Digital Commons Network^™

The Screening Of The Protective Antigens Of Aeromonas Hydrophila Using The Reverse Vaccinology Approach: Potential Candidates For Subunit Vaccine Development, Ting Zhang, Minying Zhang, Zehua Xu, Yang He, Xiaoheng Zhao, Hanliang Cheng, Xiangning Chen, Jianhe Xu, Zhujin Ding

Faculty, Staff and Student Publications

The threat of bacterial septicemia caused by Aeromonas hydrophila infection to aquaculture growth can be prevented through vaccination, but differences among A. hydrophila strains may affect the effectiveness of non-conserved subunit vaccines or non-inactivated A. hydrophila vaccines, making the identification and development of conserved antigens crucial. In this study, a bioinformatics analysis of 4268 protein sequences encoded by the A. hydrophila J-1 strain whole genome was performed based on reverse vaccinology. The specific analysis included signal peptide prediction, transmembrane helical structure prediction, subcellular localization prediction, and antigenicity and adhesion evaluation, as well as interspecific and intraspecific homology comparison, thereby screening …

A Cost-Effective And Smart Sensing Tissue-Like Testbed For Surgical Training, Lysette Zaragoza

McNair Research Journal SJSU

A low-cost tissue-like testbed with six nodes of varying stiffness was developed for surgical training to provide pressure and force feedback data through image reception to human operators. Using SolidWorks, a 3D model of the box trainer housing was created. A pad for the distribution of smartsensing nodes and microcontroller connections was designed with open spaces for the respective components. The pad was 3D-printed with PLA filament. Flat piezoelectric pressure sensors were fabricated with conductive materials and velostat sensor material. Using static and dynamic analyses, three top sensors were chosen to be used in three pressure sensing nodes. A calibration …

Understanding Our Airways: How Lung Structure And Function Is Impacted By Respiratory Infections And Immune Responses, Katherine Coll

McNair Research Journal SJSU

Understanding the underlying functions and interplaying systems that make up the respiratory system is a crucial step in the research and development of treatments for respiratory illnesses. In this literature review, I explore the complex biochemical processes that occur in the pulmonary epithelium and endothelium. As epithelial and endothelial cells serve a multitude of functions such as host protection and nutrient regulation, discussing the interplay between these cells and intercellular junctions and their immediate impact on the respiratory system is essential to understanding the impact of respiratory dysfunctions and diseases. This review further examines the different types of intercellular junctions …

The Impact Of Culture On Health Perceptions And Help-Seeking Behaviors Among Older Latinos With Co-Occurring Diabetes And Depression: A Literature Review, Alejandra M. Aguirre

McNair Research Journal SJSU

Diabetes is one of the most common health disparities in the United States today and disproportionately affects older Latino populations. Increased recognition of the bidirectional relationship between diabetes and mental health has led to more awareness and treatments for diabetes and depression. Despite high prevalence rates, diabetes and depression are commonly undiagnosed and untreated in older Latinos. Existing literature reports that factors including genetic and behavioral factors, low socioeconomic status (SES), limited healthcare access, and language barriers may prevent this population from seeking professional treatment. Prior research also suggests that culturally based stigma toward these conditions can negatively impact health …

Front Matter, Maria Cruz

McNair Research Journal SJSU

No abstract provided.

Full Issue

McNair Research Journal SJSU

No abstract provided.

A Student Bill Of Rights, Balkhiis Noor, Olivia Monestime, Julia Hines, David Peterson Del Mar

Amplify: A Journal of Writing-as-Activism

This Student Bill of Rights was created by two sections of Immigration, Migration, and Belonging, a year-long Freshman Inquiry class largely composed of students from under-represented backgrounds.

Effects Of Polyethylene Microplastic And Nanoplastics Particles On Santa Monica Mountain Fern Gametophytes, Breanna Colunga, Thomas Vandergon

Summer Undergraduate Research in Biology Program

No abstract provided.

Microbiologist Fred Tenover ’76 Joins Ud Faculty, With Focus On Faith And Science, Dave Larsen

College of Arts and Sciences Newsroom

Fred Tenover first learned the importance of integrating faith and science as a University of Dayton student, working in the biology lab of the late Br. Don Geiger, S.M.

