It's nice to be back in the swing of things. It was kinda strange on Tuesday to put gloves back on...it felt like forever ago when I last used a pipette and did an experiment. Things are starting to move forward with my project, which is nice, and we are starting a new section in Cell Bio. I also gave my last presentation in my journal club class last night, and it went really well. Now I just have to make sure to read (or at least skim) the articles for class for the rest of the semester and I will be good to go.
The director of the Microbiology department, who is very interactive with the grad students in his program, likes to send the first year micro students with a few upperclassmen out to dinner during the week after the exam. I went last week with three other first years and two upper classmen to Buddakan, an asian fusion restaurant in center city. We all got $50 to "play with" which we used to its fullest (did not cover alcohol though...fortunately, since I'm not a drinker that wasn't a big deal for me). The food was very good, and I was excited to have "real" sashimi again! (I haven't had good sashimi/sushi since going to Japan a year ago). It was a really nice dinner, and the restaurant wasn't too pricey; I could definitly see myself going there again once in a while.
All in all, it's been a good week, with two major accomplishments out of the way. I suddenly find I have a lot more free time now that my presentations are done and my first exam is out of the way. I still can't wait to see how I did though!
Thursday, October 22, 2009
Monday, October 19, 2009
Grad Diary 10/19/09
So......I just took my exam.
Actually, that wasn't so bad.
The exam time was 6:00pm to 9:00pm. Class this morning and last Friday was solely review sessions given by the TA's, and they were marginally useful. They were useful in that I felt I could explain the topics as well or maybe even better (or at least clearer) than they did, which made me feel I knew what I was talking about.
Anyway, as I said, they gave us three hours, but they designed it so that a "well prepared" student should only take an hour and a half.
I was done on my first run through in an hour.
I went through the exam one more time and spent some time thinking carefully about one or two questions that were a little trickier. Even then, I was sitting at an hour and ten minutes of test-taking time. I sat for maybe another five minutes trying to decide if I should wait any longer or just hand it in...I mean, I was done REALLY early, and I knew people would notice. Fortunately another student walked down and dropper off her exam at that point, so I took this as a cue to do to the same (at least I wasn't first). And yes, I'm sure some of my friends noticed.
I'm not that surprised, to be honest; I normally take tests really fast (I was definitely that guy in college), and I was already pretty familiar with the material. Still, I can't wait to get the results back just to see.
Anyway, all in all, the exam wasn't too bad (although the last question was quite strange), and now it's time to work on my presentation for Wednesday...
Actually, that wasn't so bad.
The exam time was 6:00pm to 9:00pm. Class this morning and last Friday was solely review sessions given by the TA's, and they were marginally useful. They were useful in that I felt I could explain the topics as well or maybe even better (or at least clearer) than they did, which made me feel I knew what I was talking about.
Anyway, as I said, they gave us three hours, but they designed it so that a "well prepared" student should only take an hour and a half.
I was done on my first run through in an hour.
I went through the exam one more time and spent some time thinking carefully about one or two questions that were a little trickier. Even then, I was sitting at an hour and ten minutes of test-taking time. I sat for maybe another five minutes trying to decide if I should wait any longer or just hand it in...I mean, I was done REALLY early, and I knew people would notice. Fortunately another student walked down and dropper off her exam at that point, so I took this as a cue to do to the same (at least I wasn't first). And yes, I'm sure some of my friends noticed.
I'm not that surprised, to be honest; I normally take tests really fast (I was definitely that guy in college), and I was already pretty familiar with the material. Still, I can't wait to get the results back just to see.
Anyway, all in all, the exam wasn't too bad (although the last question was quite strange), and now it's time to work on my presentation for Wednesday...
Wednesday, October 14, 2009
Grad Diary 10/14/09
I haven't been doing any experiments this week for two reasons. First of all, my results were kind of...interesting. Una suggested I take a day or two to think about it, come up with some hypotheses and some simple experiments to get a handle on what's going on. More importantly, though, next Monday evening is the first exam for my Cell Biology class. The first exam is especially notorious for tripping people up because many people are still trying to figure out how prepare and how to approach the problems. Fortunately they have posted the exam from the previous two years, which has been a really great help in giving me an idea of the kinds of questions and answers they are looking for.
