Browsing by Author "Tong, Rong"

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    Anticancer nanoparticulate polymer-drug conjugate
    Feng, Quanyou; Tong, Rong (Wiley, 2016-08-26)
    We review recent progress in polymer-drug conjugate for cancer nanomedicine. Polymer-drug conjugates, including the nanoparticle prepared from these conjugates, are designed to release drug in tumor tissues or cells in order to improve drugs’ therapeutic efficacy. We summarize general design principles for the polymer-drug conjugate, including the synthetic strategies, the design of the chemical linkers between the drug and polymer in the conjugate, and the in vivo drug delivery barriers for polymer-drug conjugates. Several new strategies, such as the synthesis of polymerdrug conjugates and supramolecular-drug conjugates, the use of stimulus-responsive delivery, and triggering the change of the nanoparticle physiochemical properties to over delivery barriers, are also highlighted.
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    Bayesian-optimization-assisted discovery of stereoselective aluminum complexes for ring-opening polymerization of racemic lactide
    Wang, Xiaoqian; Huang, Yang; Xie, Xiaoyu; Liu, Yan; Huo, Ziyu; Lin, Maverick; Xin, Hongliang; Tong, Rong (Nature Research, 2023-06-20)
    Stereoselective ring-opening polymerization catalysts are used to produce degradable stereoregular poly(lactic acids) with thermal and mechanical properties that are superior to those of atactic polymers. However, the process of discovering highly stereoselective catalysts is still largely empirical.We aim to develop an integrated computational and experimental framework for efficient, predictive catalyst selection and optimization. As a proof of principle, we have developed a Bayesian optimization workflow on a subset of literature results for stereoselective lactide ring-opening polymerization, and using the algorithm, we identify multiple new Al complexes that catalyze either isoselective or heteroselective polymerization. In addition, feature attribution analysis uncovers mechanistically meaningful ligand descriptors, such as percent buried volume (%Vbur) and the highest occupied molecular orbital energy (Eₕₒₘₒ), that can access quantitative and predictivemodels for catalyst development.
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    Computational and Data-Driven Design of Perturbed Metal Sites for Catalytic Transformations
    Huang, Yang (Virginia Tech, 2024-05-23)
    We integrate theoretical, computational and data-driven approaches for the sake of understanding, design and discovery of metal based catalysts. Firstly, we develop theoretical frameworks for predicting electronic descriptors of transition and noble metal alloys, including a physics model of d-band center, and a tight-binding theory of d-band moments to systematically elucidate the distinct electronic structures of novel catalysts. Within this framework, the hybridization of semi-empirical theories with graph neural network and attribution analysis enables accurate prediction equipped with mechanistic insights. In addition, novel physics effect controlling surface reactivity beyond conventional understanding is uncovered. Secondly, we develop a computational and data-driven framework to model high entropy alloy (HEA) catalysis, incorporating thermodynamic descriptor-based phase stability evaluation, surface segregation modeling by deep learning potential-driven molecular simulation and activity prediction through machine learning-embedded electrokinetic model. With this framework, we successfully elucidate the experimentally observed improved activity of PtPdCuNiCo HEA in oxygen reduction reaction. Thirdly, a Bayesian optimization framework is employed to optimize racemic lactide polymerization by searching for stereoselective aluminum (Al) -complex catalysts. We identified multiple new Al-complex molecules that catalyzed either isoselective or heteroselective polymerization. In addition, feature attribution analysis uncovered mechanistically meaningful ligand descriptors that can access quantitative and predictive models for catalyst development.
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    Design and Synthesis of Supramolecular Structures for the Controlled Release of Sulfur Signaling Species
    Carrazzone, Ryan Joseph (Virginia Tech, 2022-02-08)
    In the early 2000s, hydrogen sulfide (H₂S) was added to the family of molecules known as gasotransmitters, a class of endogenously produced and freely diffusing biological signaling molecules. Since this discovery, biologists and chemists have sought to understand the physiological roles of H₂S and to elucidate the potential benefits of exogenous H₂S delivery. As a result, many synthetic small molecule donor compounds have been created to deliver H₂S in response to various biologically relevant stimuli. Furthermore, macromolecular and supramolecular H₂S donor systems have been created to protect donors in the biological milieu, extend release kinetics, or control H₂S release conditions. Thus, H₂S-donating nanostructures with precisely tuned release rates provide invaluable tools for further investigating the biological roles and therapeutic potential of H₂S. This work describes two polymer micelle systems for the controlled delivery of H₂S. The first system is based on H2S-releasing polymer amphiphiles with varying degrees of a plasticizing comonomer incorporated into the core-forming block. The glass transition temperature of the core-forming block varied predictably with incorporation of the plasticizing comonomer. Accordingly, the half-life of H₂S release decreased from 4.2 h to 0.18 h with increasing core-forming block mobility. The second system is based on H₂S releasing polymer amphiphiles with varying degrees of crosslinking in the core-forming block. The crosslinked system was designed to achieve control over H₂S release rate with minimal dilution of donor in the core-forming block. The half-life of H₂S release increased from 117 min to 210 min with increasing crosslink density in the core-forming block, further demonstrating that H₂S release rates can be precisely controlled by tuning micelle core mobility. Beyond control over H₂S release rate, further study of the biological roles of H₂S requires donor systems with precisely triggered release. To this end, this dissertation also discusses efforts to investigate fundamental micelle–unimer relationships. This section includes an evaluation of the impact of core-forming block mobility on micelle–unimer coexistence utilizing a model polymer amphiphile system. Unimer populations correlated with glass transition temperatures of the core-forming block, suggesting the need to consider micelle core mobility when discussing polymer chain phase behavior of amphiphilic block copolymers. Finally, this work discloses new methods for the radical polymerization of poly(olefin sulfones) with control over molecular weight. POSs are a unique class of polymers with great potential for stimuli-responsive depolymerization to generate sulfur dioxide (SO₂), a signaling gas related to H₂S.
