Life Sciences Commons^™

Upper Thermal Limits Of Freshwater Mussels (Bivalvia, Unionoida) In Ramped Temperature Exposures, Kathryn Rae Cottrell Martin

Graduate Theses/Dissertations

The purpose of this study was to determine the upper thermal limits of unionids. Three species of juvenile freshwater mussels were tested in lab experiments mimicking a diel pattern of temperature change (increasing 6 h, peak 2 h, and decreasing 8 h). The peak temperature fatal to half of the exposed population (LT50) was tested with respect to species, population, age, and seasonal acclimation. Mortality was monitored for 2 weeks after exposure. The smallest size classes were tested in a thermal cycler instrument, a novel application for testing mussels. LT50s for juveniles less than 3 weeks old were within 2-3°;C …

Determination Of Evolutionary History Of Big Bluestem Populations Through Chloroplast Dna Analysis, Tej Man Tamang

Master's Theses or Doctor of Nursing Practice

Andropogon gerardii Vitman (big bluestem) is one of the most dominant and widely distributed grasses of the North American prairie. It is widely used in restoration projects for the recovery of grassland ecosystems. A. gerardii demonstrates genetic and adaptive variation among populations across the prairie. With the objective to understand the evolutionary relationship between the A. gerardii populations, two noncoding chloroplast DNA (cpDNA) spacers (rpl32-trnL(UAG) and trnQ(UUG)-rps16) were studied. Similarly, genetic differentiation among the populations was also calculated based on the spacers. The trnQ(UUG)-rps16 spacer had more polymorphic sites than the rpl32-trnL(UAG) spacer. A phylogenetic tree based on combined cpDNA …

Encoding Of Saltatory Tactile Velocity In The Adult Orofacial Somatosensory System, Rebecca Custead

College of Education and Human Sciences: Dissertations, Theses, and Student Research

Processing dynamic tactile inputs is a key function of somatosensory systems. Spatial velocity encoding mechanisms by the nervous system are important for skilled movement production and may play a role in recovery of motor function following neurological insult. Little is known about tactile velocity encoding in trigeminal networks associated with mechanosensory inputs to the face, or the consequences of movement.

High resolution functional magnetic resonance imaging (fMRI) was used to investigate the neural substrates of velocity encoding in the human orofacial somatosensory system during unilateral saltatory pneumotactile inputs to perioral hairy skin in 20 healthy adults. A custom multichannel, scalable …

Soybean Tolerance To Soybean Aphid (Aphis Glycines Matsumura) Herbivory, Lia Marchi Werle

Department of Entomology: Dissertations, Theses, and Student Research

This research examined the soybean aphid tolerant soybean KS4202 and its possible role in soybean aphid management. Studies documented the stage at which the tolerance response was initially expressed, quantified the relationship between cumulative aphid-days (CADs) and yield loss, and determined economic injury levels (EILs) for the soybean aphid tolerant KS4202 soybean. At high aphid infestation levels, aphids negatively impacted yield for KS4202 and K03-4686 (susceptible) plants that were infested at V1 stage; however, KS4202 expressed tolerance to the soybean aphid at low aphid infestation levels. No significant differences in the yield parameters were detected for KS4202 when infested at …

Mechanism Of Triglyceride Lowering Action Of Akkermansia Muciniphila And Fenugreek In A Genetic Induced Hyperlipidemia, Jing Shen

Department of Nutrition and Health Sciences: Dissertations, Theses, and Student Research

Hyperlipidemia is a condition of abnormally elevated levels of lipids and/or lipoproteins in the blood circulation. It is usually accompanied with obesity, type 2 diabetes, insulin resistance, hypertension and non-alcoholic fatty liver diseases (NAFLD) and has become a great threat to human health. New therapeutic strategies are needed for the prevention and treatment of both genetic intervention-induced hyperlipidemia and environmentally induced hyperlipidemia. In this study, we determined the therapeutic effects of a diseaseprotecting gut bacteria, Akkermansia muciniphila, and an annual legume, fenugreek, on hypertriglyceridemia induced by genetic depletion of cAMP responsive binding protein H (CREBH KO) in mice. We found …

