Biology Commons^™

Robust Embeddings Of Genetics, Anatomy, And State Decoded From A Neuron’S Activity, Aidan Schneider

Arts & Sciences Graduate Student Theses and Dissertations

Neural spike trains are shaped by both extrinsic inputs and intrinsic structural constraints. While prior work has focused on how spike timing encodes externally driven variables, such as stimuli or behavior, this dissertation explores whether principles that organize neural activity in space and time—such as genetic cell type, anatomical location, and arousal state—are also embedded in the spiking output of individual neurons. I hypothesize that these organizing principles are not quenched as irrelevant variability, but rather multiplexed within the neural code itself. To test this, I attempt to decode these principles from the spike trains of neurons recorded in behaving …

Vibrio Cholerae Endemic To The Lower Rio Grande Delta Segregate Into Urban And Rural Phylotypes, Daniele Provenzano, Jeffrey W. Turner, Jorge Duran-Gonzalez, David A. Laughlin, David Silva, Viviana Trevino, Miguel F. Gonzales, Boris Ermolinsky, Stefan Pukatzki

School of Integrative Biological & Chemical Sciences Faculty Publications

The lifestyle of Vibrio cholerae is primarily environmental, yet a chance encounter with a human host can lead to cholera, a potentially lethal form of diarrhea. Strains belonging to O1 and O139 serogroups have pandemic potential, but the contribution of non-O1/non-O139 serovars towards the genesis of cholera remains unclear. Endemic V. cholerae lineages were investigated given several historical accounts describing cholera epidemics and sporadic, contemporary cholera-like outbreaks along the lower Rio Grande Delta (LRGD). Seven isolates were recovered from an urban segment of the Rio Grande and six from a rural segment where the river empties into the Gulf of …

Genetic Gain And Loss In The Evolution Of Amniote T Cell Receptor And Immunoglobulin Genes, Jordan M. Sampson

Biology ETDs

The immune system of most jawed vertebrates consists of three major cell types: αβ T cells, γδ T cells, and B cells. Every species evaluated contains the loci that encode the highly conserved αβ T cells, however, γδ T cells are less conserved and have been lost in squamate reptiles. The loci that encode the B cell receptor have also varied across evolution. Seven immunoglobulin (Ig) heavy chain isotypes have been identified in amniotes: IgM, IgD, IgY, IgG, IgE, IgO, and IgA. Some are found in most species (IgM and IgD) and others only in specific lineages (IgY or IgG). …

​​Site Fidelity Is Associated With The Social Experience Of Forked Fungus Beetles (Bolitotherus Cornutus), Joo Yeon Kim , '22, C. W. Wood, E. D. Brodie Iii, Vincent A. Formica

Biology Faculty Works

Consistently returning to or remaining within a specific location, a behavior known as site fidelity, is a useful metric for quantifying animal space use. When multiple individuals display similar site fidelity patterns, they are likely to interact, shaping the degree and quality of their social interactions. However, the link between the expression of site fidelity behavior and an individual’s social experience has not been thoroughly investigated. In this study we examined (1) how intrinsic individual properties (body size and sex) predicted variation in site fidelity and (2) whether site fidelity was linked to the social experience of individuals in wild …

Scientific Note: Garden Loosestrife (Lysimachia Vulgaris, Primulaceae), An Emerging Invasive Plant Species Of Riparian Corridors In The Mid-Atlantic Region, Christopher T. Martine, Amy L. Jewitt, Claire M. Ciafre, Kaitlin G. Henry, Elizabeth H. Williams, Pj Newhart, Melody P. Sain

Faculty Journal Articles

Lysimachia vulgaris (garden loosestrife, Primulaceae) is an herbaceous perennial native to Europe that has been identified as an aggressive invasive species in parts of North America. The status of the species in the Mid-Atlantic region of the US, however, is poorly determined. Using recent field observations (from iNaturalist, iMapInvasives, and EDDMapS records) we here report localized incursions of L. vulgaris in the Susquehanna River Valley of central Pennsylvania, along with notes on its ecology, threats to native plant communities, and broader distribution in the state.

