Biotechnology Commons^™

Interplay Of Periodontal Bacterial Metabolites In The Progression Of Coronary Artery Disease: A System Biological Approach, Janakiraman V

Annual Research Symposium

Purpose:

The purpose of this study is to investigate the intricate relationship between periodontal disease (PD) and coronary artery disease (CAD), as evidenced by epidemiological associations. Metalloproteinase inhibitor (TIMP1) plays a pivotal role in cellular signaling, differentiation, cell death, and migration by binding to target metalloproteinases, forming complexes with other molecules (collagenases) to inactivate them. However, the expression of TIMP1 is reduced in both PD and CAD, leading to an upregulation of other metalloproteinases. This research explores the hypothesis that metabolites released from (Porphyromonas gingivalis), a prevalent bacterium in atherosclerotic patients, may inhibit TIMP1, thereby influencing CAD progression. …

Us Public Opinion About The Safety Of Gene Editing In The Agriculture And Medical Fields And The Amount Of Evidence Needed To Improve Opinions, Brandon R. Mcfadden, Joy N. Rumble, Kathryn A. Stofer, Kevin M. Folta

Agricultural Economics and Agribusiness Faculty Publications and Presentations

Introduction: Implementation of gene editing in agriculture and medicine hinges on public acceptance. The objectives of this study were to explore U.S. public opinion about gene editing in agricultural and medical fields and to provide more insight into the relationship between opinions about the safety of gene editing and the potential impact of evidence to improve opinions about safety.

Methods: Data were from two samples of U.S. respondents: 1,442 respondents in 2021 and 3,125 respondents in 2022. Survey respondents provided their opinions about the safety of gene editing in the agricultural and medical fields and answered questions about the number …

Mechanistic And Engineering Studies Of Lov Photoreceptors In Yeast, Matthew M. Cleere

Dissertations, Theses, and Capstone Projects

A variety of cellular biosensors have evolved which can translate electromagnetic radiation from the environment into biological functions. Light-Oxygen-Voltage (LOV) domains in particular, are a group of photoreceptors that respond to blue wavelengths of light and can become a cellular photoswitch by converting this stimulus through their attached effector domains. For instance, the Helix-Turn-Helix (HTH) DNA-binding activity of the bacterial transcription factor EL222 and the Regulator of G-protein Signaling (RGS) in the fungal membrane associating protein BcLOV4 are both induced by blue-light sensing LOV domains. While previous work has provided the field with a structural characterization of LOV proteins in …

Investigation Of Alzheimer’S Amyloid-Β Protein Aggregation With A New Fluorescent Dye., Emma Alberty

Undergraduate Research Symposium

Alzheimer’s Disease (AD) is the most common form of dementia characterized by the impairment of at least two brain functions such as memory loss and judgement. AD is a progressive illness that can last as many as 20 years. AD is largely considered to be caused by the formation of extracellular amyloid plaques and intracellular neurofibrillary tangles. A better understanding of the structure and function of these plaques may lead to clearer understanding of the disease. To analyze amyloid plaques, aggregation assays are often used. During these assays we begin with monomer and place the sample in biological conditions to …

Chromosome‑Level Assembly And Analysis Of Camelina Neglecta: A Novel Diploid Model For Camelina Biotechnology Research, Shuo Wang, Rostislav Y. Blume, Zhi‑Wei Zhou, Shaoping Lu, Tara J. Nazarenus, Yaroslav B. Blume, Weibo Xie, Edgar B. Cahoon, Ling‑Ling Chen, Liang Guo

Department of Biochemistry: Faculty Publications

Camelina neglecta is a new diploid Brassicaceae species, which has great research value because of its close relationship with the hexaploid oilseed crop Camelina sativa. Here, we report a chromosome-level assembly of C. neglecta with a total length of 210 Mb. By adopting PacBio sequencing and Hi-C technology, the C. neglecta genome was assembled into 6 chromosomes with scaffold N50 of 29.62 Mb. C. neglecta has undergone the whole-genome triplication (γ) shared among eudicots and two whole-genome duplications (α and β) shared by crucifers, but it has not undergone a specific whole-genome duplication event. By synteny analysis …

