Showing papers by "Academy of Sciences of the Czech Republic published in 2021"

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

Abstract: In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

An evidence review of face masks against COVID-19.

Abstract: The science around the use of masks by the public to impede COVID-19 transmission is advancing rapidly. In this narrative review, we develop an analytical framework to examine mask usage, synthesizing the relevant literature to inform multiple areas: population impact, transmission characteristics, source control, wearer protection, sociological considerations, and implementation considerations. A primary route of transmission of COVID-19 is via respiratory particles, and it is known to be transmissible from presymptomatic, paucisymptomatic, and asymptomatic individuals. Reducing disease spread requires two things: limiting contacts of infected individuals via physical distancing and other measures and reducing the transmission probability per contact. The preponderance of evidence indicates that mask wearing reduces transmissibility per contact by reducing transmission of infected respiratory particles in both laboratory and clinical contexts. Public mask wearing is most effective at reducing spread of the virus when compliance is high. Given the current shortages of medical masks, we recommend the adoption of public cloth mask wearing, as an effective form of source control, in conjunction with existing hygiene, distancing, and contact tracing strategies. Because many respiratory particles become smaller due to evaporation, we recommend increasing focus on a previously overlooked aspect of mask usage: mask wearing by infectious people ("source control") with benefits at the population level, rather than only mask wearing by susceptible people, such as health care workers, with focus on individual outcomes. We recommend that public officials and governments strongly encourage the use of widespread face masks in public, including the use of appropriate regulation.

High and rising economic costs of biological invasions worldwide

Abstract: Biological invasions are responsible for substantial biodiversity declines as well as high economic losses to society and monetary expenditures associated with the management of these invasions1,2 The InvaCost database has enabled the generation of a reliable, comprehensive, standardized and easily updatable synthesis of the monetary costs of biological invasions worldwide3 Here we found that the total reported costs of invasions reached a minimum of US$1288 trillion (2017 US dollars) over the past few decades (1970-2017), with an annual mean cost of US$268 billion Moreover, we estimate that the annual mean cost could reach US$1627 billion in 2017 These costs remain strongly underestimated and do not show any sign of slowing down, exhibiting a consistent threefold increase per decade We show that the documented costs are widely distributed and have strong gaps at regional and taxonomic scales, with damage costs being an order of magnitude higher than management expenditures Research approaches that document the costs of biological invasions need to be further improved Nonetheless, our findings call for the implementation of consistent management actions and international policy agreements that aim to reduce the burden of invasive alien species

Martini 3 : A general purpose force field for coarse-grained molecular dynamics

Abstract: The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 ( http://cgmartini.nl ), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability. The updated model allows more accurate predictions of molecular packing and interactions in general, which is exemplified with a vast and diverse set of applications, ranging from oil/water partitioning and miscibility data to complex molecular systems, involving protein-protein and protein-lipid interactions and material science applications as ionic liquids and aedamers.

The burden of heat-related mortality attributable to recent human-induced climate change

Abstract: Climate change affects human health; however, there have been no large-scale, systematic efforts to quantify the heat-related human health impacts that have already occurred due to climate change. Here, we use empirical data from 732 locations in 43 countries to estimate the mortality burdens associated with the additional heat exposure that has resulted from recent human-induced warming, during the period 1991-2018. Across all study countries, we find that 37.0% (range 20.5-76.3%) of warm-season heat-related deaths can be attributed to anthropogenic climate change and that increased mortality is evident on every continent. Burdens varied geographically but were of the order of dozens to hundreds of deaths per year in many locations. Our findings support the urgent need for more ambitious mitigation and adaptation strategies to minimize the public health impacts of climate change.

