Biochemistry, Biophysics, and Structural Biology Commons^™

Roles Of Bacterial Toxin Receptor And Piwi-Interacting Rna Of Pacific White Shrimp Penaeus Vannamei In Response To Vibrio Parahaemolyticus-Causing Acute Hepatopancreatic Necrosis Disease Infection, Waruntorn Luangtrakul

Chulalongkorn University Theses and Dissertations (Chula ETD)

Acute hepatopancreatic necrosis disease (AHPND) or Early mortality syndrome (EMS) caused by virulent strains of Vibrio parahaemolyticus AHPND (VPAHPND) has been a leading cause of significant losses of shrimp production. In this study, we aim to explore the response and the role of immune-related gene/protein and small RNA in the VPAHPND-infected shrimp. This research was divided into 2 parts. In the first part, we identified candidate genes of VPAHPND toxin receptor and further confirmed its function as a VPAHPND toxin receptor. APN has been reported as a Cry toxin from Bacillus thuringiensis, whose structure is similar to VPAHPND toxin. Therefore, …

Metabolite Profiling And Gene Expression Analysis In Starch And Sugar Metabolisms Of Ripening Durian Durio Zibethinus Pulp, Lalida Sangpong

Chulalongkorn University Theses and Dissertations (Chula ETD)

Durian (Durio zibethinus L.), an economically important fruit of Southeast Asian countries, expresses unique flavor at the edible ripe stage, resulting from metabolic changes during the ripening process. Nevertheless, the study in such modulations is still limited. In the first manuscript, we profiled metabolites from unripe and ripe pulps of durian cv. Monthong using capillary electrophoresis- (CE) and gas chromatography- (GC) time-of-flight mass spectrometry (TOF/MS) and obtained the total 94 ripening-related metabolites from a combination of the two datasets, of which we focused on flavor-related metabolites. For sugar, sucrose is the most abundant sugar that increased during ripening, and the …

Protective Effects Of Tiger Milk Mushroom (Lignosus Rhinocerus) Extracts On Oxidative Stress-Induced Neurotoxicity And Aging In Ht22 Cells And C. Elegans, Parinee Kittimongkolsuk

Chulalongkorn University Theses and Dissertations (Chula ETD)

Lignosus rhinocerus (LR) or Tiger Milk Mushroom, a fork medicinal mushroom, has been reported for several pharmacological effects including asthma treatment, anti-inflammatory, anti-proliferative, immuno-modulating effects, promote neurite outgrowth in PC-12 cells, anti-HIV-1 activity, and antioxidants properties. However, the antioxidant properties have only focus on in vitro and no or few studies have reported their protective effects in mouse hippocampal (HT22) cells and Caenorhabditis elegans (C. elegans). This study aims to investigate the neuroprotective effect of three extracts of LR against oxidative stress in both HT22 cells and. C. elegans as well as longevity in C. elegans. In HT22 cells, we …

Generation Of Neural Stem Cells (Nscs) From Human Fibroblasts Using Qq-Modified Sox2 And Neurod1 Proteins, Abdullah Ibrahim Alhomoudi

Wayne State University Theses

The generation of induced neural stem cells (iNSCs) and induced neuronal cells (iNCs) from somatic cells provides new avenues for basic research and potential transplantation therapies for neurological diseases. However, clinical applications must consider the tumor formation capabilities of the implanted cells, the inability of iNCs to self-renew in culture, and reprogramming methods that use retroviral transduction which permanently alter genetic network of the cells. Here we report the generation of protein-induced neural stem cells (piNSCs) from human dermal fibroblasts using QQ-SON pluripotent reprogramming as a tool to quickly reset the time clock of the human somatic fibroblasts to a …

Can The Carbon And Nitrogen Isotope Values Of Offspring Be Used As A Proxy For Their Mother's Diet? Using Foetal Physiology To Interpret Bulk Tissue And Amino Acid Δ15N Values, Nico Lübcker, John P. Whiteman, Seth D. Newsome, Robert P. Millar, P.J. Nico De Bruyn