It's been really weird coming to lab and not actually doing any experiments. On the other hand, it's been nice to spend the time to prepare and practice; I'm feeling pretty confident. One big difference with the exam is that the questions are all experimentally based. Therefore, the fact that the exam is open note/book actually doesn't help you that much. What we have to do is apply our knowledge of a system (say, vesicular trafficking) and interpret experimental results that are thrown at us. This interpretation requires a knowledge of the techniques (and what they do and don't tell you) as well as a basic understanding of the subject (which can be supplemented by notes). But coming up with the interpretation, and then designing new experiments to answer new questions, are all coming from you, not from your notes. Fortunately, I did get some of that with my last cell bio class, though I would say it made up between 30 and 50% of any given test.
I'm not terribly concerned about the exam - the material is all pretty familiar to me anyway, and the practice exams have been very useful - but Monday will be the day of truth. We'll see. Needless to say, this weekend will be wholly devoted to it.
It's been really weird coming to lab and not actually doing any experiments. On the other hand, it's been nice to spend the time to prepare and practice; I'm feeling pretty confident. One big difference with the exam is that the questions are all experimentally based. Therefore, the fact that the exam is open note/book actually doesn't help you that much. What we have to do is apply our knowledge of a system (say, vesicular trafficking) and interpret experimental results that are thrown at us. This interpretation requires a knowledge of the techniques (and what they do and don't tell you) as well as a basic understanding of the subject (which can be supplemented by notes). But coming up with the interpretation, and then designing new experiments to answer new questions, are all coming from you, not from your notes. Fortunately, I did get some of that with my last cell bio class, though I would say it made up between 30 and 50% of any given test.
I'm not terribly concerned about the exam - the material is all pretty familiar to me anyway, and the practice exams have been very useful - but Monday will be the day of truth. We'll see. Needless to say, this weekend will be wholly devoted to it.
Friday, October 9, 2009
Fall Rotation Profiles
I've been working in my fall rotation lab for a few weeks now, as you already know, and I thought now would be good time to give you all an introduction to the lab in a manner similar to my last lab intro.
The O'Doherty Lab
Una O'Doherty is an MD/PhD at Penn who is currently studying mechanisms of HIV latency. HIV latency is the primary reason HIV infection remains a treatable but non-curable disease. Latency - it's establishment, maintenance, and reactivation - is the next big frontier for HIV research. The O'Doherty lab is investigating whether a low-level of viral replication and infection continues despite therapy, and whether naive/resting cells are able to be infected by HIV.
Una's lab was actually one that caught my eye when I was looking at Penn, and during my interviews she was one of my interviewers. Even during interviews we hit it off great and I knew that if I went to Penn I wanted to do a rotation with her.
Una runs her lab differently than Dr. Fraser. For one, it is a lot smaller (more on that in a minute), and she likes to keep it that way so that she can spend a lot of time with her grad students. The lab atmosphere in general is super-collaborative; a major lab philosophy is that we talk a lot about our experiments with each other, give a lot of thought and feedback, and thereby do the experiments much better in the long run. Lab members regularly talk to each other not just to get feedback on their own experiments, but to also see what other people are doing. This is greatly facilitated by the fact that the lab is so small, and the net effect is a very strong community feel, and everyone is very willing to help you out or give advice.
Finally, while the atmosphere is very congenial and collaborative, Una has from the get-go pushed me to start thinking independently about my project and to take my researching skills to the next level; while I certainly started that in my last rotation, it was more self-motivated than now.
The lab just finished applying for a new grant not too long ago, so things have been pretty crazy, but now that things are settling down I am getting more time to talk with Una on an individual basis, which has been really fantastic.
Overall, the lab dynamic and level of involvement is exactly what I am looking for.
Technician
The lab has one tech, Jenny Yu. Jenny has a master's and is closer to my mom's age (actually, her kids are close in age to me and my siblings, which is kinda funny). She is an extremely skilled and knowledgeable researcher who has experience in a lot of different biological fields. She is also technically excellent, and is definitely a major asset to the lab. She does a lot of experimental work with other people in the lab and has a few projects of her own as well. In fact, the project I am working on came directly from Jenny and therefore I am working under her wing this semester, which is great because my technique will hopefully increase due to her instruction.
As the lab tech, she also handles all of the vendors and lab supplies. In this area, I am constantly astounded by Jenny's talent for getting a lot of stuff for pretty a great price. Jenny is a master haggler, something I have enjoyed watching frequently in the lab. Even more impressive, she does it in a way that usually ends up with both parties in a win-win situation, and for that reason she is well known among the vendors as a great customer. (Indeed, when a new sales representative for Invitrogen stopped by our lab to introduce herself, we mentioned that Jenny was our lab tech and the sales rep immediately recognized her name and was excited to be working with her).
