Genetics and Genomics Commons^™

Longitudinal Assessment Of The Bovine Ocular Bacterial Community Dynamics In Calves, Alison Bartenslager, Nirosh D. Aluthge, John Dustin Loy

Department of Animal Science: Faculty Publications

Background: Infectious Bovine Keratoconjunctivitis (IBK), commonly known as pinkeye, is one of the most significant diseases of beef cattle. As such, IBK costs the US beef industry at least 150 million annually. However, strategies to prevent IBK are limited, with most cases resulting in treatment with antibiotics once the disease has developed. Longitudinal studies evaluating establishment of the ocular microbiota may identify critical risk periods for IBK outbreaks or changes in the microbiota that may predispose animals to IBK.

Results: In an attempt to characterize the establishment and colonization patterns of the bovine ocular microbiota, we conducted a longitudinal study …

Utilizing An Electronic Feeder To Measure Individual Mineral Intake, Feeding Behavior, And Growth Performance Of Cow–Calf Pairs Grazing Native Range, Kacie L. Mccarthy, Michael Undi, Stephanie Becker, Carl R. Dahlen

Department of Animal Science: Faculty Publications

Crossbred Angus cow–calf pairs (n = 28 pairs) at the Central Grasslands Research Extension Center (Streeter, North Dakota) were used to evaluate an electronic feeder to monitor individual mineral intake and feeding behavior and their relationship with growth performance and liver mineral concentrations. Cows and calves were fitted with radio frequency identification ear tags that allowed access to an electronic feeder (SmartFeed system; C-Lock Inc., Rapid City, South Dakota) and were provided ad libitum minerals (Purina Wind and Rain Storm, Land O’Lakes, Inc., Arden Hills, MN). Mineral intake, number of visits, and duration at the feeder were recorded over …

A New Vine Snake (Reptilia, Colubridae, Oxybelis) From Peru And Redescription Of O. Acuminatus, Robert C. Jadin, Michael J. Jowers, Sarah A. Orlofske, William E. Duellman, Christopher Blair, John C. Murphy

Publications and Research

The Brown Vine Snake, Oxybelis aeneus, was until recently considered a single species, distributed from southern Arizona through the Neotropics into southeastern Brazil. However, newly conducted research restructured the species with a substantial taxonomic revision, recognizing five additional taxa (i.e. O. koehleri, O. microphthalmus, O. potosiensis, O. rutherfordi, O. vittatus) in this species complex. This revision focused on populations in North America, Central America, and northern South America while neglecting the southern portion of its distribution. Here, we examine the taxonomic history of the complex and use it along with specimen data to resurrect O. acuminatus from southeastern Brazil. Finally, …

Single-Locus Species Delimitation And Ecological Niche Modeling Provide Insights Into The Evolution, Historical Distribution, And Taxonomy Of The Pacific Chorus Frogs, Robert C. Jadin, Sarah A. Orlofske, Tereza Jezkova, Christopher Blair

Publications and Research

The Pacific chorus frogs are a complex of three wide-ranging species (i.e. Hyliola hypochondriaca, Hyliola regilla, Hyliola sierra) whose current taxonomy remains unresolved. We conducted species delimitation analyses of these taxa using fragments of the cytochrome b and 12S–16S mtDNA genes to assess the species diversity. Importantly, we included samples from new locations throughout the range to better understand species distributions and identify potential contact zones among clades. Our analyses revealed three slightly parapatric but distinct species-level clades. Molecular dating revealed that these species began diverging in the Pleistocene c. 1.4 Mya with H. hypochondriaca and …

Age, Growth, And Mortality Of Atlantic Tripletail In The North-Central Gulf Of Mexico, Amanda E. Jefferson, Matthew B. Jargowsky, Meagan N. Schrandt, Pearce T. Cooper, Sean P. Powers, John Dindo, J. Marcus Drymon

