Biochemistry Commons^™

Optimizing Electrode Design For Microbial Fuel Cells Used For Wastewater Treatment, Lindsay Nichols, John A. Hogan

STAR Program Research Presentations

Microbial fuel cells (MFC) utilize bacteria to generate an electrical current that can be used in the decomposition of sludge and human urine. In a MFC there is an anode (for oxidation of organic compounds), cathode (reduction of oxygen or carbon dioxide), and a proton exchange membrane (PEM, allows protons to migrate); reduction-oxidation reactions between the anode and cathode produce a measurable current. Bacteria that are found in sludge can be used to produce electrons in a voltaic cell, but optimizing conditions for harnessing the energy is crucial to making a MFC efficient. Research has shown that the ratios of …

Synthesis Of 4-Azidocoumarins And Their Use In Copper-Catalyzed Azide-Alkyne Cycloaddition Reactions, Anthony J. Netsuri

Dissertations and Theses

Triazole-containing compounds have shown great biological activity ranging from antiviral, antibacterial, to anticancer, to name a few. Coumarin derivatives have also shown interesting biological activities. The combination of these bioactive compounds appears to have great promise for new and future medicines. In this work, various 4-azido-coumarins were synthesized via the transformation of the 4-hydroxy derivatives to 4-benzotriazolyloxy coumarins by reaction with the peptide coupling agent (benzotriazol-1-yloxy)tris-(dimethylamino)phosphonium hexafluorophosphate (BOP), and 1,8-diazabicycloundec-7-ene (DBU) as the base, in tetrahydrofuran (THF) solvent. The 4-benzotriazolyloxy coumarins were converted to the 4-azidocoumarins by reaction with sodium azide (NaN3), and the overall process was simplified to a …

Spatial Patterns Of Mercury In Atmospheric Deposition, Soils And Lake Biota In The Adirondack Park, New York, Xue Yu

Civil and Environmental Engineering - Dissertations

Mercury (Hg), as a trace element cycling in the environment, poses a serious health threat to both humans and wildlife due to its toxicity. Atmospheric deposition is the main source of Hg to most remote environments. The Adirondack Park in New York State of the United States receives moderate Hg deposition, and is a region characterized by relatively high concentrations of Hg in the terrestrial and especially aquatic biota. It is important to understand the mechanisms that contribute to the sensitivity of this region to Hg inputs. In my research, studies of the spatial patterns of Hg in atmospheric deposition, …

Capillary And Microchip Electrophoresis For The Monitoring Of Disease Causing Amyloid Proteins, Elizabeth Nancy Pryor

Graduate Theses and Dissertations

The detection of oligomers and aggregates formed by two amyloid proteins, insulin and amyloid-beta (AB), is of particular importance due to the role which these species play in Diabetes and Alzheimer's disease, respectively. However, existing techniques are limited in the ability to detect insulin and AB; oligomers due to the fact that these early aggregates are transient, present at low concentrations, and difficult to isolate. Improvements must be made to existing techniques or alternative techniques must be explored in order to identify and quantify the size of these oligomeric and aggregate species without disrupting their structure.

Capillary and microchip electrophoresis …

The Contribution Of Oxidative Stress In The Protein Damage And Dna Lesion In Alzheimer's Disease Neuropathology, Cheng Zhang

Doctoral Dissertations

Glutathione (GSH) plays an essential role in the intracellular antioxidant defense against the oxidant radicals, especially the ·OH radical. To understand the early and progressive cellular changes in Alzheimer's disease (AD) development, we investigated reduced glutathione/oxidized glutathione (GSH/GSSG) status in a double mutated AD transgenic mouse model (B6.Cg-Tg), which carries Swedish amyloid precursor protein mutation (APPswe) and exon 9 deletion of the PSEN1 gene. Likewise, S-glutathionylation (Pr-SSG) is a specific post-translational modification (PTM) of cysteine residues by the addition of glutathione. S-glutathionylated proteins induced by oxidative stress play an essential role in understanding the pathogenesis of the aging …

