Lack of correlation between vertical distribution and carrier frequency, and preference for open spaces in arboreal katydids that use extreme ultrasound, in Gorgona, Colombia (Orthoptera: Tettigoniidae)

Male Tettigoniidae emit sound to attract conspecific females. The sound is produced by stridulation. During stridulation the forewings open and close, but it is during the closing stroke that the scraper contacts the file teeth to generate the predominant sound components, which are amplified by adjacent wing cells specialized in sound radiation. The sounds usually exceed the sonic boundary and might occur above 40 kHz, reaching extreme ultrasonic frequencies of 150kHz in some species. Here we test the hypothesis that Tettigoniidae species should prefer microhabitats that favour efficient signal transmission, i.e. that there is a relationship of sound frequency with the vertical distribution of the species (from ground to canopy) at Gorgona National Natural Park, Colombia. We sampled 16 trees and four different altitudinal levels between 1 and 20m above the understory vegetation. We placed collecting blankets separated by vertical distances of 5m, and knocked insects down using the technique known as fogging. We found no correlation between vertical distribution and carrier frequency, but there was a preference for open spaces (below the canopy and above the understory) in species using extreme ultrasound. This is the first quantitative description of the vertical distribution in neotropical species of the family Tettigoniidae and its relationship to the calling song frequency

The hylEfm gene in pHylEfm of Enterococcus faecium is not required in pathogenesis of murine peritonitis

<p>Abstract</p> <p>Background</p> <p>Plasmids containing <it>hyl</it>_{<it>Efm </it>}(pHyl_Efm) were previously shown to increase gastrointestinal colonization and lethality of <it>Enterococcus faecium </it>in experimental peritonitis. The <it>hyl</it>_{<it>Efm </it>}gene, predicting a glycosyl hydrolase, has been considered as a virulence determinant of hospital-associated <it>E. faecium</it>, although its direct contribution to virulence has not been investigated. Here, we constructed mutants of the <it>hyl</it>_<it>Efm</it>-region and we evaluated their effect on virulence using a murine peritonitis model.</p> <p>Results</p> <p>Five mutants of the <it>hyl</it>_<it>Efm</it>-region of pHyl_EfmTX16from the sequenced endocarditis strain (TX16 [DO]) were obtained using an adaptation of the PheS* system and were evaluated in a commensal strain TX1330RF to which pHyl_EfmTX16was transferred by mating; these include <it>i</it>) deletion of <it>hyl</it>_{<it>Efm </it>}only; <it>ii</it>) deletion of the gene downstream of <it>hyl</it>_{<it>Efm </it>}(<it>down</it>) of unknown function; <it>iii</it>) deletion of <it>hyl</it>_{<it>Efm </it>}plus <it>down</it>; <it>iv</it>) deletion of <it>hyl</it>_<it>Efm</it>-<it>down </it>and two adjacent genes; and <it>v</it>) a 7,534 bp deletion including these four genes plus partial deletion of two others, with replacement by <it>cat</it>. The 7,534 bp deletion did not affect virulence of TX16 in peritonitis but, when pHyl_{EfmTX16Δ7,534}was transferred to the TX1330RF background, the transconjugant was affected in <it>in vitro </it>growth versus TX1330RF(pHyl_EfmTX16) and was attenuated in virulence; however, neither <it>hyl</it>_{<it>Efm </it>}nor <it>hyl</it>_<it>Efm</it>-<it>down </it>restored wild type function. We did not observe any <it>in vivo </it>effect on virulence of the other deletions of the <it>hyl</it>_<it>Efm</it>-region</p> <p>Conclusions</p> <p>The four genes of the <it>hyl</it>_{<it>Efm </it>}region (including <it>hyl</it>_<it>Efm</it>) do not mediate the increased virulence conferred by pHyl_EfmTX16in murine peritonitis. The use of the markerless counterselection system PheS* should facilitate the genetic manipulation of <it>E. faecium </it>in the future.</p

Autoantibodies Against Proteins Previously Associated With Autoimmunity in Adult and Pediatric Patients With COVID-19 and Children With MIS-C

The antibody profile against autoantigens previously associated with autoimmune diseases and other human proteins in patients with COVID-19 or multisystem inflammatory syndrome in children (MIS-C) remains poorly defined. Here we show that 30% of adults with COVID-19 had autoantibodies against the lung antigen KCNRG, and 34% had antibodies to the SLE-associated Smith-D3 protein. Children with COVID-19 rarely had autoantibodies; one of 59 children had GAD65 autoantibodies associated with acute onset of insulin-dependent diabetes. While autoantibodies associated with SLE/Sjögren’s syndrome (Ro52, Ro60, and La) and/or autoimmune gastritis (gastric ATPase) were detected in 74% (40/54) of MIS-C patients, further analysis of these patients and of children with Kawasaki disease (KD), showed that the administration of intravenous immunoglobulin (IVIG) was largely responsible for detection of these autoantibodies in both groups of patients. Monitoring in vivo decay of the autoantibodies in MIS-C children showed that the IVIG-derived Ro52, Ro60, and La autoantibodies declined to undetectable levels by 45-60 days, but gastric ATPase autoantibodies declined more slowly requiring >100 days until undetectable. Further testing of IgG and/or IgA antibodies against a subset of potential targets identified by published autoantigen array studies of MIS-C failed to detect autoantibodies against most (16/18) of these proteins in patients with MIS-C who had not received IVIG. However, Troponin C2 and KLHL12 autoantibodies were detected in 2 of 20 and 1 of 20 patients with MIS-C, respectively. Overall, these results suggest that IVIG therapy may be a confounding factor in autoantibody measurements in MIS-C and that antibodies against antigens associated with autoimmune diseases or other human proteins are uncommon in MIS-C

