Biology Commons^™

The Past, Present, And Future Of Predator–Prey Interactions In A Warming World: Using Species Distribution Modeling To Forecast Ectotherm–Endotherm Niche Overlap, Jessica L. Hill, Matthew Grisnik, Ryan J. Hanscom, Jeet Sukumaran, Timothy E. Higham, Rulon W. Clark

Biology

Climate change has the potential to disrupt species interactions across global ecosystems. Ectotherm–endotherm interactions may be especially prone to this risk due to the possible mismatch between the species in physiological response and performance. However, few studies have examined how changing temperatures might differentially impact species' niches or available suitable habitat when they have very different modes of thermoregulation. An ideal system for studying this interaction is the predator–prey system. In this study, we used ecological niche modeling to characterize the niche overlap and examine biogeography in past and future climate conditions of prairie rattlesnakes (Crotalus viridis) and Ord's kangaroo …

Human Population Density And Blue Carbon Stocks In Mangroves Soils, Shih Chieh Chien, Charles Knoble, Jennifer Adams Krumins

Department of Biology Faculty Scholarship and Creative Works

Mangrove soils provide many important ecosystem services such as carbon sequestration, yet they are vulnerable to the negative impacts brought on by anthropogenic activities. Research in recent decades has shown a progressive loss of blue carbon in mangrove forests as they are converted to aquaculture, agriculture, and urban development. We seek to study the relationship between human population density and soil carbon stocks in urban mangrove forests to quantify their role in the global carbon budget. To this end, we conducted a global analysis, collecting mangrove soil carbon data from previous studies and calculating population density for each study location …

A Dietary Variety: Analyzing The Impacts Of Diverse Vs Worm-Exclusive Diets On The Blanding’S Turtle (Emydoidea Blandingii), Caitlin F. Copenhaver

Honors Program: Senior Projects (Public)

The endangered Blanding’s turtle (Emydoidea blandingii) is a species with a generally diverse diet in their freshwater wetland habitats; they consume prey such as crayfish and snails. In captivity, these options often become more limited due to logistical reasons. As ex situ conservation efforts such as captive rearing and head-starting are becoming more popular for this species, it will be important to gain more insight on how these more limited diets might affect these turtles. This study describes a comparison between diets in six captive Blanding’s turtles from September to November of 2023, with three turtles receiving only …

Experimental Evolution Under Varying Sex Ratio And Behavioral Plasticity In Response To Perceived Competitive Environment Independently Affect Calling Effort In Male Crickets, Jack T. Mckermitt, Bert Foquet, Will Kuna, John Hunt, Ben M. Sadd, Scott K. Sakaluk

Faculty Publications – Biological Sciences

The operational sex ratio (OSR) is a key component influencing the magnitude of sexual selection driving the evolution of male sexual traits, but males often also retain the ability to plastically modulate trait expression depending on the current environment. Here we employed an experimental evolution approach to determine whether the OSR affects the evolution of male calling effort in decorated crickets, a costly sexual trait, and whether plasticity in calling effort is altered by the OSR under which males have evolved. Calling effort of males from 2 selection regimes maintained at different OSRs over 18–20 generations (male vs. female biased) …

Impact Of Sodium Benzoate And A High Fat Diet On Kidney Of Mice., Anna Lipinski

College of Arts & Sciences Senior Theses

Sodium Benzoate (SB) is a commonly utilized food preservative with potential therapeutic uses for neurological conditions such as Alzheimer’s disease and hepatic encephalopathy. Consumption of SB is generally regarded as safe (GRAS), by the Food and Drug Administration, at amounts of 0.1% by weight of food. However, previous reports indicate that SB exposure may induce histological alterations in kidney structures and promote oxidative stress. Thus, with increasing obesity rates and fatty diets, the effects of SB coupled to a high fat diet (HFD) remain to be determined. This study addressed the hypothesis that SB with a HFD will increase extracellular …

Effects Of Anthropogenic Noise On The Provisioning Behavior Of Western Bluebirds And Artificial Light At Night On Nestling Development, Kerstin H. Ozkan

