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Engineering Of Polyketide Biosynthetic Pathways For Bioactive Molecules, Siyuan Wang 2016 Utah State University

Engineering Of Polyketide Biosynthetic Pathways For Bioactive Molecules, Siyuan Wang

All Graduate Theses and Dissertations

Polyketides are a large group of structurally diverse natural products that have shown a variety of biological activities. These molecules are synthesized by polyketide synthases (PKSs). PKSs are classified into three types based on their sequence, primary structure, and catalytic mechanism. Because of the bioactivities of polyketide natural products, this study is focused on the engineering of PKS pathways for efficient production of useful bioactive molecules or structural modification to create new molecules for drug development.

One goal of this research is to create an efficient method to produce pharmaceutically important molecules. Seven biosynthetic genes from plants and bacteria were ...


Rational Design Of Rama-Labeled Nanoparticles For A Dual-Modaility, Light Scattering Immunoassay On A Polystyrene Seubstrate, Nathan D. Israelsen, Donald Wooley, Cynthia Hanson, Elizabeth Vargis 2016 Utah State University

Rational Design Of Rama-Labeled Nanoparticles For A Dual-Modaility, Light Scattering Immunoassay On A Polystyrene Seubstrate, Nathan D. Israelsen, Donald Wooley, Cynthia Hanson, Elizabeth Vargis

Biological Engineering Faculty Publications

Background: Surface-enhanced Raman scattering (SERS) is a powerful light scattering technique that can be used for sensitive immunoassay development and cell labeling. A major obstacle to using SERS is the complexity of fabricating SERS probes since they require nanoscale characterization and optical uniformity. The light scattering response of SERS probes may also be modulated by the substrate used for SERS analysis. A typical SERS substrate such as quartz can be expensive. Polystyrene is a cheaper substrate option but can decrease the SERS response due to interfering Raman emission peaks and high background fluorescence. The goal of this research is to ...


Microbubble Assisted Polyhydroxybutyrate Production In Escherichia Coli, Kadriye Innan, Fulya Ay Sal, Asif Rahman, Ryan J. Putman, Foster A. Agblevor, Charles D. Miller 2016 Utah State University

Microbubble Assisted Polyhydroxybutyrate Production In Escherichia Coli, Kadriye Innan, Fulya Ay Sal, Asif Rahman, Ryan J. Putman, Foster A. Agblevor, Charles D. Miller

Biological Engineering Faculty Publications

Background

One of the potential limitations of large scale aerobic Escherichia coli fermentation is the need for increased dissolved oxygen for culture growth and bioproduct generation. As culture density increases the poor solubility of oxygen in water becomes one of the limiting factors for cell growth and product formation. A potential solution is to use a microbubble dispersion (MBD) generating device to reduce the diameter and increase the surface area of sparged bubbles in the fermentor. In this study, a recombinantE. coli strain was used to produce polyhydroxybutyrate (PHB) under conventional and MBD aerobic fermentation conditions.

Results

In conventional ...


Automated Solid-Substrate Cultivation Of The Anaerobic Bacterium Clostridium Thermocellum, Mathew J. Ruwaya 2016 University of Kentucky

Automated Solid-Substrate Cultivation Of The Anaerobic Bacterium Clostridium Thermocellum, Mathew J. Ruwaya

Theses and Dissertations--Biosystems and Agricultural Engineering

The organism Clostridium thermocellum grows on cellulosic substrates and produces ethanol, acetate, lactate, formic acid, and CO2. The organic acids produced alter the growth environment in which the bacteria grows and ultimately inhibit bacterial growth. One method which has been used successfully to maintain the system at acceptable growth conditions is to intermittently flush out the spent media and metabolic products and replace with new fermentation media. Our goal was to design and build an automated system that will automatically flush the spent media from the growing culture and resupply new media without manual intervention. An automated control system ...


