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Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants
No full textAdditional data associated with the publication "Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants" Nature Plants, 2025.
Abstract:
The plant hormone auxin regulates a wide variety of transcriptional responses depending on the cell type, environment, and species. How this diversity is achieved may be related to the specific complement of auxin signalling components in each cell. The levels of activators (class-A AUXIN RESPONSE FACTORS) and repressors (class-B ARFs) are particularly important. Tight regulation of ARF protein levels is likely key in determining this balance. Through comparative analysis of novel, dominant mutants in maize and the moss Physcomitrium patens, we have discovered a ~500-million-year-old mechanism of class-B ARF protein level regulation mediated by proteasome degradation, important in determining cell fate decisions across land plants. Thus, our results add a key piece to the puzzle of how auxin regulates plant development.
These datasets are in addition to those included in the supplmentary materials in the paper, the raw sequence data provided in the NCBI GEO deposit, and the github pages (https://github.com/ThePlantShapeLab/Truffula )
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The raw sequence data associated with the project is available to download at GEO accession numbers GSE293375, GSE293431, GSE293432Please see README_Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants.txt file for information on each datase
Effect of deliberate physical damage and repair on the icephobicity of oil-infused elastomer coatings
No full textOil-infused elastomers have shown promise as anti-icing coatings, but their softness has led to durability concerns. The effect of damage is investigated to study the resilience of the icephobicity of silicone elastomer coatings with and without oil-infusion. Physical damage is applied to specimens by abrading with grit paper or cutting with a scalpel. Surface characterization reveals morphological changes in the coatings due to damage and de-icing on the surfaces, along with changes in the static water contact angle. Abrasion of the surfaces does not overwhelmingly or universally worsen the ice adhesion strength. Some damage even lowers the ice adhesion strength, possibly due to Cassie-Baxter wetting. However, it decreases the average freezing time. Cutting causes accelerated deterioration to ice adhesion strength and worsens freezing time. Though damage to the oil-infused coatings is greater, changes in icephobicity are similar to coatings without oil-infusion. Re-coating is an effective method of repairing even severely damaged surfaces and recovering icephobicity. We show oil-infused elastomers have durable icephobicity and are effective anti-icing coatings
Metagenomic analysis of dietary fiber-induced modulations in the caecal microbiota of chickens (ANI 99% MAGs: ENA project PRJEB77488)
No full textDietary fibers offer a potential solution to rising feed costs and feed–food competition. They are known to impact the health of birds by shaping their gut microbiota. Understanding of how dietary Fibers (soluble and insoluble) modulate caecal microbiota can help in devising targeted manipulation strategies to improve Fiber fermentation and ultimately enhance chicken productivity. Birds were divided into five different dietary groups (1) basal diet (CG): corn/soya-based diet; (2) GA: basal diet + 1% inulin; (3) GB: basal diet + 4% inulin; (4) GC: basal diet + 1% ARBOCEL; (5) GD: basal diet + 4% ARBOCEL. DNA from caecal contents was isolated, and shotgun metagenomic sequencing was performed. Raw sequencing files, primary assemblies, bins, and metagenome assembled genomes (MAGs) that were dereplicated at the species level (95% ANI) have been uploaded to the European Nucleotide Archive (project PRJEB77488). This dataset contains all MAGs produced from this project, dereplicated at the strain level (99% ANI)
Cardiovascular profile of Cushing Syndrome in mice
No full textCushing Syndrome, reflecting endogenous overproduction of ACTH or exogenous exposure to glucocorticoid medication, increases cardiovascular risk. Hypertension is a major factor but underlying mechanisms are not clearly defined. We modelled Cushing Syndrome in male C57BL/6J mice with prolonged ACTH infusion and measured blood pressure on control diet and following high salt intake. In a separate group we assessed renal function and salt excretion, the in vivo pressure natriuresis response and ex vivo artery function. We found that ACTH infusion impairs sodium excretion and causes a transition to non-dipping and salt-sensitive BP. Renal hemodynamic and tubular abnormalities impair the pressure natriuresis response. Our findings provide a landscape of the complex physiological response to ACTH excess that may contribute to poor cardiovascular health in Cushing Syndrome
