Genetics and Genomics Commons^™

Analysis Of Complex Vertebrate Genomes: Computational Challenges And Solutions, Jeramiah J. Smith

Commonwealth Computational Summit

No abstract provided.

Discovery Of Sex-Specific Regions In A Salamander Genome, Nataliya Y. Timoshevskaya, Melissa C. Keinath, Jeramiah J. Smith

Commonwealth Computational Summit

Biological Aspects:

Salamander (Ambystoma mexicanum) has a gigantic genome: ~32,000,000,000 bases (10X of size of human genome)

Sex is determined by a pair of morphologically identical chromosomes:

• ZZ in male
• ZW in female

Object:

• Find (if there are any) genomic differences between chromosomes W and Z

Workflow:

1. Sequencing and de novo assembly of the reference salamander genome
2. Alignment of short sequences from male and female genomes to the reference
3. Coverage analysis

The Lamprey Genome: Illuminating Genomic Change Across Eons And Embryogenesis, Jeramiah J. Smith, Courtney K. M. Waterbury, Melissa C. Keinath, Cody B. Saraceno, Vladimir A. Timoshevskiy, Nataliya Y. Timoshevskaya

Commonwealth Computational Summit

The lamprey genome provides unique insights into both the deep evolutionary history of vertebrate genomes and the maintenance of genome structure/integrity over development. The lamprey lineage diverged from all other vertebrates approximately 500 million years ago. As such, comparisons between lamprey and other vertebrates permit reconstruction of ancient duplication and rearrangement events that defined the fundamental architecture and gene content of all extant vertebrate genomes. Lamprey also undergoes programmatic changes genome structure that result in the physical elimination of ~20% of its genomic DNA (~0.5Gb from a ~2 Gb genome) from all somatic cell lineages during early embryonic development. Here, …

Use Of Hpc To Analyze Changes In Gene Expression During Fruit Fly Spermiogenesis, Sepideh Dadkhah, Douglas A. Harrison, Jeramiah J. Smith

Commonwealth Computational Summit

In the fruit fly, Drosophila melanogaster, JAK/STAT signaling during spermiogenesis is known to play a crucial role in the maintenance of stem cells of the testis. Recent studies in our lab have shown that activation of the JAK/STAT pathway in somatic cyst cells is also required for the later stages of spermiogenesis like individualization.

The main goal of this project is to characterize the events downstream of JAK/STAT signaling in spermiogenesis and more specifically to determine the mechanism by which JAK/STAT activation regulates individualization, a later stage in spermiogenesis where 64 individual spermatids are formed from a 64-interconnected spermatid …

Background, Needs And Expectations For Genetic Counseling In Adults With Ehlers-Danlos Syndrome, Pooja Swaroop

Post & Beyond

Ehlers-Danlos Syndrome (EDS) is a heterogeneous group of heritable connective

tissue disorders. Patients with EDS often show a wide range of

clinical manifestations, which most often include joint hypermobility, connective

tissue fragility and skin hyperextensibility. The symptomatology of

individuals with EDS-Hypermobile Type (EDS-HT) is complex and can range

in severity from mild to profound with several studies reporting multisystem

involvement. In addition to the aforementioned symptoms, there

is a significant risk for comorbid psychiatric disorders. Currently, genetics

professionals and genetic counselors act primarily as diagnosticians and

provide tertiary support for the ongoing care, coordination and management

of patients with EDS. …

Bioinformatic Analysis Of The Evolution And Function Of Parasitoid Wasp Venom, Nathan T. Mortimer

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

G-Onramp: Create Genome Browsers That Enable Undergraduate Students To Participate In Collaborative Genome Annotations, Wilson Leung, Yating Liu, Luke Sargent, Jeremy Goecks, Sarah C.R. Elgin

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Chromosome Conformation In Context, James Taylor

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

A Systems Level Approach To Temporal Expression Dynamics In Drosophila Reveals Clusters Of Long Term Memory Genes, Julianna Bozler, Balint Kacsoh, Giovanni Bosco