Fern Gametophyte Response To Desiccation Is More Similar To Moss Gametophytes Than To Fern Sporophytes, Paola Moreno, Marinna Grijalva, Samuel Fitzgerald, Reem Al Dabagh, Stephen Davis, Helen Holmlund

Summer Undergraduate Research in Biology Program

No abstract provided.

Effects Of Aerosol Residues Benzene And Vinyl Chloride On A549 Lung Epithelial Cells, Alexis Thornburgh, Thomas Vandergon

Summer Undergraduate Research in Biology Program

No abstract provided.

Chaparral Fern Gametophytes Experience Microclimates With More Moisture And More Moderate Temperatures Than Fern Sporophytes, Samuel Fitzgerald, Marinna Grijalva, Paola Moreno, Reem Al Dabagh, Stephen Davis, Helen Holmlund

Summer Undergraduate Research in Biology Program

No abstract provided.

Association Between Estrogen-Related Genetic And Microbial Factors In Breast Tissue: Implications For Breast Cancer Risk, Rachel Yutong Jiang, Ariana Mccaw, Leah Stiemsma

Summer Undergraduate Research in Biology Program

No abstract provided.

Mathematically Modeling How Trapping Regimes That Target Specific Crayfish Life Stages Impact Removal Efficacy, Relena Pattison, Courtney Davis

Summer Undergraduate Research in Biology Program

No abstract provided.

Understanding The Role Of Dna Methylation In Carbon Black-Induced Endoplasmic Reticulum Stress Response Elements (Erse), Tyler Mcdonald, Antonio Gomez, Jay Brewster

Summer Undergraduate Research in Biology Program

No abstract provided.

The Minutes Of The Marshall University Staff Council Meeting, July 2023, Marshall University Staff Council

Staff Council Minutes

No abstract provided.

Age-Related Changes In Circadian Regulation Of The Human Plasma Lipidome, Shadab A. Rahman, Rose M. Gathungu, Vasant R. Marur, Melissa St. Hilaire, Karine Scheuermaier, Marina Belenky, Jackson S. Struble, Charles A. Czeisler, Steven W. Lockley, Elizabeth B. Klerman, Jeanne F. Duffy, Bruce S. Kristal

Computer and Data Science Faculty Publications

Aging alters the amplitude and phase of centrally regulated circadian rhythms. Here we evaluate whether peripheral circadian rhythmicity in the plasma lipidome is altered by aging through retrospective lipidomics analysis on plasma samples collected in 24 healthy individuals (9 females; mean ± SD age: 40.9 ± 18.2 years) including 12 younger (4 females, 23.5 ± 3.9 years) and 12 middle-aged older, (5 females, 58.3 ± 4.2 years) individuals every 3 h throughout a 27-h constant routine (CR) protocol, which allows separating evoked changes from endogenously generated oscillations in physiology. Cosinor regression shows circadian rhythmicity in 25% of lipids in both …

The Structural Characterization And Bioactivity Assessment Of Nonspecific Lipid Transfer Protein 1 (Nsltp1) From Caraway (Carum Carvi) Seeds, Taibah Aldakhil, Saud O. Alshammari, Bushra Siraj, Bishoy El-Aarag, Shamshad Zarina, David Salehi, Aftab Ahmed

Pharmacy Faculty Articles and Research

Background

Carum carvi (caraway) of the Apiaceae family has been used in many cultures as a cooking spice and part of the folk medicine. Previous reports primarily focus on the medicinal properties of caraway seed essential oil and the whole seeds extract. However, no effort has been made to study caraway proteins and their potential pharmacological properties, including nonspecific lipid transfer protein (nsLTP), necessitating further research. The current study aimed to characterize nonspecific lipid transfer protein 1 (nsLTP1) from caraway seed, determine its three-dimensional structure, and analyze protein–ligand complex interactions through docking studies. We also evaluated nsLTP1 in vitro cytotoxic …

Mekki Selected For Prestigious Johnson & Johnson Internship, Micah Hardge

Browse All News

No abstract provided.

