Biochemistry Commons^™

Sugarcane Bagasse Hydrolysis Enhancement Using Bsa, Antonio Carlos Freitas Dos Santos

Open Access Theses

Lignocellulose is composed of polysaccharides linked to lignin and other aromatic compounds, making the sugars not readily available to fermentation. This entails that biomass must go through the unit operations of pretreatment and enzyme hydrolysis. Pretreatment opens the structure to allow the enzymes to act on and hydrolyze cellulose and hemicellulose to glucose and/or xylose which in turn are fermented to ethanol. Concomitantly, the enzymes interact with soluble phenols and insoluble solids derived from lignin that inhibit hydrolysis. This leads to high enzyme loadings and higher production costs. Soluble phenols can be eliminated through washing. Insoluble lignin, however, demands another …

Antibacterial Activity Of Essential Oil Encapsulated Sodium Iota-Carrageenan Fibers, Carlos D. Carter

Open Access Theses

Spoilage microorganisms cause food waste and loss of quality. While the foodborne pathogen outbreaks lead to thousands of hospitalizations and deaths. Essential oils (EOs), plant extracts, possess the required antimicrobial activities and thus their usage stands out as a feasible approach for controlling the undesirable bacterial growth in food systems. However, EOs are highly volatile and lose their activity upon exposure to environmental conditions. In this regard, their encapsulation in Generally Recognized As Safe (GRAS) matrices such as food grade polysaccharides especially iota-carrageenan could be one of the viable alternatives. Iota-carrageenan, sulfated polysaccharide from marine algae, is being used in …

The Role Of Hif1alpha And Hif2alpha In Muscle Development And Satellite Cell Function, Shiqi Yang

Open Access Theses

Hypoxia inducible factors (HIFs) are central mediators of cellular responses to fluctuations of oxygen, an environmental regulator of stem cell activity. Muscle satellite cells are myogenic stem cells whose quiescence, activation, self-renewal and differentiation are influenced by microenvironment oxygen levels. However, the in vivo roles of HIFs in quiescent satellite cells and activated satellite cells (myoblasts) are poorly understood. Expression analyses indicate that HIF1α and HIF2α are preferentially expressed in pre- and post-differentiation myoblasts, respectively. Interestingly, double knockout of HIF1α and HIF2α (HIF1α/2α dKO) in embryonic myoblasts results in apparently normal muscle development and growth. However, HIF1α/2α dKO in postnatal …

Enhancing Silymarin Fractionation Via Molecular Modeling Using The Conductor-Like Screening Model For Real Solvents, Emma C. Brace

Open Access Theses

The market for bio-based products from plant sources is on the rise. There is a global challenge to implement environmentally clean practices for the production of fuels and pharmaceuticals from sustainable resources. A significant hurdle for discovery of comparable plant-derived products is the extensive volume of trial-and-error experimentation required. To alleviate the experimental burden, a quantum mechanics based molecular modeling approach known as the COnductor-like Screening Model for Real Solvents (COSMO-RS) was used to predict the best biphasic solvent system to purify silymarins from an aqueous mixture. Silymarins are a class of flavonolignans present in milk thistle ( Silybum marianum …

An Active Site Loop Mutant Of A Zinc Metallo-Deubiquitinase Suggests The Importance Of Loop Dynamics To Catalysis, Amy N. Bueno

Open Access Theses

AMSH is a conserved zinc metalloprotease that functions with endosomal sorting complexes required for transport (ESCRT) machinery in order to down regulate and degrade cell-surface receptors. It has been shown to have high specificity toward Lys63-linked polyubiquitin chains, a signal used for receptor down regulation by ESCRT machinery. It has previously been found that Sst2, an AMSH orthologue from fission yeast, contains a flexible "loop" near the proximal ubiquitin binding site, composed of residues L402 and F403. The different mobility of the side chains of these residues contribute to the opening and closing conformation of the catalytic cleft which allow …

Support Needs Of Young Ovarian Cancer Survivors: A Pilot Study, Aurelie Chuong

Open Access Theses

Purpose. Young ovarian cancer survivor (18 years old or older but diagnosed before the age of 34 years old) support needs (i.e., physical and daily living, psychological, sexual, patient care and support, health system and information) were examined to guide the design and implementation of future young adult and adolescent cancer support groups and interventions. Method. This cross-sectional pilot study included 11 young ovarian cancer survivors. The Supportive Care Needs Survey Short Form 34 (SCNS-SF34) was used and open-ended questions were added. Results. The calculated standardized scores for the SCNS-SF34 survey results showed that sexuality needs were ranked highest (41.7 …

New Strategies To Reveal Protein Candidates In Protein-Protein Interactome Study, Meng-Chieh Chen

Open Access Theses

Comprehensive protein-protein interaction network analysis can help reveal protein functions in a system-wide manner. A reliable knowledgebase of interaction networks is not only important for selecting the candidates for drug therapies, but also for evaluating the disease risk. In current interaction databases, 322579 interactions comprised of 56460 proteins have been reported (statistical analysis from APID: Agile Protein Interaction DataAnalyzer; http://bioinfow.dep.usal.es/apid/index.htm). The huge datasets are contributed mainly by yeast -two -hybrid (Y2H) screening and affinity-purification followed by mass spectrometry (AP-MS). High false positive rates and failing to cover certain interaction categories are the limitations of these two methods. Here, we developed …

Abcb11 Functions With B1 And B19 To Regulate Rootward Auxin Transport, Jesica Elyse Reemmer

