Wet Lab Experiments to Validate Proposed Gene Calls in Kytococcus sedentarius

Matthew Spink

Koury Lab-qPCR Instrument: The instrument shown in the image is often used to get quantitative results in the Koury Lab.

qPCR Instrument, which is often used to get quantitative results in the Koury Lab.

Undergraduate Student Project

Introduction

The genomic code contains seemingly endless amounts of information. Have you ever thought of studying a part of the genome that has never been looked at before?

My name is Matthew Spink. I'm a junior chemical engineering major at the University at Buffalo. For the past three years, I have worked under Dr. Koury in his lab and before that I took part in a high school outreach program that he is the co-PI of. One of the focuses in Dr. Koury's lab, which is partly funded by the ELN and NSF, is to understand the functions of genes in the bacteria called Kytococcus sedentarius. My work has been focused on understanding one set of genes that has never been looked at before.

Not only is it interesting to explore genes that have never been looked at before, but understanding my genes better will improve computer programs that can analyze genes a lot faster than human beings can. Data gathered by these programs is and will continue to be used to generate cutting-edge medicine that treats and cures diseases.  Exploring the genome improves and saves lives.

Abstract

Manual annotation of genes in the genome of Kytococcus sedentarius were performed and we hypothesized potential computer pipeline annotation errors in a gene incorrectly predicted to be a pseudogene and in the genes surrounding that locus. Research presented here was initiated to test these hypotheses. Initial experiments involved more detailed annotations of the genes in question as well as documentation of expression of the genes through qPCR. Manual annotation of the pseudogene strongly suggests that the predicted frameshift mutation does not exist and that the gene actually encodes for functional transcriptional regulator. qPCR results suggest that the transcriptional regulator is not expressed at basal growth condition. qPCR results support the hypothesis that a nearby gene, predicted to be a hypothetical protein, along with a nearby gene that encodes for a histidine kinase are expressed at basal conditions of growth.

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