Biological Engineering Commons^™

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 …

In-Cage Surface Wetting System For Cooling Poultry In Transport, Ryan Clark

Biological and Agricultural Engineering Undergraduate Honors Theses

Abstract

Poultry health and mortality rates are important considerations in poultry production, as companies can minimize product loss and appeal to a consumer base whose concern for animal welfare continues to grow. Although animal welfare is a consideration for the entire poultry production process, this project focuses on the live-haul phase of the process, specifically during transport from grow houses to processing facilities. During the summer months, broiler chickens being transported can suffer from heat stress that can lead to death. This project consists of the designing and testing of an in-cage surface wetting system to minimize heat stress incidents …

Silane Modulation Of Protein Conformation And Self-Assembly, Abul Bashar Mohammad Giasuddin

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This research focused on development of nanoparticle- based therapeutics against amyloid fibrils. Amyloid fibrils are associated with various diseases such as Parkinson’s, Huntington’s, mad cow disease, Alzheimer’s, and cataracts. Amyloid fibrils develop when proteins change their shape from a native form to a pathogenic “misfolded” form. The misfolded proteins have the ability to recruit more native proteins into the pathogenic forms, which self-assemble into amyloid fibrils that are hallmarks of the various protein-misfolding diseases listed above. Amyloid fibrils are highly resistant to degradation, which may contribute to the symptoms of amyloid diseases. Synthetic drugs, natural compounds, and antibodies are widely …

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 …

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 …

Pharmacokinetic Modeling Of 99mtc-Hmpao Images Of Isolated Perfused Rat Lungs, Katherine C. Barry

Master's Theses (2009 -)

The single-photon emission tomography (SPECT) imaging biomarker technetium-labeled hexamethylpropyleneamine oxime (99mTc-HMPAO) exists in two forms, the oxidized, cell-permeable form and the reduced, cell-impermeable form. Recent studies revealed that the lung uptake of 99mTc-HMPAO increases early in rat models of human acute lung injury. Lung uptake of 99mTc-HMPAO is the net result of multiple cellular and vascular processes, many of which can vary with acute illness. Thus, when a change in the lung uptake of 99mTc-HMPAO is detected, it is unclear how much of this change is due to alteration in the activity of the targeted cellular process versus alteration of …

Tumor-Targeted Double Emulsions For Ultrasound-Triggered Delivery Of Molecular Therapeutics., Connor S Centner

Electronic Theses and Dissertations

Cancer is the second leading cause of death in the United States, with 1.74 million new cancer cases diagnosed and 610,000 cancer deaths expected in 2018 alone. Current treatments often result in negative systemic effects and ineffective treatment of the tumor. Drug delivery vehicles have been developed for more effective local delivery methods, but many drug delivery vehicles lack spatial and temporal control. Targeted double emulsions are a new class of drug delivery vehicles which present a promising option for a high payload and controlled delivery. The purpose of our project was to develop and characterize an aptamer-chelated double emulsion …

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. …

Probing The Effects Of Substrate Stiffness On Astrocytes Mechanics, Ariege Bizanti

Electronic Theses and Dissertations

Astrocytes are among the most functionally diverse population of cells in the central nervous system (CNS) as they are essential to many important neurological functions including maintaining brain homeostasis, regulating the blood brain barrier, and preventing build-up of toxic substances within the brain, for example. Astrocyte importance to brain physiology and pathology has inspired a host of studies focused on understanding astrocyte behavior primarily from a biological and chemical perspective. However, a clear understanding of astrocyte dysfunction and their link to disease has been hampered by a lack of knowledge of astrocyte behavior from a biomechanical perspective. Furthermore, astrocytes (and …

Efficient One‑Step Fusion Pcr Based On Dual‑Asymmetric Primers And Two‑Step Annealing, Yilan Liu, Jinjin Chen, Anders Thygesen

Department of Chemical and Biomolecular Engineering: Faculty Publications

Gene splicing by fusion PCR is a versatile and widely used methodology, especially in synthetic biology. We here describe a rapid method for splicing two fragments by one-round fusion PCR with a dual-asymmetric primers and two-step annealing (ODT) method. During the process, the asymmetric intermediate fragments were generated in the early stage. Thereafter, they were hybridized in the subsequent cycles to serve as template for the target full-length product. The process parameters such as primer ratio, elongation temperature and cycle numbers were optimized. In addition, the fusion products produced with this method were successfully applied in seamless genome editing. The …

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 …

Regulation Of Pituitary Progenitor Differentiation By Β-Catenin, Julie Leann Youngblood

Theses and Dissertations

The pituitary gland is a critical organ that is necessary for many physiological processes, including growth, reproduction, and stress response. These vital processes are regulated through the secretion of pituitary hormones from specialized cell types. Pituitary hormone-producing cells arise from a common pool of pituitary progenitors in the developing Rathke’s pouch, and mutations that disrupt the formation and differentiation of pituitary progenitors often result in hypopituitarism, pituitary adenomas, or craniopharyngiomas. Thus, it is necessary to determine the mechanisms of pituitary development in order to understand the ways in which these congenital defects and tumors develop and disrupt pituitary function. Canonical …

A Collaborative Solution To Harmful Algal Blooms In Utah, Kyle Hillman, Bethany Jensen, Ammon Balle

Research on Capitol Hill

Harmful algal blooms (HABs)…

• affect Utah Lake, Scofield Reservoir, Jordanelle Reservoir, Mantua Lake, and other water bodies throughout Utah
• are toxic to public health, the environment, and the economy

Characterization And Engineering Of Human Proteins As Therapeutic Candidates, Kyungbo Kim

