University of New Hampshire, Durham
Cleveland State University
Charleston Southern University
University of the Pacific
The Graduate Center, City University of New York
Wofford College
University of San Francisco
Utah State University
Claremont Colleges
Deephtlv: A Deep Learning Framework For Detecting Human T-Lymphotrophic Virus 1 Integration Sites,
2023
The Texas Medical Center Library
Deephtlv: A Deep Learning Framework For Detecting Human T-Lymphotrophic Virus 1 Integration Sites, Johnathan Jia, Johnathan Jia
The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)
In the 1980s, researchers found the first human oncogenic retrovirus called human T-lymphotrophic virus type 1 (HTLV-1). Since then, HTLV-1 has been identified as the causative agent behind several diseases such as adult T-cell leukemia/lymphoma (ATL) and a HTLV-1 associated myelopathy or tropical spastic paraparesis (HAM/TSP). As part of its normal replication cycle, the genome is converted into DNA and integrated into the genome. With several hundreds to thousands of unique viral integration sites (VISs) distributed with indeterminate preference throughout the genome, detection of HTLV-1 VISs is a challenging task. Experimental studies typically use molecular biology …
Reconstructing Mutational Lineages In Breast Cancer By Multi-Patient-Targeted Single Cell Dna Sequencing,
2023
The Texas Medical Center Library
Reconstructing Mutational Lineages In Breast Cancer By Multi-Patient-Targeted Single Cell Dna Sequencing, Jake Leighton
The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)
Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer with high rates of metastasis and recurrence, where TNBC patients have a poor 5-year survival and ~50% are non-responsive to chemotherapy. Aneuploidy is a cancer hallmark that is pervasive in over 90% of breast cancer patients and is indicative of complex genomic rearrangements that are acquired during tumor initiation. Although copy number aberrations have been extensively studied in relation to aneuploidy and TNBC initiation, little is currently known regarding the timing and impact of single nucleotide variants (SNVs) contributing to these early transformative genomic events. Paramount to novel …
Physiological And Transcriptomic Responses Of Two Artemisia Californica Populations To Drought: Implications For Restoring Drought-Resilient Native Communities,
2023
Chapman University
Physiological And Transcriptomic Responses Of Two Artemisia Californica Populations To Drought: Implications For Restoring Drought-Resilient Native Communities, Hagop S. Atamian Dr., Jennifer L. Funk
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
As climate change brings drier and more variable rainfall patterns to many arid and semi-arid regions, land managers must re-assemble appropriate plant communities for these conditions. Transcriptome sequencing can elucidate the molecular mechanisms underlying plant responses to changing environmental conditions, potentially enhancing our ability to screen suitable genotypes and species for restoration. We examined physiological and morphological traits and transcriptome sequences of coastal and inland populations of California sagebrush (Artemisia californica), a critical shrub used to restore coastal sage scrub vegetation communities, grown under low and high rainfall environments. The populations are located approximately 36 km apart but …
The Genomic Dynamics Of Fermented Food Microbes,
2023
University of Massachusetts Amherst
The Genomic Dynamics Of Fermented Food Microbes, Katherine Chacon Vargas
Doctoral Dissertations
Along with the agriculture and domestication revolution, humans have utilized bacteria, yeasts, and molds for millennia in the production of traditionally fermented foods and beverages. Fermentation is a very ancient practice of high relevance nowadays since it contributes with a great variety of foods worldwide. Microbial fermentation allows metabolic transformation of the raw food materials leading to biochemical changes that played a key role in food preservation, health benefits, nutrition, flavors, and texture, among others. Food fermentation practices could diverge from traditional artisanal spontaneous fermentation to industrialize methods with specialized microbial starters and although fermented environments tend to be very …
Analysis Of Ssa4 Reporter Expression By Q-Pcr,
2023
Belmont University
Analysis Of Ssa4 Reporter Expression By Q-Pcr, Susveen Sharanshi, Rebecca Adams
Belmont University Research Symposium (BURS)
The synthesis of genome-encoded proteins via mRNA translation is integral to cell survival. In eukaryotes, such as S. cerevisiae, the mRNA that is produced in the nucleus must be exported to the cytoplasm for translation to occur, and this process is highly regulated. Specifically, the export of mRNA occurs via travel through nuclear pore complexes (NPCs), which are selective doorways embedded in the nuclear envelope. During cellular stress, such as heat shock, the cell needs to regulate gene expression to permit survival, and mRNA export is one step at which this occurs. At these high temperatures, a cell’s proteins …
Be-03 Effects Of Dietary Iron On Taxonomic Composition And Function Of The Zebrafish Gut Microbiome,
2023
Presbyterian College
Be-03 Effects Of Dietary Iron On Taxonomic Composition And Function Of The Zebrafish Gut Microbiome, Megan D. Whisonant, Jeremiah L. Jackson, Sam L. Evans, Stuart Gordon Ph.D.
