Biochemistry, Biophysics, and Structural Biology Commons^™

Exploring The Roles Of Stress, Codon Usage, And Rna Modifications In Myotonic Dystrophy Type 1, Afrooz Golestanian

Legacy Theses & Dissertations (2009 - 2024)

Myotonic dystrophy (DM), the most common form of muscular dystrophy, is a neuromuscular disease caused by microsatellite repeat expansions. It can represent a multi-systemic autosomal dominant disease with DM1 and DM2 subtypes. A cytosine-thymine-guanine (CTG) triplet repeat in the 3’ untranslated region (3’UTR) of myotonic dystrophy protein kinase (DMPK) gene causes DM1 disease, which leads to the production of a longer, abnormal and toxic mRNA. The toxic DMPK mRNA sequester the splicing proteins such as Muscle blind-like (MBNL) and rbFOX which leads to gene expression alteration. Repeat associated non-AUG (RAN) translation also occurs in DM1. Mitochondrial dysregulation has also been …

The Photo-Transformation Of Free Methionine In The Presence Of Surrogate And Standard Isolate Dissolved Organic Matter Under Sunlit Irradiation, Benjamin J. Mohrhardt

Dissertations, Master's Theses and Master's Reports

Sulfur (S)-containing amino acids are key sources of carbon, nitrogen, and sulfur involved in protein synthesis, protein function, and providing energy for microbial growth. Dissolved free and combined methionine is one of two S-containing amino acids incorporated into proteins and has been attributed to their stability and function. The oxidation of methionine has received considerable attention given its ubiquitous presence in most biological systems and has been associated with losses in protein function and pathological disorders. In natural waters, methionine is rapidly and selectively taken up by microorganisms to achieve cellular requirements of carbon, nitrogen, and sulfur. The abiotic transformation …

Dissecting The Cellular Landscape And Transcriptome Network In Viral Myocarditis By Single-Cell Rna Sequencing, Ninaad Lasrado, Nicholas Borcherding, Rajkumar Arumugam, Timothy K. Starr, Jay Reddy

School of Veterinary and Biomedical Sciences: Faculty Publications

Coxsackievirus B3 (CVB3)-induced myocarditis is commonly employed to study viral pathogenesis in mice.Chronically affected micemaydevelop dilated cardiomyopathy, which may involve the mediation of immune and nonimmune cells. To dissect this complexity, we performed single-cell RNA sequencing on heart cells from healthy and myocarditic mice, leading us to note significant proportions of myeloid cells, T cells, and fibroblasts. Although the transcriptomes of myeloid cells were mainly of M2 phenotype, the Th17 cells, CTLs, and Treg cells had signatures critical for cytotoxic functions. Fibroblasts were heterogeneous expressing genes important in fibrosis and regulation of inflammation and immune responses. The intercellular communication networks …

Identification And Characterization Of Transcription Factors Regulating Methionine Gamma-Lyase Gene Expressionin Durian Durio Zibethinus M. Pulps, Pinnapat Pinsorn

Chulalongkorn University Theses and Dissertations (Chula ETD)

Durian (Durio zibethinus L.) is an economic fruit crop in Southeast Asia. In Thailand, more than 200 durian varieties are found. Among them, two commercial cultivars which are Chanee and Monthong are mainly cultivated. Durian fruit releases a strong sulfuryl odor containing ethanethiol, methanethiol, and hydrogen sulfide during ripening. Methionine γ-lyase (MGL) is an enzyme responsible for α, γ-elimination of L-methionine into methanethiol, ammonia, and α-ketobutyrate. MGL gene is highly expressed in durian pulps during ripening concurring with methanethiol production during ripening. However, the function of durian MGL (DzMGL) has not been characterized. Thus, the enzymatic activity assay towards L-methionine, …

Characterization Of L-Malic Acid-Capped Cds Quantum Dots And Examination Of The Nanoncrystal's Biosensor Ability, Andrei A. Potapenko

