Category Archives: Culturing

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 5

The day began with an excellent lecure by Dr. Liz Karr over archea, and then a trip to the Sam Noble Museum of Natural History.

The students enjoyed their time off, but after a quick lunch it was back into the lab for a lecture by Rao Uppalapati covering various topics, including cellulosic bioenergy, and a practical demonstration of lignin staining methods.

After this, it was time to check on the molecular work from the day before, as well as begin the process of isolating colonies from the landfill, and seeing how well various other experiments were going.

Because of the student’s dedication, they finished just before dinner, and spent the rest of the night in relaxation!

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 4

Today was molecular day- and what a day it was! The student’s started with lectures from Dr. Robert Cichewicz and Dr. Paul A Lawson, before jumping into the lab.

The day was a long one, but with the student’s enthusiasm, determination, and skill the day of extraction, PCR amplification, gel electrophoresis, and cloning was a complete success!

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 3

Day three was busy- it was time to sample the duckpond, and some of Norman’s finest compost! We repeated the same set of experiments for both sites that had been done the day before with the Norman landfill.

Progress was quick, and after leaving, we prepared plates for the molecular work for the day to come!

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 !!