Biotechnology Commons^™

Study Of The Assembly Trigger For Spider Silk Proteins, Katina Zhu, Amanda Lee, Megan Lau, Sungkyung Lee, Kaden Chen, Katherine Yoo, David Eum, Daniel Eum, Austin Cho, Jiho Choi

Pacific Undergraduate Research and Creativity Conference (PURCC)

No abstract provided.

Pyrus Calleryana Extracts Reduce Germination Of Native Grassland Species, Suggesting The Potential For Allelopathic Effects During Ecological Invasion, Michaela J. Woods, Jonathan T. Bauer, Dena Schaeffer, Ryan W. Mcewan

Biology Faculty Publications

Invasive plant species’ success may be a result of allelopathy, or the release of secondary metabolites that are harmful for surrounding plant species. Allelopathy can be mediated through the abiotic environment by chemical sorption or transformation, so the substrate on which interactions occur can lead to differential outcomes in allelopathic potential. One aggressive invader, Pyrus calleryana, has become dominant in many ecosystems throughout Eastern US, and has reduced the abundance of native species where it invades. Thus, our goal was to identify if P. calleryana had allelopathic potential by testing the impact of leaf and flower leachate on gemination …

From Deep Mutational Mapping Of Allosteric Protein Landscapes To Deep Learning Of Allostery And Hidden Allosteric Sites: Zooming In On “Allosteric Intersection” Of Biochemical And Big Data Approaches, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

The recent advances in artificial intelligence (AI) and machine learning have driven the design of new expert systems and automated workflows that are able to model complex chemical and biological phenomena. In recent years, machine learning approaches have been developed and actively deployed to facilitate computational and experimental studies of protein dynamics and allosteric mechanisms. In this review, we discuss in detail new developments along two major directions of allosteric research through the lens of data-intensive biochemical approaches and AI-based computational methods. Despite considerable progress in applications of AI methods for protein structure and dynamics studies, the intersection between allosteric …

Dairy Bioactives And Functional Ingredients With Skin Health Benefits, Aleksandra Augustyniak, Davide Gottardi, Barbara Giordani, James Gaffey, Helena Mcmahon

Publications

The potential of whey from Italian cheese productions to support skin health and anti-ageing mechanism was studied. The effect of whey on dermal and epidermal cells was evaluated. Whey inhibited the activity of elastase and tyrosinase enzymes by 60% and 32%, respectively. Whey cytotoxicity against tested skin cell lines, human fibroblasts (HDFa) and keratinocytes (HaCaT) was not observed. Moreover, the antioxidant activity of the samples was noted, after treatment with whey intracellular ROS level was decreased by 87% in comparison with the hydrogen peroxide-treated cells. Fibroblasts produced a significant amount of extracellular matrix molecules, collagen I, elastin and glycosaminoglycans as …

Surveillance And Stewardship: Where Infection Prevention And Antimicrobial Stewardship Intersect, Fred C. Tenover, Debra A. Goff

Biology Faculty Publications

Colonization with multidrug-resistant organisms (MDROs) is a risk factor for subsequent infection. Surveillance for MDROs, including methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, extended-spectrum beta-lactamase-producing Enterobacterales, and carbapenemase-producing organisms, is commonly conducted in hospitals to prevent spread of MDROs, in part to reduce the potential for additional infections. Although colonization is a risk factor for infection, data on colonization with various MDROs are often not considered when selecting anti-infective therapy. There are conflicting data on the strength of the positive and negative predictive values of the colonization test results to guide therapeutic strategies. Defining therapeutic strategies for patients with complicated or …

A Trial Of Fire And Ice: Assessment Of Control Techniques For Pyrus Calleryana Invasion Of Grasslands In Southwestern Ohio, Usa, Margaret E. Maloney, Eric B. Borth, Grace Dietsch, Mary C. Lloyd, Ryan W. Mcewan

Biology Faculty Publications

Pyrus calleryana (Callery pear) is an invasive plant that threatens ecosystems in the eastern United States. We investigated the efficacy of various control techniques on P. calleryana invasion in grasslands. Treatments were applied to (a) P. calleryana stems that had experienced mowing annually for several years and were sprouting (n = 100 stems; “trees-sprouting”) and (b) stems that had established ca. 10 years earlier, had never been cut, and were single-stemmed trees (n = 40 stems; “trees-intact”). In both experiments, existing stems were cut and randomly assigned one of the following treatments: cut only (control), burning, freezing, or herbicide, and …

