Biology Commons^™

Drivers Of Decadal Vegetation Change In Northern Alaska, Jacob Allen Harris

Masters Theses

The Arctic is experiencing rapid climate change. This research documents vegetation change near Atqasuk and Utqiaġvik, Alaska. At each location, 30 plots distributed in a matrix across the landscape, were sampled annually from 2010 to 2019 using a point frame. For every encounter we recorded the height and classified it into eight broad functional groups (deciduous shrubs, evergreen shrubs, forbs, graminoids, bryophytes, lichens, litter and standing dead vegetation); for vascular plants we also identified the species. We found a consistent increase in plant stature and cover over time which was dramatic at Atqasuk. Graminoid cover and height increased at both …

Introduction To Neutrosophic Genetics, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

Neutrosophic Genetics is the study of genetics using neutrosophic logic, set, probability, statistics, measure and other neutrosophic tools and procedures. In this paper, based on the Neutrosophic Theory of Evolution (that includes degrees of Evolution, Neutrality (or Indeterminacy), and Involution) – as extension of Darwin’s Theory of Evolution, we show the applicability of neutrosophy in genetics, and we present within the frame of neutrosophic genetics the following concepts: neutrosophic mutation, neutrosophic speciation, and neutrosophic coevolution.

Adding The Third Dimension To Studies Of Parallel Evolution Of Morphology And Function: An Exploration Based On Parapatric Lake-Stream Stickleback, Grant E. Haines, Yoel E. Stuart, Dieta Hanson, Tania Tasneem, Daniel I. Bolnick, Hans Ce Larsson, Andrew P. Hendry

Biology: Faculty Publications and Other Works

Recent methodological advances have led to a rapid expansion of evolutionary studies employing three-dimensional landmark-based geometric morphometrics (GM). GM methods generally enable researchers to capture and compare complex shape phenotypes, and to quantify their relationship to environmental gradients. However, some recent studies have shown that the common, inexpensive, and relatively rapid two-dimensional GM methods can distort important information and produce misleading results because they cannot capture variation in the depth (Z) dimension. We use micro-CT scanned threespine stickleback (Gasterosteus aculeatus Linnaeus, 1758) from six parapatric lake-stream populations on Vancouver Island, British Columbia, to test whether the loss …

Associative Nitrogen Fixation Linked With Three Perennial Bioenergy Grasses In Field And Greenhouse Experiments, Jayani J. Wewalwela, Yuan Tian, Janet R. Donaldson, Brian S. Baldwin, Jac J. Varco, Brett Rushing, Haoliang Lu, Mark A. Williams

Faculty Publications

© 2020 The Authors. Associative nitrogen (N₂)‐fixation (ANF) by bacteria in the root‐zone of perennial bioenergy grasses has the potential to replace or supplement N fertilizer and support sustainable production of biomass, but its application in marginal ecosystems requires further evaluation. In this study, we first combined both greenhouse and field experiments, to explore the N₂ fixation effects of three temperate feedstocks Miscanthus × giganteus (giant miscanthus, Freedom), Panicum virgatum (switchgrass, Alamo), and Saccharum sp. (energycane, Ho 02‐147). In field studies across three growing seasons, plant and soil pools of candidate feedstocks were partially composed of N …

Soil Response To Fire Frequency In The Northern Columbia Basin Sagebrush Steppe, Leslie C. Nichols

Boise State University Theses and Dissertations

Fire is one of the most significant disturbances in an ecosystem, as it is capable of altering the physical, chemical, and biological properties of soil, and the fire frequency in semi-arid ecosystems is increasing. These changes can potentially alter plant-soil feedbacks that may affect post-fire recovery of the native plant and soil communities and lead to an ecosystem state change. However, there is much uncertainty about the magnitude of change as soils are exposed to more fires, because soil recovery and changes in fire severity following a first fire mediate the impact of successive fires on soil properties. To improve …