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    Development of Controlled Ring-Opening Polymerization of  O-Carboxyanhydrides
    Zhong, Yongliang (Virginia Tech, 2020-10-27)
    The aim of my Ph.D. thesis is to summarize my research on the development of ring-opening polymerization (ROP) of O-carboxyanhydrides (OCAs) to synthesize functionalized, degradable polyesters. Biodegradable polyesters are promising alternatives to conventional petroleum-based non-degradable polyolefins and they are widely used in everyday applications ranging from clothing and packaging to agriculture and biomedicine. Commercially available polyesters, such as poly(lactic-co-glycolic acid), poly(lactic acid), and polycaprolactone, hydrolyze in physicochemical media. They have been approved by FDA and widely used for medical applications. However, the lack of side-chain functionality in polyesters and in corresponding monomers greatly plagues their utility for applications that demand physicochemical properties such as high stiffness, tensile strength and elasticity. Increasing efforts have been devoted to the introduction of pendant groups along the polymer chain in order to modify and modulate the physicochemical properties of polyesters and thereby to expand their applications. Over the last decade, OCAs have emerged as an alternative class of highly active monomers for polyester polymerization. OCAs are prepared from amino acids and thus have a richer range of side chain functionalities than lactone or lactide. Like lactones, OCAs can undergo ROP to obtain polyesters. Unfortunately, current ROP methods, especially those involving organocatalysts, result in uncontrolled polymerization including epimerization for OCAs bearing electron-withdrawing groups, unpredictable molecular weights (MWs), or slow polymerization kinetics. Based on our recent success of Ni/Ir photoredox catalysis allowing for rapid synthesis of high-MWs polyesters, we further explore new polymerization chemistry to use earth-abundant metal complexes to replace expensive rare-earth metal photocatalysts, and practice the polymerization in moderate and energy-efficient reaction conditions. This thesis introduces novel photoredox and electrochemical earth-abundant metal catalysts that overcome above difficulties in the ROP chemistry of OCAs, and allow for the preparation of stereoregular polyesters bearing abundant side-chain functionalities in a highly controlled manner. Specifically, various highly active metal complexes have been developed for stereoselective ROP of OCAs, either using light or electricity, to synthesize syndiotactic or stereoblock copolymers with different thermal properties. Additionally, simple purification protocols of OCAs have also been initially studied, which potentially paves the way to bulk production of functional monomers. In this thesis, I first describe newly-developed photoredox Co/Zn catalysts to achieve a controlled ROP of enantiopure OCAs under mild reaction conditions (Chapter 2). Such discovery is extended to the combination use of Co catalysts with various Zn/Hf complexes that enable stereoselective controlled ROP of racemic OCAs for the preparation of stereoregular polyesters (Chapter 3). The mechanistic studies of the aforementioned developments lead to the application of such a catalytic system in controlled electrochemical ROP of OCAs (Chapter 4). Such chemistry can also be translated to stereoselectively electrochemical ROP of racemic OCAs to either syndiotactic or stereoblock polyesters, allowing precise control of polyester's tacticity and sequence (Chapter 5). An overview future work has been summarized (Chapter 6).
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    Development of Implantable Optical Fibers for Immunotherapeutics Delivery and Tumor Impedance Measurement
    Chin, Ai Lin (Virginia Tech, 2021-11-30)
    Immune checkpoint blockade antibodies have promising clinical applications but suffer from disadvantages such as severe toxicities and moderate patient-response rates. None of the current delivery strategies, including local administration aiming to avoid systemic toxicities, can sustainably supply drugs over the course of weeks; adjustment of drug dose, either to lower systemic toxicities or to augment therapeutic response, is not possible. Herein, an implantable miniaturized device has been developed using electrode-embedded optical fibers with both local delivery and measurement capabilities over the course of a few weeks. The combination of local immune checkpoint blockade antibodies delivery via this device with photodynamic therapy elicits a sustained anti-tumor immunity in multiple tumor models. Named Implantable Miniature Optical Fiber Device (IMOD), this device uses tumor impedance measurement for timely presentation of treatment outcomes, and allows modifications to the delivered drugs and their concentrations, rendering IMOD as outstandingly valuable for on-demand delivery of potent immunotherapeutics without exacerbating toxicities. Rigorous studies performed using IMOD are presented and discussed in the follow chapters, followed by exploration of proposed work to expand the breadth of functions offered by this implantable biomedical platform.
