Genomics Commons^™

Systematics Of Disk-Winged Bats (Thyroptera), Courtney L. Klumpp

Capstone Showcase

This thesis investigates the evolutionary relationships among disk-winged bats in the genus Thyroptera, a small group of Neotropical bats known for the adhesive suction disks on their wings and feet that allow them to roost inside tightly rolled leaves. The distinctive morphology and behavior of these bats have not been extensively documented, and their phylogenetic relationships remain only partially resolved. The goal of this research is to better understand how these species are related to one another and to determine whether the five recognized species of Thyroptera form a single monophyletic group. To address this question, morphological and genetic …

Using Lrr Standard Deviation As A Genotype Quality Control Measure And Its Downstream Effect On Cnv Calling., Adam Dunne

ORBioM (Open Research BioSciences Meeting)

Background:

Log R Ratio (LRR) is a genotype intensity measurement returned alongside routine genotype results and used to detect structural variation in the genome known as copy number variation (CNVs). Although LRR standard deviation (SD) is commonly applied as a quality control measure in CNV studies, limited research has explored its effect on genotype quality and the potential impact on CNV calling.

Methods:

A total of 720,152 genotypes were available on 716,234 cattle. Among these were 1,044 cattle that had duplicate genotype samples where one sample was considered gold standard (LRR SD < 0.3, Call Rate ≥ 0.95). Genotype concordance was calculated for all duplicates. PennCNV was used to call CNVs and concordance among CNV calls per duplicate animal was determined using the Jaccard index.

Results:

Across all 720,152 cattle samples, the mean …

Diagnostic And Clinical Utility Of Oncoscan Microarray And Ngs-Based Sequencing In Pediatric Solid Tumors: Children’S Mercy Hospital’S Experience, Aravindh Nagarajan, Lisa Lansdon, Midhat Farooqi, Lei Zhang, Elena Repnikova

Research Days

This papers attempts to evaluate the diagnostic and clinical utility of microarray-based OS+ in detecting clinically relevant genetic alterations in FFPE solid tumor samples and to compare the yield of somatic mutation detection by WGS/WES in pediatric solid tumors at Children’s Mercy Hospital - Kansas City.

Early Hematopoietic Differentiation Of An Inducible Pluripotent Stem Cell Model Of Infant Lymphoblastic Leukemia, Meagan Vacek, Jacqelyn Nemechek, Irina Pushel, Bradley Thornton, Priyanka Kumar, Jay L. Vivian, John M. Perry

Research Days

This abstract describes our work regarding the differentiation of human inducible pluripotent stem cells into hematopoietic stem and progenitor cells as the groundwork for the development of a genomics driven inducible pluripotent stem cell model of KMT2A rearranged infant acute lymphoblastic leukemia.

Genome Analysis Of Aeromonas Hydrophila Strain S14-452, Zarin Tasnim Raya

Undergraduate Research Conference

The Aeromonas hydrophila are gram-negative, opportunistic bacteria that can infect many groups of organisms, mainly fish and amphibians. In channel catfish, A. hydrophila causes fatal bacterial septicemia, leading to massive economic losses for catfish farmers. Therefore, an understanding of its genome will aid in identifying its virulence factors, metabolic pathways and survival mechanisms within the host. This study details the draft genome sequence of A. hydrophila strain S14-452, isolated from channel catfish exhibiting bacterial septicemia during a disease outbreak at a catfish farm.

A. hydrophila strain S14-452 was sequenced using the Illumina iSeq 100 System. Assembly was performed with SPAdes, …

The Impact Of Temperature And Humidity On The Transcriptome Of Symbiochloris Reticulata In Relation To Lobaria Pulmonaria’S Genepools, Ioana Violeta Ardelean, Christoph Scheidegger, Mihai Miclaus

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

Woolly Mammoth Genomic Adaptations To The Extreme Climate Shifts Of The Ice Age, David Diez-Del-Molino

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

A Genomics Driven Induced Pluripotent Stem Cell Model Of Infant Acute Lymphoblastic Leukemia - Early Results, Meagan Vacek, Jacqelyn Nemechek, Irina Pushel, Bradley Thornton, Molly Leyda, Priyanka Prem Kumar, Midhat Farooqi, Jay L. Vivian, Erin M. Guest, John M. Perry

Research Days

While the cure rates for pediatric ALL have improved over the decades, infants with ALL (iALL) have not benefitted from these advances and continue to have a devastating prognosis. Unfortunately progress in treatment has also been slowed by inadequate research models. With this project, we address this unmet need by investigating a novel model to understand the cellular and molecular changes that occur during iALL onset and progression.

Characterisation Of Sex Chromosome Aneuploidy In Female Cattle Using Genotype Information, Cliona Ryan

ORBioM (Open Research BioSciences Meeting)

Background

Aneuploidy is a genetic condition characterized by the loss (monosomy) or gain (trisomy) of one or more chromosomes. Aneuploidy affecting the sex chromosomes often leads to infertility. The objective of this study was to estimate the prevalence of sex chromosome aneuploidy in a large juvenile population using routinely available genotype intensity information.

