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Beginning in 2019 and quickly spreading internationally, the Coronavirus disease Covid-19 became the first pandemic that many people have witnessed firsthand along with the severe disruption to their daily lives. A key field of research for Covid-19 that is studied by epidemiologists, biologists, and computer scientists alike is modeling the spread of Covid-19 in order to better predict future outbreaks of the pandemic and evaluate potential strategies to reduce infections, hospitalizations, and deaths. This thesis proposes a method of modeling Covid-19 spread and interventions for local environments based on different levels of perspective. The goal for this thesis is to be able to present a model of Covid-19 in terms of surrounding areas in San Luis Obispo including the unique mobility dynamic currently held in the global pandemic. Furthermore, we use our model to explore different methods of ensuring a low infection rate such as isolation methods and mobility restrictions.

Infectious diseases caused by viruses such as influenza A virus (IAV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pose major threats to human health. Glycosylation, a post-translational modification critical for biological functions including receptor recognition and binding, cell adhesion, and protein folding, is a key mediator of the interaction between viruses and host cells. IAV and SARS-CoV-2 recognize and bind to glycans on host cells prior to uptake by the cells; by the same token, the glycoproteins hemagglutinin of IAV and the spike protein of SARS-CoV-2 are the targets of both host immune molecules and vaccines. The diversity of glycans, structures made up of oligosaccharide residues in complex, branched configurations, can in part be attributed to the push and pull of evolutionary pressures from infectious disease agents such as these viral pathogens. Evolving host glycans may gain the ability to evade recognition by viruses, and likewise, the evolution of viral glycans may result in viral evasion from immune responses. Thus, for a complete understanding of host-pathogen interactions, detailed characterization of glycoproteins that quantitatively measures changes in glycosylation is necessary. However, a number of factors makes quantitative characterization of glycoproteins difficult. Firstly, glycans are highly heterogeneous with dozens of possible glycans at a given glycosylation site and different occupancy levels at each site. Secondly, a particular glycoform may have very low abundance, making the signals difficult to detect. Thirdly, it is difficult to achieve deep, quantitative measurement of glycoprotein glycans using conventional liquid chromatography-mass spectrometry experiments. The usual mass spectrometry methods are not adequate because they are biased towards selecting higher abundance precursors, which leave many glycopeptide glycoforms undetected. This dissertation begins with an assessment of the current state-of-the-art of glycoproteomics using mass spectrometry to give context to our primary research discussed in subsequent chapters. Chapter 2 describes the use of a modified Tanimoto similarity coefficient to quantify the glycosylation similarity between two variants of a strain of IAV, wild-type and mutant, both expressed in embryonated chicken eggs. Our results indicate that even subtle changes in the amino acid sequence of hemagglutinin can result in measurably distinct glycosylation. Chapter 3 expands the number of comparisons of IAV strains made in the previous chapter to include strains produced in a mammalian expression vector, Madin-Darby canine kidney cells. We show that the choice of expression system can change the population of glycoforms at some but not necessarily all glycosylation sites. In addition, we explore data-independent acquisition mass spectrometry to improve upon sensitivity and selectivity of glycopeptide identification. In Chapter 4, this data-independent acquisition method is applied to the quantitative characterization of SARS-CoV-2 spike protein. The work presented here provides a significant contribution toward improving the confident detection and assignment of site-specific glycopeptides. Furthermore, understanding how to measure changes in glycosylation in related viral glycoprotein variants offers opportunities to include consideration of specific glycosylations in the design of vaccines to potentially improve efficacy against continually evolving viruses.