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    Droplet-Based Microfluidics for High-Throughput Single-Cell Omics Profiling
    Zhang, Qiang (Virginia Tech, 2022-09-06)
    Droplet-based microfluidics is a powerful tool permitting massive-scale single-cell analysis in pico-/nano-liter water-in-oil droplets. It has been integrated into various library preparation techniques to accomplish high-throughput scRNA-seq, scDNA-seq, scATAC-seq, scChIP-seq, as well as scMulti-omics-seq. These advanced technologies have been providing unique and novel insights into both normal differentiation and disease development at single-cell level. In this thesis, we develop four new droplet-based tools for single-cell omics profiling. First, the developed Drop-BS is the first droplet-based platform to construct single-cell bisulfite sequencing libraries for DNA methylome profiling and allows production of BS library of 2,000-10,000 single cells within 2 d. We applied the technology to separately profile mixed cell lines, mouse brain tissues, and human brain tissues to reveal cell type heterogeneity. Second, the new Drop-ChIP platform only requires two steps of droplet generation to achieve multiple steps of reactions in droplets such as single-cell lysis, chromatin fragmentation, ChIP, and barcoding. Third, we aim to establish a droplet-based platform to accomplish high-throughput full-length RNA-seq (Drop-full-seq), which both current tube-based and droplet-based methods cannot realize. Last, we constructed an in-house droplet-based tool to assist single-cell ATAC-seq library preparation (Drop-ATAC), which provided a low-cost and facile protocol to conduct scATAC-seq in laboratories without the expensive instrument.
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    Electrochemical Carbon Dioxide Reduction for Renewable Carbonaceous Fuels and Chemicals
    Han, Xue (Virginia Tech, 2023-03-15)
    Electrochemical CO2 reduction reaction (ECO2RR) powered by renewable electricity possesses the potential to store intermittent energy in chemical bonds while producing sustainable chemicals and fuels. Unfortunately, it is hard to achieve low overpotential, high selectivity, and activity simultaneously of ECO2RR. Developing efficient electrocatalysts is the most promising strategy to enhance electrocatalytic activity in CO2 reduction. Herein, we designed novel Bi-Cu2S heterostructures by a one-pot wet-chemistry method. The epitaxial growth of Cu2S on Bi results in abundant interfacial sites and these heterostructured nanocrystals demonstrated high electrocatalytic performance of ECO2RR with high current density, largely reduced overpotential, near-unity FE for formate production (Chapter 2). Meanwhile, we see a lot of opportunities for catalysis in a confined space due to their tunable microenvironment and active sites on the surface, leading to a broad spectrum of electrochemical conversion schemes. Herein, we reveal fundamental concepts of confined catalysis by summarizing recent experimental investigations. We mainly focus on carbon nanotubes (CNTs) encapsulated metal-based materials and summarize their applications in emerging electrochemical reactions, including ECO2RR and more (Chapter 3). Although we were able to obtain high activity and selectivity toward C1 products, it is more attractive to go beyond C1 chemicals to produce C2 products due to their high industrial value. Herein, we designed Ag-modified Cu alloy catalysts that can create a CO-rich local environment for enhancing C-C coupling on Cu for C2 formation. Moreover, Ag corporate in Cu can chemically improve the structural stability of Cu lattice. (Chapter 4) Nevertheless, advanced electrocatalytic platforms cannot be developed without a fundamental understanding of binding configurations of the surface-adsorbed intermediates and adsorbate-adsorbate interaction on the local environment in electrochemical CO2 reduction. In this case, we make discussions of recent developments of machine learning based models of adsorbate-adsorbate interactions, including the oversimplified linear analytic relationships, the cluster expansion models parameterized by machine learning algorithms, and the highly nonlinear deep learning models. We also discuss the challenges of the field, particularly overcoming the limitations of pure data driven models with the integration of computational theory and machine learning of lateral interactions for catalyst materials design. (Chapter 5).
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    Epigenomic and Transcriptomic Changes in the Onset of Disease
    Naler, Lynette Brigitte (Virginia Tech, 2021-05-19)
    Current sequencing technologies allows researchers unprecedented insight into our biology, and how these biological mechanisms can become distorted and lead to disease. These aberrant mechanisms can be brought about by many causes, but some occur as a result of genetic mutations or external factors through the epigenome. Here, we used our microfluidic technology to profile the epigenome and transcriptome to study such aberrant mechanisms in three different diseases and illnesses: breast cancer, chronic inflammation, and mental illness. We profiled the epigenome of breast tissue from healthy women with the BRCA1 mutation to understand how the mutation may facilitate eventual breast cancer. Epigenomic changes in breast cells suggest that cells in the basal compartment may differentiate into a different cell type, and perhaps become the source of breast cancer. Next, we compared the epigenome and genome of murine immune cells under low-grade inflammation and acute inflammation conditions. We found that low-grade inflammation preferentially utilizes different signaling pathways than in acute inflammation, and this may lead to a non-resolving state. Finally, we analyzed the effect of the maternal immune activation on unborn offspring, and how these changes could cause later mental illness. The insights we made into these diseases may lead to future therapies.
