Digital Commons Network^™

Cluster Analysis To Explore Morphological Variation Of Banana (Musa Spp.): A Case Study In Jember And Lumajang, East Java, Indonesia, Halimatus Sa'diyah, Vega Kartika Sari, Riza Yuli Rusdiana, Achmad Chaqiqotul Khofi

Jurnal Kultivasi

Banana (Musa spp.) is an important horticultural plant with a high variety in Indonesia; yet, knowledge on the morphological characteristics of indigenous bananas in East Java remains inadequate. This research aims to identify the variation and classify banana cultivars in East Java based on morphological character. The exploration was conducted using the accidental sampling method. The observations include 15 qualitative and 9 quantitative characters. Descriptive statistics were used to evaluate the data, followed by cluster analysis using the average linkage method and Euclidean distance. The exploration resulted in 15 banana cultivars with varying morphology. The cluster analysis shows banana cultivars …

Geographic Divergence Of Methicillin-Resistant Staphylococcus Aureus St5-Scc Mec I In The Aftermath Of A Major Earthquake And Tsunami: Impact Of A Plasmid Harboring Heavy Metal Resistance Genes, Jose R W Martínez, Manuel Alcalde-Rico, Estefanía Jara-Videla, Jinnethe Reyes, Lina P Carvajal, Sandra Rincon, Rafael Ríos, Lorena Diaz, Ana Quesille-Villalobos, Roberto Riquelme-Neira, Lina Rivas, Ahmed M Moustafa, Blake Hanson, Eduardo A Undurraga, Jorge Olivares-Pacheco, Patricia García, Rafael Araos, Paul J Planet, César A Arias, Jose M Munita

Faculty, Staff and Student Publications

Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health menace. The global spread of MRSA is characterized by successive waves of epidemic clones dominating specific geographical regions. The acquisition of genes encoding resistance to heavy metals (HMRGs) is thought to be a key feature in the geographic divergence of MRSA. However, the cause-effect relationship between the presence of HMRGs and the divergence of MRSA clones remains to be clarified. In this study, we assessed the role that HMRGs may have played in the evolutionary divergence of the MRSA ST5-SCCmecI lineage in Latin America. We conducted a genomic characterization …

An In Vivo Microscopy Dataset For The Characterization Of Leukocyte Death, Alain Pulfer, Diego Ulisse Pizzagalli, Miguel Palomino Segura, Nina Germic, Tommaso Virgilio, Mauro Di Pilato, Pau Carrillo Barbera, Elisa Palladino, Paola Antonello, Marcus Thelen, Hans-Uwe Simon, Rolf Krause, Santiago F Gonzalez

Faculty, Staff and Student Publications

Recent advancements in intravital microscopy have enabled the study of cell death in vivo under various experimental conditions, such as infection and cancer. However, the limited throughput of this technology, together with a lack of openly accessible datasets, affects the development of algorithms for the automatic detection and characterization of cell death, which in turn require the integration of extensive and curated datasets. To address these needs, we present a curated dataset of microscopy videos depicting the death of neutrophils, eosinophils, and dendritic cells, acquired in the spleen and in the lymph node of mice under inflammatory conditions. The dataset …

Antioxidant Activity (2-2-Diphenil-1-Picrilhydrazil Radical-Scavenging Assay) And Phytochemicals Of Mimosa Invisa Colla And Mimosa Pigra L. Grown At Different Terrestrial Habitats, Irawati Chaniago, Ryan Budi Setiawan, Ardi, Doni Hariandi, Winda Purnama Sari

Jurnal Kultivasi

Giant false sensitive plants (Mimosa invisa Colla) and giant sensitive plants (Mimosa pigra L.) are invasive plant species in the tropics and native to America. They are widely distributed in different ecosystems and soil types. Apart from being considered woody shrub weeds, these plant species can be used as herbal medicine for their antioxidant activities. An experiment to study the antioxidant activities and phytochemicals of M. invisa and M. pigra grown at 200 m from the coastline and close to the riverbank (riparian abandoned land) was carried out from March to November 2023. Weed leaves were collected as purposive randomized …

Agronomic Performance And Stability Of Padjadjaran Hybrid Maize In Different Agroecosystems, Farhan Fadhillah, Fiky Yulianto Wicaksono, Yuyun Yuwariah, Dedi Ruswandi

