Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.

Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have reanalyzed publicly available mass spectrometry proteomics data sets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we identified 15,565 phosphosites on serine, threonine, and tyrosine residues on rice proteins. We identified sequence motifs for phosphosites, and link motifs to enrichment of different biological processes, indicating different downstream regulation likely caused by different kinase groups. We cross-referenced phosphosites against the rice 3,000 genomes, to identify single amino acid variations (SAAVs) within or proximal to phosphosites that could cause loss of a site in a given rice variety and clustered the data to identify groups of sites with similar patterns across rice family groups. The data has been loaded into UniProt Knowledge-Base─enabling researchers to visualize sites alongside other data on rice proteins, e.g., structural models from AlphaFold2, PeptideAtlas, and the PRIDE database─enabling visualization of source evidence, including scores and supporting mass spectra.

Phosphorylation in the Plasmodium falciparum Proteome: A Meta-Analysis of Publicly Available Data Sets.

Malaria is a deadly disease caused by Apicomplexan parasites of the Plasmodium genus. Several species of the Plasmodium genus are known to be infectious to humans, of which P. falciparum is the most virulent. Post-translational modifications (PTMs) of proteins coordinate cell signaling and hence regulate many biological processes in P. falciparum homeostasis and host infection, of which the most highly studied is phosphorylation. Phosphosites on proteins can be identified by tandem mass spectrometry (MS) performed on enriched samples (phosphoproteomics), followed by downstream computational analyses. We have performed a large-scale meta-analysis of 11 publicly available phosphoproteomics data sets to build a comprehensive atlas of phosphosites in the P. falciparum proteome, using robust pipelines aimed at strict control of false identifications. We identified a total of 26,609 phosphorylated sites on P. falciparum proteins, split across three categories of data reliability (gold/silver/bronze). We identified significant sequence motifs, likely indicative of different groups of kinases responsible for different groups of phosphosites. Conservation analysis identified clusters of phosphoproteins that are highly conserved and others that are evolving faster within the Plasmodium genus, and implicated in different pathways. We were also able to identify over 180,000 phosphosites within Plasmodium species beyond falciparum, based on orthologue mapping. We also explored the structural context of phosphosites, identifying a strong enrichment for phosphosites on fast-evolving (low conservation) intrinsically disordered regions (IDRs) of proteins. In other species, IDRs have been shown to have an important role in modulating protein-protein interactions, particularly in signaling, and thus warranting further study for their roles in host-pathogen interactions. All data have been made available via UniProtKB, PRIDE, and PeptideAtlas, with visualization interfaces for exploring phosphosites in the context of other data on Plasmodium proteins.

Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation.

Public phosphorylation databases such as PhosphoSitePlus (PSP) and PeptideAtlas (PA) compile results from published papers or openly available mass spectrometry (MS) data. However, there is no database-level control for false discovery of sites, likely leading to the overestimation of true phosphosites. By profiling the human phosphoproteome, we estimate the false discovery rate (FDR) of phosphosites and predict a more realistic count of true identifications. We rank sites into phosphorylation likelihood sets and analyze them in terms of conservation across 100 species, sequence properties, and functional annotations. We demonstrate significant differences between the sets and develop a method for independent phosphosite FDR estimation. Remarkably, we report estimated FDRs of 84, 98, and 82% within sets of phosphoserine (pSer), phosphothreonine (pThr), and phosphotyrosine (pTyr) sites, respectively, that are supported by only a single piece of identification evidence─the majority of sites in PSP. We estimate that around 62 000 Ser, 8000 Thr, and 12 000 Tyr phosphosites in the human proteome are likely to be true, which is lower than most published estimates. Furthermore, our analysis estimates that 86 000 Ser, 50 000 Thr, and 26 000 Tyr phosphosites are likely false-positive identifications, highlighting the significant potential of false-positive data to be present in phosphorylation databases.

A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome.

Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have re-analysed publicly available mass spectrometry proteomics datasets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we identified 15,522 phosphosites on serine, threonine and tyrosine residues on rice proteins. We identified sequence motifs for phosphosites, and link motifs to enrichment of different biological processes, indicating different downstream regulation likely caused by different kinase groups. We cross-referenced phosphosites against the rice 3,000 genomes, to identify single amino acid variations (SAAVs) within or proximal to phosphosites that could cause loss of a site in a given rice variety. The data was clustered to identify groups of sites with similar patterns across rice family groups, for example those highly conserved in Japonica, but mostly absent in Aus type rice varieties - known to have different responses to drought. These resources can assist rice researchers to discover alleles with significantly different functional effects across rice varieties. The data has been loaded into UniProt Knowledge-Base - enabling researchers to visualise sites alongside other data on rice proteins e.g. structural models from AlphaFold2, PeptideAtlas and the PRIDE database - enabling visualisation of source evidence, including scores and supporting mass spectra.

