Classes for the spring semester started a few weeks ago, and like last semester, my course load is relatively light. I only have two classes, but both are very interesting (to me).
The first class is somewhat of an extension from last semester's Cell Biology class, and is focused on Genetic Regulation (of mostly eukaryotic cells). This is similar to a class I took this time last year as I finished up undergrad (Biochemistry II) which was a molecular biology course focused on nucleic acids, the Central Dogma (regarding transcription and translation), etc. This class will focus more on regulatory mechanisms at all levels, and will hopefully expand my knowledge of cell cycle checkpoints, etc. I am most excited about the content regarding chromatin modifications and epigenetics, since this is really where genetics is moving forward and is already exploding in terms of discovery.
That being said, I am actually even more excited for my other class, which is a cell biology based Immunology class. I haven't taken immunology yet, so I am anticipating this will be a bit harder for me and require more preparation, but I find the content so interesting (and complicated!) that I doubt I will have trouble drumming up the motivation to study. The "suggested" textbook (required for me!) looks to be extremely well put together, and I am already impressed with the way the figures are laid out. After doing a rotation in an HIV lab I quickly discovered that my lack of immunology background would severely cripple me if I were to be serious about doing virology, especially HIV work, so I am really excited about this class.
Both classes meet only twice a week for 1.5 hrs, and the genetics class has a weekly discussion section with TA's where we discuss weekly papers that parallel the course content. I don't have classes on Fridays, and this has proven to be a great breath of fresh air already. Both classes have a midterm in March and a final exam. All in all, not too stressful at the moment. We'll see how things go once exams roll around...
Friday, January 29, 2010
Thursday, January 28, 2010
iNSPIRE
This semester I started a second volunteering experience similar to the SSEA, but a little more structured and with a different demographic.
The program is called "iNSPIRE" and is run by iPRAXIS, a non-profit whose goals include providing exposure and education within the sciences to students from K-12. The iNSPIRE program has a few components, and at this time of the academic year they partner with a number of Philadelphia Schools for the annual Science Fair. Other activities include career days and even lessons/classroom activities.
I got an e-mail about the program through a graduate student listserv (similar but different from how I learned about SSEA), and I saw this as another opportunity to interact with students and develop my teaching/mentoring skills. This program required a little more legwork from me (including submitting various background checks, etc) and recruits a wide range of volunteers including undergraduate and graduate students, teachers, professors and professionals.
Today was my second day with the program, and so far it looks like it will be a good run. I am at the Alain Lock Elementray School, which houses K-8, and is literally blocks away from my apartment (which isn't so convenient considering I'm usually at the lab before hand). We come in every Thursday for a class period (about 1hr 15min) and we guide our group (avg. 4 students) work through a science fair project.
These first two weeks have been much more educational for me than for my students, by far. The school is a public school in the heart of West Philadelphia, so in many ways it is very different from the schools I went to growing up (which were in upper-middle class, suburban, predominantly white public schools). I remember the first day I arrived at the school, the first thing I noticed was the enhanced security...it wasn't severe, but it was not as inconspicuous as it was in my high school. At least one of the guards looked like (and probably was) an actual officer. I signed into the visitor desk at the front and was directed to the office, where they cleared me to go to the classroom upstairs. On my way up I encountered a young, white woman who was probably no more than two or three years older than me, patiently dragging (literally) a small child (maybe 2nd grade?) who was clearly being sent to the office. The rest of the class followed in tow, orbiting the pair like a cloud of electrons (or perhaps a plasma membrane? ha ha, I love science). The kid was yelling and complaining but the teacher just calmly tugged him inch by inch down the hallway. As I gingerly picked my way past and started up the stairs I asked myself "what I have I gotten myself into?"
Once I got to the classroom, I discovered I was a bit early, and saw that the class was wrapping up. I introduced myself to the other "Scienteers" (as we are called) most of whom were on their way out. I met Scott, the coordinator for the program and whom I had been e-mailing to set things up.
