Biology Commons^™

Optimizing Crispr/Cas9 Gene Targeting To Investigate Cone Photoreceptor Development In The Chick Retina, Diana Y. Kim

Dissertations and Theses

Many human eye conditions result in the loss of vision, due to the degeneration of cone photoreceptors in the retina. Thus, the development of methods to regenerate these cone photoreceptors is an active area of study. In order to find ways to regenerate cones, the molecular pathways and gene regulatory networks that a retinal progenitor cell takes to develop into a postmitotic cone photoreceptor needs to be well understood. In an attempt to answer this question, this paper studies the effect of CRISPR/Cas9-mediated mutagenesis of two key transcription factors, Otx2 and Nr2e3, on retinal progenitor cells and cone photoreceptors throughout …

Quantifying Protein Copy Number In Super-Resolution Using An Imaging Invariant Calibration, Francesca Cella Zanacchi, Carlo Manzo, Raffaella Magrassi, Nathan D. Derr, Melike Lakadamyali

Biological Sciences: Faculty Publications

The use of super-resolution microscopy in recent years has revealed that proteins often form small assemblies inside cells and are organized in nanoclusters. However, determining the copy number of proteins within these nanoclusters constitutes a major challenge because of unknown labeling stoichiometries and complex fluorophore photophysics. We previously developed a DNA-origami-based calibration approach to extract protein copy number from super-resolution images. However, the applicability of this approach is limited by the fact that the calibration is dependent on the specific labeling and imaging conditions used in each experiment. Hence, the calibration must be repeated for each experimental condition, which is …

Natural History Note: Anolis Sagrei Foraging On A Patch Of Obvious Prey, Stuart V. Nielsen, Aaron M. Bauer, Tony Gamble

Biological Sciences Faculty Research and Publications

No abstract provided.

A Multitrophic Perspective On Biodiversity–Ecosystem Functioning Research, Nico Eisenhauer, Holger Schielzeth, Andrew D. Barnes, Kathryn Barry, Aletta Bonn, Ulrich Brose, Helge Bruelheide, Nina Buchmann, Francois Buscott, Anne Ebeling, Olga Ferlian, Grégoire T. Freschet, Darren P. Giling, Stephan Hättenschwiler, Helmut Hillebrand, Jes Hines, Forest Isbell, Eva Koller-France, Birgitta König-Ries, Hans De Kroon, Sebastian T. Meyer, Alexandru Milcu, Jörg Müller, Charles A. Nock, Jana S. Petermann, Christiane Roscher, Christoph Scherber, Michael Scherer-Lorenzen, Bernhard Schmid, Andreas Schuldt, Teja Tscharntke, Manfred Türke, Nicole M. Van Dam, Fons Van Der Plas, Anja Vogel, Cameron Wagg, David A. Wardle, Alexandra Weigelt, Wolfgang W. Weisser, Christian Wirth, Malte Jochum

Biological Sciences Faculty Research and Publications

Concern about the functional consequences of unprecedented loss in biodiversity has prompted biodiversity–ecosystem functioning (BEF) research to become one of the most active fields of ecological research in the past 25 years. Hundreds of experiments have manipulated biodiversity as an independent variable and found compelling support that the functioning of ecosystems increases with the diversity of their ecological communities. This research has also identified some of the mechanisms underlying BEF relationships, some context-dependencies of the strength of relationships, as well as implications for various ecosystem services that mankind depends upon. In this paper, we argue that a multitrophic perspective of …

Capsaicin As A Tool For Repelling Southern Flying Squirrels From Red-Cockaded Woodpecker Cavities, Robert T. Meyer, James A. Cox

