Collagen Xi Impact On Structure And Function Of The Vertebrate Inner Ear In A Zebrafish Model,
2021
Boise State University
Collagen Xi Impact On Structure And Function Of The Vertebrate Inner Ear In A Zebrafish Model, Makenna Hardy
Boise State University Theses and Dissertations
The ear is essential to maintaining balance and hearing; both of which can be linked to one another and significantly impact a person’s quality of life. Although aging and damage are more common reasons for hearing loss, congenital ear defects still have a considerable impact on our population. The function of the ear can be affected by structural deformities to the ear and its components which results in hearing loss. Mutations and single nucleotide polymorphisms in the gene encoding Collagen XI alpha one chain (COL11A1) protein can play a role in hearing and balance dysfunction in humans as seen in …
Enhancing The Interoperability Of Glycan Data Flow Between Chebi, Pubchem, And Glygen.,
2021
George Washington University
Enhancing The Interoperability Of Glycan Data Flow Between Chebi, Pubchem, And Glygen., Rahi Navelkar, Gareth Owen, Venkatesh Mutherkrishnan, Paul Thiessen, Tiejun Cheng, Evan Bolerlton, Nathan Edwards, Michael Tiemeyer, Matthew P Campbell, Maria Martin, Jeet Vora, Robel Kahsay, Raja Mazumder
Biochemistry and Molecular Medicine Faculty Publications
Glycans play a vital role in health, disease, bioenergy, biomaterials, and bio-therapeutics. As a result, there is keen interest to identify and increase glycan data in bioinformatics databases like ChEBI and PubChem, and connecting them to resources at the EMBL-EBI and NCBI to facilitate access to important annotations at a global level. GlyTouCan is a comprehensive archival database that contains glycans obtained primarily through batch upload from glycan repositories, glycoprotein databases, and individual laboratories. In many instances, the glycan structures deposited in GlyTouCan may not be fully defined or have supporting experimental evidence and citations. Databases like ChEBI and PubChem …
Overcoming Obstacles In Protein Expression In The Yeast Pichia Pastoris: Interviews Of Leaders In The Pichia Field,
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=FyC9xXVLyD0). This review describes …
Characterizing Multivalent Interactions Between Folded Protein Domains And Intrinsically Disordered Regions Or Peptide Substrates,
2021
Syracuse University
Characterizing Multivalent Interactions Between Folded Protein Domains And Intrinsically Disordered Regions Or Peptide Substrates, Tongyin Zheng
Dissertations - ALL
Protein-protein interactions (PPIs) play central roles in most biological processes. Studying PPIs is a fundamental step in understanding the molecular basis of cellular processes such as cell-cell contact, enzyme activity, and transient assembly of signaling complexes or cellular structures. In this work, we employed a combination of biophysical and biochemical methods to characterize PPIs, with a focus on interactions between structured domains and intrinsically disordered regions or peptide substrates.The subject of Chapter two is prolyl isomerase Ess1, which is an essential enzyme found in Saccharomyces cerevisiae. Ess1 regulates the transcription and co-transcriptional RNA processing by catalyzing the isomerization of serine-proline …
Late Embryogenesis Abundant Proteins And Mitochondrial Membranes From An Animal Extremophile: Insights Into Severe Water Stress,
2021
Louisiana State University and Agricultural and Mechanical College
Late Embryogenesis Abundant Proteins And Mitochondrial Membranes From An Animal Extremophile: Insights Into Severe Water Stress, John Marcus Anderson
LSU Doctoral Dissertations
This dissertation focuses on two major topics germane to mechanisms by which animals tolerate extreme water stress. First, the impact of transgenic expression of late embryogenesis abundant proteins (LEA) on water stress tolerance of the fruit fly Drosophila melanogaster was investigated. The overall aim was to extend current understanding of the protective properties of LEA proteins documented with isolated cells to a desiccation-sensitive organism during exposure to drying and hyperosmotic stress. Four lines of D. melanogaster were created that expressed transgenes encoding selected LEA proteins originally identified in embryos of the extremophile Artemia franciscana. After 80% tissue water loss, …
Screening Next-Generation Fluorine-19 Probe And Preparation Of Yeast-Derived G Proteins For Gpcr Conformation And Dynamics Study,
2021
University of South Florida
Screening Next-Generation Fluorine-19 Probe And Preparation Of Yeast-Derived G Proteins For Gpcr Conformation And Dynamics Study, Wenjie Zhao
USF Tampa Graduate Theses and Dissertations
