Biology Commons^™

Simple Structural Differences Between Coding And Noncodingdna, Kenneth J. Locey, Ethan P. White

Biology Faculty Publications

Background

The study of large-scale genome structure has revealed patterns suggesting the influence of evolutionary constraints on genome evolution. However, the results of these studies can be difficult to interpret due to the conceptual complexity of the analyses. This makes it difficult to understand how observed statistical patterns relate to the physical distribution of genomic elements. We use a simpler and more intuitive approach to evaluate patterns of genome structure.

Methodology/Principal Findings

We used randomization tests based on Morisita's Index of aggregation to examine average differences in the distribution of purines and pyrimidines among coding and noncoding regions of 261 …

Species Compositionand Abundance Of Mammalian Communities, K. M. Thibault, S. R. Supp, M. Griffin, Ethan P. White, S.K. Morgan Ernest

Biology Faculty Publications

Ecologists have long sought to understand the mechanisms underlying the assembly and structure of communities. Such understanding is relevant to both basic science and conservation-related issues. The macroecological approach to this problem involves asking scientific questions using a large number of communities in order to elucidate generalities in pattern and process. Such analyses are typically conducted using a substantial amount of data from a particular taxonomic group across a diversity of systems. Large community databases are available for a number of taxa, but no publicly available database exists for mammals. Given the logistical challenges of collecting such data de novo, …

Bioinformatic Identification Of Small Rna (And Their Targets) In The Testis Of Clawed Frogs (Xenopus And Silurana): Implications For Male Fertility, M.J. Madison-Villar

Biology Dissertations - Archive

Chapter one sets the stage for this project, which lies somewhere near the intersection of speciation, genome, and reproductive biology. Chapter two identifies miRNA with shared expression profiles (Silurana and Xenopus). These miRNA are pulled from a subset that has retained testis expression despite a hybridization induced WGD event early in the Xenopus lineage (~21-41 MYA). Allopolyploidization is a revolutionary mechanism of genome evolution, and this event should have afforded an opportunity for diversification and changes in the expression of what are generally highly conserved transcript regulators. It is inferred that the miRNA identified in this study retained testis expression …

Variation, Systematics, And Relationships Of The Leptodactylus BolivianusComplex (Amphibia: Anura: Leptodactylidae), W. R. Heyer, Rafael O. De Sá

Biology Faculty Publications

A cluster of morphologically similar frogs of the genus Leptodactylus having a pair of distinct dorsolateral folds on the dorsum and well-developed lateral fringes on the toes has never been systematically evaluated by examining materials from throughout its geographic range. The species involved are herein referred to as members of the Leptodactylus bolivianus complex. There have been three names proposed for members of this complex: Leptodactylus bolivianus Boulenger, 1898; Leptodactylus insularum Barbour, 1906; and Leptodactylus romani Melin, 1941. The collective range for the L. bolivianus complex is from Costa Rica southward through Panama, extending across northern South America (east of …

Altitudinal Variation Of Freeze Tolerance In The Pacific Chorus Frog, Pseudacris Regilla, Sara Healas

Undergraduate Honors Theses

This study compares the physiological responses to freezing of Pacific Chorus frogs (Pseudacris regilla) from low-elevation and high-elevation sites. During the winter months, Pacific Chorus frogs have the ability to freeze solid and revive upon thawing. They survive freezing because they store massive amounts of glycogen that they convert into glucose once freezing starts. Glucose is use (1) to protect the cells during freezing and (2) to support general metabolism through the entire winter. The hypothesis is that the frogs collected at the high-elevation site will have more glucose stored as glycogen because these frogs have to survive …

Investigating The Effects Of The Plasticizers Bisphenol A And Di (2-Ethylhexyl) Phthalate On Dopaminergic Neurons In A C. Elegans Parkinson's Disease, Amanda Valera

Undergraduate Honors Theses

Parkinson's disease (PD) is a neurodegenerative disorder characterized by loss of dopamine (DA) containing neurons in the substantia nigra of the brain. Though the cellular pathways that lead to PD are varied and not well understood, elevated levels of reactive oxygen species (ROS) and inhibition of the mitochondrial electron transport chain enzyme complex I have been associated with PD pathogenesis. Environmental factors such as the plasticizers bisphenol A (BPA) and di(2-ethylhexyl) phthalate (DEHP) may also be involved in PD pathogenesis. In this research, three strains of the nematode Caenorhabditis elegans (C. elegans), a wild-type N2 strain, a ROS-sensitive nnt …

The Impact Of Tricaine Methanesulfonate, 2-Phenoxyethanol, And Carvone-Methyl Salicylate On The Innate Immune Response Of Zebrafish (Danio Rerio), Charles R. Wulff

