Biotechnology Commons^™

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) …

Examination Of The Time Delayed Induction Between Prior Encapsulation Of Catalytic Enzymes In P22 Virus-Like Particles, Andrea Hernandez Irias

Chemistry Theses

Protein cages found in nature have the ability to protect and develop new nanomaterials in order to enhance catalytic reactions. This is due to the ability of these organelle structures to mimic protein-based organelles such as Virus-Like Particles (VLPs). VLPs have the ability to not only resemble virus protein structures but to encapsulate enzymes while retaining their activity. This research examines the in vitro encapsulation withing the bacteriophage P22 derived VLP, and show that some enzymes may require a delay in encapsulation to allowed proper folding

and maturation before they can be encapsulated inside P22 as fully active enzymes. Exploring …

Ncoa4 Regulates Iron Recycling And Responds To Hepcidin Activity And Lipopolysaccharide In Macrophages, Cole A. Guggisberg, Juyoung Kim, Jaekwon Lee, Xiaoli Chen, Moon-Suhn Ryu

Biochemistry -- Faculty Publications

Macrophages, via erythrophagocytosis, recycle iron from effete erythrocytes to newly developing red blood cells. Conversion of potentially cytotoxic levels of iron from its heme into nonheme form during iron recycling is safely accomplished via coordinated regulations of cellular iron transport and homeostasis. Herein, we demonstrate the roles and regulation of NCOA4 (nuclear receptor coactivator 4)-mediated ferritinophagy in macrophages after erythrophagocytosis using the mouse macrophage cell line J774 cells. Ferritin in J774 cells increased with the rise of nonheme iron by erythrocyte ingestion and declined when total cellular iron contents subsequently decreased. NCOA4, a selective autophagic cargo receptor for ferritin, was …

Editorial: Mitochondria, Metabolism And Cardiovascular Diseases, Jun-Ichiro Koga, Xinghui Sun, Masuko Ushio-Fukai

Biochemistry -- Faculty Publications

No abstract provided.

My Summer Working With Two-Spotted Spider Mites, Renée A. Smith

Undergraduate Student Research Internships Conference

Two-spotted spider mites are a polyphagous pest, capable of eating a magnitude of food crops which causes a large problem for Canadian agriculture. Their ability to consume various crops stems from their ability to adapt to various chemical defence mechanisms. This ability allows them to acquire resistance to many commonly used pesticides. This has resulted in large infections in Canadian farms with few options to prevent the pests from affecting crop yields. Take a look at my project if you'd like to see how the Grbic lab is working to combat this issue using genetic engineering techniques!

Exploring The Use Of Covellite As A Proxy For Corrosion Of Native Copper By Sulphur Reducing Bacteria, Manan K. Joshi

Undergraduate Student Research Internships Conference

We are analyzing the effect of sulphate reducing bacteria on native copper, and using that evidence to further support the initiative of having a deep geological repository to store nuclear material. Sulphate reducing bacteria are a concern for the deep geological repository as they cause the corrosion of regular copper. However native copper has gone billions of years without corrosion, which could either mean that it had not been exposed to sulphate reducing bacteria over the billions of years, or native copper is able to withstand corrosion despite the contact of sulphate reducing bacteria. We can find out by trying …

Deep Learning Prediction Of Chemical-Induced Dose-Dependent And Context-Specific Multiplex Phenotype Responses And Its Application To Personalized Alzheimer’S Disease Drug Repurposing, You Wu, Qiao Liu, Yue Qiu, Lei Xie

Publications and Research

Predictive modeling of drug-induced gene expressions is a powerful tool for phenotype-based compound screening and drug repurposing. State-of-the-art machine learning methods use a small number of fixed cell lines as a surrogate for predicting actual expressions in a new cell type or tissue, although it is well known that drug responses depend on a cellular context. Thus, the existing approach has limitations when applied to personalized medicine, especially for many understudied diseases whose molecular profiles are dramatically different from those characterized in the training data. Besides the gene expression, dose-depen- dent cell viability is another important phenotype readout and is …

A Rapid And Ultra-Sensitive Biosensing Platform Based On Tunable Dielectrophoresis For Robust Poc Applications, Yu Jiang

Doctoral Dissertations

With the ongoing pandemic, there have been increasing concerns recently regarding major public health issues such as abuse of organophosphorus compounds, pathogenic bacterial infections, and biosecurity in agricultural production. Biosensors have long been considered a kernel technology for next-generation diagnostic solutions to improve food safety and public health. Significant amounts of effort have been devoted to inventing novel sensing mechanisms, modifying their designs, improving their performance, and extending their application scopes. However, the reliability and selectivity of most biosensors still have much to be desired, which holds back the development and commercialization of biosensors, especially for on-site and point-of-care (POC) …

