Digital Commons Network^™

Soil Microbiome Effect On Seedling Diseases And High Throughput Isolate Identification, Annalaysia Smith, Mara Krone, Santiago Mideros

MICRO-CCS student projects

The soil microbiome has a substantial effect on disease suppression. Organic farming is a practice used to create a more diverse microbiome which can create disease suppression. Different agricultural practices such as fertilization and rotation system are known to affect the microbiome (Schlatter et al 2017). Therefore, it is important to study the effects of different microbiomes on disease suppression. Furthermore, methods are necessary for quantifying the effect of disease suppression on specific pathogen populations. To do this, it is important to properly identify the pathogens.

Objectives:

1. Test if different nitrogen treatments cause variations in organic soils disease suppression. …

Efficacy And Evolutionary Dynamics Of 222 Nm Far-Uvc Against Vibrio Cholerae, Kadicha Madakimova, Angus Wu, Nkrumah Grant

MICRO-CCS student projects

The Far-UVC light at 222 nm wavelength (UV222) is one of the emerging methods of disinfection of bacteria in public spaces such as hospitals and labs.

• Does not penetrate human skin and does not cause harm to eyes making it a safer alternative to conventional UV systems.

• Primarily targets proteins preventing regrowth and repair pathways.

However, the potential for bacterial adaptation following sublethal UV222 exposure remains largely unknown.

Central question: How does QS transcriptional state influence the efficacy and resistance profile of V. cholerae to UV222 nm irradiation?

Hypothesis: Qurom-sensing transcriptional state determines V. cholerae susceptibility to UV222 nm UV …

The Gravity Of The Ukraine War: Measuring Conflict Impacts On European Grain Trade, Stefan Bonchis

Graduate Theses and Dissertations

This thesis investigates the heterogeneous structural disruptions caused by the war in Ukraine on the European Union’s agricultural trade architecture, focusing on three critical commodities: wheat, maize, and sunflower seeds. Employing a structural gravity model framework across all 27 EU Member States, the study evaluates two conflict episodes, the 2014 Crimea annexation and the 2022 full-scale invasion, to identify the net beneficiaries and heavily impacted nations within the EU agricultural trade network. The empirical strategy utilizes a dual-test design to capture the full scope of the disruption. Test A (Ukraine towards the EU trade) reveals a distinct geographic logic in …

Investigation Into Molecular Bases Of Pregnancy-Associated Malaria, Nicole Pozo

Biochemistry and Molecular Biology

Plasmodium falciparum causes the most severe and deadly form of malaria and remains a major global health problem, especially in sub-Saharan Africa (Milner, 2018). The parasite infects and multiplies inside red blood cells, leading to fever, anemia, organ damage, and death if untreated (Milner, 2018; Song et al., 2022). It is especially dangerous because it avoids the immune system by changing surface proteins called Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), which are encoded by more than 60 var genes. By switching between these genes, the parasite hides from immune detection and creates repeated waves of infection (Deitsch & Dzikowski, …

Using Zebrafish To Investigate The Innate Immune Response To R132h Mutant Glioma, Mikaela L. Fairbanks

All NMU Master's Theses

Gliomas are the most commonly occurring brain tumor found in adults. The most dominant mutation found in glioma is in the isocitrate dehydrogenase 1 (IDH1) gene. IDH converts isocitrate into α-ketoglutarate (α-KG), but the mutated form of it will take α-KG and further convert it into D-2-hydroxyglutarate (D-2-HG). Mutated IDH1 glioma (mIDH1) produces a higher concentration of D-2-HG than the wild-type IDH1 glioblastoma (wtIDH1). These mIDH1 tumors tend to have a better prognosis, growing slower and having less inflammation than the wtIDH1 counterpart, potentially due to the increased D-2-HG. However, the effects of mIDH1 and D-2-HG on the innate immune …

Identification Of Conditionally Essential Genes Required For Salmonella Enterica Serovar Typhimurium Adaptation To The Chicken Cecal Extract Through Ex Vivo Modeling And Transposon Insertion Sequencing, Deborah Bukola Olubanjo

