Howe, Daniel

Daniel K. Howe – AG – Veterinary Science

The Howe lab studies the closely related coccidian parasites Sarcocystis neurona, Neospora spp., and Toxoplasma gondii. Of particular interest is the understanding of S. neurona’s capacity to cause an uncommon neurologic syndrome called Equine Protozoal Myeloencephalitis (EPM). A primary objective of the research is to gain a better comprehension of the molecular biology of this parasite, and to use this information to improve our ability to understand and control EPM. To this end, the lab was part of a multi-investigator effort that produced two annotated genome sequences for S. neurona. These annotated genomes along with large gene expression datasets that we’ve generated are tremendous investigative resources, allowing the lab to now pursue research projects that utilize contemporary “omics” approaches for studying S. neurona and related species.

Comparison of RNA seq data from various time points in the life cycle of the coccidian parasite S. neurona.

Differential analysis of mRNA produced by S. neurona both as extracellular invasive merozoites and as intracellular propagating schizonts using Illumina RNA-Seq data. The project lead is Dr. Dan Howe (professor in Veterinary Science), while data analysis will be performed by Jamie Norris (graduate student in Veterinary Science) and Dr. Sriveny Dangoudoubiyam (Scientist 1 in Veterinary Science).

Software:

This project will primarily rely on open-source software such as Trinity, HiSat2, SAMtools, RSEM and other similar software.

Trimmomatic(http://www.usadellab.org/cms/?page=trimmomatic)
Trinity (https://github.com/trinityrnaseq/trinityrnaseq/wiki)
Bowtie2(http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml)q
SAMtools (http://samtools.sourceforge.net/)
Hisat2 (https://ccb.jhu.edu/software/hisat2/index.shtml)
RSEM(https://deweylab.github.io/RSEM/)
Cufflinks(http://cole-trapnell-lab.github.io/cufflinks/)

Comparison of genomes from several S. neurona isolates and the closely-related species Sarcocystis falcatula

This project seeks to use Illumina genome sequence data to compare and contrast wild type parasite isolates to the reference genome from the SN3 isolate, which has been passaged continuously through cell culture throughout the past two decades. The project lead is Dr. Dan Howe (professor in Veterinary Science), and the data analysis will be performed by Jamie Kaj Norris (graduate student in Veterinary Science).

Software:

This project will rely on open-source software including HISAT2, Samtools, Bedtools, and other similar software.

Students:

Suri, Parul - Graduate

Dangoudoubiyam, Sriveny - Scientist

Jamie K Norris, Graduate, Added on MCC, 04/26/2023