A Dynamic Run-Profile Energy-Aware Approach For Scheduling Computationally Intensive Bioinformatics Applications, Sachin Pawaskar, Hesham Ali

Computer Science Faculty Proceedings & Presentations

High Performance Computing (HPC) resources are housed in large datacenters, which consume exorbitant amounts of energy and are quickly demanding attention from businesses as they result in high operating costs. On the other hand HPC environments have been very useful to researchers in many emerging areas in life sciences such as Bioinformatics and Medical Informatics. In an earlier work, we introduced a dynamic model for energy aware scheduling (EAS) in a HPC environment; the model is domain agnostic and incorporates both the deadline parameter as well as energy parameters for computationally intensive applications. Our proposed EAS model incorporates 2-phases. In …

Funciones Sensoriales En Niños Menores De 3 Años Diagnosticados Con Trastorno Del Espectro Autista (Tea) / Sensory Processing In Toddlers Diagnosed With Autism Spectrum Disorder (Asd), Juliana Gutiérrez, Megan Chang, Erna Imperatore Blanche

Faculty Research, Scholarly, and Creative Activity

Spanish: Las dificultades de procesamiento sensorial en niños con Trastorno del Espectro Autista (TEA) están ampliamente descritos en la literatura principalmente mediante el uso de encuestas a padres y observaciones. Con menor frecuencia se han descrito las dificultades de procesamiento sensorial en niños menores de 3 años de edad que han sido posteriormente diagnosticados con TEA. Este studio retrospectivo está basado en 84 niños (28 diagnosticados con TEA, 28 con retraso en el desarrollo, y 28 niños con desarrollo típico) entre 18 y 36 meses de edad que asistieron a un programa de intervención temprana y cuyos padres completaron el …

Large Deletions At The Shox Locus In The Pseudoautosomal Region Are Associated With Skeletal Atavism In Shetland Ponies, Nima Rafati, Lisa S. Andersson, Sofia Mikko, Chungang Feng, Terje Raudsepp, Jessica Pettersson, Jan Janecka, Ove Wattle, Adam Ameur, Gunilla Thyreen, John E. Eberth, John Huddleston, Maika Malig, Ernest Bailey, Evan E. Eichler, Göran Dalin, Bhanu Chowdary, Leif Andersson, Gabriella Lindgren, Carl-Johan Rubin

Maxwell H. Gluck Equine Research Center Faculty Publications

Skeletal atavism in Shetland ponies is a heritable disorder characterized by abnormal growth of the ulna and fibula that extend the carpal and tarsal joints, respectively. This causes abnormal skeletal structure and impaired movements, and affected foals are usually killed. In order to identify the causal mutation we subjected six confirmed Swedish cases and a DNA pool consisting of 21 control individuals to whole genome resequencing. We screened for polymorphisms where the cases and the control pool were fixed for opposite alleles and observed this signature for only 25 SNPs, most of which were scattered on genome assembly unassigned scaffolds. …

Machine Learning Methods For Medical And Biological Image Computing, Rongjian Li

Computer Science Theses & Dissertations

Medical and biological imaging technologies provide valuable visualization information of structure and function for an organ from the level of individual molecules to the whole object. Brain is the most complex organ in body, and it increasingly attracts intense research attentions with the rapid development of medical and bio-logical imaging technologies. A massive amount of high-dimensional brain imaging data being generated makes the design of computational methods for efficient analysis on those images highly demanded. The current study of computational methods using hand-crafted features does not scale with the increasing number of brain images, hindering the pace of scientific discoveries …

Impacts Of Mowing Treatments On Smooth Bromegrass (Bromus Inermis) Belowground Bud Bank, L. Xu, J. Young, A. Boe, J. R. Hendrickson, N. H. Troelstrup Jr.

