Genomics Commons^™

Precision Medicine, Ancestry, Genetics And Race, Lucio Miele

School of Medicine Faculty Publications

DiscoverBMB, March 25 - 28, 2023, Seattle, WA

Physio-Psycho-Social Interaction Mechanism In Dyadic Health Of Young And Middle-Aged Stroke Survivors And Their Spousal Caregivers: A Longitudinal Observational Study Protocol, Dandan Xiang, Zhen-Xiang Zhang, Song Ge, Wen Na Wang, Bei-Lei Lin, Su-Yan Chen, Er-Feng Guo, Peng-Bo Zhang, Zhi-Wei Liu, Hui Li, Yong-Xia Mei

Faculty, Staff and Student Publications

Introduction: In recent years, stroke has become more common among young people. Stroke not only has a profound impact on patients' health but also incurs stress and health threats to their caregivers, especially spousal caregivers. Moreover, the health of stroke survivors and their caregivers is interdependent. To our knowledge, no study has explored dyadic health of young and middle-aged stroke survivors and their spousal caregivers from physiological, psychological and social perspectives. Therefore, this proposed study aims to explore the mechanism of how physiological, psychological and social factors affect dyadic health of young and middle-aged stroke survivors and their spousal caregivers. …

A Rare Metastatic Mesenteric Malignant Pecoma With Tsc2 Mutation Treated With Palliative Surgical Resection And Nab-Sirolimus: A Case Report, Luke Meredith, Timothy Chao, Avinoam Nevler, Atrayee Basu Mallick, Rajan Singla, Peter Mccue, Wilbur Bowne, Wei Jiang, Md, Phd

Kimmel Cancer Center Faculty Papers

BACKGROUND: Malignant perivascular epithelioid cell tumors (PEComas) are exceedingly rare malignant mesenchymal neoplasms with characteristic morphological and immunohistochemical (IHC) patterns. However, some malignant PEComas are poorly differentiated with atypical histopathological features, making a definitive diagnosis difficult. PEComas are most commonly found in females and often show either TSC1 or TSC2 alterations, which result in the activation of the mTOR pathway, or TFE3 fusions. Given these molecular characteristics, mTOR inhibitors have recently been approved by the FDA in the treatment of malignant PEComas, particularly in those with TSC1/2 alterations. Therefore, molecular analyses may be helpful for both the diagnostic workup of …

The Genomics Of Autism-Related Genes Il1rapl1 And Il1rapl2: Insights Into Their Cortical Distribution, Cell-Type Specificity, And Developmental Trajectories, Jacob Weaver

MUSC Theses and Dissertations

Neuropsychiatric disorders have a significant impact on modern society. These disorders affect a large percentage of the population: schizophrenia has a world-wide prevalence of 1% and autism spectrum disorders (ASD) affects 1 in 59 school-aged children in the US. There is substantial evidence that most neuropsychiatric disorders have a genetic component. Thus, with the advent of high throughput sequencing much effort has gone into identifying genetic variants associated with these disorders. The emerging picture from these studies is a complex one where hundreds of genes with small effects interact with a varied landscape of common variants to result in disease. …

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 …

Anomalies In The Mitochondrial Genomes Of Members Of Aliciidae, Boloceroididae, And Gonactiniidae (Actiniaria:Metridioidea), Isabel Pen

2023 Midwest Ecology & Evolution Conference

Analysis of gene sequences from three mitochondrial and two nuclear genes for a broad sampling of actiniarian taxa proposed a novel grouping of the families Aliciidae, Boloceroididae, and Gonactiniidae. (Rodríguez et al., 2014). Although previously unlinked, the association of these taxa was credible given the consistency of the genetic data and the shared occurrence of anatomical traits, including complex column structures (Aliciidae and Boloceroididae), tentacular sphincters (Boloceroididae and Gonactiniidae), and retention of juvenile musculature in adults (Boloceroididae and Gonactiniidae). Although the mitochondrial genome structure of actiniarians is generally conserved, complete mitochondrial genomes identify unusual gene orders (Alicia sansibarensis: …

Everything But The Lab Sink: Using 1,000 Phylogenomically Informative Markers To Resolve Historically Messy Species Groups In Anastrepha Fruit Flies (Diptera: Tephritidae), Kristie J. Schmidt