I took a few minutes to collect myself and figure out what exactly I had thrown myself into. Ms. McGinness, another young white woman (again, probably two or three years ahead of me, if even that) was apparently taught seventh and eighth graders. I was surprised (and happy) to see the classroom outfitted with a smart board, and I later saw that she also had about twenty Mac notebooks which stayed in the classroom (locked) but which the students used every day they were with us.
These two weeks showed me the incredible juxtaposition of the difficulties inherent in teaching inner city kids (mainly behavior issues) and the lack of funds (making certain things inaccessible) buttressed by clear attempts to improve the educational potential of the classroom, evidenced by the costly smart boards and laptops.
Honestly, the kids themselves were not very different from middle school students anywhere else. The only possible exception was a more frequent disregard for authority and rules, which made running the classroom much more about controlling out-of-line behavior than about actually teaching...to a degree that was more reminiscent of elementary school.
My group of students included (initially) Amir, Jermirr, and Tyree, and they were later joined by Laneigh, a soft spoken girl who quickly proved to be very creative and the most engage of all of them in the project. I initially had my doubts about how well my group was going to work together, but by the end of the first day (where we came up with our hypothesis) all of them seemed to be on board and interested in the project. Today was the second day, and they all continued to show interest and worked well together (meaning there was no bickering our other behavior problems), which was definitely not true for some of the other groups.
I think it will be a good run with these kids, but only time will tell. So far the experience has already been richly rewarding for me, and I am looking forward to being re-immersed in the drama of middle school...and to later extricating myself from it. I have been quickly reminded why I decided that teaching anything below high school was simply not an option for me, ha ha. Still, it should be fun, and I am looking forward to the coming months.
The program is called "iNSPIRE" and is run by iPRAXIS, a non-profit whose goals include providing exposure and education within the sciences to students from K-12. The iNSPIRE program has a few components, and at this time of the academic year they partner with a number of Philadelphia Schools for the annual Science Fair. Other activities include career days and even lessons/classroom activities.
I got an e-mail about the program through a graduate student listserv (similar but different from how I learned about SSEA), and I saw this as another opportunity to interact with students and develop my teaching/mentoring skills. This program required a little more legwork from me (including submitting various background checks, etc) and recruits a wide range of volunteers including undergraduate and graduate students, teachers, professors and professionals.
Today was my second day with the program, and so far it looks like it will be a good run. I am at the Alain Lock Elementray School, which houses K-8, and is literally blocks away from my apartment (which isn't so convenient considering I'm usually at the lab before hand). We come in every Thursday for a class period (about 1hr 15min) and we guide our group (avg. 4 students) work through a science fair project.
These first two weeks have been much more educational for me than for my students, by far. The school is a public school in the heart of West Philadelphia, so in many ways it is very different from the schools I went to growing up (which were in upper-middle class, suburban, predominantly white public schools). I remember the first day I arrived at the school, the first thing I noticed was the enhanced security...it wasn't severe, but it was not as inconspicuous as it was in my high school. At least one of the guards looked like (and probably was) an actual officer. I signed into the visitor desk at the front and was directed to the office, where they cleared me to go to the classroom upstairs. On my way up I encountered a young, white woman who was probably no more than two or three years older than me, patiently dragging (literally) a small child (maybe 2nd grade?) who was clearly being sent to the office. The rest of the class followed in tow, orbiting the pair like a cloud of electrons (or perhaps a plasma membrane? ha ha, I love science). The kid was yelling and complaining but the teacher just calmly tugged him inch by inch down the hallway. As I gingerly picked my way past and started up the stairs I asked myself "what I have I gotten myself into?"
Once I got to the classroom, I discovered I was a bit early, and saw that the class was wrapping up. I introduced myself to the other "Scienteers" (as we are called) most of whom were on their way out. I met Scott, the coordinator for the program and whom I had been e-mailing to set things up.
