Other than that, I feel like I’ve made some really good contacts at the University of Texas – always good for networking and future opportunities. I have a few new friends and a better look at graduate level research. Now, at home, I’ve turned to studying for the GRE and being slightly worried about the graduation test I have to take as a math major. Trying to be positive and gear up my brain for my last year of college! I can’t believe I’m going to be a college graduate in less than a year …assuming I accomplish everything, haha!! I’ll be moving back to Elon so soon and then getting right back into the swing of classes, organizations, working and everything else in life!

MONDAY,  7/13

Today we started a new set of C.diff. PFGE with old bacteria samples we had tried to use before. We had an issue with the concentration of one of the enzymes we were working with, trying to figure out how to make it up the right way. We are still stuck on the enzyme digestion part, but Jane found an article comparing 2 different enzymes in PFGE, the one we’re using and another, and you could see a clear difference in the results showing that the other enzyme works for this process much better. I think we’ve ordered some to try for next week… just in time for me to be finishing up!

TUESDAY, 7/14

It was my birthday! I kept working on PFGE processes, the one started Monday and started a new one today. I also saw a presentation about how to give a good science presentation but it was geared toward older people who haven’t used much PowerPoint, so it was actually ironically boring because I knew the main points: don’t read from the slides, make the text big enough, and don’t use too much animation.

WEDNESDAY, 7/15

I went to a presentation for MBID on TB vaccines. A Ph.D. student was working on some specific biochemical aspect of developing a better TB vaccine. I couldn’t follow some of it, because it was about the cytokines and chemokines, which I don’t know anything about. However, a little bit of epidemiology about TB was included and that was an interesting aspect to see. We also had a birthday celebration for recent birthdays at the School of Public Health. It was a fun potluck!

THURSDAY, 7/16

I kept going with the PFGE, as usual, and did some IBS study samples. I had lunch with my aunt who was in town and that was really great! I also worked a lot on sorting through the data for the charts I hope to compile. I have a presentation to give on Tuesday and my final presentation coming up, so I have a lot of work to finish on that very, very soon! I am still confused about how to talk about the results and exactly what is going on, but I hope to talk to Dr. Jiang about that in the coming days via email since she is in Mexico working on another study.

FRIDAY, 7/17

Not much to show for today, as I went in only for a couple of hours to see a presentation and finish 20 minutes worth of work left to do for the week: checking the results. Again, nothing, but like I said, we have narrowed down the enzyme issue and hope to have that resolved for next time. The presentation I went to was on drug resistance at the molecular level and things binding to each other and something called quac… I am really going to need to switch to a biochemistry major if I plan on doing some of the research the other people are working on, but that doesn’t really interest me anyway. I just sit back and try to follow as much as possible but still get really lost in the terminology. It’s like listening to a presentation in Russian!

MONDAY, 7/6

Today I discussed in detail the abstract I am working on with Dr. Jiang. We talked about the important things that need to be included and how my presentation will be set up for when I present in just a couple of weeks. This abstract is going to be a little different than others I have done at Elon, because it really has to reflect the depth of all the research I have done in the last few weeks in 250 words. I don’t have the luxury of elaborating in a long academic paper, so I’ve got to keep it short and to the point. We ran another PFGE gel today as well.

TUESDAY, 7/7

The PFGE gel did not show anything good today, as usual. We still have problems with the enzyme digestion stage. I spent a good bit of time researching other types of testing and results for typing of C.diff. and helped the lab tech Audrey cap a bunch of pepstone stab bottles for samples being collected in Mexico.

WEDNESDAY, 7/8

We were only able to run 7 samples in the PFGE gel process today because we didn’t have enough buffer for all of the samples we wanted to use. Dr. Jiang and I talked about how the results of our research will be displayed for my presentation. We will use a dendrogram, which is a chart that graphically shows the “distance” or difference between objects, in this case, bacteria strains. I did a lot more pepstone stab capping! Also, I saw a presentation for MBID by PhD candidate Jennifer Kerr who is doing research about proteins and pilluses in plants. I didn’t know nearly enough about biochemistry to follow, but she talked a lot about the process of research and her experience in graduate school, which was helpful to all of us. Some tips on grad school applications:
1. Don’t talk about the specs of your research in your personal statement, but rather discuss the question you asked in the research you did and what became of it. Talk about the thought process and the reasoning behind the method moreso than the method itself.
2. Get a LOR from people who know your capabilities in terms of research.
3. Seek out someone you are interested in doing graduate research with and mention their work in your personal statement. If at all possible, talk to them (on the phone!!).
4. Community outreach, tutoring, TAing, and campus involvement are all options in grad school.

