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We present the first national DNA barcode resource that covers the native flowering plants and conifers for the nation of Wales (1143 species). Using the plant DNA barcode markers rbcL and matK, we have assembled 97.7% coverage for rbcL, 90.2% for matK, and a dual-locus barcode for 89.7% of the native Welsh flora. We have sampled multiple individuals for each species, resulting in 3304 rbcL and 2419 matK sequences. The majority of our samples (85%) are from DNA extracted from herbarium specimens. Recoverability of DNA barcodes is lower using herbarium specimens, compared to freshly collected material, mostly due to lower amplification success, but this is balanced by the increased efficiency of sampling species that have already been collected, identified, and verified by taxonomic experts. The effectiveness of the DNA barcodes for identification (level of discrimination) is assessed using four approaches: the presence of a barcode gap (using pairwise and multiple alignments), formation of monophyletic groups using Neighbour-Joining trees, and sequence similarity in BLASTn searches. These approaches yield similar results, providing relative discrimination levels of 69.4 to 74.9% of all species and 98.6 to 99.8% of genera using both markers. Species discrimination can be further improved using spatially explicit sampling. Mean species discrimination using barcode gap analysis (with a multiple alignment) is 81.6% within 10×10 km squares and 93.3% for 2×2 km squares. Our database of DNA barcodes for Welsh native flowering plants and conifers represents the most complete coverage of any national flora, and offers a valuable platform for a wide range of applications that require accurate species identification.

Genome size varies among individuals within plant species and their populations. Interspecific variation in plant genome size is associated with phenology, climate, and latitude and longitude—suggesting that genome size may be linked with environmental adaptation—but the evolutionary significance of intraspecific variation in genome size remains unresolved. In particular, little is known regarding how selection under different climatic and micro‐environmental conditions shapes intraspecific variation in genome size. We measured genome size within Festuca ovina populations collected from grassland plots exposed to 16 years of experimental drought treatment at the Buxton Climate Change Impacts Laboratory. We assessed whether genome size was associated with either drought treatment or fine‐scale heterogeneity in soil depth within grassland plots. Genome size varied by up to 1.28‐fold among F. ovina individuals, but was not associated with either drought treatment or plant phenotypes (cell size, flowering time, and biomass). Genome size was, however, negatively associated with fine‐scale variation in soil depth, implying that abiotic and biotic conditions linked with soil depth impose either direct or indirect selection on genome size. We suggest that the higher nutrient availability and reduced competition associated with shallow soils enable individuals with larger genomes to persist locally within the grassland. Intraspecific variation in plant genome size could allow adaptation to changing environmental conditions. Using the world's longest running drought manipulation experiment, we make a long‐term experimental test of the relationship between population‐level plant genome size and drought. We show that while plant genome size is not altered by drought treatment, it is associated with fine‐scale natural heterogeneity in soil depth.

Up to 10% of patients with systemic sclerosis (SSc) develop pulmonary arterial hypertension (PAH). This risk persists throughout the disease and is time dependent, suggesting that SSc is a susceptibility factor. Outcome for SSc-PAH is poor compared with heritable or idiopathic forms, despite clinical and pathological similarities. Although susceptibility in heritable PAH and idiopathic PAH is strongly associated with gene mutations leading to reduced expression of bone morphogenetic protein receptor (BMPR) II, these mutations have not been observed in SSc-PAH. To explore BMPRII expression and function in a mouse model of SSc (TβRIIΔk-fib) that is susceptible to developing pulmonary hypertension and in SSc lung. BMPRII and downstream signaling pathways were profiled in lung tissue and fibroblasts from the TβRIIΔk-fib model, which develops pulmonary vasculopathy with pulmonary hypertension that is exacerbated by SU5416. Complementary studies examined SSc or control lung tissue and fibroblasts. Our study shows reduced BMPRII, impaired signaling, and altered receptor turnover activity in a transforming growth factor (TGF)-β-dependent mouse model of SSc-PAH. Similarly, a significant reduction in BMPRII expression is observed in SSc lung tissue and fibroblasts. Increased proteasomal degradation of BMPRII appears to underlie this and may result from heightened TGF-β activity. We found reduced BMPRII protein in patients with SSc-PAH and a relevant mouse model associated with increased proteasomal degradation of BMPRII. Collectively, these results suggest that impaired BMP signaling, resulting from TGF-β-dependent increased receptor degradation, may promote PAH susceptibility in SSc and provide a unifying mechanism across different forms of PAH.

