it was published before I was even fully trained in the lab, but I wasn't aware of this until around a month into SRI. At first this was kind of discouraging. To be honest, I wasn't sure I wanted to stay in the Gorsich lab anyway so when the opportunity presented itself to switch I had to fight hard not to take it. After a lot of thinking I decided to stay in the lab despite the fact that familiarity was really all I had there. What I learned last Friday affirmed to me once and for all that this was the right decision. 

As you might expect, losing the entire semester's worth of writing and the first month of summer for research really did not leave much room for anything else. I spent most of the time that I was in lab on my feet skating around everyone else to check optical densities or make time points or to do any of the other work that needed to be done at the time. What this meant was that I didn't have time to stay current regarding the articles in my field or to begin reading up on the parts of my research that had changed since my first project was cut short. So, a couple days ago when things started to wind down a little bit that's exactly what I did. 

My original project was titled "Characterization of ribonucleoprotein (RNP) granules in yeast exposed to fermentation inhibitor furfural." The benefit of this project was that it was relatively straightforward but had the potential to produce some pretty fundamental information to the fields of cell and molecular biology. Basically all I had to do was transform the P-body and stress granule marker plasmids into the yeast and grow them in the presence of furfural, periodically preparing slides from the culture to look at under fluorescence microscopy for formation for the RNPs. I admit it was pretty simple stuff, but it was engaging enough for my first project.

After I ended that project, the new focus of my research became comparative in nature. Whereas before I was only concerned with whether RNPs formed, now that we know they do in the presence of furfural (thanks, Iwaki), I am tasked with seeing if the overexpression of ZWF1, a gene important in the pentose phosphate pathway, effects their formation in the yeast. There is good reason to think that it will, but that's for another post.

So there I was consulting genome databases and the latest articles on ZWF1 when I come across an interesting piece of information: yeast ZWF1 is a homolog to a gene in humans. That is, humans have the same gene which is involved in the same relative process.

So here's where it gets sciencey. Brace yourselves.

ZWF1 in both humans and yeast codes for a protein, zwf1p, better known as glucose 6-phosphate dehydrogenase (G6PD). G6PD is an enzyme that catalyzes the first step - the rate-determining, irreversible one - in the pentose phosphate pathway, a mechanism which reduces NADP+ to NADPH. Basically, these activated carrier complexes are vital for cells - whether human or yeast - because they comprise one of the only methods biological organisms have for dealing with oxidative stress. So, NADPH reduces a molecule called glutathione. Reduced glutathione acts as a mop for free radicals in the system, removing the pressure of the oxidative stress, which is all well and good, but that's only part of why ZWF1 is so interesting.

Often in organisms diseases or afflictions amount to problems with a single gene or protein. Such is the case with hemolytic anemia, or G6PD deficiency. Hemolytic anemia is the result of a person having a low RBC count. There can be many things that case this but with G6PD deficiency, the resulting hemolytic anemia is caused by, you guessed it, a problem with G6PD - the enzyme that is coded from ZWF1, the gene whose homolog I work with in yeast. From what I understand, some event results in relatively inactive G6PD, which means a halted pentose phosphate pathway, which means no reduction of NADP+ to NADPH, which means no reduction of glutathione, which means its a free radical family reunion up in that cell. Further, erythrocytes have no other mechanism for dealing with oxidative stress -they rely solely on the pentose phosphate pathway, so those sucker just burst from all that stress resulting in the low RBC count a.k.a. hemolytic anemia.

Point is, unannounced to me, I've been working on some pretty rad medical stuff in addition to the implications overexpression of ZWF1 has on fermentation.

Fucking intense, am I right? 

Don't Even Ask: Responses to an 'All-About-Me' Interview

1. What do you know to be true, unquestionably beyond doubt, certain with every cell of your being, completely, passionately, righteously certain? -- Absolutely nothing.

2. What was the dumbest thing you used to believe? What changed your mind? -- I used to believe that sex was some sort of taboo, criminal thing. I reasoned that that is why it is done in secret. And I think puberty changed my mind. That and the internet.

3. What do you know the most about? -- I wonder if this is asking "what do you know more about than any other person?" or "of the things you know, which do you know the most about?"

4. Why do you do what you do? -- See determinism. https://en.wikipedia.org/wiki/Determinism

5. One word: breakthrough. What comes to mind? -- Frankly, what immediately comes to mind is how inconsequential and boring this question seems. But when I think of the word breakthrough I think of how I typically hear it accompanied with scientific. 

