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- Genre: Doctoral Dissertation
- Creators: Acharya, Abhinav
- Creators: Smith, Barbara
- Status: Published
Description
The world today needs novel solutions to address current challenges in areas spanning areas from sustainable manufacturing to healthcare, and biotechnology offers the potential to help address some of these issues. One tool that offers opportunities across multiple industries is the use of nonribosomal peptide synthases (NRPSs). These are modular biological factories with individualized subunits that function in concert to create novel peptides.One element at the heart of environmental health debates today is plastics. Biodegradable alternatives for petroleum-based plastics is a necessity. One NRPS, cyanophycin synthetase (CphA), can produce cyanophycin grana protein (CGP), a polymer composed of a poly-aspartic acid backbone with arginine side chains. The aspartic backbone has the potential to replace synthetic polyacrylate, although current production costs are prohibitive. In Chapter 2, a CphA variant from Tatumella morbirosei is characterized, that produces up to 3x more CGP than other known variants, and shows high iCGP specificity in both flask and bioreactor trials. Another CphA variant, this one from Acinetobacter baylyi, underwent rational protein design to create novel mutants. One, G217K, is 34% more productive than the wild type, while G163K produces a CGP with shorter chain lengths. The current structure refined from 4.4Å to 3.5Å.
Another exciting application of NRPSs is in healthcare. They can be used to generate novel peptides such as complex antibiotics. A recently discovered iterative polyketide synthase (IPTK), dubbed AlnB, produces an antibiotic called allenomycin. One of the modular subunits, a dehydratase named AlnB_DH, was crystallized to 2.45Å. Several mutations were created in multiple active site residues to help understand the functional mechanism of AlnB_DH. A preliminary holoenzyme AlnB structure at 3.8Å was generated although the large disorganized regions demonstrated an incomplete structure. It was found that chain length is the primary factor in driving dehydratase action within AlnB_DH, which helps lend understanding to this module.
ContributorsSwain, Kyle (Author) / Nannenga, Brent (Thesis advisor) / Nielsen, David (Committee member) / Mills, Jeremy (Committee member) / Seo, Eileen (Committee member) / Acharya, Abhinav (Committee member) / Arizona State University (Publisher)
Created2022
Description
Sutures, staples, and tissue glues remain the primary means of tissue approximation and vessel ligation. Laser-activated tissue sealing is an alternative approach that conventionally employs light-absorbing chromophores and nanoparticles for converting near-infrared (NIR) laser to heat. The local increase in temperature engenders interdigitation of sealant and tissue biomolecules, resulting in rapid tissue sealing. Light-activated sealants (LASE) were developed in which indocyanine green (ICG) dye is embedded within a biopolymer matrix (silk or chitosan) for incisional defect repair. Light-activated tissue-integrating sutures (LATIS) that synergize the benefits of conventional suturing and laser sealing were also fabricated and demonstrated higher efficacies for tissue biomechanical recovery and repair in a full-thickness, dorsal surgical incision model in mice compared to commercial sutures and cyanoacrylate skin glue. Localized delivery of modulators of tissue repair, including histamine and copper, from LASE and LATIS further improved healed skin strength. In addition to incisional wounds, histamine co-delivered with silk fibroin LASE films accelerated the closure of full thickness, splinted excisional wounds in immunocompetent BALB/c mice and genetically obese and diabetic db/db mice, resulting in faster closure than Tegaderm wound dressing. Immunohistochemistry analyses showed LASE-histamine treatment enhanced wound repair involving mechanisms of neoangiogenesis, myofibroblast activation, transient epidermal EMT, and also improve healed skin biomechanical strength which are hallmarks of improved healing outcomes. Benefit of temporal delivery was further investigated of a second therapeutic (growth factor nanoparticles) in modulating wound healing outcomes in both acute and diabetic wounds. The hypothesis of temporal delivery of second therapeutic around the ‘transition period’ in wounds further improved wound closure kinetics and biomechanical recovery of skin strength. Laser sealing and approximation, together with delivery of immunomodulatory mediators, can lead to faster healing and tissue repair, thus reducing wound dehiscence, preventing wounds moving towards chronicity and lowering incidence of surgical site infections, all of which can have significant impact in the clinic.
