Biology Commons^™

Life On The Quarry Wall Vs The Quarry Floor: Parthenocissus Quinquefolia, Lily Monnett, Quincie Simmons, Lauren Kyburz

Annual Student Research Poster Session

Parthenocissus quinquefolia, Virginia creeper, is found in two parts of the DePauw Nature Park quarry: vertically along the quarry wall and on large rock piles on the quarry floor. I looked into how these different habitats influenced the growth form, stress responses, and fitness of the P. quinquefolia growing in them. P. quinquefolia on the wall has higher chlorophyll a content and higher water content. There was also a higher percentage of flowering individuals on the quarry wall than on the floor. Lastly, the two habitats had vastly different morphological growth forms, with those on the wall having very long …

Effects Of Large Mammal Exclusion On Seedling Communities Depend On Plant Species Traits And Landscape Protection In Human-Modified Costa Rican Forests, Nohemi Huanca-Nuñez, Robin L. Chazdon, Sabrina E. Russo

School of Biological Sciences: Faculty Publications

1. Large terrestrial herbivorous mammals (LTH-mammals) influence plant community structure by affecting seedling establishment in mature tropical forests. Many of these LTH-mammals frequent secondary forests, but their effects on seedling establishment in them are understudied, hindering our understanding of how LTH-mammals influence forest regeneration in human-modified landscapes.

2. We tested the hypothesis that the strength of LTH-mammals' effects on seedling establishment depends on landscape protection, forest successional stage and plant species' traits using a manipulative field experiment in six 1-ha sites with varying successional age and landscape protection. In each site, we established 40 seedling plot-pairs, with one plot excluding LTH-mammals and …

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Gaxin2-Xo3 Surface Pyramids Interaction With Formaldehyde: Thermodynamic And Sensing Analysis, Mudar Ahmed Abdulsattar

Karbala International Journal of Modern Science

GaxIn2-xO3 surface pyramids' electronic structures are investigated using density functional theory, including dispersion corrections. Application of GaxIn2-xO3 surface pyramids as a gas sensor for formaldehyde is also performed and compared with experimental findings. These findings show that the energy gap of these pyramids follows closely with the bulk values. The energy gap increases between the two limits, In2O3 and Ga2O3. Applying GaxIn2-xO3 surface pyramids as a gas sensor uses transition state theory formalism. Thermodynamic quantities such as activation Gibbs energy, enthalpy, and entropy are needed for temperature-dependent calculations. A comparison of sensor response which is proportional to reaction rate as …

Seed Coatings Containing Capsaicin Reduce Seed Removal In Temperate Woody Species, Brian M. Connolly, Francesca Lanni, John L. Orrock, Peter W. Guiden

Biology Faculty Scholarship

Coating seeds in taste-averting chemical defenses (e.g., capsaicin from Capsicum spp.) can reduce rodent seed predation, and thus might promote plant establishment and forest regeneration. However, the efficacy of such seed coatings remains unknown for many woody plant species, and seed coatings have not been evaluated across different habitats where forest managers might seek to promote forest regeneration. We used two complementary seed-removal experiments in closed-canopy forests (Michigan) and an old field undergoing reforestation (New York) to examine whether coating seeds of four native tree species (Acer rubrum, Fagus grandifolia, Pinus banksiana, and Pinus resinosa) with chili …

Reimagining Large River Management Using The Resist–Accept–Direct (Rad) Framework In The Upper Mississippi River, Nicole K. Ward, Abigail J. Lynch, Erik A. Beever, Joshua Booker, Kristen L. Bouska, Holly Embke, Jeffrey N. Houser, John F. Kocik, David J. Lawrence, Mary Grace Lemon, Doug Limpinsel, Madeline R. Magee, Bryan M. Maitland, Owen Mckenna, Andrew Meier, John M. Morton, Jeffrey D. Muehlbauer, Robert Newman, Devon C. Oliver, Heidi M. Rantala, Greg G. Sass, Aaron Shultz, Laura M. Thompson, Jennifer L. Wilkening

