Biomedical Engineering and Bioengineering Commons^™

Hydrotreating Of Guaiacol: A Comparative Study Of Red Mud-Supported Nickel And Commercial Ni/Sio2-Al2o3 Catalysts, Hossein Jahromi, Foster Agblevor

Biological Engineering Faculty Publications

Upgrading of bio-oil through catalytic hydrotreating was investigated with guaiacol as a model compound. A nickel supported on red mud (Ni/RM) hydrotreating catalyst was developed and compared to the standard Ni/SiO₂-Al₂O₃ catalysts under similar experimental conditions. The Ni/RM catalyst was characterized by inductively coupled plasma atomic emission spectrometry (ICP-AES), X-ray diffraction analysis (XRD), scanning electron microscopy (SEM), BET specific surface area, and temperature programmed reduction (TPR). The effects of reaction temperature (300, 350, 400 °C) and initial hydrogen pressure (4.83 MPa (700 psi), 5.52 MPa (800 psi), and 6.21 MPa (900 psi)) on products distribution …

Microfluidic Chip For Non-Invasive Analysis Of Tumor Cells Interaction With Anti-Cancer Drug Doxorubicin By Afm And Raman Spectroscopy, Han Zhang, Lifu Xiao, Qifei Li, Xiaojun Qi, Anhong Zhou

Biological Engineering Faculty Publications

Raman spectroscopy has been playing an increasingly significant role for cell classification. Here, we introduce a novel microfluidic chip for non-invasive Raman cell natural fingerprint collection. Traditional Raman spectroscopy measurement of the cells grown in a Polydimethylsiloxane (PDMS) based microfluidic device suffers from the background noise from the substrate materials of PDMS when intended to apply as an in vitro cell assay. To overcome this disadvantage, the current device is designed with a middle layer of PDMS layer sandwiched by two MgF2slides which minimize the PDMS background signal in Raman measurement. Three cancer cell lines, including a human lung cancer …

3d Tissue Engineering, An Emerging Technique For Pharmaceutical Research, Gregory Jensen, Christian Morrill, Yu Huang

Biological Engineering Faculty Publications

Tissue engineering and the tissue engineering model have shown promise in improving methods of drug delivery, drug action, and drug discovery in pharmaceutical research for the attenuation of the central nervous system inflammatory response. Such inflammation contributes to the lack of regenerative ability of neural cells, as well as the temporary and permanent loss of function associated with neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and traumatic brain injury. This review is focused specifically on the recent advances in the tissue engineering model made by altering scaffold biophysical and biochemical properties for use in the treatment of neurodegenerative diseases. …

In Vivo Raman Spectroscopy For Biochemical Monitoring Of The Human Cervix Throughout Pregnancy, Christine M. O'Brien, Elizabeth Vargis, Amy Rudin, James C. Slaughter, Giju Thomas, J. Michael Newton, Jeff Reese, Kelly A. Bennett, Anita Mahadevan-Jansen

Biological Engineering Faculty Publications

Background

The cervix must undergo significant biochemical remodeling to allow for successful parturition. This process is not fully understood, especially in instances of spontaneous preterm birth. In vivo Raman spectroscopy is an optical technique that can be used to investigate the biochemical composition of tissue longitudinally and noninvasively in human beings, and has been utilized to measure physiology and disease states in a variety of medical applications.

Objective

The purpose of this study is to measure in vivo Raman spectra of the cervix throughout pregnancy in women, and to identify biochemical markers that change with the preparation for delivery and …

Hydrodeoxygenation Of Acetic Acid As A Model Compound For The Aqueous Phase Catalytic Pyrolysis Oils, Hossein Jahromi, Foster Agblevor

Biological Engineering Faculty Publications

Catalytic pyrolysis of biomass generates organic, aqueous, gaseous and solid fractions. The organic fraction can be easily hydrotreated to produce hydrocarbons, but the aqueous phase that contains between 10 to 25% soluble organics can pose challenges in wastewater treatment. The aqueous fraction from the catalytic pyrolysis of Pinyon Juniper wood was characterized for its organic content. The fraction contained about 15 wt% organic compounds determined from Karl Fischer analysis. The organic fractions were further characterized using gas chromatography and mass selective detection (GC/MS). The analysis showed that the dissolved organics were composed of acetic acid, ketones, aldehydes, and phenolic compounds. …

Physical Disruption Of Cell-Cell Contact Induces Vegf Expression In Rpe Cells, Fahrad Farjood, Elizabeth Vargis

