Biochemistry, Biophysics, and Structural Biology Commons^™

Characterizing The Requirement Of The Cmi/Trr Compass-Like Complex During Drosophila Development, Timothy Nickels

Master's Theses

The MLR family of COMPASS-like complexes are histone methyltransferase complexes that are associated with the activation of gene enhancers. In D. melanogaster, Cara mitad (Cmi, also known as Lpt) and Trithorax related (Trr) are central subunits of a complex orthologous to mammalian Lysine methyltransferase 2 C and D (KMT2C and KMT2D, also known as MLL3 and MLL2/4) that catalyze H3K4 monomethylation. Previous studies have demonstrated that mutations in these genes are associated with cancer and developmental disorders, but the mechanisms by which these alterations contribute to disease states are unknown. The Cmi-containing COMPASS-like complex and orthologous vertebrate complexes have been …

Peptide-Drug Conjugate For Her2-Targeted Drug Delivery, Yan Wang

University of the Pacific Theses and Dissertations

Recent strategies for anticancer drug design have been focused on utilizing antibody as a drug or targeted moiety for targeted drug delivery. Antibody−drug conjugates (ADCs) have become a promising new class of targeted therapeutic agents for treatment of cancer. ADCs are designed to preferentially direct a cytotoxic drug to a cell-surface antigen recognized by an antibody. However, there are some challenges in developing ADCs, such as limited solid tumor penetration, high manufacturing costs and antibody-drug stoichiometry. Smaller molecules such as peptides have been shown to specifically bind to cancer related targets. These peptides can be used to form peptide-drug conjugates …

Investigations On Cancer Cell Biological Effects Of Cdk8 Inhibitor Q-12, Zhixin Lu

University of the Pacific Theses and Dissertations

Over the past two decades, protein kinases have been intensively investigated as targets to treat neoplastic diseases. Many protein kinase inhibitors not only have therapeutic potential but are becoming invaluable reagents for the study of cell signaling.

We aspired to use our Cyclin-Dependent Kinase 8 inhibitor, Q-12, as a probe for biomarker discovery for CDK8 inhibitor sensitive tumor types. Q-12 shows potent inhibition of cell viability and induction of apoptosis process in some triple-negative breast cancer and colorectal cancer cell lines in vitro. Western blot results indicate that the reduction of STAT1 phosphorylation could be a robust indicator of CDK8 …

Design And In Vitro Characterization Of Lipids With A Ph-Sensitive Conformational Switch And Their Liposomes For Anticancer Drug Delivery, Shen Zhao

University of the Pacific Theses and Dissertations

The traditional anticancer drugs are distributed in vivo through systemic blood circulation with a very small portion reaching the tumor site. Targeted drug delivery systems are developed in efforts to concentrate the drug molecules in the tissue of interest while reducing the drug distribution to healthy tissues to reduce the side effects. Liposomes are colloidal systems composed of amphiphilic molecules that assemble into vesicle structures in aqueous media. They are common carriers for targeted drug delivery with the advantages of low toxicity, low immunogenicity and the ability of encapsulating both lipophilic and hydrophilic drugs.

Prior research indicated the advantages of …

Adverse Pregnancy Outcomes And Imbalance In Angiogenic Growth Mediators And Oxidative Stress Biomarkers Is Associated With Advanced Maternal Age Births: A Prospective Cohort Study In Ghana, Enoch Odame Anto, William K. Owiredu, Samuel A. Sakyi, Cornelius A. Turpin, Richard K. Ephraim, Linda A. Fondjo, Christian Obirikorang, Eric Adua, Emmanuel Acheampong

Research outputs 2014 to 2021

Background Advanced maternal age (AMA) has been associated with negative pregnancy outcomes. Oxidative stress (OS) and defective placental dysfunction are contributing factors. This study determined the association between AMA and adverse pregnancy outcomes, OS biomarkers and angiogenic growth mediators (AGMs) in normal pregnancies. Methods This prospective cohort study conducted at the Obstetrics and Gynaecology (O&G) Department of the Komfo Anokye Teaching Hospital (KATH) finally included 175 normal pregnant women comprising, 58 AMA (35–45 years), 55 (30–34 years) and 62 optimal childbearing age (20–29 years). Venous blood samples were collected at 28–32 weeks for soluble fms-like tyrosine kinase-1 (sFlt-1), placental growth …