Theses and Dissertations--Pharmacy

Protein engineering has been a useful tool in the fight against human diseases. Human insulin was the first recombinant DNA-derived therapeutic protein (Humulin^®) approved by the US FDA in 1982. However, many of the early protein drugs were only recombinant versions of natural proteins with no modification of their primary amino acid sequence and most of them did not make optimal drug products mainly due to their short half-life or suboptimal affinity, leading to poor therapeutic efficacy. The difficulty in the large-scale production of some therapeutic proteins was another important issue. In the past three decades, different protein …

The Visual Ecology Of Speyeria Mormonia, Natalie Sanchez Gonzalez

Theses and Dissertations

Variations in environmental factors such as temperature, precipitation, and day length during larval development are known to affect morphological traits in butterflies related to their visual ecology, including eye size and wing color. These vision-related traits are important for the ability of diurnal butterfly species to detect mates, especially at long distances. Thus, changes in environmental conditions may result in phenotypic modifications to butterflies which may alter their visual ecology and subsequently, their reproductive fitness. To study the interaction of phenotypic plasticity and visual ecology in the Mormon Fritillary, Speyeria mormonia, I set up a natural-laboratory experiment at the Rocky …

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 …

Molded Features In Pdms For Fabricating Bacterial Cellulose For Various Geometries, Mitchell Habegger

Williams Honors College, Honors Research Projects

The purpose of producing features on bacterial cellulose (BC) is to facilitate the elongation and alignment for cells, in this case Normal Human Dermal Fibroblast (NHDF) cells. The elongated cells have applications in wound healing, tissue engineering, disease diagnostics, and many other fields. Experiments were run to test the effectiveness of transferring features to BC sheets from features induced by fracturing on polydimethylsiloxane (PDMS) and those duplicated from molds with existing features. The features were duplicated to BC sheets by either air drying or Guided Assembly-Based Biolithography (GAB). The research results showed that fracture inducing on PDMS produced very small …

Integration Of Biology, Ecology And Engineering For Sustainable Algal‑Based Biofuel And Bioproduct Biorefinery, James Allen, Serpil Unlu, Yaşar Demirel, Paul N. Black, Wayne R. Riekhof

Department of Chemical and Biomolecular Engineering: Faculty Publications

Despite years of concerted research efforts, an industrial-scale technology has yet to emerge for production and conversion of algal biomass into biofuels and bioproducts. The objective of this review is to explore the ways of possible integration of biology, ecology and engineering for sustainable large algal cultivation and biofuel production systems. Beside the costs of nutrients, such as nitrogen and phosphorous, and fresh water, upstream technologies which are not ready for commercialization both impede economic feasibility and conflict with the ecological benefits in the sector. Focusing mainly on the engineering side of chemical conversion of algae to biodiesel has also …

The Effects Of Emerging Technology On Healthcare And The Difficulties Of Integration, Skyler J. Pavlish-Carpenter

Honors Undergraduate Theses

Background: Disruptive technology describes technology that is significantly more advanced than previous iterations, such as: 3D printing, genetic manipulation, stem cell research, innovative surgical procedures, and computer-based charting software. These technologies often require extensive overhauls to implement into older systems and must overcome many difficult financial and societal complications before they can be widely used. In a field like healthcare that makes frequent advancements, these difficulties can mean that the technology will not be utilized to its full potential or implemented at all.

Objective: To determine the inhibiting factors that prevent disruptive technology from being implemented in conventional healthcare.

Methods: …

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 …

Plants As Biofactories To Produce Mammalian Tumor Suppressor Micrornas, John Lachlan Macarthur

Theses and Dissertations

MicroRNAs (miRNAs) are small noncoding single stranded RNAs that are considered master regulators of gene expression. They are also an emerging class of therapeutic agents with significant potential for the prevention and treatment of many diseases, including cancer. Many different forms of cancer are associated with loss or reduced accumulation of one or more miRNAs that function as tumor suppressors. In animal models, restoration of missing tumor suppressor miRNAs prevents the initiation, progression and/or spread of the disease. However, the current absence of an efficient method for delivery of therapeutic miRNAs is a critical barrier to their use. The research …

Changes Of Dispersal Ability In An Isolated Population, Connor Bacon

Theses and Dissertations

Dispersal is a core mechanism in the maintenance of metapopulations. It maintains genetic diversity by connecting subpopulations and generates new populations to replace those that die out. However, as populations become more isolated, as occurs in habitat fragmentation, dispersal becomes more difficult. This should lead to selective pressure against dispersive individuals, causing a reduction in dispersal traits. Over time, this can lead to variation in dispersal traits among populations. We examine this idea using an extreme case of isolation in Euphydryas gillettii, a population that has remained completely isolated for forty years. By comparing this population to a baseline established …

Screening Of Novel Active Salicylic Acid Analogs And Identification Of A Bacterial Effector Targeting Key Proteins Involved In Salicylic Acid-Mediated Defense, Ian Palmer

Theses and Dissertations

The master regulator of salicylic acid (SA)-mediated plant defense, NPR1 (NONEXPRESSER OF PR GENES 1), and its paralogs NPR3 and NPR4 act as SA receptors. After the perception of a pathogen, plant cells produce SA in the chloroplast. In the presence of SA, NPR1 protein is reduced from oligomers to monomers, and translocated into the nucleus. There, NPR1 binds to TGA and WRKY transcription factors to induce expression of plant defense genes. EDS1 and PBS3 are two key proteins involved in SA biosynthesis. Previous research has shown that several plant pathogens produce SA hydroxylases. These pathogen-produced hydroxylases act to degrade …