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Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10−8. When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10−8 threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.
Bipolar disorder (BD) is a heritable mental illness with complex etiology. While the largest published genome-wide association study identified 64 BD risk loci, the causal SNPs and genes within these loci remain unknown. We applied a suite of statistical and functional fine-mapping methods to these loci, and prioritized 22 likely causal SNPs for BD. We mapped these SNPs to genes, and investigated their likely functional consequences by integrating variant annotations, brain cell-type epigenomic annotations, brain quantitative trait loci, and results from rare variant exome sequencing in BD. Convergent lines of evidence supported the roles of SCN2A, TRANK1, DCLK3, INSYN2B, SYNE1, THSD7A, CACNA1B, TUBBP5, PLCB3, PRDX5, KCNK4, AP001453.3, TRPT1, FKBP2, DNAJC4, RASGRP1, FURIN, FES, YWHAE, DPH1, GSDMB, MED24, THRA, EEF1A2, and KCNQ2 in BD. These represent promising candidates for functional experiments to understand biological mechanisms and therapeutic potential. Additionally, we demonstrated that fine-mapping effect sizes can improve performance and transferability of BD polygenic risk scores across ancestrally diverse populations, and present a high-throughput fine-mapping pipeline (https://github.com/mkoromina/SAFFARI).
Background: Pythium ultimum (P. ultimum) is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species. Results: The P. ultimum genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny with related Phytophthora species, including the potato blight pathogen Phytophthora infestans. Whole transcriptome sequencing revealed expression of 86% of genes, with detectable differential expression of suites of genes under abiotic stress and in the presence of a host. The predicted proteome includes a large repertoire of proteins involved in plant pathogen interactions although surprisingly, the P. ultimum genome does not encode any classical RXLR effectors and relatively few Crinkler genes in comparison to related phytopathogenic oomycetes. A lower number of enzymes involved in carbohydrate metabolism were present compared to Phytophthora species, with the notable absence of cutinases, suggesting a significant difference in virulence mechanisms between P. ultimum and more host specific oomycete species. Although we observed a high degree of orthology with Phytophthora genomes, there were novel features of the P. ultimum proteome including an expansion of genes involved in proteolysis and genes unique to Pythium. We identified a small gene family of cadherins, proteins involved in cell adhesion, the first report in a genome outside the metazoans. Conclusions: Access to the P. ultimum genome has revealed not only core pathogenic mechanisms within the oomycetes but also lineage specific genes associated with the alternative virulence and lifestyles found within the pythiaceous lineages compared to the Peronosporaceae.
Um zu überprüfen, ob sich die Artenzusammensetzung alpiner Kalk-Magerrasen (Blaugras-Horstseggenrasen, Polsterseggenrasen) im Nationalpark Berchtesgaden während der letzten drei Jahrzehnte geändert hat, wurden Vegetationsaufnahmen aus den 1980er Jahren 2013/14 zum zweiten Mal wiederholt vegetationskundlich erfasst.
Ziel der Arbeit war es, durch den Vergleich der Aufnahmenkollektive Vegetationsveränderungen während der letzten drei Jahrzehnte aufzuzeigen und diese als allogene oder autogene Prozesse zu interpretieren. Dabei wurde insbesondere der Frage nachgegangen, ob anthropogene Stickstoff-Einträge als Hauptursache für mögliche Veränderungen angesehen werden können.
Tatsächlich konnten ausgeprägte floristische Veränderungen im Vergleichszeitraum aufgezeigt werden. So hat sich seit den 1980er Jahre die mittlere Artenzahl sowohl im Polsterseggenrasen als auch im Horstseggenrasen um mehr als 10 Arten pro Aufnahmefläche erhöht. Im Polsterseggenrasen wurde ferner eine signifikante Abnahme der mittleren Kontinentalitätszahlen nachgewiesen.