Human–Wildlife Interactions

The southern flying squirrel (Glaucomys volans) is an important kleptoparasite of cavities excavated by the imperiled red-cockaded woodpecker (Dryobates borealis). Flying squirrel usurpation of cavities may affect woodpecker productivity, but current efforts to manage flying squirrels are costly and time consuming. We assessed whether capsaicin could deter flying squirrel use of woodpecker cavities on a site in southwest Georgia, USA. Twenty-nine cavity tree clusters received 4 treatments: capsaicin, water, air, and a control (no treatment). Only capsaicin both removed more flying squirrels from the cavity immediately after its application and decreased the probability of a flying …

Pursue Undergraduate Research Journal Volume 2 (Issue 1) 2019

Pursue: Undergraduate Research Journal

The scholarly journal, “PURSUE: Undergraduate Research Journal” (ISSN 2473-6201), provides undergraduates an avenue to publish their original research abstracts and articles in the following areas: psychology, sociology, biology, chemistry, physics, engineering, computer science, mathematics, humanities, agriculture, architecture, health, business, and education (this list is not exclusive).

The original research articles included in this journal are peer reviewed and selected by the journal’s Editorial Board. The review process allows undergraduate researchers to receive feedback from notable scientists in their field of study and teach them about the publication process. Publication of their work will not only inform the scientific community; it …

Occurrence Of The Sinus Nematode Skrjabingylus Sp. (Nematoda: Metastrongyloidea) Inferred From Sinus Lesions In Arkansas Mustelidae And Mephitidae, With Review Of Relevant Literature, C. Renn Tumlison, Terry Tumlison

Journal of the Arkansas Academy of Science

Nasal nematodes of the genus Skrjabingylus occur in the mammalian families Mustelidae and Mephitidae, and have been found from Canada to Costa Rica. Ingestion of infected snails, frogs, snakes, or mice can lead to infection of these mammalian hosts. Infection often causes pathology to bones in the sinus region, which may lead to discoloration, enlargement, and fenestrations of the bone. Examination of museum specimens for bone lesions or other evidence of infection has been used to evidence prior infection, but prevalence and intensity cannot be interpreted without actually recovering the parasite. We examined Mustelids and Mephitids in collections of mammals …

Distribution, Habitat, And Life History Aspects Of The Dwarf Crayfishes Of The Genus Cambarellus (Decapoda: Cambaridae) In Arkansas, Henry W. Robison, Chris T. Mcallister

Journal of the Arkansas Academy of Science

The dwarf crayfishes of the genus Cambarellus are represented in Arkansas by only 2 species: Cambarellus (Pandicambarus) puer (Hobbs) and C. (P.) shufeldtii (Faxon). Both species are quite small and uncommonly encountered in the state. Between 1972 and 2018, we made 368 crayfish collections throughout the 75 counties of Arkansas. A total of 34 collections (our collections, plus museum specimens), and those previously collected by Reimer (1963) yielded a total of 304 specimens of C. puer and 12 collections of C. shufeldtii returned 54 specimens of C. shufeldtiii. Herein, we document these …

Parasites (Trematoda, Nematoda, Phthiraptera) Of Two Arkansas Raptors (Accipitriformes: Accipitridae; Strigiformes: Strigidae), Chris T. Mcallister, Lance A. Durden, Charles R. Bursey, John A. Hnida, Vasyl V. Tkach, Tyler J. Achatz

Journal of the Arkansas Academy of Science

Very little is known about the helminth parasites of hawks and owls of Arkansas. We had the opportunity to salvage 2 road-killed raptors, a red-shouldered hawk (Buteo lineatus) and a great horned owl (Bubo virginianus) from the state and examine them for ecto- and endoparasites. Found were chewing lice (Degeeriella fulva) and a nematode (Porrocaecum angusticolle) on/in B. lineatus, and 3 digenean trematodes (Echinoparyphium sp., Strigea elegans, Neodiplostomum americanum), and nematode eggs (Capillaria sp.) in B. virginianus. We document 6 new distributional records for these parasites.