Jurnal Kultivasi

The development of high-yielding hybrid maize is a strategic step to address global food demand amidst climate change. This study evaluates the agronomic performance of 14 maize genotypes—10 newly developed F1 hybrids and 4 commercial checks—under two planting densities (95,000 and 55,000 plants/ha) across three agroecosystems (lowland, midland, and highland). The objectives were to identify superior and adaptive genotypes and analyze genotype × environment interactions using AMMI and GGE biplot methods. Genotype G12 exhibited the highest yield (338.4 g/plant) at high density, especially in the highland, but showed poor stability. In contrast, G5 demonstrated consistent performance and stability across environments. …

Greenhouse Gas Emissions From Flood-Irrigated Rice As Affected By Phosphorus Fertilizer Source, Chandler M. Arel, Kristofor R. Brye, Diego Della Lunga, Trenton L. Roberts, Richard Adams

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Research into alternative phosphorus (P) fertilizer sources that may be able to supplement P resources is necessary. Struvite (MgNH4PO4 · 6H2O) can be made by removing excess nutrients from waste sources and may reduce greenhouse gas (GHG) emissions from cropping systems. This study sought to quantify GHG [i.e., methane (CH4), nitrous oxide (N2O), and carbon dioxide (CO2)] fluxes, season-long emissions, and net GHG emissions from chemically precipitated struvite (CPST) and synthetic and real-wastewater-derived electrochemically precipitated struvite (ECST) compared to monoammonium phosphate (MAP) and an unamended control (UC) from flood-irrigated rice (Oryza sativa) grown in P-deficient, silt loam soil in a …

Pilrα Sustains Microglial Capacity To Process Myelin In A Mouse Model Of Demyelination, Kent Lin

Arts & Sciences Graduate Student Theses and Dissertations

Alzheimer's disease (AD) is characterized by amyloid-β (Aβ) plaques, neurofibrillary tangles, and neurodegeneration. Microglia, the resident immune cells of the central nervous system (CNS), play a crucial role in AD pathogenesis by containing the spreading of Aβ plaques. Genetic studies have associated a variant of the receptor Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRα) with reduced risk for AD. PILRα is a receptor found on myeloid cells, such as microglia, that binds to endogenous cell surface glycoproteins and sends inhibitory signals within the cell. Additionally, it serves as an entry receptor for Herpes Simplex Virus 1. To elucidate the role …

Pluredecadal Patterns Of The Harmful Algal Blooms In The Highly Dynamic Marine Ecosystem Of Alexandria (Egypt): A Review, Samia K. Mikhail, Wagdy Labib

Blue Economy

The long-term study of phytoplankton variability in the coastal waters of Alexandria encounters significant challenges due to several factors such as inconsistency in sampling efforts conducted across various spatial and temporal scales, limitations of short-term monitoring methods, rapid urbanization and economic expansion, and their diverse eco-environmental impacts. The article analyzes a quantitative and qualitative dataset on algal bloom variabilities in Alexandria marine ecosystem from 1992 to 2023, highlighting changes in bloom patterns and trends such as annual cycles, short-term trends, rapid turnover rates of bloom structures, recurrent blooms of various classes, escalation in the frequency and magnitude, unusual episodic events, …

Induction Of Diabetic Cardiomyopathy In A Three-Dimensional Myocardial Model, Maelyn Andreasen

Student Research Symposium

Diabetic cardiomyopathy: Impairs and damages heart tissue through chronic exposure to hyperglycemia, or high blood sugar, in diabetic individuals

The Effects Of Different Types Of Fertilizer On The Growth Of Pseudomonas Frederiksbergenis, Aspen Curtis, Nadia Greding, Kylie Fluckiger, Samantha Clements

Student Research Symposium

Which fertilizers will promote the growth of the isolate of Pseudomonas frederiksbergensis (P. frederiksbergensis)?

Pseudomonas Parafulva Confirmed To Have Antifungal Properties When Grown In Conjunction With Botrytis Cinerea, Caden Dupee, Kylee Eldredge, Zachary Elmer, Joshua Hartvigsen

Student Research Symposium

Widespread antibiotic use has led to antibiotic resistance of infectious bacteria. (Young, 2017) As part of the TinyEarth Program, the lab group collected and tested local soil samples for bacteria with hopes of finding novel antibiotic properties. From the soil samples, a bacteria was isolated, subsequently sequenced, and determined to be Pseudomonas parafulva. P. parafulva is a Gram-negative bacterium that has been known to frequent rice paddies of eastern Asian countries and has been collected in select regions of North America, including that of Cache Valley. P. parafulva has been linked to anti-fungal activities on plants. (Lui et …

Diets And Environmental Impacts - Generational Outlook, Aspen Hopper, Melanie Jex

Student Research Symposium

How different diets impact the environment: Are we aware?

