Biochemistry Commons^™

Identification And Functional Characterization Of Genes And Micrornas From Penaeus Vannamei In Response To Pathogens And Heat Stress, Pakpoom Boonchuen

Chulalongkorn University Theses and Dissertations (Chula ETD)

In the present day, high-throughput (HT) sequencing techniques provide in-depth data on how the transcripts are expressed and regulated and in this case shed light on how innate immunity responds to different stimuli. Acute Hepatopancreatic Necrosis Disease (AHPND) caused by Vibrio parahaemolyticusproducing Pir toxin (VPAHPND) is a current severe bacterial disease in shrimp. Suppression subtractive hybridization (SSH) was used to identify differentially expressed genes (DEGs) in hepatopancreas and hemocyte of VPAHPND-challengedPenaeus vannamei. The hemocyaninand Vago5 were found as up-regulated genes in hepatopancreas and hemocyte of VPAHPND-infectedP. vannamei, respectively. Their functions in shrimp immunity against VPAHPNDinfection were then characterized. The native …

Anticancer Activity Of Mansonone G Derivatives Against Human Non-Small Cell Lung Cancer: Computational And Mechanistic Study, Panupong Mahalapbutr

Chulalongkorn University Theses and Dissertations (Chula ETD)

Epidermal growth factor receptor (EGFR) and DNA topoisomerase II (Topo II) are the key molecular targets for non-small cell lung cancer (NSCLC) due to its major contribution to complex signaling cascades modulating the survival of cancer cells. In the present study, mansonone G (MG), a naturally occurring quinone-containing compound, and its semi-synthetic ether derivatives were subjected to theoretically and experimentally investigate the anticancer effects on EGFR/Topo II-mediated signaling pathways in NSCLC cell lines expressing wild-type EGFR (A549) and mutant EGFR (H1975). In vitro cytotoxicity screening results demonstrated that butoxy MG (MG3) was more susceptible to H1975 mutant cells (IC50 of …

L-Pipecolic Acid Production In Thra Knockout Escherichia Coli, Suttilak Khuanwilai

Chulalongkorn University Theses and Dissertations (Chula ETD)

L-pipecolic acid (L-PA) is a non-proteinogenic amino acid, however, it is an important precursor and a key ingredient of many pharmaceutically compound syntheses such as immunosuppressants and anesthetics. The production of amino acids via fermentation of microorganisms are getting attention, one of the widely used is an engineered E. coli. L-PA production in the engineered E. coli uses L-lysine in its cell as a substrate. This research aimed to increase L-PA production by thrA knockout. The thrA encodes homoserine dehydrogenase I, the enzyme which draws the intermediate in L-lysine biosynthesis pathway to synthesize L-threonine. The group II intron insertion was …

Effects Of Mutations Of Levansucrase From Bacillus Licheniformis Rn-01 On Levan Oligosaccharides Binding, Thassanai Sitthiyotha

Chulalongkorn University Theses and Dissertations (Chula ETD)

Produced by levansucrase that uses sucrose as a substrate, levan and levan oligosaccharides (GFn) have potential applications in food and pharmaceutical industries such as prebiotics, anti-obesity and anti-tumor agents. Previous study reported that N251A and N251Y mutants of levansucrase from Bacillus licheniformis RN-01 could effectively produce short-chain oligosaccharides upto GF3, instead of long-chain levan synthesis. This study hypothesized that these mutations probably reduced GF3 binding affinity in the active site of levansucrase that contains fructosyl-Asp93 intermediate and caused GF3 to be in an unfavorable orientation for transfructosylation; therefore, levansucrase could not effectively extend GF3 to GF4. However, these mutations probably …

Transcriptome Of Rice Oryza Sativa L. Over-Expressing Oscam1-1 Gene And Characterization Of Salt Stress-Responsive Isocitrate Lyase Gene, Worawat Yuenyong

Chulalongkorn University Theses and Dissertations (Chula ETD)

The previous study of OsCam1-1 showed that the transgenic KDML105 rice over-expressing OsCam1-1 was more tolerant to salt stress than the wild type, so to investigate the role of calmodulin encoded by OsCam1-1 in the salt-responsive mechanism, the transcriptome approach using RNA-seq technique was applied. Transcriptome profile of the transgenic KDML105 rice over-expressing OsCam1-1 under 4 hr of salt stresss (150 mM NaCl) revealed that several cell processes were affected; signaling, hormone-mediated regulation, transcription, secondary metabolism, stress responses, lipid metabolism, glycolysis, TCA cycle, glyoxylate cycle, photosynthesis, and carbohydrate metabolism. Photosynthesis rate and stomatal conductance at day 3 and 5 of …

Functional Characterization Of Inhibitor Of Kappa B Kinase In Black Tiger Shrimp Penaeus Monodon Antiviral Signaling Pathway, Zittipong Nhnhkorn

Chulalongkorn University Theses and Dissertations (Chula ETD)

The IKK-NF-κB signaling cascade is one of the crucial responsive mechanisms in inflammatory and immune responses. The key kinase proteins called inhibitor of kappa B kinases (IKKs) serve as the core elements involved in cascade activation. Here, the complete open reading frames of IKK homologs including PmIKKβ, PmIKKε1 and PmIKKε2, from the black tiger shrimp Penaeus monodon were identified and characterized for their functions in shrimp antiviral responses. The PmIKK transcripts were widely expressed in various examined tissues and the PmIKKε protein was detected in all three types of shrimp hemocytes. Only the PmIKKε1 and PmIKKε2 were responsive to white …

Comparative Toxicology Of Nio And Ni(Oh)₂ Nanoparticles, Melissa Hope Cambre

Masters Theses

“Understanding the potential toxicity of nanoparticles (NPs) is important to ensure that these new products do not impose harmful effects to human and environmental health. Paper I is a literature review in which we discuss characteristics of nanomaterials, with an emphasis on transition metal oxide nanoparticles that influence cytotoxicity. Identification of those properties may lead to the design of more efficient and safer nanosized products for various industrial purposes and provide guidance for assessment of human and environmental health risk. We then investigate biochemical and molecular mechanisms of cytotoxicity that include oxidative stress-induced cellular events and alteration of the pathways …

Assembly And Trafficking Of The Cystic Fibrosis Transmembrane Conductance Regulator And Associated Proteins, Zhihui Zhang

Theses and Dissertations--Chemistry

Cystic Fibrosis (CF) is an autosomal recessive genetic disease that leads to severe malfunction in many organs, but particularly the lungs. The primary cause of this malfunction is the decrease of the airway surface liquid layer on the lung epithelium. The lack of hydration leads to mucus build up on the epithelial lining, leading to blockage of airways. The underlying cause of CF is the dysfunction of the cystic fibrosis transmembrane conductance regulator (CFTR), which results from mutations in the protein. Almost 90% of CF patients are caused by the deletion of the phenylalanine at position 508 of CFTR, which …

Evaluation Of Ispe For Inhibitor Design In The Non-Mevalonate Pathway, Kataryzna Barbara Hoerchler

Graduate Research Theses & Dissertations

There is an urgent need to discover new antibiotics to combat the emergence of drug resistant Novel antibiotics that target unique pathways different from existing therapies are promising targets. The non-mevalonate pathway (MEP), which was discovered in the 1990’s, is essential for most bacteria, plants and apicomplexan parasites. Inhibition of the non-mevalonate is an attractive pharmaceutical target, since it is not present in mammals. Many compounds have surfaced as potential inhibitors, but none have made it to market. This thesis investigates the fourth step in the MEP pathway involving the enzyme 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) from Escherichia coli (Ec), Burkholderia thailandensis …

Understanding Carbohydrate Recognition Mechanisms In Non-Catalytic Proteins Through Molecular Simulations, Abhishek A. Kognole

Theses and Dissertations--Chemical and Materials Engineering

Non-catalytic protein-carbohydrate interactions are an essential element of various biological events. This dissertation presents the work on understanding carbohydrate recognition mechanisms and their physical significance in two groups of non-catalytic proteins, also called lectins, which play key roles in major applications such as cellulosic biofuel production and drug delivery pathways. A computational approach using molecular modeling, molecular dynamic simulations and free energy calculations was used to study molecular-level protein-carbohydrate and protein-protein interactions. Various microorganisms like bacteria and fungi secret multi-modular enzymes to deconstruct cellulosic biomass into fermentable sugars. The carbohydrate binding modules (CBM) are non-catalytic domains of such enzymes that …

