Biology Commons^™

Pcb Remediation In Transitional Floodplain Forests Along The Housatonic River, Soleil Laurin

Scripps Senior Theses

Human development affects natural environments in more ways than climate change, from the introduction of nonnative species and deforestation to pollution and urbanization. This is a case study examining the effects of PCB remediation on transitional floodplain forest along the Housatonic River in Western Massachusetts. The Housatonic River had previously been contaminated with PCBs and portions had been remediated. This study aims to determine the effects this remediation had on transitional floodplain forests, as well as provide a preliminary biodiversity assessment for sites that are planned to be remediated of PCBs by the Environmental Protection Agency. The study was carried …

Genetic Diversity Of Paxistima Canbyi A. Gray: Conserving A Rare Plant Species Endemic To The Eastern United States, Isaac Buabeng

Master’s Theses

Premise: The glacial cycles of the Pleistocene period likely had a profound impact on the genetic diversity and phylogeographic patterns of numerous plant taxa in North America. However, the genetic diversity of rare, limestone-endemic woody species has not been highlighted. This study assesses genetic diversity in Paxistima canbyi A. Gray (Canby’s mountain lover or rat stripper), a rare limestone endemic small woody plant.

Methods: We investigated the genetic diversity of P. canbyi using genomic Single Nucleotide Polymorphism (SNP) data from 165 individuals from 14 populations sampled from across the entire range distribution. We first; de novo assembled the SNP …

Response Of Helenium Amarum To Environmental Stressors In The Presence Of Mycorrhizal Fungi And Its Role As A Pollinator Resource, Austin Jameson, Lisa Horth

Biological Sciences Faculty Publications

Globally, climate change is causing shifts in precipitation patterns. Shifting precipitation patterns can be a stressor for many species. One species that is experiencing such stress is Helenium amarum Raf (H. Rock). H. amarum, thrives in dry upland pastures and low-lying grassy and sandy habitat in the mid-Atlantic (USA), where it persists despite storm-driven standing water. Helenium amarum is a species that is toxic to livestock and has been found outside its native range. Temperature and light impacts on germination are already known, but the role of water availability and potential ameliorating effects of mycorrhizae during water stress have …

Environmental Implications Of Modern Food Production: An Analysis For The Conscious Consumer, Jessica T. Coming

Cal Poly Humboldt theses and projects

This project explores the pathways by which agriculture affects the environment and determines which foods have the greatest climate, water, and land impacts. Agricultural effects on the environment are extensive, from loss of habitat and declines in regional biodiversity to disruption of global nutrient cycles and climate change. Global food production accounts for 26-34% of annual anthropogenic greenhouse gas emissions, makes up 38-46% of habitable land, and is responsible for 70% of freshwater extraction. The effect of agriculture on the environment is most significantly dictated by what type of food is being produced. Animal-based food products consistently have the highest …

South America Holds The Greatest Diversity Of Native Daisies (Asteraceae) In The World: An Updated Catalogue Supporting Continental-Scale Conservation, Andrés Moreira-Muñoz, Marcelo Monge, Mariana A. Grossi, Fabio Andrés Ávila, Vanezza Morales-Fierro, Gustavo Heiden, Berni Britto, Stephan Beck, Jimi N. Nakajima, Vanina G. Salgado, Juan Facundo Rodríguez-Cravero, Diego G. Gutiérrez

Publications and Research

Asteraceae is the world’s richest plant family and is found on all continents, in environments ranging from the coast to the highest mountains. The family shows all growth forms and, as in other angiosperm families, species richness is concentrated in tropical regions. South America has the highest diversity of Asteraceae in the world, yet taxonomic and distributional knowledge gaps remain. This study compiles an updated catalog of Asteraceae native to South America, based on national and regional checklists and ongoing large-scale flora projects. The resulting checklist includes a total of 6,940 species and 564 genera native to South America to …

Quantifying The Ecological Effects Of Salix Fragilis On Riparian Habitat In Kittitas County, Washington, Landon Shaffer

All Master's Theses

Invasive species threaten plant community structure and function globally. Riparian areas, the zone near streams where water influences vegetation, are especially sensitive to invasive species colonization, suffering large-scale shifts in community composition. Salix fragilis (crack willow) is a nonnative riparian species abundant in the lower elevation tributaries of central Washington. Some speculate whether this willow should be listed as invasive in Washington, despite a lack of regional supporting evidence. I studied riparian communities dominated by either S. fragilis or native species in the Kittitas Valley and measured biodiversity, quantified differences in solar attenuation, and compared leaf decomposition rates to learn …

