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Description
Ideas from coding theory are employed to theoretically demonstrate the engineering of mutation-tolerant genes, genes that can sustain up to some arbitrarily chosen number of mutations and still express the originally intended protein. Attention is restricted to tolerating substitution mutations. Future advances in genomic engineering will make possible the ability to synthesize entire genomes from scratch. This presents an opportunity to embed desirable capabilities like mutation-tolerance, which will be useful in preventing cell deaths in organisms intended for research or industrial applications in highly mutagenic environments. In the extreme case, mutation-tolerant genes (mutols) can make organisms resistant to retroviral infections.
An algebraic representation of the nucleotide bases is developed. This algebraic representation makes it possible to convert nucleotide sequences into algebraic sequences, apply mathematical ideas and convert results back into nucleotide terms. Using the algebra developed, a mapping is found from the naturally-occurring codons to an alternative set of codons which makes genes constructed from them mutation-tolerant, provided no more than one substitution mutation occurs per codon. The ideas discussed naturally extend to finding codons that can tolerate t arbitrarily chosen number of mutations per codon. Finally, random substitution events are simulated in both a wild-type green fluorescent protein (GFP) gene and its mutol variant and the amino acid sequence expressed from each post-mutation is compared with the amino acid sequence pre-mutation.
This work assumes the existence of synthetic protein-assembling entities that function like tRNAs but can read k nucleotides at a time, with k greater than or equal to 5. The realization of this assumption is presented as a challenge to the research community.
An algebraic representation of the nucleotide bases is developed. This algebraic representation makes it possible to convert nucleotide sequences into algebraic sequences, apply mathematical ideas and convert results back into nucleotide terms. Using the algebra developed, a mapping is found from the naturally-occurring codons to an alternative set of codons which makes genes constructed from them mutation-tolerant, provided no more than one substitution mutation occurs per codon. The ideas discussed naturally extend to finding codons that can tolerate t arbitrarily chosen number of mutations per codon. Finally, random substitution events are simulated in both a wild-type green fluorescent protein (GFP) gene and its mutol variant and the amino acid sequence expressed from each post-mutation is compared with the amino acid sequence pre-mutation.
This work assumes the existence of synthetic protein-assembling entities that function like tRNAs but can read k nucleotides at a time, with k greater than or equal to 5. The realization of this assumption is presented as a challenge to the research community.
ContributorsAmpofo, Prince Kwame (Author) / Tian, Xiaojun (Thesis advisor) / Kiani, Samira (Committee member) / Kuang, Yang (Committee member) / Arizona State University (Publisher)
Created2019
Description
Wearable assistive devices have been greatly improved thanks to advancements made in soft robotics, even creation soft extra arms for paralyzed patients. Grasping remains an active area of research of soft extra limbs. Soft robotics allow the creation of grippers that due to their inherit compliance making them lightweight, safer for human interactions, more robust in unknown environments and simpler to control than their rigid counterparts. A current problem in soft robotics is the lack of seamless integration of soft grippers into wearable devices, which is in part due to the use of elastomeric materials used for the creation of most of these grippers. This work introduces fabric-reinforced textile actuators (FRTA). The selection of materials, design logic of the fabric reinforcement layer and fabrication method are discussed. The relationship between the fabric reinforcement characteristics and the actuator deformation is studied and experimentally verified. The FRTA are made of a combination of a hyper-elastic fabric material with a stiffer fabric reinforcement on top. In this thesis, the design, fabrication, and evaluation of FRTAs are explored. It is shown that by varying the geometry of the reinforcement layer, a variety of motion can be achieve such as axial extension, radial expansion, bending, and twisting along its central axis. Multi-segmented actuators can be created by tailoring different sections of fabric-reinforcements together in order to generate a combination of motions to perform specific tasks. The applicability of this actuators for soft grippers is demonstrated by designing and providing preliminary evaluation of an anthropomorphic soft robotic hand capable of grasping daily living objects of various size and shapes.