Stability Of Modified Host-Parasitoid Model With Allee Effect, Özlem A. Gümüs, A. G. Maria Selvam, R. Janagaraj

Applications and Applied Mathematics: An International Journal (AAM)

This paper deals with a host-parasitoid model subject to Allee effect and its dynamical behavior. Steady state points of the proposed host-parasitoid model are computed. Stability properties are analyzed with eigen values of Jacobian matrix which are determined at the steady states. Theoretical findings are supported by numerical illustrations and enhanced by pictorial representations such as bifurcation diagrams, phase portraits and local amplifications for different parameter values. Existence of chaotic behavior in the system is established via bifurcation and sensitivity analysis of the system at the initial conditions. Various phase portraits are simulated for a better understanding of the qualitative …

The Effects Of White-Nose Syndrome On Cave-Dwelling Bats During Their Pre-Hibernation Season In Eastern Nebraska, Maggie Bockart

Theses/Capstones/Creative Projects

White-nose syndrome (WNS) is currently the leading cause of death to North American bats and was first documented in the United States in 2006 on the East Coast. Infection with the fungus Pseudogymnoascus destructans (Pd) causes bats to arise from hibernation with unnecessary frequency, leading to depletion of fat reserves that are imperative for extended periods of torpor. In October 2014, biologists surveyed the activity levels of bats at Fontenelle Forest in eastern Nebraska using acoustic detectors and determined what species of bats were present and their relative abundance before being exposed to WNS. By returning to the …

Improving Collaborations Between Empiricists And Modelers To Advance Grassland Community Dynamics In Ecosystem Models, Kevin R. Wilcox, Kimberly J. Komatsu, Meghan L. Avolio, Nathan P. Lemoine

Biological Sciences Faculty Research and Publications

No abstract provided.

The Response Of Lianas To 20 Yr Of Nutrient Addition In A Panamanian Forest, Stefan A. Schnitzer, Sergio Estrada Villegas, S. Joseph Wright

Biological Sciences Faculty Research and Publications

Over the past two decades, liana density and basal area have been increasing in many tropical forests, which has profound consequences for forest diversity and functioning. One hypothesis to explain increasing lianas is elevated nutrient deposition in tropical forests resulting from fossil fuels, agricultural fertilizer, and biomass burning. We tested this hypothesis by surveying all lianas ≥1 cm in diameter (n = 3,967) in 32 plots in a fully factorial nitrogen (N), phosphorus (P), and potassium (K) addition experiment in a mature tropical forest in central Panama. We conducted the nutrient-addition experiment from 1998 until present and we first …

A Guide To Freshwater Aquariums, Noah Savastano

Senior Honors Projects

The objective of this project was to create a complete guide, useful for someone of any aquarium expertise level, describing how to set up and care for an aquarium. This guide explains the science behind processes involved in setting up and maintaining an aquarium. It also educates the reader on how to properly prioritize the safety of the fish. A full text was first created including all relevant information gathered from scholarly texts and online sources. Original photographs were incorporated as a supplement to the text. Fish and aquatic plants were drawn to further illustrate the concepts that were described …

A Two-Clone Approach To Study Signaling Interactions Among Neuronal Cells In A Pre-Clinical Alzheimer’S Disease Model, Catherine J. Yeates, Ankita Sarkar, Prajakta Deshpande, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

To understand the progression of Alzheimer's disease, studies often rely on ectopic expression of amyloid-beta 42 (Aβ42) throughout an entire tissue. Uniform ectopic expression of Aβ42 may obscure cell-cell interactions that contribute to the progression of the disease. We developed a two-clone system to study the signaling cross talk between GFP-labeled clones of Aβ42-expressing neurons and wild-type neurons simultaneously generated from the same progenitor cell by a single recombination event. Surprisingly, wild-type clones are reduced in size as compared with Aβ42-producing clones. We found that wild-type cells are eliminated by the induction of cell death. Furthermore, aberrant activation of c-Jun-N-terminal …