Honors Theses

Anesthesia plays a vital role in the maintenance of aquaculture species, where it is used to minimize stress during complex handling tasks such as transport, assessment, and harvesting. However, anesthetics have been shown to suppress the innate immune response, which could impact immunity and increase risk of infection. Tricaine methanesulfonate (MS-222) and 2-Phenoxyethanol (2-PE) represent two of the most commonly used anesthetics in aquaculture, with R-(+)-carvone, in the form of carvone-methyl salicylate (CMS) has recently been proposed as an alternative anesthetic for food fish. These three anesthetics were used to assess the influence of anesthetics on the immune system of …

Social Dimensions Of Lake Ecology: Stakeholder Perception Surveys Used To Design Effective Lake Management Plans, Laurie Nannini

Masters Theses

Lake conservation management plans have exhibited varying levels of success through out Illinois. Recent research, in eutrophic lakes shows that pollution at any level stabilizes when stakeholder cooperation is enhanced by high conformist tendency and social concern. Involving stakeholders in preliminary stages of lake management plans creates more legitimacy and connectedness with the local government as well as stakeholder involvement with management plans. Public opinion data also allows policy makers to sustainably involve stakeholders in management plans. Members of the Illinois Lake Management Association were surveyed on their perceived threats to lakes, preferences on lake facilities and activities. Responses were …

Is Anthropogenic Habitat Change The Driving Force Of Rapid Evolution Of Southeastern U.S. Coastal Deer Populations?, Nicole L. Storm

Masters Theses

Many factors, such as genetics, food availability and the exact food species, can affect the growth rate and asymptotic size of animals. Since the I 960's, the coastal areas and islands in Georgia, North Carolina, and South Carolina have become vacation destinations with large and lavish resort communities built to accommodate the large number of visitors to areas that were once called home by just a small number of residents. These developments brought with them non-native plants and improved soil quality for both native and non-native plants. During this same time period, the whitetailed deer ( Odocoileus virginianus) native to …

Biosolar Conversion Of N2 And H2o To Ammonia By Engineered N2-Fixing Cyanobacteria, Seth T. Harris

The Journal of Undergraduate Research

The cyanobacterium Anabaena sp. PCC 7120 is capable of using solar energy to produce ammonia through conversion of atmospheric dinitrogen in differentiated cells called heterocysts. Harnessing this system could enable cyanobacteria to be used in ammoniafertilizer production, creating a renewable alternative to the current Haber-Bosch process. The genes patA and alr3304 in the Anabaena 7120 genome are important in heterocyst formation; an increase in heterocyst formation is seen with over-expression of patA or inactivation of alr3304. This research aims to create a novel mutant that forms more heterocysts by simultaneously over-expressing patA and inactivating alr3304, producing higher amounts of ammonia. …

Skeletal Muscle Gender Dimorphism From Proteomics, Kalina Dimova, Lauren Ann Metskas, Mohini Kulp, Stylianos P. Scordilis

Biological Sciences: Faculty Publications

Gross contraction in skeletal muscle is primarily determined by a relatively small number of contractile proteins, however this tissue is also remarkably adaptable to environmental factors such as hypertrophy by resistance exercise and atrophy by disuse. It thereby exhibits remodeling and adaptations to stressors (heat, ischemia, heavy metals, etc.). Damage can occur to muscle by a muscle exerting force while lengthening, the so-called eccentric contraction. The contractile proteins can be damaged in such exertions and need to be repaired, degraded and/or resynthesized; these functions are not part of the contractile proteins, but of other much less abundant proteins in the …

A Molecular Ecological Survey Of Tick (Ixodes Scapularis) Population Density And Their Infection Rates With Borrelia Burgdorferi At The New Jersey School Of Conservation, Nathaly M. Salazar-Vasquez

Theses, Dissertations and Culminating Projects

Studying vector populations of the Ixodes scapularis tick is of major importance in New Jersey, an endemic area of Lyme disease. This species of tick is a vector for various disease pathogens including the bacterium that causes Lyme disease, Borrelia burgdorferi. This study focused on Ixodes scapularis tick surveillance at the New Jersey School of Conservation, in Sussex County, New Jersey. Collection of host-seeking ticks began in July 2009 and has continued until December of 2010, by drag-cloth sampling in order to monitor tick abundances of all life-cycle stages.

In 2010 relative abundances for larvae and nymphal stages declined as …

Evolution Through Developmental Changes: How Alterations In Development Cause Evolutionary Changes In Anatomy, Scott F. Gilbert

Biology Faculty Works

No abstract provided.

Research, Monitoring, Assessment And Development Plan 2010 – 2011, Department Of Fisheries

Fisheries Occasional Publications

No abstract provided.

