Life Sciences Commons^™

Positional Plasticity In Regenerating Amybstoma Mexicanum Limbs Is Associated With Cell Proliferation And Pathways Of Cellular Differentiation, Catherine D. Mccusker, Antony Athippozhy, Carlos Diaz-Castillo, Charless Fowlkes, David M. Gardiner, S. Randal Voss

Biology Faculty Publications

BACKGROUND: The endogenous ability to dedifferentiate, re-pattern, and re-differentiate adult cells to repair or replace damaged or missing structures is exclusive to only a few tetrapod species. The Mexican axolotl is one example of these species, having the capacity to regenerate multiple adult structures including their limbs by generating a group of progenitor cells, known as the blastema, which acquire pattern and differentiate into the missing tissues. The formation of a limb regenerate is dependent on cells in the connective tissues that retain memory of their original position in the limb, and use this information to generate the pattern …

Initial Characterization Of The Large Genome Of The Salamander Ambystoma Mexicanum Using Shotgun And Laser Capture Chromosome Sequencing, Melissa C. Keinath, Vladimir A. Timoshevskiy, Nataliya Y. Timoshevskaya, Panagiotis A. Tsonis, S. Randal Voss, Jeramiah J. Smith

Biology Faculty Publications

Vertebrates exhibit substantial diversity in genome size, and some of the largest genomes exist in species that uniquely inform diverse areas of basic and biomedical research. For example, the salamander Ambystoma mexicanum (the Mexican axolotl) is a model organism for studies of regeneration, development and genome evolution, yet its genome is ~10× larger than the human genome. As part of a hierarchical approach toward improving genome resources for the species, we generated 600 Gb of shotgun sequence data and developed methods for sequencing individual laser-captured chromosomes. Based on these data, we estimate that the A. mexicanum genome is ~32 Gb. …

Seed Germination Ecology Of The Cold Desert Annual Isatis Violascens (Brassicaceae): Two Levels Of Physiological Dormancy And Role Of The Pericarp, Yuan M. Zhou, Juan J. Lu, Dun Y. Tan, Carol C. Baskin, Jerry M. Baskin

Biology Faculty Publications

The occurrence of various species of Brassicaceae with indehiscent fruits in the cold deserts of NW China suggests that there are adaptive advantages of this trait. We hypothesized that the pericarp of the single-seeded silicles of Isatis violascens restricts embryo expansion and thus prevents germination for 1 or more years. Thus, our aim was to investigate the role of the pericarp in seed dormancy and germination of this species. The effects of afterripening, treatment with gibberellic acid (GA₃) and cold stratification on seed dormancy-break were tested using intact silicles and isolated seeds, and germination phenology was monitored in …

Incidence Of West Nile Virus In House Sparrow Nestlings In Relation To Parental Effort, Natalie Mickelsen

Kaleidoscope

The house sparrow, Passer domesticus, is known to be an important host of West Nile (WN) virus and may contribute to the transmission of WN virus to humans. However, little is known about the factors that influence the occurrence of WN virus in birds. I conducted a study to determine if parental care was related to the rates of WN virus infections among nestling birds. I observed house sparrow nests for one hour periods noting the time the male and female parent spent on the nest box, in the nest box, and the number of food trips, as measures …

Disruption Of Daily Rhythms By High-Fat Diet Is Reversible, Katrina L. Branecky, Kevin D. Niswender, Julie S. Pendergast

Biology Faculty Publications

In mammals a network of circadian clocks coordinates behavior and physiology with 24-h environmental cycles. Consumption of high-fat diet disrupts this temporal coordination by advancing the phase of the liver molecular clock and altering daily rhythms of eating behavior and locomotor activity. In this study we sought to determine whether these effects of high-fat diet on circadian rhythms were reversible. We chronically fed mice high-fat diet and then returned them to low-fat chow diet. We found that the phase of the liver PERIOD2::LUCIFERASE rhythm was advanced (by 4h) and the daily rhythms of eating behavior and locomotor activity were altered …

Maintenance Of Brucellosis In Yellowstone Bison: Linking Seasonal Food Resources, Host-Pathogen Interaction, And Life-History Trade-Offs, John J. Treanor, Chris Geremia, Michael A. Ballou, Duane H. Keisler, Patrick J. White, John J. Cox, Phillip H. Crowley

