Biochemistry, Biophysics, and Structural Biology Commons^™

Delineating The Role Of Mir-124 For The Activation Of Neuronal Program, Ya-Lin Lu

Arts & Sciences Electronic Theses and Dissertations

The ectopic expression of two brain-enriched microRNAs (miRNAs), miR-9/9* and miR-124 (miR-9/9*-124), can robustly and efficiently reprogram human skin fibroblasts into neurons. The miRNAs act as repressors of non-neuronal genes in fibroblasts for the induction of the neuronal program. This process is analogous to neurogenesis in vivo when the expression of miR-9/9* and miR-124 represses anti-neurogenic genes such as REST or NRSF (neuron-restrictive silencer factor/repressor element-1 silencing transcription factor). Although we have some mechanistic insights into how miR-9/9*-124 drives fate conversion by acting as negative regulators of gene expression, little remained understood of the role of miRNAs as positive regulators …

Specificity Of Ssb Binding To Its Interacting Proteins And Multiple Allosteric Effects Of Ssb C-Terminal Tail On Assembly And Dna Binding Of E. Coli Recor Proteins, Min Kyung Shinn

Arts & Sciences Electronic Theses and Dissertations

The homo-tetrameric E. coli single strand (ss) DNA binding (SSB) protein is an essential component in DNA maintenance for its role in binding and protecting single stranded DNA intermediates via its N-terminal DNA binding domain (DBD). SSB also acts as a hub to recruit at least 17 SSB interacting proteins (SIPs) involved in DNA replication, recombination, and repair via its 9 amino acid C-terminal acidic tip region. A 56 amino acid intrinsically disordered linker connects the DBD and the acidic tip and plays a role in cooperative binding to ssDNA. Using isothermal titration calorimetry, I determined that the SSB-Ct peptides …

Mechanisms Of Cross-Presentation By Cdc1s, Derek James Theisen

Arts & Sciences Electronic Theses and Dissertations

Classical dendritic cells (cDCs) are specialized antigen presenting cells that can be divided into distinct subsets based on the types of pathogens they respond to and the type of immune response they generate. The cDC1 subset is specialized in priming CD8 T cell responses through the process of cross-presentation. During cross-presentation, exogenous protein antigens are taken up by cDC1 and presented on MHCI molecules, allowing for the priming of CD8 T cells during conditions when DCs themselves are not directly infected. The ability to cross-present in vivo is unique to cDC1, and is essential for anti-viral responses and rejection of …

Bumpy Road Ahead: Overcoming Dna Replication Obstacles One Barrier At A Time, Melanie Anne Sparks

Arts & Sciences Electronic Theses and Dissertations

DNA replication must occur efficiently and timely every cell cycle to protect the integrity of the genome. Stalled or slowed replication forks lead to replication stress that can cause replication fork collapse, and potentially genome instability. Scattered throughout the genome are tightly bound proteins, such as transcription factors, that are necessary for cell function and survival. These proteins have the potential to impede timely DNA replication. Furthermore, genomic DNA is packaged around histone octamers into structures called nucleosomes that both compact the DNA and provide an additional layer of information and regulation termed epigenetics. Thus, DNA replication is not only …

Engineering Natural Competence Into The Fast-Growing Cyanobacterium Synechococcus Elongatus Utex 2973, Kristen Elizabeth Wendt

Arts & Sciences Electronic Theses and Dissertations

Synechococcus elongatus UTEX 2973 is the fastest growing cyanobacterium discovered to date. Using water, carbon dioxide, and light alone, this organism can double in 1.5 hours under optimal conditions. The accelerated doubling exhibited by Synechococcus 2973 makes it a prime candidate to serve as a model photoautotrophic system. However, Synechococcus 2973 lacks one highly desirable feature: it cannot undergo natural transformation. This thesis seeks to engineer this capacity into this fast-growing system in order to create an organism that is both fast growing and naturally competent. Synechococcus 2973 is a unique platform because it is >99% genetically identical to another …

Triclosan Disrupts Immune Cell Function By Depressing Ca2+ Influx Via Acidification Of The Cytoplasm, Suraj Sangroula

Electronic Theses and Dissertations

Triclosan (TCS) is an antimicrobial agent that was effectively banned by the FDA from hand soaps in 2016, hospital soaps in 2017, and hand sanitizers in 2019; however, TCS can still be found in a few products. At consumer-relevant, non-cytotoxic doses, TCS inhibits the functions of both mitochondria and mast cells, a ubiquitous cell type. Via the store-operated Ca²⁺ entry mechanism utilized by many immune cells, mast cells undergo antigen-stimulated Ca²⁺ influx into the cytosol, for proper function. Previous work showed that TCS inhibits Ca²⁺ dynamics in mast cells, and here we show that TCS also inhibits …

Glycan-Dependent Adherence And Skin Colonization Of Staphylococcus Epidermidis Mediated By The Surface Protein Aap., Paroma Roy

