Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus

The order Picornavirales includes several plant viruses that are currently classified into the families Comoviridae (genera Comovirus, Fabavirus and Nepovirus) and Sequiviridae (genera Sequivirus and Waikavirus) and into the unassigned genera Cheravirus and Sadwavirus. These viruses share properties in common with other picornavirales (particle structure, positive-strand RNA genome with a polyprotein expression strategy, a common replication block including type III helicase, a 3C-like cysteine proteinase and type I RNA-dependent RNA polymerase). However, they also share unique properties that distinguish them from other picornavirales. They infect plants and use specialized proteins or protein domains to move through their host. In phylogenetic analysis based on their replication proteins, these viruses form a separate distinct lineage within the picornavirales branch. To recognize these common properties at the taxonomic level, we propose to create a new family termed “Secoviridae” to include the genera Comovirus, Fabavirus, Nepovirus, Cheravirus, Sadwavirus, Sequivirus and Waikavirus. Two newly discovered plant viruses share common properties with members of the proposed family Secoviridae but have distinct specific genomic organizations. In phylogenetic reconstructions, they form a separate sub-branch within the Secoviridae lineage. We propose to create a new genus termed Torradovirus (type species, Tomato torrado virus) and to assign this genus to the proposed family Secoviridae

Regulatory B Cells - Implications in Autoimmune and Allergic Disorders

B lymphocytes are a major player in the immune system and their best understood effector functions are antibody production, presentation of antigens to T cells and modulation of immune responses via cytokine production. Most B cell functions are considered to amplify immune responses, but it has also been demonstrated that due to production of immunosuppressive cytokines or antibodies, B cells can down-regulate immune responses and have the ability to induce tolerance. These B cells with regulatory capacity (Breg cells) have been shown to suppress effector functions of various target cells including T cells, dendritic cells and macrophages, and can even convert effector T cells into regulatory T cells. The most prominent mechanism of Breg mediated suppression is the release of anti-inflammatory cytokines such as IL-10 and TGF-β. Additional suppression mechanisms via cell-cell contact, involving surface molecules such as program death-1 (PD-1), CD80/CD86 and FasL mediating target cell apoptosis, have been described as well. Most importantly, Breg cells have been implicated in various inflammatory conditions, such as allergic and autoimmune diseases. There is evidence for Breg deficiencies in human SLE patients and various adoptive transfer experiments in mouse models of autoimmune and allergic diseases indicate that Breg cells are capable of suppressing disease development. In this review we endeavour to give an overview of the current knowledge about regulatory B cell immunobiology and their implications in allergic and autoimmune conditions.published_or_final_versio

Cationic Copper Iminophosphorane Complexes as CuAAC Catalysts:A Mechanistic Study

We have combined Cu K-edge X-ray absorption spectroscopy with NMR spectroscopy (1H and 31P) to study the Cu-catalyzed azide–alkyne cycloaddition (CuAAC) reaction under operando conditions. A variety of novel, well-defined CuI iminophosphorane complexes were prepared. These ligands, based on the in situ Staudinger reduction when [Cu(PPh3)3Br] is employed, were found to be active catalysts in the CuAAC reaction. Here, we highlight recent advances in mechanistic understanding of the CuAAC reaction using spectroscopic and kinetic investigations under strict air-free and operando conditions. A mononuclear Cu triazolide intermediate is identified to be the resting state during catalysis; cyclization and protonation both have an effect on the rate of the reaction. A key finding of this study includes a novel group of highly modular CuI complexes that are active in the base-free CuAAC reaction

Confinement Effects in Catalysis Using Well-Defined Materials and Cages

This review focuses on the effects that confinement of molecular and heterogeneous catalysts with well-defined structure has on the selectivity and activity of these systems. A general introduction about catalysis and how the working principles of enzymes can be used as a source of inspiration for the preparation of catalysts with enhanced performance is provided. Subsequently, relevant studies demonstrate the importance of second coordination sphere effects in a broad sense (in homogeneous and heterogeneous catalysis). Firstly, we discuss examples involving zeolites, MOFs and COFs as heterogeneous catalysts with well-defined structures where confinement influences catalytic performance. Then, specific cases of homogeneous catalysts where non-covalent interactions determine the selectivity and activity are treated in detail. This includes examples based on cyclodextrins, calix[n]arenes, cucurbit[n]urils, and self-assembled container molecules. Throughout the review, the impact of confined spaces is emphasized and put into context, in order to get a better understanding of the effects of confinement on catalyst performance. In addition, this analysis intends to showcase the similarities between homogeneous and heterogeneous catalysts, which may aid the development of novel strategies

