Gene Function in Caenorhabditis elegans

Hello everyone. My name is Mikayla Bonnett and I am now working with Dr. Matthew Marcello and his research group to study the reproduction and gene function in Caenorhabditis elegans. The title of my project is The Function of T20B12.7 in Caenorhabditis elegans. The purpose of this project is to develop a better understanding of the C. elegans genome and possibly be able to apply what is learned to the human genome. The goal of this project is to learn the function of the T20B12.7 gene. The objectives in the lab are to perform RNA interference and deletion experiments on the C. elegans’ gene T20B12.7.
C. elegans are a nematode with a genome about 30 times smaller than the human genome. Even though it is smaller it still encodes for more than 22,000 proteins, which is slightly lower than the human genome. They make very good model organisms for laboratory work because they are small in size, transparent, and easy to grow, so they are very easily managed and taken care of in the lab. Additionally, they have a rapid life cycle and well annotated genome which is helpful to receive results in a timely manner.
The main method used to answer the research question is RNA interference (RNAi). C. elegans respond very well to RNAi experiments. RNA interference is a tool used in experiments to prevent gene expression/function. This interruption can lead to the identification of the function of a gene. The RNAi effect is achieved when double stranded DNA (dsDNA) in the cytoplasm is cut up by a protein called Dicer. The dsDNA into single stranded DNA (siDNA) pieces and then binds to another protein called Argonaute, which forms RISC, RNA-induced silencing complex. The target messenger RNA (mRNA), which is a perfect base compliment to target site, goes through this complex and is cleaved and degraded. The mRNA of a gene is the RNA that is translated into a protein and a protein is what performs gene function. If the mRNA is degraded before it can be translated then the protein of that gene will never be formed, so the gene function cannot be carried out.
T20B12.7 is a C. elegans gene that is involved in embryo development, gamete generation, nematode larval development and receptor-mediated endocytosis. The gene is a ortholog of human ciapin1, which is the cytokine induced apoptosis inhibitor 1. It has several phenotypes such as slow growth, early larval lethal, sterile progeny, and embryonic lethal. The protein associated with this gene is an Anamorsin homolog. When RNAi is applied to this gene, the effect will be observed and compared with wildtype (normal) worms. The phenotype that is observed is what occurs when the worms lacks the protein from the interrupted gene. From there the function can be determined.
So far during this semester I have selected my gene of interest by using the C.elegans’ database Wormbase, which has a record of all the information known about C. elegans genomes. I also used Ortholist, which helps identify orthologs between humans and C. elegans. And to learn about the proteins associated with each gene I search through the databases UniProt and SMART Genomes. Additionally, I have started to examine wildtype worms under the microscope and practice picking and transferring the worms to new plates. I have also started to learn how to perform exploratory data analysis so I will be able to analyze the data that I collect form my experiments.

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