Biochemistry, Biophysics, and Structural Biology Commons^™

Photosynthetic Efficiency And Mesophyll Conductance Are Unaffected In Arabidopsis Thaliana Aquaporin Knock-Out Lines, Johannes Kromdijk, Katarzyna Głowacka, Stephen P. Long

Department of Biochemistry: Faculty Publications

Improving photosynthetic efficiency is widely regarded as a major route to achieving much-needed yield gains in crop plants. In plants with C₃ photosynthesis, increasing the diffusion conductance for CO₂ transfer from substomatal cavity to chloroplast stroma (g_m) could help to improve the efficiencies of CO₂ assimilation and photosynthetic water use in parallel. The diffusion pathway from substomatal cavity to chloroplast traverses cell wall, plasma membrane, cytosol, chloroplast envelope membranes, and chloroplast stroma. Specific membrane intrinsic proteins of the aquaporin family can facilitate CO₂ diffusion across membranes. Some of these aquaporins, such as PIP1;2 …

Serotonin 5-Ht2a And 5-Ht2c Receptors Regulate Rat Maternal Behavior Through Distinct Behavioral And Neural Mechanisms, Jun Gao, Lina Nie, Yu Li, Ming Li

Department of Psychology: Faculty Publications

Serotonin 5-HT_2A and 5-HT_2C receptors play important yet distinctive roles in the regulation of rat maternal behavior. The present study investigated their neural substrates and explored the possible behavioral mechanisms (i.e., behavioral organization or maternal motivation). Sprague-Dawley postpartum females were microinjected with either a selective 5-HT_2A agonist (TCB-2, 0.4 or 4.0 μg/side) or a 5-HT_2C agonist (MK212, 2.5 or 5.0 μg/side) into the medial prefrontal cortex (mPFC) or ventral tegmental area (VTA). Ten and 60 min later, their maternal activities were observed in the home cage; and their motivational responses towards pups were examined in a …

Size-Dependent Interactions Of Lipid-Coated Gold Nanoparticles: Developing A Better Mechanistic Understanding Through Model Cell Membranes And In Vivo Toxicity, Arek M. Engstrom, Ryan A. Faase, Joe E. Baio, Marilyn R. Mackiewicz, Stacey L. Harper

Chemistry Faculty Publications and Presentations

Introduction: Humans are intentionally exposed to gold nanoparticles (AuNPs) where they are used in variety of biomedical applications as imaging and drug delivery agents as well as diagnostic and therapeutic agents currently in clinic and in a variety of upcoming clinical trials. Consequently, it is critical that we gain a better understanding of how physiochemical properties such as size, shape, and surface chemistry drive cellular uptake and AuNP toxicity in vivo. Understanding and being able to manipulate these physiochemical properties will allow for the production of safer and more efficacious use of AuNPs in biomedical applications.
Methods and Materials: Here, …

Antifungal Defense Molecules From Bacterial Symbionts Of North American Trachymyrmex Ants, Georgia Scherer

CMC Senior Theses

Defensive symbioses, in which microbes provide molecular defenses for an animal host, hold great potential as untapped sources of therapeutically useful antibiotics. Fungus-growing ants use antifungal defenses from bacterial symbionts to suppress pathogenic fungi in their nests. Preliminary chemical investigations of symbiotic bacteria from this large family of ants have uncovered novel antifungal molecules with therapeutic potential, such as dentigerumycin and selvamicin.

In this study, the bacterial symbionts of North American Trachymyrmex fungus-growing ants are investigated for antifungal molecules. Plate-based bioassays using ecologically-relevant fungal pathogens confirmed that these bacteria have antifungal activity. In order to purify and identify the antifungal …

Investigating The Role Of Centromeric Repeats In Female Meiotic Drive, Jocelyn Crawford

CMC Senior Theses

Female meiotic drive is an unequal transmission of alleles that arises through the competition of paired chromosomes for inclusion in the egg, resulting in an increase in frequency of the driven alleles regardless of their effect on fitness of the individual. In Mimulus guttatus (monkeyflower) second filial generations, driven alleles display transmission advantages resulting in the virtual elimination of recessive homozygotes, while the equivalent lines lacking drive elements conform to traditional Mendelian segregation population ratios. Centromeres have been identified as mechanistic drive elements due to their role in chromosomal segregation during female meiosis, with Mimulus providing the best documented case …

Novel Post-Translational Modification And Function Of Fus: The Relevance To Amyotrophic Lateral Sclerosis, Alexandra Arenas