Biological Sciences Faculty Publications

The measurement of bulk tissue nitrogen (δ¹⁵N) and carbon isotope values (δ¹³C) chronologically along biologically inert tissues sampled from offspring can provide a longitudinal record of their mothers' foraging habits. This study tested the important assumption that mother-offspring stable isotope values are positively and linearly correlated. In addition, any change in the mother-offspring bulk tissues and individual amino acids that occurred during gestation was investigated. Whiskers sampled from southern elephant seal pups (Mirounga leonina) and temporally overlapping whiskers from their mothers were analyzed. This included n = 1895 chronologically subsampled whisker segments for bulk …

Characterization Of The Tsc/Dyrk1a Interaction, Supriya Joshi

Theses and Dissertations

The Tuberous sclerosis complex (TSC) includes TSC1, TSC2 and the TBC1D7 subunits that together function as a principal inhibitor of the mTOR protein kinase complex 1 (mTORC1). mTORC1 is a master regulator of cell growth and proliferation that responds to signaling cues such as growth factors and nutrient availability. Proteomic studies in our lab revealed an interaction between the TSC subunits and DYRK1A, a ubiquitous protein kinase encoded by a gene located in the Down syndrome (DS) region on human chr21. In this study, we sought to validate the interaction of the TSC components with DYRK1A and to determine the …

Characterizing Glycosaminoglycan And Glycosaminoglycan-Oligo Interactions With Cancer Stem Cells And Their Regulators, Rahaman Navaz Gangji

Theses and Dissertations

Tumor metastasis and recurrence account for more than 90% of cancer-associated deaths and are thought to occur due to a small subpopulation of neoplastic cells known as cancer stem cells (CSCs). Because CSCs are resistant to conventional chemotherapy, there is a critical need to develop CSC-targeting agents. Microenvironmental components, especially glycosaminoglycans (GAGs), play a key role in regulating CSC phenotype. GAGs such as heparan sulfate (HS) interact with hundreds of proteins and influence a variety of biological processes including tumor proliferation, angiogenesis, metastasis and stem cell biology.

Recently, the Desai and Patel laboratories have demonstrated that a hexasaccharide form of …

Regulation Of Vascular And Lymphatic Endothelial Barrier Function By Sphingosine-1-Phosphate, Jacqueline Bellaci

Theses and Dissertations

Endothelial cells play an important role in maintaining homeostasis, and disruption of the endothelial barrier have been linked to a number of different pathologies, including cancer metastasis. The vascular endothelial barrier is known to be regulated by a variety of factors, including sphingosine-1-phosphate (S1P), a bioactive lipid metabolite, which has been shown to improve barrier function. However, most studies to date have been focused on the vascular endothelium, and the regulation of the lymphatic endothelial barrier has not been thoroughly investigated. We found that prior to any stimulation the lymphatic endothelial cells (LECs) had a lower trans-endothelial resistance (TER) in …

Structural Features Contributing To Methylenedioxypyrovalerone (Mdpv) Analog Inhibition Of The Human Dopamine Transporter, Zachary R. Spires

Theses and Dissertations

Monoamine transporters (MATs) are transmembrane neurotransmitter sodium symporters consisting of the dopamine, norepinephrine, and serotonin transporters: DAT, NET, and SERT, respectively. Following an action potential and neurotransmitter vesicular release, MAT-mediated reuptake of these neurotransmitters in the presynaptic membrane contributes to the termination of monoaminergic neurotransmission. MATs are the targets of many drugs providing therapeutic benefits or taken recreationally. One of these drugs is methylenedioxypyrovalerone (MDPV), an abused synthetic cathinone that is a high potency uptake inhibitor of the human DAT (hDAT). In contrast, MDPV is a low potency uptake inhibitor of the Drosophila melanogaster dopamine transporter (dDAT). The reasons for …

The Impact Of Aging And Mechanical Injury On Alveolar Epithelial And Macrophage Responses In Acute Lung Injury And Inflammation, Michael S. Valentine

Theses and Dissertations

Patients with severe lung pathologies, such as Acute Respiratory Distress Syndrome (ARDS), often require mechanical ventilation as a clinical intervention; however, this procedure frequently exacerbates the original pulmonary issue and produces an exaggerated inflammatory response that potentially leads to sepsis, multisystem organ failure, and mortality. This acute lung injury (ALI) condition has been termed Ventilator-Induced Lung Injury (VILI). Alveolar overdistension, cyclic atelectasis, and biotrauma are the primary injury mechanisms in VILI that lead to the loss of alveolar barrier integrity and pulmonary inflammation. Stress and strains during mechanical ventilation are believed to initiate alveolar epithelial mechanotransduction signaling mechanisms that contribute …