Yes / The on-going COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) has posed an extraordinary threat to global public health, wealth and well-being. As the carrier of human life and production, infrastructures need to be upgraded to mitigate and prevent the spread of viral diseases. Developing multifunctional/smart civil engineering materials to fight viruses is a promising approach to achieving this goal. In this perspective, the basic introduction on virus and its structure is provided. Then, the current design principles of antiviral materials and structures are examined. Subsequently, the possibility of developing active/passive antiviral civil engineering materials (including cementitious composites, ceramics, polymers and coatings) is proposed and envisaged. Finally, the future research needs and potential challenges to develop antiviral civil engineering materials are put forward. The proposed strategies to develop multifunctional/smart antiviral civil engineering materials will aid in the construction of smart infrastructures to prevent the spread viruses, thus improving human life and health as well as sustainability of human society. / The authors would like to thank the National Science Foundation of China (51978127, 52178188, and 51908103) and the Fundamental Research Funds for the Central Universities (DUT21RC(3)039) for providing funding to carry out this investigation.

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Contemporary diagnostics rely on expensive, time-consuming, and optically-limited mechanisms that prevent at-home point-of-care molecular diagnostics with the accuracy of laboratory tools and the convenience of affordability. In this Thesis, biosensing was explored with commercial two-dimensional (2D) materials which have been investigated extensively over the last two decades yielding a variety of sensor metrics for detecting biomolecules. 2D materials have intrinsic properties that depend on the quality of material and substrate surface being employed. Here, graphene/SiO2 and monolayer hexagonal boron nitride (hBN) capping layer on graphene/SiO2 field-effect transistors (FETs) were used. Until recently, monolayer hBN has not been commercially available at the wafer-scale and has been observed in the literature to augment the properties of graphene-based devices and better control of processing repeatability. The work in this Thesis combines biochemistry with the wafer-scale production and surface-dependent properties of graphene and monolayer hBN/graphene via a FET fabrication process circumventing the use of photoresist. This was done to avoid photoresist resin that may contaminate the transducer surface and contribute to repeatability issues when studying biochemistry with 2D materials. Briefly, surface engineering of graphene/SiO2 and hBN/graphene/SiO2 was done, and the transfer characteristics were measured as a function of either the concentration of protons, genes, or proteins. Compared to bare 2D materials, the pH sensitivity of the shift in Dirac voltage was enhanced to -99 mV/pH when using 8.6 nm of Al2O3 on hBN/graphene/SiO2 FET. Graphene devices were then engineered for sensing SARS-CoV-2 genome with a signal-to-noise ratio of 3 at 100 aM and a linearized sensitivity of +22 mV/molar decade of SARS-CoV-2 ribonucleic acid and a dynamic range of four orders of magnitude. This was done by conjugating single-stranded deoxyribonucleic acid to sub-percolation threshold gold nanofilms deposited directly on the graphene sensing mesa. Finally, the 2D devices were studied for detecting SARS-CoV-2 spike protein after being functionalized with rabbit immunoglobulin G (IgG) monoclonal antibody (mAb). Additionally, preliminary work was done regarding the partial reduction and fragmentation of anti-SARS-CoV-2 spike protein human mAb IgG in an approach to leverage gold-thiol chemistry for covalently bonding the IgG to the 2D sensing mesa. In summary, the utilization of wide- and zero-bandgap nanomaterials may have profound implications in augmenting molecular diagnosis and treatment of disease through economically decentralizing biosensing. / 2024-01-20T00:00:00Z

The COVID-19 pandemic has heightened the need for fine-scale analysis of the clustering of cases of infectious disease in order to better understand and prevent the localized spread of infection. The students living on the University of Massachusetts, Amherst campus provided a unique opportunity to do so, due to frequent mandatory testing during the 2020-2021 academic year, and dense living conditions. The South-West dormitory area is of particular interest due to its extremely high population density, housing around half of students living on campus during normal conditions. Using data gathered by the Public Health Promotion Center (PHPC), we analyzed the clustering of SARS-CoV 2 cases in three-dimensional space as well as time within and between the three tallest occupied buildings in the Southwest dormitory area, John Quincy Adams, Kennedy, and Coolidge. We used the SaTScan program and its Space-Time Permutation Model, which searches for areas with a greater than expected number of cases. Analysis was done at various levels of spacial detail. Additionally, this analysis was compared to the purely temporal surveillance method, CDC’s Early Aberration Reporting System (EARS). Analysis with SaTScan at the room and floor level showed multiple significant clusters within the Coolidge dormitory building. Floor-level analysis was found to be as sensitive as and less burdensome than room-level analysis. We recommend using scan statistics in conjunction with other methods such as purely temporal scans and wastewater analysis to detect and respond to outbreaks on campus.