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Cage: A Tool For Identifying Genes With Correlated Spatiotemporal Expression, Basheer Becerra

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Functional Characteristics And Genomic Sequencing Of Antarctic Environmental Isolates, Amanda Kemper, Christina Aigner, Michelle Tigges, Sara Anderson

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Study Of Antidepressant Molecular Structure Leading To Safer Dosing, Meera Garg

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Performing A Genetic Screen To Identify Factors That Promote Lncrna-Dependent Gene Repression, Chrishan Fernando, Cecilia Yiu, Sara Cloutier, Siwen Wang, Elizabeth Tran

The Summer Undergraduate Research Fellowship (SURF) Symposium

Long non-coding RNAs (lncRNAs) were once thought not to have useful functions in organisms but rather to be products of aberrant transcription. However, roles are being found for lncRNAs in beneficial processes such as controlling gene expression. In some of these cases, lncRNAs form R-loops in vivo. R-loops are nucleic acid structures consisting of hybridized strands of single-stranded DNA (ssDNA) and single-stranded RNA (ssRNA) as well as the displaced strand of ssDNA. Formation of these R-loops is important for gene regulation by the lncRNAs. However, factors that promote formation of lncRNA R-loops are not known. The gene PHO84 is being …

Tumor Formation In Response To Loss Of Chromatin Remodeler Chd5 In Zebrafish, Taylor R. Sabato, Erin L. Sorlien, Dr. Joseph P. Ogas

The Summer Undergraduate Research Fellowship (SURF) Symposium

Chromodomain helicase DNA binding protein 5 (CHD5) has been identified as a tumor suppressor in humans. Deletion or mutation of CHD5 has been observed in numerous cancers, including neuroblastoma and melanoma. We hypothesize that chd5 is also a tumor suppressor in zebrafish, a powerful model system to study tumorigenesis. Many genes involved in tumorigenesis are conserved in zebrafish, and they develop fully penetrant tumor phenotypes. We have created chd5 knock-out zebrafish using CRISPR/Cas9 and are monitoring them for tumor development. In addition to the chd5 knock-outs, we are undertaking a double-mutant approach by coupling loss …

Using Mathematical Models Of Biological Processes In Genome-Wide Association Studies Of Psychiatric Disorders, Amy Cochran

Biology and Medicine Through Mathematics Conference

No abstract provided.

Software Development For Genome Sequence Analysis, David Farr

Symposium Of University Research and Creative Expression (SOURCE)

The cost of genome sequencing has decreased rapidly, expanding availability for many biological applications (Muir 2016). For example, researchers can now obtain genome sequences from multiple populations under different types of selection. Comparison of these sequences allows for identification of chromosome regions and specific genes associated with adaptive evolution (Kelly 2013). As an increasing number of researchers engage in this type of inquiry, many have created in-house computer scripts to analyze the raw sequence data (e.g., Kelly 2013), creating a gap in both continuity and standardization.

Using a test dataset and preliminary results from an ongoing artificial selection experiment in …

Genetic Variation In Concentration Of The 33-Mer Protein Subcomponent In Wheat, Robert L. Paris, Kaleb M. Pauley, Ryan K. Lokkesmoe, Sarah E. Lyon, James C. Dunlap, Julia M. Pierre, Timothy Vanwingerden, Finny J. Johns, Kyle J. Kilchrist, Tyler J. Reid, Caleb M. Winn

The Research and Scholarship Symposium (2013-2019)

Celiac Disease is a hypersensitive response to gluten caused by HLA-DQ2 or HLA-DQ8 T-cell presentation, initiating destruction of intestinal epithelial cells. Currently, the only remedy for those suffering from celiac disease is elimination of all gluten from the diet. Studies indicate that an indigestible fragment of the gluten molecule, alpha-gliadin subcomponent 33-mer, rich in proline and glutamine, is responsible for the hypersensitivity response. Determination of 33-mer concentration in wheat lines could be beneficial to future development of wheat lines with reduced 33-mer concentration. Protein from wheat flour was extracted and subjected to ELISA techniques in order to quantify the concentration …

Regulation Of Brown Adipocyte Gene Expression By The Histone 3 Lysine 4 Demethylase Kdm1b, Vy P. Tran

Georgia State Undergraduate Research Conference

No abstract provided.