Un(Der)Explored Links Between Plant Diversity And Particulate And Mineral-Associated Organic Matter In Soil, Šárka Angst, Gerrit Angst, Kevin E. Mueller, Markus Lange, Nico Eisenhauer

Biological, Geological, and Environmental Faculty Publications

Plant diversity can alter soil carbon stocks, but the effects are difficult to predict due to the multitude of mechanisms involved. We propose that these mechanisms and their outcomes can be better understood by testing how plant diversity affects particulate organic matter (POM) and mineral-associated organic matter (MAOM) depending on whether MAOM storage is "saturated" and the total soil organic matter pool is limited by plant inputs. Such context-dependency of plant-diversity effects on POM, MAOM, and total soil organic matter helps explain inconsistencies in plant-diversity-soil-carbon relationships across studies. Further illumination of this context-dependency is required to better predict consequences of …

Redundant Functions Of Mir156-Targeted Squamosa Promoter Binding Protein-Like Transcription Factors In Promoting Cauline Leaf Identity, Darren Manuela, Liren Du, Qi Zhang, Yifei Liao, Tieqiang Hu, Jim P. Fouracre, Mingli Xu

Faculty Publications

No abstract provided.

Occupancy Sampling To Examine Spatial Distribution Of Oklahoma Salamanders (Eurycea Tynerensis) Among Headwater Streams In The Ozark Highlands, Sophia Anreder

Biological Sciences Undergraduate Honors Theses

Water conditions are changing globally due to climate change (Gleick, 1989). Headwater streams specifically are vulnerable to changes in hydrology, water quality, and physical characteristics from anthropogenic practices due to their small watersheds with shallow soils, yet they are often not a priority in conservation (Campbell et al., 2011; Abell et al., 2017). Within streams, plethodontid (i.e., lungless) salamanders, which are also sensitive to environmental changes, may be restricted in their distribution due to undefined stream characteristics and predation by fish (Welsh and Droege, 2002; Kuhajda et al., 2015). To better understand the pressures that influence stream salamander occupancy, I …

Identification Of Novel Components Of The Retinal Determination Gene Network In Drosophila Cell Lines, Robert Drewell, Jacqueline Dresch

Biology

The retinal determination genetic network controls the development of the visual system in all seeing animals through the molecular regulation of cells to adopt an eye tissue fate. The compound eye of the fruit fly, Drosophila melanogaster, is an excellent model system to study the complex mechanisms within the network that regulate specification of cellular identity during embryogenesis. In Drosophila, the two Pax6 paralogues, eyeless and twin of eyeless, sit at the very pinnacle of the network and their expression early in development activates critical downstream components of the retinal determination pathway. In this study, we investigate the expression of …

Investigating The Threshold Of Opa1-Mediated Mitochondrial Fusion In Shsy5y Cells, Jorge Alberto Elizondo

Theses and Dissertations

Mitochondrial dynamics occurring under stress-induced conditions in SHSY5Y neuroblastoma cells provide insight into the OPA1-mediated mitochondrial fusion threshold in cells of varying energetic demands. Mitochondria are dynamic structures that are continuously balancing fusion and fission, depending on cellular needs. The ability to fuse and divide relies on the maintenance of the mitochondrial transmembrane potential. Stress-induced conditions in SHSY5Y cells were induced via utilization of carbonyl cyanide m-chlorophenylhydrazone (CCCP), a protonophore that disrupts the transmembrane potential. OMA1 protein reacts to the loss of transmembrane potential and subsequently cleaves the fusion-active isoforms of OPA1, L-OPA1. This causes an accumulation of S-OPA1, the …

Circannual And Kinship Cues Shape Reproduction And Epigenetic Aging In Peromyscus, Kim Tuyen Huynh Dam