Master's Theses

Sensory environments are rapidly changing due to increased human activity in urban and non-urban areas alike. For instance, background sounds can interfere with parent-offspring communication and mask cues reflective of predation risk, resulting in elevated vigilance at the cost of provisioning. In chapter 1, we studied nestling provisioning behavior among Western Bluebirds (Sialia mexicana) in response to short-term (1 hr) and long-term (continuous exposure throughout nesting period) noise exposure. Provisioning rates were lower at nests exposed to short-term experimental traffic noise compared to exposure to ambient background sounds. Trial order strongly influenced provisioning behavior, with the decline in …

Herptile Gut Microbiomes: A Natural System To Study Multi-Kingdom Interactions Between Filamentous Fungi And Bacteria, Lluvia Vargas-Gastélum, Alexander S. Romer, Marjan Ghotbi, Jason W. Dallas, Reed. N. Alexander, Kylie C. Moe, Kerry L. Mcphail, George F. Neuhaus, Leila Shadmani, Joseph W. Spatafora, Jason E. Stajich, Javier F. Tabima, Donald M. Walker

Biology

Reptiles and amphibians (herptiles) are some of the most endangered and threatened species on the planet and numerous conservation strategies are being implemented with the goal of ensuring species recovery. Little is known, however, about the gut microbiome of wild herptiles and how it relates to the health of these populations. Here, we report results from the gut microbiome characterization of both a broad survey of herptiles, and the correlation between the fungus Basidiobolus, and the bacterial community supported by a deeper, more intensive sampling of Plethodon glutinosus, known as slimy salamanders. We demonstrate that bacterial communities sampled from frogs, …

Genome Editing Using Crispr-Cas9 In Annual Killifish Species, Keria Moritsugu-Vandehey

University Honors Theses

CRISPR-Cas9 genome editing has been used successfully to knock out genes in model organisms such as zebrafish, turquoise killifish, and cichlid fish. CRISPR-Cas9 genome editing has not been verified in the annual killifish, Austrofundulus limnaeus. We hypothesize that targeted editing of the tyrosinase gene in embryos of A. limnaeus will lead to fish without the ability to produce black pigment. Embryos at the 1-cell stage were injected with a Cas9 cocktail containing a mix of guide RNA molecules that target the genomic sequence of the tyrosinase gene and either an mRNA coding for the Cas9 protein or Cas9 protein. …

Coralai: Emergent Ecosystems Of Neural Cellular Automata, Aidan A. Barbieux, Aidan A. Barbieux

Master's Theses

Artificial intelligence has traditionally been approached through centralized architectures and optimization of specific metrics on large datasets. However, the frontiers of fields spanning cognitive science, biology, physics, and computer science suggest that intelligence is better understood as a multi-scale, decentralized, emergent phenomenon. As such, scaling up approaches that mirror the natural world may be one of the next big advances in AI. This thesis presents Coralai, a framework for efficiently simulating the emergence of diverse artificial life ecosystems integrated with modular physics. The key innovations of Coralai include: 1) Hosting diverse Neural Cellular Automata organisms in the same simulation that …

Rhizobia-Legume Symbiosis Mediates Direct And Indirect Interactions Between Plants, Herbivores And Their Parasitoids, Carlos Bustos-Segura, Adrienne L. Godschalx, Lucas Malacari, Sergio Rasmann, Fanny Deiss, Daniel Ballhorn, Betty Benrey

Biology Faculty Publications and Presentations

Microorganisms associated with plant roots significantly impact the quality and quantity of plant defences. However, the bottom-up effects of soil microbes on the aboveground multitrophic interactions remain largely under studied. To address this gap, we investigated the chemically- mediated effects of nitrogen-fixing rhizobia on legume-herbivore-parasitoid multitrophic interactions. To address this, we initially examined the cascading effects of the rhizobia bean association on herbivore caterpillars, their parasitoids, and subsequently investigated how rhizobia influence on plant volatiles and extrafloral nectar. Our goal was to understand how these plant- mediated effects can affect parasitoids. Lima bean plants (Phaseoulus lunatus) inoculated with rhizobia exhibited …

Foraminifera As A Model Of Eukaryotic Genome Dynamism, Caitlin Timmons, Kristine Le, H. B. Rappaport, Elinor G. Sterner, Xyrus X. Maurer-Alcaláh, Susan T. Goldstein, Laura A. Katz

