Biotechnology Commons^™

Contributions Of Vibrational Spectroscopy To Virology: A Review, Iqra Chaudhary, Naomi Jackson, Denise Denning, Luke O'Neill, Hugh Byrne

Articles

Vibrational spectroscopic techniques, both infrared absorption and Raman scattering, are high precision, label free analytical techniques which have found applications in fields as diverse as analytical chemistry, pharmacology, forensics and archeometrics and, in recent times, have attracted increasing attention for biomedical applications. As analytical techniques, they have been applied to the characterisation of viruses as early as the 1970s, and, in the context of the coronavirus disease 2019 (COVID-19) pandemic, have been explored in response to the World Health Organisation as novel methodologies to aid in the global efforts to implement and improve rapid screening of viral infection. This review …

Molecular-Level Control Over Ionic Conduction And Ionic Current Direction By Designing Macrocycle-Based Ionomers, Shyambo Chatterjee, Ehsan Zamani, Seefat Farzin, Iman Evazzade, Oghenetega Allen Obewhere, Tyler James Johnson, Vitaly Alexandrov, Shudipto Konika Dishari

Department of Chemical and Biomolecular Engineering: Faculty Publications

Poor ionic conductivity of the catalyst-binding, submicrometer- thick ionomer layers in energy conversion and storage devices is a huge challenge. However, ionomers are rarely designed keeping in mind the specific issues associated with nanoconfinement. Here, we designed nature-inspired ionomers (calix-2) having hollow, macrocyclic, calix[4]arene-based repeat units with precise, sub-nanometer diameter. In ≤100 nm-thick films, the in-plane proton conductivity of calix-2 was up to 8 times higher than the current benchmark ionomer Nafion at 85% relative humidity (RH), while it was 1−2 orders of magnitude higher than Nafion at 20−25% RH. Confocal laser scanning microscopy and other synthetic techniques allowed us …

Consumer Preferences For Lab Grown Meat: The Effect Of Information On Consumer Choice, Aryn Blumenberg

Food Science Undergraduate Honors Theses

Global population growth and increased meat demand present challenges for the agricultural industry to produce meat sustainably. In-vitro meat (IVM) is an alternative that could reduce negative impacts associated with livestock production. The goal of this study was to examine consumers’ preferences for IVM. A choice experiment was created with twelve choice tasks that varied across five attributes: production method (IVM or conventional), carbon trust label, organic label, animal welfare label, and price. 1,120 US consumers were randomly assigned to one of four information treatments, differing by information presented regarding IVM: 1) neutral (baseline), 2) positive, 3) negative, and 4) …

Evaluation Of Current Methods To Detect Cellular Leucine-Rich Repeat Kinase 2 (Lrrk2) Kinase Activity, Belén Fernández, Vinita G. Chittoor-Vinod, Jillian H. Kluss, Kaela Kelly, Nicole Bryant, An Phu Tran Nguyen, Syed A. Bukhari, Nathan J. Smith, Antonio Jesús Lara Ordóñez, Elena Fdez, Marie-Christine Chartier-Harlin, Thomas J. Montine, Mark A. Wilson, Darren J. Moore, Andrew B. West, Mark R. Cookson, R. Jeremy Nichols, Sabine Hilfiker

Department of Biochemistry: Faculty Publications

Background: Coding variation in the Leucine rich repeat kinase 2 gene linked to Parkinson’s disease (PD) promotes enhanced activity of the encoded LRRK2 kinase, particularly with respect to autophosphorylation at S1292 and/or phosphorylation of the heterologous substrate RAB10.

Objective: To determine the inter-laboratory reliability of measurements of cellular LRRK2 kinase activity in the context of wildtype or mutant LRRK2 expression using published protocols.