ContributorsGhosh, Deepanjan (Author) / Rege, Kaushal (Thesis advisor) / Acharya, Abhinav (Committee member) / Holloway, Julianne (Committee member) / DiCaudo, David (Committee member) / P. Leung, Kai (Committee member) / Arizona State University (Publisher)
Created2021
Description
According to the World Health Organization, cancer is one of the leading causes of death around the world. Although early diagnostics using biomarkers and improved treatments with targeted therapy have reduced the rate of cancer related mortalities, there remain many unknowns regarding the contributions of the tumor microenvironment to cancer progression and therapeutic resistance. The tumor microenvironment plays a significant role by manipulating the progression of cancer cells through biochemical and biophysical signals from the surrounding stromal cells along with the extracellular matrix. As such, there is a critical need to understand how the tumor microenvironment influences the molecular mechanisms underlying cancer metastasis to facilitate the discovery of better therapies. This thesis described the development of microfluidic technologies to study the interplay of cancer cells with their surrounding microenvironment. The microfluidic model was used to assess how exposure to chemoattractant, epidermal growth factor (EGF), impacted 3D breast cancer cell invasion and enhanced cell motility speed was noted in the presence of EGF validating physiological cell behavior. Additionally, breast cancer and patient-derived cancer-associated fibroblast (CAF) cells were co-cultured to study cell-cell crosstalk and how it affected cancer invasion. GPNMB was identified as a novel gene of interest and it was shown that CAFs enhanced breast cancer invasion by up-regulating the expression of GPNMB on breast cancer cells resulting in increased migration speed. Lastly, this thesis described the design, biological validation, and use of this microfluidic platform as a new in vitro 3D organotypic model to study mechanisms of glioma stem cell (GSC) invasion in the context of a vascular niche. It was confirmed that CXCL12-CXCR4 signaling is involved in promoting GSC invasion in a 3D vascular microenvironment, while also demonstrating the effectiveness of the microfluidic as a drug screening assay. Taken together, the broader impacts of the microfluidic model developed in this dissertation include, a possible alternative platform to animal testing that is focused on mimicking human physiology, a potential ex vivo platform using patient-derived cells for studying the interplay of cancer cells with its surrounding microenvironment, and development of future therapeutic strategies tailored toward disrupting key molecular pathways involved in regulatory mechanisms of cancer invasion.
ContributorsTruong, Danh, Ph.D (Author) / Nikkhah, Mehdi (Thesis advisor) / LaBaer, Joshua (Committee member) / Smith, Barbara (Committee member) / Mouneimne, Ghassan (Committee member) / Vernon, Brent (Committee member) / Arizona State University (Publisher)
Created2018
Description
Tissue approximation and repair have been performed with sutures and staples for centuries, but these means are inherently traumatic. Tissue repair using laser-responsive nanomaterials can lead to rapid tissue sealing and repair and is an attractive alternative to existing clinical methods. Laser tissue welding is a sutureless technique for sealing incised or wounded tissue, where chromophores convert laser light to heat to induce in tissue sealing. Introducing chromophores that absorb near-infrared light creates differential laser absorption and allows for laser wavelengths that minimizes tissue damage.
In this work, plasmonic nanocomposites have been synthesized and used in laser tissue welding for ruptured porcine intestine ex vivo and incised murine skin in vivo. These laser-responsive nanocomposites improved tissue strength and healing, respectively. Additionally, a spatiotemporal model has been developed for laser tissue welding of porcine and mouse cadaver intestine sections using near-infrared laser irradiation. This mathematical model can be employed to identify optimal conditions for minimizing healthy cell death while still achieving a strong seal of the ruptured tissue using laser welding. Finally, in a model of surgical site infection, laser-responsive nanomaterials were shown to be efficacious in inhibiting bacterial growth. By incorporating an anti-microbial functionality to laser-responsive nanocomposites, these materials will serve as a treatment modality in sealing tissue, healing tissue, and protecting tissue in surgery.
In this work, plasmonic nanocomposites have been synthesized and used in laser tissue welding for ruptured porcine intestine ex vivo and incised murine skin in vivo. These laser-responsive nanocomposites improved tissue strength and healing, respectively. Additionally, a spatiotemporal model has been developed for laser tissue welding of porcine and mouse cadaver intestine sections using near-infrared laser irradiation. This mathematical model can be employed to identify optimal conditions for minimizing healthy cell death while still achieving a strong seal of the ruptured tissue using laser welding. Finally, in a model of surgical site infection, laser-responsive nanomaterials were shown to be efficacious in inhibiting bacterial growth. By incorporating an anti-microbial functionality to laser-responsive nanocomposites, these materials will serve as a treatment modality in sealing tissue, healing tissue, and protecting tissue in surgery.