The starting point of the work is that an analysis of the value bases of critical social issues is difficult to carry out in any qualified sense from an unstructured basis and that attempts to do so easily result in relatively superficial discussions of particular issues. Instead, we suggest how this might be viewed from a more holistic ethical and systems theological perspective.  In doing so, we review a new framework that aims to distil relevant issues regarding necessary trade-offs and how this can be done. Broadly speaking, this consists of a kind of Socratic dialogue that systematically examines the value base of the decisions that need to be made, as well as whether the effects of the decisions become unacceptable and thus need to be modified vis-a-vis the normative system embraced by the decision-maker. We discuss the role of theologians in this and emphasize that they should take a larger place in discussions on how to deal with complex societal crises, and the main point of this work is therefore to demonstrate the importance of a systematic and transparent method for filtering out critical components from ethical and theological standpoints, and to clarify the effects of the trade-offs between fundamental values that are made in real decision-making situations.

Angiotensin-converting enzyme 2 (ACE2) has been identified as the cellular entry receptor for the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). High ACE2 tissue expression and low glycine levels were suggested to increase susceptibility for SARS-CoV-2 infection and increasing circulating ACE2 has been proposed as one possible strategy to combat COVID-19. In humans, aerobic physical exercise induces an increase in plasma ACE2 in some individuals. However, it is not clear whether glycine and ACE2 levels depend on intrinsic exercise capacity or on exercise training. We used rats selectively bred for high intrinsic exercise capacity (HCR) or low exercise capacity (LCR) and tested the influence of this genetic predetermination and/or aerobic exercise on metabolites, ACE2 tissue expression and circulating ACE 2. ACE2 expression was measured in different tissues in the sedentary animals and again after 4 weeks of high-intensity aerobic exercise in both LCRs and HCRs. Sedentary HCRs exhibited significantly higher circulating ACE2 concentrations compared to LCRs, but a lower expression of ACE2 in all investigated tissues except for adipose tissue. Body weight was negatively correlated with serum ACE2 and positively correlated with ACE2 expression in the heart. Aerobic exercise caused a significant decrease in ACE2 expression in the lung, heart, muscle, and kidney both in LCRs and HCRs. Our results suggest that ACE2 expression, circulating ACE2 and glycine serum concentration are related to aerobic intrinsic exercise capacity and can be influenced with exercise. These results may support the hypothesis that physically fit individuals have a lower susceptibility for COVID-19 infection.