Mechanisms Of Adsorption Of Copper And Silver Ions On Carbon Materials In An Open Circuit, Mikhail M. Goldin

Faculty Publications and Presentations

No abstract provided.

Effective Numbers Of Electrons As A Criterion Of Carbon Suitability As A Hemosorbent, Mogely Khubutiya, Boris Grafov, Mikhail M. Goldin, Alexei Davydov, Vladimir Kolesnikov, Mark Goldin

Faculty Publications and Presentations

The number of medical applications of electrochemistry has grown in recent years due to the increased applications of electrochemical concepts to various systems of the organism. This includes electrochemically controlled hemosorption detoxification, where the removal of toxicants is controlled by changing the potential of the hemosorbent. It is important to avoid Faradaic processes in the course of hemosorption, which can lead to the addition of electrochemically modified toxicants to blood. The probability of their occurrence should depend on the open-circuit potential of the activated carbon. In order to elucidate the identification of Faradaic reactions, a model system was investigated. The …

Biology Department Newsletter, No.1, Sacred Heart University

Biology Newsletter

No abstract provided.

National Park Service Nonnative Plant Control In The Indiana Dunes National Lakeshore, Jacob Halpin, Laurie Eberhardt, Laura Thompson

Symposium on Research and Creative Expression (SORCE)

Invasive plants have become a growing threat to plant diversity and hydrology in the Indiana Dunes National Lakeshore. Invasive plants compete with native plants for nutrients and sunlight, and certain invasive species have been known to completely take over certain areas of wetlands, nearly destroying entire ecosystems. The Dunes Lakeshore contains over 1,400 plants species and is one of the top ten most diverse national parks in the United States. The mission statement of the National Park Service is to “preserve for the educational, inspirational, and recreational use of the public certain portions of the Indiana Dunes.” In order …

Humanized Mouse Models Of Hiv Infection, Paul W. Denton, J. Victor Garcia

Biology Faculty Publications

Because of the limited tropism of HIV, in vivo modeling of this virus has been almost exclusively limited to other lentiviruses such as SIV that reproduce many important characteristics of HIV infection. However, there are significant genetic and biological differences among lentiviruses and some HIV-specific interventions are not effective against other lentiviruses in non-human hosts. For these reasons much emphasis has recently been placed on developing alternative animal models that support HIV replication and recapitulate key aspects of HIV infection and pathogenesis in humans. Humanized mice, CD34+ hematopoietic progenitor cell transplanted immunodeficient mice and in particular mice also implanted with …

Exploring The Population Dynamics Of Wintering Bald Eagles Through Long-Term Data, Julie Beckstead, Alexandra N. Lagasse, Scott R. Robinson

Biology Faculty Scholarship

THE ECOLOGICAL QUESTION

How does a bald eagle population change over time at a winter migratory stopover and which factors influence its abundance?

ECOLOGICAL CONTENT

Bald eagle biology, conservation biology, endangered species, population ecology, and migration ecology (stopover)

WHAT STUDENTS DO

Guided Approach: Students will generate questions about bald eagle numbers influenced by weather and food availability. Students will then use graphing software (JMP or Excel) to compile the data in a graphical form to answer their questions.

Open-ended Approach: Students will generate their own hypotheses of interest from the larger bald eagle data set. This approach is encouraged for …

Comparison Genomics Of Oryza Rufipogon Chromosome Eight Centromere With Other Species Centromeres, Kalyani Ginjupalli

Theses, Dissertations and Culminating Projects

Centromeres are playing a key role in proper segregation of sister chromatids during mitosis and meiosis. At the centromere region in the chromosome, spindle microtubules attached to the kinetochores that direct the chromosome segregation during mitosis and meiosis. Although centromeric function is conserved among different organisms, there is no conservation of centromeric DNA sequences ranging from budding yeast which has a consensus sequence of approximately 125 base pairs (bp) on each chromosome to Caenorhabditis elegans species which has a holocentric centromere that spans the entire chromosome. However, there are some common proteins that form the kinetochore, such as CENH3 and …

Rho Kinase Regulates Basement Membrane Dynamics To Coordinate Salivary Gland Branching Morphogenesis And Tissue Organization, William Patrick Daley

Legacy Theses & Dissertations (2009 - 2024)

Branching morphogenesis is a developmental mechanism utilized by many organs, including the salivary gland, lung, kidney, and mammary gland, to increase the epithelial surface area for secretion or absorption. The embryonic submandibular salivary gland (SMG) is a classic model for studying tissue morphogenesis in three dimensions ex vivo. Salivary gland development requires distinct but overlapping processes: morphogenesis, the actual physical rearrangement of cells into complex three dimensional structures, and cytodifferentiation, the process by which these cells begin to take on their own specialized function. Polarization, or the organization of cells into a cohesive tissue structure, also occurs concurrently during organ …

Biogeographic Consequences Of Historic And Contemporary Climate Change In Boreal Forest Birds, Joel Ralston

Legacy Theses & Dissertations (2009 - 2024)

In this dissertation, I combine ecological niche models (ENMs), which can be extrapolated through time to predict historic and future changes in species distributions, with mitochondrial and nuclear genetic markers to study the biogeographic consequences of historic and contemporary climate change on boreal forest birds, and in particular Blackpoll Warbler.