University Faculty and Staff Publications

In the southeastern USA and the Gulf of Mexico (GOM), Atlantic Tripletail Lobotes surinamensis are increasingly targeted by recreational anglers, indicating that stock status should be assessed. A critical need for such assessments is age-specific data; however, previous studies have drawn conflicting conclusions regarding the most appropriate structure for aging. Moreover, growth parameters and mortality rates for GOM Atlantic Tripletail are unknown. Therefore, the goals of this study were to (1) evaluate sagittal otoliths and first dorsal spines as aging structures; (2) model combined and sex-specific growth; and (3) estimate mortality rates for GOM Atlantic Tripletail. From 2012 to 2019, …

Psxii-19 Urine Metabolomics Analysis Associated With Feed Efficiency On Crossbred Steers During The Growing And Finishing Period On Forage- And Concentrate- Based Diets., Virginia M. Artegoitia, John Newman, Ronald M. Lewis, Andrew P. Foote, Harvey C. Freetly

Department of Animal Science: Faculty Publications

A discovery project to identify non‐invasive biomarkers that can detect subtle metabolic discrepancies for cattle feed efficiency was performed using untargeted and targeted urine metabolomics by ultra-performance liquid chromatography-mass spectrometry. Individual feed intake and body weight gain were measured in crossbred steers (n = 80) on a forage-based growing ration (stage-1) followed by a high-concentrate diet finishing ration (stage- 2). Urine was collected on study days 0, 21, 42, 63, and 83 for each dietary stage. In total, 28 steers with the greatest and the least average daily-gain (ADG) within 0.32 SD of the mean of dry-matter-intake (DMI) were used. …

Epigenetic Clock And Methylation Study Of Oocytes From A Bovine Model Of Reproductive Aging, Pawel Kordowitzki, Amin Haghani, Joseph A. Zoller, Caesar Z. Li, Ken Raj, Matthew L. Spangler, Steve Horvath

Department of Animal Science: Faculty Publications

Cattle are an attractive animal model of fertility in women due to their high degree of similarity relative to follicle selection, embryo cleavage, blastocyst formation, and gestation length. To facilitate future studies of the epigenetic underpinnings of aging effects in the female reproductive axis, several DNA methylation-based biomarkers of aging (epigenetic clocks) for bovine oocytes are presented. One such clock was germane to only oocytes, while a dual-tissue clock was highly predictive of age in both oocytes and blood. Dual species clocks that apply to both humans and cattle were also developed and evaluated. These epigenetic clocks can be used …

Relationship Between Urinary Energy And Urinary Nitrogen Or Carbon Excretion In Lactating Jersey Cows, D. L. Morris, Jeffrey L. Firkins, C. Lee, W. P. Weiss, Paul J. Kononoff

Department of Animal Science: Faculty Publications

Measurement of urinary energy (UE) excretion is essential to determine metabolizable energy (ME) supply. Our objectives were to evaluate the accuracy of using urinary N (UN) or C (UC) to estimate UE and ultimately improve the accuracy of estimating ME. Individual animal data (n = 433) were used from 11 studies with Jersey cows at the University of Nebraska–Lincoln, where samples were analyzed after drying (n = 299) or on an as-is basis (n = 134). Dried samples resulted in greater estimated error variance compared with as-is samples, and thus only as-is samples were used for final models. The as-is …

Distribution And Diversity Of Heliothine And Other Lepidopteran Nudiviruses, Emrah Ozel

Theses and Dissertations--Entomology

Helicoverpa zea nudivirus 2 (HzNV-2) is the only known sterilizing and sexually-transmitted insect virus and causes pathological symptoms in H. zea reproductive tissues. HzNV-2 has features that make it a candidate as a H. zea (corn earworm) control agent, such as the ability to cause asymptomatic (latent) and symptomatic (lytic) infections and the ability to influence mating behavior of its host to favor virus spread. HzNV pathology has been studied and its genome sequenced, however, its prevalence in natural populations is largely unknown. In this study, we developed and used a low-cost PCR-based molecular survey to investigate HzNV-2 prevalence and …

24andmore: Using Genome-Wide Snps To Investigate The Genetic Diversity Of Iowa Walleye (Sander Vitreous) Broodstock, Rachel Ann Mcdonnell

