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Development of a next generation SNP genotyping array for wheat
High-throughput genotyping arrays have provided a cost-effective, reliable and interoperable system for genotyping hexaploid wheat and its relatives. Existing, highly cited arrays including our 35K Wheat Breeder's array and the Illumina 90K array were designed based on a limited amount of varietal sequence diversity and with imperfect knowledge of SNP positions. Recent progress in wheat sequencing has given us access to a vast pool of SNP diversity, whilst technological improvements have allowed us to fit significantly more probes onto a 384-well format Axiom array than previously possible. Here we describe a novel Axiom genotyping array, the ‘Triticum aestivum Next Generation’ array (TaNG), largely derived from whole genome skim sequencing of 204 elite wheat lines and 111 wheat landraces taken from the Watkins ‘Core Collection’. We used a novel haplotype optimization approach to select SNPs with the highest combined varietal discrimination and a design iteration step to test and replace SNPs which failed to convert to reliable markers. The final design with 43 372 SNPs contains a combination of haplotype-optimized novel SNPs and legacy cross-platform markers. We show that this design has an improved distribution of SNPs compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous array. We also demonstrate the improved performance of TaNGv1.1 for Genome-wide association studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available with supporting marker annotations and initial genotyping results freely available
Port Sunlight's Star: Sophie Somers
Port Sunlight Village Trust Blog Pos
Data from: Stochastic character mapping, Bayesian model selection, and biosynthetic pathways shed new light on the evolution of habitat preference in cyanobacteria
Cyanobacteria are the only prokaryotes to have evolved oxygenic photosynthesis paving the way for complex life. Studying the evolution and ecological niche of cyanobacteria and their ancestors is crucial for understanding the intricate dynamics of biosphere evolution. These organisms frequently deal with environmental stressors such as salinity and drought, and they employ compatible solutes as a mechanism to cope with these challenges. Compatible solutes are small molecules that help maintain cellular osmotic balance in high-salinity environments, such as marine waters. Their production plays a crucial role in salt tolerance, which, in turn, influences habitat preference. Among the five known compatible solutes produced by cyanobacteria (sucrose, trehalose, glucosylglycerol, glucosylglycerate, and glycine betaine), their synthesis varies between individual strains. In this study, we work in a Bayesian stochastic mapping framework, integrating multiple sources of information about compatible solute biosynthesis in order to predict the ancestral habitat preference of Cyanobacteria. Through extensive model selection analyses and statistical tests for correlation, we identify glucosylglycerol and glucosylglycerate as the most significantly correlated with habitat preference, while trehalose exhibits the weakest correlation. Additionally, glucosylglycerol, glucosylglycerate, and glycine betaine show high loss/gain rate ratios, indicating their potential role in adaptability, while sucrose and trehalose are less likely to be lost due to their additional cellular functions. Contrary to previous findings, our analyses predict that the last common ancestor of Cyanobacteria (living at around 3180 Ma) had a 97% probability of a high salinity habitat preference and was likely able to synthesize glucosylglycerol and glucosylglycerate. Nevertheless, cyanobacteria likely colonized low-salinity environments shortly after their origin, with an 89% probability of the first cyanobacterium with low-salinity habitat preference arising prior to the Great Oxygenation Event (2460 Ma). Stochastic mapping analyses provide evidence of cyanobacteria inhabiting early marine habitats, aiding in the interpretation of the geological record. Our age estimate of ~2590 Ma for the divergence of two major cyanobacterial clades (Macro- and Microcyanobacteria) suggests that these were likely significant contributors to primary productivity in marine habitats in the lead-up to the Great Oxygenation Event, and thus played a pivotal role in triggering the sudden increase in atmospheric oxygen
NMR metabolomic modeling of age and lifespan:A multicohort analysis