Interactions Between New Zealand Mud Snails (Potamopyrgus Antipodarum) And Toxic Cyanoabacteria (Anabaena) In Baduwa’T (Mad River), Humboldt County, California, Cecilia F. Kennelly

Cal Poly Humboldt theses and projects

Invasive species in freshwater systems are circulated around the globe, wreaking havoc on natural communities. The New Zealand mud snail (Potamopyrgus antipodarum) is a very successful aquatic invader that has established populations in freshwater streams, lakes, and rivers around the globe. The goal of this project was to evaluate the interactions of invasive New Zealand mud snails (NZMS) and toxic cyanobacteria Anabaena in the Mad River in Humboldt County, California. These two species of concern are found in similar habitats along the river, but their whether NZMS consume Anabaena or affect toxin production is unknown. First, I conducted …

A Taxonomic Revision Of The Genus Hydnora (Hydnoraceae), Sebastian A. Hatt, Chris J. Thorogood, J. F. Bolin, Lytton J. Musselman, Duncan D. Cameron, Olwen M. Grace

Biological Sciences Faculty Publications

A systematic monograph is presented for Hydnora (Hydnoraceae), a poorly known genus of holoparasitic plants distributed across Africa, Madagascar and southern Arabia. Species of Hydnora are characterised by their underground habit, unusual fleshy flowers and complete absence of leaves or photosynthetic tissue. This is the first detailed monograph of the genus Hydnora since 1935 and is informed by a comprehensive survey of herbarium specimens and literature. Detailed descriptions, full synonymy, distribution maps and discussion concerning confusable taxa are provided for each species, along with notes on ethnobotany, ecology and conservation. We place particular emphasis on the taxonomic value of osmophore …

Facilitative And Competitive Interactions Among Dune Grass Species In Monoculture And Polyculture Communities, Anne M. Sciolino

Theses and Dissertations

Coastal dunes are natural barriers between land and sea and are imperative to the protection and preservation of inland ecosystems and human infrastructure. However, due to global warming, seal level rise, and coastal development, coastal dunes are under constant threat of destruction. Restoration efforts have been implemented to rebuild the protective function of dunes through the planting of dune building grasses. Dune grasses build and maintain these vital sand dunes. However, little is known about facilitative and competitive relationships among the grasses. In order to maximize restoration efforts, research is needed to better understand the biotic interactions among restorative grass …

Characterizing The Targeting Pathway Of Chloroplast Outer Membrane Protein Oep18 In Arabidopsis Thaliana And Other Targeting Signals Utilized By Outer Envelope Membrane Proteins, Ceaira Hiemstra

Theses and Dissertations (Comprehensive)

Approximately 95% of chloroplast proteins are encoded by nuclear DNA and are post-translationally targeted to the chloroplast. Over half of the 138 known or predicted chloroplast outer membrane (OM) proteins are predicted to utilize four non-canonical targeting pathways. The first two pathways are characterized by containing a single α-helical transmembrane domain (TMD) within the first or last 50 amino acids (AAs), the third pathway is utilized by β-barrels, and the last requires an N-terminal cleavable transit peptide (TP). Recently, a fifth novel pathway called Toc159-like (TOC159L) has been characterized by the presence of a C-terminal reverse TP in Toc159. Subsequent …

Investigating Changing Macronutrient Dynamics At A Plant, Microbe And Plant-Microbe Interactions Scale, Emel Kangi

Graduate Theses, Dissertations, and Problem Reports (ETD)

Nutrient limitation drives forest ecosystem processes by altering net primary production, belowground (C) investments, and microbial activity. As such, the availability of essential macronutrients, such as nitrogen (N) and phosphorus (P), can severely impact plant growth, microbial decomposition, and the strength of plant-microbial interactions. However, our understanding of plant and microbe responses to changing nutrient availability, and the extent to which nutrient availability affects plant-microbe interactions, remains somewhat limited. Therefore, in this dissertation, I aimed to investigate nutrient limitation on a plant, microbe, and plant-microbe interaction level. First, to connect the phenotypic responses of nutrient-limited plants to key molecular mechanisms, …

Building Better Biofuel Crops: A Field Evaluation Of Transgenic Populus Modified To Improve Feedstock Performance For Bioenergy Use, Molli Elisabeth Coombs

Graduate Theses, Dissertations, and Problem Reports (ETD)