Dissertations and Theses @ UNI

The stocking of Sander vitreus in Iowa waterbodies is one of the primary tools used by the Iowa Department of Natural Resources (DNR) to ensure healthy populations for enjoyable fishing experiences. A substantial amount of time and money goes into this effort, so stocking efficiency is vital. Knowledge of genetic diversity contained in the broodstock increases this efficiency by having a better understanding of which strain will survive and contribute to the fishery in certain environments. The objective of this study is to investigate the genetic diversity of Iowa S. vitreus broodstock to identify genetic ancestry and quantify the genetic …

Exploring The Genetic Variability Of Zebra Mussels Dreisenna Polymoprha, Maxwell Carr

Journal of Earth and Life Science

Zebra Mussels Dreisenna polymorpha are one of the most well-known invasive species here in the United States. This species can take over watersheds very quickly, causing damage to both the ecosystem and man-made structures. The basic physical behavior of this species has been well documented, but the invasive North American Zebra Mussel is much more aggressive and therefore causes more damage in the Great Lakes region compared to its native waters. Genetic variation may be playing a very large role in how and why D. polymorpha is causing such large problems for stakeholders in the United States. This review cites …

Enviromental Dna Analysis Of A Critically Endangered Cavefish, Katelyn Gitner

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Solifuge (Camel Spider) Reproductive Biology: An Untapped Taxon For Exploring Sexual Selection, Alfredo V. Peretti, David E. Vrech, Eileen Hebets

Eileen Hebets Publications

The exploration of new and diverse animal groups in the study of sexual selection is both necessary and important to help better understand broad patterns and test sexual selection hypotheses regarding the evolutionary origins and maintenance of reproductive tactics and associated traits. Solifuges are, in this matter, an exceptional group and very little explored from the sexual selection point of view. At first glance, mating is apparently quite simple and conserved within this arachnid order, but solifuge reproductive behavior is unique among arachnids and more diverse than previously thought. In particular, these voracious animals appear to exhibit high sexual conflict, …

Spiders (Araneae) Collected As Prey By The Mud-Dauber Wasps Sceliphron Caementarium And Chalybion Californicum (Hymenoptera: Sphecidae) In Southeastern Nebraska1, Tyler B. Corey, Earl Agpawa, Eileen Hebets

Eileen Hebets Publications

Predator diets represent a potential interaction between local prey availability, prey antipredator defenses, and predator foraging behavior. Female spider-specialist muddauber wasps (Hymenoptera: Sphecidae) collect spiders and provision them intact, but paralyzed, to their developing larvae, providing a unique means of quantifying the diversity and abundance of prey that they capture. Mud-dauber wasps are hypothesized to be a major source of selection on antipredator defenses in web-building spiders, and the spiny and thickened abdomens of female spiny orb-weaving spiders (Araneae: Araneidae) are hypothesized to function as antiwasp defenses. We inventoried spider prey from nests of the mud-dauber wasps Sceliphron caementarium (Drury) …

Multisensory Integration Supports Configural Learning Of A Home Refuge In The Whip Spider Phrynus Marginemaculatus, Kaylyn A.S. Flanigan, Daniel D. Wiegmann, Eileen Hebets, Verner Peter Bingman

Eileen Hebets Publications

Predator diets represent a potential interaction between local prey availability, prey antipredator defenses, and predator foraging behavior. Female spider-specialist muddauber wasps (Hymenoptera: Sphecidae) collect spiders and provision them intact, but paralyzed, to their developing larvae, providing a unique means of quantifying the diversity and abundance of prey that they capture. Mud-dauber wasps are hypothesized to be a major source of selection on antipredator defenses in web-building spiders, and the spiny and thickened abdomens of female spiny orb-weaving spiders (Araneae: Araneidae) are hypothesized to function as antiwasp defenses. We inventoried spider prey from nests of the mud-dauber wasps Sceliphron caementarium (Drury) …

Visual Control Of Refuge Recognition In The Whip Spider Phrynus Marginemaculatus, Kaylyn A.S. Flanigan, Daniel D. Wiegmann, Patrick Casto, Vincent J. Coppola, Natasha R. Flesher, Eileen Hebets, Verner Peter Bingman