Biology Faculty Publications

Background Large-river decision-makers are charged with maintaining diverse ecosystem services through unprecedented social-ecological transformations as climate change and other global stressors intensify. The interconnected, dendritic habitats of rivers, which often demarcate jurisdictional boundaries, generate complex management challenges. Here, we explore how the Resist–Accept–Direct (RAD) framework may enhance large-river management by promoting coordinated and deliberate responses to social-ecological trajectories of change. The RAD framework identifies the full decision space of potential management approaches, wherein managers may resist change to maintain historical conditions, accept change toward different conditions, or direct change to a specified future with novel conditions. In the Upper Mississippi …

Meiosis In Budding Yeast, G. Valentin Borner, Andreas Hochwagen, Amy J. Macqueen

Biological, Geological, and Environmental Faculty Publications

Meiosis is a specialized cell division program that is essential for sexual reproduction. The two meiotic divisions reduce chromosome number by half, typically generating haploid genomes that are packaged into gametes. To achieve this ploidy reduction, meiosis relies on highly unusual chromosomal processes including the pairing of homologous chromosomes, assembly of the synaptonemal complex, programmed formation of DNA breaks followed by their processing into crossovers, and the segregation of homologous chromosomes during the first meiotic division. These processes are embedded in a carefully orchestrated cell differentiation program with multiple interdependencies between DNA metabolism, chromosome morphogenesis, and waves of gene expression …

Warmer Temperature Overrides The Effects Of Antidepressants On Amphibian Metamorphosis And Behavior, Peter Fong, Aylin Doganoglu, Eleanor Sandt, Sierra Turbeville

Biology Faculty Publications

Climate change can exacerbate the effects of environmental pollutants on aquatic organisms. Pollutants such as human antidepressants released from wastewater treatment plants have been shown to impact life-history traits of amphibians. We exposed tadpoles of the wood frog Lithobates sylvaticus to two temperatures (20°C and 25°C) and two antidepressants (fluoxetine and venlafaxine), and measured timing of metamorphosis, mass at metamorphosis, and two behaviors (startle response and percent motionless). Antidepressants significantly shortened time to metamorphosis at 20°C, but not at 25°C. At 25°C, tadpoles metamorphosed significantly faster than those at 20°C independent of antidepressant exposure. Venlafax- ine reduced body mass at …

Abalone Resource Of Western Australia: Harvest Strategy: 2021-2026 : Version 2.2, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Management Papers

This harvest strategy has been developed and revised in line with the Department’s Harvest Strategy Policy for Aquatic Resources (Department of Fisheries 2015) and is consistent with relevant national harvest strategy policies and guidelines (e.g. Sloan et al. 2014; Department of Agriculture and Water Resources 2018a, b). It makes explicit the performance indicators, reference levels, and harvest control rules designed to achieve the specific long- and short-term management objectives for the resource, and the broader goals of ESD and EBFM.

The publication of this harvest strategy is intended to make the decision-making considerations and processes for the management of specified …

Determining The Structure And Function Of A Bacteriophage Called Leozinho, Leonardo Rodrigues Venturotti

Biology Student Work

A research team, having discovered a bacteriophage named Leozinho a couple of years ago, embarked on a mission to unravel the structure of an unidentified gene, gp_61. They utilized ESMatlas, Foldseek, and ChimeraX to predict the structure of gp_61 and afterwards various laboratory procedures were employed to facilitate the growth of the gene. Ultimately, the experiment was concluded with the successful cloning of gp_61 into a plasmid vector for protein expression.

