Duke University | Howard Hughes Undergraduate Program

Well, tomorrow is the final day of the HHRF program this summer, so things are rapidly finishing up. This summer has definitely been very informative, especially since I'd not been in a lab before and thus, prior to just a couple weeks ago, had no idea what the research life was all about. Now I have at least a taste of what it means to be a research scientist.

First of all, I've noticed that research scientists generally work very independently. By that I mean that it is, in fact, rather unusual for all the researchers in a lab to have similar projects. Instead, it is far more common for everyone to be working on related but different projects, meaning each person is essentially on his or her own when it comes to optimizing experiments, figuring out protocols, etc. While others in the lab may have expertise in certain areas, everyone is still generally working independently.

I've also noticed things about the way research scientists communicate. Researchers are generally very skilled at taking in information that comes in the form of numbers or test results - any sort of empirically gathered evidence is easy for researchers to handle. Conversely, researchers generally don't seem to dig language-based info quite as much. Perhaps this is a function of their focus on results gathered in the lab, or of their extreme specialization in the particular things they are good at (rendering communication difficult between researchers)...but whatever the reason, I have observed that researchers would generally rather convey and receive information in the form of data rather than purely in word form.

Finally, I've learned a lot of interesting things about PhD tracks in general. I've come to realize that there's a ton of variability from lab to lab as to how hands-on the PI is, what the lab environment is like, what kind of funding is available, what kind of hours you're expected to put in, etc. Unlike law school or med school, for instance, PhD programs have no set time in which to complete the degree requirements - you simply keep going until you're finished (kind of), which could take anywhere from 4 or 4.5 to 6.5 years. And on a day-to-day basis, the research life (whether for grad students, post-docs, research associates, or whatever else) has a unique, open-ended feel: There's always more work to be done, and for that reason you can pretty much determine your own hours and work as much or as little as you like, assuming you still get your work done in the end. I think it's fair to say that not too many jobs have this kind of flexibility.

So as I say, it's definitely been informative to learn these things about the research life. Working in a cancer bio lab this summer has only reinforced my belief that my future career should involve something medically-related, and whether that career will involve me earning an MD, a PhD, or an MD-PhD (or something else! though I doubt it), I don't yet know. I enjoy writing and working with people, so perhaps some career which incorporated these skills along with a focus on medicine would be good for me. I'm not entirely sure yet; this requires a lot more exploration, but I've got time.

So. This past summer has been kinda crazy, in the sense that at many times I've felt almost overwhelmed by the number of new skills and techniques I needed to learn simply in order to get some basic results. I think I've picked up many of the basics of lab work over the summer, starting with pipetting and doing serial dilutions, and extending to doing Western blots, visualizing gels with UV radiation, getting spec readings on purified DNA or RNA samples, and plating cells. And don't forget learning how (and to what extent) to follow instructions within scientifc protocols. This last one is, in fact, quite important, because, as I've learned, every lab varies in terms of the specific conditions (types of machines, solutions, etc) they are using, so whereas a paper or a protocol may advise 65C for the annealing temp in a PCR reaction, we may have to use 53C because we have a fast-heating machine and they have a slow-heating one. Or whatever. Any minor difference from lab to lab could throw off an entire experiment, and you just have to learn to be aware of that and be willing to go back and try different things (or anticipate what will need to be changed or played around with) in order to optimize the results you are getting.

And optimization is something else. Before starting this summer (that is to say, before I knew what I was getting myself into), I was really excited about the work being done in the lab I'd been assigned to. And to be fair, I still am; I still think the principle of this cancer bio research is really fascinating. But good grief, the optimization! Ok, here's what happened in my case: I first spent a couple weeks just learning stuff. Then I did several Dox trials (each with at least 1 day of incubation/exposure time involved), just trying to get the conditions right and figure out what amounts of Dox were the best at causing cell death. Then I did an siRNA trial, with 2- and 3-day exposure times. Then I did 3 chimera experiments, each with 2- and 3-day exposure times. (Although the second experiment didn't really count, since I'd forgotten a critical step, which we realized after looking at my 2-day data, so there wasn't any point in doing a 3-day reading. But it still took up time.) And for any one of those steps - Dox, siRNA, or chimera - I could continue optimizing indefinitely if I wanted, just to fine-tune all the conditions needed. That's crazy!

In conclusion, I think this summer was really just more surprising than anything else. As I've said several times over the past couple blogs, I really had no idea what research was all about prior to doing the HHRF, so if nothing else I do now have a feel for life in a lab setting - it's definitely been a crazy eight weeks!

It's now week 7 of the program, and we've had the chance to hear a number of seminars up to this point. Judging from these, there are several things that, in my opinion, make a good seminar:

(1) Mindfulness of time. This may sound elementary, but I've observed that all the speakers I like the most have been cognizant of their allotted time and are careful not to talk past when they're supposed to be done. I know you are enamored of your research - that is, of course, why you do it - and even if I feel the same way, I'm not so crazy about your job that I can just drop all my commitments for later that evening. I really like when the speaker respects the audience enough to bear in mind that he/she is speaking on their time as well.

(2) Engaging the audience. Several of my favorite speakers have stopped for questions, or even posed questions to us, in the middle of their talks. I think all the speakers have probably said or felt that the seminars were pretty informal, so questions in the middle of the talk were acceptable, but only a few speakers (in my mind, the better ones) really seemed to encourage audience participation.

