Biology Commons^™

Painted Redstarts In South Texas, 2013-2014, Timothy Brush

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

No abstract provided.

Changes In Fish Populations In The Lower Canyons Of The Rio Grande, Gary P. Garrett, Robert Edwards

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

The Lower Canyons of the Rio Grande suffer from environmental degradation that has negatively impacted native fish populations and their distributions. Macrhybopsis aestivalis (speckled chub), Notropis jemezanus (Rio Grande shiner), Rhinichthys cataractae (longnose dace) and Cycleptus elongatus (blue sucker) populations appear to have suffered recent declines. Although diminished water quantity is likely an important factor in these declines, related changes in channel morphology precipitated by massive stands of Arundo donax (giant reed) and Tamarix sp. (salt cedar) may also be responsible. These invasive exotics have essentially channelized the river, disrupted normal sediment distribution and reduced shallow, low-velocity habitats. Much of …

A Central Support System Can Facilitate Implementation And Sustainability Of A Classroom-Based Undergraduate Research Experience (Cure) In Genomics, Jeremy Buhler, Elaine Mardis, Wilson Leung, Christopher Shaffer, Jennifer Threlfall, Sarah C.R. Elgin, David Lopatto, Charles Hauser, Christopher Jones, Don Paetkau, Vidya Chandrasekaran, David Dunbar, Christy Mackinnon, Joyce Stamm, Consuelo Alvarez, Daron Barnard, James Bedard, April Bednarski, Satish Bhalla, John Braverman, Martin Burg, Hui-Min Chung, Randall Dejong, Justin Diangelo, Chunguang Du, Todd Eckdahl, Julia Emerson, Amy Frary, Donald Frohlich, Anya Goodman, Yuying Gosser, Shubha Govind, Adam Haberman, Amy Hark, Arlene Hoogewerf, Diana Johnson, Lisa Kadlec, Marian Kaehler, Catherine Silver-Key, Nighat Kokan, Olga Kopp, Gary Kuleck, Jane Lopilato, Juan Martinez-Cruzado, Gerard Mcneil, Stephanie Mel, Alexis Nagengast, Paul Overvoorde, Susan Parrish, Mary Preuss, Laura Reed, Gloria Regisford, Dennis Revie, Srebrenka Robic, Jennifer Roecklien-Canfield, Anne Rosenwald, Michael Rubin, Kenneth Saville, Stephanie Schroeder, Karim Sharif, Mary Shaw, Gary Skuse, Christopher Smith, Mary Smith, Sheryl Smith, Eric Spana, Mary Spratt, Aparna Sreenivasan, Jeffrey Thompson, Matthew Wawersik, Michael Wolyniak, James Youngblom, Leming Zhou

Biology Faculty Research

In their 2012 report, the President's Council of Advisors on Science and Technology advocated "replacing standard science laboratory courses with discovery-based research courses"-a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education Partnership, a nationwide faculty consortium that aims to provide undergraduates with a research experience in genomics through a scheduled course (a classroom-based undergraduate research experience, or CURE). We examine the common barriers encountered in implementing a CURE, program elements of most value to faculty, ways in which a shared core support system can help, and the …

Another Look At The Root Of The Angiosperms Reveals A Familiar Tale, Bryan T. Drew, Brad R. Ruhfel, Stephen A. Smith, Michael J. Moore, Barbara G. Briggs, Matthew A. Gitzendanner, Pamela S. Soltis, Douglas E. Soltis

Faculty & Staff Scholarship

Since the advent of molecular phylogenetics more than 25 years ago, a major goal of plant systematists has been to discern the root of the angiosperms. While most studies indicate that Amborella trichopoda is sister to all remaining extant flowering plants, support for this position has varied with respect to both the sequence data sets and analyses employed. Recently, Goremykin et al. (2013) questioned the “Amborella-sister hypothesis” using a “noise-reduction” approach and reported a topology with Amborella + Nymphaeales (water lilies) sister to all remaining angiosperms. Through a series of analyses of both plastid genomes and mitochondrial genes, we continue …

Endogenous Ros Levels In C. Elegans Under Exogenous Stress Support Revision Of Oxidative Stress Theory Of Life-History Tradeoffs, Samson W. Smith, Leigh C. Latta Iv, Dee R. Denver, Suzanne Estes

