Non-Additive Effects of Genotypic Diversity Increase Floral Abundance and Abundance of Floral Visitors

Background: In the emerging field of community and ecosystem genetics, genetic variation and diversity in dominant plant species have been shown to play fundamental roles in maintaining biodiversity and ecosystem function. However, the importance of intraspecific genetic variation and diversity to floral abundance and pollinator visitation has received little attention. Methodology/Principal Findings: Using an experimental common garden that manipulated genotypic diversity (the number of distinct genotypes per plot) of Solidago altissima, we document that genotypic diversity of a dominant plant can indirectly influence flower visitor abundance. Across two years, we found that 1) plant genotype explained 45 % and 92 % of the variation in flower visitor abundance in 2007 and 2008, respectively; and 2) plant genotypic diversity had a positive and non-additive effect on floral abundance and the abundance of flower visitors, as plots established with multiple genotypes produced 25 % more flowers and received 45 % more flower visits than would be expected under an additive model. Conclusions/Significance: These results provide evidence that declines in genotypic diversity may be an important but little considered factor for understanding plant-pollinator dynamics, with implications for the global decline in pollinators due t

Evaluation of ground-level and space-borne sensor as tools in monitoring nitrogen nutrition status in immature and mature oil palm

Monitoring nitrogen (N) in oil palm is crucial for the production sustainability. The objective of this study is to examine the capability of visible (Vis), near infrared (NIR) and a combination of Vis and NIR (Vis + NIR) spectral indices acquired from different sensors for predicting foliar N content of different palm age groups. The N treatments varied from 0 to 2 kg per palm, subjected according to immature, young mature and prime mature classes. The Vis + NIR indices from the ground level-sensor that is green + red + NIR (G + R + NIR) was the best index for predicting N for immature palms (R2 = 0.91), while Vis indices blue + red (B + R) and Green Red Index from the space-borne sensor were significantly useful for N assessment of young and prime mature palms (R2 = 0.70 and 0.50), respectively. The application of vegetation indices for monitoring N status of oil palm is beneficial to examine extensive plantation areas

Attentional learning helps language acquisition take shape for atypically developing children, not just children with Autism Spectrum Disorders

The shape bias-generalising labels to same shaped objects-has been linked to attentional learning or referential intent. We explore these origins in children with typical development (TD), autism spectrum disorders (ASD) and other developmental disorders (DD). In two conditions, a novel object was presented and either named or described. Children selected another from a shape, colour or texture match. TD children choose the shape match in both conditions, children with DD and 'high-verbal mental age' (VMA) children with ASD (language age > 4.6) did so in the name condition and 'low-VMA' children with ASD never showed the heuristic. Thus, the shape bias arises from attentional learning in atypically developing children and is delayed in ASD

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits

Acceptance and Commitment Therapy plus usual care for improving quality of life in people with motor neuron disease (COMMEND) : a multicentre, parallel, randomised controlled trial in the UK

Background Motor neuron disease is a progressive, fatal neurodegenerative disease for which there is no cure. Acceptance and Commitment Therapy (ACT) is a psychological therapy incorporating acceptance, mindfulness, and behaviour change techniques. We aimed to evaluate the effectiveness of ACT plus usual care, compared with usual care alone, for improving quality of life in people with motor neuron disease. Methods We conducted a parallel, multicentre, two-arm randomised controlled trial in 16 UK motor neuron disease care centres or clinics. Eligible participants were aged 18 years or older with a diagnosis of definite or laboratory-supported probable, clinically probable, or possible familial or sporadic amyotrophic lateral sclerosis; progressive muscular atrophy; or primary lateral sclerosis; which met the World Federation of Neurology's El Escorial diagnostic criteria. Participants were randomly assigned (1:1) to receive up to eight sessions of ACT adapted for people with motor neuron disease plus usual care or usual care alone by a web-based system, stratified by site. Participants were followed up at 6 months and 9 months post-randomisation. Outcome assessors and trial statisticians were masked to treatment allocation. The primary outcome was quality of life using the McGill Quality of Life Questionnaire-Revised (MQOL-R) at 6 months post-randomisation. Primary analyses were multi-level modelling and modified intention to treat among participants with available data. This trial was pre-registered with the ISRCTN Registry (ISRCTN12655391). Findings Between Sept 18, 2019, and Aug 31, 2022, 435 people with motor neuron disease were approached for the study, of whom 206 (47%) were assessed for eligibility, and 191 were recruited. 97 (51%) participants were randomly assigned to ACT plus usual care and 94 (49%) were assigned to usual care alone. 80 (42%) of 191 participants were female and 111 (58%) were male, and the mean age was 63·1 years (SD 11·0). 155 (81%) participants had primary outcome data at 6 months post-randomisation. After controlling for baseline scores, age, sex, and therapist clustering, ACT plus usual care was superior to usual care alone for quality of life at 6 months (adjusted mean difference on the MQOL-R of 0·66 [95% CI 0·22–1·10]; d=0·46 [0·16–0·77]; p=0·0031). Moderate effect sizes were clinically meaningful. 75 adverse events were reported, 38 of which were serious, but no adverse events were deemed to be associated with the intervention. Interpretation ACT plus usual care is clinically effective for maintaining or improving quality of life in people with motor neuron disease. As further evidence emerges confirming these findings, health-care providers should consider how access to ACT, adapted for the specific needs of people with motor neuron disease, could be provided within motor neuron disease clinical services

