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Abstract Bacterial RNA helicase ρ is a genome sentinel that terminates the synthesis of damaged and junk RNAs that are not translated by the ribosome. It is unclear how ρ is regulated during dormancy or stress, when translation is inefficient and RNAs are vulnerable to ρ-mediated release. We use cryogenic electron microscopy, biochemical, and genetic approaches to show that substitutions of residues in the connector between two ρ domains or ADP promote the formation of extended Escherichia coli ρ filaments. By contrast, (p)ppGpp induces the formation of transient ρ dodecamers. Our results demonstrate that ADP and (p)ppGpp nucleotides bound at subunit interfaces inhibit ρ ring closure that underpins the hexamer activation, thus favoring the assembly of inactive higher-order oligomers. Connector substitutions and antibiotics that inhibit RNA and protein syntheses trigger ρ aggregation in the cell. These and other recent data implicate aggregation as a widespread strategy to tune ρ activity.

Abstract Many bacteriophages modulate host transcription to favor expression of their own genomes. Phage satellite P4 polarity suppression protein, Psu, a building block of the viral capsid, inhibits hexameric transcription termination factor, ρ, by presently unknown mechanisms. Our cryogenic electron microscopy structures of ρ-Psu complexes show that Psu dimers clamp two inactive, open ρ rings and promote their expansion to higher-oligomeric states. ATPase, nucleotide binding and nucleic acid binding studies revealed that Psu hinders ρ ring closure and traps nucleotides in their binding pockets on ρ. Structure-guided mutagenesis in combination with growth, pull-down, and termination assays further delineated the functional ρ-Psu interfaces in vivo. Bioinformatic analyses revealed that Psu is associated with a wide variety of phage defense systems across Enterobacteriaceae, suggesting that Psu may regulate expression of anti-phage genes. Our findings show that modulation of the ρ oligomeric state via diverse strategies is a pervasive gene regulatory principle in bacteria.

BackgroundA strong association between multiple sclerosis (MS) and Epstein-Barr virus (EBV) has been established but the exact role of EBV in MS remains controversial. Recently, molecular mimicry between EBNA1 and specific GlialCAM, CRYAB and ANO2 peptides has been suggested as a possible pathophysiological mechanism. The aim of this study was to analyse anti-EBV antibodies in MS patients against (I) EBV lifecycle proteins, (II) putative cross-reactive peptides, and (III) during treatment.MethodsIn this retrospective cross-sectional study, 258 serum samples were included consisting of EBV-negative (n = 25) and EBV-positive (n = 36) controls, 192 MS samples including untreated relapsing-remitting MS (RRMS) with and without relapses, secondary progressive MS (SPMS) and primary progressive MS (PPMS) patients, and 106 patients on 8 different treatment regimens. IgG and IgM antibody titers against EBV docking/fusion proteins (gp350, gh/gp42, gh/gL/gp42), immediate early antigen (BZLF1), early antigens (EA p85, EA P138, EA P54), capsid antigens (VCA P18, VCA P23, VCA gp125) and late antigens (EBNA1) were measured. Specific EBNA1 and GlialCAM, CRYAB and ANO2 peptides were synthesized and also incorporated in our custom magnetic bead based multiplex assay.ResultsWe observed significantly elevated IgG antibody titers in EBV-positive controls, RRMS with and without relapse, SPMS and PPMS patients for all lifecycle antigens except for several early antigens when compared to EBV-negative controls. Significantly higher IgG antibody titers were observed in RRMS patients for fusion proteins and EBNA1 peptides when compared to EBV-positive controls. An MS specific response was observed for ANO2 but not for GlialCAM or CRYAB. No significant treatment effects or a specific IgM response were detectable.ConclusionThe MS-specific, differential antibody response to EBV antigens confirms an altered immunological response to EBV in MS patients. EBV reactivation does not appear to play an important role in MS pathogenesis and no differential antibody signatures were observed between MS disease phases. The MS-specific anti-ANO2 antibody response suggests a potential role for EBNA1 as an antigenic driver, although the exact role of anti-ANO2 antibodies needs to be determined. The precise pathophysiological role of EBV in MS remains uncertain and requires further investigation.