Projecting the continental accumulation of alien species through to 2050

Abstract: Biological invasions have steadily increased over recent centuries. However, we still lack a clear expectation about future trends in alien species numbers. In particular, we do not know whether alien species will continue to accumulate in regional floras and faunas, or whether the pace of accumulation will decrease due to the depletion of native source pools. Here, we apply a new model to simulate future numbers of alien species based on estimated sizes of source pools and dynamics of historical invasions, assuming a continuation of processes in the future as observed in the past (a business-as-usual scenario). We first validated performance of different model versions by conducting a back-casting approach, therefore fitting the model to alien species numbers until 1950 and validating predictions on trends from 1950 to 2005. In a second step, we selected the best performing model that provided the most robust predictions to project trajectories of alien species numbers until 2050. Altogether, this resulted in 3,790 stochastic simulation runs for 38 taxon-continent combinations. We provide the first quantitative projections of future trajectories of alien species numbers for seven major taxonomic groups in eight continents, accounting for variation in sampling intensity and uncertainty in projections. Overall, established alien species numbers per continent were predicted to increase from 2005 to 2050 by 36%. Particularly, strong increases were projected for Europe in absolute (+2,543 ± 237 alien species) and relative terms, followed by Temperate Asia (+1,597 ± 197), Northern America (1,484 ± 74) and Southern America (1,391 ± 258). Among individual taxonomic groups, especially strong increases were projected for invertebrates globally. Declining (but still positive) rates were projected only for Australasia. Our projections provide a first baseline for the assessment of future developments of biological invasions, which will help to inform policies to contain the spread of alien species.

Plant- or microbial-derived? A review on the molecular composition of stabilized soil organic matter

Abstract: Soil organic matter (SOM) represents a major reservoir of stored carbon (C). However, uncertainties regarding the composition and origin of stabilized SOM hinder the implementation of sustainable management strategies. Here, we synthesize data on the contribution of plant- and microbial-derived compounds to stabilized SOM, i.e., aggregates and mineral-associated organic matter (MAOM), and review the role of environmental factors influencing this contribution. Extrapolating amino sugar concentrations in soil based on molecular stoichiometry, we find that microbial necromass accounts for ~50% (agroecosystems) or less (forest ecosystems) of the C stabilized within aggregates and MAOM across studies. This implies that plant biomolecules, including lipids, lignin, and sugars, might account for a substantial portion (≥50%) of the organic matter protected by minerals and aggregates. Indeed, plant-specific sugars and lipids can each account for as much as 10% of organic C within mineral soil fractions, and most reported quantities of plant-specific lipids and lignin in mineral soil fractions are likely underestimates due to irreversible sorption to minerals. A relatively balanced contribution of plant and microbial biomolecules to stabilized SOM in aggregates and MAOM is inconsistent with recent suggestions that stable SOM is comprised mostly of microbial compounds. Land use and soil type appear to profoundly affect the contribution of plant and microbial compounds to stabilized SOM. Consistent with studies of bulk soils, favorable conditions for microbial proliferation in grasslands or fertile Chernozems or Luvisols appear to increase the contribution of microbial compounds, while less favorable conditions for microbial proliferation in forest soils or Podzols/Alisols appear to favor the abundance of plant compounds in stabilized SOM. Combined with a tight link between substrate quality and the abundance of microbial compounds in stabilized SOM, and a potentially inverse relationship between substrate quality and the abundance of plant compounds, these results provide evidence that plant biomolecules might be preferentially stabilized by organo-mineral interactions in some ecosystems. Various areas warrant further research. For example, difficulties in distinguishing direct and indirect effects of temperature and precipitation on the composition of stabilized SOM may be overcome by long-term observational studies that include climate manipulations. Knowledge gaps in the contribution of plant and microbial compounds to stabilized SOM in soil layers below 30 cm depth may simply be closed by extending the sampling depth. Moreover, a refined focus on soil fauna, with potentially strong effects on microbial and plant compounds in stabilized SOM, will provide new insights into SOM dynamics. Future studies should quantify both microbial and plant biomolecules in mineral soil fractions to allow direct comparisons and overcome limitations in existing data. For example, because biomarker-based estimates of microbial-derived C can only indirectly estimate the maximum amount of plant-derived C, exhaustive studies of plant biomarker concentrations could be conducted, including estimates of plant-specific lipids, sugars, and lignin (and biomarkers released following mineral dissolution). Generally, more integrative studies, e.g., combining molecular and isotopic tracers of organic matter inputs with targeted sampling of mineral fractions, are required to improve knowledge of the formation and persistence of stabilized SOM.