What makes a biochemist? Here, we introduce the Biochemical Literacy Framework (BCLF) comprised seven key skills: critical thinking, self‐management, communication, information literacy, visual literacy, practical skills and content knowledge. This BCLF is intended to facilitate further consultation and discussion towards defining the context and qualities of a biochemist. When developing meaningful curricula, institutions must engage with the desired disciplinary attributes of their graduates. Successfully employed in several areas, including psychology and chemistry, disciplinary literacies provide structure for the development of core competencies‐pursuing progressive education. To this end, we have sought to develop a comprehensive blueprint of a graduate biochemist, providing detailed insight into the development of skills in the context of disciplinary knowledge. The Biochemical Literacy Framework (BCLF) aspires to encourage innovative course design in both the biochemical field and beyond through stimulating discussion among individuals developing undergraduate biochemistry degree courses based on pedagogical best practice. Here, we examine the concept of biochemical literacy aiming to start answering the question: What must individuals do and know to approach and transform ideas in the context of the biochemical sciences? The BCLF began with the guidance published by relevant learned societies – including the Royal Society of Biology, the Biochemical Society, the American Society for Biochemistry and Molecular Biology and the Quality Assurance Agency, before considering relevant pedagogical literature. We propose that biochemical literacy is comprised of seven key skills: critical thinking, self‐management, communication, information literacy, visual literacy, practical skills and content knowledge. Together, these form a dynamic, highly interconnected and interrelated meta‐literacy supporting the use of evidence‐based, robust learning techniques. The BCLF is intended to form the foundation for discussion between colleagues, in addition to forming the groundwork for both pragmatic and exploratory future studies into facilitating and further defining biochemical literacy.

NKX2-5 is a member of the homeobox-containing transcription factors critical in regulating tissue differentiation in development. Here, we report a role for NKX2-5 in vascular smooth muscle cell phenotypic modulation in vitro and in vascular remodeling in vivo. NKX2-5 is upregulated in scleroderma patients with pulmonary arterial hypertension. Suppression of NKX2-5 expression in smooth muscle cells halted vascular smooth muscle proliferation and migration, enhanced contractility, and blocked the expression of extracellular matrix genes. Conversely, overexpression of NKX2-5 suppressed the expression of contractile genes (ACTA2, TAGLN, CNN1) and enhanced the expression of matrix genes (COL1) in vascular smooth muscle cells. In vivo, conditional deletion of NKX2-5 attenuated blood vessel remodeling and halted the progression to hypertension in a mouse chronic hypoxia model. This study revealed that signals related to injury such as serum and low confluence, which induce NKX2-5 expression in cultured cells, is potentiated by TGF-β and further enhanced by hypoxia. The effect of TGF-β was sensitive to ERK5 and PI3K inhibition. Our data suggest a pivotal role for NKX2-5 in the phenotypic modulation of smooth muscle cells during pathological vascular remodeling and provide proof of concept for therapeutic targeting of NKX2-5 in vasculopathies.

PurposeConcept maps have been described as a valuable tool for exploring curriculum knowledge. However, less attention has been given to the use of them to visualise contested and tacit knowledge, i.e. the values and perceptions of teachers that underpin their practice. This paper aims to explore the use of concept mapping to uncover academics’ views and help them articulate their perspectives within the framework provided by the concepts of pedagogic frailty and resilience in a collaborative environment.Design/methodology/approachParticipants were a group of five colleagues within a Biochemical Science Department, working on the development of a new undergraduate curriculum. A qualitative single-case study was conducted to get some insights on how concept mapping might scaffold each step of the collaborative process. They answered the online questionnaire; their answers were “translated” into an initial expert-constructed concept map, which was offered as a starting point to articulate their views during a group session, resulting in a consensus map.FindingsEngaging with the questionnaire was useful for providing the participants with an example of an “excellent” map, sensitising them to the core concepts and the possible links between them, without imposing a high level of cognitive load. This fostered dialogue of complex ideas, introducing the potential benefits of consensus maps in team-based projects.Originality/valueAn online questionnaire may facilitate the application of the pedagogic frailty model for academic development by scaling up the mapping process. The map-mediated facilitation of dialogue within teams of academics may facilitate faculty development by making explicit the underpinning values held by team members.

