Exploring intra- and intergenomic variation in haplotype-resolved pangenomes.

With advances in long-read sequencing and assembly techniques, haplotype-resolved (phased) genome assemblies are becoming more common, also in the field of plant genomics. Computational tools to effectively explore these phased genomes, particularly for polyploid genomes, are currently limited. Here we describe a new strategy adopting a pangenome approach.

Dynamics of SARS-CoV-2 lineages in children and adults in 2021 and 2022.

Purpose: We aimed to describe SARS-CoV-2 lineages and diversity in children and adults in Estonia and similarity to travel-related cases and neighbouring countries.

Methods: SARS-CoV-2 sequences in 2021-2022 from a nationwide study were included. The proportion of predominant lineages in Estonian regions and among travel-related cases was described by multinomial logistic regression.

Lactuca super-pangenome reduces bias towards reference genes in lettuce research.

Background: Breeding of lettuce (Lactuca sativa L.), the most important leafy vegetable worldwide, for enhanced disease resistance and resilience relies on multiple wild relatives to provide the necessary genetic diversity. In this study, we constructed a super-pangenome based on four Lactuca species (representing the primary, secondary and tertiary gene pools) and comprising 474 accessions.

Incorporation of nitrogen in antinutritional Solanum alkaloid biosynthesis.

Steroidal glycoalkaloids (SGAs) are specialized metabolites produced by hundreds of Solanum species including food crops, such as tomato, potato and eggplant. Unlike true alkaloids, nitrogen is introduced at a late stage of SGA biosynthesis through an unknown transamination reaction. Here, we reveal the mechanism by which GLYCOALKALOID METABOLISM12 (GAME12) directs the biosynthesis of nitrogen-containing steroidal alkaloid aglycone in Solanum.

Metadata for Data dIscoverability aNd Study rEplicability in obseRVAtional Studies (MINERVA): Development and Pilot of a Metadata List and Catalogue in Europe.

Purpose: Metadata for data dIscoverability aNd study rEplicability in obseRVAtional studies (MINERVA), a European Medicines Agency-funded project (EUPAS39322), defined a set of metadata to describe real-world data sources (RWDSs) and piloted metadata collection in a prototype catalogue to assist investigators from data source discoverability through study conduct.

Methods: A list of metadata was created from a review of existing metadata catalogues and recommendations, structured interviews, a stakeholder survey, and a technical workshop. The prototype was designed to comply with the FAIR principles (findable, accessible, interoperable, reusable), using MOLGENIS software.

Cross-species transcriptomics reveals differential regulation of essential photosynthesis genes in Hirschfeldia incana.

Photosynthesis is the only yield-related trait not yet substantially improved by plant breeding. Previously, we have established H. incana as the model plant for high photosynthetic light-use efficiency (LUE).

Adaptation of Fusarium Head Blight Pathogens to Changes in Agricultural Practices and Human Migration.

Fusarium head blight (FHB) is one of the most destructive wheat diseases worldwide. To understand the impact of human migration and changes in agricultural practices on crop pathogens, here population genomic analysis with 245 representative strains from a collection of 4,427 field isolates of Fusarium asiaticum, the causal agent of FHB in Southern China is conducted. Three populations with distinct evolution trajectories are identifies over the last 10,000 years that can be correlated with historically documented changes in agricultural practices due to human migration caused by the Southern Expeditions during the Jin Dynasty.

Pseudomolecule-scale genome assemblies of Drepanocaryum sewerzowii and Marmoritis complanata.

The Nepetoideae, a subfamily of Lamiaceae (mint family), is rich in aromatic plants, many of which are sought after for their use as flavors and fragrances or for their medicinal properties. Here, we present genome assemblies for two species in Nepetiodeae: Drepanocaruym sewerzowii and Marmoritis complanata. Both assemblies were generated using Oxford Nanopore Q20 + reads with contigs anchored to nine pseudomolecules that resulted in 335 Mb and 305 Mb assemblies, respectively, and BUSCO scores above 95% for both the assembly and annotation.

Oxygen-to-ammonium-nitrogen ratio as an indicator for oxygen supply management in microoxic bioanodic ammonium oxidation.

Microbial electrolysis cells (MECs) have been proven effective for oxidizing ammonium (NH), where the anode acts as an electron acceptor, reducing the energy input by substituting oxygen (O). However, O has been proved to be essential for achieving high removal rates MECs. Thus, precise control of oxygen supply is crucial for optimizing treatment performance and minimizing energy consumption.

Orbital-selective time-domain signature of nematicity dynamics in the charge-density-wave phase of LaEuSrCuO.

Understanding the interplay between charge, nematic, and structural ordering tendencies in cuprate superconductors is critical to unraveling their complex phase diagram. Using pump-probe time-resolved resonant X-ray scattering on the (0 0 1) Bragg peak at the Cu [Formula: see text] and O [Formula: see text] resonances, we investigate nonequilibrium dynamics of [Formula: see text] nematic order and its association with both charge density wave (CDW) order and lattice dynamics in La[Formula: see text]Eu[Formula: see text]Sr[Formula: see text]CuO[Formula: see text]. The orbital selectivity of the resonant X-ray scattering cross-section allows nematicity dynamics associated with the planar O 2[Formula: see text] and Cu 3[Formula: see text] states to be distinguished from the response of anisotropic lattice distortions.

