Biology Commons^™

Mutations That Separate The Functions Of The Proofreading Subunit Of The Escherichia Coli Replicase, Zakiya Whatley, Kenneth N. Kreuzer

Biology Faculty Publications

The dnaQ gene of Escherichia coli encodes the Ɛ subunit of DNA polymerase III, which provides the 3' - 5' exonuclease proofreading activity of the replicative polymerase. Prior studies have shown that loss of Ɛ leads to high mutation frequency, partially constitutive SOS, and poor growth. In addition, a previous study from our laboratory identified dnaQ knockout mutants in a screen for mutants specifically defective in the SOS response after quinolone (nalidixic acid) treatment. To explain these results, we propose a model whereby, in addition to proofreading, Ɛ plays a distinct role in replisome disassembly and/or processing of stalled replication …

Sex Differences In Spatial Memory In Brown-Headed Cowbirds: Males Outperform Females On A Touchscreen Task, Mélanie F. Guigueno, Scott A. Macdougall-Shackleton, David F. Sherry

Biology Publications

Spatial cognition in females and males can differ in species in which there are sex-specific patterns in the use of space. Brown-headed cowbirds are brood parasites that show a reversal of sex-typical space use often seen in mammals. Female cowbirds, search for, revisit and parasitize hosts nests, have a larger hippocampus than males and have better memory than males for a rewarded location in an open spatial environment. In the current study, we tested female and male cowbirds in breeding and non-breeding conditions on a touchscreen delayed-match-to-sample task using both spatial and colour stimuli. Our goal was to determine whether …

Accurate Alternative Measurements For Female Lifetime Reproductive Success In Drosophila Melanogaster, Trinh T X Nguyen, Amanda Moehring

Biology Publications

Fitness is an individual's ability to survive and reproduce, and is an important concept in evolutionary biology. However, accurately measuring fitness is often difficult, and appropriate fitness surrogates need to be identified. Lifetime reproductive success, the total progeny an organism can produce in their lifetime, is thought to be a suitable proxy for fitness, but the measure of an organism's reproductive output across a lifetime can be difficult or impossible to obtain. Here we demonstrate that the short-term measure of reproductive success across five days provides a reasonable prediction of an individual's total lifetime reproductive success in Drosophila melanogaster. However, …

Insights Into The Origin Of Dna Methylation Differences Between Monozygotic Twins Discordant For Schizophrenia, Melkaye G. Melka, Christina A. Castellani, Richard O'Reilly, Shiva M. Singh

Biology Publications

BACKGROUND: DNA methylation differences between monozygotic twins discordant for schizophrenia have been previously reported. However, the origin of methylation differences between monozygotic twins discordant for schizophrenia is not clear. The findings here argue that all DNA methylation differences may not necessarily represent the cause of the disease; rather some may result from the effect of antipsychotics.

METHODS: Methylation differences in rat brain regions and also in two pairs of unrelated monozygotic twins discordant for schizophrenia have been studied using genome-wide DNA methylation arrays at Arraystar Inc. (Rockville, Maryland, USA). The identified gene promoters showing significant alterations to DNA methylation were …

Mathematical Modeling Of Two-Dimensional Unsteady Flow In Growing Tumor, N. Gracia, D. N. Riahi, R. Roy

Applications and Applied Mathematics: An International Journal (AAM)

We investigate the problem of unsteady fluid flow in growing solid tumors. We develop a mathematical model for a growing tumor whose boundary is taken as a sphere, and the unsteady fluid flow within the tumor is assumed to be two dimensional with respect to the radial distance and the latitudinal angle in spherical coordinates. The expressions for the time, radial and latitudinal variations of the flow velocity, pressure, and the two investigated drug concentrations within the tumor were determined analytically. We calculated these quantities in the tumor as well as in a corresponding normal tissue. We find, in particular, …

The Characterization Of A Vital Wisconsin Waterway: A Biological Assessment Of The Lower Fox River From 2006-2014, Emily L. Kiehnau

Lawrence University Honors Projects

The Lower Fox River has historically been used as a navigational crossroads, a waste disposal system, and source of hydroelectric power. Over the years, heavy use of the river has negatively affected water quality and the overall health of the system. Unhealthy rivers cannot function properly. Biological assessment based on animal surveys are often used to determine river health. I used data from the Lawrence University and Fox River Navigational System Authority invasive species-monitoring project to explore how the distribution of animals in the Fox River has changed over time and across locations. Monitoring surveys have taken place between June …

