Digital Commons Network^™

Exploring The Sulfide Tolerance Of Ectosymbiotic Niphargus Amphipods From The Frasassi Caves, Central Italy, Jan Bauermeister, Karoline Assig, Sharmishtha Dattagupta

International Journal of Speleology

Two species of the crustacean amphipod genus Niphargus inhabit the sulfidic groundwaters of the Frasassi caves in central Italy, and both harbor filamentous, sulfide-oxidizing Thiothrix ectosymbionts. As sulfide is toxic to most aerobic organisms, it appeared possible that the ectosymbionts could help their Niphargus hosts with detoxification processes. In this study, mortality due to sulfide was compared between Niphargus individuals with ectosymbionts and individuals whose ectosymbionts had been killed by antibiotic treatment. Both Frasassi-dwelling Niphargus species revealed exceptionally high tolerances to sulfide compared to other amphipod species studied so far. Niphargus individuals without viable ectosymbionts tolerated sulfide levels exceeding those …

An Investigation Of Alternative Oxidase Presence, Expression, And Regulation In The Moss Physcomitrella Patens, Karina I. Neimanis

Theses and Dissertations (Comprehensive)

Alternative oxidase (AOX) is an inner mitochondrial membrane protein that introduces a branch point at ubiquinone within the respiratory electron transport system (ETS). The AOX protein bypasses two sites of proton translocation within the ETS and as a result the yield of ATP per oxygen consumed is significantly reduced. Although AOX appears to be energetically wasteful, recent studies have revealed that AOX has a wide taxonomic distribution. AOX multigene families, transcripts, protein levels, and enzymatic activity have been most thoroughly characterized in many angiosperm (flowering) plants. Given the data available for angiosperm AOXs, evidence of non-angiosperm AOXs in the primary …

Mechanisms Of Nitrogenous Waste Excretion During The Complex Life Cycle Of The Sea Lamprey (Petromyzon Marinus), James M. Neal Mr.

Theses and Dissertations (Comprehensive)

Sea lampreys (Petromyzon marinus) are a phylogenetically ancient jawless fish, with a multi-staged life cycle characterized by a prolonged suspension-feeding larval stage, which is followed by metamorphosis into parasitic lampreys that feed on the protein-rich blood of fishes. The switch from a nutrient poor to protein-rich diet in the sea lamprey is associated with an increased capacity to deaminate excess amino acids and to excrete ammonia and urea following metamorphosis. The focus of this thesis was to determine if changes in nitrogenous waste transporter protein abundance facilitate ammonia and urea excretion during different stages of the sea lamprey …

Does Ecosystem Disturbance Alter The Capacity Of Dissolved Organic Matter To Mitigate The Impact Of Copper To Hyalella Azteca?, Kelly Livingstone

Theses and Dissertations (Comprehensive)

The potential for aquatic ecosystem recovery as a result of dissolved organic matter (DOM) protecting against metal toxicity has become a significant area of research in environmental toxicology. It is a well-characterized relationship that DOM binds free metal ions in a concentration-dependant manner, making them unavailable for toxic action and a reduction in toxicity is seen. Less understood is source variability and how the upland terrestrial environment influences the protective quality of DOM. The aim of this study was to examine the influence of land disturbance (logging, fire, smelter emissions) on DOM quality by comparing the protective capacity of different …

The Conservation Status Of The World’S Reptiles, Tony Gamble

Biological Sciences Faculty Research and Publications

Effective and targeted conservation action requires detailed information about species, their distribution, systematics and ecology as well as the distribution of threat processes which affect them. Knowledge of reptilian diversity remains surprisingly disparate, and innovative means of gaining rapid insight into the status of reptiles are needed in order to highlight urgent conservation cases and inform environmental policy with appropriate biodiversity information in a timely manner. We present the first ever global analysis of extinction risk in reptiles, based on a random representative sample of 1500 species (16% of all currently known species). To our knowledge, our results provide the …

A Transgenic Minipig Model Of Huntington's Disease, Monika Baxa, Marian Hruska-Plochan, Stefan Juhas, Petr Vodicka, Antonin Pavlok, Jana Juhasova, Atsushi Miyanohara, Tetsuya Nejime, Jiri Klima, Monika Macakova, Silvia Marsala, Andreas Weiss, Svatava Kubickova, Petra Musilova, Radek Vrtel, Emily M. Sontag, Leslie Thompson, Jan Schier, Hana Hansikova, David S. Howland, Elena Cattaneo, Marian Difiglia, Martin Marsala, Jan Motlik