Natural Resource Management Faculty Publications

Introduced in the 1880s for improving forage production and controlling soil erosion, smooth bromegrass (Bromus inermis Leyss) has invaded and is threating numerous native prairie ecosystems and wildlife habitats in the Northern Great Plains. Land managers of the mixed-grass prairie ecosystems currently spend significant resources attempting to control invasive species and restore native grasslands with various management strategies including grazing, prescribed burning, herbicide application and seeding native species. Unfortunately, many studies have showed that such management efforts have minimal short-term effects. Without sustained effort, persistence and resurgence of smooth bromegrass is inevitable.

Heterochrony Of Cranial Bones In Amniota And The Phylogenetic Placement Of Testudines, Kathleen Sagarin

Masters Theses

The study of developmental systems may help to resolve the disagreement between morphological data and molecular data when it comes to the placement of Testudines among Amniota. Among other unique morphological adaptations, turtles possess an anapsid (unfenestrated) condition of the temporal region of the skull. If turtles are descended from diapsids, as molecular data suggests, this implies a rapid transformation of the temporal region from the diapsid condition to the anapsid condition. This study specifically addressed temporal bone heterochony among amniotes using the methods of Continuous Analysis (Germain and Laurin 2009) and Parsimov-based Genetic Inference (Harrison and Larsson 2008) to …

Communiqué: College Of Humanities, Arts & Sciences Alumni Magazine,Volume 5, Summer 2016, University Of Northern Iowa. College Of Humanities, Arts, And Sciences.

Communiqué: College of Humanities, Arts & Sciences Alumni Magazine

Contents:

-- Dean's Message
-- Candid: Fortepan Iowa
-- News in Short
-- Art + Science = "Big Bang"
-- Frontline Philosophy: Herrera
-- Pressing Forward: North American Review
-- CHAS Applause
-- Book Nook
-- Away in the Alpine
-- Printing Press
-- Nepal
-- Expanding Horizons
-- Donor Feature: Gary Sholten
-- National Science Foundation Funding
-- Metal Casting Center Moves
-- Transitions
-- Yager Awards
-- Students in the News
-- Coding Against Cancer
-- Dean's Fund Donor Listing
-- Alumni News

Plant Growth Promotion By Bradyrhizobium Japonicum Under Heavy Metal Stress, M. Seneviratne, S. Gunaratne, T. Bandara, L. Weerasundara, Nishanta Rajakaruna, G. Seneviratne, M. Vithanage

Biological Sciences

The increase in usage of heavy metals in different industrial activities causes their existence in effluents. Excessive concentrations of these heavy metals pollute soil and water. Heavy metals cause toxicities and other harmful effects not only in humans and animals but also in plants and soil microorganisms. Heavy metals disrupt many biochemical and physiological activities in bacteria, including growth, development, enzyme and hormone production. Indole acetic acid (IAA) is one of the most important hormones in plants, which is secreted by both bacteria and plants. The present study assessed the effects of Ni, Pb and Cu on the growth of …

Phamdb: A Web-Based Application For Building Phamerator Databases, James G. Lamine, Randall J. Dejong, Serita M. Nelesen

University Faculty Publications and Creative Works

PhamDB is a web application which creates databases of bacteriophage genes, grouped by gene similarity. It is backwards compatible with the existing Phamerator desktop software while providing an improved database creation workflow. Key features include a graphical user interface, validation of uploaded GenBank files, and abilities to import phages from existing databases, modify existing databases and queue multiple jobs. Availability and implementation: Source code and installation instructions for Linux, Windows and Mac OSX are freely available at https://github.com/jglamine/phage. PhamDB is also distributed as a docker image which can be managed via Kitematic. This docker image contains the application and all …

Differential Association Of Vitronectin And Fibronectin With Glass And Electrospun Fibers Of A Poly (D-Lysine) /Poly (Acrylic Acid), Syed Muhammad Sohaib Zafar Zafar

USF Tampa Graduate Theses and Dissertations

Proteins represent major constituent of the extracellular matrix which plays an important role in the formation, maintenance and remodeling of tissues, this project focuses on adsorption of two specific serum proteins fibronectin (FN) and vitronectin (VTN) responsible for mediating cell matrix interaction through integrin binding, tripeptide Arg-Gly-Asp (RGD) sequence found in these protein features are recognized by αβV₃ integrin which ultimately helps in clot formation.

