Biology Commons^™

E. Coli B3639 And B3634 Are Orthologs Of Mrub_2047 And Mrub_1372, Rong Zheng, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2047 and Mrub_1372. We predict that Mrub_2047 encodes the enzyme fused 4'-phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN-binding (DNA coordinates 2083590..2084816 on the forward strand), which is the first and the second steps of the CoA biosynthesis pathway (KEGG map number 00770). It catalyzes the conversion of (R)-4’-phosphopantothenate to (R)-4’-phosphopantothenoyl-L-cysteine and the conversion of (R)-4’-phosphopantothenoyl-L-cysteine to 4’-phosphopantetheine. The E. coli K12 MG1655 ortholog …

Mrub_0258 Gene Is An Ortholog Of The B4226 Gene (Ppa) Found In Escherichia Coli; Mrub_1198 Gene Is An Ortholog Of The B2501 Gene (Ppk) Found In Escherichia Coli;, Brandon M. Wills, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_0258 and Mrub_1198. We predict that Mrub_0258 encodes the enzyme inorganic pyrophosphatase (226403..226942), which is indirectly involved with the oxidative phosphorylation pathway (KEGG map number 00190). It catalyzes the conversion of the diphosphate ions made by Mrub_1198 into two orthophosphate ions, which can then be used by ATP synthase to produce energy. The E. coli K12 MG1655 ortholog is predicted …

Trait Responses Of Invasive Aquatic Macrophyte Congeners: Colonizing Diploid Outperforms Polyploid, Rebecca E. Drenovsky, Brenda J. Grewell, Meghan J. Skaer Thomason, C. J. Futrell, M. Iannucci

Biology

Understanding traits underlying colonization and niche breadth of invasive plants is key to developing sustainable management solutions to curtail invasions at the establishment phase, when efforts are often most effective. The aim of this study was to evaluate how two invasive congeners differing in ploidy respond to high and low resource availability following establishment from asexual fragments. Because polyploids are expected to have wider niche breadths than diploid ancestors, we predicted that a decaploid species would have superior ability to maximize resource uptake and use, and outperform a diploid congener when colonizing environments with contrasting light and nutrient availability. A …

Progress In Pathogen Detection By Whole-Genome Sequencing, Chung Wong

Chemistry & Biochemistry Faculty Works

No abstract provided.

Further Support For Thermal Ecosystem Engineering By Wandering Albatross On Marion Island, Steven L Chown, Justine D. Shaw, Tanya M Haupt, Brent J Sinclair

Biology Publications

On sub-Antarctic Marion Island, wandering albatross (Diomedea exulans) nests support high abundances of tineid moth, Pringleophaga marioni, caterpillars. Previous work proposed that the birds serve as thermal ecosystem engineers by elevating nest temperatures relative to ambient, thereby promoting growth and survival of the caterpillars. However, only 17 days of temperature data were presented previously, despite year-long nest occupation by birds. Previous sampling was also restricted to old and recently failed nests, though nests from which chicks have recently fledged are key to understanding how the engineering effect is realized. Here we build on previous work by providing nest temperature data …

Similar Metabolic Rate-Temperature Relationships After Acclimation At Constant And Fluctuating Temperatures In Caterpillars Of A Sub-Antarctic Moth., Steven L Chown, Tanya M Haupt, Brent J Sinclair

Biology Publications

Temperature compensation in whole-animal metabolic rate is one of the responses thought, controversially, to characterize insects from low temperature environments. Temperature compensation may either involve a change in absolute values of metabolic rates or a change in the slope of the metabolic rate - temperature relationship. Moreover, assessments of compensation may be complicated by animal responses to fluctuating temperatures. Here we examined whole animal metabolic rates, at 0 °C, 5 °C, 10 °C and 15 °C, in caterpillars of the sub-Antarctic moth, Pringleophaga marioni Viette (Tineidae), following one week acclimations to 5 °C, 10 °C and 15 °C, and fluctuating …

Comparative Population Genomics Of Latitudinal Variation In Drosophila Simulans And Drosophila Melanogaster, Heather E. Machado, Alan O. Bergland, Katherine R. O'Brien, Emily L. Behrman, Paul S. Schmidt, Dmitri A. Petrov