Oxidative Effects Of Nanosecond Pulsed Electric Field Exposure In Cells And Cell-Free Media, Olga N. Pakhomova, Vera A. Khorokhorina, Angela M. Bowman, Raminta Rodaitė-Riševičienė, Gintautas Saulis, Shu Xiao, Andrei G. Pakhomov

Bioelectrics Publications

Nanosecond pulsed electric field (nsPEF) is a novel modality for permeabilization of membranous structures and intracellular delivery of xenobiotics. We hypothesized that oxidative effects of nsPEF could be a separate primary mechanism responsible for bioeffects. ROS production in cultured cells and media exposed to 300-ns PEF (1–13 kV/cm) was assessed by oxidation of 2′, 7′-dichlorodihydrofluoresein (H₂DCF), dihidroethidium (DHE), or Amplex Red. When a suspension of H₂DCF-loaded cells was subjected to nsPEF, the yield of fluorescent 2′,7′dichlorofluorescein (DCF) increased proportionally to the pulse number and cell density. DCF emission increased with time after exposure in nsPEF-sensitive Jurkat …

Microfluidic Separation Of Live And Dead Yeast Cells Using Reservoir-Based Dielectrophoresis, Saurin Patel, Daniel Showers, Pallavi Vedantam, Tzuen-Rong Tzeng, Shizhi Qian, Xiangchun Xuan

Mechanical & Aerospace Engineering Faculty Publications

Separating live and dead cells is critical to the diagnosis of early stage diseases and to the efficacy test of drug screening, etc. This work demonstrates a novel microfluidic approach to dielectrophoretic separation of yeast cells by viability. It exploits the cell dielectrophoresis that is induced by the inherent electric field gradient at the reservoir-microchannel junction to selectively trap dead yeast cells and continuously separate them from live ones right inside the reservoir. This approach is therefore termed reservoir-based dielectrophoresis (rDEP). It has unique advantages as compared to existing dielectrophoretic approaches such as the occupation of zero channel space and …

Structural Basis Of Substrate Recognition In Thimet Oligopeptidase And Development Of Nanoparticles For Therapeutic Enzyme Delivery, Jonathan Mark Wagner

Theses and Dissertations--Molecular and Cellular Biochemistry

Neuropeptidases are responsible for degradation of signaling peptides in the central nervous system and periphery. Some neuropeptidases have also been shown to play a role as part of the cell’s hydrolytic machinery responsible for breaking down proteins and peptides into amino acids, and these enzymes therefore influence small peptide availability for antigen presentation. A better understanding of how neuropeptidases recognize their substrates could lead to therapeutics that modulate the activity of these important enzymes. Alternatively, re-engineering these enzymes to selectively hydrolyze undesirable peptides could make them attractive as therapeutics themselves. A key question in understanding the activity of these enzymes …

Integrated Assessment Of Anthropogenic, Climate, And Policy Induced Changes Of Phosphorus Export In The United States Laurentian Great Lakes Watersheds, Meredith Ballard Labeau

Dissertations, Master's Theses and Master's Reports - Open

Anthropogenic activities have increased phosphorus (P) loading in tributaries to the Laurentian Great Lakes resulting in eutrophication in small bays to most notably, Lake Erie. Changes to surface water quality from P loading have resulted in billions of dollars in damage and threaten the health of the world’s largest freshwater resource. To understand the factors affecting P delivery with projected increasing urban lands and biofuels expansion, two spatially explicit models were coupled. The coupled models predict that the majority of the basin will experience a significant increase in urban area P sources while the agriculture intensity and forest sources of …

Bifunctional Bisphosphonates For Delivering Biomolecules To Bone, Jivan N. Yewle

Theses and Dissertations--Chemistry

Active targeting with controlled delivery of therapeutic agents to bone is an ideal approach for treatment of several bone diseases. Since bisphosphonates (BPs) are known to have high affinity to bone mineral and are being widely used in treatment of osteoporosis, they are well-suited for drug targeting to bone. For this purpose, bifunctional hydrazine-bisphosphonates (HBPs) with spacers of various lengths and lipophilicity were synthesized and studied. Crystal growth inhibition assays demonstrated that the HBPs with shorter spacers bound more strongly to bone mineral, hydroxyapatite (HA), than did alendronate. HBPs were also demonstrated to be non-toxic to MC3T3-E1 pre-osteoblasts. The targeted …