Will climate mitigation ambitions lead to carbon neutrality? An analysis of the local-level plans of 327 cities in the EU

Abstract: Cities across the globe recognise their role in climate mitigation and are acting to reduce carbon emissions. Knowing whether cities set ambitious climate and energy targets is critical for determining their contribution towards the global 1.5 °C target, partly because it helps to identify areas where further action is necessary. This paper presents a comparative analysis of the mitigation targets of 327 European cities, as declared in their local climate plans. The sample encompasses over 25% of the EU population and includes cities of all sizes across all Member States, plus the UK. The study analyses whether the type of plan, city size, membership of climate networks, and its regional location are associated with different levels of mitigation ambition. Results reveal that 78% of the cities have a GHG emissions reduction target. However, with an average target of 47%, European cities are not on track to reach the Paris Agreement: they need to roughly double their ambitions and efforts. Some cities are ambitious, e.g. 25% of our sample (81) aim to reach carbon neutrality, with the earliest target date being 2020.90% of these cities are members of the Climate Alliance and 75% of the Covenant of Mayors. City size is the strongest predictor for carbon neutrality, whilst climate network(s) membership, combining adaptation and mitigation into a single strategy, and local motivation also play a role. The methods, data, results and analysis of this study can serve as a reference and baseline for tracking climate mitigation ambitions across European and global cities.

2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Abstract: In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

A guest-assisted molecular-organization approach for >17% efficiency organic solar cells using environmentally friendly solvents

Abstract: The power conversion efficiencies (PCEs) of laboratory-sized organic solar cells (OSCs), usually processed from low-boiling-point and toxic solvents, have reached high values of over 18%. However, there is usually a notable drop of the PCEs when green solvents are used, limiting practical development of OSCs. Herein, we obtain certificated PCEs over 17% in OSCs processed from a green solvent paraxylene (PX) by a guest-assisted assembly strategy, where a third component (guest) is employed to manipulate the molecular interaction of the binary blend. In addition, the high-boiling-point green solvent PX also enables us to deposit a uniform large-area module (36 cm2) with a high efficiency of over 14%. The strong molecular interaction between the host and guest molecules also enhances the operational stability of the devices. Our guest-assisted assembly strategy provides a unique approach to develop large-area and high-efficiency OSCs processed from green solvents, paving the way for industrial development of OSCs. Organic solar cells processed from green solvents are easier to implement in manufacturing yet their efficiency is low. Chen et al. devise a guest molecule to improve the molecular packing, enabling devices with over 17% efficiency.

Jet energy scale and resolution measured in proton-proton collisions at s =13 TeV with the ATLAS detector

Abstract: Jet energy scale and resolution measurements with their associated uncertainties are reported for jets using 36-81 fb$^{-1}$ of proton-proton collision data with a centre-of-mass energy of $\sqrt{s}=13$ TeV collected by the ATLAS detector at the LHC. Jets are reconstructed using two different input types: topo-clusters formed from energy deposits in calorimeter cells, as well as an algorithmic combination of charged-particle tracks with those topo-clusters, referred to as the ATLAS particle-flow reconstruction method. The anti-$k_t$ jet algorithm with radius parameter $R=0.4$ is the primary jet definition used for both jet types. Jets are initially calibrated using a sequence of simulation-based corrections. Next, several $\textit{in situ}$ techniques are employed to correct for differences between data and simulation and to measure the resolution of jets. The systematic uncertainties in the jet energy scale for central jets ($|\eta| 2.5$ TeV). The relative jet energy resolution is measured and ranges from ($24 \pm 1.5$)% at 20 GeV to ($6 \pm 0.5$)% at 300 GeV.