ContributorsLopez Arellano, Francisco Javier (Author) / Santello, Marco (Thesis advisor) / Zhang, Wenlong (Thesis advisor) / Buneo, Christopher (Committee member) / Arizona State University (Publisher)
Created2019
Description
Stroke remains a leading cause of adult disability in the United States. In recent studies, chronic vagus nerve stimulation (VNS) has been proven to enhance functional recovery when paired with motor rehabilitation training after stroke. Other studies have also demonstrated that delivering VNS during the onset of a stroke may elicit some neuroprotective effects as observed in remaining neural tissue and motor function. While these studies have demonstrated the benefits of VNS as a treatment or therapy in combatting stroke damage, the mechanisms responsible for these effects are still not well understood or known. The aim of this research was to further investigate the mechanisms underlying the efficacy of acute VNS treatment of stroke by observing the effect of VNS when applied after the onset of stroke. Animals were randomly assigned to three groups: Stroke animals received cortical ischemia (ET-1 injection), VNS+Stroke animals received acute VNS starting within 48 hours after cortical ischemia and continuing once per day for three days, or Control animals which received neither the injury nor stimulation. Results showed that stroke animals receiving acute VNS had smaller lesion volumes and larger motor cortical maps than those in the Stroke group. The results suggest VNS may confer neuroprotective effects when delivered within the first 96 hours of stroke.
ContributorsOkada, Kristen Yuri (Author) / Kleim, Jeffrey A (Thesis advisor) / Si, Jennie (Thesis advisor) / Helms Tillery, Stephen (Committee member) / Arizona State University (Publisher)
Created2019
Description
Extracellular Vesicles (EVs), particularly exosomes, are of considerable interest as tumor biomarkers since tumor-derived EVs contain a broad array of information about tumor pathophysiology including its metabolic and metastatic status. However, current EV based assays cannot distinguish between EV biomarker changes by altered secretion of EVs during diseased conditions like cancer, inflammation, etc. that express a constant level of a given biomarker, stable secretion of EVs with altered biomarker expression, or a combination of these two factors. This issue was addressed by developing a nanoparticle and dye-based fluorescent immunoassay that can distinguish among these possibilities by normalizing EV biomarker level(s) to EV abundance, revealing average expression levels of EV biomarker under observation. In this approach, EVs are captured from complex samples (e.g. serum), stained with a lipophilic dye and hybridized with antibody-conjugated quantum dot probes for specific EV surface biomarkers. EV dye signal is used to quantify EV abundance and normalize EV surface biomarker expression levels. EVs from malignant (PANC-1) and nonmalignant pancreatic cell lines (HPNE) exhibited similar staining, and probe-to-dye ratios did not change with EV abundance, allowing direct analysis of normalized EV biomarker expression without a separate EV quantification step. This EV biomarker normalization approach markedly improved the ability of serum levels of two pancreatic cancer biomarkers, EV EpCAM, and EV EphA2, to discriminate pancreatic cancer patients from nonmalignant control subjects. The streamlined workflow and robust results of this assay are suitable for rapid translation to clinical applications and its flexible design permits it to be rapidly adapted to quantitate other EV biomarkers by the simple swapping of the antibody-conjugated quantum dot probes for those that recognize a different disease-specific EV biomarker utilizing a workflow that is suitable for rapid clinical translation.
