Asher Haug-Baltzell Abstracts
Asher Haug-Baltzell Abstracts
Ph.D. Student
Genetics GIDP
Plant and Animal Genome Conference XXIV
San Francisco, CA
January 9-13, 2016
Professional Abstracts
Lay Audience Abstracts
Abstract #1: Poster and Talk (in "Genome Management and Analysis with CoGe" workshop)
Title: High-Performance and Complex Information Visualization for Genomic Data
Due to recent advances in sequencing technologies and corresponding decreases in sequencing costs, biological researchers are awash in data. This surge of genome datasets, combined with the vast collection of already available data, is incredibly exciting for researchers. However, the scale of the available information and complex relational nature pose significant challenges, particularly when performing comparisons of many genomes and datasets. The Comparative Genomics platform CoGe is working towards developing novel visualizations that will allow for researchers to draw meaningful conclusions from such massive genomic datasets. With a current database of nearly 25,000 genomes for 17,000 species, a huge collection of experimental data, and underlying infrastructure for computational pipeline integration and execution, CoGe is uniquely positioned to begin investigating these new visualizations. Over the last year, CoGe has implemented two new data visualization tools: a high- performance dot-plot viewer and a three-dimensional three-genome synteny browser, both discussed here. These systems are important steps for increasing researchers’ ability to visualize and interact with high-dimensionality data, both through modern web-based technologies and newly-available virtual reality environments.
Abstract #2: Talk (in "Polyploidy" session)
Title: "A polyploid origin for dopamine receptors across the vertebrates"
Dopamine is an important central nervous system transmitter that functions through two classes of receptors (D1 and D2) to influence a diverse range of biological processes in vertebrates. With roles in regulating neural activity, behavior, and gene expression, there has been great interest in understanding the function and evolution dopamine and its receptors. In this study, we use a combination of sequence analyses, microsynteny analyses, and phylogenetic relationships to identify and characterize both the D1 (DRD1A, DRD1B, DRD1C, and DRD1E) and D2 (DRD2, DRD3, and DRD4) dopamine receptor gene families in 43 recently sequenced bird genomes representing the major ordinal lineages across the avian family tree. We show that the common ancestor of all birds possessed at least seven D1 and D2 receptors, followed by subsequent independent losses in some lineages of modern birds. Through comparisons with other vertebrate and invertebrate species we show that two of the D1 receptors, DRD1A and DRD1B, and two of the D2 receptors, DRD2 and DRD3, originated from a whole genome duplication event early in the vertebrate lineage, providing the first conclusive evidence of the origin of these highly conserved receptors. Our findings provide insight into the evolutionary development of an important modulatory component of the central nervous system in vertebrates, and will help further unravel the complex evolutionary and functional relationships among dopamine receptors.
Abstract #1 (Poster and Talk): High-Performance and Complex Information Visualization for Genomic Data
For the past several years the cost of sequencing a genome has been plummeting. Today, the costs have reached just about $1000 for a whole genome, and there are companies that will provide individuals with limited sequencing for ~$100. The low costs and easy availability have created a surge in genomic data, much of which is being made available for researchers. This "big data" of genomics will be key in understanding many genomic mechanisms, but with it comes many challenges especially in management and comparative analysis. My lab built and operates the comparative genomics platform "CoGe", one of the leading resources for genome management and analysis. Recently, we have been looking at developing novel visualizations that harness modern technologies to allow researchers to draw meaningful conclusions from such massive genomic datasets. This year we have implemented two new data visualization tools, both of which will be discussed in this talk and poster. The first is a high- performance, web-based visualization that allows researchers to identify conserved regions between two genomes. The second is a 3D visualizer for looking at conserved regions across three genomes. This 3D browser can be launched in a traditional web browser, but is also enabled for virtual reality providing an immersive, interactive experience. These two systems are important for the future of genomics as they allow researchers to identify genome-wide patterns of conservation. Additionally, they are helping to design and test the technologies and approaches that will eventually allow for many-genome (10+) comparisons.
Abstract #2 (Talk): A polyploid origin for dopamine receptors across the vertebrates
Dopamine (DA), well known for its role as the "reward molecule", is an incredibly important central nervous system transmitter that regulates a wide variety of behaviors and responses. Dopamine functions through 7+ receptors, which allows it control numerous and diverse processes. In this study, we identified the DA receptors in 50 recently sequenced bird genomes. We then used these newly- identified receptors in combination with known receptors from human, mouse, and select other vertebrate and invertebrate species to uncover the evolutionary history of dopamine receptors, not just within birds but across all vertebrates. We provide the first conclusive evidence that four of the receptors originated from a unique duplication event (a whole genome duplication), finally settling a long-standing hypothesis. Our findings are important for two reasons. First, understanding their evolution will help unravel the complex functional relationships among dopamine receptors. Secondly, understanding dopamine receptors has significant implications both in human health and agricultural applications, as dopamine receptors are responsible for many disease conditions in humans and control important breeding behaviors in feed animals. This study promises to help both fields, and has been widely circulated since its publication in October 2015.