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Htra1 Prevents And Reverses Α-Synuclein Aggregation, Rendering It Non-Toxic And Seeding Incompetent, Sheng Chen

Arts & Sciences Graduate Student Theses and Dissertations

Protein misfolding and accumulation of misfolded species are associated with multiple neurodegenerative diseases, including Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). α-Synuclein (α-Syn) misfolding and accumulation into Lewy bodies is closely linked to Parkinson’s disease. In ALS and FTD, TDP-43 and FUS are found to be aggregated in disease pathology. These proteins aggregate and associate with both a toxic gain of function of misfolded form and a loss of function due to misfolding. Therefore, it is critical to understand molecular mechanisms by which cells can prevent protein misfolding and how the cell can reverse the aggregation …

Cyclobutanone Inhibitors Of Diaminopimelate Desuccinylase (Dape) As Potential New Antibiotics, Thahani Shifna Habeeb Mohammad, Emma H. Kelley, Cory T. Reidl Dr., Katherine Konczak, Megan Beulke, Janielle Javier, Ken W. Olsen, Daniel P. Becker Ph.D.

Chemistry: Faculty Publications and Other Works

Based on our previous success in using cyclobutanone derivatives as enzyme inhibitors, we have designed and prepared a 37-member library of α-aminocyclobutanone amides and sulfonamides, screened for inhibition of the bacterial enzyme diaminopimelate desuccinylase (DapE), which is a promising antibiotic target, and identified several inhibitors with micromolar inhibitory potency. Molecular docking suggests binding of the deprotonated hydrate of the strained cyclobutanone, and thermal shift analysis with the most potent inhibitor (3y, IC50 = 23.1 µM) enabled determination of a Ki value of 10.2 +/− 0.26 µM and observed two separate Tm values for H. influenzae DapE (HiDapE).

Effect Of Passivation And Surface Treatment Of A Laser Powder Bed Fusion Biomedical Titanium Alloy On Corrosion Resistance And Protein Adsorption, Saman Nikpour, Jeffrey Henderson, Sina Matin, Heng-Yong Nie, Jonas Hedberg, Vahid Dehnavi, Yara Hosein, David Holdsworth, Mark Biesinger, Yolanda Hedberg

Chemistry Publications

The biomedical titanium alloy Ti6Al4V has excellent corrosion resistance and biocompatibility and is, therefore, widely used in orthopedic and orthodontic implants. Biomedical implants are increasingly fabricated by additive manufacturing, such as laser powder bed fusion (LPBF). These manufacturing protocols often include sandblasting, surface finish, and passivation. This study aims to investigate the effect of different surface finishes and the commonly used ASTM F86-13 nitric acid passivation for LPBF Ti6Al4V on its corrosion resistance, metal release, and surface changes in benign (bovine serum albumin in a pH 7.4 buffer) and harsh (hydrochloric acid at pH 1.5) solutions using various electrochemical and …

Genome-Wide Profiling Of Novel Conserved Zea Mays Micrornas Along With Their Key Biological, Molecular And Cellular Targets And Validation Using An Rt-Pcr Platform, Abdul Baqi, Sami Ullah, Muhammad Ayub, Muhammad Zafar Saleem, Ghulam Mustafa Khan, Asad Ullah

Karbala International Journal of Modern Science

MicroRNAs (miRNAs), which are typically non-coding RNAs that start off as endogenous molecules and regulate post-transcriptional levels of gene expression by mRNA degradation or translational repression. They are 18–26 nucleotides long, evolutionarily conserved and essential for predicting novel miRNAs in a variety of plants. Maize (Zea mays) is a significant food and forage crop in the globe today. In the present study, many maize miRNAs have been found to be associated with both plant development and responses to stress. In this study, 66 unique conserved maize miRNAs from 65 different miRNA families were predicted using several genomics-based methods …

The Role Of Cu (0-0.03) And Zn (0.02) Substitution On The Structural, Optical And Magnetic Properties Of Mgo Nanoparticles, S. Naseem Shah, Atif Dawar, Yasmeen Bibi, Abid Ali, M. Asif Siddiqui