A Kinesin Adapter Directly Mediates Dendritic Mrna Localization During Neural Development In Mice, Hao Wu, Jing Zhou, Tianhui Zhu, Ivan Cohen, Jason Dictenberg

Publications and Research

Motor protein-based active transport is essential for mRNA localization and local translation in animal cells, yet how mRNA granules interact with motor proteins remains poorly understood. Using an unbiased yeast two–hybrid screen for interactions between murine RNA-binding proteins (RBPs) and motor proteins, here we identified protein interaction with APP tail-1 (PAT1) as a potential direct adapter between zipcode-binding protein 1 (ZBP1, a β-actin RBP) and the kinesin-I motor complex. The amino acid sequence of mouse PAT1 is similar to that of the kinesin light chain (KLC), and we found that PAT1 binds to KLC directly. Studying PAT1 in mouse …

Influence Of Diet And Abiotic Factors On The Survival And Reproduction Of Calanoid Copepod Pseudodiaptomus Annandalei, Abd Aziz Fatin Fatihah

Student Works (2020-2029)

The calanoid copepod, Pseudodiaptomus annandalei, due to its good nutritional value and significance as a natural diet of many tropical fish, is a superior live feed for marine fish larvae. Fish larvae needs a sustainable supply of good quality live feed for optimal growth and survival. Aims of this study were to investigate the effects of (1) marine mircroheterotrophs grown in palm oil mill effluent (POME) as copepod diet and (2) abiotic factors i.e. salinity (ppt), temperature (˚C), pH, photoperiod and light intensity on the survival and nauplii production of P. annandalei. Both biotic and abiotic experiments were conducted with …

Evaluation Of Wound Healing Potential, Antioxidant Activity, Acute Toxicity And Gastro Protective Effect Of 2-Pentadecanone In Ethanol Induced Gastric Mucosal Ulceration In Rats, Kamran Sareh

Student Works (2020-2029)

Wound is an injury to normal tissue that can happen either externally or internally such as wound in skin tissue or stomach tissue. Compound 2-pentadecanone a ketone derivative, has been identified in some plants, and was reported to have anti-bacterial, antioxidant and anti-inflammatory activities. The aim of this study was to evaluate skin wound healing and gastro-protective potential effect of 2-pentadecanone in Sprague dawley rats. Acute toxicity assay was performed to detect safety of 2-pentadecanone. In the evaluation of skin wound healing, dorsal neck of rats were induced wounds and topically treated with 2-pentadecanone for 10 days. Meanwhile, for gastroprotective …

Acid Hydrolysis-Based Sugarcane Bagasse Biorefining For Levulinic Acid Production: Dynamic Mechanistic Modeling Under Varying Operating Conditions, Emília S. Lopes, Julio C.J. Gariboti, Luis H.Z. Feistel, Elmer Ccopa Rivera, Rubens Mac Iel Filho, Laura P. Tovar

Faculty Publications

© 2020, AIDIC Servizi S.r.l. The study on the lignocellulosic material conversion into bio-based platform chemicals, such as levulinic acid (LA), is one of the most promising routes to promote the development of advanced biorefineries. In this work, a dynamic mechanistic model is developed to simulate the LA production from lignocellulosic material. A wide operating range is used to estimate the parameters of the reaction kinetics. Because multi-parameter estimation problem is complex, a genetic algorithm-based optimization procedure is used to determine the optimum parameters values. Measurements are obtained for various reaction times (0 - 45 min) temperatures (150 - 200 …

Outlier Profiles Of Atomic Structures Derived From X-Ray Crystallography And From Cryo-Electron Microscopy, Lin Chen, Jing He, Angelo Facchiano