School of Biological Sciences: Faculty Publications

Examples of clinal variation in phenotypes and genotypes across latitudinal transects have served as important models for understanding how spatially varying selection and demographic forces shape variation within species. Here, we examine the selective and demographic contributions to latitudinal variation through the largest comparative genomic study to date of Drosophila simulans and Drosophila melanogaster, with genomic sequence data from 382 individual fruit flies, collected across a spatial transect of 19 degrees latitude and at multiple time points over 2 years. Consistent with phenotypic studies, we find less clinal variation in D. simulans than D. melanogaster, particularly for the autosomes. Moreover, …

Female Túngara Frogs Do Not Experience The Continuity Illusion, Alexander T. Baugh, M. J. Ryan, X. E. Bernal, A. S. Rand, M. A. Bee

Biology Faculty Works

In humans and some non-human vertebrates, a sound containing brief silent gaps can be rendered perceptually continuous by inserting noise into the gaps. This so-called ‘continuity illusion’ arises from a phenomenon known as ‘auditory induction’ and results in the perception of complete auditory objects despite fragmentary or incomplete acoustic information. Previous studies of auditory induction in gray treefrogs (Hyla versicolor and H. chrysoscelis) have demonstrated an absence of this phenomenon. These treefrog species produce pulsatile (non-continuous) vocalizations, whereas studies of auditory induction in other taxa, including humans, often present continuous sounds (e.g., frequency-modulated sweeps). This study investigated the continuity illusion …

Beyond The Adaptationist Legacy: Updating Our Teaching To Include A Diversity Of Evolutionary Mechanisms, Rebecca M. Price, Kathryn E. Perez

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

A paradigm shift away from viewing evolution primarily in terms of adaptation - the "adaptationist programme" of Gould and Lewontin - began in evolutionary research more than 35 years ago, but that shift has yet to occur within evolutionary education research or within teaching standards. We review three instruments that can help education researchers and educators undertake this paradigm shift. The instruments assess how biology undergraduates understand three evolutionary processes other than natural selection: genetic drift, dominance relationships among allelic pairs, and evolutionary developmental biology (evo-devo). Testing with these instruments reveals that students often explain a diversity of evolutionary mechanisms …

High Genetic Diversity But Low Population Structure In The Frog Pseudopaludicola Falcipes (Hensel, 1867) (Amphibia, Anura) From The Pampas Of South America, José A. Langone, Arley Camargo, Rafael O. De Sá

Biology Faculty Publications

Relative to South America’s ecoregions, the temperate grasslands of the Pampas have been poorly studied from a phylogeographic perspective. Based on an intermediate biogeographic setting between subtropical forest (Atlantic Forest) and arid ecosystems (Chaco and Patagonia), Pampean species are expected to show unstable demographic histories due to the Quaternary climatic oscillations. Herein, we investigate the phylogenetic relatedness and phylogeographic history of Pseudopaludicola falcipes, a small and common frog that is widely distributed across the Pampean grasslands. First, we use molecular data to assess if P. falcipes represents a single or multiple, separately evolving cryptic lineages. Because P. falcipes is …

Effects Of A Pyrrole-Based, Microtubule-Depolymerizing Compound On Raw 264.7 Macrophages, John A. Ciemnieckia, Clarke P. Lewis, John T. Gupton, Krista J. Stenger

Biology Faculty Publications

RAW 264.7 murine macrophages were exposed to the pyrrole-based compound 3,5-Dibromo-4-(3,4-dimethoxyphenyl)-1H-pyrrole-2-carboxylic acid ethyl ester (JG-03-14), which is a known microtubule depolymerizing agent with antitumor activity [1,2,3]. In this study exposure to JG-03-14 reduced the production of pro-inflammatory molecules by macrophages activated with lipopolysaccharide (LPS). Treatment with the pyrrole-based compound decreased the concentration of tumor necrosis factor-α (TNF-α) and nitric oxide (NO) released from the macrophages. Exposure to JG-03-14 also decreased TNF-α mRNA expression levels and the protein expression levels of inducible nitric oxide synthase (iNOS), the enzyme responsible for NO production in the activated macrophages. Furthermore, JG-03-14 treatment significantly changed …

Analogous Cellular Contribution And Healing Mechanisms Following Digit Amputation And Phalangeal Fracture In Mice, Lindsay A. Dawson, Jennifer Simkin, Michelle Sauque, Maegan Pela, Teresa Palkowski, Ken Muneoka

Biology Faculty Publications

Regeneration of amputated structures is severely limited in humans and mice, with complete regeneration restricted to the distal portion of the terminal phalanx (P3). Here, we investigate the dynamic tissue repair response of the second phalangeal element (P2) post amputation in the adult mouse, and show that the repair response of the amputated bone is similar to the proximal P2 bone fragment in fracture healing. The regeneration-incompetent P2 amputation response is characterized by periosteal endochondral ossification resulting in the deposition of new trabecular bone, corresponding to a significant increase in bone volume; however, this response is not associated with bone …

Gascoyne Demersal Scalefish Managed Fishery, Department Of Fisheries

Fisheries Occasional Publications

An operators’ guide to the management arrangements 1 September 2015 – 31 August 2016.