Biological Engineering Faculty Publications

PURPOSE: To investigate the role of RPE cell-cell contact in vascular endothelial growth factor (VEGF) protein expression in cultures of primary human RPE (hRPE) cells and a human RPE cell line (ARPE-19). METHODS: Two in vitro methods, scratching and micropatterning, were used to control the physical dissociation of RPE cell-cell junctions. Scratching was performed by scoring monolayers of RPE cells with a cell scraper. Micropatterning was achieved by using a stencil patterning method. Extracellular VEGF expression was assessed by using an enzyme-linked immunosorbent assay (ELISA) kit. Immunocytochemistry (ICC) was performed to visualize the expression and localization of VEGF and intercellular …

Decoding And Reprogramming Fungal Iterative Nonribosomal Peptide Synthetases, Daya Yu, Fuchao Xu, Shuwei Zhang, Jixun Zhan

Biological Engineering Faculty Publications

Nonribosomal peptide synthetases (NRPSs) assemble a large group of structurally and functionally diverse natural products. While the iterative catalytic mechanism of bacterial NRPSs is known, it remains unclear how fungal NRPSs create products of desired length. Here we show that fungal iterative NRPSs adopt an alternate incorporation strategy. Beauvericin and bassianolide synthetases have the same C₁-A₁-T₁-C₂-A₂-MT-T_2a-T_2b-C₃ domain organization. During catalysis, C₃ and C₂ take turns to incorporate the two biosynthetic precursors into the growing depsipeptide chain that swings between T₁ and T …

Exploiting Self-Organization In Bioengineered Systems: A Computational Approach, Delin Davis, Anna Doloman, Gregory J. Podgorski, Elizabeth Vargis, Nicholas S. Flann

Biological Engineering Faculty Publications

The productivity of bioengineered cell factories is limited by inefficiencies in nutrient delivery and waste and product removal. Current solution approaches explore changes in the physical configurations of the bioreactors. This work investigates the possibilities of exploiting self-organizing vascular networks to support producer cells within the factory. A computational model simulates de novo vascular development of endothelial-like cells and the resultant network functioning to deliver nutrients and extract product and waste from the cell culture. Microbial factories with vascular networks are evaluated for their scalability, robustness, and productivity compared to the cell factories without a vascular network. Initial studies demonstrate …

Alternative Cdep Design To Facilitate Cell Isolation For Identification By Raman Spectroscopy, Cynthia Hanson, Elizabeth Vargis

Biological Engineering Faculty Publications

Dielectrophoresis (DEP) uses non-uniform electric fields to cause motion in particles due to the particles' intrinsic properties. As such, DEP is a well-suited label-free means for cell sorting. Of the various methods of implementing DEP, contactless dielectrophoresis (cDEP) is advantageous as it avoids common problems associated with DEP, such as electrode fouling and electrolysis. Unfortunately, cDEP devices can be difficult to fabricate, replicate, and reuse. In addition, the operating parameters are limited by the dielectric breakdown of polydimethylsiloxane (PDMS). This study presents an alternative way to fabricate a cDEP device allowing for higher operating voltages, improved replication, and the opportunity …

Biomanufacturing Through Igem-An International Student Competition, Asif Rahman, Ryan J. Putman, Neal Hengge, Charles D. Miller

Biological Engineering Faculty Publications

The foundations of synthetic biology are built on molecular biology and genetic engineering. One of the purposes of synthetic biology is to make biology easier to engineer by the creation of standardized biological parts and devices. There are a wide range of potential applications for synthetic biology and a variety of approaches to constructing parts and systems. Undergraduate Science, Technology, Engineering, and Mathematics (STEM) students from around the world apply synthetic biology principles at the annual International Genetically Engineered Machine (iGEM) competition to demonstrate functioning biological systems created from standardized parts. The iGEM competition will continue to add to the …

Qualitative Analysis Of Microbial Dynamics During Anaerobic Digestion Of Microalgal Biomass In A Uasb Reactor, Anna Doloman, Yousef Soboh, Andrew J. Walters, Ronald C. Sims, Charles D. Miller

Biological Engineering Faculty Publications

Anaerobic digestion (AD) is a microbiologically coordinated process with dynamic relationships between bacterial players. Current understanding of dynamic changes in the bacterial composition during the AD process is incomplete. The objective of this research was to assess changes in bacterial community composition that coordinates with anaerobic codigestion of microalgal biomass cultivated on municipal wastewater. An upflow anaerobic sludge blanket reactor was used to achieve high rates of microalgae decomposition and biogas production. Samples of the sludge were collected throughout AD and extracted DNA was subjected to next-generation sequencing using methanogen mcrA gene specific and universal bacterial primers. Analysis of the …