An ultra-deep multi-band VLA survey of the faint radio sky (COSMOS-XS): New constraints on the cosmic star formation history

We make use of ultra-deep 3 GHz Karl G. Jansky Very Large Array observations of the COSMOS field from the multi-band COSMOS-XS survey to infer radio luminosity functions (LFs) of star-forming galaxies (SFGs). Using $\sim$1300 SFGs with redshifts out to $z\sim4.6$, and fixing the faint and bright end shape of the radio LF to the local values, we find a strong redshift trend that can be fitted by pure luminosity evolution with the luminosity parameter given by $\alpha_L \propto (3.40 \pm 0.11) - (0.48 \pm 0.06)z$. We then combine the ultra-deep COSMOS-XS data-set with the shallower VLA-COSMOS $\mathrm{3\,GHz}$ large project data-set over the wider COSMOS field in order to fit for joint density+luminosity evolution, finding evidence for significant density evolution. By comparing the radio LFs to the observed far-infrared (FIR) and ultraviolet (UV) LFs, we find evidence of a significant underestimation of the UV LF by $21.6\%\, \pm \, 14.3 \, \%$ at high redshift ($3.3\,<\,z\,<\,4.6$, integrated down to $0.03\,L^{\star}_{z=3}$). We derive the cosmic star formation rate density (SFRD) by integrating the fitted radio LFs and find that the SFRD rises up to $z\,\sim\,1.8$ and then declines more rapidly than previous radio-based estimates. A direct comparison between the radio SFRD and a recent UV-based SFRD, where we integrate both LFs down to a consistent limit ($0.038\,L^{\star}_{z=3}$), reveals that the discrepancy between the radio and UV LFs translates to a significant ($\sim$1 dex) discrepancy in the derived SFRD at $z>3$, even assuming the latest dust corrections and without accounting for optically dark sources.Comment: Submitted to ApJ; 27 pages, 13 figures, 4 table

Complete Solving for Explicit Evaluation of Gauss Sums in the Index 2 Case

Let $p$ be a prime number, $q=p^f$ for some positive integer $f$, $N$ be a positive integer such that $\gcd(N,p)=1$, and let \k be a primitive multiplicative character of order $N$ over finite field \fq. This paper studies the problem of explicit evaluation of Gauss sums in "\textsl{index 2 case}" (i.e. f=\f{\p(N)}{2}=[\zn:\pp], where \p(\cd) is Euler function). Firstly, the classification of the Gauss sums in index 2 case is presented. Then, the explicit evaluation of Gauss sums G(\k^\la) (1\laN-1) in index 2 case with order $N$ being general even integer (i.e. N=2^{r}\cd N_0 where $r,N_0$ are positive integers and $N_03$ is odd.) is obtained. Thus, the problem of explicit evaluation of Gauss sums in index 2 case is completely solved

Contributions of amino acid, acylcarnitine and sphingolipid profiles to type 2 diabetes risk among South-Asian Surinamese and Dutch adults

Introduction: People of South Asian origin are at high risk of type 2 diabetes (T2D), but the underpinning mechanisms are not fully understood. We determined ethnic differences in acylcarnitine, amino acid and sphingolipid concentrations and determined the associations with T2D. Research design and methods: Associations between these metabolites and incident T2D among Dutch and South-Asian Surinamese were determined in participants from the Healthy Life in an Urban Setting (HELIUS) study (Amsterdam, the Netherlands) using Prentice-weighted Cox regression. The HELIUS study includes 95 incident T2D cases and a representative subcohort of 700 people from a cohort of 5977 participants with a mean follow-up of 4 years. Results: Concentrations of acylcarnitines were comparable between both ethnic groups. Amino acid and lactosylceramide concentrations were higher among South-Asian Surinamese than Dutch (eg, isoleucine 65.7 (SD 16.3) vs 60.7 (SD 15.6) µmol/L). Ceramide concentrations were lower among South-Asian Surinamese than Dutch (eg, Cer d18:1 8.48 (SD 2.04) vs 9.08 (SD 2.29) µmol/L). Metabolic dysregulation preceded T2D without evidence for a multiplicative interaction by ethnicity. Most amino acids and (dihydro)ceramides were associated with increased risk (eg, Cer d18:1 HR 2.38, 95% CI 1.81 to 3.12) while acylcarnitines, glycine, glutamine and lactosylceramides were associated with decreased risk for T2D (eg, LacCer d18:2 HR 0.56, 95% CI 0.42 to 0.77). Conclusions: Overall, these data suggest that the disturbances underlying amino acid and sphingolipid metabolism may be predictive of T2D risk in populations of both South Asian and European background. These observations may be used as starting point to unravel the underlying metabolic disturbances

