Life Sciences Commons^™

Fishing And Fear Effects Interact To Shape Herbivory On Coral Reefs, Bethany M. Tilton

All HCAS Student Capstones, Theses, and Dissertations

Predation influences animal behavior and shapes ecological structure and function through lethal effects and fear effects. On coral reefs, fear effects can alter the distribution and intensity of herbivory by herbivorous reef fishes. This includes the browsing functional group, which potentially reverses macroalgal phase shifts and promotes reef recovery. Herbivory by multiple functional groups may increase on coral reefs through the use of NTZs (no-take zones) but few studies have examined the extent to which small-scale NTZs (< 0.5 km²) influence fear effects and perceived predator presence on reefs. This study aimed to determine whether fear effects on browsers on …

A Rapid Site Selection Assessment As An Indicator Of Stony Coral Microfragment Outplant Success, John J. Alfirevich

All HCAS Student Capstones, Theses, and Dissertations

Microfragmentation of massive stony coral species is a technique being utilized to propagate corals asexually to help restore coral reefs. Microfragmentation consists of cutting corals into 3 cm diameter or less fragments, which boosts growth rates. However, in some locations the size of microfragments make them vulnerable to parrotfish predation and benthic overgrowth, reducing survival. As such, a method to identify key site characteristics which promotes microfragment outplant success, particularly one that can be performed quickly across multiple areas is needed. A rapid site assessment conducted prior to microfragment outplanting was performed at 12 randomly selected sites within the Kristin …

What Did Higher Profit Cow-Calf Producers Do To Be More Profitable?, Randy Saner

Center for Agricultural Profitability

Cow-calf producers are always looking at ways to cut costs and improve profits. Looking at recent data from the University of Minnesota Center for Financial Management, FINBIN Livestock Analysis for 2022 representing cow-calf operations from Nebraska, South Dakota, and North Dakota can provide producers with some ideas on ways to improve profitability.

We Are The Reason We Stand Still In The Face Of Climate Change., Sydney Hemp

Honors Theses

Many different factors can impact the way any information is received but it is especially important to see how scientific information is received because it is often backed up by a great deal of evidence, especially in the case of global climate change. Many of these factors have nothing to do with science and everything to do with social influences, political parties, and other demographic measures. Discussion of these relationships is important when discussing communication in a broad sense, but it can be even more important when bringing up things like global climate change, which has become a political topic …

The Unexpected Significance Of Myosin A In Organization Of M-Line Protein Unc-89/Obscurin Within Striated Muscle Cells Of Caenorhabditis Elegans, Kar Men Lee

Honors Theses

This research investigates the unexpected significance of Myosin A in the organization of M-line protein UNC-89/obscurin within striated muscle cells of the nematode Caenorhabditis elegans (C. elegans). The study employs immunofluorescence techniques to examine the spatial and temporal dynamics of UNC-89/obscurin and Myosin A during embryonic development. The sarcomere, a fundamental unit in muscle cells, is governed by the 'sliding filament model,' where the M-line serves as a crucial anchor for Myosin A. This research seeks to understand the relationship between muscle function in humans and C. elegans, utilizing the latter's simple anatomy and genetic tractability. The …

Novel Fire And Herbivory Regime Impacts On Forest Regeneration And Plant Community Assembly, Devri A. Tanner

Theses and Dissertations

Human activities are increasing the occurrence of megafires that have the potential to alter the ecology of forest ecosystems. The objective of this study was to understand the impact of a 610 km2 megafire on patterns of forest regeneration and herbivory of three forest types (aspen/fir, oak/maple, and pinyon/juniper) within the burn scar. Sapling density, meristem removal, and height were measured across a transect network spanning the area of the burn scar over three years from 2019-2021. The network consisted of 17 burned/unburned transect pairs in adjacent burned/unburned forest stands (6 aspen/fir, 5 oak/maple, and 6 pinyon/juniper). Species that regenerated …

