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Microbiology

University of Colorado, Boulder

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Full-Text Articles in Life Sciences

Single-Stranded Dna Viruses In Antarctic Cryoconite Holes, Pacifica Sommers, Rafaela S. Fontenele, Tayele Kringen, Simona Kraberger, Dorota L. Porazinska, John L. Darcy, Steven K. Schmidt, Arvind Varsani Nov 2019

Single-Stranded Dna Viruses In Antarctic Cryoconite Holes, Pacifica Sommers, Rafaela S. Fontenele, Tayele Kringen, Simona Kraberger, Dorota L. Porazinska, John L. Darcy, Steven K. Schmidt, Arvind Varsani

University Libraries Open Access Fund Supported Publications

Antarctic cryoconite holes, or small melt-holes in the surfaces of glaciers, create habitable oases for isolated microbial communities with tightly linked microbial population structures. Viruses may influence the dynamics of polar microbial communities, but the viromes of the Antarctic cryoconite holes have yet to be characterized. We characterize single-stranded DNA (ssDNA) viruses from three cryoconite holes in the Taylor Valley, Antarctica, using metagenomics. Half of the assembled metagenomes cluster with those in the viral family Microviridae (n = 7), and the rest with unclassified circular replication associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses (n = 7). An additional 18 virus-like circular ...


Comparison Of Microbial Communities In The Sediments And Water Columns Of Frozen Cryoconite Holes In The Mcmurdo Dry Valleys, Antarctica, Pacifica Sommers, John Lawrence Darcy, Dorota L. Porazinska, Eli M.S. Gendron, Andrew G. Fountain, Felix Zamora, Kim Vincent, Kaelin M. Cawley, Adam J. Solon, Lara Vimercati, Jenna Ryder, Steven K. Schmidt Feb 2019

Comparison Of Microbial Communities In The Sediments And Water Columns Of Frozen Cryoconite Holes In The Mcmurdo Dry Valleys, Antarctica, Pacifica Sommers, John Lawrence Darcy, Dorota L. Porazinska, Eli M.S. Gendron, Andrew G. Fountain, Felix Zamora, Kim Vincent, Kaelin M. Cawley, Adam J. Solon, Lara Vimercati, Jenna Ryder, Steven K. Schmidt

University Libraries Open Access Fund Supported Publications

Although cryoconite holes, sediment-filled melt holes on glacier surfaces, appear small and homogenous, their microbial inhabitants may be spatially partitioned. This partitioning could be particularly important for maintaining biodiversity in holes that remain isolated for many years, such as in Antarctica. We hypothesized that cryoconite holes with greater species richness and biomass should exhibit greater partitioning between the sediments and water, promoting greater biodiversity through spatial niche partitioning. We tested this hypothesis by sampling frozen cryoconite holes along a gradient of biomass and biodiversity in the Taylor Valley, Antarctica, where ice-lidded cryoconite holes are a ubiquitous feature of glaciers. We ...


Abiotic And Biotic Drivers Of Plant Range Shifts In The Alpine, Clifton Powell Bueno De Mesquita Jan 2019

Abiotic And Biotic Drivers Of Plant Range Shifts In The Alpine, Clifton Powell Bueno De Mesquita

Ecology & Evolutionary Biology Graduate Theses & Dissertations

Over the course of Earth’s biological history, organisms have many times had to shift their geographic distributions in order to track changing abiotic conditions suitable for their growth, survival, and reproduction. Now more than ever, in the new geologic epoch of the Anthropocene, organisms will have to rapidly shift their ranges to adapt to climate change and other anthropogenic disturbances. The rearrangement of organisms can be facilitated or inhibited by biotic interactions between organisms. Here I examine plant range shifts in an alpine ecosystem in response to climate warming and earlier snowmelt, as well as the role of biotic ...