Signals From Intraventricular Depth Electrodes Can Control A Brain-Computer Interface, Jerry J. Shih, Dean J. Krusienski

Electrical & Computer Engineering Faculty Publications

A Brain-Computer Interface (BCI) is a device that enables severely disabled people to communicate and interact with their environments using their brain waves. Most research investigating BCI in humans have used scalp-recorded electroencephalography (EEG). We have recently demonstrated that signals from intracranial electrocorticography (ECoG) and stereotactic depth electrodes (SDE) in the hippocampus can be used to control a BCI P300 Speller paradigm. We report a case in which stereotactic depth electrodes positioned in the ventricle were able to obtain viable signals for a BCI. Our results demonstrate that event-related potentials from intraventricular electrodes can be used to reliably control the …

Mutant Alcohol Dehydrogenase Leads To Improved Ethanol Tolerance In Clostridium Thermocellum, Steven D. Brown, Adam M. Guss, Tatiana V. Karpinets, Jerry M. Parks

Dartmouth Scholarship

Clostridium thermocellum is a thermophilic, obligately anaerobic, Gram-positive bacterium that is a candidate microorganism for converting cellulosic biomass into ethanol through consolidated bioprocessing. Ethanol intolerance is an important metric in terms of process economics, and tolerance has often been described as a complex and likely multigenic trait for which complex gene interactions come into play. Here, we resequence the genome of an ethanol-tolerant mutant, show that the tolerant phenotype is primarily due to a mutated bifunctional acetaldehyde-CoA/alcohol dehydrogenase gene (adhE), hypothesize based on structural analysis that cofactor specificity may be affected, and confirm this hypothesis using enzyme assays. …

Forward Osmosis Bag: Ground Testing The Prospect Of Using Alternative Water Sources For Drinking Water, Michaela Marie Brant, Ariella Yendler, Mona Hammoudeh, Michael T. Flynn

STAR Program Research Presentations

On the STS-135 Space Shuttle mission, to be launched July 8, 2011, a forward osmosis bag (FOB) study will be conducted. At NASA Ames this summer, the ground truth testing is being conducted for results comparisons. The FOB technology is derived from a commercial product, the X-Pack water filter. Forward osmosis operates by utilizing an established concentration gradient across a semi-permeable membrane to move water molecules from one side of the membrane to the other. This concept is exploited to harvest drinking water from grey water sources such as urine, sea water, or vehicle water. In this experiment, potassium chloride …

The Occurrence Of False Positive Tests For Gunshot Residue Based On Simulations Of The Suspect's Occupation, Christopher R. Dockery, Matthew B. Rosenberg, Kimberly Kammerdiener, Lauren E. Mcadams

Faculty Articles

Samples collected from high-risk occupations, or simulations thereof, are analyzed for elemental composition using laser-induced breakdown spectroscopy (LlBS) to determine the occurrence of false positive gunshot residue results generated in the work environment. Previous work involving the study of lifetime of detectable amounts of gunshot residue on the hands of a suspect shooter found that gunshot residue exists up to 5.27 days after a firearm discharge. However, certain environmental and/or occupational false positive tests for gunshot residue could result when sampling non-shooters. Samples collected from occupations or simulations thereof include welding, pyrotechnics, key cutting, mechanics, and paper products all of …

Determining A Method For Rendering Low Cost Cdse(Zns) Core(Shell) Quantum Dots Aqueous Soluble Via Amphiphilic Polymer Wrapping, Patrick Mcbride

Materials Engineering

Herein is described the procedure of two amphiphilic polymer wrapping techniques that may be employed for obtaining aqueous soluble quantum dots (QDs) for use in biological fluorescent imaging applications. The advent of QDs has led to new nanoscale fluorescent materials that exhibit unparalleled quantum yields (QYs), high resistance to photobleaching, tunable emissions, and
absorption over a large optical range. However, the QD synthesis employed here at Cal Poly to obtain bright, photostable CdSe(ZnS) core(shell) QDs involves the use of organic solvents and surfactants, leading to hydrophobic QDs. Since all of biology relies on aqueous solubility, this hydrophobicity creates a major …