Proposed models for shared and distinct modes of adaptation for cGAS and OAS proteins in primates.

<p>An ancestral protein (red) with template independent polymerase activity was challenged by pathogens (green), which led to gene duplications and divergence resulting in ancestral cGAS (blue) and ancestral OAS (yellow). cGAS and OAS likely faced shared and distinct inhibitors encoded by pathogens (colored hexagons). Extensive positive selection of cGAS and OAS resulted in a variety of substitutions that evade inhibition by pathogens. For cGAS, sampling of amino acid substitutions on protein surfaces (gray stars) and the expression of spliceforms that may produce molecular mimics or cGAS variant proteins that evade antagonism could provide diverse mechanisms of escape from pathogen-encoded inhibitors. Some OAS genes also fix amino acid substitutions (gray stars) and may also evade pathogens via duplications and gene fusion events evident in OAS2 and OAS3.</p

Widespread signatures of positive selection for cGAS and OAS1 across the primate lineage.

<p>Phylogenetic analyses of cGAS <b>(A,B)</b> and OAS1 <b>(C,D)</b> were carried out using sequences from 22 matching primate species. <b>(A)</b> A species tree displaying sampled primate sequences for cGAS with dN/dS (ω) values obtained from free-ratio analyses (PAML[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005203#pgen.1005203.ref045" target="_blank">45</a>], see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005203#sec013" target="_blank">Methods</a>) indicated above each branch. ω values > 1 or at least 3 nonsynonymous: 0 synonymous amino acid changes are labeled in red with the corresponding branch (red branch). <b>(B)</b> cGAS gene structure with annotated domains and catalytic residues (below). Amino acid sites with statistically significant ω values obtained from NSsites (PAML [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005203#pgen.1005203.ref044" target="_blank">44</a>]), FUBAR, and MEME (HyPhy [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005203#pgen.1005203.ref046" target="_blank">46</a>]) are indicated above the gene. <b>(C)</b> ω values for OAS1 across primate evolution. The species tree is labeled as described for the cGAS tree. <b>(D)</b> OAS1 gene structure with amino acids displaying statistical significant ω values. Actual amino acid residue refers to human reference sequence. Catalytic amino acid residues for both cGAS and OAS1 are indicated within the gene diagram.</p

cGAS and OAS1 act in parallel innate defense signaling pathways.

<p><b>(A)</b> Model of cGAS signaling. Upon detection and binding of cytoplasmic DNA from viruses (green), cGAS (blue) dimerizes and generates cGAMP, which in turn activates STING signaling (TBK1-IRF3) to promote transcription of interferon beta. <b>(B)</b> Model of OAS signaling. Upon detection and binding of double-stranded RNA in the cytoplasm from viruses (green), OAS synthesizes 2–5 oligoadenylate, which activates RNase L and leads to the destruction of viral and cellular RNAs.</p

Evolutionary histories vary across the OAS gene family in primates.

<p>Phylogenetic analyses of OAS1, OAS2, OAS3, and OASL were carried out using sequences from 11 matching primate species. <b>(A)</b> Gene structures of the OAS gene family members in primates. NTase (red) and OAS1-C (gray) domains are indicated. For OASL the ubiquitin-like domains (yellow) are also indicated. Amino acid sites with statistically significant ω values obtained from NSsites (PAML [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005203#pgen.1005203.ref044" target="_blank">44</a>]), FUBAR, and MEME (HyPhy [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005203#pgen.1005203.ref045" target="_blank">45</a>]) are indicated above the gene. <b>(B)</b> Primate species trees with ω values obtained from free-ratio analyses in PAML [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005203#pgen.1005203.ref044" target="_blank">44</a>] for each lineage. dN/dS values and lineages with ω > 1 or at least 3 nonsynonymous:0 synonymous amino acid substitutions are highlighted in red.</p