Optimization Of Micropillar Sequences For Fluid Flow Sculpting, Daniel Stoecklein, Chueh-Yu Wu, Donghyuk Kim, Dino Di Carlo, Baskar Ganapathysubramanian 2016 Iowa State University

Optimization Of Micropillar Sequences For Fluid Flow Sculpting, Daniel Stoecklein, Chueh-Yu Wu, Donghyuk Kim, Dino Di Carlo, Baskar Ganapathysubramanian

Mechanical Engineering Publications

Inertial fluid flow deformation around pillars in a microchannel is a new method for controlling fluid flow. Sequences of pillars have been shown to produce a rich phase space with a wide variety of flow transformations. Previous work has successfully demonstrated manual design of pillar sequences to achieve desired transformations of the flow cross section, with experimental validation. However, such a method is not ideal for seeking out complex sculpted shapes as the search space quickly becomes too large for efficient manual discovery.We explore fast, automated optimization methods to solve this problem. We formulate the inertial flow physics in ...


Energy Issues Affecting Corn/Soybean Systems: Challenges For Sustainable Production, Douglas L. Karlen, David Archer, Adam Liska, Seth Meyer 2015 USDA-ARS, Ames, Iowa

Energy Issues Affecting Corn/Soybean Systems: Challenges For Sustainable Production, Douglas L. Karlen, David Archer, Adam Liska, Seth Meyer

Douglas L Karlen

Quantifying energy issues associated with agricultural systems, even for a two-crop corn (Zea mays L.) and soybean (Glycine max [L.] Merr.) rotation, is not a simple task. It becomes even more complicated if the goal is to include all aspects of sustainability (i.e., economic, environmental, and social). This Issue Paper examines energy issues associated with and affecting corn/soybean rotations by first defining the size of the system from both a U.S. and global perspective and then establishing boundaries based on the Farm Bill definition of sustainability. This structured approach is essential to help quantify energy issues within ...


A Collagen Based Tissue Engineered Heart Valve Shows Excellent Functionality And Remodelling After Dynamic Conditioning, Claire Brougham, Ricardo Moreira, Tanya J. Levingstone, Stefan Jockenhoevel, Petra Mela, Fergal J. O'Brien 2015 Dublin Institute of Technology

A Collagen Based Tissue Engineered Heart Valve Shows Excellent Functionality And Remodelling After Dynamic Conditioning, Claire Brougham, Ricardo Moreira, Tanya J. Levingstone, Stefan Jockenhoevel, Petra Mela, Fergal J. O'Brien

Conference Papers

No abstract provided.


Theoretical Study Of The Pyrolysis Of Methyltrichlorosilane In The Gas Phase. 2. Reaction Paths And Transition States, Yingbin Ge, Mark S. Gordon, Francine Battaglia, Rodney O. Fox 2015 Iowa State University

Theoretical Study Of The Pyrolysis Of Methyltrichlorosilane In The Gas Phase. 2. Reaction Paths And Transition States, Yingbin Ge, Mark S. Gordon, Francine Battaglia, Rodney O. Fox

Mark S. Gordon

The kinetics for the previously proposed 114-reaction mechanism for the chemical vapor deposition (CVD) process that leads from methyltrichlorosilane (MTS) to silicon carbide (SiC) are examined. Among the 114 reactions, 41 are predicted to proceed with no intervening barrier. For the remaining 73 reactions, transition states and their corresponding barrier heights have been explored using second-order perturbation theory (MP2) with the aug-cc-pVDZ basis set. Final energies for the reaction barriers were obtained using both MP2 with the aug-cc-pVTZ basis set and coupled cluster theory (CCSD(T)) with the aug-cc-pVDZ basis set. CCSD(T)/aug-cc-pVTZ energies were estimated by assuming additivity ...


