Rich Hoff Immersion Week 1

Over the course of this week, I did some labwork in Dr. Ethel Cesarman's lab in the Pathology Department. She has been collaborating with my PI, Dr. David Erickson, on developing a device called TINY (Tiny Isothermal Nucleic acid quantification sYstem) for the point-of-care detection of Kaposi sarcoma-associated herpesvirus (KSHV) that can also be utilized in resource-limited settings where KS is more prevalent, access to sources of electrical power, especially in the field, is challenging, and power outages occur often. It performs nucleic acid quantification through a loop-mediated isothermal amplification (LAMP) reaction. During this past week, I learned how to process skin biopsies acquired from KS patients in sub-Saharan Africa and perform DNA extraction. I also quantified the concentration of the final nucleotide sample extracted from each biopsy. In total for this week, I processed 29 skin biopsies, extracted their DNA, and quantified the concentration of the nucleotide sample. Next week will be more eventful as the lab has been preoccupied with virtual conferences and new technicians will be joining the lab. Next week I will be doing qPCR of my DNA samples. A problem that has been occurring with the TINY is that some negative controls and KSHV-negative samples have been amplifying. The LAMP reaction conditions may need to be refined to prevent these false positives. One of my goals during Immersion will be aiding in the troubleshooting of this amplification problem. I met with Dr. Cesarman on Tuesday and she said that in addition to TINY troubleshooting, I can do image analysis and we can discuss other labwork. She also said that she can arrange to have me shadow different clinicians in the Pathology Department.


See the reference below for more details about the development of the TINY:
Snodgrass, R., Gardner, A., Semeere, A., Kopparthy, V. L., Duru, J., Maurer, T., ... & Erickson, D. (2018). A portable device for nucleic acid quantification powered by sunlight, a flame or electricity. Nature biomedical engineering, 2(9), 657-665.

Comments

Post a Comment

Popular posts from this blog

Week 1

For my first week of immersion I attended the OR's of a few different physicians as my clinical mentor Dr. Jason Spector of plastic surgery and reconstruction was on vacation this week. I was able to see three different hernia repairs, and one double mastectomy and bilateral DIEP flap.  I think my favorite thing I saw was the double mastectomy and bilateral DIEP flap. From what I understand, this is a procedure in which both breasts were removed and fat from the stomach is used to reconstruct the breasts. The novelty of the DIEP flap is that it does not require the removal of muscle which allows patients to recover quicker. Additionally, blood vessels from the fat in the stomach are left in tact and "hooked up" to corresponding vessels in the breast. All in all, the procedure essentially amounted to a breast reconstruction and tummy tuck. It was a 10 hour surgery that required multiple doctors and departments, as this was not just a purely cosmetic procedure- the patient ...
Read more

Week 1 - Samantha Bratcher

Image
Hi, everyone! My name is Samantha Bratcher. My clinical immersion is with Dr. Adam Talenfeld and Dr. Kyungmouk Steve Lee in the Interventional Radiology (IR) department. Although it's not very related to my field at the university (biomechanics/mechanobiology), the clinical experience has still been very interesting. The IR department is super friendly and all the clinicians have been very available to letting me shadow them. It's only been one week, but I've already learned a lot! Every day has been watching something new, from angioplasty to biopsy to embolization. I find it so crazy that they're able to thread a wire through someone's veins to practically any area of the body. It's always a bit crazy to watch. I got a video of a balloon angioplasty using this method. The balloon is inflated inside a person's veins to expand them and increase blood flow. The second video shows the veins and their quality. The rate at which the contrast dye flows through is...
Read more

Week One - Shenghao Tan

I am working with Dr. Mirella Salvatore from the infectious disease division. My research project will revolve around associations of COVID 19 patient clinical characteristics with their hostresponses throughout their hospitalization and recovery.   On the patient care side I have been following Dr. Ole Vielemeyer in ID consultation. A large part of the round is to discuss the choice of antibiotics, itsdosage and duration from lab results and examination reports. Some of the cases this week have been quite complicated and chronic; therefore, joint effort were required to provide adequate treatments. One patient had to battle both Crohn's disease and histoplasmosis, where the immunosuppressant and antibiotics used must be carefully considered to treat the histoplasma and maintain some immune system function, while not severing the GI tract. A part of medical care I learned that I haven't considered much of is the inpatient - outpatient transition: how is the treatments adjusted ...
Read more