JAK1/2 inhibition with baricitinib in the treatment of autoinflammatory interferonopathies

BACKGROUND. Monogenic IFN-mediated autoinflammatory diseases present in infancy with systemic inflammation, an IFN response gene signature, inflammatory organ damage, and high mortality. We used the JAK inhibitor baricitinib, with IFN-blocking activity in vitro, to ameliorate disease. METHODS. Between October 2011 and February 2017, 10 patients with CANDLE (chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperatures), 4 patients with SAVI (stimulator of IFN genes-associated [STING-associated] vasculopathy with onset in infancy), and 4 patients with other interferonopathies were enrolled in an expanded access program. The patients underwent dose escalation, and the benefit was assessed by reductions in daily disease symptoms and corticosteroid requirement. Quality of life, organ inflammation, changes in IFN-induced biomarkers, and safety were longitudinally assessed. RESULTS. Eighteen patients were treated for a mean duration of 3.0 years (1.5-4.9 years). The median daily symptom score decreased from 1.3 (interquartile range [IQR], 0.93-1.78) to 0.25 (IQR, 0.1-0.63) (P < 0.0001). In 14 patients receiving corticosteroids at baseline, daily prednisone doses decreased from 0.44 mg/kg/day (IQR, 0.31-1.09) to 0.11 mg/kg/day (IQR, 0.02-0.24) (P < 0.01), and 5 of 10 patients with CANDLE achieved lasting clinical remission. The patients' quality of life and height and bone mineral density Z-scores significantly improved, and their IFN biomarkers decreased. Three patients, two of whom had genetically undefined conditions, discontinued treatment because of lack of efficacy, and one CANDLE patient discontinued treatment because of BK viremia and azotemia. The most common adverse events were upper respiratory infections, gastroenteritis, and BK viruria and viremia. CONCLUSION. Upon baricitinib treatment, clinical manifestations and inflammatory and IFN biomarkers improved in patients with the monogenic interferonopathies CANDLE, SAVI, and other interferonopathies. Monitoring safety and efficacy is important in benefit-risk assessment

Immunopathological signatures in multisystem inflammatory syndrome in children and pediatric COVID-19

: Pediatric Coronavirus Disease 2019 (pCOVID-19) is rarely severe; however, a minority of children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) might develop multisystem inflammatory syndrome in children (MIS-C), with substantial morbidity. In this longitudinal multi-institutional study, we applied multi-omics (analysis of soluble biomarkers, proteomics, single-cell gene expression and immune repertoire analysis) to profile children with COVID-19 (n = 110) and MIS-C (n = 76), along with pediatric healthy controls (pHCs; n = 76). pCOVID-19 was characterized by robust type I interferon (IFN) responses, whereas prominent type II IFN-dependent and NF-κB-dependent signatures, matrisome activation and increased levels of circulating spike protein were detected in MIS-C, with no correlation with SARS-CoV-2 PCR status around the time of admission. Transient expansion of TRBV11-2 T cell clonotypes in MIS-C was associated with signatures of inflammation and T cell activation. The association of MIS-C with the combination of HLA A*02, B*35 and C*04 alleles suggests genetic susceptibility. MIS-C B cells showed higher mutation load than pCOVID-19 and pHC. These results identify distinct immunopathological signatures in pCOVID-19 and MIS-C that might help better define the pathophysiology of these disorders and guide therapy

Creative destruction in science

Drawing on the concept of a gale of creative destruction in a capitalistic economy, we argue that initiatives to assess the robustness of findings in the organizational literature should aim to simultaneously test competing ideas operating in the same theoretical space. In other words, replication efforts should seek not just to support or question the original findings, but also to replace them with revised, stronger theories with greater explanatory power. Achieving this will typically require adding new measures, conditions, and subject populations to research designs, in order to carry out conceptual tests of multiple theories in addition to directly replicating the original findings. To illustrate the value of the creative destruction approach for theory pruning in organizational scholarship, we describe recent replication initiatives re-examining culture and work morality, working parents\u2019 reasoning about day care options, and gender discrimination in hiring decisions. Significance statement It is becoming increasingly clear that many, if not most, published research findings across scientific fields are not readily replicable when the same method is repeated. Although extremely valuable, failed replications risk leaving a theoretical void\u2014 reducing confidence the original theoretical prediction is true, but not replacing it with positive evidence in favor of an alternative theory. We introduce the creative destruction approach to replication, which combines theory pruning methods from the field of management with emerging best practices from the open science movement, with the aim of making replications as generative as possible. In effect, we advocate for a Replication 2.0 movement in which the goal shifts from checking on the reliability of past findings to actively engaging in competitive theory testing and theory building. Scientific transparency statement The materials, code, and data for this article are posted publicly on the Open Science Framework, with links provided in the article