Hydrodeoxygenation Of Pinyon Juniper Catalytic Pyrolysis Oil To Hydrocarbon Fuels, Hossein Jahromi, Foster Agblevor

Biological Engineering Faculty Publications

As a renewable source, biomass is an essential option for diminishing dependence on conventional fossil fuel energy sources. Pyrolysis is a promising technology for the conversion of biomass into liquid fuels. However, several challenges associated with using pyrolysis oils such as their high acidity and low energy content inhibit their direct use as transportation fuels. We conducted a batch hydrodeoxygenation of pinyon juniper catalytic pyrolysis oil using Ni/SiO2-Al2O3 catalyst to improve the following properties of the oil: heating value, acidity, oxygen content, water content, and viscosity. During the hydrogenation process, the influence of four experimental factors; temperature, catalyst loading, residence …

Methods For Culturing Retinal Pigment Epithelial Cells: A Review Of Current Protocols And Future Recommendations, Aaron H. Fronk, Elizabeth Vargis

Biological Engineering Faculty Publications

The retinal pigment epithelium is an important part of the vertebrate eye, particularly in studying the causes and possible treatment of age-related macular degeneration. The retinal pigment epithelium is difficult to access in vivo due to its location at the back of the eye, making experimentation with age-related macular degeneration treatments problematic. An alternative to in vivo experimentation is cultivating the retinal pigment epithelium in vitro, a practice that has been going on since the 1970s, providing a wide range of retinal pigment epithelial culture protocols, each producing cells and tissue of varying degrees of similarity to natural retinal pigment …

Deposition Of Carbon Nanotube Films On Polyamide And Polypropylene Substrates: A Computer Simulation Approach, Alejandro Heredia, Maria Colin-Garcia, Maria Del Pilar Carreon-Castro, Debarati Mukherjee, Bruno Abreu, David William Britt, Joana Catarina Mendes

Biological Engineering Faculty Publications

In this work we study hydroxylated carbon nanotube (CNT) assembly on polyamide (PA) and polypropylene (PP) polymers activated by UV radiation from a theoretical and experimental perspective. Molecular computer simulation was done to understand the stable conformations and bulk properties (molecular dynamics) of the polymers before and after exposure to UV radiation at the molecular level. Our experiments suggest that PA presents more -OH active groups, producing a more hydrophilic surface, whereas PP exhibits less potential UV activation. These results suggest that it is possible a facile covalent functionalization method to tune organic polymer surface properties through SWCNT anchoring for …

The Use Of Microfluidics And Dielectrophoresis For Separation, Concentration, And Identification Of Bacteria, Cynthia Hanson, Michael Sieverts, Karen Tew, Annelise Dykes, Michaela Salisbury, Elizabeth Vargis

Biological Engineering Faculty Publications

Traditional bacterial identification methods take one to two days to complete, relying on large bacteria colonies for visual identification. In order to decrease this analysis time in a cost-effective manner, a method to sort and concentrate bacteria based on the bacteria's characteristics itself is needed. One example of such a method is dielectrophoresis, which has been used by researchers to separate bacteria from sample debris and sort bacteria according to species. This work presents variations in which dielectrophoresis can be performed and their associated drawbacks and benefits specifically to bacterial identification. In addition, a potential microfluidic design will be discussed.

Bioenergy From Wastewater-Based Biomass, Ronald C. Sims, Sean K. Bedingfield, Reese Thompson, Judith L. Sims

Biological Engineering Faculty Publications

The U.S. Department of Energy (DOE) has stated that biomass is the only renewable resource that can supplant petroleum-based liquid transportation fuels in the near term. Wastewater is beginning to be viewed as a potential resource that can be exploited for biomass production and conversion to bioenergy. We suggest that using wastewater from municipalities and industries as a resource for cultivating biomass and combining wastewater treatment with the production of biomass for bioenergy would provide benefits to both industries. Two waste-based biomass production systems that currently have large nationwide infrastructures include: (1) wastewater treatment systems that can be used to …

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

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 …

Nanoparticle Properties And Synthesis Effects On Surface-Enhanced Raman Scattering (Sers) Enhancement Factor: An Introduction, Nathan D. Israelsen, Cynthia Hanson, Elizabeth Vargis

Biological Engineering Faculty Publications

Raman spectroscopy has enabled researchers to map the specific chemical makeup of surfaces, solutions, and even cells. However, the inherent insensitivity of the technique makes it difficult to use and statistically complicated. When Raman active molecules are near gold or silver nanoparticles, the Raman intensity is significantly amplified. This phenomenon is referred to as surface-enhanced Raman spectroscopy (SERS). The extent of SERS enhancement is due to a variety of factors such as nanoparticle size, shape, material, and configuration. The choice of Raman reporters and protective coatings will also influence SERS enhancement. This review provides an introduction to how these factors …

