The Role of Torsion/Torsion Coupling in the Vibrational Spectrum of Cis−Cis HOONO

A three-dimensional model of the vibrational dynamics of HOONO is investigated. This model focuses on the couplings between the OH stretch vibration and the two torsions. The model is based on electronic energies, calculated at the CCSD(T)/cc-pVTZ level of theory and basis and dipole moment functions calculated at the CCSD/aug-cc-pVDZ level. The resulting points were fit to explicit functional forms, and the energies, wave functions, and intensities were evaluated using an approach in which the OH stretching motion was adiabatically separated from the torsional modes. It is found that the HOON torsion is strongly coupled to both the OONO torsion and OH stretch. Despite this, many of the conclusions that were drawn from earlier two-dimensional treatments, which did not include the OONO torsion, hold up on a semiquantitative level. In addition, we use this model to investigate the assignment of recently reported matrix isolated spectra of HOONO and DOONO. Finally, by comparing the results of this three-dimensional calculation to two-dimensional calculations and to the results of second-order perturbation theory, we investigate the question of how one determines the size of the reduced-dimensional system that is needed to describe the vibrational spectrum of molecules, like HOONO, that contain several large amplitude motions

Defining Neuronal Identity Using MicroRNA-Mediated Reprogramming

Cell fate reprogramming is transforming our understanding of the establishment and maintenance of cellular identity. In addition, reprogramming holds great promise to model diseases affecting cell types that are prohibitively difficult to study, such as human neurons. Overexpression of the brain-enriched microRNAs (miRNAs), miR-9/9* and miR-124 (miR-9/9*-124) results in reprogramming human somatic cells into neurons and has recently been used to generate specific neuronal subtypes affected in neurodegenerative disorders. However, the mechanisms governing the ability of miR-9/9*-124 to generate alternative subtypes of neurons remained unknown. In this thesis, I report that overexpressing miR-9/9*-124 triggers reconfiguration of chromatin accessibility, DNA methylation, and mRNA expression to induce a default neuronal state. MiR-9/9*-124-induced neurons (miNs) are functionally excitable and are uncommitted towards specific subtypes yet possess open chromatin at neuronal subtype-specific loci, suggesting such identity can be imparted by additional lineage-specific transcription factors. Consistently, we show ISL1 and LHX3 selectively drive conversion to a highly homogenous population of human spinal cord motor neurons. This work shows that modular synergism between miRNAs and neuronal subtype-specific transcription factors can drive lineage-specific neuronal reprogramming, thereby providing a general platform for high-efficiency generation of distinct subtypes of human neurons. Since many neurodegenerative diseases occur after development, modeling them requires reprogramming methods capable of generating functionally mature neurons. However, few robust molecular hallmarks existed to identify such neurons, or to compare efficiencies between reprogramming methods. Recent studies demonstrated that active long genes (\u3e100 kb from transcription start to end) are highly enriched in neurons, which provided an opportunity to identify neurons based on the expression of these long genes. We therefore worked to develop an R package, LONGO, to analyze gene expression based on gene length. We developed a systematic analysis of long gene expression (LGE) in RNA-seq or microarray data to enable validation of neuronal identity at the single-cell and population levels. By combining this conceptual advancement and statistical tool in a user-friendly and interactive software package, we intended to encourage and simplify further investigation into LGE, particularly as it applies to validating and improving neuronal differentiation and reprogramming methodologies. Using this tool, I found by single-cell RNA sequencing that microRNA-mediated neuronal reprogramming of human adult fibroblasts yields a homogenous population of mature neurons, and that LGE distinguishes mature from immature neurons. I found that LGE correlates with expression of neuronal subunits of the Swi/Snf-like (BAF) chromatin remodeling complex, such as ACTL6B/BAF53b. Finally, I found that the loss of a functional neuronal BAF complex, as well as chemical inhibition of topoisomerase I, decreases LGE and reduces spontaneous electrical activity. Together, these results provide mechanistic insights into microRNA-mediated neuronal reprogramming, and demonstrate a transcriptomic feature of functionally mature neurons

High-Throughput, Portable Microfluidic Aptamer Assay

Aptamer-based assays are a powerful platform for sensing a wide variety of biochemical targets, including drugs, disease biomarker, and biomolecules. However, aptamer assays often lack rapid identification and high-throughput screening. Performing an aptamer-based assay on a microfluidic device is a promising solution to increase throughput, portability, and sensitivity. In this paper, we present a microfluidic device capable of running aptamer-based assays. Our device utilizes normally-closed valves and a central micropump to move fluids throughout the chip. One chip could theoretically be scaled up to run multiple assays, and multiple of these microfluidic devices could be run in parallel to increase throughput. Our experiments characterized the actuation pressure needed to normally-closed valves with different size parameters, showed and characterized flow using both oil and water solutions, and demonstrated modular movement on a chip with six micropumps. Lastly, we designed a cartridge topper system to eliminate the need for pins leading to a pneumatic controller so chips could easily be switched out. By demonstrating flow and mixing, our chip is fully capable of running an aptamer-based assay