Biology Faculty Publications

The seasonal availability of food resources is an important factor shaping the life-history strategies of organisms. During times of nutritional restriction, physiological trade-offs can induce periods of immune suppression, thereby increasing susceptibility to infectious disease. Our goal was to provide a conceptual framework describing how the endemic level bovine brucellosis (Brucella abortus) may be maintained in Yellowstone bison based on the seasonality of food resources and the life-history strategies of the host and pathogen. Our analysis was based on active B. abortus infection (measured via bacterial culture), nutritional indicators (measured as metabolites and hormones in plasma), and carcass …

Kidney-Specific Reduction Of Oxidative Phosphorylation Genes Derived From Spontaneously Hypertensive Rat, Jason A. Collett, Jiffin K. Paulose, Vincent M. Cassone, Jeffrey L. Osborn

Biology Faculty Publications

Mitochondrial (Mt) dysfunction contributes to the pathophysiology of renal function and promotes cardiovascular disease such as hypertension. We hypothesize that renal Mt-genes derived from female spontaneously hypertensive rats (SHR) that exhibit hypertension have reduced expression specific to kidney cortex. After breeding a female Okamoto-Aoki SHR (SAP = 188mmHg) with Brown Norway (BN) males (SAP = 100 and 104 mmHg), hypertensive female progeny were backcrossed with founder BN for 5 consecutive generations in order to maintain the SHR mitochondrial genome in offspring that contain over increasing BN nuclear genome. Mt-protein coding genes (13 total) and nuclear transcription factors mediating Mt-gene transcription …

The Sea Lamprey Meiotic Map Improves Resolution Of Ancient Vertebrate Genome Duplications, Jeramiah James Smith, Melissa C. Keinath

Biology Faculty Publications

It is generally accepted that many genes present in vertebrate genomes owe their origin to two whole-genome duplications that occurred deep in the ancestry of the vertebrate lineage. However, details regarding the timing and outcome of these duplications are not well resolved. We present high-density meiotic and comparative genomic maps for the sea lamprey (Petromyzon marinus), a representative of an ancient lineage that diverged from all other vertebrates ~550 million years ago. Linkage analyses yielded a total of 95 linkage groups, similar to the estimated number of germline chromosomes (1n ~ 99), spanning a total of 5570.25 cM. …

Distribution Of Three Congeneric Shrub Species Along An Aridity Gradient Is Related To Seed Germination And Seedling Emergence, Liming Lai, Yuan Tian, Yongji Wang, Xuechun Zhao, Lianhe Jiang, Jerry M. Baskin, Carol C. Baskin, Yuanrun Zheng

Biology Faculty Publications

Environmental tolerance of a species has been shown to correlate positively with its geographical range. On the Ordos Plateau, three Caragana species are distributed sequentially along the precipitation gradient. We hypothesized that this geographical distribution pattern is related to environmental tolerances of the three Caragana species during seed germination and seedling emergence stages. To test this hypothesis, we examined seed germination under different temperature, light and water potentials, and monitored seedling emergence for seeds buried at eight sand depths and given different amounts of water. Seeds of C. korshinskii germinated to high percentages at 5 : 15 to 25 : …

Method, Composition, And Kit Useful For Treatment Of Alzheimer's Disease, Steven Estus, Manasi Malik, James Simpson

Biology Faculty Patents

The presently-disclosed subject matter includes methods for treating Alzheimer's disease in a subject. The subject can have Alzheimer's diseases, can be identified has being at risk for developing Alzheimer's disease, or both. The method can comprise administering a composition that includes a CD33 inhibitor, which may include a CD33 antibody. In some embodiments the composition can further comprise at least one additional component useful for treating Alzheimer's disease. The presently-disclosed subject matter also includes compositions and kits for treating Alzheimer's disease in a subject.

