Matching Items (8)
Description
An animal's ability to produce protein-based silk materials has evolved independently in many different arthropod lineages, satisfying various ecological necessities. However, regardless of their wide range of uses and their potential industrial and biomedical applications, advanced knowledge on the molecular structure of silk biopolymers is largely limited to those produced by spiders (order Araneae) and silkworms (order Lepidoptera). This thesis provides an in-depth molecular-level characterization of silk fibers produced by two vastly different insects: the caddisfly larvae (order Trichoptera) and the webspinner (order Embioptera).
The molecular structure of caddisfly larval silk from the species Hesperophylax consimilis was characterized using solid-state nuclear magnetic resonance (ss-NMR) and Wide Angle X-ray Diffraction (WAXD) techniques. This insect, which typically dwells in freshwater riverbeds and streams, uses silk fibers as a strong and sticky nanoadhesive material to construct cocoons and cases out available debris. Conformation-sensitive 13C chemical shifts and 31P chemical shift anisotropy (CSA) information strongly support a unique protein motif in which phosphorylated serine- rich repeats (pSX)4 complex with di- and trivalent cations to form rigid nanocrystalline β-sheets. Additionally, it is illustrated through 31P NMR and WAXD data that these nanocrystalline structures can be reversibly formed, and depend entirely on the presence of the stabilizing cations.
Nanofiber silks produced by webspinners (order Embioptera) were also studied herein. This work addresses discrepancies in the literature regarding fiber diameters and tensile properties, revealing that the nanofibers are about 100 nm in diameter, and are stronger (around 500 MPa mean ultimate stress) than previous works suggested. Fourier-transform Infrared Spectroscopy (FT-IR), NMR and WAXD results find that approximately 70% of the highly repetitive glycine- and serine-rich protein core is composed of β-sheet nanocrystalline structures. In addition, FT-IR and Gas-chromatography mass spectroscopy (GC-MS) data revealed a hydrophobic surface coating rich in long-chain lipids. The effect of this surface coating was studied with contact angle techniques; it is shown that the silk sheets are extremely hydrophobic, yet due to the microstructural and nanostructural details of the silk surface, are surprisingly adhesive to water.
The molecular structure of caddisfly larval silk from the species Hesperophylax consimilis was characterized using solid-state nuclear magnetic resonance (ss-NMR) and Wide Angle X-ray Diffraction (WAXD) techniques. This insect, which typically dwells in freshwater riverbeds and streams, uses silk fibers as a strong and sticky nanoadhesive material to construct cocoons and cases out available debris. Conformation-sensitive 13C chemical shifts and 31P chemical shift anisotropy (CSA) information strongly support a unique protein motif in which phosphorylated serine- rich repeats (pSX)4 complex with di- and trivalent cations to form rigid nanocrystalline β-sheets. Additionally, it is illustrated through 31P NMR and WAXD data that these nanocrystalline structures can be reversibly formed, and depend entirely on the presence of the stabilizing cations.
Nanofiber silks produced by webspinners (order Embioptera) were also studied herein. This work addresses discrepancies in the literature regarding fiber diameters and tensile properties, revealing that the nanofibers are about 100 nm in diameter, and are stronger (around 500 MPa mean ultimate stress) than previous works suggested. Fourier-transform Infrared Spectroscopy (FT-IR), NMR and WAXD results find that approximately 70% of the highly repetitive glycine- and serine-rich protein core is composed of β-sheet nanocrystalline structures. In addition, FT-IR and Gas-chromatography mass spectroscopy (GC-MS) data revealed a hydrophobic surface coating rich in long-chain lipids. The effect of this surface coating was studied with contact angle techniques; it is shown that the silk sheets are extremely hydrophobic, yet due to the microstructural and nanostructural details of the silk surface, are surprisingly adhesive to water.