A transition away from fossil fuel use is necessary for the future of energy production, and biofuels are a renewable energy option that can mitigate the impacts of fossil fuels through lowered carbon emissions and possible carbon sequestration. In order to successfully compete with fossil fuels, the production of biofuels must be sustainable and cost effective. Populus species are a biofuel crop used for bioenergy conversion from lignocellulosic biomass that have been proposed for use in feedstock plantations on marginal lands, which would avoid competition with agricultural production. Two challenges of feedstock production being faced are recalcitrance to chemical processing, …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Habitat And Demography Of The Ozark Chinquapin (Castanea Ozarkensis) At Roaring River State Park In Barry County, Missouri, Danielle Evilsizor

Electronic Theses & Dissertations

The Ozark chinquapin, Castanea ozarkensis Ashe, is a chestnut tree with a range concentrated in the Interior Highlands of North America. Like other North American members of Castanea, it was reduced from an overstory tree to an understory shrub by the invasive chestnut blight fungus (Cryphonectria parasitica [Murrill] M.E. Barr) during the early 20^th century. However, relatively little is known about the habitat of this species or its health and reproductive capability post chestnut blight. Chapter one of this study analyzed the habitat of this species through a random forest species distribution model (SDM) to predict where …

P-Ring: The Conserved Nature Of Phosphorus Enriched Cells In Seedling Roots Of Distantly Related Species, Aniruddha Acharya, Thomas C. Pesacreta

Faculty Publications - Biological Sciences

Plants require sunlight, carbon dioxide, water and mineral ions for their growth and development. Roots in vascular plants sequester water and ions from soil and transport them to the aboveground parts of the plant. Due to heterogeneous nature of soil, roots have evolved several regulatory barriers from molecular to organismic level that selectively allows certain ions to enter the vascular tissues for transport according to the physiological and metabolic demands of plant cell. Current literature profusely elaborates about apoplastic barriers, but the possibility of the existence of a symplastic regulation through phosphorous-enriched cells has not been mentioned. Recent investigations on …

Impacts Of Disturbance And Nutrient Addition On Coastal Dune Arthropod Communities, Kayla Beitzel

Honors Theses

Coastal dune ecosystems are globally distributed ecosystems that occur from the tropics to the poles and serve as the first line of defense during storms. They are critical habitats for a variety of organisms and also play a critical role in stabilizing coastal habitats. These systems face increased pressure via urban development, recreational expansion, and sea-level rise (Newman et al. 2023; Webster et al. 2005). Insects are vital consumers in coastal ecosystems and act as regulators of plant growth. Low-diversity ecosystems, like coastal dune systems, often contain a higher abundance of low-diverse insect consumers (Ripple et al. 2021), which can …

Evaluating Habitat Use By Nekton In Widgeon Grass (Ruppia Maritima), Shoal Grass (Halodule Wrightii), And Unvegetated Bottom Habitats In The Grand Bay National Estuarine Research Reserve, Jessica Woodall

Master's Theses

Seagrass beds support high biodiversity and animal abundance, serve as feeding grounds for a variety of animals, offer shelter from predation, and act as a nursery habitat for juveniles. The species composition of seagrass beds can impact their use as habitat by animals. Two common species of seagrass in the Gulf of Mexico are Ruppia maritima (widgeon grass) and Halodule wrightii (shoal grass). The shallow coastal waters of the Grand Bay National Estuarine Research Reserve (NERR) support both species, but the use of each seagrass as habitat by nekton is poorly understood, which can limit management decision-making. Nekton communities were …

Quantifying The Role Of Water Quality On Nitrogen Cycling In A Trophic Estuary, Kayla Gonzalez-Boy

Symposium of Student Scholars

Jobos Bay Estuary is an intertidal, tropical estuary located in southern Puerto Rico. The estuary covers about 12 km² and has a variety of habitats, such as seagrass beds, mangroves, mud flats, and coral reefs, which play important roles in sediment trapping and water quality maintenance. Seagrasses also serve as nursery and feeding grounds and provide shelter for macrofauna. Currently, the role of seagrasses and water quality on nitrogen (N) cycling in trophic estuaries is not well constrained. Understanding variations in sediment-based effects on N cycling rates and transformations, and how they are associated with water quality, is an …

Mimicking Biofilms: Photosynthetic Assessments Of C. Reinhardtii In 3 Physical Forms, John Michael Roesgen

