Biology geek out

[katethekitcat]

Since we're all freaking out about applications (my profile says "public health," but my program has "molecular" in the title and I'm going to be in a biology lab the next 2-5 years), I thought it would be nice to have a place where can talk about, you know, that thing we all love enough that we're willing to put ourselves through this much hell to study it for a career.

 

So, here are some jumping-off discusison points. Answer any or all, but keep grad school out of it!

 

1.) What are you interested in researching? What scientific quesiton/problem most intrigues you?

 

2.) What do you think is the biggest challenge facing researchers today (i.e. open publication vs. journals like Nature; securing funding, lack of scientific literacy, etc.)

 

3.) What's your favorite microbe, and why? (Or ecosystem, or organism, or whatever)

 

4.) Favorite lab technique? One that was hardest to master?

 

5.) Thing you're proudest of accomplishing in the lab? Biggest screw-up you ever had in lab?

 

Or suggest your own!

[Leuco]

Okay, I'll try this

1) Hmmm.  I like studying pathogens.  I like putting together molecular puzzles, and I like proteins.

 

So, ideally, I think I'd like to study how pathogens use their proteins to invade.  I am fascinated by answering these questions that no one knows how to answer, and learning the utterly impressing way these guys manage to get past every darn thing we throw at them.

 

2)  Money, for sure.  With competition, and the sad state of funding these days... :/

 

3) Favorite microbe.... hmmm.  A few.

 

I really like influenza.  I've never worked with it, but we talked about it in a class, and I love the way HA works, and it's elegant way of releasing its contents into a cell.  Dengue, too, for pretty much the same reason (and the dengue hemorrhagic fever thing).  I can't decide whether it's a bad thing to enjoy a virus that causes so many problems, but eh. Nature of the field.

 

I have worked with E. coli a lot, and I like it for that reason.  Easy to work with, fun to study, and an all-around awesome bug.

 

4) Favorite Technique: Probably protein purification and/or crystallization.  It's awesome, can generate pretty pictures, and super gratifying when it works.

Least Favorite: PCR/Cloning. So. Many. Issues.

 

5) Proudest: Either when I got my name tag on the door as a tech/RA (I finally belong somewhere, unlike being an undergrad, when they don't "officially" recognize you) or when I sort of found a (ridiculously easy) technique from the literature that ended up being pretty well used in the lab.

 

Biggest Screw-up: (as an undergrad) Spilled an ice bucket ALL OVER a very expensive, very old spec (think fancy).  It essentially destroyed the spec.  I didn't get in too much trouble, especially because it was department owned and really old, so the grad students kinda wanted a new one anyway.  Some of the other professors said that my boss told me to dump the ice bucket, haha.  I was pretty well-loved and it was a total accident, so luckily they didn't talk about kicking me out or anything.

[rexzeppelin]

Great Topic!!

 

1. Well, honestly I'm a little insecure that I haven't committed to a particular question yet. I've applied to a lot of umbrella programs to allow for some rotations to figure my interests out a little better. That said, there are definitely questions and topics that I'm interested in. Here's a couple:

 

Exploring the ways that bacterial populations with identical genotypes can demonstrate phenotypic diversity through stochastic switching really intrigues me, since it challenges the clockwork view of biology where genes have a very specific expression A->B, and instead suggests a fuzzier reality where genes code for a 'cloud' of phenotypes, mediated by epigenetics, the environment, and randomness itself.

 

Figuring out an in vitro protocol for efficient directed evolution of proteins is another question I think is really cool. If we could figure this out, you could essentially have an automated drug-design machine. Other advantages would be that you could design protocols for multi-parametric optimization and select against unwanted interactions/pH/temp/etc.

 

In addition to these I have broad interests in exploring protein structure-function relationships and cell signaling cascades

 

2.) What do you think is the biggest challenge facing researchers today (i.e. open publication vs. journals like Nature; securing funding, lack of scientific literacy, etc.)