Theses and Dissertations--Toxicology and Cancer Biology

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease characterized by the preferential death of motor neurons. Approximately 10% of ALS cases are familial and 90% are sporadic. Fused in Sarcoma (FUS) is a ubiquitously expressed RNA binding protein implicated in familial ALS and frontotemporal dementia (FTD). FUS is ubiquitously expressed in cells and has a variety of functions in the nucleus and cytoplasm. FUS mutations in the nuclear localization sequence (NLS) causes mislocalization of FUS in the cytoplasm, where it can undergo liquid-liquid phase separation and become stress granules or protein inclusions. Although FUS inclusion bodies can be found in …

Engineering Ph-Dependent Antibody Interactions Through Linked Protonation Events In Interdomain Interfaces, Hyeyoung Eom

Graduate Research Theses & Dissertations

Engineered antibodies are frequently used in life science applications, such as therapeutics and clinical diagnostics. These customized antibodies typically possess enhanced binding affinity and/or specificity, yet these interactions are only one-way binding events that cannot be easily controlled without extreme changes in conditions, such as pH, denaturant, and/or temperature that likely irreversible damage the antibody and antigen. Here, we explore the design of proton-linked binding events in the context of both antibody/hapten (i.e., a low molecular weight ligand target) and antibody/antigen complexes. Specifically, this work looks to overcome the challenges of engineering pH-dependent small ligand/protein interactions, as well as develop …

The Exploration Of Nanotoxicological Copper And Interspecific Saccharomyces Hybrids, Matthew Joseph Winans Phd

Graduate Theses, Dissertations, and Problem Reports (ETD)

Nanotechnology takes advantage of cellular biology’s natural nanoscale operations by interacting with biomolecules differently than soluble or bulk materials, often altering normal cellular processes such as metabolism or growth. To gain a better understanding of how copper nanoparticles hybridized on cellulose fibers called carboxymethyl cellulose (CMC) affected growth of Saccharomyces cerevisiae, the mechanisms of toxicity were explored. Multiple methodologies covering genetics, proteomics, metallomics, and metabolomics were used during this investigation. The work that lead to this dissertation discovered that these cellulosic copper nanoparticles had a unique toxicity compared to copper. Further investigation suggested a possible ionic or molecular mimicry …

Investigation Of Glutamate Carboxypeptidase Ii Roles In The Folate Cycle Dependent Reproduction And Development Of Caenorhabditis Elegans, Jessica M. Derham

Masters Theses

Glutamate Carboxypeptidase II (GCPII) is a transmembrane, zinc metallopeptidase that is expressed in a wide range of organisms, including roundworms, mice, and humans. In humans, GCPII is primarily expressed in the prostate, kidneys, small intestine, and central nervous system. Within the small intestine, the expected function of GCPII is to aid in the absorption of dietary folate from the intestinal lumen. GCPII cleaves excess glutamates from folate to yield monoglutamated folate which is then readily transported into the enterocyte. Folate can then be used through the one carbon metabolic cycle for the synthesis of nucleotides, conversion of homocysteine to methionine, …

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 …

Deconvolution Tools For Extracting Insight From Challenging Two-Flavin Systems, Dallas Michael Bell

Theses and Dissertations--Chemistry

Flavoproteins have long been explored for their ubiquity among a number of metabolic and energetic reactions. The flavin cofactor has the inherent benefit of distinct spectral changes associated with redox transitions; however, the double-edged sword is incurred as these distinct signatures overlap and take up much of the UV-vis spectral range. Therefore, it is crucial to create a method to demarcate the expressed redox transitions for studying these systems. The first portion of these studies discusses the creation of a program that deduces spectra for redox transitions in a single-flavin containing model protein: flavodoxin. The latter portions discuss the application …

Single-Domain Vhh Antibodies As Protein Stabilization Modules, Nourhan Mohamed Disouky Mostafa

Graduate Research Theses & Dissertations

VHH domains are the antigen-binding units found in heavy-chain-only antibodies from the Camelidae family (e.g., camels and llamas). They are considered a unique minimalist antibody scaffold due to the lack of a variable light chain domain. Despite having half the antigen-binding interface of conventional antibodies, these VHH antibodies bind their target antigens with affinities comparable to conventional antibodies. This project explored how flexible linkers connecting an anti-GFP VHH (αGFP VHH) domain to its antigen (EGFP) enhanced antigen stability and influenced oligomeric assembly. It was hypothesized that linking the anti-GFP VHH antibody to its target antigen (EGFP) will increase the local …

Seasonal Variation In Mitochondrial Bioenergetics Of The Bluegill Sunfish, Lepomis Macrochirus, From A Shallow Midwest River, Derick Isaac Lamptey