Honors Theses and Capstones

Ligand-capped quantum dots are microscopic semiconductors commonly used in biomedical research and therapy for cell imaging and drug delivery. Despite the abundance of in vivo applications, the nature of interactions between the nanocrystals and the amino acids comprising human proteins remains insufficiently investigated. In this work, we report on the synthesis, ligand exchange, and characterization of the L-malic acid-capped CdS quantum dots via various spectroscopic techniques. We also assess the ligand-capped nanocrystals as potential probes for some amino acids. We determine that in the presence of L-cysteine, the L-malic acid-capped CdS quantum dots fluorescence signal quenches drastically, thus indicating a …

Structural And Functional Characterization Of Two Poly(Aspartic Acid) Hydrolases, Amanda Jansch

College of Graduate Studies: Theses & Dissertations

Due to the accumulation of polymers in the environment, biodegradable alternatives should be used in place of commonly used polymers like poly(carboxylates). Poly(carboxylates) are water-soluble polymers (WSPs) that make up a variety of consumer products, such as detergents, descaling agents, and superabsorbent materials commonly found in diapers and feminine hygiene products. While the visible accumulation of these products may not be obvious, it is necessary to reduce the amount entering the environment. Poly(aspartic acid) (PAA) is an alternative WSP that is biodegradable through the action of three different enzymes, PahZ1_KT-1, PahZ2_KT-1, and PahZ1_KP-2. Originally …

Identification Of Glutathionylated Cysteines Regulating Cell Migration, Dhanushika Kukulage

Wayne State University Dissertations

Cell migration is vital in many physiological processes, such as wound repair and metastasis. Impaired cell migration in wound healing may result in chronic wounds, by which 6.7 million Americans are affected, and they suffer from bacterial infections, amputations, increased mortality, and depression. Reactive oxygen species (ROS) or hydrogen peroxide (H2O2) play an essential role as a second messenger in redox signaling. Evidence has been found that H2O2 takes part in regulating cell migration as well. A primary mechanism of ROS regulating redox signaling is oxidative protein modifications. Protein S-glutathionylation, one of the oxidative modifications, is the conjugation of glutathione …

Genetic Analysis Of Vibrio Cholerae During Its Hyperinfectious State In Danio Rerio (Zebrafish), Ravipaul Singh

Wayne State University Theses

ABSTRACTGENETIC ANALYSIS OF VIBRIO CHOLERAE DURING ITS HYPERINFECTIOUS STATE IN DANIO RERIO (ZEBRAFISH) by RAVIPAUL SINGH AUGUST 2022 Advisor: Dr. Jeffrey Withey Major: Biochemistry and Molecular Biology Degree: Master of Science Vibrio cholerae is a gram-negative, comma-shaped, monotrichous bacillus and the causative agent of the diarrheal disease cholera. V. cholerae is a natural resident of aquatic environments such as rivers and estuaries and is a highly motile bacterium. Upon entering the human host, V. cholerae travels to its site of colonization in the small intestine and upregulates its virulence factors. Upon escape from the host, V. cholerae can enter a …

Effect Of Allosteric Site Binding On Smyd2 Conformational Ensemble, Jacob Daniel Sobota

Wayne State University Theses

Molecular dynamics simulation allows for the simulation of proteins with precise control over what ligands are present at what sites. The conformational ensemble of a protein can be obtained from MD simulation with and without binding at an allosteric site and compared between to gain insight at what effects binding at an allosteric site has on a protein’s structure. SMYD2, a critical regulator of cellular processes, was recently found to have a novel secondary binding site with allosteric effects on its activity. The discovery of an allosteric site has implications for drug design in the inhibition of SMYD2 to treat …

Mhc Diversity Analysis Of Spheniscus Demersus For In Situ And Ex Situ Populations, Antonieta Van Den Berg Monsalve

