Integrative Biology Commons^™

Effect Of Endurance Exercise On Micrornas In Myositis Skeletal Muscle-A Randomized Controlled Study., Jessica F Boehler, Marshall W Hogarth, Matthew D Barberio, James S Novak, Svetlana Ghimbovschi, Kristy J Brown, Li Alemo Munters, Ingela Loell, Yi-Wen Chen, Heather Gordish-Dressman, Helene Alexanderson, Ingrid E Lundberg, Kanneboyina Nagaraju

Genomics and Precision Medicine Faculty Publications

Objective

To identify changes in skeletal muscle microRNA expression after endurance exercise and associate the identified microRNAs with mRNA and protein expression to disease-specific pathways in polymyositis (PM) and dermatomyositis (DM) patients.

Methods

Following a parallel clinical trial design, patients with probable PM or DM, exercising less than once a week, and on stable medication for at least one month were randomized into two groups at Karolinska University Hospital: a 12-week endurance exercise group (n = 12) or a non-exercised control group (n = 11). Using an Affymetrix microarray, microRNA expression was determined in paired muscle biopsies taken before and …

Molecular Signatures Of Differential Responses To Exercise Trainings During Rehabilitation., Yi-Wen Chen, Chris Gregory, Fan Ye, Naoe Harafuji, Donovan Lott, San-Huei Lai, Sunita Mathur, Mark Scarborough, Parker Gibbs, Celine Baligand, Krista Vandenborne

Genomics and Precision Medicine Faculty Publications

The loss and recovery of muscle mass and function following injury and during rehabilitation varies among individuals. While recent expression profiling studies have illustrated transcriptomic responses to muscle disuse and remodeling, how these changes contribute to the physiological responses are not clear. In this study, we quantified the effects of immobilization and subsequent rehabilitation training on muscle size and identified molecular pathways associated with muscle responsiveness in an orthopaedic patient cohort study. The injured leg of 16 individuals with ankle injury was immobilized for a minimum of 4 weeks, followed by a 6-week rehabilitation program. The maximal cross-sectional area (CSA) …

Changing Measurements Or Changing Movements? Sampling Scale And Movement Model Identifiability Across Generations Of Biologging Technology, Leah R. Johnson, Philipp H. Boersch-Supan, Richard A. Phillips, Sadie J. Ryan

Integrative Biology Faculty and Staff Publications

Animal movement patterns contribute to our understanding of variation in breeding success and survival of individuals, and the implications for population dynamics. Over time, sensor technology for measuring movement patterns has improved. Although older technologies may be rendered obsolete, the existing data are still valuable, especially if new and old data can be compared to test whether a behavior has changed over time. We used simulated data to assess the ability to quantify and correctly identify patterns of seabird flight lengths under observational regimes used in successive generations of wet/dry logging technology. Care must be taken when comparing data collected …

Genetic And Epigenetic Variation In Spartina Alterniflora Following The Deepwater Horizon Oil Spill, Marta Robertson, Aaron Schrey, Ashley Shayter, Christina J. Moss, Christina Richards

Integrative Biology Faculty and Staff Publications

Catastrophic events offer unique opportunities to study rapid population response to stress in natural settings. In concert with genetic variation, epigenetic mechanisms may allow populations to persist through severe environmental challenges. In 2010, the Deepwater Horizon oil spill devastated large portions of the coastline along the Gulf of Mexico. However, the foundational salt marsh grass, Spartina alterniflora, showed high resilience to this strong environmental disturbance. Following the spill, we simultaneously examined the genetic and epigenetic structure of recovering populations of S. alterniflora to oil exposure. We quantified genetic and DNA methylation variation using amplified fragment length polymorphism and methylation …

Microbe Biogeography Tracks Water Masses In A Dynamic Oceanic Frontal System, Anni Djurhuus, Philipp H. Boersch-Supan, Svein-Ole Mikalse, Alex D. Rogers