THURSDAY, 7/9

PFGE failed again, we are still working on the solution to the enzyme problem. Processed a few new samples for the IBS study.

FRIDAY, 7/10

Nothing to work on for PFGE today, but processed some IBS study samples. I also looked over the preliminary dendrogram and will begin more work on that soon. Dr. Jiang will be out the next two weeks, so I have to kick into independent mode!!

MONDAY, 6/29

Today was a really bad day for me in the lab. Why, you ask? I ruined 6 samples, dropped a petri dish and spilled a vial of blood all over myself. Joyous! I had to wait for my clothes to be clean so I could go home. I don’t know what was wrong with me, but I was just having a really off day. In terms of my acutal lab work, we started a new set of samples for my C.diff. study and had stored some samples from last week’s round of PFGE to try the last 2 days of protocol with. Meaning that we could have new results on Tuesday. The problem we think is that the samples are not properly digesting the Sma1 enzyme. Today, I also attended a talk by Dr. Sara Strom, a South American professor in the epidemiology department at M.D. Anderson Cancer Center, an affiliate of the University of Texas. She talked about prostate cancer epidemiology and the study of epidemiology in general. It was sort of like my entire last semester of Intro to Epidemiology condensed into an hour long talk focused on prostate cancer. Things I learned?

1. All men develop prostate cancer by the time they hit 90 years old. 100% of them.

2. Prostate cancer is most prevalent in African-American men, and not prevalent in African populations for the most part.

3. Prostate cancer is really over diagnosed because most men who test positive don’t have any outward symptoms or a serious case of cancer. They just have some malignant cells.

4. The Japanese have the lowest rates of prostate cancer (this is very common with many cancers). Experts link this to their low-stress and excellent diets.

5. I really like epidemiology.

TUESDAY, 6/30

The bands were still not “cutting”, meaning we were not able to see distinct results like we wanted to, again. So we started yet another 2-day process with more old samples and even another 5-day process with new samples. We’ve got three rounds of samples going at the moment, so keeping track of it all has been crazy! We have to store 2 sets of these samples because we don’t have time to finish due to the holiday. Today I also went to the C.diff. meeting that involves researchers around the medical center complex.  I went once before at the beginning of the program, but for various reasons haven’t been able to go to the weekly meeting since. Anyway, they talked about  how the studies they are working on are still in progress, mostly organizational things like IRB and collecting samples. I’ve been asked to do a presentation on my project for the meeting (usually 10-20 people!) later this month, right around the time I have to give a presentation anyway for my program. So I’m getting lots of good research presentation experience! Yay! Other things to note: I need to read more about my study’s process and if it is typical to apply this certain protocol to this certain disease. I definitely need to read more literature.

WEDNESDAY, 7/1

It’s July already and the program is half over! When did that happen? I  got paid today, though! Yay! Nothing extremely exciting, I just finished the new C.diff. PFGE  samples I started and they will incubate in the fridge until next week when I can finish it and hopefully get results. With the volume of samples we worked on this week, it may turn out that we get a lot of good results next week since we are running so many. Cross your fingers!

Hope everyone has a wonderful Fourth of July! I’m heading to a family reunion in Pennsylvania this weekend. Happy Birthday, America! (And almost to me, 12 more days!)

MONDAY, 6/22

Began the PFGE process yet again, making the bacteria in to more useful agarose plugs. We made 2 plugs for each sample so we would have extra in case of failure. Today I received a few new samples for the IBS study I have been working on. One of the stool samples I was testing seemed to test positive for blood, but I wasn’t sure, so I asked for other opinions. It took 3 tests and 4 opinions to confirm what I had thought in the first place – the test showed the positive green color that matched the control. The test used to detect blood in the sample is based on a color change, but the test has to be read very quickly, so the first two times, I wasn’t able to run down the hall fast enough to show Nadim and Mo what I thought was a positive sample. In the end, my Ph.D. mentor confirmed my results, but there was a large debate at first because IBS samples don’t typically test positive for blood.

