Who's Who - Fraser Lab

So it's been a bit longer than I initially wanted before another update, but now things are starting to slow down a bit. Today I'm going to introduce you to everyone in my lab and in the process explain the "hierarchy" of lab personnel that you may or may not be familiar with.

The set up for my lab is pretty typical for most labs, with the exception that there aren't any grad students in it except for me.

Some Background
For those without undergraduate backgrounds in biology/biochemistry skip this section unless you want to be bored to tears. This is just to give some context for what everyone in the lab is doing.

As I mentioned in my previous post, the Fraser lab studies mechanisms of latency in Herpes simplex 1 (HSV-1, currently there is no vaccine or cure). I also mentioned that Herpes simplex, when infecting epithelial cells (like skin) produces an acute infection with active replication and virion production. When these virions infect neuronal cells, however, they become latent (dormant) and do not actively transcribe most of their genes. No matter the cell type, HSV-1 DNA immediately becomes associated with histones in the host nucleus, which is thought to be a host defense mechanism to silence viral genomic material. For whatever reason (this is still being hotly investigated), in epithelial cells the histones are modified to look like "euchromatin," i.e. active replication still occurs (this is how your own genes are transcribed - they often still have histone proteins associated but in a modified state to allow for transcription). In neurons, however, these crucial histone modifications do not happen. Instead, the HSV-1 DNA becomes tightly associated with histones to form "heterochromatin" (i.e. the transcriptionally silent form of chromatin), though it does produce one transcript in high quantity. This transcript is an RNA species termed the Latency Associated Transcript (LAT), which exists as an extremely stable 1.5kb intron-like structure. It is thought that the LAT facilitates in keeping HSV-1 DNA transcriptionally silent. The exact mechanisms by which latency is relaxed in response to neuronal stress (to give rise to recurrent outbreaks characteristic of herpes infection) is not yet well understood.

With all that said you will now be able to understand what most of us are doing in the lab. I will now go down the "command line" of the lab starting with the PI going down to undergrads.

The Primary Investigator (PI)
My PI's name is Dr. Nigel Fraser, and he is a well known expert on Herpes simplex. His lab has been investigating mechanisms of HSV-1 latency for some time now. He has a one year sabbatical coming up this fall, and this summer he is busy attending conferences and setting up his sabbatical work. I don't see him much; when he's here I usually run into him once or twice a day, say hello, and maybe tell him what I am up to for the day. This is how a lot of labs function, as the PI's primary role is to manage his/her research group, and more importantly apply for funding and present at conferences. At this point I don't meet with him regularly for an update on what I'm doing, most likely because he's been out of the office half of the time thus far. Still, I know he is keeping an eye on me in other ways, and every now and then we will chat for fifteen or twenty minutes or so about what's going on in the lab and how my rotation is going.

Senior Research Assistant

A senior researcher is someone who has a PhD and a lot of experience but instead of heading their own lab, are working for another PI. This might be because of a long time as a collaborator or a really good post doc experience, etc. The senior researcher is often the second highest up person in the lab as far as experience and direction is considered, as s/he is directly below the PI. Our senior researcher is Jaewook Oh. Jaewook is Korean, and he is working on mapping the regions of the HSV-1 DNA that are commonly associated with histone proteins (nucelosomes). Right now this is being investigated using microarray technology which will allow him to probe the entire HSV-1 genome using DNA probes derived from HSV nucelosomes (this is done by purifying HSV DNA and then treating with Micrococcal nuclease, an enzyme which degrades DNA not associated with Histones). He also does a lot of ChIP (Chromosome ImmunoPrecipitation) and is investigating the histone modfications common in latent HSV DNA. I don't talk with him very much. His English is good but sometimes communicating about science kind of difficult at times (he gave a lab meeting presentation last week which at times was kind of hard to follow for this reason). He seems like an overall nice guy but when he needs to do something you better get out of his way because he can be pretty direct at times.

The Post-Doc's
A "postdoc" is a "post-doctoral fellow" which, as the name implies, is someone who has completed their PhD training and is now working in a lab as a fellowship. These fellowships are generally for two years, and are a way to get very intensive training in a technique the lab is famous for, or for exploring a very specific model or question. When full professors go on sabbatical, they sometimes do something similar (usually for a year) where they spend time in a lab to hone their skills or get a new perspective. It is expected that researchers will have at least one postdoc experience before going into industry, and two or more if you want to go into academia. In research labs, the post docs are often the "lieutenants" of the lab, in charge of very specific projects, and they often have a grad student working with them. They are considered full time employees of the PI. Our lab has a rather large number of postdocs (4). They are:

Kerry - Kerry is investigating the stability and properties of the LAT intron species. The LAT transcript can be alternatively spliced into different forms with varying structures (the major species is a lariot common to spliced-out introns but is not degraded). Her work is more genetically oriented, which is pretty cool. I don't talk with her very much either, and like Jaewook she seems nice overall but can be a little rough around the edges when she's working or needs to get something done.

Gerald - Gerald just started in the Fraser lab a month before I came. He is actually investigating the uses of HSV as a possible gene vector for neuronal-related diseases (since HSV targets neurons so efficiently). His work is more neuroscience releated and he will be working a lot with mice. He is really easy to talk to and quick to laugh, and is really approachable if you have a question about something. His wife just gave birth to their second child (a girl) last Wednesday, so we are all pretty excited for him.

