Biological Engineering Commons^™

Extracellular Matrix Nanoparticles Effects On The Lung In Vivo, Brittaney E. Ritchie

Theses and Dissertations

Acute respiratory distress syndrome (ARDS) is a life-threatening condition that causes diffuse alveolar damage and a loss of the extracellular matrix (ECM). This leads to pulmonary edema and lung function deterioration. Our lab has created decellularized porcine lung, electrosprayed ECM nanoparticles that have been previously shown to have pro-regenerative capabilities in vitro.

In this study, the ECM nanoparticle effects on young murine lungs were tested in vivo. An ECM nanoparticle suspension, previously used for the in vitro studies, was aerosolized intratracheally into the lungs using a microsprayer. 24 hours later, the lung mechanics, bronchoalveolar lavage fluid, and histology …

Noncontact Multiscale Diffuse Optical Imaging Of Deep Tissue Hemodynamics In Animals And Humans, Siavash Mazdeyasna

Theses and Dissertations--Biomedical Engineering

Blood flow (BF) impacts the delivery of oxygen and nutrients to tissues and the removal of metabolic byproducts from tissues. Imaging of BF distributions helps characterize many diseases associated with tissue hypoxia/ischemia. The purpose of this study was to develop and validate a novel, noninvasive, noncontact, high-density camera-based speckle contrast diffuse correlation tomography (scDCT) device for use in both animal and human studies. The scDCT uses a galvo-mirror to remotely deliver the focused point near-infrared light to source positions and a sensitive 2D camera to quantify spatial diffuse speckle fluctuations, resulting from the movement of red blood cells in deep …

Opendrop Software Development, Jiajun Guan

Electrical Engineering

To be able to transfer and mix solutions more efficiently and accurately during biology experiments, the Electrical Engineering department at Cal Poly University is planning to purchase or engineer the OpenDrop device. The OpenDrop device uses electro-wetting technology to control the movement of small droplets of water on a planar electrode array to transport and mix different solutions. This device is an open-source project and could be purchased online through the GaudiLab. The basic code of the system could be found in GitHub. With this code as a reference, the goal of this senior project is to develop the firmware, …

Lipemia Levels Analysis From Human Blood Samples, Zainab Ibrahim Alshoug

Dissertations, Master's Theses and Master's Reports

Worldwide, an estimated 31% of people who die each year have a cardiovascular disease (CVD), an all-encompassing group of diseases and conditions of the heart or blood vasculature. Access to portable, user-friendly tools to test lipid levels accurately and efficiently, without requiring large volume blood draws, will help improve access to wellness management by reducing costs and facilitating early screening and monitoring of CVD thus improving outcomes. Point of care micro or millifluidic chips to test biofluids that are integrated into detection units are an attractive measurement tool because of their potential for ease of use by patients at home …

Nanofiber Scaffolds As 3d Culture Platforms, Stephanie Bule

Dissertations, Master's Theses and Master's Reports

Cell culture has become the basis for understanding the fundamental mechanisms of cell, tissue and organ function. Although major advancements in uncovering the underlying processes and mechanisms of normal and diseased cell biology have been made by using two-dimensional (2D) cell culture, there is a recent shift in moving towards three-dimensional (3D) culture platforms. The motivation is to better recapitulate the microenvironment of cells in vivo to obtain results that are more indicative to actual cellular processes. In this study, electrospun nano-fibrous scaffolds made of polycaprolactone were used as a 3D culture tool to investigate difference in cell behavior and …

Alternative Upper Configurations During Agility-Based Movements: Part 1, Biomechanical Performance, Bradley S. Davidson, Kevin B. Shelburne, Moira Pyrhoda, Rachel Wathen, Nick Nelson, Sean Higinbotham, Jay Dicharry, Daniel Feeney, Kate Harrison

