Biology Commons^™

Ohio Conservation Plan, Revised 2019, For The Plains Gartersnake, Thamnophis Radix, Norman Reichenbach

Faculty Publications and Presentations

This plan outlines strategies and methods used in an ongoing study initiated in 1999 to restore a self- sustaining population of the Plains Gartersnake (Thamnophis radix) in Ohio. Restoring a self-sustaining population would require increases in the current population to where the ratios of T. radix to T. sirtalis are from 1:1 to 1:12.2 in multiple locations in Killdeer Plains Wildlife Area (KPWA). This range of ratios would be similar to what was seen between 1978-80 by Reichenbach and Dalrymple (1986) at one site in KPWA and then more recently (2002 to 2009) by Wynn and Reichenbach (2018) at two …

Pcr Analysis On The Effects Of Alpha Synuclein Treatment On C6 Rat Glioma Cells, Michael John Helmus

Masters Theses

Multiple System Atrophy (MSA) is a rare neurological disease that mainly implicates the neuronal protein, alpha synuclein, as being centrally involved in MSA pathology. Despite synucleinopathy dogma, little is known about alpha synucleins role in MSA pathogenesis. The Ide laboratory previously conducted an Affymetrix gene expression study utilizing the post-mortem pons tissue from eight individuals with MSA and five individuals without any known neurological disorders. One conclusion from that study was that downregulation of numerous mitochondrial homeostasis related genes had occurred. It is hypothesized that alpha synuclein can perturb mitochondrial homeostasis through direct interaction with mitochondria. This study utilized Reverse …

Human-Carnivore Relations: Conflicts, Tolerance And Coexistence In The American West, Juan M. Requena-Mullor

Biology Faculty Publications and Presentations

Carnivore and humans live in proximity due to carnivore recovery efforts and ongoing human encroachment into carnivore habitats globally. The American West is a region that uniquely exemplifies these human-carnivore dynamics, however, it is unclear how the research community here integrates social and ecological factors to examine human-carnivore relations. Therefore, strategies promoting human-carnivore coexistence are urgently needed. We conducted a systematic review on human-carnivore relations in the American West covering studies between 2000 and 2018. We first characterized human-carnivore relations across states of the American West. Second, we analyzed similarities and dissimilarities across states in terms of coexistence, tolerance, number …

Oil Preference In Ants And Arthropod Diversity In Urban Environments, Itzel Guzman-Hernandez

Honors Theses

The success of certain ant species in urban areas is largely unknown. Available food in the environment could affect the composition of ants in urban areas due to a possible relationship between ant physiology and diet. I tested the oil preference of ants as a function of available arthropod prey in urban environments. I hypothesized that as arthropod diversity decreased, ant abundance at oil baits would decrease. Oil is an important nutrient that can affect ant body functions and activities. Ant foraging activities have been found to be affected by lipid depletion. A food source where ants can obtain oil …

Evidence For Trait-Based Community Assembly Patterns In Hardwood Hammock Forests, Suresh C. Subedi, J. Aaron Hogan, Michael S. Ross, Jay P. Sah, Christopher Baraloto

Faculty Publications - Biological Sciences

The hardwood forests of south Florida, commonly referred to as hammocks, persist as well-drained patches of broadleaf forest, embedded in a matrix of brackish water swamp, freshwater marsh, or pineland. Little is known about the patterns of community assembly of these subtropical forest communities in the landscape mosaic of south Florida. We used a functional trait approach to understand the composition of these communities and their responses to environmental variation across four areas of south Florida: the pine rocklands and freshwater marshes in Everglades National Park, and the lower and upper Florida Keys, where the hammocks are surrounded by halophytic …

Movements And Behaviors Of Resident And Translocated Northern Map Turtles (Graptemys Geographica) In The Upper Niagara River With Artificial Basking/Nesting Platforms As A Management Strategy, Chelsea L. Moore