Development Of Novel Crispr-Based Methods For Transcriptional Control Over Bacterial Gene Expression, Katia Tarasava Jan 2019

Development Of Novel Crispr-Based Methods For Transcriptional Control Over Bacterial Gene Expression, Katia Tarasava

Materials Science & Engineering Graduate Theses & Dissertations

One of the challenges of the 21st century is creating a sustainable economy that is able to serve the needs of a growing population with the decreasing supply of natural resources. In addition to alternative energy sources, renewable economy concerns production of materials and chemicals. The chemical and polymer industries rely heavily on petroleum for manufacturing consumer goods. Many of these chemicals can be produced from renewable resources using microorganisms. However, the amounts produced are often not enough to make the process commercially viable. By rewiring cellular metabolism and regulation, it is possible to redirect metabolic flux to increase the ...


Ecological Strategies Of Soil Bacteria And Archaea, Tess Elizabeth Brewer Jan 2019

Ecological Strategies Of Soil Bacteria And Archaea, Tess Elizabeth Brewer

Molecular, Cellular, and Developmental Biology Graduate Theses & Dissertations

Soil is essential for much of life on earth. Microbes are ubiquitous in this environment – billions of microbial cells can occupy one gram of soil. Soil microbes participate in carbon sequestration, nutrient cycling, and soil formation - all critical ecosystem processes, yet are poorly understood. A key factor in this knowledge gap is the low proportion of cultivated soil microbes – by one estimate 1/3 of soil dwelling bacteria and archaea do not have a cultured representative of their phylum. In my thesis research, I have studied the bacteria and archaea that live in soil using culture-independent techniques; specifically studying the ...


How Much Does Stream-Groundwater Exchange Influence Whole-Stream Metabolism In A Small Mountain Stream?, Erin Elizabeth Jenkins Jan 2019

How Much Does Stream-Groundwater Exchange Influence Whole-Stream Metabolism In A Small Mountain Stream?, Erin Elizabeth Jenkins

Civil Engineering Graduate Theses & Dissertations

The open-channel oxygen method quantifies rates of gross primary productivity (GPP) and ecosystem respiration (ER) by employing the diel dissolved oxygen (DO) curve. This attributes stream metabolism to four processes: photosynthesis, oxidative respiration, reaeration, and groundwater flux. Groundwater flux, however, is often assumed to be negligible, which may introduce bias in estimates of metabolism. To investigate this, whole-stream metabolism and groundwater flux were measured in Como Creek, Colorado during the summer of 2018. Results from the BASE (Bayesian Single-station Estimation) metabolism model indicate that periods of anoxic groundwater input result in an overestimation of ER in baseline simulations. These data ...


Salmonella Within Macrophages--An Extreme Host-Pathogen Interface: Small Molecule Inhibitors Of Bacterial Efflux And The Roles Of Bacterial Lipid Metabolism And Mammalian Co-Culture During Infection, Abigail L. Reens Jan 2019

Salmonella Within Macrophages--An Extreme Host-Pathogen Interface: Small Molecule Inhibitors Of Bacterial Efflux And The Roles Of Bacterial Lipid Metabolism And Mammalian Co-Culture During Infection, Abigail L. Reens

Molecular, Cellular, and Developmental Biology Graduate Theses & Dissertations

Pathogens withstand extreme host environments during infection. Salmonella enterica serovar Typhimurium survives within host macrophages, immune cells intended to phagocytose and destroy pathogens. Through decades of study, we know much about how Salmonella endures this challenging niche. I leveraged this host-pathogen interface to identify small molecules that disrupt Salmonella infection of macrophages. I developed a medium-throughput fluorescence microscopy-based screening assay and image analysis pipeline to quantify intracellular bacterial load. With this platform, I identified 300 small molecules that reduce Salmonella infection of macrophages. Of the top 60 hits, I characterized three compounds that inhibit bacterial efflux pumps and sensitize Salmonella ...


Methods Of Testing Skin Mucosomes Of Anaxyrus Boreas In The Face Of Batrachocytrium Dendrobatidis, Gena Rumsey Jan 2019

Methods Of Testing Skin Mucosomes Of Anaxyrus Boreas In The Face Of Batrachocytrium Dendrobatidis, Gena Rumsey

Undergraduate Honors Theses

The microbial community of amphibians skin has demonstrated significant importance in amphibian health and disease resistance specifically in response to the pathogenic chytrid fungus Batrachochytrium dendrobatidis (Bd; Barnhart et al. 2017). Since its discovery in the late 1990s, Bd has contributed to world-wide decline in amphibian populations. Multiple naturally occurring amphibian-skin bacteria have been identified as inhibitors of Bd, including Janthinobacterium lividum (J liv; Harris et al. 2009). The McKenzie group developed a probiotic treatment of J liv as an intervention for a boreal toad population in Colorado drastically declining due to a Bd epidemic. Since wild toads cannot be ...


Analysis Of Murine Polyomavirus Dna Replication: Large T-Antigen Interaction With Host Dna Damage Repair Protein Rpa During Cellular Infection, Katherine Rose Jan 2019

Analysis Of Murine Polyomavirus Dna Replication: Large T-Antigen Interaction With Host Dna Damage Repair Protein Rpa During Cellular Infection, Katherine Rose

Undergraduate Honors Theses

Murine Polyomaviruses are dsDNA viruses that hijack the host’s DNA damage response (DDR) pathway to replicate their own genomes (Heiser et al., 2016), offering a model for human polyomavirus replication. The viral protein large T-antigen (LT) is essential for viral replication and can interact with a variety of DDR proteins in viral DNA replication centers (Brodsky & Pipas, 1998). Replication protein A (RPA) is a DDR protein complex made up of three subunits, RPA70, RPA32, and RPA14. RPA70 and RPA32 have been shown to directly interact with LT in cells over-expressing each protein, either individually or together (Banerjee et al ...


Host And Viral Molecular Patterns Relevant To Pathogenicity And Immunity, Alexander Christian Stabell Aug 2018

Host And Viral Molecular Patterns Relevant To Pathogenicity And Immunity, Alexander Christian Stabell

Molecular, Cellular, and Developmental Biology Graduate Theses & Dissertations

Patterns in nature, many going unnoticed, are a defining characteristic of life. In this thesis, I will describe four studies that I have completed during my doctoral work. These will highlight how both host immune system and viral pathogens harness non-random biological patterns to aid in immunity or increase pathogenicity, respectively. Chapter 2 will describe the evolutionary history of a component of the primate innate immune system, Schlafen11, and its involvement in the defense against viruses. I attempt to show that Schlafen11 takes advantage of the pattern of non-optimal codon usage of HIV-1 transcripts in order to inhibit viral replication ...


Biogeographic And Biogeochemical Drivers Of Microbial Community Assembly, John Lawrence Darcy Feb 2018

Biogeographic And Biogeochemical Drivers Of Microbial Community Assembly, John Lawrence Darcy

Ecology & Evolutionary Biology Graduate Theses & Dissertations

The processes of community assembly shape all groups of coexisting organisms across all environments where life is found. Even for environments that are currently sterile, when they are colonized by life, community assembly processes will occur. The processes governing formation and diversification of microbial communities are vital to an understanding of how ecosystems develop in the human body, in emerging landscapes, and everywhere else. In this dissertation, I use community assembly theory to understand how microbial communities are shaped by geography, and also by the resources available to them. Using a microcosm-based nutrient addition experiment, I show that microbial communities ...


Engineering Bacterial Gene Expression: Applications Towards Biofuels And Antibiotic Resistance, Peter Britton Otoupal Jan 2018

Engineering Bacterial Gene Expression: Applications Towards Biofuels And Antibiotic Resistance, Peter Britton Otoupal

Chemical & Biological Engineering Graduate Theses & Dissertations

Nature is rarely static. Organisms live in diverse and stressful environments that necessitate rapid response strategies for survival. Microorganisms have responded to this by evolving bet-hedging, wherein they exhibit constitutively heterogeneous gene expression to maximize fitness across numerous background. The goal of this thesis is to “hijack” this phenomenon using novel gene expression engineering techniques to alter how bacteria respond to their environments, in order to address pressing societal concerns.

This begins with a systematic exploration of how bacterial gene expression naturally responds to antibiotics and biofuels. This reveals promising gene candidates for targeted manipulation, for which a library of ...


The Role Of Dynamics Within Bama, The Central Component Of The Bam Complex, Pamela Arden Doerner Barbour Jan 2018

The Role Of Dynamics Within Bama, The Central Component Of The Bam Complex, Pamela Arden Doerner Barbour

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

BamA is an essential component of the β-­‐barrel assembly machine that folds and inserts outer membrane proteins (OMPs) into the outer membrane of Gram-­‐negative bacteria. BamA is an OMP itself comprised of two domains, a soluble periplasmic N-­‐terminal domain consisting of five polypeptide transport associated (POTRA) repeats and a C-­‐terminal 16-­‐stranded β-­‐barrel domain. The mechanism of BamA is poorly understood but structural data suggests BamA is a dynamic protein with respect to the POTRA domains and barrel. The POTRA domains, numbered 1-5 from the N- to C- termini, can be divided into two sub-domains ...


Mechanical Inference In Dynamic Ecosystems, Ryan Elman Langendorf Jan 2018

Mechanical Inference In Dynamic Ecosystems, Ryan Elman Langendorf

Environmental Studies Graduate Theses & Dissertations

Empirical studies of graphs have contributed enormously to our understanding of complex systems, growing into a more scientific exploration of communities spanning the physical, biological, and social called network science. As the quantity and types of networks have grown so has their heterogeneity in quality and specificity resulting in a wealth of datasets that are not matched by existing theoretical methods. This is especially true in ecology where the majority of interactions are indirect and unobservable even in well-studied systems. As a result ecologists continue to grapple with three fundamental questions: Most basically, (i) `How do ecosystems function?' I answered ...


The Influence Of Plant-Soil Interactions On Plant And Soil Microbial Responses To Nitrogen Deposition, Teal Steinkraus Potter Jan 2018

The Influence Of Plant-Soil Interactions On Plant And Soil Microbial Responses To Nitrogen Deposition, Teal Steinkraus Potter

Ecology & Evolutionary Biology Graduate Theses & Dissertations

How plants interact with the soil around their roots is critical to how plant species function. Given the enormous ecological complexity of soils, it remains a challenge to understand the unique associations of plants and soils across plant species. Such knowledge is needed, however, to predict plant responses to changes in their environments. This work addresses questions on the theme of understanding how plant-soil interactions differ across among plant species and impact plant responses to environmental changes. More specifically, I examined how soil chemistry, nitrogen (N) availability, microbial communities, and abiotic conditions influence both plant responses to environmental change as ...


Ecology And Evolution Of Lepidoptera-Microbe Symbiosis, Tobin Jeremy Hammer Jan 2018

Ecology And Evolution Of Lepidoptera-Microbe Symbiosis, Tobin Jeremy Hammer

Ecology & Evolutionary Biology Graduate Theses & Dissertations

Microorganisms are now recognized to be integral components of the biology of many animal and plant taxa. These symbionts can play critical roles in host development, physiology, and in the mediation of ecological interactions among hosts. The study of insect-associated microbial symbionts is of particular interest, as insects comprise an enormous fraction of terrestrial biodiversity, provide important ecosystem services, and include destructive pests and disease vectors. However, symbiotic microbial functions are well-understood for only a limited set of insect taxa, and the broader ecological relevance of insect-microbe symbiosis is often unclear. Here, I describe four studies I undertook to investigate ...


Biochar As A Soil Amendment For Willow And Cottonwood Plantings In A Riparian Restoration, Brian Clyde Sechler Jan 2018

Biochar As A Soil Amendment For Willow And Cottonwood Plantings In A Riparian Restoration, Brian Clyde Sechler

Ecology & Evolutionary Biology Graduate Theses & Dissertations

Riparian areas provide some of the most valuable ecosystem services of any habitat type, both for native flora and wildlife, as well as human society. The global degradation of these critical systems makes their restoration imperative for the preservation of overall ecological integrity since depleted riparian corridors will have cascading effects that pervade upland and downstream regions alike. In western river systems there are two key limiting factors that can lead to failures during re-vegetation efforts along riparian stream banks: one is a lack of available soil nutrients, and the other is a lack of soil moisture. Biochar has been ...


Emergence Of New Metabolic Pathways In Escherichia Coli, Michael Kristofich Jan 2018

Emergence Of New Metabolic Pathways In Escherichia Coli, Michael Kristofich

Undergraduate Honors Theses

Catalytic promiscuity provides a starting point for the evolution of new enzymes. Taking this concept further, a series of promiscuous enzymes may assemble to form the basis of a new metabolic pathway (termed “serendipitous pathway”) that may emerge and become more efficient in adapting bacterial cells that require it to grow. The Copley lab at the University of Colorado at Boulder has been observing genetic changes that improve growth of Escherichia coli cells that lack the essential gene pdxB. These genetic changes are believed to improve the flux of metabolites through one or more serendipitous pathways that make up for ...


Effect Of Variation In An Essential Folding Element On The Cobalamin Riboswitch, Marcus Urquijo Jan 2018

Effect Of Variation In An Essential Folding Element On The Cobalamin Riboswitch, Marcus Urquijo

Undergraduate Honors Theses

Riboswitches are RNA-based genetic regulatory elements that control gene expression without the need for protein cofactors. These RNA motifs are found within the 5’ untranslated regions of mRNA and promote genetic regulation by altering the structure of RNA through binding small molecule effector ligands that cause conformational changes that repress or activate translation/transcription. The env8 cobalamin riboswitch binds cyanocobalamin (CNCbl) to repress gene expression of the downstream mRNA. It accomplishes this through an interplay of two separate domains; an aptamer domain which binds the effector ligand and a regulatory domain which contains the genetic switch. Within the aptamer domain ...


Milk Hygiene And Consumption Practices In The Gambia, Jennifer Renée Washabaugh Apr 2017

Milk Hygiene And Consumption Practices In The Gambia, Jennifer Renée Washabaugh

Anthropology Graduate Theses & Dissertations

While most mammals cease milk consumption after the weaning period, humans continue drinking milk into later-life. However, the milk integrated into human diets post-infancy comes from non-human sources, such as cattle. Livestock hold great importance for the livelihoods and nourishment of low-income populations, and as agropastoralists, many Gambians rely on milk throughout their lifespans. Milk is especially integrated into early-life diets where it is commonly given to infants in unpasteurized form. While weaning, infants are especially vulnerable to illness due to exposure to new environments and foods because of their immature immune systems, and diarrheal diseases have contributed greatly to ...


Engineering Synthetic Antibiotics In Non-Traditional Pathways To Counter Antibiotic Resistance, Colleen Maxwell Courtney Jan 2017

Engineering Synthetic Antibiotics In Non-Traditional Pathways To Counter Antibiotic Resistance, Colleen Maxwell Courtney

Chemical Engineering Graduate Theses & Dissertations

Antibiotic resistance is a growing threat to global healthcare that requires immediate action to avoid the post-antibiotic era. The inherent ability of bacteria to obtain resistance and the lack of new antibiotics has led to the current antibiotic crisis. Current antibiotics are typically found through soil compound screens and only target proteins within three cellular pathways: cellular replication, cell wall biosynthesis, and protein biosynthesis. In the last decade, strains have been isolated which have resistance to nearly all available antibiotics highlighting the urgent need for intervention. In this work we investigated the rational design of non-naturally derived antibiotics which target ...


Novel Approaches To Bioengineering Target Identification: A Focus On Non-Genetic Contributions To Complex Bacterial Phenotypes, Keesha Elizabeth Erickson Jan 2017

Novel Approaches To Bioengineering Target Identification: A Focus On Non-Genetic Contributions To Complex Bacterial Phenotypes, Keesha Elizabeth Erickson

Chemical & Biological Engineering Graduate Theses & Dissertations

Many critical societal issues could be alleviated via advances in biological engineering, specifically those bolstering our ability to design complex phenotypes like bacterial tolerance, resistance, and chemical production. Complex phenotypes are controlled through overlapping regulatory mechanisms encompassing multiple systems, including metabolism, cellular structure, energy consumption, and more. Moreover, immense heterogeneity within and across bacterial populations makes it challenging to discern key genes and pathways contributing to phenotypes of interest. Thus, to enable engineering of complex bacterial phenotypes, it is essential to consider unconventional perspectives from which to identify targets.

Here, we describe efforts concentrated on non-genetic data to ascertain key ...


Engineering Synthetic Antibiotics In Non-Traditional Pathways To Counter Antibiotic Resistance, Colleen Maxwell Courtney Jan 2017

Engineering Synthetic Antibiotics In Non-Traditional Pathways To Counter Antibiotic Resistance, Colleen Maxwell Courtney

Chemical & Biological Engineering Graduate Theses & Dissertations

Antibiotic resistance is a growing threat to global healthcare that requires immediate action to avoid the post-antibiotic era. The inherent ability of bacteria to obtain resistance and the lack of new antibiotics has led to the current antibiotic crisis. Current antibiotics are typically found through soil compound screens and only target proteins within three cellular pathways: cellular replication, cell wall biosynthesis, and protein biosynthesis. In the last decade, strains have been isolated which have resistance to nearly all available antibiotics highlighting the urgent need for intervention. In this work we investigated the rational design of non-naturally derived antibiotics which target ...


Improving Diatom Enumeration Methods For Use In Predictive Bioassessment Models, Meredith A. Tyree Jan 2017

Improving Diatom Enumeration Methods For Use In Predictive Bioassessment Models, Meredith A. Tyree

Environmental Studies Graduate Theses & Dissertations

Diatoms are routinely sampled in biological assessments of water quality, but the method traditionally used to characterize diatom communities does not adequately capture species richness for use in most assessment applications. The traditional enumeration method of 300 cell (or 600 valve) fixed counts was designed to characterize the relative abundance only of dominant taxa, making it inappropriate for common bioassessment applications such as observed/expected (O/E) models, which rely on species richness. We analyzed the nature of diatom communities in reference sites of varying diversity using a measure of counting efficiency, which revealed that 600 valve fixed counts did ...


The Effects Of Climate Change On An Alpine Lake System, A Mesocosm Experiment, Matthew Richard Olivier Jan 2017

The Effects Of Climate Change On An Alpine Lake System, A Mesocosm Experiment, Matthew Richard Olivier

Environmental Studies Graduate Theses & Dissertations

Much like in the arctic, organisms inhabiting alpine ecosystems are living at the edge of their environmental tolerances, and are thus sensitive to small changes in climate. Algal communities of alpine lakes are particularly useful as indicators of environmental change due to the fact that they are typically diverse and rapidly respond to environmental changes over short time scales. During the summer of 2014, an aquatic mesocosm experiment was conducted using cattle tanks at the Niwot Ridge Long Term Ecological Research Site (NWTLTER) in the Colorado Front Range. The purpose of the experiment was to examine the effects of increased ...


Biogeographic And Biogeochemical Drivers Of Microbial Community Assembly, John Lawrence Darcy Jan 2017

Biogeographic And Biogeochemical Drivers Of Microbial Community Assembly, John Lawrence Darcy

Ecology & Evolutionary Biology Graduate Theses & Dissertations

The processes of community assembly shape all groups of coexisting organisms across all environments where life is found. Even for environments that are currently sterile, when they are colonized by life, community assembly processes will occur. The processes governing formation and diversification of microbial communities are vital to an understanding of how ecosystems develop in the human body, in emerging landscapes, and everywhere else. In this dissertation, I use community assembly theory to understand how microbial communities are shaped by geography, and also by the resources available to them. Using a microcosm-based nutrient addition experiment, I show that microbial communities ...