Ketna - Ketna just joined our lab last Wednesday. I have no idea what she will be working on, though she's been working with Gerald a lot these past few days. She seems nice, though I haven't had a chance to talk with her past my introduction. I'm hoping to catch lunch with her this week to have a longer chat. At this point her work is pretty boring as she will be doing a LOT of background reading (I'm still doing that now!).

Iryna - Iryna is originally from the Ukraine. She earned her PhD at the University of Oklahoma doing lots of genetics work, which means she has a similar background as I do (in that she has more experience with genetics and is learning virology). I have been assigned to Iryna for the summer, which thus far has worked out really well, as she also commutes into the city every day, and our schedules match up well. At first I thought she was kind of distant and direct, but then learned it was more of a function of English being her second language. She is actually fun to talk and joke with and has been a good match for me thus far in that she expects good work from me but let's me make mistakes too. Right now she is working on two projects; she is collaborating with Jaewook (above) to prepare the DNA probes for the microarray. Her major project is developing an HSV-1 strain that, when latenlty infected, can be visualized in an easy way (i.e. latently infected cells can be spotted under the microscope). Since latenly infected cells produce only LAT transcript (at high levels) this transcript is a great candidate as a molecular marker. Iryna is trying to introduce a construct with GFP (green fluorescent protein) sequence dowstream of the LAT promoter, which will create a GFP-LAT fusion protein. If this works, the virus will produce fluorescently labeled LAT's that can be visualized in a microscope (and sorted). She is currently tyring to do this via homologous recombination using HSV DNA and a plasmid with her LAT-GFP construct, which has a very low success rate (1%). If she can do it, though, it will be an extremely useful tool for studying latenly infected neurons.

Lab Technicians
The lab techs are sometimes the most neglected people in the lab, which is a shame because they are the people keeping the labs running smoothly, and they often have the most expertise with the lab's research questions (often more than the post docs). Lab techs are often people just out of undergrad or who have their master's. They do a lot of the grunt work for the lab like preparing solutions, ordering reagents, maintaining cell lines and growing virus. They often have side projects that they work on as well. They are an indispensable part of the team. Our lab tech's name is Jared. I thought he was not much older than me, and was surprised to learn he was 28. He's been working in the Fraser lab for almost seven years now, and he has a lot of expertise. He's also really fun and approachable. He went out of his way to make sure I was all set up and had everything I needed, and he has been very patient telling me how things are run in the lab (how do I dispose of this? where can I get more pipette tips? Where do you store ethanol?) He's very good at what he does, is very efficient and organized, but also the main source of lab hilarity. He's somewhat of a joker and keeps the lab environment light. He also commutes into the city and sometimes we walk back to 30th street station together after work. I feel really comfortable going to him for help (often!) and it's great having someone in the lab that you can turn to without worrying about stepping on someone's toes.

We also have a lab tech in training, Sindura, who is from India. If I remember correctly she got her Masters in biomedical engineering and is currently working with Jaewook on his project and with Jared to learn how to be a technician. She's nice to talk to, and someone else I can turn to if I have a question about where something is in the lab, though when it comes to questions regarding viral preps or protocols I still turn to Jared.

Grad Student(s)
Generally there will be a grad student or two working on their thesis project(s). Dr. Fraser doesn't currently have any grad students doing thesis work, just me doing my summer rotation which is a temporary affair anyway. You already know about me, but as far as what I'm actually doing: I am mainly learning as many techniques as possible in the lab, including growing and maintaining cells in culture, growing up virus, titering virus (purifying and quantifying virus), producing recombinant virus, etc. As far as my project is concerned, I will basically be following Iryna's work in parallel, except instead of using GFP I will be making a fusion protein with a related fluorescent protein called "mCherry." The disadvantage with using GFP is that when cells die they sometimes autofluoresce in a wavelength similar to GFP, so you can get false positives. Using mCherry (which is, predictably, red) eliminates this. We'll see how far I can get.

Undergrad(s)
Sometimes you have undergrads in the lab working on little projects to get their feet wet. At a large research university like Penn, it is usually not nearly as intensive as my experience was at Ithaca because the labs are so much bigger. Right now there are two undergrads doing a work study. There is Prioty, who was born in Bangladesh but lived most of her life in Canada. She's an undergrad at Penn, and she's studying for the MCAT's right now (God bless her) and is pretty smart. Prioty is working with Kerry on the LAT transcript. There is also Jenny, who is doing a workstudy through Drexel (which is famous for their co-ops) and is working closely with Jared. Jenny is from Vietnam originally. She's really nice and a little timid around the lab, probably because she feels everyone around her is much more experienced than her. I try to keep her at ease as much as possible. It's kind of strange to already be seeing undergrads and not count myself one of them, but I can honestly say the transition has been pretty rapid. Anyway, Prioty and Jenny are good workers and fun to talk with, and it's nice to know I'm not the only one who is trying to figure out what the hell is going on.

And that is pretty much everyone! It's quite a group! I feel fortunate that there aren't any ridiculous personality issues within the lab, which can be a real pain. Everyone pretty much keeps to themselves, though there is some soicializing every now and then (usually with the undergrads, Jared and/or Gerald). I really like the people I'm working with and feel that, while I have a lot to learn, I have the resources and the environment I need to do well and enjoy myself.

Looking forward to sharing more in the coming days. Hope you all had a great fourth of July and I hope to hear from you soon!