Distribution Of Genomic Variation In The Usda Soybean Germplasm Collection And Relationship With Phenotypic Variation, Nonoy Batiller Bandillo

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The USDA Soybean Germplasm Collection harbors a large stock of genetic diversity with potential to accelerate soybean cultivar development. The extent and nature of favorable alleles contained in the collection are not well known nor is the distribution of genetic variation and how it relates to phenotypic variation. The genotyping of the entire USDA Soybean Germplasm Collection marked the beginning of a systematic exploration of genetic diversity for genetic research and breeding. In this research, we conducted the first comprehensive analysis of population structure on the collection of ~14,400 soybean accessions [Glycine max (L.) Merr. and G. soja Siebold …

Bioaugmentation And Correlating Anaerobic Digester Microbial Community To Process Function, Kaushik Venkiteshwaran

Dissertations (1934 -)

This dissertation describes two research projects on anaerobic digestion (AD) that investigated the relationship between microbial community structure and digester function. Both archaeal and bacterial communities were characterized using high-throughput (Illumina) sequencing technology with universal 16S rRNA gene primers. In the first project, bioaugmentation using a methanogenic, aerotolerant propionate enrichment culture was investigated as a possible method to increase digester methane production. Nine anaerobic digesters, seeded with different biomass, were operated identically and their quasi steady state function was compared. Before bioaugmentation, different seed biomass resulted in different quasi steady state function, with digesters clustering into high, medium or low …

A Computational Framework For Learning From Complex Data: Formulations, Algorithms, And Applications, Wenlu Zhang

Computer Science Theses & Dissertations

Many real-world processes are dynamically changing over time. As a consequence, the observed complex data generated by these processes also evolve smoothly. For example, in computational biology, the expression data matrices are evolving, since gene expression controls are deployed sequentially during development in many biological processes. Investigations into the spatial and temporal gene expression dynamics are essential for understanding the regulatory biology governing development. In this dissertation, I mainly focus on two types of complex data: genome-wide spatial gene expression patterns in the model organism fruit fly and Allen Brain Atlas mouse brain data. I provide a framework to explore …

Machine Learning Methods For Brain Image Analysis, Ahmed Fakhry

Computer Science Theses & Dissertations

Understanding how the brain functions and quantifying compound interactions between complex synaptic networks inside the brain remain some of the most challenging problems in neuroscience. Lack or abundance of data, shortage of manpower along with heterogeneity of data following from various species all served as an added complexity to the already perplexing problem. The ability to process vast amount of brain data need to be performed automatically, yet with an accuracy close to manual human-level performance. These automated methods essentially need to generalize well to be able to accommodate data from different species. Also, novel approaches and techniques are becoming …

Selfish Mutations: The Genetic Basis Of The Paternal Age Effect, Eoin C. Whelan

Biological Sciences Theses & Dissertations

As the mean age of childrearing grows, the effect of parental age on genetic disease and child health becomes ever more important. A number of autosomal dominant disorders show a dramatic paternal age effect due to selfish mutations: substitutions that grant spermatogonial stem cells (SSCs) a selective advantage in the testes of the father but have a deleterious effect in offspring.