 

I think the the journal pay-wall is a huge issue. How can we kindle the imaginations of the next generation of scientists if they can't learn about the research being done today? I can't say how frustrating it was trying to research potential PI's and programs and constantly running into dead ends trying to look up papers. If science continues to cloister itself inside these prestigious academic clearinghouses it risks calcifying itself and further separating itself from the public at large.

 

In this country how can we hope to have strong government support for research if scientists don't make their case to the greater public for the value of the research they do? Currently it seems like the scientific community has let the ideologues on the right define science, and the recent headline showing declining Republican confidence in evolution should be an another alarm bell that we have to take action, or risk watching a slow, gradual decline of funding and research productivity.

[immuno555]

1.) I've been working in the tissue typing lab for 5 years working with HLA histocompatability and the organ transplant program at a hospital. I'd ideally like to target investigations into preventative measures to keep people from needing to go through a tedious process of the organ procurement/donation system, dialysis for 10+ years, or basically almost dead and in need of a heart liver or bone marrow transplant.

 

2.) I think depending upon your institution what ever "track" you end up going down post-doc. If it be the "academic track" or the "research track" many  universities require you to have a high output from your lab while also maintaining other academic responsibilities and (if at a hospital) clinical duties.

 

3.) I don't have a lot of experience with microbes, so my favorite protein would be anti-HLA antibodies!!!!!!!!!!!!!!! They are sneaking little suckers some times causing HUGE problems.

 

4.) I've spent a lot of time with the solid phase immunoassay luminex platform. If you aren't familiar with it, the platform basically uses flow cytometric principles in a micro scale with patented beads. You can basically customize any assay as long as you can attach the protein to the bead surface. 

 

5.) I designed and validated my own luminex assay that we are bring into clinical use (pretty awesome in my book!) 

 

So far it sounds like we are all in this for great reasons. I mean, just to get through this application process takes enough out of you!

[ion_exchanger]

I love this idea! Thanks for posting!

 

1.) What are you interested in researching? What scientific quesiton/problem most intrigues you?

I'm interested in researching infectious diseases, I find them interesting. I'm especially interested in using the structure of proteins to design vaccines. A secondary interest of mine is diseases related to protein translation. Protein translation is a really fascinating and intricate process. It amazes me how involved it is, and if just one thing goes wrong, for example the amino acid isn't activated, there are disastrous results. 

 

2.) What do you think is the biggest challenge facing researchers today (i.e. open publication vs. journals like Nature; securing funding, lack of scientific literacy, etc.)

Several answers to this question, but working in infectious diseases, I would have to say that one I have been thinking about is the smaller funding budget for diseases and disorders that "seem" less important than others. I think about those investigators a lot. 

 

3.) What's your favorite microbe, and why? (Or ecosystem, or organism, or whatever)

Lol. I would have to say E.coli. I express proteins in E.coli, I've studied E.coli's own proteins. You can do everything with E.coli. I love it. 

 

4.) Favorite lab technique? One that was hardest to master?

I would have to agree 10000000% with Leuco. I spend most of my time expressing, purifying, and attempting to crystallize proteins. I think crystallography is just the coolest thing ever. I geek out about it. When you get the purification conditions just right and are able to produce protein in large quantities, you feel great. When you optimize the conditions to produce large and/or diffraction quality crystals, you feel great!

 

Least favorite, PCR and cloning. It's so wishy washy. Sometimes it works completely, sometimes it doesn't work at all. There are sooo many components. If your polymerase was used by someone other than you and wasn't kept on ice, if your dNTP mix isn't right... I could go on and on. 

 

5.) Thing you're proudest of accomplishing in the lab? Biggest screw-up you ever had in lab?

