Biology Commons^™

Relative Importance Of Environmental Variables For Spawning Cues And Tributary Use By An Adfluvial Lake Sucker, Brian A. Hines

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The endangered June sucker (Chasmistes liorus mictus), which is only found in Utah Lake, UT, historically spawned in all streams flowing into the lake, but due to human-caused changes their spawning is restricted to the Provo River. The purpose of this study was to gain a better understanding of the spawning and early life-history of the
June sucker for recovery purposes. My specific objectives were to determine:

1. what environmental factors attract or deter June suckers to certain Utah Lake tributaries for spawning,
2. what cues June suckers to migrate upstream to spawn,
3. if June suckers use more than one …

Effect Of Voluntary Exercise And Diet On The Unfolded Protein Response In The Brain Of Mice, Yu Ho Kim

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The medical costs for many chronic diseases are increasing dramatically and placing a major financial burden on nations and individuals in both developed and developing countries. A number of chronic diseases, such as obesity, type 2 diabetes and some neurodegenerative diseases are all attenuated by a history of physical activity suggesting that they may be interconnected in some way. It has been suggested that cellular stress is a major factor promoting these chronic diseases.

Cellular stress occurs in a specific compartment within the cell, the endoplasmic reticulum, whose normal function is in the synthesis and folding of proteins into the …

The Biogeography Of Marbled Godwit (Limosa Fedoa) Populations In North America, Bridget E. Olson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The mission of the U.S. Fish and Wildlife Service (USFWS) is working with others to conserve, protect, and enhance fish, wildlife, plants, and their habitats for the continuing benefit of the American people. Toward fulfillment of that mission, a priority of the USFWS is conservation and management of migratory birds. Effective conservation actions to ensure the continued existence of a species on the landscape cannot be designed without first understanding basic life history characteristics of a species. It is common in the case of migratory birds, that we lack understanding of some of their elemental biological traits.

The Marbled Godwit, …

Linking Fruit Traits To Variation In Predispersal Vertebrate Seed Predation, Insect Seed Predation, And Pathogen Attack, Noelle G. Beckman, Helene C. Muller-Landau

Biology Faculty Publications

The importance of vertebrates, invertebrates, and pathogens for plant communities has long been recognized, but their absolute and relative importance in early recruitment of multiple coexisting tropical plant species has not been quantified. Further, little is known about the relationship of fruit traits to seed mortality due to natural enemies in tropical plants. To investigate the influences of vertebrates, invertebrates, and pathogens on reproduction of seven canopy plant species varying in fruit traits, we quantified reductions in fruit development and seed germination due to vertebrates, invertebrates, and fungal pathogens through experimental removal of these enemies using canopy exclosures, insecticide, and …

Loss-Of-Function Of Constitutive Expresser Of Pathogenesis Related Genes5 Affects Potassium Homeostasis In Arabidopsis Thaliana, Monica Borghi, Ana Rus, David E. Salt

Biology Faculty Publications

Here, we demonstrate that the reduction in leaf K+ observed in a mutant previously identified in an ionomic screen of fast neutron mutagenized Arabidopsis thaliana is caused by a loss-of-function allele of CPR5, which we name cpr5-3. This observation establishes low leaf K+ as a new phenotype for loss-of-function alleles of CPR5. We investigate the factors affecting this low leaf K+ in cpr5 using double mutants defective in salicylic acid (SA) and jasmonic acid (JA) signalling, and by gene expression analysis of various channels and transporters. Reciprocal grafting between cpr5 and Col-0 was used to determine the relative importance of …

The Decline And Conservation Status Of North American Bumble Bees, Jonathan B. Koch

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Several reports of North American bumble bee (Bombus Latreille) decline have been documented across the continent, but no study has fully assessed the geographic scope of decline. In this study I discuss the importance of Natural History Collections (NHC) in estimating historic bumble bee distributions and abundances, as well as in informing current surveys. To estimate changes in distribution and relative abundance I compare historic data assembled from a >73,000 specimen database with a contemporary 3-year survey of North American bumble bees across 382 locations in the contiguous U.S.A. Based on my results, four historically abundant bumble bees, B. …

Design Of A BiobrickTm Compatible Gene Expression System For Rhodobacter Sphaeroides, Junling Huo