ContributorsAddison, John Bennett (Author) / Yarger, Jeffery L (Thesis advisor) / Holland, Gregory P (Thesis advisor) / Wang, Xu (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2014
Description
Proteins are a fundamental unit in biology. Although proteins have been extensively studied, there is still much to investigate. The mechanism by which proteins fold into their native state, how evolution shapes structural dynamics, and the dynamic mechanisms of many diseases are not well understood. In this thesis, protein folding is explored using a multi-scale modeling method including (i) geometric constraint based simulations that efficiently search for native like topologies and (ii) reservoir replica exchange molecular dynamics, which identify the low free energy structures and refines these structures toward the native conformation. A test set of eight proteins and three ancestral steroid receptor proteins are folded to 2.7Å all-atom RMSD from their experimental crystal structures. Protein evolution and disease associated mutations (DAMs) are most commonly studied by in silico multiple sequence alignment methods. Here, however, the structural dynamics are incorporated to give insight into the evolution of three ancestral proteins and the mechanism of several diseases in human ferritin protein. The differences in conformational dynamics of these evolutionary related, functionally diverged ancestral steroid receptor proteins are investigated by obtaining the most collective motion through essential dynamics. Strikingly, this analysis shows that evolutionary diverged proteins of the same family do not share the same dynamic subspace. Rather, those sharing the same function are simultaneously clustered together and distant from those functionally diverged homologs. This dynamics analysis also identifies 77% of mutations (functional and permissive) necessary to evolve new function. In silico methods for prediction of DAMs rely on differences in evolution rate due to purifying selection and therefore the accuracy of DAM prediction decreases at fast and slow evolvable sites. Here, we investigate structural dynamics through computing the contribution of each residue to the biologically relevant fluctuations and from this define a metric: the dynamic stability index (DSI). Using DSI we study the mechanism for three diseases observed in the human ferritin protein. The T30I and R40G DAMs show a loss of dynamic stability at the C-terminus helix and nearby regulatory loop, agreeing with experimental results implicating the same regulatory loop as a cause in cataracts syndrome.
ContributorsGlembo, Tyler J (Author) / Ozkan, Sefika B (Thesis advisor) / Thorpe, Michael F (Committee member) / Ros, Robert (Committee member) / Kumar, Sudhir (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2011
Description
This paper describes an effort to bring wing structural stiffness and aeroelastic considerations early in the conceptual design process with an automated tool. Stiffness and aeroelasticity can be well represented with a stochastic model during conceptual design because of the high level of uncertainty and variability in wing non-structural mass such as fuel loading and control surfaces. To accomplish this, an improvement is made to existing design tools utilizing rule based automated design to generate wing torque box geometry from a specific wing outer mold-line. Simple analysis on deflection and inferred stiffness shows how early conceptual design choices can strongly impact the stiffness of the structure. The impacts of design choices and how the buckling constraints drive structural weight in particular examples are discussed. The model is then carried further to include a finite element model (FEM) to analyze resulting mode shapes and frequencies for use in aeroelastic analysis. The natural frequencies of several selected wing torque boxes across a range of loading cases are compared.
ContributorsMiskin, Daniel L (Author) / Takahashi, Timothy T (Thesis advisor) / Mignolet, Marc (Committee member) / Murthy, Raghavendra (Committee member) / Arizona State University (Publisher)
Created2018
Description
Structure is a critical component in drug development. This project supports antibody- facilitated structure determination for the following eleven membrane proteins: the human histamine and dopamine G protein-coupled receptors (HRH4 and DRD2) involved in a wide variety of pathologies such as allergies, inflammation, asthma, pain along with Parkinson's and schizophrenia respectively, the human cystic fibrosis transmembrane conductance regulator (CFTR), the human NaV1.8 voltage-gated sodium ion channel, the human TPC2 two-pore channel, the SARS virus proteins 3a, E and M, the MERS virus protein E and M, and the malarial chloroquine resistance transporter (PfCRT). Serum antibodies against these proteins were generated by genetic immunization, and both in vitro and in vivo expressed membrane proteins were created to characterize the serum antibodies. Plasmid clones were generated for genetic immunization, in vitro protein expression, and in vivo expression (HEK293T transfection). Serum antibodies were generated by genetic immunization of mice by gene gun. Genetic immunization promotes an immune response that allows for the generation of antibodies in the absence of purified protein. In vitro expression was accomplished through the novel technique: in vitro translation with hydrophobic magnetic beads (IVT-HMB). Transfections were performed using the HEK293T cell line to express the protein in vivo. The generated protein was then used in gel electrophoresis and silver stain and/or Western blot analyses to identify and visualize the proteins. These expressed proteins will allow for forthcoming characterization of the generated antibodies. The resulting antibodies will in turn enable structure determination of these important membrane proteins by co-crystallization.
