Botany Commons^™

A Deep Learning Framework For Processing And Classification Of Hyperspectral Rice Seed Images Grown Under High Day And Night Temperatures, Víctor Díaz-Martínez, Jairo Orozco-Sandoval, Vidya Manian, Balpreet K. Dhatt, Harkamal Walia

Department of Agronomy and Horticulture: Faculty Publications

A framework combining two powerful tools of hyperspectral imaging and deep learning for the processing and classification of hyperspectral images (HSI) of rice seeds is presented. A seed-based approach that trains a three-dimensional convolutional neural network (3D-CNN) using the full seed spectral hypercube for classifying the seed images from high day and high night temperatures, both including a control group, is developed. A pixel-based seed classification approach is implemented using a deep neural network (DNN). The seed and pixel-based deep learning architectures are validated and tested using hyperspectral images from five different rice seed treatments with six different high temperature …

Antibacterial Activity Of Native Plants In Arkansas, Kayla L. Medina, Raven L. Turner, Katie Huffman

ATU Scholars Symposium

American beautyberry (Callicarpa Americana), Sugarberry (Celtis laevigata) and Red buckeye (Aesculus pavia) are native plants of Arkansas. Plant families with species having high chemical compounds can have antimicrobial properties. In this study, the antibacterial properties of the plants are investigated against three gram positive (Bacillus cereus, Bacillus subtilis, and Staphylococcus epidermidis) and three negative bacteria (Alcaligenes faecalis, Escherichia coli, and Serratia marcescens). The disc diffusion assay method is employed to identify any potential antibacterial properties of the plants. For this experiment, 6.41 g of dehydrated plant material (leaves for both species) was combined with 50 mL of 75% ethanol creating …

Entropy And Energy Profiles Of Chemical Reactions, Johannes C. B. Dietschreit, Dennis J. Diestler, Rafael Gómez-Bombarelli

Department of Agronomy and Horticulture: Faculty Publications

The description of chemical processes at the molecular level is often facilitated by use of reaction coordinates, or collective variables (CVs). The CV measures the progress of the reaction and allows the construction of profiles that track the evolution of a specific property as the reaction progresses. Whereas CVs are routinely used, especially alongside enhanced sampling techniques, links between profiles and thermodynamic state functions and reaction rate constants are not rigorously exploited. Here, we report a unified treatment of such reaction profiles. Tractable expressions are derived for the free-energy, internal-energy, and entropy profiles as functions of only the CV. We …

Soil Microbial Community Composition Of White Oak Mountain, Tennessee, Matthew Gano, Timothy D. Trott

Research in Biology

Abstract - Soil microbial communities are responsible for nutrient cycling in terrestrial ecosystems and have symbiotic and parasitic relationships with the plant community. However, little is known about the factors that determine the soil microbial community composition. In this study we examined how spring wildflower diversity and geographical factors influence the soil microbial community composition of the second growth oak hickory forests of White Oak Mountain in Southeast Tennessee. The characterization of the soil microbial community was completed with 16S/18S/ITS rDNA amplicon sequencing of total DNA extracted from soil samples that were normalized for each sample plot. Here we characterize …

The Bellarmine Bee Bed: Organizing A Native Plant Garden Using Feedback From The Local Community, Kate Moran

Undergraduate Theses

Animal pollinators are the cornerstone of healthy ecosystems. Their survival is essential for the persistence of entire food chains: from the flowers they cross-pollinate directly, to the animals who depend on those plants for nutrition. The establishment of pollinator gardens—particularly ones that consist of native plants—is an effective way to enhance their biodiversity, abundance, and well-being.