Observations Of An Alligator (Alligator Mississippiensis) Nest And Behavior Of Hatchlings In Clark County, With Anecdotal Observations Of Other Alligator Nests In Arkansas, Allison Surf, Kevin Nordengren, C. Renn Tumlison, Kelly Irwin

Journal of the Arkansas Academy of Science

Historically, the American alligator (Alligator mississippiensis) ranged through southern and much of eastern Arkansas. By the early 1900s, alligator populations had declined due to unregulated hunting, commercial exploitation, and habitat loss. In 1961, the Arkansas Game and Fish Commission (AGFC) established protection of this species, and in 1967 the U.S. Fish and Wildlife Service listed the alligator as an endangered species. The AGFC conducted a restocking program from 1972-1984, and the species made a full recovery in Arkansas. Still, little is known about reproductive biology in the state. We observed an alligator nest near Arkadelphia, Clark Co., the mound …

Cotylogaster Occidentalis (Aspidogastrea: Aspidogastridae) From Freshwater Drum, Aplodinotus Grunniens (Actinopterygii: Sciaenidae), In Northeastern Oklahoma, Chris T. Mcallister, Anindo Choudhury

Journal of the Arkansas Academy of Science

No abstract provided.

Vitellogenin Receptor As A Target For Tick Control: A Mini-Review, Robert D. Mitchell Iii, Daniel E. Sonenshine, Adalberto A. Pérez De León

Biological Sciences Faculty Publications

While much effort has been put into understanding vitellogenesis in insects and other organisms, much less is known of this process in ticks. There are several steps that facilitate yolk formation in developing oocytes of which the vitellogenin receptor (VgR) is a key component. The tick VgR binds vitellogenin (Vg) circulating in the hemolymph to initiate receptor-mediated endocytosis and its transformation into vitellin (Vn). The conversion of Vg into Vn, the final form of the yolk protein, occurs inside oocytes of the female tick ovary. Vn is critical to tick embryos since it serves as the nutritional source for their …

Global Patterns And Drivers Of Ecosystem Functioning In Rivers And Riparian Zones, Scott D. Tiegs, David M. Costello, Mark W. Isken, Guy Woodward, Peter B. Mcintyre, Mark O. Gessner, Eric Chauvet, Natalie A. Griffiths, Alexander S. Flecker, Vicenç Acuña, Ricardo J. Albariño, Daniel C. Allen, Cecilia Alonso, Patricio Andino, Clay Arango, Jukka Aroviita, Marcus V. M. Barbosa, Leon A. Barmuta, Colden V. Baxter, Jose Checo Colón-Gaud

Biology: Faculty Publications

River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth’s biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints …

Cold Tolerance, Temperature Mediated Discontinuous Gas Exchange, And Emergence Of The Blue Orchard Mason Bee (Osmia Lignaria), Logan Kral

All Master's Theses

The relationship between low temperatures, emergence and supercooling point of Osmia lignaria were the subject of this study. One hundred sixty-eight bees were subjected to 5 pre-wintering temperature treatments (two constant temperature controls - 22^oC, 14^oC, one of which with and one without a 12h photoperiod, and three 12h:12h thermoperiod treatments – 14:10^oC, 14:5^oC, and 14:0^oC) and were then evaluated in terms of emergence time and post-emergence vigor. An additional 70 bees were tested for metabolic rate and discontinuous gas exchange in response to test temperature conditions. An additional sample …

Are Highways Stressful For Pikas?: Analysis Of Stress Hormones Of The American Pika (Ochotona Princeps) Living Adjacent To Interstate 90 In The Cascade Range Of Washington State, Thomas J. Mcintyre Iii

All Master's Theses

Roads often disrupt ecosystem connectivity, harming many wildlife populations. Wildlife crossing structures perforate the barrier-effect of roads, providing safe passage for species dispersing across roads, thereby reconnecting ecosystems. Some wildlife species live in modified habitats along roads and in habitat features within wildlife crossing structures, but their fitness in these potentially stressful environments is poorly understood. Chronic stress alters behavior, reduces reproduction, and has been linked to reduced survival. Animals affected by chronic stress in road-adjacent habitats could reduce the ability of wildlife crossing structures to improve connectivity across roads. I assessed stress hormone concentrations in a low-mobility species, the …