Eileen Hebets Publications

Amblypygids, or whip spiders, are nocturnally active arachnids which live in structurally complex environments. Whip spiders are excellent navigators that can re-locate a home refuge without relying on visual input. Therefore, an open question is whether visual input can control any aspect of whip spider spatial behavior. In the current study, Phrynus marginemaculatus were trained to locate an escape refuge by discriminating between differently oriented black and white stripes placed either on the walls of a testing arena (frontal discrimination) or on the ceiling of the same testing arena (overhead discrimination). Regardless of the placement of the visual stimuli, the …

Identification And Quantification Of 11 Airborne Biochemicals Emitted By The Brown Recluse And Another Primitive Hunting Spider Using Headspace Solid-Phase Microextraction-Gc/Ms, Zachary Foulks, Jennifer Parks, William Stoecker, Charles Kristensen, Eileen A. Hebets, Honglan Shi

Eileen Hebets Publications

Loxosceles reclusa, or brown recluse spider, is a harmful household spider whose habitat extends throughout the Midwest in the USA and other regions in the world. The pheromones and other biomolecules that facilitate signaling for brown recluses and other spider species are poorly understood. A rapid and sensitive method is needed to analyze airborne spider signaling biomolecules to better understand the structure and function of these biochemicals in order to control the population of the spiders. In this study, we developed a novel headspace solid-phase microextraction (HS-SPME)-GC/MS method to analyze potential pheromones and biomolecules emitted by the brown recluse …

Will There Be Changes In Sexually Differentiated Behaviors In Mice Manipulated For The Sry Gene As They Mature Into Adultood?, Subin Joo

CMC Senior Theses

Sexually differentiated behavior has been shown to be affected by both genes and hormones. The discovery of the SRY gene, which codes for the development of testes, lead to the development of the Four Core Genotypes model of mice, and the separation of sex chromosomes and its resulting gonadal hormones. Using the FCG model, this study aims to look at the development of sexually differentiated behavior in mice, and track how it changes throughout their life. FCG mice will be divided into individual and social housing, and repeated experiments carried out to test their reaction to both intact female and …

A Spatiotemporal Assessment Of Fish Assemblage Response To Land-Use Change And The Evaluation Of Edna Metabarcoding For Describing Diverse Fish Communities, Timothy M. Owen

Theses and Dissertations

Fish assemblages are often assessed as a biological proxy for environmental health. While humans value healthy environments for the ecosystem services and recreational opportunities they provide, it is increasingly evident that such resources can be paradoxically degraded by anthropogenic activities. In this investigation, we studied the relationship between different intensities of anthropogenic land-use change and habitat-driven fish assemblage response across multiple spatiotemporal scales. Secondarily, we explored the efficacy of eDNA metabarcoding against conventional electrofishing techniques for the purpose of describing complete fish communities. This study was conducted in the Tuckahoe Creek basin near Richmond, Virginia. This James River tributary serves …

Population Genetics Of A Reintroduced Fisher (Pekania Pennanti) Population In West Virginia, Caroline E. Harms

Graduate Theses, Dissertations, and Problem Reports (ETD)

Fishers (Pekania pennanti) were reintroduced in West Virginia in 1969 with no population wide genetic analysis ever having been conducted. Genetic analysis of reintroduced populations is vital to assess genetic diversity as an indicative of population viability. My objective was to collect fisher samples throughout West Virginia, nearby states where fisher may be migrating (PA and NY), and the New Hampshire source population to provide a full genetic interpretation of the reintroduced West Virginia population. Genetic analysis was used to measure genetic diversity, admixture or delineation of subpopulations, and effective population size. Sample location and genetic data were …

Ogre-Faced, Net-Casting Spiders Use Auditory Cues To Detect Airborne Prey, Jay A. Stafstrom, Gil Menda, Eya I. Nitzany, Eileen A. Hebets, Ronald R. Hoy

Eileen Hebets Publications

Prey-capture behavior among spiders varies greatly from passive entrapment in webs to running down prey items on foot. Somewhere in the middle are the ogre-faced, net-casting spiders (Deinopidae: Deinopis) that actively capture prey while being suspended within a frame web. Using a net held between their front four legs, these spiders lunge downward to ensnare prey from off the ground beneath them. This “forward strike” is sensorially mediated by a massive pair of hypersensitive, night-vision eyes. Deinopids can also intercept flying insects with a “backward strike,” a ballistically rapid, overhead back-twist, that seems not to rely on visual cues. Past …