Biology Faculty Publications and Presentations

Background: The oxidative stress theory of life-history tradeoffs states that oxidative stress caused by damaging free radicals directly underpins tradeoffs between reproduction and longevity by altering the allocation of energetic resources between these tasks. We test this theory by characterizing the effects of exogenous oxidative insult and its interaction with thermal stress and diet quality on a suite of life-history traits and correlations in Caenorhabditis elegans nematodes. We also quantify demographic aging rates and endogenous reactive oxygen species (ROS) levels in live animals.

Results: Our findings indicate a tradeoff between investment in reproduction and antioxidant defense (somatic maintenance) consistent with …

Pcb Effects On Development Of Behavior In Rats, Robert Witte

Honors Projects

Abstract

PCBs were originally used as industrial chemicals in many devices and applications, including electrical capacitors and transformers, lubricants, and sealants in buildings. PCBs have been investigated and their use has been slowly phased out starting in the U.S. in the 1970s. A worldwide ban was put on the use and manufacturing of PCB in 2001, however they remain in the food chain because of their lipophilic properties and their long half-life. Major sources of PCB include wild-life, fish, and other seafood. Individuals exposed to PCB during development can experience negative effects on neurobiological, cognitive, and behavior functioning in both …

The Effects That Liquid And Solid Cattle Manure Have On The Water Quality Of Drainage Ditches In Putnam County, Ohio, Janelle Horstman

Honors Projects

Lake Erie has experienced harmful algal blooms with increased frequency since the mid-1990s due to excess nutrients from Rivers, such as the Maumee River, and largely agricultural watersheds. Nonpoint source pollution from agriculture contributes to eutrophication, algal blooms, and the degradation of water quality. This creates stress on aquatic fauna, reduced aesthetic quality, odor, and limits of the water for usage of drinking, recreation, and industry. This research paper asks what the contributions of having access to manure application records, soil records, and information about antibiotics have on what is known about manure management and antibiotic resistance, which has been …

Population Structure, Size, And The Thermal Ecology Of Iowa Wood Turtles (Glyptemys Insculpta): A Comparison Between Suburban And Rural Populations, Samuel Wesley Berg

Dissertations and Theses @ UNI

Population structure, population size, and the thermal ecology of wood turtles (Glyptemys insculpta) was studied in a suburban population in Black Hawk County (BHC) and compared to a rural population in Butler County (BC), Iowa. In a suburban population of 35 wood turtles, 32 (91.4%) were adults distributed in a 1:1 sex ratio [16 (45.7%) females and 16 (45.7%) males], and 3 (8.6%) were juveniles. In the rural population, 60 (98.4% of the total population) adult turtles were distributed in a 3:2 sex ratio [36 (59.0%) females and 24 (39.3%) males], and one (1.7%) juvenile was located. Population structure was …

Squalestatin-Induced Production Of Taxol And Baccatin In Cell Suspension Culture Of Yew (Taxus Baccata L.), Sayed Asadollah Amini, Leila Shabani, Ladan Afghani, Zohreh Jalalpour, Majid Sharifi-Tehrani

Turkish Journal of Biology

Various elicitors have already been reported to enhance the production of taxol and related taxanes. In this study, effects of a fungal metabolite, squalestatin, on production of taxol and baccatin III were studied. Expressions of 4 key involved genes, ts, dbat, bapt, and dbtnbt, in suspension cultures of Taxus baccata were also detected using qPCR. Results showed that application of squalestatin significantly increased taxol and baccatin III yields. Increased expressions of the genes were in accordance with measures of taxol and baccatin accumulations in cells and medium. Production of H_{2}O_{2} has significant positive correlations with both gene expression and taxanes, …

Current Paradigms Of Cancer Chemoprevention, Rajendra G. Mehta

Turkish Journal of Biology

Cancer chemoprevention has been continually evolving ever since the term was coined in the 70s. From the original approaches of identifying chemopreventive agents from the dietary constituents based on the epidemiological data to the current status of adapting them from the molecular targets, significant understanding of cancer as a disease and its possible prevention has been achieved. The identification of the chemopreventive agent from a complex mixture of natural product extracts involves numerous steps including bioassay guided fractionation; evaluation of the extracts, fractions and isolated new chemicals selectively using in vitro and in vivo experimental models; and understanding the mechanism …

