Biology Commons^™

Leveraging Herbaria Specimens: A New 3d Imaging Protocol And Analyses Of Diversity Of West Virginia Rosids, Zachary Scott Shamblin

Theses, Dissertations and Capstones

Herbaria are repositories of plant natural history, whose data can provide insights into the life histories of plant taxa over space and time. Recent initiatives to digitize herbarium data have made studies over broad geographic and taxonomic extents possible, with the ability of scientists to access data from large databases of herbaria. Most of the digitization initiatives have focused on flat 2D herbaria sheets, but herbaria also include 3D collections, such as fungi, mosses, lichens, and dry fruits. In Chapter 1 we propose an easy and cost-effective workflow that uses free photogrammetry software to produce 3D images of 3D herbaria …

The Future Of The Big Sagebrush Ecosystem: Plant Community Response To Grazing, Wildfire, And Invasive Annual Grass In A Changing Climate, Margaret Eleanor England

Theses, Dissertations and Capstones

Climate change is increasingly affecting the plant communities across the world. In the Western United States, these changes are affecting plant communities and their risk of invasive species, as well as the frequency and severity of wildfire. Big sagebrush (Artemisia tridentata Nutt.) ecosystems of the Western United States are facing threats of increasingly frequent wildfire and invasion of the annual grass cheatgrass (Bromus tectorum L.), which may be exacerbated by global climate change. Past studies have found cheatgrass to exhibit a positive feedback loop with wildfire, and climate change is expected to facilitate expansion of the cheatgrass …

Assessment Of The Negative Role Amur Honeysuckle Has On Urban Forest Diversity, Hayley Schlabowske, Paige Lundborg, Jason Koontz, Michael Reisner

Independent Research Projects

Lonicera maackii (Amur Honeysuckle), an invasive shrub species, has out-competed native species in urban riparian zones for decades due to its ability to receive more sunlight and it also secretes an allelochemical from its leaves that negatively impacts the ecosystems. Our research question is how does Lonicera maackii affect native plant species in the herbaceous understory? Five forest communities were sampled in Northwest Illinois. Sites were separated into four different categories with L. maackii only, Garlic Mustard (Alliaria petiolata) only, Neither invasive species, and sites where both occur. There were 12 sites for each of the four categories resulting in …

Software Choice And Sequencing Coverage Can Impact Plastid Genome Assembly–A Case Study In The Narrow Endemic Calligonum Bakuense, Eka Giorgashvili, Katja Reichel, Calvinna Caswara, Vuqar Kerimov, Thomas Borsch, Michael Gruenstaeudl

Biological Sciences Faculty Publications

Most plastid genome sequences are assembled from short-read whole-genome sequencing data, yet the impact that sequencing coverage and the choice of assembly software can have on the accuracy of the resulting assemblies is poorly understood. In this study, we test the impact of both factors on plastid genome assembly in the threatened and rare endemic shrub Calligonum bakuense. We aim to characterize the differences across plastid genome assemblies generated by different assembly software tools and levels of sequencing coverage and to determine if these differences are large enough to affect the phylogenetic position inferred for C. bakuense compared to congeners. …

Environmental Gradients Impact Key Leaf Traits In Riparian Trees, Amanda Malone

Electronic Theses and Dissertations

Specific leaf area (SLA) reflects a plant’s carbon investment per area and relates to generalized leaf economics spectrum growth strategies (LES). To fill gaps of knowledge about intraspecific SLA variation and why it is often inconsistent with the LES, we studied the response of two riparian tree species along the urban-rural gradient in Northeastern Colorado: an invasive, nitrogen-fixer with broad tolerances and a nitrogen-limited and shade-intolerant native. Despite these differences, the two species responded similarly, apart from the response to the urban-rural gradient, in which lower nitrogen in rural areas was associated with a more conservative strategy in the native …

Cbp60-Db: An Alphafold-Predicted Plant Kingdom-Wide Database Of The Calmodulin-Binding Protein 60 (Cbp60) Protein Family With A Novel Structural Clustering Algorithm, Keaun Amani, Vanessa Shivnauth, Christian Castroverde

Biology Faculty Publications

Molecular genetic analyses in the model species Arabidopsis thaliana have demonstrated the major roles of different CAM-BINDING PROTEIN 60 (CBP60) proteins in growth, stress signaling, and immune responses. Prominently, CBP60g and SARD1 are paralogous CBP60 transcription factors that regulate numerous components of the immune system, such as cell surface and intracellular immune receptors, MAP kinases, WRKY transcription factors, and biosynthetic enzymes for immunity-activating metabolites salicylic acid (SA) and N-hydroxypipecolic acid (NHP). However, their function, regulation and diversification in most species remain unclear. Here we have created CBP60-DB, a structural and bioinformatic database that comprehensively characterized 1052 CBP60 gene homologs …