Gene Expression During The First 28 Days Of Axolotl Limb Regeneration I: Experimental Design And Global Analysis Of Gene Expression, S. Randal Voss, Alex Palumbo, Radha Nagarajan, David M. Gardiner, Ken Muneoka, Arnold J. Stromberg, Antony T. Athippozhy

Biology Faculty Publications

While it is appreciated that global gene expression analyses can provide novel insights about complex biological processes, experiments are generally insufficiently powered to achieve this goal. Here we report the results of a robust microarray experiment of axolotl forelimb regeneration. At each of 20 post-amputation time points, we estimated gene expression for 10 replicate RNA samples that were isolated from 1 mm of heterogeneous tissue collected from the distal limb tip. We show that the limb transcription program diverges progressively with time from the non-injured state, and divergence among time adjacent samples is mostly gradual. However, punctuated episodes of transcription …

Tissue Specific Reactions To Positional Discontinuities In The Regenerating Axolotl Limb, Malcolm Maden, Daima Avila, Molly Roy, Ashley W. Seifert

Biology Faculty Publications

We investigated cellular contributions to intercalary regenerates and 180^o supernumerary limbs during axolotl limb regeneration using the cell autonomous green fluorescent protein marker and exchanged blastemas between white and green fluorescent protein animals. After distal blastemas were grafted to proximal levels tissues of the intercalary regenerate behaved independently with regard to the law of distal transformation; graft epidermis was replaced by stump epidermis, muscle-derived cells, blood vessels, and Schwann cells of the distal blastema moved proximally to the stylopodium and cartilage and dermal cells conformed to the law. After 180^o rotation, blastemas showed contributions from stump tissues which …

Finding Our Way Through Phenotypes, Andrew R. Deans, Suzanna E. Lewis, Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, Judith A. Blake, J. Gordon Burleigh, Bruno Chanet, Laurel D. Cooper, Mélanie Courtot, Sándor Csösz, Hong Cui, Wasila Dahdul, Sandip Das, T. Alexander Dececchi, Agnes Dettai, Rui Diogo, Robert E. Druzinsky, Michel Dumontier, Nico M. Franz, Frank Friedrich, George V. Gkoutos, Melissa Haendel, Luke J. Harmon, Terry F Hayamizu, Yongqun He, Heather M. Hines, Nizar Ibrahim, Laura M. Jackson, Pankaj Jaiswal, Christina James-Zorn, Sebastian Köhler, Guillaume Lecointre, Hilmar Lapp, Carolyn J. Lawrence, Nicolas Le Novère, John G. Lundberg, James Macklin, Austin R. Mast, Peter E. Midford, István Mikó, Christopher J. Mungall, Anika Oellrich, David Osumi-Sutherland, Helen Parkinson, Martín J. Ramírez, Stefan Richter, Peter N. Robinson, Alan Ruttenberg, Katja S. Schulz, Erik Segerdell, Katja C. Seltmann, Michael Sharkey, Aaron D. Smith, Barry Smith, Chelsea D. Specht, R. Burke Squires, Robert W. Thacker, Anne Thessen, Jose Fernandez-Triana, Mauno Vihinen, Peter D. Vize, Lars Vogt, Christine E. Wall, Ramona L. Walls, Monte Westerfeld, Robert A. Wharton, Christian S. Wirkner, James B. Woolley, Matthew J. Yoder, Aaron M. Zorn, Paula Mabee

Entomology Faculty Publications

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of …

Characterization Of Two Biochars Derived From Horse Muck And Their Ability To Reduce Pathogen Transport In Soil, David Griffith

Theses and Dissertations--Biosystems and Agricultural Engineering

Biochars have been created and characterized from a variety livestock manure biomass including poultry, dairy, and swine. However, no research has been conducted on the physical and chemical makeup of biochar pyrolyzed from horse muck. Two horse muck derived biochars containing either straw (HS) or woodchip (HW) bedding were pyrolyzed at 700°C and characterized for their physical and chemical properties. Tests revealed both biochars had high alkalinity, moderate specific conductivity, and low surface area as compared to other biochars in the literature. HS contained more mineral structures than HW. Scanning electron microscopy presented differences in particle shape, size, and presence …

Cross-Talk Between The Tumor Suppressors Par-4 And P53, Tripti Shrestha Bhattarai

