Progress 09/10/13 to 09/30/16
Outputs
Target Audience:Our work was shared with scientists concerned with immune development in the foal: Postnatal changes in epigenetic modifications of neutrophils of foals are associated with increased ROS function and regulation of neutrophil function. Dindot SV, Doan RN, Kuskie KR, Hillman PR, Whitfield CM, McQueen CM, Bordin AI, Bourquin JR, Cohen ND. Dev Comp Immunol. 2018 Oct;87:182-187.PMID: 29958850 Changes/Problems:It took us a long time to work out the appropriate analytical methods for these data as this was the first report of sequential analysis of ChIP-Seq data from neutrophils in any species, let alone a species with a relatively limited annotation of the genome. What opportunities for training and professional development has the project provided?2 graduate students (Kyle Kuskie, MS and Cole McQueen, PhD) contributed to this work. For both individuals the skills in bioinformatics and epigenetics were extremely valuable. How have the results been disseminated to communities of interest?Yes, via publication. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
We learned that post-natal epigenetic modifications are associated with functional changes in neutrophils. These data indicate enviromental cues contribute to the ability of foals to fight infections and survive to meet their intended use(s). We believe that these environmental cues are likely to include the microbitiota, and this is a new line of inquiry for our laboratory.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Postnatal changes in epigenetic modifications of neutrophils of foals are associated with increased ROS function and regulation of neutrophil function.
Dindot SV, Doan RN, Kuskie KR, Hillman PR, Whitfield CM, McQueen CM, Bordin AI, Bourquin JR, Cohen ND.
Dev Comp Immunol. 2018 Oct;87:182-187. doi: 10.1016/j.dci.2018.06.012. Epub 2018 Jun 26.
PMID:
29958850
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Progress 01/01/12 to 12/31/12
Outputs
OUTPUTS: Activities - All samples have been collected and analyzed for epigenetic modifications and for reactive oxygen species. Products - A map of 2 specific histone modifications across the genome of foal neutrophils has been generated. PARTICIPANTS: INDIVIDUALS 1) Principal Investigator, Noah Cohen: Collected samples and oversaw phenotypic characterization of neutrophil function, and interpretation and reporting of results . 2) Co-Principal Investigator, Scott Dindot: Oversaw the epigenetic analysis and interpretation and reporting of results. 3) Graduate Student, Mr. Ryan Doan: Oversaw the sequencing steps and analysis of ChIP-seq results. 4) Graduate Student, Mr. Kyle Kuskie: Oversaw the isolation of neutrophil chromatin and immunoprecipitation. PARTNER ORGANIZATIONS: Additional funding for this project was provided by the Morris Animal Foundation. TARGET AUDIENCES: Target audiences include: 1) equine veterinarians; 2) horse breeders producing foals; 3) equine scientists, including geneticists; and, 4) neonatal immunologists. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Change in knowledge - We have characterized the genomic distribution of 2 histone modifications for foal neutrophils, and identified the biological pathways and processes associated with these modifications. We also have determined the biological pathways and processes for which modifications change between days 2 and 30 of life.
Publications
- No publications reported this period
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Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: We have completed blood collection, chromatin isolation and immuno-precipitation, and developing sequencing libraries. We have completed ChIP-Seq for samples from 1 foal. PARTICIPANTS: Mr. Kyle Kuskie worked (while concurrently completing an MS degree) as a technician assisting with isolating neutrophils from blood of foals, isolating chromatin from neutrophils and immunoprecipitation of chromatin. Kyle also quantified reactive oxygen species generation using flow cytometry. He has graduated and is currently employed by the Tarrant County Department of Health in their bioterrorism/biosecurity section. Mr. Ryan Doan, doctoral student,worked to develop sequencing libraries for the ChIP-Seq procedure. Ryan is expected to complete a PhD in genetics at Texas A&M University in 2013, under the direction of Dr. Scott Dindot. Ms. Courtney Brake, technician, assisted with collecting blood from foals. Dr. Scott Dindot, Co-Project Director, has supervised all stages of ChIP-Seq, and will assume responsibility for analyzing ChIP-Seq results. Dr. Dindot is Assistant Professor in the Department of Veterinary Pathobiology at Texas A&M University. Dr. Noah Cohen, Project Director, has overseen all phases of the project, with secondary role to Dr. Dindot for the ChIP-Seq. TARGET AUDIENCES: Segments that will be served by results of this study will be producers of foals (and other neonatal animals of agricultural importance), veterinarians who treat neonatal foals, and research scientists interested in understanding neonatal immune development. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
We have developed methods for ChIP-Seq for neutrophils, a method that is to our knowledge unreported.
Publications
- No publications reported this period
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Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: Activities have included acquiring flow cells for ChIP Seq, and developing protocols for isolating nuclei from neutrophils, and collecting samples from foals. The funding provided was used to obtain funding from a private foundation to support a trainee (technician/graduate student) to conduct the research. PARTICIPANTS: 1) Noah Cohen, Co-PI: Participated in acquiring blood samples from horses and foals; responsible for overseeing the design, conduct, data analysis, and interpretation of results of the study; oversight of neutrophil isolation protocols. 2) Scott Dindot, Co-PI: Participated equally in the design, conduct, data analysis, and interpretation of findings, and oversaw the ChIP-SEQ procedures 3)Kyle Kuskie, Technician/Graduate Student: Has been responsible for implementing methods for neutrophil isolation, isolation of nuclei from neutrophils, and chromatin immunoprecipitation (all steps prior to sequencing histone modifications). Partner Organizations: A grant was written to the Morris Animal Foundation to provide partnering support. Their support provides funding for the trainee (Kyle Kuskie) to participate in this project. Training or professional development: Undergraduate student workers have participated in assisting with processing blood and assisting with restraint of mares while blood is collected. TARGET AUDIENCES: Target audiences will be horse producers because results will be relevant to foal health. In addition, equine biologics manufacturers will be interested in the knowledge gained from this project as it relates to developmental changes in innate immunity, and adaptive immunity which is influenced by innate responses. Technicians, graduate students, and undergraduate students in our laboratory have learned new information about isolating neutrophils and neutrophil nuclei from horses. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Outcomes have included scientists and trainees learning more about isolating nuclei and chromatin from neutrophils of animals, specifically horses, and improved skills with the isolation and processing of neutrophils from horses.
Publications
- No publications reported this period
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