So, we had our two last speakers of this course: Dr. Boris Wawrik and Dr. Bob Nairn. Then the rest of the day was all about data analysis and compilation of the whole project so we could do a better presentation tomorrow. We were all working very hard I must say because it took us three polite “get out, leave my lab” warning from Dr. Stevenson, and the backup power out-OUT.

Looking very  forward to entertaining  the audience tomorrow !!

Miranda Sawyer

What a day? We came together and started processing our data to put it into our presentation for tomorrow. Unfortunately nature was not on our side. The power shut off just as Dr. Brad said to start wrapping things up for the night. Not only was the power off at the microbiology building but also the sooner suites, meaning no internet. The morning will be filled with work, putting the final preparation for our presentation. Charlie and I are doing the microbiology part of the presentation. I thought I didn’t know that much, but I learned more than imagined. Hopefully we can interpret in a pleasing way tomorrow.

This morning we had two lectures. Dr. Boris Wawrik spoke about the microbial environment of the Mississippi river delta. Dr. R. W. Naim talked the restoration of Tar Creek in Picher, OK. Its amazing what engineering and knowledge of chemistry is capable of doing. Although the restoration has a small affect due to more pollutants upstream, it is obvious near the source at Mayer Ranch, there is significant improval. I will be curious to see what the future will hold for his other restorations.

The most interesting part of the day was getting to see everything through the electron microscopes. We got to view many bacteria in the scanning electron and got some very interesting photos. I didn’t think it was possible to see such small detail, but technology makes it possible. We got to see some, what appeared as, filament projections off of some bacteria with the JEOL mircroscope. Super neato! Haha!

After lunch it was time to visit the Samuel Roberts Noble Microscopy Lab inside George Lynn Cross Hall, and check out TEM and SEM imaging techniques, using some of the class isolates, as well as metal coupons, and enrichments of landfill leachate. A very interesting experience!

Lab time was spent analyzing the student’s MIC experiments, and seeing what, if any antibiotics their isolates were resistant to. This was the final critical piece of data for each student in finalizing what the identity of their isolates were.

Finally, each student began to prepare their presentations, covering their isolates, how they came to an identification, and anything in the course that they found interesting or entertaining.

Well, it’s another long for the undergraduate research students as we did a lot during the day. During lecture today, our guest speaker named Dr. Tanner gave us a discussion about microorganisms in the lakes and ponds of Oklahoma. It was interesting learning about his works in researching microorganisms from ponds and how we shouldn’t fear the bacteria in them. Our next speaker, Dr. Callaghan, gave us a discussion about hydrocarbons and how they corrode pipelines that causes leaks. After lecture, we went on a field trip to a meat-testing facility in Oklahoma City. The owner of the facility gave us a tour of how they operate inside the lab and how they test meat. Not only did we learn something from that trip, but we also were given an opportunity to work for him in the near future after he gave us his business card. He was really awesome guy. After the trip, we went to lab putted antibiotics onto our microorganisms. After that, we spent the next several hours learning how to use programs which involved in DNA sequencing and others. It was a load for us to learn and we had a hard time keeping up with our professor. Our good friend and tutor, Blake Stamps, had told us that he was now leaving us now for good to go back to Texas to visit his family. We will truly miss him.

Najuma Maharjan

Very very extremely sad day and second longest day of doing research. Sad in a way that Blake left us to see his family. I really miss him. He is the best TA I have ever met in my life till date. I wish him luck and really appreciate his help and patience with students. As usual, our day started off with Dr. Tanner’s talk on funny incidents during sewage treatment plant and anaerobic hydrocarbon degradation by Amy Callaghan. Both of them were interesting and knowledgeable. After lecture, we went to Aeigis laboratories in OKC.  This was the neat trip so far. The manager of lab gave us a tour of how the things work. For instance, receiving samples, samples testing, processing and all. He also offered us to do an internship and even apply for job anytime.  Then, we headed back to our OU lab and started working on DNA sequencing and processing. We spent hours and hours using that program and had real hard time downloading things on our laptops. But finally we did it. We will be continuing the same data analysis tomorrow. Definitely missed Blake through entire lab

Patricia Pace

Dr Tanner came today to speak about an undergraduate project he had done on the lakes of Oklahoma. He was interesting and I learned a lot about science from him. It is interesting to learn of all the resistant bacteria in the Oklahoma water ways. I would really attend to take a class taught by Dr Tanner. I also listened to a lecture by Dr Callaghan. She spoke about hydrocarbon degradation. Hydrocarbons are surprisingly hard to degrade and require an enzyme to form an intermediate.

We also visited Aeigis Laboratories and spoke with Danny O. He gave us a tour of the facilities and told us how they process their samples. He gave us information regarding jobs in the science field and the types of questions employers will ask.

