Wednesday, August 20, 2008
Daily Next Six Months' Douchebag: Razzy
While this may cause a great deal of lamentation and sorrow among my legions of dedicated Razzphiles, I have to sadly announce that the "Daily Douchebag" and "Daily Dude I Want to Hit" features are indefinitely suspended.
I'm sure you all just attempted to punch your computer screens in shock and rage, but before you destroy your gateway to the internets, let me offer an explanation. The other day, one of my lovely anonymous Razzy Haters left the following comment:
Sure, make fun of world class athletes who are actually succeeding in life. Of course, you are successful, if you consider being an alcoholic a success. How about publishing some articles? So much for publish or perish: no wonder Columbia is the laughingstock of the Ivy League. By the way, you have already failed in your goal to model rhinovirus in mice (see: Bartlett et al. 2008 Nature Medicine)
I thank the commenter for recognizing my achievements in avoiding sobriety, and applaud them for picking on me in a way that I figured someone would have done a long time ago: hating on my publication record. It's true that I have not published my research in a peer-reviewed journal, primarily because, as the commenter also notes, my thesis project has been an abject disaster. I spent my first three years in graduate school working on a transgenic mouse. "Transgenic" means that it was genetically fucked with to express the human receptor for rhinovirus. In theory, this would mean that it would express said receptor in its respiratory tract, and thus be susceptible to infection with some mouse-adapted rhinoviruses we had sitting around the lab. I showed by every means possible that this mouse had integrated the transgene into its germline DNA (PCR and Southern blot), it was expressing the transgene (Northern blot and real-time quantitative PCR), and the receptor was present in the mouse trachea (immunohistochemistry). However, the mice still were not supporting virus replication, so I eventually did some flow cytometry and saw to my horror that the receptor was not present on the cell surface. Since the receptor normally is responsible for snagging the virus at the cell surface and bringing it into the cell, this was a major blow to my thesis work. After three years of doing every experiment imaginable to understand what was going on, I realized that while this mouse might be transgenic, it was never going to be susceptible to infection. With a heavy heart, I sacrificed the mice and began to plot a plan B.
Because making transgenic mice is time-consuming and expensive, I decided to instead isolate rhinoviruses that could use a mouse cell surface protein as a receptor. This means I can use any mouse to develop my model, but first I need some rhinoviruses that can grow in mice. The reason why people aren't busy doing all kinds of in vivo work with the common cold is that rhinovirus does not grow well in mouse cells at all. There is a block at the level of viral RNA replication that results in negligible production of infectious virus from mouse cells either infected with virus or transfected with viral RNA (in human cells, you can just pop the viral genetic material itself into a cell, this will be translated into viral proteins and replicated by the viral polymerase, and voila–the cell makes new virus). So I spent the next two and a half years passaging rhinoviruses capable of using the mouse LDL receptor for entry back and forth between mouse and human cells, to select variants which grow better in mouse cells. I did this through two different mouse cell lines, and finally showed that I did indeed select viruses with robust growth in mouse cells. The next step would be to try it in actual living mice.
Unfortunately, right at that time, an epidemic of mouse hepatitis virus tore through our mouse facility. The veterinarians made me stop breeding my colony for five months, which translates to NO MORE MOUSE WORK. So I spent that time trying in earnest to clone my adapted viruses, which has been a whole other technical bitch and a half that I won't get into. A few months ago, I was given the go-ahead to resume breeding, and I thought, "FINALLY! I can get these mouse experiments finished, write it up, maybe dabble in some asthma work, get Ph.ake doctored, and get a real job (or a post-doc)!" However, the technicians in my animal room have been rough with maintaining our colony and all the dams (mommy mice) have been on a gluttonous spree of eating their young. When mice get stressed, they tend to eat their newborn pups because they're stupid and gross. I tried to avoid this by instructing the mouse facility staff to add cotton nestlets (squares of cotton that the mice shred up and nest in), ensure they are eating breeder chow for maximum fertility, and not disturb cages with newborn pups (baby mice). The technicians have not heeded these formally requested instructions, so I had to send a bitchy e-mail to their boss. How many of you have ever had to address the topic of CANNIBALISM in a work e-mail?
I was just in our mouse room and noticed that many of our breeder cages did not have extra cotton nestlets and, in a few cases, breeder chow in them. Some of the cages without nestlets appeared to have been recently changed. As you may recall, I recently requested that all breeder cages not be changed if they contain newborn pups, that all breeder cages be given breeder chow, and that all breeder cages be given several cotton nestlets when changed. I made these requests to both maximize litter size and reduce cannibalization of newborn pups, which has been a problem for some time. While a certain amount of cannibalism is normal and unavoidable, I have noticed evidence in many of my breeder cages (ie: blood, viscera, and partially cannibalized pup corpses) of widespread dam cannibalization. In fact, despite having numerous cages devoted to breeding some strains of mice, I barely get several pups per month that survive to adulthood because most are neonatally cannibalized, likely because the dams are stressed by cage changes and a lack of nesting material. This is having a significant impact on my research, as it dramatically reduces the number of mice I'm able to work with. Today I noticed evidence of recent cannibalization in several breeding cages (neither of which had additional cotton nestlets in them when discovered).