Does The Presence Of Multiple Β-Lactamases In Gram-Negative Bacilli Impact The Results Of Antimicrobial Susceptibility Tests And Extended-Spectrum Β-Lactamase And Carbapenemase Confirmation Methods?, Fred C. Tenover, Caitlin M. Dela Cruz, Scott Dewell, Victoria M. Le, Isabella A. Tickler

Biology Faculty Publications

Objectives: Many multidrug-resistant Gram-negative bacilli (MDR-GNB) harbour multiple β-lactamases. The aim of this study was to assess the impact of multiple β-lactamase carriage on the accuracy of susceptibility tests and extended-spectrum β-lactamase (ESBL) and carbapenemase confirmation methods.

Methods: A total of 50 MDR-GNB, of which 29 carried multiple β-lactamases, underwent broth microdilution (BMD) and disk diffusion (DD) testing as well as confirmation tests for ESBLs and carbapenemases. Whole-genome sequencing (WGS) was used for β-lactamase gene identification.

Results: Categorical agreement of BMD and DD testing results ranged from 86.5 to 97.7% for 10 β-lactam agents. BMD and DD algorithms for ESBL …

Polyrad -- Protection Against Free Radical Damage, Hannah Kim, Yin Tse, Andrew Webb, Ethan Mudd, Muhammad Raisul Abedin, Melanie R. Mormile, Subhadeep Dutta, Kaushal Rege, Sutapa Barua

Biological Sciences Faculty Research & Creative Works

The effects of elevated levels of radiation contribute to the instability of pharmaceutical formulations in space compared to those on earth. Existing technologies are ineffective at maintaining the therapeutic efficacies of drugs in space. Thus, there is an urgent need to develop novel space-hardy formulations for preserving the stability and efficacy of drug formulations. This work aims to develop a novel approach for the protection of space pharmaceutical drug molecules from the radiation-induced damage to help extend or at least preserve their structural integrity and potency. To achieve this, free radical scavenging antioxidant, Trolox was conjugated on the surface of …

Seasonal Patterns In Stable Isotope And Fatty Acid Profiles Of Southern Stingrays (Hypanus Americana) At Stingray City Sandbar, Grand Cayman, Lisa A. Hoopes, Tonya M. Clauss, Nicole E. Browning, Alexa J. Delaune, Bradley M. Wetherbee, Mahmood Shivji, Jessica C. Harvey, Guy C.M. Harvey

Biology Faculty Articles

Ecotourism opportunities in the marine environment often rely heavily on provisioning to ensure the viewing of cryptic species by the public. However, intentional feeding of wildlife can impact numerous aspects of an animals’ behavior and ecology. Southern stingrays (Hypanus americana) provisioned at Stingray City Sandbar (SCS) in Grand Cayman have altered diel activity patterns and decreased measures of health. This study looked at seasonal changes in stable isotope (SI) and fatty acid (FA) profiles of provisioned stingrays at SCS. Plasma δ15N was higher in male stingrays (11.86 ± 1.71‰) compared to females (10.70 ± 1.71‰). Lower values for δ15N in …

Statistics Of Branched Populations Split Into Different Types, Thierry E. Huillet

Applications and Applied Mathematics: An International Journal (AAM)

Some population is made of n individuals that can be of P possible species (or types) at equilibrium. How are individuals scattered among types? We study two random scenarios of such species abundance distributions. In the first one, each species grows from independent founders according to a Galton-Watson branching process. When the number of founders P is either fixed or random (either Poisson or geometrically-distributed), a question raised is: given a population of n individuals as a whole, how does it split into the species types? This model is one pertaining to forests of Galton-Watson trees. A second scenario that …

Estimation Of Transmission Dynamics Of Covid-19 In India: The Influential Saturated Incidence Rate, - Tanvi, Rajiv Aggarwal, Ashutosh Rajput

Applications and Applied Mathematics: An International Journal (AAM)