Environmental And Adaptive Buffers That Mediate The Response Of Subalpine Ecosystems To Environmental Change, Lafe G. Conner

Student Works

This document reports the results of 4 studies of subalpine ecosystem ecology, describing ways that spatial heterogeneity in soils and plant communities mediate ecosystem responses to environmental change. Ecosystem responses to environmental change are also mediated by regional climate patterns and interannual variability in weather. In the first chapter we report the results of an experiment to test for the mediating effects of associational resistance in a forest community that experienced wide-spread beetle kill. We found that Engelmann spruce were more likely to survive a beetle outbreak when growing in low densities (host dilution) and not through other types of …

Using Ecological Niche Modeling And Genetics To Evaluate The Conservation Status Of The Texas Gartersnake, Thamnophis Sirtalis Annectens, Kayla N. Key

Biology Theses

The definition of a species has been argued extensively by philosophers and biologists resulting in the development of many different concepts which often contradict each other. An integrative approach using multiple types of data (e.g, morphological, ecological, behavioral, genetic) may be the most successful at correctly assigning taxonomic levels.Here, we use an integrative approach of ecological niche modeling and molecular genetics to investigate the taxonomy of a state imperiled gartersnake subspecies, Thamnophis sirtalis annectens, using ecological niche modeling and molecular phylogenetics analyses. Recently, it was given a conservation rank of S2 (imperiled) in the state of Texas and those that …

Genetic Changes To A Transcriptional Silencer Element Confers Phenotypic Diversity Within And Between Drosophila Species, Winslow C. Johnson, Alison J. Ordway, Masayoshi Watada, Jonathan N. Pruitt, Thomas M. Williams, Mark Rebeiz

Biology Faculty Publications

The modification of transcriptional regulation has become increasingly appreciated as a major contributor to morphological evolution. However, the role of negative-acting control elements (e.g. silencers) in generating morphological diversity has been generally overlooked relative to positive-acting “enhancer” elements. The highly variable body coloration patterns among Drosophilid insects represents a powerful model system in which the molecular alterations that underlie phenotypic diversity can be defined. In a survey of pigment phenotypes among geographically disparate Japanese populations of Drosophila auraria, we discovered a remarkable degree of variation in male-specific abdominal coloration. In testing the expression patterns of the major pigment-producing enzymes, …

Controllability Of An Eco-Epidemiological System With Disease Transmission Delay: A Theoretical Study, Samadyuti Haldar, Kunal Chakraborty, T. K. Kar

Applications and Applied Mathematics: An International Journal (AAM)

This paper deals with the qualitative analysis of a disease transmission delay induced prey preda-tor system in which disease spreads among the predator species only. The growth of the preda-tors’ susceptible and infected subpopulations is assumed as modified Leslie–Gower type. Suffi-cient conditions for the persistence, permanence, existence and stability of equilibrium points are obtained. Global asymptotic stability of the system is investigated around the coexisting equilib-rium using a geometric approach. The existence of Hopf bifurcation phenomenon is also exam-ined with respect to some important parameters of the system. The criterion for disease a trans-mission delay the induced Hopf bifurcation phenomenon …

Spatial Heterogeneity, Host Movement And Mosquito-Borne Disease Transmission, Miguel A. Acevedo, Olivia Prosper, Kenneth Lopiano, Nick Ruktanonchai, T. Trevor Caughlin, Maia Martcheva, Craig W. Osenberg, David L. Smith

Dartmouth Scholarship

Mosquito-borne diseases are a global health priority disproportionately affecting low-income populations in tropical and sub-tropical countries. These pathogens live in mosquitoes and hosts that interact in spatially heterogeneous environments where hosts move between regions of varying transmission intensity. Although there is increasing interest in the implications of spatial processes for mosquito-borne disease dynamics, most of our understanding derives from models that assume spatially homogeneous transmission. Spatial variation in contact rates can influence transmission and the risk of epidemics, yet the interaction between spatial heterogeneity and movement of hosts remains relatively unexplored. Here we explore, analytically and through numerical simulations, how …

Regulation Of Glial Cell Line-Derived Neurotrophic Factor (Gdnf) Production In Voluntary And Involuntary Muscle, John-Mary Vianney