Theses and Dissertations--Toxicology and Cancer Biology

This work describes the fascinating interplay between two tumor suppressors Prostate apoptosis response-4 (Par-4) and p53. The guardian of the genome, p53, is frequently mutated in human cancers, and may contribute to therapeutic resistance. However, p53 is intact and functional in normal tissues, and we observed that specific activation of p53 in normal fibroblasts could induce apoptosis selectively in p53-deficient cancer cells. This paracrine apoptotic effect was executed by Par-4 secreted in response to p53 activation. Accordingly, activation of p53 in wild-type mice, but not in p53^-/- or Par-4^-/- mice, caused systemic elevation of Par-4 that induced apoptosis …

Pharmacologic Induction Of The Melanocotin 1 Receptor (Mc1r) Pathway Provides Protection Against Sunburn And Enhances Expression Of Antioxidant Enzymes In The Skin, Alexandra Amaro-Ortiz

Theses and Dissertations--Toxicology and Cancer Biology

The inability to tan properly after sun exposure strongly correlates with increased incidence of skin cancer. The melanocortin 1 receptor (MC1R) is a transmembrane Gs-coupled cell surface receptor found on epidermal melanocytes that transmits pro-survival and pro-differentiation signals mediated by the second messenger cAMP. Humans carrying loss-of-function polymorphisms in MC1R signaling exhibit higher incidences of skin cancers including melanoma.

This study focused on the physiologic effects of topical application of forskolin, an adenylate cyclase activator, in extension (Mc1r^e/e) K14-SCF animals, which model the fair-skinned UV-sensitive human. Twice daily application of the drug promoted accelerated pigmentation, increased skin darkening …

Engineering Triterpene Metabolism In Tobacco, Zuodong Jiang

Theses and Dissertations--Plant and Soil Sciences

Terpenes comprise a large diverse class of natural products and many of them attract interest because of their physiological function, therapeutic and industrial values. Triterpene oils including squalene (C30), botrycococcene (C30) and their methylated derivatives (C31-C37) generated by the green algae Botryococcus braunii race B, which have recently received significant attention because of their utility for advanced biofuels. However, the slow growth habit of B. braunii makes it impractical as a robust biofuel production system. In this thesis, we firstly evaluated the potential of generating high levels of triterpene (C30) production in tobacco plants by diverting carbon flux from cytosolic …

Role Of Sox11 During Vertebrate Ocular Morphogenesis And Retinal Neurogenesis, Lakshmi Shashidharan Pillai

Theses and Dissertations--Biology

Microphthalmia, anophthalmia, and coloboma (MAC) are distinct abnormalities demonstrating a continuum of developmental eye defects that contribute to 15-20% of blindness and severe vision deficiencies in children worldwide. The genetic etiology of MAC is large, complex and encompasses the whole developmental biology of the eye. Understanding how the eye develops will aid in identifying genes and developmental pathways involved in MAC. Although investigation of the genetic architecture of congenital anomalies is growing exponentially, much work remains to be accomplished to understand the complex, genetically heterogeneous congenital anomalies, which significantly impact childhood vision.

With an interest in elucidating the mechanisms that …

Context-Dependent Individual Variation In Foraging Behaviour And Parental Care In House Sparrows, David Moldoff

Theses and Dissertations--Biology

Behaviors can exhibit a wide degree of plasticity depending on the environmental context in which they are expressed. Despite this, repeatable differences have been found among and within individuals across a wide range of taxa. For my thesis, I investigated individual differences in foraging and parental care. In the first experiment, I assessed house sparrows (Passer domesticus) for domain-generality among neophobia, habituation and associative learning as they are all responses to novelty. While the results of the study find individual differences in each of these contexts the conclusion supported separate mechanisms for each response (domain-specificity). In the second experiment, I …

Dual Functions For Insulinoma-Associated 1 In Retinal Development, Marie A. Forbes-Osborne

Theses and Dissertations--Biology

Proper visual system function requires tightly controlled proliferation of a pool of relatively homogeneous retinal progenitor cells, followed by the stepwise specification and differentiation of multiple distinct cell types. These retinal cells, both neuronal and glial, must be generated in the correct numbers, and the correct laminar location to permit the formation of synaptic connections between individual cell types. After synapses are made, constant signaling is required as part of normal retinal function, and to maintain cellular identity and connectivity. These processes rely on both extrinsic and intrinsic signaling, with regulation of gene expression by cascades of transcription factors having …