Biological Sciences Faculty Research and Publications

Background: Some promising treatments for Huntington's disease (HD) may require pre-clinical testing in large animals. Minipig is a suitable species because of its large gyrencephalic brain and long lifespan. Objective: To generate HD transgenic (TgHD) minipigs encoding huntingtin (HTT)1–548 under the control of human HTT promoter. Methods: Transgenesis was achieved by lentiviral infection of porcine embryos. PCR assessment of gene transfer, observations of behavior, and postmortem biochemical and immunohistochemical studies were conducted. Results: One copy of the human HTT transgene encoding 124 glutamines integrated into chromosome 1 q24-q25 and successful germ line transmission occurred through successive generations (F0, F1, F2 …

Image-Level And Group-Level Models For Drosophila Gene Expression Pattern Annotation, Quian Sun, Sherin Muckatira, Lei Yuan, Shuiwang Ji, Stuart Newfeld, Sudhir Kumar, Jieping Ye

Computer Science Faculty Publications

Background: Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment …

A Mesh Generation And Machine Learning Framework For Drosophila Gene Expression Pattern Image Analysis, Wenlu Zhang, Daming Feng, Rongjian Li, Andrey Chernikov, Nikos Chrisochoides, Christopher Osgood, Charlotte Konikoff, Stuart Newfeld, Sudhir Kumar, Shuiwang Ji

Computer Science Faculty Publications

Background: Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide …

Mitigating Predatory Ants Promotes Establishment Of Biological Control Of Arundo By Arundo Scale In The Cattle Fever Tick Quarantine Zone, A. Velez-Bonner, W. L. A. Osbrink, D. W. Thomas, Kenneth R. Summy, A. T. Showler, A. Perez De Leon, John A. Goolsby

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

Ant collection, identification, and control experiments were conducted to improve the establishment of the arundo scale, Rhizaspidiotus donacis, a biological control agent of Arundo donax, an invasive weed in the riparian habitats along the Rio Grande in Texas. Observational studies indicated R. donacis immatures are preyed upon by a variety of predator insects, especially ants. A survey of the principle ant species was made at sites along the Rio Grande with Arundo donax to help direct biological control strategies. We conclude that uses of ant baits can effectively control the common ant species found in these habitats and improve the …

Acyl-Lipid Metabolism, Younghua Li-Beisson, Basil Shorrosh, Fred Beisson, Mats X. Andersson, Vincent Arondel, Philip D. Bates, Sébastien Baud, David Bird, Allan Debono, Timothy P. Durrett, Rochus B. Franke, Ian A. Graham, Kenta Katayama, Amélie A. Kelly, Tony Larson, Jonathan E. Markham, Martine Miquel, Isabel Molina, Ikuo Nishida, Owen Rowland, Lacey Samuels, Katherine M. Schmid, Hajime Wada, Ruth Welti, Changcheng Xu, Rémi Zallot, John Ohlrogge

Scholarship and Professional Work - LAS

Acyl lipids in Arabidopsis and all other plants have a myriad of diverse functions. These include providing the core diffusion barrier of the membranes that separates cells and subcellular organelles. This function alone involves more than 10 membrane lipid classes, including the phospholipids, galactolipids, and sphingolipids, and within each class the variations in acyl chain composition expand the number of structures to several hundred possible molecular species. Acyl lipids in the form of triacylglycerol account for 35% of the weight of Arabidopsis seeds and represent their major form of carbon and energy storage. A layer of cutin and cuticular waxes …

Bmp Planning To Address Urban Runoff: Plaster Creek Watershed Sustain Pilot, Tetra Tech, Inc.

Watershed Reports

The Plaster Creek watershed is tributary to the Grand River in west Michigan. Plaster Creek is one of several impaired streams in this area, located in metropolitan Grand Rapids. There are several listed impairments for the Creek including 1) other indigenous aquatic life and wildlife, 2) warm water fishery, and 3) total and partial body contact recreation. Total maximum daily load (TMDL) studies were completed in 2002 for biota and E. coli to address the listed impairments. In 2008, a watershed management plan (WMP) was developed which outlines an implementation plan for water quality improvement in the watershed. This pilot …

Molecularly Imprinted Polymer Technology: A Powerful, Generic, Facile And Cost Effective Alternative For Enantio-Recognition And Separation: A Glance At Advances And Applications, Jyn Philip, Dms Mosha