Metabolomic age models have been proposed for the study of biological aging, however, they have not been widely validated. We aimed to assess the performance of newly developed and existing nuclear magnetic resonance spectroscopy (NMR) metabolomic age models for prediction of chronological age (CA), mortality, and age-related disease. Ninety-eight metabolic variables were measured in blood from nine UK and Finnish cohort studies (N ≈31,000 individuals, age range 24-86 years). We used nonlinear and penalized regression to model CA and time to all-cause mortality. We examined associations of four new and two previously published metabolomic age models, with aging risk factors and phenotypes. Within the UK Biobank (N ≈102,000), we tested prediction of CA, incident disease (cardiovascular disease (CVD), type-2 diabetes mellitus, cancer, dementia, and chronic obstructive pulmonary disease), and all-cause mortality. Seven-fold cross-validated Pearson's r between metabolomic age models and CA ranged between 0.47 and 0.65 in the training cohort set (mean absolute error: 8-9 years). Metabolomic age models, adjusted for CA, were associated with C-reactive protein, and inversely associated with glomerular filtration rate. Positively associated risk factors included obesity, diabetes, smoking, and physical inactivity. In UK Biobank, correlations of metabolomic age with CA were modest (r = 0.29-0.33), yet all metabolomic model scores predicted mortality (hazard ratios of 1.01 to 1.06/metabolomic age year) and CVD, after adjustment for CA. While metabolomic age models were only moderately associated with CA in an independent population, they provided additional prediction of morbidity and mortality over CA itself, suggesting their wider applicability.</p
"I Am Not Taking Sides as a Female At All":Co-Facilitation and Gendered Positioning in a Domestic Abuse Perpetrator Program
The facilitation of domestic abuse perpetrator programs (DAPPs) by mixed gender co-facilitation pairs brings different facilitator perspectives and enables the modeling of egalitarian and respectful male-female relationships. This study analyzed 22 video and audio recordings of community-based DAPP groups featuring male participants, and male and female facilitators. Using thematic analysis, we aimed to understand how facilitators engaged participants and whether the facilitator's gender affected this. We found an asymmetry in the positioning of the facilitators. Group participants challenged both facilitators, but especially the female facilitators. Facilitator strategies toward behavior change included softening direct challenges (female facilitators) and mobilizing the shared category of men (male facilitators). Implications from this study are for reflective practice in facilitator management and supervision specifically focused on gendered power dynamics. Skilled facilitation is key to behavior change and the gendered interplay within groups may be a crucial element in the reduction of interpersonal violence and abuse.</p
Data from Rogmann & Dubrovinsky 2024
Supplementary information for: 'A Raman spectroscopic study of CS_2 with paraffin up to 25 GPa' by E.-M. Rogmann and L.S. Dubrovinsk
Multiplicity and Educational Reproduction:Building the Intersection of Social Structures into Bourdieu's Model
Bourdieu’s model of educational reproduction is primarily about class. It may seem, then, that research showing how various factors can offset or modify the apparent effects of class on educational outcomes – not just gender or ethnicity but ‘family effects’, ‘school effects’ and ‘neighbourhood effects’ – are troublesome for the model. However, Bourdieu’s original synoptic diagram of reproduction contains all manner of caveats and allowances that can accommodate such findings – they were just never developed beyond quick acknowledgement. The purpose of this chapter is to engage in that development work. It considers, in theoretical terms, the interplay of class with myriad factors in shaping children’s relationships to the education system. In doing so, it integrates and builds on some of Bourdieu’s concepts and ideas developed later in his career, including the notion of ‘field’ and the concept of ‘social surface’. The result is a revised model of educational reproduction that still places class at the heart of the process but builds multiplicity of social positioning into the picture more rigorously. This model should then provide educational researchers with a variety of tools for making sense of observed deviations from modal tendencies in quantitative and qualitative data
Equivariant hierarchically hyperbolic structures for 3-manifold groups via quasimorphisms
Behrstock, Hagen, and Sisto classified 3-manifold groups admitting a hierarchically hyperbolic space structure. However, these structures were not always equivariant with respect to the group. In this paper, we classify 3-manifold groups admitting equivariant hierarchically hyperbolic structures. The key component of our proof is that the admissible groups introduced by Croke and Kleiner always admit equivariant hierarchically hyperbolic structures. For non-geometric graph manifolds, this is contrary to a conjecture of Behrstock, Hagen, and Sisto and also contrasts with results about CAT(0) cubical structures on these groups. Perhaps surprisingly, our arguments involve the construction of suitable quasimorphisms on the Seifert pieces, in order to construct actions on quasi-lines