Method Developments To Identify Loci And Selection Patterns Associated With Genotype By Environment Interactions In Soybean, Mary M. Happ

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

For many complex traits such as grain yield, genotype by environment (GxE) interactions are a prevalent source of phenotypic variation. Exploring the capacity of different methodologies to help describe and quantify the GxE interaction landscape for grain yield is an important step in informing plant breeders what the most viable strategies for management and exploitation of GxE may be. In this endeavor, we compared the results from multiple genome wide association studies (GWAS) that used either stability estimators as a phenotype to capture GxE variance, or directly mapped GxE in a mixed model for yield. Leading into this study, a …

Engineered Reporter Phages For Detection Of Escherichia Coli, Enterococcus, And Klebsiella In Urine, Susanne Meile, Jonas Marschall, Et Al.

2020-Current year OA Pubs

The rapid detection and species-level differentiation of bacterial pathogens facilitates antibiotic stewardship and improves disease management. Here, we develop a rapid bacteriophage-based diagnostic assay to detect the most prevalent pathogens causing urinary tract infections: Escherichia coli, Enterococcus spp., and Klebsiella spp. For each uropathogen, two virulent phages were genetically engineered to express a nanoluciferase reporter gene upon host infection. Using 206 patient urine samples, reporter phage-induced bioluminescence was quantified to identify bacteriuria and the assay was benchmarked against conventional urinalysis. Overall, E. coli, Enterococcus spp., and Klebsiella spp. were each detected with high sensitivity (68%, 78%, 87%), specificity (99%, 99%, …

Phase Ii, Open-Label Study Of Encorafenib Plus Binimetinib In Patients With Brafv600-Mutant Metastatic Non-Small-Cell Lung Cancer, Gregory J Riely, Daniel Morgensztern, Et Al.

2020-Current year OA Pubs

PURPOSE: The combination of encorafenib (BRAF inhibitor) plus binimetinib (MEK inhibitor) has demonstrated clinical efficacy with an acceptable safety profile in patients with

METHODS: In this ongoing, open-label, single-arm, phase II study, patients with

RESULTS: At data cutoff, 98 patients (59 treatment-naïve and 39 previously treated) with

CONCLUSION: For patients with treatment-naïve and previously treated

Tumor Matrix Stiffness Provides Fertile Soil For Cancer Stem Cells, Sadegh Safaei, Roya Sajed, Ahmad Shariftabrizi, Shima Dorafshan, Leili Saeednejad Zanjani, Masoumeh Dehghan Manshadi, Zahra Madjd, Roya Ghods

Kimmel Cancer Center Papers, Presentations, and Grand Rounds

Matrix stiffness is a mechanical characteristic of the extracellular matrix (ECM) that increases from the tumor core to the tumor periphery in a gradient pattern in a variety of solid tumors and can promote proliferation, invasion, metastasis, drug resistance, and recurrence. Cancer stem cells (CSCs) are a rare subpopulation of tumor cells with self-renewal, asymmetric cell division, and differentiation capabilities. CSCs are thought to be responsible for metastasis, tumor recurrence, chemotherapy resistance, and consequently poor clinical outcomes. Evidence suggests that matrix stiffness can activate receptors and mechanosensor/mechanoregulator proteins such as integrin, FAK, and YAP, modulating the characteristics of tumor cells …

Study Of Polytopic Membrane Protein Topological Organization As A Function Of Membrane Lipid Composition, Takefumi Morizumi, Kyumhyuk Kim, Hai Li, Elena G Govorunova, Oleg A Sineshchekov, Yumei Wang, Lei Zheng, Éva Bertalan, Ana-Nicoleta Bondar, Azam Askari, Leonid S Brown, John L Spudich, Oliver P Ernst

Faculty, Staff and Student Publications

Kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) is a light-gated channel used for optogenetic silencing of mammalian neurons. It selects K+ over Na+ in the absence of the canonical tetrameric K+ selectivity filter found universally in voltage- and ligand-gated channels. The genome of H. catenoides also encodes a highly homologous cation channelrhodopsin (HcCCR), a Na+ channel with >100-fold larger Na+ to K+ permeability ratio. Here, we use cryo-electron microscopy to determine atomic structures of these two channels embedded in peptidiscs to elucidate structural foundations of their dramatically different cation selectivity. Together with structure-guided mutagenesis, we show that K+ versus Na+ …

Communicating Climate To Ourselves And Others, Connor Bernier

Media and Communication Studies Summer Fellows

My Summer Fellows experience has focused on the essential importance of communication in the climate crisis, and on personal exploration to reconnect with the natural world. Grounding practices such as hiking in the woods and gardening mitigate climate anxiety, renewing environmentalists’ ability to continue their work. This presentation will discuss why how we talk about communication matters and review the climate communication scholarship. Throughout I will incorporate reflection and analysis of my outdoor experiences.