Tanzania Journal of Science

The emerging Molecularly Imprinted Polymer (MIP) technology has yielded proof of concept, harnessing nature’s fundamentals to yield recognition receptor mimics from the miniaturized basics, borrowing on the ground rules, but conveniently avoiding the complexity, fragility, instability, costs and ethics of animal based bio-affinity matrices. Thus, the impact of bio-sciences on the future of technology is not via direct use of the molecules, but rather the lessons learned. Molecular imprinting is a powerful specialty representing the generic, cost effective and facile alternative for preparation of synthetic custom-tailored receptors. It achieves this via creation of specific selective recognition sites for a pre-determined …

Chronic Stress Elevates Telomerase Activity In Rats, Annaliese K. Beery, Jue Lin, Joshua S. Biddle, Darlene D. Francis, Elizabeth H. Blackburn, Elissa S. Epel

Neuroscience: Faculty Publications

The enzyme telomerase lengthens telomeres—protective structures containing repetitive DNA sequences at chromosome ends. Telomere shortening is associated with diseases of ageing in mammals. Chronic stress has been related to shorter immune-cell telomeres, but telomerase activity under stress may be low, permitting telomere loss, or high, partially attenuating it. We developed an experimental model to examine the impacts of extended unpredictable stress on telomerase activity in male rats. Telomerase activity was 54 per cent higher in stressed rats than in controls, and associated with stress-related physiological and behavioural outcomes. This significant increase suggests a potential mechanism for resilience to stress-related replicative …

Vegf And Angiopoietin-1 Exert Opposing Effects On Cell Junctions By Regulating The Rho Gef Syx, Siu P. Ngok, Rory Geyer, Miaoliang Liu, Antonis Kourtidis, Sudesh Agrawal, Chuanshen Wu, Himabindu Reddy Seerapu, Laura J. Lewis-Tuffin, Karen L. Moodie, Deborah Huveldt, Ruth Marx, Jay M. Baraban, Peter Storz, Arie Horowitz, Panos Z. Anastasiadis

Dartmouth Scholarship

Vascular endothelial growth factor (VEGF) and Ang1 (Angiopoietin-1) have opposing effects on vascular permeability, but the molecular basis of these effects is not fully known. We report in this paper that VEGF and Ang1 regulate endothelial cell (EC) junctions by determining the localization of the RhoA-specific guanine nucleotide exchange factor Syx. Syx was recruited to junctions by members of the Crumbs polarity complex and promoted junction integrity by activating Diaphanous. VEGF caused translocation of Syx from cell junctions, promoting junction disassembly, whereas Ang1 maintained Syx at the junctions, inducing junction stabilization. The VEGF-induced translocation of Syx from EC junctions was …

What's That Hooting Sound? A Survey On Novel Sound Producing Mechanisms In Chameleons, Keyana Boka

Mahurin Honors College Capstone Experience/Thesis Projects

This research project seeks to study how chameleons generate low frequency vibrations, some audible and some not. The mechanism responsible for this 'hoot' is unknown. A modified tracheal appendage we termed “the resonator” has been hypothesized as the potential source of this sound. An anatomical survey was conducted on various chameleon species including, Chameleo melleri (Meller), Chamaeleo pardalis (Ambanja, Nosy Be, Panther, Sambava), Furcifer rhinoceratus, Chamaeleo dilepis (Flapneck), Chamaeleo rudis (Side-striped), Chamaeleo calyptratus (Veiled), Chamaeleo jacksonii (Jackson’s), Chamaeleo quadricornicus (4-horned), Chamaeleo quilensis (Flapneck), Chamaeleo senegalensis (Senegal), Chamaeleo jacksonii xantholophus (giant Jackson’s), and Rhampholean brevicaudatus (Pygmy). Each chameleon was dissected …

The Debate On Marine Mammals In Captivity, Lorna C. Scribner

Honors Theses

Are marine mammal species better off today because of captivity? Is captivity ethical and should it be continued? As this debate grows stronger, both of these sides of the argument offer substantial evidence in their favor. In this paper, I discuss data for both sides and evaluate the justifications of marine mammal captivity. Ideally, no matter the outcome, this research will educate the public on influential factors of wild and captive populations.

Quantifying Acclimation Levels Of Mimus Polyglottos In The Presence Of People, Jordan Rutherford

Honors Theses

The northern mockingbird (Mimus polyglottos) is a common bird species found in North America that in the past 150 years has expanded its distribution north. It is now commonly seen in urban and suburban areas were at one point, it was rarely seen outside of rural and forested areas. For the study, I observed northern mockingbirds at nine different sites over a period of a month between September and October 2012. After the study, I determined that there is a negative relationship between the number of people in the surrounding area and the distance when the birds flew away.