Graduate Theses and Dissertations

Salmonella enterica serovar Typhimurium (S. Typhimurium) remains a major foodborne pathogen associated with chicken, where it can persist in the intestinal tract without overt disease and contribute to zoonotic transmission. The chicken cecum represents a complex ecological niche shaped by microbial competition, host-derived substrates, short-chain fatty acids, oxygen limitation, extracellular components, and diverse metabolic gradients. Although transposon insertion sequencing (Tn-seq) has been widely used to define bacterial fitness determinants, limited work has examined genome-wide adaptation of S. Typhimurium in chicken ceca-derived ex vivo systems that preserve key features of the avian cecal environment. This dissertation investigated conditionally essential genes required …

Guide To The Erath Winery Collection, Linfield College Archives

Linfield Archives Finding Aids

The collection was donated by Richard (Dick) Erath, the founder of the Erath Winery in Dundee, Oregon. The collection contains financial information about the Winery, publicity found in newspapers and magazines, personal plans, details of the wine-making process, multiple drafts of the biographical book The Boys Up North; among much other information, and a bottle of the first commercial wine produced by the Erath Winery in 1972.

Soilless Substrates As A Critical Control Point For Mitigating Food Safety Risks Within Hydroponic Leaf Lettuce Production, Eric Nuertey Tetteh

Graduate Theses and Dissertations

The effect of hydroponic soilless substrates and microbial biocontrol agents on the persistence of foodborne pathogens in indoor lettuce production is variable depending on substrate type, pathogen species, and biocontrol formulation. This study addressed key gaps by first characterizing the ability of different substrates to support Salmonella and Listeria monocytogenes survival and then evaluating the ability of pine biochar and Bacillus subtilis to suppress pathogen persistence in selected substrates under controlled conditions. In the first experiment, the persistence of Salmonella and L. monocytogenes was evaluated in four soilless substrates: rockwool (RW), low density foam (LDF), peat moss (PM) and coco …

Valorisation Potential Of Microalgae As A Sustainable Source Of Lipids And Health Promoting Compounds, Bozena Mccarthy

Theses

The transition toward a circular bioeconomy requires sustainable strategies for managing and valorising food industry effluents while reducing reliance on environmentally damaging raw materials such as palm oil, which is associated with deforestation, biodiversity loss and greenhouse gas (GHGs) emissions. Microalgae represent a promising platform for converting nutrient rich industrial by-products into biomass and high-value compounds for food, nutraceutical and bio-based applications. Dairy processing generates large quantities of whey, creating environmental challenges due to its high organic load. Improved whey treatment and valorisation strategies are therefore essential for enhancing sustainability in food production systems. In this study, the biomass productivity …

An Emergent Seafood Nationalism Takes Hold In The United States, Owen Temby

School of Earth, Environmental, & Marine Sciences Faculty Publications

This paper introduces the concept of ‘seafood nationalism’ to describe how, since 2024–2025, the United States increasingly uses tariffs, trade remedies, food safety enforcement and origin-based rules to favour American seafood over foreign products. Federal actions include Executive Order 14276, Restoring American Seafood Competitiveness, which directs agencies to address unfair trade practices, unsafe imports and to develop a coordinated seafood trade strategy. Additional measures include a tariff package imposing a 10% duty on nearly all seafood imports and 30% on seafood from China, as well as new anti-dumping and countervailing duty orders on warm-water shrimp. This paper presents Gulf …

Comparing The Effects Of Project-Based Learning, Inquiry Learning, And Conventional Instruction On Students' Learning Motivation In Biology, Yeyen Angraini, Irwandi Irwandi, Jayanti Syahfitri

Jurnal Pendidikan Sains

Learning motivation is an important factor influencing students’ engagement, persistence, and success in Biology learning. However, classroom instruction at the senior high school level is often dominated by teacher-centered approaches, which may limit students’ active participation and motivational development. This study aimed to compare students’ learning motivation across Project-Based Learning (PjBL), Inquiry Learning, and conventional instructional approaches in Biology learning. The study employed a quantitative quasi-experimental design with a pretest–posttest approach involving three groups. Participants consisted of 85 Grade XI students from SMA Negeri 1 Talang Padang, South Sumatra, distributed across three classes: PjBL (n = 28), Inquiry (n = …