I was most proud when I could troubleshoot protein expression and purification or crystallization problems by myself without having to ask my mentor, and how proud she looked when I told her everything that happened. I was also proud when I received my first summer student as a postbac, which I thought was too soon and I thought that I would totally mess things up, but when my student became semi-independent I was a proud mama! Haha.

 

Another proud moment was when I first searched for myself in the NIH directory. I used it to find info on scientists, and now my name is listed there. EEK!

 

I haven't had a major screw up in the lab yet, knock on wood. Once I made my ion-exchange buffers and accidentally put the equivalent about 200mM salt in the wrong premade buffer, and thought I wrecked the HPLC, until someone told me that some buffers, i.e. histag purification buffers, have salt in both buffers, so no need to worry. Just a day in the lab. 

[katethekitcat]

Least favorite, PCR and cloning. It's so wishy washy. Sometimes it works completely, sometimes it doesn't work at all. There are sooo many components. If your polymerase was used by someone other than you and wasn't kept on ice, if your dNTP mix isn't right... I could go on and on. 

 

 

Woah...two people hate PCR and cloning? That's actually my favorite thing to do!

[ion_exchanger]

The concept and end result of PCR and cloning are really cool. I like how useful it is. It's just so darn frustrating! Lol. I don't seem to have the magic touch that will make things work. I would have to run PCR for 3.5 hours and hope that my product was produced, and if it wasn't, have to run it again overnight, and then come in the next morning and hope it was produced again. If PCR didn't work, it would throw my experiments off by a lot.

[Leuco]

The concept and end result of PCR and cloning are really cool. I like how useful it is. It's just so darn frustrating! Lol. I don't seem to have the magic touch that will make things work. I would have to run PCR for 3.5 hours and hope that my product was produced, and if it wasn't, have to run it again overnight, and then come in the next morning and hope it was produced again. If PCR didn't work, it would throw my experiments off by a lot.

 

Sameeee.  I spent months on PCR.  Worked for everyone else, not for me.  It frustrates me because it takes forever to troubleshoot, and it seems to be magical sometimes.  I run the exact same reaction one day, and then the next, and get different results!

I dunno.  I agree that it's very, very useful, just very, very frustrating.

[ion_exchanger]

Agreed. I feel like I'm constantly wasting reagents. When I finally get PCR to work and run my experiments, I run colony PCR to confirm that the experiment worked. When it fails the first time, I have to run it a second time to make sure the reaction didn't just mess up. Oh the uncertainty.

[persimmony]

The concept and end result of PCR and cloning are really cool. I like how useful it is. It's just so darn frustrating! Lol. I don't seem to have the magic touch that will make things work. I would have to run PCR for 3.5 hours and hope that my product was produced, and if it wasn't, have to run it again overnight, and then come in the next morning and hope it was produced again. If PCR didn't work, it would throw my experiments off by a lot.

 

Seriously. You'd think a well established concept/method such as PCR would work flawlessly every time. In theory it should! Just like everything else...

 

In the past, I could spend half a day doing genotyping that would show up no bands. Then repeat the next day with new primers maybe, and it still wouldn't work. So frustrating. Then I do the exact same thing on day 3 and voila! Magic.

 

Nowadays, PCR works ~90% of the time for me. Maybe it just works better in the winter months. Who the heck knows.

Edited January 2, 2014 by persimmony

[acetylcholine]

1.) I am interested primarily in developmental neuroscience within an evolutionary and comparative context, particularly using invertebrates for comparison.

 

2.) Money.

 

3.) Cephalopods.  They're part of why I got into what I want to do; google 'octopus brain' and you'll know why.  I intend to use them as model organisms when I embark on my post-PhD/postdoc career.

 

4.) Favorite:  Confocal microscopy.  Hardest to master:  Either video behavioral analysis or immunohistochemistry.

 

5.) Proudest:  Finishing my first project.  Biggest screw-up:  I haven't had any particularly big screw-ups.