ContributorsRodrigues, Meryl (Author) / Hu, Tony (Thesis advisor) / Nikkhah, Mehdi (Committee member) / Kiani, Samira (Committee member) / Smith, Barbara (Committee member) / Han, Haiyong (Committee member) / Arizona State University (Publisher)
Created2019
Description
Alzheimer’s disease (AD) affects over 5 million individuals each year in the United States. Furthermore, most cases of AD are sporadic, making it extremely difficult to model and study in vitro. CRISPR/Cas9 and base editing technologies have been of recent interest because of their ability to create single nucleotide edits at nearly any genomic sequence using a Cas9 protein and a guide RNA (sgRNA). Currently, there is no available phenotype to differentiate edited cells from unedited cells. Past research has employed fluorescent proteins bound to Cas9 proteins to attempt to enrich for edited cells, however, these methods are only reporters of transfection (RoT) and are no indicative of actual base-editing occurring. Thus, this study proposes a transient reporter for editing enrichment (TREE) and Cas9-mediated adenosine TREE (CasMasTREE) which use plasmids to co-transfect with CRISPR/Cas9 technologies to serve as an indicator of base-editing. Specifically, TREE features a blue fluorescent protein (BFP) mutant that, upon a C-T conversion, changes the emission spectrum to a green fluorescent protein (GFP). CasMasTREE features a mCherry and GFP protein separated by a stop codon which can be negated using an A-G conversion. By employing a sgRNA that targets one of the TREE plasmids and at least one genomic site, cells can be sorted for GFP(+) cells. Using these methods, base-edited isogenic hiPSC line generation using TREE (BIG-TREE) was created to generate isogenic hiPSC lines with AD-relevant edits. For example, BIG-TREE demonstrates the capability of converting Apolipoprotein E (APOE), a gene associated with AD-risk development, wildtype (3/3) into another isoform, APOE2/2, to create isogenic hiPSC lines. The capabilities of TREE are vast and can be applied to generate various models of diseases with specific genomic edits.
ContributorsNguyen, Toan Thai Tran (Author) / Brafman, David (Thesis advisor) / Wang, Xiao (Committee member) / Tian, Xiaojun (Committee member) / Arizona State University (Publisher)
Created2020
Description
Fusion proteins that specifically interact with biochemical marks on chromosomes represent a new class of synthetic transcriptional regulators that decode cell state information rather than deoxyribose nucleic acid (DNA) sequences. In multicellular organisms, information relevant to cell state, tissue identity, and oncogenesis is often encoded as biochemical modifications of histones, which are bound to DNA in eukaryotic nuclei and regulate gene expression states. In 2011, Haynes et al. showed that a synthetic regulator called the Polycomb chromatin Transcription Factor (PcTF), a fusion protein that binds methylated histones, reactivated an artificially-silenced luciferase reporter gene. These synthetic transcription activators are derived from the polycomb repressive complex (PRC) and associate with the epigenetic silencing mark H3K27me3 to reactivate the expression of silenced genes. It is demonstrated here that the duration of epigenetic silencing does not perturb reactivation via PcTF fusion proteins. After 96 hours PcTF shows the strongest reactivation activity. A variant called Pc2TF, which has roughly double the affinity for H3K27me3 in vitro, reactivated the silenced luciferase gene by at least 2-fold in living cells.
ContributorsVargas, Daniel A. (Author) / Haynes, Karmella (Thesis advisor) / Wang, Xiao (Committee member) / Mills, Jeremy (Committee member) / Arizona State University (Publisher)
Created2019
Description
This dissertation aimed to evaluate the effectiveness and drawbacks of promising fall prevention strategies in individuals with stroke by rigorously analyzing the biomechanics of laboratory falls and compensatory movements required to prevent a fall. Ankle-foot-orthoses (AFOs) and functional electrical stimulators (FESs) are commonly prescribed to treat foot drop. Despite well-established positive impacts of AFOs and FES devices on balance and gait, AFO and FES users fall at a high rate. In chapter 2 (as a preliminary study), solely mechanical impacts of a semi-rigid AFO on the compensatory stepping response of young healthy individuals following trip-like treadmill perturbations were evaluated. It was found that a semi-rigid AFO on the stepping leg diminished the propulsive impulse of the compensatory step which led to decreased trunk movement control, shorter step length, and reduced center of mass (COM) stability. These results highlight the critical role of plantarflexors in generating an effective compensatory stepping response. In chapter 3, the underlying biomechanical mechanisms leading to high fall risk in long-term AFO and FES users with chronic stroke were studied. It was found that AFO and FES users fall more than Non-users because they have a more impaired lower limb that is not fully addressed by AFO/FES, therefore leading to a more impaired compensatory stepping response characterized by increased inability to generate a compensatory step with paretic leg and decreased trunk movement control. An ideal future AFO that provides dorsiflexion assistance during the swing phase and plantarflexion assistance during the push-off phase of gait is suggested to enhance the compensatory stepping response and reduce more falls. In chapter 4, the effects of a single-session trip-specific training on the compensatory stepping response of individuals with stroke were evaluated. Trunk movement control was improved after a single session of training suggesting that this type of training is a viable option to enhance compensatory stepping response and reduce falls in individuals with stroke. Finally, a future powered AFO with plantarflexion assistance complemented by a trip-specific training program is suggested to enhance the compensatory stepping response and decrease falls in individuals with stroke.