Protein Engineering In The Study Of Protein Labeling And Degradation, Xinyi Zhang

Theses and Dissertations--Chemistry

Proteins are large macromolecules that play important roles in nature. With the development of modern molecular biology techniques, protein engineering has emerged as a useful tool and found many applications in areas ranging from food industry, environmental protection, to medical and life science. Biomimetic membrane incorporates biological elements, such as proteins, to form membranes that mimic the high specificity and conductance of natural biological membranes. For any application involving the usage of proteins, the first barrier is always the production of proteins with sufficient stability, and the incorporation of proteins into the artificial matrix. This thesis contains two major parts, …

Protein Suppression Of Flavin Semiquinone As A Mechanistically Important Control Of Reactivity: A Study Comparing Flavoenzymes Which Differ In Redox Properties, Substrates, And Ability To Bifurcate Electrons, John Patrick Hoben

Theses and Dissertations--Chemistry

A growing number of flavoprotein systems have been observed to bifurcate pairs of electrons. Flavin-based electron bifurcation (FBEB) results in products with greater reducing power than that of the reactants with less reducing power. Highly reducing electrons at low reduction midpoint potential are required for life processes of both aerobic and anaerobic metabolic processes. For electron bifurcation to function, the semiquinone (SQ) redox intermediate needs to be destabilized in the protein to suppress its ability to trap electrons. This dissertation examines SQ suppression across a number of flavin systems for the purpose of better understanding the nature of SQ suppression …

Study Of The Mechanism Of Action For Ru(Ii) Polypyridyl Complexes As Potential Anticancer Agents, Yang Sun

Theses and Dissertations--Chemistry

Application of chemotherapeutic agents in current cancer treatment has been limited by adverse effects as poor selectivity results in systemic toxicity; most chemotherapy approaches also experience inherited or acquired drug resistance which lead to reduced treatment outcome. Research efforts have focused on the discovery of novel chemotherapies that overcome the limitations mentioned above. Ru(II) polypyridyl complexes with anti-cancer properties have been extensively studied as traditional cytotoxic agents and photodynamic therapy agents due to their photophysical and photochemical characteristics.

Most research has focused on the design of Ru(II) polypyridyl complexes that have affinities to nucleic acids as inspired by the classic …

Steroid-Coa Ligases, Fadd17a1 And Fadd19a1, And Their Role In Cholesterol Side-Chain Degradation In Mycobacterium Tuberculosis, Johnathan Salim Abou-Fadel

Open Access Theses & Dissertations

Mycobacterium tuberculosis (Mtb) is a serious health issue arising from the increasing incidence of multi-drug resistant (MDR-TB) strains that are becoming more prevalent in high-risk countries, especially here in the Texas/Mexico border. Confirmed cases and outbreaks in schools and hospitals are more frequent in this region due to the high-volume pedestrian traffic between the two cities, and the lack of a modernized health system in Mexico. Identification of new Mtb metabolic pathways for development of novel antitubercular drugs is urgently needed. The goal of this current work investigates two Mtb fatty acyl-CoA ligase enzymes' (FadD17A1 and FadD19A1) to explore whether …

The Structural And Functional Study Of The Human Mitochondrial Hsp60 Chaperonin In Neurodegenerative Diseases, Jinliang Wang

Open Access Theses & Dissertations

Proteins are essential elements that are responsible for a variety of cellular activities within organisms, including catalyzing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules. After protein synthesis in the ribosome, the unfolded protein need to fold into their unique compact structures so that they can perform their full biological functions. The biologically active structure of a protein is referred to the native-state of the protein with biological activity. The process of protein folding is one of the most important and challenging research topics of contemporary biochemistry, especially for its central role …