Would Ecology Fail The Repeatability Test?, Stefan A. Schnitzer, Walter P. Carson

Biological Sciences Faculty Research and Publications

No abstract provided.

Mcra Gene Abundance Correlates With Hydrogenotrophic Methane Production Rates In Full-Scale Anaerobic Waste Treatment Systems, R. L. Morris, Vaibhav Panjabrao Tale, P. P. Mathai, Daniel Zitomer, James Maki

Biological Sciences Faculty Research and Publications

Anaerobic treatment is a sustainable and economical technology for waste stabilization and production of methane as a renewable energy. However, the process is under-utilized due to operational challenges. Organic overload or toxicants can stress the microbial community that performs waste degradation, resulting in system failure. In addition, not all methanogenic microbial communities are equally capable of consistent, maximum biogas production. Opinion varies as to which parameters should be used to monitor the fitness of digester biomass. No standard molecular tools are currently in use to monitor and compare full-scale operations. It was hypothesized that determining the number of gene copies …

Tyrosine Phosphorylation Based Homo-Dimerization Of Arabidopsis Rack1a Proteins Regulates Oxidative Stress Signaling Pathways In Yeast, Mercy Sabila, Nabanita Kundu, Deana Smalls, Hemayet Ullah

Department of Biology Faculty Publications

Scaffold proteins are known as important cellular regulators that can interact with multiple proteins to modulate diverse signal transduction pathways. RACK1 (Receptor for Activated C Kinase 1) is a WD-40 type scaffold protein, conserved in eukaryotes, from Chlamydymonas to plants and humans, plays regulatory roles in diverse signal transduction and stress response pathways. RACK1 in humans has been implicated in myriads of neuropathological diseases including Alzheimer and alcohol addictions. Model plant Arabidopsis thaliana genome maintains three different RACK1 genes termed RACK1A, RACK1B, and RACK1C with a very high (85-93%) sequence identity between them. Loss of function mutant in Arabidopsis indicates …

Herbivore Density Mediates The Indirect Effect Of Herbivores On Plants Via Induced Resistance And Apparent Competition, Ricardo A. Ramirez, Micky D. Eubanks

Biology Faculty Publications

Herbivore-induced plant resistance and apparent competition are two indirect ways herbivores interact. If a less damaging herbivore indirectly suppresses the abundance of a more damaging herbivore via these mechanisms, then plants may ultimately benefit. Changes in herbivore density, however, can dictate the intensity of species interactions and may play a critical role in determining the outcome of plant- and predator-mediated herbivore interactions. We tested the effects of herbivore density on the strength of indirect interactions among phloem-feeding aphids and herbivorous caterpillars and the outcome of these interactions for their shared host plant, cotton (Gossypium hirsutum). We quantified the …

Msh1 Is A Plant Organellar Dna Binding And Thylakoid Protein Under Precise Spatial Regulation To Alter Development, Kamaldeep S. Virdi, Yashitola Wamboldt, Hardik Kundariya, John D. Laurie, Ido Keren, K.R. Sunil Kumar, Anna Block, Gilles J. Basset, Steve Luebker, Christian Elowsky, Philip M. Day, Johnna L. Roose, Terry M. Bricker, Thomas Elthon, Sally A. Mackenzie

School of Biological Sciences: Faculty Publications

As metabolic centers, plant organelles participate in maintenance, defense, and signaling. MSH1 is a plantspecific protein involved in organellar genome stability in mitochondria and plastids. Plastid depletion of MSH1 causes heritable, non-genetic changes in development and DNA methylation. We investigated the msh1 phenotype using hemi-complementation mutants and transgene-null segregants from RNAi suppression lines to sub-compartmentalize MSH1 effects. We show that MSH1 expression is spatially regulated, specifically localizing to plastids within the epidermis and vascular parenchyma. The protein binds DNA and localizes to plastid and mitochondrial nucleoids, but fractionation and protein–protein interactions data indicate that MSH1 also associates with the thylakoid …

Accepting Evolution And Believing In God: How Religious Persons Perceive The Theory Of Evolution, Katherine F. Manwaring