Integrative Biology Faculty and Staff Publications

Dispersal limitation, not just environmental selection, plays an important role in microbial biogeography. The distance–decay relationship is thought to be weak in habitats where dispersal is high, such as in the pelagic environment, where ocean currents facilitate microbial dispersal. Most studies of microbial community composition to date have observed little geographical heterogeneity on a regional scale (100 km). We present a study of microbial communities across a dynamic frontal zone in the southwest Indian Ocean and investigate the spatial structure of the microbes with respect to the different water masses separated by these fronts. We collected 153 samples of free-living …

Suitability Of Laurentian Great Lakes For Invasive Species Based On Global Species Distribution Models And Local Habitat, Andrew M. Kramer, Gust Annis, Marion E. Wittmann, William L. Chadderton, Edward S. Rutherford, David M. Lodge, Lacey Mason, Dmitry Beletsky, Catherine Riseng, John M. Drake

Integrative Biology Faculty and Staff Publications

Efficient management and prevention of species invasions requires accurate prediction of where species of concern can arrive and persist. Species distribution models provide one way to identify potentially suitable habitat by developing the relationship between climate variables and species occurrence data. However, these models when applied to freshwater invasions are complicated by two factors. The first is that the range expansions that typically occur as part of the invasion process violate standard species distribution model assumptions of data stationarity. Second, predicting potential range of freshwater aquatic species is complicated by the reliance on terrestrial climate measurements to develop occurrence relationships …

Accuracy Of Climate-Based Forecasts Of Pathogen Spread, Annakate M. Schatz, Andrew M. Kramer, John M. Drake

Integrative Biology Faculty and Staff Publications

Species distribution models (SDMs) are a tool for predicting the eventual geographical range of an emerging pathogen. Most SDMs, however, rely on an assumption of equilibrium with the environment, which an emerging pathogen, by definition, has not reached. To determine if some SDM approaches work better than others for modelling the spread of emerging, non-equilibrium pathogens, we studied time-sensitive predictive performance of SDMs for Batrachochytrium dendrobatidis, a devastating infectious fungus of amphibians, using multiple methods trained on time-incremented subsets of the available data. We split our data into timeline-based training and testing sets, and evaluated models on each set …

The Role Of The Y-Chromosome In The Evolution Of Autosomally Coded Traits, Ian Kutch

Electronic Theses and Dissertations

Recent work indicates that the Y-chromosome of the fruit fly Drosophila melanogaster can influence gene regulation on the autosomes and X chromosome. This newly discovered function of the Y has the potential to dramatically shape the regulatory evolution of numerous genes that reside throughout the genome; even for genes that code for both male and female traits. Given that the mechanism underlying the Y-linked influence on gene expression in D. melanogaster appears to exist in other independently evolved heterogametic sex chromosomes, the evolutionary implications of Y-linked regulatory variation (YRV) deserves to be explored. These implications include the potential for Y-chromosomes …

Evolutionary Linkage Of Mimetic And Non-Mimetic Color Traits In A Coral Snake Mimicry Complex, John D. Curlis Jr

College of Graduate Studies: Theses & Dissertations

Color polymorphism in aposematic mimicry systems is a perplexing phenomenon for evolutionary biologists, as theoretically the benefits of converging on a model phenotype should constrain the evolution of phenotypic diversity in these systems (i.e., color polymorphism should not occur). Nevertheless, color polymorphism in mimicry systems is prevalent throughout many taxa. In some of these systems, the evolution of color polymorphism results in the existence of non-mimetic morphs, such as those that are cryptic. The case of ground snakes (Sonora semiannulata) is unique in that color polymorphism encompasses both mimetic and cryptic morphs, as well as individual mimetic and …

A Comparison Of Benthic Macroinvertebrate Assemblages Between Perennial And Intermittent Headwater Streams Of The Mattole River In Northern California, Usa, Mason S. London

