Engineering Commons^™

Coupled Oscillators: Protein And Acoustics, Angelique N. Mcfarlane

Theses

This work encompassed three different vibrational energy transfer studies of coupled resonators (metal, topological, and microtubule comparison) inspired by the lattices of microtubules from regular and cancerous cells. COMSOL Multiphysics 5.4 was utilized to design the experiment. The simulation starts with an acoustic pressure study to examine the vibrational modes present in coupled cylinders, representing α-, β-tubulin heterodimers. The Metal Study consisted of 3 models (monomer, dimer, and trimer) to choose the correct height (40 mm) and mode (Mode 1) for study. The Topological Study was run to predict and understand how the lattice structure changes over a parametric sweep …

Immobilized Phosphate-Binding Protein Systems To Remove And Recover Phosphate, Faten Bakri Hussein

Dissertations (1934 -)

Inorganic phosphorus (Pi) is a critical element for all life and a major component of DNA’s backbone. Global agriculture requires Pi to support the rapid growth of plants and high crop productivity. Yet, the mineable Pi supply needed for global agriculture is in short supply in nature and Pi reserves are unevenly distributed around the world. In contrast, surplus Pi in water poses a serious pollution problem as it can cause eutrophication. Scarcity of non-renewable Pi resources combined with pollution in the form of overabundant Pi presents a phosphorus paradox. Tackling this issue is necessary and using innovative approaches targeting …

Simulation Of Gene Regulatory Elements For Biosensing, Mallory Bates, Svetlana Harbough, Tarun Goswami

Biomedical, Industrial & Human Factors Engineering Faculty Publications

Gene regulatory studies are of significant importance in many scenarios such as mental illness. 21% of U.S adults experience mental illnesses including 1 in 4 active-duty military personnel. Mental health can be identified in the body by different biomarkers. These biomarkers potentially controlled by riboswitches, which are located in mRNA and switch “ON” or “OFF” depending on the concentration of a biomarker. In this research, a known riboswitch reengineered and its response in the presence of a biomarker investigated. We changed computationally PreQ₁, a known riboswitch that has the smallest aptamer, and then experimentally tested against biomarkers, dehydroepiandrosterone-sulfate …

Concurrent Identification, Characterization, And Reconstruction Of Protein Structure And Mixed-Mode Dynamics From Rdc Data Using Redcraft, Hanin Rafiq Omar

Theses and Dissertations

A complete understanding of the structure-function relationship of proteins requires an analysis of their dynamic behaviors and the static structure. However, all current approaches to studying dynamics in proteins have their shortcomings. A conceptually attractive and alternative approach simultaneously characterizes a protein's structure and its intrinsic dynamics⁠. Ideally, such an approach could solely rely on RDC data-carrying both structural and dynamical information. The major bottleneck in utilizing RDC data in recent years has been attributed to a lack of RDC analysis tools capable of extracting the pertinent information embedded within this complex data source.

Here we present a comprehensive strategy …

Determination Of Main Ingredients In Milk Using Akm-98 Milk Analyzer, Qobil Mukhiddinov Master, Sh Sultanova Dr., J Safarov Dr. Professor, A Aït-Kaddour Dr., Professor, D Samandarov Phd

Technical science and innovation

The aim of the research is a quick, easy, economical way to determine milk content. Nowadays, the production of cow’s milk is dominant, but the original quality of non-bovine milk, such as camel’s milk, is now better described and is experiencing growing interest. Camel’s milk, goat’s milk, ewe’s milk and buffalo’s milk have received special attention because of their recognition as potential functional foods from a nutritional point of view. It is admitted that camel’s milk presents a high nutritional quality; e.g., it has three times more vitamin C, minerals, and essential and polyunsaturated Fatty Acids than cow’s milk. It …

Computational Algorithms For Predicting Membrane Protein Assembly From Angstrom To Micron Scale, Nandhini Rajagopal

Dissertations - ALL

Biological barriers in the human body are one of the most crucial interfaces perfected through evolution for diverse and unique functions. Of the wide range of barriers, the paracellular protein interfaces of epithelial and endothelial cells called tight junctions with high molecular specificities are vital for homeostasis and to maintain proper health. While the breakdown of these barriers is associated with serious pathological consequences, their intact presence also poses a challenge to effective delivery of therapeutic drugs. Complimenting a rigorous combination of in vitro and in vivo approaches to establishing the fundamental biological construct, in addition to elucidating pathological implications …