GPCR regulates numerous diverse physiological processes relevant to diabetes, obesity, Alzheimer's diseases, and several central nervous system disorders and targets proteins in signaling pathways. It has created nearly 200 billion profits from its derivative drugs in 2018. There are near 400 structures of over 70 GPCRs have been resolved by X-ray crystallography, cryo-electron microscopy, and NMR spectroscopy. One of the current challenges that remain in the conformational transition and dynamics study using NMR spectroscopy is to obtain sufficient quantities of the G proteins and GPCRs. Pichia pastoris has shown its tremendous promise in expressing the GPCRs in a high yield, …
Evaluation Of Horizontal Gene Transfer Between Genetically Engineered Cyanobacteria And Gram-Negative Bacteria,
2021
Old Dominion University
Evaluation Of Horizontal Gene Transfer Between Genetically Engineered Cyanobacteria And Gram-Negative Bacteria, Andriana Chrysovalanti Zourou
Chemistry & Biochemistry Theses & Dissertations
As the world population is increasing and societies become more technology driven, there is an imperative to develop ‘green energy’ sources to protect our planet. Cyanobacteria that have been genetically engineered to produce organic compounds that may be burnt as fuels show great potential, as they are an environmentally friendly and self-renewable, net carbon-neutral option. However, there are potential risks in the development and use of genetically modified organisms (GMOs). We need to understand in advance the risks that GMOs may pose to our environment and to animal and human health. This will enable experimental procedures, containment strategies and policies …
Awegnn: Auto-Parametrized Weighted Element-Specific Graph Neural Networks For Molecules.,
2021
University of Kentucky
Awegnn: Auto-Parametrized Weighted Element-Specific Graph Neural Networks For Molecules., Timothy Szocinski, Duc Duy Nguyen, Guo-Wei Wei
Mathematics Faculty Publications
While automated feature extraction has had tremendous success in many deep learning algorithms for image analysis and natural language processing, it does not work well for data involving complex internal structures, such as molecules. Data representations via advanced mathematics, including algebraic topology, differential geometry, and graph theory, have demonstrated superiority in a variety of biomolecular applications, however, their performance is often dependent on manual parametrization. This work introduces the auto-parametrized weighted element-specific graph neural network, dubbed AweGNN, to overcome the obstacle of this tedious parametrization process while also being a suitable technique for automated feature extraction on these internally complex …
Host-Parasite Interactions Within Food Webs,
2021
University of Arkansas, Fayetteville
Host-Parasite Interactions Within Food Webs, Adam Zvanut Hasik
Graduate Theses and Dissertations
Parasitism is one of the most common life history strategies employed in nature, yet the effects of parasites are often thought to be minimal, and the vast majority of studies fail to consider parasites and their effects on host organisms. This is likely a problem, as the magnitude of parasite-mediated effects on their hosts can be quite large. Additionally, the effects of parasites are known to extend beyond the host to affect other species interactions. I used a series of approaches to gain a more integral understanding of host-parasite interactions by studying (1) the effects of parasites on biotic interactions …
Divergent Regulatory Roles Of Nurd Chromatin Remodeling Complex Subunits Gatad2 And Chd4 In Caenorhabditis Elegans,
2021
Florida Institute of Technology
Divergent Regulatory Roles Of Nurd Chromatin Remodeling Complex Subunits Gatad2 And Chd4 In Caenorhabditis Elegans, Nicole Lynn Golden
Theses and Dissertations
During stress, a protective cellular network known as the heat shock response (HSR) is induced to maintain protein-folding homeostasis, or proteostasis. While the HSR is essential for stress resistance, its misregulation is associated with neurodegenerative disease and cancer. Using the nematode model organism Caenorhabditis elegans, we have identified the chromatin remodeling complex NuRD (nucleosome remodeling and deacetylase) as a novel regulator of the HSR. Here, we begin with a brief introduction of the HSR and chromatin remodeling complexes in C. elegans, prior to presenting our findings in a series of two chapters. In chapter one, we outline a set of …
Genetically Encoded Multivalent Liquid Glycan Array Displayed On M13 Bacteriophage,
2021
1Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada. Pharmaceutical Chemistry Department, Faculty of Pharmacy, The British University in Egypt, El Sherouk, Egypt
Genetically Encoded Multivalent Liquid Glycan Array Displayed On M13 Bacteriophage, Amira Khalil, Mirat Sojitra, Jasmine Maghera, Emily Rodrigues, Eric J. Carpenter, Shaurya Seth, Daniel Ferrer Vinals, Todd L. Lowary
Pharmacy