Alternative Upper Configurations During Agility-Based Movements

The objective of this research was to determine if three alternative shoe closures improve biomechanical performance measures compared to a standard lace closure in agility-based movements. NCAA Division 1 and club-level male athletes recruited from lacrosse, soccer, tennis, and rugby performed four court-based movements: Lateral Skater Jump Repeats (LSJ), Countermovement Jump Repeats (CMJ), Triangle Drop Step Drill (TDS), and Anterior-Posterior Drill (AP). Each athlete performed the movements in four shoe upper closures: Standard Closure, Lace Replacement, Y Wrap, and Tri Panel. Movement completion time, Ground contact time, peak eccentric rate of force development (RFD), peak concentric GRF, peak concentric COM …

Alternative Upper Configurations During Agility-Based Movements: Part 2, Joint-Level Biomechanics, Bradley S. Davidson, Kevin B. Shelburne, Moira Pyrhoda, Rachel Wathen, Nick Nelson, Sean Higinbotham, Jay Dicharry, Daniel Feeney, Kate Harrison

Alternative Upper Configurations During Agility-Based Movements

The objective of this research was to determine if three alternative shoe closures improve biomechanical performance measures compared to a standard lace closure in agility-based movements. NCAA Division 1 and club-level male athletes recruited from lacrosse, soccer, tennis, and rugby performed four court-based movements: Lateral Skater Jump Repeats (LSJ), Countermovement Jump Repeats (CMJ), Triangle Drop Step Drill (TDS), and Anterior-Posterior Drill (AP). Each athlete performed the movements in four shoe upper closures: Standard Closure, Lace Replacement, Y Wrap, and Tri Panel. Movement completion time, Ground contact time, peak eccentric rate of force development (RFD), peak concentric GRF, peak concentric COM …

Higher Tensile Forces Across Cellular Junctions And An Intact Nuclear Linc Complex Is Required For Epithelial Function And Stability, Fnu Vani Narayanan

Theses and Dissertations

Recent advances in three-dimensional (3D) cell culture systems have provided key insights into the understanding of biochemical and physiological states of native tissue. A significant progress in the field of mechanobiology involves measuring cellular traction forces in a more native 3D environment. However, the effects of mechanical forces exerted across cellular junctions and the nuclear LINC complex, in an organized 3D system has not been investigated thus far. Epithelial cells spontaneously form acini (also known as cysts or spheroids) with a single, fluid-filled central lumen, when grown in 3D matrices. The size of the lumen is dependent on apical secretion …

Development Of A Torque-Based Device For The Quantification Of Arm Rigidity In Patients With Parkinson’S Disease, Georgina O. Miller

Theses and Dissertations

Parkinsonian rigidity is caused by the inability of the muscles to relax and extend properly, due to reduced dopamine levels and often begins on one side of the body before spreading contralaterally. The current standard for determining joint rigidity in a clinical setting is a test completed by the clinician based on the feel of the relaxed wrist and elbow joints as they are passively flexed and extended and a series of ordinal rating scales, the Movement Disorder Society’s – Unified Parkinson’s Disease Rating Scale (MDS-UPDRS), Hoehn and Yahr Scale (H&Y), and Parkinson’s Disease Questionnaire-39 (PDQ-39). These methods are used …

The Impact Of Aging And Mechanical Injury On Alveolar Epithelial And Macrophage Responses In Acute Lung Injury And Inflammation, Michael S. Valentine

Theses and Dissertations

Patients with severe lung pathologies, such as Acute Respiratory Distress Syndrome (ARDS), often require mechanical ventilation as a clinical intervention; however, this procedure frequently exacerbates the original pulmonary issue and produces an exaggerated inflammatory response that potentially leads to sepsis, multisystem organ failure, and mortality. This acute lung injury (ALI) condition has been termed Ventilator-Induced Lung Injury (VILI). Alveolar overdistension, cyclic atelectasis, and biotrauma are the primary injury mechanisms in VILI that lead to the loss of alveolar barrier integrity and pulmonary inflammation. Stress and strains during mechanical ventilation are believed to initiate alveolar epithelial mechanotransduction signaling mechanisms that contribute …

Enhanced Label Free Normal And Cancer Cells Classification Using Combined Parametric Modeling And Optical Techniques, Ayshathul Fouzia Abdul Gani

