Biological Engineering Commons^™

Whole Cell Cross-Linking To Discover Host-Microbe Protein Cognate Receptor/Ligand Pairs, Bart C. Weimer, Poyin Chen, Prerak T. Desai, Dong Chen, Jigna Shah

Biological Engineering Faculty Publications

Bacterial surface ligands mediate interactions with the host cell during association that determines the specific outcome for the host–microbe association. The association begins with receptors on the host cell binding ligands on the microbial cell to form a partnership that initiates responses in both cells. Methods to determine the specific cognate partnerships are lacking. Determining these molecular interactions between the host and microbial surfaces are difficult, yet crucial in defining biologically important events that are triggered during association of the microbiome, and critical in defining the initiating signal from the host membrane that results in pathology or commensal association. In …

Developing Droplet Based 3d Cell Culture Methods To Enable Investigations Of The Chemical Tumor Microenvironment, Jacqueline Alexandria De Lora

Biomedical Sciences ETDs

Adaptation of cancer cells to changes in the biochemical microenvironment in an expanding tumor mass is a crucial aspect of malignant progression, tumor metabolism, and drug efficacy. In vitro, it is challenging to mimic the evolution of biochemical gradients and the cellular heterogeneity that characterizes cancer tissues found in vivo. It is well accepted that more realistic and controllable in vitro 3D model systems are required to improve the overall cancer research paradigm and thus improve on the translation of results, but multidisciplinary approaches are needed for these advances. This work develops such approaches and demonstrates that new droplet-based cell-encapsulation …

Wearable Assistive Technologies For Autism: Opportunities And Challenges, Emma Mansouri Benssassi, Juan-Carlos Gomez, Louanne E. Boyd, Gillian R. Hayes, Juan Ye

Engineering Faculty Articles and Research

Autism is a lifelong developmental condition that affects how people perceive the world and interact with others. Challenges with typical social engagement, common in the autism experience, can have a significant negative impact on the quality of life of individuals and families living with autism. Recent advances in sensing, intelligent, and interactive technologies can enable new forms of assistive and augmentative technologies to support social interactions. However, researchers have not yet demonstrated effectiveness of these technologies in long-term real-world use. This article presents an overview of the social and sensory challenges of autism, which offer great opportunities and challenges for …

Comparative Analysis Of Physiological Measurements And Environmental Metrics On Predicting Heat Stress Related Events, Mckenzie Lee Barlow

Master's Theses

Exposure to high heat and humidity can lead to serious health risks, including heat exhaustion and heat stroke. Wet Bulb Globe Temperature (WBGT) and heat index have historically been used to predict heat stress events, but individualized factors are not included in the measurement. It has been shown that there is a relationship between cardiovascular measurements and heat stress, which could be used to measure heat stress risk on an individual level. Research has been done to find relationships between cardiovascular metrics in a workplace environment, however the study did not include the use of a controlled environment as a …

Radical Social Ecology As Deep Pragmatism: A Call To The Abolition Of Systemic Dissonance And The Minimization Of Entropic Chaos, Arielle Brender

Student Theses 2015-Present

This paper aims to shed light on the dissonance caused by the superimposition of Dominant Human Systems on Natural Systems. I highlight the synthetic nature of Dominant Human Systems as egoic and linguistic phenomenon manufactured by a mere portion of the human population, which renders them inherently oppressive unto peoples and landscapes whose wisdom were barred from the design process. In pursuing a radical pragmatic approach to mending the simultaneous oppression and destruction of the human being and the earth, I highlight the necessity of minimizing entropic chaos caused by excess energy expenditure, an essential feature of systems that aim …

Nutrient Limitation Of Algal Growth In Fishery Lakes, Madeline Ludwig

Biological and Agricultural Engineering Undergraduate Honors Theses

This study investigated the effect of nutrient addition on algal growth in three United States Forest Service lakes for fishery management in Arkansas. In fishery managed lakes, fertilization works by manipulating algae growth, a basal food resource in lakes, to promote the growth of the fish population. For the nutrient addition experiments, water was collected from each lake in cubitainers and spiked with nutrients; the treatments included the control, nitrogen (+N), phosphorus (+P), and nitrogen and phosphorus (+N +P). When algal growth was visually observed, a water sample was collected from each cubitainer and analyzed for chlorophyll-α. The results showed …

