Prion species barrier at the short phylogenetic distances in the yeast model

Prions are self-perpetuating and, in most cases, aggregation-prone protein isoforms that transmit neurodegenerative diseases in mammals and control heritable traits in yeast. Prion conversion requires a very high level of identity of the interacting protein sequences. Decreased transmission of the prion state between divergent proteins is termed "species barrier" and was thought to occur due to the inability of divergent prion proteins to co-aggregate. Species barrier can be overcome in cross-species infections, for example from "mad cows" to humans. We studied the counterparts of yeast prion protein Sup35, originated from three different species of the Saccharomyces sensu stricto group and exhibiting the range of prion domain divergence that overlaps with the range of divergence observed among distant mammalian species. Heterologous Sup35 proteins co-aggregated in S. cerevisiae cells. However, in vivo cross-species prion conversion was decreased and in vitro polymerization was cross-inhibited in at least some heterologous combinations, thus demonstrating the existence of prion species barrier. Our data suggests that species-specificity of prion transmission is controlled at the level of conformational transition rather than co-aggregation. We have shown the Sup35 prion domain is sufficient for the species barrier among the S. sensu stricto species, and constructed SUP35 chimeric prion domains, combining the subregions of various origins Our data demonstrated in different cross-species combinations, different modules of prion domain play a crucial role in the controlling of species-specificity of prion transmission. One essential amino acid position has been identified in S. cerevisiae and S. paradoxus system. Our data support a model suggesting that identity of the short amyloidogenic sequences is crucial for the species barrier. Sup35 originated from three different species of the S. sensu stricto group were capable of forming a prion in S. cerevisiae. However, it was not known whether they are capable of generating and maintaining the prion state in the homologous cell environment. We have constructed the S. paradoxus and S. bayanus strains with appropriate markers, and we were able to demonstrate de novo [PSI+] formation in S. paradoxus but not in S. bayanus. Our data show that [PSI+] formation is not a unique property of S. cerevisiae.Ph.D.Committee Chair: Chernoff, Yury; Committee Member: Bommarius, Andreas; Committee Member: Doyle, Donald; Committee Member: Lobachev, Kirill; Committee Member: Yi, Sooji

ALIX binds a YPX(3)L motif of the GPCR PAR1 and mediates ubiquitin-independent ESCRT-III/MVB sorting.

The sorting of signaling receptors to lysosomes is an essential regulatory process in mammalian cells. During degradation, receptors are modified with ubiquitin and sorted by endosomal sorting complex required for transport (ESCRT)-0, -I, -II, and -III complexes into intraluminal vesicles (ILVs) of multivesicular bodies (MVBs). However, it remains unclear whether a single universal mechanism mediates MVB sorting of all receptors. We previously showed that protease-activated receptor 1 (PAR1), a G protein-coupled receptor (GPCR) for thrombin, is internalized after activation and sorted to lysosomes independent of ubiquitination and the ubiquitin-binding ESCRT components hepatocyte growth factor-regulated tyrosine kinase substrate and Tsg101. In this paper, we report that PAR1 sorted to ILVs of MVBs through an ESCRT-III-dependent pathway independent of ubiquitination. We further demonstrate that ALIX, a charged MVB protein 4-ESCRT-III interacting protein, bound to a YPX(3)L motif of PAR1 via its central V domain to mediate lysosomal degradation. This study reveals a novel MVB/lysosomal sorting pathway for signaling receptors that bypasses the requirement for ubiquitination and ubiquitin-binding ESCRTs and may be applicable to a subset of GPCRs containing YPX(n)L motifs

Virtual Synchronous Generator Control Using Twin Delayed Deep Deterministic Policy Gradient Method

This paper presents a data-driven approach that adaptively tunes the parameters of a virtual synchronous generator to achieve optimal frequency response against disturbances. In the proposed approach, the control variables, namely, the virtual moment of inertia and damping factor, are transformed into actions of a reinforcement learning agent. Different from the state-of-the-art methods, the proposed study introduces the settling time parameter as one of the observations in addition to the frequency and rate of change of frequency (RoCoF). In the reward function, preset indices are considered to simultaneously ensure bounded frequency deviation, low RoCoF, fast response, and quick settling time. To maximize the reward, this study employs the Twin-Delayed Deep Deterministic Policy Gradient (TD3) algorithm. TD3 has an exceptional capacity for learning optimal policies and is free of overestimation bias, which may lead to suboptimal policies. Finally, numerical validation in MATLAB/Simulink and real-time simulation using RTDS confirm the superiority of the proposed method over other adaptive tuning methods

