Matching Items (5)
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- All Subjects: DNA
- Creators: Borges, Chad
- Resource Type: Text
- Status: Published
Description
Many industries require workers in warehouse and stockroom environments to perform frequent lifting tasks. Over time these repeated tasks can lead to excess strain on the worker's body and reduced productivity. This project seeks to develop an exoskeletal wrist fixture to be used in conjunction with a powered exoskeleton arm to aid workers performing box lifting types of tasks. Existing products aimed at improving worker comfort and productivity typically employ either fully powered exoskeleton suits or utilize minimally powered spring arms and/or fixtures. These designs either reduce stress to the user's body through powered arms and grippers operated via handheld controls which have limited functionality, or they use a more minimal setup that reduces some load, but exposes the user's hands and wrists to injury by directing support to the forearm. The design proposed here seeks to strike a balance between size, weight, and power requirements and also proposes a novel wrist exoskeleton design which minimizes stress on the user's wrists by directly interfacing with the object to be picked up. The design of the wrist exoskeleton was approached through initially selecting degrees of freedom and a ROM (range of motion) to accommodate. Feel and functionality were improved through an iterative prototyping process which yielded two primary designs. A novel "clip-in" method was proposed to allow the user to easily attach and detach from the exoskeleton. Designs utilized a contact surface intended to be used with dry fibrillary adhesives to maximize exoskeleton grip. Two final designs, which used two pivots in opposite kinematic order, were constructed and tested to determine the best kinematic layout. The best design had two prototypes created to be worn with passive test arms that attached to the user though a specially designed belt.
ContributorsGreason, Kenneth Berend (Author) / Sugar, Thomas (Thesis director) / Holgate, Matthew (Committee member) / Mechanical and Aerospace Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
DNA, RNA and Protein are three pivotal biomolecules in human and other organisms, playing decisive roles in functionality, appearance, diseases development and other physiological phenomena. Hence, sequencing of these biomolecules acquires the prime interest in the scientific community. Single molecular identification of their building blocks can be done by a technique called Recognition Tunneling (RT) based on Scanning Tunneling Microscope (STM). A single layer of specially designed recognition molecule is attached to the STM electrodes, which trap the targeted molecules (DNA nucleoside monophosphates, RNA nucleoside monophosphates or amino acids) inside the STM nanogap. Depending on their different binding interactions with the recognition molecules, the analyte molecules generate stochastic signal trains accommodating their “electronic fingerprints”. Signal features are used to detect the molecules using a machine learning algorithm and different molecules can be identified with significantly high accuracy. This, in turn, paves the way for rapid, economical nanopore sequencing platform, overcoming the drawbacks of Next Generation Sequencing (NGS) techniques.
To read DNA nucleotides with high accuracy in an STM tunnel junction a series of nitrogen-based heterocycles were designed and examined to check their capabilities to interact with naturally occurring DNA nucleotides by hydrogen bonding in the tunnel junction. These recognition molecules are Benzimidazole, Imidazole, Triazole and Pyrrole. Benzimidazole proved to be best among them showing DNA nucleotide classification accuracy close to 99%. Also, Imidazole reader can read an abasic monophosphate (AP), a product from depurination or depyrimidination that occurs 10,000 times per human cell per day.
In another study, I have investigated a new universal reader, 1-(2-mercaptoethyl)pyrene (Pyrene reader) based on stacking interactions, which should be more specific to the canonical DNA nucleosides. In addition, Pyrene reader showed higher DNA base-calling accuracy compare to Imidazole reader, the workhorse in our previous projects. In my other projects, various amino acids and RNA nucleoside monophosphates were also classified with significantly high accuracy using RT. Twenty naturally occurring amino acids and various RNA nucleosides (four canonical and two modified) were successfully identified. Thus, we envision nanopore sequencing biomolecules using Recognition Tunneling (RT) that should provide comprehensive betterment over current technologies in terms of time, chemical and instrumental cost and capability of de novo sequencing.
To read DNA nucleotides with high accuracy in an STM tunnel junction a series of nitrogen-based heterocycles were designed and examined to check their capabilities to interact with naturally occurring DNA nucleotides by hydrogen bonding in the tunnel junction. These recognition molecules are Benzimidazole, Imidazole, Triazole and Pyrrole. Benzimidazole proved to be best among them showing DNA nucleotide classification accuracy close to 99%. Also, Imidazole reader can read an abasic monophosphate (AP), a product from depurination or depyrimidination that occurs 10,000 times per human cell per day.
In another study, I have investigated a new universal reader, 1-(2-mercaptoethyl)pyrene (Pyrene reader) based on stacking interactions, which should be more specific to the canonical DNA nucleosides. In addition, Pyrene reader showed higher DNA base-calling accuracy compare to Imidazole reader, the workhorse in our previous projects. In my other projects, various amino acids and RNA nucleoside monophosphates were also classified with significantly high accuracy using RT. Twenty naturally occurring amino acids and various RNA nucleosides (four canonical and two modified) were successfully identified. Thus, we envision nanopore sequencing biomolecules using Recognition Tunneling (RT) that should provide comprehensive betterment over current technologies in terms of time, chemical and instrumental cost and capability of de novo sequencing.
