Category Archives: Student’s Reactions

Day 8- Student’s Reactions

Najuma Maharjan

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.

Day 6- Student’s Reactions

We’ll combine all of the posts from day 7 with today since we let all the students take a breather on Sunday!

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.

Day 5- Student’s Reactions


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.

Day 4- Student’s Reactions

Patricia Pace

I have never been in the lab this late. I am having a lot of fun, but I know tomorrow this late night is going to hit me. I did have a lot of fun today. Dr Cichewicz spoke to us about Race, genetics, and health. His lecture talked a lot about drugs and pharmaceuticals. Dr Lawson, the poo doctor, spoke with us microbial taxonomy and how molecular biology has affected it. After lunch I extracted environmental DNA from LF-2B leachate. Judith and I then used the PCR technique to amplify the archaeal DNA. Blake ran the gels and we repeated the Phenol and Vanillan degradation as a class. We then used the TOPO method to incorporate our DNA into a plasmid so that the bacteria could reproduce the DNA for us. I am currently waiting for Blake to return with the cells so that I can plate them and go home to sleep…hurry Blake!

Sushma Ale

We had two speakers today: Dr. Cichewicz and Dr. Lawson (who I got to introduce in front of the class). It was a very new experience. Dr. Cichewicz talked about some interesting scope in a field of microbiology as a career. Also in the lab, we did some interesting experiment by running PCR, gel making, and TOPO cloning reaction. Overall it was very long and yet very educational day!

Brandon Denton

The longest day so far. 9 A.M. to 11:20 P.M. It was a long and intense day of 2 lectures before lunch and PCR, Agarose Gel Electrophoresis,  Topo Cloning ,and Transformation of Ecoli strain Mach 1 all using the Power Biofilm kit from Invitrogen. The kit worked great!  Pushing through the day was worth it because we learned so many new subjects and molecular techniques while completing our experiments and this will give us enough time to collect and analyze data so that we will be able create our poster and present our findings on Fri, Aug 5th and is my b-day.  If you want to give me a gift, donate some money to this program or to EPSCOR). Yes….I said DATA! We started to collect absorbance readings that, when analyzed, will tell us if we have come closer to isolating Phenol and Vanillin degrading microorganisms

Day 3- Student’s Reactions

 

Patricia Pace

Wow! It feels like we’ve been here a month already! I am learning so much every day. Today Dr Najar came and spoke to us about DNA sequencing. I was quite surprised to learn that DNA is not sequenced in order, and it is a sort of puzzle they fit together after identifying the nucleotides. The Cecil Lewis, Jr came and spoke regarding evolution. I really enjoyed his lecture. He provided some interesting information on population genetics and nucleotide diversity. I loved his saying, “The lottery is a tax on people who are bad at math”. His lecture was fun and informative. We took a break for lunch. After lunch we processed some samples from the duck pond. Sushma, Judith and I used the liquid obtained from the upper duck pond to make SRB MPN tubes, overlay plates, and the formalin sample for the experiments. We also made a slurry from compost at the Norman Landfill, and used this to start an experiment for biodegradation of phenol compounds. Unfortunately, the concentration was much too high and we had to abandon that project for now. Tomorrow we plan on using the leachate we obtained Monday at the landfill to complete the biodegradation of phenol compounds project. It was a fun day, and passed very quickly. I am looking forward to tomorrow. We have a couple of lectures in the morning and in the afternoon we get to start Molecular Biology!

Jeremiah White

Today had some intriguing lectures on gene sequencing and genetics.  Dr. Fares Najar’s presentation on Sequencing Technologies and their Application introduced the group to the processes and history, processes, and methods of gene sequencing. The technology allows for deciphering of new genomes and has many more significant applications.  Dr. Cecil Lewis, Jr. lectured shortly after.  His presentation on Race, Genetics, and Health was extremely interesting.  It covered population genetics, forces of evolution, levels of diversity, and enthralling topics on human evolution.