Computational Algorithms For Predicting Membrane Protein Assembly From Angstrom To Micron Scale, Nandhini Rajagopal

Dissertations - ALL

Biological barriers in the human body are one of the most crucial interfaces perfected through evolution for diverse and unique functions. Of the wide range of barriers, the paracellular protein interfaces of epithelial and endothelial cells called tight junctions with high molecular specificities are vital for homeostasis and to maintain proper health. While the breakdown of these barriers is associated with serious pathological consequences, their intact presence also poses a challenge to effective delivery of therapeutic drugs. Complimenting a rigorous combination of in vitro and in vivo approaches to establishing the fundamental biological construct, in addition to elucidating pathological implications …

Covid-19 Serological Diagnostic Development Using A Sars-Cov-2 Rbd Foldon Fusion, Joey Emery Breckenridge Jr.

Electronic Theses and Dissertations

Serological tests are conducted to assess humoral response against viral protein antigens, to assess viral exposure and protection from pathogens. The rapid development and modularity of serological assays have proven critical to managing the current SARS-CoV-2 pandemic. The receptor binding domain of SARS-CoV-2 is within the trimeric Spike protein and serves as a highly immunogenic target for potentially neutralizing antibodies. Current receptor binding domain serological assays use recombinant monomers or dimers of the receptor binding domain. The receptor binding domain is presented to the immune system natively in the context of the Spike protein trimer. Therefore, a recombinant trimeric receptor …

Molecular Dynamic Simulation Of Protein Devices And The Parameterization Of Azides And Alkynes For Use In Unnatural Amino Acid Models, Addison Kyle Smith

Theses and Dissertations

Proteins that have been modified by attaching them to a surface or to a polyethylene glycol (PEG) molecule can see many uses in therapeutics and diagnostics -- these unique proteins are called protein devices. Current techniques can perform these functionalizations at a specific residue on the protein, but what remains is identifying what happens to protein structure when mutated, and where to perform the attachment. Both of these issues can be examined using molecular dynamic (MD) simulations. Currently, simulations of the unnatural amino acid (uAA) mutations necessary for protein device functionalization cannot be executed, and full-protein screens of all possible …

Molecular Dynamic Simulation Of Protein Devices And The Parameterization Of Azides And Alkynes For Use In Unnatural Amino Acid Models, Addison Kyle Smith

Theses and Dissertations

Proteins that have been modified by attaching them to a surface or to a polyethylene glycol (PEG) molecule can see many uses in therapeutics and diagnostics -- these unique proteins are called protein devices. Current techniques can perform these functionalizations at a specific residue on the protein, but what remains is identifying what happens to protein structure when mutated, and where to perform the attachment. Both of these issues can be examined using molecular dynamic (MD) simulations. Currently, simulations of the unnatural amino acid (uAA) mutations necessary for protein device functionalization cannot be executed, and full-protein screens of all possible …

Protease Resistant Growth Factor Formulations For The Healing Of Chronic Wounds, Tabitha Boeringer

USF Tampa Graduate Theses and Dissertations

Chronic wounds are those wounds which are refractory to treatment, often taking years to heal. These wounds are complex and may present with elevated protease levels, resulting in rapid degradation of growth factors, both native and augmented via treatment. This study’s focus was the development of a system to protect growth factors from protease mediated degradation.

The protective system consisted of chimeric fusion proteins developed to contain both a growth factor or known protease inhibitory peptide and an Elastin-Like-Peptide (ELP)component. The unique phase transitioning abilities of the ELP component allowed for the self-assembly of these chimeric fusion proteins into a …

Characterization Of Avidin And Case9 Single Protein Molecules By A Solid-State Nanopore Device, Haopeng Li

Graduate Theses and Dissertations

The shape and charge of a protein play significant roles in protein dynamics in the biological system of humans and animals. Characterizing and quantifying the shape and charge of a protein at the single-molecule level remains a challenge. Solid-state nanopores made of silicon nitride (SiNx) have emerged as novel platforms for biosensing such as diagnostics for single-molecule detection and DNA sequencing. SSN detection is based on measuring the variations in ionic conductance as charged biomolecules translocate through nanometer-sized channels driven by an external voltage applied across the membrane. In this paper, we observe the translocation of asymmetric cylindrical structure CRISPR-Cas9 …