Theses and Dissertations

Students frequently hold an incorrect view of evolution. There are several potential barriers that prevent students from engaging evolutionary theory including lack of knowledge, limited scientific reasoning ability, and religiosity. Our research provides tools for overcoming barriers related to religiosity and diagnoses the barriers preventing students from fully engaging in learning the theory of evolution. This was a two-part study. The first part of our study addressed two hypothesized barriers to learning evolutionary theory among members of The Church of Jesus Christ of Latter-day Saints (LDS or Mormon): (1) religious views stemming from incorrect understanding of the Church's neutral stance …

Hydrodynamic Loading In Concomitance With Exogenous Cytokine Stimulation Modulates Differentiation Of Bovine Mesenchymal Stem Cells Towards Osteochondral Lineages, Stephen M. Goldman, Gilda A. Barabino

Publications and Research

Background: Mesenchymal stem cells (MSCs) are viewed as a having significant potential for tissue engineering and regenerative medicine therapies. Clinical implementation of MSCs, however, demands that their preparation be stable and reproducible. Given that environmental and bioprocessing parameters such as substrate stiffness, seeding densities, culture medium composition, and mechanical loading can result in undirected differentiation of the MSC population, the objective of this study was to systematically investigate how hydrodynamic loading influences the differentiation of bone marrow-derived mesenchymal stem cells (MSCs) towards the osteochondral lineages both in the presence and absence of exogenous, inductive factors.

Methods: Expanded bovine MSCs were …

The Implications Of Chromatin Remodelers' Acetylation In Ino1 Activation, Michelle M. Esposito

Dissertations, Theses, and Capstone Projects

It is known that histone acetylases (HATs) regulate gene expression, but only recently have new functional implications about remodelers’ acetylation emerged. For instance, the HAT, Gcn5p, is capable of acetylating the catalytic subunit of the nucleosome remodeling complex SWI/SNF, Snf2p, which results in the dissociation of the complex from chromatin. The implications of this acetylation and subsequent dissociation have yet to be explored with regard to transcriptional regulation and other possible mechanisms. To further understand the implications of remodeler acetylation, I used a yeast model system examining the expression of the inositol-3-phosphate synthase gene INO1. Through chromatin immunoprecipitation (ChIP) …

When Human-Leopard Conflict Turns Deadly: A Cross-Country Situational Analysis, Julie S. Viollaz

Dissertations, Theses, and Capstone Projects

Habitat destruction and pollution are two of the main causes for the decline of the planet’s biodiversity. Yet environmentalists are now recognizing that illegal wildlife killings, both poaching and retaliatory killings due to human-wildlife conflict, are perhaps the next major threat. Biologists have researched illegal killings and their effect on species conservation, but few researchers have applied criminological principles of crime reduction to them. This research will explore the situational factors that drive retaliatory leopard killings in parts of South Africa, Kenya, and India. These factors, human and environmental, include local expectations from wildlife, sensitivity to environmental issues, communication between …

Chamber-Specific Patterns Of Epicardium Formation In Zebrafish, Sana Khan

Dissertations, Theses, and Capstone Projects

The outer cardiac layer, the epicardium, coordinates the final steps of vertebrate heart development. This cardiac tissue arises from cells in the proepicardial organ (PEO) that forms around the base of the inflow tract. Its general location is conserved across species despite morphological differences. Cellular mechanisms of migration differ across species. Three strategies of PEO migration are described: 1) The floating cyst model - PEO cells released into the pericardial cavity are directed by fluid movements to migrate onto the myocardium; 2) Villi transfer - cardiac contractions may mediate multicellular PEO villi contact to the myocardium; and 3) Tissue bridge-mediated …

Role Of Bec-1/Beclin 1 And Autophagy Genes In C.Elegans Germline Cell Proliferation, Kristina Ames

Dissertations, Theses, and Capstone Projects

Autophagy is an evolutionary conserved process involved in the cellular adaptation to stress and basal levels of autophagy are crucial for cellular metabolism and homeostasis. Cellular recycling by autophagy is characterized by the formation of distinctive double-membrane vesicles (autophagosomes) that engulf unnecessary cytoplasmic components, such as organelles and long-lived proteins. Failure to remove protein aggregates and/or damaged organelles, via autophagy, has been implicated in various medical conditions such as liver disease, neurodegenerative diseases and cancer. Autophagy may suppress or promote cellular proliferation in tumors, depending on the type and metabolic state of the cell, where autophagy is generally believed to …

Moths Fight Back: Arms Race In The Cloud Forest, Diana Pamela Rivera

Theses

Moths and bats engage in a coevolutionary arm race, where the same signals bats use to find moths are being used by moths to avoid bats. Moths evolve not only behavioral but acoustic responses to avoid predation by bats. This research examines one small component of a complex, multispecies arm race between moths and bats. In this study we found that the moth Amastus hyalina displayed both flight and acoustic responses to ultrasonic stimuli.

