Molecular Biology Commons^™

Fxs-Causing Point Mutations In Fmrp Disrupt Neuronal Granule Formation And Function, Emily L. Starke

Electronic Theses and Dissertations

Fragile X Syndrome (FXS) is a neurodevelopmental disorder caused by the disruption of Fragile X Mental Retardation Protein (FMRP) function in neurons, affecting nearly 1 in 7,500 individuals. Although FXS typically occurs from a complete loss of FMRP expression due to a CGG trinucleotide expansion within the 5’UTR of the FMR1 gene, single nucleotide polymorphisms (SNPs) within the KH domains of FMRP have been shown to severely disrupt FMRP function. FMRP is an RNA-binding translation repressor that interacts with ~4% of the neuronal transcriptome. Many target mRNAs encode for proteins important for regulating synaptic processes and modulate synaptic plasticity. It …

Effects Of Resin Chemistries On The Selective Removal Of Industrially Relevant Metal Ions Using Wafer-Enhanced Electrodeionization, Humeyra B. Ulusoy Erol, Christa N. Hestekin, Jamie A. Hestekin

Chemical Engineering Faculty Publications and Presentations

Wafer-enhanced electrodeionization (WE-EDI) is an electrically driven separations technology that occurs under the influence of an applied electric field and heavily depends on ion exchange resin chemistry. Unlike filtration processes, WE-EDI can be used to selectively remove ions even from high concentration systems. Because every excess ion transported increases the operating costs, the selective separation offered by WE-EDI can provide a more energy-efficient and cost-effective process, especially for highly concentrated salt solutions. This work reports the performance comparison of four commonly used cation exchange resins (Amberlite IR120 Na⁺, Amberlite IRP 69, Dowex MAC 3 H⁺, and …

Development Of A Dna Biosensor Using Crispr/Dcas9 On A Graphene Oxide Surface For Detecting Antibiotic Resistance Genes, Wendy Cecil

Mahurin Honors College Capstone Experience/Thesis Projects

Antibiotic resistance is a rapidly spreading global threat to human health. Previously in our lab, we developed a simple method for facile detection of antibiotic resistance genes (ARGs) in bacteria. This DNA detection system takes advantage of the CRISPR-Cas system (Clustered Regularly Interspaced Short Palindromic Repeat and CRISPRAssociated Protein). We designed CRISPR in complex with nuclease deactivated Cas9 (dCas9) on graphene oxide (GO) sheets conjugated with Cas9 antibodies. Single guide RNA (sgRNA) was customized to program dCas9 for target DNA binding. sgRNA was covalently labeled with fluorescein to provide fluorescence signal. Graphene oxide (GO) is utilized for its quenching properties …

Molecular Dynamics Of Bcs1l: A New Homology Model And The Structural Impact Of Pathogenic Mutations, Josh Deyoung, Sadie Heeringa, Rachael Baker, Amy Wilstermann

Summer Research

• Mutations to BCS1L can lead to one of three distinct rare diseases: Björnstad syndrome, BCS1L mitopathy, GRACILE syndrome
• These diseases cause a variety of symptoms in patients that range from mild (hearing loss and brittle hair) to severe and fatal (iron overload, failure to thrive, lactic acidosis, aminoaciduria, early death)

Tracking The Subcellular Localization Of Surface Proteins In Staphylococcus Aureus By Immunofluorescence Microscopy, Salvatore J. Scaffidi, Mac A. Shebes, Wenqi Yu

Molecular Biosciences Faculty Publications

Surface proteins of Staphylococcus aureus and other Gram-positive bacteria play essential roles in bacterial colonization and host-microbe interactions. Surface protein precursors containing a YSIRK/GXXS signal peptide are translocated across the septal membrane at mid-cell, anchored to the cell wall peptidoglycan at the cross-wall compartment, and presented on the new hemispheres of the daughter cells following cell division. After several generations of cell division, these surface proteins will eventually cover the entire cell surface. To understand how these proteins travel from the bacterial cytoplasm to the cell surface, we describe a series of immunofluorescence microscopy protocols designed to detect the stepwise …

Dcaf14 Promotes Stalled Fork Stability To Maintain Genome Integrity, Arik Townsend, Gabriella Lora, Justin Engel, Neysha Tirado-Class, Huzefa Dungrawala

Molecular Biosciences Faculty Publications

No abstract provided.

