Biological Engineering Commons^™

Exploring The Capacity Of Bacteria For Natural Product Biosynthesis, Ozkan Fidan

All Graduate Theses and Dissertations

This dissertation is focused on exploring the potential of bacteria for the biosynthesis of natural products with the purposes of generating novel natural product derivatives and of improving the titer of pharmaceutically important natural products.

A wide variety of compounds from various sources have been historically used in the treatment and prevention of diseases. Natural products as a major source of new drugs are extensively explored due to their huge structural diversity and promising biological activities such as antimicrobial, anticancer, antifungal, antiviral and antioxidant properties. For instance, penicillin as an early-discovered antimicrobial agent has saved millions of lives, indicating the ...

Immunofluorescence Image Feature Analysis And Clustering Pipeline For Distinguishing Epithelial-Mesenchymal Transition, Shreyas Hirway, Nadiah Hassan, Dr. Christopher Lemmon, Dr. Seth Weinberg

Biology and Medicine Through Mathematics Conference

No abstract provided.

Quantified Measurement Of The Tilt Effect In A Family Of Café Wall Illusions, Nasim Nematzadeh Dr., David Martin Powers Prof.

MODVIS Workshop

This abstract explores the tilt effect in a family of Café Wall illusions using a Classical Gaussian Receptive Field model (CRF). Our model constructs an intermediate representation called edge map at multiple scales (Fig. 1) that reveals tilt cues and clues involved in the illusory perception of the Café Wall pattern. We investigate a wide range of parameters of the stimulus including mortar width, luminance, tiles contrast, and phase of the tile displacement (the stimuli in Fig. 2). We show that this simple bioplausible model, simulating the contrast sensitivity of the retinal ganglion cells, can not only detect the tilts ...

Phylogenetic And Experimental Characterization Of An Acyl-Acp Thioesterase Family Reveals Significant Diversity In Enzymatic Specificity And Activity, Fuyuan Jing, David C. Cantu, Jarmila Tvaruzkova, Jay P. Chipman, Basil J. Nikolau, Marna D. Yandeau-Nelson, Peter J. Reilly

Marna Yandeau-Nelson

Background: Acyl-acyl carrier protein thioesterases (acyl-ACP TEs) catalyze the hydrolysis of the thioester bond that links the acyl chain to the sulfhydryl group of the phosphopantetheine prosthetic group of ACP. This reaction terminates acyl chain elongation of fatty acid biosynthesis, and in plant seeds it is the biochemical determinant of the fatty acid compositions of storage lipids.

Results: To explore acyl-ACP TE diversity and to identify novel acyl ACP-TEs, 31 acyl-ACP TEs from wide-ranging phylogenetic sources were characterized to ascertain their in vivo activities and substrate specificities. These acylACP TEs were chosen by two different approaches: 1) 24 TEs were ...

Stability Analysis Of A More General Class Of Systems With Delay-Dependent Coefficients, Chi Jin, Keqin Gu, Islam Boussaada, Silviu-Iulian Niculescu

SIUE Faculty Research, Scholarship, and Creative Activity

This paper presents a systematic method to analyse the stability of systems with single delay in which the coefficient polynomials of the characteristic equation depend on the delay. Such systems often arise in, for example, life science and engineering systems. A method to analyze such systems was presented by Beretta and Kuang in a 2002 paper, but with some very restrictive assumptions. This work extends their results to the general case with the exception of some degenerate cases. It is found that a much richer behavior is possible when the restrictive assumptions are removed. The interval of interest for the ...

Hydrodeoxygenation Of Pinyon-Juniper Catalytic Pyrolysis Oil, Hossein Jahromi

All Graduate Theses and Dissertations

Catalytic hydrodeoxygenation (HDO), is an effective process to convert oxygenated compounds to hydrocarbons. This process is widely used for improving the negative properties of biomass-derived pyrolysis oils (bio-oils) such as high acidity, poor stability, and low heating value. During this process oxygen is removed from the bio-oil in the form of water, thus the liquid product of HDO process consists of aqueous phase and hydrocarbon phase that can be easily separated. Synthesis of efficient HDO catalyst has been a major challenge in the field of bio-oil upgrading. Red mud, which is an alkaline waste from alumina industry was used to ...

Ecological Co2 Flux Of A Green Roof Ecosystem And A Typical Grassland Ecosystem, Madeline Oxner

Biological and Agricultural Engineering Undergraduate Honors Theses

The Hillside Auditorium Green Roof is a low impact development feature on the University of Arkansas campus. It retains storm water and allows plants living on the roof to take up and transpire the water. Green roofs work to mimic natural ecosystems in urban environments. A key property is ecosystem respiration, which plays a large role in the global carbon cycle and is an important biologic activity indicator. The ecosystem respiration of Hillside Auditorium Green Roof was compared to a typical grassland ecosystem at the University of Arkansas farm to determine how closely the green roof is able to mimic ...