In tethered flight the tiger moth Amastus hyalina (Arctiinae) exhibits a complex array of reactions to ultrasonic tones that includes changes in flight and production of …

Predator Diet And Trophic Position Modified With Altered Habitat Morphology, Alexander Tewfik, Susan S. Bell, Kevin S. Mccann, Kristina Morrow

Integrative Biology Faculty and Staff Publications

Empirical patterns that emerge from an examination of food webs over gradients of environmental variation can help to predict the implications of anthropogenic disturbance on ecosystems. This “dynamic food web approach” is rarely applied at the coastal margin where aquatic and terrestrial systems are coupled and human development activities are often concentrated. We propose a simple model of ghost crab (Ocypode quadrata) feeding that predicts changing dominant prey (Emerita talpoida, Talorchestia sp., Donax variablis) along a gradient of beach morphology and test this model using a suite of 16 beaches along the Florida, USA coast. …

Lianas Suppress Seedling Growth And Survival Of 14 Tree Species In A Panamanian Tropical Forest, Laura Martinez Izquierdo, Maria M. Garcia, Jennifer S. Powers, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Lianas are a common plant growth form in tropical forests, where they compete intensely with trees, decreasing tree recruitment, growth, and survival. If the detrimental effects of lianas vary significantly with tree species identity, as is often assumed, then lianas may influence tree species diversity and community composition. Furthermore, recent studies have shown that liana abundance and biomass are increasing relative to trees in neotropical forests, which will likely magnify the detrimental effects of lianas and may ultimately alter tree species diversity, relative abundances, and community composition. Few studies, however, have tested the responses of multiple tree species to the …

Consequences Of Secondary Calibrations On Divergence Time Estimates, John J. Schenk

Biology: Faculty Publications

Secondary calibrations (calibrations based on the results of previous molecular dating studies) are commonly applied in divergence time analyses in groups that lack fossil data; however, the consequences of applying secondary calibrations in a relaxed-clock approach are not fully understood. I tested whether applying the posterior estimate from a primary study as a prior distribution in a secondary study results in consistent age and uncertainty estimates. I compared age estimates from simulations with 100 randomly replicated secondary trees. On average, the 95% credible intervals of node ages for secondary estimates were significantly younger and narrower than primary estimates. The primary …

Mutations In Mtr4 Structural Domains Reveal Their Important Role In Regulating TrnaI Met Turnover In Saccharomyces Cerevisiae And Mtr4p Enzymatic Activities In Vitro, Yan Li, Joseph Burclaff, James T. Anderson

Biological Sciences Faculty Research and Publications

RNA processing and turnover play important roles in the maturation, metabolism and quality control of a large variety of RNAs thereby contributing to gene expression and cellular health. The TRAMP complex, composed of Air2p, Trf4p and Mtr4p, stimulates nuclear exosome-dependent RNA processing and degradation in Saccharomyces cerevisiae. The Mtr4 protein structure is composed of a helicase core and a novel so-called arch domain, which protrudes from the core. The helicase core contains highly conserved helicase domains RecA-1 and 2, and two structural domains of unclear functions, winged helix domain (WH) and ratchet domain. How the structural domains (arch, WH …

Is Protection Against Florivory Consistent With The Optimal Defense Hypothesis?, Adrienne L. Godschalx, Lauren Stady, Benjamin Watzig, Daniel J. Ballhorn

Biology Faculty Publications and Presentations

Background: Plant defense traits require resources and energy that plants may otherwise use for growth and reproduction. In order to most efficiently protect plant tissues from herbivory, one widely accepted assumption of the optimal defense hypothesis states that plants protect tissues most relevant to fitness. Reproductive organs directly determining plant fitness, including flowers and immature fruit, as well as young, productive leaf tissue thus should be particularly well-defended. To test this hypothesis, we quantified the cyanogenic potential (HCNp)—a direct, chemical defense—systemically expressed in vegetative and reproductive organs in lima bean (Phaseolus lunatus), and we tested susceptibility of these …