2023 Midwest Ecology & Evolution Conference

The genus Anastrepha (Diptera: Tephritidae) is long overdue for a major taxonomic revision. Of the 22 recognized species groups within Anastrepha, only ~5 are well supported clades. Molecular methods, such as traditionally used mitochondrial DNA markers, have been unsuccessful at elucidating relationships amongst Anastrepha species; therefore, a more robust phylogenomic tool is likely necessary. To accomplish this, we used Highly Multiplexed Amplicon-based Phylogenomics (HiMAP) to identify 1,000 phylogenomically informative nuclear markers. Post sequencing, we obtained data for 500+ amplicons for 90 Anastrepha spp. belonging to 18 Anastrepha species groups. Our findings agree with some aspects of the most recently …

Convergent Evolution Of Antifreeze Proteins In Two Insect Families Supported By Whole Genome And Gene Family Loci Analyses, Shaw Kagawa

2023 Midwest Ecology & Evolution Conference

Various Coleoptera (beetles) and Lepidoptera (moths) insects are known to produce highly active antifreeze peptides (AFPs), an adaptive trait that enabled them to avoid freezing and survive severe winters. These include the grain pest Tenebrio molitor (yellow mealworm), pine-boring Rhagium beetles, the fire-colored Dendroides beetles, a stag beetle, and the Choristoneura spruce budworms (moths). Insect AFPs are small peptides of ~8 to 15 kDa, consisting of several tandem 13-amino acid repeats of similar sequences, each ending with a conserved tripeptide Thr-Cys/aa-Thr motif, found to be important for ice binding. Except for the eastern spruce budworm, the evolutionary origin/s and process/es …

Novel Model For Tau Protein Expression And Function: The Honeybee Brain, Abdallah F. Sher

2023 Midwest Ecology & Evolution Conference

Scientists have long attempted to understand the mechanisms by which senescence occurs. Leading theories suggest that aging is an emergent property of natural selection’s prioritization of reproductive ability. Social insects, such as the honeybee (Apis mellifera) challenge this idea, separating colonies into reproductive and non-reproductive castes. Worker honeybees do not reproduce, suggesting that selection prioritizes tasks other than reproduction. Forager honeybees, for example, display improved cognitive and immune function compared to other behavioral phenotypes of bees, likely to support their ability to perform tasks such as navigating complex environments or making context-dependent decisions while foraging. Foragers are normally older honeybees, …

Geographic Analysis Of Sex Chromosome Polymorphism In The Virginian Wild Strawberry, Trezalka A. Budinsky

2023 Midwest Ecology & Evolution Conference

The evolution of sex chromosomes is a ubiquitous and essential diversifying mechanism in eukaryotes. Yet early stages of sex-chromosome differentiation are poorly understood. The subdioecious octoploid, Fragaria virginiana, provides a rare opportunity to study the beginnings of sex chromosome evolution due to its young, polymorphic ZW sex system. Females are ZW and males/hermaphrodites are ZZ. F. virginiana has a small sex-determining region (SDR) located on the female W chromosome that has undergone three transposition events between the strawberry's four subgenomes, resulting in three SDR haplotypes: alpha (the result of a first transposition and closest to a pre-sex chromosome ancestral …

Potential Loss Of Pheromone Receptors In The Red Milkweed Beetle, Tetraopes Tetrophthalmus (Coleoptera: Cerambycidae), Mathew A. Price

2023 Midwest Ecology & Evolution Conference

The family of longhorn beetles (Coleoptera: Cerambycidae) are characterized by their elongate antennae, which are well adapted for detecting volatile compounds. This makes them an ideal family to study odorant receptor genes (ORs), which are the rapidly evolving family of proteins that are used by insects to detect odors at the molecular level. Here, we present data on 48 ORs we have sequenced and annotated from an antennal transcriptome of a male red milkweed beetle, Tetraopes tetrophthalmus. In contrast to most cerambycids, T. tetrophthalmus is not known to produce long-range sex pheromones to attract or select mates; correspondingly, …

Renal-Hepatic-Pancreatic Dysplasia Type 2: Perinatal Lethal Condition Or A Multisystemic Disorder With Variable Expressivity, Kathryn Gunther, Essam M Imseis, Joyce P Samuel, Elizabeth A Hillman, Tiina H Ojala, Timo Jahnukainen, Paul R Hillman

Faculty, Staff and Student Publications

BACKGROUND: Renal-hepatic-pancreatic dysplasia type 2 (RHPD2) is a rare condition that has been described in the literature disproportionately in perinatal losses. The main features of liver and kidney involvement are well described, with cardiac malformations and cardiomyopathy adding additional variation to the phenotype. Many patients reported are within larger cohorts of congenital anomalies of kidney and urinary tract (CAKUT) or liver failure, and with minimal phenotypic and clinical course data.