Ms Environmental Biology Capstone Project, Dylan Brown

Regis University Student Publications (comprehensive collection)

Chapter 1- Revisiting Tamarisk Invasion in Riparian Ecosystems: An Argument Against Single Species Management of the Southwestern Willow Flycatcher (Empidonax traillii extimus)

Chapter 2- Temporal Trends of Tamarisk Remediation to Native Vegetation Establishment

Chapter 3- Assessing Effectiveness of Tamarisk Removal Treatments Through a Meta Regression Analysis

Chapter 4- Legal Challenges of Tamarisk Removal in the Southwestern United States

Sulfated Flavonoids In The Asteraceae, Alyssa Rice

Senior Honors Projects

Gypsum soils are a unique soil type with high levels of calcium and sulfur, which creates a harsh living environment for plants. To survive these conditions, plants have evolved a suite of mechanisms to survive these excess minerals, such as sulfur. In this study we aimed to determine if gypsum status was related to sulfated flavonoid production in plants of the Asteraceae. Flower and leaf tissues were collected from herbarium specimens representing gypsophiles, gypsovags, and gypsofuges. These tissues were analyzed for the presence of sulfated flavonoids using Thin Layer Chromatography (TLC). We observed sulfated flavonoid production in leaf and flower …

Dr. Laurie L. Consaul Herbarium (Uwo), Lauren H. Rego

Community Engaged Learning Final Projects

Along with the provided databased species, students scanned 257 specimens within the physical herbarium at Wester.

Bioprospecting For Improved Floral Fragrance In Wild Sunflower, Jason Anandappa

Honors Undergraduate Theses

The cultivation of crop sunflower or Helianthus annuus is a 20 billion USD industry globally. Crop wild relatives of H. annuus have a long history of being used to breed improved traits into cultivated varieties. Cultivated H. annuus is not known to have a pleasant aroma, and at times seed yield is limited by pollination services, particularly in the production of hybrid seed. Improved floral fragrance could improve pollinator attraction and would add value to ornamental sunflowers in the context of the cut-flower industry. If volatile organic compounds that together generate favorable scents are present in wild Helianthus species, they …

Investigating The Phytochemical Profiles Of Wild And Cultivated Blueberries (Vaccinium Spp.) In Central Florida, Anisa Khalid

Honors Undergraduate Theses

Blueberries (Vaccinium spp.) are valued for their high nutritional quality and flavor. There are five species in the Vaccinium genus native to the state of Florida, but only three are palatable to humans: V. myrsinites, V. darrowii, and V. corymbosum. While V. darrowii has been studied extensively due to its successful hybridization with northern highbush blueberry cultivars, V. myrsinites and wild V. corymbosum have been understudied. This study aims to 1) quantify the abundance of various phytochemicals in fruits of these wild blueberry species and compare fruit quality both among the wild taxa and two varieties of …

West Virginia Herbaria: Status, Updates, And Plans, Pamela Puppo, Katharine Gregg, Donna Ford-Werntz, James Vanderhorst, Michelle Mabry, Jeremy Keene

Biological Sciences Faculty Research

The West Virginia (U.S.A.) Herbarium Curators met on December 1st, 2021, with the intent of sharing updates on the collections, fostering collaboration, learning from each other's experiences, and identifying priorities for the collections towards the future. This article presents a summary of the herbaria that were represented in this meeting.

Modeling Jadera Haematoloma’S Phenotypic Variation In The Context Of Its Developmental Plasticity, Michael C. Yorsz

Honors Theses

Phenotypic plasticity is the ability of an organism to integrate information from environmental cues to inform the development of its phenotype and remains understudied in biology. Models of plasticity are needed because evolution in the presence of plasticity is poorly understood. Jadera haematoloma, a hemimetabolous true bug, is an excellent animal model of plasticity, exhibiting a non-linear plastic response to juvenile nutrition that biases adult development into groups with differences in flight capability, wing shape, and fecundity. However, there is a lack of literature consensus regarding the range of developmental outcomes in the species. Some publications report the presence …