Manipulating Graded Exercise Test Variables Affects The Validity Of The Lactate Threshold And Vo2peak, Nicholas A. Jamnick, Javier Botella, David B. Pyne, David Bishop

Research outputs 2014 to 2021

Background To determine the validity of the lactate threshold (LT) and maximal oxygen uptake (V_ O2max) determined during graded exercise test (GXT) of different durations and using different LT calculations. Trained male cyclists (n = 17) completed five GXTs of varying stage length (1, 3, 4, 7 and 10 min) to establish the LT, and a series of 30-min constant power bouts to establish the maximal lactate steady state (MLSS). V_ O2 was assessed during each GXT and a subsequent verification exhaustive bout (VEB), and 14 different LTs were calculated from four of the GXTs (3, 4, 7 and 10 …

Evidence For Extra-Gastric Expression Of The Proton Pump H+/K+ -Atpase In The Gills And Kidney Of The Teleost Oreochromis Niloticus, Ebtesam Barnawi

Theses and Dissertations (Comprehensive)

It is well known that stomach acid secretion by oxynticopeptic cells of the gastric mucosa is accomplished by the H⁺/ K⁺-ATPase (HKA), which is comprised of the HKα1 (gene: atp4a) and HKβ (gene: atp4b) subunits. However, the role of the HKA in extra-gastric organs such as the gill and kidney is less clear especially in fishes. This pump may contribute to active ion and/or acid-base regulation either through direct ion transport or through secondary transport proteins against unfavorable concentration gradients via the energy derived from ATP hydrolysis. In the present work I have demonstrated …

Relationships Between Factors Influencing Biofilm Formation And Pathogen Retention In Complex Rhizosphere Microbial Communities, Aaron Coristine

Theses and Dissertations (Comprehensive)

Riparian wetlands are unique habitats facilitating all forms of life. The riverbanks of these environments provide ideal conditions for bacteria, plants, and higher organisms. Of particular interest to this research was the variation in microbial community structure at high, intermediate and poor water quality impacted areas. Assessing the capabilities of plants to retain microbial pathogens was identified. Root systems and corresponding soil are ideal locations for bacterial deposition, resulting in attachment at these areas. Biofilm production in these regions is important for long-term establishment, leading to persistence and potential naturalization. Opportunistic pathogens originating from mammalian fecal matter are introduced into …

Bioinformatic Interrogation Of Phosphonate Tailoring Pathways, Monica Papinski

Theses and Dissertations (Comprehensive)

Phosphonates represent an underexploited class of natural products despite their tremendous potential for use in medicine and agriculture. Even less characterized are phosphonate-containing macromolecules such as cell wall lipids and glycans, distinguished by a P-C bond known to provide stability towards hydrolysis. Despite some progress made in revealing cell wall phosphonate tailoring (Pnt) pathways, several barriers impede the discovery and characterization of novel phosphonate biosynthetic pathways. Specifically, a large diversity of gene composition and arrangement is evident surrounding key genes established to participate in phosphonate tailoring pathways, which are identified alongside the presence of the ppm gene encoding the P-C …

Initial Functional Characterization Of Bfo 2291 And Bfo 2294 From Tannerella Forsythia; Degraders Of Chondroitin Sulfate A, Rony Eshaque, Rony Eshaque

Theses and Dissertations (Comprehensive)

Periodontitis is characterized by the inflammation of the periodontal tissues in response to bacterial action. The Global Burden of Disease (GBD) 2010 study shows that periodontitis ranks 6^thin the global prevalence of oral health conditions and affects 11% of the world population. It is initiated by the formation of biofilms containing different types of bacteria. These biofilms exist as dental plaque and contain three types of bacteria called Tannerella forsythia, Porphyromonasgingivalis, and Treponema denticola. These three types of bacteria are strongly associated with periodontitis and they are termed as the Red complex. The main focus of the …

Implementation And Performance Comparison Of Some Heuristic Algorithms For Block Sorting, Sandhya Turlapaty