Edited January 2, 2014 by acetylcholine

[ion_exchanger]

I started doing PCR regularly and for the first time this past summer during my first rotation. I was chalking my mistakes up to beginners error, but it's nice to know that there is a deeper story. I'm not the biggest screw up. Yay!

 

To add to number 2, money is definitely a challenge I think from a materials standpoint. I was spoiled during my first research project in that I really didn't have to worry about materials/reagents, and I admit I could be a bit wasteful when I first started working in the lab full time. For example, I would throw away ion exchange columns without trying to reuse them, which makes me cringe. I've since gotten a lot better. I moved to a lab where materials were not as plentiful, and I had to be even tighter. I like to start working in the lab early, and once I came in to find that there were no blue falcon tubes to be found. I ended up having to hunt around the building to find someone that had them. 

[Adenine_Monarch]

1. I "grew up" in a gene therapy laboratory so that topic has always been my baby. The idea of correcting genes (or inserting correct genes) has always fascinated me. I'm also big on immunotherapy and any form of translational medicine. My PI was a doctor and there was always a clinical side to our lab, so going from bench to bedside is a big deal to me.

 

2.) The three examples you mentioned are all problematic to me. As one poster said, it is annoying to try to research POIs and realize you have little access to their work unless you are on university servers. Money is and will always be an issue. Coming from California, I have seen just how much difference CIRM has made for researchers interested in regenerative medicine, for example. That was a boatload of money that might never have been there if votes had turned out differently. The lack of scientific literacy in the general population is definitely a peeve to me. I wish there was some better way to teach science and get people interested in it. Not knowing basic things like how the body works or how evolution works is, in my mind, tantamount to not knowing how to add or multiply....

 

3.) I guess because of my line of work, I have a particular fondness for E. coli, mice and HIV (the basis for all lentiviral vectors).

 

4.) I love DNA so I've always gotten a kick out of any sort of DNA purification (plasmid, genomic, micro whatever) especially when you do it the old fashioned way of winding it around a glass rod. I also like mouse work.
Any sort of PCR is hard to master. I have a love/hate relationship with it. Quantitative PCR was my specialty and I got pretty good at it. But it's like training a puppy; you constantly have to be on it or it gets out from under you and your data comes out looking crappy if you put that plate in on a day when you were tired... TIP: Careful, slow pipetting can make a HUGE difference....!

 

5.) I was proud of successfully troubleshooting and designing a qPCR based genotyping method for our lab. I always felt pride in passing on knowledge to other students/fellows/whoever. And I was very proud to discover clear cut evidence on a question we were asking that went straight into our paper. I also killed a large Southern blot gel tank once by accidentally pushing it off the shelf onto the bench opposite me. I also got my x and y axes mixed up on some FACs data I was presenting one time. Mortifying when my PI pointed it out and was mad at me afterwards....

[pyrocide]

1.) What are you interested in researching? What scientific quesiton/problem most intrigues you?

I've been working full-time as a lab tech in a heart development lab for the last 2 years.  In my first project I was introduced to cardiomyocyte (CM) differentiation techniques, and we focused a lot on growth factor modulation.  That didn't really catch my fancy, but my next project involved conditionally deleting a protein in mouse CMs that is involved in very early development, dsDNA repair, and histone modification. That's been really awesome--it has introduced me to heart tissue remodeling, CM cell cycling/apoptosis pathways, and of course dsDNA mechanisms, which I've been geeking out about since college. Mostly I'm looking for a lab that looks at CM responses in both developing and damaged tissue with a stronger emphasis on the molecular (and maybe even some genetic) biology of CMs. Also, as I mentioned before, I'm terribly intrigued by elucidating physical dsDNA mechanims and the big enzyme complexes involved (i.e., DNA replication, homologous recombination, dsDNA repair). I'd be so excited if I could get myself a rotation in that kind of lab. 

 

2.) What do you think is the biggest challenge facing researchers today (i.e. open publication vs. journals like Nature; securing funding, lack of scientific literacy, etc.)

