Cellular assays are the backbone of biological studies - be it for tissue modeling, drug discovery, therapeutics, or diagnostics. Two-dimensional (2D) cell culture has been deployed for several decades to garner physiologically relevant information and predict data before the cost-intensive animal testing. Although 2D techniques have been valuable for cellular assays, they have a colossal limitation - they do not adequately consider the natural three-dimensional (3D) microenvironment of the cells. As a result, they sometimes provide misleading statistics. Therefore, it is important to develop a 3D model that predicts cellular behaviors and their interaction with neighboring cells and extracellular matrix (ECM) in a more realistic manner. In recent biomedical research, various platforms have been modeled to generate 3D prototypes of tissues, spheroids, in vitro that could allow the study of cellular responses resembling in vivo environments, such as matrices, scaffolds, and devices. But most of these platforms have drawbacks such as lack of spheroid size control, low yield, or high cost associated with them. On the other hand, Amikagel is a low cost, high-fidelity platform that can facilitate the convenient generation of tumor and stem cell spheroids. Furthermore, Amikabeads are aminoglycoside-derived hydrogel microbeads derived from the same monomers as Amikagel. They are a versatile platform with several chemical groups that can be exploited for encapsulating the spheroids and investigating the delivery of bioactive compounds to the cells. This thesis is focused on engineering novel 3D tumor and stem cell models generated on Amikagel and encapsulated in Amikabeads for proximal delivery of bioactive compounds and applications in regenerative medicine.

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.

Chromatin is the dynamic structure of proteins and nucleic acids into which eukaryotic genomes are organized. For those looking to engineer mammalian genomes, chromatin is both an opportunity and an obstacle. While chromatin provides another tool with which to control gene expression, regional density can lead to variability in genome editing efficiency by CRISPR/Cas9 systems. Many groups have attempted to de-silence chromatin to regulate genes and enhance DNA's accessibility to nucleases, but inconsistent results leave outstanding questions. Here, I test different types of activators, to analyze changes in chromatin features that result for chromatin opening, and to identify the critical biochemical features that support artificially generated open, transcriptionally active chromatin.

I designed, built, and tested a panel of synthetic pioneer factors (SPiFs) to open condensed, repressive chromatin with the aims of 1) activating repressed transgenes in mammalian cells and 2) reversing the inhibitory effects of closed chromatin on Cas9-endonuclease activity. Pioneer factors are unique in their ability to bind DNA in closed chromatin. In order to repurpose this natural function, I designed SPiFs from a Gal4 DNA binding domain, which has inherent pioneer functionality, fused with chromatin-modifying peptides with distinct functions.

SPiFs with transcriptional activation as their primary mechanism were able to reverse this repression and induced a stably active state. My work also revealed the active site from proto-oncogene MYB as a novel transgene activator. To determine if MYB could be used generally to restore transgene expression, I fused it to a deactivated Cas9 and targeted a silenced transgene in native heterochromatin. The resulting activator was able to reverse silencing and can be chemically controlled with a small molecule drug.

Other SPiFs in my panel did not increase gene expression. However, pretreatment with several of these expression-neutral SPiFs increased Cas9-mediated editing in closed chromatin, suggesting a crucial difference between chromatin that is accessible and that which contains genes being actively transcribed. Understanding this distinction will be vital to the engineering of stable transgenic cell lines for product production and disease modeling, as well as therapeutic applications such as restoring epigenetic order to misregulated disease cells.

Rapid development of new technology has significantly disrupted the way radiotherapy is planned and delivered. These processes involve delivering high radiation doses to the target tumor while minimizing dose to the surrounding healthy tissue. However, with rapid implementation of these new technologies, there is a need for the detection of prescribed ionizing radiation for radioprotection of the patient and quality assurance of the technique employed. Most available clinical sensors are subjected to various limitations including requirement of extensive training, loss of readout with sequential measurements, sensitivity to light and post-irradiation wait time prior to analysis. Considering these disadvantages, there is still a need for a sensor that can be fabricated with ease and still operate effectively in predicting the delivered radiation dose.



