Blogs

       After looking at the code of the program I found myself searching for certain functions and taking very long to find them. A function tells the program “Hey! Do this if the user clicks here!” So to solve this I designed a UML diagram which shows me what the certain functions are called when a certain button is clicked. Below is the completed diagram.

“UML Diagram for Data Explorer”

             There are several different programming languages in the data explorer program which are: HTML/CSS, JavaScript, PHP, and JQuery. Having the most experience with HTML/CSS and PHP. I decide to do some research on JavaScript and JQuery. I found that JavaScript is a bit like other languages I have already used. So I had little trouble with JavaScript. JQuery on the other hand was new. Although the program used all these different languages I found myself using JavaScript the most.

By chance I discovered one of the primer sets, Cerc5, I had initially discounted actually works to selectively amplify the 28S USE. Even better this primer set seems to only amplify sequences found in the Columbia River Estuary. It so far has not been found in the Chesapeake, Amazon, Beaufort and Susquehanna samples I have tested. This is exactly what I have been trying to find- a CRE specific species of Cercozoa.

This week has been less succesfull than I had hoped. Every PCR reaction I run has amplified DNA in the control. This makes it impossible to get meaningful data. Something is contaminated with DNA but it has not been clear what reagent it is exactly. Until I find the source of the contamination I cannot proceed with project. Other than those troubles, I have been working on getting extended USE sequences for other Cercozoan species so that I may design more affective primers.

http://ambwd01.stccmop.org/datamart/virtualcolumbiariver/ptrack

http://www.amazon.com/Particles-Coastal-Ocean-Theory-Applications/dp/110706175X

http://www.nefsc.noaa.gov/drifter/particles.html

This week, I was able to reproduce my previous results using different isolates. I found that one terminal oxidase mutant consistently shows higher-than-normal β-galactosidase activity, which means that the ctaA promoter attached to the lacZ gene is being activated by something. I also found that the lab’s two isolates of ∆qox mutants have different β-galactosidase activities.

On Monday, I prepared a variety of solutions to test in the HPLC on Tuesday. Because the ascorbic acid had so obscured the 4-chloroaniline spike during last week’s HPLC run, I prepared less concentrated solutions, and also tested solutions of acetic acid and sodium hydrosulfite. Unfortunately, acetic acid did not dissolve the MnO₂ much at all, and sodium hydrosulfite was insoluble in methanol, an important requirement for our HPLC setup. Therefore, I determined that low concentrations of ascorbic acid would be our best bet for creating usable HPLC data.

This week I finished up the first stage of my project, preparing the DNA fragments that contain only the upstream and downstream segments from the genes of interest.  The next step, which I started this week is to send the fragments in for sequencing to make sure there are no unintended mutations in these regions (obviously the gene of interest will be absent). 

Monday, 07/07/14:
    I read from my CompuCell3D Reference Manual and Introduction to CompuCell pdfs to help me to make changes for my simulation. I also had a meeting with Karen about starting my simulation as a hexagonal image as opposed to square because hexagonal seem closer to a realistic start for cells.

Monday, 06/30/14: