Drought Responsive Gene Expression Regulatory Divergence Between Upland And Lowland Ecotypes Of A Perennial C4 Grass,
2016
Marshall University
Drought Responsive Gene Expression Regulatory Divergence Between Upland And Lowland Ecotypes Of A Perennial C4 Grass, John T. Lovell, Scott Schwartz, David B. Lowry, Eugene V. Shakirov, Jason E. Bonnette, Xiaoyu Weng, Mei Wang, Jenifer Johnson, Avinash Sreedasyam, Christopher Plott, Jerry Jenkins, Jeremy Schmutz, Thomas E. Juenger
Biological Sciences Faculty Research
Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C4 grass, Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. …
Diversity Of Cultured Bacteria From The Perennial Ice Block Of Scarisoara Ice Cave, Romania,
2016
Institute of Biology Bucharest
Diversity Of Cultured Bacteria From The Perennial Ice Block Of Scarisoara Ice Cave, Romania, Corina Iţcuş, Mădălina-Denisa Pascu, Traian Brad, Aurel Perşoiu, Cristina Purcarea
International Journal of Speleology
Cave ice ecosystems represent a poorly investigated glacial environment. Diversity of cave ice bacteria and their distribution in perennial ice deposits of this underground glacial habitat could constitute a proxy for microbial response to climatic and environmental changes. Scarisoara Ice Cave (Romania) hosts one of the oldest and largest cave ice blocks worldwide. Here we report on cultured microbial diversity of recent, 400, and 900 years-old perennial ice from this cave, representing the first characterization of a chronological distribution of cave-ice bacteria. Total cell density measured by SYBR Green I epifluorescence microscopy varied in the 2.4 x 104 – …
18s Rdna Dataset Profiling Microeukaryotic Populations Within Chicago Area Nearshore Waters,
2016
The Woodhall School
18s Rdna Dataset Profiling Microeukaryotic Populations Within Chicago Area Nearshore Waters, Daniel Searle, Emily Sible, Alexandria Cooper, Catherine Putonti
Bioinformatics Faculty Publications
Despite their critical role in the aquatic food web and nutrient cycling, microeukaryotes within freshwater environments are under-studied. Herein we present the first high-throughput molecular survey of microeukaryotes within Lake Michigan. Every two weeks from May 13 to August 5, 2014, we collected surface water samples from the nearshore waters of four Chicago area beaches: Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach. Four biological replicates were collected for each sampling date and location, resulting in 112 samples. Eighty-nine of these samples were surveyed through targeted sequencing of the V7 and V8 regions of the 18S rDNA gene. …
Microbial Biofilm Community Variation In Flowing Habitats: Potential Utility As Bioindicators Of Postmortem Submersion Intervals,
2016
University of Dayton
Microbial Biofilm Community Variation In Flowing Habitats: Potential Utility As Bioindicators Of Postmortem Submersion Intervals, Jennifer M. Lang, Racheal Erb, Jennifer L. Pechal, John R. Wallace, Ryan W. Mcewan, Mark Eric Benbow
Biology Faculty Publications
Biofilms are a ubiquitous formation of microbial communities found on surfaces in aqueous environments. These structures have been investigated as biomonitoring indicators for stream heath, and here were used for the potential use in forensic sciences. Biofilm successional development has been proposed as a method to determine the postmortem submersion interval (PMSI) of remains because there are no standard methods for estimating the PMSI and biofilms are ubiquitous in aquatic habitats. We sought to compare the development of epinecrotic (biofilms on Sus scrofa domesticus carcasses) and epilithic (biofilms on unglazed ceramic tiles) communities in two small streams using bacterial automated …
An Assessment Of West Virginia Watersheds Through The Use Of Geographic Information System (Gis),
2016
Marshall University, Huntington, W.Va.
An Assessment Of West Virginia Watersheds Through The Use Of Geographic Information System (Gis), Nathan Thomas Hoxie
Theses, Dissertations and Capstones
Analysis of West Virginia Department of Environmental Protection (WVDEP) agency’s Stream Condition Index and habitat assessment data compared two cycles of data. Geographic Information System (GIS) was used to develop a kriging model to project scores. Scores were calculated for Hydrologic Unit Code (HUC) eight and ten using Zonal statistics. The Getis-Ord Gi Star was used to identify high and low value clusters. Land use and impervious surface data was gathered from the United States Geological Survey (USGS) to assess impacts to watersheds. The results for WVSCI and habitat assessment showed that there was an improvement between cycles. Negative WVSCI …
Detection Of Fecal Contamination Using Molecular Methods,
2016
Augustana College, Rock Island Illinois
Detection Of Fecal Contamination Using Molecular Methods, Kristina K. Bowen
Independent Research Projects
This study explores the process of designing a molecular method to detect fecal contamination in the urban watersheds of Rock Island and Moline, Illinois. These urban watersheds are known to contain high ammonia levels and total dissolved solids based on previous studies. Additionally there is concern about the aging combined sewer and storm water system. Therefore, these watersheds are thought to have poor water quality including fecal contamination. Existing molecular methods used for detecting fecal contamination require a considerable amount of resources in the laboratory. Our goal was to design a molecular method that requires fewer resources and can continue …
Isolation And Identification Of Bacterial Endosymbionts In The Brooding Brittle Star Amphipholis Squamata,
2016
University of New Hampshire - Main Campus
Isolation And Identification Of Bacterial Endosymbionts In The Brooding Brittle Star Amphipholis Squamata, Abbey Rose Tedford
Honors Theses and Capstones
Symbiotic associations with subcuticular bacteria (SCB) have been identified and studied in numerous echinoderms, including the SCB of the brooding brittle star, Amphipholis squamata. These SCB, however, have not been studied using current next generation sequencing technologies. Previous studies on the SCB of A. squamata placed these bacteria in the genus Vibrio (γ-Proteobacteria), but subsequent studies suggested that the SCB are primarily composed of α-Proteobacteria. The present study examines the taxonomic composition of SCB associated with A. squamata from the Northwest Atlantic. DNA was extracted using a CTAB protocol and 16S rRNA sequences were amplified …
Enhancing The Industrial Potential Of Filamentous Cyanobacteria,
2016
South Dakota State University
Enhancing The Industrial Potential Of Filamentous Cyanobacteria, Tylor J. Johnson
Electronic Theses and Dissertations
The objectives of this project were to improve the industrial potential of filamentous N2-fixing cyanobacteria by increasing its biofuel tolerance, and to evaluate the economic feasibility and environmental impacts of a theoretical, cyanobacteria-based biofuel production facility. To develop a method to quantify filamentous cyanobacteria in dilute culture media, a dual-stained fluorescence assay was evaluated. While the viable cell stain (SYTO® 9) was accurate, the non-viable cell stain (propidium iodide) also bound to viable cells. Additional non-viable cell stains were evaluated, but none were accurate at quantifying viability. Thus we concluded that the viable cell stain SYTO® 9 is a reliable …
Endosymbiotic Bacteria In The Bed Bug, Cimex Lectularius L. (Hemiptera: Cimicidae),
2016
University of Kentucky
Endosymbiotic Bacteria In The Bed Bug, Cimex Lectularius L. (Hemiptera: Cimicidae), Mark H. Goodman
Theses and Dissertations--Entomology
The return of bed bugs to prominence as an urban pest has precipitated an emphatic research response from the scientific community in an effort to better understand their biology and management. However, not all aspects of bed bug biology have received equal attention. The role of symbiotic bacteria in the normal function and biology of insects is often underappreciated, and this is true of bed bugs. Bed bugs have two main endosymbiotic bacteria, a Wolbachia species and a poorly-characterized gamma-proteobacterium referred to as BLS. However, their interactions with the host are poorly understood. I explored various aspects of these symbionts …
Attached Algae As An Indicator Of Water Quality: A Study Of The Viability Of Genomic Taxonomic Methods,
2016
University of New Hampshire, Durham
Attached Algae As An Indicator Of Water Quality: A Study Of The Viability Of Genomic Taxonomic Methods, Allison R. Wood
Honors Theses and Capstones
This research involved evaluating algae as an indicator of water quality in New Hampshire's rivers, with a focus on the Great Bay Estuary. The project had three main goals. First, determining whether or not algae would work as an indicator of water quality in the great bay ecosystem, an environment where tidal currents are strong and water composition is mixed. The second goal was to compare traditional microscopic methods of taxonomy with emerging genomic methods, increasing the economic viability of attached algae monitoring. The third project goal, still underway, is to evaluate massive amounts of genomic data from the Great …
Effects Of Epichloë Coenophiala−Tall Fescue Symbiosis On Plant-Microbe-Soil Interactions In A Temperate Pasture,
2016
University of Kentucky
Effects Of Epichloë Coenophiala−Tall Fescue Symbiosis On Plant-Microbe-Soil Interactions In A Temperate Pasture, Lindsey C. Slaughter
Theses and Dissertations--Plant and Soil Sciences
Plants interact in myriad ways with microorganisms to influence ecosystem processes such as nutrient cycling, which can regulate ecosystem response to global change. One important plant-microbe symbiosis occurs between cool-season grasses and asexual fungal Epichloë endophytes, such as tall fescue (Schedonorus arundinaceus) and Epichloë coenophiala. Because the common toxic strain of the endophyte (CTE) harms grazing livestock, non-livestock toxic endophyte (NTE) strains have been developed and are increasingly deployed in pastures. Little is known about how these symbioses impact other plant-microbe interactions and microbe-mediated soil processes in grassland ecosystems. I conducted three studies to determine how E. …
Relationships Between Fecal Indicator Bacteria And Environmental Factors At Edgewater Beach,
2016
The University of Akron
Relationships Between Fecal Indicator Bacteria And Environmental Factors At Edgewater Beach, Anna M. King
Williams Honors College, Honors Research Projects
To provide more timely estimates of indicator bacteria concentrations in recreational waters, environmental agencies are using predictive models to supplement conventional bacteria enumeration methods. As a tool to develop predictive models, correlational relationships between variables can be examined, to determine the statistical significance of explanatory variables. Prior research at Lake Erie beaches suggests that environmental conditions such as average wave height, rainfall, turbidity, and water temperature may demonstrate a strong relationship to concentrations of fecal indicator bacteria Escherichia coli and Enterococcus faecalis (enterococci). These relationships were examined at Edgewater Beach in Cleveland, Ohio, using statistical correlation tests on data collected …
Sequence-Based Methods For Detecting And Evaluating The Human Gut Mycobiome,
2016
University of Nebraska-Lincoln
Sequence-Based Methods For Detecting And Evaluating The Human Gut Mycobiome, Mallory J. Suhr, Nabaraj Banjara, Heather E. Hallen-Adams
Department of Food Science and Technology: Faculty Publications
We surveyed the fungal microbiota in 16 fecal samples from healthy humans with a vegetarian diet. Fungi were identified using molecular cloning, 454 pyrosequencing and a Luminex analyte specific reagent (ASR) assay, all targeting the ITS region of the rRNA genes. Fungi were detected in each fecal sample and at least 46 distinct fungal operational taxonomic units (OTUs) were detected, from two phyla — Ascomycota and Basidiomycota. Fusarium was the most abundant genus, followed by Malassezia, Penicillium, Aspergillus, and Candida. Commonly detected fungi such as Aspergillus and Penicillium, as well as known dietary fungi Agaricus bisporus and …
Noninvasive Measurement Of Electrical Events Associated With A Single Chlorovirus Infection Of A Microalgal Cell,
2016
University of Nebraska–Lincoln
Noninvasive Measurement Of Electrical Events Associated With A Single Chlorovirus Infection Of A Microalgal Cell, Seung-Woo Lee, Eun-Hee Lee, Gerhard Thiel, James L. Van Etten, Ravi Saraf
Department of Chemical and Biomolecular Engineering: Faculty Publications
Chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1) contains a viral-encoded K+ channel imbedded in its internal membrane, which triggers host plasma membrane depolarization during virus infection. This early stage of infection was monitored at high resolution by recording the cell membrane depolarization of a single Chlorella cell during infection by a single PBCV-1 particle. The measurement was achieved by depositing the cells onto a network of one-dimensional necklaces of Au nanoparticles, which spanned two electrodes 70 μm apart. The nanoparticle necklace array has been shown to behave as a single-electron device at room temperature. The resulting electrochemical field-effect transistor …
Killer Toxin From Several Food-Derived Debaryomyces Hansenii Strains Effective Against Pathogenic Candida Yeasts,
2016
University of Nebraska-Lincoln
Killer Toxin From Several Food-Derived Debaryomyces Hansenii Strains Effective Against Pathogenic Candida Yeasts, Nabaraj Banjara, Kenneth Nickerson, Mallory J. Suhr, Heather E. Hallen-Adams
Kenneth Nickerson Papers