We then went to the lab and used our sequences we found some programs that allowed us to compare our results to national databases to find what bacteria we have. This was a lengthy process that took several hours. We also prepared Mueller-Hinton plates with the bacteria from our TSB MPN tubes. We then added antibiotic disks to look for antibiotic resistance.

This was one long day. But I had a lot of fun.

Sushma Ale

It was in the afternoon today before Blake left the lab for good. It was pretty sad highlight of the day. The other highlights were: tour to the AEGIS food testing laboratories (very very very interesting tour by Danny G. Orozco), data sequencing and data analysis on finchTv.com, and some entertainment with Dr. Stevenson three kids. Today was one of my favorite days so far, really enjoyed all part besides Blake leaving us. over all, a 5star day!

What an exhausting day. I don’t know if it was because I am tired or because we didn’t leave til 10pm. The speakers this morning were pretty interesting. I enjoyed listening to Ralph Tanner’s lecture because he made everything sound so simple and seem so simple. He was pretty funny too, especially when he was talking about trespassing to get samples and caring about catching bass rather than bluegill’s. The topic was pretty interesting. Amy Callaghan really broke everything down to a more chemistry level which really didn’t make a whole lot of sense to me because the last time I had chemistry was high school. We toured the Aeigis laboratory this afternoon. It is neat how many different ways microbiology can be applied, food testing is one. It smelled kinda funny in there, but I liked how clean it was and how they had music playing. It definitely wouldn’t be a job I would like to have because I’m not a good pipetter. Ha! And I don’t think I’d like staring at the same type of things all day. When we got back to the lab we got introduced to some very large auger plates for testing antibiotic resistance. Very simple process, I liked it! After dinner we messed around on some the computers figuring out a few different programs that read our DNA sequences and compared them to other found bacteria. Trichococcus was one which I made a tree for, which was detected in one of our samples. Unfortunately the Mac wouldn’t open to let me know which sample I was looking at but I wrote down the number for future reference. Well tomorrow we are doing a lot of data analysis that I’m looking forward to.

After lunch, it was time to jump in the van, and head off to Aegis Labs in Oklahoma City. Aegis is a high-throughput food service testing lab, and the students had a chance to see first hand how an industrial lab handles samples, and compare it to the research lab environment. Thank you again to Aegis Labs!

Back in the lab, it was time to test the student’s isolates for antibiotic resistance, and begin the process of analyzing the 16s sequence that had just been returned from the OU Zoology sequencing center. With data coming back from a number of experiments, it was time for the students to begin organizing their thoughts, and their lab notebooks for the presentations on Friday!

After this, it was off to the greenhouse to show the students firsthand the grasses used in her research.

After lunch it was off to the lab, and a talk over scanning electron microscopy (SEM) and Transmission electron microscopy (TEM).

Finally, the student’s did their own gram stains on their isolates, and used phase-contrast microscopy to image their cultures. A busy day, but one filled with plenty of data and interesting speakers!

We started our day with “Microbial Ecology of the Norman Landfill” lecture by Dr. Suflita and “Animal-Microbe-Symbioses by Anne Dunn. Both lecture discussed new things and it was pretty cool. In lab, we jot down the color of plates we inoculated last Friday. My plate has numerous growth and glad to see the result. Next, we start taking phenol and vanillan data and also checked the growth of test-tubes. At last, we get to know Q-FAME technique that is related to fatty acids. We also did gel electrophoresis and took cool snaps of DNA. Yay!!!!

Sushma Ale

First day of week 2, the lecture by Dr. Dunn was amazing! I enjoyed every slide and am looking forward to hearing Blake’s speech about quorum sensing; can’t wait.  Part II (lab) was covered by running gel and learning about FAME. 4 more days to go… we can do it ppl  J

Brandon Denton

I enjoyed the lecture from Dr. Anne Dunn( http://faculty-staff.ou.edu/D/Anne.K.Dunn-1/)  about Vibrio fischeri  and bioluminescence and symbiosis demonstrated in the Hawaiian bobtail squid (Euprymna scolopes).  Josph Suflita, Director of the OU Institute for Energy and the Environment, gave a very interesting presentation over the Norman Landfill research site from a metabolomic perspec tive.   We went to the lab after lunch for some PCR, PAGE, and a demonstration of the Q-FAME Rapid Microbial ID Method of the landfill aquifer samples.