Optimizing Genetic Manipulation Of Methanogens Through Faster Cloning Techniques, Merrisa Jennings

Biological and Agricultural Engineering Undergraduate Honors Theses

Methanogenesis is the biological production of methane. Only anaerobic archaea known as methanogens are capable of such a metabolic feat. They have strict living conditions and substrate sources which determine their rate of metabolism. This is of particular importance from a greenhouse gas reduction perspective or biogas capturing perspective. One of the best ways to optimize methanogen methane production is via genetic manipulation. The current procedures are timely though, therefore a faster cloning processes should be developed. The objective of this study was to optimize a premade genetic transformation kit known as the Gibson Kit. The Gibson Kit was supposed …

Transcriptomics To Develop Biochemical Network Models In Cyanobacteria, Bridget E. Hegarty, Jordan Peccia, Ratanachat Racharaks

Yale Day of Data

Through targeted genetic manipulations guided by network modeling, we will create a flexible, cyanobacteria-based platform for the production of biofuel-precursors and valuable chemical products. To build gene-metabolite predictive models, we have characterized Synecococcus elongatus sp. UTEX 2973’s (henceforth, UTEX 2973) gene expression and metabolite production under a number of environmental conditions.

Dynamic Classification Of Moisture Stress Using Canopy And Leaf Temperature Responses To A Step Changes Of Incident Radiation, Erin E. Stevens, George E. Meyer, Ellen T. Paparozzi

Honors Program: Senior Projects (Public)

Environmental conditions affect plant productivity and understanding how plants respond to drought stress can be measured in different ways. This study focused on measuring leaf response time to induced water stress. Leaf response time to a step increase and step decrease in radiation was computed for four species of well-watered and water-stressed plants in a controlled environment. The canopy temperature was measured with an infrared thermometer and a thermal imaging camera. Thermal images were analyzed to determine the average temperature of a selected single, unobstructed leaf at the top of the canopy. Both the canopy response time and the single …

Exogenous Fniii 12-14 Regulates Tgf-Β1-Induced Markers, Hilmi M. Humeid

Theses and Dissertations

The extracellular matrix protein Fibronectin (FN) plays an important role in cell contractility, differentiation, growth, adhesion, and migration. The 12th -14th Type III repeats of FN (FNIII 12-14), also referred to as the Heparin-II domain, comprise a highly promiscuous growth factor (GF) binding region. This binding domain aids in cellular signaling initiated from the ECM. Additionally, FN has the ability to assemble into fibrils under certain conditions, mostly observed during cell contractile processes such as those that initiate due to upregulation of Transforming Growth Factor Beta 1 (TGF-β1) [1], [2]. Previous work from our lab has shown that self-assembly of …

Enhanced Hot Electron Lifetimes In Quantum Wells With Inhibited Phonon Coupling, Hamidreza Esmaielpour, Vincent R. Whiteside, Herath P. Piyathilaka, Sangeetha Vijeyaragunathan, Bin Wang, Echo Adcock-Smith, Kenneth P. Roberts, Tetsuya D. Mishima, Michael B. Santos, Alan D. Bristow, Ian R. Sellers

Faculty & Staff Scholarship

Hot electrons established by the absorption of high-energy photons typically thermalize on a picosecond time scale in a semiconductor, dissipating energy via various phonon-mediated relaxation pathways. Here it is shown that a strong hot carrier distribution can be produced using a type-II quantum well structure. In such systems it is shown that the dominant hot carrier thermalization process is limited by the radiative recombination lifetime of electrons with reduced wavefunction overlap with holes. It is proposed that the subsequent reabsorption of acoustic and optical phonons is facilitated by a mismatch in phonon dispersions at the InAs-AlAsSb interface and serves to …

Mutagenesis Of Human Alpha-Galactosidase A For The Treatment Of Fabry Disease, Erin Stokes