Die dokumentierten floristischen Veränderungen könnten auf die globale Erwärmung und die damit verbundenen Klimaeffekte zurückzuführen sein. Auch natürlich ablaufende Sukzessionsprozesse könnten die aufgezeigten Änderungen in der Artenzusammensetzung erklären, allerdings ist die Zeitspanne von 30 Jahren zu kurz, als dass eine autogene Sukzession als der Hauptfaktor angesehen werden kann. Denkbar ist aber, dass Sukzessionsprozesse durch die globale Erwärmung heutzutage beschleunigt ablaufen. Stickstoffeinträge oder Landnutzungsänderungen spielen als Erklärungsmodell für die Vegetationsveränderungen dagegen wohl eher eine untergeordnete Rolle.
Seit 11 Jahren werden von Mitgliedern der Eurasian Dry Gassland Group (EDDG) und deren Vorgängerorganisationen Grasland-Sonderteile in Tuexenia herausgegeben. Der diesjährige Sonderteil präsentiert sechs Artikel mit unterschiedlichen Fragestellungen zu Trockenrasen und verwandten Graslandtypen aus sechs europäischen Ländern: Belgien, Bosnien-Herzegowina, Deutschland, Italien, Serbien und Ungarn. Ein Artikel behandelt syntaxonomische Aspekte der Serpentin-Steppenrasen des Balkans (s. auch Umschlagfoto). Zwei Beiträge untersuchen funktionelle Eigenschaften von Pflanzenarten im Grasland, der eine (in belgischen Trockenrasen) die Variationen funktioneller Merkmale in Abhängigkeit von den Umweltbedingungen und der andere die Mengenverhältnisse von funktionellen Merkmalen entlang eines Höhengradienten in den italienischen Alpen. Ein Artikel zeigt mithilfe eines experimentellen Ansatzes, dass artenarmes ungarisches Grasland durch Diasporenzufuhr in artenreiche Wiesen überführt werden kann, während ein anderer Beitrag ökologische Theorien am Grasland in einer ungarischen Stadt überprüft. Der sechste Artikel behandelt schließlich Vegetationsveränderungen von Steppenrasen in Nordostdeutschland nach 20 Jahren.
This Special Feature is the tenth in a series devoted to dry grasslands and edited by members of the European Dry Grassland Group (EDGG; http://www.edgg.org) or its prede-cessor Arbeitsgruppe Trockenrasen that have been published in Tuexenia since 2005 (GAL-VÁNEK et al. 2012). With this issue we celebrate our tenth anniversary of the Tuexenia Dry Grassland Special Features.
Nitrate is an abundant nutrient and electron acceptor throughout Earth’s biosphere. Virtually all nitrate in nature is produced by the oxidation of nitrite by the nitrite oxidoreductase (NXR) multiprotein complex. NXR is a crucial enzyme in the global biological nitrogen cycle, and is found in nitrite-oxidizing bacteria (including comammox organisms), which generate the bulk of the nitrate in the environment, and in anaerobic ammonium-oxidizing (anammox) bacteria which produce half of the dinitrogen gas in our atmosphere. However, despite its central role in biology and decades of intense study, no structural information on NXR is available. Here, we present a structural and biochemical analysis of the NXR from the anammox bacterium Kuenenia stuttgartiensis, integrating X-ray crystallography, cryo-electron tomography, helical reconstruction cryo-electron microscopy, interaction and reconstitution studies and enzyme kinetics. We find that NXR catalyses both nitrite oxidation and nitrate reduction, and show that in the cell, NXR is arranged in tubules several hundred nanometres long. We reveal the tubule architecture and show that tubule formation is induced by a previously unidentified, haem-containing subunit, NXR-T. The results also reveal unexpected features in the active site of the enzyme, an unusual cofactor coordination in the protein’s electron transport chain, and elucidate the electron transfer pathways within the complex.
Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrant CD19 pre-mRNA splicing events, including recently reported excision of a cryptic intron embedded within CD19 exon 2. While “exitrons” are known to exist in hundreds of human transcripts, we discovered, using reporter assays and direct long-read RNA sequencing (dRNA-seq), that the CD19 exitron is an artifact of reverse transcription. Extending our analysis to publicly available datasets, we identified dozens of questionable exitrons, dubbed “falsitrons,” that appear only in cDNA-seq, but never in dRNA-seq. Our results highlight the importance of dRNA-seq for transcript isoform validation.