Simulation Of A Rat Muscle-Tendon Unit With Hill-Type Model Dynamics And The Study Of Viscoelasticity In A Collagen Molecule Via Molecular Dynamics, Veronica Siko

West Chester University Master’s Theses

The field of biological science has established that tendons transfer muscular forces to adjacent bones, but there is a dearth of information about the underlying physical principles of these interactions and how the property of viscoelasticity (displayed in tendons as a difference in mechanical response to stress with differing stretching rates) is encompassed in the collagen of tendons. This thesis details the results of concentric and eccentric contractions of the rat muscle-tendon unit (MTU) with and without viscoelasticity (concentric contraction requires active shortening of the muscle, while eccentric contraction requires active lengthening of the muscle) (Lovering & Brooks, 2014). Once …

Photoreceptor Phosphodiesterase (Pde6): Structure, Regulatory Mechanisms, And Implications For Treatment Of Retinal Diseases, Rick H. Cote, Richa Gupta, Michael J. Irwin, Xin Wang

Faculty Publications

The photoreceptor phosphodiesterase (PDE6) is a member of large family of Class I phosphodiesterases responsible for hydrolyzing the second messengers cAMP and cGMP. PDE6 consists of two catalytic subunits and two inhibitory subunits that form a tetrameric protein. PDE6 is a peripheral membrane protein that is localized to the signaling-transducing compartment of rod and cone photoreceptors. As the central effector enzyme of the G-protein coupled visual transduction pathway, activation of PDE6 catalysis causes in a rapid decrease in cGMP levels that results in closure of cGMP-gated ion channels in the photoreceptor plasma membrane. Because of its importance in the phototransduction …

The Gene Expression Patterns Of Phanerochaete Chrysosporium And Trametes Versicolor On Diverse Lignocellulosic Feedstocks, Noor Osama Alabbasi

Masters Theses

Plant biomass is considered to be an important future starting material for fuels and chemicals, thereby decreasing our reliance on fossil fuels. While direct combustion continues to be a source of fuel, the generation of liquid fuels from plant biomass for transportation has proven to be challenging. Among the limiting factors for conversion of this material to biofuels is the recalcitrant nature of lignocellulose, the primary component of non-starch plant biomass. A strategy to overcome this dilemma is to directly or indirectly use the enzymes from white-rot fungi, which have evolved a unique ability to deconstruct lignocellulose. However, the biochemical …

A Novel Review Of Heat Shock Protein 110 Kda: A Basis For Research And Continued Experimentation Through Biochemical Analysis, Crist W. Cuffee

Theses and Dissertations

Heat shock protein 110 kDa, Hsp110, is a distinct cellular protector, different in form and function from Hsp70, a close relative of Hsp110. Functioning primarily as a holdase or in tandem with other molecular chaperones, a review of current accomplishments elucidates the uniqueness of this protein and the continued mysteries that surrounds it. Found only in eukaryotes, Hsp110 has been linked to many diseases, ranging from parasitic infection to neurodegenerative disorders. While still lacking, studies of this protein have provided much in the realm of speculation on the mechanisms behind Hsp110s’ contribution to different pathologies. This review will serve as …

Novel Roles Of Yy1 In Astrocytes, Karli A. Mockenhaupt

Theses and Dissertations

Astrocytes tile the entire central nervous system, are diverse across brain regions, and perform specialized functions fine-tuned for their neuronal circuit. Initially, astrocyte heterogeneity is generated through intrinsic programs specified by their progenitors. Then, as astrocyte mature, they are specialized by region-specific communication with surrounding cells. The molecular programs that regulate this diversity and allow for the accommodation to the needs of the local environment remains elusive. We explored a ubiquitously expressed zinc finger transcription factor, Yin Yang 1 (YY1), that both activates and represses transcription by regulating loops of active chromatin. This report describes the diverse functions of astrocytic …

Global Coordination Between Gene Expression Processes In C. Crescentus, James Raymond Aretakis

Wayne State University Dissertations

Gene expression is an essential process of all organisms which occurs in two steps, mRNA transcription, and translation and which is shut off by mRNA decay. For a bacterium to grow and divide, these steps need to be tuned to optimize the synthesis rates of thousands of proteins from their genes. Genome-wide experiments were used to determine the absolute transcription rates, mRNA degradation rates, and translation rates on a gene by gene basis in the model bacterium Caulobacter crescentus. This not only provides a system biology view of the organism’s gene expression resource allocation, but also provides a chance to …

Factor Fiction? Identifying A Putative Toxoplasma Gondii Transcriptional Complex, Julia M. Paquette