The Development Of An In Silico Vaccine Design-Based E-Module To Improve Students' Biological Literacy, Qairinasherin Qwine Ferendi, Rusdi Rusdi, Hanum Isfaeni

Jurnal Pendidikan Sains

Low levels of biological literacy among students, particularly in biotechnology, highlight the need for innovative digital learning media that facilitate meaningful and contextual learning experiences. This study aimed to develop and evaluate an interactive biotechnology e-module based on in silico vaccine design to improve students’ biological literacy. The study employed Educational Design Research (EDR) using the Hannafin and Peck model, which consists of three phases: needs assessment, development, and implementation. The participants included 73 tenth-grade science students and one biology teacher from SMAN 68 Jakarta, Indonesia. The e-module was developed using Canva and Heyzine to create an interactive flipbook integrating …

Comparative Screening Of Cytotoxic Potential Of Berberis Aristata And Senna Alexandrina Extracts, Rida Noor Akhtar, Javaria Zahoor, Rizwan Ullah Khan, Aziz Ullah, Naila Malkani

Journal of Bioresource Management

Medicinal plants provide a safe and efficient source of drugs for cancer treatment. Berberis aristata and Senna alexandrina are traditionally used to treat several ailments because they contain compounds with antimicrobial, antitoxic, anti-inflammatory, and other properties. The objective of the study was to prepare crude ethanolic extracts of B. aristata and S. alexandrina and to determine their cytotoxic potential against cancer cells. Ethanolic extracts were prepared for both plants. Hepatocellular carcinoma cells (HepG2) were used for all assays. The cytotoxicity of extracts was determined by 3‑(4,5‑Dimethylthiazol‑2‑yl)‑2,5‑diphenyltetrazolium bromide (MTT) assay using various concentrations of extracts. The obtained sub-lethal concentrations were used …

A Review On Nanoparticles: Classification And Roles In Plant Systems, Muhammad Junaid Zafar, Muhammad Shafiq, Muhammad Azeem Rana

Journal of Bioresource Management

Nanotechnology has been a new paradigm of the twenty-first century with several good breakthroughs. These tiny particles, known for their outstanding qualities, are enjoying an increasing influence in many research fields concerning foodstuff, cosmetics, electronics, and pharmacology. Synthesis of nanoparticles includes utilizing chemical processes with reducing agents, alongside employing physical techniques such as top-down and bottom-up approaches for NP formation. The biological approach, known as green synthesis, utilizes plant extracts to ensure increased safety. Biological methods also involve bacteria and fungi, known as the major sources of nanoparticles. It is acknowledged as the most effective and environmentally conscious approach, attributed …

Endophytic Actinobacteria: Deciphering Therapeutic And Industrial Potential, And Prospects Of Genome Mining In Novel Products Discovery, Yusra Waheed, Rabia Shahdin, Imran Sajid

Journal of Bioresource Management

Endophytic actinobacteria are a diverse group of Gram-positive bacteria with high G+C content, which inhabit plants’ internal tissues, and represent a significant yet underexplored reservoir of bioactive secondary metabolites. In host plants, a remarkable repertoire of metabolites, including broad-spectrum antibiotics, anticancer, antiviral, antifungal, antioxidant, and immunomodulatory compounds, is synthesized by these microbial allies, carrying significant medicinal and agricultural potential. These endophytes, in contrast to their soil relatives, have developed unique biosynthetic gene clusters (BGCs) strongly influenced by plant-associated factors, leading to the production of structurally novel metabolites. In recent years, the advances in genome mining, metagenomics, and metabolomics have accelerated …

Antimicrobial Resistance Profiles And Clinical Dynamics Of Listeriosis In Small Ruminants: A One Health Review, Muhammad Aqeel, Pervez Ahmed Khoso, Amjad Hussain Mirani, Dildar Hussain Kalhoro, Abdul Ahad Soomro

Journal of Bioresource Management

Although the incidence of listeriosis is much lower in small ruminants, it has implications for food safety, herd health and appropriate antibiotic usage as well as zoonotic potential. Both have been reported to be robust pathogens and Listeria monocytogenes is generally recognized as the most common etiologic agent, but in ovine or caprine abortion it should be included as a significant differential diagnosis. This is a narrative one health review that summarizes status of the information published to date on the epidemiology and clinical signs of infection, resistance patterns found and diagnosis and prevention methods employed in small ruminant populations. …