Karbala International Journal of Modern Science

The co-precipitation method was employed to prepared Cu (0-0.03) and Zn (0.02) dual doped MgO nanoparticles. The secondary phases of CuO and Cu₂O were observed along with the cubical phase of MgO. The doping induced effect was noticed for the crystallite size variations (14.39-19.89 nm). The morphological transformation from spherical to rice-like shape were observed. The estimated values of optical bandgap (4.66-4.45 eV) were well correlated with the crystallite size and dopant concentrations. The ferromagnetic ordering was observed at room temperature and the enchantment in the coercivity (142.27 Oe) with Zn (0.02) doping was noticed. Such type of …

Synthesis And Characterization Of Bio Based Amphiphilic Molecules, Vandana Singh

Theses and Dissertations

Among various molecular self-assemblies, low molecular weight gelators (LMWGs), that can form gels in organic solvents/water/oils, have gained much research attention due to their huge potential applications. Generally, gels are soft nanomaterials formed by the self-assembly of amphiphilic molecules into a three-dimensional fibrous network entrapping the solvent.

As these gels are formed by self-assembly via non-covalent interactions they are reversible and differ from macromolecular gels. To synthesize LMWGs, biomolecules such as fats, oils, fatty acids, lignocelluloses, sugars, amino acids, and peptides are commonly used as their inherent property favors self-assembly. In the current scenario, interest in synthesizing bio-based gelators has …

Effect Of Zwitterionic Additives On Solvation And Transport Of Sodium And Potassium Cations In (Ethylene Oxide)10: A Molecular Dynamics Simulation Study, Manh Tien Nguyen, Yuhua Duan, Qing Shao

Markey Cancer Center Faculty Publications

Sodium- (Na+) and potassium- (K+) ion batteries are cost-effective alternatives to lithium- ion (Li+) batteries due to the abundant sodium and potassium resources. Solid polymer electrolytes (SPEs) are essential for safer and more efficient Na+ and K+ batteries because they often exhibit low ionic conductivity at room temperature. While zwitterionic (ZW) materials enhance Li+ battery conductivity, their potential for Na+ and K+ transport in batteries remains unexplored. In this study, we investigated the effect of three ZW molecules (ChoPO4, i.e., 2-methacryloyloxyethyl phosphoryl- choline, ImSO3, i.e., sulfobetaine ethylimidazole, and ImCO2, i.e., carboxybetaine ethylimidazole) on the dissociation of Na+ and K+ coordination …

Hyperstructures In Chemical Hyperstructures Of Redox Reactions With Three And Four Oxidation States, Fakhry Asad Agusfrianto, Sonea Andromeda, Mariam Hariri

All Works

Hyperstructures find numerous applications across various disciplines. One notable application is in chemistry, particularly in the context of chemical reactions. In 2014, Davvaz introduced the concept of bi-hyperstructures, but their application specifically in chemical reactions, has yet to be thoroughly explored in previous studies. Thus, the primary aim of this paper is to examine and analyze the different types of bi-hyperstructures present within chemical hyperstructures. The scope of this study focuses on two types of chemical hyperstructures: redox reactions and reactions in electrochemical cells. Within these chemical hyperstructures, we investigate the possibility of bi-hyperstructures among bi-semihypergroups, bi-hypergroups, bi-H_v-semigroups, and bi-H_v-groups. …

Predicting The Reactions Of Cs2, Ocs, And Co2 With Group Iv And Group Vi Transition Metal Oxides, Marissa Shea Blair, Zachary Ryan Lee Phd, David A. Dixon Phd

Posters-at-the-Capitol

Building on a recent serious of high level electronic structure studies of Lewis acid gas reactions with metal oxide sorbents, DFT (B3LYP and ωB97X-D) and CCSD(T) methods are being used to predict the Lewis acid-base addition (physisorption) and formation of metal oxide carbonate/thiocarbonate formation (chemisorption) reactions of CS2, OCS, and CO2 of CS2, OCS, and CO2 with Group IV (MO2)n and Group VI (MO3)n (n = 1 - 3) nanoclusters. For the Group IV oxides, chemisorption to form terminal carbonates and thiocarbonates is predicted to be the most favored, with thiocarbonate ligand binding energies slightly more exothermic than their carbonate …