The main goal of this thesis is to construct a pollinator garden that maximizes the benefits for animal pollinators using feedback from local gardeners. A survey was used to gather information about the popularity and preferences of 40 flowering plants, and after analyzing the …

Divergent Metabolic Changes In Rhizomes Of Lowland And Upland Switchgrass (Panicum Virgatum) From Early Season Through Dormancy Onset, Nathan A. Palmer, Gautam Sarath, Michael J. Bowman, Aaron J. Saathoff, Serge J. Edmé, Robert B. Mitchell, Christian M. Tobias, Soundararajan Madhavan, Erin D. Scully, Scott E. Sattler

Department of Agronomy and Horticulture: Faculty Publications

High-biomass-yielding southerly adapted switchgrasses (Panicum virgatum L.) frequently suffer from unpredictable winter hardiness at more northerly sites arising from damage to rhizomes that prevent effective spring regrowth. Previously, changes occurring over the growing season in rhizomes sampled from a cold-adapted tetraploid upland cultivar, Summer, demonstrated a role for abscisic acid (ABA), starch accumulation, and transcriptional reprogramming as drivers of dormancy onset and potential keys to rhizome health during winter dormancy. Here, rhizome metabolism of a high-yielding southerly adapted tetraploid switchgrass cultivar, Kanlow—which is a significant source of genetics for yield improvement—was studied over a growing season at a northern …

Floral Visitors Of A Colorado Endemic Chasmophyte, Telesonix Jamesii (Saxifragaceae), Andrew G. Gaier, Erin Manzitto-Tripp, Julian Resasco

Western North American Naturalist

Telesonix jamesii, a rare and imperiled species of perennial saxifrage, is restricted to rocky habitats at high elevations across 21 isolated, known populations in the southern Rocky Mountains of Colorado and New Mexico. Despite its imperiled conservation status, very little is known about the natural history of T. jamesii. We studied pollination of this species during the summers of 2019–2021 at multiple locations on Pikes Peak, Colorado. We conducted a total of 899 min of pollinator surveys, identifying all floral visitors during this time period. We then examined floral visitors for the presence of T. jamesii pollen to …

Darwin Core Archive File, Stover-Ebinger Herbarium, Eastern Illinois University

Darwin Core Archive Download

ZIP file contains occurrences.csv, identivications.csv, and images.csv. The meta.xml document describes the content. Fields within the occurrences.csv file are defined by the Darwin Core exchange standard.

This file is updated as new occurrence records are added.

Herbicide Drift Vs. Crop Resilience – The Influence Of Micro-Rates, Milan Brankov, Bruno Canella Vieira, Miloš Rajković, Milena Simić, Vukadinović Jelena, Violeta Mandić, Vesna Dragičević

Department of Agronomy and Horticulture: Faculty Publications

A greenhouse study was conducted to test the effects of low herbicide dose exposure on different crops measuring visible damages, plant height, leaf area, and dry matter. Seven crops were tested: lettuce (Lactuca sativa L.) cv. Novosadska majska maslena, oil pumpkin (Cucurbita maxima Duch) cv. Olivija, oilseed rape (Brassica napus L.) cv. NS Ras, pepper (Capsicum annuum L.) cv. Kurtovska kapija, soybean (Glycine max (L.) Merr) cv. ZP Laura, sunflower (Helianthus annuus L.) cv. NS Kruna, and tomato (Solanum lycopersicum L.) cv. Dunavski Rubin. Herbicide dicamba in the range of 0.14 to 1 …

Physiological And Transcriptomic Responses Of Two Artemisia Californica Populations To Drought: Implications For Restoring Drought-Resilient Native Communities, Hagop S. Atamian Dr., Jennifer L. Funk

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

As climate change brings drier and more variable rainfall patterns to many arid and semi-arid regions, land managers must re-assemble appropriate plant communities for these conditions. Transcriptome sequencing can elucidate the molecular mechanisms underlying plant responses to changing environmental conditions, potentially enhancing our ability to screen suitable genotypes and species for restoration. We examined physiological and morphological traits and transcriptome sequences of coastal and inland populations of California sagebrush (Artemisia californica), a critical shrub used to restore coastal sage scrub vegetation communities, grown under low and high rainfall environments. The populations are located approximately 36 km apart but …