Computer Science Faculty Publications

Background: As more protein atomic structures are determined from cryo-electron microscopy (cryo-EM) density maps, validation of such structures is an important task. Methods: We applied a histogram-based outlier score (HBOS) to six sets of cryo-EM atomic structures and five sets of X-ray atomic structures, including one derived from X-ray data with better than 1.5 Å resolution. Cryo-EM data sets contain structures released by December 2016 and those released between 2017 and 2019, derived from resolution ranges 0–4 Å and 4–6 Å respectively. Results: The distribution of HBOS values in five sets of X-ray structures show that HBOS is sensitive distinguishing …

Structural And Functional Characterization Of Cazyme And Cazyme-Related Proteins From: Bacteroides Thetaiotaomicron And Porphyromonas Gingivalis: Two Abundant Colonizers Of The Human Microbiome, James Stevenson

Theses and Dissertations (Comprehensive)

The human body consists of approximately 30 trillion cells, while non-human microbes that reside on and within the body outnumber human somatic cells by a factor of 1.3 – 2.3. The interplay between our cells and those of the colonizing microorganisms affect physiology in a multitude of ways, both beneficial and detrimental. Microbes found in the oral cavity, such as the Red Complex member Porphyromonas gingivalis, are associated with pathology, namely periodontal diseases including gum deterioration, tooth decay, and loss of underlying alveolar bone. At the other end of the gastrointestinal tract, microbes such as Bacteroides thetaiotaomicron are found …

Synthesis And Biophysical Analysis Of The Cell-Penetrating Peptide Penetratin And Its Aromatic Analogues, An Le

Theses and Dissertations (Comprehensive)

Cell-penetrating peptides (CPPs) interact with biological membranes, undergo cellular intake/uptake, and may act as potential drug delivery agents. Understanding the molecular interactions of these peptides with membranes contributes to gaining a better knowledge of their potential use in medical and pharmaceutical applications to improve human health. The current research focuses on understanding the mechanisms of a CPP in interaction with different model phospholipid membranes. The peptide penetratin (primary sequence: RQIKIWFQNRRMKWKK) is an example of a CPP that can interact with and pass through biological membranes. The current thesis provides spectroscopic and calorimetric evidence that penetratin associates with lipid membranes. Circular …

Special Issue On The Third Workshop On Biological Mentality, Kenneth A. Augustyn

Michigan Tech Publications, Part 1

The Third Workshop on Biological Mentality was held from September 23, 2019 to March 2, 2020 as a series of twenty-one Monday online conferencing sessions, each consisting of a talk followed by a Q&A discussion. Like the two previous workshops [1, 2], the objective of this workshop was to seek a deeper level of understanding the physical foundations of biological mentality (whether conscious or nonconscious).

Functional Characterization Of Proteins From A Putative Chondroitin Sulfate A Degrading Operon And The Crystal Structure Of An Exo-N-Acetylgalactosamine-4-Sulfatase From Tannerella Forsythia, Peter Nguyen

Theses and Dissertations (Comprehensive)

Advanced periodontitis has been shown to have strong associations with the residence of a bacterial triad of Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola also known as the red complex. These bacteria were previously thought to be asaccharolytic, making them better suited to survive in deep in periodontal pockets where access to carbohydrates from food is limited. Information gathered from genomic analysis suggested that upregulation of an operon (BFO2285-BFO2295, BFO3043) could confer the capacity for T. forsythia to degrade chondroitin-4-sulfate, the principle glycosaminoglycan of alveolar bone tissue. Bioinformatics analysis suggested the operon was similar to an operon found in Bacteroidetes …

Fggy Carbohydrate Kinase Domain Containing Is Induced During Skeletal Muscle Atrophy And Modulates Map Kinase And Akt Signaling, Anastasia L. Smith

UNF Graduate Theses and Dissertations

Skeletal muscle atrophy can result from a range of physiological conditions, including denervation, immobilization, hindlimb unweighting, and aging. To better characterize the molecular genetic events of atrophy, a microarray was performed using skeletal muscle isolated from mice after 3 and 14 days of denervation and compared to control muscle to identify novel atrophy-induced genes. The microarray revealed that FGGY carbohydrate kinase domain containing (Fggy) is expressed in skeletal muscle and is induced in response to denervation. Bioinformatic analysis of the Fggy gene locus revealed two validated alternative isoforms, that we have termed Fggy-L-552 and Fggy-S-387, which have distinct transcription initiation …