She is really great to work with and has been a great mentor and guide these past few weeks. I am looking forward to continuing my project with her over the next few months.
Postdoctoral Fellow
The lab has one postdoc; a veterinarian by training, Angela Mexas is currently studying HIV infection of naive and memory T cells. I didn't interact with her a whole lot in the first few weeks but over time we have had more interaction and she is very friendly and helpful. She works a lot with Erin, another grad student, and a bit with Jenny, so we don't collaborate very much, but I enjoy chatting with her at lunch and around the lab.
Graduate Students
There are three full-time grad students who are in various stages of their theses. Luis Agosto is a fifth-year grad student who is planning on defending his thesis in May. He has been investigating whether HIV-1 can actively infect resting T-cells, and then moved on to test various HIV-1 mutants/constructs to develop possible gene therapy vectors using HIV machinery. He's super friendly and helpful, and lends a lot of energy to the lab. He is originally from Puerto Rico, and came to the states for his undergrad education (at Penn State Univeristy) before coming here for Grad School. Between Luis, Angela and myself, half the O'Doherty lab is fully Hispanic, which is actually kind of fun, although growing up in predominantly white communities my whole life has dulled my sense of Hispanic identity. Anyway, Luis is really smart and capable, and similar to everyone else in the lab, goes out of his way to help you out or give you advice.
Matthew Pace is a third year grad student who finished his preliminary exams (also called qualifying exams) earlier this year with flying colors. While Luis will soon be asking his committee for permission to begin writing his thesis, Matt is just getting started on his thesis, and is just now enjoying the fine pleasure of trying to get five people's schedules to line up for a first committee meeting. Similar to Luis, Matt is currently investigating different viral constructs, but with the goal of elucidating possible entry restrictions in resting T cells. Matt is the resident "organizer" of the lab, meaning that Una usually leaves it to him to handle administrative things like reserving rooms for lab meetings and sending papers out for our weekly journal club. Outside of Jenny, Matt has taken made it a point to introduce me to as many aspects of the lab as possible, including where to go to pick up cells or reagents, how to use different equipment, the ins and outs of the biosafety cabinet, etc.
Erin Graf is the final graduate student in the lab, and she just started her second year. Because she is only a year ahead of me, and because she is in the same certificate program I am, she is another great resource for me when it comes to questions about classes, rotations, etc. Her preliminary exams are in May, so until then she isn't working on a formal thesis project per se, but is rather doing some research and putting her ideas together to come up with her project. I am not as informed about her project. She is working a lot with clinical samples from HIV+ patients on retrovirals, measuring viral DNA levels to get a handle on whether there is active viral replication in resting T cells (a major question in the lab). Actually, my project is more related to hers in the respect, which I will talk about in a minute. She is also looking at elite suppressors, patients who are HIV+ but who control their virus so well that they don't need treatment and don't progress to AIDS. Our benches are close to each other, and we both make heavy use of the Real Time PCR machine so we interact a lot with each other.
My Project
My project is relatively simple to describe but very hard to do in practice. HIV is an RNA virus (meaning its genome is RNA not DNA), and as such after initial infection it needs to "reverse transcribe" it's DNA back into RNA (which is "backwards" from how most living things do it). After making DNA from RNA, this DNA is then integrated into the host cell DNA where new viruses are then made. When people are on retroviral drugs, the capacity for viral replication is greatly reduced. Una's lab proposes that, in at least some patients, viral replication still occurs, but at low levels. One way of examining this question is to look at viral DNA levels; we already have a good grasp of how to do this with viral DNA that has already been integrated, but it's been hard to directly look at viral DNA that is not integrated (episomal). My project is, in a nutshell, to develop a method to measure "linear" HIV DNA.
I won't go into the details, but suffice to say that it is pretty tricky, although I have a few methods to try out. The assay is PCR based, which is great because I already have a lot of experience with PCR. If I can get an assay that works then it will be a huge boon to the lab, but if I can't, then at least I tried (and will have learned a lot in the process).
Anyway, that, in a nutshell, is everyone in the lab. All in all, everyone has been extremely helpful and interactive, and it is full of energy. So far it is exactly the kind of lab atmosphere I am looking for and I am enjoying it immensely. All that remains is to make some progress on my project and keep up with classwork!
