HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids

BACKGROUND: The analysis of polyploid genomes is problematic because homeologous subgenome sequences are closely related. This relatedness makes it difficult to assign individual sequences to the specific subgenome from which they are derived, and hinders the development of polyploid whole genome assemblies. RESULTS: We here present a next-generation sequencing (NGS)-based approach for assignment of subgenome-specific base-identity at sites containing homeolog-specific polymorphisms (HSPs): ‘HSP base Assignment using NGS data through Diploid Similarity’ (HANDS). We show that HANDS correctly predicts subgenome-specific base-identity at >90% of assayed HSPs in the hexaploid bread wheat (Triticum aestivum) transcriptome, thus providing a substantial increase in accuracy versus previous methods for homeolog-specific base assignment. CONCLUSION: We conclude that HANDS enables rapid and accurate genome-wide discovery of homeolog-specific base-identity, a capability having multiple applications in polyploid genomics

Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat

BACKGROUND: Bread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets. Therefore each wheat gene potentially exists as a trio of A, B and D homoeoloci, each of which may contribute differentially to wheat phenotypes. We describe a novel approach combining wheat cytogenetic resources (chromosome substitution ‘nullisomic-tetrasomic’ lines) with next generation deep sequencing of gene transcripts (RNA-Seq), to directly and accurately identify homoeologue-specific single nucleotide variants and quantify the relative contribution of individual homoeoloci to gene expression. RESULTS: We discover, based on a sample comprising ~5-10% of the total wheat gene content, that at least 45% of wheat genes are expressed from all three distinct homoeoloci. Most of these genes show strikingly biased expression patterns in which expression is dominated by a single homoeolocus. The remaining ~55% of wheat genes are expressed from either one or two homoeoloci only, through a combination of extensive transcriptional silencing and homoeolocus loss. CONCLUSIONS: We conclude that wheat is tending towards functional diploidy, through a variety of mechanisms causing single homoeoloci to become the predominant source of gene transcripts. This discovery has profound consequences for wheat breeding and our understanding of wheat evolution

Sustainable pathways towards climate and biodiversity goals in the UK:the importance of managing land-use synergies and trade-offs

Agricultural and environmental policies are being fundamentally reviewed and redesigned in the UK following its exit from the European Union. The UK government and the Devolved Administrations recognise that current land use is not sustainable and that there is now an unprecedented opportunity to define a better land strategy that responds fully to the interconnected challenges of climate change, biodiversity loss and sustainable development. This paper presents evidence from three pathways (current trends, sustainable medium ambition, and sustainable high ambition) to mid-century that were co-created with UK policymakers. The pathways were applied to a national integrated food and land-use model (the FABLE calculator) to explore potential synergies and trade-offs between achieving multiple sustainability targets under limited land availability and constraints to balance food supply and demand at national and global levels. Results show that under the Current Trends pathway all unprotected open natural land would be converted to urban, agriculture and afforested land, with the consequence that from 2030 onwards tree planting targets could not be met. In contrast, the two sustainable pathways illustrate how dietary change, agricultural productivity improvements and waste reduction can free up land for nature recovery and carbon sequestration. This enables a transition to a sustainable food and land-use system that provides a net carbon sink with up to 44% of land able to support biodiversity conservation. We highlight key trade-offs and synergies, which are important to consider for designing and implementing emerging national policies. These include the strong dependence of climate, food and biodiversity targets on dietary shifts, sustainable improvements in agricultural productivity, improved land-use design for protecting and restoring nature, and rapid reductions in food loss and waste.Supplementary informationThe online version contains supplementary material available at 10.1007/s11625-022-01242-8

Measuring nasal bacterial load and its association with otitis media

BACKGROUND: Nasal colonisation with otitis media (OM) pathogens, particularly Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis, is a precursor to the onset of OM. Many children experience asymptomatic nasal carriage of these pathogens whereas others will progress to otitis media with effusion (OME) or suppurative OM. We observed a disparity in the prevalence of suppurative OM between Aboriginal children living in remote communities and non-Aboriginal children attending child-care centres; up to 60% and <1%, respectively. This could not be explained by the less dramatic difference in rates of carriage of respiratory bacterial pathogens (80% vs 50%, respectively). In this study, we measured nasal bacterial load to help explain the different propensity for suppurative OM in these two populations. METHODS: Quantitative measures (colony counts and real-time quantitative PCR) of the respiratory pathogens S. pneumoniae, H. influenzae and M. catarrhalis, and total bacterial load were analysed in nasal swabs from Aboriginal children from remote communities, and non-Aboriginal children attending urban child-care centres. RESULTS: In both populations nearly all swabs were positive for at least one of these respiratory pathogens. Using either quantification method, positive correlations between bacterial load and ear state (no OM, OME, or suppurative OM) were observed. This relationship held for single and combined bacterial respiratory pathogens, total bacterial load, and the proportion of respiratory pathogens to total bacterial load. Comparison of Aboriginal and non-Aboriginal children, all with a diagnosis of OME, demonstrated significantly higher loads of S. pneumoniae and M. catarrhalis in the Aboriginal group. The increased bacterial load despite similar clinical condition may predict persistence of middle ear effusions and progression to suppurative OM in the Aboriginal population. Our data also demonstrated the presence of PCR-detectable non-cultivable respiratory pathogens in 36% of nasal swabs. This may have implications for the pathogenesis of OM including persistence of infection despite aggressive therapies. CONCLUSION: Nasal bacterial load was significantly higher among Aboriginal children and may explain their increased risk of suppurative OM. It was also positively correlated with ear state. We believe that a reduction in bacterial load in high-risk populations may be required before dramatic reductions in OM can be achieved