Candida yeasts are the dominant fungi in the healthy human microbiome, but are well-known for causing disease following a variety of perturbations. Evaluation of fungal populations from the healthy human gut revealed a significant negative correlation between the foodborne yeast, Debaryomyces hansenii, and Candida species. D. hansenii is reported to produce killer toxins (mycocins) effective against other yeast species. In order to better understand this phenomenon, a collection of 42 D. hansenii isolates was obtained from 22 cheeses and evaluated for killer activity against Candida albicans and Candida tropicalis over a range of temperatures and pH values. Twenty three …
The Impact Of Urbanization On Mosquito-Borne Viruses,
2016
Virginia Commonwealth University
The Impact Of Urbanization On Mosquito-Borne Viruses, Nikhita Puthuveetil
Undergraduate Research Posters
Mosquito-borne diseases such as yellow fever, dengue, and West Nile are rapidly emerging across the globe. Their emergence is often aided by the growth of their vector population, or the organisms that transmit the virus to the host. Urbanization and land use often destroys the habitat of the virus and its vector. However, the virus and its vector often survive despite the changes to its environment. The goal of this paper is to find out exactly how urbanization and changes in land use affect mosquito-borne viruses and how these viruses survive despite the destruction of their habitats. To understand how …
Toxicity Of Engineered Nanomaterials To Plant Growth Promoting Rhizobacteria,
2016
University of Kentucky
Toxicity Of Engineered Nanomaterials To Plant Growth Promoting Rhizobacteria, Ricky W. Lewis
Theses and Dissertations--Plant and Soil Sciences
Engineered nanomaterials (ENMs) have become ubiquitous in consumer products and industrial applications, and consequently the environment. Much of the environmentally released ENMs are expected to enter terrestrial ecosystems via land application of nano-enriched biosolids to agricultural fields. Among the organisms most likely to encounter nano-enriched biosolids are the key soil bacteria known as plant growth promoting rhizobacteria (PGPR). I reviewed what is known concerning the toxicological effects of ENMs to PGPR and observed the need for high-throughput methods to evaluate lethal and sublethal toxic responses of aerobic microbes. I addressed this issue by developing high-throughput microplate assays which allowed me …
Tillage And Fertilization Influences On Autotrophic Nitrifiers In Agricultural Soil,
2016
University of Kentucky
Tillage And Fertilization Influences On Autotrophic Nitrifiers In Agricultural Soil, Shuang Liu
Theses and Dissertations--Plant and Soil Sciences
Nitrification is a biological oxidation of NH3 to NO2- and then to NO3-. Understanding how the nitrifier community responds to agricultural management is essential because the community composition is complex and functional distinction of subgroups occurs. Better managing nitrifiers could benefit the environment by increasing nitrogen (N) fertilizer use efficiency, decreasing NO3- leaching, and reducing NO and N2O emissions. This study examined how long-term N fertilization and tillage influenced nitrifier density, ratios, nitrification rates, and the community structure of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and nitrite-oxidizing bacteria (NOB). The …
Studies On Regulation Of Pqq-Dependent Phosphate Solubilization Among Rhizosphere Dwelling Bacteria,
2016
University of Kentucky
Studies On Regulation Of Pqq-Dependent Phosphate Solubilization Among Rhizosphere Dwelling Bacteria, Ran An
Theses and Dissertations--Plant and Soil Sciences
Plant growth promotion can be enhanced by soil- and rhizosphere-dwelling bacteria by a several different methods. One method is by promoting nutrient acquisition from soil. Phosphorus is an essential nutrient that plants obtain from soil, but in many cases it is immobilized in forms that are not available for plant uptake. Bacteria can solubilize insoluble soil phosphates by secreting gluconic acid. This chemical is produced from glucose by the activity of the bacterial enzyme glucose dehydrogenase, which requires a coenzyme called PQQ. In this dissertation, I studied the regulation of the glucose dehydrogenase enzyme and the PQQ coenzyme in the …
Diversity Of Free-Living Nitrogen Fixing Bacteria In The Badlands Of South Dakota,
2016
South Dakota State University
Diversity Of Free-Living Nitrogen Fixing Bacteria In The Badlands Of South Dakota, Bibha Dahal
Electronic Theses and Dissertations
Biological Nitrogen Fixation is carried out by a highly diverse group of members of the domains Bacteria and Archaea which express a nitrogenase enzyme complex and are termed diazotrophs. The best known diazotrophs form symbiotic associations with plants, but free-living nitrogen fixing bacteria also contribute a substantial amount of nitrogen to ecosystems, including arid lands. The aim of this study was to isolate free-living diazotrophs from the soil crusts of sod tables of South Dakota Badlands. Samples were obtained from sod tables and the surrounding base (matrix) in spring and fall of 2014. A culture dependent approach was used to …