Seeing Eye To Eye? Comparing Faculty And Student Perceptions Of Biomolecular Visualization Assessments, Josh T. Beckham, Daniel R. Dries, Bonnie L. Hall, Rarchel M. Mitton-Fry, Shelly Engelman, Charmita Burch, Roderico Acevedo, Pamela S. Mertz, Didem Vardar-Ulu, Swati Agrawal, Kristin M. Fox, Shane Austin, Margaret A. Franzen, Henry V. Jakubowski, Walter R. P. Novak, Rebecca Roberts, Alberto I. Roca, Kristen Procko

Chemistry Faculty Publications

While visual literacy has been identified as a foundational skill in life science education, there are many challenges in teaching and assessing biomolecular visualization skills. Among these are the lack of consensus about what constitutes competence and limited understanding of student and instructor perceptions of visual literacy tasks. In this study, we administered a set of biomolecular visualization assessments, developed as part of the BioMolViz project, to both students and instructors at multiple institutions and compared their perceptions of task difficulty. We then analyzed our findings using a mixed-methods approach. Quantitative analysis was used to answer the following research questions: …

Treatment Of Oil Refinery Wastewater Polluted By Heavy Metal Ions Via Adsorption Technique Using Non-Valuable Media: Cadmium Ions And Buckthorn Leaves As A Study Case, Salem Jawad Alhamd, Mohammed Nsaif Abbas, Mehrdad Manteghian, Thekra Atta Ibrahim, Karar Dawood Salman Jarmondi

Karbala International Journal of Modern Science

This study focuses on the removal of cadmium ions generated by oil refinery wastewater, employing an agricultural by-product. Buckthorn leaves, sourced from Baghdad and Diyala provinces, underwent preparation, including washing, drying, crushing, and sieving before being utilized in experiments. Batch experiments were conducted using simulated solutions to assess the impact of six key adsorption design parameters: pH, cadmium concentration, agitation speed, contact time, adsorbent dosage, and temperature. The highest adsorption efficiency, reaching 94.4367%, was directly correlated with contact time, adsorbent dosage, pH value, and agitation speed, and inversely related to other variables. Morphological studies on the treated adsorbent, indicated structural …

Rotational Spectrum And Ring Structures Of Silacyclohex-2-Ene And 1,1-Difluorosilacyclohex-2-Ene, Nicole T. Moon, Amanda J. Duerden, Thomas M.C. Mcfadden, Nathan A. Seifert, Gamil A. Guirgis, Garry S. Grubbs

Chemistry Faculty Research & Creative Works

Silacyclohex-2-ene and 1,1-difluorosilacyclohex-2-ene have been synthesized, and the chirped-pulse, Fourier-transform microwave spectra of each have been observed and analyzed from 4.9 to 23.1 GHz. Quantum chemical calculations have been performed at the B3LYP-D3BJ/Def2TZVP level of theory and predict μ_a to be the largest dipole moment component with a significantly larger value in this component for 1,1-difluorosilacyclohex-2-ene. In accordance with this prediction, the spectra were predominantly a-type with the observation of a few b- and c-type transitions. The signal-to-noise ratio was adequate in both spectra to observe ²⁹Si, ³⁰Si, and all singly substituted ¹³C isotopologues in natural …

Group 14 Metallocene Catalysts For Carbonyl Hydroboration And Cyanosilylation, Haley J. Robertson, Mallory N. Fujiwara, Allegra L. Liberman-Martin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

A series of six Group 14 metallocene compounds (M = Ge, Sn, Pb) were studied as catalysts for carbonyl hydroboration and cyanosilylation reactions at room temperature. Both bis(pentamethylcyclopentadienyl) and tetramethyldisiloxa[3]metallocenophane compounds were compared. The tin and lead metallocenophanes exhibited the highest reactivity in hydroboration and cyanosilylation reactions. Hammett analysis of aldehyde hydroboration provided a ρ value of 0.73, suggesting a buildup of negative charge during the turnover-limiting step, consistent with the transition state for hydride transfer to the carbonyl center. NMR studies of Lewis acidity indicate that the Ge, Sn, and Pb tetramethyldisiloxa[3]metallocenophane compounds are weak Lewis acids.