The central dogma of biology does not allow for the study of glycans using DNA sequencing. We report a liquid glycan array (LiGA) platform comprising a library of DNA ‘barcoded’ M13 virions that display 30–1,500 copies of glycans per phage. A LiGA is synthesized by acylation of the phage pVIII protein with a dibenzocyclooctyne, followed by ligation of azido-modified glycans. Pulldown of the LiGA with lectins followed by deep sequencing of the barcodes in the bound phage decodes the optimal structure and density of the recognized glycans. The LiGA is target agnostic and can measure the glycan-binding profile of lectins, …
Distinct Spatiotemporal Regulation Of The Cytoprotective Heat Shock Response In Caenorhabditis Elegans,
2021
Florida Institute of Technology
Distinct Spatiotemporal Regulation Of The Cytoprotective Heat Shock Response In Caenorhabditis Elegans, Rosemary Nadine Plagens
Theses and Dissertations
Every organism studied to-date utilizes the heat shock response (HSR) to maintain protein-folding homeostasis (proteostasis) during temperature or other protein-folding stress. The HSR has been well characterized using acute heat stress (HS) in single-celled models, but less is known about how distinct cell types and tissues respond to HS. Furthermore, how metazoans respond to prolonged HS at the molecular level remains relatively unexplored. The model organism C. elegans, with its genetic tractability and distinct tissues and behaviors, has been used extensively in the field to characterize the acute HSR, but with considerable variability across labs regarding HS temperature and duration. …
Mechanisms Of Spontaneous Curvature Inversion In Compressed Graphene Ripples For Energy Harvesting Applications Via Molecular Dynamics Simulations,
2021
University of Arkansas, Fayetteville
Mechanisms Of Spontaneous Curvature Inversion In Compressed Graphene Ripples For Energy Harvesting Applications Via Molecular Dynamics Simulations, James M. Mangum, Ferdinand Harerimana, Millicent N. Gikunda, Paul M. Thibado
Physics Faculty Publications and Presentations
Electrically conductive, highly flexible graphene membranes hold great promise for harvesting energy from ambient vibrations. For this study, we built numerous three-dimensional graphene ripples, with each featuring a different amount of compression, and performed molecular dynamics simulations at elevated temperatures. These ripples have a convex cosine shape, then spontaneously invert their curvature to concave. The average time between inversion events increases with compression. We use this to determine how the energy barrier height depends on strain. A typical convex-to-concave curvature inversion process begins when the ripple’s maximum shifts sideways from the normal central position toward the fixed outer edge. The …
Characterization Of Iron-Sulfur Cluster Biogenesis In Methanogenic Archaea,
2021
University of Arkansas, Fayetteville
Characterization Of Iron-Sulfur Cluster Biogenesis In Methanogenic Archaea, Thomas Modlin Deere
Graduate Theses and Dissertations
Iron-sulfur (Fe-S) clusters are among the oldest cofactors on the planet, used by proteins in almost all forms of life on Earth to carry out processes ranging from energy transfer to DNA replication. Among the organisms believed to use these Fe-S proteins more extensively than almost any others are the methanogens, an ancient lineage of archaeal microbes that produce methane as a required product of their metabolism. Methane, the primary component of commercial natural gas, is both a potent greenhouse gas and an important fossil fuel. It can also be renewably produced as a biofuel. Biogenic methane is almost entirely …
The Characterization Of Angiopoietin-Like Protein 4 Overexpression In Triple Negative Breast Cancer,
2021
University of Arkansas, Fayetteville
The Characterization Of Angiopoietin-Like Protein 4 Overexpression In Triple Negative Breast Cancer, Jodi Simeon
Graduate Theses and Dissertations
Triple Negative Breast Cancer (TNBC) is highly invasive and metastatic with approximately 15% of patients developing liver metastases. The primary treatment of metastatic TNBC is chemotherapy, however, there is an increased chance of resistance to this therapeutic technique. If Breast Cancer Liver Metastasis (BCLM) is left untreated most patients survive only 4 to 8 months with a very rare 5-year survival. Therefore, it is imperative to analyze markers and molecular pathways that TNBC cells use to progress, invade, and metastasize to the liver. The aim of this study was to examine the overexpression of angiopoietin-like 4 (ANGPTL4) in TNBC cells …
Evaluating Bioenergetics And Mitochondrial Dynamics In Patient Fibroblasts With Pathogenic Mitochondrial Dna Mutations Causing Leigh Syndrome,
2021
University of Arkansas, Fayetteville
Evaluating Bioenergetics And Mitochondrial Dynamics In Patient Fibroblasts With Pathogenic Mitochondrial Dna Mutations Causing Leigh Syndrome, Ajibola Bakare