Using Imputation As A Method Of Improving Genetic Data Analysis, Kimberly Diaz Perez

Georgia State Undergraduate Research Conference

No abstract provided.

C-Myc’S Role On Methylation Of The Gata-2 Gene In Non-Small Cell Lung Carcinoma, Jonathan D. Hajduk

Student Scholar Showcase

Lung cancer accounts for more deaths per year than any other form of cancer, resulting in a total of 158,000 deaths per year in the U.S. Non-small cell lung cancer (NSCLC) is diagnosed in greater than 224,000 Americans every year. Methylation and subsequent downregulation of certain genes has been directly linked to the uncontrolled growth of NSCLC cells. Natural killer (NK) cells are key innate immune cells responsible for apoptosis of cells with incorrect genetic code. It is believed that one component of uncontrolled NSCLC growth is due to the NK cells’ inability to detect errors within NSCLC cells. Perhaps …

Development Of An Interleukin-4-Inducing Principle From Schistosoma Mansoni Eggs (Ipse)-Specific Pcr Assay As A Quantitative Predictor Of Schistosomiasis-Associated Morbidity, Dannah Farah, Evaristis Mbanefo, Michael H. Hsieh

GW Research Days 2016 - 2020

Schistosomiasis is a neglected tropical disease affecting between 200-500 million people worldwide. The two species causing most human cases of schistosomiasis are Schistosoma mansoni and Schistosoma haematobium. The gold standard for diagnosis is parasitological detection of parasite eggs in stool using the Kato-Katz method. Counting eggs shed in stool is labor-intensive and inaccurate. Interleukin-4- inducing principle from Schistosoma mansoni eggs (IPSE) is the most abundant secreted protein from schistosome eggs. We hypothesized that the mRNA transcripts of the IPSE protein may be found in the liver tissue and stool of experimentally infected animals, and that these transcripts can be specifically …

Differential Mrna Expression In Ectopic Germinal Centers Of Myasthenia Gravis Thymus, Manjistha Sengupta, Bi-Dar Wang, Norman H. Lee, Gary Cutter, Linda L. Kusner, Henry J. Kaminski

GW Research Days 2016 - 2020

Myasthenia gravis (MG) is an autoimmune neuromuscular disorder resulting in weakness of voluntary muscles. It is caused by antibodies directed against proteins present at the post-synaptic surface of neuromuscular junction (NMJ). A characteristic pathology of patients with early onset MG is thymic hyperplasia with ectopic germinal centers (GC). However, mechanisms that trigger and maintain thymic hyperplasia are poorly characterized.

In order to determine the central mechanisms involved in the pathology, thymus samples from MG patients were assessed by histology and grouped based on appearance of GC compared to samples without them. We assessed the differential mRNA expression profiles between the …

Genetic Effect Of Drought On The California Newt, Taricha Torosa, Madeleine M. Perrault, Samantha Fiallo, Alero Arueyingho, Cindy Kim, Laiken Ritchie

Seaver College Research And Scholarly Achievement Symposium

Droughts are now a common occurrence in Southern California and are known to cause population declines in many species, and such bottlenecks can cause a loss of genetic variation. Genetic variation was examined in a population of the California newt located in Arroyo Sequit Creek in the Santa Monica Mountains. Genetic data from animals examined prior to the current drought were compared to similar data collected from the population after it experienced several years of severe drought. We hypothesized that the drought impacted population should show less genetic variation in comparison to the pre-drought population. Nevertheless, there were no genetic …

P08. Unravelling Organelle Genome Evolution Architecture Using Rna-Sequencing Data, Matheus Sanita Lima, David Roy Smith

Western Research Forum

Background: Mitochondria genomes vary from 11 Mb to 6 kb, while plastids can vary from 1 Mb to 30 kb. Non-coding DNA accounts for most of this size variation, but the mechanistic and evolutionary reasons for that are still unknown. Next generation sequencing has generated unprecedented amounts of genomic and transcriptomic data that can be used for organelle genome evolution studies. However, most of these data is used only for the study of cell nucleus. Therefore, I decided to use these untapped data source to investigate the transcription of organelle genomes in plastid-bearing protists.