Biology ETDs

Oxygenic photosynthesis supports the majority of life on Earth through the capture of energy from sunlight and the assimilation of CO₂ into basic building blocks of cells. Microalgae are fast growing and account for about half of global photosynthesis. In addition, they can be cultivated and their metabolism can be redirected to generate additional useful products ranging from biofuels to pharmaceuticals. However, the efficiency of metabolite production is severely impacted by the slow diffusion of CO₂ through water and the high energetic costs of harvesting microalgae from liquid cultures. Microalgae grow in open water, but they also form …

The Evolutionary Responses Of Life-History Strategies To Climatic Variability In Flowering Plants, James Boyko, Eric R. Hagen, Jeremy M. Beaulieu, Thais Vasconcelos

Biological Sciences Faculty Publications and Presentations

• The evolution of annual or perennial strategies in flowering plants likely depends on a broad array of temperature and precipitation variables. Previous documented climate life-history correlations in explicit phylogenetic frameworks have been limited to certain clades and geographic regions.
• To gain insights which generalize to multiple lineages we employ a multi-clade approach analyzing 32 groups of angiosperms across eight climatic variables. We utilize a recently developed method that accounts for the joint evolution of continuous and discrete traits to evaluate two hypotheses: annuals tend to evolve in highly seasonal regions prone to extreme heat and drought; and annuals tend to …

Multiple Light Signaling Pathways Control Solar Tracking In Sunflowers, Christopher J. Brooks, Hagop S. Atamian, Stacey L. Harmer

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Sunflowers are famous for their ability to track the sun throughout the day and then reorient at night to face east the following morning. This occurs by differential growth patterns, with the east sides of stems growing more during the day and the west sides of stems growing more at night. This process, termed heliotropism, is generally believed to be a specialized form of phototropism; however, the underlying mechanism is unknown. To better understand heliotropism, we compared gene expression patterns in plants undergoing phototropism in a controlled environment and in plants initiating and maintaining heliotropic growth in the field. We …

Potentially Adaptive Significance Of Genome Size Diversity Across Ecological Gradients And Seed Size In Ivesia (Rosaceae), Israel T. Borokini, Shaun R. Broderick, Zhi Gao, Joshua M. Hallas, James A. Birchler, Mary M. Peacock

Western North American Naturalist

Variation in genome size across taxa has been explained using neutral and nonadaptive theories; however, genome size variation among taxonomic groups can also be shaped by natural selection if it correlates with functional traits. This study investigated the potential adaptive significance of genome size in Ivesia, a radiating genus distributed in the western North American desert ecosystems. We estimated the genome size of 34 taxa (including 31 Ivesia taxa, 2 Potentilla taxa, and 1 Horkelia taxon) using flow cytometric methods. For each taxon, leaf samples were collected from 6 individuals in 1 location each; intraspecific genome size variation was …

Genome-Wide Association Study And Genomic Prediction Of Fusarium Wilt Resistance In Common Bean Core Collection, Kenani Chiwina, Haizheng Xiong, Gehendra Bhattarai, Ryan Dickson, Theresa Makawa Phiri, Yilin Chen, Ibtisam Alatawi, Derek Dean, Neelendra K. Joshi, Yuyan Chen, Awais Riaz, Paul Gepts, Mark Brick, Patrick Byrne, Howard Schwartz, James B. Ogg, Kristen Otto, Amy Fall, Jeremy Gilbert, Ainong Shi

Horticulture Faculty Publications and Presentations

The common bean (Phaseolus vulgaris L.) is a globally cultivated leguminous crop. Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. phaseoli (Fop), is a significant disease leading to substantial yield loss in common beans. Disease-resistant cultivars are recommended to counteract this. The objective of this investigation was to identify single nucleotide polymorphism (SNP) markers associated with FW resistance and to pinpoint potential resistant common bean accessions within a core collection, utilizing a panel of 157 accessions through the Genome-wide association study (GWAS) approach with TASSEL 5 and GAPIT 3. Phenotypes for Fop race 1 and race …

Lichens Of Iller Creek: A Checklist For The Iller Creek Unit, A Division Of Dishman Hills Conservation Area, Spokane Valley, Wa, Devin M. Mumey, Giovanna Bishop, Jessica L. Allen

2023 Symposium

The field of biodiversity documentation encompasses a broad range of research including new species discovery and description, compilation of species present in a given area, and investigation of interspecies interaction. In an era of increasingly devastating and rapid environmental change, documenting biodiversity has become increasingly important. Anthropogenic effects on urban-adjacent natural areas are especially significant, as they can cause numerous, often drastic, responses in ecosystems. Our objective here was to document the lichen biodiversity in a large urban-adjacent protected area: the Iller Creek Unit of the Dishman Hills Conservation Area in Spokane Valley, Washington. This unit encompasses a diversity of …

