Biochemistry Commons^™

Oxidative Stress, Metabolomics Profiling, And Mechanism Of Local Anesthetic Induced Cell Death In Yeast, Cory Honsinger Thomas Boone, Ryan A. Grove, Dana Adamcova, Javier Seravalli, Jiri Adamec

Department of Biochemistry: Faculty Publications

The World Health Organization designates lidocaine as an essential medicine in healthcare, greatly increasing the probability of human exposure. Its use has been associated with ROS generation and neurotoxicity. Physiological and metabolomic alterations, and genetics leading to the clinically observed adverse effects have not been temporally characterized. To study alterations that may lead to these undesirable effects, Saccharomyces cerevisiae grown on aerobic carbon sources to stationary phase was assessed over 6 h. Exposure of an LC₅₀ dose of lidocaine, increased mitochondrial depolarization and ROS/RNS generation assessed using JC-1, ROS/RNS specific probes, and FACS. Intracellular calcium also increased, assessed by …

Secs (Sinusoidal Endothelial Cells), Liver Microenvironment, And Fibrosis, Vaishaali Natarajan, Edward N. Harris, Srivatsan Kidambi

Department of Biochemistry: Faculty Publications

Liver fibrosis is awound-healing response to chronic liver injury such as alcoholic/nonalcoholic fatty liver disease and viral hepatitis with no FDA-approved treatments. Liver fibrosis results in a continual accumulation of extracellular matrix (ECM) proteins and paves the way for replacement of parenchyma with nonfunctional scar tissue. The fibrotic condition results in drastic changes in the local mechanical, chemical, and biological microenvironment of the tissue. Liver parenchyma is supported by an efficient network of vasculature lined by liver sinusoidal endothelial cells (LSECs). These nonparenchymal cells are highly specialized resident endothelial cell type with characteristic morphological and functional features. Alterations in LSECs …

Gene Duplication And Neo-Functionalization In The Evolutionary And Functional Divergence Of The Metazoan Copper Transporters Ctr1 And Ctr2, Brandon L. Logeman, L. Kent Wood, Jaekwoon Lee, Dennis J. Thiele

Department of Biochemistry: Faculty Publications

Copper is an essential element for proper organismal development and is involved in a range of processes, including oxidative phosphorylation, neuropeptide biogenesis, and connective tissue maturation. The copper transporter (Ctr) family of integral membrane proteins is ubiquitously found in eukaryotes and mediates the high-affinity transport of Cu_ across both the plasma membrane and endomembranes. Although mammalian Ctr¹ functions as a Cu_ transporter for Cu acquisition and is essential for embryonic development, a homologous protein, Ctr², has been proposed to function as a low-affinity Cu transporter, a lysosomal Cu exporter, or a regulator of Ctr¹ activity, but …

Novel Role Of The Nociceptin System As A Regulator Of Glutamate Transporter Expression In Developing Astrocytes, Logan Meyer

Theses and Dissertations

Our previous results showed that oligodendrocyte development is regulated by both nociceptin and its G-protein coupled receptor, the nociceptin/orphanin FQ receptor (NOPR). The present in vitro and in vivo findings show that nociceptin plays a crucial conserved role in both human and rodent brain astrocytes, regulating the levels of the glutamate/aspartate transporter GLAST/EAAT1. This nociceptin-mediated response takes place during a critical developmental window that coincides with astrocyte maturation and synapse formation. GLAST/EAAT1 upregulation by nociceptin is mediated by NOPR and the downstream participation of a complex signaling cascade that involves the interaction of several kinase systems, including PI-3K/AKT, mTOR and …

Sh3 And Multiple Ankyrin Repeat Domain 3 (Shank3) Affects The Expression Of Hyperpolarization-Activated Cyclic Nucleotide-Gated (Hcn) Channels In Mouse Models Of Autism, Nikhil N. Shah

Theses and Dissertations

SH3 and multiple ankyrin repeat domains 3 (SHANK3) is a multidomain scaffold protein that is highly augmented in the postsynaptic density (PSD) of excitatory glutamatergic synapses within the central and peripheral nervous systems. SHANK3 links neurotransmitter receptors, ion channels, and other critical membrane proteins to intracellular cytoskeleton and signal transduction pathways. Mutations in SHANK3 are linked with a number neuropsychiatric disorders including autism spectrum disorders (ASDs). Intellectual disability, impaired memory and learning, and epilepsy are some of the deficits commonly associated with ASDs that result from mutations in SHANK3. Interestingly, these symptoms show some clinical overlap with presentations of human …