Friction Coefficients For Dried Distillers Grains On Eight Structural Surfaces, G. C. Nyendu, S. Pflum, P. Schumacher, C. J. Bern, T. J. Brumm

Biological Engineering Faculty Publications

Static and dynamic coefficients of friction on structural surfaces play important roles in the power requirements and material selection for equipment used in handling and storing agricultural commodities. However, friction data on dried distillers grains with solubles (DDGS) is limited. Further, lack of a standardized method for determining friction coefficient on grain handling materials presents a challenge. This article describes studies carried out to determine the static coefficient of friction (•_s) and dynamic coefficient of friction (•_d) for corn DDGS at 10%, 8.2%, and 6.5% moisture content (all moistures are % wet basis) on eight structural surfaces: High-Density Polyethylene (HDPE), …

Functional Dissection And Module Swapping Of Fungal Cyclooligomer Depsipeptide Synthetases, Dayu Yu, Fuchao Xu, David Gage, Jixun Zhan

Biological Engineering Faculty Publications

BbBSLS and BbBEAS were dissected and reconstituted in Saccharomyces cerevisiae. The intermodular linker is essential for the reconstitution of the separate modules. Module 1 can be swapped between BbBEAS and BbBSLS, while modules 2 and 3 control the product profiles. BbBSLS is a flexible enzyme that also synthesizes beauvericins.

Engineered Production Of Fungal Anticancer Cyclooligomer Depsipeptides In Saccharo-Myces Cerevisiae, Dayu Yu, Fuchao Xu, Jiachen Zi, Siyuan Wang, David Gage, Jia Zeng, Jixun Zhan

Biological Engineering Faculty Publications

Two fungal cyclooligomer depsipeptide synthetases (CODSs), BbBEAS (352 kDa) and BbBSLS (348 kDa) from Beauveria bassiana ATCC 7159, were reconstituted in Saccharomyces cerevisiae BJ5464-NpgA, leading to the production of the corresponding anticancer natural products, beauvericins and bassianolide, respectively. The titers of beauvericins (33.82±1.41 mg/l) and bassianolide (21.74±0.08 mg/l) in the engineered S. cerevisiae BJ5464-NpgA strains were comparable to those in the native producer B. bassiana. Feeding D-hydroxyisovaleric acid (D-Hiv) and the corresponding L-amino acid precursors improved the production of beauvericins and bassianolide. However, the high price of D-Hiv limits its application in large-scale production of these cyclooligomer depsipeptides. Alternatively, we …

Design And Application Of An In Vivo Reporter Assay For Phenylalanine Ammonialyase, S. Wang, S. Zhang, T. Zhou, J. Zeng, Jixun Zhan

Biological Engineering Faculty Publications

Phenylalanine ammonia-lyase (PAL) is an important enzyme that links primary metabolism to secondary metabolism. Its efficiency is often a critical factor that affects the overall flux of a related metabolic pathway, the titer of the final products, and the efficacy of PAL-based therapies. Thus, PAL is a common target for metabolic engineering and it is of significant interest to screen efficient PALs for industrial and medical applications. In this study, a novel and efficient visible reporter assay for screening of PAL efficiency in Escherichia coli was established based on a plant type III polyketide biosynthetic pathway. The candidate PALs were …

Rational Reprogramming Of Fungal Polyketide First Ring Cyclization, Yuquan Xu, Tong Zhou, Zhengfu Zhou, Shiyou Su, Sue A. Roberts, William R. Montfort, Jia Zeng, Ming Chen, Wei Zhang, Min Lin, Jixun Zhan, Istvan Molnar

Biological Engineering Faculty Publications

Resorcylic acid lactones (RAL) and dihydroxyphenylacetic acid lactones (DAL) represent important pharmacophores with heat shock response and immune system modulatory activities. The biosynthesis of these fungal polyketides involves a pair of collaborating iterative polyketide synthases (iPKSs): a highly reducing iPKS (hrPKS) whose product is further elaborated by a nonreducing iPKS (nrPKS) to yield a 1,3-benzenediol moiety bridged by a macrolactone. Biosynthesis of unreduced polyketides requires the sequestration and programmed cyclization of highly reactive poly-β-ketoacyl intermediates to channel these uncommitted, pluripotent substrates towards defined subsets of the polyketide structural space. Catalyzed by product template (PT) domains of the fungal nrPKSs and …