TUESDAY, 6/23

Nothing insanely exciting happened on Tuesday. We began the next day of the PFGE process by washing and rinsing the plugs with different chemicals. The plugs stayed well in tact throughout, at least better than the past couple of weeks. I finished the DNA extraction process on 12 blood samples and began processing some new samples as well for the IBS study. Dr. Jiang had given me a reading on cluster analysis at the end of last week, which I continued reading during my down time.

WEDNESDAY, 6/24

The third day in the PFGE process went well. The plugs again stayed in tact, and it seems that we have learned each week what to tweak to make the experiment better. By keeping the bacteria and the gel at the same temperature when making the plugs, our samples were better preserved and were better able to withstand “gentle agitation” as called for by the protocol. For the MBID program Wednesday meeting, we again went to the Infectious Diseases Grand Rounds at Baylor College of Medicine. The cases today involved a man who developed a horrible lesion on his finger as a result of exposure to some type of mold on a tomato plant. He was an avid gardener. Another patient had some sort of infectious disease similar to meningitis that caused cysts in the brain to develop. The third case discussed among the doctors was about a yeast infection in the blood. After the Grand Rounds, we ate lunch with a very friendly M.D./Ph.D, Dr. Lisa Armitage. She spent some time getting to know the eight of us and talking about our different projects. It seemed that in her biochemistry/molecular biology experience, she had done a little bit of each person’s type of experiment. She knew quite a bit about what each of us were involved in and even about our mentors. She told us a little bit about her work; she intends to win the Nobel Prize for developing a test that will detect a current tuberculosis infection in the blood. Apparently, a test can determine if you have had tuberculosis at some point, but there is nothing that will show a currently active strain of tuberculosis. Dr. Armitage was very encouraging – a lot of us are struggling with our research, but she ensures that the effort will produce SOMETHING, even if it shows you what you don’t expect to see. Her decision to become an M.D./Ph.D. resulted from the idea that she just couldn’t live without being in the lab and doing research as part of her career. She took a great pay cut to be able to do both research and clinical work but seems to be very happy with this lifestyle. She loves both jobs. She was so funny and interesting and I really enjoyed the conversation we were able to have with her.

THURSDAY, 6/25

Thursday we prepared the gel for the electrophoresis process. This week, we didn’t have nearly as much trouble with the machine as last time and everything went smoothly. Dr. Jiang and I talked about the analysis portion of my project and we intend to start working on that post July 4th and also will begin writing an introduction for my presentation around that time.

FRIDAY, 6/26

The last day of the week hasn’t been going well for me. Although I get to go in later since there isn’t anything to do until the afternoon, the results have not been treating me well. We read the gel at about 2:30 PM, but under the UV light, the bands that genotype the bacteria were all bunched up at the top of the gel. I didn’t quite understand what this means but I do know that there was an issue with the enzyme that we added to the sample and that this problem may be able to be fixed on Monday. Dr. Jiang said something about cutting the sample and trying the electrophoresis again, so tomorrow we will be able to try to work with these samples again as well as start another PFGE process with new samples. After reading the unfortunate results, I headed over to the UT Rec Center for a “Science Expo”/BBQ put on for all of the students in the Graduate School summer program. They had recruited representatives from several different programs at the UT graduate school to sit at booths while we walked around to talk to them about their departments. Although none of them really fit me (neuroscience, cancer biology, cell and environmental biology, virology, etc) I was able to learn about graduate school in general and talk to a few students. I also talked to a woman who received both an MPH and a Dr.PH from UT and knows Dr. DuPont quite well. I am not sure of my exact plans post-Elon, but it was informational to talk to her about the benefits of an MPH or a Dr.PH, both programs I am still learning a lot about.

It was a pretty average week – no “Eureka!”s yet, but I still got my hands dirty in research and was able to do a few educational things, too. Next week is short because of the July 4th holiday, but I should still be able to get a lot done in the lab and there are a couple of seminars to attend as well. Keeping my fingers crossed that I see some DNA bands soon!

After work on Wednesday, I was able to go to an Astros (baseball) game with some friends from the program. It turned out to be pretty fun!!

MONDAY, 6/15

We started over with the PFGE process that didn’t work last week, using four new C.diff. samples from St. Luke’s Hospital. We created a total of 12 samples, and Jane, Dr. Jiang and I each did our own set of the four samples. This day I also processed some new blood and stool samples for IBS Study #3. Nothing eventful in the world of seminars occurred today.

