Biological Engineering Commons^™

Artificial Yeast Polarization Controlled By Chemical Gradient, James K. Nolan, Bernard Tao

The Summer Undergraduate Research Fellowship (SURF) Symposium

Engineering synthetic multicellular systems will lead to new synthetic biology technological platforms, inform developmental biology through recapitulation of natural systems and possibly unveil novel morphologies with practical applications not before reached throughout natural history (Maharbiz, 2012). Creating an exogenous molecular circuit that will polarize unicellular cells into “apical” and “basal” domains relative to a substrate plane would fulfill a missing component towards fully multicellular synthetic cellular communities (Maharbiz, 2012). To this end, a PIP₃ polarization network previously designed by Chau and associates (Chau, Walter, Gerardin, Tang, Lim 2012) was coupled to the specific activation by niacin of a recombinant …

Image Skeletal Muscle Progenitors In Situ To Investigate How The Ecm Composition Regulates Musculoskeletal Assembly, Andrew L. Schilb, Sarah Calve

The Summer Undergraduate Research Fellowship (SURF) Symposium

Regenerative medicine has difficulty with the human body’s inability to functionally repair tissues lost as a result of disease or serious accident. Through tissue engineering, there has been development of various scaffolding with the purpose of enhancing skeletal muscle regrowth and functionality. The scaffolds are typically constructed from artificial polymers or decellularized extracellular matrix (ECM) that mimics adult tissue. These standardized scaffolds are hindered though by the host since tissue engineers have not taken into account of how the composition musculoskeletal ECM during tissue repair is dramatically different than that of a homeostatic adult. Now green fluorescent protein positive (GFP+) …

Adhesive Elastomeric Proteins, Haefa Mansour, Julie Liu

The Summer Undergraduate Research Fellowship (SURF) Symposium

Sutures and staples commonly used to close surgical wounds tend to be much stiffer than the surrounding tissue, often resulting in external tissue damage. Surgical adhesives provide a promising alternative to these sutures and staples. Ideal surgical adhesives are biocompatible, able to set well and remain sticky in moist conditions, possess strong adhesive and cohesive properties, and exhibit mechanical properties that mimic those of the surrounding tissue. Unfortunately, the adhesives available today are unable to satisfactorily meet all of these criteria. We are utilizing protein engineering techniques to design, create, and test a new surgical adhesive that combines the adhesive …

Department Of Biological Systems Engineering Newsletter, October 2013

BSE Department Magazine

No abstract provided.

Life Support: Long Term Storage Of Solid Waste In An Enclosed Membrane System, Emmy O. Trieu, Michael Flynn, Rocco Mancinelli

STAR Program Research Presentations

In deep space missions, maintaining life support is of the utmost priority. In such a closed system, human waste must be stored and treated. Simulated feces (ersatz) will be inoculated with microbes representing normal fecal flora, mixed with urine brine and shredded refuse of products typically used in space missions. Composting methods often use alternating layers of waste with scraps of carboniferous materials (finely shredded refuse). By preparing membrane bags with a homogenized ersatz and carboniferous refuse mixture and membrane bags with alternating layers of ersatz and carboniferous refuse, it may be possible to monitor anaerobic thermophillic digestion of the …

Hybrid Nanostructured Textile Bioelectrode For Unobtrusive Health Monitoring, Pratyush Rai

Graduate Theses and Dissertations

Coronary heart disease, cardiovascular diseases and strokes are the leading causes of mortality in United States of America. Timely point-of-care health diagnostics and therapeutics for person suffering from these diseases can save thousands of lives. However, lack of accessible minimally intrusive health monitoring systems makes timely diagnosis difficult and sometimes impossible. To remedy this problem, a textile based nano-bio-sensor was developed and evaluated in this research. The sensor was made of novel array of vertically standing nanostructures that are conductive nano-fibers projecting from a conductive fabric. These sensor electrodes were tested for the quality of electrical contact that they made …

Zein: Novel Natural Polymer For Nanoparticle- And Film-Mediated Gene Delivery, Jessica D. Taylor

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Gene delivery, the introduction of DNA into cells, is applicable to gene therapy, DNA vaccination, functional genomics and diagnostics, tissue engineering, and drug-eluting medical devices. Particulates incorporating DNA are promising vehicles for gene delivery and overcome some of the barriers that hinder successful gene transfer, with the ability to protect DNA and provide for controlled, localized, and sustained release and transfection. Furthermore, innovative new gene delivery strategies that incorporate DNA particulates or complexes within films or coatings for devices and scaffolds could further provide for controlled and sustained transfection at the site of implant. Zein, a hydrophobic protein from corn, …