Hime: Mining And Ensembling Heterogeneous Information For Protein Interaction Predictions, Huaming Chen, Yaochu Jin, Lei Wang, Chi-Hung Chi, Jun Shen

Faculty of Engineering and Information Sciences - Papers: Part B

esearch on protein-protein interactions (PPIs) data paves the way towards understanding the mechanisms of infectious diseases, however improving the prediction performance of PPIs of inter-species remains a challenge. Since one single type of sequence data such as amino acid composition may be deficient for high-quality prediction of protein interactions, we have investigated a broader range of heterogeneous information of sequences data. This paper proposes a novel framework for PPIs prediction based on Heterogeneous Information Mining and Ensembling (HIME) process to effectively learn from the interaction data. In particular, the proposed approach introduces an ensemble process together with substantial features that …

Propuesta Preliminar De Diseño Para Un Sistema De Separación De Proteínas Del Lactosuero Usando Ultrafiltración, Natalia Monroy Pedraza

Ingeniería de Alimentos

El lactosuero es un subproducto de la elaboración de quesos, tradicionalmente es usado para alimentación animal y en muchos casos es desechado como efluente, generando un gran impacto ambiental, este cuenta aproximadamente con el 55% de los nutrientes de la leche. Dependiendo del tipo de queso se obtienen diferentes tipos de lactosuero, estos varían en su composición, sin embargo, en todos los casos la lactosa es su componente mayoritario seguido de las proteínas, siendo estas de gran valor biológico. En este trabajo se evaluó experimentalmente la separación de las proteínas contenidas en el lactosuero usando membranas de ultrafiltración, analizando la …

Development Of Functional Biomaterials Using Protein Building Blocks, Li-Sheng Wang

Doctoral Dissertations

Proteins have intrinsic molecular properties that are highly useful for materials applications, especially for biomaterials. My research has focused on translating these molecular properties to materials surface behavior. In one approach, I developed a fluorous-based thermal treatment strategy to generate stable thin films from a variety of naturally abundant proteins. The different surface properties generated from the choice of protein were utilized to modulate cell-surface interactions, prevent bacterial adhesions, and control drug loading/release. I have used nanoimprint lithography to generate patterned protein films for cell alignment. Coupling with inkjet printing deposition, I have fabricated mixed protein films with spatial and …

Eulerian Video Magnification Adaptation For Live Cell Microscopy Analysis, Paul Leamy, Jane Courtney

Session 5: Medical and Biomedical Imaging

In this paper an adaptation of the Eulerian Video Magnification technique is described for use with .TIFF files produced by a photo-conversion time lapse protocol for live cell microscopy, specifically for research into Acquired Immune Deficiency Syndrome. The tracking and characterisation of a protein found in Human Immunodeficiency Virus, to determine its dynamics and pathways is a key determinant in understanding the protein’s function. The aim of this algorithm is to process an image sequence in the temporal direction with the result being that changes in fluorescence for particular pixel locations, or regions of interest, are tracked and filtered thereby …

A Multiscale Model Of Protein Adsorption On A Nanoparticle Surface, David Power, Ian Rouse, Stefano Poggio, Erik Brandt, Hender Lopez, Alexander Lyubartsev, Vladimir Lobaskin

Articles

We present a methodology to quantify the essential interactions at the interface between inorganic solid nanoparticles (NPs) and biological molecules. Our model is based on pre-calculation of the repetitive contributions to the interaction from molecular segments, which allows us to efficiently scan a multitude of molecules and rank them by their adsorption affinity. The interaction between the biomolecular fragments and the nanomaterial are evaluated using a systematic coarse-graining scheme starting from all-atom molecular dynamics simulations. The NPs are modelled using a two-layer representation, where the outer layer is parameterized at the atomistic level and the core is treated at the …

Modeling Cell Line-Specific Recruitment Of Signaling Proteins To The Insulin-Like Growth Factor 1 Receptor, Keesha E. Erickson, Dipak Barua, For Full List Of Authors, See Publisher's Website.

