Biochemical and Biomolecular Engineering Commons^™

Understanding Glycoside Hydrolase Processivity For Improved Biomass Conversion, Suvamay Jana

Theses and Dissertations--Chemical and Materials Engineering

In nature, organisms secrete synergistic enzyme cocktails to deconstruct crystalline polysaccharides, such as cellulose and chitin, to soluble sugars. The cocktails consist of multiple classes of processive and non-processive glycoside hydrolases (GH) that aid in substrate accessibility and reduce product inhibition. Processive GHs attach to chain ends and hydrolyze many glycosidic linkages in sequence to produce disaccharide units before dissociation, and as such, are responsible for the majority of hydrolytic bond cleavages. Accordingly, processive GHs are targets for activity improvements towards efficient and economical biomass conversion. However, the mechanism and factors responsible for processivity are still not understood completely at …

Synthesis Of Difluoromethyl And Monofluoromethyl Ketones For Biological Evaluation At The Gaba-B Receptor, Mallory Maier

Honors Theses

The central nervous system communicates using neurotransmitters. Most are excitatory neurotransmitters, such as acetylcholine, dopamine, and serotonin, but

The Pharmacodynamic Functions Of Low-Dose Rapamycin As A Model For Universal Influenza Protection, William Gust

Honors Theses

One of the most sought after breakthroughs in modern influenza research is the creation of a universal influenza vaccine that would protect against all strains of avian influenza. An unlikely model for this kind of protection might be found in the mTOR inhibitor rapamycin. Traditionally used to prevent organ transplant rejection, low doses of rapamycin have been found to protect mice against infection with distinct subtypes of influenza. However, it is not understood how a partial block in this pathway provides optimal heterosubtypic immunity. Interestingly, previous experiments have shown that low dose rapamycin inhibits germinal center formation to reduce antibody …

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 …

Membrane Chromatography For Bioseparations: Ligand Design And Optimization, Zizhao Liu

Graduate Theses and Dissertations

Membrane chromatography, or membrane adsorber, represents an attractive alternative to conventional packed bed chromatography used in downstream processing. Membrane chromatography has many advantages, including high productivity, low buffer consumption and ease to scale up. This doctoral dissertation focuses on developing novel polymeric ligands for protein separations using membrane chromatography. Atom transfer radical polymerization (ATRP), known as a controlled radical polymerization technique, has been used to control the architecture of grafted polymeric ligands. The center theme of this dissertation is to develop new polymeric ligands and investigate how the polymer’s property (e.g. flexibility, hydrophobicity) and architecture (e.g. chain density, chain length) …

Conformationally Superarmed S-Ethyl Glycosyl Donors As Effective Building Blocks For Chemoselective Oligosaccharide Synthesis In One Pot, Mithila Bandara, Jagodige Yasomanee, Nigam Rath, Christian Pedersen, Mikael Bols, Alexei Demchenko

Chemistry & Biochemistry Faculty Works

A new series of superarmed glycosyl donors has been investigated. It was demonstrated that the S-ethyl leaving group allows for high reactivity, which is much higher than that of equally equipped S-phenyl glycosyl donors that were previously investigated by our groups. The superarmed S-ethyl glycosyl donors equipped with a 2-O-benzoyl group gave complete β-stereoselectivity. Utility of the new glycosyl donors has been demonstrated in a one-pot one-addition oligosaccharide synthesis with all of the reaction components present from the beginning.

Subcellular And In-Vivo Nano-Endoscopy, Surya Venkatasekhar Cheemalapati, John Winskas, Hao Wang, Karthik Konnaiyan, Arseny Zhdanov, Alison Roth, Swamy Rakesh Adapa, Andrew Deonarine, Rays H. Y. Jiang, Anna Pyayt

Chemical, Biological and Materials Engineering Faculty Publications

Analysis of individual cells at the subcellular level is important for understanding diseases and accelerating drug discovery. Nanoscale endoscopes allow minimally invasive probing of individual cell interiors. Several such instruments have been presented previously, but they are either too complex to fabricate or require sophisticated external detectors because of low signal collection efficiency. Here we present a nanoendoscope that can locally excite fluorescence in labelled cell organelles and collect the emitted signal for spectral analysis. Finite Difference Time Domain (FDTD) simulations have shown that with an optimized nanoendoscope taper profile, the light emission and collection was localized within ~100 nm. …

Materials And Techniques Used In Cranioplasty Fixation: A Review, Basel A. Khader, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Cranioplasty is the surgical repair of a deficiency or deformity of the skull. The purpose of cranioplasty is to provide protection for the brain following cranial surgery, and to offer relief to psychological disadvantages while increasing social performance. There are several materials that had been used for cranioplasty, but an ideal product has yet to be developed, hence the ongoing research into biologic and non-biologic alternatives to the existing materials. This article critiques the products currently used for cranioplasty in order to facilitate the development of new materials, which can improve patient outcomes.