Entrepreneurs can have a long-lasting impact on organizations they found, despite significant changes in the environment. Imprinting theory offers an explanation for this. Yet, knowledge of how imprinting occurs is still limited. Scholars have therefore called for more attention to processes and micro-level theories of imprinting, including the role of individuals. I therefore ask, how do entrepreneurs imprint organizations? Drawing on material from company archives, I conducted a longitudinal, historical case study of Zeiss, a German manufacturer of optical instruments, covering the period 1846–1990. I show how individual blueprints of the founder and his business partner were translated into persistent features of the organization through early decisions, teaching, role modeling, and formalized rules, which left structural, behavioral, and product imprints. The article extends theory on imprinting by shedding light on blueprints as sources of imprints, the multiple mechanisms by which individuals persistently shape core features of an organization, and the multiple organizational dimensions on which imprints are left. [ABSTRACT FROM AUTHOR]

We present magnesium alginate as an aqueous polymer electrolyte for use in magnesium batteries. Alginates are polysaccharides extracted from algae, which form hydrogel materials upon interaction with divalent and trivalent cations. They are renewable, non-toxic, biocompatible materials that are widely used in the food and pharmaceutical industries. Mg2+ is weakly bound to an alginate polymer, which results in a hydrogel-like material that contains mobile magnesium ions. We propose that this is the ideal situation for an electrolyte that behaves in a similar way as a ‘water-in-salt’ system. Magnesium alginate was successfully synthesized and characterized by FTIR, XRD, and PDF. Ionic conductivity was measured with EIS measurements; a 2 wt% magnesium electrolyte shows a conductivity of 1.8 mS/cm. During conductivity experiments, we noticed the formation of a black layer on magnesium electrodes, which can improve the ionic conductivity between the electrodes. We carefully characterized this layer with XPS and saw that it mainly consists of alginate derivatives.

Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets.

Abstract Objective Progression prediction is a significant unmet need in people with progressive multiple sclerosis (pwPMS). Studies on glial fibrillary acidic protein (GFAP) have either been limited to single center with relapsing MS or were based solely on Expanded Disability Status Scale (EDSS), which limits its generalizability to state‐of‐the‐art clinical settings and trials applying combined outcome parameters. Methods Serum GFAP and NfL (neurofilament light chain) were investigated in EmBioProMS participants with primary (PP) or secondary progressive MS. Six months confirmed disability progression (CDP) was defined using combined outcome parameters (EDSS, timed‐25‐foot walk test (T25FW), and nine‐hole‐peg‐test (9HPT)). Results 243 subjects (135 PPMS, 108 SPMS, age 55.5, IQR [49.7–61.2], 135 female, median follow‐up: 29.3 months [17.9–40.9]) were included. NfL (age‐) and GFAP (age‐ and sex‐) adjusted Z scores were higher in pwPMS compared to HC (p 3 was associated with higher risk for CDP in participants with low NfL Z score (i.e., ≤1.0) (HR: 2.38 [1.12–5.08], p = 0.025). In PPMS, GFAP Z score >3 was associated with higher risk for CDP (HR: 2.88 [1.21–6.84], p = 0.016). Risk was further increased in PPMS subjects with high GFAP when NfL is low (HR: 4.31 [1.53–12.13], p = 0.006). Interpretation Blood GFAP may help identify pwPPMS at risk of progression. Combination of high GFAP and low NfL levels could distinguish non‐active pwPMS with particularly high progression risk.

Bias in regional climate model (RCM) data makes bias correction (BC) a necessary pre-processing step in climate change impact studies. Among a variety of different BC methods, quantile mapping (QM) is a popular and powerful BC method. Studies have shown that QM may be vulnerable to reductions in calibration sample size. The question is whether this also affects the climate change signal (CCS) of the RCM data. We applied four different QM methods without subsampling and with three different subsampling timescales to an ensemble of seven climate projections. BC generally improved the RCM data relative to observations. However, the CCS was significantly modified by the BC for certain combinations of QM method and subsampling timescale. In conclusion, QM improves the RCM data that are fundamental for climate change impact studies, but the optimal subsampling timescale strongly depends on the chosen QM method.

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

The dodecameric protein kinase CaMKII is expressed throughout the body. The alpha isoform is responsible for synaptic plasticity and participates in memory through its phosphorylation of synaptic proteins. Its elaborate subunit organization and propensity for autophosphorylation allow it to preserve neuronal plasticity across space and time. The prevailing hypothesis for the spread of CaMKII activity, involving shuffling of subunits between activated and naive holoenzymes, is broadly termed subunit exchange. In contrast to the expectations of previous work, we found little evidence for subunit exchange upon activation, and no effect of restraining subunits to their parent holoenzymes. Rather, mass photometry, crosslinking mass spectrometry, single molecule TIRF microscopy and biochemical assays identify inter-holoenzyme phosphorylation (IHP) as the mechanism for spreading phosphorylation. The transient, activity-dependent formation of groups of holoenzymes is well suited to the speed of neuronal activity. Our results place fundamental limits on the activation mechanism of this kinase.

Through the use of a reversible chemical dimerizer, the splicing factor PRPF38A is re-localized to the nuclear lamina, paving the way for a systematic analysis of spatio-temporal splicing regulation.

