Biochemical and Biomolecular Engineering Commons^™

Peptoid Based Slide Coatings For Disease Detection Via Elisa Microarray Analysis, Melissa Lea Hebert

Graduate Theses and Dissertations

Poly-N-substituted glycines (peptoids) are a very versatile family of synthetic molecules that can be customized for any number of applications. In this study, we chose to use peptoids as a foundation for sandwich ELISA microarray analysis with a long term goal of creating an early detection device for complex diseases such as cancer. The peptoids were designed to self-assemble into microspheres to be used in coatings on the surface of the microarray substrates to increase the surface area available for antibody attachment. This increased antibody density would lead to an increase in the microarray analysis sensitivity and dynamic range. Studies …

Systems And Devices For Isothermal Biochemical Reactions And / Or Analysis, Robert W. Doebler Ii, Christopher Cooney, Anna Hickerson, James D. Sterling, Ali Nadim

Business and Information Technology Faculty Research & Creative Works

An isothermal reaction and analysis system may include a receiver to receive sample holders, a thermal control sub system to control a temperature of the receiver, an excitation Subsystem, a detection Subsystem and an analysis Subsystem. Excitation Sources and/or detectors are positioned to enhance data collection. Sample holders may include filters, selectively blocking and passing wavelengths or bands of electromagnetic radiation.

Temperature Control Device With A Flexible Temperature Control Surface, Phil D. Belgrader, Christopher G. Cooney, Robert D. Doebler, Anna D. Hickerson, Bruce D. Irvine, Ali D. Nadim, James D. Sterling, Reza Miraghale

Business and Information Technology Faculty Research & Creative Works

A device for controlling temperature in a reaction chamber is disclosed. The device comprises: a bladder assembly comprising a housing dimensioned to hold a reaction chamber disposed within an interior Volume of the housing; and a first temperature-control bladder disposed within the housing, the first temperature-control bladder is configured to receive a temperature-control fluid and comprises a flexible, heat conductive Surface that comes in contact with at least a portion of an exterior surface of the reaction chamber after receiving the temperature-control fluid. Also disclosed are a bladder thermal cycler, a temperature-control bladder assembly and methods for producing a thermal …

The Yin And Yang Actions Of North American Ginseng Root In Modulating The Immune Function Of Macrophages, Chike Godwin Azike, Paul Abrahams Charpentier, Jirui Hou, Hua Pei, Edmund Man King Lui

Physiology and Pharmacology Publications

BACKGROUND: Immuno-modulatory effects of ginseng, including both immuno-stimulatory and immuno-suppressive effects, have been widely reported. This study aims to determine whether the paradoxical immuno-modulatory effect is related to unique phytochemical profiles of different North American (NA) ginseng, namely aqueous (AQ) and alcoholic (ALC) extracts.

METHODS: AQ and ALC extracts were prepared and their immuno-bioactivity were studied in vitro in murine macrophages (Raw 264.7) through measuring the direct stimulatory production of pro-inflammatory mediator and cytokines as well as the suppression of lipopolysaccharide (LPS)-stimulatory response by the two extracts. Gel permeation chromatography was used to fractionate and isolate phytochemicals for characterization of …

Synthesis And Analytical Evaluation Of Folate Conjugates For Use In Cancer Cell Detection, Sneha Reddy Kuthuru

All Capstone Projects

Recent clinical studies have shown the importance of folate receptor in drug delivery system as they increase the potency and reduce toxicity of many cancer therapies. The folate receptor alpha ( FR-a) binds with high affinity for folic acid and serves for receptor mediated transport of folate into cells. Folate is necessary for DNA metabolism and thus it is speculated that rapidly dividing cancer cells have an increased requirement for folic acid. It is known that FR-a levels are elevated in specific malignant diseases (solid tumors, leukemia) and thus the FR receptor serves as useful targeting moiety for the diagnosis …

Synthesis Of An Endothelial Cell Mimicking Surface Containing Thrombomodulin And Endothelial Protein C Receptor, Karl E. Kador

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Synthetic materials for use in blood contacting applications have been studied for many years with limited success. One of the main areas of need for these materials is the design of synthetic vascular grafts for use in the hundreds of thousands of patients who have coronary artery bypass grafting, many without suitable veins for autologous grafts. The design of these grafts is constrained by two common modes of failure, the formation of intimal hyperplasia (IH) and thrombosis. IH formation has been previously linked to a mismatching of the mechanical properties of the graft and has been overcome by creating grafts …

Continuous-Flow, Rapid Lysis Devices For Biodefense Nucleic Acid Diagnostic Systems, Robert W. Doebler, Barbara Erwin, Anna Hickerson, Bruce Irvine, Denice Woyski, Ali Nadim, James D. Sterling