Theoretical Study Of The Pyrolysis Of Methyltrichlorosilane In The Gas Phase. 3. Reaction Rate Constant Calculations, Yingbin Ge, Mark S. Gordon, Francine Battaglia, Rodney O. Fox 2015 Central Washington University

Theoretical Study Of The Pyrolysis Of Methyltrichlorosilane In The Gas Phase. 3. Reaction Rate Constant Calculations, Yingbin Ge, Mark S. Gordon, Francine Battaglia, Rodney O. Fox

Mark S. Gordon

The rate constants for the gas-phase reactions in the silicon carbide chemical vapor deposition of methyltrichlorosilane (Ge, Y. B.; Gordon, M. S.; Battaglia, F.; Fox, R. O. J. Phys. Chem. A 2007, 111, 1462.) were calculated. Transition state theory was applied to the reactions with a well-defined transition state; canonical variational transition state theory was applied to the barrierless reactions by finding the generalized transition state with the maximum Gibbs free energy along the reaction path. Geometry optimizations were carried out with second-order perturbation theory (MP2) and the cc-pVDZ basis set. The partition functions were calculated within the harmonic oscillator ...


Evaluation Of Coarse-Grained Mapping Schemes For Polysaccharide Chains In Cellulose, Sergiy Markutsya, Ajitha Devarajan, John Ysrael Baluyut, Theresa Lynn Windus, Mark S. Gordon, Monica H. Lamm 2015 Iowa State University

Evaluation Of Coarse-Grained Mapping Schemes For Polysaccharide Chains In Cellulose, Sergiy Markutsya, Ajitha Devarajan, John Ysrael Baluyut, Theresa Lynn Windus, Mark S. Gordon, Monica H. Lamm

Mark S. Gordon

A fundamental understanding of the intermolecular forces that bind polysaccharide chains together in cellulose is crucial for designing efficient methods to overcome the recalcitrance of lignocellulosic biomass to hydrolysis. Because the characteristic time and length scales for the degradation of cellulose by enzymatic hydrolysis or chemical pretreatment span orders of magnitude, it is important to closely integrate the molecular models used at each scale so that, ultimately, one may switch seamlessly between quantum, atomistic, and coarse-grained descriptions of the system. As a step towards that goal, four multiscale coarse-grained models for polysaccharide chains in a cellulose-Iα microfiber are considered. Using ...


Theoretical Study Of The Pyrolysis Of Methyltrichlorosilane In The Gas Phase. 1. Thermodynamics, Yingbin Ge, Mark S. Gordon, Francine Battaglia, Rodney O. Fox 2015 Iowa State University

Theoretical Study Of The Pyrolysis Of Methyltrichlorosilane In The Gas Phase. 1. Thermodynamics, Yingbin Ge, Mark S. Gordon, Francine Battaglia, Rodney O. Fox

Mark S. Gordon

Structures and energies of the gas-phase species produced during and after the various unimolecular decomposition reactions of methyltrichlorosilane (MTS) with the presence of H2 carrier gas were determined using second-order perturbation theory (MP2). Single point energies were obtained using singles + doubles coupled cluster theory, augmented by perturbative triples, CCSD(T). Partition functions were obtained using the harmonic oscillator-rigid rotor approximation. A 114-reaction mechanism is proposed to account for the gas-phase chemistry of MTS decompositions. Reaction enthalpies, entropies, and Gibbs free energies for these reactions were obtained at 11 temperatures ranging from 0 to 2000 K including room temperature and typical ...


Storage Of Round And Square Switchgrass Bales: Effect Of Storage Time And Fungal Inoculation On Saccharification Efficiency, Noaa Frederick 2015 University of Arkansas, Fayetteville

Storage Of Round And Square Switchgrass Bales: Effect Of Storage Time And Fungal Inoculation On Saccharification Efficiency, Noaa Frederick

Theses and Dissertations

To produce fermentable sugars from lignocellulosic biomass feedstock, severe pretreatment conditions are needed (either high acid concentration, temperature, or retention times). High severities can produce toxic byproducts which inhibit enzymatic hydrolysis or fermentation. In order to reduce pretreatment severities (and thus increase enzyme and fermentation efficiency), the white-rot fungus Pleurotus ostreastus was seeded into square and round bales of Kanlow switchgrass (Panicum virgastum L.) and left in the field over a period of 9 month. The laccase producing fungus is believed to selectively degrade lignin, a common plant structural polymer, which can function as an enzymatic inhibitor. Samples were taken ...


