Genomics Commons^™

A Tissue Specific Transcriptomic, Proteomic And Phospho-Proteomic Atlas Of The Translational Machinery Of Arabidopsis Thaliana, Abdullah Salim

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Gene expression encompasses the flow of genetic information from DNA to mRNA (transcription) and from mRNA to protein (translation) along with the regulatory mechanisms underlying these processes. Omics technologies offer a powerful toolset with which to study gene expression at each of these stages. A recently published dataset integrating transcriptomic, proteomic and phospho-proteomic measurements from 30 Arabidopsis thaliana tissues provides a unique resource to explore gene expression.¹ The translational machinery (the ribosome, and its initiation, elongation, and termination factors) are a core component in gene expression. Defects in translation can be lethal or lead to major developmental defects and …

The Effects Of Mapk Signaling On The Development Of Cerebellar Granule Cells, Kerry Morgan

University Scholar Projects

The granule cells are the most abundant neuronal type in the human brain. Rapid proliferation of granule cell progenitors results in dramatic expansion and folding of the cerebellar cortex during postnatal development. Mis-regulation of this proliferation process causes medulloblastoma, the most prevalent childhood brain tumor. In the developing cerebellum, granule cells are derived from Atoh1-expressing cells, which arise from the upper rhombic lip (the interface between the roof plate and neuroepithelium). In addition to granule cells, the Atoh1 lineage also gives rise to different types of neurons including cerebellar nuclei neurons. In the current study, I have investigated the …

The Effects Of Mapk Signaling On The Development Of Cerebellar Granule Cells, Kerry Morgan

Honors Scholar Theses

The granule cells are the most abundant neuronal type in the human brain. Rapid proliferation of granule cell progenitors results in dramatic expansion and folding of the cerebellar cortex during postnatal development. Mis-regulation of this proliferation process causes medulloblastoma, the most prevalent childhood brain tumor. In the developing cerebellum, granule cells are derived from Atoh1-expressing cells, which arise from the upper rhombic lip (the interface between the roof plate and neuroepithelium). In addition to granule cells, the Atoh1 lineage also gives rise to different types of neurons including cerebellar nuclei neurons. In the current study, I have investigated the …

Genomics, Exometabolomics, And Metabolic Probing Reveal Conserved Proteolytic Metabolism Of Thermoflexus Hugenholtzii And Three Candidate Species From China And Japan, Scott C. Thomas, Devon Payne, Kevin O. Tamadonfar, Cale O. Seymour, Jian Yu Jiao, Senthil K. Murugapiran, Dengxun Lai, Rebecca Lau, Benjamin P. Bowen, Leslie P. Silva, Katherine B. Louie, Marcel Huntemann, Alicia Clum, Alex Spunde, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, I. Min Chen, Dimitrios Stamatis, T. B.K. Reddy, Ronan O’Malley, Chris Daum, Nicole Shapiro, Natalia Ivanova, Nikos C. Kyrpides, Tanja Woyke, Emiley Eloe-Fadrosh, Trinity L. Hamilton, Paul Dijkstra, Brian P. Hedlund

Life Sciences Faculty Publications

Thermoflexus hugenholtzii JAD2 , the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2 and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2 and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing “Candidatus Thermoflexus japonica,” “Candidatus Thermoflexus tengchongensis,” and “Candidatus …

Has Maize Overtaken Our Reality? A Personal Briefing, Biochemical Comparison, Agrigenomics, And History Of Maize, Nader Pahlevan

Honors Theses

Maize (Zea mays ssp. Mays) is a revolutionary cereal grain that has raced to the world’s most popular staple crop, transforming societies and impacting history. This paper aims to build and portray the story maize has created through its journey to world domination. The important details that encompass this literature are maize’s cultural significance in my life’s story, the comparison of various starches broken down into amylose and amylopectin ratios, a summative historical account on maize’s spread throughout numerous parts of the old world, and the genetical analysis of maize that explains the key features that have led …

Applications Of Comparative Genomics And Data Science To Agricultural And Clinical Research, Katrina A. Schlum

Doctoral Dissertations

The advent of inexpensive, high-throughput whole genome sequencing (WGS) technologies has led to the generation of thousands of related genomes, even from a single study. Large-scale genome analysis has resulted in hypothesis-generating approaches in the fields of clinical, human and agriculture genomics. Additionally, population-level genomic sampling has resulted in a decrease in false positives in genotype-phenotype associations and an increase in understanding of the basis of disease, antibiotic and pesticide resistance. Deeper understanding of migration, genetic divergence and evolution has also been made possible due to WGS. This research applies comparative genomics, population genomics and data science approaches to whole …

The Impact Of A Lynch Syndrome Diagnosis By Population Genomic Screening On Family Communication, Medical Management, And Lifestyle Changes, Reem Ibrahim Bux, Brooke Nicole Delehoy