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    Implantable optical fibers for immunotherapeutics delivery and tumor impedance measurement
    Chin, Ai Lin; Jiang, Shan; Jang, Eungyo; Niu, Liqian; Li, Liwu; Jia, Xiaoting; Tong, Rong (Nature Research, 2021)
    Immune checkpoint blockade antibodies have promising clinical applications but suffer from disadvantages such as severe toxicities and moderate patient–response rates. None of the current delivery strategies, including local administration aiming to avoid systemic toxicities, can sustainably supply drugs over the course of weeks; adjustment of drug dose, either to lower systemic toxicities or to augment therapeutic response, is not possible. Herein, we develop an implantable miniaturized device using electrode-embedded optical fibers with both local delivery and measurement capabilities over the course of a few weeks. The combination of local immune checkpoint blockade antibodies delivery via this device with photodynamic therapy elicits a sustained anti-tumor immunity in multiple tumor models. Our device uses tumor impedance measurement for timely presentation of treatment outcomes, and allows modifications to the delivered drugs and their concentrations, rendering this device potentially useful for on-demand delivery of potent immunotherapeutics without exacerbating toxicities.
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    Linking Thermophysical Transitions and Rheological Properties to Polymer Foaming Outcomes with Carbon Dioxide
    Sarver, Joseph Arron (Virginia Tech, 2022-06-01)
    Interest in high-pressure and supercritical fluids as physical blowing agents for polymer foaming is driving a renewed need for the fundamental understanding of polymer thermophysical and rheological properties in the presence of dense fluids. In particular, carbon dioxide is often studied as a physical blowing agent because of its readily accessible critical point (31.1 ℃ and 73.8 MPa) and relatively high solubility levels in polymer materials. The basic principle involved is to dissolve the supercritical fluid in the polymer at high pressures and then impose a pressure reduction to initiate bubble nucleation and growth. The outcomes depend on the thermophysical and rheological properties of the polymer under the prevailing process conditions in the fluid. The present dissertation explores the high-pressure characterization and foaming of thermoplastic elastomers and seeks to link polymer thermophysical and rheological properties to polymer foaming outcomes with carbon dioxide as a physical blowing agent. A major focus of this dissertation has been the development of novel high-pressure characterization techniques to understand polymer behavior at high pressure. These techniques include (1) high-pressure torsional braid analysis (HP-TBA), (2) magnetic suspension balance (MSB), and (3) unique high-pressure batch foaming cells. HP-TBA allows for the assessment of the depression in thermal transitions (Tg and/or Tm/Tc) and the changes in rheological properties like modulus or rigidity of polymer systems exposed to carbon dioxide. MSB provides for the assessment of the amount of carbon dioxide that sorbs into a polymer material at a given temperature and pressure. Unique confined foaming strategies have been developed to translate information learned from batch-scale experimentation to practical industrial applications. The polymer systems of interest are thermoplastic elastomers including poly(ethylene-co-vinyl acetate) (EVA) and poly(ethylene-co-vinyl acetate-co-carbon monoxide) (EVACO). These materials find use in numerous commercial applications including adhesives, compatibilizers, and foams. Their foams are noted to undergo significant degrees of expansion followed by unfavorable post-foaming collapse. In the first part of this study, the foaming of neat EVACO and EVA with carbon dioxide was explored. The blending of these polymers was then explored to regulate foam expansions and control the pore morphology development. The foamability of the polymers and their blends was explored under both isothermal and gradient conditions to assess the temperature effects on foaming outcomes at a given pressure. In the second part of this study foaming of EVACO was explored in relationship to the depressed thermal transitions of the polymer in the presence of carbon dioxide. Accompanying the depressed melting transition is a sharp reduction in the modulus or rigidity of the polymer material. By studying foaming outcomes near the melting transition rational windows for foaming exploration can be evaluated to generate foams that display more favorable bulk foam densities and minimal foam collapse. This part demonstrates that linking foaming conditions to the relative rigidity or melt strength of EVACO in carbon dioxide allows for the determination of the lower pressure where foaming will occur and the upper pressure beyond which further foam density reductions are not significant. The third part of this study explores the foaming of EVACO with carbon dioxide under batch, confined foaming conditions where the foam expansion is restricted in order to again control the foaming outcomes and prevent foam collapse. A practical question is the scale-up of batch foaming processes which likely will be conducted with injection molding or extrusion type processes. Studying batch foaming in confinement allows for a better understanding of the factors that may affect foam development that may be more readily translated to industrial practice. The fourth part of this study examines the role of crystallinity and block copolymer composition in altering the polymer behavior in carbon dioxide. Several EVACO polymers with varying ethylene, vinyl acetate, and carbon monoxide content have been explored to study how block copolymer composition affects the thermophysical and rheological properties along with the sorption of carbon dioxide at high pressure.
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    Living Ring-Opening Polymerization of O-Carboxyanhydrides: The Search for Catalysts
    Zhong, Yongliang; Tong, Rong (Frontiers Media, 2018-12-21)
    Biodegradable poly(a-hydroxy acids) can be synthesized by means of ring-opening polymerization (ROP) of O-carboxyanhydrides (OCAs). Numerous catalysts have been developed to control the living polymerization of OCAs. Here we review the rationale for the use of OCA, the desirable features for and important attributes of catalysts for the ROP of OCAs, and specific examples that have been developed.