Symbiotic Bacteria Can Colonize Closely-Related, But Not Distantly-Related Species Of Its Host Dictyostelium Discoideum, Rory Vu Mather

Undergraduate Research Symposium Posters

Some of the closest interactions between organisms can be found within symbioses, where different individuals live in close physiological contact and either benefit or harm the other. A powerful kind of benefit comes when bacterial symbionts produce amino acids or provide digestive capabilities outside the host’s ability, in essence taking advantage of the other’s genetic catalog. One such symbiosis is that of the social amoeba Dictyostelium discoideum and its bacterial symbionts Burkholderia agricolaris, Burkholderia hayleyella, and Burkholderia bonneia. In this symbiosis, Burkholderia provide the capability of carrying food bacteria to their host, an advantageous trait when bacterial food is rare. …

Examining The Effects Of Fadrozole, An Aromatase Inhibitor, On Testosterone And Estrogen Production Of Domestic Chicken Embryos (Gallus Gallus), Abby E. Joseph

Honors Theses

The hypothalamic-pituitary-gonadal (HPG) axis is responsible for the production of the hormones testosterone and estradiol, and testosterone is thought to contribute to regulation of the axis through a negative feedback mechanism. Regulation by negative feedback involves the product of a pathway turning off that pathway when enough product is made. However, because the enzyme P450 aromatase converts testosterone to estradiol, estradiol may also contribute to regulation of the HPG axis and other phenomena that have been attributed to testosterone, like the inhibition of immune function. Previous studies have injected birds with an aromatase inhibitor (presumably reducing estradiol production) and shown …

Analysis Of The Thermal Stability Of A Diverse Panel Of Respiratory Syncytial Virus (Rsv) Strains, Darby Deford

Undergraduate Honors Thesis Collection

Respiratory syncytial virus (RSV) is a major respiratory pathogen of young infants and the elderly and is associated with upper and lower respiratory disease. Vaccine development for RSV has been hindered by poor immunogenicity in target populations, genetic and physical instabilities, and a legacy of vaccine-enhanced disease. The fusion and attachment proteins of RSV, F and G, have been seen to be responsible for inducing the majority of neutralizing antibodies. However, little remains known about how differences in RSV F and G affect virus replication and stability. In this thesis, we proposed to examine the replication and thermal stability of …

The Gut Microbiome: Is Fecal Matter Microbial Composition A Proxy For Intestinal Microbial Composition In Studies Of The Microbiome, Enique Reyes

All Master's Theses

As many health phenomena seem to be affected directly and indirectly by the microbiome, gut microbiome research has increased in the last decade. Issues such as allergies, cancer, obesity, and other health complications have been shown to be influenced by the microbiome. Most of gut microbiome research is done by collecting and sequencing the DNA of the microbiome of the fecal matter from model organisms or human subjects. Studies that use this method of sample collection and analysis assume that fecal matter microbiomes are similar to intestinal microbiomes, and that it can be used as a proxy. At present, no …

Exploring The Efficacy Of Natural Products In Alleviating Alzheimer’S Disease Using Animal Models, Prajakta Deshpande, Neha Gogia, Amit Singh

Biology Faculty Publications

Alzheimer’s disease (hereafter AD) is a progressive neurodegenerative disorder that affects the central nervous system. There are multiple factors that cause AD, viz., accumulation of extracellular Amyloid-beta 42 plaques, intracellular hyper-phosphorylated Tau tangles, generation of reactive oxygen species due to mitochondrial dysfunction and genetic mutations. The plaques and tau tangles trigger aberrant signaling, which eventually cause cell death of the neurons. As a result, there is shrinkage of brain, cognitive defects, behavioral and psychological problems. To date, there is no direct cure for AD. Thus, scientists have been testing various strategies like screening for the small inhibitor molecule library …

