Progress 11/18/13 to 10/31/17
Outputs
Target Audience:Data has been presented at scientific meetings to the global animal genomics community. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Bonnie has taken on a key role in the histological brain atlas project and is learning skills including effective collaboration, leadership of a collaboration and effective communication. The brain atlas project has allowed Bonnie to build collaborations with multiple departments within the University of Vermont, the Animal Science department at the University of Connecticut, and an industry collaboration with NeuroScience Associates, Inc. Additional professional development opportunities for Bonnie include presenting her data at national and international meetings. Her attendance at meetings was funded in part by nationally competitive travel awards. How have the results been disseminated to communities of interest?Results of the bovine brain methylation project and the bovine brain atlas have been disseminated through the following oral and poster presentations: McKay, SD. 2017. Profiling Epigenetic Modifications in the Limbic System of the Bovine Brain. Leibniz institute for Farm Animal Biology in Dummerstorf, Germany. (Invited Presentation) Cantrell, B, H Lachance, R Funston, R Weaber and S McKay. 2017. Global Quantification of DNA Hydroxymethylation and DNA Methylation in the Bovine Brain. Proceedings of the 36th International Society for Animal Genetics Conference, Dublin, Ireland. http://www.isag.us/2017/docs/ISAG2017_Proceedings.pdf Cantrell, B., N. Jebbett, R. C. Switzer III, E. Delay, S. Zinn, S. Aborn, J. O'Neil, R. Funston, R. Weaber and S.D. McKay. 2017. Facilitation of the Bovine Epigenome in the Limbic System: An atlas of the Bovine Brain. University of Vermont Student Research Conference, Burlington, Vermont. http://www.uvm.edu/~uvmsrc/?Page=archive/2017/presentation.php&SM=archive/_archivemenu.html&pkNetidStudent=bacantre Cantrell, B., N. Jebbett, R. C. Switzer III, E. Delay, S. Zinn, S. Aborn, J. O'Neil, R. Funston, R. Weaber and S.D. McKay. 2017. Facilitation of the Bovine Epigenome in the Limbic System: An atlas of the Bovine Brain. International Plant & Animal Genome XXV, San Diego, California. https://pag.confex.com/pag/xxv/meetingapp.cgi/Paper/24366 What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Whole genome bisulfite sequencing has been performed on five tissues of the limbic system of the bovine brain for each of eight cattle. These tissues include the amygdala, cingulate gyrus, periaqueductal gray, prefrontal cortex and hippocampus. Alignment of whole genome bisulfite sequencing reads to the reference genome is underway. Subsequently, the epigenetic landscape for each tissue will be characterized by base specific identification and distribution of methylation. Differential methylation will be examined between groups of animals with extreme measures of docility. Additionally, a bovine brain atlas is under development. Brain sections being stained for Weil-myelin are currently being mounted to slides and will be stained soon. All of the Nissl stained sections have been mounted and slides are expected to be delivered at any moment. In the meantime, four undergraduate neuroscience students are working under supervision of Bonnie Cantrell, my Ph.D. student, to identify and label regions of the limbic system using the images that we currently have. The Bovine Brain Atlas will be featured in NSAlabs 2017 calendar.
Publications
- Type:
Journal Articles
Status:
Submitted
Year Published:
2017
Citation:
Cantrell BA, H Lachance, B Murdoch, RN Funston, RL Weaber and SD McKay. 2017. First Report of Global DNA Methylation in the Limbic System of Cattle with Extreme Measure of Docility. Submitted.