Miranda Sawyer

It is hard to believe it is already August and only a week of this course has gone by. For some reason I was really awake today and actually understanding what was going on. One of the lectures today talked about the landfill, and pretty much what we are doing, but put it more into perspective. The second lecture spoke about the symbiotic relationship between a squid in haiwaii and a luminescent bacteria. Very interesting stuff! Labwork today made time fly by! I’m still not an expert pipetter, but I did learn I’ve been pipetting wrong for a whole week. Whoops! Phenol and vanillan degradation is happening faster than I expected, but it could level off and slow down eventually. I hope that doesn’t happen cause it is the one experiment I am really interested in. I didn’t think it was possible for a mathematician to become a scientist, but I extracted DNA today. There is a first time for everything and this week has been full of them, but not very many people can say they have extracted DNA from an organism. Well guess what, I have! Not by myself, but I have! Ready to see what tomorrow will bring.

Following this, it was back in the lab for DNA extractions of each isolate the students have been working on, amplification of the 16s rRNA gene and running it out on agarose gels to visualize the DNA. The students did a wonderful job, and the product from PCR looked wonderful! Today we also learned about Fatty Acid Methyl Ester (FAME) analysis and identification of microbes by Nikki Johnson.

Patricia Pace

Pretty sure I have had too much fun in the sun. Today we went for a walk in the Kessler Farm field laboratories. We walked quite a bit and saw many interesting things. The most impressive and interesting to me was the creek bed. I understand and could see a number of species of plants growing there that are not indigenous to this part of Oklahoma. We then were able to go back to the suites, shower, change clothes, and have a quick lunch before returning to the Microbiology building for a lecture by Dr. Elshahed. He spoke about biofuels and how he has found anaerobic fungi that can help to overcome the problems of accessing the cellulose.

Our day off. Thanks to Dr Stevenson, Aaron and Blake we had the day off. It was a great time to rest and recharge our batteries. A group of us went to the mall and saw a movie here in Norman. Every bit as important as getting to know the campus is getting to know the surrounding area. Since this experience, in part, is to help us decide where we would like to go to graduate school, this day off was valuable in evaluating the area where we may live for 8 to 10 years. Thanks Brad, Blake, and Aaron.

Najuma Maharjan

Most interesting day so far eventhough we had to get up at 7am. We had field trip to Kessler Farm. Trip was interesting because we got to see bio blade, national wind profile, atmospheric deposition sites and greenhouse sites. After that we had nice lunch and interesting talk on anaerobic Fungi and their Role in Cellulosic Bioenergy by Mostafa Elshahed. The day was over before dinner and thus we got plenty of time to take rest and rehydrate after long week. So lets say  today is The most wonderful day  so far.

Ram Shah

Oh!! lord another hot day and field trip to Kessler Farm Field Laboratory which is around 20 miles from University of Oklahoma, I was thinking how can I made that but it was a really nice trip we went earlier in the morning to escape from the angry sun and I learned many interesting things. Kessler Farm Field was owned by a scientist Kessler he used to do research about weather and some other natural phenomena. Later this field was given to OU and now this is one of the most attracting research fields for botanist and naturalist. There are many weather information collection equipments which collect data of different kinds of weather and environmental changes. In the afternoon, we had a guest speaker, Dr. Mostafa Elshahed. He spoke about anaerobic fungi and their role in cellulosic bioenergy. After that, we did not have any lab today, so we got some rest and rehydration.

Sushma Ale

Another interesting field trip was the first part of today’s agenda; to Kestel’s farm. It was the land with diverse research going on. I learned something about white noise and sonar. Second half of the day was about a lecture on anaerobic fungi that are found on the rumen of herbivores. This was a presentation by Dr. Elscheid on a Saturday noon which was very very appreciative and educational at the same time.

It was a very nice surprise; a whole day to our self. Annoyingly enough, I was awaken around 7 a.m by a wrong call in our suites and stayed up since then. Anyway, the day is still young and is looking to run few errands. See ya’ll tomorrow, and enjoy your day off J

Jeremiah White

Today we visited the Kessler Farm Field Laboratory.  It is a large acrage that was donated to OU where a variety of studies are taking place.  The studies include biological and meterological experiments on the 350 acre farm.  Everything from temperatures, rainfall, wind, grazing, rodents, non-indegionous organisms, and more are studied on the site.  It is an amazing project with many environmental elemental factors observed.  Many more research studies will start in the future to obtain a better understanding of the Kessler Farm.

After the tour, it was a trip back to OU for a talk by Mostafa Elshahed over anaerobic fungi, and then the remainder of the day was given to the students!

Brandon Denton

Interesting indeed! Today we explored the Sam Noble Museum, where many interesting dinosaur skeletons have a home. The morning started off with a lecture about archaea by Liz Karr and after the lecture we got to here Dr. Uppalapatti speak about were the biofuel industry for Oklahoma is hopefully heading if all works according to plan, and how different bacteria affect plants and the way he goes about exploring it. In the lab we got to see our grown bacteria and extract it for further analysis. In one of our sample we have a fuzzy dot which kind of looked like a fungi of some sort, could of even been a kind of bacteria. We also recorded more data from the phenol and vanillan samples, and saw the growth in the tsb, only one or two had more growth than yesterday. I’m looking forward to tomorrow getting to go to a research site, mainly cause its outside and not in a lab.