Masters Theses

As average global temperature increase, the frequency and magnitude of extreme temperatures in shallow aquatic ecosystems are more ubiquitous. In order to understand how these changing thermal regimes affect aquatic ectotherms, it is essential to develop studies evaluating the response of ectotherms to seasonal fluctuating thermal regimes. Previous studies on fluctuating temperature regimes have reported an increased physiological stress leading to morphological, behavioral and biochemical adaptations. From the latter, the adaptive capacity and seasonal performance associated with optimal function of the oxidative phosphorylation system (OXPHOS) are key for species persistence. However, studies on this matter are scarce. This study explores …

Flavodoxin, The Hydrogen Atom Of Flavoproteins: A 19f Nmr Study Of Dynamics And Conformational Changes Utilizing Flavodoxin From Rhodopseudomonas Palustris, Taylor Varner

Theses and Dissertations--Chemistry

Flavodoxin is a small, highly stable protein that contain a single FMN cofactor used to transfer single electrons at low potentials. The organism Rhodopseudomonas palustris contains a long-chain flavodoxin. Long-chain flavodoxins are characterized by a 20 amino acid loop that is proposed to allow interactions with partner proteins. We plan to utilize this protein as a model to build our repertoire with protein fluorination and fluorine NMR in flavoproteins. This tool kit will then be applied to the study of a partner protein of interest that is capable of performing electron bifurcation. We have incorporated m-fluoro tyrosine into flavodoxin and …

Hijacking The Fusion Complex Of Human Parainfluenza Virus As An Antiviral Strategy, T. C. Marcink, E. Yariv, K. Rybkina, V. Más, F. T. Bovier, A. Des Georges, A. L. Greninger, C. A. Alabi, M. Porotto, N. Ben-Tal, A. Moscona

Advanced Science Research Center

The receptor binding protein of parainfluenza virus, hemagglutinin- neuraminidase (HN), is responsible for actively triggering the viral fusion protein (F) to undergo a conformational change leading to insertion into the target cell and fusion of the virus with the target cell membrane. For proper viral entry to occur, this process must occur when HN is engaged with host cell receptors at the cell surface. It is possible to interfere with this process through premature activation of the F protein, distant from the target cell receptor. Conformational changes in the F protein and adoption of the postfusion form of the protein …

Correction: Visible-Light Photooxidation In Water By 1o2-Generating Supramolecular Hydrogels, Sankarsan Biswas, Mohit Kumar, Andrew Levine, Ian Jimenez, Rein V. Ulijn, Adam Braunschweig

Advanced Science Research Center

Correction for ‘Visible-light photooxidation in water by ¹O₂-generating supramolecular hydrogels’ by Sankarsan Biswas et al., Chem. Sci., 2020, 11, 4239–4245, DOI: 10.1039/C9SC06481H.

Polymer Brush Hypersurface Photolithography, Carlos Carbonell, Daniel J. Valles, Alexa M. Wong, Andrea S. Carlini, Mollie A. Touve, Joanna Korpanty, Nathan C. Gianneschi, Adam B. Braunschweig

Advanced Science Research Center

Polymer brush patterns have a central role in established and emerging research disciplines, from microarrays and smart surfaces to tissue engineering. The properties of these patterned surfaces are dependent on monomer composition, polymer height, and brush distribution across the surface. No current lithographic method, however, is capable of adjusting each of these variables independently and with micrometer-scale resolution. Here we report a technique termed Polymer Brush Hypersurface Photolithography, which produces polymeric pixels by combining a digital micromirror device (DMD), an air-free reaction chamber, and microfluidics to independently control monomer composition and polymer height of each pixel. The printer capabilities are …

A Novel Pool Of Microparticle Cholesterol Is Elevatedin Rheumatoid Arthritis But Not In Systemic Lupus Erythematosus Patients, Shuai Shuai Hu, Brenton L. Cavanagh, Robert Harrington, Muddassar Ahmad, Grainne Kearns, Steve Meaney, Claire Wynne

Articles

Microparticles are sub-micron, membrane-bound particles released from virtually allcells and which are present in the circulation. In several autoimmune disorders their amountand composition in the circulation is altered. Microparticle surface protein expression has beenexplored as a differentiating tool in autoimmune disorders where the clinical pictures can overlap.Here, we examine the utility of a novel lipid-based marker—microparticle cholesterol, present in allmicroparticles regardless of cellular origin—to distinguish between rheumatoid arthritis (RA) andsystemic lupus erythematosus (SLE). We first isolated a series of microparticle containing lipoproteindeficient fractions from patient and control plasma. There were no significant differences in thesize, structure or protein content of …

A Proteomic Analysis Of Corydoras Sterbai Secretions And Tissues, Erik Powell Wictor