Dissertations

The development of label-free methods for cell classifications has been driven by the importance of early detection and identification of cancer disease. The future point-of-care (POC) treatment methods require rapid and real-time cancer screening techniques. As the labelled methods of cell classification are time-consuming processes and require a large amount of sample preparation along with skilled persons, they do not appear to be suitable for POC treatment methods. This necessitates the importance of such development. The label-free methods incorporate the biophysical properties of cells instead of biomarkers. The optical properties of cells have been frequently utilized for cell classification. This …

Development Of A Low-Cost, Open Source Miniature Rotary Cell Culture System To Simulate Microgravity Within An Irradiated Environment, Elizabeth Vargis, Jr Dennison

Browse all Datasets

A major challenge for astronauts in long-duration space travel is combatting the hazardous spaceflight environment caused by microgravity and increased levels of ionizing radiation. Microgravity damages cellular DNA by increasing the production of harmful reactive oxygen species, while ionizing radiation damages DNA by creating double-stranded DNA (dsDNA) breaks. Cellular damage due to microgravity and radiation has been investigated using ground-based models, but most models consider microgravity and ionizing radiation alone, or asynchronously. Synchronous modeling better mimics spaceflight conditions and can be used to understand the combined effects of microgravity and ionizing radiation. However, commercially available devices to model microgravity and …

Expression Systems For Synthetic Spider Silk Protein Production, Michaela R. Hugie

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Spider silk is a biodegradable and biocompatible natural material that is stronger than steel and more elastic than nylon. These properties make spider silk a desirable material for many commercial products, ranging from textiles to biomedical materials. Due to spiders’ cannibalistic and territorial nature it is impossible to farm them to produce spider silk at a high enough yield to meet product demands. Therefore, a bioengineered synthetic process is necessary to produce spider silk. Synthetic spider silk has been produced in bacteria, goats, yeast, plants, mammalian cells and silkworms, but none of these processes provided a commercially viable yield or …

Blood Glucose Predictor, Jessica Patterson

Electrical Engineering

For my senior project, I perform data analysis using statistical methods to determine body metrics that correlate with blood glucose levels. Working with Dr. Tina Smilkstein, I take repeat measurements from 6 different volunteers to establish trends in bodily metric data. The data taken includes weight, body fat, pulse rate, VO2, blood glucose, blood pressure, hours slept, and quality of sleep. Using these values, I use the program MiniTab to view results.

A few examples of correlations with blood glucose found in this project are:

• Systolic blood pressure for females had a regression line of 124.0 -0.3366*Blood Pressure. This indicates …

Review Of Naturally Occurring Ammonia In Groundwater And Its Effect On Using Chloramines For Drinking Water Disinfection In Louisiana, Athena Lindsay

Honors Capstones

No abstract provided.

Monitoring Silane Sol-Gel Kinetics With In-Situ Optical Turbidity Scanning And Dynamic Light Scattering, Abul Bashar Mohammad Giasuddin, David W. Britt

Biological Engineering Faculty Publications

Organosilanes (e.g., R’-SiOR₃) provide hydrophobic functionality in thin-film coatings, porous gels, and particles. Compared with tetraalkoxysilanes (SiOR₄), organosilanes exhibit distinct reaction kinetics and assembly mechanisms arising from steric and electronic properties of the R’ group on the silicon atom. Here, the hydrolysis and condensation pathways of n-propyltrimethoxy silane (nPM) and a tri-fluorinated analog of nPM, 3,3,3-trifluoropropyl trimethoxy silane (3F), were investigated under aqueous conditions at pH 1.7, 2.0, 3.0, and 4.0. Prior to hydrolysis, 3F and nPM are insoluble in water and form a lens at the bottom (3F) or top (nPM) of the solutions. This …

Workshop On Convergence In Biological Engineering, Keith Roper

Funded Research Records

No abstract provided.