Biological Sciences: Faculty Publications

In contrast to the canonical view that genomes cycle only between haploid and diploid states, many eukaryotes have dynamic genomes that change content throughout an individual’s life cycle. However, the few detailed studies of microeukaryotic life cycles render our understanding of eukaryotic genome dynamism incomplete. Foraminifera (Rhizaria) are an ecologically important, yet understudied, clade of microbial eukaryotes with complex life cycles that include changes in ploidy and genome organization. Here, we apply fluorescence microscopy and image analysis techniques to over 2,800 nuclei in 110 cells to characterize the life cycle of Allogromia laticollaris strain Cold Spring Harbor (CSH), one of …

The Metameric Echinoderm, Richard L. Turner

Ocean Engineering and Marine Sciences Faculty Publications

Animal phyla are distinguished by their body plans, the ways in which their bodies are organized. A distinction is made, for example, among phyla with bodies of many segments (metameric; e.g., annelids, arthropods, and chordates), others with completely unsegmented bodies (americ; e.g., flatworms and mollusks), and a few phyla with bodies of 2 or 3 regions (oligomeric; e.g., echinoderms and hemichordates). The conventional view of echinoderms as oligomeric coelomates adequately considers early development, but it fails to recognize the metameric body plan that develops in the juvenile rudiment and progresses during indeterminate adult growth. As in the 3 phyla traditionally …

Dna-Pkcs Rnaseq Data: Dna-Pkcs Wilde-Type Or Kinase-Dead Protein Regulate Basal And Etoposide-Induced Gene Expression Changes, Amanda Ashley

Chemistry & Biochemistry: Datasets

No abstract provided.

Environmental Dna Metabarcoding Of Pan Trap Water To Monitor Arthropod-Plant Interactions, Joshua H. Kestel, David L. Field, Philip W. Bateman, Nicole E. White, Karen L. Bell, Paul Nevill

Research outputs 2022 to 2026

Globally, the diversity of arthropods and the plants upon which they rely are under increasing pressure due to a combination of biotic and abiotic anthropogenic stressors. Unfortunately, conventional survey methods used to monitor ecosystems are often challenging to conduct on large scales. Pan traps are a commonly used pollinator survey method and environmental DNA (eDNA) metabarcoding of pan trap water may offer a high-throughput alternative to aid in the detection of both arthropods and the plant resources they rely on. Here, we examined if eDNA metabarcoding can be used to identify arthropods and plant species from pan trap water, and …

Reproductive Biology Of The Jellyfish Outbreak Along The Uae Coastal Waters, Amrutha Aravind

Dissertations

Jellyfish are a ubiquitous occurrence in the world’s oceans. During the past decades, dramatic spatial increases and temporal shifts in jellyfish distributions have been reported around the world. The United Arab Emirates (UAE) coastal area also has experienced several blooms along with severe adverse impacts on its economic facilities. Few studies have been conducted within the Arabian Gulf and the Sea of Oman, to identify the blooming species and the environmental parameters that favor such breakouts. The present study aimed to identify the jellyfish species found along the coastal area of UAE and trying to link their occurrence with seasonal …

Antioxidant Properties Of Kombucha Beverage Infused With Ganoderma Lucidum And Green Tea From Camellia Sinensis (L.) Kuntze With Several Fermentation Times, Rizki Rabeca Elfirta, Pamungkas Rizki Ferdian, Iwan Saskiawan, Tri Hadi Handayani, Kayla Faza Gustafri Mandalika, Rini Riffiani, Kasirah Kasirah, Ukhradiya Magharaniq Safira Purwanto

Karbala International Journal of Modern Science

Kombucha is a functional beverage produced through the fermentation of infused tea or Camelia sinensis (L.) Kuntze (CS) by a symbiotic culture of bacteria and yeast. Apparently, the substrate of kombucha can be substituted to enhance its functional properties. Ganoderma lucidum (GL) is a potential substrate reported to have health benefits. This study aims to evaluate antioxidant properties by comparing different formulations and fermentation times. The formulations prepared in the present study varied in the compositions of GL and CS substrates, namely F1 (100% GL), F2 (75% GL: 25% CS), F3 (50% GL: 50% CS), F4 (25% GL: 75% CS), …