Cal Poly Humboldt theses and projects

Intermittent streams are common throughout the world and comprise 60% or more of total river lengths in the conterminous United States. Despite their prevalence, intermittent streams are understudied, particularly first-order headwater streams, which are vital for maintaining the function, health and biotic diversity of river networks. In June 2016, I sampled five intermittent and five perennial headwater streams in the Mattole River watershed in northwestern coastal California, USA, to compare benthic macroinvertebrate (BMI) assemblages between intermittent and perennial streams. BMI samples were collected using a 500µm mesh D-net at eight randomly located riffles along a 150-m reach, and then composited, …

Molecular Diversity Of Foliar Fungal Endophytes In Relation To Defense Strategies And Disease In Whitebark Pine, Lorinda Bullington

Graduate Student Theses, Dissertations, & Professional Papers

An invasive fungal pathogen, Cronartium ribicola (the causative agent of white pine blister rust) infects and kills whitebark pine (Pinus albicaulis) throughout the western US. Blister rust has decreased whitebark pine populations by over 90% in some areas. Whitebark pine, a keystone species, has been proposed for listing under the Endangered Species Act in the U.S., and the loss of this conifer is predicted to have severe impacts on forest composition and function in high elevations. Hundreds of asymptomatic fungal species live inside whitebark pine tissue, and recent studies suggest that these fungi can influence the frequency and …

Integrated Stress And Community Perceptions: Toward An Understanding Of Human-Cougar Tolerance, Lara Brenner

Graduate Student Theses, Dissertations, & Professional Papers

Evidence suggests that cougars (Puma concolor) are beginning to recolonize their traditional range in the Midwestern and Eastern US, returning to a landscape and a social environment that have changed drastically in a century of absence. Any hope of the cougar’s persistence depends on both human tolerance of their presence and on cougar tolerance of disrupted habitat. In this thesis, we took advantage of diverse cougar policy in place in the Western US to explore variation in human attitudes and acceptability of cougars and in the cougar stress response. We validated a process to identify and extract cortisol …

Measuring Bacterial Growth Using A 3d-Printable Spectrometer, Samuel R. Bunting

Williams Honors College, Honors Research Projects

Visible light spectroscopy is a commonly used technique for measuring the growth of bacterial cultures, and growth curves provide broadly important data. However, the equipment and resources required for these experiments has been restricted to higher education and industry due to high cost and sophistication. We have previously reported on an inexpensive, 3D-printable photospectrometer called the SpecPhone. This device utilizes an iPhone as the camera, along with several other, inexpensive additions to make a fully functional spectrometer. Here, the application of the SpecPhone is expanded to the quantification of actively dividing E. coli cultures. Two protocols have been developed; one …

Wetland Connectivity And Macroinvertebrate Diversity, Samantha M. Hodgson, Jacob Pollock, Dr. Anne E. Wiley

Williams Honors College, Honors Research Projects

Wetlands are important in filtering pollutants from aquatic ecosystems and also serve as habitats for a diverse array of organisms. However, wetland-river networks are often subject to human disturbances such as dyke construction. These decreases in connectivity have the potential to impede movement of organisms and nutrients between habitats.

This study examined how the food web structure and diversity of macroinvertebrate communities differ between wetland sites connected and disconnected to nearby rivers. According to macroinvertebrate surveys in wetlands connected to nearby rivers and dyked wetlands (not connected to nearby rivers), there is an increase in average species richness and diversity …

Mitochondrial And Nuclear Patterns Of Conflict And Concordance At The Gene, Genome, And Behavioral Scales In Desmognathus Salamanders, Justin D. Kratovil