Synthesis of TiC nanotube arrays and their excellent supercapacitor performance

Nanostructured metal carbides have numerous applications in catalysis and energy storage. However, directional construction remains a significant challenge. In this work, a novel strategy for the direct synthesis of nanostructured metal carbides using nanostructured metal oxides as the precursor is developed. TiO2 nanotube arrays (TiO2 NTAs) can be successfully transformed into TiC nanotube arrays (TiC NTAs) through electro-deoxidation and carbonization reactions in a low-temperature molten salt. TiC NTAs have a highly oriented and ordered array structure, which shows the advantages of large specific surface area, direct electron transport, and good chemical stability. Here, TiC NTA electrodes and PVA-H3PO4 electrolyte gel were assembled into a flexible quasi-solid-state supercapacitor to characterize their energy storage performance. The results show that the TiC NTA electrodes exhibit a high areal capacitance of 53.3 mF cm−2, excellent cycling stability, and mechanical flexibility. Moreover, the energy densities can reach 4.6 μW h cm−2 at a power density of 78.9 μW cm−2. This work provides a new strategy for the directed synthesis of nanostructured metal carbides and demonstrates the energy storage application potential of TiC NTAs. It is expected that this work will contribute to the development of the synthesis and application of nanostructured metal carbides

A directional total variation minimization algorithm for isotropic resolution in digital breast tomosynthesis

An optimization-based image reconstruction algorithm is developed for contrast enhanced digital breast tomosynthesis (DBT) using dual-energy scanning. The algorithm minimizes directional total variation (TV) with a data discrepancy and non-negativity constraints. Iodinated contrast agent (ICA) imaging is performed by reconstructing images from dual-energy DBT data followed by weighted subtraction. Physical DBT data is acquired with a Siemens Mammomat scanner of a structured breast phantom with ICA inserts. Results are shown for both directional TV minimization and filtered back-projection for reference. It is seen that directional TV is able to substantially reduce depth blur for the ICA objects.Comment: Proceedings paper for accepted contribution to the 8th International Conference on Image Formation in X-Ray Computed Tomography (https://www.ct-meeting.org

N-linked glycosylation of protease-activated receptor-1 at extracellular loop 2 regulates G-protein signaling bias

G-protein-coupled receptors (GPCRs) are the largest class of mammalian signaling receptors and mediate vast physiological responses. The capacity to modulate GPCR signaling therapeutically is important for treatment of various diseases, and discovering new aspects of receptor signaling is critical for drug development. Protease-activated receptor-1 (PAR1) is GPCR for thrombin. Similar to other GPCRs, PAR1 is promiscuous and couples to multiple heterotrimeric G-protein subtypes in the same cell. How a single GPCR can couple to multiple G-protein subtypes concurrently has remained an enigma. We demonstrate that N-linked glycosylation of PAR1 regulates G-protein coupling specificity and differentially controls cellular responses. Thus, the status of GPCR glycosylation is a critical determinant for specifying coupling to distinct G-protein subtypes

Optimization-Based Image Reconstruction for X-Ray CT with Multispectral Data

Computed tomography (CT) has grown into a major workhorse in radiology since its emergence in the 1970's, for its noninvasiveness, three-dimensional information, and superior contrast resolution. There had been a number of major advances in the CT technology, including optimization-based reconstruction methods, which can be designed to reduce image artifacts and enable flexible scanning configuration design. More recently, there has been a renewed interest in exploring the energy information in CT imaging using multispectral scans. A number of commercial scanners are available to acquire dual-energy scan data for a range of clinical applications. On the other hand, a common limitation shared by almost all commercial dual-energy CT scanners is the significant addition of special hardware to conventional diagnostic CT, adding on to the already-expensive cost of CT systems. Part of the reason for the dependence on the special hardware to acquire dual-energy or multispectral CT data is the need to conform to the data conditions required by the reconstruction methods that include either data-domain or image-domain decomposition and the failure to take advantage of the design flexibility enabled by fully-modeled, optimization-based reconstruction methods, such as the one-step inversion methods for multispectral CT. In this dissertation work, we aim to propose a one-step, optimization-based reconstruction method and enable novel, non-standard scan configurations of potential practical significance for multispectral CT that can be readily implemented on existing conventional CT scanners with no or minimum system modification. We start with the development of the method, including a non-linear data model, a non-convex optimization program, and an algorithm for numerically solving the program, and applied the method to both simulated and real data collected from standard, full-scan and non-standard, partial-scan configurations. The results suggest that fast, low-dose, and low-cost multispectral CT can be enabled by the proposed optimization-based reconstruction and the ASD-NC-POCS algorithm