A non-linear SEIR mathematical model for coronavirus disease in India has been proposed, by incorporating the saturated incidence rate on the occurrence of new infections. In the model, the threshold quantity known as the reproduction number is evaluated which determines the stability of disease-free equilibrium and the endemic equilibrium points. The disease-free equilibrium point becomes globally asymptotically stable when the corresponding reproduction number is less than unity, whereas, if it is greater than unity then the endemic equilibrium point comes into existence, which is locally asymptotically stable under certain restrictions on the parameters value in the model. The impact of …

Dynamical Behavior Of An Eco-Epidemiological Model Incorporating Prey Refuge And Prey Harvesting, Dawit Melese, Ousman Muhye, Subrata K. Sahu

Applications and Applied Mathematics: An International Journal (AAM)

In this paper an eco-epidemiological model incorporating a prey refuge and prey harvesting with disease in the prey-population is considered. Predators are assumed to consume both the susceptible and infected prey at different rates. The positivity and boundedness of the solution of the system are discussed. The existence and stability of the biologically feasible equilibrium points are investigated. Numerical simulations are performed to support our analytical findings.

Fish And Macroinvertebrate Response To Restoration And Conservation Efforts, Madison C. Cogar

Graduate Theses/Dissertations

Fish and macroinvertebrate response to restoration and conservation efforts varies in regards to the size and structure of the system (e.g. headwater streams in WV versus large rivers such as the Mississippi River). This project reviews fish and macroinvertebrate rebound in treated acid mine drainage (AMD) streams in WV as well as macroinvertebrate drift patterns in the Mississippi and Missouri Rivers. AMD is a product of a chemical reaction resulting in an acidic water outflow from mining sites, which may harm aquatic life. As a response, passive AMD treatment systems have been installed. I tested the effectiveness of remediation by …

Spatial Use By Mammals Within Two State Parks In The Ozarks National Scenic Riverways, Benjamin Aaron Smith

Graduate Theses/Dissertations

A mammalian species inventory with comparisons between sampled sites was conducted via multiple methodologies to document presence of mammals at two Missouri state parks within the Ozark National Scenic Riverways. Camera traps, small mammal traps, acoustic detectors, and mist nets were used to detect species at the parks, and species similarity indices and occupancy analyses were used to discern use of space. A mammalian inventory was compiled for each area of inquiry. Greater diversity was found at the park with more variable habitat types. Bat activity was more in the park with a known hibernaculum, though species specific activity differed …

Large-Scale Genome Sequencing Of Mycorrhizal Fungi Provides Insights Into The Early Evolution Of Symbiotic Traits, Shingo Miyauchi, Enikő Kiss, Alan Kuo, Elodie Drula, Annegret Kohler, Marisol Sánchez-García, Emmanuelle Morin, Bill Andreopoulos, Kerrie W. Barry, Gregory Bonito, Marc Buée, Akiko Carver, Cindy Chen, Nicolas Cichocki, Alicia Clum, David Culley, Pedro W. Crous, Laure Fauchery, Mariangela Girlanda, Richard D. Hayes, Zsófia Kéri, Kurt Labutti, Anna Lipzen, Vincent Lombard, Jon Magnuson, François Maillard, Claude Murat, Matt Nolan, Robin A. Ohm, Jasmyn Pangilinan, Maíra De Freitas Pereira, Silvia Perotto, David Hibbett

Biology

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve …

Discerning Competitive Vs. Facilitative Relationships Of Weeds On Forest Restoration Efforts At La Sal Del Rey, Tx, Mylen A. Arias

Theses and Dissertations

Dryland ecosystems need effective restoration strategies to address severe degradation. It is often assumed that voluntary forb weeds either compete with or have no effect on native seedlings. In contrast, theory and empirical work suggest a potential facilitative role for such forb weeds. We conducted a manipulative weed exclusion experiment at a semi-arid site in South Texas targeted for large scale forest restoration and subsequently dominated by early successional forb weeds to discern the net effect of these weeds on the growth and survival of target thornscrub tree and shrub seedlings. Overall, weed presence did not significantly affect seedling mortality …