Metabolic Collaboration Between Cells In The Tumor Microenvironment Has A Negligible Effect On Tumor Growth, Johan Gustafsson, Fariba Roshanzamir, Anders Hagnestål, Sagar M. Patel, Oseeyi I. Daudu, Donald F. Becker, Jonathan L. Robinson, Jens Nielsen

Department of Biochemistry: Faculty Publications

The tumor microenvironment is composed of a complex mixture of different cell types interacting under conditions of nutrient deprivation, but the metabolism therein is not fully understood due to difficulties in measuring metabolic fluxes and exchange of metabolites between different cell types in vivo. Genome-scale metabolic modeling enables estimation of such exchange fluxes as well as an opportunity to gain insight into the metabolic behavior of individual cell types. Here, we estimated the availability of nutrients and oxygen within the tumor microenvironment using concentration measurements from blood together with a metabolite diffusion model. In addition, we developed an approach …

Emerging Roles Of Cullin-Ring Ubiquitin Ligases In Cardiac Development, Josue Zambrano-Carrasco, Jianqiu Zou, Wenjuan Wang, Xinghui Sun, Jie Li, Huabo Su

Department of Biochemistry: Faculty Publications

Heart development is a spatiotemporally regulated process that extends from the embryonic phase to postnatal stages. Disruption of this highly orchestrated process can lead to congenital heart disease or predispose the heart to cardiomyopathy or heart failure. Consequently, gaining an in-depth understanding of the molecular mechanisms governing cardiac development holds considerable promise for the development of innovative therapies for various cardiac ailments. While significant progress in uncovering novel transcriptional and epigenetic regulators of heart development has been made, the exploration of post-translational mechanisms that influence this process has lagged. Culling-RING E3 ubiquitin ligases (CRLs), the largest family of ubiquitin ligases, …

Augusta: From Rna-Seq To Gene Regulatory Networks And Boolean Models, Jana Musilova, Zdenek Vafek, Bhanwar Lal Puniya, Ralf Zimmer, Tomáš Helikar, Karel Sedlar

Department of Biochemistry: Faculty Publications

Computational models of gene regulations help to understand regulatory mechanisms and are extensively used in a wide range of areas, e.g., biotechnology or medicine, with significant benefits. Unfortunately, there are only a few computational gene regulatory models of whole genomes allowing static and dynamic analysis due to the lack of sophisticated tools for their reconstruction. Here, we describe Augusta, an open-source Python package for Gene Regulatory Network (GRN) and Boolean Network (BN) inference from the high-throughput gene expression data. Augusta can reconstruct genome-wide models suitable for static and dynamic analyses. Augusta uses a unique approach where the first estimation of …

Development And Evaluation Of A Mitochondrial Dna Marker For The Detection Of Rattus Rattus And Rattus Norvegicus Fecal Contamination, A'Aden Redhead

Graduate Research Showcase

No abstract provided.

The Antagonist Effect Of Pichia Kluyveri Against The Aflatoxigenic Aspergillus Flavus, Wafa Masoud

Journal of the Arab American University مجلة الجامعة العربية الامريكية للبحوث

Aspergillus flavus is one of the main fungi that are known to produce Aflatoxin B1 (AFB1). AFB1 has been detected in many food products and reported to be a carcinogenic. Using a biocontrol agent against A. flavus can safely eliminate or reduce the occurrence of AFB1 in food. Therefore, the effects of four yeast strains of Pichia kluyveri on the growth and spore germination of A. flavus were studied. In addition, the effect of exposure of A. flavus to the yeast’s headspace, as well as the effects of different headspace concentrations of 2-phenyl ethyl acetate and ethyl acetate, on the …

On-Site Estimation Of Total Sugars In Flavored Milk Using A Glucometer, Erwin Oliver V. Fundador, Karyn Thea E. Rivera, Kriza Faye A. Calumba, Noreen Grace V. Fundador