Graduate Theses and Dissertations
Leigh syndrome (LS) is a rare fatal mitochondrial disorder of infants caused by pathogenic mutations in the nuclear (nDNA) or mitochondrial DNA (mtDNA) leading to mitochondrial dysfunction. The extent to which pathogenic mtDNA variants regulate disease severity in LS is not well understood. The heterogeneous nature of this disorder, based in part by complex mitochondrial genetics, and the nuclear and mitochondrial cross-talk has made it particularly challenging to investigate and develop therapies for treating LS . While the prognosis is poor, several studies are underway to understand the pathophysiology of LS. This dissertation provides a comprehensive structural and functional analysis …
A Time-Course Characterization Of Muscle Function And Mitochondrial Markers During Colorectal Cancer-Induced Cachexia In Tumor-Bearing Male Mice,
2021
University of Arkansas, Fayetteville
A Time-Course Characterization Of Muscle Function And Mitochondrial Markers During Colorectal Cancer-Induced Cachexia In Tumor-Bearing Male Mice, Ana Cabrera Ayuso
Graduate Theses and Dissertations
Cachexia is a multisystemic and multifactorial syndrome prevalent in cancer patients. It is clinically defined by involuntary loss of >5% weight in a six-month window, despite nutritional interventions. A negative energy balance characterizes cancer cachexia (CC), it is associated with weakness and fatigue in skeletal muscle. Impaired muscle function is associated with lower quality of life in cancer patients. Defects in mitochondrial function are strongly associated with muscle wasting. This study explored muscular contractile function and mitochondrial quality control (MQC) markers in soleus, gastrocnemius, and tibialis anterior (TA) muscles of C26-induced male tumor-bearing mice during a 25-day time course. It …
Evolution Of Targeted Therapy Resistance In Eml4-Alk Positive Non-Small Cell Lung Cancer,
2021
University of South Florida
Evolution Of Targeted Therapy Resistance In Eml4-Alk Positive Non-Small Cell Lung Cancer, Robert Vander Velde
USF Tampa Graduate Theses and Dissertations
Targeted therapies have emerged as potent treatments that lead to the remission of many tumors. However, they rarely cure cancers in advanced, metastatic settings. This is due to the evolution of resistance, which in turn can be ascribed to the survival of small subpopulations of tolerant and/or resistant cells. Here we investigated the evolution of resistance to EML4-ALK inhibitors in non-small cell lung cancer (NSCLC) and demonstrated that resistance evolves gradually, from unique pre-treatment sub-populations, as multiple resistance mechanisms accumulate in a Darwinian fashion. Despite accumulating multiple changes, cells evolved, in parallel, toward similar inhibitor specific phenotypes. Evolving cells have …
Transcriptomic And Functional Investigation Of Bacterial Biofilm Formation,
2021
University of South Florida
Transcriptomic And Functional Investigation Of Bacterial Biofilm Formation, Brooke R. Nemec
USF Tampa Graduate Theses and Dissertations
Staphylococcus aureus and Acinetobacter baumannii are two highly successful human pathogens, which have adopted very different, but effective survival strategies. The success of S. aureus is attributed to the tight regulation of an arsenal of virulence factors. Conversely, A. baumannii lacks what would be considered traditional virulence factors and, instead, has developed a high tolerance for environmental stress, which allows it to persist in unforgiving environments, including nosocomial settings and the human body. One common characteristic of these two organisms is their proclivity for biofilm formation. Herein, we discuss the diverse mechanisms governing biofilm formation for A. baumannii and S. …
Cytoplasmic Polyadenylation Element Binding Protein 2 Alternative Splicing Regulates Hif1Α During Chronic Hypoxia,
2021
University of South Florida
Cytoplasmic Polyadenylation Element Binding Protein 2 Alternative Splicing Regulates Hif1Α During Chronic Hypoxia, Emily M. Mayo
USF Tampa Graduate Theses and Dissertations
Chronic pulmonary hypoxia commonly results in the sustained expression of HIF1 (hypoxia inducible factor 1), a heterodimeric transcription factor, that, if unrestrained, can result in dramatic vasculature remodeling, pulmonary arterial hypertension, and right-sided heart failure. Together, these pulmonary disorders cost approximately $100 billion annually to treat due to the limited therapeutic targets designed to inhibit HIF1 expression. In this study, we introduce a translational regulator of HIF1 expression, known as Cytosolic polyadenylation element binding proteins 2 (CPEB2). Our lab has previously demonstrated in cancer cells that alternatively spliced isoforms of CPEB2 regulate the translation of the HIF1 oxygen-dependent subunit, HIF1α, …