I present a mathematical model to analyse the normal function of the stem cell compartment, which provides a framework for SSC renewal and accommodates differences between animal systems. In order to model the SSC mutation accumulation, a Markov chain …

Regional Extinction Risk And Conservation Priorities For Persian Gulf Marine Bony Fishes, Jack Ryan Buchanan

Biological Sciences Theses & Dissertations

Around the world, protected areas are the primary conservation measure used to combat biodiversity loss; however, these are often established without comprehensive species-specific information, leading to placement in areas that often do not address the processes that threaten biodiversity. To address this, International Union for Conservation of Nature Red List assessments are being utilized to determine species-specific threats and population status at the global and sub-global levels. This study examines the regional extinction risk for all known marine bony fishes of the Persian Gulf. About 8.3% of the 471 marine bony fishes assessed are at elevated risk of regional extinction. …

Gene Set Enrichment And Projection: A Computational Tool For Knowledge Discovery In Transcriptomes, Karl Douglas Stamm

Dissertations (1934 -)

Explaining the mechanism behind a genetic disease involves two phases, collecting and analyzing data associated to the disease, then interpreting those data in the context of biological systems. The objective of this dissertation was to develop a method of integrating complementary datasets surrounding any single biological process, with the goal of presenting the response to a signal in terms of a set of downstream biological effects. This dissertation specifically tests the hypothesis that computational projection methods overlaid with domain expertise can direct research towards relevant systems-level signals underlying complex genetic disease. To this end, I developed a software algorithm named …

Gfap-Positive Radial Glial Cells Are An Essential Progenitor Population For Later-Born Neurons And Glia In The Zebrafish Spinal Cord, Kimberly Johnson, Jessica Barragan, Sarah Bashiruddin, Cody J. Smith, Chelsea Tyrrell, Michael J. Parsons, Rosemarie Doris, Sarah Kucenas, Gerald B. Downes, Carla M. Velez, Caitlin Schneider, Catalina Sakai, Narendra Pathak, Katrina Anderson, Rachael Stein, Stephen H. Devoto, Jeff S. Mumm, Michael J.F. Barresi

Biological Sciences: Faculty Publications

Radial glial cells are presumptive neural stem cells (NSCs) in the developing nervous system. The direct requirement of radial glia for the generation of a diverse array of neuronal and glial subtypes, however, has not been tested. We employed two novel transgenic zebrafish lines and endogenous markers of NSCs and radial glia to show for the first time that radial glia are essential for neurogenesis during development. By using the gfap promoter to drive expression of nuclear localized mCherry we discerned two distinct radial glial-derived cell types: a major nestin+/Sox2+ subtype with strong gfap promoter activity and a minor Sox2+ …

Royal Jelly Promotes Daf-16-Mediated Proteostasis To Tolerate Β-Amyloid Toxicity In C. Elegans Model Of Alzheimer’S Disease, Xiaoxia Wang, Min Cao, Yuqing Dong

Publications

Numerous studies have demonstrated that dietary intervention may promote health and help prevent Alzheimer's disease (AD). We recently reported that bee products of royal jelly (RJ) and enzyme-treated royal jelly (eRJ) were potent to promote healthy aging in C. elegans. Here, we examined whether RJ/eRJ consumption may benefit to mitigate the AD symptom in the disease model of C. elegans. Our results showed that RJ/eRJ supplementation significantly delayed the body paralysis in AD worms, suggesting the β-amyloid (Aβ) toxicity attenuation effects of RJ/eRJ. Genetic analyses suggested that RJ/eRJ-mediated alleviation of Aβ toxicity in AD worms required DAF-16, rather …

High-Throughput Screening Of Clinically Approved Drugs That Prime Polyethylenimine Transfection Reveals Modulation Of Mitochondria Dysfunction Response Improves Gene Transfer Efficiencies, Albert Nguyen, Jared P. Beyersdorf, Jean-Jack Riethoven, Angela K. Pannier