Business and Information Technology Faculty Research & Creative Works

Two mechanical lysis devices have been developed as compact, robust components to provide rapid sample preparation for nucleic acid diagnostic systems. One such component, known as the Micro Bead-Beater™ (μBB™, BBTM, Claremont BioSolutions, Upland, CA), is a compact device that is capable of ultrarapid lysis (>90% lysis in 30 s) of micro volumes (< 80 μL) of Bacillus spores in a continuous-flow format or in a disposable single-tube format. The μBB is also capable of processing much larger volumes of solutions containing spores or vegetative cells using a continuous-flow mode. A second mechanical lysis device designed as a disposable component is the microfluidic bead blender, which uses a small electric motor to spin vanes within the bead-laden solution. DNA quantification results using dsDNA-binding fluorescence dyes and real-time PCR are presented, comparing the lysis of Bacillus subtilis spores using the μBB™ with other well-known lysis techniques. Nanoscale imaging results obtained using scanning electron microscopy and transmission electron microscopy on B. subtilis spores lyzed using the μBB™ are also presented. © 2009, Society for Laboratory Automation and Screening. All rights reserved.

Organizational Agility, James D. Sterling

Business and Information Technology Faculty Research & Creative Works

No abstract provided.

Ala Spotlight Series V.2, James D. Sterling

Business and Information Technology Faculty Research & Creative Works

No abstract provided.

Labevolution: What's The Next Mutation?, James D. Sterling

Business and Information Technology Faculty Research & Creative Works

No abstract provided.

Building Benchmarks, James D. Sterling

Business and Information Technology Faculty Research & Creative Works

No abstract provided.

Off And Running, James D. Sterling

Business and Information Technology Faculty Research & Creative Works

No abstract provided.

Moment Analysis Of Near-Equilibrium Binding Interactions During Electrophoresis, Yousef Daneshbod, James D. Sterling, Ali Nadim

Business and Information Technology Faculty Research & Creative Works

The electrophoretic transport of three chemically reacting species, two of which can bind reversibly to form the third, is analyzed mathematically. The species are assumed to move horizontally through a long channel with different electrophoretic mobilities and diffusion coefficients. By considering small perturbations of the system about equilibrium or when one of the two binding species is much more abundant than the other, the governing advection-reaction- diffusion equations can be linearized and studied via the method of moments. The result is a set of coupled ordinary differential equations for the moments that can be solved analytically. Analysis of the long-time …

Electrowetting Droplet Microfluidics On A Single Planar Surface, Christopher G. Cooney, Chao Yi Chen, Michael R. Emerling, Ali Nadim, James D. Sterling

Business and Information Technology Faculty Research & Creative Works

Electrowetting refers to an electrostatically induced reduction in the contact angle of an electrically conductive liquid droplet on a surface. Most designs ground the droplet by either sandwiching the droplet with a grounding plate on top or by inserting a wire into the droplet. Washizu and others have developed systems capable of generating droplet motion without a top plate while allowing the droplet potential to float. In contrast to these designs, we demonstrate an electrowetting system in which the droplet can be electrically grounded from below using thin conductive lines on top of the dielectric layer. This alternative method of …

Desulfovibrio Desulfuricans G20 Tetraheme Cytochrome Structure At 1.5 A˚ And Cytochrome Interaction With Metal Complexes, Mrunalini Pattarkine, J J. Tanner, C A. Bottoms, Y H. Lee, Judy D. Wall

Faculty Works

The structure of the type I tetraheme cytochrome c3 from Desulfovibrio desulfuricans G20 was determined to 1.5 A˚ by X-ray crystallography. In addition to the oxidized form, the structure of the molybdate-bound form of the protein was determined from oxidized crystals soaked in sodium molybdate. Only small structural shifts were obtained with metal binding, consistent with the remarkable structural stability of this protein. In vitro experiments with pure cytochrome showed that molybdate could oxidize the reduced cytochrome, although not as rapidly as U(VI) present as uranyl acetate. Alterations in the overall conformation and thermostability of the metal-oxidized protein were investigated …

Modeling Of Immunoglobulin Uptake By N,N,N′,N′-Ethylenediaminetetramethylenephosphonic Acid-Modified Zirconia Particles Under Static And Dynamic Conditions, Sabyasachi Sarkar, Anuradha Subramanian

Papers in Biotechnology

A matrix developed from N,N,N′,N′-ethylenediaminetetramethylenephosphonic acid-modified zirconia beads (further referred to as r_PEZ); 25–38 μm in diameter and with a pore size of 22 ± 3 nm, was utilized for the separation of immunoglobulins (Igs). r_PEZ has been shown to bind to various Igs originating from a wide variety of species. To understand the mechanisms controlling the uptake of Igs by r_PEZ, static protein uptake experiments were carried out. The protein uptake profiles were further modeled with a kinetic rate constant model. Individual studies were undertaken for human immunoglobulin A, G and M (HIgA, HIgG and HIgM). The kinetic rate …