Demographic History Shapes North American Gray Wolf Genomic Diversity And Informs Species' Conservation, Bridgett M. Vonholdt, Daniel R. Stahler, Kristin Brzeski, Marco Musiani, Rolf O. Peterson, Michael Phillips, John Stephenson, Kent Laudon, Erin Meredith, John Vucetich, Jennifer A. Leonard, Robert K. Wayne

Michigan Tech Publications, Part 2

Effective population size estimates are critical information needed for evolutionary predictions and conservation decisions. This is particularly true for species with social factors that restrict access to breeding or experience repeated fluctuations in population size across generations. We investigated the genomic estimates of effective population size along with diversity, subdivision, and inbreeding from 162,109 minimally filtered and 81,595 statistically neutral and unlinked SNPs genotyped in 437 grey wolf samples from North America collected between 1986 and 2021. We found genetic structure across North America, represented by three distinct demographic histories of western, central, and eastern regions of the continent. Further, …

Testing The Cavefish Model: An Organism-Focused Theory Of Biological Design, Michael J. Boyle, Scott Arledge, Brian Thomas, Jeffrey P. Tomkins, Randy J. Guliuzza

Proceedings of the International Conference on Creationism

Poster Abstract

The Institute for Creation Research (ICR) is experimentally testing an engineering-based model of rapid biological adaptation: Continuous Environmental Tracking (CET). This model infers that organisms actively track conditions within specific environments to self-adjust through internal mechanisms and initiate adaptive functionality. The animal under investigation is Astyanax mexicanus (Mexican tetra), a freshwater fish with well-differentiated, interfertile morphotypes: eyed surface-dwelling fish (surface fish) with distinct pigmentation patterns, and eyeless cave-dwelling fish (cavefish) with minimal pigmentation. Aquaria within our newly established laboratory contain breeding pairs of cavefish exposed to either (A) cyclical light/dark patterns of full-spectrum high-intensity light, (B) minimal light …

Hybridization And Genetic Distances Suggest One Large Monobaramin In The Gourd Family (Cucurbitales: Cucurbitaceae), Timothy R. Brophy, Jack R. Gregory, Brigitte Townsend

Proceedings of the International Conference on Creationism

The gourds form a primarily tropical and subtropical family (Cucurbitales: Cucurbitaceae) of herbaceous climbers and woody lianas composed of approximately 960 species in 95 genera and 15 tribes. Many of these are globally important food crops and ornamentals including cucumbers, gourds, squashes, melons, pumpkins, and luffas. Utilizing published literature, there is evidence of interspecific hybridization (natural, experimental cross-pollination, and embryo/ovule culture) in five of the 15 tribes. These consist of successful crosses between 131 unique species pairs, including two intergeneric and one intertribal cross, forming eight monobaramins. In addition, species that do not hybridize directly, but hybridize with the same …

Paleo-Ontogenetic Growth Curves: Evidence For Extreme Past Animal Longevity?, Leo Hebert Iii

Proceedings of the International Conference on Creationism

One of the Bible's most ridiculed claims is its assertion that pre-Flood and immediate post-Flood humans experienced lifespans of hundreds of years. Hence, the ability to partially corroborate the Bible's claim in this regard should be of great interest to creation researchers. Paleontologists have within the last two decades become increasingly interested in using growth rings recorded in fossil forms to make inferences about past growth rates, sizes, and lifespans. Examination of these growth rings suggest that some creatures in the pre-Flood world matured quite slowly compared to similar extant forms. Also, multiple studies have shown that slower development and …

Elucidating The Relationships Between Spider Size, Joint Stiffness, And The Mechanical Frequency Response Of The Body, Reese L. Gartly

Electronic Thesis and Dissertation Repository

Spiders use vibrations to sense their surroundings. It has been suggested that the vibration perception in spiders may be altered by the mechanics of the body. I studied the biomechanics of spiders, at the level of leg joints and the whole body. To study joints, I quantified the allometry of leg joint stiffness in spiders. I found that the stiffness of spider joints increased nearly isometrically with increasing body mass, partly by having shorter and thicker leg segments and also by other unknown means. Using these data, I developed empirically validated biomechanical models which predicted the effects of mechanics on …