Dynamics And Inhibition Of Abc And Rnd Transporters Associated With Multidrug Resistances In Cancer And Pathogenic Bacteria, Hang Zhao

Biological Sciences Theses and Dissertations

The overexpression of efflux transporters is deemed to be one of the important mechanisms that contribute to Multidrug Resistance (MDR). In this dissertation, three transporters of significance were studied, the Breast Cancer Resistance Protein (BCRP/ABCG2) in a variety of cancer cells, the mtrCDE transporter from Neisseria gonorrhoeae, and the acrAB-tolC transporter from Escherichia coli. It is well known that the overexpression of BCRP in cancer cells results in these cells being resistant to the effects of many chemotherapeutics. This results in multidrug resistance for this cancer because of the fact that BCRP can transport many different types of …

The Coastal Monitor: Vol. 10 No. 2, John Tanacredi Ph.D.

The Coastal Monitor

Stephen J. Gould’s prophetic piece, “The Golden Rule: A Proper Scale for Our Environmental Crisis”, noted that, “Patience enjoys a long pedigree of favor”, which he elaborated, “usually involves a deep understanding of the fundamental principle… rarely grasped in daily life – the effects of scale.” Scientists observe changes incessantly, in dimensions and time, from microscopic conditions of cellular biology to the inconceivable distances of galaxies and their influences on Earth.

Patterns Of Cytonuclear Discordance And Divergence Between Subspecies Of The Scarlet Macaw (Ara Macao) In Central America, Matthew L. Aardema, Kari L. Schmidt, George Amato

Department of Biology Faculty Scholarship and Creative Works

The scarlet macaw, Ara macao, is a neotropical parrot that contains two described subspecies with broadly discrete geographical distributions. One subspecies, A. m. macao, is found from South America north into southwestern Costa Rica, while the second subspecies, A. m. cyanoptera, is found from eastern Costa Rica north into central Mexico. Our previous research using mitochondrial data to examine phylogeographical divergence across the collective range of these two subspecies concluded that they represent distinct evolutionary entities, with minimal contemporary hybridization between them. Here we further examine phylogenetic relationships and patterns of genetic variation between these two subspecies using a dataset …

Loggerhead Shrike Occurrence Along Urban Gradients In South Carolina’S Coastal Plain, Michelle A. Krauser, Christopher E. Hill

Biology

The urban landscape is understudied compared to less developed ecosystems, despite providing suitable habitat for wildlife, including some species of grassland birds. Loggerhead Shrikes (Lanius ludovicianus) are predatory songbirds that frequent grasslands and have been observed using grassy areas in developed and more natural landscapes, yet remain largely unstudied in developed landscapes. We investigated the effects of development, measured as impervious surface percentage, on Loggerhead Shrike occurrence in urban areas in South Carolina, U.S.A, and also tracked canopy cover (%), highway density (m/ha), non-highway road density (m/ha), total road density (m/ha), and powerline density (m/ha). The first author searched 300 …

Brilliant Bird Brains: Object Recognition In Herring Gulls (Larus Argentatus Smithsonianus), Kristen M. Covino, F. Dylan Titmuss, Joseph E. Brosseau, Dora C. Donacik, Maddie E. Ellms, Alyssa R. Nowicki, Daphne Okuyama, Jessica M. Robinson, Katherine A. Schickfus, Eliza L. Stanley, Mary Elizabeth Everett

Biology Faculty Works

The ability to recognize and associate objects with prior experiences has been demonstrated in several avian taxa. Corvids, for example, recognize visual stimuli associated with negative previous experiences and will modify their behavioral responses according to the level of perceived threat. However, the extent to which similar memory-based behaviors exist in seabirds is poorly understood. Our study investigated object recognition by Herring Gulls (Larus argentatus smithsonianus) on their breeding grounds, the site of a long-term monitoring project. When handling gulls and conducting field research, researchers wear standard bicycle helmets as a protective measure against physical aggression by nesting …

Application Of Computational Tools To Identify Variations Associated With Peromyscus Dominant Spot, Zhenhua Shang