Chemical and Biochemical Engineering Faculty Research & Creative Works

Receptor tyrosine kinases (RTKs) typically contain multiple autophosphorylation sites in their cytoplasmic domains. Once activated, these autophosphorylation sites can recruit downstream signaling proteins containing Src homology 2 (SH2) and phosphotyrosine-binding (PTB) domains, which recognize phosphotyrosine-containing short linear motifs (SLiMs). These domains and SLiMs have polyspecific or promiscuous binding activities. Thus, multiple signaling proteins may compete for binding to a common SLiM and vice versa. To investigate the effects of competition on RTK signaling, we used a rule-based modeling approach to develop and analyze models for ligand-induced recruitment of SH2/PTB domain-containing proteins to autophosphorylation sites in the insulin-like growth factor 1 …

Cross-Linking Amyloid Forming Proteins For Improved Understanding Of Early Aggregation, Gram Booth

Chemical Engineering Undergraduate Honors Theses

Alzheimer’s disease is the only disease in the ten leading causes of death in the United states that cannot be slowed, prevented, or cured. Alzheimer’s dementia and type II diabetes are the top two diseases caused by improper protein folding, aggregation, and deposition of fibrillar plaques in tissues. These plaques, originally thought to be the cause of these diseases, have been discovered to be mostly benign and representative of the later stages of the disease. The smaller, more soluble oligomeric aggregates are responsible for the death of pancreatic and neural cells. Many oligomeric species are unstable and exist only for …

Visualization And Quantification Of Lipid And Protein In Single Microalgal Cell, Hina Laghari Mohammad Shakeel

Electrical Engineering Theses

Microalgae have the potential to be used as a main source of renewable energy in the future due to their lipid contents. Microalgae are comprised of several components including carbohydrates, lipids and proteins. This lipid and protein composition needs to be quantified so the amount of usable energy can be measured. Therefore, the main objective of this thesis is to develop an image processing technique for the quantification of lipid and protein contents in single microalgal cell.

This image processing technique has made lipid quantification an easier process as compared to previous methods used to quantify lipid content. The technique …

Physicochemical And Nutritional Properties Of Extrudates From Food Grade Distiller’S Dried Grains, Garbanzo Flour, And Corn Grits, Poonam Singha, Sushil Kumar Singh, Kasiviswanathan Muthukumarappan, Padmanaban G. Krishnan

Sushil Singh

Green Chemistry Oxidative Modification Of Peptoids Utilizing Bleach And Tempo, Jesse Leland Roberts

Graduate Theses and Dissertations

Biotherapeutic drugs, derived from biological molecules such as proteins and DNA, are becoming an integral and exceptionally critical aspect of modern medicine. Compared to common pharmaceutical drugs, biotherapeutics are much larger in size and have greater target specificity, allowing them to treat many chronic diseases ranging from cancer to rheumatoid arthritis. The major issue with protein based therapeutics is that they readily undergo proteolysis, or enzymatic degradation, when administered through subcutaneous injections. Traditionally, biotherapeutic modification procedures have centered on the use of PEG derivatives. This process, called PEGylation, is unfavorable due to the increases in molecular weights of the proteins …

Development Of A Low Cost Biosensing Platform For Highly Sensitive And Specific On-Site Detection Of Pathogens And Infections, Cheng Cheng

Doctoral Dissertations

A highly sensitive, specific, real time, and field-deployable surveillance tool is critical to the control of pathogens and infections, as well as ecological impact of chemicals exposure. This work investigates the development of a low cost biosensing platform that can be used for viral disease diagnosis and chemical detection. The sensing mechanism is known as AC electrokinetics (ACEK) capacitive sensing. By applying an inhomogeneous AC electric field on sensor electrodes, positive dielectrophoresis is induced to accelerate the travel of analytes. The same applied AC signal also directly measures the capture of target by the probe on sensor surface. The realized …

Design And Engineering Of Water-Soluble Light-Harvesting Protein Maquettes, Goutham Kodali, Joshua A. Mancini, Lee A. Solomon, Tatiana V. Episova, Nicholas Roach, Christopher Hobbs, Pawel W. Wagner, Olga Mass, Kunche Aravindu, Jonathan E. Barnsley, Keith C. Gordon, David L. Officer, P. Leslie Dutton, Christopher C. Moser

Australian Institute for Innovative Materials - Papers

Natural selection in photosynthesis has engineered tetrapyrrole based, nanometer scale, light harvesting and energy capture in light-induced charge separation. By designing and creating nanometer scale artificial light harvesting and charge separating proteins, we have the opportunity to reengineer and overcome the limitations of natural selection to extend energy capture to new wavelengths and to tailor efficient systems that better meet human as opposed to cellular energetic needs. While tetrapyrrole cofactor incorporation in natural proteins is complex and often assisted by accessory proteins for cofactor transport and insertion, artificial protein functionalization relies on a practical understanding of the basic physical chemistry …