Fungal-Associated Deterioration Of Polythene Bags Collected From The Dumping Sites Of District Sialkot: A Preliminary Screening Study, Zarish Fatima, Brian Gagosh Nayyar, Ayesha Sarwar, Mah-E- Noor Abbas, Saira Fiaz, Wajiha Seerat

Journal of Bioresource Management

Polythene bags are highly inert plastic materials made from monomers of ethylene. Due to their durability, lightweight, and low-weight characteristics, polythene bags are in high demand among consumers and retailers worldwide. This widespread use of polythene bags has led to the generation of polythene waste in the environment. This study focused on the degradation of polythene bags through fungal strains in the desired region.  In this research, three identified fungal strains, namely Aspergillus niger, Aspergillus flavus, and Fusarium oxysporum, were screened using two synthetic media for degradation, such as the culture plate method (CPM) and Liquid media degradation (LMD). A …

Microalgae As Sustainable Biofactories For Bioplastic Production: Challenges And Future Perspectives: A Review, Zahraa Hussein Obaid, Noor S. Naji, Jasim M. Salman, Layla Mustafa A.A. Alkatrani

Journal of King Abdulaziz University: Marine Science

The widespread use of traditional plastics, combined with their slow breakdown, has exacerbated environmental and health problems. Therefore, it has become imperative to find alternatives. Due to their simplicity of cultivation, quick growth, tolerance to challenging growing conditions, and low cost, microalgae are being used more frequently as a bio-source for bioplastics lately. Additionally, a variety of biopolymers, including polyhydroxybutyrate, polylactic acid (PLA), starch, polyhydroxyalkanoates (PHA), protein, and cellulose, could be produced by microalgae. These polymers show promising qualities including biodegradability, biocompatibility, and non-toxicity under various cultivation conditions. The purpose of this study is to demonstrate the potential of microalgae …

Magnetically Treated Water: Enhancing Stocking Density, Water Quality, And Growth In Nile Tilapia (Oreochromis Niloticus), Mortada M. A. Hussein, Ayatollah A. H. Abd-El Said, Asmaa N. Mohammed, Fatma M. M. Korni

Journal of King Abdulaziz University: Marine Science

This study aimed to explore the potential of using magnetic treated water (MTW) to increase stocking densities of growing Nile tilapia, Oreochromis niloticus, in storage, productive, and/or rearing holding facilities with limited mortality and water loss. The experimental period was 12 weeks, with 1500 O. niloticus fingerlings acclimated with maintained water parameters. After acclimation, 1350 were randomly selected and used for experiment setting up, including its triplicates. For each replicate, 225 fingerlings were distributed in three experimental tanks of MTW units as group set A, B and C, each received 50, 75, and 100 fingerlings, respectively. Besides, 225 fingerlings …

Microplastics Contamination In Marine Environment: Sources And Management Strategies, Aishah Hamdi, Mohammad Oves, Naser Alkenani, Majed Alshaeri

Journal of King Abdulaziz University: Marine Science

Microplastics (MPs) have been identified as emerging global pollutants because of their persistence, mobility, and significant ecological impacts. These particles, which result from the degradation of plastic waste and from various industrial and consumer activities, are now widespread in marine environments. The capacity of MPs to adsorb contaminants and bioaccumulate within food webs increases their ecological and health risks, prompting substantial concern regarding their long-term consequences for marine ecosystems and human health. This review synthesizes current knowledge regarding the composition, sources, transport, mechanisms, and environmental behavior of microplastics (MPs), with particular emphasis on marine systems. In these environments, the persistence …

Exploring Staphylococcus Aureus Host-Pathogen Interaction Using Proteomic Technologies, Emilee Marlene Elizabeth Mustor