ContributorsNevisipour, Masood (Author) / Honeycutt, Claire (Thesis advisor) / Sugar, Thomas (Thesis advisor) / Artemiadis, Panagiotis (Committee member) / Abbas, James (Committee member) / Lee, Hyunglae (Committee member) / Arizona State University (Publisher)
Created2019
Description
Electromagnetic fields (EMFs) generated by biologically active neural tissue are critical in the diagnosis and treatment of neurological diseases. Biological EMFs are characterized by electromagnetic properties such as electrical conductivity, permittivity and magnetic susceptibility. The electrical conductivity of active tissue has been shown to serve as a biomarker for the direct detection of neural activity, and the diagnosis, staging and prognosis of disease states such as cancer. Magnetic resonance electrical impedance tomography (MREIT) was developed to map the cross-sectional conductivity distribution of electrically conductive objects using externally applied electrical currents. Simulation and in vitro studies of invertebrate neural tissue complexes demonstrated the correlation of membrane conductivity variations with neural activation levels using the MREIT technique, therefore laying the foundation for functional MREIT (fMREIT) to detect neural activity, and future in vivo fMREIT studies.
The development of fMREIT for the direct detection of neural activity using conductivity contrast in in vivo settings has been the focus of the research work presented here. An in vivo animal model was developed to detect neural activity initiated changes in neuronal membrane conductivities under external electrical current stimulation. Neural activity was induced in somatosensory areas I (SAI) and II (SAII) by applying electrical currents between the second and fourth digits of the rodent forepaw. The in vivo animal model involved the use of forepaw stimulation to evoke somatosensory neural activations along with hippocampal fMREIT imaging currents contemporaneously applied under magnetic field strengths of 7 Tesla. Three distinct types of fMREIT current waveforms were applied as imaging currents under two inhalants – air and carbogen. Active regions in the somatosensory cortex showed significant apparent conductivity changes as variations in fMREIT phase (φ_d and ∇^2 φ_d) signals represented by fMREIT activation maps (F-tests, p <0.05). Consistent changes in the standard deviation of φ_d and ∇^2 φ_d in cortical voxels contralateral to forepaw stimulation were observed across imaging sessions. These preliminary findings show that fMREIT may have the potential to detect conductivity changes correlated with neural activity.
The development of fMREIT for the direct detection of neural activity using conductivity contrast in in vivo settings has been the focus of the research work presented here. An in vivo animal model was developed to detect neural activity initiated changes in neuronal membrane conductivities under external electrical current stimulation. Neural activity was induced in somatosensory areas I (SAI) and II (SAII) by applying electrical currents between the second and fourth digits of the rodent forepaw. The in vivo animal model involved the use of forepaw stimulation to evoke somatosensory neural activations along with hippocampal fMREIT imaging currents contemporaneously applied under magnetic field strengths of 7 Tesla. Three distinct types of fMREIT current waveforms were applied as imaging currents under two inhalants – air and carbogen. Active regions in the somatosensory cortex showed significant apparent conductivity changes as variations in fMREIT phase (φ_d and ∇^2 φ_d) signals represented by fMREIT activation maps (F-tests, p <0.05). Consistent changes in the standard deviation of φ_d and ∇^2 φ_d in cortical voxels contralateral to forepaw stimulation were observed across imaging sessions. These preliminary findings show that fMREIT may have the potential to detect conductivity changes correlated with neural activity.