Genotoxic, Cytotoxic, And Apoptotic Effects Of Crude Extract Of Usnea Filipendula Stirt. In Vitro, Serap Çeli̇kler Kasimoğullari, Seyhan Oran, Ferda Ari, Engi̇n Ulukaya, Nazlihan Aztopal, Mehmet Sarimahmut, Şule Öztürk

Turkish Journal of Biology

Lichens are recently receiving great attention because they have potential anticancer activity. Therefore, in this study, genotoxic and antigrowth properties of lichen species Usnea filipendula Stirt. were tested against human breast cancer cell lines (MCF-7 and MDA-MB-231). Antigrowth effect was assayed by the MTT and ATP viability assays. Cell death modes (apoptosis/necrosis) were evaluated morphologically (fluorescence staining) and biochemically (caspase-cleaved cytokeratin 18, caspase-3 activity, and poly-(ADP-ribose) polymerase (PARP) cleavage). Genotoxic activity of U. filipendula was determined by using micronucleus, chromosomal aberration, and comet assays in human lymphocyte culture. U. filipendula inhibited growth in a dose-dependent manner and induced apoptosis by …

Stimulatory Effect Of Methyl Jasmonate And Squalestatin On Phenolic Metabolism Through Induction Of Lox Activity In Cell Suspension Culture Of Yew, Zohreh Jalalpour, Leila Shabani, Ladan Afghani, Majid Sharifi-Tehrani, Sayed Asadollah Amini

Turkish Journal of Biology

Cell suspension cultures of Taxus baccata were treated with 2 elicitor compounds, methyl jasmonate (MeJA) and squalestatin (S), individually and in combination for 7 days to determine if they mediated the enhancement of biosynthesis of endogenous jasmonate through induction of lipoxygenase (LOX) activity. Total phenolic compounds, total flavonoids, total antioxidants, phenylalanine ammonia-lyase (PAL), polyphenol oxidase (PPO), and LOX activities in 5-month-old yew cell cultures were studied. Our results showed that MeJA and S could stimulate production of phenol derivatives in cell suspension cultures of T. baccata. In parallel to the induction of phenolic production in elicited cells, results showed that …

Tracking Above- And Below- Ground Seed Persistence And Mortality In A Native Tallgrass Prairie Restoration, Carmen Pellish

Dissertations and Theses @ UNI

The large cost of seed and low seedling establishment rates make restoring native tallgrass prairies expensive and difficult. Tallgrass prairie restorations typically achieve seedling emergence rates of only 10%. This begs the question of what happens to the remaining 90% of seeds that do not emerge as seedlings. This thesis sought to assess or quantify the importance of seed predators and death by microorganisms or to senescence on seed survival and seedling establishment within a newly planted native tallgrass prairie restoration under typical restoration conditions. I hypothesized that small vertebrate seed predators would play be detrimental to overall seedling emergence …

Novel Cul3 Binding Proteins Function To Remodel E3 Ligase Complexes, Wananit Wimuttisuk, Mark West, Brittney Davidge, Kebing Yu, Arthur Salomon, Jeffrey D. Singer

Biology Faculty Publications and Presentations

Background: Cullins belong to a family of scaffold proteins that assemble multi-subunit ubiquitin ligase complexes to recruit protein substrates for ubiquitination via unique sets of substrate adaptor, such as Skp1 or Elongin B, and a substrate-binding protein with a conserved protein-protein interacting domain, such as leucine-rich repeats (LRR), a WD40 domain, or a zinc-finger domain. In the case of the Cullin3 (Cul3), it forms a BTB-Cul3-Rbx1 (BCR) ubiquitin ligase complex where it is believed that a BTB domain-containing protein performs dual functions where it serves as both the substrate adaptor and …

Investigation Of Angiogenic Effects Of Bioactive Borate Glass Microfibers And Beads In A Rodent Model, Richard Jeffrey Watters