Stress-induced reactive oxygen species compartmentalization, perception and signalling

Abstract: Reactive oxygen species (ROS) are essential for life and are involved in the regulation of almost all biological processes. ROS production is critical for plant development, response to abiotic stresses and immune responses. Here, we focus on recent discoveries in ROS biology emphasizing abiotic and biotic stress responses. Recent advancements have resulted in the identification of one of the first sensors for extracellular ROS and highlighted waves of ROS production during stress signalling in Arabidopsis. Enzymes that produce ROS, including NADPH oxidases, exhibit precise regulation through diverse post-translational modifications. Discoveries highlight the importance of both amino- and carboxy-terminal regulation of NADPH oxidases through protein phosphorylation and cysteine oxidation. Here, we discuss advancements in ROS compartmentalization, systemic ROS waves, ROS sensing and post-translational modification of ROS-producing enzymes and identify areas where foundational gaps remain. This Review covers the recent advancements in our understanding of reactive oxygen species production, regulation and perception in plants. It is primarily focused on stress responses and the role of NADPH oxidases.

Genetic insights into biological mechanisms governing human ovarian ageing.

Abstract: Reproductive longevity is essential for fertility and influences healthy ageing in women1,2, but insights into its underlying biological mechanisms and treatments to preserve it are limited. Here we identify 290 genetic determinants of ovarian ageing, assessed using normal variation in age at natural menopause (ANM) in about 200,000 women of European ancestry. These common alleles were associated with clinical extremes of ANM; women in the top 1% of genetic susceptibility have an equivalent risk of premature ovarian insufficiency to those carrying monogenic FMR1 premutations3. The identified loci implicate a broad range of DNA damage response (DDR) processes and include loss-of-function variants in key DDR-associated genes. Integration with experimental models demonstrates that these DDR processes act across the life-course to shape the ovarian reserve and its rate of depletion. Furthermore, we demonstrate that experimental manipulation of DDR pathways highlighted by human genetics increases fertility and extends reproductive life in mice. Causal inference analyses using the identified genetic variants indicate that extending reproductive life in women improves bone health and reduces risk of type 2 diabetes, but increases the risk of hormone-sensitive cancers. These findings provide insight into the mechanisms that govern ovarian ageing, when they act, and how they might be targeted by therapeutic approaches to extend fertility and prevent disease. Hundreds of genetic loci associated with age at menopause, combined with experimental evidence in mice, highlight mechanisms of reproductive ageing across the lifespan.

Stratification strength and light climate explain variation in chlorophyll a at the continental scale in a European multilake survey in a heatwave summer