Methanol And Dimethyl Ether From Renewable Hydrogen And Carbon Dioxide: Alternative Fuels Production And Life-Cycle Assessment, Michael J. Matzen, Yaşar Demirel

Yaşar Demirel Publications

In this work we investigate two renewably based alternative fuels; methanol and dimethyl ether. The ultimate feedstocks for production are wind-based electrolytic hydrogen and carbon dioxide captured from an ethanol fermentation process. Dimethyl ether production was modeled in ASPEN Plus using a previously simulated methanol production facility. The facilities use 18.6 metric tons (mt) of H₂ and 138.4 mt CO₂ per day. Methanol is produced at a rate 96.7 mt/day (99.5 wt%) and dimethyl ether is produced at a rate of 68.5 mt/day (99.6 wt%). A full comparative life-cycle assessment (cradle-to-grave) of both fuels was conducted to investigate …

Development And Characterization Of Oxygen Sensitive Microbial Biosensors, Jonathan Lee

Rose-Hulman Undergraduate Research Publications

Microbial biosensors are useful in detecting suboptimal conditions in a bioreactor. This detection can help in development of improved mixing methods to reduce the occurrence of these conditions. In this research, the activities of 3 promoters known to have activity under anaerobic conditions, the gadB promoter, an FNR protein activated promoter, and the pfl promoter, were tested for activity under anaerobic conditions by connecting them to a green fluorescent protein (GFP) gene. Using two types of media, Luria-Bertani (LB) and Wilms-Reuss media, the activity of these promoters under aerobic and anaerobic conditions were tested. Results indicate that while the FNR …

Biomedical Engineering, William Pitt

BYU Research Development Office Research Networking Conference

Polymeric biomedical materials and drug delivery, with recent emphasis on blood sepsis diagnostics. Today I am looking for collaboration in mathematical modeling of instabilities in sheared 2 phase flow.

Alginate Hydrogels As Three-Dimensional Scaffolds For In Vitro Culture Models Of Growth Plate Cartilage Development And Porcine Embryo Elongation, Taylor D. Laughlin

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

The establishment of in vitro culture models utilizes tissue engineering principles to design functional mimics of in vivo environments in vitro. Advantages for the use of in vitro culture models include ethical alleviation of animal models for therapeutic testing, cost efficiency, and a greater ability to study specific mechanisms via a systematic, ground-up approach to development. In this thesis, alginate hydrogels are utilized in the development of in vitro culture models of porcine embryo elongation and growth plate cartilage development. First, the effect of scaffold and modifications to the scaffold were explored in both projects. In order to modulate …

Hydrothermal Synthesis And Characterisation Of Bioactive Glass-Ceramic Nanorods, Ehsan Zeimaran, Sara Pourshahrestani, Seyed Farid Seyed Shirazi, Belinda Pingguan-Murphy, Nahrizul Adib Kadri, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

In this study fabrication of rod-like bioactive glass-ceramics (BGCs) using hydrothermal treatment based on a sol-gel precursor is reported for the first time. BGCs with composition 58 wt% SiO₂, 33 wt% CaO and 9 wt% P₂O₅ were synthesized in different thermal conditions (200 and 220 °C) and characterised with regard to morphology, chemical composition and crystallinity. The bioactivity of the materials was assessed by immersion in simulated body fluid for up to 7 days. The results revealed that as the reaction temperature increased from 200 to 220 °C, the diameter of rods was reduced from …

Raman Spectroscopic Analysis Of Fingernail Clippings Can Help Differentiate Between Postmenopausal Women Who Have And Have Not Suffered A Fracture, James R. Beattie, Niamh M. Cummins, Clare Caraher, Olive M. O'Driscoll, Aruna T. Bansal, Richard Eastell, Stuart H. Ralston, Michael D. Stone, Gill Pearson, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Raman spectroscopy was applied to nail clippings from 633 postmenopausal British and Irish women, from six clinical sites, of whom 42% had experienced a fragility fracture. The objective was to build a prediction algorithm for fracture using data from four sites (known as the calibration set) and test its performance using data from the other two sites (known as the validation set). Results from the validation set showed that a novel algorithm, combining spectroscopy data with clinical data, provided area under the curve (AUC) of 74% compared to an AUC of 60% from a reduced QFracture score (a clinically accepted …