Bioremediation Of Lead Using Spore Surface Displayed Proteins, Sofia M. Diaco

Honors Theses and Capstones

Lead is a toxic pollutant very harmful to human health since it accumulates in the body and affects the brain, liver, kidney, and bones. Fetuses can be exposed to lead during pregnancy, which can cause problems with learning later on in the baby’s life. The purpose of this project is to display a lead binding protein on bacterial spore surface for the bioremediation of lead from water. Spores from Bacillus subtilis are very robust and resistant to various harsh environments. Genetically fused to a spore surface protein, the displayed proteins demonstrate enhanced robustness and can be easily produced through sporulation …

Testing The Independence Hypothesis Of Accepted Mutations For Pairs Of Adjacent Amino Acids In Protein Sequences, Jyotsna Ramanan

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Evolutionary studies usually assume that the genetic mutations are independent of each other. However, that does not imply that the observed mutations are independent of each other because it is possible that when a nucleotide is mutated, then it may be biologically beneficial if an adjacent nucleotide mutates too.

With a number of decoded genes currently available in various genome libraries and online databases, it is now possible to have a large-scale computer-based study to test whether the independence assumption holds for pairs of adjacent amino acids. Hence the independence question also arises for pairs of adjacent amino acids within …

Activity Of Protein Kinase A Attached To Magnetic Beads, Kevin P. Lin, Tamara L. Kinzer-Ursem, Mrugesh K. Parasa

The Summer Undergraduate Research Fellowship (SURF) Symposium

Development of high throughput assays is a crucial step in developing more efficient techniques that aid in many important areas of research today such as drug development or identification of protein structure function relationships. Integration of high throughput assays into more research efforts could drastically decrease the time and cost it takes for a new drug to hit the market. Protein Kinase A (PKA) is an extensively studied protein as it is highly upregulated in cancer and is a hot spot for drug targeting. In this work, azide-tagged PKA is covalently attached to magnetic beads using azide-alkyne cycloaddition, a well-known …

Numerical Characterization Of Protein Sequences Based On The Generalized Chou's Pseudo Amino Acid Composition, Chun Li, Xueqin Li, Yan-Xia Lin

Faculty of Engineering and Information Sciences - Papers: Part A

The technique of comparison and analysis of biological sequences is playing an increasingly important role in the field of Computational Biology and Bioinformatics. One of the key steps in developing the technique is to identify an appropriate manner to represent a biological sequence. In this paper, on the basis of three physical-chemical properties of amino acids, a protein primary sequence is reduced into a six-letter sequence, and then a set of elements which reflect the global and local sequence-order information is extracted. Combining these elements with the frequencies of 20 native amino acids, a (21+λ) dimensional vector is constructed to …

Towards Data Analytics Of Pathogen-Host Protein-Protein Interaction: A Survey, Huaming Chen, Jun Shen, Lei Wang, Jiangning Song

Faculty of Engineering and Information Sciences - Papers: Part A

"Big Data" is immersed in many disciplines, including computer vision, economics, online resources, bioinformatics and so on. Increasing researches are conducted on data mining and machine learning for uncovering and predicting related domain knowledge. Protein-protein interaction is one of the main areas in bioinformatics as it is the basis of the biological functions. However, most pathogen-host protein-protein interactions, which would be able to reveal much more infectious mechanisms between pathogen and host, are still up for further investigation. Considering a decent feature representation of pathogen-host protein-protein interactions (PHPPI), currently there is not a well structured database for research purposes, not …

Conductive And Protein Resistant Polypyrrole Films For Dexamethasone Delivery, Binbin Zhang, Paul J. Molino, Alexander R. Harris, Zhilian Yue, Simon E. Moulton, Gordon G. Wallace

Australian Institute for Innovative Materials - Papers

The development of inherently conducting polymers as controllable/programmable drug delivery systems has attracted significant interest in medical bionics, and the interfacial properties of the polymers, in particular, protein adsorption characteristics, is integral to the stability of the overall performance. Herein we report a hybrid conducting system based on polypyrrole doped with an anti-inflammatory prodrug, dexamethasone phosphate (DexP), upon which post-surface modification was conducted to render the polymer more biostable. We firstly investigated the influence of the current density and DexP concentration on the physiochemical properties and surface characteristics of the resulting polymer films. Films were then surface modified with thiolated …