Enrichment Of Polycyclic Aromatic Hydrocarbon Metabolizing Microorganisms On The Oral Mucosa Of Tobacco Users, James V. Defrancesco, Lin Tao, M Paul Chiarelli, Sylvia Pavlova, Antonia Kolokythas, Joel Schwartz, Benjamin Salameh, Stefan J. Green, Guy Adami

Chemistry: Faculty Publications and Other Works

Certain soil microbes resist and metabolize polycyclic aromatic hydrocarbons (PAHs). The same is true for a subset of skin microbes. In the human mouth, oral microbes have the potential to oxidize tobacco PAHs, thereby increasing these chemicals' ability to cause cancer of adjacent epithelium. We hypothesized that we could identify, in smokers, the oral mucosal microbes that can metabolize PAH. We isolated bacteria and fungi that survived long-term in minimal media with PAHs as the sole carbon source, under aerobic conditions, from the oral mucosa in 17 of 26 smokers and two of 14 nonsmokers. Of bacteria genera that survived …

On Water Arrangements In Right- And Left-Handed Dna Structures, Liliya A. Yatsunyk, S. Neidle

Chemistry & Biochemistry Faculty Works

DNA requires hydration to maintain its structural integrity. Crystallographic analyses have enabled patterns of water arrangements to be visualized. We survey these water motifs in this review, focusing on left- and right-handed duplex and quadruplex DNAs, together with the i-motif. Common patterns of linear spines of water organization in grooves have been identified and are widely prevalent in right-handed duplexes and quadruplexes. By contrast, a left-handed quadruplex has a distinctive wheel of hydration populating the almost completely circular single groove in this structure.

Innovative Cyanine-Based Fluorescent Dye For Targeted Mitochondrial Imaging And Its Utility In Whole-Brain Visualization, Xin Yan, Xinqian Chen, Zhiying Shan, Lanrong Bi

Michigan Tech Publications

Conducting in vivo brain imaging can be a challenging task due to the complexity of brain tissue and the strict requirements for safe and effective imaging agents. However, a new fluorescent dye called Cy5-PEG2 has been developed that selectively accumulates in mitochondria, enabling the visualization of these essential organelles in various cell lines. This dye is versatile and can be used for the real-time monitoring of mitochondrial dynamics in living cells. Moreover, it can cross the blood-brain barrier, making it a promising tool for noninvasive in vivo brain imaging. Based on the assessment of glial cell responses in the hippocampus …

Attochemistry Regulation Of Charge Migration, Aderonke Folorunso

LSU Doctoral Dissertations

Charge migration (CM) is a coherent attosecond process that involves the movement of localized holes across a molecule. This phenomenon is potentially useful to understand the fundamental principles of photochemistry, such as light harvesting. The first part of this dissertation discusses the molecular modes of attosecond charge migration. In this work, we used first-principles calculations to investigate the modes of charge migration (CM) in halogenated hydrocarbon chains at attosecond timescales. We have simulated the creation of a localized hole on the halogen atom using constrained density functional theory (DFT) and then tracked its subsequent dynamics with time-dependent DFT (TDDFT). Our …

Enzymatic Degradation Of Plastic Waste: A Review Of Microbial Strategies And Future Perspectives, David Gonçalves

Seton Hall Biochemistry II Annals of Student Reviews

It is said that humans generate 2.01 billion tons of municipal waste every year and this number is projected to explode to a massive 3.40 billion tons annually by the year 2050 (Ellis, 2018). This increase in waste production perfectly underscores a growing reliance on materials that persist in ecosystems long-term. This contamination, generated from large-scale industrial practices to doing your laundry at home, is best exemplified by the proliferation of microplastics throughout the environment.

What are microplastics? The first documented use of the term microplastics can be traced to a 1990 publication in the South African Journal of Science …

Physical, Chemical, And Biological Methods Of Large-Scale Water Decontamination, Belmin Kolenovic

Seton Hall Biochemistry II Annals of Student Reviews

Considering water is the solvent of life, there is a lack of attention to what is added to it and how it impacts not only the environment but also society at large. In recent years, public scrutiny of the actions of individuals and industries concerning their negative actions on the environment has increased. General trends have seen a shift toward reusability and the reduction of pollutants. Examples include the use of reusable water bottles and the shift to biodegradable straws and paper cups. A plastic bottle casually floating atop a river is easily noticeable as a form of pollution but …

Note From The Editor, Gregory Wiedman

Seton Hall Biochemistry II Annals of Student Reviews

No abstract provided.