What I Talk About When I Talk About Integration Of Single-Cell Data, Yang Xu

Doctoral Dissertations

Over the past decade, single-cell technologies evolved from profiling hundreds of cells to millions of cells, and emerged from a single modality of data to cover multiple views at single-cell resolution, including genome, epigenome, transcriptome, and so on. With advance of these single-cell technologies, the booming of multimodal single-cell data creates a valuable resource for us to understand cellular heterogeneity and molecular mechanism at a comprehensive level. However, the large-scale multimodal single-cell data also presents a huge computational challenge for insightful integrative analysis. Here, I will lay out problems in data integration that single-cell research community is interested in and …

Radioluminescence Based Biochemical Sensing And Imaging Strategies To Measure Local Drug Release And Ph, Gretchen B. Schober

All Dissertations

In this dissertation we describe methods for measuring infection relevant biochemical analytes using radioluminescent and ultrasound luminescent materials. Films and nanoparticles fabricated with europium doped gadolinium oxysulfide (Gd₂O₂S:Eu³⁺) are used to quantitatively measure radiolabeled pharmaceutical concentration, specifically tritium labeled vancomycin (³H-vancomycin). Europium and dysprosium doped strontium aluminate is used to fabricate an ultrasound modulated, pH sensing film. These methods are indicated for theranostic evaluation of implant associated infection. Bacterial biofilms are inherently resistant to traditional antibiotic treatment and can coat biomedical implants. These biofilm related infections are difficult or impossible to eradicate …

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.

Metabolite Damage And Damage Control In A Minimal Genome, Drago Haas, Antje M. Thamm, Jiayi Sun, Lili Huang, Lijie Sun, Guillaume A.W. Beaudoin, Kim S. Wise, Claudia Lerma-Ortiz, Steven D. Bruner, Marian Breuer, Zaida Luthey-Schulten, Jiusheng Lin, Mark A. Wilson, Greg Brown, Alexander F. Yakunin, Inna Kurilyak, Jacob Folz, Oliver Fiehn, John I. Glass, Andrew D. Hanson, Christopher S. Henry, Valérie De Crécy-Lagard

Biochemistry -- Faculty Publications

Analysis of the genes retained in the minimized Mycoplasma JCVI-Syn3A genome established that systems that repair or preempt metabolite damage are essential to life. Several genes known to have such functions were identified and experimentally validated, including 5-formyltetrahydrofolate cycloligase, coenzyme A (CoA) disulfide reductase, and certain hydrolases. Furthermore, we discovered that an enigmatic YqeK hydrolase domain fused to NadD has a novel proofreading function in NAD synthesis and could double as a MutT-like sanitizing enzyme for the nucleotide pool. Finally, we combined metabolomics and cheminformatics approaches to extend the core metabolic map of JCVI-Syn3A to include promiscuous enzymatic reactions and …

Application In Medicine: Has Artificial Intelligence Stood The Test Of Time, Mir Ibrahim Sajid, Shaheer Ahmed, Usama Waqar, Javeria Tariq, Mohsin Chundrigar, Samira Shabbir Balouch, Sajid Abaidullah

Medical College Documents

Artificial intelligence (AI) has proven time and time again to be a game-changer innovation in every walk of life, including medicine. Introduced by Dr. Gunn in 1976 to accurately diagnose acute abdominal pain and list potential differentials, AI has since come a long way. In particular, AI has been aiding in radiological diagnoses with good sensitivity and specificity by using machine learning algorithms. With the coronavirus disease 2019 pandemic, AI has proven to be more than just a tool to facilitate healthcare workers in decision making and limiting physician-patient contact during the pandemic. It has guided governments and key policymakers …

Performance Of Machine Learning Classifiers In Classifying Stunting Among Under-Five Children In Zambia, Obvious Nchimunya Chilyabanyama, Roma Chilengi, Roma Chilengi, Michelo Simuyandi, Caroline C. Chisenga, Masuzyo Chirwa, Kalongo Hamusonde, Rakesh Kumar Saroj, Najeeha Talat Iqbal, Innocent Ngaruye