Undergraduate Honors Thesis Projects

The South African Penguin has been listed as endangered by the International Union for Conservation of Nature. Major histocompatibility complex (MHC) alleles provide valuable statistics because of their variation in terms of vertebrate genomes and are pertinent to immune and reproductive health. A greater number of MHC alleles correlates with survivability of a population because the genes control the immune and reproductive systems. Legacy research by Otterbein alumni and Dr. Simon Lawrance studied MHC samples from wild, in situ, and captive, ex situ, penguin populations. By comparing these populations' major histocompatibility complexes through biostatistical analysis, contributions to conservation of the …

College Of Natural Sciences Newsletter, January 2022, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 3, Issue 1

Page 1 Dean's Message
Page 2 Awards & Recognition
Page 3 Outreach in Harrisburg, SD
Page 4 Geography Alumni Named Among 'Highly Cited Researchers', 53rd Annual Geography Convention
Page 5 Geography Convention Speakers, Brookings/SDSU Day
Page 6 Media Coverage of Natural Sciences
Page 7 Open PRAIRIE Data
Page 8 Fall 2021 Dean's List
Page 9 Fall 2021 Dean's List, cont.

ฮอร์โมนเอสโตรเจนเหนี่ยวนำให้เกิดการแทรกของ Line-1 ดีเอ็นเอเข้าไปในจีโนมของเซลล์มะเร็งเต้านม, กุลจิรา โรจน์ไพศาลกิจ

Chulalongkorn University Theses and Dissertations (Chula ETD)

ในปัจจุบันโรคมะเร็งเต้านมเป็นมะเร็งที่มีอุบัติการณ์และอัตราการตายสูงที่สุดในเพศหญิงทั่วโลกรวมถึงในประเทศไทยด้วย โดยพบว่า LINE-1 ถือว่าเป็น Retrotransposon element ที่พบมากที่สุดถึง 17 % ของจีโนมและมีความสามารถในการคัดลอกแล้วแทรกตัวเองในบริเวณอื่นของจีโนมซึ่งเป็นสาเหตุของทำให้เกิดความไม่สเถียรของจีโนมอันเป็นสาเหตุของการเกิดโรคมะเร็ง และยังพบว่าการแสดงออกของLINE-1 มีผลต่อการลุกลาม, ขนาด, และระยะของโรคมะเร็งเต้านมด้วย นอกจากนี้ยังพบว่าผู้หญิงที่การได้รับฮอร์โมนเอสโตรเจนต่อเนื่องเป็นระยะเวลานานทำให้ความเสี่ยงของโรคมะเร็งเต้านมเพิ่มมากขึ้น ถึงกระนั้นยังคงไม่ทราบถึงกลไกการทำงานของเอสโตรเจน ดังนั้นผู้วิจัยจึงตั้งสมมุติฐานว่า เอสโตรเจนสามารถเหนี่ยวนำให้เกิดการแทรกของ LINE-1 ดีเอ็นเอเข้าไปในจีโนมของเซลล์มะเร็งเต้านม โดยทำการศึกษาบผลของเอสโตรเจนที่ได้รับต่อการแสดงออกของ LINE-1 mRNA และ LINE-1 โปรตีน รวมถึงผลของเอสโตรเจนที่ได้รับต่อการแทรกของ LINE-1 ดีเอ็นเอโดยวิเคราะห์จากปริมาณดีเอ็นเอในเซลล์มะเร็งเต้านม T47D ผลการทดลองพบว่าที่เอสโตรเจนมีผลทำให้การแสดงออกของ LINE-1 mRNA เพิ่มขึ้นสูงที่สุดอย่างมีนัยสำคัญที่ความเข้มข้นของเอสโตรเจน 5 nM ด้วยวิธี Realtime RT-PCR ในเซลล์มะเร็งเต้านม T47D และผลทำให้การแสดงออกของ LINE-1 mRNA เพิ่มขึ้นสูงที่สุดอย่างมีนัยสำคัญที่ 12 ชม. ด้วยวิธี Realtime RT-PCR ในเซลล์มะเร็งเต้านม T47D และเอสโตรเจนมีผลทำให้การแสดงออกของโปรตีน LINE-1 ORF1p เพิ่มขึ้นสูงที่สุดอย่างมีนัยสำคัญที่ 48 และ 72 ชม. ในเซลล์มะเร็งเต้านม T47D ด้วยวิธี Western blot โดยพบว่าการแสดงออกของโปรตีน LINE-1 ORF1p เพิ่มขึ้นสูงที่สุดอย่างมีนัยสำคัญ 72 ชม. นอกจากนี้เอสโตรเจนมีผลทำให้ปริมาณของ LINE-1 ดีเอ็นเอบริเวณ ORF2 เพิ่มขึ้นสูงที่สุดอย่างมีนัยสำคัญที่ 72 ชม.ในเซลล์มะเร็งเต้านม T47D มากที่สุดอย่างมีนัยสำคัญด้วยวิธี Real-time PCR แสดงให้เห็นว่าเอสโตรเจนมีผลทำให้เกิดการแทรกของ LINE-1 ดีเอ็นเอเข้าไปในจีโนมได้ จากผลการทดลองทั้งหมดจึงสรุปได้ว่า เอสโตรเจนมีผลต่อการเพิ่มแสดงออกของ LINE-1 mRNA และ LINE-1 โปรตีน รวมถึงเพิ่มปริมาณ LINE-1 ดีเอ็นเอ อย่างมีนัยสำคัญในเซลล์มะเร็งเต้านม T47D แสดงว่าเอสโตรเจนสามารถเหนี่ยวนำให้เกิดการแทรกของ LINE-1 ดีเอ็นเอเข้าไปในจีโนมนำไปสู่การกลายพันธุ์ของยีนและความไม่เสถียรของจีโนม