Muscle Atrophy Marker Expression Differs Between Rotary Cell Culture System And Animal Studies, Charles P. Harding, Elizabeth Vargis

Biological Engineering Faculty Publications

Muscular atrophy, defined as the loss of muscle tissue, is a serious issue for immobilized patients on Earth and for humans during spaceflight, where microgravity prevents normal muscle loading. In vitro modeling is an important step in understanding atrophy mechanisms and testing countermeasures before animal trials. The most ideal environment for modeling must be empirically determined to best mimic known responses in vivo. To simulate microgravity conditions, murine C2C12 myoblasts were cultured in a rotary cell culture system (RCCS). Alginate encapsulation was compared against polystyrene microcarrier beads as a substrate for culturing these adherent muscle cells. Changes after culture under ...

Identifying Genetic Regulators Of Cancer Stem Cell Differentiation For Glioblastoma Therapy, Ann Chen, Yang Xiao, Rong Fan, Jiangbing Zhou

Yale Day of Data

Glioblastoma multiforme (GBM) is the most common and aggressive type of primary brain cancer. Even with treatment, GBM patients have a median survival rate of less than 15 months and a five-year survival rate of 2%. Poor therapeutic outcomes may be attributed to the presence of a subpopulation of cells within tumors, known as cancer stem cells (CSCs), which are resistant to conventional radiotherapy and chemotherapy. CSCs are capable of tumor initiation, sustained self-renewal, and differentiation into terminal cell types. These terminally differentiated cells make up the bulk of the tumor and are sensitive to GBM therapies. Therefore, CSC-directed therapies ...

Investigating The Feasibility Of Using Mesoporous Silica Particles To Deliver Glucose During Anaerobic Fermentation, Megan E. Walz

Theses and Dissertations--Biosystems and Agricultural Engineering

The study presented herein investigated a potential low-energy method to separate and concentrate glucose from a lignocellulosic hydrolysate. The motivation for this method was twofold: 1) to provide the fermentation microorganism an optimal glucose concentration and 2) to supply a fermentation media free of inhibitory compounds. Two sizes of porous silica particles (with 7 nm and 2.3 nm pores) were synthesized and their ability to adsorb glucose from solution confirmed. Next, the ability of two different microorganisms, Saccharomyces cerevisiae and Streptococcus bovis, to utilize sugars adsorbed to the porous silica particles was investigated.

Both the 7 nm and 2 ...

Manipulation Of The Precursor Supply For High-Level Production Of Longifolene By Metabolically Engineered Escherichia Coli, Yujin Cao, Rubing Zhang, Wei Liu, Guang Zhao, Wei Niu, Jiantao Guo, Mo Xian, Huizhou Liu

Chemical and Biomolecular Engineering -- All Faculty Papers

Longifolene is a naturally occurring tricyclic sesquiterpene widely used in many different fields. Up to now, this valuable terpene was mainly manufactured from the high-boiling fraction of certain pine resins. Microbial production can be a promising alternative to the extraction from natural plant sources. Here, we present the metabolic engineering strategy to assemble biosynthetic pathway for longifolene production in Escherichia coli. E. coli was rendered to produce longifolene by heterologously expressing a codon optimized longifolene synthase from Picea abies. Augmentation of the metabolic flux to farnesyl pyrophosphate (FPP) by different FPP synthases conferred a 1.8-fold increase in longifolene production ...

Assessing Biofiltration Without Ozonation For Removal Of Trihalomethane Precursors In Drinking Water At The Beaver Water District Drinking Water Treatment Plant, Sana Ajaz

Theses and Dissertations

Biofiltration without pre-ozonation has the capability to remove natural organic matter (NOM) fractions that serve as precursors of disinfection byproducts (DBPs), which include the four regulated trihalomethanes (THMs) and dichloroacetonitrile (DCAN). Rapid small-scale column tests (RSSCTs) and Pilot Plant filters operated at empty-bed contact times (EBCTs) of 4, 8, and 16 minutes were used to evaluate the performance of nutrient-amended (free ammonia and phosphorus) biofiltration for THM and DCAN precursor removal, as measured using formation potential (FP) tests. NOM surrogates – which include dissolved organic carbon (DOC), specific ultraviolet absorbance (SUVA254) and fluorescence-PARAFAC components – were measured weekly throughout the 30-week study ...

Identification And Engineering Of Nonribosomal Peptide Biosynthetic Systems, Fuchao Xu

All Graduate Theses and Dissertations

This research focuses on the understanding and engineering of nonribosomal peptide biosynthetic pathways in Streptomyces coelicolor CH999, Escherichia coli BAP1 and Saccharomyces cerevisiae BJ5464-NpgA. The biosynthetic systems of indigoidine from bacteria and beauvericin/bassianolide from fungi were studied in this research. The production of these valuble products was significantly increased by enhancing their synthetic pathway with metabolic engineering approaches.

Indigoidine is a bacterial natural product with antioxidant and antimicrobial activities. Its bright blue color resembles the industrial dye indigo, thus representing a new natural blue dye that may find uses in industry. Indigo is a dark blue crystalline powder and ...