The Stab Resistance of Bombyx Mori Silk Cocoons (Data)
No full textData related to the paper "The Stab Resistance of Bombyx Mori Silk Cocoons", the abstract for which follows: This study considers the mechanical response of Bombyx mori silk cocoons to knife stabbing, a simple but controlled way of simulating predaceous penetration. Here, we stab test both entire cocoons (EC) and cocoon wall segments (CWS) statically and dynamically, and note that the process can be broken down in three stages. The first stage involves material deflection, the second is knife penetration, and the third is knife perforation. It is found that ca. 95 % of the kinetic energy is lost during the penetration stage. There are noticeable differences in strain between the equatorial (
= 13 %) and meridional (
= 1.5 %) directions before and after the stabbing of EC specimens (p <0.001). The apparent area of the cocoon is noted to be on average 7 % lower after stabbing than it is prior to being stabbed (p <0.01). It is found that while compression of the cocoon from stabbing results in equatorial expansion (with a Poisson's ratio, ν = 0.25), in the meridional direction the cocoon contracts (ν = -0.05) thus displaying auxetic behavior. Force-deflection curves are different in CWS specimens as compared to EC specimens, and this is attributable to natural curvatures in CWS specimens remaining even after a being flattened for mounting and testing. Differences between EC and CWS specimens are also noticeable in the sizes of the stab footprints, with EC samples exhibiting 33 % smaller footprints than CWS samples (p < 0.001). It is concluded that testing whole cocoon structures provides a more accurate understanding of their properties as compared to cut and flattened structures. This is because flattening cocoon wall specimens induces delamination and multiple failure zones, reducing the natural stab resistance of the material.Excel file containing stress-strain data from tensile testing of the Bombyx mori cocoon wall:
Stress-strain data.xls
Excel file containing raw data for the dimensional changes in Bombyx mori cocoons along with their standard deviations and changes in normalised area of full cocoons:
Dimensional changes.xls
Excel file containing data for the stab force comparison of Bombyx mori cocoon wall and the entire cocoon:
Stab force comparison.xls
Excel file containing continuous force-displacement data from the Instron testing, presenting a comparison of the Bombyx mori cocoon wall and the entire cocoon:
Stab force against displacement.xls
Excel file containing data for the comparison of knife stab footprint for the static and dynamic testing:
Stab footprint area EC vs CWS.xl
CLAW: a Phase Differentiation and Biomechanical Modeling Software for Animal Claws
Get PDFCLAW is a software that provides an integrated platform for the high-resolution phase differentiation (material differentiation), and biomechanical modeling of animal claws. The workflow begins by converting two-dimensional (2D) DICOM slices from computer tomography (CT) scans into a three-dimensional (3D) volumetric model. From this 3D volume, users can perform segmentation to differentiate between regions of alpha-keratin, beta-keratin, and bone. Based on the segmented volume, the software enables the creation of single-material and composite-material meshes using 3D Delaunay tetrahedralization, based on machine learning to generate accurate surface, voxel, and volumetric meshes. After meshing, users can assign material properties (currently limited to a single material) to the whole claw, and perform finite element–based stress analysis under different loading conditions. The workflow ensures high geometric fidelity and supports the reproducible modeling of complex biological structures
Teaching that Matters for Migrant Students (TEAMS): Understanding Levers of Integration in Scotland, Finland and Sweden
No full textTEAMS is an international project conducted by teams of researchers from the Universities of Edinburgh, Jyväskylä, Stockholm, and Turku, led by Dr. Nataša Pantić at the University of Edinburgh and supported by the NordForsk British-Nordic research programme. This three-year project has addressed the need to understand the challenges and opportunities for schools as they respond to the increasing number of migrants in classrooms. The project used mixed methods, including social network analysis and qualitative fieldwork.