Abstract: Output Status: Forthcoming/Available Online Additional co-authors: Jolanda Verspagen, Maria van Herk, Maria G. Antoniou, Nikoletta Tsiarta, Valerie McCarthy, Victor C. Perello, Danielle Machado-Vieira, Alinne Gurjao de Oliveira, Dubravka Spoljaric Maronic, Filip Stevic, Tanja Žuna Pfeiffer, Itana Bokan Vucelic, Petar Žutinic, Marija Gligora Udovic, Anđelka Plenkovic-Moraj, Ludek Blaha, Rodan Geris, Marketa Frankova, Kirsten Seestern Christoffersen, Trine Perlt Warming, Tonu Feldmann, Alo Laas, Kristel Panksep, Lea Tuvikene, Kersti Kangro, Judita Koreiviene, Jurate Karosiene, Jurate Kasperoviciene, Ksenija Savadova-Ratkus, Irma Vitonyte, Kerstin Haggqvist, Pauliina Salmi, Lauri Arvola, Karl Rothhaupt, Christos Avagianos, Triantafyllos Kaloudis, Spyros Gkelis, Manthos Panou, Theodoros Triantis, Sevasti-Kiriaki Zervou, Anastasia Hiskia, Ulrike Obertegger, Adriano Boscaini, Giovanna Flaim, Nico Salmaso, Leonardo Cerasino, Sigrid Haande, Birger Skjelbred, Magdalena Grabowska, Maciej Karpowicz, Damian Chmura, Lidia Nawrocka, Justyna Kobos, Hanna Mazur-Marzec, Pablo Alcaraz-Parraga, Elzbieta Wilk-Wozniak, Wojciech Krzton, Edward Walusiak, Ilona Gagala-Borowska, Joana Mankiewicz-Boczek, Magdalena Toporowska, Barbara Pawlik-Skowronska, Michal Niedzwiecki, Wojciech Peczula, Agnieszka Napiorkowska-Krzebietke, Julita Dunalska, Justyna Sienska, Daniel Szymanski, Marek Kruk, Agnieszka Budzynska, Ryszard Goldyn, Anna Kozak, Joanna Rosinska, Elzbieta Szeląg-Wasielewska, Piotr Domek, Natalia Jakubowska-Krepska, Kinga Kwasizur, Beata Messyasz, Aleksandra Pelechata, Mariusz Pelechaty, Mikolaj Kokocinski, Beata Madrecka-Witkowska, Iwona Kostrzewska-Szlakowska, Magdalena Frąk, Agnieszka Bankowska-Sobczak, Michal Wasilewicz, Agnieszka Ochocka, Agnieszka Pasztaleniec, Iwona Jasser, Ana M. Antao-Geraldes, Manel Leira, Vitor Vasconcelos, Joao Morais, Micaela Vale, Pedro M. Raposeiro, Vitor Goncalves, Boris Aleksovski, Svetislav Krstic, Hana Nemova, Iveta Drastichova, Lucia Chomova, Spela Remec-Rekar, Tina Elersek, Lars-Anders Hansson, Pablo Urrutia-Cordero, Andrea G. Bravo, Moritz Buck, William Colom-Montero, Kristiina Mustonen, Don Pierson, Yang Yang, Christine Edwards, Hannah Cromie, Jordi Delgado-Martin, David Garcia, Jose Luis Cereijo, Joan Goma, Mari Carmen Trapote, Teresa Vegas-Vilarrubia, Biel Obrador, Ana Garcia-Murcia, Monserrat Real, Elvira Romans, Jordi Noguero-Ribes, David Parreno Duque, Elisabeth Fernandez-Moran, Barbara Ubeda, Jose Angel Galvez, Nuria Catalan, Carmen Perez-Martinez, Eloisa Ramos-Rodriguez, Carmen Cillero-Castro, Enrique Moreno-Ostos, Jose Maria Blanco, Valeriano Rodriguez, Jorge Juan Montes-Perez, Roberto L. Palomino, Estela Rodriguez-Perez, Armand Hernandez, Rafael Carballeira, Antonio Camacho, Antonio Picazo, Carlos Rochera, Anna C. Santamans, Carmen Ferriol, Susana Romo, Juan Miguel Soria, Arda Ozen, Tunay Karan, Nilsun Demir, Meryem Beklioglu, Nur Filiz, Eti Levi, Ugur Iskin, Gizem Bezirci, Ulku Nihan Tavsanoglu, Kemal Celik, Koray Ozhan, Nusret Karakaya, Mehmet Ali Turan Kocer, Mete Yilmaz, Faruk Maras¸lioglu, Ozden Fakioglu, Elif Neyran Soylu, Meral Apaydin Yagci, Sakir Cinar, Kadir Capkin, Abdulkadir Yagci, Mehmet Cesur, Fuat Bilgin, Cafer Bulut, Rahmi Uysal, Koker Latife, Reyhan Akcaalan, Meric Albay, Mehmet Tahir Alp, Korhan Ozkan, Tugba Ongun Sevindik, Hatice Tunca, Burcin Onem, Hans Paerl, Cayelan C. Carey, Bastiaan W. Ibelings

