Science
The Chapman Chronicles, vol. II.
Abstract: It's hard to describe exactly what I'm doing at work through this blog for several reasons; some of the procedures I have performed haven't been published yet, so I can't talk about them, and many of the other tasks I've done are challenging to describe in detail for my readers without the benefit of some background in molecular biology or science research. I will give a general overview of what I've done so far in my project, and describe in more detail a few of the interesting episodes of the past week, including (but not limited to) performing top secret science procedures, watching exchange columns, and eating pie.
These past two weeks, I have been working on several different related mini-projects with Amber, my mentor. The general goal behind each of these projects is to express a protein that has been mutated in specific places, and then perform a range of tests on it either to better understand the structure of the protein itself, or to develop new methods for analyzing protein structure. I won't delve into specifics, but so far I have inserted a point mutation into a plasmid and amplified the DNA; I have also expressed two different mutated versions of the protein in E. coli cells and isolated our desired protein from all the other gunk in bacterial cells. We performed some tests on one of these proteins using really expensive machines today, and I learned what each piece of equipment does and what our results mean. The other is being crystalized in a different lab; we will have results within the next few days!
It's fun, interesting and challenging to learn about Amber's research in molecular biology and the tools she uses to obtain and study her results; it's taken two weeks, but by now I've reached a point where I can find things around the lab without needing to ask somebody for them, perform lab procedures with less-than-constant supervision, and generally be helpful around the lab. One of my least favorite lab procedures so far has been eluting protein through columns; the procedure allows the isolation of a desired protein from a solution containing lots of dissolved material, which is cool, but requires that I watch solutions drip through plastic columns for a good chunk of my day, which is less than exciting.
Another excellent aspect of my senior project thus far has been the cuisine available to me in the lab. Perhaps I say this because I enjoyed a particularly delightful day food-wise today, but the variety of food choices has been consistently satisfactory (the adjective, not the verbal equivalent). Today I enjoyed a cold-brew latte which tasted like creamy deliciousness; and for lunch I had a bowl of ramen from the downstairs cafeteria, which was pleasingly heavy on the pulled pork and vegetables. The Farrens lab has also had a couple of birthdays this week (happy birthday John and Emily), so Amber brought in a homemade strawberry rhubarb pie. The pie was good and definitely worth the kidney stones I'll probably get, because rhubarb is notoriously high in oxalates.
To the readers of my blog who are science teachers, I leave you with this final question: what happens to your tongue when you eat capsaicin and menthol at the same time?
Photo guide:
3931: Watching columns drip.
3927: The sweet view from the lab window.
3928: The bacteria food from last week!
Margaret's Grand Adventure: My first week at OHSU! (Day 4)
Day 4:
Today was another clinic day, and my time there was cut short by my visit to see the Dalai Lama speak--what an absolutely amazing experience!!
In the morning Dr Hansen and i met with 2 of the 4 scheduled patients because 2 didn't show up. One of the ones that did arrive wanted a breast augmentation. They had received a free muscle flap to reconstruct one breast after chemotherapy. During this consultation, Dr Hansen explained that radiated skin usually hardens in a process called capsular contracture, but any skin around an implant is prone to a similar result.
Another term that I learned (I forgot to mention in in my post about day 3) is surgical procedure called a lumpectomy, in which only a small portion (or lump) of a breast is removed.
Another patient wanted cosmetic breast implants, and this demonstrates a different side of Dr Hansen's services. She mostly operates on cancer-related cases but also performs purely cosmetic procedures. Another area of her practice (one i forgot to mention in m day 3 post about a patient) is the female to male / male to female transition surgeries. Dr Hansen commented that this is a newly booming part of her practice, and that she specializes in performing breast removals (mastectomies) and breast implants.
A surgical note: often the nipple is grafted onto the newly reconstructive breasts straight from the old breasts, and this is as 'simple' and removing the nipple, removing several layers of epidermis on the reconstructed breast, and sewing on the nipple.
