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Inner Ear Development And Advances In Inner Ear Organoid Formation, Paige Avery 2021 University of Louisville

Inner Ear Development And Advances In Inner Ear Organoid Formation, Paige Avery

The Cardinal Edge

The inner ear houses the cochlea which contains hair cells responsible for the transduction of sound waves. The process of forming these hair cells responsible for hearing is a complicated process consisting of many signaling factors that allow ectoderm to form into the otic placode, the otic vesicle, and finally prosensory cells such as hair cells (Schlosser, 2006). Loss of these hair cells contributes to deafness and hearing loss throughout life, and regeneration of these cells may serve as a therapeutic agent for those with irreversible damage. This review looks at the development of the otic placode and hair cells ...


Novel Pilot Development Of A Closed-Loop Sustainable System Between Biogas Renewable Energy, Distilling, And Aquaculture By Vermiculture Of Stillage Wastes, Samuel C. Kessler 2021 University of Louisville

Novel Pilot Development Of A Closed-Loop Sustainable System Between Biogas Renewable Energy, Distilling, And Aquaculture By Vermiculture Of Stillage Wastes, Samuel C. Kessler

The Cardinal Edge

This study provides a mixed-methods approach in analyzing a potential closed-loop system between renewable biogas production from anaerobic digestion, vermiculture production, aquaculture production, and organic wastes with a particular focus on stillage wastes. Such system may hold significant promise for significantly reducing organic carbon and methane emissions from its components, and should be assessed for such. The 2021 IPCC report essentially identified methane reduction as the single fastest way to slow global warming (IPCC, 2021), making the study and implementation of methane-reducing systems and supportive policy for them critical. Knowledge gaps to implementing this system were qualitatively identified as disconnect ...


Improving Healthspan Through Patient-Derived Artificial Organs From Induced Pluripotent Stem Cells And Two-Photon Polymerization, Connor Espenshade 2021 University of Pennsylvania

Improving Healthspan Through Patient-Derived Artificial Organs From Induced Pluripotent Stem Cells And Two-Photon Polymerization, Connor Espenshade

Protocols and Reports

Senescence, from the shortening of telomeres, accumulation of mutations, epigenetic hypomethylation, and other causes, begins an eventual cycle of decline in every patient. Stem cells disappear as a function of age, which in turn impairs cellular replication. Moreover, when fully differentiated cells are induced back into induced pluripotent stem cells (iPSCs), they not only revert to a state of pre-differentiation, but also to a younger cellular age. Their aging clocks turn back: their telomeres become longer and DNA methylation reverts back to an earlier age. It should therefore be possible to use iPSCs to replace the missing stem cells from ...


Phenotype Bias Determines How Natural Rna Structures Occupy The Morphospace Of All Possible Shapes, Fatme Ghaddar, Dr Kamaludin Dingle, Dr Petr Sulc, Prof Ard A. Louis 2021 Gulf University for Science and Technology, Kuwait

Phenotype Bias Determines How Natural Rna Structures Occupy The Morphospace Of All Possible Shapes, Fatme Ghaddar, Dr Kamaludin Dingle, Dr Petr Sulc, Prof Ard A. Louis

Undergraduate Research Symposium

The relative prominence of developmental bias versus natural selection is a long standing controversy in evolutionary biology. Here we demonstrate quantitatively that developmental bias is the primary explanation for the occupation of the morphospace of RNA secondary structure (SS) shapes. By using the RNAshapes method to define coarse-grained SS classes, we can measure the frequencies that non-coding RNA SS shapes appear in nature. Our main findings are firstly that only the most frequent structures appear in nature; the vast majority of possible structures in the morphospace have not yet been explored. Secondly, and perhaps more surprisingly, these frequencies are accurately ...