Oxidation Kinetics Of Silver Thin Films For Antimicrobial Applications In The Health Care Industry, Sean D. Morham

Materials Engineering

To determine if varying city water qualities from around the United States can support a developing “oxidation corrosion of silver thin films” method of creating aqueous ionic silver solutions for the anti-microbial treatment of healthcare linens, a test was devised holding all variables constant with the exception of water quality parameters. This corrosion style test was done in order to assess a pass/fail criteria of 25 ppb ionic silver concentration in the aqueous solutions which resulted from the corrosion of silver thin film coated substrates. Above 25 ppb being a pass, below 25 ppb being a fail. While varying the …

Evaluation Of Delivery Conditions For Cutaneous Plasmid Electrotransfer Using A Multielectrode Array, Bernadette Ferraro, Loree C. Heller, Yolmari L. Cruz, Siqi Guo, Amy Donate, Richard Heller

Bioelectrics Publications

Electroporation (EP) is a simple in vivo method to deliver normally impermeable molecules, such as plasmid DNA, to a variety of tissues. Delivery of plasmid DNA by EP to a large surface area is not practical because the distance between the electrode pairs, and therefore the applied voltage, must be increased to effectively permeabilize the cell membrane. The design of the multielectrode array (MEA) incorporates multiple electrode pairs at a fixed distance to allow for delivery of plasmid DNA to the skin, potentially reducing the sensation associated with in vivo EP. In this report, we evaluate the effects of field …

An Apoptosis Targeted Stimulus With Nanosecond Pulsed Electric Fields (Nspefs) In E4 Squamous Cell Carcinoma, Wei Ren, Stephen J. Beebe

Bioelectrics Publications

Stimuli directed towards activation of apoptosis mechanisms are an attractive approach to eliminate evasion of apoptosis, a ubiquitous cancer hallmark. In these in vitro studies, kinetics and electric field thresholds for several apoptosis characteristics are defined in E4 squamous carcinoma cells (SCC) exposed to ten 300 ns pulses with increasing electric fields. Cell death was [95% at the highest electric field and coincident with phosphatidylserine externalization, caspase and calpain activation in the presence and absence of cytochrome c release, decreases in Bid and mitochondria membrane potential (Δψm) without apparent changes reactive oxygen species levels or in Bcl2 and Bclxl levels. …

A Cell Electrofusion Microfluidic Device Integrated With 3d Thin-Film Microelectrode Arrays, Ning Hu, Jun Yang, Shizhi Qian, Sang W. Joo, Xiaolin Zheng

Mechanical & Aerospace Engineering Faculty Publications

A microfluidic device integrated with 3D thin film microelectrode arrays wrapped around serpentine-shaped microchannel walls has been designed, fabricated and tested for cell electrofusion. Each microelectrode array has 1015 discrete microelectrodes patterned on each side wall, and the adjacent microelectrodes are separated by coplanar dielectric channel wall. The device was tested to electrofuse K562 cells under a relatively low voltage. Under an AC electric field applied between the pair of the microelectrode arrays, cells are paired at the edge of each discrete microelectrode due to the induced positive dielectrophoresis. Subsequently, electric pulse signals are sequentially applied between the microelectrode arrays …

Computer Simulation Of A Hollow-Fiber Bioreactor: Heparan Regulated Growth Factors-Receptors Binding And Dissociation Analysis, Changjiang Zhang

University of Kentucky Doctoral Dissertations

This thesis demonstrates the use of numerical simulation in predicting the behavior of proteins in a flow environment.