ContributorsDrotar, Beniamin (Author) / Fromme, Petra (Thesis director) / Hansen, Debra T. (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
When scientific software is written to specify processes, it takes the form of a workflow, and is often written in an ad-hoc manner in a dynamic programming language. There is a proliferation of legacy workflows implemented by non-expert programmers due to the accessibility of dynamic languages. Unfortunately, ad-hoc workflows lack a structured description as provided by specialized management systems, making ad-hoc workflow maintenance and reuse difficult, and motivating the need for analysis methods. The analysis of ad-hoc workflows using compiler techniques does not address dynamic languages - a program has so few constrains that its behavior cannot be predicted. In contrast, workflow provenance tracking has had success using run-time techniques to record data. The aim of this work is to develop a new analysis method for extracting workflow structure at run-time, thus avoiding issues with dynamics.
The method captures the dataflow of an ad-hoc workflow through its execution and abstracts it with a process for simplifying repetition. An instrumentation system first processes the workflow to produce an instrumented version, capable of logging events, which is then executed on an input to produce a trace. The trace undergoes dataflow construction to produce a provenance graph. The dataflow is examined for equivalent regions, which are collected into a single unit. The workflow is thus characterized in terms of its treatment of an input. Unlike other methods, a run-time approach characterizes the workflow's actual behavior; including elements which static analysis cannot predict (for example, code dynamically evaluated based on input parameters). This also enables the characterization of dataflow through external tools.
The contributions of this work are: a run-time method for recording a provenance graph from an ad-hoc Python workflow, and a method to analyze the structure of a workflow from provenance. Methods are implemented in Python and are demonstrated on real world Python workflows. These contributions enable users to derive graph structure from workflows. Empowered by a graphical view, users can better understand a legacy workflow. This makes the wealth of legacy ad-hoc workflows accessible, enabling workflow reuse instead of investing time and resources into creating a workflow.
The method captures the dataflow of an ad-hoc workflow through its execution and abstracts it with a process for simplifying repetition. An instrumentation system first processes the workflow to produce an instrumented version, capable of logging events, which is then executed on an input to produce a trace. The trace undergoes dataflow construction to produce a provenance graph. The dataflow is examined for equivalent regions, which are collected into a single unit. The workflow is thus characterized in terms of its treatment of an input. Unlike other methods, a run-time approach characterizes the workflow's actual behavior; including elements which static analysis cannot predict (for example, code dynamically evaluated based on input parameters). This also enables the characterization of dataflow through external tools.
The contributions of this work are: a run-time method for recording a provenance graph from an ad-hoc Python workflow, and a method to analyze the structure of a workflow from provenance. Methods are implemented in Python and are demonstrated on real world Python workflows. These contributions enable users to derive graph structure from workflows. Empowered by a graphical view, users can better understand a legacy workflow. This makes the wealth of legacy ad-hoc workflows accessible, enabling workflow reuse instead of investing time and resources into creating a workflow.