Compounds Released From Biomass Deconstruction: Understanding Their Effect On Cellulose Enzyme Hydrolysis And Their Biological Activity, Angele Djioleu 2015 University of Arkansas, Fayetteville

Compounds Released From Biomass Deconstruction: Understanding Their Effect On Cellulose Enzyme Hydrolysis And Their Biological Activity, Angele Djioleu

Theses and Dissertations

The effect of compounds produced during biomass pretreatment on cellulolytic enzyme was investigated. Liquid prehydrolyzates were prepared by pretreating switchgrass using 24 combinations of temperature, time, and sulfuric acid concentration based on a full factorial design. Temperature was varied from 140°C to 180°C; time ranged from 10 to 40 min; and the sulfuric acid concentrations were 0.5% or 1% (v/v). Identified products in the prehydrolyzates included xylose, glucose, hydroxymethylfurfural (HMF), furfural, acetic acid, formic acid, and phenolic compounds at concentration ranging from 0 to 21.4 g/L. Pretreatment conditions significantly affected the concentrations of compounds ...


Removal Of Trace Organic Compounds In Domestic Wastewater Using Recirculating Packed-Bed Media Filters, Brittani Nikole Perez 2015 University of Tennessee - Knoxville

Removal Of Trace Organic Compounds In Domestic Wastewater Using Recirculating Packed-Bed Media Filters, Brittani Nikole Perez

Masters Theses

Pharmaceuticals and personal care products (PPCPs) are commonly detected in the environment resulting from their survival from conventional wastewater treatment systems. More information is needed about the fate and transfer of these trace organic compounds in domestic wastewater and their associated risks so that efficient strategies for their removal can be developed for both large/small scale treatment systems. This study aimed to determine whether onsite wastewater treatment systems were capable of providing PPCP removal, in addition to quantifying different forms of removal (biodegradation/sorption). A column study was constructed to determine the removal efficiencies of 3 target PPCPs, endocrine ...


Label-Free Surface-Enhanced Raman Spectroscopy-Linked Immunosensor Assay (Slisa) For Environmental Surveillance, vinay bhardwaj 2015 Florida International University

Label-Free Surface-Enhanced Raman Spectroscopy-Linked Immunosensor Assay (Slisa) For Environmental Surveillance, Vinay Bhardwaj

FIU Electronic Theses and Dissertations

The contamination of the environment, accidental or intentional, in particular with chemical toxins such as industrial chemicals and chemical warfare agents has increased public fear. There is a critical requirement for the continuous detection of toxins present at very low levels in the environment. Indeed, some ultra-sensitive analytical techniques already exist, for example chromatography and mass spectroscopy, which are approved by the US Environmental Protection Agency for the detection of toxins. However, these techniques are limited to the detection of known toxins. Cellular expression of genomic and proteomic biomarkers in response to toxins allows monitoring of known as well as ...


Three-Dimensional Confocal Microscopy Indentation Method For Hydrogel Elasticity Measurement, Donghee Lee, Md Mahmudur Rahman, You Zhou, Sangjin Ryu 2015 University of Nebraska-Lincoln

Three-Dimensional Confocal Microscopy Indentation Method For Hydrogel Elasticity Measurement, Donghee Lee, Md Mahmudur Rahman, You Zhou, Sangjin Ryu

Md Mahmudur Rahman

No abstract provided.


Harnessing Notch Signaling For Biomaterial Scaffold-Based Bone Regeneration, Helena P. Lysandrou, Chunhui Jiang, Naagarajan Narayanan, Shihuan Kuang, Meng Deng 2015 Purdue University

Harnessing Notch Signaling For Biomaterial Scaffold-Based Bone Regeneration, Helena P. Lysandrou, Chunhui Jiang, Naagarajan Narayanan, Shihuan Kuang, Meng Deng

The Summer Undergraduate Research Fellowship (SURF) Symposium

Bone fracture has recently become prevalent, especially with an increasingly aging population. Current bone grafts procedures, including autografts and allografts, are hindered by multiple factors, such as limited supplies and inconsistent bone healing. Scaffold-based bone tissue engineering emerges as a prospective strategy to aid in bone regeneration through delivery of growth factors such as bone morphogenic proteins (BMPs). However, the use of BMPs suffers from several drawbacks such as protein instability and immunogenicity. Therefore, there exists a great need for the development of novel therapies to promote bone healing. Notch signaling, a pathway critical for cell-fate determination has been shown ...