Late Postemergence Glufosinate-Based Programs For Glyphosate-Resistant Palmer Amaranth Control In Dicamba/Glufosinate/Glyphosate-Resistant Soybean, Vipan Kumar, Jatinder S. Aulakh, Rui Liu, Amit J. Jhala

Department of Agronomy and Horticulture: Faculty Publications

Glyphosate-resistant (GR) Palmer amaranth (Amaranthus palmeri S. Watson) is widespread in the Central Great Plains. Introduction of newly developed dicamba/glufosinate/glyphosate (DGG)-resistant soybean varieties allows postemergence (POST) applications of dicamba and glufosinate for in-season control of GR Palmer amaranth. Limited information exists on the effectiveness of glufosinate applied late-POST for tall (70–90 cm) GR Palmer amaranth control in DGG-resistant soybean. The objectives of this study were to (1) determine the effectiveness of late-POST glufosinate-based programs for GR Palmer amaranth control, and (2) determine the impact of those programs on soybeans grain yields. Ten glufosinatebased programs were tested in a field …

A Leaf-Level Spectral Library To Support High-Throughput Plant Phenotyping: Predictive Accuracy And Model Transfer, Nuwan K. Wijewardane, Huichun Zhang, Jinliang Yang, James C. Schnable, Daniel P. Schachtman, Yufeng Ge

Department of Agronomy and Horticulture: Faculty Publications

Leaf-level hyperspectral reflectance has become an effective tool for high-throughput phenotyping of plant leaf traits due to its rapid, low-cost, multi-sensing, and non-destructive nature. However, collecting samples for model calibration can still be expensive, and models show poor transferability among different datasets. This study had three specific objectives: first, to assemble a large library of leaf hyperspectral data (n=2460) from maize and sorghum; second, to evaluate two machine-learning approaches to estimate nine leaf properties (chlorophyll, thickness, water content, nitrogen, phosphorus, potassium, calcium, magnesium, and sulfur); and third, to investigate the usefulness of this spectral library for predicting external datasets …

Decadal Patterns Of Adaptation And Trait Variation Of The Dominant Prairie Grass Across The Midwest Rainfall Gradient And Response To Drought, Jack Sytsma

2023 Midwest Ecology & Evolution Conference

Frequent droughts are predicted to impact grasslands but intraspecific variation in response to drought is not well-known. Big bluestem (Andropogon gerardii) is a grass distributed across the Midwest rainfall gradient (MAP500-1200mm/yr) giving rise to climate-adapted ecotypes. This dominant grass is important for cattle forage and conservation. Reciprocal gardens were established in 2009 in ecological communities (driest to wettest: Colby, Hays, Manhattan, KS to Carbondale IL) and measured for over a decade. Rainfall was reduced using rainout shelters in three sites. Cover and biomass were monitored in plots over time, and height, width, photosynthetic rate, SPAD, and reproductive phenology …

Documenting Plant Biodiversity At The Eastern Michigan University Owned Parsons Center For Arts And Sciences, Emily R. Edwards Mrs.

2023 Midwest Ecology & Evolution Conference

Eastern Michigan University (EMU) owns an 86-acre property in northwest Michigan called the Parsons Center for Arts and Sciences. No botanical research has been done at the Center. A comprehensive plant species list will provide important resources for EMU students, all Parsons users (e.g., artists and community members), and county biologists. This research aims to collect and identify as many plant species at the site as possible and create two online, publicly available databases of the plant list and collection. Such a collection will bring awareness to the Parsons Center and add to its botanical value.