SC Upstate Research Symposium
A healthy gut microbiota is essential to promote host health and well-being, therefore, effects of dietary components on the gut microbiome are important to investigate as the gastrointestinal tract can be a major route of infection. Iron—an essential component of heme and iron-sulfur proteins—plays a central role in many biological activities, including oxygen transport and cellular respiration.
In particular, the iron homeostasis system is one of the best characterized due to iron's causative relationship with iron-deficiency anemia. Dietary iron supplementation is a commonly used treatment for iron deficiency anemia; however, the known direct impacts of iron on the gut microbiome …
Acoustic Telemetry Provides Insights For Improving Conservation And Management At A Spawning Aggregation Site Of The Endangered Nassau Grouper (Epinephelus Striatus),
2023
University of the Virgin Islands
Acoustic Telemetry Provides Insights For Improving Conservation And Management At A Spawning Aggregation Site Of The Endangered Nassau Grouper (Epinephelus Striatus), Richard S. Nemeth, Elizabeth Kadison, Jonathan Jossart, Mahmood Shivji, Bradley Wetherbee, Jordan Matley
Biology Faculty Articles
Nassau grouper (Epinephelus striatus, Serranidae) were one of the most important fishery species in the Caribbean, but are now listed as critically endangered. Population collapse in most places occurred primarily by fishers targeting their spawning aggregation sites, where thousands of fish gathered during full moon periods from December to April. Identifying management options for protecting this vulnerable period is crucial for their survival. In the US Virgin Islands, we tagged 24 Nassau grouper with acoustic transmitters at a fish spawning aggregation (FSA) site called the Grammanik Bank, a 1.5 km2, marine protected area (MPA) closed each year from …
Margalefidinium Polykrikoides Cyst Resuspension In The Lafayette River, A Sub-Tributary Of The Chesapeake Bay,
2023
Old Dominion University
Margalefidinium Polykrikoides Cyst Resuspension In The Lafayette River, A Sub-Tributary Of The Chesapeake Bay, Gabrielle Greaney, Eduardo Perez Vega, Katherine Crider, Dreux Chappell, Kimberly Powell, Richard Hale, Peter Bernhardt, Margaret Mulholland
Undergraduate Research Symposium
Harmful Algal Blooms are a collection of algae in a body of water that can cause serious environmental issues and health problems in both people and aquatic organisms. Dinoflagellates are microscopic, unicellular, and eukaryotic organisms that are well known for forming harmful algal blooms because of eutrophication. Coastal Virginia suffers from HABs in the Chesapeake Bay and its tributaries. A common species of dinoflagellate, known as Margalefidinium polykrikoides exists in the Chesapeake Bay. The purpose of this study is to determine if sediment resuspension produced by wind generated surface gravity waves cause cysts (dinoflagellate resting stages) to be suspended into …
Functional Analysis Provides Insight Into Missing Heritability,
2023
WSU SOM Class of 2024
Functional Analysis Provides Insight Into Missing Heritability, Scott L. Baughan, Michael A. Tainsky, Fatima Darwiche
Medical Student Research Symposium
Accurate ascertainment of genetic risk can be potentially lifesaving for patients who inherit cancer promoting mutations. However, even with the most extensive panel testing clinically available, a large number of patients will test negative despite family history of cancer or test positive for a variant of unknown significance (VUS). For these patients, clinical management is complicated; patients want to know their risk, and may fear disease they are not at great risk for (benign VUS) or they may not be given access to potentially lifesaving early screening procedures (pathogenic VUS). ATM has proven a challenge to clinicians due to its …
Identifying Non-Traditional Slippery Sequences Associated With Translational Frameshifts,
2023
Purdue University
Identifying Non-Traditional Slippery Sequences Associated With Translational Frameshifts, Aaron J. Gin, Kari Lynn Clase
Graduate Industrial Research Symposium
Genetic frameshifts are a mutation in which