Purpose: Despite the high number of patients with phalangeal fractures, evidence-based recommendations for the treatment of specific phalangeal fractures could not be concluded from the literature. The purpose of the present study was to assess current epidemiological data, classification of the fracture type, and mode of treatment.
Methods: This study presents a retrospective review of 261 patients with 283 phalangeal fractures ≥ 18 years of age who were treated in our level I trauma centre between 2017 and 2018. The data were obtained by the analysis of the institution’s database, and radiological examinations.
Results: The average age of the patients was 40.4 years (range 18–98). The ratio of male to female patients was 2.7:1. The two most typical injury mechanisms were crush injuries (33%) and falls (23%). Most phalangeal fractures occurred in the distal phalanx (P3 43%). The 4th ray (D4 29%) was most frequently affected. The P3 tuft fractures, and the middle phalanx (P2) base fractures each accounted for 25% of fracture types. A total of 74% of fractures were treated conservatively, and 26% required surgery, with Kirschner wire(s) (37%) as the preferred surgical treatment. The decision for surgical treatment correlated with the degree of angular and/or rotational deformity, intraarticular step, and sub-/luxation of specific phalangeal fractures, but not with age and gender.
Conclusions: Our findings demonstrated the popularity of conservative treatment of phalangeal fractures, while surgery was only required in properly selected cases. The correct definition of precise fracture pattern in addition to topography is essential to facilitate treatment decision-making.
In non-hadronic axion models, which have a tree-level axion-electron interaction, the Sun produces a strong axion flux by bremsstrahlung, Compton scattering, and axiorecombination, the "BCA processes." Based on a new calculation of this flux, including for the first time axio-recombination, we derive limits on the axion-electron Yukawa coupling gae and axion-photon interaction strength ga using the CAST phase-I data (vacuum phase). For ma <~ 10 meV/c2 we find ga gae < 8.1 × 10−23 GeV−1 at 95% CL. We stress that a next-generation axion helioscope such as the proposed IAXO could push this sensitivity into a range beyond stellar energy-loss limits and test the hypothesis that white-dwarf cooling is dominated by axion emission.
The Transylvanian Plateau in Romania is well known to host large areas of a variety of dry grassland types, still traditionally managed by low-intensity mowing or grazing. While this natural heritage is now under threat from changes in agricultural practices, the diversity of Transylvanian dry grasslands is still little understood. There is a lack of both field data sampled with standardised methods and a syntaxonomic treatment with modern statistical methods and supra-regional perspective. Therefore, the European Dry Grassland Group (EDGG) carried out its first international Research Expedition in Transylvania 2009 to study syntaxonomy, vegetation-environment relationships, and biodiversity patterns of these communities. In various locations across Transylvania, we sampled 10-m² vegetation plots (n = 82) and nested-plot series from 0.0001 m² to 100 m² (n = 20), including all vascular plant, bryophyte, and lichen species, as well as structural and soil data. The vegetation classification was carried out with modified TWINSPAN, followed by determination of diagnostic species with phi values and a small-scale re-assignment of relevés with the aim of crispness maximisation. Both TWINSPAN and ordination revealed three major groups of syntaxa, which were matched to three orders from the class of basiphilous dry grasslands, Festuco-Brometea, represented by one alliance each: rocky dry grasslands (Stipo pulcherrimae-Festucetalia pallentis: Seslerion rigidae); xeric grasslands on deep soils (Festucetalia valesiacae: Stipion lessingianae) and meso-xeric grasslands on deep soils (Brachypodietalia pinnati: Cirsio-Brachypodion pinnati). We accepted nine association-level units plus two that potentially merit association status but were only represented by one relevé each. Most of the units could be identified with one or several previously described associations. To support nomenclatural stability, we provide a nomenclatural revision and designate nomenclatural types where previously there were none. Further, we used DCA ordination and analysis of variance to determine the main environmental drivers of floristic differentiation and to determine ecological and structural differences between the vegetation types. The strongest differentiation occurred along the aridity gradient with the dense, particularly diverse stands on more or less level sites on the one hand (Brachypodietalia pinnati) and the more open, less diverse stands on steep south-facing slopes on the other end of the gradient (Stipo pulcherrimae- Festucetalia pallentis, Festucetalia valesiacae). The two xeric orders were then separated along the second DCA axis, with the Stipo pulcherrimae-Festucetalia pallentis inhabiting the stone-rich sites at higher altitudes while the Festucetalia valesiacae occur on soft, deep substrata at lower altitudes. The analysed dry grassland communities have extraordinarily high -diversity at all spatial scales for all plants and for vascular plants, but are relatively poor in bryophytes and lichens. Some formerly mown stands of the Festuco sulcatae-Brachypodietum pinnati (Brachypodietalia pinnati) are even richer in vascular plant species than any other recorded vegetation type worldwide on the spatial scales of 0.1 m² (43) and 10 m² (98); the respective relevés are documented here for the first time. Also, the b-diversity of the grasslands was unexpectedly high, with a mean z-value of 0.275. Despite its limited extent, the methodological thoroughness of this study allows us to shed new light on the syntaxonomy of dry grasslands in Romania and to raise the awareness that Transylvania still hosts High Nature Value grasslands that are bio - diversity hotspots at a global scale but at the same time are highly endangered through changes in agricultural practices.