Masters Theses

"The primary objective of this research project was to evaluate the effects of three different compositions of bioactive glass microfibers (45S5, 13-93B3, and 13-93B3Cu) and bioactive glass beads (13-93, 13-93B3, and 13-93B3Cu) on angiogenesis in subcutaneous tissue in the SKH1 'hairless' mouse. Microvascular responses to the bioactive glass implants were investigated via three experimental approaches: noninvasive vital imaging of microvasculature in dorsal skin windows; quantitative histomorphometry of microvascular densities; and quantitative PCR measurements of mRNA expression of pro-angiogenic cytokines VEGF and FGF-2. The live imaging of dorsal skin window preparations in the hairless SKH1 showed the formation of a halo-like …

Energy Tradeoffs Between Food Assimilation, Growth, Metabolism And Maintenance, Lihong Jiao

Masters Theses

"The effect of metabolic rate (MR) on organisms' health maintenance is a long-standing puzzle and empirical data on this issue is contradictory. A theoretical model was developed for understanding animal's energy budget under the food condition of Ad libitum (AL) and food restriction. This model offers a framework for understanding the role of MR and health maintenance mechanism from the perspective of energy tradeoff between food assimilation, growth, metabolism and maintenance. Hornworm (Manduca sexta larva) has been selected as an model to test the energetic tradeoff under different food supply and ambient temperatures. The changes in energy budget can …

Molecular Phylogenetic Relationships Of North American Dermacentor Ticks Using Mitochondrial Gene Sequences, Kayla L. Perry

College of Graduate Studies: Theses & Dissertations

Dermacentor is a recently evolved genus of hard ticks (Family Ixodiae) that includes 36 known species worldwide. Despite the importance of Dermacentor species as vectors of human and animal disease, the systematics of the genus remain largely unresolved. This study focuses on phylogenetic relationships of the eight North American Nearctic Dermacentor species: D. albipictus, D. variabilis, D. occidentalis, D. halli, D. parumapertus, D. hunteri, and D. andersoni, and the recently re-established species D. kamshadalus, as well as two of the Neotropical Dermacentor species D. nitens and D. dissimilis (both formerly Anocentor). We sequenced portions of the mitochondrial …

The Prevalence And Effect Of Wolbachia Infection On The Brown Widow Spider (Latrodectus Geometricus), Brittany Dane' Arrington

College of Graduate Studies: Theses & Dissertations

Wolbachia was recently identified in the Brown Widow Spider (Latrodectus geometricus). This symbiont has not previously been found in this genus, therefore the consequences on the host’s population dynamics are unknown. The frequency of endosymbiont infection can provide insight into the population dynamics of the host as this bacteria is known to alter host life history. In my 1^st chapter I determine the prevalence of Wolbachia pipentis infection in in the Brown Widow Spider (Latrodectus geometricus) from five locations in the Southeastern United States. Infection frequency differed significantly among sampling locations, ranging from 20% to …

Microbial Communities Colonizing Leaves During Early Decomposition Stages, Stephanie Harper

College of Graduate Studies: Theses & Dissertations

Microbial communities associated with decaying leaves play an important role in the cycling of nutrients in stream ecosystems. In headwater streams that are deemed as heterotrophic, bacteria and fungi are main drivers of organic matter decomposition and thus partly responsible for facilitating the cycling of nutrients from leaves that fall into the stream. The main objective of this study was to compare microbial community composition between different leaf types during breakdown in stream ecosystems. To achieve this objective, I used a combination of field and laboratory trials. Field experiments were performed at the Luquillo Experimental Forest using Dacryodes excelsa and …

Epistasis In Predator-Prey Relationships, Iuliia Inozemtseva

College of Graduate Studies: Theses & Dissertations

Epistasis is the interaction between two or more genes to control a single phenotype. We model epistasis of the prey in a two-locus two-allele problem in a basic predator- prey relationship. The resulting model allows us to examine both population sizes as well as genotypic and phenotypic frequencies. In the context of several numerical examples, we show that if epistasis results in an undesirable or desirable phenotype in the prey by making the particular genotype more or less susceptible to the predator or dangerous to the predator, elimination of undesirable phenotypes and then genotypes occurs.