Comments
timely NYT articles for you
Check out yesterday's NYT Op Ed, written by Angelina Jolie, about her recent double mastectomy, and today's piece in the Health section describing how genetic testing is leading to more and more women electing to have surgery before being diagnosed with breast cancer.
Pure, sweet hope
Miss Margaret! What thoughtful, informative posts! Your first week sounds incredibly educational and varied--let's hope your dark past doesn't catch up with you and cut your job short!
I love your attitude, as always. I, too, find that the best way to deal with the blows that life throws at us is to concentrate on the beauty and hope that emerge--just like you've noticed in the patients you've seen. And a visit with His Holiness doesn't hurt, either!
An idea: since you need some photos, can you show us what you look like all suited up? I'd love to see you in your glory.
Miss you!!!
Nichole
Margaret's Grand Adventure: My first week at OHSU! (Day 3)
Day 3:
Today we spent the day at the clinic for preop (pre-operation) and postop (post-operation) consultations. One of the patients had received a mastectomy and needed to reconstruct one or more of their breasts. Another patient had implants but needed an augmentation to fix existing complications with the breasts' appearances.
Interesting fact: saline implants can remain in place for life, while medical professionals recommend replacing silicone implants every 10 years or so.
Another patient had sustained a crush injury to their pointer finger and met with Dr Hansen during the recovery process to determine the best course of action as the finger continue to heal. The finger had sustained multiple fractures, as well as concentrated cell death and partial amputation.
Another patient in the clinic had battled a reoccurring type of cancer, which contributed to an infected open-leg wound with tissue damage, inflammation, and decay, as well as bone visibility. After a failed skin flap graft the options were limited to a transverse free muscle flap from the back area, or an amputation.
What surprises and inspires me most is the energy and passion that remains so vividly alive in these patients, despite the hardships they have had and will continue to endure. Their vibrant spirits are catching, and they give me hope; pure, sweet, hope.
Comments
This is fascinating; thanks
This is fascinating; thanks for the thoughtful and detailed posts! Given the longevity of saline, why would one choose silicone implants instead?
Margaret's Grand Adventure: My first week at OHSU! (Day 2)
Day 2:
Today was a SURGERY day!! After arriving at OHSU South (the upper campus) I suited up in my scrubs, hair covering, surgical mask, booties, and Dansko clogs. The clogs were essential, practically every surgeon, nurse, technician, anesthesiologist, and person in between wears these Dansko clogs, and the shoes' strong arch support helps relieve stress on the feet, knees, and back during a long day in the OR (operating room).
The first surgery I watched was the tail end of a facial surgery. The patient had suffered facial drooping as a result of an accident, and Dr Hansen reopened the old scar and repaired muscle damage. As you know, I cannot release the names or specifics of patients (I don't even know most of them), but I will discuss the types of procedures from a surgical standpoint.
The second surgery was a rather unusual one, even from Dr Hansen's extensive experience. The surgery was called a labiaplasty, or a surgical reduction of the labia. The labia minora and majora are the folds of skin surrounding the human vulva, and anatomically these are found in the female sex genitals. This was an interesting procedure to watch, and the whole process didn't take long. During the labiaplasty, Dr Hansen and one of her residents removed wedge-shaped flaps from the patient's labia and sutured the remaining tissue together, with a net result of reduced labia size.
The last surgery of the day was a bilateral breast implantation. I believe that the patient had sizer implants in place to stretch the tissue and make room for the permanent implants, and those were removed during the procedure. The surgeons chose a permanent implant size by testing different sizers to test the shape of breasts. The sizer implants can be re-sterilized and used again, while the permanent implants cannot, so they surgeons wanted to be sure of what they wanted before inserting the permanent ones. I loved watching the miracle of the whole process; everything from the surgeons' ability to create breasts from skin and silicone, to the anesthesiologist's ability to put the patient under and then bring them back again. I look forward to many more days like this one!
Margaret's Grand Adventure: My first week at OHSU!