Structural Basis Of Signal Transduction Within Environmental Sensing Pas Regulated Ser/Thr Kinases, Roksana Azad

Dissertations, Theses, and Capstone Projects

To sense environmental cues, nature has evolved molecular switches that are widely used across life. This process often relies on environmentally controlled PPIs (Protein-Protein Interactions) within a sensory domain that senses various stimuli and alters the functional activities of downstream effectors. This study focused on the superfamily of PAS (Per-ARNT-Sim) environmental sensory domains and their roles in regulating two Ser/Thr Kinases (STKs). PAS domains achieve their regulatory control by internally binding small molecule ligands/cofactors (e.g., O₂ binding to heme …

Effects Of Measurement Methods And Growing Conditions On Phenotypic Expression Of Photosynthesis In Seven Diverse Rice Genotypes, Megan Reavis, Larry C. Purcell, Andy Pereira, Kusum Naithani

Biological Sciences Faculty Publications and Presentations

Introduction: Light response curves are widely used to quantify phenotypic expression of photosynthesis by measuring a single sample and sequentially altering light intensity within a chamber (sequential method) or by measuring different samples that are each acclimated to a different light level (non-sequential method). Both methods are often conducted in controlled environments to achieve steady-state results, and neither method involves equilibrating the entire plant to the specific light level.

Methods: Here, we compare sequential and non-sequential methods in controlled (greenhouse), semi-controlled (plant grown in growth chamber and acclimated to field conditions 2-3 days before measurements), and field environments. We selected …

How Plants Cope With Stress, Nabila Riaz

Dartmouth College Ph.D Dissertations

Iron (Fe) is one of the essential micronutrients required by both plants and animals. In humans, Fe deficiency causes anemia, the most prevalent nutritional disorder in the world today. Most people rely on plant-based foods as their major Fe source, but plants are a poor source of dietary Fe.

Fe deficiency has many adverse effects on photosynthesis, which is not surprising given that 95% of foliar Fe is found in chloroplast. The Gueirnot lab had previously showed that the bHLH transcription factors ILR3 and PYE are required for photoprotection during Fe deficiency by preventing ROS damage to photosystem II (PSII). …

Isolation Of Arabidopsis Thaliana Plants Homozygous For An Insertional Inactivation Mutation Within Atprp4., Sydney Raitz, Timothy D. Trott

Research in Biology

The AtPRP4 gene in Arabidopsis thaliana has been shown to function in several specific parts of the plant’s cell wall. It is shown to be expressed in the seeds, radicles, roots, leaves, inflorescences, and embryos of Arabidopsis thaliana. These patterns have suggested unique functions for ATPRP4 in determining cell-type-specific wall structure during the development of a plant as well as contributing to defense reactions against physical damage to the plant and pathogen infection within the plant. In this study, a simple DNA prep was performed on the true leaves of Arabidopsis thaliana. Subsequent PCR reactions were performed using …

Examining The Restoration Potential Of Prescribed Fire And Tree Girdling Treatments On A Fire Dependent Ecosystem: Ecosystem Responses And Management Implications, Rebecca Daigle

Masters Theses

Oak savannas have greatly declined since the 1800s and management is needed to maintain these rare community types. A combination of prescribed burns and mechanical thinning are a common practice to increase forb abundance and biodiversity. This study examines the viability of another technique to thin the canopy called girdling, which was used in conjunction with low-intensity prescribed burns. Early summer prescribed burns were conducted in 2017, 2019, and 2021, while girdling treatments were implemented in 2017 and 2019. The study was conducted in Kent County, Michigan at two degraded former oak savanna communities. In 2022, we collected data to …

Investigating The Role Of Plant Traits And Interactions In Emergent Wetland Nutrient Removal, Andrew Ryan Sample

Theses and Dissertations

Increasing wetland restoration in the Lower Mississippi Alluvial Valley has been identified as a method to reduce nutrient loading in the Gulf of Mexico. Wetlands have historically been used to treat water through processes facilitated by wetland plants, and relatively few species and plant traits have been identified as important in carrying out these processes. This study focuses on some of those species and traits and aims to identify species differences and plant traits that may be important for wetland nutrient mitigation. Chapter I provides background information on nutrient pollution, wetland biogeochemical mechanisms for nutrient sequestration, and the focal species …