Dissertations, Theses, and Capstone Projects

Fabry disease is an X-linked lysosomal storage disorder caused by the deficiency of the enzyme, α-galactosidase A, which results in the accumulation of the lipid substrate. This accumulation results in obstruction of blood flow in patients and early demise at approximately 40-60 years of age. There is currently only one FDA approved treatment (Fabrazyme) classified as an enzyme replacement therapy. However, approximately 88% of patients experience a severe immune response that, rarely, can be fatal and is a huge cost burden at average $250,000 a year per patient. The structure of α-galactosidase A has been previously determined to be a …

Rice Hull Bioreactor For Recirculating Aquaculture, Marlon A. Greensword

LSU Doctoral Dissertations

The engineering of floating media biofilters has been optimized over the years. The backwashing process has made them more energy and water efficient. Likewise, moving bed bioreactors (MBBR) are gaining interest and popularity because they are relatively affordable to build. Yet, developing countries’ aquaculture production remains largely excluded from the advances made in recirculating aquaculture systems (RAS). This discrepancy is partially driven by the high costs of media such plastic beads and Kaldnes (KMT) media, commonly used in MBBR.

This dissertation evaluates the usability and profitability of rice hulls (RH), an abundant by-product in many developing nations, as a sinking …

Establishing A Lung Model For Evaluation Of Engineered Lung Microbiome Therapies, Kathryn F. Atherton, Stephen Miloro, Jenna Rickus

The Summer Undergraduate Research Fellowship (SURF) Symposium

Benzene, a toxin and carcinogen found in air polluted by cigarette smoke, car exhaust, and industrial processes, is associated with the development of leukemia and lymphoma. Other than avoiding exposure, there is no current method to deter the effects of benzene. One potential strategy to prevent these effects is to engineer the bacteria of the human lung microbiome to degrade benzene. To evaluate this novel approach, we must verify that the bacteria remain viable within the lung microenvironment. To do so, lungs were harvested from rats and swabbed to determine the contents of the original lung microbiome. Then green fluorescent …

The Response Of Schwann Cells To Weak Dc Electric Fields, Alexander T. Lai, Jianming Li

The Summer Undergraduate Research Fellowship (SURF) Symposium

Schwann cells are glial cells that serve the vital role of supporting neurons in the peripheral nervous system. While their primary function is to provide insulation (myelin) for axons, they also help regenerate injured axons by digesting severed axons and providing scaffolding to guide the regeneration process. This specific role of Schwann cells makes them highly important cellular targets following nerve injury. Although some efforts have been made to encourage Schwann cell migration after nerve damage, the use of electric fields to control cell responses remain unexplored; therefore, this experiment serves to characterize the behavior of Schwann cells to weak …

Evaluating Thermal Comfort Of Broiler Chickens During Transportation Using Heat Index And Simulated Electronic Chickens, Kaushik Luthra

Graduate Theses and Dissertations

Broilers experience high physiological stress during pre-slaughter transport, especially under extremes of thermal environment. Characterization of thermal environment on the trailer is crucial to identify stress-prone regions during transportation. At the same time, Broilers experience high physiological stress during pre-slaughter transport, especially under extremes of thermal environment. Characterization of thermal environment on the trailer is crucial to identify stress-prone regions during transportation. At the same time, quantification of heat loss of the broilers loaded on trailers is important in understanding the well-being of the broilers. We have developed four electronic chickens (E-chickens) to simulate the sensible heat loss of live …

Mushroom Inoculation On Switchgrass Feedstock During Storage: Effects Of Subsequent Pre-Processing For Intended Biofuels Production, Amandeep Singh Turay

Graduate Theses and Dissertations

The objective of this project was to examine the effect of fungal treatment and liquid hot water pretreatment of switchgrass combine in view of increasing glucose release. The fungal treatment consisted of incubating Pleurotus ostreatus in square switchgrass bales, at 50% moisture content for 25 days, 54 days, and 82 days. The digestibility of the switchgrass biomass was subsequently evaluated using Accelerase 1500 enzyme. Lignin is an important barrier to enzymatic hydrolysis, and it was stipulated that incubation with P. ostreatus would disrupt plant cell walls, resulting in enhanced saccharification. Three different concentrations of P. ostreatus were evaluated: 0%, 2%, …

Mri Applications In Tissue Engineering, Shadi Othman

Science Seminar Series

Shadi Othman of the School of Engineering and Computer Science Bioengineering Program, will speak on his research on MRI applications in tissue engineering.