The O'Doherty Lab
Una O'Doherty is an MD/PhD at Penn who is currently studying mechanisms of HIV latency. HIV latency is the primary reason HIV infection remains a treatable but non-curable disease. Latency - it's establishment, maintenance, and reactivation - is the next big frontier for HIV research. The O'Doherty lab is investigating whether a low-level of viral replication and infection continues despite therapy, and whether naive/resting cells are able to be infected by HIV.
Una's lab was actually one that caught my eye when I was looking at Penn, and during my interviews she was one of my interviewers. Even during interviews we hit it off great and I knew that if I went to Penn I wanted to do a rotation with her.
Una runs her lab differently than Dr. Fraser. For one, it is a lot smaller (more on that in a minute), and she likes to keep it that way so that she can spend a lot of time with her grad students. The lab atmosphere in general is super-collaborative; a major lab philosophy is that we talk a lot about our experiments with each other, give a lot of thought and feedback, and thereby do the experiments much better in the long run. Lab members regularly talk to each other not just to get feedback on their own experiments, but to also see what other people are doing. This is greatly facilitated by the fact that the lab is so small, and the net effect is a very strong community feel, and everyone is very willing to help you out or give advice.
Finally, while the atmosphere is very congenial and collaborative, Una has from the get-go pushed me to start thinking independently about my project and to take my researching skills to the next level; while I certainly started that in my last rotation, it was more self-motivated than now.
The lab just finished applying for a new grant not too long ago, so things have been pretty crazy, but now that things are settling down I am getting more time to talk with Una on an individual basis, which has been really fantastic.
Overall, the lab dynamic and level of involvement is exactly what I am looking for.
Technician
The lab has one tech, Jenny Yu. Jenny has a master's and is closer to my mom's age (actually, her kids are close in age to me and my siblings, which is kinda funny). She is an extremely skilled and knowledgeable researcher who has experience in a lot of different biological fields. She is also technically excellent, and is definitely a major asset to the lab. She does a lot of experimental work with other people in the lab and has a few projects of her own as well. In fact, the project I am working on came directly from Jenny and therefore I am working under her wing this semester, which is great because my technique will hopefully increase due to her instruction.
As the lab tech, she also handles all of the vendors and lab supplies. In this area, I am constantly astounded by Jenny's talent for getting a lot of stuff for pretty a great price. Jenny is a master haggler, something I have enjoyed watching frequently in the lab. Even more impressive, she does it in a way that usually ends up with both parties in a win-win situation, and for that reason she is well known among the vendors as a great customer. (Indeed, when a new sales representative for Invitrogen stopped by our lab to introduce herself, we mentioned that Jenny was our lab tech and the sales rep immediately recognized her name and was excited to be working with her).
She is really great to work with and has been a great mentor and guide these past few weeks. I am looking forward to continuing my project with her over the next few months.
Postdoctoral Fellow
The lab has one postdoc; a veterinarian by training, Angela Mexas is currently studying HIV infection of naive and memory T cells. I didn't interact with her a whole lot in the first few weeks but over time we have had more interaction and she is very friendly and helpful. She works a lot with Erin, another grad student, and a bit with Jenny, so we don't collaborate very much, but I enjoy chatting with her at lunch and around the lab.
Graduate Students
There are three full-time grad students who are in various stages of their theses. Luis Agosto is a fifth-year grad student who is planning on defending his thesis in May. He has been investigating whether HIV-1 can actively infect resting T-cells, and then moved on to test various HIV-1 mutants/constructs to develop possible gene therapy vectors using HIV machinery. He's super friendly and helpful, and lends a lot of energy to the lab. He is originally from Puerto Rico, and came to the states for his undergrad education (at Penn State Univeristy) before coming here for Grad School. Between Luis, Angela and myself, half the O'Doherty lab is fully Hispanic, which is actually kind of fun, although growing up in predominantly white communities my whole life has dulled my sense of Hispanic identity. Anyway, Luis is really smart and capable, and similar to everyone else in the lab, goes out of his way to help you out or give you advice.
Matthew Pace is a third year grad student who finished his preliminary exams (also called qualifying exams) earlier this year with flying colors. While Luis will soon be asking his committee for permission to begin writing his thesis, Matt is just getting started on his thesis, and is just now enjoying the fine pleasure of trying to get five people's schedules to line up for a first committee meeting. Similar to Luis, Matt is currently investigating different viral constructs, but with the goal of elucidating possible entry restrictions in resting T cells. Matt is the resident "organizer" of the lab, meaning that Una usually leaves it to him to handle administrative things like reserving rooms for lab meetings and sending papers out for our weekly journal club. Outside of Jenny, Matt has taken made it a point to introduce me to as many aspects of the lab as possible, including where to go to pick up cells or reagents, how to use different equipment, the ins and outs of the biosafety cabinet, etc.