Laboratory Automation Curriculum At Keck Graduate Institute, James D. Sterling

Business and Information Technology Faculty Research & Creative Works

A novel curriculum in laboratory automation and high-throughput technologies has been developed at the Keck Graduate Institute (KGI) over the past five years as part of the professional master's degree program in applied life sciences. The goal of this curriculum has been four-fold: (1) motivate study by describing the need for automation through several example problems in combinatorial biological discovery, (2) provide elements of fundamental engineering science that are required for the development of the technologies and tools that enable automation, (3) provide opportunities for the students to see and use state-of-the-art instruments, learn about existing industry standards, and to …

Laboratory Automation Education, James D. Sterling

Business and Information Technology Faculty Research & Creative Works

No abstract provided.

Resolution Of Multiple Ssdna Structures In Free Solution Electrophoresis, Eve F. Fabrizio, Ali Nadim, James D. Sterling

Business and Information Technology Faculty Research & Creative Works

By using high concentrations of buffer, electroosmotic flow within uncoated channels of a microfluidic chip was minimized, allowing the free solution electrophoretic separation of DNA. More importantly, because of the ability to efficiently dissipate heat within these channels, field strengths as high as 600 V/cm could be applied with minimal Joule heating (< 2 °C). As a result of the higher field strengths, separations within an 8-cm-long channel were achieved within a few minutes. However, when the electrophoretic separation of single-stranded DNA (ssDNA) less than 22 bases in length was performed, containing the fluorophore Texas Red as an end label, more than the expected single peak was observed at this high electric field. On the other hand, the free solution electrophoresis of a double-stranded DNA (dsDNA) consisting of a random sequence did exhibit the expected single peak. The appearance of these multiple peaks for ssDNA is shown to be dependent upon the base content and sequence of the ssDNA as well as on the chemical structure of the fluorophore used to tag the DNA for detection. Specifically, the peaks can be attributed to different secondary structures that result either from hydrophobic interactions between the DNA bases and an uncharged fluorescent dye or from G-quadruplexes within guanine-rich strands.

Sequence Dependent Mobility Of Short Oligonucleotides In Free-Solution Electrophoresis, James D. Sterling, Eve F. Fabrizio, Ali Nadim

Business and Information Technology Faculty Research & Creative Works

No abstract provided.

Method, Apparatus And Article For Microfluidic Control Via Electrowetting, For Chemical, Biochemical And Biological Assays And The Like, James D. Sterling

Business and Information Technology Faculty Research & Creative Works

An active-matrix microfluidic platform employs thin film transistor active ("TFT") matrix liquid crystal display ~ technology to manipulate small samples of fluid for chemical, biochemical, or biological assays without moving parts, for example, using a two-dimensional matrix array of drive electrodes. The active-matrix microfluidic platform may employ existing active matrix 0 addressing schemes and/or commercial "off-the-shelf" animation software to program assay protocols. A feedback subsystem may > determine an actual location of a fluid in the microfluidic structure, and provides location information to for display, for example, on an active-matrix display, and/or to control movement of one or more fluid bodies …

Studies On The Formation Of Dna-Cationic Lipid Composite Films And Dna Hybridization In The Composites, Murali Sastry, Vidya Ramakrishnan, Mrunalini Pattarkine, Krishna N. Ganesh

Faculty Works

The formation of composite films of double-stranded DNA and cationic lipid molecules (octadecylamine, ODA) and the hybridization of complementary single-stranded DNA molecules in such composite films are demonstrated. The immobilization of DNA is accomplished by simple immersion of a thermally evaporated ODA film in the DNA solution at close to physiological pH. The entrapment of the DNA molecules in the cationic lipid film is dominated by attractive electrostatic interaction between the negatively charged phosphate backbone of the DNA molecules and the protonated amine molecules in the thermally evaporated film and has been quantified using quartz crystal microgravimetry (QCM). Fluorescence studies …

Cationic Surfactant Mediated Hybridization And Hydrophobization Of Dna Molecules At The Liquid/Liquid Interface And Their Phase Transfer, Murali Sastry, Ashavani Kumar, Mrunalini Pattarkine, Vidya Ramakrishnan, Krishna N. Ganesh

Faculty Works

Hybridization of complementary oligonucleotides mediated by a cationic surfactant at the water/hexane interface leads to hydrophobic, double-helical DNA which may be readily phase transferred to the organic phase and cast into thin films on solid substrates.