Molecular Mechanism Of Damage-Associated Molecular Patterns In Association With Acute Hepatopancreatic Necrosis Disease Resistance Of Heat Stressed-Shrimp Penaeus Vannamei, Supitcha Wanvimonsuk

Chulalongkorn University Theses and Dissertations (Chula ETD)

Non-lethal heat shock (NLHS) is known to enhance resistance to acute hepatopancreatic necrosis disease caused by Vibrio parahaemolyticus (VPAHPND) in the Pacific white shrimp Penaeus vannamei. Generally, cell damage induced by stresses leads to the release of damage-associated molecular patterns (DAMPs), molecules that act as endogenous danger signals to promote immune response. The first part of this research aims to study molecular mechanism of DAMPs that can enhance innate immunity upon NLHS treatment on VPAHPND resistance. We identified and characterized the candidate NLHS-induced DAMP that can activate innate immune responses against VPAHPND. The candidate DAMP genes were retrieved from the …

Type-B Energetic Processes And Their Associated Scientific Implications, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

Recently, our work has identified two thermodynamically distinct types (A and B) of energetic processes naturally occurring on Earth. Type-A energy processes such as the classical heat engines, ATP hydrolysis, and many of the known chemical, electrical, and mechanical processes apparently follow well the second law of thermodynamics; Type-B energy processes, for example, the newly discovered thermotropic function that isothermally utilizes environmental heat energy to do useful work in driving ATP synthesis, follow the first law of thermodynamics (conservation of mass and energy) but do not have to be constrained by the second law, owing to its special asymmetric functions. …

A Look Into Alzheimer’S Disease—Interventions At The Molecular Level, Priscila Feliciano Nieves

Honors Undergraduate Theses

There are puzzle pieces to the cure for Alzheimer’s Disease (AD), and such can emerge by inspecting the biomolecular interactions and their effects on neuronal cells. The upcoming presented literature review will cover the molecular changes caused by AD pathological progression, explore the relationship between non-AD molecules and AD molecules in the body, and analyze potential contributing factors in AD. In addition, the information to be provided will highlight medicinal alternatives respective to a particular stage in AD.