Quantifying The Heterogeneity Of The Immunoglobulin G N-Glycome In An Ageing Australian Population: The Busselton Healthy Ageing Study, Alyce Russell

Theses: Doctorates and Masters

The use of immunoglobulin G N-glycomics to study chronic non-communicable disorders and other complex phenotypes emerged following the Human Genome Project. The consortium discovered that most phenotypes were too complex to be explained by genetics alone. Thus, the biological importance of epigenetics was recognised; heritable modifications to gene expression rather than the genome itself. Nglycosylation is a form of epigenetic regulation known as a post-translational modification. It stabilises the immunoglobulin G structure and alters downstream responses elicited by the antibody and is extensively studied as a candidate biomarker in the post-genomic era.

The N-glycosylation of immunoglobulin G itself is complex, …

Amyloid Proteins And Fibrils Stability, Farbod Mahmoudinobar

Dissertations

Compared to globular proteins that have a stable native structure, intrinsically disordered peptides (IDP) sample an ensemble of structures without folding into a native conformation.One example of IDP is the amyloid-beta(Abeta) protein which is the main constituent of senile plaques in the brain of Alzheimer's patients.Understanding the process by which IDPs undergo structural changes to form oligomers that eventually aggregate into senile plaques/amyloid fibrils may significantly advance the development of novel therapeutic methods to treat neurodegenerative diseases, for which there is no cure to date. This dissertation has two main objectives. The first one is to investigate and identify structural …

Architecture Of The Chromatin Remodeler Rsc And Insights Into Its Nucleosome Engagement., Avinash B Patel, Camille M Moore, Basil J Greber, Jie Luo, Stefan A Zukin, Jeff Ranish, Eva Nogales

Articles, Abstracts, and Reports

Eukaryotic DNA is packaged into nucleosome arrays, which are repositioned by chromatin remodeling complexes to control DNA accessibility. The

Does The Seedling Emergence Technique Limit The Detection Of Seeds Of Miombo Species In Miombo Woodlands?, Halima M. Amir, Mkabwa L. K Manoko

Journal of Humanities and Social Sciences

Seedling emergence technique frequently used in soil seed bank studies indicates that seeds of Miombo species are not present in the soil seed bank. Does this method limit the detection of seeds of Miombo species in the soil seed bank? This question has not been investigated systematically. The present study aims to find out whether the seedling emergency method limits the detection of seeds of Miombo species in the soil seed bank of Miombo woodlands. In the investigation, seedling emergence and extraction methods were used to estimate soil seed bank in Miombo woodlands. Data were obtained from 50 circular plots …

Effects Of Seasons And Zonation On Biochemical Contents Of Two Seagrass Species Along Dar Es Salaam Coast, Tanzania, Wamwi M. Mbaga, Esther F. Mvungi

Tanzania Journal of Science

Accumulation and allocation of biochemicals in plants are affected by various factors. The influence of seasons and vertical zonation on biochemical contents of seagrasses Cymodocea rotundata and Thalassia hemprichii from Mjimwema seagrass meadow along the coast of Dar es Salaam were assessed. Samples were collected in 2016 during wet/rainy (April–May) and dry (June–July) seasons. Concentrations of crude protein, soluble carbohydrates, phosphorus, lipid, and proline were determined using standard methods. Significant higher levels of phosphorus, lipid, protein and proline were observed during the dry season than in wet season (p < 0.05). Likewise, seagrass population occurring at the shore zone expressed higher levels of biochemical contents than those found at the subtidal zones. The highest concentration of protein was recorded in Thalassia hemprichii (5.8 mg/g dw)), while those of lipid and carbohydrates (27.1 and 53.1 mg/g dw, respectively) were recorded in Cymodocea rotundata. The two species studied did not vary significantly in their biochemical concentrations in both seasons. Generally it was observed that the concentrations of studied biochemicals were up-regulated during the dry season and varied depending on the locations where the seagrass grow. Thus, both season and zonation played roles in biochemical accumulation in the seagrasses understudy, however not interactively.