Biology Theses

Urbanization and degradation of riparian zones has contributed to the decline of fish and wildlife populations throughout the world. Northern Map Turtles (Graptemys geographica) in the upper Niagara River face similar declines due to shoreline development and the concurrent loss of backwater habitats and terrestrial nesting sites. A project was initiated in which basking/nesting platforms were created, and Northern Map Turtles from a Lake Erie population were translocated into the river. Resident and translocated turtles were tracked using biotelemetry and their habitat use, behaviors, and swimming paths were compared. Translocated turtles exhibited homing behavior and had longer home …

Interactions Between Earliest Linearbandkeramik Farmers And Central European Hunter Gatherers At The Dawn Of European Neolithization, Alexey G. Nikitin, Peter Stadler, Nadezhda Kotova, Maria Teschler-Nicola, T. Douglas Price, Jessica Hoover, Douglas J. Kennett, Losif Lazaridis, Nadin Rohland, Mark Lipson, David Reich

Open Access Publishing Support Funded Articles

Archaeogenetic research over the last decade has demonstrated that European Neolithic farmers (ENFs) were descended primarily from Anatolian Neolithic farmers (ANFs). ENFs, including early Neolithic central European Linearbandkeramik (LBK) farming communities, also harbored ancestry from European Mesolithic hunter gatherers (WHGs) to varying extents, reflecting admixture between ENFs and WHGs. However, the timing and other details of this process are still imperfectly understood. In this report, we provide a bioarchaeological analysis of three individuals interred at the Brunn 2 site of the Brunn am Gebirge-Wolfholz archeological complex, one of the oldest LBK sites in central Europe. Two of the individuals had …

The Implementation Of Qpcr Beach Monitoring Methods: Analysis Of A Multi-Lab Validation Study And The Role Of Environmental Parameters On A Comparison Of Colilert And Qpcr Methods, Molly J. Lane

Masters Theses

Public beaches are routinely tested for potentially pathogenic bacteria to protect beachgoers from possible illness. An EPA approved method, Colilert™, used for testing E. coli in recreational water requires 18 – 22 hours before a result is reported but, recreators have already contacted unsafe water before the beach is closed. My study focused on a U.S. EPA proposed qPCR method (Draft Method C) to quantify E. coli in recreational waters that can provide same-day results. In Chapter 2, I examined the calibration procedure used to validate Draft Method C and compared standard curve intercept and slope estimates calculated with a …

Impacts Of Shoreline Restoration And Source Of Nutrient Enrichment On Macrophytes And Epiphytic Algal Communities, Paige Marie Kleindl

Masters Theses

Macrophytes and their epiphytic algal communities are integral for optimizing littoral ecosystem functioning in lakes. Epiphytic algae’s placement on the plant’s surface can reduce light and nutrient availability (i.e., nitrogen and phosphorus) for the host macrophyte. Macrophyte and epiphytic algal proximity complicates these primary producer group interactions and responses to bioavailable nutrients in the water column or porewater. For example, epiphytic algae may have a competitive advantage over surface water nutrients compared to macrophytes, which may have a competitive advantage over porewater nutrients via root systems.

Muskegon Lake’s industrial history and designation as an Area of Concern prompted shoreline restoration, …

Habitat Use Of The Climate-Sensitive Snowshoe Hare (Lepus Americanus) In The Manistee National Forest In Michigan’S Lower Peninsula, Spencer D. West

Masters Theses

Snowshoe hares (Lepus americanus) are a wide-ranging lagomorph that are important forest herbivores and a popular game species throughout their range. Across the southern boundary of their geographic range, snowshoe hares are experiencing population declines and possible extirpation due to increased predation pressure driven by climate change induced camouflage mismatch, competition for forage, degraded and fragmented habitat. One method of reversing the negative trends in snowshoe hare distribution is to increase and improve available hare habitat. A specific habitat analysis for local regions will most effectively advise managers how to target habitat management. I radio-collared 11 snowshoe hares in the …

