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- Annual Symposium on Biomathematics and Ecology Education and Research (7)
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Articles 1 - 26 of 26
Full-Text Articles in Life Sciences
Analysis Of Complex Vertebrate Genomes: Computational Challenges And Solutions, Jeramiah J. Smith
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
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:
- Sequencing and de novo assembly of the reference salamander genome
- Alignment of short sequences from male and female genomes to the reference
- 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Using Imputation As A Method Of Improving Genetic Data Analysis, Kimberly Diaz Perez
Georgia State Undergraduate Research Conference
No abstract provided.
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
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
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 …
P08. Unravelling Organelle Genome Evolution Architecture Using Rna-Sequencing Data, Matheus Sanita Lima, David Roy Smith
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
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
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
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 …
Penetrance Estimates For Incidental Genomic Findings In Acmg-59, James A. Diao
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 …