I took a few minutes to collect myself and figure out what exactly I had thrown myself into. Ms. McGinness, another young white woman (again, probably two or three years ahead of me, if even that) was apparently taught seventh and eighth graders. I was surprised (and happy) to see the classroom outfitted with a smart board, and I later saw that she also had about twenty Mac notebooks which stayed in the classroom (locked) but which the students used every day they were with us.
These two weeks showed me the incredible juxtaposition of the difficulties inherent in teaching inner city kids (mainly behavior issues) and the lack of funds (making certain things inaccessible) buttressed by clear attempts to improve the educational potential of the classroom, evidenced by the costly smart boards and laptops.
Honestly, the kids themselves were not very different from middle school students anywhere else. The only possible exception was a more frequent disregard for authority and rules, which made running the classroom much more about controlling out-of-line behavior than about actually teaching...to a degree that was more reminiscent of elementary school.
My group of students included (initially) Amir, Jermirr, and Tyree, and they were later joined by Laneigh, a soft spoken girl who quickly proved to be very creative and the most engage of all of them in the project. I initially had my doubts about how well my group was going to work together, but by the end of the first day (where we came up with our hypothesis) all of them seemed to be on board and interested in the project. Today was the second day, and they all continued to show interest and worked well together (meaning there was no bickering our other behavior problems), which was definitely not true for some of the other groups.
I think it will be a good run with these kids, but only time will tell. So far the experience has already been richly rewarding for me, and I am looking forward to being re-immersed in the drama of middle school...and to later extricating myself from it. I have been quickly reminded why I decided that teaching anything below high school was simply not an option for me, ha ha. Still, it should be fun, and I am looking forward to the coming months.
Spring Rotation Lab Profiles
I've been in my final rotation for about two weeks now and I think I am ready to give you all a quick tour of the members of the lab and the general questions being addressed in the lab.
Primary Investigator
Dr. Jianxin You (she goes by "Jen") is an assistant professor at Penn; she joined the school two years ago and is on track for getting tenure in a couple of years. Her research is on the Human Pailloma Virus (HPV). Most strains cause benign warts, genital warts, and in a few cases, persistent infection may lead to cervical cancer in women (the second most common cancer in women).
To understand her research interests I will have to give you a really quick primer on HPV genomics; HPV is a DNA virus which maintains its genome an independent circular episome within the nucleus. The major way that HPV maintains its episome within the host cells is by physically tethering the episome to host chromosomes so that, when cells divide, the episomes are similarly segregated among the daughter cells. A major constituent of this "tether" had been previously found to be a viral protein (called "E2"), but it was not certain how this protein bound to host chromosomes. Jian published an important paper in 2005 that demonstrated that the E2 protein binds to both the HPV genome (which was already very well established) but also to a host protein called Brd4, which is a chromatin-associating protein. Ever since that paper she has been focused on elucidating all the functions and implications host Brd4 may have on HPV gene expression, viral persistence in the host, etc. Her lab uses a variety of experimental approaches including proteomics, molecular biology, and cell biology based techniques.
I got interested in Jian's research after she gave a "chalk talk" back in September (chalk talks were short presentations given by faculty where they explained their research and possible rotation projects). I was also really interested in working in a lab where I could expand my technique repertoire beyond nucleic acid work (i.e. I am getting tired of PCR!!!).
So far Jian has been giving me a lot of one-on-one time, which I really like. I've been reading a LOT of papers to get some background on HPV and on Brd4, etc, and then reviewing what I learned with Jian to make sure I am getting up to speed.
Jian has a small lab, and currently does not have any permanent graduate students (mostly because she is so new), though a couple have rotated with her.
Post Docs
There are three post docs in Jian's lab, although technically Jing has a full-time position. They are all originally from China and have spent varying amounts of time in the US:
Junpeng Yan is a relatively quiet but really nice and friendly post doc, and he shares the other half of my bench (so he's my benchmate). He is currently working on elucidating possible Histone Acetyl Transferase (HAT) activity in Brd4 and a special fusion protein Brd4Nut, which is present in a really rare but very aggressive carcinoma. After a few days of warming up to each other, he is a bit more talkative with me (I think he's just shy) and has been really helpful with finding reagents/equipment and answering basic questions.