Methods: Benchmark western blot assessments of phospho-LRRK2 and phospho-RAB10 were performed in parallel with in situ immunological approaches in HEK293T, mouse embryonic fibroblasts, and lymphoblastoid cell lines. Rat brain tissue, with or without adenovirus-mediated …

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 …

Expression And Functional Characterization Of Avocado Dgat1 And Pdat1 In Arabidopsis And Camelina, Josphat Kiunga

Electronic Theses and Dissertations

The study is aimed to determine the role of avocado DGAT1 and PDAT1 in seed oil synthesis. Triacylglycerol (TAG) has a nutritional and industrial value and is essential for plant growth. DGAT1 and PDAT1 catalyze the final step of TAG Assembly. We hypothesized that both PaPDAT1 and PaDGAT1, although predominantly expressed in non-seed tissues, could contribute to oil accumulation in seeds. Agrobacterium transformants with PaPDAT1 and PaDGAT1 cloned in pCAMBIA were generated to test this. Subsequently, the Agrobacterium-mediated transformation of Arabidopsis mutant lines and camelina was carried out by floral dipping. The T₁ camelina seeds …

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 …

Unraveling The Genetic Architecture Of Somatic Embryogenesis In Upland Cotton, Adam M. Canal

All Theses

Somatic embryogenesis is the de novo development of asexual embryos because of the plasticity of the plant cell. In tissue culture, the biochemical and genetic mechanisms of dedifferentiated callus tissues can be reprogrammed to transdifferentiate into developed, polarized embryos, which can ultimately regenerate into whole plants. Although this rarely occurs in nature, scientists have exploited this process for decades to regenerate whole plants following gene transformation or for micropropagation. While some species are amenable to in vitro regeneration, upland cotton is particularly recalcitrant, with regenerative potential being confined to only several genotypes. The lack of elite, regenerable genotypes greatly restricts …

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 …

Regulatory Amendments Of The Strategic Policy For The Job Creation In Indonesia: Research And Innovation Aspect, Putera Prakoso Bhairawa, Widianingsih Ida, Ningrum Sinta, Suryanto, Rianto Yan

ASEAN Journal on Science and Technology for Development

The Job Creation Law, enacted in Indonesia in November 2020, has provided a new understanding of the sectors, such as investment and business activities, employment, and ease of conducting business, that are directly related to various aspects of regulatory adjustment. Research and innovation related to regulatory adjustments have received growing attention in recent years. This article thus attempts to reveal regulatory amendments from the strategic policy of job creation, particularly in terms of research and innovation, grouped into four topics: 1) conducting research and innovation activities; 2) supporting human resources and expertise; 3) stipulating policy support for facilitation, licensing, and …

Deepening Knowledge Of Nutrient Dynamics In Coastal Waters, Meirinawati Hanny, Wahyudi A'An Johan

ASEAN Journal on Science and Technology for Development

Nutrients are important compounds in waterbodies that regulate primary productivity and phytoplankton growth, the basis of food webs. Increased nutrient concentration has become a serious concern because it causes eutrophication and threatens the sustainability of ecosystems. Eutrophication is the process of nutrient enrichment in water bodies that affects their productivity and decreases water quality. Although information about nutrient distribution, limiting nutrients, and nutrient budgets is important for coastal water management, studies of wide-scale nutrient dynamics in Indonesian waters remain limited. To provide comprehensive data on nutrients, this review summarized the concentrations and compositions of nutrients in coastal waters, compared the …

Coastal Vulnerability Assessment For Community Resilience On Abrasion: Case Of Bugel Coast, Kulon Progo Regency, Indonesia, Ramadhan Cahyadi, Dina Ruslanjari, Diana Puspitasari, Gading Dita Indasari, Naufal Sandro

ASEAN Journal on Science and Technology for Development

The coastal boundary can be optimized for settlement and agriculture site based on a spatial plan for Kulon Progo Regency 2012–2032 within a minimum distance of 100m from the coastline. The location of ring 1 local transmigration settlement on the Bugel Coast is less than 100 m. The increasing trend in coastal erosion caused by climate change is a major contributing factor to the reduction of coastal borders. Thus, rapid assessment of coastal erosion vulnerability is necessary to determine an effective coastal management response. This paper aims to analyze the coastal erosion level using vulnerability assessment, geomorphology of coastal areas, …