Changes In Walleye Fecundity And Egg Size Before, During, And After Rehabilitation Of The Red Lakes Fishery, Benjamin J. Miller, Benjamin D. Erb

Journal of Earth and Life Science

The Red Lakes in northern Minnesota experienced a major Walleye Sander vitreus fishery crash in the late 20th century, but has since recovered to record abundances and supports a major commercial and recreational fishery. Fecundity is an integral aspect of recruitment that can contribute greatly to the understanding of fishery population dynamics. To elucidate the effects of varying Walleye densities and exploitation rates on fecundity and egg size in years 1989 (overexploited fishery), 2004 (recovering fishery), and 2017 (recovered fishery), we analyzed linear models that related fecundity or egg size to morphological features for these three sampling periods. Walleyes were …

Goldeye Hidon Alosoides Calorimetry In Red Lake, Jesse Mendel

Journal of Earth and Life Science

Goldeye Hiodon alosoides are found across North America and are a relatively unstudied group of fish as they have had no economic value in the past. Ecologically speaking, these fish could have importance to the waters that they inhabit, as they are prey to fishes like Walleyes Sander vitreus, Northern Pike Esox lucius, and Muskellunge Esox masquinongy. These fish could potentially be vital to predatory fishes because of the amount of oil found in these fish, creating gram for gram more energy than compared to other consumable substances. The average energy density for all Goldeye was 6.73 …

Examining Black Bullhead Ameiurus Melas Age And Growth In Shallow Minnesota Lakes, Michael S. Collins, Anna M. Medina

Journal of Earth and Life Science

Ageing methods, population age structures, and growth trajectories for Black Bullhead Ameiurus melas were evaluated for six populations from shallow lakes divided between two ecoregions in Minnesota, USA. A total of 693 fish were collected in July and August 2018 and measured for total lengths (TL) and weights (g). We collected ageing structures from 320 of these fish. Crosssections of lapillar otoliths (n=191) and pectoral spine structures (n=75) were used to estimate age by two readers in a blind reading procedure. Fish caught ranged in total lengths from ~40 to 350 mm and weighed between 8 and 380 g. Black …

Multistate Survey Of American Dog Ticks (Dermacentor Variabilis) For Rickettsia Species, Joy A. Hecht, Michelle E.J. Allerdice, Elizabeth A. Dykstra, Laura Mastel, Rebecca J. Eisen, Tammi L. Johnson, Holly D. Gaff, Andrea S. Varela-Stokes, Jerome Goddard, Benedict B. Pagac, Christopher D. Paddock, Sandor E. Karpathy

Biological Sciences Faculty Publications

Dermacentor variabilis, a common human-biting tick found throughout the eastern half and along the west coast of the United States, is a vector of multiple bacterial pathogens. Historically, D. variabilis has been considered a primary vector of Rickettsia rickettsii, the causative agent of Rocky Mountain spotted fever. A total of 883 adult D. variabilis, collected between 2012 and 2017 from various locations in 12 states across the United States, were screened for rickettsial DNA. Tick extracts were evaluated using three real-time PCR assays; an R. rickettsii-specific assay, a Rickettsia bellii-specific assay, and a Rickettsia genus-specific …

Optimizing De Novo Genome Assembly From Pcr-Amplified Metagenomes, Simon Roux, Gareth Trubl, Danielle Goudeau, Nandita Nath, Estelle Couradeau, Nathan A. Ahlgren, Yuanchao Zhan, David Marsan, Feng Chen, Jed A. Fuhrman, Trent R. Northen, Matthew B. Sullivan, Virginia I. Rich, Rex R. Malmstrom, Emiley A. Eloe-Fadrosh