Gag Grouper (Mycteroperca Microlepis) Neurocranium, Sierra Potts, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

10 cm neurocranium from Gag Grouper, Mycteroperca microlepis, collected from Snapper Mike's on 05/11/2023 by Sierra Potts

Resolution Of The Tetrabothrius Jagerskioeldi Cryptic Species Complex Among Holarctic Alcidae (Charadriiformes): Cestodes Among Fraterculinae—Exploring Marine Diversity, Host Range, And Dynamic Oceanography In The Greater North Pacific, Eric P. Hoberg, Kaylen Marie Soudachanh, Svetlana K. Bondarenko

MANTER: Journal of Parasite Biodiversity

In the biosphere, limits for diversity among species, communities, and biomes are revealed through intensive and extensive field-based inventory and assembly of voucher specimens and associated informatics examined in a phylogenetic, historical, ecological, and biogeographic arena. Archival resources for specimens and information contribute to a cumulative view of faunal structure and assembly under a comparative umbrella. Ultimately, species definitions, and inclusive partitions among populations and lineages, are fundamental in articulating hypotheses that examine interactions about evolution, the nature of organisms, and the condition of environments across space and time. We conclude our proposals establishing species limits for tapeworms of the …

Convolutional Neural Network-Based Gene Prediction Using Buffalograss As A Model System, Michael Morikone

Dissertations and Doctoral Documents from University of Nebraska-Lincoln, 2023–

The task of gene prediction has been largely stagnant in algorithmic improvements compared to when algorithms were first developed for predicting genes thirty years ago. Rather than iteratively improving the underlying algorithms in gene prediction tools by utilizing better performing models, most current approaches update existing tools through incorporating increasing amounts of extrinsic data to improve gene prediction performance. The traditional method of predicting genes is done using Hidden Markov Models (HMMs). These HMMs are constrained by having strict assumptions made about the independence of genes that do not always hold true. To address this, a Convolutional Neural Network (CNN) …

Factors Affecting Forage Quality And The Subsequent Response In Production And Energy Metabolism In Lactating Jersey Cows, Kassidy Kate Buse

Dissertations and Doctoral Documents from University of Nebraska-Lincoln, 2023–

Forage quality is the potential of a forage to produce a production response in animals. Because of how essential they are in dairy cattle rations, forages can have major influence on the behavior and production of dairy cattle. In experiment 1, the effect of forage fragility on the rumen environment and digestibility was evaluated. Increasing the inclusion of a less fragile forage led to greater rumen retention time, which resulted in lower rumen pH and greater NDF digestibility. Experiment 2 evaluated the effects of diets high in either corn silage or alfalfa haylage supplemented with either corn- or soybased protein …

Effects Of Dimerization On The Deacylase Activities Of Human Sirt2., Jie Yang, Nathan I Nicely, Brian P Weiser

Rowan-Virtua School of Osteopathic Medicine Faculty Scholarship

Human sirtuin isoform 2 (SIRT2) is an NAD+-dependent enzyme that functions as a lysine deacetylase and defatty-acylase. Here, we report that SIRT2 readily dimerizes in solution and in cells and that dimerization affects its ability to remove different acyl modifications from substrates. Dimerization of recombinant SIRT2 was revealed with analytical size exclusion chromatography and chemical cross-linking. Dimerized SIRT2 dissociates into monomers upon binding long fatty acylated substrates (decanoyl-, dodecanoyl-, and myristoyl-lysine). However, we did not observe dissociation of dimeric SIRT2 in the presence of acetyl-lysine. Analysis of X-ray crystal structures led us to discover a SIRT2 double mutant (Q142A/E340A) that …

Characterization Of Adipocyte Mechanical Properties And Stretch Control Of Mechanosignaling In Adipocytes, Tasneem Bouzid