Howdy there! This week I spent 5 wonderful, jam-packed, intense days shadowing Dr. Julie Hansen at OHSU. She's a reconstructive plastic surgeon there and I got to follow here around her clinic and her operating room. Dr. Hansen and I met during my advanced biology class when I shadowed her for several days, and during that time I also got to know the plastic surgery residency coordinator, Amanda Kotsovos.
Now let me summarize each day of senior projects so far one at a time, starting with the first:
Day 1:
I showed up to the south campus of OHSU bright and early in the morning (so much for sleeping in on senior projects, eh?), and I met with Dr. Hansen for the first time in several months. We discussed the possible directions/focuses of the project and then she showed me around her office in Mackenzie Hall and introduced me to some of the staff. Next Dr Hansen had to make some phone calls and do paper work, so Amanda and I went to the parking office to get my ID badge. However, we ran into an snafu: the regulations changed and became stricter since my last visit (unbeknownst to Amanda, Dr Hansen, or me). Instead of a 5 minute process similar to what I experienced in the fall, I suddenly had to take several online classes, pass several online tests, and get a background check. I received a temporary 2 week pass, and Amanda and I returned to Dr Hansen's office where I spent all day passing the classes and tests. However, it wasn't that bad, and I learned more about hospital regulations and expectations, especially in regard to patients' private information. We're still awaiting the results of the background check, and we all joke that my "dark past" will come back to haunt me (haha, just kidding). After all the bouncing around and test taking I got few minutes to browse through a plastic surgery journal before heading off to track practice. It never occured to me that science magazines would have different advertisements than non-scienctific ones, but it makes perfect sense now that I think about it. Still, I don't know whether I'll ever be able to consider the ad selling leeches as 'normal.' It read, "Leeches! On call 24 hours. Just like you."
It's the little things that me you simle, right?
science News
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Have you read the research
Have you read the research articles that Amber gave you earlier this week? Can you give us a general overview of that research? And since you're keeps us informed of your culinary experiences, I have to ask if you are enjoying the Tuesday farmers' markets?
"Sort of" on both counts.
I've read one of the four papers she's given me---the 1999 publication that began this line of research---and plan to read the others this week. In the 1999 publication, Steve Mansoor (a former graduate student in the Farrens lab) et al. explores fluorescence as a potential method for deducing the structure of a protein. He creates many different mutations of the T4 lysozyme by removing all cysteines from the protein, then substituting a single cysteine for a different amino acid in each mutant; the resulting protein contains only one cysteine at a known and controlled location. He then binds a fluorescent label to the cysteine in each of his mutants, and performs a range of tests and analysis to determine whether the protein's fluorescence correlates to its other properties. He concludes that the fluorescent label can be attached to the protein without substantially altering its function at exposed and partially buried sites, that one can deduce the solvent accessibility of a site (degree to which the site is exposed to a solvent in which the protein is dissolved) by fluorescence emission (wavelength of light emitted by the fluorophore) and steady-state anisotropy values (I know what the first is, and do not understand the second), and that he couldn't draw conclusions about 3D structure of the protein from fluorescence excitation, fluorescence lifetime, and quantum yield values (understand each of these: the wavelength which excites the fluorophore most, the length of time at which the fluorophore remains in an excited state, and the fraction of times that the protein will fluoresce per photon).
In the 2002 paper, he studies the degree to which tryptophan quenches the label's fluorescence---the label's fluorescence diminishes with the proximity of tryptophan; I can't really discuss it because I've only skimmed the article.
I haven't enjoyed a Tuesday farmer's market, but I enjoyed a Saturday one a few days ago. Ate crepes which were good but overpriced, cheesecake, kettle corn and pita chips. All very tasty.
ps. Nice view!
When I worked at OHSU I was in the sub-basement...
Capsaicin + menthol = OUCH!
Were you able to show off your previous understanding of exchange columns? (Yes, they can be quite slow!)
Sadly, this is not really an answer...
Unfortunately, the exchange process is one of the things that I'm not allowed to talk about. It's a very cool set of reactions, however, so look for future publications by the Farrens lab!