Dissertations

Glia cell line-derived neurotrophic factor (GDNF) is a survival factor for subpopulations of neurons, including somatic and autonomic motor neurons. These neurons depend, in part, on GDNF that is synthesized and secreted by their target tissues. It has been shown that a number of tissues in the periphery express GDNF and these target tissues differ in their composition, function, and in the case of different muscle cell types, their contractile characteristics. Whether the processes regulating GDNF production in these different tissues is similar or different is poorly understood. The broad goal of this study is to examine factors that normally …

The Biological Consequences Of Kaolin Geophagia, Deloris Alexander, Desire Richardson, Lakisha Odom, Kara Cromwell, Dejuana Grant, Micoya Myers, Eddy Cadet, Hamid Mahama, Vijaya Rangari, Ralphenia Pace, Ramble Ankumah, Kokoasse Kpomblekou-A, Curtis Fluker

Professional Agricultural Workers Journal

Abstract

Kaolin geophagia is associated with the relief of gastrointestinal distress, but it may also cause adverse health effects on the body. This study was designed to: assess kaolin composition; test if 129SvEv mice would consume kaolin and determine the consequences of consumption; and assess rotational stress modulation of consumption. Thirteen kaolin samples were purchased from Alabama and Georgia stores. Chemical and physical properties were characterized for each sample using a Munsell chart, pH meter, Energy Dispersive Spectroscopy, Transmission Electron Microscopy, Visible Near-InfraRed Spectra, and Inductively Coupled Plasma-Optical Emission Spectrometry. Kaolin was then given to mice as food supplements and …

Isolation And Epidemiological Analysis Of Verotoxigenic E. Coli From Patients With Acute Gastroenteritis: A Prospective Study Aiming To Reduce The Burden Of Infection In The Cork Region., Shirley Ross

Masters

Verotoxigenic Escherichia coli (VTEC) is a serious gastrointestinal pathogen associated with morbidity and mortality in the first world, as accentuated by the O104 VTEC outbreak in Germany in 2011. Molecular detection of Verotoxin (VT) has increased the detection of VTEC across Europe however, Ireland still has the highest incidence and isolation is still a key step in the confirmation of infection and the control and prevention of outbreaks. Currently no standard protocol exists for the detection, isolation and characterisation of non-O157 VTEC and it is feared that due to this that the prevalence of VTEC is under-reported. This body of …

Reproductive Ecology And Hatchling Behavior Of Olive Ridley Sea Turtles In Honduras, Noemi Duran Royo

Loma Linda University Electronic Theses, Dissertations & Projects

In this dissertation, I investigated the reproductive ecology and hatchling behavior of the olive ridley (Lepidochelys olivacea) sea turtle population nesting in Pacific Honduras. I begin by reviewing olive ridley reproduction, human use of this species, and past and present conservation on nesting beaches. I also propose a conservation strategy to improve nesting beach conservation programs in developing countries. In the first of four empirical studies, I used microsatellite markers to assess multiple paternity levels of the Honduran population, and found evidence for multiple paternity in 75% of the nests examined. This rate, higher than expected for a population of …

Climatic Variation And Seed Persistence: Freeze-Thaw Cycles Lower Survival Via The Joint Action Of Abiotic Stress And Fungal Pathogens, Brian M. Connolly, John L. Orrock

Biology Faculty Scholarship

Global climate change is altering thermal cycles in soils during late winter, a transition that may directly threaten seed survival via abiotic stress, facilitate infection by soil-borne pathogens, or both. Using field-collected soil and seeds of the perennial bunchgrass Elymus canadensis, we tested the hypothesis that soil freeze–thaw events limit survival within the soil through direct effects on seed persistence and amplification of soil pathogen attack using a factorial experiment that manipulated freeze–thaw cycles (constant freeze vs. freeze–thaw) and fungicide addition. Freeze–thaw treatment resulted in lower seedling emergence and delayed emergence time relative to constant-freeze controls. Fungicide-treated soils had …

Bioinformatics For The Comparative Genomic Analysis Of The Cotton (Gossypium) Polyploid Complex, Justin Thomas Page

Theses and Dissertations

Understanding the composition, evolution, and function of the cotton (Gossypium) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). Specifically, read-mapping (a fundamental part of next-generation sequence analysis) cannot adequately differentiate reads as belonging to one genome or the other. These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we developed PolyCat to categorize reads according to their genome of origin based on homoeo-SNPs that differentiate the two genomes. We re-sequenced the genomes of extant diploid relatives of tetraploid cotton …

Quantitative Detection Of Syntrophic Fatty Acid-Degrading Bacterial Communities In Methanogenic Environments, Prince Peter Mathai, Daniel Zitomer, James Maki

