May+2013

For this month I am now going to begin to look into the Cowden-Dahl lab and her research

From what I discovered so far, her lab is specifically focused on ovarian cancer research. It is targeting the over expression of an epidermal growth factor receptor which causes ovarian cancer progression. She is focused on genes that are directly accountable to this receptor. Her lab is " investigating how the ARID3B transcription factor is regulated by EGFR signaling and its involvement in cancer". ARID3B has been found to be over expressed in those with ovarian cancer. ARID3B stands for at-rich interactive domain 3B.



For me, the beginning of understanding has to start at the molecular level. I am beginning by researching the gene to understand its origin, its involvement in homo sapiens, its lineage (which is similar to running a gene ontology), and knowing its chromosome location. Entrez on ncbi is the easiest place to have all the information about a specific gene displayed.

Another gene she has looked at is PEA3 which was found to be over expressed in 92% of stage 3 and 4 ovarian cancer patients in one study. It is an ETS family transcription factor that is elevated in advanced and metastatic (progressive) ovarian cancer and regulates prometastatic matrix metalloproteinases (MMPs) in other cell types.

In conclusion, the Dahl lab is concerned primarily with ovarian cancer research and attempting to find which genes are responsible for these ovarian tumors that correspond with low survival rates. By targeting the genes, a way to have them under expressed would be a way to fight the caner and promote overall survival in its victims.

In Conclusion for the Year...
In conclusion for the entire year I have learned new skills in both biology and computer science. I began the year by looking at scientific papers and writing about a specific blood disease called alpha thalassemia and all of the background behind it. I learned the effects it has on the blood stream and how it effects the human being. I looked at the disease on a molecular level to truly understand what it is and what it does.

I then began understanding and using matlab. I performed practice programs and even wrote my own program. I learned how to manipulate programs that already exist to do exactly what I individually need. I also learned the basics behind matlab and basic commands. I began by writing a very basic program and then extended my knowledge to write a bit more complicated program using graphs and a GUI. A GUI is a graphical user interface and created a GUI all my own. From writing 2 of my own GUI's I was then able to begin looking at the bioinformatics tools and using them in some online exercises. I was able to use many of the tools to my advantage and was a great tool.

I then was able to combine my knowledge of both biology and computer science through biotechnology by completing a project in matlab using real life data from Francis Raycoft. Francis supplied me with data from his lab and used the information to help sort through a long list of different genes. The data was linked to some of my research from last year and it required much filtering to get down to a final list. I learned how to run a gene ontology and its importance.A gene ontology is used to classify and link certain characteristics of an organism and finds its ancestry. This helps to find paths that are related especially among gene knock down. Along with that, I learned how organisms are classified and why links between genes and characteristics are so important. I ran a gene ontology on matlab and learned all of the skills necessary to run one. I tried multiple websites to get an idea of what a gene ontology is and used the largest website responsible for documenting genes used for gene ontologies (the Gene Ontology). I have also learned more in depth the importance, usefulness, and meaning of ncbi and all the very valuable tools it has. I have learned to use their search engine, ENTREZ, BLAST, and tools built into the system. I have learned to search ncbi to find the information I would like and to cross check information. I completed 2 online exercises about ncbi and using its search engine to run a blast on a nucleotide sequence and to take an organism and run a taxonomy on it. I then later used ncbi to blast a few nucleotide sequences I had known from last year. I learned that the more bp you have while running a BLAST the more accurate your results will be. But even without a long line of bp, it is still very possible to find the gene you are searching for.

I have also read and learned to better comprehend scientific papers and synthesize the information within them. And from looking at a few more papers than last year, I have also been able to interpret and understand figures within the papers and the different methods in which information is gathered in this field. And with scientific papers I have finished the year by looking at the Dahl lab and her research in ovarian cancer. Her lab has targeted genes responsible for ovarian tumors and those genes that are over expressed in cancer patients.