The Effects Of Biodiversity On Plant Parasitic Nematodes, Josh Lund

Student Research Symposium

The Dilution Effect Hypothesis¹ argues that biodiversity reduces pathogen transmission risk due to dilution of susceptible hosts, enhanced microbial communities that suppress pathogens, interference competition, nutrient heterogeneity, and ecological stability.

A Look Into Frugivorous Interactions With Psychotria And Palicourea In Barro Colorado Island, Panama, Madison Smart, Gerald Schneider, Elsa Jos

Student Research Symposium

Importance of Seed Dispersal

• Seed dispersal is a vital ecological process that influences plant population dynamics and ecosystem structure.
• Half of all seed-bearing plants rely on frugivorous animals to disperse their seeds to new locations, promoting plant recruitment

How Peribacillus Simplex Influences Plant Growth In The Presence Of Pesticide, David Tolman, Luke Wilkinson, Tanner Thompson, Tori Richardson

Student Research Symposium

P. simplex is known for its biocontrol, bioremediation, antibiotic producing, and sustainable agriculture properties

Determining The Kinetic Basis Of Crispr-Cas12a2 Function, Sobita Kunwar, Thomson Hallmark, Dylan Keiser, Bronson Naegle, Sudeshna Manna, Aaron Thomas, Chase L. Beisel

Student Research Symposium

CRISPR- Cas (Clustered Regularly Interspaced Short Palindromic Repeats- CRISPR associated) systems are bacterial adaptive immune systems that protect bacteria against mobile genetic elements such as viruses and plasmids^1,2.

Investigating The Oxytocin System Of The Brain In The Molecular Basis Of Self-Control, Kenzie Wachtel

Student Research Symposium

• Oxytocin (OXT) is a neuropeptide involved in social behaviors such as pair-bonding, maternal behavior, and attachment¹. At the core of these social bonds is reward. OXT has many interactions with neural reward circuits to produce the pleasurable effects of social contact².

Response To Induced Herbivory, Isis Cordova

Student Research Symposium

Herbivore attacks trigger complex changes in plant primary and secondary metabolisms. Secondary metabolites (SM), are hypothesized to respond synergistically to repeated herbivore attacks (Fig. 1).

Unearthing Connections: Characterizing Populations Of Local Harvester Ants, Carson Lyman

Student Research Symposium

What is Hybridization?

• Hybridization is the combination of two different species or subspecies, to create hybrid offspring¹.
• The offspring inherits some genetic material from both parents and so exhibits characteristics of both.

Determining Antibiotic Efficacy On A Species Of Pseudomonas Bacteria Isolated From A Soil Sample, Austin Taylor, Peyton Wells, Alyssa Smith

Student Research Symposium

The Pseudomonas genus contains a variety of species of bacteria that play essential roles in soil health, plant growth, and microbial competition. Certain species exhibit biocontrol properties by producing antimicrobial compounds to protect plants from harmful pathogens. While our Pseudomonas species is normally non-pathogenic to plants and humans, it could transfer antimicrobial resistance genes to harmful pathogens in the environment. By studying the Minimum Inhibitory Concentration (MIC) of the isolated bacteria to several common antibiotics, we could identify antibiotic-sensitive strains that could be used in agriculture, or antimicrobial-producing strains that could serve as natural defenses for plants.

What Nesting Materials Are Best For An Insect Hotel?, Madison Smart

Student Research Symposium

• Native insects are important for pollination, natural pest management, and other ecological processes.