Crystal Structure Of (2-{[(8-Aminona­Phthalen-1-Yl)Imino]­Meth­Yl}-4,6-Di-Tert-Butyl­Phenolato-Κ3n,N′,O)Bromido­Nickel(Ii), Patrick O’Brien, Matthias Zeller, Wei-Tsung Less

Chemistry: Faculty Publications and Other Works

The title compound, [NiBr(C25H29N2O)], contains an NiII atom with a slightly distorted square-planar coordination environment defined by one O and two N atoms from the 2-{[(8-aminonaphthalen-1-yl)imino]methyl}-4,6-di-tert-butylphenolate ligand and a bromide anion. The Ni—O and Ni—N bond lengths are slightly longer than those observed in the phenyl backbone counterpart, which can be attributed to the larger steric hindrance of the naphthyl group in the structure of the title compound. The molecule as a whole is substantially distorted, with both the planar naphthalene-1,8-diamine and imino–methyl– phenolate substitutents rotated against the NiN2OBr plane by 38.92 (7) and 37.22 (8), respectively, giving the molecule …

Detection Of Semi-Polar Vitamins And Nutrients In Biological Samples, Jennifer Janovick

Williams Honors College, Honors Research Projects

Metabolomics is used to examine metabolite fluctuations in biological systems and enables the diagnosis of metabolic disorders and the identification of new therapeutic targets.¹ Liquid chromatography-mass spectrometry (LC-MS) was utilized to develop a new method using a T3 column to separate small molecule nutrients and vitamins in a tissue sample. Initial tests of column performance used standard solutions; the amount of metabolites identified and the elution profile of these metabolites was examined. Both the standard solution and sample of brain tissue were tested with the final method developed. Six metabolites were identified in the standard and 31 were identified …

Mutations In Rhodopsin Transmembrane Helix 5 And Dimerization Interface, Margaret Pinkevitch

Williams Honors College, Honors Research Projects

G protein coupled receptors (GPCRs) are membrane proteins with many functional roles. This family of receptors is expansive, with several subfamilies. Here, a member of subfamily A, rhodopsin (Rho) is studied. Mutations in rhodopsin have been linked to the disease retinitis pigmentosa (RP). Some of these mutations have been found to disrupt the dimerization/oligomerization of Rho at the TM4/TM5 proposed dimerization interface, causing pathogenesis of RP. In this study, two mutations of transmembrane helix 5 were investigated for changes in dimerization and stability, cell trafficking, and signaling. It was found that the V209M and F220C mutations did not result in …

The Interaction Between Ceramide-1-Phosphate And Group Iva Cytosolic Phospholipase A2 And Its Role In Wound Healing, Patrick Macknight

Theses and Dissertations

The sphingolipid, ceramide-1-phosphate (C1P), directly binds and activates Group IVA cytosolic phospholipase A₂ (cPLA₂a) to generate eicosanoids. Due to the role of eicosanoids in wound healing, we choose to use our novel genetic mouse model expressing cPLA₂a with an ablated C1P interaction site (KI) to examine the cPLA₂a/C1P interaction in wound healing. Wound closure rate was not affected, but wound maturation was dramatically enhanced by loss of the C1P/cPLA₂α interaction based on the following findings. Wounds in KI mice displayed: i) increased infiltration of dermal fibroblasts into the wound environment; ii …

Dielectric Properties Of Isolated Adrenal Chromaffin Cells Determined By Microfluidic Impedance Spectroscopy, A. C. Sabuncu, M. Stacey, G. L. Graviso, N. Semenova, P. T. Vernier, N. Leblanc, I. Chatterjee, J. Zaklit

Bioelectrics Publications

Knowledge of the dielectric properties of biological cells plays an important role in numerical models aimed at understanding how high intensity ultrashort nanosecond electric pulses affect the plasma membrane and the membranes of intracellular organelles. To this end, using electrical impedance spectroscopy, the dielectric properties of isolated, neuroendocrine adrenal chromaffin cells were obtained. Measured impedance data of the cell suspension, acquired between 1 kHz and 20 MHz, were fit into a combination of constant phase element and Cole-Cole models from which the effect of electrode polarization was extracted. The dielectric spectrum of each cell suspension was fit into a Maxwell-Wagner …