:-( Last Class :-(

Well we all knew this roller coaster of a ride would end sometime. On Monday, we were lectured on qPCR by Mr. Jun. I learned a few things that I had not known prior to his lecture. Following his presentation, I gave my presentation on what I think is novel organism. I am sorry it I seemed a little nervous. I’ve never been too good at presenting in front of classes. We then headed to class to perform casein, oxidase and catalase tests on our strains. The positive result for oxidase is the appearance of blue pigment after application to a colony streaked on filter paper. The positive result of catalase would be the formation of bubbles after a loopful of specimen is placed in a droplet of 3% hydrogen peroxide. There seemed to be no correlation between the oxidase and catalase results. On Wednesday, we had our last class of the semester. We had a short review of what will be covered on the final and then we had a party to celebrate the successful semester. I really enjoyed this class this semester. I got to meet a lot of interesting people that have shown the dedication required to succeed. It’s kind of sad that it’s all over, now I got to find a job. I wish everybody the best of luck in pursuing their goals. It has truly been a pleasure this semester.

Semester at a Glance....

This semester was very short, at least it seemed that way. We started out doing simple tests for our research project, but as the semester went on, we did things like PCR and gamma radiation tolerance. My favorite part of this class was being able to gain research experience. Many students lack this important and now, I have it and it will set me apart from the rest. Another nice factor of the lab is that the work we did may eventually get published in an IJSEM publication. This surely will set me apart from other students, if I decide to go to med school one day. My least favorite part of the lab was being there from 130-5pm every Monday and Wednesday, although some days went by fast. Throughout this semester, Dr. Rainey was very helpful. I’m extremely happy that all of our media was pre-made and we didn’t have to do it ourselves. I think that this is an important component of the lab. If we had to make the media ourselves, we would’ve lost a lot of time and wouldn’t have been able to do as many tests. I must say, in doing the different tests, many our plates were contaminated. In the beginning we may not have used proper streaking technique, but once contamination became too frequent, we did. Even though we used proper techniques we were still plagued by contamination. Every time, it was the same strains, those that grew on 1/10 PCA. I’m convinced that those strains are pure at all.
This past week we did tests such as caseinase, catalase, and oxidase. If the organism is able to break down caseinase a clearing will be seen in the opaque, white media. If the organism is positive for catalase bubbles of oxygen will be produced in the hydrogen peroxide. If an organism produces oxidase it will turn blue once inoculated with hydrogen peroxide. We had strains that were positive for all of these tests. The last day we talked about the dreaded final (just kidding you guys) and had frozen Krispey Kreme and had delicious Papa Johns pizza. I also bought popsicles. We all had a BLAST (get it), even though we waited 10 minutes for Larry to show up to class.... I enjoyed this class and I know that Rainey can't wait for his next 4126 class so that they can continue with this project.

On Monday,

we turned in our masterpieces (IJSEM paper). However, there was still work to be done. Previously in the class, we made a list of all the tests left to be done, so today we were able to mark a few off the list. We streaked our 26 strains onto agar plates containing casein. We will check them in a couple of weeks. A clearing in the milky media we be a positive test. We also performed tests for catalase and oxidase. The catalase tests was familiar to most of us having taken general micro lab back in the day. Cells were inoculated into a small drop of hydrogen peroxide. The presence of bubbles denotes a positive test (the bubbles are oxygen). For the oxidase tests, cells were placed on filter paper. A drop of oxidase solution was placed onto of the cells. A color change, mostly a blue color change, denotes a positive test. The majority of our strains were positive for catalase and negative for oxidase. The results of these tests are on the spreadsheet. Unfortunately, the Luedemann (1968) paper did not perform catalase or oxidase tests to compare my strains to.
We also determined that our soil isolate, GB-20, grew the best on R2A and 1/10 PCA.
On Wednesday, we enjoyed pizza and donuts, courtesy of Dr. Rainey. Thank you!!! They were delicious. We also talked about the final, database, and lab notebook which are all due or take place on Monday. Yikes! Finals week got here so fast.

The End is Near......

This week we had our final classes of the semester. On Monday, we had a presentation by Jun a Post Doc in Dr. Moe’s lab he told us about quantitative PCR. We had an idea about how it works from the Salazaar paper that we read it talked about qPCR with a set of primers specific for the family Geodermatophilacea. After the presentation we had a few test to run. Milk agar plates were streaked these plates are used to test caseinase activity and should be graded in 2 wks. Also tested were oxidase and catalase which give almost instantaneous results. To test catalase we took a look of our isolates and placed it in a drop of 3% H2O2 if oxygen bubbles began to form then it was positive if no bubbles negative. To test oxidase we took a loopful of isolate and smeared it onto a filter paper made of cellulose. Then we added the oxidase reagent which was at 1% concentration to the smear if it turns dark purple to black it was positive. Light blue is the natural reaction between the paper and the reagent and is a negative test result. Interestingly about our results is that we had because of the variability within each genus for the oxidase test result that some of our isolates would be positive and some negative however all of our isolates were catalase positive but oxidase negative.
Wednesday was a discussion about what is going to be on the final and what is expected of us in our database/ excel sheet and our lab journals which are all due on the day of the final. After the discussion we had an end of the semester party with pizza and donuts.

LAST BLOG!!!