Characterization Of Murine Breast Cancer Cell Lines For Anti-Cancer Vaccine, Haven N. Frazier

Biological Sciences Undergraduate Honors Theses

Breast cancer is the most commonly diagnosed cancer in women and the second leading cause of cancer death among women in the United States (1). While treatments involving radiation and chemotherapy currently exist, disease must be detected early in order for the treatments to be somewhat effective, and there is no effective treatment after metastasis occurs (2). Additionally, current therapies do not mitigate tumor immunosuppression. Decreasing the tumor-associated immunosuppressive conditions while activating antitumor immunity could prevent recurrence and metastasis, possibly leading to an effective treatment for cancer (3). Tumor cell vaccines could possibly address this issue and have become a …

Differentiation And Containment Of Derived Pancreatic Beta Cells, Caden Duffy, Alonzo Cook Ph.D.

Biomedical Engineering Western Regional Conference

Currently, the only permanent cure for Type 1 Diabetes is a pancreatic or islet transplant. With the shortage of donors, we are progressing research towards alternative therapies by differentiating induced pluripotent stem cells into derived pancreatic β-cells that can be transplanted and used as treatment for Type 1 Diabetes. We are investigating methods to increase the yield of fully derived, insulin producing pancreatic β-cells and are additionally researching the use of hydrophilized expanded polytetrafluoroethylene for use in cell containment devices. These devices could offer a future alternative for islet transplantation in human patients.

Fractionation And Characterization Of Lignin Streams From Genetically Engineered Switchgrass, Enshi Liu

Theses and Dissertations--Biosystems and Agricultural Engineering

Development of biomass feedstocks with desirable traits for cost-effective conversion is one of the main focus areas in biofuels research. As suggested by techno-economic analyses, the success of a lignocellulose-based biorefinery largely relies on the utilization of lignin to generate value-added products, i.e. fuels and chemicals. The fate of lignin and its structural/compositional changes during pretreatment have received increasing attention; however, the effect of genetic modification on the fractionation, depolymerization and catalytic upgrading of lignin from genetically engineered plants is not well understood. This study aims to fractionate and characterize the lignin streams from a wild-type and two genetically engineered …

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 …

Characterization Of Molecular Communication Based On Cell Metabolism Through Mutual Information And Flux Balance Analysis, Zahmeeth Sayed Sakkaff

School of Computing: Dissertations, Theses, and Student Research

Synthetic biology is providing novel tools to engineer cells and access the basis of their molecular information processing, including their communication channels based on chemical reactions and molecule exchange. Molecular communication is a discipline in communication engineering that studies these types of communications and ways to exploit them for novel purposes, such as the development of ubiquitous and heterogeneous communication networks to interconnect biological cells with nano and biotechnology-enabled devices, i.e., the Internet of Bio-Nano Things. One major problem in realizing these goals stands in the development of reliable techniques to control the engineered cells and their behavior from the …

Examination Of Pseudomonas Fluorescence As A Recombinant Expression Host: Cloning, Expression, And Chromatography, Ahmed K.Ali Elmasheiti

Graduate Theses and Dissertations

In an effort to expand the pool of bacterium useful for biotechnology applications, Pseudomonas fluorescens, a common gram negative microbe, was examined for its ability to function in a recombinant setting. P. fluorescens is ubiquitous in nature and was initially identified as a soil bacterium found in dirt and is typically associated with plant material. Past literature indicates that it shared characteristics common to Escherichia coli and Bacillus subtilis, including simple growth conditions and potential cloning vectors, providing motivation to look into both the upstream and downstream characteristics of this bacterium. First, it was demonstrated that P. fluorescens could be …