UNF Graduate Theses and Dissertations

An implementation framework has been developed in this thesis for a well-known APX-hard combinatorial optimization problem known as Block Sorting. The motivation for the study of this problem comes from applications such as computational biology and optical character recognition. While existing Block Sorting research has been theoretically focused on the development and analysis of several approximation algorithms for Block Sorting, little or no work has been carried out thus far on the implementation of the proposed approximation algorithms. The conceptualization of an implementation framework and illustrating its use by experimenting with the existing approximation algorithms will provide means for discovering …

New Insights Into The "Manna From Heaven" Hypothesis, Clare Laubenthal

Honors Program Theses

Titan’s atmosphere is unique in that its atmospheric chemistry is thought to be similar to that of the Earth’s atmosphere during the Archean Era, when bacterial life dominated the Earth¹. Tholins form as a result of the radiation of organic gases by ultraviolet light. These molecules are considered alike to the prebiotic hazes that formed in the atmosphere of Earth during the Archean Era and which allowed for the eventual development of microbial life² . This study investigated whether Earth soil bacteria can grow, using laboratory created tholin analogs, or aerosols, as a nutrient source. This study …

Rates And Patterns Of Evolution In A Duplicated Genome In The Family Catostomidae, Megann Michelle Schmidt

Honors Program Theses

Whole genome duplication (WGD) is a process in which the entire genome of an organism is duplicated, making redundant genes which are subject to unique evolutionary forces. Various modes of selection create different genetic fates such as retention of ancestral function, development of new function, or loss of function. Because of these differing fates, WGD is hypothesized to be a major driving force behind diversification. In this project, DNA sequences from fish species in the family Catostomidae were examined to observe patterns of evolution following a known WGD. Gene trees were generated for 179 loci to determine the amount of …

Prebiotic Potential Of Aerosols, Emma Rae Shipley

Honors Program Theses

A triple quadrupole gas chromatograpy mass spectrometer (GC/MS/QQQ) was used to determine prebiotic molecules of interest in plasma and photochemical aerosols. Glycolic acid was further studied using isotopically doped gases. Plasma and photochemical aerosol analogs were shown to have nucleobases and a few amino acids. Each type of aerosol was also the source of glycolic acid, a precursor to glycine. Using ¹⁸O doped CO, it was determined that contamination was not a source of oxygen in the samples. Using different combinations of ¹³C doped gases in 1:1 combinations of CO and CH₄, it was determined that …

A Discrete Loop In Serca N-Domain Plays A Role In Serca Headpiece Dynamics And Function, Olga N. Raguimova

Dissertations

The sarco/endoplasmic reticulum calcium ATPase (SERCA) is the major regulator of Ca2+ levels in the cell. Deficient calcium handling in the heart has been linked to heart failure, a leading cause of death in developed countries. As of today, targeting SERCA to enhance cardiac function has not been successful due to lack of details about SERCA structural dynamics during Ca2+ transport.

In my research, I utilized MD simulations and variety of physical assays to determine the role of Nβ5-β6 loop in regulation of SERCA structural dynamics during Ca2+ transport. Previous MD simulations by our lab predicted that the Nβ5-β6 loop …

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 …

Dna Lesions Produced From The Reaction Of Diols And 5-Formylcytosine And Their Effects On Dna Replication, Brock Allen

University of the Pacific Theses and Dissertations

Nucleic acids are complex macromolecules that are susceptible to both endogenous and exogenous damage. This study explored damage resulting from interactions with environmental nucleophilic toxins, such as a variety of diols and amines found in industry. These nucleophiles can react with electrophilic groups, such as 5-formylcytosine. 5-formylcytosine is an oxidation product of the epigenetic base 5-methylcytosine. It is typically removed by thymine DNA glycosylase (TDG) but is known to accumulate in the genome, making the formyl group susceptible to attack. In this study we used GC/MS and ESI-MS to show that DNA lesions from the nucleophilic addition reaction of toxins …

Comparison Between The Structure-Function Relationship In The Wild Type Gαi1 Protein And Its Oncogenic Mutant, Jesse Lee Goossens