Healing Sanctuary, Kammy Downs

Master's Theses or Doctor of Nursing Practice

The natural world has hidden wisdom and resources that are disregarded as we misuse our responsibility to care for them. The benefits of being in tune with nature have been traded for a culture that manipulates nature on the altar of expediency, waste, and unquenchable desire. Healing Sanctuary presents a duality. My work speaks about the relationship between the seen and unseen, represented by ten larger-than-life drawings of medicinal herbal plants that have had a profound physical healing effect on me. At the same time, plants, roots, and seeds create visceral metaphors for mental health. Our accomplishments, outlook on life, …

A Flora Of Coyote Ridge And Flat, Inyo County, California, Martin Purdy

CGU Theses & Dissertations

California’s Sierra Nevada mountain range contains a disproportionate share of the state’s plant diversity and is one of the most floristically diverse regions of its size in the United States. The high Sierra Nevada, in particular, has been identified as an important center of species richness and endemism within California. Anthropogenic climate warming is expected to disproportionately affect mountain ecosystems, and models have predicted serious habitat contraction and extirpation for many alpine plant taxa. A specimen-based inventory of the vascular and non-vascular plants of Coyote Ridge and Flat was conducted to establish baseline data for one such sensitive alpine and …

Genome-Wide Identification Of Wrky Transcription Factor Encoding Genes In Amborella Trichopoda Baill. (Amborellaceae), Bijaya Pradhan

Electronic Theses and Dissertations

WRKY transcription factors (TFs) are DNA-binding proteins, which play important roles in managing plant stresses and regulating growth and development processes. The WRKY TF family has expanded significantly through genome/gene duplications in the plant evolutionary process. Although the WRKY TFs have been identified in hundreds of plant species, they are yet to be identified in Amborella trichopoda, a species that represents the most basal group of Angiosperms. The main objectives of this study were to conduct genome-wide identification of the WRKY gene family in A. trichopoda and to assess their homologs in Angiosperms. In this study, we identified …

Callery Pear Removal Experiment: Trees-Intact (Medlar Conservation Area), Margaret E. Maloney, Eric B. Borth, Grace Dietsch, Mary C. Lloyd, Ryan W. Mcewan

Five Rivers MetroParks Collaboration Data Archive

The invasive tree Callery pear (Pyrus calleryana) is problematic in open habitats in the American Midwest. We investigated the efficacy of various control techniques on P. calleryana invasion in grasslands. Treatments were applied to P. calleryana stems that were single-stemmed trees (around 7 years; n = 40 stems), and response of those stems was measured.

Callery Pear Removal Experiment: Trees-Sprouting (Stillwater Conservation Area), Margaret E. Maloney, Eric B. Borth, Grace Dietsch, Mary C. Lloyd, Ryan W. Mcewan

Five Rivers MetroParks Collaboration Data Archive

The invasive tree Callery pear (Pyrus calleryana) is problematic in open habitats in the American Midwest. We investigated the efficacy of various control techniques on P. calleryana invasion in grasslands. Treatments were applied to P. calleryana stems that had experienced mowing annually for several years and were sprouting (n = 100 stems) and response of those stems was measured.

Largemouth Bass In The Upper Mississippi River: An Evaluation Of Management Strategies And Understanding Potential Factors Influencing Dynamic Rate Functions, Kylie Beth Sterling

Graduate Theses/Dissertations

The Upper Mississippi River (UMR) supports ecologically and economically important commercial and recreational fisheries. One recreational fishery in the UMR is the Largemouth Bass fishery. Recreational fisheries can be effectively managed using information on population dynamics, though little is known about Largemouth Bass population dynamics in large river ecosystems. Therefore, the objectives of this study were to 1) evaluate recruitment, growth, and mortality of three Largemouth Bass populations in the UMR, specifically within Pools 4, 8, and 13, and 2) to use those estimates of recruitment, growth and mortality to inform exploitation models to evaluate best management practices for each …

Environmental Effects On Biomass Allocation And Small Plot Evaluations Of Aquatic Pesticides For Control Of Nitellopsis Obtusa (Starry Stonewort) Collected From Lake Koronis In Stearns County, Minnesota, Patrick J. Carver

All Graduate Theses, Dissertations, and Other Capstone Projects

Phenology is the study of critical life stages in plants in relation to shifts in environmental factors during seasonal changes. Starry stonewort is a green macro alga in the family Characeae native to Eurasia. Much of the Midwestern United States has been invaded by this species. Starry stonewort has been seen to have late season growth patterns in its invaded range. This study found that this growth pattern was dependent upon water temperature and light transmittance both of which affect biomass production and senescence. It was hypothesized that peak biomass would occur in the late summer (August), however we observed …