La supervivencia de los organismos superiores depende de que sus células se organicen y actúen de manera sincronizada para cumplir funciones específicas, para lo cual es fundamental la comunicación intercelular. Este proceso es básico para la vida de todas las células, pero es la razón de ser en las neuronas que están especializadas en recibir información, procesarla y comunicarla a otras células. En el sistema nervioso, la principal forma de comunicación se realiza a través de la sinapsis química, en la que una neurona libera un mensajero químico, el neurotransmisor, que es reconocido por un receptor presente en otra célula permitiéndole responder al mensaje. La acetilcolina es uno de los principales neurotransmisores utilizados por las neuronas, y sus receptores, tanto metabotrópicos como ionotrópicos, están expresados en muchos tipos celulares. Los receptores ionotrópicos de acetilcolina, llamados receptores nicotínicos, son canales catiónicos pentaméricos que pertenecen a la familia de receptores Cys-loop. El receptor nicotínico de acetilcolina α7 es un homopentámero que exhibe propiedades funcionales particulares fundamentales para su rol neuromodulador, incluyendo la elevada permeabilidad al Ca2+ y la capacidad para transformar respuestas ionotrópicas transitorias en eventos más sostenidos de señalización metabotrópica. Es uno de los receptores nicotínicos más abundantes en el sistema nervioso, aunque también se encuentra presente en otros tejidos. En el sistema nervioso central cumple un rol importante en procesos de cognición, atención y memoria, al regular la liberación de neurotransmisores, mediar la transmisión sináptica rápida y modular la excitabilidad neuronal. Una disminución de su actividad se ha asociado con diversos desórdenes neurológicos y neurodegenerativos, incluyendo esquizofrenia, autismo y enfermedad de Alzheimer. El receptor α7 también se expresa en células no neuronales, tales como -entre otras-, los astrocitos, la microglía, los linfocitos B y T, las células epiteliales, los macrófagos, cumpliendo un rol importante en inmunidad, inflamación y neuroprotección. Las acciones neuromoduladoras, neuroprotectoras y antinflamatorias sistémicas del receptor nicotínico de acetilcolina α7 junto a sus propiedades únicas de activación, desensibilización, permeabilidad al Ca2+ y rol dual ionotrópico-metabotrópico, lo han convertido en un blanco farmacológico emergente muy importante en diversos desórdenes neurológicos, neurodegenerativos e inflamatorios. Este trabajo de tesis se basó en el estudio de los aspectos moleculares relacionados a diferentes tipos de modulación de las funciones ionotrópicas y metabotrópicas del receptor nicotínico de acetilcolina α7 humano. Para ello se utilizaron principalmente técnicas electrofisiológicas a nivel de canal único y de corrientes macroscópicas, en conjunto con análisis de proteínas por western blot y ensayos de movimiento de Ca2+ intracelular. El capítulo I se centró en el estudio de la modulación de las funciones ionotrópicas y metabotrópicas del receptor α7 por eventos de fosforilación/desfosforilación. Se demostró que favorecer el estado desfosforilado de las tirosinas del dominio intracelular de α7 potencia la actividad ionotrópica del receptor. A nivel de corrientes unitarias, el efecto potenciador involucró un aumento en la frecuencia y duración de los episodios de activación, mientras que a nivel de corrientes macroscópicas se manifestó por una disminución en la velocidad de decaimiento de la corriente, y un aumento en la tasa de recuperación desde el estado desensibilizado. Por el contrario, la desfosforilación de las tirosinas tuvo un efecto negativo en la actividad metabotrópica del receptor, estudiada por western blot a partir de la vía de ERK 1/2. Además, a diferencia de lo observado para las tirosinas, las alteraciones en el estado de fosforilación de serinas y treoninas del dominio intracelular no ocasionaron cambios importantes en la actividad ionotrópica de α7 en las condiciones experimentales aquí utilizadas. En síntesis, los resultados presentados en este capítulo ponen en evidencia que la fosforilación de las tirosinas, si bien es absolutamente necesaria para la actividad metabotrópica de α7 mediada por la vía ERK 1/2, actúa como un modulador negativo de la actividad ionotrópica del receptor. El capítulo II abordó el estudio de la asociación funcional entre un fragmento peptídico de la glicoproteína S del SARS-CoV-2 (Y674-R685) y el receptor nicotínico de acetilcolina α7 humano. La asociación entre SARS-CoV-2 y los receptores nicotínicos fue propuesta en forma de hipótesis al comienzo de la pandemia. Más adelante, simulaciones de dinámica molecular mostraron que el fragmento