Dissertations and Doctoral Documents from University of Nebraska-Lincoln, 2023–

Obesity has reached global epidemic levels in recent decades and is the leading risk factor for type-2 diabetes (T2D). Adipose tissue behaves as a link between obesity and T2D, with dysfunctional extracellular matrix (ECM) remodeling, adipokine secretion and lipid metabolism leading to insulin resistance. The extracellular mechanophysical milieus is understood to regulate adipocyte differentiation and function through activation of mechanosensory machinery and related pathways. Therefore, exploring the adipocytic response to mechanical loading can provide great pathophysiological insight into obesity and T2D. Adipose tissue is exposed to various compound forces due to weight-bearing and movement, and adipocyte stiffness influences stress distribution …

Examination Of The Prevalence And Behaviors Of Pathogenic And Spoilage Bacteria At Multiple Stages In The Meat Processing Chain, Samuel C. Watson

Dissertations and Doctoral Documents from University of Nebraska-Lincoln, 2023–

As long as there is food, there will also be bacteria that are capable of compromising the quality and safety of food. This dissertation aims to study bacteria capable of spoiling meat, causing illness, or both. The literature review summarizes the understanding of several bacterial pathogens, current issues in combating those pathogens in the food supply, and how spoilage Pseudomonas behave in the meat supply. Chapter 2 explored the impact of organic acid treatments on the spoilage microbiome of raw beef during extended storage. While Pseudomonas and Yersinia were both present in significant levels, Lactococcus was determined to be the …

Chromosome 10q2432 Variants Associate With Brain Arterial Diameters In Diverse Populations: A Genome-Wide Association Study, Minghua Liu, Farid Khasiyev, Sanjeev Sariya, Antonio Spagnolo-Allende, Danurys L Sanchez, Howard Andrews, Qiong Yang, Alexa Beiser, Ye Qiao, Emy A Thomas, Jose Rafael Romero, Tatjana Rundek, Adam M Brickman, Jennifer J Manly, Mitchell Sv Elkind, Sudha Seshadri, Christopher Chen, Saima Hilal, Bruce A Wasserman, Giuseppe Tosto, Myriam Fornage, Jose Gutierrez

Journal Articles

BACKGROUND: Brain arterial diameters (BADs) are novel imaging biomarkers of cerebrovascular disease, cognitive decline, and dementia. Traditional vascular risk factors have been associated with BADs, but whether there may be genetic determinants of BADs is unknown.

METHODS AND RESULTS: The authors studied 4150 participants from 6 geographically diverse population-based cohorts (40% European, 14% African, 22% Hispanic, 24% Asian ancestries). Brain arterial diameters for 13 segments were measured and averaged to obtain a global measure of BADs as well as the posterior and anterior circulations. A genome-wide association study revealed 14 variants at one locus associated with global BAD at genome-wide …

A Novel Software For Organelle Genome-Based Baraminology Studies, Matthew Cserhati

Proceedings of the International Conference on Creationism

Background

There are 24,165 organelle DNA sequences at the Organelle Genome webpage at the NCBI website, as of June 19, 2022. Of these, 14,799 are mitochondrial genomes and 8,050 are chloroplast genomes. Since organelle genomes are very small and very abundant within the cell, they are easy to isolate and sequence. This means that there is a very large number of organelle genome data available for baraminologists to explore and analyze. Using organelle genomes is a quick way to map a large number of species to their respective baramins in preliminary baraminology studies.