Host And Viral Molecular Patterns Relevant To Pathogenicity And Immunity, Alexander Christian Stabell Jan 2017

Host And Viral Molecular Patterns Relevant To Pathogenicity And Immunity, Alexander Christian Stabell

Molecular, Cellular, and Developmental Biology Graduate Theses & Dissertations

Patterns in nature, many going unnoticed, are a defining characteristic of life. In this thesis, I will describe four studies that I have completed during my doctoral work. These will highlight how both host immune system and viral pathogens harness non-random biological patterns to aid in immunity or increase pathogenicity, respectively. Chapter 2 will describe the evolutionary history of a component of the primate innate immune system, Schlafen11, and its involvement in the defense against viruses. I attempt to show that Schlafen11 takes advantage of the pattern of non-optimal codon usage of HIV-1 transcripts in order to inhibit viral replication ...


A Cross-Scale Assessment Of Historical Fire Severity Patterns, Landscape Dynamics, And Methodological Challenges In Mixed-Severity Fire Regimes Of The Northern U.S. Rockies, Cameron Edwards Naficy Jan 2017

A Cross-Scale Assessment Of Historical Fire Severity Patterns, Landscape Dynamics, And Methodological Challenges In Mixed-Severity Fire Regimes Of The Northern U.S. Rockies, Cameron Edwards Naficy

Geography Graduate Theses & Dissertations

Forests characterized by mixed-severity fire regimes (MSFR) exhibit high spatio-temporal variability of fire frequency and severity. These forests comprise much of western North America, but their ecological dynamics, spatial ecology, resilience mechanisms, and biophysical drivers are poorly understood. MSFR forests provide rich spatio-temporal data that predate landscape changes and alterations to disturbance regimes that have occurred since Euro-American colonization. However, the relative scarcity of large historical datasets and some persistent methodological limitations have impeded robust reconstructions of historical MSFRs, creating substantial debate and confusion. We address these problems by developing an extensive dataset of dendroecological records and geospatial maps of ...


Bathing In Bacteria: Mycobacteria Relative Abundance On Showerhead Biofilms, Robin G. Hacker-Cary Jan 2017

Bathing In Bacteria: Mycobacteria Relative Abundance On Showerhead Biofilms, Robin G. Hacker-Cary

Undergraduate Honors Theses

Mycobacterium is a genus of Actinobacteria that contains many human pathogens, causing diseases such as tuberculosis, leprosy, and nontuberculous mycobacteria (NTM) lung disease. Diagnosed cases of NTM lung disease, are increasing rapidly across the United States. Recent studies have indicated that this respiratory infection is acquired through the inhalation of aerosolized mycobacteria derived from the biofilms found on the inside of household showerheads.

To asses the factors that influence mycobacteria abundance on the interior biofilms of showerheads we analyzed bacterial and protistan communities from showerhead samples gathered across the United States. Further, we investigated water chemistry, specifically total chorine concentration ...


Correlative Light And Electron Microscopy On Mouse Polyomavirus-Infected Fibroblasts, Christina Henderson Jan 2017

Correlative Light And Electron Microscopy On Mouse Polyomavirus-Infected Fibroblasts, Christina Henderson

Undergraduate Honors Theses

Polyomaviruses are small, DNA tumor viruses that can infect multiple species, including humans. In recent years, the number of identified human polyomaviruses (huPyV) has grown. To identify possible therapeutic targets for huPyVs, a better understanding of virus infection at the structural level is needed. Confocal microscopy allows for the visualization of fluorescently-tagged proteins but without seeing the cell’s subcellular structures, functional information can be lost. Electron microscopy provides structural insight but does not always provide biological or biochemical details. Combining these two approaches can relate biological function to structural information about virus replication. Polyomaviruses (PyV) co-opt host proteins that ...