Development Of Genomic Resources In Vitis Riparia For Discoveries On Pre- And Post-Transcriptional Molecular Regulators Of Early Induction Into Endodormancy, Michael Robben

Electronic Theses and Dissertations

Grapevine is one of the most important fruit crops in the world, responsible for billions in global sales annually. The largest threat to grapevine and other crop production is global climate change resulting human activities. This brings unpredictable and drastic changes in ambient air temperatures to many climates in which grapes are grown. Lower temperatures and inclement weather are already responsible for millions in lost revenue due to tissue damage of established plants. Thus, protecting grapevine crops from weather-related damage is the biggest concern to growers aside from pathogen- and diseaserelated crop damage. The primary mechanism for winter survival in …

Exploring Bioprocessing Technologies For Diverse Industrial Application Of Canola, Ahmad Fawzi N Alhomodi

Electronic Theses and Dissertations

Globally, canola is the second largest oilseed crop after soybean, which is processed for the commercial production of high value oil. The industrial processing steps for canola oil extraction include preprocessing (cleaning, pressing, flaking, and cooking), mechanical pressing, and/or organic solvents. This process results in large quantities of protein-rich (~ 40% dry basis) meal as a co-product. The meal is used partially in animal diet (<30% inclusion) due to high levels of antinutritional factors (ANFs) such as high fibers, phytic acid, and glucosinolates, and low metabolizable energy. Thus, this research was designed to examine various bioprocessing technologies (i.e., traditional sprouting, solid state fermentation, submerged state fermentation, co-culture fermentation, mild pretreatments, and their combinations) for possible advancement in canola use. Canola seed sprouting for 6-day period led to an increase in protein content and a reduction in ANFs and oil content of sprouts compared to ungerminated seed. Subsequent submerged state fermentation of 6- day old sprouts using three different strains (Aureobasidium pullulans, Trichoderma reesei and Neurospora crassa) further increased protein content and lowered ANFs. Solid-state fermentation of 144 h old sprouts using A. pullulans, N. crassa and T. reesei enhanced the protein content and reduced ANFs of sprouts. Sprouting canola seed for three days helped in hull removal, leading to high protein meal accompanied by low fiber and phytic acid level. Three-day seed sprouting had no effect on oil yield, but free fatty acid content was higher compared to seed oil. Co-culture fermentation of HECM under solid state process showed maximum reduction in fiber content with co-culture of A. pullulans and N. crassa while a combination of A. pullulans and T. reesei promoted the highest GLS and phytic acid reductions compared to other combinations, which indicated the advantage of coculture inoculation over monoculture in terms of ANFs reduction. Mild pretreatment of HECM using deionized water resulted in washed HECM (WHECM) with lower soluble sugars and GLS compared to untreated HECM, whereas protein and amino acid were concentrated due to the removal of soluble components. WHECM compared to HECM showed higher protein digestibility when fed to rainbow trout. Subsequent mono- and coculture fermentation of HECM and WHECM under submerged process resulted in higher protein and amino acid content and lower ANFs levels compared to uninoculated controls. The results of cellulase, endoglucanase and β-glucosidase activity indicated the crucial role of used substrates, fungi, fermentation modes (solid state/submerged stated) and inoculation methods (mono-/co-culture) on enzyme activities.

The Effects Of Average Annual Temperature On Flowering Times And Flower Count, Angela Copploe

Williams Honors College, Honors Research Projects

Over a course of 15 years, three different species of flowers were examined to see the relationship between the increase in average annual temperature, flowering time, and flower count.

Getting To The Root Cause: The Genetic Underpinnings Of Root System Architecture And Rhizodeposition In Sorghum, Farren Smith

Graduate Theses, Dissertations, and Problem Reports (ETD)

Plants are some of the most diverse organisms on earth, consisting of more than 350,000 different species. To understand the underlying processes that contributed to plant diversification, it is fundamental to identify the genetic and genomic components that facilitated various adaptations over evolutionary history. Most studies to date have focused on the underlying controls of above-ground traits such as grain and vegetation; however, little is known about the “hidden half” of plants. Root systems comprise half of the total plant structure and provide vital functions such as anchorage, resource acquisition, and storage of energy reserves. The execution of these key …

Determinants Of Population Genetic Structure In Chamaecrista Fasciculata (Michx.) Greene (Fabaceae) In The Southeastern United States, Mahboubeh Hosseinalizadeh Nobarinezhad, Lisa E. Wallace