Theses and Dissertations

Evolutionary success is defined by the ability of a species to adapt and survive across many generations. This success is not determined by any single attribute but rather includes the entrenched, complex system that could be associated with biological rhythms, reproductive strategies, and regulations of epigenetic and genetic components. By using closed Peromyscus colonies as a model and by coupling mathematical modeling, analyses of breeding records, epigenetic studies, and in vitro and in vivo experiments, this dissertation aims to discover how Peromyscus adjusts to the internal and external pressures to ensure their survival and preserve evolutionary fitness in controlled environments. …

Exploring The Ancestry And Mutational Signatures Of Free-Breeding Dogs From Chernobyl And The Galápagos Islands, Gabriella Jean Spatola

Theses and Dissertations

Two free-breeding dog populations, one in Chernobyl, Ukraine, and the other on the Galápagos Islands, Ecuador, exist on opposite sides of the globe, yet both hold unique scientific potential to further our understanding of free-breeding dog population dynamics and evolutionary processes related to their environments. In the following studies, blood samples from more than 400 individual Chernobyl dogs were collected and their genomes were analyzed alongside over 1500 purebred and 200 global free-breeding dogs, describing genetic relationships and the extent of admixture with purebred migrants. Importantly, the sampled Chernobyl dogs had long-term exposures to ionizing radiation because of the 1986 …

Hybrid Penstemon Flowers: Colors, Pigments, And Detectability & Experimental Teaching: Evaluating The Impact Of Active Learning, Josh Thomas Edward Stevens

Theses and Dissertations

Shifts to different primary pollinators are often accompanied by changes in suites of floral traits. Understanding how and why these floral adaptations evolve is a central goal in evolutionary biology. Within the genus Penstemon, the transition from bee-pollinated to hummingbird-pollinated flowers is a common evolutionary pattern. These pollinator shifts have caused several closely related species to exhibit distinct pollination syndromes. One example of this evolutionary phenomenon can be seen within the sister species P. eatonii (hummingbird-pollinated) and P. laevis (bee-pollinated). These two species form several hybrid zones, in which hybrid individuals exhibit colors resembling both parental species, along with a …

Investigating The Immunomodulatory Effects Of Cdk8/19 Inhibitor Senexin631 In A Her2-Positive Breast Cancer Model, Stephen O'Rourke

Theses and Dissertations

HER2-positive (HER2⁺) breast cancer is aggressive and often develops resistance to anti-HER2 therapies. CDK8 and CDK19, transcription-associated cyclin-dependent kinases (tCDKs) in the Mediator complex, are dysregulated in HER2⁺ breast cancer, correlate with poor survival, and support transcriptional escape driving therapeutic resistance. Previous studies Previous studies in immune-deficient models demonstrated that CDK8/19 inhibition (CDK8/19i) reduces pro-tumor macrophages (M2Φs), but its role in immune-competent tumors and innate immune–mediated tumor control remains unclear. Since HER2⁺ tumors are often immunogenic and anti-HER2 therapies rely on innate immune activation, reprogramming immunosuppressive M2Φ toward an M1Φ-like phenotype could enhance antitumor immunity. We hypothesized that CDK8/19i modulates …

Lianas Reduce Tree Height With Negative Consequences For Carbon Storage And Growth Estimates, Xingyan Cao, Frieke Van Coillie, Sruthi M. Krishna Moorthy, Kasper Coppieters, Barbara D'Hont, Stefan A. Schnitzer, Geertje M. F. Van Der Heijden, Hans Verbeeck, Félicien Meunier

Biological Sciences Faculty Research and Publications

1. Current evidence suggests that liana (woody vine) competition with trees could be threatening the carbon sink by reducing carbon uptake and storage in tropical forests. Previous studies investigating forest demography in liana removal experiments have, however, assumed similar allometries for trees, regardless of the amount of lianas they support. Yet, recent observations suggest that liana load may alter tree shape and structure, including height, which could result in an underestimation of the liana effects on forest carbon stocks and tree growth.
2. In this study, we used terrestrial laser scanning (TLS) in a liana removal experiment in Gigante Peninsula, Panama, collected …

Teratogenic Effects Of Serotonin Receptor 2b Disruption On The Migration And Cardiac Derivatives Of The Cardiac Neural Crest, Brian K. Wells, Gwyneth K. Garramone, Amira Mahomed, Max Ezin

Biology Faculty Works

Background: Cardiac neural crest cells (cNCCs) are critical for heart development, and their disruption can result in congenital heart defects. Serotonin (5-HT) signaling, specifically via 5-HT2B and 5-HT2C receptors, regulates diverse physiological processes, including neural crest migration. This study investigates how modulation of 5-HT2B and 5-HT2C receptor activity impacts cNCC migration and the development of their derivatives, with relevance to serotonergic drug safety during pregnancy.