Dissertations

Many signal transduction pathways are regulated by guanine nucleotide-binding (G?) proteins, which function as molecular switches fluctuating between active and inactive conformations. Proper function depends on three flexible switch regions that are involved in the relatively slow hydrolysis of GTP. Deep sequencing studies have found mutations in the GNAS and GNAI1 genes involved in tumorigenesis, among which include a mutation corresponding to a highly conserved arginine residue in the switch II region. A mutation in GNAI1 encoding an R208Q change in G?i1 has been linked to intestinal cancers. We investigated the molecular basis of oncogenesis of this mutant by studying …

Inhibition Of Mutant Egfr In Nsclc Promotes Endothelin-1-Mediated Nsclc Disease Progression, Stephen Ollosi

Master's Theses

Angiogenesis in NSCLC has been identified as important therapeutic target in combination with EGFR TKIs. However, only small incremental advancements have been made for the use of angiogenesis inhibitors in NSCLC and it remains elusive why the inhibition of VEGF-mediated neovascularization is not therapeutically efficacious. I present experimental evidence that a subpopulation of NSCLC cells with EGFR TKI-induced EMT contributes toward the attenuation of the response to EGFR TKI therapy. One of the hallmarks of cancer is heterogeneity and I have previously demonstrated that tumor heterogeneity within NSCLC cells lines harboring EGFR kinase domain mutations gives rise to divergent resistance …

Identification Of Genes And Metabolites Involved In Durian Durio Zibethinus Fruit Ripening, Pinnapat Pinsorn

Chulalongkorn University Theses and Dissertations (Chula ETD)

Durian (Durio zibethinus M.), a major economic fruit, actively produces infamous sulfur-containing compounds during ripening. However, sulfur metabolism which is important in this fruit is rarely investigated. In this study, the integration of metabolomics using CE-TOF/MS and transcriptomics using de novo RNA-seq assembly was performed to reveal metabolic changes involved in sulfur metabolism and chemical composition related to fruit quality. During ripening, the expression level of genes involved in sulfur metabolism is concurred with the reduced sulfate ion content in placenta and the up-accumulation of sulfur metabolism-related metabolites in pulps. It is noteworthy that durian pulps highly accumulate γ-glutamylcysteine (γ-EC) …

Development Of Simple Devices For Point-Of-Care Screening Of Bacterial Infection And Inflammatory Markers, Julaluk Noiphung

Chulalongkorn University Theses and Dissertations (Chula ETD)

A paper-based analytical devices (PADs) provides a great benefit in medical diagnostics, especially in the developing world. The first part of this dissertation describes the effect of sample viscosity on PADs for the measurement of pH and nitrite concentration in human saliva. Preliminary study found that viscosity had a significant effect on the calibration curve of nitrite and a consistent curve could be generated after added washing buffer. Nitrite measurement in artificial saliva with viscosity 1.87-5.10 mPa-s was tested on the proposed device and also showed a good correlation with the standard spectrophotometry method (p=0.8484, paired sample t-test, n=20). Moreover, …

Polyamine Accumulation And Responses Of Mango Fruit To Postharvest Polyamine Application, Bussarin Wonnabussapawich

Chulalongkorn University Theses and Dissertations (Chula ETD)

Mango (Mangifera indicia L.) is a popular tropical fruit which has a great value in both domestic and international markets. Mango is a climacteric fruit which ethylene production increases dramatically, thus leading to a quick ripening process and a short postharvest life. Polyamines (PAs) have been reported to be involved in fruit ripening. Changes in endogenous free polyamines accumulation were measured in two mango cultivars; ‘Nam Dok Mai No.4’ and ‘Nam Dok Mai Si Tong’. Mangoes were allowed to ripen at 25±1 ºC after harvest. It was found that ‘Nam Dok Mai No.4’ mango exhibited higher ethylene production, respiration rate, …

Functional Characterization Of Heat Shock Proteins During Stress Response In Pacific White Shrimp Penaeus Vannamei And Brine Shrimp Artemia Franciscana, Wisarut Junprung

Chulalongkorn University Theses and Dissertations (Chula ETD)