ContributorsAshok Kumar, Neeta (Author) / Sadleir, Rosalind J (Thesis advisor) / Greger, Bradley (Committee member) / Muthuswamy, Jitendran (Committee member) / Tillery, Stephen H (Committee member) / Sohn, SungMin (Committee member) / Arizona State University (Publisher)
Created2020
Description
The CRISPR/Cas9 gene-editing tool is currently in clinical trials as the excitement about its therapeutic potential is exponentially growing. However, many of the developed CRISPR based genome engineering methods cannot be broadly translated in clinical settings due to their unintended consequences. These consequences, such as immune reactions to CRISPR, immunogenic adverse events following receiving of adeno-associated virus (AAV) as one of the clinically relevant delivery agents, and CRISPR off-target activity in the genome, reinforces the necessity for improving the safety of CRISPR and the gene therapy vehicles. Research into designing more advanced CRISPR systems will allow for the increased ability of editing efficiency and safety for human applications. This work 1- develops strategies for decreasing the immunogenicity of CRISPR/Cas9 system components and improving the safety of CRISPR-based gene therapies for human subjects, 2- demonstrates the utility of this system in vivo for transient repression of components of innate and adaptive immunity, and 3- examines an inducible all-in-one CRISPR-based control switch to pave the way for controllable CRISPR-based therapies.
ContributorsMoghadam, Farzaneh (Author) / Kiani, Samira (Thesis advisor) / LaBaer, Josh (Committee member) / Ebrahimkhani, Mo (Committee member) / Arizona State University (Publisher)
Created2020
Description
Gene circuit engineering facilitates the discovery and understanding of fundamental biology and has been widely used in various biological applications. In synthetic biology, gene circuits are often constructed by two main strategies: either monocistronic or polycistronic constructions. The Latter architecture can be commonly found in prokaryotes, eukaryotes, and viruses and has been largely applied in gene circuit engineering. In this work, the effect of adjacent genes and noncoding regions are systematically investigated through the construction of batteries of gene circuits in diverse scenarios. Data-driven analysis yields a protein expression metric that strongly correlates with the features of adjacent transcriptional regions (ATRs). This novel mathematical tool helps the guide for circuit construction and has the implication for the design of synthetic ATRs to tune gene expression, illustrating its potential to facilitate engineering complex gene networks. The ability to tune RNA dynamics is greatly needed for biotech applications, including therapeutics and diagnostics. Diverse methods have been developed to tune gene expression through transcriptional or translational manipulation. Control of RNA stability/degradation is often overlooked and can be the lightweight alternative to regulate protein yields. To further extend the utility of engineered ATRs to regulate gene expression, a library of RNA modules named degradation-tuning RNAs (dtRNAs) are designed with the ability to form specific 5’ secondary structures prior to RBS. These modules can modulate transcript stability while having a minimal interference on translation initiation. Optimization of their functional structural features enables gene expression level to be tuned over a wide dynamic range. These engineered dtRNAs are capable of regulating gene circuit dynamics as well as noncoding RNA levels and can be further expanded into cell-free system for gene expression control in vitro. Finally, integrating dtRNA with synthetic toehold sensor enables improved paper-based viral diagnostics, illustrating the potential of using synthetic dtRNAs for biomedical applications.
ContributorsZhang, Qi (Author) / Wang, Xiao (Thesis advisor) / Green, Alexander (Committee member) / Brafman, David (Committee member) / Tian, Xiaojun (Committee member) / Plaisier, Christopher (Committee member) / Arizona State University (Publisher)
Created2020