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Progress 10/01/15 to 09/30/16
Outputs
Target Audience:Data has been presented at scientific meetings to the global animal genomics community. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Bonnie has taken on a key role in the histological brain atlas project and is learning skills including effective collaboration, leadership of a collaboration and effective communication. Additional professional development opportunities for Bonnie include presenting her data at national and international meetings. Her attendence at meetings was funded in part by nationally competitive travel awards. How have the results been disseminated to communities of interest?To date, results of the global DNA Methylation project and the bovine brain atlas have been desiminated through the following poster presentations: Cantrell, B, H Lachance, R Funston, R Weaber and S McKay. 2016. Novel Analysis of Global DNA Methylation in the Limbic System of the Bovine Brain. Proceedings of the 35th International Society for Animal Genetics Conference, Salt Lake City, Utah. Cantrell, B., N. Jebbett, R. C. Switzer III, E. Delay, S. Zinn, S. Aborn, J. O'Neil, R. Funston, R. Weaber and S.D. McKay. 2017. Facilitation of the Bovine Epigenome in the Limbic System: An atlas of the Bovine Brain. International Plant & Animal Genome XXV, San Diego, California. https://pag.confex.com/pag/xxv/meetingapp.cgi/Paper/24366 What do you plan to do during the next reporting period to accomplish the goals?In the next reporting period, whole genome bisulfite sequencing data will be analyzed. The epigenetic landscape for each tissue will be characterized by base specific identification and distribution of methylation. Differential methylation will be examined between groups of animals with extreme measures of docility. In regards to the bovine brain atlas, components of the limbic system will be identified and labeled.
Impacts
What was accomplished under these goals?
Data generated from measures of global DNA methylation have been used to identify functionally distinct regions of the bovine brain that will be used for a more in-depth analysis. Global measures of DNA Methylation were generated from nine tissues of the limbic system of the bovine brain in six animals with extreme measures of docility (N=3 per groups). Subsequently, five tissues of the limbic system of the bovine brain from eight cattle have been dissected, DNA extracted and submitted for whole genome bisulfite sequencing. This tissues include the amygdala, cingulate gyrus, periaqueductal gray, prefrontal cortex and hippocampus. The epigenetic landscape for each tissue will be characterized by base specific identification and distribution of methylation. Differential methylation will be examined between groups of animals with extreme measures of docility. We are currently focusing on developing the bovine brain atlas. The brain of a Holstein steer was fixed through perfusion in the maxillary artery with paraformaldehyde perfusion fixative produced by Electron Microscopy Sciences (Hatfield, PA) and extracted from the skull for further perfusion. The brain was sectioned into 60 micrometer coronal sections and stained with thionine or Weil-myelin every sixth section at NeuroScience Associates (Knoxville, TN). High resolution images of the brain were developed during sectioning for the construction of a three-dimensional brain atlas.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
1. Murdoch, B., G. Murdoch, S. Greenwood and S. McKay. (2016). Nutritional Influence on Epigenetic Marks and Effect on Livestock Production. Frontiers in Genetics 7(182). doi: 10.3389/fgene.2016.00182.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2016
Citation:
3. Cantrell, B.A., R.L. Weaber, R.N. Funston, H. Lachance and S.D. McKay. (2016). P2011 Novel analysis of global DNA methylation in the limbic system of the bovine brain. Journal of Animal Science 94(7supplement4), 43-43. doi: 10.2134/jas2016.947supplement443x.
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Progress 10/01/14 to 09/30/15
Outputs
Target Audience:Data has been presented at scientific meetings to the global animal genomics community. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Bonnie has taken a key role in the histological brain atlas project. Specifically, she secured an in-kind gift to fund the project and has been the project leader for the University of Vermont team. In doing so, she is learning how to collaborate, effectively communicate, manage time and manage money. Furthermore, Bonnie secured funding from the University of Vermont College of Agriculture and Lifesciences to travel to Tennessee to assist with the sectioning and staining of the brain. How have the results been disseminated to communities of interest?To date, results of this project have been disseminated to the animal genomics community through a poster presentation entitled "Investigating Extreme Measures of Docility and Global DNA Methylation in the Bovine Brain" at the 2015 Plant and Animal Genome conference in San Diego, CA. An abstract of the poster and a pdf copy of the poster can be found online at the following website: https://pag.confex.com/pag/xxiii/webprogram/Paper14108.html. What do you plan to do during the next reporting period to accomplish the goals?Within the next year, we plan on identifying the specific regions of the limbic system that will undergowhole genome bisulfite sequencing. We plan on securing an intact bovine brain for subsequent generation of the brain atlas.
Impacts
What was accomplished under these goals?