Brandon Denton

We started the day off with a presentation by Dr. Fares Najar titled “Sequencing Technologies and their Applications”.  This presentation included detailing a comparison and contrast of the Sanger and Pyrosequencing methods of sequencing. It was very interesting, informative, and full of information.   Dr. Cecil Lewis gave the second presentation over population genetics that included a genetic trace of humans and gave results that showed a common ancestry to sub Saharan Africa.  I found one particular question very interesting.  Is sickle cell anemia an evolutionary adaptation for a resistance to malaria? He showed that populations in Africa with a high rate of malaria also have a high rate of persons with sickle cell anemia who are resistant to malarial infection.  We broke for lunch and then returned and took a trip to the OU duck pond to take soil and water samples.  We then inoculated several different types of growth media with samples taken from the duck pond and compost from the landfill in order to enumerate and eventually isolate various types of microbes including cellulose degrading anaerobes.  Very interesting day and things are starting to click and overhead light bulbs are getting brighter.   I can’t wait for data!

Judith Zounon

We started the day off with a presentation by Dr. Fares Najar titled “Sequencing Technologies and their Applications”.  This presentation included detailing a comparison and contrast of the Sanger and Pyrosequencing methods of sequencing. It was very interesting, informative, and full of information.   Dr. Cecil Lewis gave the second presentation over population genetics that included a genetic trace of humans and gave results that showed a common ancestry to sub Saharan Africa.  I found one particular question very interesting.  Is sickle cell anemia an evolutionary adaptation for a resistance to malaria? He showed that populations in Africa with a high rate of malaria also have a high rate of persons with sickle cell anemia who are resistant to malarial infection.  We broke for lunch and then returned and took a trip to the OU duck pond to take soil and water samples.  We then inoculated several different types of growth media with samples taken from the duck pond and compost from the landfill in order to enumerate and eventually isolate various types of microbes including cellulose degrading anaerobes.  Very interesting day and things are starting to click and overhead light bulbs are getting brighter.   I can’t wait for data!

Day 2- Student’s Reactions

Jeremiah White

Today was the first day of fieldwork, an adventure out to the Norman Landfill to gather leachate samples.  Samples were taken from five different well sites at different locations on the landfill and the surrounding area.  The goal was to gather samples of microbes from leachate to bring back to OU for microbial study.  Liquid was pumped at same depths along water table at locations and collected in specific containers and filters.  After the landfill fieldwork as award of sustenance was enjoyed a tasty local BBQ eatery!  The second half of the day was spent in the OU lab inoculating the leachate samples into different media, made yesterday.  Aliquots of the samples were taken and added to specific types of media to gauge population count, identify type of respiration and trophic level, microbial function in leachate environment, and isolation of microbes in the leachate samples.  It will be stimulating to see the microbes soon discovered, what roles are played in leachate environment, and the array of experimental methods used in the process!  Kudos to Dr. Stevenson, Blake Stamps, and Aaron!

Charlie Ung

This morning, our research group was picked up by Dr. Stevenson in his van and drove all the way to the Norman Police Department located on the landfill. We began extracting leachate from a well by using a pump machine. We learned how to take samples and how to filter them out of the liquid waste.  After learning how to take samples, out group was then divided into two groups to take samples of the next four wells. It whole process was fun as we were working together and at the same time being social with one another. After the long day out at the field, we then went out to eat lunch, which was fun as we were hanging out and resting. After eating, we went straight to lab and started creating colonies by putting the leachate in mediums. I personally, thought it was an important learning experience since I will later be working in a laboratory environment similar to this in the near future. Not only was it a learning experience, but I thought it was a bonding experience as our team started becoming friends. This was ultimately demonstrated when part of the group agreed to hang out after dinner to go swimming!

Najuma Maharjan

Our first field trip to Norman Landfill was a great success. We sampled five wells as directed by Dr. Stevenson and his co-workers. After that we used those samples to inoculate various media like SRB MPN tubes, TSB MPN tubes and TSA plates. We have set those inoculated plates and tubes to monitor growth over the next 24-96 hours. Hopefully we will get accurate results soon. So far, it was absolutely a new experienced and exciting day.

Kristen Worthen

Today I and my lab partner Sushma did inoculations from a sample obtained from well 35 at the Norman landfill. First, we made SRB MPN’s of dilutions from 10-1 to 10-5, in triplicate, and began to let them incubate. This set of tubes was anaerobic. We then made TSB MPN’s from the leachate from the same well, diluting from 10-1 through 10-5, again in triplicate. This set of tubes was aerobic. We then made PBS dilution tubes from 10-1 through 10-4, and used these to inoculate TSA plates at 10-2 through 10-5. This process was also done in triplicate. Cellulose agar plates were then inoculated from the PBS dilution series, just as for the TSA plates. Finally, we made cellulose overlay plates by spreading 1mL of undiluted leachate onto each of three salt plates and overlaying them with cellulose. All the plates and tubes were then allowed to incubate.