Chemical Strategies For Tailoring Properties Of Nanomaterials Produced By Pulsed Laser Interaction In Liquid Environments, Katharine M. Tibbetts

Chemistry Publications

Interactions of intense ultrashort laser pulses with liquid media and at solid-liquid interfaces produce plasmas with high densities of reactive chemical species that promote the formation of nanomaterials. This work discusses the current understanding of laser-induced chemical reactions in aqueous medium involving hydrated electrons and hydroxyl radicals, and the effects of chemical additives on these reactions. Two chemical strategies are presented for controlling the composition of the laser-induced plasma and nanomaterial properties. First, adding chemical scavengers of hydroxyl radicals will be shown to inhibit metal oxidation, enabling the synthesis of ligand-free Ag and Au-Ag alloy nanoparticles by reduction of Au …

A Qualitative Inquiry To The Impact Of Peer Teaching On Undergraduate Chemistry Students, Marcus Sambar

Theses and Dissertations

This study investigates the impact of peer teaching on undergraduate STEM majors, particularly those who serve as peer teachers for introductory chemistry courses. While previous research has predominantly focused on the benefits of peer tutoring for the tutored students, the reciprocal impact on peer teachers remains underexplored. The main purpose of this study is to quantify the differences between peer teachers and comparable students who do not engage in teaching, with a specific focus on problem-solving approaches and the ability to explain STEM concepts. The assessment included coding students' work to reveal strategy use and provide a means of comparison …

Research Trends And Impact Report On Aggregation-Induced Emission (Aie), 2001-2021, Elsevier Analytical Services

Public Reports

Since the concept of AIE was first proposed in China in 2001, it has gradually grown to a field of science that attracts dedicated researchers from around the world. Elsevier's data analytics team used AIE experts' interpretation of current theoretical, technological, and industrial development trends in the field for reference to collect AIE-related global scientific publications (from the Scopus database) to serve as a publication set in the field of AIE. This was undertaken to present, accurately and objectively, the development of AIE research over the past two decades and the latest scientific advancements in the field; to facilitate the …

Mechanism Of Protein Aggregation Inhibition By Arginine: Blockage Of Anionic Side Chains Favors Unproductive Encounter Complexes, Lars Konermann, Yuen K. Ng

Chemistry Publications

Aggregation refers to the assembly of proteins into non-physiological higher order structures. While amyloid has been studied extensively, much less is known about amorphous aggregation, a process that interferes with protein expression and storage. Free arginine (Arg⁺) is a widely used aggregation inhibitor, but its mechanism remains elusive. Focusing on myoglobin (Mb), we recently applied atomistic molecular dynamics (MD) simulations for gaining detailed insights into amorphous aggregation (Ng et al., J. Phys. Chem. B 2021, 125, 13099). Building on that approach, the current work for the first time demonstrates that MD simulations can directly elucidate aggregation …

Md Simulations Of Peptide-Containing Electrospray Droplets: Effects Of Parameter Settings On The Predicted Mechanisms Of Gas Phase Ion Formation, Lars Konermann, Kasra Hanifi, Pablo M. Scrosati

Chemistry Publications

Electrospray ionization (ESI) mass spectrometry (MS) is widely used for interrogating peptides, proteins, and other biomolecular analytes. A growing number of laboratories use molecular dynamics (MD) simulations for uncovering ESI mechanisms by modeling the behavior of highly charged nanodroplets. The outcome of any MD simulation depends on certain assumptions and parameter settings, and it is desirable to optimize these factors by benchmarking computational data against experiments. Unfortunately, benchmarking of ESI simulations is difficult, because experimentally generated gaseous ions do not generally retain any features that would reveal their formation pathway [e.g., the charged residue mechanism (CRM) or the ion evaporation …

Aggregation And Oligomerization Characterization Of Ss-Lactoglobulin Protein Using A Solid-State Nanopore Sensor, Mitu C. Acharjee, Brad Ledden, Brian Thomas, Xianglan He, Troy Messina, Jason Giurleo, David Talaga, Jiali Li