Biological Sciences Faculty Research and Publications

In methanogenic habitats, volatile fatty acids (VFA), such as propionate and butyrate, are major intermediates in organic matter degradation. VFA are further metabolized to H2, acetate and CO2 by syntrophic fatty acid-degrading bacteria (SFAB) in association with methanogenic archaea. Despite their indispensable role in VFA degradation, little is known about SFAB abundance and their environmental distribution. To facilitate ecological studies, we developed four novel genus-specific quantitative PCR (qPCR) assays, with primer sets targeting known SFAB: Syntrophobacter, Smithella, Pelotomaculum and Syntrophomonas. Primer set specificity was confirmed using in silico and experimental (target controls, clone libraries and melt-curve analysis) …

Selfish Mitochondrial Dna Proliferates And Diversifies In Small, But Not Large, Experimental Populations Of Caenorhabditis Briggsae, Wendy S. Phillips, Anna Luella Coleman-Hulbert, Emily S. Weiss, Dana K. Howe, Sita Ping, Riana I. Wernick, Suzanne Estes, Dee R. Denver

Biology Faculty Publications and Presentations

Evolutionary interactions across levels of biological organization contribute to a variety of fundamental processes including genome evolution, reproductive mode transitions, species diversification, and extinction. Evolutionary theory predicts that so-called “selfish” genetic elements will proliferate when the host effective population size (N_e) is small, but direct tests of this prediction remain few. We analyzed the evolutionary dynamics of deletion-containing mitochondrial DNA (ΔmtDNA) molecules, previously characterized as selfish elements, in six different natural strains of the nematode Caenorhabditis briggsae allowed to undergo experimental evolution in a range of population sizes (N = 1, 10, 100, and 1,000) for a maximum …

Environmental And Adaptive Buffers That Mediate The Response Of Subalpine Ecosystems To Environmental Change, Lafe G. Conner

Theses and Dissertations

This document reports the results of 4 studies of subalpine ecosystem ecology, describing ways that spatial heterogeneity in soils and plant communities mediate ecosystem responses to environmental change. Ecosystem responses to environmental change are also mediated by regional climate patterns and interannual variability in weather. In the first chapter we report the results of an experiment to test for the mediating effects of associational resistance in a forest community that experienced wide-spread beetle kill. We found that Engelmann spruce were more likely to survive a beetle outbreak when growing in low densities (host dilution) and not through other types of …

Protein Domain Linker Prediction: A Direction For Detecting Protein – Protein Interactions, Maad Mohammad Hasan Shatnawi

Dissertations

Protein chains are generally long and consist of multiple domains. Domains are the basic of elements of protein structures that can exist, evolve and function independently. The accurate and reliable identification of protein domains and their interactions has very important impacts in several protein research areas. The accurate prediction of protein domains is a fundamental stage in both experimental and computational proteomics. The knowledge is an initial stage of protein tertiary structure prediction which can give insight into the way in which protein works. The knowledge of domains is also useful in classifying the proteins, understanding their structures, functions and …

Lessons From Pollution Control: Response To Heller And Hobbs 2014, Robert L. Fischman, James Salzman

Articles by Maurer Faculty

Heller and Hobbs (2014) provide an incisive analysis of the challenges inherent in setting endpoint states as conservation goals. The social construct of nature, nonequilibrium ecosystems, global climate change, large-scale transformations of the landscape, and increasing population and economic activity confound efforts to establish conservation goals. Stakeholders often disagree on endpoint targets, whereas competing notions of historic fidelity and future flexibility frustrate our ability to articulate success, never mind actually achieve it. As Heller and Hobbs describe, this leaves managers in the bind of finding the “balance between future-looking management emphasizing change and past-looking management emphasizing persistence.” As a result, …

Erika Dyck. Facing Eugenics: Reproduction, Sterilization, And The Politics Of Choice, Garland E. Allen

Biology Faculty Research

[Book review of Erika Dyck. Facing Eugenics: Reproduction, Sterilization, and the Politics of Choice. Toronto: University of Toronto Press, 2013.]