Theses and Dissertations--Biology

Advancements in molecular sequencing have revealed unexpected cryptic genetic diversity and contrasting evolutionary histories within genes and between genomes of many organisms; often in disagreement with recognized taxonomy. Incongruent patterns between the mitochondrial and nuclear evolutionary history can have several plausible explanations, but widespread systematic conflict inevitably challenges our conceptions of species boundaries when there is discordance between coevolving and coinherited genomes. It is unknown to what degree mitonuclear conflict drives the process of divergence, or how ubiquitous these patterns are across the tree of life. To understand the evolutionary relevance of intergenomic discordance we must identify the conflicting patterns …

Neural Circuitry For Target Selection And Action Selection In Animal Behavior, Daizaburo Shizuka, Eileen Hebets, Kim L. Hoke

Papers in Behavior in Biological Sciences

Animal behaviorists have long strived for a comprehensive understanding of the proximate and ultimate causes of complex behavior, and we propose that recent advances in neurobiology can help reshape or clarify this behavior-oriented understanding. We begin with an overview of current views of neural circuit mechanisms that mediate target selection and action selection. In target selection, different stimuli compete for priority in sensory-motor process- ing. Action selection is the process by which multiple possible motor actions compete for priority in a manner which balances the needs of the animal with opportunities or threats in the environment. We next discuss spatial …

Using Molecular Genetic And Demographic Tools To Improve Management Of Ex Situ Avian Populations, Gina Ferrie

Electronic Theses and Dissertations

Small populations, specifically those that are isolated from others, are more prone to extinction than larger inter-connected populations. The risks that these small isolated populations face include loss of genetic diversity due to founder effects and inbreeding due to population bottlenecks, as well as demographic uncertainty due to fluctuating fecundity and mortality rates and impacts of external environmental factors. Ex situ populations, including those managed as conservation breeding programs with species recovery aims, as well as those that do not have reintroduction goals but are managed for long term population sustainability, suffer from the same extinction risks as small and …

Reproductive Life History And Signal Evolution In A Multi-Species Assemblage Of Electric Fish, Joseph Waddell

Electronic Theses and Dissertations

Animals that co-occur in sympatry with multiple closely-related species use reproductive mate attraction signals not only to assess the quality of a potential conspecific mate (sexual selection), but also to discriminate conspecifics from heterospecifics (species recognition). However, the extent to which sexual selection and species recognition may interact, or even conflict, is poorly known. Neotropical electric fish offer unrivaled opportunities for understanding this problem. They generate simple, stereotyped mate attraction signals that are easy to record and quantify, and that are well-understood from the neurobiological perspective. Additionally, they live in electrically-crowded environments, where multiple congeners live and reproduce in close …

The Status Of Snapping Turtles (Chelydra Serpentina) In Virginia: Population Viability, Demography, Regulatory Analysis, And Conservation, Benjamin C. Colteaux

Theses and Dissertations

Snapping turtles (Chelydra serpentina) are being harvested in unprecedented numbers in the United States (US) to meet the needs of international markets. Over three million live snapping turtles from farm and wild caught stock were exported from the US to Asia in 2012-14 alone. In the Commonwealth of Virginia, records indicate that 29,860 snapping turtles were commercially harvested between 2000 and 2015. Size limits are often used to regulate harvest pressure in snapping turtles and other game species. I analyzed the historic harvest of eleven US states to test the efficacy of minimum-size limit regulations at reducing commercial …

Diversity And Evolution Of Fruits In Cuscuta (Dodders; Convolvulaceae), Anna Ho

Theses and Dissertations (Comprehensive)

Cuscuta (dodder) is a genus of roughly 200 species of obligate stem parasites with sub-cosmopolitan distribution. The fruit, generally regarded as a capsule, has a thin pericarp containing one to four seeds and opening at the base (circumscissile dehiscence; DE), or remaining closed (indehiscent; IN). IN has evolved multiple times in Cuscuta from DE, and is most common in the North American clades of subgenus Grammica. In addition, some species produce fruits that open irregularly. Characteristics pertaining to the fruits of Cuscuta are important as their seeds contribute most to their distribution and prevalence across the globe, and their reduced …