ASEAN Journal on Science and Technology for Development

Sugar has been linked to obesity and chronic diseases. Unfortunately some "healthy products," such as flavored milk, contain high sugar. In the Philippines, such an issue is made worse by local brands not putting nutritional labels on their products. Thus, a cheap, home-based method to measure total sugars should be beneficial. In this paper, we have shown that after incubation with invertase and lactase, a glucometer can be used to measure total sugars in flavored milk on-site. All experiments except the weighing of invertase and lactose were done in a home setting for actual proof of concept. The total sugar …

Molecular Identification To Verify The Existence Of Helicotylenchus Dihystera In Coffee Plants At East Java, Indonesia, Ankardiansyah Pandu Pradana, Toyoshi Yoshiga

ASEAN Journal on Science and Technology for Development

Spiral nematodes Helicotylenchus sp. are known to infect a variety of plants, including coffee. This is in line with the studies and surveys of nematodes in Indonesia. However, to date, there has been no study reporting the nematode with molecular analysis. In this study, we surveyed the nematodes in Arabica coffee plantations in Bondowoso regency – Indonesia. These spiral nematodes were collected in DESS solution for morphological, morphometric and molecular analysis. The morphometric analysis was carried out under an Olympus BH-2 compound microscope with an attached calibrated Toupcam M20 camera. The molecular analysis was performed on the total DNA from …

Species Distribution Modelling Using Bioclimatic Variables On Critically Endangered Endemic Species (Macrocephalon Maleo) In Sulawesi, Septianto Aldiansyah, Khalil Abdul Wahid

ASEAN Journal on Science and Technology for Development

The island of Sulawesi isolates migratory fauna from Asia and Australia and creates animal combinations such as the Maleo (Macrocephalon Maleo). The Maleo population is experiencing a downward trend due to habitat fragmentation, deforestation and threats by humans. This study aims to model the potential distribution of Maleo using several famous current and future models as a result of climate change throughout the island of Sulawesi, not only in its natural habitat, but beyond its natural habitat. Bioclimatic variables and in situ attendance data were used in this study. The method used is Maximum Entropy by evaluating the GLM, SVM …

The Musical Descriptor Using Fast Fourier Transform (Fft): Examples In P Ramlee Songs, Ahmad Faudzi Musib, Sinin Hamdan, Kuryati Kipli, Aaliyawani Ezzerin Sinin, Johari Abdullah

ASEAN Journal on Science and Technology for Development

The musical descriptor can be characterize using quantitative evaluation of audio sounds. This paper evaluates the musical descriptors for P Ramlee instrumental songs utilizing the Fast Fourier Transform (FFT) from the audio sounds signal. In this study, Python programming language is used to develop a series of custom scripts to calculate the musical descriptors. The approach involved constructing musical descriptors from instrumental music through analysis and digital processing of the spectra. The signal data were first transformed using the FFT to extract frequencies and intensities, which are crucial for identifying the spectral signature of musical sounds. The FFT is particularly …

Effect Of Monoclonal Antibodies Ma-33h1f7 And Ma-8h9d4 On Pai-1 In Cells Activated With Tgfβ, Srikar Modukuri

Biotechnology Theses

This study investigates the impact of monoclonal antibody treatment on plasminogen activator inhibitor-1 (PAI-1) expression and secretion in transforming growth factor beta (TGFβ) activated pleural human mesothelial cells. In this study, we examined total PAI-1 levels in conditioned media from human pleural mesothelial cells under various conditions using immunoblot and enzyme-linked immunosorbent assay techniques (ELISA). Specifically, we targeted PAI-1 with monoclonal antibodies (mAbs) MA-33H1F7 and MA-8H9D4, which bind to unique epitopes on PAI-1. A reduction in PAI-1 levels was observed between control and antibody-treated cells by immunoblot analysis of cell conditioned media. ELISA results also revealed a reduction in total …

