Tuesday, August 4, 2009

RET 2009 Final Reflection – working at Prof. Erin Cram’s Worm Lab

Prior to coming to the lab, I had been on email communication with Prof. Cram so that I was able to get started with background reading on our potential projects. The readings included background information on the soil nematode, C. elegans, a review on the Distal Tip Migration – the main focus of the Cram Worm Lab. I had the best summer experience working with Prof. Erin Cram learning using molecular biology techniques to identify proteins that interact with each other. . Prof. Erin spent time giving us an overview of the research project, helped us get familiarize with the instrumentation and techniques used our experiments. She set us up with a graduate student Mouna Ibourk who helped us with the Yeast Two Hybrid Experiments. We felt we were very much part of the lab group as we were able to participate into eh group meeting, the journal club and friendly academic exchanges with all the graduate students and undergraduate students in the lab.

Prof. Erin Cram personally helped us get settled with the norms and protocols in the lab including getting our lab safety and hygiene training during the first week. She was always available to answer our questions and helped us understand the experiment procedures. She also introduced us to the various basic references including my favorite – “Integrated Genomics” .

The project that we were involved with relied on two molecular biology approaches to study functional genomics or more specifically which proteins affect the proper development and migration of the distal tip cell in the nematode C. elegans. Yeast Two Hybrid Screening allowed us to test whether the SIAH-1 protein interacted with CACN-1, a novel protein discovered and studied in the lab. We also performed RNAi silencing experiments where SIAH-1 depletions were accomplished by feeding the C. elegans with bioengineered (transformed) bacteria. By doing so, the worms were not able to make the SIAH-1 protein by degrading the rna that codes for the protein. My lab experience helped me see how bioinformatics in the form of protein amino acid sequence available on the web accessible data bases can be used to design either the whole protein or in our case a part of the protein. Our experiments started with these primers which were inserted in the worm cDNA cloned and then transformed into bacteria which were then fed to the worms. One of the most important thing that we learned is that the timing protocol for yeast, e.coli and C. elegans were different and careful planning was needed so that observations and data collection can be accomplished during the weekday. While we did not have enough time to collect more data, we were fortunate to be able to finish this preliminary study and identify the relative importance of the SIAH-1 protein in distal tip development and migration in C. elegans. The highlight of the lab experience was that we were able to prepare two plasmids pUN63 and pUN64 both containing the SIAH-1 fragment that now reside in the Cram Worm Lab -80°C plasmid repository, available for future investigations.

My experience helped me gain appreciation for the C. elegans and work on genes and proteins. The best tie-in to my lesson plan is the importance of covalent and non-covalent (intermolecular) molecular interactions are in biological recognition. This is relevant in the cascade of reaction mechanism and signaling processes involved in cancer metastasis, immune response and proper development of an organism.

The experience made me realize that I want to spend time exploring the connections between the shapes of molecules and how they interact with each other, with genetics and biology. My lesson plan will include exploring the interactions by creating water, amino acids, DNA and globulin models both with space filling models as well as with a software that will help in better visualization of the electrostaic potential interactions on the surfaces of a molecule.

The lab notebook used for recording of experimental data used in the lab was novel to me. It gave me a chance to put it into practice and allowed me to see the practical aspects of using their method. The lab uses a three ring binder, loose sheets and a plastic sleeve for each page.

I definitely learned a lot this summer and provided me with great inspiration on teaching more science applications across disciplines.

Hurray for the C. elegans!!!

Mary Espanol

1 comment:

kcarrette said...

Week 5 in the lab:
This week I continued to work to maintain and monitor the algae stock in the lab. Two days during the week I collected 50ml samples from each reactor. Those samples were double filtered. The filters were used for chlorophyll testing and the filtered solution used for ammonia, pH, and IC measurement. These tests generally took me a day to conduct.
During this week I also prepared paraformeldehyde and conducted FISH preparation for Nehreen’s IFAS system. This required me to take samples from the IFAS reactor; make slides of each of the samples; and take the samples to hybridize.

During the last week of my lab (week 6) I reviewed the pictures of slides that I took at the beginning of my summer research. These pictures were of the bacteria from the IFAS (Fixed Activated Sludge System). From these pictures I quantified the bacteria by comparing stained cells vs. unstained cells.