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.