Theses and Dissertations

Peromyscus are the most prevalent mammalian species in North America, and they're employed extensively in both laboratory and field studies. P. maniculatus and P. polionotus, the deer mouse and the old-field mouse, are closely related and can produce viable and fertile hybrid offspring. However, a comprehensive database of polymorphisms, particularly in those kept as living stocks and supplied to university researchers, is lacking. In chapter 2, we performed comparative genomic study on P. maniculatus and P. polionotus and used the polymorphic data to identify the range of genetic complexity that underlies physiological and behavioral differences between two species. We also …

The Effect Of Antibiotics On Immune Cell Infiltration Of Colon In A Mouse Model Of Early Onset Colorectal Cancer, Valerie Hinsch

Theses and Dissertations

Early onset colorectal cancer (EOCRC) is an aggressive form of colorectal cancer diagnosed before the age of 50. While colorectal cancer cases in patients 50 years and older have been declining, EOCRC cases have been steadily increasing globally in the last few decades, and the cause is unknown. Many agents, called exposomes, have been associated with EOCRC based on their emergence and prevalence prior to and in parallel with the rise in EOCRC cases. Among these are antibiotics (Abx). Abx are indispensable in our fight against infectious diseases, however their overuse is becoming a global epidemic. They are prescribed globally, …

Dephosphorylation Of Mpk6 And Mpk3 By Phosphatases Modulates Responses To Herbivory In Arabidopsis, Claire Teresa Hann

Theses and Dissertations

As sessile organisms, plants rely on extracellular signals and chemical responses to defend against stressors. Extracellular stress signals inducing defense responses originate both from biotic or abiotic threats, and from products of tissue damage or hormones. In defense against herbivores, essential responses include rapid generation of jasmonic acid (JA) at the wound site, followed by the global expression of genes that impede digestion and growth. Early defense gene expression amplifies JA production, while later JA-responsive gene expression causes the accumulation of defense products. MAP kinase (MAPK) pathways play a central role in mediating the perception of self, non-self, and hormonal …

College Of Natural Sciences Newsletter, September - October 2023, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 1 Dean's Message
Page 2 New Faculty an Staff for the Fall 2023 Semester
Page 3 Awards
Page 4 Student Ambassadors in CNS
Page 5 Meet our Jacks
Page 6-8 Events
Page 9-11 Media Coverage of CNS
Page 12-13 Spring 2023 Dean's List
Page 14 Open PRAIRIE Data

Farnesol Brain Transcriptomics In Cns Inflammatory Demyelination, William J. Doyle, Dana Walters, Xutong Shi, Kristina Hoffman, Krisztian Magori, Jean-Baptiste Roullet, Javier Ochoa-Repáraz

Biology Faculty Publications and Presentations

Background: Farnesol (FOL) prevents the onset of experimental autoimmune encephalomyelitis (EAE), a murine model of multiple sclerosis (MS).

Objective: We examined the transcriptomic profile of the brains of EAE mice treated with daily oral FOL using next-generation sequencing (RNA-seq).

Methods: Transcriptomics from whole brains of treated and untreated EAE mice at the peak of EAE was performed.

Results: EAE-induced mice, compared to naïve, healthy mice, overall showed increased expression in pathways for immune response, as well as an increased cytokine signaling pathway, with downregulation of cellular stress proteins. FOL downregulates pro-inflammatory pathways and attenuates the immune response in EAE. FOL …

Pollinators Of Gonzaga University, Sophie O'Shei, Gary Chang

Biology Student Scholarship

This data is from a public science project conducted by Sophie O'Shei (Gonzaga '24) investigating pollinator diversity in and around Gonzaga's campus. Photos of plants and pollinators were submitted using iNaturalist, an online platform and app that allows users to upload photos of animals, plants, insects, etc. and identifies their species using AI. It also tracks where photos were taken. Users were then able to go through uploaded images and suggest what species they identify in the photo, which can confirm or correct the AI's identification.