ContributorsAcűna, Ruben (Author) / Bazzi, Rida (Thesis advisor) / Lacroix, Zoé (Thesis advisor) / Candan, Kasim (Committee member) / Arizona State University (Publisher)
Created2015
Description
ABSTRACT The accretion of juvenile island-arc lithosphere by convergent tectonism during the Paleoproterozoic, in conjunction with felsic volcanism, resulted in the assembly, ductile to partial brittle deformation, uplift, and northwest-directed thrusting of rocks in the McDowell Mountains region and adjacent areas in the Mazatzal Orogenic belt. Utilizing lithologic characteristics and petrographic analysis of the Proterozoic bedrock, a correlation to the Alder series was established, revising the stratigraphic sequences described by earlier works. The central fold belt, composed of an open, asymmetric syncline and an overturned, isoclinal anticline, is cut by an axial-plane parallel reactivated thrust zone that is intruded by a deformed Paleoproterozoic mafic dike. Finite strain analyses of fold geometries, shear fabrics, foliations, fold vergence, and strained clasts point to Paleoproterozoic northwest-directed thrusting associated with the Mazatzal orogen at approximately 1650 million years ago. Previous studies constrained the regional P-T conditions to at least the upper andalusite-kyanite boundary at peak metamorphic conditions, which ranged from 4-6 kilobars and 350-450⁰ Celsius, although the plasticity of deformation in a large anticlinal core suggests that this represents the low end of the P-T conditions. Subsequent to deformation, the rocks were intruded by several granitoid plutons, likely of Mesoproterozoic age (1300-1400 Ma). A detailed analysis of Proterozoic strain solidly places the structure of the McDowell Mountains within the confines of the Mazatzal Orogeny, pending any contradictory geochronological data.
ContributorsVance, Brad (Author) / Reynolds, Stephen J. (Thesis advisor) / Semken, Steven (Committee member) / Stump, Edmund (Committee member) / Arizona State University (Publisher)
Created2012
Description
The key to success is hard work and determination. Achieving success is always under construction. This project began as a simple analysis of the firm's progress, as at the time it was in desperate need of new clients and a marketing strategy to strengthen its visibility on campus.Through this evaluation, our team found that the firm was in an abysmal state and the previously noted problems were not the only issues of concern. From our research we found that in order for the firm to grow and become a successful student run consulting firm, there are several interorganizational issues that need to be understood and addressed. The intention of New Venture Group and the Consulting Scholars academic program is to provide students the opportunity to garner practical learning experiences. These potential opportunities are not taken full advantage of because of the afflicting problems that exist. The purpose of this thesis is to understand what problems exist within the firm and the next steps that should be taken to resolve them.
ContributorsBaskin, Connor (Co-author) / Farr, Austin (Co-author) / Chou, Alexandra (Co-author) / Laub, Jeffrey (Thesis director) / Taylor, Todd (Committee member) / Department of Supply Chain Management (Contributor) / Department of Economics (Contributor) / Department of Marketing (Contributor) / Department of Finance (Contributor) / School of International Letters and Cultures (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor) / Department of Information Systems (Contributor) / W. P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
In the present study, I will focus on several aspects of parenting (monitoring, structure, positive parenting, harsh discipline) and the relations with social competence. The larger study, on which this paper is based, was intended to study multiple types of parenting behaviors and social competencies, and development of measures was culturally and developmentally informed (including focus groups and pilot collection). However, utilizing each dimension that emerged from analyses of the parenting behaviors and social competence measures would result in a study with too large a scope. I will include each aspect of parenting that emerged in analyses. However, I will focus on just one of the two factors of social competence that emerged in analyses for adolescents. This first factor includes prosocial behavior (helping and sharing; Eisenberg et al., 2006) and also is composed of general social competence items capturing adolescents’ use of manners and politeness. For the purposes of this paper, I will refer to this first factor as “social competence,” and I will draw on the general social competence literature and prosocial behavior literature.
ContributorsMahajan, Ananyaa (Author) / Eggum, Natalie (Thesis director) / Spinrad, Tracy (Committee member) / Barrett, The Honors College (Contributor) / Department of Psychology (Contributor) / Sanford School of Social and Family Dynamics (Contributor)
Created2023-05