Lipophilic And Hydrophilic Quantitative Analysis Of Antioxidant Activity In Tomatoes And Tomato Products, Anna Tran Dinh

Masters Theses, 2010-2019

The amount of antioxidants present in food varies depending on environmental conditions in which produce was grown and how products were processed prior to consumption. It would, therefore, be useful to quantify antioxidant activities in these foods. This study focused on quantitative analysis of antioxidant activities in commercially produced whole tomatoes and processed tomato products. For commercially processed tomatoes, diced tomatoes had total antioxidant activities (TAA) ranging from 1.243 to 2.243 μmol TE/g fresh weight (fw), juice 1.573 to 6.86 μmol TE/g fw, paste 6.3 to 13.248 μmol TE/g fw, sauce 1.62 to 3.168 μmol TE/g fw, and soup 1.073 …

The Influence Of Ubiquitin-Related Modifier Protein Urm1 On Prion Formation, Jacob Beaver

Honors Theses

Prions are infections proteins that are auto-catalyzing (form by altering a regular protein into the structurally different prion form), and are the cause of many common diseases such as Alzheimer's, Parkinson's, Huntington's, and Bovine Spongiform encephalopathy (or Mad Cow disease). This experiment tested the effect of three different plasmids, pH317, pER62 and pmp46 on prion formation in both wild-type and Urm1 deletion mutants in the yeast Saccharomyces cerevisiae. The proposed hypothesis was overexpression of the prion forming protein would increase the frequency of prion formation, as well as yield less sustainable prion amyloids (or prion aggregations) that are easier to …

Effects Of Selenium On The Freshwater Alga Chlamydomonas Reinhardtii With And Without The Proteasome Inhibitor Mg132, E. Patrick Vallentine

Honors Theses

Selenium is a required nutrient in animal life but has not been shown to be needed in plants. The model plant cell Chlamydomonas reinhardtii may be an exception as it appears to increase its growth rate in the presence of selenium. Because selenium has the same valence state as sulfur it may be incorporated into proteins as the modified amino acid selenocysteine. This incorporation of selenocysteine into protein may disrupt the disulfide bridges that give proteins the correct conformation. Misfolded proteins can wreak havoc on a cell. This stress can be measured through several parameters. Chlorophyll levels, glutathione levels, growth, …

A Tree Theory Case Study In Steinernema, Camille Eileen Finlinson Porter

Theses and Dissertations

It is widely assumed that current phylogenetic methods are fairly accurate at recovering the evolutionary relationships among different species, but evaluating the relative success of this enterprise is a difficult task. This study addresses some fundamental questions associated with generating phylogenetic trees. The complete genomes of five species of Steinernema were sequenced and assembled. Genes were predicted in AUGUSTUS and orthologous genes were found from those data using OrthoMCL. I aligned 3890 genes in MAFFT and eliminated poorly aligned positions with GBlocks. I created individual trees for each gene as well as a supermatrix tree in PAUP*, using a closely …

Coexistence Of Sympatric Taxa Of Chamaecrista Section Xerocalyx: Addressing The Interplay Between Morphology And Biotic Interactions, Beatriz Baker-Méio

Dissertations

Animal-plant interactions may prevent gene flow and promote divergent selection among closely related plants, ultimately leading to formation of new species. This may be the case for Chamaecrista sect. Xerocalyx, in which two or more of the 24 varieties often are encountered in the same area, with marked morphological and phenological differences among them. Over a broad geographical range, however, the morphological gaps among varieties disappear. Several biotic interactions contribute to the fitness of Chamaecrista species. Their flowers are pollinated by bees, and herbivores attack their leaves, flowers, fruits, and seeds. In addition, all species produce extrafloral nectar, which …

The Effects Of Climate Change And Overexploitation On Birds And Mammals: Phenological Shifts, Range Shifts, And Population Changes, Rachel Denny

Honors Theses

Our world is changing more than many individuals could imagine. Climate change is not a hoax. Comprehensive empirical records of changes since 1900 in local, regional, and global temperature clearly indicate that Earth is warming more rapidly than ever in recorded history. In response, some bird species are already shifting, both phenologically (timing) and geographically. However, the majority of birds are not shifting or not shifting fast enough, and this is resulting in population declines. A much smaller number of studies suggest that mammals are also shifting phenologically and geographically.