Initial field-work was conducted …

A Tale Of Two Scents: Scent Preferences Of Naïve And Experienced Pollinators, Scout N. Steinhiser

2023 Midwest Ecology & Evolution Conference

Mounting evidence of pollinator decline and its repercussions on agriculture and plant diversity means that scientists must work to understand the details of plant-pollinator interactions. Though there are many facets to the relationship between plants and pollinators, one major mediator of this relationship is scent. As much is already known about the scent make-up of Narcissus and its pollinator partners, it is a great model system for additional research. This is also true for the insect species Vanessa cardui, a generalist pollinator found worldwide that has most likely come into contact with Narcissus and its scent. The objective of this …

Trait Variation In Bryophytes At Karst Cave Entrances, Chenoa Briggs

2023 Midwest Ecology & Evolution Conference

Cave entrances are critical ecosystems in their role as ecotones between the interior cave environment and the surrounding external environment. Bryophytes are highly sensitive to environmental changes and many species found at caves are specialists to those habitats. This study aims to identify how functional traits of bryophytes are affected by the cave environment. Bryophytes and environmental variables were sampled from six cave entrances. Functional trait data was collected from literature. The data from this study supplies information on the functional traits of bryophytes and can provide insight into the effects of environmental pressures on community assembly.

Geographic Analysis Of Sex Chromosome Polymorphism In The Virginian Wild Strawberry, Trezalka A. Budinsky

2023 Midwest Ecology & Evolution Conference

The evolution of sex chromosomes is a ubiquitous and essential diversifying mechanism in eukaryotes. Yet early stages of sex-chromosome differentiation are poorly understood. The subdioecious octoploid, Fragaria virginiana, provides a rare opportunity to study the beginnings of sex chromosome evolution due to its young, polymorphic ZW sex system. Females are ZW and males/hermaphrodites are ZZ. F. virginiana has a small sex-determining region (SDR) located on the female W chromosome that has undergone three transposition events between the strawberry's four subgenomes, resulting in three SDR haplotypes: alpha (the result of a first transposition and closest to a pre-sex chromosome ancestral …

The Influence Of Cover Crops On Plant-Soil Microbe Interactions Of Native Prairie Forbs, Josh C. Poland

2023 Midwest Ecology & Evolution Conference

Tallgrass prairies are abundant and rich habitats where soil microbial communities frequently interact with native grass and forb species. Cover crops increase available soil nutrients and promote healthy soil microbial communities in agriculture, and therefore may provide similar benefits to restoration. A prairie restoration in Madison Co, IL was initiated in autumn 2021 using areas with two different cover crop types, NLS Soil Health Mix and Winter Oat, as well as areas with no cover crops. A greenhouse project exposed five native forb species (Monarda fistulosa, Rudbeckia hirta, Pycnanthemum virginianum, Desmodium canadensis (legume), and Asclepias incarnata …

Bryophytes At Cave Entrances Across A Range Of Anthropogenic Disturbance, Morghan Mccool

2023 Midwest Ecology & Evolution Conference

Cave entrances are critical ecosystems in their role as ecotones between the interior cave environment and the surrounding external environment. Bryophytes serve as ecosystem engineers of cave entrance microhabitats. This study piloted a method to quantify anthropogenic disturbance unique to cave entrances and characterize the bryophyte assemblages at caves in urban and other natural areas. Bryophytes and environmental variables were sampled from cave entrances; bryophytes were identified, alpha and beta diversity values were computed. So far, 144 species of bryophytes, 36 of which were state records, have been identified across 6 sites. By improving knowledge of bryophyte communities, park managers …

A Phylogenetic Evaluation Of Proposed Segregates Of A. Canadense, Brett Lambert

2023 Midwest Ecology & Evolution Conference

Brett Lambert- 1^st Year Master’s Student at The Ohio State University

Department of Evolution, Ecology, and Organismal Biology (Freudenstein Lab)

Title: A phylogenetic evaluation of proposed segregates of Asarum canadense

Abstract: The wild gingers (Asarum: Aristolochiaceae) are rhizomatous forbs native to Europe, Asia, and North America. A member of subgenus Asarum (A. canadense) is currently circumscribed as containing two varieties, A. canadense var. reflexum and A. canadense var. acuminatum. These varieties have previously been recognized as distinct species based on morphological variation. This project will evaluate variation across A. canadense using molecular (maximum likelihood and …