The recent outbreak of MHV has taken its toll on my ability to perform mouse work, and now that our room is cleared, I was hoping to have access to as many mice as possible. I believe that the requests I have made will significantly reduce the cannibalism problem which has plagued our colony since I was able to resume breeding following clearance of MHV from our room. Would you please ensure that the requests for special care of our breeder cages are being rigorously implemented?
The facility manager was very apologetic and assured me she would have a staff meeting to address these issues and they would be handled. God willing, in three weeks I will have mice to complete my thesis with. This still means another nine months of work, which is where suspension of my "Daily Whatever" posts comes in.
Those of you who are suffering alongside me in the trenches of scientific research funded by the elusive NIH RO1 grant know that thanks to our current president's hatred of all things involving "stem cells," the entire NIH budget has been drastically cut and everyone is having a hard time getting grants to fund their labs. My PI (boss), who is extremely well-regarded in his field and who writes a fucking textbook on the subject to prove it, has experienced the trials of securing funding as much as more junior faculty who aren't endowed full professors at an Ivy League school. Therefore, our lab has four students on one grant, which is too many. You would think that in the interest of supporting research which will yield papers and grant money and thus enhance its reputation, Columbia would use its considerable financial resources to help out, but you would think wrong. Columbia doesn't give a fuck because they haven't gotten any bad press for it, and that's the only thing which spurs this institution to do ANYTHING. That is why, as anonymous hater pointed out, Columbia is the laughingstock of the Ivy League. Instead, my department's brilliant solution to our lab funding problem is to get rid of students. Because three of the students on my PI's grant (including myself) are sixth years, they are graduating all of us ASAP.
You might think, "But Razzy, you complain about grad school all the time! Don't you want to get Ph.ake doctored like tomorrow?" While I absolutely would love to move on to my post-doctoral life, I don't want to do it before I publish my dope-ass mouse model. Unlike anonymous, I don't believe that I have "failed" at my project because another group published a model before I did. Other models have been published similar to that one which have many drawbacks. The specific paper anonymous cites shows viral RNA replication in mice, but virtually no production of infectious virus. I consider production of infectious virus critical to a useful model, because what's the point of using an animal model if it doesn't mimic the human disease? When you get a cold, you shed tons of infectious virus out your nose. That's how the damn disease is transmitted. I probably could have demonstrated production of negative strand RNA two years ago and published it, but my standards for a model require production of infectious virus by infected mice. The fact that Bartlett et al published their subpar model in a demi-Nature journal only goes to show that there is a substantial need for this kind of experimental system, and the rhinovirologist community will take what they can get. That's why when I complete my experiments, my paper is going to rule everybody's face off. However, I won't be able to do that if I have to graduate in December, a prospect that was sprung on me last week.
I have worked it out with my department to graduate in February, which should give me enough time to complete my experiments, submit one or two papers for publication, defend a thesis I am proud of, and get a real job. This timeline is feasible, but mandates working extremely long hours. I have worked hard throughout graduate school and have experienced many setbacks due to events beyond my control. However, now that I'm on the homestretch, I don't want to give the haters any ammunition suggesting that I didn't overcome all of it with some hot publications and the respect of my scientific peers. Therefore, if I'm going to get up at 5 a.m. to write for four hours every day, it's going to have to be papers rather than blog posts. I'm still going to do my best to write at least one thing every day, but I just can't justify researching and writing (usually copiously) about a minimum of two topics. I love writing this blog and I am sad that I have to dial it back a little, but sometimes you have to prioritize your life, and what you want to do takes a backseat to what you need to do. I need to blind some bitches with science for the next six months, so please be patient with my reduced output of Razzification during that time. I promise at the end, you'll have some SWEET peer-reviewed journal articles to read! TRUST!
Labels: excuses, grad school bullshit, Razzification, Razzy Haters, science, viruses rule
Comments:
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Your PI should have adhered to the LPU philosophy and forced you to scoop Bartlett. Waiting until you have something "whole" to publish is so 1970's.
# posted by 
: 8/20/2008 3:48 PM
: 8/20/2008 3:48 PM
Wow, I can't WAIT to read your thesis! Make us all proud, Razzy (including yourself)! We're rooting for you.
And I will miss your Daily Douchebag/Dude I want to hit. Props for staying true to your inner nerd, though. =D
And I will miss your Daily Douchebag/Dude I want to hit. Props for staying true to your inner nerd, though. =D
I got in one little comment and Razzy got scared and said she moving with her writing and science in Colubmia.
Wow...
I'll be waiting with bated breath for your article.
Wow...
I'll be waiting with bated breath for your article.
# posted by : 8/20/2008 10:36 PM
: 8/20/2008 10:36 PM
I think I'd be more concerned about this news if I were a mouse.
Am I mistaken or is this the first time you've used the word "sobriety" in one of your posts?
Am I mistaken or is this the first time you've used the word "sobriety" in one of your posts?
# posted by : 8/20/2008 11:19 PM
: 8/20/2008 11:19 PM
Razzy - you do what you have to and do not forget... DO NOT LET THE FUCKERS GET YOU DOWN.
Nic xx
Nic xx
# posted by : 8/21/2008 12:04 PM
: 8/21/2008 12:04 PM 
This blog thrived before the Dude and the Douchebag were introduced; it'll still rock even with them on hiatus.
Do what you need to do, Raz; that is so say, continue to kick ass.
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Do what you need to do, Raz; that is so say, continue to kick ass.
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