Money. There's no money for grants, no money for new researchers, and no money for new grad students.

 

3.) What's your favorite microbe, and why? (Or ecosystem, or organism, or whatever)

My senior project was on Pseudomonas aeruginosa, which is your pretty standard microbe, I guess. It turns blue sometimes, which is pretty cool. C. elegans is pretty fun--rol mutants are the best. Stem cells are fussy monsters. I have to say I like mice the best, mostly because I've got the dexterous fingers to handle the more complex procedures mice often require.

 

4.) Favorite lab technique? One that was hardest to master?

Favorite: adult cardiomyocyte isolation. I'm proud to say I can keep my hands still enough to successfully perform mouse heart cannulations.

Hardest: For some reason I just had the worst time mastering western blotting. Back in college I completely botched the WB section of the Intro Bio Lab, and I wasn't given much of a protocol when I had to do it in my heart research lab. Troubleshot everything before realizing my chemiluminescent detection reagent a coworker recommended wasn't potent enough. That was rough.  

 

5.) Thing you're proudest of accomplishing in the lab? Biggest screw-up you ever had in lab?

Proudest accomplishment: early in my time at the heart lab, the lab just could not get its heart differentiations to work. Just.. nothing. Not even early mes-endoderm markers (growth factor quality control is terrible and it should feel terrible. ><) Bossman had me try out a new protocol, and I was the first to get a cardiomyocyte + culture the lab had seen in like a year. The cells didn't even beat, but it still felt like Christmas. 
Biggest screw up: On my first neonatal cardiomyocyte isolation ever, I tried a Percoll separation (reduces fibroblasts and other small cells from your sample) since that is what the grad student who had the project before me used to reduce fibroblasts. Before I ran the Percoll, I had a beautiful yield of cells, but lost every single one of them after spinning down the column. Turns out there was a miscommunication and bossman did not want me to run the Percoll--turns out he hates using the Percoll column since it usually reduces yield something fierce. CM isolation kits are very expensive and he was very upset with me for a while after that. He still brings it up whenever I have a new protocol to learn.  

[ion_exchanger]

 

4.) Favorite lab technique? One that was hardest to master?

Favorite: adult cardiomyocyte isolation. I'm proud to say I can keep my hands still enough to successfully perform mouse heart cannulations.

Hardest: For some reason I just had the worst time mastering western blotting. Back in college I completely botched the WB section of the Intro Bio Lab, and I wasn't given much of a protocol when I had to do it in my heart research lab. Troubleshot everything before realizing my chemiluminescent detection reagent a coworker recommended wasn't potent enough. That was rough.  

 

 

 

I have a love hate relationship with western blots. I think they are pretty cool and love the information they provide, but yes finding the right tricks to make them work is a little annoying. Sometimes my results are a little inconsistent. I also have a problem with developing the film. When I first started running them, I was wasting so much film because I couldn't decide how long to expose them. Everyone's film was so much prettier and cleaner than my film. 

[astaroth27]

1.) I second gene therapy. Huzzah! I am more of a genetics person than an immunology person but both topics fascinate me.

 

2.) Money, definately. However, it is just a symptom of our misplaced priorities in this world. I don't want to go into politics but I think we could all agree here that scientific research is underfunded and dismissed by people who don't understand it.

 

3.) C. difficile! I have never studied a more pervasive organism. Study it at your own risk but good luck getting rid of it when you are done.

 

4.) Favorite: Anything I have never done before. Once I master something I don't have an interest in personally doing it anymore.

Hardest: Plasmid construction. It is a skill I am glad I learned before grad school but I have only recently been able to get a plasmid I made myself to function as a vector.

 

5.) My proudest accomplishment was one of my first. Genetically engineering some bacteria to smell like popcorn butter based on my own experimental design was a proud day. Maybe not the most practical experiment but it made me a gene therapy believer.