Biomedical Engineering and Bioengineering Commons^™

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 …

Modeling De Novo Granulation Of Anaerobic Sludge, Anna Doloman, Honey Varghese, Charles D. Miller, Nicholas Flann

Computer Science Faculty and Staff Publications

Background: A unique combination of mechanical, physiochemical and biological forces influences granulation during processes of anaerobic digestion. Understanding this process requires a systems biology approach due to the need to consider not just single-cell metabolic processes, but also the multicellular organization and development of the granule.

Results: In this computational experiment, we address the role that physiochemical and biological processes play in granulation and provide a literature-validated working model of anaerobic granule de novo formation. The agent-based model developed in a cDynoMiCs simulation environment successfully demonstrated a de novo granulation in a glucose fed system, with the average specific methanogenic …

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 …

A Computational Study Of Vegf Production By Patterned Retinal Epithelial Cell Colonies As A Model For Neovascular Macular Degeneration, Qanita Bani Baker, Gregory J. Podgorski, Elizabeth Vargis, Nicholas Flann

Biology Faculty Publications

Background: The configuration of necrotic areas within the retinal pigmented epithelium is an important element in the progression of age-related macular degeneration (AMD). In the exudative (wet) and non-exudative (dry) forms of the disease, retinal pigment epithelial (RPE) cells respond to adjacent atrophied regions by secreting vascular endothelial growth factor (VEGF) that in turn recruits new blood vessels which lead to a further reduction in retinal function and vision. In vitro models exist for studying VEGF expression in wet AMD (Vargis et al., Biomaterials 35(13):3999–4004, 2014), but are limited in the patterns of necrotic and intact RPE epithelium they can …