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Nonviral gene delivery methods are advantageous over viral vectors in terms of safety, cost, and flexibility in design and application, but suffer from lower gene transfer efficiency. In addition to modifications to nucleic acid design and nonviral carriers, new tools are sought to enhance transfection. Priming is the pharmacological modulation of transfection efficiency and transgene expression, and has demonstrated transfection increase in several compounds, for example, chloroquine and glucocorticoids. To develop a library of transfection priming compounds, a highthroughput screen was performed of the NIH Clinical Collection (NCC) to identify clinical compounds that prime polyethylenimine (PEI) transfection. HEK293T cells were …

The Maintenance Of Phenotypic Divergence Through Sexual Selection: An Experimental Study In Barn Swallows Hirundo Rustica, Rebecca Safran, Yoni Vortman, Brittany R. Jenkins, Joanna K. Hubbard, Matt Wilkins, Rachel J. Bradley, Arnon Lotem

School of Biological Sciences: Faculty Publications

Previous studies have shown that sexual signals can rapidly diverge among closely related species. However, we lack experimental studies to demonstrate that differences in trait-associated reproductive performance maintain sexual trait differences between closely related populations, in support for a role of sexual selection in speciation. Populations of Northern Hemisphere distributed barn swallows Hirundo rustica are closely related, yet differ in two plumage-based traits: ventral color and length of the outermost tail feathers (streamers). Here we provide experimental evidence that manipulations of these traits result in different reproductive consequences in two subspecies of barn swallow: (H. r. erythrogaster in North …

01. From Cemetery Prairies To National Tallgrass Prairies: Proceedings Of The 24th North American Prairie Conference, Roger Anderson, Chris Benda

North American Prairie Conference Proceedings

Program booklet, abstracts, and all manuscripts for the 24th North American Prairie Conference held July 17-20, 2016, at Illinois State University.

The Contribution Of The Pineal Gland On Daily Rhythms And Masking In Diurnal Grass Rats, Arvicanthis Niloticus, Dorela D. Shuboni, Amna A. Agha, Thomas K. H. Groves, Andrew J. Gall

Faculty Publications

Melatonin is a hormone rhythmically secreted at night by the pineal gland in vertebrates. In diurnal mammals, melatonin is present during the inactive phase of the rest/activity cycle, and in primates it directly facilitates sleep and decreases body temperature. However, the role of the pineal gland for the promotion of sleep at night has not yet been studied in non-primate diurnal mammalian species. Here, the authors directly examined the hypothesis that the pineal gland contributes to diurnality in Nile grass rats by decreasing activity and increasing sleep at night, and that this could occur via effects on circadian mechanisms or …

The Explorations Program: Benefits Of Single-Session, Research- Focused Classes For Students And Postdoctoral Instructors, Jeremy L. Hsu, Anna M. Wrona, Sarah E. Brownell, Waheeda Khalfan

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We present an update to Explorations, a program at Stanford University that allows undergraduates in an introductory biology course to explore specialized topics in the biological sciences while providing graduate students and postdoctoral scholars the unique opportunity to develop and teach single-session, research-focused classes. We provide an assessment of eight iterations of the program, using program attendance, student and instructor evaluations, senior exit surveys, course grades, and completion of undergraduate honors theses to assess the impact of our program on students and instructors. Students rated their experiences highly, and most reported that the program had a positive impact on their …

Telomere Estimates By Qpcr In American Kestrel Birds, Esteban Palencia, Julie A. Heath (Mentor), Eric J. Hayden (Mentor)

Idaho Conference on Undergraduate Research

Telomeres are highly conserved repeated sequences found at the ends of linear chromosomes. Measuring telomere length has been used to estimate the ages of individuals in several species. The research presented here focuses on developing telomere length estimates in the American Kestrel (Falco sparverius), using Quantitative Polymerase Chain Reaction (qPCR). The verification of a primer pair that can amplify a reference gene and serve to normalize the telomere qPCR data is vitally important. The gene for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was preferably chosen because it occurs in a single copy in most birds. However, the Kestrel genome has not …