TUESDAY, 6/16

Today was PFGE Day #2, another 8 AM arrival but fairly early afternoon departure (3:30ish). We washed the samples with different buffer chemicals today. We also had to prepare the chemicals used in the protocol, which took the longest time. There was a lot of math involved in terms of calculating dilutions and concentrations to use in the chemicals, but there were things like molecular weight and molarity that I am still learning about in order to be able to do the correct math to make up the recipes. Dr. Jiang did all the calculations for the chemicals this week, but had some reassurance and double-checking from Jane and myself. Nothing eventful for my programs today, either.

WEDNESDAY, 6/17

For PFGE, we did more washing of samples with chemicals and waiting for incubation, which took a while (6 hour incubation periods leaves lots of time for internet research). The most exciting part of today was the tour of the Clinical Microbiology Lab at UT’s Memorial Hermann Hospital, which is the main teaching hospital for UT Medical School. Dr. Audrey Wanger, the director of the clinical micro lab at both Memorial Hermann and the Lyndon B. Johnson County Hospital gave us the tour. The MHH lab receives samples from all over the hospital as well as from smaller facilities that don’t have the capacity for more extensive testing on samples. The samples are cultured for various things, based on what the physician orders. There was a main area of the lab, where general testing for staph bacteria, strep bacteria, yeasts and other organisms are tested for, mostly the typical tests ordered in a hospital. There were two other testing rooms off the main area, one is specifically for TB and fungal cultures, and they keep the room negatively pressurized so that if TB or fungus somehow got into the air (there is a lot of protection to ensure that doesn’t happen), then the air would stay in that room instead of spreading into the bigger area. There is also another room specifically for further molecular based testing, especially for viruses and more complex things to detect. Some other interesting facts learned: Most of the technicians doing the lab tests are either 2 year or 4 year trained personnel and they are specifically certified in laboratory technology. I had no idea there was a special type of certification or school you can go to for this — lab tech school. Also, Dr. Wanger meets with infectious disease specialists from Memorial Hermann every morning and they video conference with ID specialists at LBJ Hospital to go over special or interesting or unique diseases they come across in cultures. Dr. Wanger said that LBJ typically sees stranger cases because (insert public health knowledge here!!!) people who go to the county hospitals are typically less insured and wait until the last possible moment to receive treatment. So, you see much more developed and worse cases of certain diseases there versus at Memorial Hermann. This entire lab tour was sponsored by the infectious diseases grant that is also paying me more money for my stipend. We got free lunch afterward as well, and the 8 of us in the program finally started talking to each other more to learn about what we are all interested in doing after undergrad.

THURSDAY, 6/18

Today, we washed the samples and rinsed with buffers again to start the PFGE workings for the day. Later in the afternoon, after several incubations, we made the larger gel and put the samples into the PFGE machine, which gave us a lot of trouble when we tried to start it up. The machine wasn’t working properly at first, but with 4 heads and an hour later, we finally got it going. I was supposed to attend a presentation at the graduate school today, but it got cancelled. I also ran a blood and a stool sample for IBS Study #3.

FRIDAY, 6/19

Sadly, the big day at the end of the week where we were to see final results ended on a bad note. The gel did not show any bands under UV light viewing, meaning something was wrong in the process of our protocol. We eventually figured out that two of the chemicals were made with the wrong concentration of one or two items…. One buffer we made was 200 times stronger than it was supposed to be!! Dr. Jiang went back to look at it and did something regarding molecular weight to fix it so that it WILL work next week! The game plan at this point is for me to read about cluster analysis, which is what we will use to analyze the data set as a whole for my end results. She intends to give me some data that has already been collected so that I can at least get a head start on the analysis part. We will keep stabbing at this PFGE process until we get it right! On another note, I attended a talk at the graduate school this afternoon about liver regeneration, given by a notable researcher at MD Anderson Cancer Center (part of the University of Texas). Dr. Michelle Barton, the speaker, gave a very interesting presentation about p53, a protein that is a major tumor suppressor in human organs. I didn’t follow the majority of the biochemistry part of the presentation, but she did speak about Promethius and liver regeneration as well as the general idea of the experiments they have been conducting in mice to learn about how p53 works and how liver regeneration research may help advance general knowledge about cancer. Another interesting public health note, developing countries with higher rates of hepatitis infection have much higher rates of liver cancer because p53 is reduced in hepatitis patients. This makes sense if you think about demographic transition, which we learned in epidemiology this past semester, that as you move from 3rd world to 1st world, you see a change from prominently infectious diseases to mostly chronic diseases.