Overview Of The Zoonotic Potential And Coinfection Of Sars-Cov-2 In Indonesia, Muhammad Khaliim Jati Kusala, Ni Luh Putu Indi Dharmayanti

Karbala International Journal of Modern Science

In the ASEAN region, Indonesia has the highest overall COVID-19 infection score. The SARS-CoV-2 pandemic first emerged in China and then transmitted sporadically throughout the world. Animals and humans can be infected with the corona virus, so this disease is classified as a zoonotic disease. This review aims to gather information regarding the potential of SARS-CoV-2 as a zoonotic disease and coinfections with several other pathogens in Indonesia. This study collected data demonstrating the potential for COVID-19 to be transmitted from humans to animals, as an evidenced by positive test results for the Bat Coronavirus Antigen in bats. Cats have …

Physical Properties Of Odorants Affect Behavior Of Trained Detection Dogs During Close-Quarters Searches, Daniel Mejia, Lydia Burnett, Nicholas Hebdon, Peter Stevens, Alexis Shiber, Clay Cranston, Lauryn Degreeff, Lindsay D. Waldrop

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Trained detection dogs have a unique ability to find the sources of target odors in complex fluid environments. How dogs derive information about the source of an odor from an odor plume comprised of odorants with different physical properties, such as diffusivity, is currently unknown. Two volatile chemicals associated with explosive detection, ammonia (NH₃, derived from ammonium nitrate-based explosives) and 2-ethyl-1-hexanol (2E1H, associated with composition C4 plastic explosives) were used to ascertain the effects of the physical properties of odorants on the search behavior and motion of trained dogs. NH₃ has a diffusivity 3.6 times that of …

Resolution Of Respect: Conrad Alan Istock (1936–2023), Steven Hecht Orzack, Julia Bell, Judith Bronstein, William Etges, Shripad Tuljakpurkar

Biological Sciences Faculty Publications and Presentations

Conrad Istock was an important contributor to the emerging field of evolutionary ecology starting in the 1960s. His best-known work in this area blended theory and field and laboratory studies of pitcher-plant mosquitoes. Conrad died March 8, 2023, in Ithaca, New York, USA.

Proteomic Dataset For Decellularization Of Porcine Auricular Cartilage, Roxanne N. Stone, Xinzhu Pu, Julia Thom Oxford

Biology Faculty Publications and Presentations

Objectives Osteoarthritis (OA) is a major concern in the United States and worldwide. Development and validation of robust decellularization techniques is critical in generating suitable bioscaffolds for future OA treatment options.

Data descriptions In the present study, proteins from porcine auricular cartilage before and after decellularization were extracted, digested, and identified using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The data represents protein profiles of both non-decellularized and decellularized porcine auricular cartilage. This data is intended to be useful to scientists who are interesting in generating biomaterials for potential relevant clinical applications using decellularized cartilage tissue.

A Test Of The Gleaner–Opportunist Trade-Off Among Photosynthetic Traits In Cryptophyte Algae, Jake A. Swanson, Matthew J. Greenwold, Tammi L. Richardson, Jeffry L. Dudycha

Biology Faculty Publications and Presentations

As photosynthetic producers, phytoplankton form the foundation of aquaticfood webs. Understanding the relationships among photosynthetic traits inphytoplankton is essential to revealing how diversification of these traitsallows phytoplankton to harvest energy from different light environments. Weinvestigated whether the diversification of 15 species of cryptophytes, a phy-lum of phytoplankton with diverse light-capturing pigments, showed evidenceof trade-offs among photosynthetic performance traits as predicted by the gleaner-opportunist resource exploitation framework. We constructed photo-synthesis versus irradiance (P–E) curves and rapid light curves (RLCs) to estimate parameters characterizing photosynthetic performance and electrontransport rate. We inferred the evolutionary relationships among the 15 specieswith ultraconserved genomic elements and …

Divergent Proteomic Profiles Of Opium Poppy Cultivars, Setenay Aykanat, Mine Türktaş