Tools And Strategies For The Patterning Of Bioactive Molecules And Macromolecules, Daniel J. Valles 2021 The Graduate Center, City University of New York

Tools And Strategies For The Patterning Of Bioactive Molecules And Macromolecules, Daniel J. Valles

Dissertations, Theses, and Capstone Projects

Hypersurface Photolithography (HP) is a printing method for fabricating structures and patterns composed of soft materials bound to solid surfaces and with ~1 micrometer resolution in the x, y, and z dimensions. This platform leverages benign, low intensity light to perform photochemical surface reactions with spatial and temporal control of irradiation, and, as a result, is particularly useful for patterning delicate organic and biological material. In particular, surface- initiated controlled radical polymerizations can be leveraged to create arbitrary polymer and block- copolymer brush patterns. Chapter 1 will review the advances in instrumentation architectures from our group that have made these ...


Biocontrol Of Foodborne Pathogens Using Bacteriophages, Dzhuliya Ignatova, Erion Hogan, Simone Dakare, Jean Lu 2021 Kennesaw State University

Biocontrol Of Foodborne Pathogens Using Bacteriophages, Dzhuliya Ignatova, Erion Hogan, Simone Dakare, Jean Lu

Symposium of Student Scholars

Biocontrol of Foodborne Pathogens Using Bacteriophages

Dzhuliya Ignatova, Erion Hogan, Simone Dakare, and Jean Lu

Department of Molecular and Cellular Biology

Abstract

Salmonella and Shigella are two important groups of foodborne bacterial pathogens. Salmonella cause an illness called salmonellosis while Shigella cause shigellosis (bacillary dysentery). The most common symptoms of these illnesses are abdominal cramps, diarrhea, and fever. Shigella can also cause bloody diarrhea. It was estimated that each year Salmonella cause 93.8 million cases of gastroenteritis and 155,000 deaths globally. Shigella causes 164.7 million cases and 1.1 million deaths throughout the world yearly. People get ...


Complimenting A Chlamydomonas Reinhardtii Mutation Using Cell Penetrating Peptides, Matthew McKenzie 2021 Kennesaw State University

Complimenting A Chlamydomonas Reinhardtii Mutation Using Cell Penetrating Peptides, Matthew Mckenzie

Symposium of Student Scholars

Complimenting a Chlamydomonas reinhardtii Mutation Using Cell Penetrating Peptides

Matthew McKenzie and Jennifer L. Cooper

Chlamydomonas reinhardtii is a photosynthetic model organism most notable for its easily manipulatable genetics. C. reinhardtii uses flagella to swim and optimize its growth conditions in the light. We plan to use cell penetrating peptides (CPPs) to compliment C. reinhardtii that is affected with the IFT46 mutation. Cell penetrating peptides are short peptides that can move across a cell membrane. The novel CPP that we are using is called TaT-CaM. It consists of the trans-activator of transcription (TaT) and the calmodulin domain (CaM) that binds ...


Consumer Valuation Of And Attitudes Towards Novel Foods Produced With Npets: A Review, John C. Beghin, Christopher R. Gustafson 2021 University of Nebraska-Lincoln and Iowa State University

Consumer Valuation Of And Attitudes Towards Novel Foods Produced With Npets: A Review, John C. Beghin, Christopher R. Gustafson

Economics Working Papers

We review the emerging international body of evidence on attitudes and willingness to 10 pay (WTP) for novel foods produced with New Plant Engineering Techniques (NPETs). NPETs include genome/gene editing, cisgenesis, intragenesis, RNA interference and others. These novel foods are often beneficial for the environment and human health and more sustainable under increasingly prevalent climate extremes. These techniques can also improve animal welfare and disease resistance when applied to animals. Despite these promising attributes, evidence suggests that many, but not all consumers, discount these novel foods relative to conventional ones. Our systematic review sorts out findings to identify conditioning ...