A novel convection-diffusion-reaction computational model is first introduced to simulate fibroblast growth factor (FGF-2) binding to its receptor (FGFR) on cell surfaces and regulated by heparan sulfate proteoglycan (HSPG) under flow in a bioreactor. The model includes three parts: (1) the flow of medium using incompressible Navier-Stokes equations; (2) the mass transport of FGF-2 using convection-diffusion equations; and (3) the cell surface binding using chemical kinetics. The model consists of a set of coupled nonlinear partial differential equations (PDEs) for flow and …

Negative Dielectrophoretic Capture Of Bacterial Spores In Food Matrices, Mehti Koklu, Seungkyung Park, Suresh D. Pillai, Ali Beskok

Mechanical & Aerospace Engineering Faculty Publications

A microfluidic device with planar square electrodes is developed for capturing particles from high conductivity media using negative dielectrophoresis (n-DEP). Specifically, Bacillus subtilis and Clostridium sporogenes spores, and polystyrene particles are tested in NaCl solution (0.05 and 0.225 S/m), apple juice (0.225 S/m), and milk (0.525 S/m). Depending on the conductivity of the medium, the Joule heating produces electrothermal flow (ETF), which continuously circulates and transports the particles to the DEP capture sites. Combination of the ETF and n-DEP results in different particle capture efficiencies as a function of the conductivity. Utilizing 20 μm height DEP chambers, “almost complete” and …

Transesterification And Recovery Of Intracellular Lipids Using A Single Step Reactive Extraction, Daniel R. Nelson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

A single-step, extractive reaction for extraction of lipids such as biodiesel components, omega-3 fatty acids, or other triglycerides from microbial cells was examined. Conventional methods for lipid extraction use toxic solvents, and require multiple steps and long processing times. When the goal is to produce fatty acid methyl esters or FAMEs, the extracted lipids are subjected to a separate transesterification reaction with simple alcohols in the presence of an acid or base catalyst. A simplified, single-step reactive extraction method can be applied that combines the sequential extraction followed by transesterification using acidified alcohols - a process known as in situ …

Combining Molecular And Imaging Biomarkers To Enhance Maldi Biomarker Analysis, Ayyappa Chowdary Vadlamudi

Electrical & Computer Engineering Theses & Dissertations

This thesis presents a three-step method to predict prostate cancer (PCa) regions on biopsy tissue samples based on high confident, low resolution PCa regions marked by a pathologist. First, a prediction model is designed to predict PCa regions using matrix-assisted laser desorption mass spectrometry (MALDI-MS) tissue imaging data from one prostate tissue slice. Second, a texture analysis technique is applied to a high magnification optical image for the same purpose from an adjacent tissue slice. Finally, those two results are fused to obtain the PCa regions that will assist MALDI imaging biomarker analysis. Experiments show that the texture analysis based …

Electroporation-Mediated Delivery Of A Naked Dna Plasmid Expressing Vegf To The Porcine Heart Enhances Protein Expression, W. G. Marshall Jr., B. A. Boone, J. D. Burgos, S. I. Gografe, M. K. Baldwin, M. L. Danielson, M. J. Larson, D. R. Caretto, Y. Cruz, B. Ferraro, L. C. Heller, K. E. Ugen, M. J. Jaroszeski, R. Heller

Bioelectrics Publications

Gene therapy is an attractive method for the treatment of cardiovascular disease. However, using current strategies, induction of gene expression at therapeutic levels is often inefficient. In this study, we show a novel electroporation (EP) method to enhance the delivery of a plasmid expressing an angiogenic growth factor (vascular endothelial growth factor, VEGF), which is a molecule previously documented to stimulate revascularization in coronary artery disease. DNA expression plasmids were delivered in vivo to the porcine heart with or without coadministered EP to determine the potential effect of electrically mediated delivery. The results showed that plasmid delivery through EP significantly …

Dielectrophoretic Choking Phenomenon In A Converging-Diverging Microchannel, Ye Ai, Shizhi Qian, Sheng Liu, Sang W. Joo

Mechanical & Aerospace Engineering Faculty Publications

Experiments show that particles smaller than the throat size of converging-diverging microchannels can sometimes be trapped near the throat. This critical phenomenon is associated with the negative dc dielectrophoresis arising from nonuniform electric fields in the microchannels. A finite-element model, accounting for the particle-fluid-electric field interactions, is employed to investigate the conditions for this dielectrophoretic (DEP) choking in a converging-diverging microchannel for the first time. It is shown quantitatively that the DEP choking occurs for high nonuniformity of electric fields, high ratio of particle size to throat size, and high ratio of particle's zeta potential to that of microchannel. © …