The project collected new data on teachers’ beliefs, practices and social networks, and the integration experiences of migrant students, including:
· Quantitative survey data of teachers’ social networks (n =359 (wave 1) – 416 (w2) – 341 (w3))
· Quantitative survey data on student engagement in schools (n=394 (w1) – 973 (w3))
· Online log data on teacher interaction for migrant student support (n=126(w1) – 78 (w2) – 81 (w3))
· Qualitative interview data on school staff/students’ beliefs (n=44/8(w1)–33/20(w2)–17/19(w3))
· Qualitative observations data on school staff practices and interactions (~120 h of fieldwork notes in total)
· Policy review data (~80 documents
Sensing The Direction of Leadership and Social Identity in Dance Education_Interview data
No full textThe Social Identity in Leadership (SIL) model, recently applied in sports coaching environments argues that leadership is best understood in terms of the relationship between the leader and followers within a particular social or cultural group. SIL addresses how individuals who share a common social identity collaborate to lead other members of the community and influence them. Despite potential application benefits, this theory has yet to be defined and contextualised in dance environments. Accordingly, the aim of this study was to determine current approaches to the delivery of dance with regard to motivating learners to initiate then sustain and extend their engagement. Specifically, we sought to discover the approaches to leadership currently applied by dance teachers and to determine if principles of SIL are used. Based on a review of current literature about the application of SIL in teaching and coaching contexts, semi-structured interviews were conducted with nine experienced dance teachers recruited from a network of experienced dance teachers in the UK using a purposive sampling approach. The range of experience the dance teachers had was from 5-20 years, with an overall mean of 11 years of dance teaching. The interviews lasted between 10 and 44 min, the variation in the duration of the interviews and relevant transcripts is attributed to each participant’s ability to articulate their understanding of SIL as this is a relatively new concept and terminology to be applied to dance. Five themes emerged from the data that provide evidence to suggest that, whist not as yet clearly defined, principles of SIL were employed by the dance teachers
Incidence, severity, risk factors and outcomes of SARS-CoV-2 reinfections during the Omicron period: a systematic review and meta-analysis
No full textOur previous systematic review estimated the cumulative incidence of SARS-CoV-2 reinfections as 1.16% (1.01%-1.33%) during the pre-Omicron period. The Omicron variant that emerged in November 2021 was significantly genetically distinct from the previous SARS-CoV-2 variants and thus, more transmissible and posed an increased risk of SARS-CoV-2 reinfections in the population. We, therefore, conducted a fresh systematic review and meta-analysis to estimate the SARS-CoV-2 reinfection burden during the Omicron period. We searched CINAHL, Medline, Global Health, Embase, and WHO COVID-19 in October 2023 for studies reporting the SARS-CoV-2 reinfection incidence during the Omicron period. The quality of the included studies was assessed using the Joanna Briggs Institute checklists. Random effects meta-analyses were conducted to estimate the incidence, and requirement of hospitalisation of SARS-CoV-2 reinfections. Symptomatic severity of reinfections and case fatality rates were analysed narratively. Thirty-six studies were included. We estimated the reinfection cumulative incidence during the Omicron period based on data from 28 studies. We also presented the cumulative incidence of SARS-CoV-2 reinfections by age-groups, vaccination status, and in healthcare workers. Data were limited on disease severity and long-term outcomes. The dataset contains information on the study characteristics of included studies, and overall incidence data, incidence data stratified by different variables (mainly age, sex, vaccination status, comorbidity status, and occupation) and severity and outcomes data reported in included studies
Targeting TRPM3 As a Potential Therapeutic Approach for Autosomal Dominant Polycystic Kidney Disease
No full textAbstract
Cystic diseases, especially autosomal dominant polycystic kidney disease (ADPKD; incidence approx. 1/1000), are a leading cause of renal failure, caused by appearance and growth of renal cysts that can lead to renal failure in middle age. Most ADPKD cases are caused by mutations in PKD1 or PKD2, encoding polycystin-1 (PC1) and polycystin-2 (PC2). PC1 is a mechanosensor that controls PC2, a Ca2+-permeable cation channel that, by regulating cytoplasmic Ca2+, prevents adenylyl cyclase producing cyst-promoting concentrations of cAMP. In other systems, there is evidence for PC2 interacts with TRPM3. We therefore examined the effect of pharmacological activators and inhibitors of TRPM3 on cyst formation in cultured mouse kidney rudiments exposed to a range of concentrations of forskolin, a cAMP-elevating drug commonly used experimentally to induce cysts in cultured kidneys. We found that TRPM3 inhibitors (isosakuranetin, primidone, diclofenac) increased cyst formation, while TRPM3 activators (CIM0216 and nifedipine) greatly reduced cyst formation and reduced the sensitivity of kidneys to forskolin. These preclinical, in-vitro data suggest that TRPM3 may be a promising target in ADPKD management