Finally done...

I am very excited to let you guys know that i finally finished my poster for the ASU conference presentation. It was not easy at all and I believe it was the same for my other peers. Now, I am glad that I am done with the hardest part. Remember that I told you guys that I was having trouble writing the introduction because I could not find any references or somebody that has done something similar to my project. Well, I finally came up with a good introduction for my project. This was the last component I wrote for my project and i was very glad that I ended up with something good. Now, it is over with writing and drawing, I am getting ready for the ASU presentation this Monday coming up March 4th. Like we all know it is not easy to stand before a lot people to do a presentation or to speak. Until now I do not know if we are going to present one by one or if we are just going to stand near our poster and people will stop by and ask questions. Hopefully it will be the second one. Anyways, I am getting ready for both. I am more than excited to be there on Monday and meet these varieties of people from all over the place and see what kind of research they are doing and also find out about the new discoveries in science. On Friday afternoon around two, Dijana brought the printed posters in the lab. They were looking very nice in the 3x3 size. I looked for mine and it was looking perfectly great and exactly like I wanted it. Supposedly, one person will bring the poster to ASU on Monday and we will get it from there but I preferred taking mine home in order to practice at home and then know pretty much that I have on the poster and also be ready for eventual questions. Now, I believe everything is ready and I am just waiting for Monday to go present. I am very excited and I am looking forward to doing good on my presentation. Wish me good luck guys!!!

Below is a picture of my poster

What a week!

This week was a rough week for me. Everything started first with a cold that I caught and which did not give me any chance to breathe just for a second. And on top of that I lost my cell phone in the library downstairs and i have not found it until now. It was horrible! Anyways life goes on and I have to be strong and fulfill my engagement. Since I finished the practical part of my research project, I was in lab this week trying to finish up writing my lab report and the poster for the presentation at ASU conference. It is on march 4th and it is around the corner so I better work hard to get it done on time. I spent this week in lab trying to write the introduction. But unfortunately, I could not figure out something good. For some reason, I am still having trouble writing the introduction of my project. I spent countless of hours trying to research if anybody has done a similar research but unfortunately I did not see anything similar. Last week, I started with the material and methods part which I finished it this week. After that, I began the results and discussion part. I have all the results of my tests recorded in my lab notebook so I used it to create a spreadsheet on Microsoft Excel in which I documented my results. Now I just need to insert this spreadsheet in the results and discussion part along with my two phylogenetic trees that I already made. After that I will focus on drawing a conclusion of my experiment and then go back to the introduction. I hoping by that time I will have the inspiration to figure out something good. As usual, I was in the STEM Program this week helping student with their and any questions they might. It is a great pleasure for me to be able to impact students' life and give them the taste of success. I really enjoy doing that! For next week in the lab, I will try to finish the component of my poster presentation and start to build the actual for the conference. I am looking forward to finishing this poster in the next two weeks so that I can have some time to revise before March 4th.

Below is the picture of a tree similar to the one i constructed.

       

Putting everything together

I spent this week in the lab trying to write the component of my poster presentation at ASU conference on March 4th. Last week, I had my two phylogenetic trees done so this week I am focusing on writing an introduction to my research project as well as the material and methods, the results and finally a conclusion. The abstract, which is the first component of my poster presentation was done during the week of January 7th and submitted to ASU so I do not have to worry about that one anymore. Now, I am working on the introduction. I looked for some peer reviewed journals in our school library databases to see if anybody has done this type of research project before, so that I can use some of their findings as reference to write my introduction but I have not seen the exact project but some project similar to it. I was having trouble writing the introduction so I when talked to Matt who helped me by giving some informations that I should consider putting in the introduction. When I was stuck on the introduction, I realized the material and methods which are something that I already did will be easier to write so I decided to write this part before going back to the introduction. So, I end up writing the materials and methods part. In this part, I just listed the names of the different species of bacteria that I am working with and then briefly describe the steps followed to do the experiments. I also listed the biochemical tests that were performed on the bacteria without giving the results of the test because there is a section reserved for that. I guess this part of report is the easiest to write because the only thing you do is just put in word what you do practically versus writing an introduction which required you to look for references to support your project. I am looking forward to finishing the material and methods this week and focus on the introduction as well as the rest of my poster presentation.
I was very busy this week during my office hours at the STEM Program helping students with their math homework. I enjoy doing that because I think this is a great experience and you learn more when you are trying to explain something to somebody.

Below is the picture of the bacteria that I worked with: Escherichia Coli  (microscope view)

                                                   Gram negative-bacilli

In the World of Biology Art

This week, I was in lab trying to figure out how to turn a complicated phylogenetic tree to a simple and meaningful tree in order to be able to interpret it. After many attempts, i finally end up with a tree (picture below). This tree was constructed using the parsimonious idea which is a method used to construct a type of phylogenetic tree based on the idea that the best route is the one that require the fewest evolutionary changes. So, that was the idea that i used to come up with my phylogenetic tree. Like i said, i used this week trying to figure it out and i was not easy at all because after each trial i have to go back and check with the original tree generated by the computer software to see if everything matches very well. The bad thing with this is you are not going to know ahead if what you are doing is actually right or wrong until you finish it and then check. And i did like three trials before getting it right. After doing that, I used the flowchart in the Microsoft Word to represent the tree. This procedure also took me awhile to do because the tree was too long and i have to find a way to put it on one page. So pretty much this week in the lab, it was all about drawing, drawing and drawing. That is when the beauty of art comes in the biology. I spent also some of my time in the lab trying to read my peers' blogs to see what they are doing. I can tell that everybody is working on an exciting project and the blogs look good. I wish good luck to everybody especially those that will be presenting at the ASU conference. Next week, the game plan in the lab will be to finish up completely with the tree by doing some resizing and also annotation. I am also looking forward of interpreting these trees and start putting up my poster for the ASU conference. I am very excited to be selected for such a conference. I think this will be a very great experience for me and also for each and every one of us presenting there. As a student, this opportunity is one of the best that can happen to me and I am so grateful.
                                       I started from this...

    to construct this...