Insights Into Halophilic Microbial Adaptation: Analysis Of Integrons And Associated Genomic Structures And Characterization Of A Nitrilase In Hypersaline Environments, Sarah Sonbol 2021 American University in Cairo

Insights Into Halophilic Microbial Adaptation: Analysis Of Integrons And Associated Genomic Structures And Characterization Of A Nitrilase In Hypersaline Environments, Sarah Sonbol

Theses and Dissertations

Hypersaline environments are extreme habitats that can be exploited as biotechnological resources. Here, we characterized a nitrilase (NitraS-ATII) isolated from Atlantis II Deep brine pool. It showed higher thermal stability and heavy metal tolerance compared to a closely related nitrilase.

We also studied integrons in halophiles and hypersaline environments. Integrons are genetic platforms in which an integron integrase (IntI) mediates the excision and integration of gene cassettes at specific recombination sites. In order to search for integrons in halophiles and hypersaline metagenomes, we used a PCR-based approach, in addition to different bioinformatics tools, mainly IntegronFinder.

We found that integrons and ...


Understanding The Adhesion Mechanism In Mycelium-Assisted Wood Bonding, Wenjing Sun 2021 The University of Maine

Understanding The Adhesion Mechanism In Mycelium-Assisted Wood Bonding, Wenjing Sun

Electronic Theses and Dissertations

The increasing environmental awareness has led to an increased interest in developing more sustainable materials as alternatives to petroleum-derived products. Among different nature-based products, fungal-mycelium-based bio-composites have gained considerable attention in various applications. Multiple materials with different densities and structures and potential applications can be fabricated by inoculating filamentous white-rot fungi in lignocellulosic materials and other substrates. Different from lower-density as-grown foam-like mycelium composites, higher-density mycelium-lignocellulosic panels have the potential to replace commercial particleboard and fiberboard bonded by petroleum-based resins. This kind of composite can be produced by directly adding heat and pressure to the low-density foams or by assembling ...


Functional Characterization Of Arogenate Dehydratase Isoforms In Soybean, Ramtin Sirjani 2021 The University of Western Ontario

Functional Characterization Of Arogenate Dehydratase Isoforms In Soybean, Ramtin Sirjani

Electronic Thesis and Dissertation Repository

Phenylalanine flux is partitioned between phenylpropanoid and protein synthesis. The mechanisms behind the metabolic channeling of phenylalanine are largely unknown. Arogenate dehydratase (ADT) enzymes, which catalyze the last and rate-limiting step in the synthesis of phenylalanine in plants, have been shown to interact with the isoflavonoid metabolon in the cytosol. Cytosolic phenylalanine, however, can only be synthesized through prephenate dehydratase (PDT) activity. In this study, putative soybean ADTs (GmADTs) were characterized for their ADT and PDT activity. This was done using complementation assays with two different knockout yeast strains, aro8aro9 and pha2, which lack prephenate aminotransferase and PDT activity, respectively ...


Overcoming Obstacles In Protein Expression In The Yeast Pichia Pastoris: Interviews Of Leaders In The Pichia Field, Zoe Ingram, Abha Patkar, Dahoon Oh, Kevin K. Zhang, Christina Chung, Joan Lin-Cereghino, Geoff P. Lin-Cereghino 2021 University of the Pacific

Overcoming Obstacles In Protein Expression In The Yeast Pichia Pastoris: Interviews Of Leaders In The Pichia Field, Zoe Ingram, Abha Patkar, Dahoon Oh, Kevin K. Zhang, Christina Chung, Joan Lin-Cereghino, Geoff P. Lin-Cereghino

Pacific Journal of Health

The yeast Pichia pastoris (also known as Komagataella pastoris) has been used for over 30 years to produce thousands of valuable, heterologous proteins, such as insulin to treat diabetes and antibodies to prevent migraine headaches. Despite its success, there are some common, stubborn problems encountered by research scientists when they try to use the yeast to produce their recombinant proteins. In order to provide those working in this field with strategies to overcome these common obstacles, nine experts in P. pastoris protein expression field were interviewed to create a written review and video (https://www.youtube.com/watch?v=Q1oD6k8CdG8 ...