A couple of people from the program came over to watch a movie on Friday night, which was fun. There are a few people that I get along with pretty well so far, and we’re already planning to do some fun things next weekend, perhaps going to an Astros game. Yesterday, I went tubing on the Comal River in New Braunfels, which was really fun! It was really crowded, but relaxing to float down the river for a few hours. Thankfully, I didn’t get much sunburn, only a couple of patches on my legs.  We also went to the most enormous outlet mall I have ever seen – 2 side by side, for that matter – in San Marcos earlier today. Somehow I didn’t spend a dime on anything, which is impressive for me. But, I’m getting around Texas a little bit, which is fun and new and therefore a little refreshing!

MONDAY, 6/8

I began my work on PFGE or “pulsed field gel electrophoresis” for the Clostridium difficile bacteria samples we had growing in the lab. Jane and Dr. Jiang worked with me the first day, where we scraped the cultured C. diff. bacteria from agarose plates and processed them into little gel plugs that incubated in a solution for a few hours. This was only day 1 of a five day process that is very meticulous and can’t be corrected throughout. You either do it right the entire way through or it doesn’t come out. On Monday, I also had lunch with Jeticia, a student at UTSPH pursuing an MPH. I just got to chat with her while we ate our packed lunches outside – asking questions about what she liked and the benefits of going into an MPH program straight out of undergrad. In the afternoon, I processed three new stool samples, including one for the IBS #2 study – something that was supposed to be closed out but will have a sample come in every so often. I also began processing 2 new blood samples for IBS #3. I finally got my hands on a username for the computer to keep in contact with people! Last, I had a seminar from 3:00-4:30 to end the day. The seminar took place in the graduate school research building and was given by a post-(multiple)doc(s) about “Ethics in Biomedical Sciences”. Dr. Pickering spoke about keeping track of your data, lab notebooks, the idea of intellectual property, animals in research, research with humans, biosafety and biodefense and the scientist’s role in society. Since he specialized in biodefense, he spent a lot of time talking about that area. One interesting thing I learned was that the coding for the polio virus is available to the public in some sort of database. At some point in recent history, people at a university were able to replicate the polio virus, mostly just to show that someone could create it from scratch. We talked about whether or not this kind of behavior should be permitted and what the necessity for knowing how to create infectious diseases is… if there is any at all.

TUESDAY, 6/9

I began day 2 of the process for PFGE, where I spent a lot of time waiting, as I did throughout the week. The plugs containing the C. diff. bacteria were washed in a buffer and incubated for 6 hours, washed again with the same buffer and incubated overnight. I again processed new blood and stool samples for IBS #3. The most exciting part of my day, and surprisingly so, was a seminar I went to about “Making Life Easier: Strategies for Productivity” by a woman who is the director of faculty development at UT’s medical school. Interestingly enough, she was a CPO, or certified professional organizer, and her life revolves around trying to make everyone else’s simpler and more productive and effective. She was really funny in her talk and I did pick up a few tips about saving time. 1) You don’t always “have a minute” when someone asks. It always turns into 20 minutes and a waste of time. 2) Multitasking DECREASES productivity. You spend so much time trying to shift your brain between tasks that you lose the time you could have spent focusing and accomplishing one task. 3) Turn off your email notification pop-ups and put your calls directly to voicemail when you’re trying to get something important done. She most importantly inspired me to make a list of things to do by the time I’m 30. Reasonable goals with a very real deadline – 10 years can always be pushed back from year to year, but you only turn 3o once – could actually be accomplished! Lastly, I took some time after the seminar getting to know a couple of the other students in the program, Aaron and Tim. I actually enjoy getting to know their backgrounds and interests to see what types of people I have the potential to work with in the future.

WEDNESDAY, 6/10

I came in early to begin the long PFGE process for today. At 8:15, I washed the bacteria gel plugs with a buffer again, and had to wait 6 hours before washing them with another type of buffer solution 3 times for 30 minutes each. In the meantime, I finished most of the previous blood samples and put them through the entire DNA extraction process. Some of these samples were for the IBS #3 (genetics and IBS) study and some were C. diff. patient blood samples. In the afternoon, a high school student Catherine came in who is going to be working in the lab over the next year as a part time gig to see what scientific research is all about. She’s a bright girl – over 2300 on the SAT and pre-med. It is really cool to see that such a big university reaches out to the local school community to get students involved in real lab science.