The dissertation discusses the development of a sensor that changes color upon exposure to therapeutic levels of ionizing radiation used during routine radiotherapy. The underlying principle behind the sensor is based on the formation of gold nanoparticles from its colorless precursor salt solution upon exposure to ionizing radiation. Exposure to ionizing radiation generates free radicals which reduce ionic gold to its zerovalent gold form which further nucleate and mature into nanoparticles. The generation of these nanoparticles render a change in color from colorless to a maroon/pink depending on the intensity of incident ionizing radiation. The shade and the intensity of the color developed is used to quantitatively and qualitatively predict the prescribed radiation dose.

The dissertation further describes the applicability of sensor to detect a wide range of ionizing radiation including high energy photons, protons, electrons and emissions from radioactive isotopes while remaining insensitive to non-ionizing radiation. The sensor was further augmented with a capability to differentiate regions that are irradiated and non-irradiated in two dimensions. The dissertation further describes the ability of the sensor to predict dose deposition in all three dimensions. The efficacy of the sensor to predict the prescribed dose delivered to canine patients undergoing radiotherapy was also demonstrated. All these taken together demonstrate the potential of this technology to be translatable to the clinic to ensure patient safety during routine radiotherapy.

In the United States, 12% of women are typically diagnosed with breast cancer, where 20-30% of these cases are identified as Triple Negative Breast Cancer (TNBC). In the state of Arizona, 810 deaths occur due to breast cancer and more than 4,600 cases are diagnosed every year (American Cancer Society). The lack of estrogen, progesterone, and HER2 receptors in TNBC makes discovery of targeted therapies further challenging. To tackle this issue, a novel multi-component drug vehicle is presented. Previously, we have shown that mitoxantrone, a DNA damaging drug, can sensitize TNBC cells to TRAIL, which is a protein that can selectively kill cancer cells. In this current study, we have formulated aminoglycoside-derived nanoparticles (liposomes) loaded with mitoxantrone, PARP inhibitors, for delivery to cancer cells. PARP inhibitors are helpful in preventing cancer cells from repairing their DNA following damage with other drugs (e.g. mitoxantrone). Various treatment liposome groups, consisting of lipid-containing polymers (lipopolymers) synthesized in our laboratory, were formulated and characterized for their size, surface charge, and stability. PARP inhibitors and treatment of cells for in-vitro and in-vivo experiments with these liposomes resulted in synergistic death of cancer cells. Finally, studies to evaluate the pre-clinical efficacy of these approaches using immuno-deficient mouse models of TNBC disease have been initiated.

New forms of carbon are being discovered at a rapid rate and prove to be on the frontier of cutting edge technology. Carbon possesses three energetically competitive forms of orbital hybridization, leading to exceptional blends of properties unseen in other materials. Fascinating properties found among carbon allotropes, such as, fullerenes, carbon nanotubes, and graphene have led to new and exciting advancement, with recent applications in defense, energy storage, construction, and electronics. Various combinations of extreme strength, high electrical and thermal conductivity, flexibility, and light weight have led to new durable and flexible display screens, optoelectronics, quantum computing, and strength enhancer coating. The quest for new carbon allotropes and future application persists.

Despite the advances in carbon-based technology, researchers have been limited to sp3 and sp2 hybridizations. While sp3 and sp2 hybridizations of carbon are well established and understood, the simplest sp1 hybridized carbon allotrope, carbyne, has been impossible to synthesize and remains elusive. This dissertation presents recent results in characterizing a new sp1 carbon material produced from using pulsed laser ablation in liquid (PLAL) to ablate a gold surface that is immersed in a carbon rich liquid. The PLAL technique provides access to extremely non-thermal environmental conditions where unexplored chemical reactions occur and can be explored to access the production of new materials. A combination of experimental and theoretical results suggests gold clusters can act as stabilizing agents as they react and adsorb onto the surface of one dimensional carbon chains to form a new class of materials termed “pseudocarbynes”. Data from several characterization techniques, including Raman spectroscopy, UV/VIS spectroscopy, and transmission electron microscopy (TEM), provide evidence for the existence of pseudocarbyne. This completely new material may possess outstanding properties, a trend seen among carbon allotropes, that can further scientific advancements.