Ecological Feedbacks Stabilize A Turf-Dominated Ecosystem At The Southern Extent Of Kelp Forests In The Northwest Atlantic, Colette Feehan, Sean P. Grace, Carla A. Narvaez

Department of Biology Faculty Scholarship and Creative Works

Temperate marine ecosystems globally are undergoing regime shifts from dominance by habitat-forming kelps to dominance by opportunistic algal turfs. While the environmental drivers of shifts to turf are generally well-documented, the feedback mechanisms that stabilize novel turf-dominated ecosystems remain poorly resolved. Here, we document a decline of kelp Saccharina latissima between 1980 and 2018 at sites at the southernmost extent of kelp forests in the Northwest Atlantic and their replacement by algal turf. We examined the drivers of a shift to turf and feedback mechanisms that stabilize turf reefs. Kelp replacement by turf was linked to a significant multi-decadal increase …

Developing Approaches That Leverage Next Generation Sequencing To Study Broad Biological Problems, Nicole Hales

Biology Dissertations - Archive

The advent of Next Generation Sequencing has been an extremely powerful tool in transforming the way we answer biological questions today. With the price per base pair continuously decreasing, and throughput, sequencing speed and quality of sequence reads increasing, NGS has allowed scientists to develop novel biological applications that have led to significant findings. During my dissertation, I leveraged several non-model organisms across various projects to develop new approaches of NGS to study a broad range of biological questions, including (1) understanding the genetic processes underlying transgenerational plasticity in Daphnia, (2) using Hi-C sequencing to study vertebrate genome structure and …

Leveraging The Dynamic Repeat Element Landscape Of Squamate Reptile Genomes To Understand Broad Patterns Of Vertebrate Genome Evolution And Transposable Element Biology, Giulia Im Pasquesi

Biology Dissertations - Archive

Vertebrate genomes are mostly composed of transposable elements (TE), mobile DNA sequences that have shaped genome structure and evolution by promoting positive (e.g., regulatory network rewiring, embryo development) and negative (e.g., ectopic recombination, disease) genomic processes. Leveraging genomic and transcriptomic data from diverse vertebrate species, I present novel lines of evidence that underscore the unique value of squamate reptile genomes for investigating properties of TE landscape evolution. This dissertation demonstrates that squamate genomes defy paradigms of amniote repeat element evolution set by mammals and birds, in particular: that greater variability in TE content is found between major lineages, that genome …

Mammal Species Inventory Using Various Trapping Methods In Zone 4 Of Billy Barquedier National Park, Belize During Rainy Season, Mersady Redding

Animal Science Undergraduate Honors Theses

Belize is a small country, but it is extremely ecologically diverse. Based on the few studies conducted in Belize, the abundance of mammals is low but diversity is high. Particular findings note the number and identity of species differed between four sites in the Maya Mountains of Belize, indicating that a data set from a single site is not representative of the Neotropical region. Insufficient data is available to estimate current species richness of many areas in Belize, including Billy Barquedier National Park (BBNP). The objective of this study was to explore trapping and documentation methods of terrestrial mammals in …

Freshwater Turtle Community Composition In Mined Land Strip Pit Lakes And The Effects Of Learned Trap Avoidance On Capture Rates Of Sternotherus Odoratus And Trachemys Scripta, Ethan Craig Hollender

Graduate Theses/Dissertations

Turtles are among the most threatened groups of organisms on the planet and as such are in need of protected habitat where healthy communities can be maintained. The reclamation of land that was formerly the site of surface strip mining provides a matrix of reclaimed terrestrial landscapes rich with lakes and ponds that have the potential to function as such habitat. To determine the suitability of these habitats for turtle communities, I compared the turtle communities of strip pit lakes and natural lakes in southeastern Kansas. Of the seven species of aquatic turtle I encountered, Common Snapping Turtles (Chelydra …