Bacterial RNA helicase ρ is a genome sentinel that terminates the synthesis of damaged and junk RNAs that are not translated by the ribosome. It is unclear how ρ is regulated during dormancy or stress, when translation is inefficient and RNAs are vulnerable to ρ-mediated release. We use cryogenic electron microscopy, biochemical, and genetic approaches to show that substitutions of residues in the connector between two ρ domains or ADP promote the formation of extended Escherichia coli ρ filaments. By contrast, (p)ppGpp induces the formation of transient ρ dodecamers. Our results demonstrate that ADP and (p)ppGpp nucleotides bound at subunit interfaces inhibit ρ ring closure that underpins the hexamer activation, thus favoring the assembly of inactive higher-order oligomers. Connector substitutions and antibiotics that inhibit RNA and protein syntheses trigger ρ aggregation in the cell. These and other recent data implicate aggregation as a widespread strategy to tune ρ activity. Bacterial transcription factor Rho (ρ) is a key regulator of transcription termination. Here, the authors show that Escherichia coli ρ forms inactive oligomers and filaments in the presence of stress-associated nucleotides (p)ppGpp and ADP. [ABSTRACT FROM AUTHOR]

Behavioural hydrological modelling aims not only at predicting the discharge of an area within a model, but also at understanding and correctly depicting the underlying hydrological processes. Here, we present a new approach for the calibration and evaluation of water balance models, exemplarily applied to the Riveris catchment in Rhineland-Palatinate, Germany. For our approach, we used the behavioural model WaSiM. The first calibration step is the adjustment of the evapotranspiration (ETa) parameters based on MODIS evaporation data. This aims at providing correct evaporation behaviour of the model and at closing the water balance at the gauging station. In a second step, geometry and transmissivity of the aquifer are determined using the Characteristic Delay Curve (CDC). The portion of groundwater recharge was calibrated using the Delayed Flow Index (DFI). In a third step, inappropriate pedotransfer functions (PTFs) could be filtered out by comparing dominant runoff process patterns under a synthetic precipitation event with a soil hydrological reference map, Then, the discharge peaks were adjusted based on so-called signature indices. This ensured a correct depiction of high-flow volume in the model. Finally, the overall model performance was determined using signature indices and efficiency measures. The results show a very good model fit with values for the NSE of 0.88 and 0.9 for the KGE in the calibration period and an NSE of 0.81 and a KGE of 0.89 for the validation period. Simultaneously, our calibration approach ensured a correct depiction of the underlying processes (groundwater behaviour, runoff patterns). This means that our calibration approach allows selecting a behaviourally faithful one from many possible parameterisation variants. [ABSTRACT FROM AUTHOR]

Many bacteriophages modulate host transcription to favor expression of their own genomes. Phage satellite P4 polarity suppression protein, Psu, a building block of the viral capsid, inhibits hexameric transcription termination factor, ρ, by presently unknown mechanisms. Our cryogenic electron microscopy structures of ρ-Psu complexes show that Psu dimers clamp two inactive, open ρ rings and promote their expansion to higher-oligomeric states. ATPase, nucleotide binding and nucleic acid binding studies revealed that Psu hinders ρ ring closure and traps nucleotides in their binding pockets on ρ. Structure-guided mutagenesis in combination with growth, pull-down, and termination assays further delineated the functional ρ-Psu interfaces in vivo. Bioinformatic analyses revealed that Psu is associated with a wide variety of phage defense systems across Enterobacteriaceae, suggesting that Psu may regulate expression of anti-phage genes. Our findings show that modulation of the ρ oligomeric state via diverse strategies is a pervasive gene regulatory principle in bacteria. Many bacteriophages can modulate host transcription. Here, the authors uncover the anti-termination mechanism of phage satellite P4 protein, Psu. Psu dimers clamp two open rings of the termination factor ρ, promote ρ hyper-oligomerization, and trap nucleotides in ρ's binding pockets. [ABSTRACT FROM AUTHOR]

We present magnesium alginate as an aqueous polymer electrolyte for use in magnesium batteries. Alginates are polysaccharides extracted from algae, which form hydrogel materials upon interaction with divalent and trivalent cations. They are renewable, non-toxic, biocompatible materials that are widely used in the food and pharmaceutical industries. Mg2+ is weakly bound to an alginate polymer, which results in a hydrogel-like material that contains mobile magnesium ions. We propose that this is the ideal situation for an electrolyte that behaves in a similar way as a 'water-in-salt' system. Magnesium alginate was successfully synthesized and characterized by FTIR, XRD, and PDF. Ionic conductivity was measured with EIS measurements; a 2 wt% magnesium electrolyte shows a conductivity of 1.8 mS/cm. During conductivity experiments, we noticed the formation of a black layer on magnesium electrodes, which can improve the ionic conductivity between the electrodes. We carefully characterized this layer with XPS and saw that it mainly consists of alginate derivatives. [ABSTRACT FROM AUTHOR]