A Quick Measure of Theory of Mind in Autistic Adults: Decision Accuracy, Latency and Self-Awareness.

Autistic adults often experience difficulties in taking the perspective of others, potentially undermining their social interactions. We evaluated a quick, forced-choice version of the Adult Theory of Mind (A-ToM) test, which was designed to assess such difficulties and comprehensively evaluated by Brewer et al. (2017). The forced-choice version (the A-ToM-Q) demonstrated discriminant, concurrent, convergent and divergent validity using samples of autistic (N = 96) and non-autistic adults (N = 75). It can be administered in a few minutes and machine-scored, involves minimal training and facilitates large-scale, live, or web-based testing. It permits measurement of response latency and self-awareness, with response characteristics on both measures enhancing understanding of the nature and extent of perspective taking difficulties in autistic individuals.

Mutualism has its limits: consequences of asymmetric interactions between a well-defended plant and its herbivorous pollinator.

Concern for pollinator health often focuses on social bees and their agricultural importance at the expense of other pollinators and their ecosystem services. When pollinating herbivores use the same plants as nectar sources and larval hosts, ecological conflicts emerge for both parties, as the pollinator's services are mitigated by herbivory and its larvae are harmed by plant defences. We tracked individual-level metrics of pollinator health-growth, survivorship, fecundity-across the life cycle of a pollinating herbivore, the common hawkmoth, Hyles lineata, interacting with a rare plant, Oenothera harringtonii, that is polymorphic for the common floral volatile (R)-(-)-linalool. Linalool had no impact on floral attraction, but its experimental addition suppressed oviposition on plants lacking linalool. Plants showed robust resistance against herbivory from leaf-disc to whole-plant scales, through poor larval growth and survivorship. Higher larval performance on other Oenothera species indicates that constitutive herbivore resistance by O. harringtonii is not a genus-wide trait. Leaf volatiles differed among populations of O. harringtonii but were not induced by larval herbivory. Similarly, elagitannins and other phenolics varied among plant tissues but were not herbivore-induced. Our findings highlight asymmetric plant-pollinator interactions and the importance of third parties, including alternative larval host plants, in maintaining pollinator health. This article is part of the theme issue 'Natural processes influencing pollinator health: from chemistry to landscapes'.

Proteomic characterization of GSK3ß knockout shows altered cell adhesion and metabolic pathway utilisation in colorectal cancer cells.

Glycogen-specific kinase (GSK3ß) is an integral regulator of the Wnt signalling pathway as well as many other diverse signalling pathways and processes. Dys-regulation of GSK3ß is implicated in many different pathologies, including neurodegenerative disorders as well as many different tumour types. In the context of tumour development, GSK3ß has been shown to play both oncogenic and tumour suppressor roles, depending upon tissue, signalling environment or disease progression. Although multiple substrates of the GSK3ß kinase have been identified, the wider protein networks within which GSK3ß participates are not well known, and the consequences of these interactions not well understood. In this study, LC-MS/MS expression analysis was performed using knockout GSK3ß colorectal cancer cells and isogenic controls in colorectal cancer cell lines carrying dominant stabilizing mutations of ß-catenin. Consistent with the role of GSK3ß, we found that ß-catenin levels and canonical Wnt activity are unaffected by knockout of GSK3ß and therefore used this knockout cell model to identify other processes in which GSK3ß is implicated. Quantitative proteomic analysis revealed perturbation of proteins involved in cell-cell adhesion, and we characterized the phenotype and altered proteomic profiles associated with this. We also characterized the perturbation of metabolic pathways resulting from GSK3ß knockout and identified defects in glycogen metabolism. In summary, using a precision colorectal cancer cell-line knockout model with constitutively activated ß-catenin we identified several of the diverse pathways and processes associated with GSK3ß function.

Measuring Theory of Mind in Adults with Autism Spectrum Disorder.