Honors Theses and Capstones

Toxoplasma gondii is a highly prevalent protozoan parasite that is estimated to infect 30-50% of the global population, though there is no treatment for chronic infection and current treatments for acute infection may have serious side effects. Transcription is a tightly regulated process in T. gondii, allowing the parasite to successfully invade and replicate within host cells, and it is thus a promising avenue to study gene regulation and to investigate possible novel therapeutics. In our lab’s previous research, a TFIID-like complex was identified in T. gondii and found to be associated with the parasite specific bromodomain protein BDP3. …

Exploring The Connection Between The Spontaneous Regression Seen In Neuroblastomas, Hypertumors, And Reactive Oxygen Species, Shahad Musa, Manitha Mulpuru

AUCTUS: The Journal of Undergraduate Research and Creative Scholarship

Peto’s Paradox is defined as the lack of correlation between larger animals and cancer risk. Under the assumption that all cells have equal risk of becoming cancerous, larger animals should have greater rates of cancer. However, the inverse is true. Determining the cause of this variation may allow a supplemental approach to cancer treatment. A combination of two reasons may account for this correlation including hypertumors and metabolism. Hypertumors, or cheater cells, are hypothesized to suppress cancer growth through spontaneous autophagic degradation and overexpression of the RAS g-protein. Both of these characteristics are exhibited in Neuroblastomas. An anticancer drug used …

Host Factors Affecting Group Ii Intron Retrotransposition, Justin Michael Waldern

Legacy Theses & Dissertations (2009 - 2024)

Group II introns are self-splicing mobile elements that are thought to be the evolutionary ancestors of eukaryotic retrotransposons, the spliceosome, and spliceosomal introns. Yet, little is known about how group II introns have coevolved within their native hosts or about the corresponding host biology.Using the Ll.LtrB intron in its native host, Lactococcus lactis, I first sought to identify host factors that influence retrotransposition. Since retrotransposition can be costly to the host organism, group II introns must achieve a delicate balance between self-proliferation and host preservation. By utilizing the native host organism, my goal was to unearth retrotransposition-related mechanisms that have …

Retrotransposon-Mediated Transduction Of An Environmental Cue To Regulate Centrosome Fate, Shawn Patrick Murphy

Legacy Theses & Dissertations (2009 - 2024)

In 1969, the enrichment of mobile element repeat sequences led Britton and Davidson to propose the hypothesis that gene expression in higher eukaryotes is regulated through the exaptation of mobile elements. In this work, I have explored the hypothesis that mobile elements can also be harnessed by the host to regulate asymmetric cell division, thereby determining cell fate. Retrotransposons are ubiquitous eukaryotic mobile elements that transpose through an RNA intermediate. They are often active in cell types that divide asymmetrically to yield daughter cells with different fates, such as embryonic stem cells, germline stem cells, neuronal stem cells and the …

The Phosphodiesterase, Rv0805, Is An Unheralded Component Of Tb Complex Mycobacterial Physiology In And Beyond Camp Homeostasis, James R. Mcdowell

Legacy Theses & Dissertations (2009 - 2024)

Phosphodiesterases (PDEs) are integral components of 3’,5’-cyclic adenosine monophosphate (cAMP) signaling pathways by degrading cAMP to modulate the concentration, duration, and localization of the cAMP signal which maintains the specificity of cAMP pathways. The human pathogen, Mycobacterium tuberculosis (Mtb) has a unique cAMP network architecture with at least 15 adenylyl cyclases (ACs) that generate cAMP, but only one characterized PDE, Rv0805, which is found exclusively in pathogenic mycobacteria. Rv0805 can influence Mtb cAMP levels but the absence of Rv0805 orthologs in non-pathogenic mycobacteria and apparent separation of Rv0805 from cAMP directed roles led to numerous questions surrounding PDE function in …

Identification Of Ires Activity In Cellular Mrnas And Viral Rna Using A Circular Rna Construct, Priyanka Sehta

Legacy Theses & Dissertations (2009 - 2024)

Translation initiation is a critical step in the process of protein synthesis. The canonical way of translation initiation involves ribosomes being recruited to the 7-methyl guanosine cap present at the 5’end of the untranslated region (5’ UTR) of the RNAs. However, viral RNAs and some cellular mRNAs lack this 5’ cap structure and thus deploy an alternate non-canonical translation initiation mechanism. In non-canonical translation initiation, ribosome recruitment is facilitated by the RNA secondary structures called Internal Ribosome Entry Site (IRES) present most often in the 5’ UTR. To measure IRES-mediated translation, the dual luciferase assay has been the gold standard. …

Role Of Rna Helicases In The Drosophila Germline, Patrick Blatt

Legacy Theses & Dissertations (2009 - 2024)