Human Genetics Theses

The purpose of population genomic screening programs is to help in prevention and treatment of conditions that takes into account an individual’s unique genetics, environmental, and lifestyle factors. Through this “genome-first” approach, individuals at increased lifetime risk for certain conditions are identified, allowing them and their relatives to qualify for preventative medical care and surveillance (Schwartz et al., 2018). An example institution that utilizes this approach is Geisinger’s MyCode Community Initiative, where their goal is to “make healthcare better” through research and its application to patient care (MyCode Community Health Initiative, n.d.). MyCode reports back medically actionable results for conditions …

Validation Of Anti-Oxidative Stress Genes From Genome-Wide Screening Of Escherichia Coli, Carson Ercanbrack

Chemistry & Biochemistry Undergraduate Honors Theses

The primary purpose of this project is to evaluate the genes that play a role in the oxidative stress response in Escherichia coli. In doing so, the entire genome of E. coli was subject to throughput in which individual genes were determined to have a role in the bacteria’s oxidative stress response. Moreover, this project focused on the validation of the genes that were able to pass the initial throughput stage. The genes were subject to two forms of validation. In the first validation technique, candidate genes were overexpressed and minimum inhibitory concentrations of hypochlorous acid were taken. Following, a …

Involvement Of The Ino80 Chromatin Remodeling Complex In Cell Division And Genomic Stability, Ethan Chen

Biomedical Engineering Undergraduate Honors Theses

Cell division is a vital biological process for growth and development in both single and multi-cellular organisms—whereby the cell must duplicate its organelles and genome in entirety and appropriately distribute the copied contents to the daughter cells. Cells undergo a cycle of two distinct phases: interphase and mitosis. During interphase, the cell replicates its genomic DNA (in the form of chromosomes) located within the nucleus. DNA replication is carried out in a euchromatin state, where the chromosome structure is loose and easily accessible by DNA polymerase and other replication enzymes. Upon the completion of replication, chromatin is condensed into highly …

Computational Approaches To Delineate Transcriptional And Functional Heterogeneity In Pancreatic Cancer, Sanjana Srinivasan

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

Pancreatic ductal adenocarcinoma (PDAC) is an incurable disease characterized by poor survival, dense desmoplastic stroma and activating mutations in KRAS (>90%). These tumors are highly complex ecosystems composed of molecularly distinct sub-populations that exhibit a spectrum of genetic features and associated phenotypes. Despite recent advances in the transcriptomic characterization of PDAC into at least two tumor subtypes, this alone has been insufficient to define more specific patterns of oncogenic dependency. To fully leverage advancements in next generation sequencing and functional genomics, we have sought to establish computational methodologies to aid in refined target discovery, and to develop a novel …

The Diversity And Evolution Of Phenazine Biosynthesis Pathways In Enterobacterales, Christian Leise

Honors Theses

Enterobacterales is an order of Gram-negative bacteria that encompasses plant and animal pathogens and organisms of industrial importance. Some of these bacteria produce secondary metabolites classified as phenazines (Phz). Studies in other groups of microorganisms revealed that phenazines are redox-active and exhibit broad antibacterial, antifungal, and antiparasitic activity. Enterobacterales are known to produce phenazines, but details about the diversity, biochemistry, and function of phenazine metabolites in these organisms are missing. In this work, we screened the National Center for Biotechnology Information (NCBI) GenBank for genome sequences of phenazine-producing (Phz+) Enterobacterales. Additionally, genomes of Phz+ strains Pectobacterium carotovorum cc303 and …

Mixture Model Approaches To Integrative Analysis Of Multi-Omics Data And Spatially Correlated Genomic Data, Ziqiao Wang

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

Integrative genomic data analysis is a powerful tool to study the complex biological processes behind a disease. Statistical methods can model the interrelationships of the involved gene activities through jointly analyzing multiple types of genomic data from different platforms (vertical integration), or improve the power of a study through aggregating the same type of genomic data across studies (horizontal integration). In this dissertation, we propose statistical methods and strategies for integrative multi-omics data in association analysis of disease phenotypes, with an emphasis on cancer applications.