Recent European drought extremes beyond Common Era background variability

Abstract: Europe’s recent summer droughts have had devastating ecological and economic consequences, but the severity and cause of these extremes remain unclear. Here we present 27,080 annually resolved and absolutely dated measurements of tree-ring stable carbon and oxygen (δ13C and δ18O) isotopes from 21 living and 126 relict oaks (Quercus spp.) used to reconstruct central European summer hydroclimate from 75 bce to 2018 ce. We find that the combined inverse δ13C and δ18O values correlate with the June–August Palmer Drought Severity Index from 1901–2018 at 0.73 (P < 0.001). Pluvials around 200, 720 and 1100 ce, and droughts around 40, 590, 950 and 1510 ce and in the twenty-first century, are superimposed on a multi-millennial drying trend. Our reconstruction demonstrates that the sequence of recent European summer droughts since 2015 ce is unprecedented in the past 2,110 years. This hydroclimatic anomaly is probably caused by anthropogenic warming and associated changes in the position of the summer jet stream. European summer droughts in recent years are anomalously severe compared with those of the previous 2,000 years, according to a synthesis of annually resolved tree-ring carbon and oxygen isotope records.

Overview: State-of-the Art Commercial Membranes for Anion Exchange Membrane Water Electrolysis

Abstract: One promising way to store and distribute large amounts of renewable energy is water electrolysis, coupled with transport of hydrogen in the gas grid and storage in tanks and caverns. The intermittent availability of renewal energy makes it difficult to integrate it with established alkaline water electrolysis technology. Proton exchange membrane (PEM) water electrolysis is promising, but limited by the necessity to use expensive platinum and iridium catalysts. The expected solution is anion exchange membrane (AEM) water electrolysis, which combines the use of cheap and abundant catalyst materials with the advantages of PEM water electrolysis, namely a low foot print, large operational capacity, and fast response to changing operating conditions. The key component for AEM water electrolysis is a cheap, stable, gas tight and highly hydroxide conductive polymeric AEM. Here we present target values and technical requirements for AEMs, discuss the chemical structures involved and the related degradation pathways, and give an overview over the most prominent and promising commercial AEMs (Fumatech Fumasep® FAA3, Tokuyama A201, Ionomr Aemion™, Dioxide materials Sustainion®, and membranes commercialized by Orion Polymer), and review their properties and performances of water electrolyzers using these membranes.

Long-read sequence assembly: a technical evaluation in barley

Abstract: Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read assemblies are clearly superior to the current barley reference sequence based on short-reads. Assemblies derived from accurate long reads excel in most metrics, but the CCS approach was the most cost-effective strategy for assembling tens of barley genomes. A downsampling analysis indicated that 20-fold CCS coverage can yield very good sequence assemblies, while even five-fold CCS data may capture the complete sequence of most genes. We present an updated reference genome assembly for barley with near-complete representation of the repeat-rich intergenic space. Long-read assembly can underpin the construction of accurate and complete sequences of multiple genomes of a species to build pan-genome infrastructures in Triticeae crops and their wild relatives.

A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes.

Abstract: Rye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, an elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted for 98.47% of the estimated genome size (7.86 Gb), with 93.67% of the contigs (7.25 Gb) assigned to seven chromosomes. Repetitive elements constituted 90.31% of the assembled genome. Compared to previously sequenced Triticeae genomes, Daniela, Sumaya and Sumana retrotransposons showed strong expansion in rye. Further analyses of the Weining assembly shed new light on genome-wide gene duplications and their impact on starch biosynthesis genes, physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye. This genome sequence promises to accelerate genomic and breeding studies in rye and related cereal crops. A high-quality genome assembly of Weining rye sheds new light on gene duplications and their effects on starch biosynthesis genes, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions.