Directed Carbapenemase Testing Is No Longer Just For Enterobacterales: Cost, Labor, And Workflow Assessment Of Expanding Carbapenemase Testing To Carbapenem-Resistant P. Aeruginosa, Fred C. Tenover, Christian M. Gill, Poonam Rajkotia, Amity L. Roberts, David P. Nicolau

Biology Faculty Publications

Molecular carbapenem-resistance testing, such as for the presence of carbapenemases genes, is commonly implemented for the detection of carbapenemase-producing Enterobacterales. Carbapenemase-producing P. aeruginosa is also associated with significant morbidity and mortality, although; prevalence may be underappreciated in the United States due to a lack of carbapenemase testing. The present study sought to compare hands-on time, cost and workflow implementation of carbapenemase gene testing in Enterobacterales and P. aeruginosa isolates versus sending out isolates to a public health laboratory (PHL) for testing to assess if in-house can provide actionable results. The time to carbapenemase gene results were compared. Differences in cost …

Evaluation Of Ionic Liquid Treatment As An Alternative To Chemical Fixation And Dehydration In The Preparation Of Biofilms For Scanning Electron Microscopy, Molly Shreve

Mahurin Honors College Capstone Experience/Thesis Projects

Scanning electron microscopes (SEM) give researchers the ability to observe very small features on biological specimens at the nanometer scale, which is a much higher resolution than what can be obtained with a light microscope. To be observed under SEM, unlike light microscopes, samples must be dry, conductive, and able to withstand electron bombardment. Preparation methods have been developed that work well for samples composed mainly of proteins and lipids, but these fail for samples that are predominantly carbohydrates, such as bacterial biofilms. When carbohydrates of these biofilms are dehydrated, they tend to shrink and collapse, and their normal hydrated …

Mechanisms Of Stimulation By Intestinal Endothelial Cells During Hiv Infection Of Activated Cd4+ T Cells, Anding Shen, Timothy Kim, Sarah Logan, Zihan Zhang

Summer Research

Under antiretroviral therapy, the viral persistence of HIV is enabled by latent viral reservoirs, particularly in resting CD4+ T cells. Recent studies reveal interactions between endothelial cells and T cells allowing for latent infection of resting and activated CD4+ T cells. We focused our investigation on the stimulation of activated T cells by intestinal endothelial cells (IECs), due to the prominent gut pathology of HIV and predominance of an activated T cell phenotype in the gut. While prior research shows the involvement of soluble factors like IL-6 in stimulation of resting T cells, our results from transwell cultures suggest the …

Understanding The Non-Canonical Function Of Ezh1/2 In Gene Activation, Visakuo Tsurh, Longxia Xu, Xiaobing Shi

Summer Research

Enhancers of Zeste homolog proteins (EZH1 and EZH2) play a critical role in regulating gene transcription during development. The typical function of EZH2 and its homolog EZH1 is catalyzing the trimethylation of histone three at lysine 27 (H3K27) to repress gene expression through the PRC2 complex. In cancer, EZH2 is often over-expressed or mutated, leading to the silencing of tumor suppressor genes and a worse prognosis of the disease. Research on EZH1 and EZH2 in cancer has focused on their canonical function and has culminated in therapies that target their enzymatic activity. However, studies have found that drugs that inhibit …

Biomechanics Of Mantis Prey Capture, Danielle S. Taylor

Honors Theses

Mantis species have a variety of different morphologies, so do the extreme forms of mantis limbs trade prey catching capability for camouflage? We hypothesize that some extreme forms of mantis limbs that are associated with cryptic species may be associated with a tradeoff of the capability of those limbs. Previous research has developed 2D morphologies of several hundred species of mantises. We are creating a 3D morphology by using micro dissection, micro CT imaging to construct our 3D biomechanical model. We found the attachment points of the ligaments and muscles from a Tenodera forearm and have constructed a 2D biomechanical …

Deep Learning-Based Technique For The Perception Of The Cervical Cancer, Aya Haraz, Hossam El-Din Moustafa, Abeer Twakol Khaleel, Ahmed H. Eltanboly

Mansoura Engineering Journal

In third-world countries, cervical cancer is the most prevalent and leading cause of death. It is affected by a variety of factors, including smoking, poor nutritional status, immunological inadequacy, and prolonged use of contraception. The Pap smear test, which is intended to prevent cervical cancer, finds preneoplastic changes in cervical epithelial cells. This study framework classified cervical cancer cells from Pap smears into five specified cell types using machine learning-based classification algorithms. The SIPaKMeD database is used in this investigation. This public dataset, which was manually cropped from 966 cluster cell images taken from Pap smear slides, has 4045 isolated …