Investigation Of Sulfur Cycling In Marine Sponge Cinachyrella Spp. From A South Florida Reef, Shelby K. Cain

All HCAS Student Capstones, Theses, and Dissertations

Symbionts within marine sponges are actively participating in the biogeochemical cycles. Among them, the role of symbiont microbes in the sulfur cycle remains a mystery. This study measured the abundance of microbes within the genus Cinachyrella before and after exposure to hydrogen sulfide. A four-part study was conducted: a) five-hour drop experiments, b) vertical distribution experiments, c) five-hour uptake experiments, and d) long-term exposure experiments. The five-hour drop experiment utilized a microsensor to measure sulfide levels, which was lowered 1.0 mm every thirty minutes for a total of 5 hours. Three trials were performed, each with one sponge and a …

Novel Polymorphisms Of Zrsr2 And Gpm6b Gene Homologs And Their Use In Sex Identification Of Bovine And Porcine Species, Evan K. Peterson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Accurate and cost-effective PCR based sex identification is important in animal production because it gives producers the ability to determine the sex of embryos prior to transfer, saving time and money. The most efficient PCR sex identification assays work by using a single primer pair to amplify a specific target region located on the Y-chromosome and a second, separate target region on the X-chromosome.

This thesis reports the design of two novel assays. The first assay was designed to target the Zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2 (ZRSR2) gene found on the X-chromosome and its Y-chromosome …

A Transgenic Pig Model Expressing A Cmv-Zsgreen1 Reporter Across An Extensive Array Of Tissues, Amy T. Desaulniers, Rebecca A. Cederberg, Elizabeth P. Carreiro, Channabasavaiah B. Gurumurthy, Brett R. White

Department of Animal Science: Faculty Publications

Since genetic engineering of pigs can benefit both biomedicine and agriculture, selecting a suitable gene promoter is critically important. The cytomegalovirus (CMV) promoter, which can robustly drive ubiquitous transgene expression, is commonly used at present, yet recent reports suggest tissue-specific activity in the pig. The objective of this study was to quantify ZsGreen1 protein (in lieu of CMV promoter activity) in tissues from pigs harboring a CMV-ZsGreen1 transgene with a single integration site. Tissue samples (n=35) were collected from neonatal hemizygous (n=3) and homozygous (n=3) piglets and ZsGreen1 abundance was determined via immunoblotting. ZsGreen1 was detected in all tissues, except …

Using Triallelic Snps For Determining Parentage In North American Yak (Bos Grunniens) And Estimating Cattle (B. Taurus) Introgression, Theodore S. Kalbfleisch, Jessica L. Petersen, R. G. Tait Jr., Jiansheng Qiu, Veronica Basnayake, Peter H. Hackett, Michael P. Heaton

Department of Animal Science: Faculty Publications

Background: Genetic testing for pedigree accuracy is critical for managing genetic diversity in North American (NA) yak (Bos grunniens ), a population expanded mostly from imported zoological park specimens. DNA testing also enhances species conservation by identifying recent B. taurus F1 hybrid ancestors (within three generations). Biallelic single nucleotide polymorphisms (SNPs) can accomplish either task, but increases the marker count and costs necessary to achieve both. Our aim was to identify novel, multifunctional, triallelic yak SNPs (tySNPs), with each having two alleles for yak parentage testing, and a third allele for identifying recent cattle introgression.