Special Issue Editorial: Business Innovation For The Sustainable Development Goals, Mohamed Saleem Nazmudeen, Fadzliwati Mohiddin, Stephen Singaraju, Seyed M Buhari

ASEAN Journal on Science and Technology for Development

Welcome to this special issue of the ASEAN Journal on Science and Technology for Development (AJSTD), focused on “Business Innovation for the Sustainable Development Goals (SDGs)." This collection features a robust ensemble of 30 papers that not only highlight innovative business practices across the ASEAN region but also align these innovations with the Sustainable Development Goals. These contributions span a diverse range of disciplines, grouped into five broad categories: Management and Strategy, Financial Innovations, Marketing and Consumer Behavior, Information Technology and Systems, and Environmental and Social Impact.

Implementing Unmanned Aerial Vehicles To Collect Human Gait Data At Distance And Altitude For Identification And Re-Identification, Donn E. Bartram

Graduate Theses, Dissertations, and Problem Reports (ETD)

Gait patterns are a class of biometric information pertaining to the way a person moves and poses. Gait information is unique to each person and can be used to identify and reidentify people. Historically, this task has been achieved through the use of multiple ground-based imaging sensors. However, as Unmanned Aerial Vehicles (UAVs) advance, they present the opportunity to evolve the process of persons identification and re-identification. Collecting human gait data using UAVs at distances ranging from 20m to 500m and altitudes ranging from 0m to 120m is a challenging task. The current biometric data collection methods, primarily designed for …

Role Of Extracytoplasmic Function (Ecf) Sigma Factors In The Survival And Symbiosis Of Nitrogen-Fixing Bradyrhizobium Under Desiccation Stress And Comparative Analysis Of Desiccation-Tolerant Rhizobial Isolates, Mohammad Kamruzzaman

Biology Dissertations - Archive

Rhizobia are soil bacteria that facilitate biological nitrogen fixation (BNF) through a symbiotic relationship with legumes such as soybeans. As an eco-friendly alternative to chemical nitrogen fertilizers, rhizobial inoculants can enhance plant growth and yield. However, they face various stresses, including drought (i.e., desiccation). Rhizobia can manage desiccation stress by accumulating trehalose, a disaccharide produced by genes such as otsA, otsB, and treS. Extracytoplasmic function (ECF) sigma factors sense external signals and regulate these desiccation-related genes during the stress. Previous studies have highlighted the importance of EcfG in response to desiccation stress and symbiosis. Based on the protein sequence …

Temporal Distribution Of Potential Waterborne Pathogens In Sequiota Spring, William J. Durstock

Graduate Theses/Dissertations

Waterborne pathogens from human fecal matter pose a significant health risk in karst environments, where domestic wastewater can easily be transferred to the shallow groundwater system via old, leaky septic tanks and damaged sewer lines. This study monitored fecal indicator bacteria (FIB) and potential pathogens in Sequiota Spring located in the karst region of southwest Missouri, using Microbial Source Tracking (MST) and Illumina DNA sequencing of bacterial 16S rRNA genes. MST identified high levels of human fecal indicator bacteria (HFIB) (up to 110,000 cells/L) in July 2020. By June 2022, HFIB levels had dropped significantly (55-fold reduction) after the City …

Development And Application Of Guided Mode Resonance Biosensor Platforms For Highly Sensitive And Real-Time Cell Killing Assays, Seyedmohsen Vaziri

Electrical Engineering Dissertations - Archive

In this work, we developed and investigated the cancer cell killing efficacy of different instances using real-time high-sensitivity measurements facilitated by Guided-Mode Resonance (GMR) sensors. The GMR biosensor technology detects shifts in the spectral peak caused by changes in the refractive index of the surrounding medium, offering a label-free method for monitoring cellular events.

A549 cell line wild type and HER2 knockout (lung cancer cells) were exposed to different concentrations of Triton X-100 and ADC (Herceptin with αHFc-CL-DMDM). The GMR-based cell killing assay demonstrated exceptional sensitivity and specificity, with shifts in wavelength exhibiting a robust correlation with cell viability and …