Momentum-dependent scaling exponents of nodal self-energies measured in strange metal cuprates and modelled using semi-holography.

The anomalous strange metal phase found in high-T cuprates does not follow the conventional condensed-matter principles enshrined in the Fermi liquid and presents a great challenge for theory. Highly precise experimental determination of the electronic self-energy can provide a test bed for theoretical models of strange metals, and angle-resolved photoemission can provide this as a function of frequency, momentum, temperature and doping. Here we show that constant energy cuts through the nodal spectral function in (Pb,Bi)SrLaCuO have a non-Lorentzian lineshape, consistent with a self-energy that is k dependent.

SARS-CoV-2 clade dynamics and their associations with hospitalisations during the first two years of the COVID-19 pandemic.

Background: The COVID-19 pandemic was characterised by rapid waves of disease, carried by the emergence of new and more infectious SARS-CoV-2 virus variants. How the pandemic unfolded in various locations during its first two years has yet to be sufficiently covered. To this end, here we are looking at the circulating SARS-CoV-2 variants, their diversity, and hospitalisation rates in Estonia in the period from March 2000 to March 2022.

Integration of biocompatible hydrogen evolution catalyst developed from metal-mix solutions with microbial electrosynthesis.

Microbial conversion of CO to multi-carbon compounds such as acetate and butyrate is a promising valorisation technique. For those reactions, the electrochemical supply of hydrogen to the biocatalyst is a viable approach. Earlier we have shown that trace metals from microbial growth media spontaneously form in situ electro-catalysts for hydrogen evolution.

Revealing cellular (poly)sulphide storage in electrochemically active sulphide oxidising bacteria using rotating disc electrodes.

Sulphide oxidising bacteria (SOB) have the potential to be used for bioelectrochemical removal, i.e. oxidation, of sulphide from waste streams.

The genomic and enzymatic basis for iridoid biosynthesis in cat thyme (Teucrium marum).

Iridoids are non-canonical monoterpenoids produced by both insects and plants. An example is the cat-attracting and insect-repelling volatile iridoid nepetalactone, produced by Nepeta sp. (catmint) and aphids.

Development of an explainable artificial intelligence model for Asian vascular wound images.

Chronic wounds contribute to significant healthcare and economic burden worldwide. Wound assessment remains challenging given its complex and dynamic nature. The use of artificial intelligence (AI) and machine learning methods in wound analysis is promising.

Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding.

Lettuce (Lactuca sativa L.) is a leafy vegetable crop with ongoing breeding efforts related to quality, resilience, and innovative production systems. To breed resilient and resistant lettuce in the future, valuable genetic variation found in close relatives could be further exploited.

An Efficient Triplex TaqMan Quantitative PCR to Detect a Blackleg-Causing Lineage of in Potato Based on a Pangenome Analysis.

is an important bacterial pathogen causing blackleg (BL) in potatoes. Nevertheless, is often detected in seed lots that do not develop any of the typical blackleg symptoms in the potato crop when planted. Field bioassays identified that strains can be categorized into two distinct classes, some able to cause blackleg symptoms and some unable to do it.

Naturalistic driving study on the impact of an aftermarket blind spot monitoring system on the driver's behaviour of heavy goods vehicles and buses on reducing conflicts with pedestrians and cyclists.

The risk being severely or fatally injured in crashes with heavy goods vehicle and buses is much higher compared to other vehicles. Especially vulnerable road users such as pedestrian and cyclists are at high risk. In the European Union 4600 pedestrian and more than 2000 cyclists were killed in 2019.

Enhancement of Ammonium Oxidation at Microoxic Bioanodes.

Bioelectrochemical systems (BESs) are considered to be energy-efficient to convert ammonium, which is present in wastewater. The application of BESs as a technology to treat wastewater on an industrial scale is hindered by the slow removal rate and lack of understanding of the underlying ammonium conversion pathways. This study shows ammonium oxidation rates up to 228 ± 0.

Vicarious touch: Overlapping neural patterns between seeing and feeling touch.

Simulation theories propose that vicarious touch arises when seeing someone else being touched triggers corresponding representations of being touched. Prior electroencephalography (EEG) findings show that seeing touch modulates both early and late somatosensory responses (measured with or without direct tactile stimulation). Functional Magnetic Resonance Imaging (fMRI) studies have shown that seeing touch increases somatosensory cortical activation.

The effect of anxiety and depression on cognition in older adults with severe-to-profound hearing loss.

Purpose: To evaluate the effect of anxiety and/or depression on cognition in older adults with severe-to-profound hearing loss.

Methodology: In total, 83 older subjects (age of 55 years or older) with post-lingual, bilateral, severe-to-profound hearing loss were enrolled in this study between April 2014 and March 2021. The Repeatable Battery for Assessment of Neuropsychological Status for Hearing-impaired individuals (RBANS-H) and the Hospital Anxiety and Depression Scale (HADS) were used to measure cognition and anxiety/depression.