a nucleotide skip leads to a shift in the
reading frame. In viruses, these frameshifts
can be programmed using a slippery
sequence to bypass the stop codon
associated with the initial protein. This
allows for variable control of protein
expression. In bacteriophages, translational
frameshifts have been identified but only a
few have been proven experimentally. Using
experimental data and comparative
genomics, non-traditional slippery
sequences can be identified as assisting in
controlling the protein coding throughout
viruses. Novel slippery sequences can aid in
the understanding of protein expression in
biological environments and further the …
Functional Annotation Of The Animal Genomes:
An Integrated Annotation Resource For The
Horse,
2023
University of California- Davis
Functional Annotation Of The Animal Genomes: An Integrated Annotation Resource For The Horse, Sichong Peng, Anna R. Dahlgren, Callum G. Donnelly, Erin N. Hales, Jessica Lynn Petersen, Rebecca R. Bellone, Ted Kalbfleisch, Carrie J. Finno
Faculty Papers and Publications in Animal Science
The genomic sequence of the horse has been available since 2009, providing critical resources for discovering important genomic variants regarding both animal health and population structures. However, to fully understand the functional implications of these variants, detailed annotation of the horse genome is required. Due to the limited availability of functional data for the equine genome, as well as the technical limitations of short-read RNAseq, existing annotation of the equine genome contains limited information about important aspects of gene regulation, such as alternate isoforms and regulatory elements, which are either not transcribed or transcribed at a very low level. To …
Intellectual Disability Related To De Novo Germline Loss Of The Distal End Of The P-Arm Of Chromosome 17: A Case Report,
2023
Noorda College of Osteopathic Medicine
Intellectual Disability Related To De Novo Germline Loss Of The Distal End Of The P-Arm Of Chromosome 17: A Case Report, Eden Pope, Matthew Huertas, Amar Paul, Braden Cunningham, Matthew Jennings, Ryan Perry, Stephanie Chavez, John A. Kriak, Kyle B. Bills, David W. Sant
Annual Research Symposium
Hypothesis/Purpose: In this report we present a case of a 20-year-old female with congenital intellectual disability, stunted growth, and hypothyroidism. Competitive genetic hybridization (CHG) revealed a loss of 17p13.3, and the deletion was not present in either parent. This deletion has not previously been characterized, but mutations on the p-arm of chromosome 17 are responsible for Miller-Dieker Syndrome and Isolated Lissencephaly Sequence, both of which share symptoms in common with the patient.
Methods: Peripheral mononuclear cells (PBMCs) were used for karyotyping and competitive genetic hybridization (CHG). Bioinformatic analysis was carried out using the Genome Data Viewer (ncbi.nlm.nih.gov/genome/gdv).
Results: Karyotype was …
Vitamin C Contributes To Epigenetic Regulation Of Genes Related To Diabetic Retinopathy In Retinal Endothelial Cells,
2023
Noorda College of Osteopathic Medicine
Vitamin C Contributes To Epigenetic Regulation Of Genes Related To Diabetic Retinopathy In Retinal Endothelial Cells, Elizabeth L. Turner, Jonathon Reynolds, Walker Kay, Marianne Becnel, Matthew Conway, Alexander Kim, John A. Kriak, Kyle B. Bills, David W. Sant
Annual Research Symposium
No abstract provided.
Determination Of Feasibility And Plausibility Of Using Various Biological Samples For Remote Genetic Testing,
2023
Noorda College of Osteopathic Medicine
Determination Of Feasibility And Plausibility Of Using Various Biological Samples For Remote Genetic Testing, Cole Farnsworth, Molly Henley, Walker Kay, Varos Victer Manukyan, Jonathon Reynolds, John A. Kriak, Kyle B. Bills, David W. Sant
Annual Research Symposium
No abstract provided.
Effects Of B4galnt1 Expression On Metastatic Phenotype And Response To Treatment In Osteosarcoma Cell Lines,
2023
Roseman University of Health Sciences
Effects Of B4galnt1 Expression On Metastatic Phenotype And Response To Treatment In Osteosarcoma Cell Lines, Fatemeh Zareihajiabadi
Annual Research Symposium
No abstract provided.