Unbiased Automated Quantitation Of Ros Signals In Live Retinal Neurons Of Drosophila Using Fiji/Imagej, Prajakta Deshpande, Neha Gogia, Anuradha Venkatakrishnan Chimata, Amit Singh 2021 University of Dayton

Unbiased Automated Quantitation Of Ros Signals In Live Retinal Neurons Of Drosophila Using Fiji/Imagej, Prajakta Deshpande, Neha Gogia, Anuradha Venkatakrishnan Chimata, Amit Singh

Biology Faculty Publications

Numerous imaging modules are utilized to study changes that occur during cellular processes. Besides qualitative (immunohistochemical) or semiquantitative (Western blot) approaches, direct quantitation method(s) for detecting and analyzing signal intensities for disease(s) biomarkers are lacking. Thus, there is a need to develop method(s) to quantitate specific signals and eliminate noise during live tissue imaging. An increase in reactive oxygen species (ROS) such as superoxide (O2•-) radicals results in oxidative damage of biomolecules, which leads to oxidative stress. This can be detected by dihydroethidium staining in live tissue(s), which does not rely on fixation and helps prevent ...


A Multi-Approach And Multi-Scale Platform To Model Cd4+ T Cells Responding To Infections, Kenneth Y. Wertheim, Bhanwar Lal Puniya, Alyssa La Fleur, Ab Rauf Shah, Matteo Barberis, Tomáš Helikar 2021 University of Nebraska-Lincoln

A Multi-Approach And Multi-Scale Platform To Model Cd4+ T Cells Responding To Infections, Kenneth Y. Wertheim, Bhanwar Lal Puniya, Alyssa La Fleur, Ab Rauf Shah, Matteo Barberis, Tomáš Helikar

Biochemistry -- Faculty Publications

Immune responses rely on a complex adaptive system in which the body and infections interact at multiple scales and in different compartments. We developed a modular model of CD4+ T cells, which uses four modeling approaches to integrate processes at three spatial scales in different tissues. In each cell, signal transduction and gene regulation are described by a logical model, metabolism by constraint-based models. Cell population dynamics are described by an agent-based model and systemic cytokine concentrations by ordinary differential equations. A Monte Carlo simulation algorithm allows information to flow efficiently between the four modules by separating the time scales ...


An Exploration Of The Properties Of Repair Template Dna That Promote Precision Genome Editing, Krishna S. Ghanta 2021 University of Massachusetts Medical School

An Exploration Of The Properties Of Repair Template Dna That Promote Precision Genome Editing, Krishna S. Ghanta

GSBS Dissertations and Theses

CRISPR/Cas9 induced DNA breaks can be precisely repaired by cellular homology-directed repair (HDR) pathways using exogenously provided template DNA (donor). However, the full potential of precision editing is hindered in many model systems by low cutting efficiencies, low HDR efficiencies and, cytotoxicity related to Cas9 and donor DNA. In this thesis, I address these challenges and present methods that we developed to increase HDR efficiencies in multiple model organisms.

In Caenorhabditis elegans, we show that by reducing toxicity high editing efficiencies can be achieved with single stranded oligonucleotide (ssODN) donors. We demonstrate that melting dsDNA donors dramatically improves the ...


Development Of High Value Oil Traits Using The Model Oilseed Crop Camelina Sativa, Evan Updike 2021 University of Nebraska-Lincoln

Development Of High Value Oil Traits Using The Model Oilseed Crop Camelina Sativa, Evan Updike

Theses and Dissertations in Biochemistry

Plant oils are an important source of food, fuel, and feed in our society today. The oil found in the seeds of plants is composed almost entirely of triacylglycerol (TAG) molecules, which consist of three fatty acids esterified to a glycerol backbone. As crude oil supplies decline, vegetable oils are gaining traction as a renewable substitute to petroleum-based materials in fuels, lubricants, and specialty oleochemicals. However, as it currently stands vegetable oils do not possess the properties necessary to fill the void of a petroleum free world.

To address this problem, plant biotechnologists have done extensive work on genetic engineering ...