Water Column Ammonium Concentration And Salinity Influence Nitrogen Uptake And Growth Of Spartina Alterniflora, Rachel Mactavish

College of Graduate Studies: Theses & Dissertations

Salt marsh macrophytes, such as Spartina alterniflora, play a critical role in uptake and transformation of inorganic nitrogen before it reaches coastal waters, thereby reducing the potential for eutrophication. Although nitrogen availability typically limits S. alterniflora growth, it may be possible to exceed the nitrogen uptake capacity of S. alterniflora. Increasing either nitrogen concentrations or salinity are key factors regulating S. alterniflora nitrogen uptake. Investigating the effects of nutrients and salinity on S. alterniflora is important given that increases in inorganic nitrogen supply to surface waters from agriculture and urbanization occur simultaneously with freshwater withdrawals that reduce flow and increase …

The Effects Of Herbicide On The Endangered Herb Baptisia Arachnifera And Preliminary Nutrient Survey Of Leaf Tissue And Soil, Ruth Ann C. Steinbrecher

College of Graduate Studies: Theses & Dissertations

Baptisia arachnifera (Hairy Rattleweed) is an endangered herbaceous legume that only occurs in Wayne and Brantley Counties of Georgia, United States. Many of the remaining populations exist in areas now managed for timber. This study investigated the effects of Imazapyr, an herbicide commonly used in timber management, on health and vitality of B. arachnifera under both field and greenhouse conditions. This study also analyzed leaf and soil samples from six populations of B. arachnifera to determine the nutrient content of the leaves. A recensus of a B. arachnifera population was also conducted in a site without commercial timber management. In …

Effects Of Organic And Conventional Agricultural Practices On Soil Microbial Communities And Molecular Detection Of Soil Borne Disease, Holli K. Milner

College of Graduate Studies: Theses & Dissertations

Agricultural practices affect soil microbial communities and health through the input of pesticides, herbicides, fertilizers, and cycling of crop rotation. By examining the microbial community structure, we analyzed how microbial species respond to the environment that individual farms create. Early detection of soil borne disease is essential for agricultural success. However, monitoring incidence of disease based on plant growth response to pathogenic inoculation may not reveal the amount of pathogenic DNA in soil. A comparative study of tomato production systems was conducted by analysis of soil microbial community structure from four farms in Southeast Georgia for the years 2012 and …

"Mining" For A Reference Condition In Southern West Virginia Streams, Matthew Rouch

Theses and Dissertations

Quarterly samples were used to estimate assemblage-level (all species combined) fish production within three minimally-impacted, southern West Virginia streams. The total annual fish production estimate was highest in Slaunch Fork (37.52 kg∙ha^-1∙y^-1), a tributary of the Tug Fork River, and lowest in Cabin Creek (10.59 kg∙ha^-1∙y^-1), a Guyandotte River tributary. Creek Chub Semotilus atromaculatus, Mottled Sculpin Cottus bairdii and Blacknose Dace Rhinicthys atratulus were the most abundant species among sites, accounting for >90% of all sampled individuals. Reference condition criteria were also selected and metrics calculated for each of the three …

Effect Of Gamma Ray Irradiation And Cryopreservation On Pollen Stainability, In Vitro Germination, And Fruit Set In Citrus, Manoj Kundu, Anil Dubey, Manish Srivastav, Surendra Malik, Bhupinder Singh

Turkish Journal of Biology

The present work analyzed the stainability and in vitro germinability of the gamma-ray-irradiated fresh and cryopreserved pollens of 3 Citrus species: C. limon, C. limetta, and C. sinensis. Fruit set after pollinating 75 flowers of C. grandis with irradiated and nonirradiated (control) fresh and cryopreserved pollen was also assessed. Results showed that in solid and liquid culture media the highest in vitro germination values were detected in fresh (61.45% and 62.53%, respectively) as well as cryopreserved (53.17% and 55.36%, respectively) C. sinensis nonirradiated pollens. However, at a higher irradiation dose of 500 Gy in both culture media, the minimum reduction …