Artificial Intelligence (AI) has the potential to greatly improve the delivery of healthcare and other services that advance population health and wellbeing. However, the use of AI in healthcare also brings potential risks that may cause unintended harm. To guide future developments in AI, the High-Level Expert Group on AI set up by the European Commission (EC), recently published ethics guidelines for what it terms “trustworthy” AI. These guidelines are aimed at a variety of stakeholders, especially guiding practitioners toward more ethical and more robust applications of AI. In line with efforts of the EC, AI ethics scholarship focuses increasingly on converting abstract principles into actionable recommendations. However, the interpretation, relevance, and implementation of trustworthy AI depend on the domain and the context in which the AI system is used. The main contribution of this paper is to demonstrate how to use the general AI HLEG trustworthy AI guidelines in practice in the healthcare domain. To this end, we present a best practice of assessing the use of machine learning as a supportive tool to recognize cardiac arrest in emergency calls. The AI system under assessment is currently in use in the city of Copenhagen in Denmark. The assessment is accomplished by an independent team composed of philosophers, policy makers, social scientists, technical, legal, and medical experts. By leveraging an interdisciplinary team, we aim to expose the complex trade-offs and the necessity for such thorough human review when tackling socio-technical applications of AI in healthcare. For the assessment, we use a process to assess trustworthy AI, called 1Z-Inspection® to identify specific challenges and potential ethical trade-offs when we consider AI in practice.
Pathogens possess the ability to adapt and survive in some host species but not in others–an ecological trait known as host tropism. Transmitted through ticks and carried mainly by mammals and birds, the Lyme disease (LD) bacterium is a well-suited model to study such tropism. Three main causative agents of LD, Borrelia burgdorferi, B. afzelii, and B. garinii, vary in host ranges through mechanisms eluding characterization. By feeding ticks infected with different Borrelia species, utilizing feeding chambers and live mice and quail, we found species-level differences in bacterial transmission. These differences localize on the tick blood meal, and specifically complement, a defense in vertebrate blood, and a polymorphic bacterial protein, CspA, which inactivates complement by binding to a host complement inhibitor, Factor H (FH). CspA selectively confers bacterial transmission to vertebrates that produce FH capable of allele-specific recognition. CspA is the only member of the Pfam54 gene family to exhibit host-specific FH-binding. Phylogenetic analyses revealed convergent evolution as the driver of such uniqueness, and that FH-binding likely emerged during the last glacial maximum. Our results identify a determinant of host tropism in Lyme disease infection, thus defining an evolutionary mechanism that shapes host-pathogen associations.
An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations.
Wastewater-based epidemiology (WBE) has demonstrated its importance to support SARS-CoV-2 epidemiology complementing individual testing strategies. Due to their immune-evasive potential and the resulting significance for public health, close monitoring of SARS-CoV-2 variants of concern (VoC) is required to evaluate the regulation of early local countermeasures. In this study, we demonstrate a rapid workflow for wastewater-based early detection and monitoring of the newly emerging SARS-CoV-2 VoCs Omicron in the end of 2021 at the municipal wastewater treatment plant (WWTP) Emschermuendung (KLEM) in the Federal State of North-Rhine-Westphalia (NRW, Germany).