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

Protein aggregation is linked to many chronic and devastating neurodegenerative human diseases and is strongly associated with aging. This work demonstrates that protein aggregation and oligomerization can be evaluated by a solid-state nanopore method at the single molecule level. A silicon nitride nanopore sensor was used to characterize both the amyloidogenic and native-state oligomerization of a model protein ß-lactoglobulin variant A (βLGa). The findings from the nanopore measurements are validated against atomic force microscopy (AFM) and dynamic light scattering (DLS) data, comparing βLGa aggregation from the same samples at various stages. By calibrating with linear and circular dsDNA, this study …

Evolution Of A Self-Renewing, Participant-Centered Workshop Series In Bmb Assessment, Ludmila Tyler, Peter J. Kennelly, Shelly Engelman, Kirsten F. Block, Jennifer C. Bobenko, Jaclyn Catalano, Jesica A. Jones, Margaret I. Kanipes-Spinks, Yang Mooi Lim, Jennifer Loertscher, Tejiri Olafimihan, Hailey Reiss, Territa L. Upchurch-Poole, Yufeng Wei, Kimberly J. Linenberger Cortes, Victoria Del Gaizo Moore

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

We present as a case study the evolution of a series of participant-centered workshops designed to meet a need in the life sciences education community—the incorporation of best practices in the assessment of student learning. Initially, the ICABL (Inclusive Community for the Assessment of Biochemistry and Molecular Biology/BMB Learning) project arose from a grass-roots effort to develop material for a national exam in biochemistry and molecular biology. ICABL has since evolved into a community of practice in which participants themselves—through extensive peer review and reflection—become integral stakeholders in the workshops. To examine this evolution, this case study begins with a …

Efficient Sabre-Sheath Hyperpolarization Of Pyruvate And Other Alpha-Ketocarboxylates And Ultra-High-Qualityfactor Wireless Masing Magnetic Resonance Sensing Of Hyperpolarized Contrast Media, Isaiah Olabisi Adelabu

Wayne State University Dissertations

Over the years, there has been research geared towards mitigating disease conditions such as cancers and tumors by molecular sensing of their aberrant metabolism in humans and animal models of diseases. Some of these biomolecules of interest are pyruvate, α-ketoglutarate, and ketoisocaproate, that play a central role in eukaryotic and human metabolic pathways. Nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) have become predominant in investigating and imaging cancers and tumors for early detection and treatment. Although conventional NMR spectroscopy is limited by low sensitivity, we overcame this barrier through the use of hyperpolarization techniques. NMR hyperpolarization improves …

Development Of Microfluidic Thermal Gel Electrophoresis For Biological Analysis, Mario Ambrocio Cornejo

Wayne State University Dissertations

ABSTRACTDEVELOPMENT OF MICROFLUIDIC THERMAL GEL ELECTROPHORESIS FOR BIOLOGICAL ANALYSIS by MARIO AMBROCIO CORNEJO May 2024 Advisor: Dr. Thomas H. Linz Major: Chemistry (Analytical Chemistry) Degree: Doctor of Philosophy The molecular biology that takes place within cells is vital to the over function of an organism. Healthy cellular function is crucial to a wide web of interconnected processes that need to be balanced and regulated. When these processes become abnormal, disease states are developed. The mapping of biological networks has led to the development of gene therapy and more accurate diagnostic tests. However, there are still vital biomolecules that due to …

Exploiting Light To Probe Biological Processes, Madeline Denison

Wayne State University Dissertations

Metal complexes have many advantages as biochemical tools due to their rich photophysical properties and unique geometry. Metal-based complexes are commonly reported as emissive probes or photoactivatable biological agents. Long emission lifetimes of metal complexes allow for the use of lifetime gating which eliminates autofluorescence found in assays, a distinct advantage over short-lived organic fluorophores. This work utilizes this powerful technique to generate reversible, emissive probes for monitoring CYP3A4 active site occupancy. In addition to the emissive properties of metals, metals can also be used as photodynamic therapy (PDT) and photochemotherapy (PCT) agents. These light-activated strategies provide important spatiotemporal control …