Acute hepatopancreatic necrosis disease (AHPND) caused by the bacterium Vibrio parahaemolyticus carrying toxin produced plasmid (VPAHPND), has led to severe mortalities in farmed penaeid shrimp throughout Asia. Our studies demonstrated that a chronic non-lethal heat shock (chronic-NLHS) could enhance resistance of the Pacific white shrimp Penaeus vannamei to VPAHPND infection. Shrimp exposed to chronic-NLHS (28 °C to 38 °C, 5 min for 7 days) had higher survival rate (>50%) than that of the control non-heated shrimp (20%) when they were challenged with VPAHPND. The qRT-PCR analysis revealed that the expression of heat shock proteins, LvHSP70 and LvHSP90, as well …

Production And Purification Of Mannan Oligosaccharide And Its Role In Tight Junction Assembly In Epithelial Cells, Chatchai Nopvichai

Chulalongkorn University Theses and Dissertations (Chula ETD)

Mannan Oligosaccharide (MOS) is well-known as prebiotic supplement that help increasing life quality of livestocks and animals. Many reports revealed that MOS supplement can help improve intestinal morphology, enhancing growth performance, raising body weight, and increasing metabolic and stress response. MOS feeding also affected several biological processes in peripheral blood mononuclear cells in pigs and modulates expression of many immune-related genes that helps to prevent and reduce the severity of viral infection. However, the mechanism of action of MOS is remained unclear and the production, purification, identification of bioactive MOS molecular type is needed. In this study, we developed a …

Drug Resistance Mechanism Of Ns3/4a Protease And Identification Of Potent Compounds Inhibiting Reverse Transcriptase Of Hepatitis Virus, Jirayu Kammarabutr

Chulalongkorn University Theses and Dissertations (Chula ETD)

Viral Hepatitis has become a public health concern which caused 1.34 million deaths in 2015 and 95% of sickness and untimely deaths come from chronic hepatitis B and C virus infections. The epidemic of viral hepatitis B and C affects around 325 million people worldwide and is 10 times more than the global HIV epidemic. Hepatitis C virus (HCV), which is the main cause of hepatitis C, has a high mutation rate due to the lack of proofreading activity of the RNA polymerase enzyme. One of an attractive target for anti-HCV drug design and development is the NS3/4A serine protease. …

Effect Of Feedback-Resistant Arog Overexpression On L-Phenylalanine Production In Escherichia Coli, Maria Ulfah

Chulalongkorn University Theses and Dissertations (Chula ETD)

L-Phenylalanine (L-Phe) is one of the most important amino acids in food and pharmaceutical industries. It is widely used as a nutritional supplement and a precursor for the synthesis of food additives. The market of L-Phe has been stimulated by increasing demand for the low-calorie sweetener, aspartame. In Escherichia coli, the key enzyme which catalyzes the first committed step of aromatic amino acid biosynthesis pathway is 3-deoxy-D-arabino-heptulosonate-7- phosphate synthase (DAHP-synthase). The enzyme has 3 isoforms, AroG, AroF and AroH, which are feedback inhibited by L-Phe, L-Tyr and L-Trp, respectively. AroG, encoded by aroG, is the major isoform contributed about 80% …

Functional Characterization Of White Spot Syndrome Virus-Responsive Mir-750 In Black Tiger Shrimp Penaeus Monodon, Nichaphat Kanoksinwuttipong

Chulalongkorn University Theses and Dissertations (Chula ETD)

In the RNA interference (RNAi) process, small RNAs called microRNAs (miRNAs) modulate gene expression post-transcriptionally by acting as guides to direct Argonaute (Ago)-containing RNA-induced silencing complexes (RISCs) to targeted mRNAs. The Penaeus monodon miR-750 was previously reported as the highly upregulated miRNA during white spot syndrome virus (WSSV) infection. In this study, the computational program and 2D gel electrophoresis technique were used to identify miR-750 target genes. Bioinformatic analysis suggested that the predicted target mRNAs of miR-750 were ubiquitin-conjugating enzyme E2 Q1 gene (UbcQ1), Actin1 (Act1) and Sarcoplasmic calcium-binding protein (Scp). Furthermore, the alteration of protein expression in the stomach …

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 …