Isolation And Characterization Of Potential Lactic Acid Producing Bacteria From Fermented Fruit Juice, Than Wah Wah, Maw Saw Sandar, Htun Reemon

ASEAN Journal on Science and Technology for Development

Lactobacillus species are used as probiotics to inhibit human pathogens because of their ability to produce antimicrobial substances. However, when different kinds of antibiotics are used, the antibiotic resistance of drug-resistant bacteria increases. In this study, lactic acid-producing bacteria with antimicrobial activity were isolated and used as probiotics to inhibit six human pathogens, namely Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Bacillus cereus, Salmonella typhi, and Shigella boydii. Nine bacterial isolates were obtained from the crude juice of sugar cane (Saccharum officinarum), strawberry (Fragaria ananassa), and fruit pulp of palm (Borassus flabellifer). Among them, three bacterial isolates (S1, SC, and PP) …

Grand Design For Merapi Irrigation Channel System Using Watershed And River Region Approaches Based On Community Development In Yogyakarta, Indonesia, Suprayogi Slamet, Gunawan Totok, Murti Sigit Heru, Prihantarto Wikan Jaya, Alatas Masrur

ASEAN Journal on Science and Technology for Development

This paper proposes a grand design for Merapi Irrigation Channel, an irrigation channel system spanning from Turi to Cangkringan District in Yogyakarta, Indonesia. This design is based on Geographic Information System research to assess the feasibility of the system from two aspects, namely geophysics using site selection approaches (watershed and river region) and community aspirations, analyze potential water resource availability to support its sustainability, and construct a grand design. Primary data acquired from IKONOS image interpretation were used to collect geophysical and ?eld data for parameter mapping, and spatial data were modeled using Geographic Information System technology to determine paths, …

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 …

Diversity Of Bacteriophage In Burkholderia Species, Abigail Price

Honors Projects

Bacteriophages are viruses that infect and replicate within bacteria and offer the potential of a therapeutic alternative to chronic infections that do not respond to antibiotic-based therapies. B. vietnamiensis is one of a number of Burkholderia species involved with chronic drug resistant infections in the lungs of individuals with compromised respiratory systems, as found in those with chronic obstructive pulmonary disease and, most especially, are of particular significance in patients with cystic fibrosis. The diversity of the Burkholderia species is explored by using online databases and looking at bacteriophage or phage-encoding viruses found in B. vietnamiensis. The open reading frames …

The Synthesis And Purification Methodology Of An Intermolecular Pyrophosphate Sensor: Applications For The Quantitative Polymerase Chain Reaction, Ethan Gevedon

Honors Projects

The optimized synthesis and purification methodology for an intermolecular pyrophosphate sensor scaffold molecule was performed: high performance liquid chromatography afforded the scaffold in excellent purity and yield. The applications of the sensor assembly in the quantitative polymerase chain reaction were discussed, and preliminary results show that

Generating Improved Rna Localization Reporters Using The U1hp-U1a System, Ryan Dannemiller, Rebecca Adams Phd

[Archive] Belmont University Research Symposium (BURS)

Generating Improved RNA Localization Reporters Using the U1hp-U1A System

Ryan Dannemiller, Rebecca Adams, PhD. Belmont University, Nashville, TN.

Messenger mRNA (mRNA) is genetic material that is used to bridge between DNA in the nucleus and protein-making machinery in the cytoplasm of eukaryotic cells. The processes of transcription and translation are physically separated, so the localization of mRNA dictates whether the encoded protein can be generated. In order to observe the localization of specific transcripts in response to stimuli, tools are needed to track location of mRNA. For example, in response to heat shock and ethanol stress, most mRNA is retained …

Europium-Doped Cerium Oxide Nanoparticles For Microglial Aβ Clearance And Homeostasis, Jatin Machhi, Pravin Yeapuri, Milica Markovic, Milankumar Patel, Wenhui Yan, Yaman Lu, Jacob D. Cohen, Mahmudul Hasan, Mai Mohamed Abdelmoaty, You Zhou, Huangui Xiong, Xinglong Wang, R. Lee Mosley, Howard E. Gendelman, Bhavesh D. Kevadiya