The Relationship Between Biofilm Production And Human Respiratory Cell Attachment And Invasion By Acinetobacter Baumannii, Rachel A. Pearson

Theses and Dissertations

Acinetobacter baumannii is an opportunistic gram-negative bacterial pathogen that causes many nosocomial infections in immunocompromised individuals. Common infections include catheter-associated urinary tract infections, ventilator-associated pneumonia, skin and soft tissue infections, and bloodstream infections that often lead to septicemia. Increasing multidrug resistance (MDR) in A. baumannii warrants new approaches to understanding its virulence mechanisms and pathogenicity. As a first step in infection, A. baumannii can attach to host cells, providing a surface for the bacteria to grow and perhaps facilitating biofilm formation and subsequent tissue invasion. In this study, we evaluated antibiotic resistance and characterized biofilm formation, attachment, invasion, and surface …

Non-Native Leaf Litter Modifies Algal Resources With Effects On Tadpole Growth, Spencer L. Cruz

Theses and Dissertations

Leaf litter species play a key role in determining the quality and quantity of algal resources in aquatic ecosystems as a cross-boundary subsidy. The invasion of non-native plant species into forests can alter aquatic resources. I investigated the effects of non-native leaf litter species on algal resources and green frog, Lithobates clamitans, development using a randomized complete block experiment that lasted 288 days. In experimental ponds, I added two non-native and two native leaf litter species in the presence and absence of tadpoles. Early in the experiment, Japanese honeysuckle and Chinese privet decreased periphyton N:P ratios and stimulated tadpole …

Δscope: A New Method To Quantify 3d Biological Structures And Identify Differences In Zebrafish Forebrain Development, Morgan S. Schwartz, Jake Schnabl, Mackenzie P.H. Litz, Benjamin Baumer, Michael Barresi

Biological Sciences: Faculty Publications

Research in the life sciences has traditionally relied on the analysis of clear morphological phenotypes, which are often revealed using increasingly powerful microscopy techniques analyzed as maximum intensity projections (MIPs). However, as biology turns towards the analysis of more subtle phenotypes, MIPs and qualitative approaches are failing to adequately describe these phenotypes. To address these limitations and quantitatively analyze the three-dimensional (3D) spatial relationships of biological structures, we developed the computational method and program called ∆SCOPE (Changes in Spatial Cylindrical Coordinate Orientation using PCA Examination). Our approach uses the fluorescent signal distribution within a 3D data set and reorients the …

The Concept Of The Hologenome, An Epigenetic Phenomenon, Challenges Aspects Of The Modern Evolutionary Synthesis, Adena Collens, Emma Kelley, Laura A. Katz

Biological Sciences: Faculty Publications

John Tyler Bonner's call to re-evaluate evolutionary theory in light of major transitions in life on Earth (e.g., from the first origins of microbial life to the evolution of sex, and the origins of multicellularity) resonate with recent discoveries on epigenetics and the concept of the hologenome. Current studies of genome evolution often mistakenly focus only on the inheritance of DNA between parent and offspring. These are in line with the widely accepted Neo-Darwinian framework that pairs Mendelian genetics with an emphasis on natural selection as explanations for the evolution of biodiversity on Earth. Increasing evidence for widespread symbioses complicates …

Toward Understanding The Mechanism Of Protein Targeting In The Chloroplast Signal Recognition Particle Pathway, Mercede Furr

Graduate Theses and Dissertations

Protein targeting is a vital cellular function. The signal recognition particle (SRP) pathway is a universally conserved targeting system present in the cytosol and used to co-translationally target many proteins to the inner membrane of prokaryotes and the endoplasmic reticulum of eukaryotes. The chloroplast has a homologous SRP system which post-translationally targets light harvesting chlorophyll binding proteins (LHCPs) to the thylakoid membrane for integration. The chloroplast SRP (cpSRP) is a heterodimer with a 54 kDa subunit equivalent to SRP54 in the canonical pathway. In addition, cpSRP contains a novel 43 kDa subunit which is a unique and irreplaceable component. cpSRP43 …