Plant roots sense soil compaction through restricted ethylene diffusion

Abstract: Soil compaction represents a major challenge for modern agriculture. Compaction is intuitively thought to reduce root growth by limiting the ability of roots to penetrate harder soils. We report that root growth in compacted soil is instead actively suppressed by the volatile hormone ethylene. We found that mutant Arabidopsis and rice roots that were insensitive to ethylene penetrated compacted soil more effectively than did wild-type roots. Our results indicate that soil compaction lowers gas diffusion through a reduction in air-filled pores, thereby causing ethylene to accumulate in root tissues and trigger hormone responses that restrict growth. We propose that ethylene acts as an early warning signal for roots to avoid compacted soils, which would be relevant to research into the breeding of crops resilient to soil compaction.

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment: DUNE Collaboration.

Abstract: The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE’s sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach.

Economic costs of invasive alien species across Europe

Abstract: Funding Information: The authors acknowledge the French National Research Agency (ANR-14-CE02-0021) and the BNP-Paribas Foundation Climate Initiative for funding the InvaCost project that allowed the construction of the InvaCost database. The present work was conducted following a workshop funded by the AXA Research Fund Chair of Invasion Biology and is part of the AlienScenario project funded by BiodivERsA and Belmont-Forum call 2018 on biodiversity scenarios. AN acknowledges funding from EXPRO grant no. 19-28807X (Czech Science Foundation) and long-term research development project RVO 67985939 (The Czech Academy of Sciences). CC was supported by Portuguese National Funds through Fundation para a Ci?ncia e a Tecnologia (CEECIND/02037/2017; UIDB/00295/2020 and UIDP/00295/2020). RNC was funded by a research fellowship from the Alexander von Humboldt Foundation. TWB acknowledges funding from the European Union?s Horizon 2020 research and innovation programme under the Marie Sk?odowska-Curie grant no. 747120. MG and CD were funded by the BiodivERsA-Belmont Forum Project ?Alien Scenarios? (BMBF/PT DLR 01LC1807C). NK was partially supported by the Russian Federationn Foundation for Basic Research (grant no.19-04-01029-A) [national literature survey] and the basic project of Sukachev Institute of Forest SB RAS (project no. 0287-2021-0011) [InvaCost database contribution]. DR thanks InEE-CNRS who supports the network GdR 3647 ?Invasions Biologiques?. Funds for AJT, EA and LBM contracts come from the AXA Research Fund Chair of Invasion Biology of University Paris Saclay. BL, DR and FC are French agents (affiliated, respectively, to the Mus?um National d?Histoire Naturelle, University of Rennes and Centre National de la Recherche Scientifique); their salaries, for which they are grateful, are typically not accounted for in assessment of costs on biological invasions. At last, the authors want to express their thanks for the translation of the abstract to other European languages, namely to Paride Balzani, Antonin Kouba, Sandra Hodic, and ROS Educational Consultancy Ltd & Garnock Media Ltd

Neuronal enhancers are hotspots for DNA single-strand break repair

Abstract: Defects in DNA repair frequently lead to neurodevelopmental and neurodegenerative diseases, underscoring the particular importance of DNA repair in long-lived post-mitotic neurons1,2. The cellular genome is subjected to a constant barrage of endogenous DNA damage, but surprisingly little is known about the identity of the lesion(s) that accumulate in neurons and whether they accrue throughout the genome or at specific loci. Here we show that post-mitotic neurons accumulate unexpectedly high levels of DNA single-strand breaks (SSBs) at specific sites within the genome. Genome-wide mapping reveals that SSBs are located within enhancers at or near CpG dinucleotides and sites of DNA demethylation. These SSBs are repaired by PARP1 and XRCC1-dependent mechanisms. Notably, deficiencies in XRCC1-dependent short-patch repair increase DNA repair synthesis at neuronal enhancers, whereas defects in long-patch repair reduce synthesis. The high levels of SSB repair in neuronal enhancers are therefore likely to be sustained by both short-patch and long-patch processes. These data provide the first evidence of site- and cell-type-specific SSB repair, revealing unexpected levels of localized and continuous DNA breakage in neurons. In addition, they suggest an explanation for the neurodegenerative phenotypes that occur in patients with defective SSB repair.