This week was the most exciting of the semester!!! On Monday, we performed oxidase, catalase, and casein tests on each of our 26 strains. Most of the strains tested positive for catalase (meaning they produced oxygen bubbles when mixed with hydrogen peroxide) and negative for oxidase (did not turn a dark blue/purple when mixed with solution on filter paper). We will not know the results of the casein tests because these will be recorded during the summer. We also took another look at our dessication plates and re-scored them, if necessary. My group found that not much had changed since the last time we viewed these plates. On Wednesday, we talked about our final exam and what we needed for our database. We also had a party which was wonderful (thank you, Dr. Rainey!!). This week was extra exciting since we received our presentation grades and I also got into medical school. I can't believe summer break is almost here!

all good things must come to an END!!!

So this week was rather bitter sweet. On Monday there were two presentations. First there was the qPCR presentation, presented by Jun. Last, but definitely not least came Larry's presentation on his his new found species, Geodermatophilus geauxtigeris. I learned a few things about qPCR (Quantitative PCR). First, qPCR cannot combine with single stranded DNA. However, it can combine with double stranded DNA. When attached to double stranded DNA it absorbs light at 488 nanometers, and emits light at 520 nanometers. The advantage of qPCR is it can recognize the presence of and quantify the target gene. In addition, I learned a few new things about an unknown species from the family of Geodermatophilaceae thanks to Mr. Roach.
In addition to presentations we streaked our strains unto plates which contained casein and performed catalase and oxidase test. Catalase test was performed by adding a loop full of the strain to hydrogen peroxide, and checking for bubbles. The oxidase test was performed by adding an solution to and checking for the formation of a color.
Wednesday brought on the tears. We got good news as well as bad. The good news was that Lauren had been accepted into med school (YAY LAUREN)...however, the bad news was that we may never be able to work alongside each other again :(
All in all this has been a great semester and I love all of you!!!!♥

Blog

On Monday, after turning in the final drafts to our IJSEM papers, we attended a presentation on Real-Time PCR. Real-Time PCR was used in the Salazar 2006 paper in determining the GEO primers, which we used when performing PCR throughout the class. Then we streaked casein plates and tested for oxidase and catalase. The oxidase experiment was preformed by spreading the culture onto filter paper. Then we added a drop of oxidase solution to the culture, and observed for a color change. The catalase experiment was performed by placing a loop with culture into a drop of hydrogen peroxide and observing for the formation of bubbles. The results from catalase and oxidase were put into the spread sheet. Before leaving, we looked at the progress of our Gobi isolate and noted on which media the organism was growing best on. On Friday, we attended our final class. We received our grades from our presentations and had a lab party with donuts and pizza thanks to Dr. Rainey. Then before we left we had a discussion about the final, lab books, and the database.

Final Blog

This was our last week of class. On Monday we had a little lecture on qPCR which is used to not only detect fragments of DNA but quantify the amount of DNA present. We also streaked our strains on casein plates and preformed oxidase and catalase tests. All twenty-six of our strains were catalase positive and oxidase negative. Weird. Wednesday was our class party. It was awesome!! We also discussed the final coming up on Monday and our databases and notebooks that are due next week. I have really enjoyed this class and working with everyone! I feel as if I have learned a lot and gained knowledge that will be extremely useful in the future. Thanks to Eugene for making all the media, Cristi for the study guide and of course Dr. Rainey! See yall at the final!

CONGRATULATIONS TO LAUREN

One of our esteemed classmates got some very good news this past week:

LAUREN GOT ACCEPTED TO MEDICAL SCHOOL

Here Lauren is giving her 4126 presentation on her research findings

WE WISH LAUREN ALL THE BEST FOR THE FUTURE

WE ARE EXPECTING MORE GREAT THINGS FROM HER...........

the new 4126 was a BLAST (not an EZTAXON)....

BIOL 4126 was only taught once before in Spring 2003 - then Rainey served as the Assoc Dean in BASC for 5 years before finding the light and coming back from the dark side. The first 4126 was a very different "beast" to that of this semester. In fact it was taught in a different world, a world with no BLOGs or AirSet, in fact Al Gore had just finished inventing the internet and was starting on his next invention.......

The new format and the components included seemed to work well for everyone and a real hands on research experience was had by all. On the basis of the comments on the BIOL 4126 survey (thanks to those who completed it) there is not too much to change in the format and components of the class. The next class will work on a different set of strains that belong to a different family of bacteria.

At the end of the semester we have made new discoveries (that strains are resistant to radiation and desiccation and that it differs between strains and genera) and collected a set of data that can be used to describe some new species of the family Geodermatotophilaceae. There is still some data to collect and this will be done in the summer and a paper(s) will be submitted to IJSEM in late Summer/early Fall. We will all be coauthors on the paper(s) along with Keren (Keren Ray - first student from RaineyLab who went to Med School in 1999 and is now a Peds Doc in Baton Rouge) and Danielle (who you all met and is finishing her PA training) who isolated the strains in the first place.

The class party was fun and Rainey was impressed with these GOLD shoes some of our classmates had on - he wanted a pair. That was until today - now he wants a pair of these:
but he needs a pay raise as these cost $540 not $5.40 or $54.00 but $540 and guess who is wearing them? Click on the picture above to see the whole story :-)