If we do not alter our current behaviors soon, Earth …

Marine Fungi Of U.S. Gulf Of Mexico Barrier Island Beaches: Biodiversity And Sampling Strategy, Allison Kathleen Walker

Dissertations

Marine fungi are an important but often overlooked component of marine ecosystems. Primarily saprotrophic, they are vital to coastal nutrient cycling processes and food webs. However, basic marine fungal distribution data are lacking in many parts of the world, as is knowledge of the sampling intensity required to characterize the biodiversity of these communities. The roles of substrate, season and latitude in shaping intertidal ascomycete community structure were examined for the U.S. Gulf of Mexico, and the role of sampling frequency on species richness estimates was also addressed. Best sampling practices were developed and 750 collections of beach detritus, sand …

Management Of Biological And Chemical Constituents For The Advancement Of Intensive, Minimal-Exchange, Biofloc-Based Shrimp (Litopenaeus Vannamei) Aquaculture, Andrew James Ray

Dissertations

Intensive, minimal-exchange, biofloc-based shrimp aquaculture systems may provide a sustainable alternative to traditional shrimp culture. Through a series of experiments, this document explores the effects of several key management strategies on water quality, isotopic distribution, and shrimp production.

An experiment evaluated the effects of managing suspended solids (biofloc) concentration at two levels. It was found that using a higher flow rate to larger settling chambers resulted in significantly lower biofloc and nitrate concentrations, and significantly improved shrimp growth rate. A second experiment compared systems with clear water and systems with biofloc. The filters in the clear water systems prevented biofloc …

Differential Expression Of Alpha 4 Integrins On Effector Memory T Helper Cells During Bordetella Infections. Delayed Responses In Bordetella Pertussis, Tzvia Abramson, Tuan M. Nguyen, Dipti Ravindra, Brian Kwong, Sana Waheed, Ryan Ferguson, Nicole Tarlton, Victoria Wu, Christopher S. Sequeira, Martina Bremer

Faculty Publications, Biological Sciences

Bordetella pertussis (B. pertussis) is the causative agent of whooping cough, a respiratory disease that is reemerging worldwide. Mechanisms of selective lymphocyte trafficking to the airways are likely to be critical in the immune response to this pathogen. We compared murine infection by B. pertussis, B. parapertussis, and a pertussis toxin-deleted B. pertussis mutant (BpΔPTX) to test the hypothesis that effector memory T-helper cells (emTh) display an altered pattern of trafficking receptor expression in B. pertussis infection due to a defect in imprinting. Increased cell recruitment to the lungs at 5 days post infection (p.i.) with B. parapertussis, and to …

Species Shout-Outs From Abdul To Zebra: Encouraging Nonmajors To Communicate In The Biology Classroom, Christina P. Colon

Publications and Research

No abstract provided.

Influences Of A Cladophora Bloom On The Diets Of Amblema Plicata And Elliptio Dilatata In The Upper Green River, Kentucky, Jennifer Maria Yates

Masters Theses & Specialist Projects

Freshwater mussels are the most imperiled group of freshwater invertebrates globally. Recent research suggests a better understanding of mussel feeding ecology may facilitate and improve conservation efforts. The use of stable isotopes is becoming an increasingly common method to study aquatic food webs. Carbon (C) and nitrogen (N) are two of the most frequently employed elements in food web studies. Differences in natural abundance of ¹³C/¹²C can indicate which food sources are the basal sources of carbon incorporated into a consumer’s tissue, while the ratio of ¹⁵N /¹⁴N provides a method of assessing trophic …

A Symbiotic View Of Life: We Have Never Been Individuals, Scott F. Gilbert, J. Sapp, A. I. Tauber

Biology Faculty Works

The notion of the "biological individual" is crucial to studies of genetics, immunology, evolution, development, anatomy, and physiology. Each of these biological subdisciplines has a specific conception of individuality, which has historically provided conceptual contexts for integrating newly acquired data. During the past decade, nucleic acid analysis, especially genomic sequencing and high-throughput RNA techniques, has challenged each of these disciplinary definitions by finding significant interactions of animals and plants with symbiotic microorganisms that disrupt the boundaries that heretofore had characterized the biological individual. Animals cannot be considered individuals by anatomical or physiological criteria because a diversity of symbionts are both …

Review Of "Fifty Animals That Changed The Course Of History" By E. Chaline, John B. Jenkins

Biology Faculty Works

No abstract provided.