Patricia Pace

Today was our first field trip. We went to the Norman Landfill. The class sampled a total of 5 wells. We then were able to return to the lab and use this leachate to inoculate some media. Hopefully we were successful and will see some growth in our tubes that we can use later in our experiments. We worked well together, and because of this left the lab at a reasonable hour. I also was informed on the building I need to visit to apply for a temporary parking permit so that I can drive to and from class. All in all it has been a good day.

Sushma Ale

Field trip turned out better than anticipated. The weather was just favorable to bear the heat for two and some hour outdoor. The tricky part of the day was to be able to stick the needle and the vent needle into the sample bottles. In this attempt, I squirt leachate all over myself several times which is why my favorite part of the day was pipeting and streaking plates after we returned to the lab. It was not only inside an air conditioning, but also we were able to spare some extra time for ourselves. It was a tiresome afternoon and we definitely deserved it !!

Day 1- Student’s Reactions

Each day we’ll post paragraphs from the students, and how they felt about the course for the day. Here are the reactions from day one!

Sushma Ale

1st lecture by Dr. Stevenson was a great start. Even though the itinerary seemed a little too overwhelming, positive attitude and enthusiasm was highly encouraged. Day 1 was very exciting: new lab coat, new lab notebooks, new folder, and new techniques added a whole lot of NEW EXPERIENCE. My most exciting part of the day was working in the anaerobic chamber; I felt like a mini astronaut!!

Miranda Day

Today was definitely a day of learning. Being a math major in a science lab feels a little out of my league, but it was very interesting to learn how a microbiology lab works. I’ve never worn a lab coat before, so I felt pretty cool wearing it.

Najuma Maharjan

Thank you so much Blake Stamps and Dr. Brad Stevenson- awesome and wonderful host for the first day of class. Met some great friends and heard amazing lecture full of curiosity this morning.  Food provided was healthy and delicious. It was super fascinating to be able to use microbiology lab tools especially on the very top of OU building with amazing scenery time and again. I really had a joyful day and hoping it to be the same in coming days. Like Dr. Stevenson said this morning I believe I will definitely walk away with more knowledge and new experience than I had before I came here. Once again thank you so much for this awesome program. I greatly appreciate it!

Patricia Pace

Yesterday we Dr Stevenson spoke about the course for the first time. We learned what the experiment involved that we are attempting to perform. We also got our lab notebooks and were instructed on how to use them. Jason Masoner then came and spoke about the landfill we would be visiting. After lunch Dr Michael McInerney lectured regarding the nutritional requirements of anaerobes and demonstrated how to inoculate a vial of media. Later in the afternoon Judith, Sushma, Christine, and I were able to make the broth for some aerobic plates. After dinner we each practiced making media vials for anaerobes using the glove-box station. It was a fun and interesting day.

Jeremiah White

Today started off with an overview of the course objectives by Dr. Stevenson.  We also were informed about his work and area interest in microbiology.  Our first guest speaker was Jason Masoner with USGS from the Norman landfill.  He informed us of the leachate plume and the landfill’s importance in national landfill research.  A trip is planned Tuesday to take samples form the sites.  Dr. McInerney spoke second on the nutritional requirements and media design for anaerobes.  His lecture included why anaerobes need the nutrients and how to isolate and culture these microbes.  He wrapped the lecture up with a demonstration of isolating, culturing, and spinning a sample in anaerobic media tube.  The rest of the day the group mixed the mediums used for the course.  The day was ended in Dr. Stevenson’s Lab where everyone got some experience in the anaerobic chambers.

Ram D. Shah

Today, the first day was a great starting day. I got a clear vision about the whole summer course. It will be interesting, challenging and knowledgeable. Day was started with Dr. Stevenson’s speech about the outlines and goal of this summer course then Jason Masoner, the first guest speaker of this course, explained us about the Norman Landfill site where we are going tomorrow. Today, we did some laboratory experiments too, we did some medium preparations.

… More to come!