ContributorsSen, Suman (Author) / Lindsay, Stuart (Thesis advisor) / Zhang, Peiming (Thesis advisor) / Gould, Ian R. (Committee member) / Borges, Chad (Committee member) / Arizona State University (Publisher)
Created2016
Description
For reading DNA bases more accurately, a series of nitrogen-containing aromatic heterocycles have been designed and synthesized as candidates of universal reader to interact with all naturally occurring DNA nucleobases by hydrogen bonding interaction and eventually is used to read DNA by recognition tunneling. These recognition molecules include 6-mercapto-1H-benzo[d]imidazole-2-carboxamide, 5-(2-mercaptoethyl)-1H-imidazole-2-carboxamide, 5-(2-mercaptoethyl)-4H-1,2,4-traizole-3-carboxamide and 1-(2-mercaptoethyl)-1H-pyrrole-3-carboxamide. Their formation of hydrogen bonding complexes with nucleobases was studied and association constants were measured by proton NMR titration experiments in deuterated chloroform at room temperature. To do so, the mercaptoethyl chain or thiol group of these reading molecules was replaced or protected with the more lipophilic group to increase the solubility of these candidates in CDCl3. The 3' and 5' hydroxyl groups of deoxyadenosine (dA), deoxyguanosine (dG), deoxycytidine (dC) and thymidine (dT) were protected with tert-butyldimethylsilyl (TBDMS) to eliminate hydrogen bonding competition from the hydroxyl protons with these candidates as well as to increase the solubility of the nucleosides in CDCl3 for NMR titration experiment. Benzimidazole and imidazole containing readers exhibited the strongest H-bonding affinity towards DNA bases where pyrrole containing reader showed the weakest affinity. In all cases, dG revealed the strongest affinity towards the readers while dA showed the least.
The molecular complex formation in aqueous solution was studied by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry. The formation of both 1:1 and 2:1 complexes between one or two reading molecules and a DNA nucleotide were observed by ESI mass. A series of amino acids and carbohydrates were also examined by mass spectrometry to show the formation of non-covalent complexes with imidazole reader in aqueous solution. The experimental results were compared by calculating energies of ground state conformers of individual molecules and their complexes using computer modeling study by DFT calculations. These studies give insights into the molecular interactions that happen in a nanogap during recognition tunneling experiments.
The molecular complex formation in aqueous solution was studied by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry. The formation of both 1:1 and 2:1 complexes between one or two reading molecules and a DNA nucleotide were observed by ESI mass. A series of amino acids and carbohydrates were also examined by mass spectrometry to show the formation of non-covalent complexes with imidazole reader in aqueous solution. The experimental results were compared by calculating energies of ground state conformers of individual molecules and their complexes using computer modeling study by DFT calculations. These studies give insights into the molecular interactions that happen in a nanogap during recognition tunneling experiments.
ContributorsBiswas, Sovan (Author) / Lindsay, Stuart (Thesis advisor) / Zhang, Peiming (Thesis advisor) / Borges, Chad (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2016
Description
In order for assistive mobile robots to operate in the same environment as humans, they must be able to navigate the same obstacles as humans do. Many elements are required to do this: a powerful controller which can understand the obstacle, and power-dense actuators which will be able to achieve the necessary limb accelerations and output energies. Rapid growth in information technology has made complex controllers, and the devices which run them considerably light and cheap. The energy density of batteries, motors, and engines has not grown nearly as fast. This is problematic because biological systems are more agile, and more efficient than robotic systems. This dissertation introduces design methods which may be used optimize a multiactuator robotic limb's natural dynamics in an effort to reduce energy waste. These energy savings decrease the robot's cost of transport, and the weight of the required fuel storage system. To achieve this, an optimal design method, which allows the specialization of robot geometry, is introduced. In addition to optimal geometry design, a gearing optimization is presented which selects a gear ratio which minimizes the electrical power at the motor while considering the constraints of the motor. Furthermore, an efficient algorithm for the optimization of parallel stiffness elements in the robot is introduced. In addition to the optimal design tools introduced, the KiTy SP robotic limb structure is also presented. Which is a novel hybrid parallel-serial actuation method. This novel leg structure has many desirable attributes such as: three dimensional end-effector positioning, low mobile mass, compact form-factor, and a large workspace. We also show that the KiTy SP structure outperforms the classical, biologically-inspired serial limb structure.
ContributorsCahill, Nathan M (Author) / Sugar, Thomas (Thesis advisor) / Ren, Yi (Thesis advisor) / Holgate, Matthew (Committee member) / Berman, Spring (Committee member) / Artemiadis, Panagiotis (Committee member) / Arizona State University (Publisher)
Created2017
Description
Fluoroquinolone antibiotics have been known to cause severe, multisystem adverse side effects, termed fluoroquinolone toxicity (FQT). This toxicity syndrome can present with adverse effects that vary from individual to individual, including effects on the musculoskeletal and nervous systems, among others. The mechanism behind FQT in mammals is not known, although various possibilities have been investigated. Among the hypothesized FQT mechanisms, those that could potentially explain multisystem toxicity include off-target mammalian topoisomerase interactions, increased production of reactive oxygen species, oxidative stress, and oxidative damage, as well as metal chelating properties of FQs. This review presents relevant information on fluoroquinolone antibiotics and FQT and explores the mechanisms that have been proposed. A fluoroquinolone-induced increase in reactive oxygen species and subsequent oxidative stress and damage presents the strongest evidence to explain this multisystem toxicity syndrome. Understanding the mechanism of FQT in mammals is important to aid in the prevention and treatment of this condition.
ContributorsHall, Brooke Ashlyn (Author) / Redding, Kevin (Thesis director) / Wideman, Jeremy (Committee member) / Borges, Chad (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05