Therapies For Mitochondrial Disorders, Kayli Sousa Smyth, Anne Mulvihill

SURE Journal: Science Undergraduate Research Experience Journal

Mitochondria are cytoplasmic, double-membrane organelles that synthesise adenosine triphosphate (ATP). Mitochondria contain their own genome, mitochondrial DNA (mtDNA), which is maternally inherited from the oocyte. Mitochondrial proteins are encoded by either nuclear DNA (nDNA) or mtDNA, and both code for proteins forming the mitochondrial oxidative phosphorylation (OXPHOS) complexes of the respiratory chain. These complexes form a chain that allows the passage of electrons down the electron transport chain (ETC) through a proton motive force, creating ATP from adenosine diphosphate (ADP). This study aims to explore current and prospective therapies for mitochondrial disorders (MTDS). MTDS are clinical syndromes coupled with abnormalities …

A Pooling Strategy For Detecting Carbapenem Resistance Genes By The Xpert Carba-R Test In Rectal Swab Specimens, Fred C. Tenover, Peng Zhang, Qi Wang, Chaoe Zhou, Feifei Zhang, Xinghui Gao, Yi-Wei Tang, Hui Wang

Biology Faculty Publications

Rapid and accurate detection of carriers of carbapenemase-producing organisms (CPO) in hospitalized patients is critical for infection control and prevention. This study aimed to evaluate a pooling strategy for the detection of carbapenem resistance genes (CRG) in multiple specimens using the Xpert Carba-R test. Two rectal swabs each were collected from 415 unique patients. One swab was tested by Carba-R on the five specimen-pooled strategy. The other swab was tested individually by culture followed by DNA sequence analysis for CRG as the reference. At the first 5:1 pooling testing, 22 of 83 pools were positive, which yielded 34 positives from …

Heterodimerization Between Chemokine Receptors Cxcr4 And Ccr7 And Its Role In Cancer, Maryam Naveed Muhammad Tariq

Theses

In physiology, the functional and physical interactions between cell surface receptors for signal molecules such as hormones, neurotransmitters, and cytokines, provides an important mechanism of diversity and regulation of signal transduction. Therefore, investigating the functional interactions between these receptors is of great importance for understanding their role in physiology and pathophysiology with potential application in drug discovery. In this context, numerous evidences support the implication of two chemokine receptors, CXCR4 and CCR7, in many cancer types. In this study, we hypothesized that the functional, and perhaps the physical interaction, occurring between CXCR4 and CCR7 may constitute one of the key …

Screening For Endophytic Actinobacteria To Enhance Growth And Salinity Tolerance Of Tomato Plants In The United Arab, Amira Hamdy Hassan

Theses

Salinity is one of the most decisive environmental factors limiting the productivity of crop plants, mainly in arid and semi-arid regions. An eco-friendly technology can be used to boost crop production in saline areas by using plant growth-bacteria. Endophytic actinobacteria that produce the enzyme 1-Aminocyclopropane-1-Carboxylic acid (ACC) Deaminase (ACCD) can modulate the levels of Ethylene (ET) in plants to reduce the effect of abiotic stresses including high salt stress. The main objectives of this study were to: (1) Evaluate endophytic actinobacterial isolates from healthy tomato plants cultivated in the UAE that are capable of producing ACCD in vitro; (2) …

Effect Of Carnosol On G Protein-Coupled Receptor Signaling In Cancer Cells, Laith Jehad Ahmad Abudawood

Theses

Carnosol is a plant polyphenol compound known for its beneficial properties against human diseases such as cancer and diabetes. However, the exact molecular and cellular mechanisms involved, and its molecular targets are not fully known. Carnosol was shown to bind and to modulate specific intracellular signaling proteins in cancer cell lines. In this study, we hypothesized that carnosol may pharmacologically target specific cell surface receptors including G Protein-Coupled Receptors (GPCRs) and Receptor Tyrosine Kinase (RTKs). Therefore, we tested the pharmacological effect of carnosol on the following receptors: Insulin Receptor (IR), Chemokine CXCL12 Receptor (CXCR4), Angiotensin II (AngII) Receptor (AT1R), Glucagon-Like …

Leaf Phenology And Freeze Tolerance Of The Invasive Tree Pyrus Calleryana (Roseaceae) And Potential Native Competitors, Margaret E. Maloney, Abby Hay, Eric B. Borth, Ryan W. Mcewan