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    Locally Administered Particle-Anchored Cytokines Safely Enhance Cancer Immunotherapy
    Niu, Liqian (Virginia Tech, 2024-05-16)
    Cancer immunotherapy has long been proposed as a powerful approach to curing tumors, based on the natural function of the immune system in protecting its host with specificity, thus holding the potential for developing long-term memory that prevents tumor recurrence. However, the immunosuppressive feature of the tumor microenvironment prevents the patients' own immune system from functioning normally in the fight against cancer. As one of the most potent cancer immunotherapies, immunostimulatory cytokines have been shown to elicit anti-tumor immune responses in preclinical studies, but their clinical application is limited by severe immune-related adverse events upon systemic administration. None of the current delivery strategies can fully address issues of toxicities and sustainably supply cytokines over the course of a few days without compromising cytokines' structural integrity. Herein, we have developed a novel formulation to anchor potent cytokine molecules to the surface of large-sized particles (1 µm) for local cancer treatment. The cytokines are confined in tumors and have minimal systemic exposure over a few days following intratumoral injection, thereby eliciting anti-tumor immunity while avoiding the systemic toxicities caused by the circulating cytokines. Such particle-anchored cytokines can be synergistic with other immunotherapies, including immune checkpoint blockade antibodies and tumor antigens, to safely promote tumor regressions in various syngeneic tumor models and genetically engineered murine tumor models.
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    Low-Input and Single-Cell Transcriptomic Technologies and Their Application to Disease Studies
    Zhou, Zirui (Virginia Tech, 2023-12-19)
    With the rapid progress of next-generation sequencing (NGS) technologies, new tools and methods have emerged to investigate the transcriptomics of various organisms. RNA sequencing (RNA-seq) employs NGS to evaluate the presence and abundance of RNA transcripts in biological samples. This technique offers a comprehensive snapshot of the RNA dynamics within cells. With the ability to profile the entire transcriptome of organisms rapidly and accurately, RNA-seq has become the state-of-the-art method for transcriptome profiling, surpassing the traditional microarray approach. Single-cell RNA sequencing (scRNA-seq) was introduced in 2009 to profile the single-cell gene expression in highly heterogeneous samples such as brain tissue and tumors. The advancement of scRNA-seq technologies enables the in-depth transcriptomic study in each cell subtype. When selecting an scRNA-seq method, researchers must weigh the trade-off between profiling more single cells versus obtaining more comprehensive transcripts per cell, while considering the overall costs. The throughput of full-length scRNA-seq methods is usually lower, as each single cell needs to be processed separately to produce scRNA-seq libraries. However, full-length methods enable the researchers to investigate the splicing variants and allele-specific expression. Non-full-length methods only capture the 3' or 5' ends of transcripts, which limits their application in isoform detection, but as cells are pooled after barcoding for cDNA synthesis, the throughput is 2–3 orders of magnitude higher than full-length methods. We developed a droplet-based platform for full-length single-cell RNA-seq, which enabled the efficient recovery of full-length mRNA from individual cells in a high-throughput manner. The developed platform can process ~8,000 single cells within 2 days and detect ~20% more genes compared to Drop-seq. Besides scRNA-seq technology development, we also applied a low-input RNA-seq method to study the transcriptomics in different biological samples. When handling precious biological samples, a low-input method is necessary to profile the transcriptome of homogeneous cell populations. We first studied the epigenomic and transcriptomic regulations in colorectal cancer (CRC) using MOWChIP-seq, a low-input high-throughput method, in conjunction with our low-input RNA-seq approach. Fusobacterium nucleatum (Fnn) is closely related to the progression of cancers like CRC and pancreatic cancer. However, the molecular mechanisms of how Fnn adjusts the tumor microenvironment (TME) and leads to poor clinical outcomes are still unclear. In this in-vitro study, we characterized how hypoxia, an important TME ignored by previous research, facilitates Fnn infection of CRC and corresponding alterations of global epigenome and transcriptome. We infer that hypoxia has similar effects as Fnn infection alone on the CRC cells. The Fnn infection under hypoxia further boosts the proliferation and progression of CRC. We then applied our low-input RNA-seq method to study brain neuroscience and immunology. Psychedelics like DOI show promising clinical efficacy in patients with psychiatric conditions. Although psychedelics exhibit rapid antidepression action and long-lasting effectiveness compared to conventional treatment, their acute psychotic symptoms and potential for drug abuse discourage their application in clinical practice. In this case, it is important to comprehend the molecular mechanisms responsible for psychedelics' clinical efficacy. This understanding can pave the way for the development of improved treatments that do not rely on psychedelics. After profiling the transcriptome of mouse brain samples exposed to psychedelics with different post-exposure times, we concluded that the psychedelic-induced transcriptomic variations are more transient than epigenomic changes. In the second brain neuroscience project, we first applied 3-color FACS sorting to differentiate four neuron and non-neuron subtypes in human postmortem prefrontal cortex tissues. Then we profiled the gene expression of the four subtypes and validated the FACS sorting by examining the expression of marker genes. Differentially expressed genes between each subtype and the others were extracted and proceeded to gene ontology analysis. We identified unique altered biological pathways related to each subtype. The immunology research focuses on revealing the difference between low-grade inflammation and monocyte exhaustion, as well as the unique biological pathways they regulate. Therefore, we profiled the transcriptome of bone marrow-derived monocytes stimulated by PBS control, a low- or high-dose LPS. In addition to wild-type mice, we also included TRAM-deficient and IRAK-M-deficient mice. We concluded that low-dose LPS specifically regulates the TRAM-dependent pathway of TLR4 signaling, and high-dose LPS exclusively upregulates exhaustion markers by impacting metabolic and proliferative pathways.