Local Delivery Of Ctla-4 Blockade Inhibits Growth Of Pancreatic Tumors, Jack Baltz

Biomedical Engineering Undergraduate Honors Theses

Immune checkpoint blockade has demonstrated great potential in activating antitumor immunity. Ipilimumab is a monoclonal antibody which targets cytotoxic T-lymphocyte antigen-4. CTLA-4 belongs to the CD28 class of receptors and is found on the surface of CD4⁺ and CD8⁺ T cells. CTLA-4 acts to suppress the immune system when bound to CD80 and CD86 receptors on antigen presenting cells. Ipilimumab, or anti-CTLA-4, has shown to be effective in significantly extending the survival of patients with metastatic melanoma. However, systemic delivery of Ipilimumab also induces significant side effects such as: colitis, dermatitis, uveitis, and hypophysitis. In order to minimize …

Development Of A Simple Handheld Biosensor For Waterborne Pathogens, Bryce C. Jones

Chemical Engineering Undergraduate Honors Theses

Current methods of detecting waterborne pathogens involve testing strips which take 24-48 hours to yield results, or require expensive equipment in order to function. In minimalist environments, these two technologies are not always applicable to test water quality. With the emergence of a new method of PCR, named LAMP PCR, it is possible to quickly and accurately detect pathogen DNA in a water sample. In order to scale this technique into a simple device, the aspects of the reaction must be accommodated, and a visual detection method chosen. A handheld device which keeps the isothermal LAMP PCR stable for the …

Targeted Drug Delivery Using Peptoid Based Nanospheres, Kaylee J. Smith

Chemical Engineering Undergraduate Honors Theses

While medicine has improved greatly in the last couple of decades, there are negative side effects that accompany many drugs. Undesirable side effects could be greatly reduced if non-systemic drug delivery systems were used because the medicine would harm diseased cells at a much higher rate than it does healthy cells. One possible non-systemic drug delivery system is peptoid nanospheres. These nanospheres will then be linked to another peptoid that is engineered to attach almost exclusively to diseased cells.

This research project is focused on designing peptoids that will form nanospheres in solution. Four specific peptoids were synthesized and tested …

Investigating The Modulation Of Aggregating Amyloid Beta 40, Marlee J. Motes

Chemical Engineering Undergraduate Honors Theses

Amyloid beta protein has been linked to the formation of Alzheimer’s disease in patients.¹ Plaques form from amyloid beta fibrils. The formation of these plaques between neural connections in the brain are associated with Alzheimer’s disease.² The reduction of the formation of fibrils can be linked to utilizing protein mimics. The protocols that are used to reproduce the simulation of amyloid beta in the brain can be very important. Also, the structure of the protein mimic that is being used to inhibit the formation of fibrils can determine how the amyloid beta plaques are reduced.

The structure of sequence KLLFFLFFLLK …

Model Validation And Transition To Turbulence In Orbiting Culture Dishes., Jonathan Michael D. Thomas

Electronic Theses and Dissertations

Wall shear stress (WSS) is commonly accepted as the primary influence affecting characteristics of anchored endothelial cells when subjected to fluid flow. Orbital shakers are commonly used to study cellular responses due to their ease of use, ability to run several experiments simultaneously, and since they exert physiologically relevant oscillatory shear. These studies require comprehensive resolution of WSS, however the fluid dynamics inside orbiting culture dishes has not yet been well described since the flow is complex and difficult to quantify analytically. A computational fluid dynamics (CFD) model of flow in an orbiting dish has been developed that yields detailed …

Cloning, Fed-Batch Expression And Purification Of A Novel Anti-Candida Peptide And Development Of A Cleavage Resistant Variant Of Green Fluorescence Protein, Rudra Palash Mukherjee

Graduate Theses and Dissertations

This work illustrates that the intelligent design of a bioprocess for the production of peptides of various length is possible by having a prior knowledge of desired product, cell line, fermentation conditions, and choices for downstream recovery. Cloning, expression, and recovery of a novel 12-mer anti-Candida peptide served as an illustrative case for a proposed Escherichia coli platform. The antifungal peptide, expressed as a fusion to GFPUV during high call density fed-batch, was recovered from cell lysate, concentrated using ion exchange chromatography, and finally cleaved with cyanogen bromide. The platform was capable of producing active peptide capable of arresting the …