Sunny Li is another post-doc, and though she's not as quiet as Junpeng, they are both always pretty busy so I haven't gotten to know her very well yet. She is a little more direct but just as helpful as Junpeng when I've been trying to find things in the lab. Sunny is working on a couple of projects, but one of her bigger ones is further elucidating Brd4/E2 interactions.
Jing Jiao is a full time research specialist in the lab. She has been at Penn for a couple of years now in another lab and recently moved to Jian's lab (this past December). We are both learning together where everything is in lab. She does a lot of tissue culture and bacteria work, but I'm not entirely sure what she is working on.
All three of them are super friendly and really nice, and I have enjoyed getting to know them bit by bit over the past two weeks. They are really focused and busy most of the time, so there isn't as much chit-chat during the day, but that hasn't bothered me so far.
Undergraduates
There are two undergrads in the You lab. Susan is an upperclassman (I think a senior?), and she has worked in the lab for a while now. This semester she is wrapping things up and organizing her research, so I am pretty sure she is done once this semester ends. She comes in once a week for a couple of hours so I don't interact with her very much, but she seems nice enough.
The other undergrad, Sante, is working in the lab as a technician. I think he is a second or third year. He comes in most every day in the afternoon and works for a couple of hours, but he is very, very quiet and keeps to himself so I haven't gotten to know him at all so far.
And that's basically everyone in the lab. They are all pretty quiet and keep to themselves mostly, but when engaged they are really friendly and helpful, and so far this hasn't bothered me. Unlike Dr. Fraser's lab, which was similarly quiet, there is a much stronger sense of collaboration between everyone, and I don't feel nearly as isolated as I did in Dr. Fraser's lab.
As for my own project, I am initially working on characterizing and troubleshooting a GFP-tagged E2 construct which could be used as a means of visualizing HPV episomes in cells (the construct has already been made, I am just characterizing and assaying it). I am also reading A LOT, and I may get new project ideas as my reading progresses.
So far things are going well and I think it will be a good final rotation. I'll be keeping you updated!
Primary Investigator
Dr. Jianxin You (she goes by "Jen") is an assistant professor at Penn; she joined the school two years ago and is on track for getting tenure in a couple of years. Her research is on the Human Pailloma Virus (HPV). Most strains cause benign warts, genital warts, and in a few cases, persistent infection may lead to cervical cancer in women (the second most common cancer in women).
To understand her research interests I will have to give you a really quick primer on HPV genomics; HPV is a DNA virus which maintains its genome an independent circular episome within the nucleus. The major way that HPV maintains its episome within the host cells is by physically tethering the episome to host chromosomes so that, when cells divide, the episomes are similarly segregated among the daughter cells. A major constituent of this "tether" had been previously found to be a viral protein (called "E2"), but it was not certain how this protein bound to host chromosomes. Jian published an important paper in 2005 that demonstrated that the E2 protein binds to both the HPV genome (which was already very well established) but also to a host protein called Brd4, which is a chromatin-associating protein. Ever since that paper she has been focused on elucidating all the functions and implications host Brd4 may have on HPV gene expression, viral persistence in the host, etc. Her lab uses a variety of experimental approaches including proteomics, molecular biology, and cell biology based techniques.
I got interested in Jian's research after she gave a "chalk talk" back in September (chalk talks were short presentations given by faculty where they explained their research and possible rotation projects). I was also really interested in working in a lab where I could expand my technique repertoire beyond nucleic acid work (i.e. I am getting tired of PCR!!!).
So far Jian has been giving me a lot of one-on-one time, which I really like. I've been reading a LOT of papers to get some background on HPV and on Brd4, etc, and then reviewing what I learned with Jian to make sure I am getting up to speed.
Jian has a small lab, and currently does not have any permanent graduate students (mostly because she is so new), though a couple have rotated with her.