Intron and gene size expansion during nervous system evolution

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McCoy, M. J., & Fire, A. Z. Intron and gene size expansion during nervous system evolution. BMC Genomics, 21(1), (2020): 360, doi:10.1186/s12864-020-6760-4.Background The evolutionary radiation of animals was accompanied by extensive expansion of gene and genome sizes, increased isoform diversity, and complexity of regulation. Results Here we show that the longest genes are enriched for expression in neuronal tissues of diverse vertebrates and of invertebrates. Additionally, we show that neuronal gene size expansion occurred predominantly through net gains in intron size, with a positional bias toward the 5′ end of each gene. Conclusions We find that intron and gene size expansion is a feature of many genes whose expression is enriched in nervous systems. We speculate that unique attributes of neurons may subject neuronal genes to evolutionary forces favoring net size expansion. This process could be associated with tissue-specific constraints on gene function and/or the evolution of increasingly complex gene regulation in nervous systems.This study was supported by the following programs, grants, and fellowships: 2018 Grass Fellowship in Neuroscience (Grass Foundation), 2019 Whitman Fellowship at the Marine Biological Laboratory, and the Stanford Genomics Training Program (5T32HG000044–22; PI: M. Snyder) to MJM, and R01GM37706/R35GM130366 to AZF. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Convexity estimates for hypersurfaces moving by convex curvature functions

We consider the evolution of compact hypersurfaces by fully nonlinear, parabolic curvature flows for which the normal speed is given by a smooth, convex, degree-one homogeneous function of the principal curvatures. We prove that solution hypersurfaces o

Development of boldness and docility in yellow-bellied marmots

Peer reviewedPostprin

Synthesis of an Ionic Covalent Organic Framework Through Orthogonal Dynamic Covalent Chemistry

Orthogonal dynamic organic chemistry is a rapidly developing field of chemistry focusedon the use of multiple dynamic covalent bonds to form complicated multifunctional organicarchitectures with relative ease. In contrast with traditional approaches in chemistry, dynamiccovalent chemistry allows for the facile formation of compounds through the rearrangement ofbonds driven by thermodynamic stability. In this work, spiroborate and imine linkages areinvestigated as a new orthogonal dynamic covalent system. The formation of the spiroborategroup is observed in a system alongside imine formation, illustrating the first instance of aspiroborate-imine orthogonal dynamic covalent system. Here, the small molecule modeling,synthesis optimization, structural characterization, and ion conductivity is reported for anorthogonal imine and spiroborate linked covalent organic framework. Ethanol as a solvent andscandium triflate as a catalyst were found to best favor the formation of this orthogonal polymer.The current system was found to have some crystallinity as a covalent organic framework.Furthermore, the polymer was found to have potential as a solid-state electrolyte with areasonable room temperature ion conductivity (1.44 x 10-5 S&middot;cm-1) and a low activation energyfor lithium-ion conduction (0.16 eV&middot;atom<span

Grounding a future in place: incorporating small town character into a mixed-use town center in Castle Rock, CO

Master of Landscape ArchitectureDepartment of Landscape Architecture/Regional and Community PlanningAmir GoharSmall cities in America are largely made of suburban developments, and as they continue to grow they must consider ways of transitioning their growth into something more responsible. A city can grow more responsibly by minimizing sprawl and increasing the density of developments; however, when doing this the city risks altering its visual character with large buildings that feel out of place. This report demonstrates how Castle Rock, Colorado can increase building density, without jeopardizing the key characteristics and experiential qualities that contribute to the city’s sense of place. In order for a city to successfully implement high-density developments grounded in the character, history, and cultural of the community, the city must first identify how community members perceive the character of their environment. Semi-structured interviews with Castle Rock residents reveal the key qualities that contribute to the character and sense of place within the community. Precedent studies inform common strategies used by similar development across the country, and site analysis reveals the opportunities and constraints presented by the site and its surroundings. A projective design is created by synthesizing the findings from semi-structured interviews, precedent studies, and site analysis, to create a mixed-use town center in Castle Rock, Colorado. This project demonstrates how Castle Rock can introduce an alternative form of growth that is more responsible, and more reflective of the city’s character and sense of place

Changes in dietary patterns and body composition within 12 months of liver transplantation

Background: Cardiometabolic risk factors are increasing in liver transplant recipients (LTR). Influencing dietary factors have not been assessed. The aim of this observational study was to assess changes in weight, metabolic function, dietary intake and eating behaviours in the first year after orthotopic liver transplantation (OLT). Methods: Consecutive recruitment of 17 patients (14 males) awaiting OLT at a single tertiary hospital. Dietary intake, food behaviours and anthropometry were recorded at baseline, and 6 and 12 months posttransplant. Results: By 12 months, patients had gained on average 7.3% of body weight. The prevalence of overweight or obesity increased from baseline 53% to 77% (P=0.001). By 6 months, 65% (n=11/17) of patients had altered glucose metabolism. Dietary intake was consistent with a Western-style dietary pattern with high saturated fat. Over half of the patients (69%, n=11/16) reported low to no depressive feelings and rated their self-esteem as good (53%, n=9/16). The Power of Food Scale increased between pre and post-transplant, indicating a stronger appetitive drive. Conclusions: Weight gain occurs early post-transplant, with significant metabolic dysfunction present within 6 months, however is not associated with significant psychological distress. Early dietary intervention designed to limit weight gain and target cardiometabolic health is recommended for this unique patient population