Erin Graf is the final graduate student in the lab, and she just started her second year. Because she is only a year ahead of me, and because she is in the same certificate program I am, she is another great resource for me when it comes to questions about classes, rotations, etc. Her preliminary exams are in May, so until then she isn't working on a formal thesis project per se, but is rather doing some research and putting her ideas together to come up with her project. I am not as informed about her project. She is working a lot with clinical samples from HIV+ patients on retrovirals, measuring viral DNA levels to get a handle on whether there is active viral replication in resting T cells (a major question in the lab). Actually, my project is more related to hers in the respect, which I will talk about in a minute. She is also looking at elite suppressors, patients who are HIV+ but who control their virus so well that they don't need treatment and don't progress to AIDS. Our benches are close to each other, and we both make heavy use of the Real Time PCR machine so we interact a lot with each other.
My Project
My project is relatively simple to describe but very hard to do in practice. HIV is an RNA virus (meaning its genome is RNA not DNA), and as such after initial infection it needs to "reverse transcribe" it's DNA back into RNA (which is "backwards" from how most living things do it). After making DNA from RNA, this DNA is then integrated into the host cell DNA where new viruses are then made. When people are on retroviral drugs, the capacity for viral replication is greatly reduced. Una's lab proposes that, in at least some patients, viral replication still occurs, but at low levels. One way of examining this question is to look at viral DNA levels; we already have a good grasp of how to do this with viral DNA that has already been integrated, but it's been hard to directly look at viral DNA that is not integrated (episomal). My project is, in a nutshell, to develop a method to measure "linear" HIV DNA.
I won't go into the details, but suffice to say that it is pretty tricky, although I have a few methods to try out. The assay is PCR based, which is great because I already have a lot of experience with PCR. If I can get an assay that works then it will be a huge boon to the lab, but if I can't, then at least I tried (and will have learned a lot in the process).
Anyway, that, in a nutshell, is everyone in the lab. All in all, everyone has been extremely helpful and interactive, and it is full of energy. So far it is exactly the kind of lab atmosphere I am looking for and I am enjoying it immensely. All that remains is to make some progress on my project and keep up with classwork!
Friday, October 2, 2009
Grad Diary 10/2/09
This week, lab was hell.
For whatever reason(s), nothing seemed to work. My experiments gave weird results and I couldn't even do the most mundane of things like a gel extraction. I think there is some type of karmic law that states that the first two weeks in a new lab, everything goes beautifully and you develop a sense that you can make real progress in your project. Then...WHAM. Equipment fails, experiments go wrong, calculations never produce the same answer twice, and you feel completely incompetent.
Fortunately, I know from my research at Ithaca and from my summer rotation that this is a common occurrence in research. Still, I wish it wasn't happening so early in my rotation! I feel like the only thing I'm proving at this point is that I have poor lab technique...Which is, of course, an exaggeration. No one else in the lab, my PI included, is too concerned about it...they know I will figure it out and they don't think my technique is bad, I'm just having "one of those weeks."
And mercifully, today I have begun dissecting what has been going wrong and starting to move out of my rut, with a lot of help from Jenny, the lab technician that is taking me under her wing. Still, it's been an incredibly stressful week. Thank God for the weekend.
For whatever reason(s), nothing seemed to work. My experiments gave weird results and I couldn't even do the most mundane of things like a gel extraction. I think there is some type of karmic law that states that the first two weeks in a new lab, everything goes beautifully and you develop a sense that you can make real progress in your project. Then...WHAM. Equipment fails, experiments go wrong, calculations never produce the same answer twice, and you feel completely incompetent.
Fortunately, I know from my research at Ithaca and from my summer rotation that this is a common occurrence in research. Still, I wish it wasn't happening so early in my rotation! I feel like the only thing I'm proving at this point is that I have poor lab technique...Which is, of course, an exaggeration. No one else in the lab, my PI included, is too concerned about it...they know I will figure it out and they don't think my technique is bad, I'm just having "one of those weeks."
And mercifully, today I have begun dissecting what has been going wrong and starting to move out of my rut, with a lot of help from Jenny, the lab technician that is taking me under her wing. Still, it's been an incredibly stressful week. Thank God for the weekend.
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