Gametogenesis, the process of creating egg or sperm, is required for launching successive generations of sexually reproducing organisms. The developmental milestones that occur during gamete production have been studied for decades and are of critical interest to gain insight to conserved features of human fertility. Drosophila has been used for over a century as an efficient research model and remains pivotal in uncovering fundamental biological paradigms. During Drosophila egg production, or oogenesis, several developmental transitions must be traversed to ensure completion of oogenesis including: Germline Stem Cell (GSC) maintenance and differentiation, mitotic and meiotic cell divisions, and production of maternally …

Functional Characterization Of Threonine 49 Phosphorylation Of Cytochrome C, Antoine Khobeir

Wayne State University Theses

Cytochrome c (Cytc) is a pivotal multifunctional mitochondrial protein that serves as a single electron carrier between complexes III and IV of the electron transport chain. It has important roles in both cellular respiration and apoptosis. The novel Thr49 (T49) phosphorylation of Cytc likely affects mitochondrial respiration, membrane potential, ROS production, ATP production, and apoptosis. Based on the functional characterization of previously mapped phosphorylation sites (Tyr97, Tyr48, Thr28, Ser47, Thr58) of the lab, we hypothesize that T49 phosphorylation will lead to controlled respiration, optimal intermediate mitochondrial membrane potential, lower ROS production, and inhibition of apoptosis compared to unphosphorylated Cytc. Here …

Novel Role Of Endoplasmic Reticulum-Associated Degradation In The Regulation Of Ceruloplasmin, Stephen William Hippleheuser

Wayne State University Theses

Ceruloplasmin (Cp) is a secreted ferroxidase produced by the hepatocytes that assists in the transport of iron throughout the human body. In human aceruloplasminemia patients, due to Cp deficiency excess intracellular iron buildup leads to ailments like liver cirrhosis, neurodegeneration, and blindness. We recently found that the biogenesis of Cp in the endoplasmic reticulum (ER) is regulated by a principal ER quality-control process, ER-associated degradation (ERAD). ERAD clears misfolded ER proteins for cytosolic proteasomal degradation, with the Sel-1 suppressor of lin-12-like (Sel1L)-HMG-CoA reductase degradation 1 (Hrd1) protein complex representing the most conserved branch in mammals. Interestingly, we found that Sel1L-Hrd1 …

Abc Transporters In Glioblastoma: Anticancer Drug Transport And Transporter Regulation At The Blood-Brain Barrier, Julia A. Schulz

Theses and Dissertations--Pharmacy

Glioblastoma is one of the deadliest cancers, with a median survival of only one year. Even after aggressive treatment consisting of surgical resection, radiation, and chemotherapy, most glioblastoma patients suffer from tumor recurrence within 6-9 months. One reason for treatment failure of anticancer drugs is the blood-brain barrier that protects the brain by impeding xenobiotic uptake from the blood. To this end, efflux transporters at the human blood-brain barrier, such as P-glycoprotein (ABCB1) and Breast Cancer Resistance Protein (ABCG2), prevent many compounds, including anticancer drugs, from entering the brain. Thus far, approaches to deliver anticancer drugs across the blood-brain barrier …

'Induction Of Apoptosis, Cytotoxicity And Radiosensitization By Novel 3,4-Dihydroquinazolinone Derivatives, Eman Ramadan, Amira Khalil

Pharmacy

Twenty new quinazolinone derivatives bearing a piperonyl moiety were designed and synthesized. The structures of the target compounds were in agreement with the microanalytical and spectral data. Compounds 4-10, 13, 14 and 17-27 were screened for their cytotoxic activity against HepG-2 and MCF-7 cancer cell lines. The target compounds showed IC₅₀ in the range of 2.46-36.85 µM and 3.87-88.93 µM for HepG-2 and MCF-7, respectively. The promising compounds 7, 19, 26 and 27 were selected to measure their EGFR inhibitory activity. The IC₅₀ values of the promising compounds were in the range of 146.9-1032.7 nM for EGFR in …

Post-Translational Modification And Degradation Mechanisms Of The Aryl Hydrocarbon Receptor, Yujie Yang

University of the Pacific Theses and Dissertations

The aryl hydrocarbon receptor (AHR) is a transcription factor first discovered to be activated by exogenous ligands, such as dioxins, and helps promote downstream gene (e.g. CYP1A1) transcription to metabolize the toxicants. With the reports of various AHR targets genes, the expression levels and activities of AHR have been implicated in many physiological and pathological situations. Understanding how AHR protein level is regulated would provide more information to target AHR. AHR stays in the cytosol in the absence of ligand in a complex with HSP90, p23 and XAP2. After ligand activation, AHR translocates into the nucleus, fulfilling its transactivation function …