Production And Biocompatibility Of Spider Silk Proteins In Goat Milk, Richard E. Decker Jr

All Graduate Theses and Dissertations

Due to its strength, flexibility, and biocompatibility, spider silk is a highly appealing material for applications in the medical field. Unfortunately, natural spider silk is difficult to obtain in large quantities because spiders are territorial and cannibalistic, making them impractical to farm. Synthetic spider silk proteins produced by transgenic hosts such as bacteria and goats have made it possible to obtain the quantities of spider silk needed to study it more fully and to investigate its potential uses. The spider silk proteins produced in our laboratory do not have an optimal purification method to remove all of the non-biocompatible contaminants ...

Computational Investigation Of The Interactions Between Bioactive Compounds And Biological Assemblies, Tye D. Martin

Shared Knowledge Conference

Design of small molecules is an ongoing focus for developing agents against pathogenic viruses and bacteria that are threats to worldwide health. Viruses such as Zika feature assemblies of repeat peptide subunits or capsid proteins which are potential targets for antiviral compounds. Other protein assemblies are implicated in pathology of Alzheimer’s Disease (AD) and additional neurodegenerative diseases characterized by large assemblies of misfolded proteins such as amyloid-beta (Aβ) and tau. Recent studies on a class of conjugated polyelectrolytes (CPEs) with phenylene ethynylene moieties and charged functional groups have shown potential both as bioactive antimicrobials and theragnostic sensing agents for ...

The Subject Librarian Newsletter, Engineering And Computer Science, Fall 2017, Buenaventura "Ven" Basco

Buenaventura "Ven" Basco

No abstract provided.

Microfluidic Electrical Impedance Spectroscopy, John J. Foley

Master's Theses and Project Reports

The goal of this study is to design and manufacture a microfluidic device capable of measuring changes in impedance valuesof microfluidic cell cultures. Tocharacterize this, an interdigitated array of electrodes was patterned over glass, where it was then bonded to a series of fluidic networks created in PDMS via soft lithography. The device measured ethanol impedance initially to show that values remain consistent over time. Impedance values of water and 1% wt. saltwater were compared to show that the device is able to detect changes in impedance, with up to a 60% reduction in electrical impedance in saltwater. Cells were ...

Cost-Effective Paper-Based Diagnostic Using Split Proteins To Detect Yeast Infections, Zachary R. Berglund, Kevin V. Solomon, Mohit S. Verma, Moiz Rasheed, Zachary Hartley, Kevin Fitzgerald, Kok Zhi Lee, Janice Chan, Julianne Dejoie, Makayla Schacht, Alex Zavala

The Summer Undergraduate Research Fellowship (SURF) Symposium

The common yeast infection, vulvovaginal candidiasis, affects three out of four women throughout their lifetime and can be spread to their child in the form of oral candidiasis (thrush). This disease is caused by the fungal pathogen Candida albicans, which is also a major cause of systemic candidiasis, a rarer but deadly disease with up to a 49% lethality rate. Current widely-used diagnostic methods include cell cultures, pH tests, and antibody detection, to assist effective treatment. Despite availability of various diagnostic methods, there is no inexpensive, rapid, and accurate way to detect C. albicans infection. This project aims to develop ...

Improving Biomanufacturing Production With Novel Elp-Based Transcriptional Regulators, Juya Jeon, Logan R. Readnour, Kevin V. Solomon

The Summer Undergraduate Research Fellowship (SURF) Symposium

Microbes can be used to produce valuable drugs, chemicals, and biofuels, but their potential has not been fully realized due to low production yields. To improve biomanufacturing processes and yield, we are developing novel, transcriptional regulators using biosynthesis technology in order to improve cellular health and overall production. Our regulator contains elastin-like polypeptides (ELPs), which make ideal sensors since they exhibit a sharp, inverse phase transition to indicators of cell health such as intracellular pH and ionic strength, and external stimuli such as temperature. We hypothesize that ELP can be fused to transcription factors to control expression of target genes ...

Rapid Sample Processing Of Foodborne Pathogens Using Cross-Flow Microfiltration, Casey Bomrad, Michael R. Ladisch, Linda Liu, Jessica Lynn Zuponcic, Eduardo Ximenes

The Summer Undergraduate Research Fellowship (SURF) Symposium

Foodborne illnesses are a prominent issue, causing 48 million illnesses annually. The Escherichia coli O157:H7 outbreak in romaine lettuce is a recent example. The source of the pathogen was contaminated irrigation water. The most common methods for detecting foodborne pathogens involve cultivation and enrichment of food samples. The enrichment steps are time-consuming, taking 24 to 72 hours to complete. Our study aims to accelerate irrigation water sample preparation for pathogenic microorganism fast detection through cross-flow microfiltration. This is accomplished by a device called a continuous cell concentration and recovery device (C3D). The C3D uses cross-flow microfiltration in a hollow ...