Methods

Chicken embryos at HH8 were treated with 50 μL of 20 μM 1-Methylpsilocin (1-MP), an inverse agonist of 5-HT2B and agonist of 5-HT2C, and collected at HH14 to assess cNCC migration. Embryos were pre-treated …

Mammals Of Malheur National Wildlife Refuge And Surrounding Harney County, Oregon, John E. Cornely, Leslie N. Carraway

Monographs of the Western North American Naturalist

Malheur National Wildlife Refuge (NWR), located in southeastern Oregon, is part of the National Wildlife Refuge System (NWRS) of the United States. Currently, NWRS includes more than 568 NWRs, 38 Wetland Management Districts, and 5 Marine National Monuments. Malheur NWR, like a majority of the refuges in the NWRS, was established for the conservation of migratory birds. Many of these NWRs also provide significant habitat for mammals. Malheur NWR, one of the oldest (established 1908) and largest refuges in the system, is one of those with significant habitat for mammals. In addition to the refuge, we have included Harney County, …

Pollination And Essential Oil Production Of Lavandula Angustifolia Mill. (Lamiaceae), Riley B. Jackson, Tyler M. Wilson, Joseph S. Wilson, Zabrina Ruggles, Lindsey Topham Wilson, Chris Packer, Jacob G. Young, Christopher R. Bowerbank, Richard E. Carlson

Biology Faculty Publications

Lavandula angustifolia Mill., lavender, is an aromatic plant in the Lamiaceae family. Lavender, which is native to the Mediterranean region but cultivated throughout the world, is an important economic plant. Several studies have investigated two aspects of this aromatic plant: (1) which pollinators, particularly bees, pollinate lavender, and (2) the composition of lavender essential oil. However, little research has been conducted to investigate how pollination affects either the yield or phytochemistry of lavender. The current study, which was conducted in North America, investigates which bee species visit lavender and how pollination affects plant chemistry, specifically the essential oil produced by …

Blue Light Is A Key Factor In Regulating Stomatal Movement, Transpiration Rate And Aba Metabolism Under Varying Vapour Pressure, Sheona Noemi Innes, Sara Brunborg Jakobsen, Rikke Bryn Røsåsen, Haider Ali, Knut Asbjørn Solhaug, Jorunn Elisabeth Olsen, Sissel Torre

Research outputs 2022 to 2026

Vapour pressure deficit (VPD) and blue light (BL) are import signals for stomatal regulation and highly relevant during cultivation of economically important crops such as cucumber in controlled environments. However, the information about combined effects of VPD and BL and the regulation of abscisic acid (ABA) in this respect, is limited and seems to vary between species. This study investigated how moderate (1.12 kPa) or low (0.28 kPa) VPD combined with 5% or 30% BL affect the foliar ABA metabolism, transpiration rate, nutrient uptake, and growth in well-watered cucumber plants (Cucumis sativus ‘Quatro’). Additional BL, regardless of VPD, resulted in …

In Vivo Pulse-Chase In Caenorhabditis Elegans Reveals Intestinal Histone Turnover Changes Upon Starvation, Christopher Borchers, Kara Osburn, Hyun Cheol Roh, Scott T. Aoki

Faculty Work Comprehensive List

The ability to study protein dynamics and function in the authentic context of a multicellular organism is paramount to better understand biological phenomena in animal health and disease. Pulse-chase of self-labeling fusion protein tags provides the opportunity to label proteins of interest and track those proteins over time. There are currently several challenges associated with performing in vivo protein pulse-chase in animals, such as cost, reproducibility, and accurate detection methods. The Caenorhabditis elegans model organism has attributes that alleviate many of these challenges. This work tests the feasibility of applying the Halo modified enzyme (HaloTag) for in vivo protein pulse-chase …