Draft Genome Of The Common Snapping Turtle, Chelydra Serpentina, A Model For Phenotypic Plasticity In Reptiles, Debojyoti Das, Sunil Kumar Singh, Jacob Bierstedt, Alyssa Erickson, Gina L. J. Galli, Dane A. Crossley Ii, Turk Rhen

Biology Faculty Publications

Turtles are iconic reptiles that inhabit a range of ecosystems from oceans to deserts and climates from the tropics to northern temperate regions. Yet, we have little understanding of the genetic adaptations that allow turtles to survive and reproduce in such diverse environments. Common snapping turtles, Chelydra serpentina, are an ideal model species for studying adaptation to climate because they are widely distributed from tropical to northern temperate zones in North America. They are also easy to maintain and breed in captivity and produce large clutch sizes, which makes them amenable to quantitative genetic and molecular genetic studies of …

Spirituality As A Moderator Between Ptss And Cardiovascular Reactivity, Kriti Sharda

Honors Scholar Theses

Posttraumatic stress symptoms (PTSS) can be distressing and produce robust cardiovascular symptoms, such as increased heart rate and blood pressure, which have been implicated in higher risk of developing cardiovascular disease (CVD). Identifying factors that may reduce symptoms may suggest therapeutic strategies. One such potential factor is spirituality, given that spirituality is associated with both reducing PTSS and with preventing or improving CVD. We sampled 63 young college women who indicated being exposed to unwanted sexual contact. We asked them to write about their experience while we took heart rate (HR), systolic blood pressure (SBP) and diastolic blood pressure (DBP) …

Developing Methods To Survey, Collect, Process, And Screen Endemic Entomopathogenic Fungi Against The Asian Citrus Psyllid In The Lower Rio Grande Valley, Jonathan Cisneros

Theses and Dissertations

The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama (Hemiptera: Liviidae), vectors “Candidatus Liberibacter spp.”, the causative agent of Citrus Greening Disease. Managing ACP is imperative given the continuous increase in HLB positive trees. An aspect of integrated pest management (IPM) is the use of entomopathogenic fungi for the biological control of D. citri.

In order to identify endemic entomopathogenic fungi actively infecting D. citri, ACP were collected from local residential areas, surface sterilized, and plated on a semi-selective agar medium. Collection of over 9,300 samples from 278 sites throughout the LRGV led to the positive identification of …

Disturbance, Defense And Fitness In Silverleaf Nightshade (Solanum Elaeagnifolium) In Their Native Range In South Texas, Jesus Chavana

Theses and Dissertations

The role of human disturbance in accelerating weed growth is well understood. While most of these studies have focused on soil mediated disturbance, mowing is also a management practice that could impact weed traits. Using silver leaf nightshade (Solanum elaeagnifolium), a noxious and invasive weed, we asked whether continuous mowing affects growth and plant defense traits. We found that mowed plants produced significantly less fruits, had lower total seed fitness, but had higher seed mass, and germinated significantly faster. When three common herbivores were allowed to feed on the seedlings; tobacco hornworm (Manduca sexta), a generalist Solanaceae caterpillar gained more …

Interactive Effects Of Heat Stress And Pesticides Co-Exposure On Swimming Behavior, Oxidative Stress, Antioxidant Expression, And Redox Status In Common Goldfish (Carassius Auratus), Brittney Danielle Lacy

Theses and Dissertations

Aquatic ecosystems are inundated by environmental pesticides. This study, observed the dose-dependent effects of pesticides cocktail (metalachlor, linuron, isoproturon, tebucanazole, aclonifen, atrazine, pendimethalin, and azinphos-methyl) and elevated temperature (32 °C for 4-week exposure) on morphology of gills and kidneys, and expression of nitrotyrosine protein (NTP), dinitrophenyl protein (DNP), catalase (CAT), superoxidase dismutase (SOD), Na+/K+-ATPase, renin, and apoptosis in tissues of goldfish. Additionally, the effects on the free-swimming behavior were also observed. Histological analysis showed wide-spread damage in tissues at higher temperature and pesticides co-exposure. Immunohistochemical analysis demonstrated alterations in NTP, DNP, CAT and SOD expressions in tissues at higher temperature …