Muon reconstruction and identification efficiency in ATLAS using the full Run 2 pp collision data set at √ s = 13 TeV

Abstract: This article documents the muon reconstruction and identification efficiency obtained by the ATLAS experiment for 139 $$\hbox {fb}^{-1}$$ fb - 1 of pp collision data at $$\sqrt{s}=13$$ s = 13 TeV collected between 2015 and 2018 during Run 2 of the LHC. The increased instantaneous luminosity delivered by the LHC over this period required a reoptimisation of the criteria for the identification of prompt muons. Improved and newly developed algorithms were deployed to preserve high muon identification efficiency with a low misidentification rate and good momentum resolution. The availability of large samples of $$Z\rightarrow \mu \mu $$ Z → μ μ and $$J/\psi \rightarrow \mu \mu $$ J / ψ → μ μ decays, and the minimisation of systematic uncertainties, allows the efficiencies of criteria for muon identification, primary vertex association, and isolation to be measured with an accuracy at the per-mille level in the bulk of the phase space, and up to the percent level in complex kinematic configurations. Excellent performance is achieved over a range of transverse momenta from 3 GeV to several hundred GeV, and across the full muon detector acceptance of $$|\eta |<2.7$$ | η | < 2.7 .

Contribution of macromolecules to brain 1H MR spectra: Experts' consensus recommendations

Abstract: Proton MR spectra of the brain, especially those measured at short and intermediate echo times, contain signals from mobile macromolecules (MM). A description of the main MM is provided in this consensus paper. These broad peaks of MM underlie the narrower peaks of metabolites and often complicate their quantification but they also may have potential importance as biomarkers in specific diseases. Thus, separation of broad MM signals from low molecular weight metabolites enables accurate determination of metabolite concentrations and is of primary interest in many studies. Other studies attempt to understand the origin of the MM spectrum, to decompose it into individual spectral regions or peaks and to use the components of the MM spectrum as markers of various physiological or pathological conditions in biomedical research or clinical practice. The aim of this consensus paper is to provide an overview and some recommendations on how to handle the MM signals in different types of studies together with a list of open issues in the field, which are all summarized at the end of the paper.

The Weyl BMS group and Einstein’s equations

Abstract: We propose an extension of the BMS group, which we refer to as Weyl BMS or BMSW for short, that includes super-translations, local Weyl rescalings and arbitrary diffeomorphisms of the 2d sphere metric. After generalizing the Barnich-Troessaert bracket, we show that the Noether charges of the BMSW group provide a centerless representation of the BMSW Lie algebra at every cross section of null infinity. This result is tantamount to proving that the flux-balance laws for the Noether charges imply the validity of the asymptotic Einstein’s equations at null infinity. The extension requires a holographic renormalization procedure, which we construct without any dependence on background fields. The renormalized phase space of null infinity reveals new pairs of conjugate variables. Finally, we show that BMSW group elements label the gravitational vacua.

Safeguarding freshwater life beyond 2020 : recommendations for the new global biodiversity framework from the European experience

Abstract: Plans are currently being drafted for the next decade of action on biodiversity-both the post-2020 Global Biodiversity Framework of the Convention on Biological Diversity (CBD) and Biodiversity Strategy of the European Union (EU). Freshwater biodiversity is disproportionately threatened and underprioritized relative to the marine and terrestrial biota, despite supporting a richness of species and ecosystems with their own intrinsic value and providing multiple essential ecosystem services. Future policies and strategies must have a greater focus on the unique ecology of freshwater life and its multiple threats, and now is a critical time to reflect on how this may be achieved. We identify priority topics including environmental flows, water quality, invasive species, integrated water resources management, strategic conservation planning, and emerging technologies for freshwater ecosystem monitoring. We synthesize these topics with decades of first-hand experience and recent literature into 14 special recommendations for global freshwater biodiversity conservation based on the successes and setbacks of European policy, management, and research. Applying and following these recommendations will inform and enhance the ability of global and European post-2020 biodiversity agreements to halt and reverse the rapid global decline of freshwater biodiversity.