Cloning And Characterization Of Bacterial Mannanase Isolated From Dynastes Hercules Larvae, Sitipon Leerawatthanakun

Chulalongkorn University Theses and Dissertations (Chula ETD)

Bacterial isolate HM7 was isolated from Dynastes hercules larvae excrement. It was identified as Bacillus sp. by 16S rRNA gene analysis. When the bacteria were cultured for β-mannanase production in medium containing konjac flour it had the highest specific activity of 138 U/mg at 36 h, and when cultured in medium containing coconut meal it had the highest specific of 114 U/mg at 48 h. The 1089 base pairs long of a β-mannanase encoding gene (Man26HM7) was successfully cloned and expressed in Escherichia coli BL21 (DE3), using pET21-b expression system. The enzyme was purified and characterized. The optimal condition MAN26HM7catalysis …

Mechanisms Of Phytochemicals From Murraya Koenigii And Stevia Rebuadiana In Cell Model Of Diabetes, Hepatocellular Carcinoma And Cholangiocarcinoma Under Hyperglycemic Conditions, Nattakarn Nooron

Chulalongkorn University Theses and Dissertations (Chula ETD)

Diabetes mellitus (DM) is a group of metabolic disorders in which high blood glucose levels over a prolonged period, caused by deficiency of insulin production from the pancreas, or by the insulin resistance. Several epidemiological studies suggest that diabetic population is not only at increased risk of cardiovascular complications, but also at substantially higher risk of many types of malignancies. Hyperglycemia induced free radical reactive oxygen species (ROS) production, which is a major cause of cell injury and organ damage, especially affects pancreatic beta cells. Whereas insulin resistance in skeletal muscle tissue and adipocyte are the major sites of postprandial …

ความหลากชนิดของนกที่ใช้ประโยชน์จากหลังคาเขียวในกรุงเทพมหานคร, ปรมินทร์ เสนานันท์สกุล

Chulalongkorn University Theses and Dissertations (Chula ETD)

หลังคาเขียวเพิ่มพื้นที่สีเขียวในเมืองและอาจรองรับสังคมนกโดยให้ที่พักพิง อาหารและแหล่งน้ำ งานวิจัยนี้ศึกษาความหลากชนิดของนกและรูปแบบการใช้ประโยชน์บนหลังคาเขียว 7 แห่งในกรุงเทพมหานครที่มีขนาดพื้นที่และสัดส่วนพื้นที่สีเขียวแตกต่างกัน โดยสำรวจนกบนหลังคาเขียวทุกเดือนระหว่างเมษายน 2559-พฤษภาคม 2560 พบนกรวม 26 ชนิดและนกส่วนใหญ่เป็นนกประจำถิ่น พบนก 7-18 ชนิดบนหลังคาเขียว นกกินปลีอกเหลือง Cinnyris jugularis เป็นนกที่พบบนทุกหลังคาเขียว นกกระจอกบ้าน Passer montanus เป็นนกที่มีความชุกชุมสูงสุดโดยมักปรากฏเป็นฝูงใหญ่ พบนกอพยพบางชนิด เช่น นกอัญชันป่าขาเทา Rallina eurizonoides นกแซงแซวสีเทา Edolius leucophaeus นกขมิ้นท้ายทอยดำ Oriolus chinensis นกกระเบื้องผา Monticola solitarius และนกอีเสือสีน้ำตาล Lanius cristatus การหาอาหารและการเกาะพักเป็นรูปแบบการใช้ประโยชน์ที่มีความถี่สูงสุด (ร้อยละ 47 และ 31 ตามลำดับ) นกใช้ไม้ยืนต้นสำหรับการเกาะพักและการเคลื่อนที่ ลักษณะทางกายภาพและชีวภาพบางประการส่งผลต่อสังคมนกที่ใช้ประโยชน์บนหลังคาเขียว ดังนั้นหลังคาเขียวจึงมีศักยภาพในการอนุรักษ์ความหลากหลายทางชีวภาพในระบบนิเวศเมือง

Enzymatically Active Microspheres For Self-Propelled Colloidal Engines, Jungeun Park

