The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing

DNA methylation, the addition of a methyl (CH3) group to a cytosine residue, is an evolutionarily conserved epigenetic mark involved in a number of different biological functions in eukaryotes, including transcriptional regulation, chromatin structural organization, cellular differentiation and development. In the social amoeba Dictyostelium, previous studies have shown the existence of a DNA methyltransferase (DNMA) belonging to the DNMT2 family, but the extent and function of 5-methylcytosine in the genome are unclear. Here, we present the whole genome DNA methylation profile of Dictyostelium discoideum using deep coverage replicate sequencing of bisulfite-converted gDNA extracted from post-starvation cells. We find an overall very low number of sites with any detectable level of DNA methylation, occurring at significant levels in only 303-3432 cytosines out of the ∼7.5 million total cytosines in the genome depending on the replicate. Furthermore, a knockout of the DNMA enzyme leads to no overall decrease in DNA methylation. Of the identified sites, significant methylation is only detected at 11 sites in all four of the methylomes analyzed. Targeted bisulfite PCR sequencing and computational analysis demonstrate that the methylation profile does not change during development and that these 11 cytosines are most likely false positives generated by protection from bisulfite conversion due to their location in hairpin-forming palindromic DNA sequences. Our data therefore provide evidence that there is no significant DNA methylation in Dictyostelium before fruiting body formation and identify a reproducible experimental artifact from bisulfite sequencing. © 2023 The Author(s). Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics

Deep Learning for Vanishing Point Detection Using an Inverse Gnomonic Projection

We present a novel approach for vanishing point detection from uncalibrated monocular images. In contrast to state-of-the-art, we make no a priori assumptions about the observed scene. Our method is based on a convolutional neural network (CNN) which does not use natural images, but a Gaussian sphere representation arising from an inverse gnomonic projection of lines detected in an image. This allows us to rely on synthetic data for training, eliminating the need for labelled images. Our method achieves competitive performance on three horizon estimation benchmark datasets. We further highlight some additional use cases for which our vanishing point detection algorithm can be used.Comment: Accepted for publication at German Conference on Pattern Recognition (GCPR) 2017. This research was supported by German Research Foundation DFG within Priority Research Programme 1894 "Volunteered Geographic Information: Interpretation, Visualisation and Social Computing

Reduced-symmetry two-dimensional solitons in photonic lattices

We demonstrate theoretically and experimentally a novel type of localized beams supported by the combined effects of total internal and Bragg reflection in nonlinear two-dimensional square periodic structures. Such localized states exhibit strong anisotropy in their mobility properties, being highly mobile in one direction and trapped in the other, making them promising candidates for optical routing in nonlinear lattices.Comment: 5 pages, 4 figure

Event Tracker: a Text Analytics Platform for Use During Disasters

Emergency management organisations currently rely on a wide range of disparate tools and technologies to support the monitoring and management of events during crisis situations. This has a number of disadvantages, in terms of training time for new staff members, reliance on external services, and a lack of integration (and hence poor transfer of information) between those services. On the other hand, Event Tracker is a new solution that aims to provide a unified view of an event, integrating information from emergency response officers, the public (via social media) and also volunteers from around the world. In particular, Event Tracker provides a series of novel functionalities to realise this unified view of the event, namely: real-time identification of critical information, automatic grouping of content by the information needs of response officers, as well as real-time volunteers management and communication. This is supported by an efficient and scalable back-end infrastructure designed to ingest and process high-volumes of real-time streaming data with low latency

Autonomous multi-platform observations during the Salinity Processes in the Upper-ocean Regional Study

Author Posting. © The Oceanography Society, 2017. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 30, no. 2 (2017): 38–48, doi:10.5670/oceanog.2017.218.The Salinity Processes in the Upper-ocean Regional Study (SPURS) aims to understand the patterns and variability of sea surface salinity. In order to capture the wide range of spatial and temporal scales associated with processes controlling salinity in the upper ocean, research vessels delivered autonomous instruments to remote sites, one in the North Atlantic and one in the Eastern Pacific. Instruments sampled for one complete annual cycle at each of these two sites, which are subject to contrasting atmospheric forcing. The SPURS field programs coordinated sampling from many different platforms, using a mix of Lagrangian and Eulerian approaches. This article discusses the motivations, implementation, and first results of the SPURS-1 and SPURS-2 programs.SPURS is supported by multiple NASA grants, with important additional contributions from the US National Science Foundation, NOAA, and the Office of Naval Research, as well as international agencies. SVP drifters are deployed with support from NASA and the NOAA funded Global Drifter Program at the Lagrangian Drifter Laboratory of the Scripps Institution of Oceanography. SVP-S2 drifters are provided by NOAA-AOML and NASA. PRAWLER mooring development is supported by NOAA’s Office of Oceanic and Atmospheric Research, Ocean Observing and Monitoring Division, and by NOAA/PMEL

Rationally designed immunogens enable immune focusing following SARS-CoV-2 spike imprinting