The first mitochondrial DNA (mtDNA) studies in …

New Analyses Suggest That All Horses (Perissodactyla: Equidae) Belong To A Single Holobaramin, Timothy R. Brophy, Jack R. Gregory

Proceedings of the International Conference on Creationism

The horse family (Perissodactyla: Equidae) is composed of approximately 35 genera, primarily extinct forms from Cenozoic sediments, that include the modern genus Equus. The equids, along with some other extinct perissodactyls (e.g., palaeotheriids) form the superfamily (or clade) Equoidea. Our previous research confirmed the conclusions of several other baraminological analyses that all members of the horse family belong to the same monobaramin. No baraminological studies, however, have detected consistent discontinuity between the horses and any outgroup taxa. The goal of this study is to investigate potential discontinuity and holobaraminic status of horses and other similar taxa using new datasets …

Messages In The Genetic Code: The Dram Form, John M. Demassa

Proceedings of the International Conference on Creationism

Does the Genetic code contain non-structural information or even intelligible messages? The present work offers a mathematical investigation of the genetic code using a novel numeric procedure applied to both nucleobases and amino acids found in standard code tables. The numeric two step procedure amounts to an atom count of all the atoms in standard genetic code tables and shall be called Compound Numeric Triangulation. The first step called Compound Numeric Indexing (CNI) converts the DNA codon table (purines and pyrimidines),the RNA codon table (purines and pyrimidines) and the 20 standard amino acids into representative index numbers. In this step, …

Molecular And Morphological Analyses Confirm That All Loons (Aves: Gaviiformes) Form A Single Holobaramin, Timothy R. Brophy, Mary-Clark A. Matthews, Mckayla M. Guillory, Alexis M. Ramerth

Proceedings of the International Conference on Creationism

Loons or divers (Aves: Gaviiformes), a group of waterbirds found primarily in the Northern Hemisphere, are comprised of several extinct taxa as well as an extant family (Gaviidae) with one genus (Gavia) and five species. Recent phylogenetic studies suggest that the Sphenisciformes (penguins) and Procellariiformes (petrels, albatrosses, and shearwaters) form a sister group to the loons. Our previous research, based on hybridization, morphological, and vocalization data, found that all extant loons form a single holobaramin (i.e., created kind). This previous study, however, was inconclusive as to the membership of fossil taxa within the kind. The goal of the …

The Exquisite Design Of Somatic Hypermutation To Enhance Antibody Diversity, Binding Affinity And Self-Tolerance, Frank Maas

Proceedings of the International Conference on Creationism

Somatic hypermutation (SHM) of antibody genes is commonly cited as preeminent evidence of the Darwinian “survival of the fittest” in nature. Just as SHM generates antibodies with the strongest binding affinity through a process of random mutation and selection in somatic cells of an individual, the same process occurring in germ cells on a population level can result in macroevolution according to proponents of the latter theory. Although SHM appears to produce point mutations randomly, such mutations are actually generated by a well-designed intricate mechanism contributing to species preservation. Non-random characteristics of SHM are summarized as well as recent findings …

Microplastics, Macro-Problems: Abundance Of Man-Made Materials In The Waters And Sediments Of Florida State Parks, Luciana M. Banquero, Kate Mclendon, Andres Alatorre, Mackenzie Daniels, Savanna Freeman, Cassidy Starke, Katherine Harris, Sidney J. Busch

The Pegasus Review: UCF Undergraduate Research Journal

Man-made materials (MMM) are pollutants introduced to the environment by human activity. Microplastics (MP) are a type of MMM that threaten living organisms through bioaccumulation. The term MMM also encompasses pollutants produced from natural materials, such as rayon and microfibrillated cellulose, which are used in food packaging. This study aims to determine the extent of MMM pollution within estuaries in two of Florida’s state parks, as well as the effectiveness of using restored vegetation on shorelines to reduce MMM pollution. Tomoka State Park and Gamble Rogers State Park were selected at the request of the Florida Department of Environmental Protection. …

Determining The Extent Of Pioneer Mangrove Acidification On Intertidal Oyster Reefs, Cindy Whitten, Andres Alatorre, Nicole Campbell, Savanna Freeman, Sydney Henderson, Kate Mclendon, Connor Wright, June Davison, Madison Ganci, Katherine Harris