Theses & Dissertations

Skin-dwelling coagulase-negative staphylococci (CoNS), a group of bacteria that includes Staphylococcus epidermidis, has been implicated to promote skin immunity and antimicrobial defense and prohibit colonization of skin by pathogens like S. aureus. As a skin inhabitant, S. epidermidis lives in tight association with corneocytes, the cells that constitute the uppermost layer of the skin epidermis. Yet the molecular mechanism responsible for adhesion of S. epidermidis to corneocytes remains poorly understood. Our study indicated that Accumulation-associated protein (Aap), a cell-wall anchored, fibrillar adhesin mediates bacterial-host interaction, demonstrated by significantly higher corneocyte binding by Aap-positive 1457 mutants as compared to …

Testing The Combined Module Swapping And Repair By Modification Strategies: A Step Toward Universal Toolbox, Catherine A. Martini

Biology Theses

The crux of synthetic biology is the engineering of biological components to modulate the activity of specific DNA-based promoter(s) to drive gene expression; thus, providing a means to modulate pathways between signal detection and cellular response. However, the longstanding frustration of synthetic biologists has been the inability to transfer those engineered components between cellular systems — this lack of “modular universality” or “universal toolbox” impedes research by forcing a metaphorical reinvention of the wheel in new systems. The modular swapping strategy expanded the available “toolbox” with customizable hybrid repressors formed from “swapping” the DNA-recognition modules (DRMs) and environmental-sensing modules (ESMs) …

A Chemical Interpretation Of Protein Electron Density Maps In The Worldwide Protein Data Bank, Sen Yao, Hunter N. B. Moseley

Molecular and Cellular Biochemistry Faculty Publications

High-quality three-dimensional structural data is of great value for the functional interpretation of biomacromolecules, especially proteins; however, structural quality varies greatly across the entries in the worldwide Protein Data Bank (wwPDB). Since 2008, the wwPDB has required the inclusion of structure factors with the deposition of x-ray crystallographic structures to support the independent evaluation of structures with respect to the underlying experimental data used to derive those structures. However, interpreting the discrepancies between the structural model and its underlying electron density data is difficult, since derived sigma-scaled electron density maps use arbitrary electron density units which are inconsistent between maps …

Foliage Type Controls Mercury Input, Storage, And Release In The Boreal Forest, Madelaine J R Anderson

Electronic Thesis and Dissertation Repository

Mercury (Hg) is a naturally occurring element with a complex biogeochemical cycle. Forests act as net sinks for both carbon (C) and Hg as foliage accumulates Hg with time. Litterfall represents a main input of C and Hg into forest soils. My aim was to investigate how foliage type (coniferous, deciduous) governs the input of Hg into forests with a field-based study that measured Hg accumulation over a growing season, and then investigate the storage and release of Hg from foliar tissues into soil with a laboratory-based incubation experiment. Results from the field-based study demonstrate deciduous leaves have more linear …

Identification Of Predation Events In Wild Fish Using Novel Acoustic Transmitters, Amy A. Weinz, Jordan K. Matley, Natalie V. Klinard, Aaron T. Fisk, Scott F. Colborne

Great Lakes Institute for Environmental Research Publications

Background: Acoustic telemetry is a commonly used tool to gain knowledge about aquatic animal ecology through the study of their movements. In telemetry studies researchers must make inferences regarding the movements and the fates of tagged animals. Until recently, predation has been inferred in telemetry data using a variety of methods including abrupt changes in movement patterns or habitat use. An acoustic telemetry transmitter has been developed to detect predation events of tagged animals, and while they have performed well in controlled laboratory trials, literature regarding the application of these novel transmitters in field settings is limited. The objective of …

Differential Expression Of Rna In The Rat Peripheral Nervous System Following Nerve Injury And Treatment With Pain-Relieving Celecoxib-Loaded Nanomedicine, Andrea Stevens

Electronic Theses and Dissertations

The neuroinflammatory response to peripheral nerve injury is associated with chronic pain and significant changes in the expression profiles of RNAs in neurons, glia and infiltrating immune cells: a neuro-immune triad. Chronic constriction injury (CCI) of the rat sciatic nerve provides an opportunity to mimic neuropathic injury and quantitatively assess behavior and differential gene expression in individual animals. Macrophages that phagocytose intravenously injected nanoemulsion carrying the non-steroidal anti-inflammatory, NSAID, Celecoxib, naturally accumulate at the site of injury resulting in relief of CCI behavioral hyper-sensitivity. It is not known beyond the inhibition of cyclooxygenase-2 (COX-2) activity and the reduction in prostaglandin …

Analysis Of Olfactory Mrna Cap Modifications Using Rnaseh And Lc-Ms, Ilinca M. Giosan

Theses and Dissertations

In the olfactory system, olfactory sensory neurons (OSNs) express odorant receptors (ORs) in a singular fashion through unknown mechanisms. Published data supports the notion that singularity is achieved, in part, through a modification the mRNA strand, perhaps in its 5’cap region. This theoretical study aims to test this 5’cap hypothesis.