Contributions Of Citizen Science Data To Butterflies Of The Lower Rio Grande Valley, Akane Jazmyn Benitez

Theses and Dissertations

Citizen science-provided insect data inherently exhibits variability in accuracy. In the Lower Rio Grande Valley (LRGV), butterfly occurrence reporting is predominantly reliant on citizen science contributions. My research compared fieldwork conducted monthly over a year to occurrence records submitted by visitors at the National Butterfly Center and in Mission, Hidalgo County, Texas. I hypothesized that butterfly occurrences at the Center would be maximized during the fall and minimized during winter and summer months. My research findings revealed that butterfly taxa richness is contingent upon the following factors: 1) the impact of citizen science submitting reports, and 2) monthly butterfly activity …

Activation Of Toll-Like Receptor 2 Promotes The Expression Of Inflammatory Mediators And Cell Proliferation Of Human Polycystic Kidney Disease Cells, Yang Zhang, Matthew Plansinis, Sophia Peak, Elisabeth Weber, Aiping Wei, Yu Xu, Madelyn Ross, Abigail Leagjeld, Darren P. Wallace, Yan Zhang

Michigan Tech Publications

Autosomal dominant polycystic kidney disease (ADPKD) is characterized by the progressive enlargement of fluid-filled cysts, leading to a decline in renal function. Toll-like receptors (TLR)-2 and TLR4 are pattern recognition receptors and components of the innate immune response. We found that mRNA levels for TLR2 and TLR4, an adaptor protein MyD88, and the transcription factor NF-κB were elevated in the kidneys of ADPKD patients and PKD mice. There was decreased expression of IκBα, an inhibitory protein sequestering NF-κB in the cytosol, and increased NF-κB nuclear translocation in human ADPKD kidneys compared with normal human kidneys (NHK). Pam3CSK4, a synthetic TLR2 …

The Effort To Improve Students’ Problem-Solving Ability: Physics E-Modules For High School Students, Hidayatullah Hana Putra, Edi Supriana, Nasikhuddin Nasikhuddin, Annisa U. Yana, Suhailee Sohnui

Jurnal Pendidikan Sains

Physics teachers in Indonesia still face obstacles during learning, such as students who are less active and have difficulty in solving physics problems. The physics learning media used are also still not very interesting and are not based on authentic problem solving. Therefore, this study focuses on the development of PBL-based e-modules on work and energy to improve the physics problem-solving abilities of high school students. This research and development used the ADDIE design and was tested on 90 high school students in High School 1 Sumber Pucung Malang in the 2022/2023 academic year. The questionnaire instrument was used in …

Ethnoscience-Based Science Learning Through Composite Board Making Utilizing Eggshell Waste And Water Hyacinth Fiber (Eichornia Crassipes), Asep Khaidir Arpan, Yulia Sukmawardani, Pina Pitriana, Ade Yeti Nuryantini

Jurnal Pendidikan Sains

The demand for boards continues to increase every year, while overexploitation of wood leads to environmental degradation and forest loss. On the other hand, eggshell and water hyacinth waste continues to grow without optimal utilization. This research aims to make composite boards based on eggshell waste and water hyacinth fibers and analyze the potential of ethnoscience in science learning. This research used a qualitative descriptive method with a literature and documentation study approach. The materials used in this experiment are eggshell waste, water hyacinth fiber, and polyester resin. The composite board was made by mixing water hyacinth fiber and eggshell …

Contextual Approach To Improve Problem Solving Skills In Ipas Subject At Elementary School: A Study Development Of Teaching Materials, Nur Hidayah, Sumarno Sumarno, Joko Siswanto