Turkish Journal of Biology

We examined the proteomic profiles of three registered opium poppy cultivars (Papaver somniferum L.) having different alkaloid contents. The study was conducted on both the stem and capsule organs. A high number of differentially expressed proteins (DEPs) were identified between the cultivars and the organs. We analyzed DEPs for their contribution in GO terms and KEGG pathways. The up-regulated DEPs were significantly enriched in photosynthesis and translation, for morphine-rich and noscapine-rich cultivars, respectively. The data depicted that photosynthesis is crucial for Benzylisoquinoline alkaloid (BIA) biosynthesis, but different processes are also effective on morphine and noscapine biosynthesis, which occur at different …

Tnfr1 Signaling Is Positively Regulated By Jak-2 And C-Src Via Tyrosine Phosphorylation, Fatma Zehra Hapi̇l Zevkli̇ler, Fatma Ece Çopuroğlu, Mustafa Gökhan Ertosun, Ufuk Mert, Derya Özeş, Osman Nidai Özeş

Turkish Journal of Biology

Background/aim: Tumor necrosis factor alpha (TNFα, a.k.a. TNF) is a pleiotropic cytokine that exerts most of its effects through type 1 TNF receptor (TNFR1). Following TNF binding, TNFR1 recruits TRADD (tumor necrosis factor receptor type 1-associated DEATH domain). This interaction triggers formation of signalosome complexes which have been claimed to induce apoptosis (via downstream caspase activations), inflammation (via NF-kappaB) and stress pathways (JNK & p38). However, the mechanism underlying TNF-induced ERK and AKT activation is not completely revealed. TNFR1 is known to constitutively bind c-Src and JAK2, and these enzymes were previously demonstrated to modulate TNF signaling. Therefore, we hypothesized …

Prognostic Gene Biomarkers For C-Src Inhibitor Si162 Sensitivity In Melanoma Cells, Seyhan Türk, Ayşegül Yilmaz, Ümit Yavuz Malkan, Gülberk Uçar, Can Türk

Turkish Journal of Biology

Background/aim: Early detection and treatment are crucial in combating malignant melanoma. Src is an important therapeutic target in melanoma due to its association with cancer progression. However, developing effective Src-targeting drugs remains challenging and personalized medicine relies on biomarkers and targeted therapies for precise and effective treatment. This study focuses on Si162, a newly synthesized c-Src inhibitor, to identify reliable biomarkers for predicting Si162 sensitivity and explore associated biological characteristics and pathways in melanoma cells. Materials and methods: Primary melanoma cells (M1, M21, M24, M84, M133, M307, and M2025) were obtained from patients diagnosed with melanoma. Si162 cytotoxicity tests were …

Expression Patterns Of M6a Rna Methylation Regulators Under Apoptotic Conditions In Various Human Cancer Cell Lines, Azime Akçaöz Alasar, Buket Sağlam, İpek Erdoğan Vatansever, Bünyamin Akgül

Turkish Journal of Biology

Background/aim: Cancer is a complex disease that involves both genetic and epigenetic factors. While emerging evidence clearly suggests that changes in epitranscriptomics play a crucial role in cancer pathogenesis, a comprehensive understanding of the writers, erasers, and readers of epitranscriptomic processes, particularly under apoptotic conditions remains lacking. The aim of this study was to uncover the changes in the expression of m6A RNA modifiers under apoptotic conditions across various cancer cell lines. Materials and methods: Initially, we quantified the abundance of m6A RNA modifiers in cervix (HeLa and ME180), breast (MCF7 and MDA-MB-231), lung (A549 and H1299), and colon (CaCo2 …

Theranostic Potential Of A Novel Aptamer Specifically Targeting Her2 In Breast Cancer Cells, Fulya Küçükcankurt, Samet Uçak, Nedret Altiok

Turkish Journal of Biology

Background/aim: The overexpression of HER2 is correlated with poorer outcomes and therapeutic resistance in breast cancer patients. While HER2-targeted therapies have shown improvement, prognosis remains poor for HER2-positive breast cancer patients, and these treatments have limitations. Therefore, it is crucial to explore effective molecular strategies for early detection and treatment of HER2-positive breast cancers. Materials and methods: In this study, we employed the cell-SELEX method to generate a selective aptamer capable of recognizing HER2 in its native conformation within breast cancer cells, for theranostic applications. Utilizing an adherent cell-SELEX approach, we developed and explored a DNA aptamer, named HMAP7, which …