Biology

Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes can now be generated from nanogram to subnanogram amounts of DNA. However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. Methods. Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified …

Nuclear Envelope Organization In Dictyostelium Discoideum, Petros Batsios, Ralph Gräf, Michael P. Koonce, Denis A. Larochelle, Irene Meyer

Biology

The nuclear envelope consists of the outer and the inner nuclear membrane, the nuclear lamina and the nuclear pore complexes, which regulate nuclear import and export. The major constituent of the nuclear lamina of Dictyostelium is the lamin NE81. It can form filaments like B-type lamins and it interacts with Sun1, as well as with the LEM/HeH-family protein Src1. Sun1 and Src1 are nuclear envelope transmembrane proteins involved in the centrosome-nucleus connection and nuclear envelope stability at the nucleolar regions, respectively. In conjunction with a KASH-domain protein, Sun1 usually forms a so-called LINC complex. Two proteins with functions reminiscent of …

Analysis Of Dunc-13 And Its Role In The Formation Of Ethanol Tolerance In Drosophila Melanogaster, Charles Cook

Honors Theses

Alcoholism is a costly disease that is responsible for a significant portion of the global disease burden, yet there is much is left to know about how this disease develops. Tolerance plays a critical role in predisposing an individual to alcohol abuse. Recently, the active zone of presynaptic neurons has been implicated as an ethanol effector. In this study, we examined the role that a presynaptic active zone protein, Dunc13, plays in the formation of tolerance to alcohol. Dunc13 is an ortholog of mammalian Unc13-1, and through the use of Drosophila as a model system, we show that genetic reduction …

The Developmental And Behavioral Effects Of Early Life Stage Cannabinoid Exposure, Mariegene E. Almand

Honors Theses

As of 2019, marijuana legalization and decriminalization is sweeping the globe. Patients are increasingly using cannabis-derived compounds including Δ9-tetrahydrocannabinol (THC) and cannabidiol (CBD) for treatment of diseases as diverse as epilepsy, Parkinson’s disease, and cancer. Furthermore, mothers are claiming that CBD oil decreases uncomfortable pregnancy side effects. While the adverse effects of chronic cannabinoid use and of cannabinoids on pregnancy have been previously investigated, the exact function of the endocannabinoid system, and its primary receptors, cannabinoid receptors 1 and 2, involved in producing these outcomes is still unclear. In this study, two strains of zebrafish embryos, namely fli and cnr2-/- …

Microbial Communities Associated With Dragonfly Nymphs Raised In Varying Concentrations Of Amoxicillin, Michelle Basha

Honors Theses

The bacteria on and within an organism make up that organism’s microbiome. Given interest in the use of antibiotics in agriculture and the effect of microbes on human health, more studies are needed on the microbial community composition of different organisms and how it responds to antibiotic use. This study investigated changes in the amount of antibiotic resistant bacteria present in dragonfly nymphs exposed to differing concentrations of amoxicillin. Next generation sequencing of the 16S rRNA gene was used to identify cultures of these antibiotic resistant bacteria. Increasing the concentration of antibiotics the dragonfly nymphs were exposed to resulted in …

Analysis Of Atlantic And Northern Gulf Coast Wetland Bacterial Extracellular Enzyme Activity, Noah Kippenbrock

Honors Theses

Sea-level rise is projected to cause saltwater marshes to migrate landward replacing brackish and freshwater marshes. Coastal wetlands are important sinks of carbon, phosphorous, and nitrogen, so it is important to understand the function of their microbial communities. This study aims to categorize the difference in function between different spatially distinct wetland marsh types in advance of the expected alteration of the wetland ecosystems. Extracellular microbial enzymatic activity was measured to understand organic matter decomposition and nutrient mineralization in different marsh types. We measured the activities of the extracellular enzymes β-glucosidase, NAGase, peroxidase, phenol oxidase, and phosphatase across sites along …