Methods: Genome sequences were …

Exploring A Novel Substrate-Borne Vibratory Signal In The Wolf Spider Schizocosa Floridana, Malcolm F. Rosenthal, Eileen Hebets, Rowan H. Mcginley, Cody Raiza, James Starrett, Lin Yan, Damian O. Elias

Eileen Hebets Publications

Animals communicate using a diversity of signals produced by a wide array of physical structures. Determining how a signal is produced provides key insights into signal evolution. Here, we examine a complex vibratory mating display produced by male Schizocosa floridana wolf spiders. This display contains three discrete substrate-borne acoustic components (known as “thumps”, “taps”, and “chirps”), each of which is anecdotally associated with the movement of a different body part (the pedipalps, legs, and abdomen respectively). In order to determine the method of production, we employ a combination of high-speed video/audio recordings and SEM imaging of possible sound-producing structures. Previous …

Testing The Hypothesized Antipredator Defence Function Of Stridulation In The Spiny Orb-Weaving Spider, Micrathena Gracilis, Tyler B. Corey, Eileen A. Hebets

Eileen Hebets Publications

The observable diversity of antipredator defenses across organisms demonstrates predation’s impact on trait evolution. The functions of many traits that are presumed to have an antipredator function have never been directly tested. The spiny orb-weaving spider, Micrathena gracilis, for example, stridulates when grasped. While stridulation was first hypothesized to be an antipredator defense nearly 50 years ago, no data exist to support this hypothesis. To explore the form and function of M. gracilis stridulation, we first quantified the behavioral and acoustical properties of sound production. Next, using laboratory assays, we directly tested the effect of stridulation on survival with …

Mandibulofacial Dysostosis Attributed To A Recessive Mutation Of Cyp26c1 In Hereford Cattle, Renae L. Sieck, Anna M. Fuller, Patrick S. Bedwell, Jack A. Ward, Stacy K. Sanders, Shi-Hua Xiang, Sichong Peng, Jessica Lynn Petersen, David J. Steffen

Department of Animal Science: Faculty Publications

In spring 2020, six Hereford calves presented with congenital facial deformities attributed to a condition we termed mandibulofacial dysostosis (MD). Affected calves shared hallmark features of a variably shortened and/or asymmetric lower mandible and bilateral skin tags present 2–10 cm caudal to the commissure of the lips. Pedigree analysis revealed a single common ancestor shared by the sire and dam of each affected calf. Whole-genome sequencing (WGS) of 20 animals led to the discovery of a variant (Chr26 g. 14404993T>C) in Exon 3 of CYP26C1 associated with MD. This missense mutation (p.L188P), is located in an α helix of …

Genomic Adaptations To Salinity Resist Gene Flow In The Evolution Of Floridian Watersnakes, Rhett M. Rautsaw, Tristan D. Schramer, Rachel Acuña, Lindsay N. Arick, Mark Dimeo, Kathryn P. Mercier, Michael Schrum, Andrew J. Mason, Mark J. Margres, Jason L. Strickland, Christopher L. Parkinson

Publications and Research

The migration-selection balance often governs the evolution of lineages, and speciation with gene flow is now considered common across the tree of life. Ecological speciation is a process that can facilitate divergence despite gene flow due to strong selective pressures caused by ecological differences; however, the exact traits under selection are often unknown. The transition from freshwater to saltwater habitats provides strong selection targeting traits with osmoregulatory function. Several lineages of North American watersnakes (Nerodia spp.) are known to occur in saltwater habitat and represent a useful system for studying speciation by providing an opportunity to investigate gene flow …

Not Withering On The Evolutionary Vine: Systematic Revision Of The Brown Vine Snake (Reptilia: Squamata: Oxybelis) From Its Northern Distribution, Robert C. Jadin, Christopher Blair, Sarah A. Orlofske, Michael J. Jowers, Gilson A. Rivas, Laurie J. Vitt, Julie M. Ray, Eric N. Smith, John C. Murphy

Publications and Research

The genus Oxybelis currently is composed of four taxa despite numerous studies suggesting and describing multiple taxa within the O. aeneus complex. Here, we utilize a multilocus molecular dataset (i.e. cyt b, ND4, 12S, 16S, cmos, PRLR, 3663 bp) to conduct phylogenetic analyses to assess the evolutionary history of Oxybelis. Our molecular analyses find three major lineages of Oxybelis (i.e. O. aeneus complex, O. brevirostris, O. fulgidus complex) with a sister relationship between O. brevirostris and the O. aeneus complex to the exclusion of the O. fulgidus complex. More specifically, O. aeneus appears to harbor at least …