Comparison Of Standard And Environmental Dna Methods For Estimating Chinook Salmon Smolt Abundance In The Klamath River, California, Doyle Joseph Coyne

Cal Poly Humboldt theses and projects

Evaluating abundance of juvenile salmonids is critical to conservation and management. Current abundance estimation involves use of rotary screw traps and mark-recapture studies. Use of environmental DNA (eDNA) in water samples offers a noninvasive and less expensive approach that may potentially improve or eventually replace traditional monitoring. Here I evaluate the utility of eDNA to predict weekly abundance estimates of outmigrating Chinook salmon (Oncorhynchus tshawytscha) smolts in the Klamath River, California. A total of 15 water samples were collected per week over the 17-week smolt outmigration in both 2019 and 2020. Chinook salmon eDNA concentration in each water …

Auxin-Induced Degradation Of Dream Proteins, Lin-9 And Lin-54, In Caenorhabditis Elegans, Karli E. Chosa

Dissertations, Master's Theses and Master's Reports

The Dp, Retinoblastoma, E2F, And MuvB (DREAM) complex mediates transcriptional repression and is highly conserved throughout a number of species, including vertebrates, Drosophila melanogaster, and Caenorhabditis elegans. Differing from mammalian DREAM, C.elegans DRM, appears to act solely in a repressive role, with the MuvB subcomplex (LIN-9, LIN-37, LIN-52, LIN-53, and LIN-54) playing a key role in the repression of genes. In this study, we use the auxin-inducible degron (AID) system, an effective, fast-acting, tool used in the degradation of degron-tagged proteins to individually deplete two key proteins of the MuvB subcomplex, LIN-9 and LIN-54, in C. elegans. The …

Applications Of Machine Learning In Microbial Forensics, Ryan B. Ghannam

Dissertations, Master's Theses and Master's Reports

Microbial ecosystems are complex, with hundreds of members interacting with each other and the environment. The intricate and hidden behaviors underlying these interactions make research questions challenging – but can be better understood through machine learning. However, most machine learning that is used in microbiome work is a black box form of investigation, where accurate predictions can be made, but the inner logic behind what is driving prediction is hidden behind nontransparent layers of complexity.

Accordingly, the goal of this dissertation is to provide an interpretable and in-depth machine learning approach to investigate microbial biogeography and to use micro-organisms as …

The Effects Of Increasing Positively Charged Metal Ions Within Synovial Fluid, Kandisi Anyabwile

Williams Honors College, Honors Research Projects

Osteoarthritis is a degenerative joint disease that affects 10% of men and 13% of women over age of 60. It is the degradation of the cartilage between two bones; obesity, age, overuse, or injury are major contributors to the development of this disease. The joint is incapsulated by the synovial sac filled with a viscous solution that aids in lubrication referred to as synovial fluid. If the synovial sac is ruptured due to injury, positive ions (K⁺, Na⁺, Ca²⁺, and Fe³⁺) may affect viscoelastic properties within the sac. The purpose of this …

Titanium Dioxide Nanoparticles Binding To Human Blood Plasma Proteins, Morgan Miller

Williams Honors College, Honors Research Projects

Titanium Dioxide (TiO₂, titania) nanoparticles are widely studied in cosmetology, food administration, and medical fields. This is due to the nanoparticles’ suitable properties, specific combination of strength and high corrosion resistance. With the increasing attention to these particles, there is concern with potential health complications. Some of the complications involved with titania nanoparticles include blood clots and immune reactions (Sit et al., 2019). In this study, we continue the study conducted in the Sahai research group (J. Chen. MS thesis, 2020), on the binding of titania nanoparticles with blood plasma proteins, focusing on potential effects of shape only. …

Leveraging Chemical And Computational Biology To Probe The Cellulose Synthase Complex, B. Kirtley Amos

Theses and Dissertations--Plant and Soil Sciences

Cellular expansion in plants is a complex process driven by the constraint of internal cellular turgor pressure by an expansible cell wall. The main structural element of the cell wall is cellulose. Cellulose is vital to plant fitness and the protein complex that creates it is an excellent target for small molecule inhibition to create herbicides. In the following thesis many small molecules (SMs) from a diverse library were screened in search of new cellulose biosynthesis inhibitors (CBI). Loss of cellular expansion was the primary phenotype used to search for putative CBIs. As such, this was approached in a forward …