THURSDAY, 6/11

This was the third PFGE day where I repeated a lot of washing and waiting. We washed the plugs in different buffers, one included an enzyme intended to amplify the bacteria and help isolate the strains. I had to leave a little early to make it to another seminar, so I couldn’t be there at the time that the rest of the gel process was completed, but Dr. Jiang showed me essentially what happened. A gel was poured into about a 6 by 6 inch mold with something in place to make little holes to put all the bacteria plugs into. That block of gel, once solidified, was put into a machine that completed the real PFGE part of the process. The machine sent electric waves through the gel to separate the bacteria into different bands that identify what strain of bacteria is contained in the plug. The machine is very complicated looking and I am still trying to understand the entire process, but this is the simplest explanation I can make at this point in time. The gel sat in the machine for around 20 hours, so we completed it the next day. While waiting for incubations, I spent a lot of time on the Internet looking up scholarly articles about C. diff. and reading through the current research about it. I could go on and on about the issues involved with it, especially in hospitals, but I can explain that in more detail when I wrap up my research. Since I will be repeating this PFGE process over and over again the next few weeks, it might be more interesting to talk about the research I’ve been reading than repeat the process in the blog every week. At 4:00 on Thursday, I went to a boring but informational seminar on “The Anatomy of a Research Article”. A woman was talking about the process of writing a scientific research paper following the IMRAD model: Introduction, Methods, Results and Discussion. Major highlights were 1) Be as explicit as possible, don’t make your reader guess your hypothesis, purpose or strategy. 2) Provide enough detail that someone could repeat your exact process as well as statistics of how good your data is (p values, etc). 3) The discussion section of your paper should not repeat your results, but talk about your findings in context of your field of study, its importance to scientific research, comparing your research to other studies and addressing both strengths and limitations to your work. For the most part, I felt like prior experience in research and having spent the last semester writing a 35 page undergraduate thesis would have exempt me from this talk, but it was still informational.

FRIDAY, 6/12

I came in later to the lab today since I wouldn’t be able to do anything with the PFGE until about 3:00 PM. I spent most of the morning processing some blood samples, looking at my new GRE vocabulary book, and learning and researching more more about PFGE, which is used for genotyping and identification of pathogenic organisms. It is considered the gold standard in terms of processing pathogenic organisms in infectious disease research. I attended a noontime seminar with my fellow research students that was a talk by a biochemistry professor. He addressed the history of the P450 protein, which I know nothing about and I don’t know much about biochemistry so I didn’t follow 95% of his talk. He was an interesting guy though, a priest and a scientist, and he discussed how the two studies differed so much and completed different parts of him, if that makes any sense. After the seminar, I went back to the lab for more PFGE and C. diff. research before taking the gel out of the PFGE machine at 3:00. We then stained the gel with ethium bromide, which is apparently very poisonous and there was a special waste disposal for it and anything that touched it. We cleaned out the PFGE machine while we waited for the gel to be stained. Then, we did the last part, trying to view the gel under a UV light to tell us what bacteria we were looking at. Unfortunately, the process didn’t properly work. We didn’t see bands like we were supposed to, rather we saw smears across the gel. Although I spent a week doing these samples and it didn’t turn out, I have learned more than I ever knew about lab processing and working with bacteria, and my comfort level in the lab is much higher than before I started this process. I have a better idea of how to make sure it turns out better next week, and we’ll just have to pick back up and try again. Next week, Jane, Dr. Jiang and I will each do the PFGE process with only 3 samples, all the same samples, to be sure the process is working. Dr. Jiang and Jane don’t have a lot of PFGE experience with bacteria, so we are all learning about it. Hopefully we’ll see some better results next Friday.