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The concept of introducing engineering principles of abstraction and standardization into synthetic biology has received increasing attention in the past several years and continues to be in the forefront of synthetic biology. One direction being pursued by synthetic biologists is creation of modular biological parts (BioBrick^TM) that can be readily synthesized and mixed together in different combinations. However, most standard BioBrick^TM parts in the Registry were designed for E. coli, although synthesis of specific BioBrick^TM parts for other bacteria, such as for yeast and cyanobacteria, have begun. Besides, at the present time, there are only …

Characterization And Application Of Dynamic In Vitro Models Of Human Airway, Hemangkumar J. Patel

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In recent years, respiratory diseases have emerged as a leading cause of mortality across the globe. In the United States alone respiratory diseases are the fourth leading cause of deaths annually. Moreover, with the rapid increase of industrialization and urbanization, the occurrences of respiratory diseases are expected to remain high with strong chances of increasing in the future. To ameliorate the epidemic of respiratory disease, it is first important to understand its underlying mechanisms.

Respiratory research studies in animals have elucidated the chronological order of the pathological events and systemic responses inside the lung, but understanding the response of individual …

The Role Of Phosphoinositide Signaling In Breast Cancer Metastasis Suppressor 1-Mediated Metastasis Suppression Of Human Breast Carcinoma Cells, Sitaram Harihar

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Breast cancer is the most common non-skin cancer in women and the second most common cause of cancer-related death in U.S. women. Despite numerous advances in treatment strategies against breast cancer, the presence of undetected distant metastasis of the primary tumor remains the main cause of mortality. Current screening and detection methods such as mammograms are simply not sensitive enough to detect formation of metastasis. Further, currently available therapies against metastatic breast cancer do not provide a complete cure for the disease. Thus, understanding the biology and molecular factors involved in cancer metastasis will help aid in preventing the onset …

A Study On The Applications And Toxicity Assessments Of Carbon Nanotubes In Tissue Engineering, Rena Baktur

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Carbon nanotubes (CNTs) are one of the most popular nanomaterials. There has been increasing interest in the development and applications of carbon nanotubes due to their huge potential in industrial and medical applications. Recent applications of carbon nanotubes include development of scaffolds and drug delivery systems. Despite rapidly emerging applications of CNTs, little is known about the impact of CNTs on cellular processes, especially mesenchymal stem cell (MSC)'s differentiation. Also, the effects of nanoparticle exposure under different conditions on cellular responses have not been well characterized yet.

To characterize the effects of CNTs on creating nanoscale scaffolds for tissue engineering, …

The High Cost Of Cheap Coal; Why Can't We Move To Renewable Energy, Cameron Dale Bartlett

Undergraduate Honors Capstone Projects

This article addresses the historic and current use of coal as the main source of electric power throughout the United States. Coal powered power plants remain an important part of the history and industrialization of the United States, even though there are many detrimental health and environmental impacts associated with its use. A slowly growing trend has been emerging with research on and use of renewable energy to replace fossil fuels, such as coal. Greater public awareness and involvement will help drive the slowly emerging use of renewable energy. This article looks at the current barriers that are prohibiting the …

Is Wildlife Going To The Dogs? Impacts Of Feral And Free-Roaming Dogs On Wildlife Populations, Julie K. Young, Kirk A. Olson, Richard P. Reading, Sukh Amgalanbaatar, Joel Berger

Wildland Resources Faculty Publications

In human-populated landscapes, dogs (Canis familiaris) are often the most abundant terrestrial carnivore. However, dogs can significantly disrupt or modify intact ecosystems well beyond the areas occupied by people. Few studies have directly quantified the environmental or economic effects of free-roaming and feral dogs. Here, we review wildlife-dog interactions and provide a case study that focuses on interactions documented from our research in Mongolia to underscore the need for studies designed to best determine how dogs affect native wildlife and especially imperiled populations. We suggest additional research, public awareness campaigns, and the exclusion of dogs from critical wildlife habitat. The …

Temperature Increase Effects On Sagebrush Ecosystem Forbs: Exprimental Evidence And Range Manager Perspectives, Hilary Louise Whitcomb

Green Canyon Environmental Research Area, Logan Utah

No abstract provided.

Relative Changes In Krillabundance Inferred From Antarctic Fur Seal, T. Huang, L. Sun, John M. Stark, Y. Wang, Z. Cheng, Q. Yang, S. Sun

John M. Stark

No abstract provided.