Biology Faculty Publications

Pyrus calleryana is one of the most problematic invasive species in the eastern United States. The mechanisms that enable Py. calleryana to establish and outcompete native plants are not fully understood but likely include a profile of advantageous traits. Extended leaf phenology is a characteristic noted in many woody invasive plants. Leaf phenology of Py. calleryana and two native woody species, Populus deltoides and Platanus occidentalis, was observed in natural areas near Dayton, OH from December 2019 to November 2020. A frost event in May also gave us the serendipitous opportunity to assess frost tolerance of these species. We …

Visualizing Hormonal Effects On Cardiomyocyte Hypertrophic Growth Dynamics Using Digital Holographic Microscopy: Does Size Matter?, Jacquelyn Simmons

McNair Research Journal SJSU

Heart disease continues to be the leading cause of death in the United States. Humans are unable to regenerate their heart tissue following an injury. However, neonatal mice are able to regenerate their heart tissue when cardiomyocytes (CMs) proliferate. This regenerative ability is lost approximately one week after birth when proliferating mononucleated CMs become binucleated and can no longer complete the cell-cycle. Recent studies have shown the combined inhibition of thyroid hormone (T3) and norepinephrine (NE) increases CM proliferation, promotes heart regeneration, and reduces cell size in vivo. Using digital holographic microscopy, the aim of this study was to (1) …

Mechanisms Of Carbapenemase-Mediated Resistance Among High-Risk Pseudomonas Aeruginosa Lineages In Peru, Isabella A. Tickler, Juan Carlos Gomez De La Torre, Luis Alvarado, Anne E. Obradovich, Fred C. Tenover

Biology Faculty Publications

Objectives: Pseudomonas aeruginosa is one of the leading causes of healthcare-associated infections globally. High-risk carbapenemase-encoding P. aeruginosa clones are disseminating in many regions. The aim of this study was to learn more about the lineages and mechanisms of resistance of P. aeruginosa circulating in Peru.

Methods: A total of 141 carbapenemase-producing isolates recovered from hospitalized and ambulatory patients in Lima were sequenced and analyzed to infer their lineages through whole-genome sequence typing (wgST) and to identify their antimicrobial resistance genes.

Results: wgST identified nine sequence types (STs); ST111 and ST357 were the most frequently encountered (44.0% and 38.3%, respectively), followed …

Tau-Dependent Neurodegeneration And Alleviation By Etas®50, Clifford Tyree Castleberry

Theses (2016-Present)

Brain growth factors are a broad group of molecules that enable the brain to adapt to stress. In a study on Alzheimer’s mice (APP), we tested the role of an asparagus supplement, ETAS®50, to mitigate the stress caused by the Alzheimer’s condition in this mouse model. Gene expression data revealed regulation of genes related to neuronal growth and function, such as tau, which were severely stressed in the APP mice to be alleviated.

Increasing The Resilience Of Plant Immunity To A Warming Climate, Jong Hum Kim, Christian Castroverde, Shuai Huang, Chao Li, Richard Hilleary, Adam Seroka, Reza Sohrabi, Diana Medina-Yerena, Bethany Huot, Jie Wang, Sharon Marr, Mary Wildermuth, Tao Chen, John Macmicking, Sheng Yang He

Biology Faculty Publications

Extreme weather conditions associated with climate change affect many aspects of plant and animal life, including the response to infectious diseases. Production of salicylic acid (SA), a central plant defence hormone, is particularly vulnerable to suppression by short periods of hot weather above the normal plant growth temperature range via an unknown mechanism. Here we show that suppression of SA production in Arabidopsis thaliana at 28 °C is independent of PHYTOCHROME B (phyB) and EARLY FLOWERING 3 (ELF3), which regulate thermo-responsive plant growth and development. Instead, we found that formation of GUANYLATE BINDING PROTEIN-LIKE 3 (GBPL3) defence-activated biomolecular condensates (GDACs) …

Optimization Of Palmitic Acid Production In Chloroidium Sp. Utex 3007 As A Sustainable Source Of Palm Oil Alternative, Amnah Salem Alzahmi

Theses

The increase in palm oil consumption and production has resulted in removing up to 90% of trees in some tropical forests. The green microalgae Chloroidium sp. UTEX 3007 can be an alternative sustainable source of palm oil due to its high palmitic acid content. The objective of this study was to generate a mutant Chloroidium population that is capable of producing and accumulating elevated levels of palmitic acid and to characterize the obtained populations’ lipid contents. The palmitic acid production optimization in Chloroidium sp. UTEX 3007 was conducted via a workflow of ultraviolet (UV) mutagenesis and sorting of high-lipid producing …