We develop a new strategy based on horizontal integration by leveraging publicly available datasets into …

Dynamics Of Hybrid Zones At A Continental Scale, Bradley T. Martin

Graduate Theses and Dissertations

Hybridization has traditionally been viewed as a happenstance that negatively impacts populations, but is now recognized as an important evolutionary mechanism that can substantially impact the evolutionary trajectories of gene pools, influence adaptive capacity, and contravene or reinforce divergence. Physiographic processes are important drivers of dispersal, alternately funneling populations into isolation, promoting divergence, or facilitating secondary contact of diverged populations, increasing the potential for hybridization. In North America, glacial-interglacial cycles and geomorphological changes have provided a dynamic backdrop over the last two million years that promoted such oscillations of population contraction and expansion. These biogeographic processes have resulted in regional …

Understanding The Genetics Of Schizophrenia, Matthew Toohey

Thinking Matters Symposium

Schizophrenia has been considered heritable for a long time, but only with the advent of new technologies such as whole-genome sequencing and genome-wide association studies can we begin to identify specific molecular causes of schizophrenia. This poster will review some of the genetic variants that research groups have associated with schizophrenia. Current research has indicated that schizophrenia is a polygenic disease and has been linked to many genes. Some of these common risk variants are in protein coding sections of the DNA. These proteins are often linked to neurological development or immune system function. Other variants that have been associated …

307— Cooperation Of Selfish Genetic Elements In Stalk-Eyed Flies, Suhani Patel, Ben Mcpherson

GREAT Day

SGEs are selfish genetic elements that increase the likelihood of their own transmission regardless of the host’s best interest. Transposable elements (TEs) and meiotic drivers are both types of SGEs. SGEs subsequently result in genetic conflict as they disrupt functional elements in the genome. We are working to better understand the cooperation of selfish genetic elements in Stalk-Eyed flies. Transposable elements are counteracted by small non-coding RNA molecules called piRNA. These RNA molecules work by reducing the expression of TEs by degrading TE RNA transcripts. Prior work in stalk-eyed flies has shown that TEs are expressed at a higher rate …

Annotation Of The Genome Of Drosophilia Ananassae, Landon Kehr

Celebration of Scholarship 2021

This project involves the use of software to annotate the genome of D. ananassae in collaboration with the Genomics Education Partnership. Annotations include coding regions and transcription start sites for specific genes that are homologous to D. melanogaster genes.

Comparative Genomics For D. Ananassae, Hailey Chang, Tia Watkins

Celebration of Scholarship 2021

The purpose of this project is to utilize comparative genomics tools to characterize specific genes in D. Ananassae. This is done in collaboration with the Genomics Education Partnership.

An Ensemble Of The Icluster Method To Analyze Longitudinal Lncrna Expression Data For Psoriasis Patients, Suyan Tian, Chi Wang

Internal Medicine Faculty Publications

BACKGROUND: Psoriasis is an immune-mediated, inflammatory disorder of the skin with chronic inflammation and hyper-proliferation of the epidermis. Since psoriasis has genetic components and the diseased tissue of psoriasis is very easily accessible, it is natural to use high-throughput technologies to characterize psoriasis and thus seek targeted therapies. Transcriptional profiles change correspondingly after an intervention. Unlike cross-sectional gene expression data, longitudinal gene expression data can capture the dynamic changes and thus facilitate causal inference.

METHODS: Using the iCluster method as a building block, an ensemble method was proposed and applied to a longitudinal gene expression dataset for psoriasis, with the …

A Whole-Genome Scan For Association With Invasion Success In The Fruit Fly Drosophila Suzukii Using Contrasts Of Allele Frequencies Corrected For Population Structure, Laure Olazcuaga, Anne Loiseau, Hugues Parrinello, Mathilde Paris, Antoine Fraimout, Christelle Guedot, Lauren M. Diepenbrock, Marc Kenis, Jinping Zhang, Xiao Chen, Nicolas Borowiec, Benoit Facon, Heidrun Vogt, Donald K. Price, Heiko Vogel, Benjamin Prud'homme, Arnaud Estoup, Mathieu Gautier

Life Sciences Faculty Publications

Evidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here, we characterized the genome response of the spotted wing drosophila Drosophila suzukii during the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic …

The Giant Axolotl Genome Uncovers The Evolution, Scaling, And Transcriptional Control Of Complex Gene Loci, Siegfried Schloissnig, Akane Kawaguchi, Sergej Nowoshilow, Francisco Falcon, Leo Otsuki, Pietro Tardivo, Nataliya Timoshevskaya, Melissa C. Keinath, Jeramiah J. Smith, S. Randal Voss, Elly M. Tanaka

Biology Faculty Publications

Vertebrates harbor recognizably orthologous gene complements but vary 100-fold in genome size. How chromosomal organization scales with genome expansion is unclear, and how acute changes in gene regulation, as during axolotl limb regeneration, occur in the context of a vast genome has remained a riddle. Here, we describe the chromosome-scale assembly of the giant, 32 Gb axolotl genome. Hi-C contact data revealed the scaling properties of interphase and mitotic chromosome organization. Analysis of the assembly yielded understanding of the evolution of large, syntenic multigene clusters, including the Major Histocompatibility Complex (MHC) and the functional regulatory landscape of the Fibroblast Growth …