Investigation Of Dna Hybridization In Localized Systems In Close Proximity, Ashley M. Sewsankar

Honors Undergraduate Theses

Hybridization of two or more DNA or RNA strands is well documented for the process taking place with all strands free in solution or when one strand is immobilized on a substrate. This study contributes to the investigation of the hybridization process when two single DNA strands (ssDNA) are in close proximity. We took advantage of an X sensor in which hybridization of four DNA strands enables the formation of a DNA four-way junction (crossover or X) structure. We immobilized multiple layers of crossover structures to study its hybridization being triggered by short ssDNA coming from solution and further investigate …

Peripheral And Central Glucose Flux In Type I Diabetes, Jelena Anna Juras

Theses and Dissertations--Neuroscience

Diabetes is a complex metabolic disorder, of which high blood glucose concentration is the primary hallmark. Type I diabetes mellitus (T1DM) is characterized by the lack of insulin production, due to a poorly understood autoinflammatory cascade. In the words of historian Barnett “Diabetes may no longer be a death sentence, but for more and more people in the 21st century, it will become a life sentence”, making it the focal point of many research groups. It is estimated that around 20 million individuals worldwide live with T1DM.

Effects of long-term chronically elevated blood glucose are not only seen in micro/macro-vascular …

Building Tools For Improved Modulation Of The Human Gabaa Receptor, A Central Nervous System Target For The Treatment Of Anxiety, Garrett Edward Zinck

Theses and Dissertations--Pharmacy

In the U.S., anxiety is recognized as an increasing range of mentally and physically debilitating psychiatric health disorders with significant economic repercussions. Over the last 20 years, several novel anti-anxiety therapies have entered the drug development pipeline, but none have made it to market.

The work in this dissertation focused on structurally modifying valerenic acid (VA), a structurally unique carboxylated sesquiterpene acid found in Valeriana officinalis. VA is putatively reported to have allosteric modulatory activity of the human GABA_A receptor, a ligand-gated ion channel responsible for attenuating neurotransmissions. Structural modeling of VA’s GABA_A receptor interaction suggests that …

Apoe Genotype And Cerebral Glucose Metabolism: A Multi-Omics Approach, Holden C. Williams

Theses and Dissertations--Physiology

Apolipoprotein E (APOE) is encoded by the APOE gene, present in humans as three main isoforms (E2, E3, and E4). E4 carriers face up to a 15-fold increased risk for developing late-onset Alzheimer’s disease (AD), while E2 carriers are protected. Understanding the risk conferred by E4 has been an extensive research focus for nearly three decades, but the exact mechanism has yet to be proven. Many studies have demonstrated attenuated roles of E4 in classical hallmarks of AD, notably amyloid processing and neurofibrillary formation, which normally present later in disease progression. How APOE influences hallmarks that present much earlier are …

A Study Of Cobalt (Iii) Oxide Nanoparticle Delivery Of Sirna Molecules Directed Against Signaling Intermediates Of The P2y2 Receptor, Rachel Blair Stroud

Graduate Theses/Dissertations

G protein-coupled receptors are evolutionarily ubiquitous sensors of extracellular signals, propagating intracellular signal cascades through heterotrimeric G proteins. P2Y₂ receptors are GPCRs which are activated by extracellular nucleotides to mediate signaling cascades via Gαq coupling. Many GPCRs are subject to a common mechanism for signal termination involving phosphorylation of the C-terminal tail followed by β-arrestin binding and subsequent endocytic internalization of the complex. This effect has been described for the P2Y₂ R in the 1321N1 astrocytoma cell line, and UTP-induced activation and desensitization profiles have been previously defined. There is need to develop molecular vehicles for safe and …