Biomass Estimation Of Marine Biofilms On Plastic Surfaces, Kian Banihashemi, Fernando Javier Gil

Biological Sciences

Plastics have become a major source of marine pollution, which threatens food safety and quality, human health, and marine ecosystems. Due to the drastic negative effects of plastics in a marine environment, alternative biodegradable plastics are being generated that are more eco-friendly and have less environmental impact. Though some of these plastics are known to biodegrade, the process of degradation for bioplastics has not been heavily studied in a marine environment. This pilot project sought to both quantify the process of biodegradation and compare across different methods for effectiveness of biomass estimation, which serves as an indicator of biodegradation. Plastics …

Rhizosphere-Competent Actinobacterial Isolates With Acc Deaminase Activity Alleviate Salt Stress In Tomato Plants In The Uae, Alaa Ahmed Abbas Elbadawi

Biology Theses

Tomato (Solanum lycopersicum) is one of the most popular vegetables in the world, including the United Arab Emirates (UAE). Salinity is a global menace to plant growth and development, causing significant economic losses to tomato and other crop plants. It is well-known that 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCD) can increase plant tolerance to environmental stresses. This can be attributed to the increased activity of the enzyme ACCD, which breaks down ACC [the immediate precursor of ethylene (ET)] to ammonia and α-ketobutyrate, to lower the overproduction of ET levels in planta and to reduce the damages caused …

Functional Role Of Ppal And Potential For Moss In Industrial Applications., Susana Perez Martinez

Electronic Theses and Dissertations

This dissertation is an examination and characterization of the functional roles of PPAL. PROTEIN PRENYLTRANSFERASE ALPHA SUBUNIT-LIKE (PPAL) is a recently discovered gene. PPAL homologs are present in all plants and many animals, where its function is largely unknown. It is possible that PPAL could participate in prenylation processes since it shares similarity to the α subunits of known prenylation enzymes. Prenylation is a post-translational modification of proteins that involves the addition of a lipid moiety to proteins to facilitate membrane targeting and association and promote protein-protein interactions. Prenylation has important roles in plant growth and development, including …

Alterations Of The Gut Mycobiome In Patients With Ms - A Bioinformatic Approach, Saumya Shah

Honors Scholar Theses

The mycobiome is the fungal component of the gut microbiome and is implicated in several autoimmune diseases. However, its role in multiple sclerosis (MS) has not been studied. We performed descriptive and formal statistical tests using the R language to characterize the gut mycobiome in people with MS (pwMS) and healthy controls. We found that the microbiome composition of multiple sclerosis patients is different from healthy people. The mycobiome had significantly higher alpha diversity and inter-subject variation in pwMS than controls. Additionally, Saccharomyces and Aspergillus were over-represented in pwMS. Different mycobiome profiles, defined as mycotypes, were associated with different bacterial …

Identifying Genetic Differences Among African American And Caucasian Triple Negative Breast Cancer Genotypes, Christopher Jordan Dixon

Theses (2016-Present)

Triple negative breast cancers (TNBC) are closely related to basal-like cancers and classified based on their molecular signatures and their progenitor cell type. TNBCs lack the presence of three common types of receptors known to fuel breast cancer growth: estrogen receptors (ER), progesterone receptors (PR), and human epidermal growth factor receptors 2 (HER2neu). TNBC represent 10-20% of all molecular breast cancer subtypes. Even though genomic and transcriptome analyses show that many of the molecular signatures associated with TNBC are not related to ethnicity, clinicians and researchers find that African American (AA) TNBC women have higher mortality rates compared to Caucasian …

Students Interest And Thoughts On Stem, Chrisitine Girtain

STEM Month

I am Juan Sebastian Bohorquez Mora, I am a sophomore student at Toms River High School North. I am interested in biofuels because I believe they are a good option to replace fossil fuels. I am also interested in duckweed because biofuels are made out of crops, and people need to eat those crops. That’s when duckweed comes in and it can be used as a feedstock for ethanol production which is a biofuel. Bioethanol is a type of biofuel and it is derived from the corn’s starch. Instead of making ethanol from the corn’s starch, we can use duckweed …

Annual Faculty Research Symposium 2022, Oakwood University

Proceedings

No abstract provided.