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    Low-Input Multi-Omic Studies of Brain Neuroscience Involved in Mental Diseases
    Zhu, Bohan (Virginia Tech, 2022-09-13)
    Psychiatric disorders are believed to result from the combination of genetic predisposition and many environmental triggers. While the large number of disease-associated genetic variations have been recognized by previous genome-wide association studies (GWAS), the role of epigenetic mechanisms that mediate the effects of environmental factors on CNS gene activity in the etiology of most mental illnesses is still largely unclear. A growing body of evidence suggested that the abnormalities (changes in gene expression, formation of neural circuits, and behavior) involved in most psychiatric syndromes are preserved by epigenetic modifications identified in several specific brain regions. In this thesis, we developed the second generation of one of our microfluidic technologies (MOWChIP-seq) and used it to profile genome-wide histone modifications in three mental illness-related biological studies: the effect of psychedelics in mice, schizophrenia, and the effect of maternal immune activation in mice offspring. The second generation of MOWChIP-seq was designed to generate histone modification profiles from as few as 100 cells per assay with a throughput as high as eight assays in each run. Then, we applied the new MOWChIP-seq and SMART-seq2 to profile the histone modification H3K27ac and transcriptome, respectively, using NeuN+ neuronal nuclei from the mouse frontal cortex after a single dose of psychedelic administration. The epigenomic and transcriptomic changes induced by 2,5-Dimethoxy-4-iodoamphetamine (DOI), a subtype of psychedelics, in mouse neuronal nuclei at various time points suggest that the long-lasting effects of the psychedelic are more closely related to epigenomic alterations than the changes in transcriptomic patterns. Next, we comprehensively characterized epigenomic and transcriptomic features from the frontal cortex of 29 individuals with schizophrenia and 29 individually matched controls (gender and age). We found that schizophrenia subjects exhibited thousands of neuronal vs. glial epigenetic differences at regions that included several susceptibility genetic loci, such as NRXN1, RGS4 and GRIN3A. Finally, we investigated the epigenetic and transcriptomic alterations induced by the maternal immune activation (MIA) in mice offspring's frontal cortex. Pregnant mice were injected with influenza virus at GD 9.5 and the frontal cortex from mice pups (10 weeks old) were examined later. The results offered us some insights into the contribution of MIA to the etiology of some mental disorders, like schizophrenia and autism.
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    Microfluidics for Low Input Epigenomic Analysis and Its Application to Brain Neuroscience
    Deng, Chengyu (Virginia Tech, 2021-01-06)
    The epigenome carries dynamic information that controls gene expression and maintains cell identity during both disease and normal development. The inherent plasticity of the epigenome paves new avenues for developing diagnostic and therapeutic tools for human diseases. Microfluidic technology has improved the sensitivity and resolution of epigenomic analysis due to its outstanding ability to manipulate nanoliter-scale liquid volumes. In this thesis, I report three projects focusing on low-input, cell-type-specific and spatially resolved histone modification profiling on microfluidic platforms. First, I applied Microfluidic Oscillatory Washing-based Chromatin Immunoprecipitation followed by sequencing (MOWChIP-seq) to study the effect of culture dimensionality, hypoxia stress and bacterium infection on histone modification landscapes of brain tumor cells. I identified differentially marked regions between different culture conditions. Second, I adapted indexed ChIPmentation and introduced mu-CM, a low-input microfluidic device capable of performing 8 assays in parallel on different histone marks using as few as 20 cells in less than 7 hours. Last, I investigated the spatially resolved epigenome and transcriptome of neuronal and glial cells from coronal sections of adult mouse neocortex. I applied unsupervised clustering to identify distinct spatial patterns in neocortex epigenome and transcriptome that were associated with central nervous system development. I demonstrated that our method is well suited for scarce samples, such as biopsy samples from patients in the context of precision medicine.