SATURDAY, 6/13

Yes, Saturday! Jeff and I went out to Dr. Steve Norris’ house in Pearland, south of the outerbelt around Houston, for a mexican barbeque. Other students from the MBID program and I were welcomed to the Norris home, a beautiful house on a beautiful lake where we were even able to go on a paddleboat! My friends from the program, Tyler, Tim and Aaron were there as well as another student, Justin. The other 4 students involved didn’t show, but they missed out on WONDERFUL fajitas and sopapilla cheesecake! The Norris’ were wonderful hosts and we had a lot of fun talking with faculty mentors involved in the program and going out on the lake for a little paddle-boating. We all had a great time, and one of the faculty mentors even played a little Johnny Cash on the piano – he was fabulous! So, the lesson here was that even nerds in microbiology research can have a good time on the weekends.

Next week I’ll be doing the PFGE process over again and looking forward to going tubing down a river in New Braunfels, near Austin, next weekend with a few friends!

MONDAY 6/1

 I ran three new blood samples with Audrey, a research associate in the lab who has introduced me to the DNA extraction process for the IBS study I will be helping out on. I also stored the corresponding stool samples in the huge and very cold lab freezer. We made some more media, or petri dishes with different chemicals that incubate bacteria in order to perform what is commonly called a “culture” (mostly for stool samples). The ones we made Monday included horse blood! This is apparently because some bacteria need blood in order to grow. I also learned about the RNA and DNA coding process for norovirus research from a Ph.D. student working in the lab named Nadim. His research involves a study in Mexico focusing on norovirus as a major cause of traveler’s diarrhea. 

TUESDAY 6/3

I again ran some samples of blood and stool for the IBS study. I also met with Dr. Herbert DuPont, the primary mentor on the research project I’ll be handling on my own the next 7 weeks. He explained to me the objective of my Clostridium difficile research, isolating strains of bacteria from stool samples of C.diff. patients at St. Luke’s Episcopal hospital, where Dr. DuPont is the Chief of Internal Medicine. Previous studies of C.diff. in other hospitals have shown that about 50% of C.diff. cases stem from only 2 bacteria strains, and the other 50% of cases come from numerous bacteria strains. This idea has great implications for the control of C.diff., which is an infectious disease of diarrhea that runs rampant among elderly patients in hospitals. Essentially, these patients are being treated for a particular condition while in the hospital and given antibiotics as part of their treatment. These antibiotics destroy the good flora in the colon, and this combined with a repressed immune system leaves the elderly patient very susceptible to the C.diff. bacteria that is spread through the hospital by doctors, nurses, med students, etc. Hopefully, I will be able to isolate the different bacteria strains that are causing St. Luke’s so many problems, and they might be able to use said research for public health control measures. Dr. DuPont also took me to the weekly C.diff. meeting in the Medical Center, taking place at St. Luke’s every Tuesday at 11 AM. Physicians, researchers and students from around the city meet to discuss the current C.diff. studies occurring around the Medical Center facilities, and each week someone gives a short presentation. This week, a PharmD student Carrie Shuman presented on the microbiological idea of bacterial translocation of C.diff., or the spread of bacteria cells to vital organs throughout the body. The research I will be working on is a new topic of interest for this group of about 20 people, so I have the opportunity to present to them about my research at the end of the summer or even in the midst of finding conclusions.

WEDNESDAY 6/4

I processed approximately 50 blood samples, some of which were incomplete, incubating at room temperature before the next stage of DNA extraction. I also had one new blood and stool sample that came in the early afternoon. I was introduced to the other Molecular Basis of Infectious Diseases grant students along with the program coordinator, Dr. Steve Norris, today at a lunch we had together. Before the lunch, we went to another city wide meeting at Baylor College of Medicine, also in the Medical Center. One of the great thing about having over 40 hospitals and universities in such a small area is the accessibility to different seminars, meetings and other learning experiences. The City Wide Infectious Diseases Grand Rounds is a fascinating meeting that takes place every Wednesday at 12:00 noon. Infectious disease physicians from around Houston attend and three “mystery” cases are presented to the attendees (around 50-70), sort of like CSI but infectious disease cases. The doctors in attendance then guess what disease the patient has and talk about treatment options. One of today’s cases was about an IV drug user infected with Clostridium sorelli, which brought up the topic of  C.diff.  and it was neat to see that “my” disease is a topic of interest to them! Another case involved an HIV patient that had Histoplasma which caused a yeast infection to grow in his brain! The third case was a 2 year old that had a lung abscess which turned out to be Streptococcus pneumonaiae. Following the grand rounds meeting, the other seven MBID students and Dr. Norris and I had pizza and talked about some of the upcoming programs, like seminars, meetings and a barbeque at Dr. Norris’ house this coming Saturday.