Effects Of Post-Translational Histone Modifications On Transcription Rate,
2023
Roseman University of Health Sciences
Effects Of Post-Translational Histone Modifications On Transcription Rate, Aaron Bohn
Annual Research Symposium
No abstract provided.
Presentation Of Paired P- And Q-Arm Mosaic Deletions On Chromosome 18 Associated With Neuropsychiatric Symptoms,
2023
Noorda College of Osteopathic Medicine
Presentation Of Paired P- And Q-Arm Mosaic Deletions On Chromosome 18 Associated With Neuropsychiatric Symptoms, Jackson Nielsen, Laura Minor, John Dougherty Jr., Paige Moore, Kailee Edwards, Brandon Burrell, Jameson Williams, John A. Kriak, David W. Sant, Kyle B. Bills
Annual Research Symposium
No abstract provided.
Was Kaposi’S Sarcoma-Associated Herpesvirus Introduced Into
China Via The Ancient Silk Road? An Evolutionary Perspective,
2023
Fudan University
Was Kaposi’S Sarcoma-Associated Herpesvirus Introduced Into China Via The Ancient Silk Road? An Evolutionary Perspective, Zhenqiu Liu, Qiwen Fang, Jialu Zuo, Veenu Minhas, Charles Wood, Na He, Tiejun Zhang
Virology Papers
Kaposi’s sarcoma-associated herpesvirus (KSHV) has become widely dispersed worldwide since it was first reported in 1994, but the seroprevalence of KSHV varies geographically. KSHV is relatively ubiquitous in Mediterranean areas and the Xinjiang Uygur Autonomous Region, China. The origin of KSHV has long been puzzling. In the present study, we collected and analysed 154 KSHV ORF-K1 sequences obtained from samples originating from Xinjiang, Italy, Greece, Iran and southern Siberia using Bayesian evolutionary analysis in BEAST to test the hypothesis that KSHV was introduced into Xinjiang via the ancient Silk Road. According to the phylogenetic analysis, 72 sequences were subtype A …
Paternal Ages And Genetic Diseases And Congenital Anomalies,
2023
University of Central Florida
Paternal Ages And Genetic Diseases And Congenital Anomalies, Neda Hamood
The Pegasus Review: UCF Undergraduate Research Journal
he purpose of this research is to investigate the link between Advanced Paternal Ages (APA) (i.e., APA ≥ 35 years and APA ≥ 50 years) and genetic diseases and congenital anomalies. Currently, the relationship between both APA and genetic diseases and congenital anomalies remains unclear. There is room for improvement, however, to investigate systematically the relationship between specific congenital anomalies in newborns and APA. More recently, the link between APA (as opposed to existing studies analyzing Advanced Maternal Age alone) and genetic diseases has been recognized by researchers, epidemiologists, and various health experts. Thus, this study serves to examine the …
The Clinical And Genetic Spectrum Of Autosomal-Recessive Tor1a-Related Disorders,
2023
Harvard Medical School, United States
The Clinical And Genetic Spectrum Of Autosomal-Recessive Tor1a-Related Disorders, Afshin Saffari, Tracy Lau, Homa Tajsharghi, Ehsan Ghayoor Karimiani, Ariana Kariminejad, Stephanie Efthymiou, Giovanni Zifarelli, Tipu Sultan, Mehran Beiraghi Toosi, Shahnaz Ibrahim
Department of Paediatrics and Child Health
In the field of rare diseases, progress in molecular diagnostics led to the recognition that variants linked to autosomal-dominant neurodegenerative diseases of later onset can, in the context of biallelic inheritance, cause devastating neurodevelopmental disorders and infantile or childhood-onset neurodegeneration. TOR1A-associated arthrogryposis multiplex congenita 5 (AMC5) is a rare neurodevelopmental disorder arising from biallelic variants in TOR1A, a gene that in the heterozygous state is associated to torsion dystonia-1 (DYT1 or DYT-TOR1A), an early-onset dystonia with reduced penetrance. While 15 individuals with TOR1A-AMC5 have been reported (less than 10 in detail), a systematic investigation of the full disease-associated spectrum has …