Genetic Relationships Using Mitochondrial Versus Nuclear Markers: Is The Catfish Rag1 Gene Suitable For Species Differentiation In The Family Pangasiidae?, Huong Thanh Hoang

Graduate Theses and Dissertations

The Mekong River located in Southeast Asia is a global “hotspot” for aquatic biodiversity. It includes an extensive variety of fish species second only to the Amazon River in South America. Recent studies have revealed the impacts of anthropogenic and climate factors on this river system. Such impacts can result in the formation of barriers, which divide a species population and impede gene flow between separated sub-populations. Barriers influence evolutionary trajectories resulting in the generation of geographic variants or subspecies from an ancestral population. Catfish (Teleostei: Siluriformes) are a key species of the Mekong River ecosystem and are an essential …

Finding And Analyzing De Novo Mutations In The Exomes Of Parent-Offspring Trios Of Spontaneous Chiari Malformation Type 1 Patients, Brian Leon Ricardo

Arts & Sciences Graduate Student Theses and Dissertations

Chiari Malformation Type 1 (CM1) is a neurodevelopmental disorder that occurs when one of the cerebellar tonsils herniates past the foramen magnum causing headaches, motor or sensory deficits, sleep apnea, and difficulty swallowing. This disorder is estimated to affect 1% of the population but due to the need of neuroimaging for diagnosis and the presence of asymptomatic patients there is still uncertainty about the exact proportion of the population affected. CM1 often presents itself with other neurodevelopmental disorders such as syringomyelia, scoliosis, and known genetic syndromes such as Klippel-Feil and Marfan syndromes. Twin, family, and familial clustering studies have established …

Effects Of Water Table Depth And Edaphic Characteristics On Plant Diversity In A Southern Mississippi Pitcher Plant Bog, Patrick Kirby

Master's Theses

This study examined the effects that water table depth and soil characteristics have on plant species richness and species composition within pitcher plant bogs across seasons. Eight piezometers were installed at random distances to monitor long-term water table depth and pressure fluctuations along a ~710-meter line transect traversing upland and bog habitats. Vegetation sampling quadrats (n=128) were set up near each piezometer. Cover data and water table depths were collected in spring and late summer. Soil samples collected from each treatment group were used to obtain soil texture and nutrient data. The summer collection period yielded a total gdiversity of …

Ywha (14-3-3) Protein Isoforms And Their Interactions With Cdc25b Phosphatase In Mouse Oogenesis And Oocyte Maturation, Alaa A. Eisa, Santanu De, Ariana Detwiler, Eva Gilker, Alexander C. Ignatious, Srinivasan Vijayaraghavan, Douglas Kline

Biology Faculty Articles

Background

Immature mammalian oocytes are held arrested at prophase I of meiosis by an inhibitory phosphorylation of cyclin-dependent kinase 1 (CDK1). Release from this meiotic arrest and germinal vesicle breakdown is dependent on dephosphorylation of CDK1 by the protein, cell cycle division 25B (CDC25B). Evidence suggests that phosphorylated CDC25B is bound to YWHA (14-3-3) proteins in the cytoplasm of immature oocytes and is thus maintained in an inactive form. The importance of YWHA in meiosis demands additional studies.