Ex Situ Conservation Of Dianthus Giganteus D’Urv. Subsp. Banaticus (Heuff.) Tutin By In Vitro Culture And Assessment Of Somaclonal Variability By Molecular Markers, Liliana Jarda, Anca Butiuc Keul, Maria Hohn, Andrzej Pedryc, Victoria Cristea

Turkish Journal of Biology

Ex situ conservation of Dianthus giganteus subsp. banaticus was obtained by in vitro culture on different culture media supplemented with phytohormones. Assessment of somaclonal variability over a period of preservation by in vitro culture is required prior to introduction and acclimatization in natural habitats. In this study we used 2 types of molecular markers, ISSR and multilocus SSR markers, which allow comparison of different alleles, to assess the somaclonal variability of endemic taxa Dianthus giganteus subsp. banaticus after a period of 24 months of preservation by in vitro culture. The assessment of somaclonal variability of D. giganteus subsp. banaticus shows …

Genotoxic Effects Of Zinc Oxide And Titanium Dioxide Nanoparticles On Root Meristem Cells Of Allium Cepa By Comet Assay, Eşref Demi̇r, Nuray Kaya, Bülent Kaya

Turkish Journal of Biology

Nanogenotoxicity is an emergent field, relevant for estimating the potential genotoxic risk of nanomaterials. In this study we investigated the genotoxic potential of zinc oxide (ZnO, Keywords: Zinc oxide nanoparticles, titanium dioxide nanoparticles, Allium cepa, comet assay, genotoxicity, DNA damage

Development Of An Improved Rna Interference Vector System For Agrobacterium-Mediated Plant Transformation, Umut Toprak, Cathy Coutu, Doug Baldwin, Martin Erlandson, Dwayne Hegedus

Turkish Journal of Biology

Plant-mediated RNA interference (RNAi) has shown a great potential in pest control and requires i) subcloning of sense/antisense regions in compatible vectors, ii) transfer of the silencing cassette into a binary vector, iii) transformation of Agrobacterium tumefaciens with desired binary plasmids, and iv) transformation of plants with Agrobacterium. The procedure is long and should ensure plasmid backbone stability; however, plasmid recombination due to antibiotic selection is a common problem. pGSA1252 is an RNAi silencing binary vector allowing direct cloning of hairpin structure; however, it possesses a chloramphenicol selection marker leading to plasmid recombination in various Agrobacterium strains. To solve this …

The Genus Crocus, Series Crocus (Iridaceae) In Turkey And 2 East Aegean Islands: A Genetic Approach, Osman Erol, Hi̇lal Betül Kaya, Levent Şik, Meti̇n Tuna, Levent Can, Muhammed Bahatti̇n Tanyolaç

Turkish Journal of Biology

In this study, a total of 26 Crocus specimens from different locations across Turkey and 2 East Aegean islands (Chios and Samos) were analyzed using 12 amplified fragment length polymorphism (AFLP) primer combinations to obtain information on genetic diversity, population structure, and genetic relationships. A total of 369 polymorphic AFLP bands were generated and scored as binary data. Genetic similarities were determined. Cluster analysis revealed 4 major groups among the 26 genotypes examined in this study. The nuclear DNA contents (2C) of the 26 Crocus specimens were found to range from 5.08 pg in C. asumaniae to 9.75 pg in …

Molecular Characterization Of The Encoding Regions And Tissue Expression Analyses For 3 Novel Buffalo Akt Genes, Akt1, Akt2, And Akt3, Chunfeng Wu, Lixian Liu, Jinlong Huo, Dalin Li, Yueyun Yuan, Feng Yuan, Yongwang Miao

Turkish Journal of Biology

The objective of this study was to obtain the complete coding sequences (CDSs) of 3 buffalo genes (AKT1, AKT2, and AKT3) using reverse-transcriptase polymerase chain reaction and to depict their molecular characterizations and tissue expression patterns in buffalo. The buffalo AKT1, AKT2, and AKT3 CDSs were 1443 bp, 1446 bp, and 1440 bp in length and encoded 480, 481, and 479 amino acids, respectively. Nine, 13, and 3 nucleotide differences were found in the CDSs between buffalo and other bovine species. Phylogenetic analyses showed that buffalo AKT1 and AKT2 have close genetic relationships with other species in the family Bovidae, …