Snow-Albedo Feedback In Northern Alaska: How Vegetation Influences Snowmelt, Lucas C. Reckhaus

Theses and Dissertations

This paper investigates how the snow-albedo feedback mechanism of the arctic is changing in response to rising climate temperatures. Specifically, the interplay of vegetation and snowmelt, and how these two variables can be correlated. This has the potential to refine climate modelling of the spring transition season. Research was conducted at the ecoregion scale in northern Alaska from 2000 to 2020. Each ecoregion is defined by distinct topographic and ecological conditions, allowing for meaningful contrast between the patterns of spring albedo transition across surface conditions and vegetation types. The five most northerly ecoregions of Alaska are chosen as they encompass …

The Role Of Spine In Causing Lameness In Horses, Raja Zabeeh Ullah Khan

English Language Institute

Lameness is one of the most important problems of horses. It influences all communities who keep horses. Recent studies have shown the significance of spinal muscles and vertebrae in inducing lameness in horses. The field has not been explored much and requires application of biomechanics to define the role of spine in inducing lameness in horses. This presentation highlights the importance of spine in inducing lameness in horses by relating the solution with biomechanics.

Structure And Evolution Of Lizard Immunity Genes, Trent Santonastaso

University of New Orleans Theses and Dissertations

One of the most important gene families to play a role in adaptive immunity is the major histocompatibility complex (MHC). MHC class II loci are considered to be the most variable loci in the vertebrate genome, and studies have shown that this variability can be maintained through complex co-evolutionary dynamics between host and parasite. Despite the rich body of research into the MHC, there is comparatively little understanding of its genomic architecture in reptiles. Similarly, loci associated with innate immunity have received little attention in reptiles compared to other vertebrates. In the first chapter, we investigated the structure and organization …

The Investigation Of Surface Structures On Various Pathogens And Their Interactions With The Human Immune System, Carmen M. Villalobos

Biomedical Engineering ETDs

The cell surface is the first interface the host immune system encounters and

its investigation has led to a better understanding of cellular biology and types of

pathways that pathogens target in a host cell. The cell surface has evolved to include

many functions such as manipulation of the cytoskeleton, cell signaling, membrane

trafficking, adhesion, and integration into host tissue. The pathogens of interest are

the pathogenic fungus, Candida albicans, and the parasite, Giardia lamblia and we

investigate the consequences of drug treatments on the cell surface, leading to

promising new targets.

Building An Ins-1 Cdna Library For A Genome-Wide Crispr-Cas9 Screen, Idongesit Ekpo

Undergraduate Honors Theses

By the year 2040, an estimated 642 million people are expected to have diabetes globally. Diabetes results from an elevation of metabolic stressors, such as glucotoxicity, lipotoxicity, oxidative stress and apoptosis. In type 2 diabetes, these stressful conditions contribute to the malfunction and loss of functional insulin-producing β-cells. Current treatment methods for diabetes include insulin therapy, islet transplant and anti-diabetes medication. These treatments are not curative and ignore other factors that contribute to the pathogenesis of diabetes beyond insulin resistance and islet β-cell failure. Previous research on β-cells has focused on ways to replace functional β-cell mass, trigger β-cell proliferation, …

Needles In A Haystack Of Protein Diversity: Interrogation Of Complex Biological Samples Through Specialized Strategies In Bottom-Up Proteomics Uncover Peptides Of Interest For Diverse Applications, Manuel I. Villalobos Solis

Doctoral Dissertations

Peptide identification is at the core of bottom-up proteomics measurements. However, even with state-of the-art mass spectrometric instrumentation, peptide level information is still lost or missing in these types of experiments. Reasons behind missing peptide identifications in bottom-up proteomics include variable peptide ionization efficiencies, ion suppression effects, as well as the occurrence of chimeric spectra that can lower the efficacy of database search strategies. Peptides derived from naturally abundant proteins in a biological system also have better chances of being identified in comparison to the ones produced from less abundant proteins, at least in regular discovery-based proteomics experiments. This dissertation …

Community Dynamics And Function Of Algae And Bacteria During Winter In Central European Great Lakes, George S. Bullerjahn, Robert Michael L. Mckay, Gábor Bernát, Ondřej Prášil, Lajos Vörös, Károly Pálffy, Nóra Tugyi, Boglárka Somogyi

Great Lakes Institute for Environmental Research Publications

Abundant phytoplankton and bacteria were identified by microscopy and high-throughput 16S rRNA tag Illumina sequencing of samples from water- and ice phases collected during winter at two central European Great Lakes, Balaton and Fertő (Neusiedlersee). Bacterial reads at all sites were dominated (>85%) by Bacteroidetes and Proteobacteria. Amongst phototrophs, microscopy and 16S sequencing revealed that both phytoplankton and cyanobacteria were represented, with a median of 1500 cyanobacterial sequence reads amongst 13 samples analyzed. The sequence analysis compared replicate Balaton and Fertő ice and water samples with an outgroup from three Hungarian soda lakes. In particular, both water and ice …