Graduate Research Opportunities

I am no longer accepting new graduate or undergraduate students.

Read About Previous Completed Research Projects

Genetics of Pulmonary Hypertension Syndrome

In collaboration with Dr. Orlowski, in Poultry Science, we are mapping genes affecting resistance and susceptibility to Ascites; a.k.a. Idiopathic Pulmonary Arterial Hypertension (IPAH), or Pulmonary Hypertension Syndrome (PHS). This disease affects meat-type chickens and is similar to the disease in humans. We have identified regions on chromosome Z and 2, that segregate with resistance and are working to determine the contributions of each of these regions. In addition, we are pursuing the chicken as a medical model for PHS in humans.

This project is supported by a grant from USDA 2018-2021.

Alia Parveen

Alia Parveen (CEMB PhD 2019) used whole genome resequencing to examine copy number variations associated with PHS. The resequencing data identified 28 candidate QTLs controlling ascites.

Visit her webpage.

Duaa Al-Mansaf

Duaa Al-Mansaf (PhD 2022) examined tissue and gender specific expression of the CPQ gene to elucidate how expression of this gene contributes to ascites phenotype. She used Mass Spectrometry to identify biomarkers predictive of ascites.

Layla Al-Mitib

Layla Al-Mitib (PhD candidate) is examining the role of mitochondrial biogenesis in muscle myopathies and ascites phenotype in broilers. She is using histological means to look for mitochondrial dysfunction and degeneration associated with ascites.

Katherine Lee

Katie Lee (PhD 2022) used marker assisted selection in broilers to show that QTLs we identified by whole genome resequencing can shift ascites resistance without affecting production traits.

Shatovisha Dey

Shatovisha Dey (PhD 2017) used genome resequencing and qPCR to examine associations of the UTS2D and AGTR1 genes with PHS. She also used whole genome resequencing to identify a major determinant of ascites on chromosome 2. She is now a postdoc at IUPUC.

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Khaloud AlZahrani

Khaloud AlZahrani (MS 2013; PhD 2018) used genome resequencing and qPCR to examine associations of the HTR2B gene with PHS. She also performed ATACseq on pulmonary arteries to identify genes affected in response to hypoxia

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Byron Marciniak

Byron Marciniak (BIOL BS 2018) isolated RNAs from different tissues to study expression of candidate genes associated with ascites.

Timothy Licknack

Timothy Licknack (MS candidate) was a graduate student with Dr. Anthony. He generated RNAseq data to investigate cardiac hypertrophy and hypoxia in young broiler chicks. .

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Katy Tarrant

Katy Tarrant (PhD 2016) examined a region on GgaZ for association with PHS and production traits. She is now a faculty member at California State Fresno.

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Adnan Alrubaye

Adnan Alrubaye (PhD 2013) examined the affects of several loci on PHS in breeding lines. He used qPCR to examine expression levels for several candidate genes. He is now a faculty member in the Department of Biological Sciences and the Department of Poultry Science, and Associate Director of the Cell and Molecular Biology program at the University of Arkansas.

Candace Timmerman

Candace Timmerman (PhD 2009) used SSR and VNTRs to investigate population structure in Timber Rattlesnakes and to map the chicken genome for ascites QTLs.

Cassandra Hunter

Cassandra Hunter was a 2007 Carver Student from UAPB working on the PHS project.

Russell Burks

Russell Burks (BS Honors 2011) identified SNPs in a serotonin receptor affecting PHS in the chicken.

Bacterial Chrondronecrosis and Osteomyelitis (BCO) in Lameness in Broilers

In collaboration with Dr. Robert Wideman and Dr. Adnan Alrubaye in Poultry Science, we are investigating the bacteria involved in BCO as found in lame chickens. Dr. Wideman developed a wire-floor model for inducing lameness. Our laboratory has been contributing through molecular identification of bacteria isolated from necrotic lesions of the femoral and tibial heads. We have been developing methods to understand the spread of the infection within a flock and to develop management methods to reduce or eliminate the spread. We have developed a bacterial epidemic model for the spread of BCO lameness in broilers on litter flooring to mimic the spread of the infection. We are using that litter-flooring model to identify management strategies, and feed supplements to prevent the spread of the infection.

Simon Ekesi

Simon Ekesi (CEMB PhD 2020) examined pathogenesis models and preventatives for BCO induced by Staphylococci. He used embryo lethality and monocyte survival to compare BCO isolates from several genera. He compared the genomes of E. coli and S. aureus isolates from BCO outbreaks to determine the phylogenomic relationships.

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Abdulkarim Shwani

Abdulkarim Shwani (PhD 2023) investigated the phylogenomic relationships between BCO pathogens and other Staphylococcus species. He used Directed Genome Evolution to identify virulence determinants in BCO pathogens. He developed a system for inexpensive capture of bacterial samples from the air with rapid DNA extraction for qPCR.

Amer Hasan

Amer Hasan (PhD 2022) investigated the role of gut integrity in resistance to BCO pathogens. He examined how stress, and pre-biotics can modify gut integrity.

Sonali Lenaduwe

Sonali Lenaduwe (CEMB MS 2021) analyzed S. agnetis for the physiological conditions that trigger biofilm formation. She worked with Abdulkarim on the specific genetic determinants for survival of S. agnetis in macrophages.

Sura Zaki

Sura Zaki (CEMB PhD 2021) developed PCR assays for distinguishing Staphylococcus species involved in BCO. She also worked on chicken macrophage function in bacterial clearance and S. agnetis survival in chicken macrophage.

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Adnan Alrubaye

Adnan Alrubaye (PhD 2013) cultured the bacteria from lesions and used PCR and sequencing to genotype isolates for 16S rDNA. Dr. Al-Rubaye is now a faculty member in Biological Sciences, and the Department of Poultry Science. He directs all of the bird work on the BCO project, and is the Associate Director for the CEMB gradute program.

Karah Baggett

Karah Baggett (BS Honors 2016) sequenced and analyzed two previously undescribed small plasmids from chicken isolates of S. agnetis.

Molecular Genomics in Non-Model Organisms

With Dr. Steve Beaupré and a consortium of investigators from MCBIOS we are sequencing and assembling the genome for Crotalus horridus (Timber Rattlesnake) in the Southeastern United States.

With Dr. Tsunemi Yamashita (Arkansas Tech University) we are sequencing and assembling the genome for Centroides vittatus (scorpion) to understand its phylogenomics and toxin repertoire.

Matthew Ford

Matthew Ford (BS Honors) analyzed variations in mtDNA in fragmented Timber Rattlesnake populations.

Kylee Emerson

Kylee Emerson (BS Honors) developed PCR assays for mtDNA variations in Timber Rattlesnakes.

Brenda Flack

Brenda Flack (CEMB PhD 2010) used microsatellite markers to look at populations gene flow and multiple paternity in Timber Rattlesnakes.

Scott Nichols

Scott Nichols (BS Honors Biology) analyzed the transcriptome of the scorpion Centruroides vitattus and mapped toxin genes onto our genome assembly. He annotated a large contig for multiple genes.