An Indigoidine Biosynthetic Gene Cluster From Streptomyces Chromofuscus Atcc 49982 Contains An Unusual Indb Homologue, Dayu Yu, Fuchao Xu, Jonathan Valiente, Siyuan Wang, Jixun Zhan

Biological Engineering Faculty Publications

A putative indigoidine biosynthetic gene cluster was located in the genome of Streptomyces chromofuscus ATCC 49982. The silent 9.4-kb gene cluster consists of five open reading frames, named orf1, Sc-indC, Sc-indA, Sc-indB, and orf2, respectively. Sc-IndC was functionally characterized as an indigoidine synthase through heterologous expression of the enzyme in both Streptomyces coelicolor CH999 and Escherichia coli BAP1. The yield of indigoidine in E. coli BAP1 reached 2.78 g/l under the optimized conditions. The predicted protein product of Sc-indB is unusual and much larger than any other reported IndB-like protein. The N-terminal portion of this enzyme resembles IdgB and the …

Looking Below The Surface Of Breast Tissue During Surgery, A Mahadevan-Jansen, Md Keller, Elizabeth Vargis, B Caldwell, T-Q Nguyen, Ndm Granja, M Sanders, Mc Kelley

Biological Engineering Faculty Publications

In this article, we present a method that provides prompt detection of the presence of cancer cells inside the 2-mm margin of tissue surrounding the tumor after excision using spatially offset Raman spectroscopy (SORS). SORS was developed to detect subtle changes in soft tissue spectra in the 100–2000 μm range and tested on excised breast tissues. The results display a very high specificity and sensitivity (100% and 95%, respectively) of classification between positive and negative tumor margins. SORS is a clinically feasible method, suitable for the real-time, intraoperative assessment of tumor margins at the micrometer level.

Selective Biochlorination Of Hydroxyquinolines By A Flavin-Dependent Halogenase, Fuchao Xu, Amanda Merkley, Dayu Yu, Jixun Zhan

Biological Engineering Faculty Publications

Rdc2 is a flavin-dependent halogenase from Pochonia chlamydosporia. Through the introduction of a His₆-tag to both the N- and C-termini, the isolation yield of Rdc2 from Escherichia coli using Ni-NTA affinity chromatography was increased by three-fold. In vitro reaction of Rdc2 and a flavin reductase (Fre) with seven different hydroxyquinolines revealed that 3-hydroxyquinoline (3), 5-hydroxyquinoline (5), 6-hydroxyquinoline (6), and 7-hydroxyquinoline (7) can be specifically halogenated. These products were prepared by incubating the corresponding substrates with IPTG-induced E. coli BL21(DE3)/Rdc2. They were respectively characterized as 3-hydroxy-4-chloroquinoline (3a), 5-hydroxy-6-chloroquinoline (5a), 5-chloro-6-hydroxyquinoline (6a), and 7-hydroxy-8-chloroquinoline (7a) by NMR and MS …

Pyrene Fate Affected By Humic Acid Amendment In Soil Slurry Systems, Y. Liang, D. Sorensen, Ronald C. Sims, Joan Mclean

Biological Engineering Faculty Publications

Background

Humic acid (HA) has been found to affect the solubility, mineralization, and bound residue formation of polycyclic aromatic hydrocarbons (PAHs). However, most of the studies on the interaction between HA and PAH concentrated on one or two of the three phases. Few studies have provided a simple protocol to demonstrate the overall effects of HA on PAH distribution in soil systems for all three phases.

Methods

In this study, three doses of standard Elliott soil HA (ESHA), 15, 187.5, and 1,875 μg ESHA/g soil slurry, were amended to soil slurry systems. ¹⁴C-pyrene was added to the systems along …

The Power Of Soil: Using It To Our Advantage, Judith L. Sims, R. Otis

Biological Engineering Faculty Publications

No abstract provided.

Temperature Effect On Tert-Butyl Alcohol (Tba) Biodegradation Kinetics In Hyporheic Zone Soils, M. H. Greenwood, Ronald C. Sims, J. E. Mclean, W. J. Doucette

Biological Engineering Faculty Publications

Background

Remediation of tert-butyl alcohol (TBA) in subsurface waters should be taken into consideration at reformulated gasoline contaminated sites since it is a biodegradation intermediate of methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE), and tert-butyl formate (TBF). The effect of temperature on TBA biodegradation has not been not been published in the literature.

Methods

Biodegradation of [U ¹⁴C] TBA was determined using hyporheic zone soil microcosms.

Results

First order mineralization rate constants of TBA at 5°C, 15°C and 25°C were 7.84 ± 0.14 × 10^-3, 9.07 ± 0.09 × 10^-3, and 15.3 ± 0.3 …