THURSDAY 6/5

I finished the DNA extraction process on the 50 blood samples in progress and finished up other stool samples in the lab. I met with Dr. Zhi-Dong Jiang, my other mentor, to discuss the process of the environmental samples related to my project. Someone is swabbing the rooms of C.diff.  patients in 5 areas: around the bed frame, on the floor around the bed, the bathroom sink, toilet and the light switch in the bathroom. These samples will then be tested for C.diff. bacteria to find out what surfaces are spreading the bacteria to the patients. Dr. Jiang showed me how to log these samples and the other lab employee, Jane, showed me how to put these samples through the culture process. I also attended the UT School of Public Health employee appreciation lunch with everyone in the lab and met some new employees that work on the other side of the hall!

That was it for my work this week – I took off on Friday to go home for my brother’s high school graduation. I’ll be starting in full force tomorrow to get going on my project; it will take at least a week to process only one group of samples for my research! All in all, I am really enjoying all the opportunities I have as part of the program, from working with a very renown researcher Dr. DuPont, to the hospitality of all of the lab employees and especially Dr. Jiang, as well as all of the seminars and meetings and educational things I can take part in! Oh, and last, I was on the way back to Houston today, and the man sitting next to me on the plane happened to talk to me, telling me that his sister is the DIRECTOR OF INFECTIOUS DISEASES for the state of Ohio! HOW AWESOME! She managed protocol for the swine flu and dealt with the cases when it hit Ohio a couple months ago. He gave me his contact information and hopefully I’ll be able to meet his sister and see what she does at work!

It’s hot here already, and June isn’t even here yet! I got down to Houston on Monday and used my day off on Tuesday to get familiar with downtown, the medical center and the METRO system! It’s a very different and at times confusing city life… especially when it takes you an hour and a half to get home when you took the right bus line number but the one you happen to get on went a slightly different route than the one you should have been on. Oh well, I’ve been getting a lot of reading in.

The first day of my program was semi-bearable. The morning consisted of getting to know the program directors and fellow students as well as learning about the facilities and the premise of the program. We got ahead of schedule though, and spent about an hour waiting around with nothing to do until general orientation started in the afternoon. It was a pleasant four hours learning about lab safety, using animals in the laboratory and radiation safety. There were people falling asleep during some of the talks. Then I made my way back to the apartment.

Thursday I was introduced to the School of Public Health labs, which I had seen before, but this time I was shown all the equipment. Audrey, the woman in charge of facilitating the labs for Drs. DuPont and Jiang (my mentors) was able to get me started doing some work even though both the faculty members were gone. I learned a little bit about making agar in a petri dish and got settled with a desk and computer (the one I am currently working on).

Today, I met Dr. Zhi-Dong Jiang, one of my mentors on the projects I’ll be working on. She explained to me what I really wanted to hear: the two projects I will be doing this summer. One is completely my own and the other is a related project that needs some work done while I’m here. The first project, which I will be in charge of, involves isolating different bacteria related to C. difficile that causes IBS in patients. I will be working on testing different stool samples — laugh now, and forever hold your peace because it’s all you’ll be hearing about for the next two months! These samples will be cultured and then I will use UV lights to identify which bacteria strains appear. The bacteria takes a lot of time to grow on the agar, so it seems that I won’t be extremely busy during the day, because the tests take only a few hours to do but several days to go through the entire process with different incubation times. So, when I have free time, I will be working on the other project involving identifying DNA from blood samples of patients with IBS. My mentors, Dr. Herbert DuPont and Dr. Jiang, are trying to identify genetic factors that contribute to the contraction of IBS. It’s a very interesting concept, and I am certainly getting all the gory details behind it.

This afternoon, I will be trained to work with the blood samples with Audrey. Next week she and Jane Chen, another lab employee, will help show me the cultures for the bacteria and how to run those tests. Then I’ll be starting on my own the week of June 7! The plan is to have my data by July 17 so I can do the analysis the next week before presenting my research to the other MBID students at the end of the program. I was worried at first, but my mentors definitely have a clear-cut plan of what I’m getting into, and it sounds interesting. I am really hoping that the meticulous testing leads to some good results that I can analyze, which I think will be the best part about the whole thing for me.

I’m taking my lunch break and then hoppin’ to it! Looking forward to a fun weekend in the hot sun by the pool!