Role Of Glycolytic Metabolism In Glioblastoma Multiforme, Shreya Udawant

Theses and Dissertations

PI3K/AKT/mTOR signaling pathway is activated in 90% of all Glioblastoma Multiforme (GBM) tumors. We used a dual targeting approach to interfere with the phosphoinositide 3-kinase- mammalian target of rapamycin (PI3K-mTOR) pathway by treating U87MG GBM cells with NVP-BEZ235 (PI3K and mTOR a dual inhibitor) and, their downstream effects on molecular regulation on glycolytic genes were investigated using RNA-sequencing and gene set enrichment analysis (GSEA). RNA-seq identified 7803 differentially regulated genes in response to NVP-BEZ235. GSEA identified two glycolysis-related gene sets had significant differences (P < 0.05) in gene expression between control and NVP-BEZ235 treated samples. The GSEA core enrichment reported 17 and 35 genes were significantly downregulated (P adj < 0.05) in response to NVP-BEZ235 treatment in two different glycolysis related gene sets. We validated the expression of genes using qRT-PCR in U87MG cells as well as other GBM cell lines. Our results suggest novel insights on hallmark metabolic reprogramming associated with the PI3K-mTOR inhibition and provides advances in developing molecular targeted therapies.

Drivers Of Rickettsial Pathogen Transmission And Spillover In Local Tick Populations In Southeastern Virginia, Alexandra Cumbie

Biomedical Sciences Theses & Dissertations

Cases of spotted fever group rickettsiosis are becoming more prevalent in the United States. In Virginia, there are three human-biting ticks which are largely responsible for the spread of rickettsial pathogens and the increase in disease cases. These species include Dermacentor variabilis, Amblyomma americanum, and Amblyomma maculatum; all of which are vectors of rickettsial agents to vertebrate hosts. These species are sympatric as adults and have the potential to share large and small mammal hosts. Their interactions on and off host and their associated rickettsiae were the focus of this dissertation work. Amblyomma americanum is the vector …

Ixodes Scapularis Src Kinase Is Required For Rickettsial Pathogen Survival In Ticks, Jeremy W. Turck

Biological Sciences Theses & Dissertations

Anaplasma phagocytophilum is an obligate intracellular bacterium that causes disease in humans and animals. It is the causative agent for human anaplasmosis. A. phagocytophilum uses certain strategies to infect both vertebrates and invertebrates. It uses Ixodes scapularis ticks as a vector for spreading infection to other mammal species. This bacterium has a specific path for infection through the salivary glands of its vector host. It also suppresses certain functions such as the inhibition of apoptosis and ROS production in order to increase its survival in ticks. Src kinase, a non-receptor protein-tyrosine kinase, is a major player in cell signaling. Src …

Assessment Of Genetic Diversity In Largetooth Sawfish, Pristis Pristis, Populations Over The 20th Century, Ann Fearing

Master's Theses

The Critically Endangered Largetooth Sawfish, Pristis pristis, experienced global declines in range and abundance over the past century and Australia is now their last stronghold. This research aimed to understand whether these declines have been accompanied by a reduction in levels of genetic diversity. Using P. pristis tissue samples sourced from natural history specimens, three fragments (616-bp, 386-bp, 141-bp) in the mitochondrial DNA (mtDNA) control region were PCR-amplified. At each fragment, significant genetic structure was found in P. pristis overall (Φ_ST=0.946, N=9; 0.813, N=54; 0.771, N=99). The Indo-West Pacific and Atlantic/Eastern Pacific each harbor genetically distinct lineages of …