6. What has been one of your most memorable experiences in your career? -- If I can just replace career with education, as it's pretty much the extent of any career I've had so far, I think visiting OWS in Manhattan with my freshman SOC221 professor was the most memorable experience I've had so far.

7. What global policy, credo, practice, or law would you like to decree? -- Hm... probably something environmental. 40 lashings for improperly recycled plastics would be a good place to start. (I do it for teh lulz).

8. What experience tested your mettle but made you a better person? -- In a word, McNair.

9. Finish this sentence: "It's a good day when..." -- it's not a bad one. I find that defining everything that isn't absolutely terrible as okay helps to make it okay, and the likelihood of running into a bad day when you call most days good is lower than the alternative.

10. When was the last time you thought, "Yes! That person has got it going on!"? -- Probably a couple of days ago after watching an E. Warren video wherein she lambastes a couple of reporters who clearly didn't know who the hell they were talking to, or what the hell it was about. E. Warren's got it going on.

11. What question in your life has had the biggest impact on you? -- This one. This one being asked right now. Dat impact.

12. What are you positively addicted to? -- The World Wide Web.

13. What's the best advice you were ever given in terms of business? -- Spoken by a wise man I once knew: fb;gm.

14. What's the most common life advice that you give your friends? -- "Named must your fear be before banish it you can." (Also, lol @ "friends").

15. What the first thing that comes to mind when you hear the word devotion? -- Religion.

16. What are you most interested in? I like rhetoric and philosophy. Like, a lot.

17. What are you incredibly grateful for? -- All the stuff everyone else already said added together +1.

18. What's your form of service to the world? -- There is a quote that says something along the lines of "your place in the world is where your passion meets one of its greatest needs." I tend to agree with this, but service is different than place, so I'm going to modify it: your service to the world is what you do in your place in the world where your passion meets one of its greatest needs. Unfortunately I haven't really figured out the "passion" and "greatest needs of the world" parts yet, so the best thing I can do for now is find my place. And a step toward service is kind of like service, right?


"Something inspirational" - Someone Important.

"What's chronic, repetitive or inflamed in your life?" - Danielle LaPorte

"Try not to over think everything." This short and sweet sentence is probably the best advice I've ever been given, and it's some of the only advice I can never seem to follow. So it lingers in my thoughts, subtly haunting me from day-to-day. But the advice itself is only a reminder of what's really getting at me.

What seems to be the biggest problem I face is an overwhelming feeling of futility. When I give reality any real thought I always end up with the same eerie, shrill feeling: none of this really amounts to much of anything. Not really. Steeped in convention and inherited values, I get the feeling that we are all just blindly, steadily marching toward oblivion with smiles more or less painted on our faces. I've convinced myself that this isn't the product of emotion but logic. It's reason that has led me to this conclusion, eagerly pushing me toward the edge of optimism (and indeed sanity if I can admit that) to a bird's eye view of the abyss that awaits everything and everyone anyone has ever valued. In the end, I ask myself, what is it all for?

I'm not religious. I see the value in faith - I was raised in a deeply religious family with pastors for grandparents, so I've seen that side of things - but it's just not my narcotic. I'm not convinced of eternal happiness or existence. When I think about the universe and (to the best of my ability) consider its scale and immensity, I can't help but realize just how fragile everything we know and value is. In the scheme of the universe we are less than inconsequential, and at any time some cataclysmic event could reduce all of the knowledge and history ever recorded since the beginning of time to dust. And calling what would be left of our existence dust is probably being generous - there's no guarantee that there would even be a trace left after such an event. Neil deGrasse Tyson says, "the universe doesn't care about us," and although he says this in a comedic and conversational tone, I doubt he finds the idea much more comfortable than anyone else who has given that truth any serious thought.

This sense of meaninglessness is not conducive to anything. I know that. I know that living life with the thought that everything is coming to an end sooner or later is, in itself, useless (I'm sure you can appreciate the irony in this by now). But that doesn't comfort me, and I'm not sure that it should. As a scientist, I probe the world in search for truth. And as far as I can see, it's true that we are on a collision course with another galaxy with plenty of asteroids and other space debris to encounter along the way. It's true that everything we've ever created from the Mona Lisa and the Prius to Central Michigan University and the friends we have there is hurling toward its place in the utter, inescapable chasm of nothingness that awaits.

This idea is was it chronic in my life. This is what I struggle with from day to day to say nothing of things far less existential such as finances and my research.