Jurnal Pendidikan Sains

The objective of this study is to assess the validity, practicality, and efficacy of instructional materials. We refer to this research as research and development, with a focus on the creation of teaching materials. The research design proposed by Borg and Gall consists of six steps: identification of potential and difficulties, data collecting, product design, design validation, design revision, and product trial. The utilized instruments comprise expert and practitioner validity sheets, teacher and student response surveys, and validation sheets for teaching materials and modules, as well as pretest and posttest questions. Experts performed the validity assessment, attaining a score of …

Teaching Materials Containing Kse To Support Character Education In Mathematics Subjects In Elementary Schools, Kunaenah Kunaenah, Rasiman Rasiman, Bagus Ardi Saputro

Jurnal Pendidikan Sains

The purpose of the study was to determine the validity, practicality, and effectiveness of teaching materials containing KSE to support character education in mathematics lesson content. This study employs a development research approach based on Borg and Gall's research design. The subjects of the study were in class V at public elementary school Kaliboyo. The data collection instruments used were validity sheets, response questionnaires, validation sheets, and observation sheets. The findings show that experts carried out the validity test, achieving a value of 93.30% in the very valid category. The practicality test results were derived from various sources: students' questionnaires, …

Development Of Differentiated Teaching Modules With A Scientific Approach To Improve Elementary School Students’ Science Literacy, Supriyanto Supriyanto, Joko Sulianto, Achmad Buchori

Jurnal Pendidikan Sains

The study aim is to determine the validity, practicality, and effectiveness of teaching materials. This type of research involves the development and creation of teaching module products. The research design used is ADDIE (Analysis, Design, Development, Implementation, Evaluation). The instruments used are validity sheets for experts and practitioners, teacher response questionnaires, teaching module validation sheets, and pretest and posttest questions. The findings show that experts conducted the validity test, achieving a score of 92.22 in the very valid category. The practicality test was obtained from the teacher questionnaire, which was stated as practical with an average value of 91.25, and …

Differentiated Teaching Module Using Problem Solving Model: Numerical Ability Of Elementary School Students, Risa Alifatin, Agus Sutono, Ida Dwijayanti

Jurnal Pendidikan Sains

This study aims to develop a differentiated teaching module using the problem-solving model that is valid, practical, and effective to improve students' numerical abilities. This study uses the ADDIE Model research and development approach. The sample in this study was class III of elementary school Tenggulangharjo as an experimental class totaling 22 students and class III of elementary school Karangtengah as a control class totaling 19 students. Data analysis used the t-test and N-Gain test. The study found that (1) the average validity score of the three parts of the Differentiated Teaching Module was 3.74, which is 93.62%, placing it …

Analysis Of Students' Creative Thinking Skills In Learning Hydrocarbons By Using Daily Life-Based Practicum Method, Yenni Kurniawati, Laras Dyaz Handayani, Dea Ramadani, Nurhikmah Sari

Jurnal Pendidikan Sains

Creative thinking skill is a competence of the 21st century that is needed very much and needs to be increased by utilizing chemistry in life. This research aimed at analyzing student creative thinking skills in experimental and control groups and finding out the effect of the daily life-based practical work learning method on student creative thinking skills. This research was conducted in the eleventh grade at High School 1 Pekanbaru on the hydrocarbon lesson. The quasi-experimental method was used in this research with pretest-posttest and non-equivalent control group designs. The instruments used in this research were essay tests, observation, and …

Exploring Students’ Perceptions Of Science Laboratory Practices: A Comparative Study Between Rural And Urban Schools, Safrida Dwiningsih, Ina Lestari, Roma Ismi, Sri Wahyu Rahmadina, Masdalena Sinaga, M. Rahmad

Jurnal Pendidikan Sains

This study aims to analyze students' perceptions of the implementation of science laboratory practicums at public middle school 020 Pekanbaru and public middle school 7 Pangkalan Kuras, Riau Province. Using a quantitative survey method, this study involved 75 student respondents. The instrument used was a questionnaire consisting of 26 statements, analyzed descriptively. The results show that students' perceptions of the preparation, implementation, and conclusion stages of the practicum fall into the "good" category, with urban schools having a higher percentage. In conclusion, the implementation of practicums in urban schools is better than in rural schools, bringing attention to the need …