The project started during Earth Week 2023, giving students, staff, and other members …

Compensating For Effects Of Autotomy On Locomotion In Stink Bugs (Halyomorpha Halys), Lilian C. Jubb

Longwood Senior Thesis Proposal

Autotomy is the voluntary release of an appendage, typically to avoid predation or entrapment. Autonomy of a single leg can have minimal effects on locomotion in arthropods with more than six legs. Hexapods, however, use a double-tripod gait which is completely disrupted with the loss of a single leg, thus locomotor performance should be greatly reduced leading to lower survival. Autotomy is so costly to locomotion that some insects regenerate a lost limb in a subsequent molt leading to reduced investment in other important functions (e.g. reproduction). Autotomy persists in adult hexapods with no opportunity for regeneration, which suggests some …

Transcriptomics Of Temporal- Versus Substrate-Specific Wood Decay In The Brown-Rot Fungus Fibroporia Radiculosa, Byoungnam Min, Steven Ahrendt, Anna Lipzen, Cristina E. Toapanta, Robert A. Blanchette, Dan Cullen, David Hibbett

Biology

Brown-rot fungi lack many enzymes associated with complete wood degradation, such as lignin-attacking peroxidases, and have developed alternative mechanisms for rapid wood breakdown. To identify the effects of culture conditions and wood substrates on gene expression, we grew Fibroporia radiculosa in submerged cultures containing Wiley milled wood (5 days) and solid wood wafers (30 days), using aspen, pine, and spruce as a substrate.

Genome Assembly Of The Foot-Flagging Frog, Staurois Parvus: A Resource For Understanding Mechanisms Of Behavior, Mika A. Holtz, Riccardo Racicot, Doris Preininger, Adam M.M. Stuckert, Lisa A. Mangiamele

Biological Sciences: Faculty Publications

Elaborate and skilled movements of the body have been selected in a variety of species as courtship and rivalry signals. One roadblock in studying these behaviors has been a lack of resources for understanding how they evolved at the genetic level. The Bornean rock frog (Staurois parvus) is an ideal species in which to address this issue. Males wave their hindlimbs in a "foot-flagging"display when competing for mates. The evolution of foot flagging in S. parvus and other species is accompanied by increases in the expression of the androgen receptor gene within its neuromuscular system, but it remains unclear what …

Cannabinoid Receptor Type 1 Regulates Sequential Stages Of Migration And Morphogenesis Of Neural Crest Cells And Derivatives In Chicken And Frog Embryos, Amira Mahomed, Daljit Girn, Afrin Pattani, Brian K. Wells, Chloe C. King, Sonya Patel, Harsimran Kaur, Christina M. Noravian, Jessica Sieminski, Chi Pham, Halley Dante, Maxellende Ezin, Tamira Elul

Biology Faculty Works

The main cannabinoid receptor CB1R first shows expression during early neurula stage in chicken (Gallus gallus) embryos, and at early tailbud stage in the frog (Xenopus laevis) embryos. This raises the question of whether CB1R regulates similar or distinct processes during the embryonic development of these two species. Here, we examined whether CB1R influences the migration and morphogenesis of neural crest cells and derivatives in both chicken and frog embryos. Early neurula stage chicken embryos were exposed to arachidonyl-2ʹ-chloroethylamide (ACEA; a CB1R agonist), N-(Piperidin-1-yl)-5-(4-iodophenyl)-1-(2,4-dichlorophenyl)-4-methyl-1H-pyrazole-3-carboxamide (AM251; a CB1R inverse agonist) or Blebbistatin (nonmuscle Myosin II inhibitor) in ovo and examined during …

Characterizing Allosteric Regulation And Conformational Dynamics In Staphylococcus Aureus Pyruvate Carboxylase, Amanda Joan Laseke

Dissertations (1934 -)