In this study, the differences in delivery of methylated and unmethylated prokaryotic

DNA in mammalian cells was investigated. 3 plasmids, DH5-α, ER2925 and

GM272 were extracted and transformed from E. coli bacteria. DH5-α is the regular

methylated plasmid, however,ER2925 and GM272 lack Dam and Dcm enzymes which

methylate adenine and internal cytosine in prokaryotes respectively, hence they are

unmethylated. The 3 plasmids were delivered via different delivery vectors in two

cell lines, UMUC3 and MDA-MB-231 which are human bladder cancer cell line and

human triple negative breast cancer cell line, respectively.

Luciferase and BCA assay were carried out to quantify transgene expression to

compare the efficacy of gene delivery in three aforementioned plasmids. In addition,

hydrodynamic diameter and zeta potential was measured for all delivery vectors, to

correlate with other transgene expression data. The results show that methylated

plasmid has significantly higher transgene expression in mammalian cell lines. This

can be either a result of smaller size and more positive zeta potential that the methylated

plasmid had, or a result of having Dam and Dcm enzymes which enhance binding

of DNA and transcription factors and enhance gene expression. Having smaller size

and more positive zeta potential was proven to be the case for the methylated plasmid

in this study. However the latter hypothesis should be investigated furthermore.

Current wound closure technology is limited, and lacks key elements \u2014 such as the formation of an immediate seal \u2014 that could otherwise resolve some of the common and life threatening complications associated with certain surgeries. Previous research has produced nanosealants capable of providing that immediate seal through the use of laser activation with a near infrared laser. Here, we have developed a biocompatible suture utilizes the same mechanics to provide the tensile strength needed to replace or supplement existing suture lines. Laser activated tissue integrating sutures (LATIS), are shown to have 75% of the tensile strength of commercially available PGA sutures, while still exhibiting the same laser mediated localized heating effect at power densities of as low as 1.6 W/cm2. LATIS has been shown to reach the temperature ranges needed for protein interdigitation, but suffers from low wet mechanical strength. Preparatory steps or solvents for chemical crosslinking generally dehydrate LATIS sutures, causing a shriveling effect that weakens the overall mechanical strength of the suture. To resolve this, a new method of drying, by which LATIS sutures are dried under tension on a suspended platform, has been shown to decrease control suture strength, but restore the strength of chemically treated LATIS sutures to the level of control sutures or above. These promising results suggest that follow-up work with chemical cross-linkers may produce the increases in LATIS wet strength that are needed for its implementation in deeper tissue surgeries.

Proton beam therapy (PBT) is a state-of-the-art radiotherapy treatment approach that uses focused proton beams for tumor ablation. A key advantage of this approach over conventional photon radiotherapy (XRT) is the unique dose deposition characteristics of protons, resulting in superior healthy tissue sparing. This results in fewer unwanted side effects and improved outcomes for patients. Current available dosimeters are intrinsic, complex and expensive; hence cannot be used to determine the dose delivered to the tumor routinely. Here, we report a hydrogel based plasmonic nanosensor for measurements of clinical doses in ranges between 2-4 GyRBE. In this nanosensor, gold ions, encapsulated in a hydrogel, are reduced to gold nanoparticles following irradiation with proton beams. Formation of gold nanoparticles renders a color change to the originally colorless hydrogel. The intensity of the color can be used to calibrate the hydrogel nanosensor in order to quantify different radiation doses employed during treatment. The potential of this nanosensor for clinical translation was demonstrated using an anthropomorphic phantom mimicking a clinical radiotherapy session. The simplicity of fabrication, detection range in the fractionated radiotherapy regime and ease of detection with translational potential makes this a first-in-kind plasmonic colorimetric nanosensor for applications in clinical proton beam therapy.

In a dormant state, cancer cells survive chemotherapy leaving the opportunity for cancer cell relapse and metastasis ultimately leading to patient death. A novel aminoglycoside-based hydrogel ‘Amikagel’ developed in Dr. Rege’s lab serves as a platform for a 3D tumor microenvironment (3DTM) mimicking cancer cell dormancy and relapse. Six Amikagels of varying mechanical stiffness and adhesivities were synthesized and evaluated as platforms for 3DTM formation through cell viability and cell cycle arrest analyses. The impact of fetal bovine serum concentration and bovine serum albumin concentration in the media were studied for their impact on 3DTM formation. These experiments allow us to identify the best possible Amikagel formulation for 3DTM.