Identifying Compensatory Mutations In The Envelope Protein Of Japanese Encephalitis Virus That Restore Neurovirulence, Nathan Taylor, Jiyoun Kim

Student Research Symposium

• Japanese Encephalitis Virus (JEV) is a positive sense, single stranded Enveloped virus

Solving The Structure Of An Ancestral Protein Tyrosine Phosphatase, Natalie Turcsanski, Edna Armah

Student Research Symposium

Protein tyrosine phosphatases (PTPs) regulate cell signaling by removing phosphate groups from tyrosine residues. Malfunction of these enzymes can lead to diseases such as diabetes and cancer. A conserved feature among PTPs is the catalytic acid loop, essential for phosphate removal. Computational analysis of PTP structures revealed that ancestral PTPs have considerable variation in conformations of this loop, sparking interest in their further study. The Asgard group, identified as ancestral to eukaryotic PTPs, was successfully expressed and purified under optimized conditions. Current efforts focus on optimizing crystallization to obtain larger crystals for structural analysis. This project will investigate the allosteric …

Vaccine Stabilization With Spider Silk, Mallory Wootton

Student Research Symposium

Most vaccines must be stored between 2 - 8°C to maintain their efficacy, with some vaccines requiring temperatures as low as -70°C for long-term storage. These temperature requirements pose issues for vaccine distribution, notably to remote/rural areas, in hotter climates, and low- and middle-income countries which are largely dependent on vaccine imports. [1]

Determining The Function Of Type Iv-B Crispr-Cas Systems, Eric Jenkins, Brendon Guinn

Student Research Symposium

CRISPR-Cas systems are a diverse group of prokaryotic adaptive immune systems that defend against Mobile Genetic Elements (MGEs) such as bacteriophages and plasmids. CRISPR-associated (Cas) proteins bind to guide RNAs (crRNAs) transcribed from a DNA repeat array (CRISPR array) containing spacers complementary to MGEs. Upon infection by a MGE, the Cas protein-crRNA complex binds to the target sequence in the invaders genome and cleaves the nucleic acid.

Distributor-Specific Variability In Balb/C Mouse Mortality Following Sars-Cov-2-Ma10 Infection, Taylor Kerr

Student Research Symposium

In recent years SARS-COV-2 has become a rapidly expanding area of research. To model human infections, this virus was adapted to mice enabling valuable insight into these processes.² Mice are often an effective research model due to their low cost, short reproduction time, and ability to adapt to a wide variety of viruses. Research into these immunological responses is crucial in developing vaccines, treatments, and furthering our understanding of this virus' behavior.¹ However, genetic variability in mouse models may be confounding previous and on-going research.

Activation Of Enkephalinergic Neurons Modulate Pain Within The Brain, Lucy N. Scribner, Oakley M. Statham, Greydon R. Durrant, Callie M. Newson

Student Research Symposium

The endogenous opioid system, consisting of three neuropeptides and canonical receptors, is ubiquitously expressed throughout the brain and is heavily involved in modulating pain[1]. However, research has placed tremendous focus on investigating the receptors of this system, and less attention has been devoted to the peptides. One such opioid peptide, enkephalin, is notably absent within the pain center of the brain, the periaqueductal gray (PAG)[2]. To further understand the role enkephalins play in modulating pain, we aimed to target and activate specific enkephalin-containing neurons that connect to the PAG. By activating these enkephalinergic projections, we hypothesized that this would lead …

Effects Of C-Section Birth On Vasopressin 1a Receptors In The Prairie Vole Brain, Caleb Hart

Student Research Symposium

The goal of this study was to understand how the brain might change depending on the birth experience: a vaginal birth or a cesarean section. C-sections have been associated with an increased risk of obesity and other behavioral and metabolic health conditions that are related to the function of hypothalamic hormones in the brain¹. Vasopressin is one neuropeptide hormone that is produced in the hypothalamus and influences a variety of metabolic functions and behaviors, including water balance and social pair bonding². This study used prairie voles to assess the effect of birth experience on the brain …

Seasonal And Sex-Based Variation In Coyote Responses To Social Olfactory Stimuli, Giuliana Carneiro

Student Research Symposium

Coyotes (Canis latrans) are socially complex, often forming strong pair bonds that can persist across multiple breeding seasons³. Scent marking, particularly urine marking, is a key form of communication used to establish territory, convey reproductive status, and maintain social hierarchies¹. This behavior is influenced by factors such as sex and season, and is central to understanding their social dynamics⁴. This preliminary study is part of a broader investigation into coyote behavior, specifically examining how these factors affect responses to olfactory stimuli from familiar and unfamiliar individuals².

In this study, coyote …

Drivers Of Recruitment For A Population Of Cutthroat Trout In Northern Utah, Abbigail Lane, Austin Garner

Student Research Symposium

• Understanding recruitment dynamics informs effective management of sensitive populations (Camp et al. 2020).