DNA methylation is a chemical modification to DNA base pairs that has the potential to regulate gene expression. Gene expression directly influences the phenotype of an organism. Therefore, DNA methylation is an epigenetic modification of DNA that regulates gene transcription and may influence variation in economically important phenotypes in agricultural species. We are working towards generating a comprehensive survey of methylation in the bovine brain and investigating differential methylation between two groups of cattle with extreme measures of docility. Our primary objective is to generate a map of the limbic system of the bovine brain methylome. Decreased cost of next generation sequencing has enabled us to perform whole genome bisulfite sequencing on five different tissues in each of eight cattle (4 high and 4 low docility). This change in sequencing strategy will yieldsingle base pair resolution sequencing data. Subsequently, it was deemed necessary to generate a histological atlas of the bovine brain. The histological brain atlas project was funded by an in-kind gift in excess of $100,000 from NeuroScience Associates (https://www.neuroscienceassociates.com/).
Publications
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2015
Citation:
1. Cantrell, B, H Lachance, R Funston, R Weaber and SD McKay. 2015. Investigating Extreme Measures of Docility and Global DNA Methylation in the Bovine Brain. International Plant & Animal Genome XXIII, San Diego, California. https://pag.confex.com/pag/xxiii/webprogram/Paper14108.html
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Progress 11/18/13 to 09/30/14
Outputs
Target Audience: This research has provided my graduate student, Bonnie Cantrell, with the opportunity to become engaged in the animal genomics community through learning and performing fundamental epigenetics research and presenting that research at the Plant and Animal Genomics Conference. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? My graduate student Bonnie Cantrell, had the opportunity to present a poster entitled "Investigating Extreme Measures of Docility and Global DNA Methylation in the Bovine Brain" at the 2015 Plant and Animal Genome conference in San Diego, CA. Her attendance and presentation at this conference provided Bonnie with professional development opportunities including networking with members of the global animal genomics community. How have the results been disseminated to communities of interest? To date, results of this project have been disseminated to the animal genomics community through a poster presentation entitled "Investigating Extreme Measures of Docility and Global DNA Methylation in the Bovine Brain" at the 2015 Plant and Animal Genome conference in San Diego, CA. An abstract of the poster and a pdf copy of the poster can be found online at the following website: https://pag.confex.com/pag/xxiii/webprogram/Paper14108.html. What do you plan to do during the next reporting period to accomplish the goals? Within the next year we expect to generate libraries for methyl binding domain sequencing (MBD-Seq). Five brain regions with significant differences in global DNA methylation levels between groups of cattle will undergo MBD-Seq. This method of next generation sequencing will be utilized to determine the genomic locations for methylation in brain regions for each of six cattle. Next, generated sequence reads from all six animals will be compiled for each brain region and NextGENe (SoftGenetics, State College, PA) software will be used to align sequence reads to the UMD3.1 bovine reference genome assembly for identification of methylated regions.
Impacts
What was accomplished under these goals?
DNA methylation is a chemical modification to DNA base pairs that has the potential to regulate gene expression. Gene expression directly influences the phenotype of an organism. Therefore, DNA methylation is an epigenetic modification of DNA that regulates gene transcription and may influence variation in economically important phenotypes in agricultural species. We are working towards generating a comprehensive survey of methylation in the bovine brain and investigating differential methylation between two groups of cattle with extreme measures of docility. Brains from six cattle (3 high and 3 low docility) have been dissected and nine functionally distinct regions of the brain have been harvested. Harvested brain regions include the bed nucleus of the stria terminalis, amygdala, hippocampus, prefrontal cortex, dorsal raphe, hypothalamus, periaqueductal gray, cingulate cygrus and nucleus accumbens. Our primary objective is to generate a map of the bovine brain methylome. Towards that end, we have measured global DNA methylation levels for each of the nine brain regions harvested from each of the six cattle. Brain regions with significant differences in global DNA methylation levels between groups of cattle will undergo next generation sequencing. Within the next year we expect to generate libraries for methyl binding domain sequencing (MBD-Seq). This method of next generation sequencing will be utilized to determine the genomic locations for methylation in brain regions for each of six cattle. Subsequently, analysis will be undertaken to determine the extent of methylation in each brain region. This is the first step in enhancing our knowledge of the bovine brain methylome and its association to an economically important behavioral phenotype in cattle.
Publications
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2015
Citation:
" Bonnie Cantrell, Hannah Lachance, Rick Funston, Robert Weaber and Stephanie McKay. 2015. Investigating Extreme Measures of Docility and Global DNA Methylation in the Bovine Brain. International Plant & Animal Genome XXIII, San Diego, California.
https://pag.confex.com/pag/xxiii/webprogram/Paper14108.html
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