Eliciting antibodies to surface-exposed viral glycoproteins can generate protective responses that control and prevent future infections. Targeting conserved sites may reduce the likelihood of viral escape and limit the spread of related viruses with pandemic potential. Here we leverage rational immunogen design to focus humoral responses on conserved epitopes. Using glycan engineering and epitope scaffolding in boosting immunogens, we focus murine serum antibody responses to conserved receptor binding motif (RBM) and receptor binding domain (RBD) epitopes following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike imprinting. Although all engineered immunogens elicit a robust SARS-CoV-2-neutralizing serum response, RBM-focusing immunogens exhibit increased potency against related sarbecoviruses, SARS-CoV, WIV1-CoV, RaTG13-CoV, and SHC014-CoV; structural characterization of representative antibodies defines a conserved epitope. RBM-focused sera confer protection against SARS-CoV-2 challenge. Thus, RBM focusing is a promising strategy to elicit breadth across emerging sarbecoviruses without compromising SARS-CoV-2 protection. These engineering strategies are adaptable to other viral glycoproteins for targeting conserved epitopes

FIRED (Fire Events Delineation): An Open, Flexible Algorithm and Database of US Fire Events Derived from the MODIS Burned Area Product (2001-2019)

Harnessing the fire data revolution, i.e., the abundance of information from satellites, government records, social media, and human health sources, now requires complex and challenging data integration approaches. Defining fire events is key to that effort. In order to understand the spatial and temporal characteristics of fire, or the classic fire regime concept, we need to critically define fire events from remote sensing data. Events, fundamentally a geographic concept with delineated spatial and temporal boundaries around a specific phenomenon that is homogenous in some property, are key to understanding fire regimes and more importantly how they are changing. Here, we describe Fire Events Delineation (FIRED), an event-delineation algorithm, that has been used to derive fire events (N = 51,871) from the MODIS MCD64 burned area product for the coterminous US (CONUS) from January 2001 to May 2019. The optimized spatial and temporal parameters to cluster burned area pixels into events were an 11-day window and a 5-pixel (2315 m) distance, when optimized against 13,741 wildfire perimeters in the CONUS from the Monitoring Trends in Burn Severity record. The linear relationship between the size of individual FIRED and Monitoring Trends in Burn Severity (MTBS) events for the CONUS was strong (R2 = 0.92 for all events). Importantly, this algorithm is open-source and flexible, allowing the end user to modify the spatio-temporal threshold or even the underlying algorithm approach as they see fit. We expect the optimized criteria to vary across regions, based on regional distributions of fire event size and rate of spread. We describe the derived metrics provided in a new national database and how they can be used to better understand US fire regimes. The open, flexible FIRED algorithm could be utilized to derive events in any satellite product. We hope that this open science effort will help catalyze a community-driven, data-integration effort (termed OneFire) to build a more complete picture of fire.</p

SARS-CoV-2 mRNA vaccination elicits robust antibody responses in children

Publisher Copyright: Copyright © 2022 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY)Although children have been largely spared from coronavirus disease 2019 (COVID-19), the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) with increased transmissibility, combined with fluctuating mask mandates and school reopenings, has led to increased infections and disease among children. Thus, there is an urgent need to roll out COVID-19 vaccines to children of all ages. However, whether children respond equivalently to adults to mRNA vaccines and whether dosing will elicit optimal immunity remain unclear. Here, we aimed to deeply profile the vaccine-induced humoral immune response in 6- to 11-year-old children receiving either a pediatric (50 μg) or adult (100 μg) dose of the mRNA-1273 vaccine and to compare these responses to vaccinated adults, infected children, and children who experienced multisystem inflammatory syndrome in children (MIS-C). Children elicited an IgG-dominant vaccine-induced immune response, surpassing adults at a matched 100-μg dose but more variable immunity at a 50-μg dose. Irrespective of titer, children generated antibodies with enhanced Fc receptor binding capacity. Moreover, like adults, children generated cross-VOC humoral immunity, marked by a decline of omicron-specific receptor binding domain, but robustly preserved omicron spike protein binding. Fc receptor binding capabilities were also preserved in a dose-dependent manner. These data indicate that both the 50- and 100-μg doses of mRNA vaccination in children elicit robust cross-VOC antibody responses and that 100-μg doses in children result in highly preserved omicron-specific functional humoral immunity.publishersversionPeer reviewe

Source identification and distribution reveals the potential of the geochemical Antarctic sea ice proxy IPSO25

The presence of a di-unsaturated highly branched isoprenoid (HBI) lipid biomarker (diene II) in Southern Ocean sediments has previously been proposed as a proxy measure of palaeo Antarctic sea ice. Here we show that a source of diene II is the sympagic diatom Berkeleya adeliensis Medlin. Furthermore, the propensity for B. adeliensis to flourish in platelet ice is reflected by an offshore downward gradient in diene II concentration in >100 surface sediments from Antarctic coastal and near-coastal environments. Since platelet ice formation is strongly associated with super-cooled freshwater inflow, we further hypothesize that sedimentary diene II provides a potentially sensitive proxy indicator of landfast sea ice influenced by meltwater discharge from nearby glaciers and ice shelves, and re-examination of some previous diene II downcore records supports this hypothesis. The term IPSO25-Ice Proxy for the Southern Ocean with 25 carbon atoms-is proposed as a proxy name for diene II