Many Labs 5:Testing pre-data collection peer review as an intervention to increase replicability

Replication studies in psychological science sometimes fail to reproduce prior findings. If these studies use methods that are unfaithful to the original study or ineffective in eliciting the phenomenon of interest, then a failure to replicate may be a failure of the protocol rather than a challenge to the original finding. Formal pre-data-collection peer review by experts may address shortcomings and increase replicability rates. We selected 10 replication studies from the Reproducibility Project: Psychology (RP:P; Open Science Collaboration, 2015) for which the original authors had expressed concerns about the replication designs before data collection; only one of these studies had yielded a statistically significant effect (p < .05). Commenters suggested that lack of adherence to expert review and low-powered tests were the reasons that most of these RP:P studies failed to replicate the original effects. We revised the replication protocols and received formal peer review prior to conducting new replication studies. We administered the RP:P and revised protocols in multiple laboratories (median number of laboratories per original study = 6.5, range = 3?9; median total sample = 1,279.5, range = 276?3,512) for high-powered tests of each original finding with both protocols. Overall, following the preregistered analysis plan, we found that the revised protocols produced effect sizes similar to those of the RP:P protocols (?r = .002 or .014, depending on analytic approach). The median effect size for the revised protocols (r = .05) was similar to that of the RP:P protocols (r = .04) and the original RP:P replications (r = .11), and smaller than that of the original studies (r = .37). Analysis of the cumulative evidence across the original studies and the corresponding three replication attempts provided very precise estimates of the 10 tested effects and indicated that their effect sizes (median r = .07, range = .00?.15) were 78% smaller, on average, than the original effect sizes (median r = .37, range = .19?.50)

Determination of phospholipids in oat samples by HPLC-ELSD and HPLC-ESI-MS

Oat (Avena sativa L.) is an important crop produced in various regions of Europe and North America. Oat lipids are a heterogeneous mixture of acyl lipids and unsaponifiable components. The neutral lipids are mainly triacylglycerols (TAGs) and account for 50–60% of total oat lipids. Oat oil is also rich in polar lipids; that is, phospholipids (6–26%) and glycolipids (6–17%). Characterization of oat polar lipids has largely been performed by thin-layer chromatography, but the characterization of phospholipid classes has been poorly studied. The aim of our work was the determination of different phospholipids in Romanian oat samples. To this end, one commercial sample (Comun) and four pure varieties (Jeremy, Lovrin 1, Lovrin 27-T and Mures) were used. HPLC-ELSD results allowed to establish that phosphatidylglycerol (PG), phosphatidylcholine (PC), and lyso-PC were the most representative phospholipids in all the oat samples, except for Mures variety where phosphatidylethanolamine (PE), PC, and lyso-PC were the principal phospholipids. Additionally, HPLC-ESI MS analysis showed that C16:0, C16:1, C18:0, C18:1, C18:2, C18:3, C20:0 and C20:1 were the fatty acids bounded to the phospholipid glycerol chain

Alternative splicing and subfunctionalization generates functional diversity in fungal proteomes.

Alternative splicing is commonly used by the Metazoa to generate more than one protein from a gene. However, such diversification of the proteome by alternative splicing is much rarer in fungi. We describe here an ancient fungal alternative splicing event in which these two proteins are generated from a single alternatively spliced ancestral SKI7/HBS1 gene retained in many species in both the Ascomycota and Basidiomycota. While the ability to express two proteins from a single SKI7/HBS1 gene is conserved in many fungi, the exact mechanism by which they achieve this varies. The alternative splicing was lost in Saccharomyces cerevisiae following the whole-genome duplication event as these two genes subfunctionalized into the present functionally distinct HBS1 and SKI7 genes. When expressed in yeast, the single gene from Lachancea kluyveri generates two functionally distinct proteins. Expression of one of these proteins complements hbs1, but not ski7 mutations, while the other protein complements ski7, but not hbs1. This is the first known case of subfunctionalization by loss of alternative splicing in yeast. By coincidence, the ancestral alternatively spliced gene was also duplicated in Schizosaccharomyces pombe with subsequent subfunctionalization and loss of splicing. Similar subfunctionalization by loss of alternative splicing in fungi also explains the presence of two PTC7 genes in the budding yeast Tetrapisispora blattae, suggesting that this is a common mechanism to preserve duplicate alternatively spliced genes