Post Docs
There are three post docs in Jian's lab, although technically Jing has a full-time position. They are all originally from China and have spent varying amounts of time in the US:
Junpeng Yan is a relatively quiet but really nice and friendly post doc, and he shares the other half of my bench (so he's my benchmate). He is currently working on elucidating possible Histone Acetyl Transferase (HAT) activity in Brd4 and a special fusion protein Brd4Nut, which is present in a really rare but very aggressive carcinoma. After a few days of warming up to each other, he is a bit more talkative with me (I think he's just shy) and has been really helpful with finding reagents/equipment and answering basic questions.
Sunny Li is another post-doc, and though she's not as quiet as Junpeng, they are both always pretty busy so I haven't gotten to know her very well yet. She is a little more direct but just as helpful as Junpeng when I've been trying to find things in the lab. Sunny is working on a couple of projects, but one of her bigger ones is further elucidating Brd4/E2 interactions.
Jing Jiao is a full time research specialist in the lab. She has been at Penn for a couple of years now in another lab and recently moved to Jian's lab (this past December). We are both learning together where everything is in lab. She does a lot of tissue culture and bacteria work, but I'm not entirely sure what she is working on.
All three of them are super friendly and really nice, and I have enjoyed getting to know them bit by bit over the past two weeks. They are really focused and busy most of the time, so there isn't as much chit-chat during the day, but that hasn't bothered me so far.
Undergraduates
There are two undergrads in the You lab. Susan is an upperclassman (I think a senior?), and she has worked in the lab for a while now. This semester she is wrapping things up and organizing her research, so I am pretty sure she is done once this semester ends. She comes in once a week for a couple of hours so I don't interact with her very much, but she seems nice enough.
The other undergrad, Sante, is working in the lab as a technician. I think he is a second or third year. He comes in most every day in the afternoon and works for a couple of hours, but he is very, very quiet and keeps to himself so I haven't gotten to know him at all so far.
And that's basically everyone in the lab. They are all pretty quiet and keep to themselves mostly, but when engaged they are really friendly and helpful, and so far this hasn't bothered me. Unlike Dr. Fraser's lab, which was similarly quiet, there is a much stronger sense of collaboration between everyone, and I don't feel nearly as isolated as I did in Dr. Fraser's lab.
As for my own project, I am initially working on characterizing and troubleshooting a GFP-tagged E2 construct which could be used as a means of visualizing HPV episomes in cells (the construct has already been made, I am just characterizing and assaying it). I am also reading A LOT, and I may get new project ideas as my reading progresses.
So far things are going well and I think it will be a good final rotation. I'll be keeping you updated!
Tuesday, January 19, 2010
Grad Diary 1/19/10
Today's virology seminar aptly summed my current feelings regarding my lab rotations. I have found that, even with only a week or so into Jian's lab, I am really enjoying my time here and the interactions I've been having with everyone in the lab. I am wondering if this lab will become a strong contender against Una's lab, which I have, up to this point, been so sure I was going to join.
At virology seminar I walked in with Jian and we sat near the front. Una happened to walk in a bit late (and she almost never goes to these seminars) and since we were in the front, sat on my other side. I was literally caught between two PI who I know would love to keep me in their lab. It was really ironic, and this irony was not lost on the rest of Una's lab, who were also in attendance.
I am trying to remain honest to both PI's by indicating my interest in each lab, but I foresee my thesis lab decision to be a bit harder than I initially anticipated. We shall see...
At virology seminar I walked in with Jian and we sat near the front. Una happened to walk in a bit late (and she almost never goes to these seminars) and since we were in the front, sat on my other side. I was literally caught between two PI who I know would love to keep me in their lab. It was really ironic, and this irony was not lost on the rest of Una's lab, who were also in attendance.
I am trying to remain honest to both PI's by indicating my interest in each lab, but I foresee my thesis lab decision to be a bit harder than I initially anticipated. We shall see...
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