USF Tampa Graduate Theses and Dissertations

Staphylococcus aureus deploys an arsenal of virulence effectors to remodel the host environment during infection, while simultaneously the host mounts an immune response to contain and eliminate this bacterium. This dynamic interplay defines the host-pathogen interface and shapes infection outcome. In this context, the secreted proteases represent a major arm of S. aureus pathogenesis, promoting bacterial persistence in the host by dismantling immune defenses, cleaving host signaling molecules and reshaping the host proteome. However, traditional substrate-by-substrate characterization cannot reveal the full scope of proteolytic activity occurring during infection. To address this, we developed Terminal Amine-Guanidination of Substrates-Charge Reversal (TAGS-CR), a …

Near-Infrared Spectroscopy For Monitoring Bovine Respiratory Syncytial Virus Infection In Experimentally Challenged Calves, Erin Blanchard, Jelena Muncan, Grace Beddingfield, Cassandra Barber, Florencia Meyer, Santiago Cornejo, Merrilee Thoresen, Amelia Woolums, Carrie Vance

Endeavors: Mississippi State Undergraduate Research Journal

Bovine respiratory disease (BRD) is a multifactorial disease complex that causes significant economic loss in the cattle industry. Bovine respiratory syncytial virus (BRSV), one of the primary viruses included in BRD, primarily targets the lower respiratory tract and causes a wide variety of subclinical and clinical signs. Current diagnosis techniques require off-site laboratory testing, creating delays that allow BRSV to spread through herds and highlighting the need for rapid diagnostic methods. The objective of the study was to evaluate near-infrared spectroscopy as a diagnostic tool for BRSV detection across varying infection severities. Twenty-two Holstein bull calves were reared in research …

Microplastic Analysis In Fish Larvae (Family: Gonostomatidae And Myctophidae) From The Banggai Sea, Indonesia, Noer Kholis, Luqman Ilyas Ardito, Luqmanul Hakim, Augy Syahailatua, Agus Saleh Atmadipoera, Rina Zuraida, Tuan Nurul Sabiqah Tuan Anuar, Mufti Petala Patria

Makara Journal of Science

Microplastic pollution is recognized as a threat to marine ecosystems, yet its impacts on early life stages of mesopelagic fishes remain poorly understood. This study investigated the occurrence and characteristics of microplastic ingestion in fish larvae of the families Myctophidae and Gonostomatidae from the Banggai Sea, Indonesia. Morphometric measurements and microplastic content were analyzed in 40 larvae (20 per family). Gonostomatidae larvae, despite being smaller in total length, exhibited significantly larger mouth widths and ingested more microplastic particles (mean = 3.90 ± 0.72 particles) than Myctophidae (mean = 3.40 ± 0.38 particles). Correlation analysis showed no significant relationships between morphometric …

Screening For The Suitable Signal Peptide For Secreted Nattokinase Expression In E. Coli Using An In Silico Approach: Precursor Vs. Mature Forms, Dewi Purwani Caya Ningsih, Kartika Sari Dewi, I Wayan Martadi Santika, Ade Andriani, Joko Pebrianto Trinugroho, Muhammad Yusuf

Makara Journal of Science

Nattokinase (NK), an enzyme with thrombolytic activity, has been widely used in treating cardiovascular disease. The expression of NK in the E. coli cell host is favored due to its several benefits, though it often results in inclusion bodies. Appropriate signal peptides can be attached to the N-terminus of a protein to initiate a secretory expression system, thus preventing the nascent protein from aggregating in the cytoplasm. This study aimed to identify suitable signal peptides for the secretory expression of active NK in E. coli and to investigate the impact of pre-protein in NK secretion using an in silico approach. …

Closing The Gaps: Reforming Maryland Controls On Veterinary Antimicrobial Distribution, Samantha Capaldo, Kerry Mcclaughry

Journal of Food Law & Policy

Antimicrobials have been used in livestock and other food animals in the United States (“U.S.”) since the late 1940s. An antimicrobial is “[a]ny natural, synthetic, or semisynthetic substance that can eradicate or prevent the growth of microbes,” including “[a]ntibacterial, antifungal, antiparasitic, and antiviral medications.” Antimicrobial use in food animals is subject to a complex statutory and regulatory framework at both the state and federal levels. Antimicrobial use in food animals has been widely criticized for contributing to antimicrobial-resistant bacterial infections in humans. In response to this criticism, the U.S. Food and Drug Administration (“FDA”) and several states, including Maryland, have …