(3) Explaining jargon or specific terms used. Some of what I thought were the better speakers were sure to explain the terminology they were using, which was great. It seems that, fairly often, researchers can become caught up in the lingo of their lab, and so even though FGF-8 might be the most basic thing to them, I may have no idea what that is and thus require an explanation. The only caveat to this is that speakers should be careful not to over-explain. For instance, you don't need to tell me what mitosis is. (I don't think any speaker did this exactly, but someone explained what I thought was a comparable term in terms of level of ease or obviousness, and I didn't think that was quite appropriate. I may still be an undergrad, but I have had biology classes in my life.) 

(4) Using humor effectively. If you know you can make decent jokes to lighten the mood of a presentation like this, do so. If not, please don't try.

Also, as for general comments on the nature of the seminar (which will not be affected by how "good" or "bad" the speaker is): I think it's quite difficult to achieve a good line-up of speakers. There's definitely been a lot of diversity of topics represented, which is great, but more often than not I find simple factors - like my tiredness at the end of the day - standing in the way of my really getting the most out of the seminars. I've truly enjoyed about 3 or 4 of the seminars (I think was largely because the speakers were good and perhaps I just had more energy on those days). For the rest I've just found it poor timing to have a seminar at the end of a presumably long day of research for everyone, with the lights turned off for optimal PowerPoint viewing and/or induction of sleep (it's hard to tell)... And I think on those days - though perhaps I was just particularly tired - it wouldn't have made a difference how "good" the speaker was.

But cheers to drawing near the conclusion of 8 weeks of research - wish me luck on my abstract and poster!

Salutations. I'm back in the lab for Week 6 of research, and on the whole things seem to be going well. The PhD with whom I work primarily on a day-to-day basis has been out of town for the past couple days and won't be returning till later this week...although she left me a detailed to-do list, I have admittedly been a little frazzled by having to work on my own (this is, you may recall, not just my 6th week in this particular lab, but also only my 6th week in any lab setting at all, so it's a little disconcerting to have to fly solo at this point in the game). Last week was not too bad as for being on my own, but I got to start off the morning and week today with troubles pouring my acrylamide gel. I did learn, however, (several attempts later) that clamps and thin separators (as opposed to the thicker ones) are, in fact, necessary to properly pour a gel.

In any case, I'm trying to continue to look at the big picture of my research and keep in mind how my overall timeline is progressing. You might remember that my project is divided into four phases: I'm effectively done with the first (apoptosis assay with just siRNA), am wrapping up the second (synthesis of chimera; I should be basically finished when the sequencing results return for the plasmid and when I've annealed the antisense strands to yield a full chimera), and am soon to move on to the third and fourth phases (validation using qRT-PCR/"real time," and testing the full chimera on LNCaPs respectively). It probably sounds a little slanted, as I've really only got 2 of the 4 phases done and I'm more than halfway done with the research program this summer, but a large chunk of my initial time here was spent just learning the basics, so I think I should come at least reasonably close to finishing my project this summer. I'll be sure to give an update on how the sequencing and annealing turn out.

...The results of plasmid sequencing are now back. I haven't really gotten a chance to analyze them yet, but judging just from the length of the sequences sent back to me (and I don't even know if this is a valid thing to go off of), it appears that I got good data on some and bad data on others. Well, as Kristi would say, "That's science." All in all though, I think that in my four days of relative independence (Kristi was out of town so I was basically on my own in the lab for the first time), things went fairly well. I got bands on my acrylamide gel (woo hoo! That doesn't always happen), had a successful transcription, and was able to do all the necessary calculations for and then actually go through with plating cells...though not necessarily all in that order. I haven't made it to the validation step of RT-PCR yet, but that can wait till tomorrow. So what does that mean in terms of the phases? I suppose I'm pretty much as done as I'll ever be with Phases 1 and 2, I'm into Phase 4 (now that I've plated cells with the chimeras to test if the chimeras cause cell death), and I will soon be starting with Phase 3 (validating through RT-PCR that my siRNA is, in fact, killing cells particularly by knocking down the target gene).

The one thing I'm mildly concerned about is putting together an abstract and a poster for the conclusion of the Howard Hughes program. I feel that I've not been here long enough to have really substantial results - results which I'm proud of and confident in putting forward - so I'm a little confused as to how I'm to go about exhibiting my data. But as I figure that out, I'll let you know. One thing I do know is that fabricating data is unacceptable within the scientific community. I'm glad I read the Poehlman article, which informed me that making stuff up is generally frowned upon within the scientific community.

Howdy. I'm now in the middle of my 5th week of research this summer - it's hard to believe that not only are we past the halfway mark, but also, due to the deadline of poster submission to allow time for printing, there are really only 2 wks of research remaining as far as results that will actually make it to the poster. Unbelievable!

What I've been working on lately is more with synthesis of my chimera. Assuming my most recent PCR worked (I'm keeping my fingers crossed), I'll be able to do a gel extraction, followed by purification, then I'll grow up bacteria colonies and send these off for sequencing. All of this will simply allow me to make sure that what I've actually been making is in fact the same as what I think I've been making all this time. At this molecular biology level, nothing's visible to the naked eye so it seems that there's a lot of guesswork involved.

(later...) I did in fact get my plasmids all prepped and ready to go, and sent them for synthesis on Friday. I expect to have the results from that tomorrow (Tuesday). In addition, I've been working toward running a chimera experiment to see if the full-blown chimera induces apoptosis in my LNCaP cells. I've transcribed (converted DNA to RNA) and am currently running out the 3 chimeras (the experimental, the control which has a mutant aptamer, and the control which has a mutant siRNA) on an acrylamide gel. If that works, I'll extract the genetic material from the gel, purify, and eventually anneal the anti-sense RNA strand to the siRNA portion (as transcription gave me only one long RNA strand, whereas a true chimera includes a, by definition, duplexed siRNA) in order to do my chimera experiment. Hopefully all goes as planned!