Bioengineered Cell Niche For Skeletal Muscle Regeneration, Nicole M. Whittern, Naagarajan Narayanan, Chunhui Jiang, Owen Jones, Jay Gilbert, Michael Whittern, Shihuan Kuang, Meng Deng 2015 Purdue University

Bioengineered Cell Niche For Skeletal Muscle Regeneration, Nicole M. Whittern, Naagarajan Narayanan, Chunhui Jiang, Owen Jones, Jay Gilbert, Michael Whittern, Shihuan Kuang, Meng Deng

The Summer Undergraduate Research Fellowship (SURF) Symposium

Skeletal muscles can self-repair minor strains, lacerations, and contusions; however, in cases of volumetric muscle lossand muscle degenerative diseases, tissue fails to regenerate. Current cell-based therapies, such as myoblast transplantation, have significant drawbacks of low survival rates and engraftment efficacy, mainly due to the absence of supportive cell microenvironment. Scaffolds that mimic the natural cell microenvironment provide a robust platform to support cell adhesion, migration, proliferation, and differentiation. Electrospinning is a versatile technology platform used for fabricating the fiber scaffold that mimics the extracellular matrix. Thus, we aim to reconstitute the cell microenvironment through development of aligned fiber scaffolds by ...


Proteoglycan Mimic Of The Glycocalyx To Treat Endothelial Dysfunction, Victoria Messerschmidt, Alyssa Panitch, James R. Wodicka 2015 Purdue University

Proteoglycan Mimic Of The Glycocalyx To Treat Endothelial Dysfunction, Victoria Messerschmidt, Alyssa Panitch, James R. Wodicka

The Summer Undergraduate Research Fellowship (SURF) Symposium

Patients with kidney failure usually undergo hemodialysis, a process by which toxins produced by the body are filtered from the blood, in order to survive. The preferred form for vascular access is called an arteriovenousfistula (AVF), a surgically created connection between an artery and vein that is utilized to undergo dialysis. However, AVFs have a failure rate of 50-60%. One of the contributions to AVF failure is endothelial cell dysfunction and loss of glycocalyx, which allows neutrophils and other native cells into the media of the vessel, which causes an inflammatory response. Our lab addresses endothelial dysfunction by mimicking the ...


A Novel Synthetic Yeast For Enzymatic Biodigester Pretreatment, Tianyu Tan, Mark S. Aronson, Arren Liu, Jill H. Osterhus, Melissa Robins, Suraj Mohan, Erich Leazer, Bowman Clark, Alexa Petrucciani, Katherine Lowery, James Welch, Casey Martin, Helena Lysandrou, Michael E. Scharf, Jenna Rickus 2015 Purdue University

A Novel Synthetic Yeast For Enzymatic Biodigester Pretreatment, Tianyu Tan, Mark S. Aronson, Arren Liu, Jill H. Osterhus, Melissa Robins, Suraj Mohan, Erich Leazer, Bowman Clark, Alexa Petrucciani, Katherine Lowery, James Welch, Casey Martin, Helena Lysandrou, Michael E. Scharf, Jenna Rickus

The Summer Undergraduate Research Fellowship (SURF) Symposium

Lignin, a complex organic polymer, is a major roadblock to the efficiency of biofuel conversion as it both physically blocks carbohydrate substrates and poisons biomass degrading enzymes, even if broken down to monomer units. A pretreatment process is often applied to separate the lignin from biomass prior to biofuel conversion. However, contemporary methods of pretreatment require large amounts of energy, which may be economically uncompelling or unfeasible. Taking inspiration from several genes that have been isolated from termites and fungi which translate to enzymes that degrade lignin, we want to establish a novel “enzymatic pretreatment” system where microbes secrete these ...


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