Emergency Action Plan: Home, Family, Pets, And Livestock, Kristin Black, Michael Pate, Callahan K. Adams

All Current Publications

This document is an emergency family action plan designed to help your entire household prepare for emergencies. It aligns with the Youth Emergency Preparedness and Animal Project Safety Program available through Utah State University (USU). It can be taught by FFA teachers, 4-H leaders, Extension faculty/staff, and afterschool program educators. The Emergency Action Plan is intended for youth to bring home, lead their families in completing the sections, and guide them in preparing for and practicing emergency preparedness.

Bovine Tuberculosis In The Middle East And North Africa: A Systematic Review And Meta-Analysis On Prevalence And Mycobacterium Bovis Clonal Complexes, Tsegaye Shamebo, Aboma Zewude, Temesgen Mohammed, Nabeeha Abdelgaleel Hassan, Mohammed Saleh Albreiki, Yassir Mohammed Eltahir, Atef Oreiby, Robert Barigye, Markos Tibbo, Ali Artaman, Gobena Ameni

All Works

Introduction – Bovine tuberculosis (bTB) is endemic in the Middle East and North Africa (MENA) region causing major threat to dairy production and milk consumers. This paper presents a comprehensive systematic review and meta-analysis of bTB prevalence and Mycobacterium bovis clonal complexes in the MENA region based on studies published between 2000 and 2025. Methods – A comprehensive literature search was conducted in PubMed, Scopus, Web of Science, Embase, and relevant regional databases. Thirty-eight studies met the criteria and included in the meta-analysis. Random-effects meta-analysis was used to estimate pooled prevalence. Additional analyses were done on sensitivity, meta-regression, and publication …

Rna G-Quadruplexes Function As A Tunable Switch Of Fus Phase Separation, Jenny L. Carey, Miyuki Hayashi, Emily A. Welebob, Laura R. Ganser, Huan Wang, Kerry Buckhaults, Jacquelyn A. Depierro, Zheng Shi, James Shorter, Sua Myong, Aaron R. Haeusler, Lin Guo

Department of Biochemistry and Molecular Biology Faculty Papers

Fused in sarcoma (FUS) undergoes liquid-liquid phase separation (LLPS) to support essential cellular functions, but aberrant phase transitions promote toxic aggregation in neurodegenerative disease. Short RNA oligonucleotides can reverse this behavior, yet the structural determinants that govern RNA activity remain poorly defined. Here, we identify RNA G-quadruplexes (rG4s) as tunable structural motifs that potently modulate FUS LLPS. rG4 activity depends on its concentration and is modulated by rG4 length and stability: increasing repeat number switches rG4s from inhibitor to nucleator of FUS assembly, whereas chemical modifications that stabilize rG4 enhance inhibitory function and render these activities resilient to ionic perturbation. …

Understanding The Needs And Practices Of Cut Flower Growers In Louisiana, Jessie M. Hoover

LSU Doctoral Dissertations

The specialty cut flower industry is expanding nationwide, including southeastern states such as Louisiana. Existing studies and market analyses focus on national trends of other regions with established floriculture networks, leaving a critical gap in understanding the unique challenges and opportunities faced by growers in Louisiana. This lack of data limits the ability of extension professionals, policymakers, and industry stakeholders to develop targeted strategies that support local production and market development. This study used qualitative case study methods to investigate the practices, challenges, and needs of 13 specialty cut flower growers in Louisiana. The study utilized Urie Bronfenbrenner’s (1979, 1986) …

Air Pollution And Public Health: Global Evidence And Implications, Mohammed Obaid Al-Mansoori

Al-Bahir

Globally, the issue of air pollution keep being one of most serious challenges that affecting environment and human health, coming from emissions of industries, transport, agriculture and also from the fuel people use in homes, in addition to natural events that make the situation worse. This review try to bring together the available evidences about the sources, types, and the health impacts of the main air pollutants, including the gaseous ones like SO₂, O₃, NO₂, and CO, and the particulate matter (PM₁₀, PM₂.₅). Exposure for short or long time to these pollutants is linked with many harmful outcomes, such as …