Circrna Ldlr Promotes Proliferation And Aerobic Glycolysis Of Gastric Cancer Cells By Targeting Chd1 With Mir-449b-5p, Fanye Zeng, Juntao Zhao, Mengting Tong, Wenting He, Nan Li, Yuxiang Fan, Yanhua Zhu, Liping Zhang, Hongliang Zhang

Turkish Journal of Biology

Background/aim: Circular RNAs can serve as detection biomarkers and therapeutic targets for tumors. Our study aimed to elucidate the mechanisms associated with circRNA LDLR (circLDLR) in gastric cancer (GC) proliferation and aerobic glycolysis. Materials and methods: Expression signatures of circLDLR, miR-449b-5p, and CHD1 were examined in GC samples using quantitative PCR. Proliferation ability of MKN-45 cells was assessed via CCK-8 and EdU assays, and cell apoptosis was measured by flow cytometry. Glucose uptake, lactate production, ATP/ADP ratios, and NAD+/NADH ratios in cell supernatants were quantified to evaluate aerobic glycolysis. Subcellular isolation assay, quantitative PCR, immunoblot analysis, RNA immunoprecipitation (RIP), and …

Beneficial Effects Of A Novel Polyherbal Formulation On The Skeletal Muscle Antioxidant Status, Inflammation, And Muscle-Signaling Proteins In Exercised Rats, Mehmet Tuzcu, Oğuzhan Özdemi̇r, Cemal Orhan, Nurhan Şahi̇n, Abhijeet Morde, Muralidhara Padigaru, Prakash Bhanuse, Kazım Şahi̇n

Turkish Journal of Biology

Background/aim: Exhausting exercise can damage muscle tissue due to free radical interactions. It is hypothesized that the increase in free radicals following muscle injury, either due to oxidative damage to biomolecules or the activation of inflammatory cytokines, may lead to secondary muscle damage. This study investigated the effects of a novel joint health formula (JHF) containing bisdemethoxycurcumin-enriched curcumin, 3-O-Acetyl-11-keto-beta-boswellic acid-enriched Boswellia (AKBA), and Ashwagandha on exhaustion time, grip strength, antioxidant status, and muscle-signaling proteins in exhaustively exercised rats. Materials and methods: Twenty-eight rats were divided into four groups: Control (C), exercise (E), E + JHF 100 (100 mg/kg), and E …

Effect Of Thymol On Oxidative Stress And Reelin Signaling Pathway In Alzheimer's Disease Model, Barış Bi̇tmez, Burcu Çevreli̇, Emel Kaşikçi

Turkish Journal of Biology

Background/aim: The purpose of this study was to investigate how thymol affects cognitive functions and the levels of MDA, GSH, Aβ1-42, ApoE, reelin, and LRP8 in an AD model induced in male Wistar albino rats with the application of D-galactose (D-gal) and aluminum chloride (AlCl3). Materials and methods: In this work, 3-month-old male Wistar albino rats were used. Group 1 served as the Control, Group 2 received 0.5 mL/day saline + 0.5 mL/day sunflower oil, Group 3 was administered 200 mg/kg/day AlCl3 + 60 mg/kg/day D-gal, Group 4 received 30 mg/kg/day thymol, and Group 5 was administered 200 mg/kg/day AlCl3 …

Relation Of Life Sciences Students’ Metacognitive Monitoring To Neural Activity During Biology Error Detection, Mei Grace Behrendt, Caron Clark, Mckenna Elliott, Joseph Dauer

Department of Educational Psychology: Faculty Publications

Metacognitive calibration—the capacity to accurately self-assess one’s performance—forms the basis for error detection and self-monitoring and is a potential catalyst for conceptual change. Limited brain imaging research on authentic learning tasks implicates the lateral prefrontal and anterior cingulate brain regions in expert scientific reasoning. This study aimed to determine how variation in undergraduate life sciences students’ metacognitive calibration relates to their brain activity when evaluating the accuracy of biological models. Fifty undergraduate students enrolled in an introductory life sciences course completed a biology model error detection task during fMRI. Students with higher metacognitive calibration recruited lateral prefrontal regions linked in …