Biological Sciences Faculty Publications

Chamaecrista fasciculata is a widely distributed, phenotypically variable species in the eastern U.S. Whereas studies have demonstrated genetic structure and local adaptation in northern areas of its distribution, there has been no comparison of genetic variability among populations at the southern extent where phenotypic variation is more complex. We characterized genetic variation at 14 microsatellite loci for populations in Mississippi and Alabama and compared this to variation in a phenotypic trait, leaf pubescence. Geographic distance, climatic variables, and elevation were evaluated as factors to explain the observed patterns of genetic diversity. A significant amount of variation (19%) resided among populations, …

The Challenges Of Growing Orchids From Seeds For Conservation: An Assessment Of Asymbiotic Techniques, Devani Jolman, Martín I. Batalla, Alexis Hungerford, Pryce Norwood, Noah Tait, Lisa E. Wallace

Biological Sciences Faculty Publications

Lewis Knudson first successfully germinated orchid seeds asymbiotically on artificial medium in 1922. While many orchid species have since been grown asymbiotically, the tremendous variation in how species respond to artificial medium and growth conditions ex situ has also become apparent in the past century. In this study, we reviewed published journal articles on asymbiotic orchid seed germination to provide a summary of techniques used and to evaluate if these differ between terrestrial and epiphytic species, to identify areas where additional research is needed, and to evaluate whether asymbiotic germination could be used more often in ex situ conservation. We …

Stomatal Conductance And Reed Canary Grass Suppression Traits Of Native Michigan Trees, David E. Martinez, Dave Warners

Student Papers and Reports

Reed canary grass (Phalaris arundinacea), a prominent invasive understory species, threatens native Michigan biodiversity statewide. A notable affected area includes a stretch of agricultural land along Schooley Drain in Caledonia, MI, located in the headwaters of the Plaster Creek watershed. Our study pursues the following questions: “Do native trees provide enough shade to reduce the growth of Reed canary grass?” and “Which native trees best transpire water from a floodplain?”: To answer these questions, we continued the evaluation of seven different species of native Michigan trees to investigate which species best inhibits the growth of reed canary grass …

The Emma Cole Project: Reevaluating The Flora Of Grand Rapids, William Hofmann, Hayden Janssen, Martin Vanderschoot, Garrett Crow, Dave Warners

Student Papers and Reports

In 1901, botanist and teacher Emma Cole published an account of all the vascular plants in the Grand Rapids area, which is the most comprehensive documentation of the flora in the area today. The vicinity of Grand Rapids has been developed significantly since then, and with it the surrounding natural spaces have also been greatly altered. Over the past 7 years, Calvin University’s Emma Cole Project has been inventorying the flora of greater Grand Rapids and comparing modern plant life with the flora during Cole’s time 120 years ago. This project strives to both verify species’ presence around Grand Rapids …

Botanical Assessments Of High-Quality Southern Shrub-Carr And Hardwood Swamp Wetlands In The Undeveloped Lowell Regional Greenspace, Kent County, Michigan, Garrett Crow, Dave Warners, Haley R. Weesies, Jonathon D. Walt, Zachary Hartwig, Carolyn H. Koehn

Faculty and Professional Research

The 2019–2023 Masterplan for Kent County Parks includes the future development of acquired properties that have been designated as the Lowell Regional Greenspace (528 acres), occupying nearly the entirety of Section 22 of Lowell Charter Township in Kent County, Michigan. Four wetlands located in the same drainage basin along Karen Creek in the Lowell Regional Greenspace were inventoried for floristic quality assessments during the summers of 2016, 2018, 2019, and 2021. One of the wetlands was forested and determined to be a southern hardwood swamp community type. The other three wetlands are best classified as shrub-carr communities. In the southern …

Observing Gravitropism In Brassica Rapa Roots, Trang Ly, Maya O'Callagham, Lan Poeschl, Adil Saeed, George Zorn

UROP Posters

The objective of this experiment is to observe the effect of gravitropism on the orientation of Brassica rapa (B. rapa) roots. Specifically, amyloplasts that reside at the bottom of root tips act as gravity sensors. As plants are disturbed from upright orientation, roots automatically grow according to the downward pull of gravity. It is hypothesized that as the angle of rotation increases, the angle of root growth is inversely proportional. Five plants containing four seeds of B. rapa were grown over the course of 10 days. Each plates, aside from the control, were rotated once 90°, 80°, and 270° to …