ContributorsUrie, Russell Ricks (Author) / Rege, Kaushal (Thesis advisor) / Acharya, Abhinav (Committee member) / DeNardo, Dale (Committee member) / Holloway, Julianne (Committee member) / Thomas, Marylaura (Committee member) / Arizona State University (Publisher)
Created2019
Description
Abnormally low or high blood iron levels are common health conditions worldwide and can seriously affect an individual’s overall well-being. A low-cost point-of-care technology that measures blood iron markers with a goal of both preventing and treating iron-related disorders represents a significant advancement in medical care delivery systems. Methods: A novel assay equipped with an accurate, storable, and robust dry sensor strip, as well as a smartphone mount and (iPhone) app is used to measure total iron in human serum. The sensor strip has a vertical flow design and is based on an optimized chemical reaction. The reaction strips iron ions from blood-transport proteins, reduces Fe(III) to Fe(II), and chelates Fe(II) with ferene, with the change indicated by a blue color on the strip. The smartphone mount is robust and controls the light source of the color reading App, which is calibrated to obtain output iron concentration results. The real serum samples are then used to assess iron concentrations from the new assay and validated through intra-laboratory and inter-laboratory experiments. The intra-laboratory validation uses an optimized iron detection assay with multi-well plate spectrophotometry. The inter-laboratory validation method is performed in a commercial testing facility (LabCorp). Results: The novel assay with the dry sensor strip and smartphone mount, and App is seen to be sensitive to iron detection with a dynamic range of 50 - 300 µg/dL, sensitivity of 0.00049 µg/dL, coefficient of variation (CV) of 10.5%, and an estimated detection limit of ~15 µg/dL These analytical specifications are useful for predicting iron deficiency and overloads. The optimized reference method has a sensitivity of 0.00093 µg/dL and CV of 2.2%. The correlation of serum iron concentrations (N=20) between the optimized reference method and the novel assay renders a slope of 0.95, and a regression coefficient of 0.98, suggesting that the new assay is accurate. Lastly, a spectrophotometric study of the iron detection reaction kinetics is seen to reveal the reaction order for iron and chelating agent. Conclusion: The new assay is able to provide accurate results in intra- and inter- laboratory validations and has promising features of both mobility and low-cost.
ContributorsSerhan, Michael (Author) / Forzani, Erica (Thesis advisor) / Raupp, Gregory (Committee member) / Acharya, Abhinav (Committee member) / Hu, Tony (Committee member) / Smith, Barbara (Committee member) / Arizona State University (Publisher)
Created2020
Description
Genome wide association studies (GWAS) have identified polymorphism in the Apolipoprotein E (APOE) gene to be the most prominent risk factor for Alzheimer’s disease (AD). Compared to individuals homozygous for the APOE3 variant, individuals with the APOE4 variant have a significantly elevated risk of AD. On the other hand, longitudinal studies have shown that the presence of the APOE2 variant reduces lifetime risk of developing AD by 40 percent. While there has been significant research that has identified the risk-inducing effects of APOE4, the underlying mechanisms by which APOE2 influences AD onset and progression have not been extensively explored. The hallmarks of AD pathology manifest in human neurons in the form of extracellular amyloid deposits and intracellular neurofibrillary tangles, whereas astrocytes are the primary source of the APOE protein in the brain. In this study, an isogenic human induced pluripotent stem cell (hiPSC)-based system is utilized to demonstrate that conversion of APOE3 to APOE2 greatly reduced the production of amyloid-beta (Aβ) peptides in hiPSC-derived neural cultures. Mechanistically, analysis of pure populations of neurons and astrocytes derived from these neural cultures revealed that mitigating effects of APOE2 is mediated by cell autonomous and non-autonomous effects. In particular, it was demonstrated the reduction in Aβ and pathogenic β-C-terminal fragments (APP-βCTF) is potentially driven by a mechanism related to non-amyloidogenic processing of amyloid precursor protein (APP), suggesting a gain of protective function of the APOE2 variant. Together, this study provides insights into the risk-modifying effects associated with the APOE2 allele and establishes a platform to probe the mechanisms by which APOE2 enhances neuroprotection against AD.
ContributorsRaman, Sreedevi (Author) / Brafman, David (Thesis advisor) / Smith, Barbara (Committee member) / Plaiser, Christopher (Committee member) / Wang, Xiao (Committee member) / Tian, Xiaojun (Committee member) / Arizona State University (Publisher)
Created2021
Description
While various collision warning studies in driving have been conducted, only a handful of studies have investigated the effectiveness of warnings with a distracted driver. Across four experiments, the present study aimed to understand the apparent gap in the literature of distracted drivers and warning effectiveness, specifically by studying various warnings presented to drivers while they were operating a smart phone. Experiment One attempted to understand which smart phone tasks, (text vs image) or (self-paced vs other-paced) are the most distracting to a driver. Experiment Two compared the effectiveness of different smartphone based applications (app’s) for mitigating driver distraction. Experiment Three investigated the effects of informative auditory and tactile warnings which were designed to convey directional information to a distracted driver (moving towards or away). Lastly, Experiment Four extended the research into the area of autonomous driving by investigating the effectiveness of different auditory take-over request signals. Novel to both Experiment Three and Four was that the warnings were delivered from the source of the distraction (i.e., by either the sound triggered at the smart phone location or through a vibration given on the wrist of the hand holding the smart phone). This warning placement was an attempt to break the driver’s attentional focus on their smart phone and understand how to best re-orient the driver in order to improve the driver’s situational awareness (SA). The overall goal was to explore these novel methods of improved SA so drivers may more quickly and appropriately respond to a critical event.
ContributorsMcNabb, Jaimie Christine (Author) / Gray, Dr. Rob (Thesis advisor) / Branaghan, Dr. Russell (Committee member) / Becker, Dr. Vaughn (Committee member) / Arizona State University (Publisher)
Created2017