Pyruvate carboxylase (PC) produces oxaloacetate from pyruvate and bicarbonatein an ATP-dependent manner. The catalytic activity of PC places it at a pivotal intersection between catabolism and anabolism. Understanding the essential metabolic role of PC requires a more complete description of how its activity is regulated and how that regulation is manifested through changes in conformational dynamics. PC activity is regulated by the mutually exclusive binding of the allosteric activator, acetyl-CoA, and the allosteric inhibitor, L-aspartate. The binding site for acetyl- CoA has largely been identified, but the binding location for the acetyl moiety is unknown. Given that the acetyl moiety …

The Role Of Insulin Signaling In Controlling Oogenesis In Drosophila Melanogaster, Tancia W. Bradshaw

Theses and Dissertations

Adult stem cell activity responds to organismal nutrient status to maintain and support tissue homeostasis. Despite the intricate relationship between dietary input, adipose tissue and peripheral organ function, we are at the tip of the iceberg regarding our understanding of the cellular and molecular mechanisms underlying adipose communication to other tissues. The Drosophila ovary receives nutritional signals from the fat body with multiple nutrient-sensing pathways functioning in adipocytes to control distinct stages of oogenesis. Insulin/insulin-like growth factor signaling (IIS) within adult adipocytes remotely controls oocyte production at distinct stages of oogenesis. The PI3K/Akt1 axis in adipocytes promotes germline stem cell …

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

Horticulture Faculty Publications and Presentations

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

Miocene Phytolith And Diatom Dataset From 10.3myo Diatomite Formation, Fernley, Nevada, Usa, Jacopo Niccolò Cerasoni, Megan C. O'Toole, Richa Patel, Yoel E. Stuart

Biology: Faculty Publications and Other Works

Phytoliths are opal silica particles formed within plant tissues. Diatoms are aquatic, single-celled photosynthetic algae with silica skeletons. Phytolith and diatom morphotypes vary depending on local environmental and climatic conditions and because their silicate structures preserve well, the study of phytolith and diatom morphotypes can be used to better understand paleoclimatic and paleoenvironmental dynamics and changes. This article presents original data from an 820cm-deep stratigraphy excavated at the Hazen diatomite deposits, a high-elevation desert paleolake in the Fernley District, Northern Nevada, USA. The site has been studied for an assemblage of fossilized threespine stickleback, Gasterosteus doryssus, that reveal adaptive …

Role Of G1p3-Rab5 Interaction In Breast Cancer Gene Expression, Madelyn Terrell

Honors Theses

Breast cancer is one of the most common cancers worldwide with millions of cases diagnosed each year. Despite modern treatments, over 40% of patients can expect to relapse after initial cancer eradication. Consequently, it is crucial to unravel the mechanisms by which breast cells confer their cancerous properties to develop novel treatments that improve patient survival. G1P3 is a mitochondrial localized protein found to be upregulated 50x in estrogen receptorpositive breast cancer and is correlated with overall poor patient survival. G1P3-overexpressing cells display increased amounts of interferon-stimulated genes (ISGs) and G1P3 as an ISG indicates these genes potential to promote …

Sex And Stress Modulate Pupal Defense Response In Tobacco Hornworm, Sukhman Singh, Sakshi Watts, Ishveen Kaur, Isabella Rodriguez, Jessica Ayala, Dariela Rodriguez, Elian Martin, Rupesh R. Kariyat

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

In insects, larval and adult defenses against predators have been well studied. However, pupal (also known as resting stage) defenses have been overlooked and not examined thoroughly. Although some pupa possess antipredator strategies such as hairs, spines, cryptic coloration, and exudation of chemicals, few studies have tested these responses and the factors affecting them. Here, we investigated the behavioral responses in tobacco hornworm Manduca sexta that pupates in soil by introducing an external stimulus using vibrations from an electric toothbrush to mimic predation. We observed that M. sexta made violent wriggling (twitching), followed by pulsating movements in response to the …