Najuma Maharjan

As usual we had two speakers. First one was Liz Karr “Molecular Biology of the Archaea”and second was Dr. Rao Uppalapati “Trackling plant pathogens in the functional genomic era” Dr. Uppalapati not only talked about above particular topic but also discussed scopes of microbiology and biology as a whole. It was nice to know various research opportunities that we were unaware of. He handout some notes and useful sheets from the Sam Noble Foundation.

Jeremiah White

Today started off with a lecture from Dr. Liz Karr, Molecular Biology of the Archaea.  It included the unique phylogenetic characteristics and her interest in the molecular biology of archaea. We looked at the extreme environments the archaea are found in.  Next Dr. Rao Uppalapati from the Sam Noble Foundation spoke on Tackling Plant Pathogens in Functional Genomic Era.  The last part of the day was spent in the lab isolating colonies from our TSB and MPN and picking clones from yesterday’s work. It was another exciting day of new experiences and knowledge!

Charlie Ung

Today, during lecture, a guest speaker came and discussed about Archaea. She told us about how they work, and how they could thrive in extremely hot temperatures. Some of the things she discussed were linked to what we had done in lab, such as DNA cloning and PCR. After that, we took a trip to the museum. It was really fun moment we had together. The artifacts, display fossils, and lectures were so interesting that we had all separated as we were discovering things that were new to us. After that, we went to lab and guest speaker, Dr. Uppalapati discussed about plant diseases. We then looked at some plants under the microscope. After his discussion with the class, we continued on with our lab experiment and diluted the colonies that we had created from the previous day onto another medium. After that, we left early around six o’clock and treated ourselves with the bunch of food at Couch Cafeteria during Freshman Orientation Day.

Patricia Pace

Today was one of my favorite days of this experience. From the speakers, to the experiments I enjoyed the day thoroughly. Dr. Karr came in the morning to speak about Achaea. The lecture was exciting and enlightening. Then after lunch Dr. Uppalapati spoke to us regarding plant pathogens and cellulosic biofuels. This lecture was one of my favorite of the week. Not just because the information was so detailed and informative, but also because Dr. Uppalapati was so excited about teaching us about his research. His excitement was infectious and helped us to learn and want to learn more. Finally, we went to the lab and checked our colonies for growth. Finding that my MLS38-B16S colonies grew well I was able to put 96 different colonies into a 96 well plate. We also had two members of the group check the growth in the TBS MPN tubes and found the last dilution that was positive. We used that dilution to streak a plate. We also checked our TSA plates and were able to streak three additional plates from those plates. I am happy with the progress of this course thus far, and cannot believe all we have accomplished. I am excited for next week as I expect and fear that there will be a number of tasks that I have never been exposed to before.

Ram Shah

Today was a fun day. In the morning we had a guest speaker Dr. Liz Karr. She spoke about the molecular biology of the Archaea. She told us how some Archaea can survive even in the extreme high temperature. In the afternoon, we went to Sam Noble Museum of Natural History. We saw some extinct animal fossils like dinosaurs and historical stuffs of the Oklahoman lives. We enjoyed a lot, I especially enjoyed the rotational video of bugs eating on a dead reptile. After lunch, we had another speaker, Dr. Rao Uppalapati, he is a scientist in The Samuel Roberts Nobel Foundation. He gave us some ideas of his biotechnology research and his effort on making some biofuels from switch grass. After his discussion, we started our lab. We diluted the colonies of microbes from the previous day medium into a new medium.

Sushma Ale

Here we are on the end of our first week weekdays. We had Dr. Karr give us some more interesting facts about Achaea and there was a trip to the Sam Noble Natural history Museum after the lecture. It was a delightful tour of the museum, except the very first part where I go yelled at by a cop for climbing up that “elephant looking thingy.”

Miranda Sawyer

Interesting indeed! Today we explored the Sam Noble Museum, where many interesting dinosaur skeletons have a home. The morning started off with a lecture about archaea by Liz Karr and after the lecture we got to here Dr. Uppalapatti speak about were the biofuel industry for Oklahoma is hopefully heading if all works according to plan, and how different bacteria affect plants and the way he goes about exploring it. In the lab we got to see our grown bacteria and extract it for further analysis. In one of our sample we have a fuzzy dot which kind of looked like a fungi of some sort, could of even been a kind of bacteria. We also recorded more data from the phenol and vanillan samples, and saw the growth in the tsb, only one or two had more growth than yesterday. I’m looking forward to tomorrow getting to go to a research site, mainly cause its outside and not in a lab.