Y674-R685 no solo tiene afinidad por α7, sino que penetra profundamente en el bolsillo de unión a agonista del receptor. En este capítulo, en primer lugar, se demostró que el fragmento Y674-R685 actúa como un agonista silente de α7, ya que es capaz de provocar corrientes unitarias y macroscópicas del receptor, pero solo en presencia de un modulador alostérico positivo. Por otro lado, se demostró que Y674-R685 también ejerce una modulación negativa de α7, que se evidenció por una profunda disminución, dependiente de la concentración, en la duración de los episodios de activación de los canales potenciados y en la amplitud de las respuestas macroscópicas provocadas por la acetilcolina. De esta manera, utilizando distintos enfoques electrofisiológicos, se develó la existencia de una interacción funcional entre el fragmento Y674-R685 de la glicoproteína S del SARS-CoV-2 y el receptor α7 que proporciona las bases moleculares para seguir explorando la participación de los receptores nicotínicos en la fisiopatología de la COVID-19. El capítulo III se basó en el estudio del receptor α7 como blanco del cannabidiol, lo cual resulta de gran interés debido al uso expandido de este fitocannabinoide para tratar diferentes condiciones patológicas gracias a sus propiedades terapéuticas y a la ausencia de efectos psicoactivos. Para ello se exploró el efecto del cannabidiol en las funciones ionotrópicas y metabotrópicas de α7 mediante técnicas electrofisiológicas y ensayos de movimiento de Ca2+ intracelular. En lo que respecta a las funciones ionotrópicas, se demostró que el cannabidiol produce una rápida disminución de la actividad del canal a nivel de corrientes unitarias evidenciada por la reducción en la frecuencia de los episodios de activación. Este efecto fue dependiente de la concentración y se dio con una CI50 en el rango submicromolar, lo que indica una potente modulación negativa. Por otra parte, el cannabidiol también produjo una modulación negativa en la función metabotrópica de α7 que se evidenció por una marcada disminución en las respuestas de Ca2+ intracelular tras la activación del receptor. Estos resultados demuestran que el cannabidiol ejerce una modulación negativa de α7 de relevancia farmacológica que debe tenerse en cuenta a la hora de evaluar los posibles usos terapéuticos del fitocannabinoide. En conjunto, los resultados presentados en esta tesis amplían el entendimiento de los aspectos moleculares relacionados con la modulación de las funciones ionotrópicas y metabotrópicas del receptor nicotínico de acetilcolina α7 en distintas condiciones, a saber, fisiológicas (eventos de fosforilación/desfosforilación), patológicas (fragmento peptídico derivado de la glicoproteína S del SARS-CoV-2) y terapéuticas (cannabidiol). / The survival of higher organisms depends on the ability of their cells to be well organized and to behave in a synchronized manner to fulfill specific functions for which intercellular communication is of pivotal importance. This process is basic for the life of all cells, but it is the raison d'être in neurons that are specialized in receiving information, processing it, and communicating it to other cells. In the nervous system, the main form of communication is carried out via the chemical synapse, in which a neuron releases a chemical messenger, the neurotransmitter, which is identified by a receptor present in another cell, allowing it to respond to the message. Acetylcholine is one of the main neurotransmitters used by neurons, and its receptors, both metabotropic and ionotropic, are expressed in many cell types. Ionotropic acetylcholine receptors, called nicotinic receptors, are pentameric cation channels belonging to the Cys-loop receptor family. The α7 nicotinic acetylcholine receptor is a homopentamer with particular functional properties critical to its neuromodulatory role, including high Ca2+ permeability and the ability to transform transient ionotropic responses into more sustained metabotropic signaling events. It is one of the most abundant nicotinic receptors in the nervous system, although it is also present in other tissues. In the central nervous system, it plays an important role in cognition, attention, and memory, by regulating the release of neurotransmitters, mediating rapid synaptic transmission, and modulating neuronal excitability. A decrease in α7 activity has been associated with various neurological and neurodegenerative disorders, such as schizophrenia, autism, and Alzheimer's disease. The α7 receptor is also expressed in non-neuronal cells; namely, astrocytes, microglia, B and T lymphocytes, epithelial cells, and macrophages, and plays an important role in immunity, inflammation, and neuroprotection. The