Initially, available primers detecting Omicron-related mutations were rapidly validated in a central laboratory. Subsequently, RT-qPCR analysis of purified SARS-CoV-2 RNA was performed in a decentral PCR laboratory in close proximity to KLEM. This decentralized approach enabled the early detection of K417N present in Omicron in samples collected on 8th December 2021 and the detection of further mutations (N501Y, Δ69/70) in subsequent biweekly sampling campaigns. The presence of Omicron in wastewater was confirmed by next generation sequencing (NGS) in a central laboratory with samples obtained on 14th December 2021. Moreover, the relative increase of the mutant fraction of Omicron was quantitatively monitored over time by dPCR in a central PCR laboratory starting on 12th December 2021 confirming Omicron as the dominant variant by the end of 2021.
In conclusions, WBE plays a crucial role in surveillance of SARS-CoV-2 variants and is suitable as an early warning system to identify variant emergence. In particular, the successive workflow using RT-qPCR, RT-dPCR and NGS demonstrates the strength of WBE as a versatile tool to monitor variant spreading.
Wastewater-based SARS-CoV-2 epidemiology (WBE) has been established as an important tool to support individual testing strategies. The Omicron sub-variants BA.4/BA.5 have spread globally, displacing the preceding variants. Due to the severe transmissibility and immune escape potential of BA.4/BA.5, early monitoring was required to assess and implement countermeasures in time. In this study, we monitored the prevalence of SARS-CoV-2 BA.4/BA.5 at six municipal wastewater treatment plants (WWTPs) in the Federal State of North Rhine-Westphalia (NRW, Germany) in May and June 2022. Initially, L452R-specific primers/probes originally designed for SARS-CoV-2 Delta detection were validated using inactivated authentic viruses and evaluated for their suitability for detecting BA.4/BA.5. Subsequently, the assay was used for RT-qPCR analysis of RNA purified from wastewater obtained twice a week at six WWTPs. The occurrence of L452R carrying RNA was detected in early May 2022, and the presence of BA.4/BA.5 was confirmed by variant-specific single nucleotide polymorphism PCR (SNP-PCR) targeting E484A/F486V and NGS sequencing. Finally, the mutant fractions were quantitatively monitored by digital PCR, confirming BA.4/BA.5 as the majority variant by 5 June 2022. In conclusion, the successive workflow using RT-qPCR, variant-specific SNP-PCR, and RT-dPCR demonstrates the strength of WBE as a versatile tool to rapidly monitor variants spreading independently of individual test capacities.
Electromagnetic calorimeter (ECAL) is being developed to complement dilepton spectrometer HADES. ECAL will enable the HADES@FAIR experiment to measure data on neutral meson production in heavy ion collisions at the energy range of 2-10 AGeV on the beam of future accelerator SIS100@FAIR. We will report results of the last beam test with quasi-monoenergetic photons carried out in MAMI facility at Johannes Gutenberg Universität Mainz.
We present first data on sub-threshold production of Ks0 mesons and Λ hyperons in Au+Au collisions at sNN=2.4 GeV. We observe an universal 〈Apart〉 scaling of hadrons containing strangeness, independent of their corresponding production thresholds. Comparing the yields, their 〈Apart〉 scaling, and the shapes of the rapidity and the pt spectra to state-of-the-art transport model (UrQMD, HSD, IQMD) predictions, we find that none of them can simultaneously describe these observables with reasonable χ2 values.
We investigate identical pion HBT intensity interferometry in central Au+Au collisions at 1.23A GeV. High-statistics π−π− and π+π+ data are measured with HADES at SIS18/GSI. The radius parameters, derived from the correlation function depending on relative momenta in the longitudinally comoving system and parametrized as three-dimensional Gaussian distribution, are studied as function of transverse momentum. A substantial charge-sign difference of the source radii is found, particularly pronounced at low transverse momentum. The extracted source parameters agree well with a smooth extrapolation of the center-of-mass energy dependence established at higher energies, extending the corresponding excitation functions down towards a very low energy.
The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.