Dissertations and Theses

Micro- and nano-motors have attracted numerous attentions from various scientific areas due to their potential applications. Most studies on self-propelled colloidal engines have exploited catalytic decomposition of hydrogen peroxide to drive the motor. Since the hydrogen peroxide is caustic, it is not suitable to use in biological applications, encouraging people to develop “greener” fuels. The aim of this research is to study a new transduction mechanism for self-propulsion not tied to hydrogen peroxide, and which can in particular be used with biological molecules as fuels. In this study, we focus on making particles with enzymatic activity which can effectively decompose …

Study Of Molecular Interactions Of Glycosaminoglycans And Glycosaminoglycan Mimetics With Their Protein Targets, Daniel K. Afosah

Theses and Dissertations

Glycosaminoglycans (GAGs) are complex linear chain carbohydrate molecules found on virtually all animal cell surfaces. Owing to their negatively charged nature, GAGs interact with a number of different proteins. Thus, although they have great potential as therapeutic agents, their apparent promiscuous interactions increase their side effect risk. GAG mimetics, including GAG oligosaccharides and non-saccharide GAG mimetics (NSGMs) are viable approaches to address this. This work discusses sulfated benzofuran thrombin inhibitors with submaximal protease inhibition, sulfated diflavonoid inhibitors of plasmin and GAG oligosaccharides with selectivity for human neutrophil elastase (HNE).

Anticoagulants are very important for the treatment of thrombotic diseases. The …

Reversal Of The Npc Phenotype By Start Domain Proteins, Tavis H. Sparrer

Theses and Dissertations

Niemann Pick Type C (NPC) disease is a fatal childhood neurological disease caused by mutations in the NPC-1 protein, resulting in cholesterol buildup in the late endosomes. StarD4 and StarD5 are cholesterol binding proteins that play a role in the intracellular cholesterol transport. In this study we overexpress StarD4 and StarD5 in in vitro and in vivo models, and find evidence of amelioration of the NPC phenotype. This study demonstrates that the overexpression of these proteins has the potential to be a therapeutic treatment for NPC disease.

Optimization Of In Vitro Transcription/Translation Conditions For In Vitro Compartmentalization Studies And Synthesis Of 4-Fluorohistidine, Christine Ring

Theses and Dissertations

Genetic code expansion allows the incorporation of non-canonical amino acids with a variety of new functional groups: fluorescent amino acids,^1-3 azides,^4-6 alkynes,^5-10 and photocrosslinkers.^4,11,12 This incorporation requires the evolution of new tRNA/aminoacyl tRNA sythetase pairs. Traditionally screenings of novel tRNA/aminoacyl tRNA synthetase pairs have been done in vivo. While these in vivo screenings have proven robust, they are limited in multiple ways: non-canonical amino acids (ncAAs) must be nontoxic and bioavailable. Furthermore, library size is limited by transformation efficiency. Lastly, in vivo screenings require substantial amounts of the target ncAA, which is often not available …

Biochemical Analysis Of Putative Single-Stranded Nucleic Acid Binding Proteins In Porphyromonas Gingivalis, Steve H. Kokorelis

Theses and Dissertations

Proteins that bind to both DNA and RNA embody the ability to perform multiple functions by a single gene product. These nucleic acid binding proteins in prokaryotes can play a vital role in many cellular processes, including replication, transcription, gene expression, recombination, and repair, to name a few. Nucleic acid binding proteins have unique functional characteristics that stem from their structural attributes that have evolved in a widely-conserved manner. In Escherichia coli (E. coli), the highly-conserved histone-like protein, HU, which predominates as a heterodimer of HUα and HUβ, has been found to bind to both dsDNA and ssDNA. …

Biochemical And Histological Differences Between Costal And Articular Cartilages, Michael W. Stacey

Bioelectrics Publications

Biologically, costal cartilage is an understudied tissue type and much is yet to be learned regarding underlying mechanisms related to form and function, and how these relate to disease states, specifically chest wall deformity. Chest wall deformities have a component of inheritance, implying underlying genetic causes; however the complexity of inheritance suggests multiple genetic components. At our Centre investigations were performed on gene expression of key select genes from costal cartilage removed at surgery of patients with chest wall deformity to show high expression of decorin, a key player in collagen fiber formation and growth. Also, the degree of tissue …