neuromodulatory, neuroprotective, and systemic anti-inflammatory actions of α7, together with its unique activating, desensitizing, Ca2+ permeability, and dual ionotropic-metabotropic properties, have made the receptor a very important emerging drug target in various neurological, neurodegenerative, and inflammatory disorders. This P.D. thesis work was based on the study of molecular aspects related to different types of modulation of the ionotropic and metabotropic functions of the human α7 nicotinic acetylcholine receptor. To this end, electrophysiological techniques at the single channel and macroscopic current levels were mainly used, as well as protein analysis by western blot and intracellular Ca2+ movement assays. Chapter I focused on the study of α7 receptor ionotropic and metabotropic function modulation by phosphorylation/dephosphorylation events. It was shown that favoring the dephosphorylated state of α7 intracellular domain tyrosine residues potentiates its ionotropic activity. At the single-channel level, this potentiating effect involved an increase in the frequency and duration of activation episodes, while at the macroscopic level it was manifested by a decrease in the rate of current decay and by an increase in the rate of recovery from the desensitized state. In contrast, tyrosine dephosphorylation had a negative effect on receptor metabotropic activity, studied by western blot from ERK 1/2 pathway. In addition, unlike what was observed for tyrosine residues, alterations in the phosphorylation status of serine and threonine residues present in the intracellular domain did not cause any significant changes in α7 ionotropic activity under the experimental conditions used. Summing up, the results collected in this chapter show that tyrosine phosphorylation, although it is absolutely necessary for α7 metabotropic activity mediated by ERK 1/2 pathway, acts as a negative modulator of receptor ionotropic activity. Chapter II focused on the study of the functional association between a peptide fragment of SARS-CoV-2 S glycoprotein (Y674-R685) and human α7 nicotinic acetylcholine receptor. The association between SARS-CoV-2 and nicotinic receptors was hypothesized at the beginning of the pandemic. Later, molecular dynamics simulations showed that the Y674-R685 fragment not only has affinity for α7 but also penetrates deep into its agonist-binding pocket. In this chapter, it was firstly stated that the Y674-R685 fragment acts as a silent α7 agonist, since it is capable of triggering single-channel and macroscopic currents, but only in the presence of a positive allosteric modulator. On the other hand, it was shown that Y674-R685 also exerts α7 negative modulation, which was evidenced by a profound concentration-dependent decrease in the duration of acetylcholine-induced activation episodes from potentiated channels and macroscopic responses. In this way, using different electrophysiological approaches, the existence of functional interaction between SARS-CoV-2 S glycoprotein Y674-R685 fragment and α7 receptor was revealed, which provides the molecular bases to further explore nicotinic receptor participation in COVID-19 pathophysiology. Chapter III was based on the study of the α7 receptor as a target of cannabidiol, which is of great interest due to the expanded use of this phytocannabinoid to treat different pathological conditions thanks to its therapeutic properties and the absence of psychoactive effects. To this end, the effect of cannabidiol on α7 ionotropic and metabotropic functions was explored using electrophysiological techniques and intracellular Ca2+ movement assays. Regarding ionotropic functions, it was shown that cannabidiol produces a rapid decrease in single-channel activity evidenced by the reduction in activation episodes frequency. This concentration-dependent effect occurred with an IC50 in the submicromolar range, indicating a potent negative modulation. On the other hand, cannabidiol also produced a negative modulation in α7 metabotropic function that was evidenced by a marked decrease in intracellular Ca2+ responses after receptor activation. These results demonstrate that cannabidiol exerts α7 negative modulation of pharmacological relevance that must be taken into account when evaluating possible therapeutic uses of the phytocannabinoid. Taken together, the results presented in this thesis broaden the understanding of molecular aspects related to the modulation of α7 nicotinic acetylcholine receptor ionotropic and metabotropic functions under different conditions, namely physiological (phosphorylation/dephosphorylation events), pathological (SARS-CoV-2 S glycoprotein fragment) and therapeutic (cannabidiol).