A Functional Study Of Ampa And Kainate Receptors, Yan Han

Legacy Theses & Dissertations (2009 - 2024)

The ionotropic glutamate receptors are localized in the pre- and postsynaptic membrane of neurons and mediate the majority of fast excitatory synaptic transmission. These receptors are divided into three subtypes: α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA), kainic acid, and N-methyl-D-aspartic acid (NMDA) receptors. My thesis work focused on AMPA and kainate receptor subtypes.

Creating Rna Aptamers To Modulate Function Of Human Estrogen Receptor Alpha, Daiying Xu

Legacy Theses & Dissertations (2009 - 2024)

ABSTRACT

Design And Application Of Composite Rna Aptamers, Shengchun Wang

Legacy Theses & Dissertations (2009 - 2024)

aptamers are being developed as an essential tool in many fields of biological research. Their utility is not limited to being protein inhibitors; a lot of novel functions can be realized. However, in vivo application of RNA aptamers still faces many challenges. The aim of this dissertation is to design and apply composite aptamers in multiple expression and delivery systems to address some critical issues, such as correct folding, high level production, degradation by nucleases, excessive consumption of cellular resource and potential toxic effect.

Bringing The Dead Compartment Of A Plant Cell To Life: A Novel Imaging Technique Resurrects The Dynamic Nature Of The Apoplast, Doug Van Hoewyk

Biology

No abstract provided.

Floristic And Environmental Characteristics Of Sub-Boreal Peatlands Of Minnesota And Western Wisconsin, Kevin Douglas Clement

All Graduate Theses, Dissertations, and Other Capstone Projects

Peatland communities in the sub-boreal region of Minnesota and western Wisconsin were characterized by floristic composition, structure and environmental characteristics to determine the natural variation among peatland communities in the region and their shared associations with the boreal and temperate peatlands of North America. Floristic classification revealed five, distinct peatland community types, identified as Sphagnum Bogs, Herbaceous Fens, Forested Fens, Rich/Calcareous Fens and Phalaris anrundinacea dominated peatlands. Differences among sub-boreal peatlands largely reflected changes in the significant indicator and dominant plant species identified, which were found to exhibit high fidelities to a particular peatland community type. Floristic variations among sub-boreal …

An Assessment Of Histone-Modification Antibody Quality, Thea Egelhofer, Aki Minoda, Sarit Klugman, Kyungjoon Lee, Paulina Kolasinska-Zwierz, Artyom Alekseyenko, Ming-Sin Cheung, Daniel Day, Sarah Gadel, Andrey Gorchakov, Tingting Gu, Peter Kharchenko, Samantha Kuan, Isabel Latorre, Daniela Linder-Basso, Ying Luu, Queminh Ngo, Marc Perry, Andreas Rechtsteiner, Nicole Riddle, Yuri Schwartz, Gregory Shanower, Anne Vielle, Julie Ahringer, Sarah C.R. Elgin, Mitzi Kuroda, Vincenzo Pirrotta, Bing Ren, Susan Strome, Peter Park, Gary Karpen, R Hawkins, Jason Lieb

Biology Faculty Research

We have tested the specificity and utility of more than 200 antibodies raised against 57 different histone modifications in Drosophila melanogaster, Caenorhabditis elegans and human cells. Although most antibodies performed well, more than 25% failed specificity tests by dot blot or western blot. Among specific antibodies, more than 20% failed in chromatin immunoprecipitation experiments. We advise rigorous testing of histone-modification antibodies before use, and we provide a website for posting new test results (http://compbio.med.harvard.edu/antibodies/).

Distributions And Abundances Of Microstegium Vimineum Along Forest Roadsides At The Grassy Hill Natural Area, Franklin County, Virginia, Gregory D. Turner

Virginia Journal of Science

In summer 2005, plots were surveyed along roads passing through forest habitats at the Grassy Hill Natural Area Preserve in Franklin County, Virginia to assess the distributions and abundances of Microstegium vimineum in transects located at increasing distances away from roadsides into forest interiors. Across plots, Microstegium was encountered almost exclusively in roadside transects, where abundances were relatively high. While forest composition and topographic features were similar across plots, percent canopy cover and leaf litter depth were greater in interior compared to roadside transects due to undisturbed tree canopies and ground cover located in interior plot areas. Results imply that …