METHODS: An independent series of phenotypes and prognosis was aggregated from the literature. In this literature review, we describe an additional patient with RHPD2, provide a clinical update on the …

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 …

Rare Variant Enrichment Analysis Supports Greb1l As A Contributory Driver Gene In The Etiology Of Mayer-Rokitansky-Küster-Hauser Syndrome, Angad Jolly, Haowei Du, Christelle Borel, Na Chen, Sen Zhao, Christopher M Grochowski, Ruizhi Duan, Jawid M Fatih, Moez Dawood, Sejal Salvi, Shalini N Jhangiani, Donna M Muzny, André Koch, Konstantinos Rouskas, Stavros Glentis, Efthymios Deligeoroglou, Flora Bacopoulou, Carol A Wise, Jennifer E Dietrich, Ignatia B Van Den Veyver, Antigone S Dimas, Sara Brucker, V Reid Sutton, Richard A Gibbs, Stylianos E Antonarakis, Nan Wu, Zeynep H Coban-Akdemir, Lan Zhu, Jennifer E Posey, James R Lupski

Faculty, Staff and Student Publications

Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by aplasia of the female reproductive tract; the syndrome can include renal anomalies, absence or dysgenesis, and skeletal anomalies. While functional models have elucidated several candidate genes, only WNT4 (MIM: 603490) variants have been definitively associated with a subtype of MRKH with hyperandrogenism (MIM: 158330). DNA from 148 clinically diagnosed MRKH probands across 144 unrelated families and available family members from North America, Europe, and South America were exome sequenced (ES) and by family-based genomics analyzed for rare likely deleterious variants. A replication cohort consisting of 442 Han Chinese individuals with MRKH was …

Protocol To Identify The Core Gene Supported By An Essential Gene In E. Coli Bacteria Using A Genome-Wide Suppressor Screen, Isao Masuda, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

We describe here a genome-wide screening approach to identify the most critical core reaction among a network of many that are supported by an essential gene to establish cell viability. We describe steps for maintenance plasmid construction, knockout cell construction, and phenotype validation. We then detail isolation of suppressors, whole-genome sequencing analysis, and reconstruction of CRISPR mutants. We focus on E. coli trmD, which encodes an essential methyl transferase that synthesizes m1G37 on the 3'-side of the tRNA anticodon. For complete details on the use and execution of this protocol, please refer to Masuda et al. (2022).

Srtsim: Spatial Pattern Preserving Simulations For Spatially Resolved Transcriptomics, Jiaqiang Zhu, Lulu Shang, Xiang Zhou

Faculty, Staff and Student Publications

Spatially resolved transcriptomics (SRT)-specific computational methods are often developed, tested, validated, and evaluated in silico using simulated data. Unfortunately, existing simulated SRT data are often poorly documented, hard to reproduce, or unrealistic. Single-cell simulators are not directly applicable for SRT simulation as they cannot incorporate spatial information. We present SRTsim, an SRT-specific simulator for scalable, reproducible, and realistic SRT simulations. SRTsim not only maintains various expression characteristics of SRT data but also preserves spatial patterns. We illustrate the benefits of SRTsim in benchmarking methods for spatial clustering, spatial expression pattern detection, and cell-cell communication identification.

A Biallelic Frameshift Indel In Ppp1r35 As A Cause Of Primary Microcephaly, Moez Dawood, Gulsen Akay, Tadahiro Mitani, Dana Marafi, Jawid M Fatih, Alper Gezdirici, Hossein Najmabadi, Kimia Kahrizi, Jaya Punetha, Christopher M Grochowski, Haowei Du, Angad Jolly, He Li, Zeynep Coban-Akdemir, Fritz J Sedlazeck, Jill V Hunter, Shalini N Jhangiani, Donna Muzny, Davut Pehlivan, Jennifer E Posey, Claudia M B Carvalho, Richard A Gibbs, James R Lupski

Faculty, Staff and Student Publications

Protein phosphatase 1 regulatory subunit 35 (PPP1R35) encodes a centrosomal protein required for recruiting microtubule-binding elongation machinery. Several proteins in this centriole biogenesis pathway correspond to established primary microcephaly (MCPH) genes, and multiple model organism studies hypothesize PPP1R35 as a candidate MCPH gene. Here, using exome sequencing (ES) and family-based rare variant analyses, we report a homozygous, frameshifting indel deleting the canonical stop codon in the last exon of PPP1R35 [Chr7: c.753_*3delGGAAGCGTAGACCinsCG (p.Trp251Cysfs*22)]; the variant allele maps in a 3.7 Mb block of absence of heterozygosity (AOH) in a proband with severe MCPH (-4.3 SD at birth, -6.1 SD by …

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, 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, 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.