University of the Pacific Theses and Dissertations

Defensive mechanisms vary widely in the animal kingdom ranging from physical defenses like spines to chemical defenses such as toxins. Toxins in these secretions and tissues can fluctuate from enzymes to lipids to uncharacterized chemicals. Next generation -omics technology and mass spectrometry are extremely important in analyzing these samples because of their ability to distinguish minute amounts of toxic substance within a complicated sample. The goal of this experiment was to look at secretions and tissues from Corydoras sterbai. All samples in this study were proteolyzed using a mixture of Trypsin and Lys-C, fractionated, and run through nanoLC-MS/MS analysis using …

Proteomic Analysis Of Fetal Rat Neural Stem Cells After Treatment With Hericium Erinaceus, Bright Adam Test

University of the Pacific Theses and Dissertations

The fungus, Hericium erinaceus, has outstanding chemical properties, displaying health benefits in digestive, hepatic, and nervous tissues. Its ease of accessibility and use makes it one of the most common substances used for treatment in Eastern medicine. More and more recent research is confirming the incredible health benefits of this fungus, especially the impact that is seen on nervous tissue growth and recovery post-treatment. Such neurite outgrowth and myelin sheath regeneration could illustrate the beginning of the cure to lifelong neurodegenerative diseases such as Multiple Sclerosis. In this first-of-its-kind study, we cultured and differentiated fetal rat neural stem cells while …

Tools To Evaluate Nanodiamond-Mediated Delivery Of Tiopronin For Cataract Prevention, Justin Beltz

Doctoral Dissertations

”There is a growing demand for non-surgical means of cataract treatment. This dissertation presents three bodies of work that reflect the early-stage development of eye drop formulations aimed at delaying cataract progression. These formulations consist of the antioxidant 2-mercaptopropionylglycine (MPG) loaded onto nanodiamond particles.

Cataractogenesis is linked to oxidative damage to lens proteins. To investigate the potential of MPG for protection against oxidative damage, A549 cells were incubated in 0.6 mM tert-butylhydroperoxide (tBHP). Cells exposed to tBHP without MPG exhibited elevated levels of reactive oxygen species, which led to the depletion of the vital antioxidant glutathione and, ultimately, apoptosis. Co-administration …

Selectivity For Allosteric Effectors Of Bacterial Adp-Glucose Pyrophosphorylase: Structural And Functional Studies, Mashael Alghamdi

Dissertations

The biosynthesis of the intracellular polysaccharide in bacteria and plants, glycogen and starch, respectively, controlled by the key regulatory step that catalyzed by ADP-Glucose Pyrophosphorylase (ADP-Glc PPase). ADP-Glc PPase is an allosteric enzyme regulated by metabolites produced of the principle carbon assimilation pathway in each organism. Agrobacterium tumefaciens enzyme activated by fructose 6-phosphate (Fru6P) and pyruvate, whereas Escherichia coli enzyme activated by fructose 1,6-bisphosphate (FBP), and both enzymes inhibited by AMP. Here, we targeted the allosteric regulation of the A. tumefaciens enzyme, examined some residues that may impact the regulation mechanism (Ser72, His71, Arg75, Ser351, Ser334, Arg368, Asn350, and Asp291), …

Human Isocitrate Dehydrogenase Enzymes, Joseph Valentein Roman

Dissertations

Mammals have three forms of isocitrate dehydrogenase (ICDH) that each catalyze the oxidative decarboxylation of isocitrate forming alpha-ketoglutarate (AKG), carbon dioxide and reduced pyridine nucleotide. The intra-mitochondrial, citric acid cycle enzyme is ICDH III that exists as a hetero tetramer and uses NAD+ as a substrate. ICDH I and ICDH II are both dimeric enzymes that reside in the cytosol and use NADP+. While, the precise function of the cytosolic ICDHs is not known, active site variants of both ICDH I and II cause a variety of cancers. The R132H variant of ICDH1 is one of the most common alterations. …

Controlled Release Of Fibroin Repeat-Tagged Proteins From Silk Hydrogel, Jaturong Promsuk

Chulalongkorn University Theses and Dissertations (Chula ETD)

Protein-based biologic drugs such as growth factors are playing important roles in modern medicine. These proteins can be used to stimulate local tissue repair. Growth factors are often incorporated into a scaffold, such as a hydrogel, and then put into the desired area of the body to achieve therapeutic effects. However, diffusion of these growth factors outside of the designated area or inappropriate release time can have deleterious consequences, such as inducing tumors in other areas of the body or uncontrolled inflammation. Therefore, this project aims to create a model to study diffusion of protein from hydrogel by using green …

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 …

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 …