Hip Proprioceptors Preferentially Modulate Reflexes Of The Leg In Human Spinal Cord Injury, Tanya Onushko, Allison S. Hyngstrom, Brian D. Schmit

Biomedical Engineering Faculty Research and Publications

Stretch-sensitive afferent feedback from hip muscles has been shown to trigger long-lasting, multijoint reflex responses in people with chronic spinal cord injury (SCI). These reflexes could have important implications for control of leg movements during functional activities, such as walking. Because the control of leg movement relies on reflex regulation at all joints of the limb, we sought to determine whether stretch of hip muscles modulates reflex activity at the knee and ankle and, conversely, whether knee and ankle stretch afferents affect hip-triggered reflexes. A custom-built servomotor apparatus was used to stretch the hip muscles in nine chronic SCI subjects …

Stent Graft Blush, Vanessa Barrett, Thomas Matzinger, Mike Morelli

Mechanical Engineering

In order to better understand Type IV endoleaks (“blush”), the Cal Poly Senior Project team GraftTest has developed a blush evaluation system able to mimic several of the aorta’s environmental parameters. Capable of both pressure and flow rate control, this bench top system accommodates Medtronic’s wide range of abdominal and thoracic aortic stent grafts. Having researched endoleaks, stent grafts, and numerous other factors affecting stent graft blush, a system was developed with the aim of assessing and comparing the performance of Medtronic’s stent grafts with regard to blush. Furthermore, this system has been designed to provide reliable and repeatable results …

Beach Wheelchair Project, Rory Aronson, Joshua Marcum, Samuel Coyne, Alex Hayes, Alexa Colburn, Max Hessel, Benedikt Strauss, Marvin Rimmele, Marco Pietsch

Mechanical Engineering

The Beach Wheelchair, Sandcrawler, is a machine intended to help give people with disabilities the full beach experience. The non-profit organization Bridge II Sports sponsored this project, and tasked us with developing the design and fabricating a prototype. This chair has several features including a linkage mechanism that raises and lowers a chair relative to an external frame, hand crank drive with Gates Carbondrive belt and sprockets, buoyant Wheeleez balloon tires, and much more.

Computational Capabilities Of Leaky Integrate-And-Fire Neural Networks For Liquid State Machines, Amin Almassian, Christof Teuscher

Student Research Symposium

We analyze the computational capability of Leaky Integrate-and-Fire (LIF) Neural Networks used as a reservoir (liquid) in the framework of Liquid State Machines (LSM). Maass et. al. investigated LIF neurons in LSM and their results showed that they are capable of noise-robust, parallel, and real-time computation. However, it still remains an open question how the network topology affects the computational capability of a reservoir. To address that question, we investigate the performance of the reservoir as a function of the average reservoir connectivity. We also show that the dynamics of the LIF reservoir is sensitive to changes in the average …

Controlling Bacterial Persister Cells With Low Level Electric Currents, Henry Lars Peterson

Renée Crown University Honors Thesis Projects - All

Bacterial persister cells present a growing concern as they inherit the ability to tolerate high concentrations of antibiotics and repopulate after an antibiotic treatment leading to chronic diseases. Pseudomonas aeruginosa causes many human infections including skin infections and those associated with burn injuries, and implanted medical devices, and are associated with Cystic Fibrosis. Recently, the Ren Lab developed a novel approach to eliminate persister cells of P. aeruginosa, including those in biofilms, using low level electric currents. To evaluate the safety of this method and to better understand how the underlying elements, this study focused on the cytotoxicity of …

Optimization Of Polyhydroxybutyrate Production In Recombinant Escherichia Coli Through Metabolic Modeling And Simulation, Yoshitaro Heshiki

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

The objective of this study is to optimize the growth media and genes to maximize PHB production computer simulations, and to evaluate the simulation results through experiments. In order to achieve this objective, the metabolism of E. coli that produces PHB was modeled using the existing E. coli genome-scale metabolic networks. To identify the best additional nutrient for PHB production, carbon sources, minerals, amiano acids, nitrogen sources, and sulfur sources were examined by production potential analysis. Strain design was conducted to find the unwanted reactions to overexpress PHB synthesis pathway.

Cationic Starch Synthesis, Development, And Evaluation For Harvesting Microalgae For Wastewater Treatment, Renil John Anthony

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Microalgae are the preferred crop for the production of biodiesel. Microalgae are microplants that have the ability to harness sunlight more efficiently than other plants and store 20-80% lipids per g of dry algae in their cells. Microalgae have the extraordinary ability to grow in brackish water or wastewater. Microalgae can be grown in municipal wastewater to uptake phosphorus and nitrogen and remediate the wastewater of these nutrients. Microalgae thus cultivated accomplishes a dual role of wastewater treatment and provides a sustainable feedstock for biofuels and other bioproducts.

