The Wait Finally Ends

Hey guys, it's Katie from the Children's Hospital of Philadelphia again.

So last week I received some news that I thought would be good, our probe was ordered and should arrive any day!  On the day Dr. Peretz and Dr. Crider came to visit my PI told me that even if it didn't arrive I would be able to start my project.  Unfortunately, that didn't end up happening and I was told to wait for delivery.  Almost a week later, we found out that the probe would not be arriving at all and I was given the go ahead to start my project.  With only a week to do a month's work of work I haven't had much down time.  Our project includes extracting, plating, and analyzing over 200 patient samples for HSV 1 and HSV 2.  The samples are run through a real time PCR thermocycler for amplification and the results are presented on a computer system.  I can't show you on the blog because I don't have access to my pictures yet but I will come poster time.  Anyway, the plate we are using has 96 wells all of which are filled with 50 mL of liquid.  Picture a tear drop in a miniature thimble and you kind of get the idea.  Our trial includes 4 different assays, two of which are type common (don't differentiate between HSV1 and HSV2) and the others are type specific (they tell you which one it is).  Each assay has a different target sequence so we are comparing the sensitivity and specificity of each.

My days now consist of arriving at the lab, retrieving my samples from the refrigerator, and moving to the amplification area.  Plating one run takes about an hour because you have to wait for your samples and master mixes to thaw, spin down your master mix, and then proceed to the actual aliquoting  of sample and master mix.  I generally get 2-4 plates done a day and I am down to my final run today.  By the end of today I should have my data ready to be analyzed and I will begin the long process of condensing a binder full of material into four spreadsheets.  Sounds fun right?

Overall I am enjoying my time in the lab.  Although I had more downtime and waiting time than anyone originally expected my project is coming along and things are looking pretty good. 

PROJECT!!!!

Hey it's Katie again from the Children's Hospital of Philadelphia.  Finally after 7 long months of waiting I finally have my project.  In Dr. Hodinka's lab, the primary goal of research is to improve their clinical outcomes.  With that in mind, he has assigned me to two new projects.  The one which has taken up the majority of my time is the HSV (Herpes Simplex Virus) comparison study.  Mike (a med-tech) and I are comparing 5 different HSV assays (three type specific and two type independent assays).  Mike and I are waiting for one more probe (a PCR agent that emits florescence when replication is occuring) before we can officially begin the study.

My other project is developing a new corona virus assay.  Corona virus is a respiratory virus that is most known for the SARS outbreak a few years ago.   However, this outcome is pretty rare and coronavirus usually results in the common cold.  Its name originated from the sun shaped rash that can sometimes develop on the patient's skin. The assay I will be developing tests for 4 strains of the virus.  So far this project has involved pulling past respiratory samples and doing a lot of paper work.  At this point I have over 700 patient samples on file, and that is just from one month!  Once we get a little deeper into the project I will fill you guys in on more details but I just wanted to check in!

Added Responsibility - Week 2

Finally, a little more responsibility.  The end of my first week in lab finished with a bang as I was invited to take the validation of a new assay to completion.  Because this lab processes active patient samples, each test and modality used needs to be validated before hand.  This involves running the new and old test side by side and comparing results, specificity, and sensitivity.  Because all samples used in a validation are from previous patients, not current ones, I was able to run some of the tests.  The new assay we were testing was for HepB, both the initial antibody testing and the confirmatory assay.  In total we ran about 500 samples (at least 3 times each) and ended up with a 14 page excel sheet to prove it.  This project was a major improvement over the beginning of my week and offered some hope for the future.

My expectations were met toward the beginning of my second week.  Having observed most of the benches and tests in the lab, my PI Dr. Hodinka decided that I should get more hands on experience.  One of the tests he wanted me to run was a Western Blot HIV confirmatory assay.  This test detects proteins in a sample (HIV antibody in this case) by binding them to a strip.  Each band on the strip represents a different protein and the intensity of each band can indicate the severity of the virus present.  The blot that I ran compared two lots of controls; a high positive, low positive, and negative control.  Because this test is slightly outdated, it is preformed over night and is very labor intensive.  I had to mix my reagents and manually add them to my plate.  

HIV Western Blot      

The most exciting part of the week in my opinion was the indication that my project would begin sometime next week.  Because most advances made in the field of clinical virology in the future will be in the molecular testing area, Dr. Hodinka will most likely give me a project involving PCR of some kind.  After months of having no clue what I would be doing in the lab, this little inkling has me pretty excited.  Being the "gold standard" of molecular testing, RT-PCR (real time polymerase chain reaction) is highly specific and is a relatively efficient way of identifying and diagnosing viruses present in sample.  Differently from traditional end point PCR, real time PCR can detect amplification as it is happening and accurately report how severe an infection is based on the number of cycles it took a positive sample to pass a threshold.  This is a very useful piece of information for clinicians when making a diagnosis.

Overall I am very excited about the remainder of my time in the lab.  The people who work here are very friendly and always willing to explain something or offer insight when I need it.

The First of Many 12 Hour Days - Week 1

At 5:00 AM on the dot a sharp ring echoed through my room signaling the beginning of my time working in The Children's Hospital of Philadelphia (CHOP).  Two hours, two train rides and a taxi ride later I walked through the doors of the hospital.  Immediately the impact this experience would have on my life began to show.  All around me hung posters and images of the patients and doctors involved in this life saving institution.  Through the EXP program I was now a part of CHOP, which I think is pretty cool.

Because my lab is not soley research based there are a few unique protocols I had to follow before I started any work.  I was trained in the safetly regulations for the hospital and I took a tour through the different sections of the lab.  As the main Virology lab for the hospital, technicians are constantly running samples and testing patients who are waiting for their diagnosis.  As if that weren't enough work, several of the techs are responsible for validating new diagnostic modalities and equiptment that will be implemented in the future.  And just in case that didn't cover it, they were (are) now responsible for a 17 year old high school student from Peddie (me). 

After my first three days in the lab I have seen several steps of the process of diagnosing patients.  From processing to analysis each step must be done with care and accuracy EVERY TIME.  If not the results could be dire.  As a minor and not an official employee of CHOP it will be a while before I am cleared to do substantial work in the lab.  With that being said, there has not been a moment in the lab where I haven't been learning something.  Each member of Dr. Hodinka's team is about as knowledgable in their field as it gets and they always have something new to share. 

After my two week introduction to the lab is over I will recieve my project for the remaining four weeks. SO far the name of the game has been patience... learning how to take my time and STAR (the background of every computer in the lab) S-top T-hink A-ct R-eview: make sure all of your actions are well intended and appropriate.  I am excited for the remainder of my time in the lab and what new challenges await me.