Physiological Strategies During Animal Diapause: Lessons From Brine Shrimp And Annual Killifish., Jason E. Podrabsky, Steven C. Hand

Biology Faculty Publications and Presentations

Diapause is a programmed state of developmental arrest that typically occurs as part of the natural developmental progression of organisms that inhabit seasonal environments. The brine shrimp Artemia franciscana and annual killifish Austrofundulus limnaeus share strikingly similar life histories that include embryonic diapause as a means to synchronize the growth and reproduction phases of their life history to favorable environmental conditions. In both species, respiration rate is severely depressed during diapause and thus alterations in mitochondrial physiology are a key component of the suite of characters associated with cessation of development. Here, we use these two species to illustrate the …

One Fish, Two Fish, Red Fish, Blue Fish: The Analysis Of The Specter Cell Cycle Mutant In Zebrafish, Tetiana Petrachkova

Masters Theses

Cell division is controlled by genes that regulate the cell cycle. Here we show that the zebrafish specter (spr) mutant is mutation in the cyclin B1 gene, a gene necessary for the G2 to M transition of the cell cycle.

The spr mutation mapped to the cyclin B1 gene. Sequencing showed a transition (C139→T) that caused a nonsense mutation in exon 2 of the cyclin B1 gene. In situ hybridization of cyclin B1 revealed that the mRNA is absent in the mutant embryo by gastrulation. We found that the earliest visible mutant phenotype was a darkening of the head caused …

Microbial Community Analysis From Petroleum-Contaminated Sediments With High Magnetic Susceptibility, Anja E. Williams

Masters Theses

Microbial biodegradation is an increasingly incorporated method of hydrocarbon mineralization during oil spill cleanup. To monitor biodegradation, magnetic susceptibility (MS) is a geophysical tool that detects changes in sediments’ magnetism, possibly caused by microbial activity, for example by anaerobic iron reduction that can induce magnetite formation. Furthermore, the high input of carbon from an oil spill makes other required nutrients, like nitrogen, limiting. The first study goal was to characterize the microbial communities present at high levels of MS with 16S rRNA gene clone libraries at the petroleum-contaminated site in Bemidji, Minnesota. Sequences with high similarity to known iron-reducers were …

Generation And Assessment Of Muscular Mutations In Caenorhabditis Elegans, Katie N. Reget

DePaul Discoveries

A study of egg laying muscular mutations in C. elegans was conducted over a span of ten weeks. Parent (EGL-19) and wild type (N2) were exposed to mutagenesis and integration mutation techniques to generate genetic and physical different mutants. Overall, four genetic, physical and phenotypically unique worms were generated for the process of mutagenesis. The worms used in the process of integration were found to have shortened life spans, reduced size and decrease numbers of progeny.

Predation In A Natural Community Of Marine Mollusks: Using Morphology To Determine Predator-Prey Ecology, Danielle N. Araiza, Erica Valdez

DePaul Discoveries

Predatory gastropod mollusks in the family Naticidae feed on bivalve mollusks and leave distinctive markings in the form of countersunk circular boreholes on the shells. These boreholes possess both an inner borehole diameter (IBD) and an outer borehole diameter (OBD) which are proportional to the size of the predator. It has been proposed that the ratio of IBD to OBD can be used to identify predator species. Variation in the ratio of the IBD to OBD was examined in two prey species (Dwarf surf clam, Incongruous ark clam) collected from Otter Island beach in South Carolina to determine if clams …

Chronic Inflammation As A Result Of Hepatitis C Virus Infection: A Review Of The Literature, Samantha L. Lane

DePaul Discoveries

Approximately 170 million people are infected with Hepatitis C virus (HCV) worldwide^5,6. It is estimated that roughly 80% of those infected suffer from persistent infection with the virus; this persistence of infection is progressive, and over time can lead to fibrosis, cirrhosis, and hepatocellular carcinoma⁷. Chronic inflammation and apoptotic deregulation are both hallmarks of chronic HCV infection, and many molecular pathways are initiated in both the innate and adaptive immune responses during infection with this viral pathogen. The aim of this review was to survey some of the major molecular mechanisms responsible for the induction of …

Lignocellulose Metabolism In A Fungus-Gardening Ant Symbiosis, Alexandria Demilto

Biology Theses

Fungus-gardening ants exhibit a unique interaction with specific fungi in an obligatory symbiosis; ants feed and prune their fungal symbiont in exchange for nourishment. Cellulose is the most abundant plant compound found on earth and may serve as a rich carbon source to ants. Recent studies show that leaf-cutting (Atta and Acromyrmex) ants' fungus does not typically digest cellulose, but there have been few comparisons to the other higher attine fungus gardening ants. In this study, I measured the lignocellulose consumption of the higher fungus-gardening ants Trachymyrmex septentrionalis and Trachymyrmex arizonensis. Colonies were fed either a diet of Texas Red …