This study focused on efficiently harvesting microalgae from water using modified starch. …

Department Of Biological Systems Engineering Newsletter, Volume 7, Number 2, April 2013

BSE Department Magazine

No abstract provided.

Atypical Glycolysis In Clostridium Thermocellum, Jilai Zhou, Daniel G. Olson, D. Aaron Argyros, Yu Deng, Walter M. Van Gulik, Johannes P. Van Dijken, Lee R. Lynd

Dartmouth Scholarship

Cofactor specificities of glycolytic enzymes in Clostridium thermocellum were studied with cellobiose-grown cells from batch cultures. Intracellular glucose was phosphorylated by glucokinase using GTP rather than ATP. Although phosphofructokinase typically uses ATP as a phosphoryl donor, we found only pyrophosphate (PPi)-linked activity. Phosphoglycerate kinase used both GDP and ADP as phosphoryl acceptors. In agreement with the absence of a pyruvate kinase sequence in the C. thermocellum genome, no activity of this enzyme could be detected. Also, the annotated pyruvate phosphate dikinase (ppdk) is not crucial for the generation of pyruvate from phosphoenolpyruvate (PEP), as deletion of the ppdk gene did …

The Effects Of Hydrostatic Pressure On Early Endothelial Tubulogenic Processes, Ryan M. Underwood

Theses and Dissertations--Biomedical Engineering

The effects of mechanical forces on endothelial cell function and behavior are well documented, but have not been fully characterized. Specifically, fluid pressure has been shown to elicit physical and chemical responses known to be involved in the initiation and progression of endothelial cell-mediated vascularization. Central to the process of vascularization is the formation of tube-like structures. This process—tubulogenesis—is essential to both the physiological and pathological growth of tissues. Given the known effects of pressure on endothelial cells and its ubiquitous presence in the vasculature, we investigated pressure as a magnitude-dependent parameter for the regulation of endothelial tubulogenic activity. To …

Noninvasive Near-Infrared Diffuse Optical Monitoring Of Cerebral Hemodynamics And Autoregulation, Ran Cheng

Theses and Dissertations--Biomedical Engineering

Many cerebral diseases are associated with abnormal cerebral hemodynamics and impaired cerebral autoregulation (CA). CA is a mechanism to maintain cerebral blood flow (CBF) stable when mean arterial pressure (MAP) fluctuates. Evaluating these abnormalities requires direct measurements of cerebral hemodynamics and MAP. Several near-infrared diffuse optical instruments have been developed in our laboratory for hemodynamic measurements including near-infrared spectroscopy (NIRS), diffuse correlation spectroscopy (DCS), hybrid NIRS/DCS, and dual-wavelength DCS flow-oximeter. We utilized these noninvasive technologies to quantify CBF and cerebral oxygenation in different populations under different physiological conditions/manipulations. A commercial finger plethysmograph was used to continuously monitor MAP. For investigating …

Metacom: Automated Data Processing And Analysis Of Metagenomic Community Sequences, Cody A. Tramp, Charles D. Miller

Browse all Datasets

Advances in next generation sequencing technology have allowed metagenomic researchers to study the composition of bacterial communities through analysis of the vast numbers of sequence reads that these technologies generate. It is not feasible to analyze and interpret this large amount of data manually and individual research groups must create automated scripts and programs to analyze this data. Here, we present MetaCom, a program that offers a common set of analysis and organizational tools that can be used by research groups in the analysis of environmental samples. MetaCom is an open-source software tool that can process next generation sequencing output, …

Bacillus Thuringiensis: Transgenic Crops, Julie A. Peterson, John J. Obrycki, James D. Harwood

Department of Entomology: Faculty Publications

Bacillus thuringiensis (Bt) crops, genetically modified to express insecticidal toxins that target key pests of corn, cotton, rice, potato, and other crops, have been rapidly adopted and have become dominant fixtures in agroecosystems throughout the world. Due to the constitutive nature of Bt toxin expression, insecticidal proteins may be found in nearly all plant tissues, presenting multiple sources for Bt toxins to enter the environment, thus creating complex direct and indirect pathways for non-target organisms to be exposed to insecticidal proteins. The environmental impacts of Bt crops have been widely debated, although both benefits and risks do exist. Benefits of …