Antigenic evolution of SARS coronavirus 2

SARS coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, emerged in China in December 2019. Vaccines developed were very effective initially, however, the virus has shown remarkable evolution with multiple variants spreading globally over the last three years. Nowadays, newly emerging Omicron lineages are gaining substitutions at a fast rate, resulting in escape from neutralization by antibodies that target the Spike protein. Tools to map the impact of substitutions on the further antigenic evolution of SARS-CoV-2, such as antigenic cartography, may be helpful to update SARS-CoV-2 vaccines. In this review, we focus on the antigenic evolution of SARS-CoV-2, highlighting the impact of Spike protein substitutions individually and in combination on immune escape.</p

FLEET: Butterfly Estimation from a Bipartite Graph Stream

We consider space-efficient single-pass estimation of the number of butterflies, a fundamental bipartite graph motif, from a massive bipartite graph stream where each edge represents a connection between entities in two different partitions. We present a space lower bound for any streaming algorithm that can estimate the number of butterflies accurately, as well as FLEET, a suite of algorithms for accurately estimating the number of butterflies in the graph stream. Estimates returned by the algorithms come with provable guarantees on the approximation error, and experiments show good tradeoffs between the space used and the accuracy of approximation. We also present space-efficient algorithms for estimating the number of butterflies within a sliding window of the most recent elements in the stream. While there is a significant body of work on counting subgraphs such as triangles in a unipartite graph stream, our work seems to be one of the few to tackle the case of bipartite graph streams.Comment: This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version was published in Seyed-Vahid Sanei-Mehri, Yu Zhang, Ahmet Erdem Sariyuce and Srikanta Tirthapura. "FLEET: Butterfly Estimation from a Bipartite Graph Stream". The 28th ACM International Conference on Information and Knowledge Managemen

Ariel - Volume 2 Number 5

Editors Delvyn C. Case, Jr. Paul M. Fernhoff News Editors Richard Bonanno Robin A. Edwards Features Editors Stephen P. Flynn Steven A. Ager Lay-Out Editor Carol Dolinskas Contributing Editors Michael J. Blecker W. Cherry Light Eugenia Miller Lin Sey Edwards Jack Guralnik Tom Williams James Noco

AP-1cFos/JunB/miR-200a regulate the pro-regenerative glial cell response during axolotl spinal cord regeneration

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sabin, Keith Z., Jiang, Peng, Gearhart, Micah D., Stewart, Ron, & Echeverri, Karen. AP-1cFos/JunB/miR-200a regulate the pro-regenerative glial cell response during axolotl spinal cord regeneration. Communications Biology, 2(91), (2019), doi:10.1038/s42003-019-0335-4.Salamanders have the remarkable ability to functionally regenerate after spinal cord transection. In response to injury, GFAP+ glial cells in the axolotl spinal cord proliferate and migrate to replace the missing neural tube and create a permissive environment for axon regeneration. Molecular pathways that regulate the pro-regenerative axolotl glial cell response are poorly understood. Here we show axolotl glial cells up-regulate AP-1cFos/JunB after injury, which promotes a pro-regenerative glial cell response. Injury induced upregulation of miR-200a in glial cells supresses c-Jun expression in these cells. Inhibition of miR-200a during regeneration causes defects in axonal regrowth and transcriptomic analysis revealed that miR-200a inhibition leads to differential regulation of genes involved with reactive gliosis, the glial scar, extracellular matrix remodeling and axon guidance. This work identifies a unique role for miR-200a in inhibiting reactive gliosis in axolotl glial cells during spinal cord regeneration.This reseach was supported by a Regenerative Medicine Minnesota Grant and a NIH NCID R01 to KE. KZS has been supported by a NIH T32 GM113846 grant

Substantial improvements not seen in health behaviors following corner store conversions in two Latino food swamps.

BackgroundThe effectiveness of food retail interventions is largely undetermined, yet substantial investments have been made to improve access to healthy foods in food deserts and swamps via grocery and corner store interventions. This study evaluated the effects of corner store conversions in East Los Angeles and Boyle Heights, California on perceived accessibility of healthy foods, perceptions of corner stores, store patronage, food purchasing, and eating behaviors.MethodsHousehold data (n = 1686) were collected at baseline and 12- to 24-months post-intervention among residents surrounding eight stores, three of which implemented a multi-faceted intervention and five of which were comparisons. Bivariate analyses and logistic and linear regressions were employed to assess differences in time, treatment, and the interaction between time and treatment to determine the effectiveness of this intervention.ResultsImprovements were found in perceived healthy food accessibility and perceptions of corner stores. No changes were found, however, in store patronage, purchasing, or consumption of fruits and vegetables.ConclusionsResults suggest limited effectiveness of food retail interventions on improving health behaviors. Future research should focus on other strategies to reduce community-level obesity

Probing the active site of homoserine trans-succinylase

AbstractHomoserine trans-succinylase is the first enzyme in methionine biosynthesis of Escherichia coli and catalyzes the activation of homoserine via a succinylation reaction. The in vivo activity of this enzyme is subject to tight regulation by several mechanisms, including repression and activation of gene expression, feedback inhibition, temperature regulation and proteolysis. This complex regulation reflects the key role of this enzyme in bacterial metabolism. Here, we demonstrate – using proteomics and high-resolution mass spectrometry – that succinyl is covalently bound to one of the two adjacent lysine residues at positions 45 and 46. Replacing these lysine residues by alanine abolished the enzymatic activity. These findings position the lysine residues, one of which is conserved, at the active site

Indication for π+π−\pi^+ \pi^- scattering in p+pp+p collisions at sNN=\sqrt{s_{_{NN}}} = 200 GeV

A $\rho(770)^0$ mass shift of about -40 MeV/$c^2$ was measured in $p+p$ collisions at $\sqrt{s_{_{NN}}} =$ 200 GeV at RHIC. Previous mass shifts have been observed at CERN-LEBC-EHS and CERN-LEP. We will show that phase space does not account for the $\rho(770)^0$ mass shift measured at RHIC, CERN-LEBC-EHS and CERN-LEP and conclude that there are significant scattering interactions in $p+p$ collisions.Comment: 11 pages and 7 figure