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    New Microfluidic Technologies for Studying Histone Modifications and Long Non-Coding RNA Bindings
    Hsieh, Yuan-Pang (Virginia Tech, 2020-06-01)
    Previous studies have shown that genes can be switched on or off by age, environmental factors, diseases, and lifestyles. The open or compact structures of chromatin is a crucial factor that affects gene expression. Epigenetics refers to hereditary mechanisms that change gene expression and regulations without changing DNA sequences. Epigenetic modifications, such as DNA methylation, histone modification, and non-coding RNA interaction, play critical roles in cell differentiation and disease processes. The conventional approach requires the use of a few million or more cells as starting material. However, such quantity is not available when samples from patients and small lab animals are examined. Microfluidic technology offers advantages to utilize low-input starting material and for high-throughput. In this thesis, I developed novel microfluidic technologies to study epigenomic regulations, including 1) profiling epigenomic changes associated with LPS-induced murine monocytes for immunotherapy, 2) examining cell-type-specific epigenomic changes associated with BRCA1 mutation in breast tissues for breast cancer treatment, and 3) developing a novel microfluidic oscillatory hybridized ChIRP-seq assay to profile genome-wide lncRNA binding for numerous human diseases. We used 20,000 and 50,000 primary cells to study histone modifications in inflammation and breast cancer of BRCA1 mutation, respectively. In the project of whole-genome lncRNA bindings, our microfluidic ChIRP-seq assay, for the first time, allowed us to probe native lncRNA bindings in mouse tissue samples successfully. The technology is a promising approach for scientists to study lncRNA bindings in primary patients. Our works pave the way for low-input and high-throughput epigenomic profiling for precision medicine development.
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    Non-Covalent Interactions in the Design and Performance of Macromolecules for Biological Technologies
    Pekkanen, Allison Marie (Virginia Tech, 2017-06-30)
    Supramolecular, or non-covalent, interactions remain a hallmark of biological systems, dictating biologic activity from the structure of DNA to protein folding and cell-substrate interactions. Harnessing the power of supramolecular interactions commonly experienced in biological systems provides numerous functionalities for modifying synthetic materials. Hydrogen bonding, ionic interactions, and metal-ligand interactions highlight the supramolecular interactions examined in this work. Their broad utility in the fields of nanoparticle formulations, polymer chemistry, and additive manufacturing facilitated the generation of numerous biological materials. Metal-ligand interactions facilitated carbon nanohorn functionalization with quantum dots through the zinc-sulfur interaction. The incorporation of platinum-based chemotherapeutic cisplatin generated a theranostic nanohorn capable of real-time imaging and drug delivery concurrent with photothermal therapies. These nanoparticles remain non-toxic without chemotherapy, providing patient-specific. Furthermore, metal-ligand interactions proved vital to retaining quantum dots on nanoparticle surfaces for up to three days, both limiting their toxicity and enhancing their imaging potential. Controlled release of biologics remain highly sought-after, as they remain widely regarded as next-generation therapeutics for a number of diseases. Geometry-controlled release afforded by additive manufacturing advances next-generation drug delivery solutions. Poly(ether ester) ionomers composed of sulfonated isophthalate and poly(ethylene glycol) provided polymers well suited for low-temperature material extrusion additive manufacturing. Ionic interactions featured in the development of these ionomers and proved vital to their ultimate success to print from filament. Contrary to ionic interactions, hydrogen bonding ureas coupled poly(ethylene glycol) segments and provided superior mechanical properties compared to ionic interactions. Furthermore, the urea bond linking together poly(ethylene glycol) chains proved fully degradable over the course of one month in solution with urease. The strength of these supramolecular interactions demanded further examination in the photopolymerization of monofunctional monomers to create free-standing films. Furthermore, the incorporation of both hydrogen bonding acrylamides and ionic groups provided faster polymerization times and higher moduli films upon light irradiation. Vat photopolymerization additive manufacturing generated 3-dimensional parts from monofunctional monomers. These soluble parts created from additive manufacturing provide future scaffolds for controlled release applications. Controlled release, whether a biologic or chemotherapeutic, remains a vital portion of the biomedical sciences and supramolecular interactions provides the future of materials for these applications.
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    Photocatalyst-independent photoredox ring-opening polymerization of O-carboxyanhydrides: stereocontrol and mechanism
    Zhong, Yongliang; Feng, Quanyou; Wang, Xiaoqian; Yang, Lei; Korovich, Andrew G.; Madsen, Louis A.; Tong, Rong (2021-03-14)
    Photoredox ring-opening polymerization of O-carboxyanhydrides allows for the synthesis of polyesters with precisely controlled molecular weights, molecular weight distributions, and tacticities. While powerful, obviating the use of precious metal-based photocatalysts would be attractive from the perspective of simplifying the protocol. Herein, we report the Co and Zn catalysts that are activated by external light to mediate efficient ring-opening polymerization of O-carboxyanhydrides, without the use of exogenous precious metal-based photocatalysts. Our methods allow for the synthesis of isotactic polyesters with high molecular weights (>200 kDa) and narrow molecular weight distributions (M-w/M-n < 1.1). Mechanistic studies indicate that light activates the oxidative status of a Co-III intermediate that is generated from the regioselective ring-opening of the O-carboxyanhydride. We also demonstrate that the use of Zn or Hf complexes together with Co can allow for stereoselective photoredox ring-opening polymerizations of multiple racemic O-carboxyanhydrides to synthesize syndiotactic and stereoblock copolymers, which vary widely in their glass transition temperatures.