P120 Catenin Regulates Inflammation In Macrophage, Xiaoqing Guan

Wayne State University Dissertations

Objective: p120 catenin (p120ctn) has been reported to play a critical role in maintenance of the stability of adherens junctions. It also has potential anti-inflammatory effects in epithelial and endothelial cells. This research was designed to evaluate the effects of p120ctn on inflammatory responses in human macrophages upon LPS stimulation, as well as the possible mechanism by which p120ctn regulates LPS-induced proinflammatory response in macrophages. Methods: THP-1 cells were induced to differentiate into macrophages by PMA. The isoforms of p120ctn were identified via RT-PCR and Western blot. The expression of p120ctn was examined by Western blot in THP-1 derived macrophages …

Understanding The Mechanism Of Oxidative Stress Generation By Oxidized Dopamine Metabolites: Implications In Parkinson's Disease, Nihar Mehta

Wayne State University Dissertations

Oxidation of dopamine to toxic metabolites is considered to be one of the prime factors involved in the death of dopaminergic neurons in Parkinson’s disease. Some dopamine oxidation products have the capability to redox cycle in the presence of molecular oxygen, further contributing to oxidative stress. Therefore, our aim here was to study the redox cycling of dopamine oxidized metabolites and elucidate the underlying mechanism by which they cause oxidative stress.

Redox reactions involve transfer of one or more electrons between two compounds

resulting in either oxidation or reduction. In redox cycling, a compound undergoes

alternate oxidation and reduction, transferring …

Functional Analysis Of Sin3 Isoforms In Drosophila, Nirmalya Saha

Wayne State University Dissertations

he multisubunit SIN3 complex is a global transcriptional regulator. In Drosophila, a single Sin3A gene encodes different isoforms of SIN3, of which SIN3 187 and SIN3 220 are the major isoforms. Previous studies have demonstrated functional non-redundancy of SIN3 isoforms. The role of SIN3 isoforms in regulating distinct biological processes, however, is not well characterized. In addition, how the components of the SIN3 complex modulate the gene regulatory activity of the complex is not well understood. In this study, I identified the biological processes regulated by the SIN3 isoforms. Additionally, I explored how Caf1-55 impacts the gene regulatory activity of …

Plaster Creek Bacterial Monitoring And Source Tracking Project - Final Report, Randall J. Dejong

Faculty and Professional Research

The objective of this project was to identify important sources of bacterial loading in Plaster Creek (Kent County). The following goals were set to reach this objective: 1) the relative contributions of bacterial loading for 10 major tributaries will be assessed and the five most egregious contributors will be prioritized; 2) molecular markers will be used to try to identify the primary taxonomic sources, and 3) to pinpoint bacterial loading locations using molecular markers and scent-trained canines in sub-watersheds.

Mechanisms Of Thai Medicinal Plant Extracts On The Attenuation Of Glutamate-Mediated Neurotoxicity, Anchalee Prasansuklab

Chulalongkorn University Theses and Dissertations (Chula ETD)

As the world population ages, neurodegenerative diseases, particularly Alzheimer's disease, are becoming a major public health concern with increasing incidence and prevalence worldwide while no cure currently exists. To challenge this situation, herbal medicine may provide a potential alternative treatment as use of natural-derived substances has been proven to be effective in the prevention and/or treatment of several diseases. During the past decades, increasing evidence has implicated excessive glutamate levels in the pathway of neuronal cell death. Thailand is a place known for cultivating a variety of tropical plants and herbs, so far many of them have never been examined …

Effects Of Plant Extracts On Melanin Biosynthesis And Melanogenetic Gene Expression In B16f10 Melanoma Cells, Moragot Chatatikun

Chulalongkorn University Theses and Dissertations (Chula ETD)

Ultraviolet radiation from sunlight is a significant environmental factor in skin damage and can induce hyperpigmentation disorder and aesthetic problem. Development of novel whitening phytochemical compounds from natural products has been become trends recently. The purpose of this study was to find some plant extracts that reduce melanin synthesis and melanogenetic gene expression in alpha-MSH-induced B16F10 mouse melanoma cells. To screen total phenolics and flavonoids, antioxidant activity, and anti-mushroom tyrosinase activity, we used 13 plants which were extracted with petroleum ether, dichloromethane and ethanol solvents, subsequently. We found that total phenolic content of 13 plants extracts was found in the …