Department of Paediatrics and Child Health

Stunting is a global public health issue. We sought to train and evaluate machine learning (ML) classification algorithms on the Zambia Demographic Health Survey (ZDHS) dataset to predict stunting among children under the age of five in Zambia. We applied Logistic regression (LR), Random Forest (RF), SV classification (SVC), XG Boost (XgB) and Naïve Bayes (NB) algorithms to predict the probability of stunting among children under five years of age, on the 2018 ZDHS dataset. We calibrated predicted probabilities and plotted the calibration curves to compare model performance. We computed accuracy, recall, precision and F1 for each machine learning algorithm. …

Methanogen Metabolic Flexibility, Sean Carr

Dissertations and Theses in Biological Sciences

Methanogens are obligately anaerobic archaea which produce methane as a byproduct of their respiration. They are found across a wide diversity of environments and play an important role in cycling carbon in anaerobic spaces and the removal of harmful fermentation byproducts which would otherwise inhibit other organisms. Methanogens subsist on low-energy substrates which requires them to utilize a highly efficient central metabolism which greatly favors respiratory byproducts over biomass. This metabolic strategy creates high substrate:product conversion ratios which is industrially relevant for the production of biomethane, but may also allow for the production of value-added commodities. Particularly of interest are …

Fuzzy C-Means Clustering And Pseudo-Coloring-Based Pest Detection Of Ripe-Fruit Health Monitoring System Using 2-D Aggrotech Images, Ayush Kumar Tungo, Rishita Padhan, Tanaya Priyadarshini Pradhan, Mandakini Dehury, Roshan Kumar Jena

Graduate Research in Engineering and Technology (GRET)

Fruits are the gift of almighty to nature. Fresh fruit promote good health and having rich source of micronutrients, vitamins and fiber value. But due to its high sugar level on ripping stage different type of pest are attracted by its smell and effects on harvesting. This paper focuses on identification of the pest on ripe fruits using Fuzzy C Means (FCM) clustering for segmentation and simultaneously highlights the segmented insects with Pseudo-coloring using Pseudo-color image processing techniques. IoT integrated Drone based images are inputted as the dataset to perform detection of pest on fruit monitoring system. Before clustering-based segmentation …

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) …

Variation On A Theme: The Structures And Biosynthesis Of Specialized Fatty Acid Natural Products In Plants, Samuel Scott, Edgar B. Cahoon, Lucas Busta

Biochemistry -- Faculty Publications

Plants are able to construct lineage-specific natural products from a wide array of their core metabolic pathways. Considerable progress has been made toward documenting and understanding, for example, phenylpropanoid natural products derived from phosphoenolpyruvate via the shikimate pathway, terpenoid compounds built using isopentyl pyrophosphate, and alkaloids generated by the extensive modification of amino acids. By comparison, natural products derived from fatty acids have received little attention, except for unusual fatty acids in seed oils and jasmonate-like oxylipins. However, scattered but numerous reports show that plants are able to generate many structurally diverse compounds from fatty acids, including some with highly …

Functional Requirements For A Samd14-Capping Protein Complex In Stress Erythropoiesis, Suhita Ray, Linda Chee, Yichao Zhou, Meg A. Schaefer, Michael J. Naldrett, Sophie Alvarez, Nicholas T. Woods, Kyle J. Hewitt

Papers from the Nebraska Center for Biotechnology

Acute anemia induces rapid expansion of erythroid precursors and accelerated differentiation to replenish erythrocytes. Paracrine signals—involving cooperation between stem cell factor (SCF)/Kit signaling and other signaling inputs—are required for the increased erythroid precursor activity in anemia. Our prior work revealed that the sterile alpha motif (SAM) domain 14 (Samd14) gene increases the regenerative capacity of the erythroid system in a mouse genetic model and promotes stress-dependent Kit signaling. However, the mechanism underlying Samd14’s role in stress erythropoiesis is unknown. We identified a protein-protein interaction between Samd14 and the α- and β-heterodimers of the F-actin capping protein (CP) complex. Knockdown of …

Bio-Vascular 3d, Wisdom Shadrach

ORBioM (Open Research BioSciences Meeting)

Cardiovascular disease is a leading cause of mortality and morbidity across the world and according to the world health organization account for 32% of mortality rate globally. There still remain a need to develop better in vitro vascular models that would aid further in-depth understanding of cardiovascular pathogenesis and proposed therapeutic intervention.

This study intends to characterize four novel medically relevant synthetic polymer scaffolds, and one hydrogel, for their biocompatibility and potential application in a tissue engineered blood vessel (TEBV). A primary human endothelial cell line derived from the vein of the umbilical cord (HUVEC), and a human primary smooth …