Methods

Genotype and genotype intensity data was available on 145,476 female dairy and beef cattle below 15 months of age at the time of genotyping, with no recorded progeny. Genotype intensity data included the LogR Ratio (LRR), R-value (the sum of X and Y SNP probe intensities), …

The Detection Of Putative Recessive Lethal Haplotypes In Irish Sheep Populations, Rory Mcauley

ORBioM (Open Research BioSciences Meeting)

In livestock populations, recessive lethal alleles are a known contributor to poor reproductive performance due to embryonic death in homozygous individuals. Despite their lethal effect in the recessive form, these alleles may be maintained at high frequencies among carrier animals because of their positive pleiotropic effects on economically important traits. Although several such recessive alleles have been identified in cattle and pig populations, limited studies have been completed in sheep, and none within Irish sheep populations. Genotype data for 69,034 animals from five major Irish sheep breeds genotyped on a variety of panels was available for this study. Only animals …

Multiple Rsv Strains Infecting Hep-2 And A549 Cells Reveal Cell Line-Dependent Differences In Resistance To Rsv Infection, Anubama Rajan, Felipe-Andres Piedra, Letisha Aideyan, Trevor Mcbride, Matthew Robertson, Hannah L. Johnson, Gina Marie Aloisio, David Henke, Cristian Coarfa, Fabio Stossi, Vipin Kumar Menon, Harshavardhan Doddapaneni, Donna Marie Muzny, Sara Joan Javornik Cregeen, Kristi Louise Hoffman, Joseph Petrosino, Richard A. Gibbs, Vasanthi Avadhanula, Pedro A. Piedra

Research Symposium

Background: Respiratory syncytial virus (RSV) is the major viral driver of a global pediatric respiratory disease burden disproportionately borne by the poor¹. Thus, RSV, like SARS-CoV-2, combines with congenital and environmental and host-history-dependent factors to create a spectrum of disease with greatest severity most frequently occurring in those least able to procure treatment.

Methods: Here we apply whole genome sequencing and a suite of other molecular biological techniques to survey host-virus dynamics in infections of two distinct cell lines (HEp2 and A549) with four strains representative of known RSV genetic diversity.

Results: We observed non-gradient patterns of RSV …

Microrna-34a And Long Non-Coding Rna Malat1 Is Associated With Hpv Status And Viral Load In Premalignant Cervical Lesions, Orlando Solis-Coronado, Juan A. García-Quiñones, Mariel Aracely Oyervides-Muñoz, Victor Treviño, Celia N. Sanchez-Dominguez, Antonio A. Pérez-Maya, Diana Cristina Perez-Ibave, Oscar Vidal-Gutierrez, Juan Francisco González-Guerero, Genaro A. Ramírez-Correa, María Lourdes Garza-Rodríguez

Research Symposium

Background: Cervical cancer (CC) is one of the most common gynecological malignancies in the world, and human papillomavirus (HPV) infection is the most important risk factor for their development. Although there are methods for the early detection of CC and HPV infection, but there are not highly sensitive and specific, for it´s necessary to investigate alternatives such as miR-34a and MALAT1, implicated in the pathogenesis of CC. The objective was to evaluate the association of HPV status, viral load, the presence of coinfections, and the grade of CC precursor lesions with miR-34a and MALAT1 expression in patients with high …

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, …

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 …

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.

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.

Genetic Variations In The Myostatin Gene Among Irish Cattle Breeds, Cliona Ann Ryan

ORBioM (Open Research BioSciences Meeting)

No abstract provided.

Development Of Cloning Vehicles For Expression Of Gc-Maf In Yeast, Tammy Tran, Seohyun Lee, Jane Yu, Wilson Wu

Pacific Undergraduate Research and Creativity Conference (PURCC)

No abstract provided.

Proteomic Analysis Of The Expression Of Masp1 Dragline Silk Protein In E. Coli, Sophie Rae Pazzo, Rajan Amit Patel, Kamrin Athwal, Edward Kim

Pacific Undergraduate Research and Creativity Conference (PURCC)

No abstract provided.

Spr-5; Met-2 Maternal Reprogramming Cooperates With The Dream Complex To Regulate Developmental Cell Fates, Jazmin Dozier, Sandra Nguyen, Brandon Carpenter

Symposium of Student Scholars

Histone methylation is a post-transcriptional modification to the N-terminal tails of histone core proteins that regulates DNA accessibility, and consequently, gene expression. Like DNA, histone methylation can be inherited between generations, and is highly regulated during embryonic development. At fertilization, histone methylation must undergo maternal reprogramming to reset the epigenetic landscape in the new zygote. During maternal reprogramming of histone methylation in the nematode, C. elegans, H3K4me (a modification associated with active transcription) is removed by the H3K4 demethylase, SPR-5, and H3K9me (a modification associated with transcriptional repression) is subsequently added by the histone methyltransferase, MET-2. Recently, it was …

Microbial Diversity And Community Structure In Sediments Associated With The Seagrass (Thallassia Testudinum) In Apalachicola Bay, Florida, Rahma Ahmed, Thomas Mcelroy, Troy Mutchler

Symposium of Student Scholars

Seagrass is an angiosperm which provides many ecosystem services in coastal areas, such as providing food, shelter and nurseries for many species, and decreasing the impact of waves on shorelines. A global assessment reported that 29% of known seagrass meadows are in a state of decline due to the effects of human activity. Seagrass is commonly found in shallow marine waters where they form meadows containing a microbiome that plays an important role in providing nutrients for seagrass growth, though little is known about the microorganisms within the seagrass meadow sediments. Our project collected sediments from seagrass meadows and adjacent …

Identification And Comparison Of Arbuscular Mycorrhizal Fungi And Soil Microbiomes Between American Chestnuts And Surrounding Hardwoods, Sarah Andrews, Geoffrey Eger, Isabella Vahle

Symposium of Student Scholars

Background/Questions/Methods

The introduction of the Chinese chestnut blight in 1904 decimated native American chestnut (Castanea dentata (Marshall) Borkh.) populations. In this study we aim to: 1) document the location of individual chestnuts in our vicinity; 2) document healthy versus blight infected individuals; 3) characterize putative differences in the soil microbiome between infected and non-infected individuals, as well as between chestnuts and hardwood neighbors. With this information we hope to provide new insights into mechanisms that may enhance blight and fungal resistance in American chestnuts through the understanding of the interactions between the trees and their surrounding soil microbiome.

Soil …

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 …