Characterization Of The Growth Factor Receptor Network Oncogenes In Lung Cancer, Ashley Duche 2021 Chapman University

Characterization Of The Growth Factor Receptor Network Oncogenes In Lung Cancer, Ashley Duche

Pharmaceutical Sciences (MS) Theses

Lung cancer remains the leading cause of cancer related deaths worldwide, reportedly contributing to 1.8 million of the 10.0 million mortalities documented in the year 2020. Although advancements have been made in therapeutics and diagnostic methods, formulation of effective treatments and development of drug resistance continues to be a challenge. These challenges arise from our lack of understanding of intricate signaling pathways, such as the Growth Factor Receptor Network (GFRN), which contributes to complex lung tumor heterogeneity allowing for drug resistance development. In this study, gene expression signatures of six GFRN oncogenes overexpressed in human mammary epithelial cells ...


Marker-Assisted Selection To Determine The Introgression Of Rpv-3 Mediated Downy Mildew Resistance In 'Chambourcin' X 'Caberenet Sauvignon' Grapevine Population, Kavya Sri Tummala 2021 Missouri State University

Marker-Assisted Selection To Determine The Introgression Of Rpv-3 Mediated Downy Mildew Resistance In 'Chambourcin' X 'Caberenet Sauvignon' Grapevine Population, Kavya Sri Tummala

MSU Graduate Theses

Downy mildew caused by the fungus, Plasmopara viticola in the grapes is one of the major diseases affecting crop yield throughout the world. Breeding grapes via conventional methods for the downy mildew resistance will take approximately 25-30 years to fully evaluate and release new cultivars. Because of the long breeding cycle in woody plant species like grape, developing DNA markers linked to genes or quantitative trait loci (QTLs) for horticultural traits can greatly accelerate the breeding process and allow a much more accurate selection of progeny. This study aims to determine the presence of resistance in the 267 F1 genotypes ...


Investigation Into The Evolution Of Heterogeneity Within Secondary Replicons And Their Maintenance In Genus Variovorax, Christopher Ne Ville 2021 California State University - San Bernardino

Investigation Into The Evolution Of Heterogeneity Within Secondary Replicons And Their Maintenance In Genus Variovorax, Christopher Ne Ville

Electronic Theses, Projects, and Dissertations

Approximately 10% of all bacterial genomes sequenced thus far contain a secondary replicon. This considerable genetic reservoir contains many potentially mobilizable elements, allowing for the formation of many unique secondary replicons. This property of bacterial populations vastly increases the genomic diversity available to species that effectively take up and maintain these replicons. Members of the genus Variovorax have extensive heterogeneity in genome architecture, including sequenced isolates containing plasmids, megaplasmids, and chromids. Using available Illumina data on the NCBI database, we have completed these assemblies using 3rd generation sequencing methods on 17 members of this genus. We have sequenced, assembled ...


Euadb: A Resource For Covid-19 Test Development And Comparison, Alyssa Woronik, Henry W. Shaffer, Karin Kiontke, Jon M. Laurent, Ronald Zambrano, Mariah Daley, Jef D. Boeke, David H. Fitch 2021 Sacred Heart University

Euadb: A Resource For Covid-19 Test Development And Comparison, Alyssa Woronik, Henry W. Shaffer, Karin Kiontke, Jon M. Laurent, Ronald Zambrano, Mariah Daley, Jef D. Boeke, David H. Fitch

Biology Faculty Publications

Due to the sheer number of COVID-19 (coronavirus disease 2019) cases there is a need for increased world-wide SARS-CoV-2 testing capability that is both efficient and effective. Having open and easy access to detailed information about these tests, their sensitivity, the types of samples they use, etc. would be highly useful to ensure their reproducibility, to help clients compare and decide which tests would be best suited for their applications, and to avoid costs of reinventing similar or identical tests. Additionally, this resource would provide a means of comparing the many innovative diagnostic tools that are currently being developed in ...


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