Deficits in Theory of Mind (ToM)-the ability to interpret others' beliefs, intentions and emotions-undermine the ability of individuals with Autism Spectrum Disorder (ASD) to interact in socially normative ways. This study provides psychometric data for the Adult-Theory of Mind (A-ToM) measure using video-scenarios based in part on Happé's (Instructions for theory of mind story task, 1999) Strange Stories test. The final items discriminated IQ-matched adults with ASD from controls on the social but not the physical items. Additional validity data included a two-component principal components solution, correlations with existing ToM scales, and the absence of correlations with self-report measures of empathy and social anxiety (not requiring inferences about the intent of others). The expected group differences in ToM were accompanied by marked variability in the ASD sample.

Pancreaticoduodenectomy for nonampullary duodenal lesions: indications and results.

BACKGROUND: Pancreaticoduodenectomy (PD) is a complex procedure, associated with a definite risk of mortality and 30-50% risk of complications. For nonampullary duodenal lesions, PD can carry a higher morbidity as they are more commonly associated with a soft pancreas and narrow-calibre main pancreatic ducts. It is therefore paramount that the risks and benefits of surgery are considered carefully in this group of patients. A preoperative histological diagnosis for duodenal lesions is normally achieved by endoscopic biopsy. In this study, we aim to assess the outcome of PD in patients with nonampullary duodenal lesions and correlate the preoperative endoscopic histology work-up with the definitive postoperative pathology. MATERIALS AND METHODS: We reviewed a prospectively collected PD database from January 2007 to December 2013. Demographic and clinical data were included. Preoperative endoscopic histology was compared with final specimen histology to assess concordance. RESULTS: Forty patients (55% women, mean age 69.4 years, range 45-83 years) underwent PD for duodenal lesions over a 7-year time period. The most common presenting symptom was epigastric pain (32.5%), followed by anaemia (20%). Overall, the complication rate was 55%, with the most frequent adverse event being pancreatic fistula in 13/40 (32.5%). The perioperative mortality was 2/40 (5%). Duodenal adenocarcinoma (65%) was the most common postoperative histological diagnosis. The mean tumour size was 36 mm (range 5-103 mm) and a median of 13 nodes were harvested. The median length of stay was 15 days (range 7-66 days). Overall, 12/40 patients (30%) had a preoperative diagnosis of high-grade dysplasia. The postoperative specimen in this subgroup of patients was reviewed carefully and only 3/12 (25%) patients had high-grade dysplasia in the resection specimen. In the remaining patients, 3/12 (25%) had adenocarcinoma in the resection specimen and 6/12 patients (50%) had low-grade dysplasia. CONCLUSION: PD carries a high mortality and morbidity, especially for duodenal lesions. We recommend a careful endoscopic review after the index case with a high-definition optical evaluation of duodenal lesions. This, in addition to an experienced histological assessment of the index biopsy material, forms an essential prerequisite in aiding the multidisciplinary team in the decision-making process with respect to triage of these lesions to conservative management, surveillance, endoscopic resection or finally surgical resection.

Low-flow active and passive sampling of VOCs using thermal desorption tubes: theory and application at an offset printing facility.

While air sampling techniques using adsorbent-based collection, thermal desorption and chromatographic analysis have found a niche in ambient air sampling, occupational applications have been more limited. This paper evaluates the use of thermal desorption techniques for low flow active and passive sampling configurations which allow conveniently long duration sampling in occupational settings and other high concentration environments. The use of an orifice enables flows as low as 0.5 ml min(-1) and sampling periods up to several days without significant biases. A model is used to predict sampling rates of a passive sampler encompassing an orifice, a void space, glass wool, and the adsorbent. Laboratory and field tests conducted at a commercial offset printing facility, which contained a variety of volatile organic compounds (primarily aromatic but also a few chlorinated and terpene compounds at levels from 1 to 67,000 microg m(-3)), are used to evaluate the approach. Tenax GR and Carbosieve SIII, both singly and together, were employed as adsorbents. Side-by-side tests comparing high flow, low flow and passive samplers show excellent agreement and high linearity (r = 0.95) for concentrations spanning nearly five orders of magnitude. Active samplers were tested at flows as low as 0.5 ml min(-1), compared to typical flows up to 40 ml min(-1). Passive samplers demonstrated a linear range and agreement with predictions for adsorbate loadings from approximately 1 ng to nearly 10 microg. Using a chemical mass balance receptor model, concentrations in the facility were apportioned to solvents, inks and other indoor and outdoor sources. Overall, the use of low flow active and passive sampling approaches employing thermal desorption techniques provides good performance and tremendous flexibility that facilitates use in many applications, including workplace settings.