The Pegasus Review: UCF Undergraduate Research Journal

The Indian River Lagoon (IRL) stretches 251 kilometers along Florida’s east coast and is one of the most biodiverse estuaries in North America. Mosquito Lagoon, the northernmost portion of the IRL, is home to mangroves and intertidal oyster reefs that provide numerous ecosystem services. These two habitats are overlapping as climate change drives mangroves poleward. Scientists have documented mangrove expansion and the transition of oyster reef habitat to mangrove islands. Past studies have shown large, adult mangrove stands drive soil acidification. The goal of this study was to understand if stand-alone, or pioneer, Rhizophora mangle (red mangroves) and Avicennia germinans …

Jun Upregulation Drives Aberrant Transposable Element Mobilization, Associated Innate Immune Response, And Impaired Neurogenesis In Alzheimer’S Disease, Chiara Scopa, Samantha Barnada, Maria Cicardi, Mo Singer, Davide Trotti, Marco Trizzino

Farber Institute for Neuroscience Faculty Papers

Adult neurogenic decline, inflammation, and neurodegeneration are phenotypic hallmarks of Alzheimer's disease (AD). Mobilization of transposable elements (TEs) in heterochromatic regions was recently reported in AD, but the underlying mechanisms are still underappreciated. Combining functional genomics with the differentiation of familial and sporadic AD patient derived-iPSCs into hippocampal progenitors, CA3 neurons, and cerebral organoids, we found that the upregulation of the AP-1 subunit, c-Jun, triggers decondensation of genomic regions containing TEs. This leads to the cytoplasmic accumulation of HERVK-derived RNA-DNA hybrids, the activation of the cGAS-STING cascade, and increased levels of cleaved caspase-3, suggesting the initiation of programmed cell death …

Dataset For The Incorporation Of Climate Change Into A Multiple Stressor Risk Assessment For The Chinook Salmon (Oncorhynchus Tshawytscha) Population In The Yakima River, Washington Usa, Wayne Landis, Chelsea J. Mitchell, John D. Hader, Rory Nathan, Emma E. Sharpe

Environmental Sciences Faculty and Staff Publications

Data files available below

This data set is in support of Landis et al (in press 2024). A key question in understanding the implications of climate change is how to integrate ecological risk assessments that focus on contaminants with the environmental alterations from climate projections. This article summarizes the results of integrating selected direct and indirect effects of climate change into an existing Bayesian network previously used for ecological risk assessment. The existing Bayesian network Relative Risk Model (BN-RRM) integrated the effects of organophosphate pesticides concentrations, water temperature, and dissolved oxygen levels on the Chinook salmon population in the Yakima …

Evaluating The Effectiveness Of The Internal Transcribed Sequences (Its) As Dna Barcodes To Estimate Fungal Diversity, Jailisa Linares

All HCAS Student Capstones, Theses, and Dissertations

Universal phylogenetic markers such as the nuclear ribosomal internal transcribed sequences (ITS), specifically ITS1 and ITS2, are routinely used to estimate fungal diversity in environmental samples. However, numerous studies report differences in the performance and efficacy of ITS1 and ITS2 in documenting fungal diversity. To better understand the implications of using ITS1 versus ITS2, a comprehensive representation of the diverse fungal taxa was necessary to conduct a meta-analysis of their use across multiple fungal taxa. In order to address this, a thorough literature review was conducted to compare and contrast the use of ITS1 and ITS2 as effective DNA barcodes. …

Psammocora Stellata Distribution At Devil's Crown, Floreana Island, Galápagos Islands, Ecuador, María José Guarderas Sevilla

All HCAS Student Capstones, Theses, and Dissertations

In the Galápagos Archipelago, the free-living nodular coral Psammocora stellata is a common species that does not form reef structures. However, it is a key component of the ecosystem by increasing habitat complexity and, consequently, species diversity. This species experienced a drastic decline in Devil’s Crown channel, Floreana Island, where it disappeared after the 1982-83 El Niño-Southern Oscillation, presumably by displacement of unattached colonies by strong surface waves and currents. This assemblage has now recovered to pre-impact levels. A combination of underwater photoquadrats from 2007 and 2009 and recent (2023) orthomosaics were used to determine changes in coral densities and …