Nebraska Center for Biotechnology: Faculty and Staff Publications

Alzheimer’s disease (AD) is the most common neurodegenerative disorder. Pathologically, it is characterized by the deposition of amyloid beta (Aβ) plaques and presence of neurofibrillary tangles. These drive microglia neuroinflammation and consequent neurodegeneration. While the means to affect Aβ plaque accumulation was achieved how it affects disease outcomes remains uncertain. Cerium oxide (CeO₂) reduces Aβ plaques, oxidative stress, inflammation, and Alzheimer’s disease (AD) signs and symptoms. Specifically, CeO₂ nanoparticles (CeO₂NPs) induces free radical scavenging and cell protective intracellular signaling. This can ameliorate the pathobiology of an AD-affected brain. In order to investigate, CeO₂NPs …

Annual Faculty Research Symposium 2022, Oakwood University

Proceedings

No abstract provided.

Characterization Of Erinacine-A, Justice Brakache

Symposium of Student Scholars

The wood-rot fungus known as the lion’s mane mushroom (H. erinaceus) has a long history of usage in ancient eastern medicine, noted for its health-boosting properties, particularly to neurological health. Claims include this mushroom’s ability to stimulate nerve growth as well as prevent the progression of neurodegenerative diseases such as dementia. Recent studies on the subject have shown promising data supporting these anecdotal claims, proving the ability of extracts from this mushroom to stimulate nerve growth factor (NGF) in human cells, among other beneficial findings. This study seeks to assess the effectiveness of the diterpenoid erinacine-A, present in H. …

Improving Photosynthetic Efficiency In Microalgae Through The Genetic Engineering Of Energy Sensors And Photoreceptors, Taylor L. Britton

Biology ETDs

Through photosynthesis microalgae can convert sunlight, water, and CO₂ into chemical energy that can be used to generate carbon neutral biofuels and biomass. With an ever-increasing demand and need for petroleum substitutes it is imperative that we improve the output of industrial-relevant crops such as microalgae. One important way of improving output in algae is by understanding the roles that stress and energy conversion is regulated in these organisms. Photosynthetic organisms fundamentally depend on light- and sugar-driven metabolic and signaling networks, which integrate environmental cues to govern and sustain growth and survival. SnRKs (SNF1-related protein kinases) and the photoreceptor …

Healthcare Simulation: A Key To The Future Of Medical Education - A Review, Omair Ayaz, Faisal Wasim Ismail

Medical College Documents

Aim: Simulation originates from its application in the military and aviation. It is implemented at various levels of healthcare education and certification today. However, its use remains unevenly distributed across the globe due to misconception regarding its cost and complexity and to lack of evidence for its consistency and validity. Implementation may also be hindered by an array of factors unique to the locale and its norms. Resource-poor settings may benefit from diverting external funds for short-term simulation projects towards collaboration with local experts and local material sourcing to reduce the overall cost and achieve long-term benefits. The recent shift …

Als-Associated Kif5a Mutations Abolish Autoinhibition Resulting In A Toxic Gain Of Function, Desiree M. Barron, Adam R. Fenton, Sara Saez-Atienzar, Anthony Giampetruzzi, Aparna Sreeram, Shankaracharya, Pamela J. Keagle, Victoria R. Doocy, Nathan J. Smith, Eric W. Danielson, Megan Andresano, Mary C. Mccormack, Jaqueline Garcia, Valérie Bercier, Ludo Van Den Bosch, Jonathan R. Brent, Claudia Fallini, Brian J. Traynor, Erica L.F. Holzbaur, John E. Landers

Biochemistry -- Faculty Publications

Understandingthepathogenicmechanismsof diseasemutations is critical toadvancingtreatments.ALS-associated mutations in the gene encoding the microtubulemotor KIF5A result in skipping of exon 27 (KIF5ADExon27) and the encoding of a protein with a novel 39 amino acid residue C-terminal sequence. Here, we report that expression of ALS-linked mutant KIF5A results in dysregulated motor activity, cellular mislocalization, altered axonal transport, and decreased neuronal survival. Single-molecule analysis revealed that the altered C terminus of mutant KIF5A results in a constitutively active state. Furthermore,mutant KIF5A possesses altered protein and RNA interactions and its expression results in altered gene expression/splicing. Taken together, our data support the hypothesis that causative …