Open Access Theses

Auxin transport is essential for the architecture and development of erect plants. In a network of transporters directing auxin flows, ATP-Binding Cassette (ABC) transporters are a ubiquitous family of proteins that actively transport important substrates, including auxins, across the plasma membrane. ABCB1 and ABCB19 have been shown to account for the majority of rootward auxin transport, but residual fluxes to the root tip in Arabidopsis b1b19 double mutants implies the involvement of at least one additional auxin transporter in this process. Of specific interest, the severe dwarfism seen in abcb1abcb19 is strikingly reminiscent of that seen in mutants defective in …

Efficacy Of Cleaning Method For Removal Of Exogenous Welding Fume Contamination From Nail Tissue Prior To Use As A Biomarker For Welding Fume Manganese Exposure, Jeffrey Corral Bainter

Open Access Theses

Nail tissue has been proposed as a biomarker for body burden of occupational exposure to manganese from welding fumes. Though recent studies have shown correlation between manganese exposure and both nail tissue concentration as well as concentrations in dopaminergic regions of the brain, concerns of the validity of nail tissue as a biomarker have arisen due to the potential for exogenous contamination of Mn to undermine the quantization of endogenous Mn in nail. Previous studies have used a cleaning method of 1% Triton X-100 surfactant plus sonication in order to attempt to remove exogenous welding fume contamination. Determination of the …

1,25-Dihydroxyvitamin D Alters Lipid Metabolism And Epithelialto- Mesenchymal Transition In Metastatic Epithelial Breast Cancer Cells, Alle Nicole Barnard

Open Access Theses

Evidence suggests that high vitamin D status (marked by serum 25-hydroxyvitamin D, 25(OH)2 D) is associated with a decreased risk of breast cancer. It has been established that 1,25-dihydroxyvitamin D (1,25(OH) 2 D) can alter glycolysis and the Krebs cycle of breast cancer cells (Jiang et al., 2010; Zheng et al., 2013) but little information is available on 1,25(OH) 2 D's alterations of lipid metabolism in breast cancer cells. Thus, the current research investigates if there was an effect of 1,25(OH) 2 D on proteins that regulate lipid metabolism in MCF10A, MCF10A-ras, MCF10CA1h, and MCF10CA1a epithelial breast cancer cells. While …

Investigation Into The Control Of Melittin Secondary Structure And Antimicrobial Activity, Zachary B. Molinets

Open Access Theses

Antimicrobial resistance has been an exponentially growing problem since the discovery of antibiotics. Antibiotics have been misused for many years and this misuse has grown into a real problem for the medical community. While there are countless safeguards to prevent infection by a resistant strain of bacteria, there are still many plagued by it and must be treated with sometimes dangerous antibiotics. Melittin, along with many other peptides, contain potent antimicrobial properties, but are also toxic toward enthrocytes. The control of the secondary structure of peptides provides the key to adjusting their activity.

Key Residues Of Human Cytoplasmic Protein Tyrosine Phosphatase-A And -B For Substrate Binding And Specificity, Byunghyun Park

Open Access Theses

Reversible tyrosine phosphorylation plays an important role in signaling pathways that are essential for regulating cellular growth, differentiation and metabolism. Moreover, several human diseases such as diabetes, obesity and cancers are associated with the deregulation of protein tyrosine phosphatases (PTPs). Several studies provide evidence that PTPs not only contribute to cellular differentiation, but over-expression of these molecules also leads to transformation of non-transfomed cells as well. Based on these results, designing specific PTP inhibitors may ultimately function as potential therapeutic agents to treat various diseases including cancer, diabetes, and autoimmune diseases. EphA2 is a receptor tyrosine kinase which is hypo-phosphorylated …

Developing An Unstructured Model To Investigate The Effect Of Ethanol On Product Yields For Glucose And Xylose Cofermentation In Saccharomyces Cerevisiae 424a (Lnh-St), Shane D. Clingenpeel

Open Access Theses

Production of bio-ethanol from lignocellulose requires the efficient fermentation of glucose and xylose, even in the presence of inhibitors. The desired product, ethanol itself, will inhibit the fermentation. A further understanding of how ethanol affects the organism is critical to overcoming its inhibition.

This thesis evaluated the effect of ethanol on the cofermentation of glucose and xylose in two different cases. The first case had an unstructured model created for Saccharomyces cerevisiae 424A (LNH-ST), a genetically modified strain of yeast capable of cofermenting glucose and xylose. The differential equations were based around sugar consumption, and the product yields were investigated …

Interaction Between Maltose Binding Protein And Escherichia Coli Maltose Transporter, Yan Huang

Open Access Theses

The ATP-binding cassette (ABC) transporter superfamily is one of the largest families of transport proteins. The ABC transporters are responsible for selective permeability of solute across membranes energized by ATP hydrolysis, which occurs in all domains of life. Maltose transporter is an ABC importer that mediates maltose/maltodextrin uptake in bacteria and archaea. It is identified as an essential virulence factor in pathogenic species of Streptococcis pyogenes and Vibrio cholera (1, 2). Escherichia coli maltose transporter is a well-characterized system with crystal structures and exclusive biochemical studies available. Knowledge of the E. coli maltose transport mechanism will lead to a better …

Development Of A Starch-Based Mussel-Mimetic Adhesive Polymer, Jeffrey Kazimir De Kozlowski

Open Access Theses

Mussel-mimetic adhesive polymers have gained lots of attention for their strong adhesive strength, moisture resistance, and unique ability to crosslink. These properties are mainly attributed to the high content of catecholic 3,4-dihydroxyphenylalanine (DOPA) in mussel adhesive proteins. While there has been success in creating mussel-mimetic synthetic polymers, less effort has been given to create a renewable, green, biocompatible counterpart. This thesis explores the possibilities of starch-based mussel-mimetic adhesives. Carboxymethyl starch of various molecular weights and degree of substitution was synthesized and subsequent conjugation of dopamine to these polymers by 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide was investigated. The polymers suffered from very low substitution (DScatechol …