Methods: I mapped the transcriptomes over …

P02. Production Of A Protein Subunit Vaccine For Mannheimia Haemolytica In Lettuce Chloroplasts, Coby K. Martin

Western Research Forum

The cattle industry worldwide is ravaged by bovine respiratory disease (BRD), a bacterial disease caused by Mannheimia haemolytica. We have designed a chimeric protein subunit vaccine against M. haemolytica based on recent evidence demonstrating the protective potential of antigens against a virulence factor, leukotoxin, in addition to a surface lipoprotein. Plant-based production of this protein vaccine provides a safe and inexpensive alternative to traditional production methods. Plant-base production also supports the use of an edible vaccine that will deliver antigens to pharyngeal tissues to provide local immunization against M. haemolytica to prior to its progression into the lungs. Chloroplasts …

Molecular Regulation Of Stem Cell Behavior During Tissue Repair And Cancer Formation, Nestor J. Oviedo

Science Seminar Series

Oviedo will be presenting his work on identifying the mechanisms of adult stem cell fate determination based on their topographical location in the adult body. Understanding stem cell fate determination is crucial because tissue repair and neoplastic growth are greater in anterior than in posterior regions of adult animals. Despite its critical implications for stem cell biology, carcinogenesis and regenerative medicine, this physiological phenomenon has remained overlooked. Recent findings from his group provide intriguing evidence implying DNA repair mechanisms and cellular signaling through post-translational modifications regulate stem cell fate decision depending on their topographical location in the adult body. We …

Genetic Variants Contributing To Frontotemporal Dementia With Parkinsonism, Elizabeth C. Oduwo

UNO Student Research and Creative Activity Fair

Frontotemporal dementia with parkinsonism (FTDP) is a neurodegenerative disease characterized by disturbances in cognition, language, and personality, which also has features of parkinsonism. This disease is associated with multiple genes including two located close together on chromosome 17: MAPT and GRN. Human and medical genetics can be used to identify the genes that contribute to the risk of this disease.

Earlier work in the Chase lab had identified a large Mennonite kindred (MEN-1) where parkinsonism and dementia were found in five members of a nuclear family. These symptoms parallel those seen in FTDP and all of the affected members share …

Taxonomic Placement Of The Nidulariaceae Of Nebraska And Iowa Based On Molecular And Morphological Data, Goodmond H. Danielsen Iv

UNO Student Research and Creative Activity Fair

Proper taxonomic and molecular study is necessary to better organize closely related species that may not only be used for human needs, but also in the quest for knowledge of how the world around us works. Though important, the taxonomic placement of Nebraskan and Iowan bird’s nest fungi (Nidulariaceae) is not well documented. Here, phylogenetic analysis is used to place the Nidulariaceae of Nebraska and Iowa in the tree of life using molecular and morphological techniques. Based on these results and results of further work done on these specimens, it will be possible to better place the Nidulariaceae of Nebraska …

Penetrance Estimates For Incidental Genomic Findings In Acmg-59, James A. Diao

Yale Day of Data

The dropping costs and rising popularity of next-generation sequencing has introduced the possibility of personalizing medical treatments and screening for genetic diseases. Still, the clinical community’s understanding remains incomplete, with limited consensus on the proper interpretation for many genetic variants. Thus, the standard procedure when returning sequencing results has been to report findings only in genes related to the diagnostic indication, and not incidental findings in other genes. To balance the threat of false positives with the medical benefits of true findings, the American College on Medical Genetics and Genomics (ACMG) recommends an exception: that clinical sequencing laboratories seek and …