Robust Cullin-Ring Ligase Function Is Established By A Multiplicity Of Poly-Ubiquitylation Pathways, Spencer Hill, Kurt Reichermeier, Daniel C. Scott, Lorena Samentar, Jasmin Coulombe-Huntington, Luisa Izzi, Xiaojing Tang, Rebeca Ibarra, Thierry Bertomeu, Annie Moridian, Michael J. Sweredoski, Nora Caberoy, Brenda A. Schulman, Frank Sicheri, Mike Tyers, Gary Kleiger

Life Sciences Faculty Research

The cullin-RING ligases (CRLs) form the major family of E3 ubiquitin ligases. The prototypic CRLs in yeast, called SCF enzymes, employ a single E2 enzyme, Cdc34, to build poly-ubiquitin chains required for degradation. In contrast, six different human E2 and E3 enzyme activities, including Cdc34 orthologs UBE2R1 and UBE2R2, appear to mediate SCF-catalyzed substrate polyubiquitylation in vitro. The combinatorial interplay of these enzymes raises questions about genetic buffering of SCFs in human cells and challenges the dogma that E3s alone determine substrate specificity. To enable the quantitative comparisons of SCF-dependent ubiquitylation reactions with physiological enzyme concentrations, mass spectrometry was employed …

Nanomaterials For Biosensing Lipopolysaccharide, Palak Sondhi, Helal Maruf, Keith Stine

Chemistry & Biochemistry Faculty Works

Lipopolysaccharides (LPS) are endotoxins, hazardous and toxic inflammatory stimulators released from the outer membrane of Gram-negative bacteria, and are the major cause of septic shock giving rise to millions of fatal illnesses worldwide. There is an urgent need to identify and detect these molecules selectively and rapidly. Pathogen detection has been done by traditional as well as biosensor-based methods. Nanomaterial based biosensors can assist in achieving these goals and have tremendous potential. The biosensing techniques developed are low-cost, easy to operate, and give a fast response. Due to extremely small size, large surface area, and scope for surface modification, nanomaterials …

Peroxiredoxin 6 And Inflammation In Alzheimer's Disease, Jared Ferrell-Penniman

Biological Sciences Theses and Dissertations

Alzheimer’s disease (AD) is known for its debilitating symptoms and poor prognosis. However, despite intense research into neurodegenerative diseases, there are few therapies targeted at the underlying mechanisms of the disease. Oxidative stress (OS) and inflammation are cellular phenomena thought to be key to the progression of the disease. Critically, peroxiredoxin 6 (Prx6), an antioxidant protein with multiple functions, has been identified from mammalian studies as a potential regulator of both OS and inflammation that may have a specific effect on AD. This project seeks to elucidate the role of Prx6 in AD as well as the underlying mechanisms. Drosophila …

Functional Implications Of Nlrp1 Variants For Autoimmune Disease, Laura J. Westhoff

Undergraduate Honors Theses

NLRP1 is a protein-coding human gene that plays a crucial role in the NLRP1 inflammasome. Variants to the NLRP1 gene have been associated with autoimmune and autoinflammatory diseases. We examined the effects of polymorphisms at two SNPs on cytokine levels and NLRP1 gene expression in 50 human volunteers without diagnosed autoimmune disease. NLRP1 was genotyped at SNPs rs2670660 and rs12150220 and individuals who were homozygous at one or more SNP were selected for further analysis. Serum IL-18 and IL-1β levels were quantified using ELISA. NLRP1 gene expression was measured using real-time PCR. A strong linkage was found between genotypes of …

Transcription Regulation Of Human Il1b Gene In Monocytes And Lymphoid Cd4 T Cells, Sree H. Pulugulla

Electronic Theses and Dissertations

Cytokines are key regulators of the inflammatory response and play an important role in facilitating intercellular communication between various immune cell types. Interleukin‑1β (IL‑1β) is a potent pro-inflammatory cytokine that is required for robust initiation of innate immune response and subsequent development of adaptive immunity. IL-1β is first synthesized as an inactive cytoplasmic, non‑glycosylated, precursor molecule (proIL‑1β) by monocytes and macrophages in response to invading pathogenic microbes. The activation of caspase‑1 by inflammasomes cleaves proIL-1β into mature biologically active IL-1β that is released from cells via a non-classical, endoplasmic reticulum‑independent secretory pathway directly from the cytoplasm via Gasdermin D membrane …