Modelling Annual Scintillation Velocity Variations of FRB 20201124A

Compact radio sources exhibit scintillation, an interference pattern arising from propagation through inhomogeneous plasma, where scintillation patterns encode the relative distances and velocities of the source, scattering material, and Earth. In Main et al. 2022, we showed that the scintillation velocity of the repeating fast radio burst FRB20201124A can be measured by correlating pairs of burst spectra, and suggested that the scattering was nearby the Earth at $\sim0.4\,$kpc from the low values of the scintillation velocity and scattering timescale. In this work, we have measured the scintillation velocity at 10 epochs spanning a year, observing an annual variation which strongly implies the screen is within the Milky Way. Modelling the annual variation with a 1D anisotropic or 2D isotropic screen results in a screen distance $d_{l} = 0.24\pm0.04\,$pc or $d_{l} = 0.37\pm0.07\,$pc from Earth respectively, possibly associated with the Local Bubble or the edge of the Orion-Eridanus Superbubble. Continued monitoring, and using measurements from other telescopes particularly at times of low effective velocity will help probe changes in screen properties, and distinguish between screen models. Where scintillation of an FRB originates in its host galaxy or local environment, these techniques could be used to detect orbital motion, and probe the FRB's local ionized environment.Comment: 5 pages, 5 Figures, submitted to MNRAS Letter

The Lantern Vol. 41, No. 1, Fall 1974

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Structural Analysis to Determine the Core of Hypoxia Response Network

The advent of sophisticated molecular biology techniques allows to deduce the structure of complex biological networks. However, networks tend to be huge and impose computational challenges on traditional mathematical analysis due to their high dimension and lack of reliable kinetic data. To overcome this problem, complex biological networks are decomposed into modules that are assumed to capture essential aspects of the full network's dynamics. The question that begs for an answer is how to identify the core that is representative of a network's dynamics, its function and robustness. One of the powerful methods to probe into the structure of a network is Petri net analysis. Petri nets support network visualization and execution. They are also equipped with sound mathematical and formal reasoning based on which a network can be decomposed into modules. The structural analysis provides insight into the robustness and facilitates the identification of fragile nodes. The application of these techniques to a previously proposed hypoxia control network reveals three functional modules responsible for degrading the hypoxia-inducible factor (HIF). Interestingly, the structural analysis identifies superfluous network parts and suggests that the reversibility of the reactions are not important for the essential functionality. The core network is determined to be the union of the three reduced individual modules. The structural analysis results are confirmed by numerical integration of the differential equations induced by the individual modules as well as their composition. The structural analysis leads also to a coarse network structure highlighting the structural principles inherent in the three functional modules. Importantly, our analysis identifies the fragile node in this robust network without which the switch-like behavior is shown to be completely absent

Engineering Yarrowia lipolytica to Produce Glycoproteins Homogeneously Modified with the Universal Man3GlcNAc2 N-Glycan Core

Yarrowia lipolytica is a dimorphic yeast that efficiently secretes various heterologous proteins and is classified as “generally recognized as safe.” Therefore, it is an attractive protein production host. However, yeasts modify glycoproteins with non-human high mannose-type N-glycans. These structures reduce the protein half-life in vivo and can be immunogenic in man. Here, we describe how we genetically engineered N-glycan biosynthesis in Yarrowia lipolytica so that it produces Man3GlcNAc2 structures on its glycoproteins. We obtained unprecedented levels of homogeneity of this glycanstructure. This is the ideal starting point for building human-like sugars. Disruption of the ALG3 gene resulted in modification of proteins mainly with Man5GlcNAc2 and GlcMan5GlcNAc2 glycans, and to a lesser extent with Glc2Man5GlcNAc2 glycans. To avoid underoccupancy of glycosylation sites, we concomitantly overexpressed ALG6. We also explored several approaches to remove the terminal glucose residues, which hamper further humanization of N-glycosylation; overexpression of the heterodimeric Apergillus niger glucosidase II proved to be the most effective approach. Finally, we overexpressed an α-1,2-mannosidase to obtain Man3GlcNAc2 structures, which are substrates for the synthesis of complex-type glycans. The final Yarrowia lipolytica strain produces proteins glycosylated with the trimannosyl core N-glycan (Man3GlcNAc2), which is the common core of all complex-type N-glycans. All these glycans can be constructed on the obtained trimannosyl N-glycan using either in vivo or in vitro modification with the appropriate glycosyltransferases. The results demonstrate the high potential of Yarrowia lipolytica to be developed as an efficient expression system for the production of glycoproteins with humanized glycans