Results

Messenger RNA for multiple isoforms of the YWHA protein family was detected in mouse oocytes and eggs. All seven mammalian YWHA …

Evaluation Of Pheromone Mating Disruption For California Red Scale Control In Commercial California Citrus, Joel Timothy Leonard

Master's Theses

California red scale (CRS), Aonidella aurantii, is an increasingly injurious insect pest for the California citrus industry due to insecticide resistance, changing weather patterns, and shifting trade regulations. The presence of the insect on fruit, damages the rind of the fruit and high populations can cause dieback of branches as well as lower yields. Pheromone mating disruption of CRS has the potential to alleviate population control concerns and reduce insecticide use. The efficacy of the pheromone mating disruption technique for pest management of CRS was determined using the products CheckMate® CRS and Semios CRS Plus. CheckMate® CRS was evaluated …

Effects Of Infanticide Risk And Timber Harvest On American Black Bear Space Use, D. Cody Norton

All NMU Master's Theses

Space use is an important aspect of bear ecology that maybe influenced by infanticide risk and timber harvest. I used generalized linear mixed models (GLMM) to determine if female American black bear (Ursus americanus) space use was consistent with avoidance behavior to reduce infanticide risk in the Upper Peninsula of Michigan during the 2009–2011 and 2013–2014 breeding seasons. Females with cubs occupied core areas and home ranges of similar size and relative probability of male use to females without cubs. Additionally, females with cubs did not reduce movements during times of day when male movements were greatest. Female …

Integrating Social Dimensions Into Spatial Connectivity Planning For Grizzly Bears, Abigail Sage

Boise State University Theses and Dissertations

In anthropogenic landscapes, which prevail globally, preserving key habitat corridors or routes between wildlife populations is vital for long-term species persistence. Animals moving through these corridors can encounter a number of barriers, including roads, fences, or other human land-uses. Additionally, people unwilling to cohabitate with wildlife can also kill animals considered nuisances or disturb animals in ways that reduce their fitness. The spatial patterns of human tolerance therefore play an important role in the efficacy of habitat corridors. Although there are large bodies of research on habitat corridors and human attitudes toward wildlife, studies that examine the spatial interaction of …

Characterization Of Plasmids Harbored By Vibrio Cholerae Isolates Endemic To The Rio Grande Delta, Viviana Trevino

Theses and Dissertations

Cholera is a diarrheal disease responsible for considerable morbidity and mortality globally. Epidemics along the Rio Grande Delta were reported during the 1850s, and the etiological agent Vibrio cholerae, remains endemic, thus presenting a unique opportunity for a study of historical and biological relevance. V. cholerae strains were isolated from two locations: the Rio Grande River under a bridge linking Brownsville to Matamoros (site 21) and where the river empties into the Gulf of Mexico (site 42). Two strains from site 21, and one from site 42 were selected to isolate, subclone, sequence, assemble and annotate extra-chromosomal elements. Results …

Role Of Topoisomerase Ii Alpha In Dna Topology And T Cell Responses During Chronic Viral Infections, Stella Chinyere Ogbu

Electronic Theses and Dissertations

The clearance of viruses is largely dependent upon the activation of T cells to generate a robust immune response. However, host responses are suppressed during chronic viral infections. In this thesis, we explored the role of Top2α in DNA topology in individuals with chronic HBV, HCV, and HIV infections. We found that Top2α protein expression and activity were low in T cells derived from chronically virus-infected individuals compared to healthy subjects. Using CD4⁺ T cells treated with Top2α inhibitor or poisoner as a model, we demonstrated that Top2α inhibition disrupts the DNA topology, suppresses DNA repair kinase (ATM), and …

Age And Seasonal Change In The Chronobiology Of A Spider With An Exceptionally Long-Period Circadian Clock, Shae Crain

Electronic Theses and Dissertations

This study examines locomotor activity in samples of Frontinella pyramitela collected over its active season (April-October) to investigate whether seasonality and/or age may help explain the exceptional variability typically found in spider clock systems. Despite its noteworthy variability (%CV= 7.7), we have found that Frontinella has a mean free-running period of 28.4±2.18 hours that does not significantly vary over time. There is no correlation between day length and free-running period, indicating that varying length of FRP is not a function of photoperiod length. In LD 12:12 h, the window of activity is significantly smaller in April, gradually widening as the …