Application Of Micro-Scale 3d Printing In Pharmaceutics, Andrew Kjar, Yu Huang

Biological Engineering Faculty Publications

3D printing, as one of the most rapidly-evolving fabrication technologies, has released a cascade of innovation in the last two decades. In the pharmaceutical field, the integration of 3D printing technology has offered unique advantages, especially at the micro-scale. When printed at a micro-scale, materials and devices can provide nuanced solutions to controlled release, minimally invasive delivery, high-precision targeting, biomimetic models for drug discovery and development, and future opportunities for personalized medicine. This review aims to cover the recent advances in this area. First, the 3D printing techniques are introduced with respect to the technical parameters and features that are …

Mechanisms Of Reduced Vascular Tone Following Arteriogenesis Induced By Femoral Artery Ligation, Christopher Hatch

Biomedical Engineering

The presence of a developed, native collateral network can decrease the severity of ischemic injury proceeding arterial occlusion. The collateral network must under arteriogenesis to enlarge and increase blood flow to the ischemic region. Although there has been tremendous effort attempting to understand the mechanisms of arteriogenesis, no therapies have been successful in improving patient outcome. To better understand the mechanisms involved in arteriogenesis, the effect of nitric oxide production, myogenic tone, and a-adrenergic receptors were evaluated as these have been identified as playing an important role in vascular injury. Arteriogenesis was induced by ligating the femoral artery between the …

Optimization Of Biogas Production By Use Of A Microbially Enhanced Inoculum, Anna Doloman

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

A renewable energy source, biogas, comprises of methane (80%) and carbon dioxide (15%), and is a great alternative to the conventional fossil-based fuels, such as coal, gas and oil. Biogas is created during anaerobic biological digestion of waste materials, such as landfill material, animal manure, wastewater, algal biomass, industrial organic waste etc. A biogas potential from organic waste in the United States is estimated at about 9 million tons per year and technology allows capture of greenhouse gases, such as methane and carbon dioxide, into a form of a fuel. In the light of global climate change and efforts to …

Investigation Of The Biosynthetic Process Of Indigoidine, Yi Chen

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

Indigoidine is a natural blue dye with antioxidant and antimicrobial activities. It has also been used as an indicator for gene expression based on its distinctive blue color. Similar to the industry blue dye indigo, indigoidine has a promising potential to be applied in industry as a blue dye. However, the indigoidine production level in the original microorganisms was very low. Heterologous expression of the responsible synthetase gene in Escherichia coli can facilitate the fast and large-scale production of indigoidine. Also, a good understating of the working mechanism of the synthetase is favorable for the industrial application.

In our previous …

Discovery And Engineering Of An Endophytic Pseudomonas Strain From Taxus Chinensis For Efficient Production Of Zeaxanthin Diglucoside, Ozkan Fidan, Jixun Zhan

Biological Engineering Faculty Publications

Background

Endophytic microorganisms are a rich source of bioactive natural products. They are considered as promising biofertilizers and biocontrol agents due to their growth-promoting interactions with the host plants and their bioactive secondary metabolites that can help manage plant pathogens. Identification of new endophytes may lead to the discovery of novel molecules or provide new strains for production of valuable compounds.

Results

In this study, we isolated an endophytic bacterium from the leaves of Taxus chinensis, which was identified as Pseudomonas sp. 102515 based on the 16S rRNA gene sequence and physiological characteristics. Analysis of its secondary metabolites revealed …

A Study Of Protein And Peptide-Directed Nanoparticle Synthesis For Catalytic Materials, Abdollah Mosleh

Graduate Theses and Dissertations

Nanoparticles have received much attentions due to their unique properties that makes them suitable candidates for a broad range of applications. As the size of particles decreases, their surface area-to-volume ratio would increase which is the main cause of much attention. In addition to the size, their morphologies and compositions may also play important roles for defining unique properties. Nanoparticle synthesis include both bottom-up and top-down strategies. To control the process of inorganic nanoparticles synthesis one could follow the bottom-up approach to have atom-level control over their compositions, morphologies, phases, and sizes which is the subject of this work. Due …

Visualizing Ischemic Skin Flap Necrosis Through Phasor Analysis Of Autofluorescence Lifetime Images, Hallie Ramser Toomer