Studies Of Intracellular Trafficking Of Phospholipids Triggered By Osh6, Ilham Hassoon Kadhim

Theses and Dissertations

Yeast vacuoles (mammalian lysosomes) and their closely related organelle late endosomes (LE) play a central role in anti-aging processes since they host the target of rapamycin complex 1 (TORC1). A recent study showed that the vacuolar TORC1 stimulates protein synthesis and cell growth while the late endosomal TORC1 inhibits autophagy, an anti-aging process. This raises a question as to which membrane trafficking pathways toward LE/vacuoles are critical in controlling endosomal TORC1 and anti-aging processes. Members of the family of oxysterol-binding proteins mediate non-vesicular lipid transport between membranes and contribute to longevity in different manners. We previously found that a 2-fold …

Plant Stem Undergraduate Symposium, David Britt

Biological Engineering Faculty Publications

No abstract provided.

Effect Of An Education Intervention On Nursing Students' Knowledge Of And Attitudes Toward Caring For Transgender And Gender Nonconforming People, Tanya N. Carmichael

Dissertations

Transgender and gender nonconforming (TGNC) people experience inequities in accessing health care, quality of care, and health outcomes. Rates of stress, depression, suicidal ideation/attempts, smoking, alcohol and substance use, and certain sexually transmitted infections are higher among TGNC people. Barriers to accessing care for TGNC people include social and economic marginalization; fear, stigma, and discrimination; and health care professionals (HCPs) with limited experience and knowledge about caring for TGNC people. Lack of knowledge and biased attitudes toward gender minorities within health care contribute to care that is substandard, delayed or refused outright; non-use of existing evidence-based guidelines for TGNC-related care; …

Dynamic Mapping Of Proteome Trafficking Within And Between Living Cells By Transitid, Wei Qin, Joleen S Cheah, Charles Xu, James Messing, Brian D Freibaum, Steven Boeynaems, J Paul Taylor, Namrata D Udeshi, Steven A Carr, Alice Y Ting

Faculty, Staff and Students Publications

The ability to map trafficking for thousands of endogenous proteins at once in living cells would reveal biology currently invisible to both microscopy and mass spectrometry. Here, we report TransitID, a method for unbiased mapping of endogenous proteome trafficking with nanometer spatial resolution in living cells. Two proximity labeling (PL) enzymes, TurboID and APEX, are targeted to source and destination compartments, and PL with each enzyme is performed in tandem via sequential addition of their small-molecule substrates. Mass spectrometry identifies the proteins tagged by both enzymes. Using TransitID, we mapped proteome trafficking between cytosol and mitochondria, cytosol and nucleus, and …

A Novel Statistical Method For Decontaminating T-Cell Receptor Sequencing Data, Ruoxing Li, Mehmet Altan, Alexandre Reuben, Ruitao Lin, John V Heymach, Hai Tran, Runzhe Chen, Latasha Little, Shawna Hubert, Jianjun Zhang, Ziyi Li

Faculty, Staff and Student Publications

The T-cell receptor (TCR) repertoire is highly diverse among the population and plays an essential role in initiating multiple immune processes. TCR sequencing (TCR-seq) has been developed to profile the T cell repertoire. Similar to other high-throughput experiments, contamination can happen during several steps of TCR-seq, including sample collection, preparation and sequencing. Such contamination creates artifacts in the data, leading to inaccurate or even biased results. Most existing methods assume 'clean' TCR-seq data as the starting point with no ability to handle data contamination. Here, we develop a novel statistical model to systematically detect and remove contamination in TCR-seq data. …