A Bifunctional Nanocomposites Based Electrochemical Biosensor For In-Field Detection Of Pathogenic Bacteria In Food, Meng Xu

Graduate Theses and Dissertations

This research focused on the application of electrochemical biosensors for the rapid detection of pathogenic bacteria, Escherichia coli O157:H7 and Salmonella Typhimurium, in foods. The possible presence of pathogenic bacteria in foods has always been a great threat to the wellbeing of people and the revenue of food companies. Therefore, the demand for rapid and sensitive methods to detect foodborne pathogens is growing. In this research, an impedimetric immunosensor was first developed for the rapid detection of E. coli O157:H7 and S. Typhimurium in foods. It was based on the techniques of immunomagnetic separation, enzyme labelling, and electrochemical impedance spectroscopy …

A Portable And Automatic Biosensing Instrument For Detection Of Foodborne Pathogenic Bacteria In Food Samples, Zhuo Zhao

Graduate Theses and Dissertations

Foodborne diseases are a growing public health problem. In recent years, many rapid detection methods have been reported, but most of them are still in lab research and not practical for use in the field. In this study, a portable and automatic biosensing instrument was designed and constructed for separation and detection of target pathogens in food samples using nanobead-based magnetic separation and quantum dots (QDs)-labeled fluorescence measurement. The instrument consisted of a laptop with LabVIEW software, a data acquisition card (DAQ), a fluorescent detector, micro-pumps, stepper motors, and 3D printed tube holders. First, a sample in a syringe was …

Importance Of Heat And Pressure For Solubilization Of Recombinant Spider Silk Proteins In Aqueous Solution, Justin A. Jones, Thomas I. Harris, Paula F. Oliveira, Brianne E. Bell, Abdulrahman Alhabib, Randolph V. Lewis

Biology Faculty Publications

The production of recombinant spider silk proteins continues to be a key area of interest for a number of research groups. Several key obstacles exist in their production as well as in their formulation into useable products. The original reported method to solubilize recombinant spider silk proteins (rSSp) in an aqueous solution involved using microwaves to quickly generate heat and pressure inside of a sealed vial containing rSSp and water. Fibers produced from this system are remarkable in their mechanical ability and demonstrate the ability to be stretched and recover 100 times. The microwave method dissolves the rSSPs with dissolution …

Development Of In Vivo Systems For Detecting And Studying Ribosome Inhibition By Small Molecules, Shijie Huang

Chemistry and Chemical Biology ETDs

The ribosome is the quintessential antibacterial drug target, with many structurally and mechanistically distinct classes of antibacterial agents acting by inhibiting ribosome function. Detecting and quantifying ribosome inhibition by small molecules and investigating their binding modes and mechanisms of action are critical to antibacterial drug discovery and development efforts. To develop a ribosome inhibition assay that is operationally simple, yet provides direct information on the drug target and the mechanism of action, we have developed engineered E. coli strains harboring an orthogonal ribosome controlled green fluorescent protein reporter that produce fluorescent signal when the O-ribosome is inhibited. As a proof …

Ionic Basis Of Ventricular Action Potentials, Ariel L. Escobar

Science Seminar Series

Dr. Escobar will talk about his cutting-edge approach to understanding molecular mechanisms underlying electrical activity in the heart.

Nanobubbles Provide Theranostic Relief To Cancer Hypoxia, Christopher M. Long, Pushpak N. Bhandari, Joseph Irudayaraj

The Summer Undergraduate Research Fellowship (SURF) Symposium

Hypoxia is a common motif among tumors, contributing to metastasis, angiogenesis, cellular epigenetic abnormality, and resistance to cancer therapy. Hypoxia also plays a pivotal role in oncological studies, where it can be used as a principal target for new anti-cancer therapeutic methods. Oxygen nanobubbles were designed in an effort to target the hypoxic tumor regions, thus interrupting the hypoxia-inducible factor-1α (HIF-1α) regulatory pathway and inhibiting tumor progression. At less than 100nm, oxygen nanobubbles act as a vehicle for site-specific oxygen delivery, while also serving as an ultrasound contrast agent for advanced imaging purposes. Through in vitro and in vivo studies, …