Graduate Theses and Dissertations

Necrotic skin flaps are difficult to predict and treat due to the lack of quantitative biomarkers. Label-free multiphoton microscopy is well suited for non-invasively monitoring skin metabolism through NAD(P)H and other intrinsic fluorophores, and offers immediate future directions for assessing necrosis in the clinic. The objective of this study was to assess whether phasor FLIM could be used to evaluate skin flap status and treatment efficacy in ex vivo skin sections. Phasor maps revealed differences in growth factor treatment and region, but changes in skin flap autofluorescence at 755nm excitation and 460nm emission were not just related to NAD(P)H. A …

Characterization Of Biofilms In A Synthetic Rhizosphere Using Hollow Fiber Root-Mimetic Systems, Michelle Bonebrake

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The area around a plant’s roots hosts a complex and diverse microbial community. This environment can include a large number of bacteria that live on the surface of the root and benefit from the nutrients that the roots exude into the soil. These microbes can in turn be beneficial to the plant by protecting the roots from harmful fungi or stressful environmental conditions such as drought. In this thesis, several root-mimetic systems (RMSs) were developed for the study and growth of plant-beneficial bacteria in the laboratory environment. The RMS uses a porous hollow fiber used in hemodialysis as a surface …

Spiderworms: Using Silkworms As Hosts To Produce A Hybrid Silkworm-Spider Silk Fiber, Ana Laura Licon

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Spider silk has received significant attention due to its fascinating mechanical properties. Given the solitary and cannibalistic behavior of spiders, spider silk farming is impractical. Unlike spiders, silkworms are capable of producing large quantities of a fibrous product in a manner mimetic to spiders, and there already exists an industry to process cocoons into threads and textiles for many applications. The combination of silk farming (sericulture), a millennia old practice, and modern advancements in genetic engineering has given rise to an innovative biomaterial inspired by nature; transgenic silkworm silk.

This project focuses on the creation of chimeric silkworm-spider silk fibers …

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

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

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 …

Modified Substrate Specificity Of A Methyltransferase Domain By Protein Insertion Into An Adenylation Domain Of The Bassianolide Synthetase, Fuchao Xu, Russell Butler, Kyle M. May, Megi Rexhepaj, Dayu Yu, Jiachen Zi, Yi Chen, Yonghong Liang, Jia Zeng, Joan Hevel, Jixun Zhan

Chemistry and Biochemistry Faculty Presentations

Background: Creating designer molecules using a combination of select domains from polyketide synthases and/or nonribosomal peptide synthetases (NRPS) continues to be a synthetic goal. However, an incomplete understanding of how protein-protein interactions and dynamics affect each of the domain functions stands as a major obstacle in the field. Of particular interest is understanding the basis for a class of methyltransferase domains (MT) that are found embedded within the adenylation domain (A) of fungal NRPS systems instead of in an end-to-end architecture.

Results: The MT domain from bassianolide synthetase (BSLS) was removed and the truncated enzyme BSLS-ΔMT was recombinantly expressed. The …

Design, Development, And Field Testing A Visnir Integrated Multi-Sensing Soil Penetrometer, Nuwan K. Wijewardane

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

The research community in soil science and agriculture lacks a cost-effective and rapid technology for in situ, high resolution vertical soil sensing. Visible and near infra-red (VisNIR) technology has the potential to be used for such sensor development due to its ability to derive multiple soil properties rapidly using a single spectrum. Such efforts must, however, overcome a few challenges: (i) a dry ground soil spectral library that can be used to predict the target soil properties accurately, (ii) a robust design which can acquire high quality VisNIR spectra of soil, (iii) an effective method that can link field intact …

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

Biomedical Engineering ETDs

Small, biologically active molecules with unique properties and applications are potential solutions to a wide range of threats to global health including infectious agents and neurodegenerative disease. Experimental studies on a class of oligomeric p-phenylene ethynylenes (OPEs) have shown potential both as bioactive antimicrobials and fluorescent sensing agents for tracking amyloid-β (Aβ) aggregates found in Alzheimer’s Disease (AD). A second type of small molecule with potential applications in AD therapy, curcumin, has been found to interfere with Aβ fibril growth. Curcumin also attenuates Aβ-membrane interactions and Aβ toxicity. Our goal has been to use computational techniques to better understand the …