Hybridization Of Dna By Sequential Immobilization Of Oligonucleotides At The Air-Water Interface, Murali Sastry, Vidya Ramakrishnan, Mrunalini Pattarkine, Anand Gole, K. N. Ganesh

Faculty Works

The hybridization of DNA by sequential electrostatic and hydrogen-bonding immobilization of single-stranded complementary oligonucleotides at the air-water interface with cationic Langmuir monolayers is demonstrated. The complexation of the single-stranded DNA molecules with octadecylamine (ODA) Langmuir monolayers was followed in time by monitoring the pressure-area isotherms. A large (and slow) expansion of the ODA monolayer was observed during each stage of complexation in the following sequence: primary single-stranded DNA followed by complementary single-stranded DNA followed by the intercalator, ethidium bromide. Langmuir-Blodgett (LB) films of the ODA-DNA complex were formed on different substrates and characterized using quartz-crystal microgravimetry (QCM), Fourier transform infrared …

Anion Induced Blue To Purple Transition In Bacteriorhodopsin, Mrunalini Pattarkine, Anil K. Singh

Faculty Works

Purple membrane (PM, λ" role="presentation">λmax" role="presentation">max 570 nm) of H. halobium on treatment with sulphuric acid changes its colour to blue (λ" role="presentation">λmax" role="presentation">max 608 nm). The purple chromophore can be regenerated from the blue chromophore by exogeneous addition of anions such as CI−" role="presentation">− and HPO42−" role="presentation">2−4. Chloride ion is found to be more effective than the dibasic phosphate ion in regenerating the purple chromophore. Nevertheless, one thing common to the anion regeneration is that both CI−" role="presentation">− and HPO42−" role="presentation">2−4 show marked pH effect. At pH 1.0 the efficiency of …

A Lattice Boltzmann Subgrid Model For High Reynolds Number Flows, S. Hou, James D. Sterling, S. Chen, G. D. Doolen

Business and Information Technology Faculty Research & Creative Works

A sub grid turbulence model for the lattice Boltzmann method is proposed for high Reynolds number fluid flow applications. The method, based on the standard Smagorinsky sub grid model and a single-time relaxation lattice Boltzmann method, incorporates the advantages of the lattice Boltzmann method for handling arbitrary boundaries and is easily implemented on parallel machines. The method is applied to a two-dimensional driven cavity flow for studying dynamics and the Reynolds number dependence of the flow structures. The substitution of other sub grid models, such as the dynamic sub grid model, in the framework of the LB method is discussed.

Gas Dynamic Unstart In Superdetonative Ram Accelerators, Kaveh Ghorbanian, James D. Sterling

Business and Information Technology Faculty Research & Creative Works

In this paper we analyze the reflection of non-reacting shock waves as oblique detonation waves. The 2D, steady, inviscid analysis makes use of detonation polar diagrams to identify incident shock angles that lead to reflected detonations, with and without detonation Mach stem formation. The implications of the results for design and operation of superdetonative ram accelerators are explored. The influence of the projectile forebody geometry, the propellant composition, and the takeover velocity is described. We conclude with a discussion of the significance of these parameters on superdetonative ram accelerator unstart phenomena.

Enhanced Combustion Pulsejet Engines For Mach 0 To 3 Applications, J. Sterling, K. Ghorbanian, T. Sobota

Business and Information Technology Faculty Research & Creative Works

In this paper, we discuss the cyclic operation of an enhanced combustion pulsejet engine (ECPE) applicable in the Mach number range of 0 to 3. The geometry of this engine naturally provides for integration into a new combined cycle engine with ramjets. As in the operation of conventional pulsejets, an ECPE provides engine aspiration, charge compression, combustion and expansion without the use of turbomachinery. The use of modern electronics, fuel injection, and feedback control offers the potential for performance improvements that could make the ECPE a cost-effective competitor for the turbojet engine. This article describes the operating cycle of a …

Influence Of Formation Processes On Oblique Detonation Wave Stabilization, K. Ghorbanian, J. D. Sterling

Business and Information Technology Faculty Research & Creative Works

In this article we report steady, two-dimensional, inviscid solutions for the near field and far field of a supersonic reactive flow over a variable-double-ramp geometry. The incident shock wave compresses and heats the reactants that will combust after flowing some induction length. Upon reaction, a detonation wave forms and intersects the leading wave at some distance from the ramp surface. In this article, reaction-polar diagrams are developed, and the detonation branch solutions are used to investigate the wave interaction processes that may lead to a steady three-wave structure. By considering this formation process new oblique detonation wave stabilization criteria based …

Lattice Boltzmann Thermohydrodynamics, F. J. Alexander, S. Chen, J. D. Sterling

Business and Information Technology Faculty Research & Creative Works

We introduce a lattice Boltzmann computational scheme capable of modeling thermohydrodynamic flows of monatomic gases. The parallel nature of this approach provides a numerically efficient alternative to traditional methods of computational fluid dynamics. The scheme uses a small number of discrete velocity states and a linear, single-time relaxation collision operator. Numerical simulations in two dimensions agree well with exact solutions for adiabatic sound propagation and Couette flow with heat transfer. © 1993 The American Physical Society.