         

Phylogenetic analysis of 15 bacteria based on morphology and metabolism

This project consists of determining the cell shape of the bacteria(bacilli or cocci) and the gram(positve or negative) of the bacteria species. And also through biochemical tests, determine which bacteria is closely related to which. I started the project by inoculating 15 individual bacterial cells onto a Petri plate. These different bacteria are: Salmonella, Bacillus Subtilis, Enterococcus Aureus, Staphilococcus Epidermis, Micrococcus Luteus, Proteus Vulgaris, Providencia Stuartii, Serratia Marcescens, Streptococcus Mutans, Streptococcus Salivarius. First I did the gram staining of these bacteria and determine their cell shape and the gram. After that, I proceeded to a bunch of biochemical tests such as catalase test, oxydase test, glucose fermentation, mannitol fermentation, lactose fermentation, tryptone broth, TSB with 6.5%, TSI and the blood agar. For each fermentation test, I have to test for gas and acid so I did like 145 tests and I can tell that it was not easy at all. After all these tests, i put my results in a spreadsheet and interpret them. Hierarchical cluster analysis and median-joining phylogenetic analysis were used to interpret the result. I used a special software to do the phylogenetic trees. Right now, I am in the process of interpreting the result and I also have to reconstruct the trees and draw them in a simple and meaningful way. So, for the next two weeks, my task will be to draw the phylogenetic trees, interpret the results and then put together a poster for my presentation. This is a really good project because it thought how to deal with bacteria, how to do gram staining of bacteria and how to perform all these biochemical tests.It also helped me know how to use special software to analyze statistical data. This project really gave me a hand on working in the lab.
Below are some pictures of my tests and gram staining slides.

Effect of aging on learning in Drosophila melanogaster

My passion for fruit fly pushes me to look for a peer review journal on flies that I want to share with you. We all know that as people age, they tend to have memory dysfunctions and their learning ability decrease. To study the effect of age on learning, a researcher, Eric Le Bourg, did some experiment on fruit- fly Drosophila melanogaster to see the relationship between age and learning. He chose flies because they have a short life span and they can study many generations and also they have a well-known genetics. This journal article studies the effects of aging on learned suppression of photopositive tendencies in Drosophila melanogaster. To begin his experiment, the researcher makes the hypothesis that as flies age, the ability to learn decreases. To test his hypothesis, he proceeded to three different experiments. He used light as a conditioned stimulus associated an aversive unconditioned stimulus, the taste of quinine, and the darkened arm which was not associated with an aversive stimulus. It turned out that flies run away from light to avoid the quinine. He pointed out that quinine does not induce sensitization and has been used for many decades in learning studies using D. melanogaster because of its bitter taste.

The first experiment tested whether flies of different ages can avoid lighted vial associated with an aversive stimulus. The second tested if they can avoid the lighted vial associated with a strong (quinine) or weak (distilled water) aversive stimulus. Before both experiment, half of the flies were subjected to training with the aversive stimulus that will be used in the experiment. In the third experiment, one half of the flies was subjected to training with a lighted vial containing a paper wetted with quinine and the other half was subjected to 16 trials with a lighted vial containing a dry paper and after that, the same group of flies to 16 training trials with another lighted vial containing a paper wetted with quinine on each trial.

These experiments have shown flies of all age learn to avoid the light when it is associated with quinine or water. Quinine has a bitter taste that flies do not like and the water prevent them from flying that is why they avoid these two stimuli. However, the learning score in the older age flies decrease little bit compared to the first week age flies. Therefore, it can be concluded that age had different effects on locomotor activity and learning. Old flies walk slower but the locomotion had a slight effect on learning.

After reading this, my question is, does this conclusion also apply to human? As we grow old, do we really get stupid or we know everything but we just don’t want to talk?

                                  Drosophila melanogaster

Click here to read this article

Citation:
Eric Le Bourg, Effects of aging on learned suppression of photopositive tendencies in Drosophila melanogaster, Neurobiology of Aging, Volume 25, Issue 9, October 2004,
Pages 1241-1252, ISBN 0197-4580, 10.1016/j.neurobiolaging.2003.12.004.
(http://www.sciencedirect.com/science/article/pii/S0197458004000326)

Fruit flies and learning

This week I met with Jon Hayashi, a temp faculty member in the Biosciences Department at PC who is a good resource for the type research field that I am interesting in. We discussed about school, work and the kind of research that I want to do. After discussion, I told him that I would like to do something that has to do with genes in drosophila. So, he showed me a bunch of experiments on drosophila to look at and have an idea of what I want to do. He also gave me an article on Genetic approaches to learning in fruit flies and some videos of experiments. After looking through all these experiments, I decided to focus on fruit flies and learning.

In this area, Dr. Josh Dubnau of Cold Spring Harbor Laboratory did the T-Maze experiment to test the memories in fruit flies. After the experiment, it turned out that flies can learn. They can form a short term memory and also a long term memory if they are trained for a long period of time. To conclude his experiment, Dr Josh Dubnau stated that, “We're beginning to uncover the fact that many of the genes that are important for memory in flies are probably also important for memory in distantly related animals, even humans”.

For me, this experiment is amazing and I probably be doing something similar for my internship to learn more about fruit flies and their brain.

Here is the video of the experiment