Impact of early applied upper limb stimulation: The EXPLICIT-stroke programme design

Main claims of the literature are that functional recovery of the paretic upper limb is mainly defined within the first month post stroke and that rehabilitation services should preferably be applied intensively and in a task-oriented way within this particular time window. EXplaining PLastICITy after stroke (acronym EXPLICIT-stroke) aims to explore the underlying mechanisms of post stroke upper limb recovery. Two randomized single blinded trials form the core of the programme, investigating the effects of early modified Constraint-Induced Movement Therapy (modified CIMT) and EMG-triggered Neuro-Muscular Stimulation (EMG-NMS) in patients with respectively a favourable or poor probability for recovery of dexterity.BioMechanical EngineeringMechanical, Maritime and Materials Engineerin

First report of Soybean Mosaic Virus in commercially grown soybean in the Netherlands

In July 2020, plants with crinkled, chlorotic, occasionally necrotic leaves, typical for Soybean Mosaic Virus (SMV), were observed in eight soybean fields (Glycine max L.) in Flevoland, The Netherlands (Supp. Fig. 1). Disease incidence varied from 5-50% and the plants affected often occurred in small or extensive patches. Leaves from several symptomatic plants were sampled from each of two fields planted with soybean variety Green Shell or Summer Shell. Total RNA was extracted from one plant leaf sample per field using InviTrap Spin Plant RNA Mini Kit (Invitek, Germany). One-tube RT-PCRs employing potyvirus generic primers P9502 and CPUP (Van der Vlugt et al, 1999) and SMV-specific primers SMV-dT (5'-TTTTTTTTTTTTTTTAGGACAAC-3') and SMV-Nib-Fw (5'-CAAGGATGARTTTAAGGAG-3') combined with Sanger sequencing confirmed the presence of SMV in all leaf samples. To exclude the presence of other agents in the samples, total RNA from each cultivar was used in standard Illumina library preparation with ribosomal RNA depletion followed by sequencing on an Illumina NovaSeq6000 (paired-end, 150 bp) which yielded 66,579,158 reads (Summer Shell) and 223,953,206 reads (Green Shell). After quality trimming in CLC Genomics Workbench 20.0.4 (CLC-GWB; Qiagen, Hilden), four million reads were randomly sampled for de novo assembly. Contigs over 500 nucleotides (nts) in length with a minimum of 500 reads were annotated by BLASTn against NCBI GenBank. This identified one contig of 9,883 nts (6,233,397 reads) in Summer Shell and one contig of 9,727 nts (3,139,927 reads) in Green Shell with clear homology to SMV (E-value = 0.0). No other viruses were identified in the datasets. Reference assemblies against the SMV reference sequence (NC_002634) mapped 24,090,763 reads (36.2%) for Summer Shell and 175,459,637 reads (78.3%) for Green Shell. Extracted consensus sequences for SMV in both soybean cultivars were 9,584 nts long (excluding the poly-A tail). Sequence data from the de novo and reference assemblies were combined into consensus sequences which showed over 98% overall nt sequence identity to NC_002634 and 99.6% to each other. Both consensus sequences were deposited in GenBank under accession numbers MW822167 (SMV-Summer Shell) and MW822168 (SMV-Green Shell). In addition, the presence of SMV in the field samples was confirmed with an inoculation assay. Leaf samples from both fields were ground in phosphate buffer (0.1M, pH 7.2) and inoculated on cotyledons and first expanded leaves of soybean plants (unknown cv.) 12 days post-germination. Plants showed veinal chlorosis in systemic leaves from 12 days post-inoculation, which developed into veinal necrosis. SMV infections were confirmed by RT-PCR in systemic, chlorotic leaf samples of all symptomatic plants using the SMV-specific primers described above. To our knowledge, this is the first report of SMV in The Netherlands. As soybean is a relatively new but expanding crop in this country, information about emerging diseases is highly relevant. SMV can be transmitted via seeds and aphids, where seeds can serve as primary source of virus inoculum (Cui et al., 2011; Hartman et al., 2016; Hajimorad et al., 2018). Weeds and non-commercial plants can also serve as origin of SMV, particularly in subsequent growing seasons, although this virus infects a limited host range of six plant families (Cui et al., 2011; Hill & Whitham, 2014). Special monitoring would be advised for the recurrence and possible damage by SMV in Dutch soybean fields