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    Pressurized Mixtures of Ionic Liquids as Process Solvents for Biomass
    Williams, Michael Lawrence (Virginia Tech, 2021-01-04)
    The present thesis investigates the application of pressurized mixtures of imidazolium-based ionic liquids with traditional organic solvents for the dissolution and extraction of lignocellulosic biomass, with bamboo as a specific example of renewable biomass. The approach has been unconventional in that the focus has been on solvent mixtures in which the ionic liquid is the minor component. The objective has been to combine the solvating power of the ionic liquid with a traditional solvent such as ethanol to modulate the outcomes of solubility and extractions by tuning the parameters of fluid composition, temperature, and pressure. Working with mixtures of ionic liquids in traditional solvents as process solvents lowers the viscosity of the medium and thus reduces the transport limitations that are often encountered when working with pure ionic liquids. Among other potential advantages are the reductions in overall process cost that are associated with ionic liquids, potentially easier recovery of post-extraction products, and the recycling of the ionic liquids. This thesis has also addressed another important question regarding the thermal stability of the ionic liquids as a processing medium at elevated temperatures and pressures over time, which may negatively impact their recovery and reuse, and may lead to environmentally unacceptable consequences. The dissolution experiments were carried out in a specially designed high-pressure view-cell equipped with sapphire windows for visual or optical observations. Evaluations were made employing standard characterization tools such as Thermogravimetric Analysis (TGA), Fourier Transform Infrared Spectroscopy (FTIR), UV-Vis Spectroscopy, and Scanning Electron Microscopy (SEM). Thermal stability studies were carried out using a combination of a view-cell and fiber optic UV-Vis capability at high pressures (up to 350 bar) and temperatures (up to 150 ℃). The dissolution of bamboo was first explored using mixtures of 1-ethyl-3-methylimidazolium acetate ([EMIM]Ac) with ethanol at temperatures from 100 to 150 ℃ and pressures from 35 to 350 bar over 4 or 24 h extraction times. The fluid mixtures employed were in the range of 1 - 40 wt % ionic liquid, which is in contrast to relevant dissolution experiments reported in the literature which either use pure ionic liquids or have the ionic liquids as the majority component. The effects of changing the temperature, pressure, and solvent composition on the removal of different components of the bamboo were assessed. Temperature played the most significant role in the amount of material extracted from the bamboo, with higher temperatures resulting in the removal of more lignin than cellulose and greater conversion of crystalline cellulose to the less recalcitrant amorphous form of cellulose. The concentration of ionic liquid in solution was also important, with higher concentrations resulting in more dissolved biomass. Finally, increasing the pressure resulted in higher amounts of dissolved biomass. The next series of studies focused on rigorously assessing the stability of 1-alkyl-3-methylimidazolium acetate and chloride ionic liquids with alkyl chain lengths from 2 to 10 under both isothermal and non-isothermal conditions via thermogravimetric analysis. Isothermal degradation experiments were conducted at temperatures ranging from 100 to 225 ℃ over time periods ranging from two hours to three weeks. Non-isothermal degradation experiments were conducted at heating rates of 5, 10, 15, and 20 ℃/min from room temperature to 650 ℃. The activation energies and pre-exponential factors were assessed with isoconversional integral methods; the activation energies () ranged from 115 to 157 kJ/mol, and the pre-exponential factors (()) ranged from 24-38. The degradation reactions could be described as 1st order, as they often are in the literature, but were best fit by the 3-dimensional reaction model. Ionic liquids with longer alkyl chains on their imidazolium rings decomposed more quickly and at lower temperatures. The thermal stability of the most promising ionic liquids ([EMIM]Ac, [BMIM]Ac, [EMIM]Cl, and [BMIM]Cl) were then assessed more closely at the possible biomass processing conditions that were being considered. The primary interest was determining the effects of various cosolvents on the thermal stability of these ionic liquids at the process temperatures and pressures, from 100 to 150 ℃ and 35 to 350 bar. These evaluations were carried out in the same high-pressure view cell in which the extraction experiments were conducted. To assess the degradation of the ionic liquids, time-evolved UV spectra of the mixtures were generated. It was found that more protic solvents such as water attenuated the degradation of the ionic liquids, whereas aprotic solvents such as DMF significantly exacerbated their degradation. Among the ionic liquids evaluated, it was found that [BMIM]Cl had the greatest stability in ethanol at 150 ℃. The bamboo extraction experiments were then continued with mixtures of [BMIM]Cl in ethanol. The results showed that higher temperatures are necessary to extract lignin and cellulose, with [BMIM]Cl's thermal stability at these temperatures giving it the advantage over [EMIM]Ac. In this system as well it was shown that higher concentrations of ionic liquid facilitated the extraction of more biomass. However, biomass constituents that dissolve into mixtures with lower concentrations of ionic liquid readily precipitate back out of solution when the mixture is returned to room conditions. Along with the results of the studies with [EMIM]Ac, the experiments conducted with [BMIM]Cl show that an increase in pressure results in greater amounts of dissolved biomass holding other conditions constant. The thesis, in summary, presents for the first time (a) the use of ionic liquids as a minor component in organic solvents as a potential biomass processing media, (b) the thermal stability of ionic liquids in a cosolvents at high pressures and temperatures, and (c) experimental results showing that pressure can enhance the amount that can be extracted from biomass with mixtures of ionic liquids in a cosolvent like ethanol.