UMSL Genomics:Research

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RNA Virus Discovery In Wild Birds of Northeastern Brazil

This research will be performed to help prediction and prevention of outbreak that could affect avifauna. We will use RNA-Seq to identify novel viral agents in wild birds. For this we will use RNA extracted from cloacae and oropharyngeal swabs from different bird species of `Caatinga` and Atlantic Forest biomes of Northeastern Brazil. RNA will be purified, reverse-transcribed into cDNA, and sequenced using the Illumina platform. The goal is to identify putative viral agents by using the Trinity program to assemble transcriptomes de novo from RNA-seq data and command-line BLAST to differentiate between bird and virus contigs.


Circadian clocks exist in many organisms and are rhythmically regulating expression of genes responsible for a variety of cellular processes. The Groucho gene is very important in the early stages of development in fruit flies and it is known to be rhythmically expressed in the fly brain. How Groucho is regulating circadian genes is less clear. Using RNAi, knock down experiments are performed using genes known to regulate circadian rhythms. The long term goal is identification of genes driven by the circadian clock, the mechanisms through which regulation occurs and how these genes influence behavior.
More specifically,
1. Identification of genes that contribute to regulating Groucho
2. Identification of circadian output genes Groucho has a role in regulating.

Computational simulations to determine the best parameters for profiling circadian transcriptional rhythms

RNA-Sequencing (RNA-Seq) is becoming extensively used to systematically profile transcripts’ cycling pattern. However, it consumes a great deal of time, money, and resources, and analysis of the huge amounts of data is not trivial. Meanwhile, it is not always necessary to generate maximum data sizes for each experiment. Our aim is to determine an appropriate balance where we can get enough data for our research with a considerably low cost.
Based on experimental data, we are doing computational simulation to test the right depth of RNA-Seq for circadian expression study. Depth is the time that a nucleotide gets sequenced. It is determined by genome length, average read length, and reads number. We are testing the robustness and accuracy of the post-analysis results under different reads numbers since we are working specifically with Drosophila, Illumina MiSeq. There are other factors, like organism, sample density that also affect the results. We will also evaluate these factors later in our project.

UMSL Genomics
Department of Biology
University of Missouri, St. Louis

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