On The Use Of Log-Transformation Vs. Nonlinear Regression For Analyzing Biological Power-Laws, Xiao Xiao, Ethan P. White, M. B. Hooten, Susan L. Durham

Biology Faculty Publications

Power-law relationships are among the most well-studied functional relationships in biology. Recently the common practice of fitting power-laws using linear regression on log-transformed data (LR) has been criticized, calling into question the conclusions of hundreds of studies. It has been suggested that nonlinear regression (NLR) is preferable, but no rigorous comparison of these two methods has been conducted. Using Monte Carlo simulations we demonstrate that the error distribution determines which method performs better, with LR better characterizing data with multiplicative lognormal error and NLR better characterizing data with additive, homoscedastic, normal error. Analysis of 471 biological power-laws shows that both …

Dissimilatory Nitrate Reductionpathways In An Oligotrophic Aquatic Ecosystem: Spatial And Temporal Trends, I. J. Washbourne, C. L. Crenshaw, Michelle A. Baker

Biology Faculty Publications

Elevated nitrate (NO₃⁻) concentrations can cause eutrophication, which may lead to harmful algal blooms, loss of habitat and reduction in biodiversity. Denitrification, a dissimilatory process that removes NO₃⁻ mainly as dinitrogen gas (N₂), is believed to be the dominant NO₃⁻ removal pathway in aquatic ecosystems. Evidence suggests that a less well-studied process, dissimilatory nitrate reduction to ammonium (DNRA), which retains nitrogen (N) in the system, may also be important under favorable conditions. Using stable isotope tracers in sealed microcosms, we measured the potential for NO₃⁻ losses due to DNRA …

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, …

Relative Changes In Krillabundance Inferred From Antarctic Fur Seal, T. Huang, L. Sun, John M. Stark, Y. Wang, Z. Cheng, Q. Yang, S. Sun

Biology Faculty Publications

Antarctic krill Euphausia superba is a predominant species in the Southern Ocean, it is very sensitive to climate change, and it supports large stocks of fishes, seabirds, seals and whales in Antarctic marine ecosystems. Modern krill stocks have been estimated directly by net hauls and acoustic surveys; the historical krill density especially the long-term one in the Southern Ocean, however, is unknown. Here we inferred the relative krill population changes along the West Antarctic Peninsula (WAP) over the 20th century from the trophic level change of Antarctic fur seal Arctocephalus gazella using stable carbon (d13C) and nitrogen (d15N) isotopes of …

The Selaginella Genome Identifies Changes In Gene Content Associated With The Evolution Of Vascular Plants, J. A. Banks, T. Nishiyama, M. Hasebe, J. L. Bowman, M. Gribskov, C. Depamphilis, Paul G. Wolf

Biology Faculty Publications

Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in …

The Evolution Of Chloroplast Genes And Genomes In Ferns, Paul G. Wolf, J. P. Der, A. M. Duffy, J. B. Davidson, A. L. Grusz, K. M. Pryer

Biology Faculty Publications

Most of the publicly available data on chloroplast (plastid) genes and genomes come from seed plants, with relatively little information from their sister group, the ferns. Here we describe several broad evolutionary patterns and processes in fern plastid genomes (plastomes), and we include some new plastome sequence data. We review what we know about the evolutionary history of plastome structure across the fern phylogeny and we compare plastome organization and patterns of evolution in ferns to those in seed plants. A large clade of ferns is characterized by a plastome that has been reorganized with respect to the ancestral gene …

De Novo Characterization Of The Gametophyte Transcriptome In Bracken Fern, Pteridium Aquilinum, J. P. Der, M. S. Barker, N. J. Wickett, C. W. Depamphilis, Paul G. Wolf

Biology Faculty Publications

Because of their phylogenetic position and unique characteristics of their biology and life cycle, ferns represent an important lineage for studying the evolution of land plants. Large and complex genomes in ferns combined with the absence of economically important species have been a barrier to the development of genomic resources. However, high throughput sequencing technologies are now being widely applied to non-model species. We leveraged the Roche 454 GS-FLX Titanium pyrosequencing platform in sequencing the gametophyte transcriptome of bracken fern (Pteridium aquilinum) to develop genomic resources for evolutionary studies.