Micro, Nano Encapsulation Methods For Sustained Release Drug Formulations And Biomimetic Applications, Shantanu Balkundi

Doctoral Dissertations

The Layer-by-Layer (LbL) assembly technique was used to obtain a new type of protein/polyphenol microcapsule based on naturally occurring polyphenol (-)-epigallocatechin gallate (EGCG) and gelatin, type A. The dependence of permeability on the molecular weight of permeating substances was studied and compared with commonly used polyallylamine/polystyrene sulfonate capsules. A quartz crystal microbalance was used to monitor the regularities of EGCG adsorption in alternation with type A and B Gelatins and electrophoretic mobility measurements were used that indicated that the nature of assembly was dependent on Gelatin properties. It was shown that EGCG retains its antioxidant activity in the LbL assemblies. …

Temperature Influence And Heat Management Requirements Of Microalgae Cultivation In Photobioreactors, Thomas Hagen Mehlitz

Master's Theses

Microalgae are considered one of the most promising feedstocks for biofuel production for the future. The most efficient way to produce vast amounts of algal biomass is the use of closed tubular photobioreactors (PBR). The heat requirement for a given system is a major concern since the best algae growth rates are obtained between 25-30 °C, depending on the specific strain. A procedure to determine temperature influence on algal growth rates was developed for a lab-scale PBR system using the species Chlorella. A maximum growth rate of 1.44 doublings per day at 29 °C (optimal temperature) was determined. In addition, …

Regulation Of Intracellular Calcium Concentration By Nanosecond Pulsed Electric Fields, Shaka S. Scarlett, Jody A. White, Peter F. Blackmore, Karl H. Schoenbach, Juergen Kolb

Bioelectrics Publications

Changes in [Ca²⁺]_i response of individual Jurkat cells to nanosecond pulsed electric fields (nsPEFs) of 60 ns and field strengths of 25, 50, and 100 kV/cm were investigated. The magnitude of the nsPEF-induced rise in [Ca²⁺]_i was dependent on the electric field strength. With 25 and 50 kV/cm, the [Ca²⁺]_i response was due to the release of Ca²⁺ from intracellular stores and occurred in less than 18 ms. With 100 kV/cm, the increase in [Ca²⁺]_i was due to both internal release and to influx across the plasma …

Pressure-Driven Transport Of Particles Through A Converging-Diverging Microchannel, Ye Ai, Sang W. Joo, Xiangchun Xuan, Shizhi Qian

Mechanical & Aerospace Engineering Faculty Publications

Pressure-driven transport of particles through a symmetric converging-diverging microchannel is studied by solving a coupled nonlinear system, which is composed of the Navier-Stokes and continuity equations using the arbitrary Lagrangian-Eulerian finite-element technique. The predicted particle translation is in good agreement with existing experimental observations. The effects of pressure gradient, particle size, channel geometry, and a particle's initial location on the particle transport are investigated. The pressure gradient has no effect on the ratio of the translational velocity of particles through a converging-diverging channel to that in the upstream straight channel. Particles are generally accelerated in the converging region and then …

Comparison Of Electrically Mediated And Liposome-Complexed Plasmid Dna Delivery To The Skin, Loree C. Heller, Mark J. Jaroszeski, Domenico Coppola, Richard Heller

Bioelectrics Publications

BACKGROUND: Electroporation is an established technique for enhancing plasmid delivery to many tissues in vivo, including the skin. We have previously demonstrated efficient delivery of plasmid DNA to the skin utilizing a custom-built four-plate electrode. The experiments described here further evaluate cutaneous plasmid delivery using in vivo electroporation. Plasmid expression levels are compared to those after liposome mediated delivery.

METHODS: Enhanced electrically-mediated delivery, and less extensively, liposome complexed delivery, of a plasmid encoding the reporter luciferase was tested in rodent skin. Expression kinetics and tissue damage were explored as well as testing in a second rodent model.

RESULTS: Experiments …