The development of pulmonary arterial hypertension in scleroderma remains an important contributor to mortality in this condition, despite substantial improvements in outcomes due to modern therapeutic strategies. No animal models of scleroderma develop this important complication. We describe the constitutive vascular phenotype of a mouse model of scleroderma and show that pulmonary endothelial injury replicates the pathological changes of pulmonary arterial hypertension seen in human disease. The TβRIIΔk-fib mouse strain expresses a kinase-deficient type II transforming growth factor β (TGFβ) receptor driven by a fibroblast-specific promoter leading to ligand-dependent upregulation of TGFβ signalling; this mouse strain replicates key fibrotic features of scleroderma. We did structural, biochemical, and functional assessments of pulmonary and systemic vessels, including in-vivo haemodynamic studies, before and after vascular endothelial growth factor receptor (VEGFR) inhibition with SU5416, which induced pulmonary endothelial cell apoptosis. These assessments included biochemical analysis of the TGFβ, endothelin, and VEGF signalling axes in vivo; tissue sections; and explanted pulmonary arterial smooth muscle cells. In the TβRIIΔk-fib mouse strain, a constitutive pulmonary vasculopathy with medial thickening, a perivascular proliferating chronic inflammatory cell infiltrate, and mildly raised pulmonary artery pressures resemble the well-described chronic hypoxia model of pulmonary hypertension. After administration of SU5416, the pulmonary vascular phenotype was more florid, with pulmonary arteriolar luminal obliteration by apoptosis-resistant proliferating endothelial cells; the result was right ventricular hypertrophy confirming haemodynamically significant pulmonary arterial hypertension. Altered TGFβ, endothelin, and ligand and receptor expression of VEGF were consistent with a scleroderma phenotype. This study replicates key features of scleroderma-associated pulmonary arterial hypertension in a mouse model. Our results suggest that pulmonary endothelial cell injury in a genetically susceptible mouse strain triggers this complication and support functional interplay between TGFβ, endothelin, and VEGF that provides insight into pathogenesis. Arthritis Research UK.

Accurate acquisition of phenotypic data is critical for cataloguing and utilising genetic variation in cultivated crops, landraces, and their wild relatives. The collection of phenotypic data using handwritten notes often introduces errors which can and should be avoided. Electronic data collection is crucial for ensuring error prevention and data standardisation and thus ensuring high-quality, reliable data. This paper describes the development of GridScore NEXT, a new plant phenotyping application that significantly advances the state of the art for collecting field trial data in plant genetics, pre-breeding and crop improvement research. Building on its predecessor, GridScore, the development of GridScore NEXT was driven by real life, in the field interactions with expert user groups across a number of crops. This iterative design methodology allowed the development and testing of new features. Collaborators from the 'Biodiversity for Opportunities, Livelihoods and Development' (BOLD) project, focusing on crops including rice, grasspea, and alfalfa, along with barley, potato, vegetable and blueberry teams, provided invaluable insights through training sessions and interviews and in the field use of the application. Key improvements to GridScore NEXT include enhanced data collection tools, supporting individual plant phenotyping within plots and enabling new data types such as GPS coordinates and image traits. GridScore NEXT provides customisable user defined validation rules to help prevent errors and incorporates barcode scanning for accurate, efficient data capture. The application offers an increased toolbox of data visualizations over its predecessor including heatmaps and statistical box plots, which aid in identifying potential data issues and understanding trial performance in the field. GridScore NEXT is cross-platform and can operate without an internet connection, making it ideal for field use in remote areas. Its adoption has led to standardisation of methods, significant error reduction, and the timely sharing of data, enabling quicker decision-making in pre-breeding and characterisation experiments. GridScore NEXT is available under an open-source (Apache 2.0) licence and freely available to all with no restrictions. It offers self-hosting options for enhanced data security and privacy. GridScore NEXT shows broad applicability across a diverse range of not only plant phenotyping experiments, but any experiment that requires the collection of accurate data.

Background Many reports from the UK government and other organisations highlight a need for a plant aware workforce, and some enumerate specific areas of plant science where there is a skills shortage. We have undertaken a systematic analysis of the content of degree programmes that advertise as teaching plant biology to determine if the UK Higher Education (HE) sector is delivering the graduates required to meet the skills gaps reported. Results Our data reveals a highly mixed picture of delivery from 1‐ to 4‐year courses, modules ranging from 10 to 40 credits, and Higher Education Institutions (HEIs) providing variable information on their websites. Our analysis shows that on average (irrespective of credit) a module covers three subject areas. Most courses have little plant content and it is generally taught with other subjects on a module. The most substantial plant‐specific subject teaching is delivered on 18 courses we have identified as Plant Science courses. Conclusion Overall, the UK HE sector is not delivering graduates with the skill set outlined in numerous reports as required to enable food production in a changing climate. Any prospective student (or employer) will find it virtually impossible to determine which degree will deliver the skills they need as there is no plant curriculum offered across the board, and specific information is hidden within module descriptors on websites. If the skills outlined as being essential for the economy and society are truly important, then a new approach is required.