Developing An Electroporation Method For Transforming Streptomyces Nymphaeiformis, Heather Knott, Stephen Baron

Honors Projects

Streptomyces species are notoriously difficult to transform. Streptomyces nymphaeiformis is no different, so a method of electroporation was used to attempt to transform the cells. Multiple growth stages were used in order to alter the degree of development of the cell wall. The procedure did not kill the cells, but the cells were not transformed. Due to the lack of transformation with S. nymphaeiformis, transformation was attempted on two other Streptomyces strains, S. lividans and S. coelicolor. Neither was successfully transformed to thiostrepton (tsr) resistance, nor did they grow on a plate lacking thiostrepton. One possibility for the …

Comparative Modeling And Evolutionary Comparison Of Serine Protease, A Timber Rattlesnake Venom Protein, Qawer Ayaz

Theses

The aim of this study is to create a homology model of VG35 serine protease and evaluate the evolutionary comparison of secondary structure on basis of protein model using YASARA. This method was furthermore used to predict the potential epitopes which can help in the investigation of future studies.

The VG35 was used to run a BLAST search which gave most resembled serine protease of different species which was then translated and modeled in YASARA. The modeled protein data was then used to determine the secondary structure. This was then used for evolutionary comparison of all proteins to VG35. Then …

A Computational Assessment Of The Allosteric Modulation Of Gabaa Receptor, Abdel Rahman Atef Aly

Theses

γ-aminobutyric acid (GABA) type A receptor (GABA_AR) is a pentameric ligand gated ion channel and a member of the Cys-loop superfamily. It is targeted by several clinically significant allosteric modulators. The role of individual subunits of the receptor has been very extensively studied. However, the exact molecular pathway upon which the receptor is activated remains elusive. The main objective of this study was to probe the molecular activation pathway for the orthosteric GABA and to understand how two of the most well-established positive (PAM) and negative (NAM) allosteric modulators tend to modulate the receptor. Three independent long scale …

Synthesis Of A Streptavidin-Conjugated Agarose Resin For Purification Of Biotin-Tagged Biomolecules, Sydney Thomas

Senior Theses

Streptavidin, a bacteria-derived protein, and the small molecule biotin display extremely high-affinity binding. Researchers have taken advantage of this uniquely strong interaction in a myriad of detection, labeling, and purification techniques, one of which is affinity chromatography. Streptavidin can be immobilized onto a solid support, and this streptavidin-conjugated material can be used to capture biotin-tagged molecules with exceedingly high strength and specificity. In this project, a protocol was developed for synthesizing an agarose-based streptavidin resin for use as an affinity chromatography medium. Additionally, two fluorescence-based assays were developed for quantifying the amount of streptavidin conjugated to each resin and for …

Rna Sequencing Reveals That Cyp3a5 Sirna Treatment Induces Cell Cycle Blockade And Senescence In Mdapca2b Human Prostate Cancer Cells, Jeetesh Sharma

Annual Research Symposium

No abstract provided.

The Design, Construction, And Testing Of A Recombinant Dna Vaccine For Brucella Abortus And Brucella Melitensis, Stephanie Lynn Korle

LSU Doctoral Dissertations

Brucella spp. are a bacterium that cause brucellosis, a zoonotic disease, which is commonly seen in cattle, sheep, goats, swine, and canines. Brucellosis is a problem worldwide, although it is eradicated in some countries (Garin-Bastuji et al. 1998). The reason for designing recombinant DNA (rDNA) vaccines opposed to utilizing the live-attenuated vaccines on the market is that they cannot be given to pregnant animals without potentially causing abortion, while an rDNA vaccine should be safe for pregnant animals since it does not contain viable bacteria. Also, there are no serological tests that can accurately distinguish between an animal vaccinated …