Clinical, radiologic, pathologic, and molecular characteristics of long-term survivors of diffuse intrinsic pontine glioma (DIPG): a collaborative report from the International and European Society for Pediatric Oncology DIPG registries

Purpose Diffuse intrinsic pontine glioma (DIPG) is a brainstem malignancy with a median survival of &lt; 1 year. The International and European Society for Pediatric Oncology DIPG Registries collaborated to compare clinical, radiologic, and histomolecular characteristics between short-term survivors (STSs) and long-term survivors (LTSs). Materials and Methods Data abstracted from registry databases included patients from North America, Australia, Germany, Austria, Switzerland, the Netherlands, Italy, France, the United Kingdom, and Croatia. Results Among 1,130 pediatric and young adults with radiographically confirmed DIPG, 122 (11%) were excluded. Of the 1,008 remaining patients, 101 (10%) were LTSs (survival ≥ 2 years). Median survival time was 11 months (interquartile range, 7.5 to 16 months), and 1-, 2-, 3-, 4-, and 5-year survival rates were 42.3% (95% CI, 38.1% to 44.1%), 9.6% (95% CI, 7.8% to 11.3%), 4.3% (95% CI, 3.2% to 5.8%), 3.2% (95% CI, 2.4% to 4.6%), and 2.2% (95% CI, 1.4% to 3.4%), respectively. LTSs, compared with STSs, more commonly presented at age &lt; 3 or &gt; 10 years (11% v 3% and 33% v 23%, respectively; P &lt; .001) and with longer symptom duration ( P &lt; .001). STSs, compared with LTSs, more commonly presented with cranial nerve palsy (83% v 73%, respectively; P = .008), ring enhancement (38% v 23%, respectively; P = .007), necrosis (42% v 26%, respectively; P = .009), and extrapontine extension (92% v 86%, respectively; P = .04). LTSs more commonly received systemic therapy at diagnosis (88% v 75% for STSs; P = .005). Biopsies and autopsies were performed in 299 patients (30%) and 77 patients (10%), respectively; 181 tumors (48%) were molecularly characterized. LTSs were more likely to harbor a HIST1H3B mutation (odds ratio, 1.28; 95% CI, 1.1 to 1.5; P = .002). Conclusion We report clinical, radiologic, and molecular factors that correlate with survival in children and young adults with DIPG, which are important for risk stratification in future clinical trials

The effect of web based depression interventions on self reported help seeking: randomised controlled trial [ISRCTN77824516]

BACKGROUND: To date, there has been very little work investigating behaviour changes induced by interventions that are designed to increase help seeking. The present paper examines the effects of two Internet depression websites on help seeking. METHODS: 414 individuals with elevated scores on a depression assessment scale were randomly allocated to a depression information website, a cognitive-behavioural skills training website (CBT) or an attention control condition. Reports of help seeking for specific treatments, from specific sources and for categories of treatments were assessed. RESULTS: Relative to the control, the depression information site was associated with decreases in seeking support from friends and family, the use of music and of everyday treatments and no increase in seeking evidence based interventions. The CBT site was associated with the report of help seeking for CBT, massage and exercise. CONCLUSION: Methods to encourage the use of evidence-based treatments need further research to determine whether the assistance sought is evidence based and whether there are unintended effects

Reduced Complexity Model Intercomparison Project Phase 1: introduction and evaluation of global-mean temperature response

Reduced-complexity climate models (RCMs) are critical in the policy and decision making space, and are directly used within multiple Intergovernmental Panel on Climate Change (IPCC) reports to complement the results of more comprehensive Earth system models. To date, evaluation of RCMs has been limited to a few independent studies. Here we introduce a systematic evaluation of RCMs in the form of the Reduced Complexity Model Intercomparison Project (RCMIP). We expect RCMIP will extend over multiple phases, with Phase 1 being the first. In Phase 1, we focus on the RCMs' global-mean temperature responses, comparing them to observations, exploring the extent to which they emulate more complex models and considering how the relationship between temperature and cumulative emissions of CO2 varies across the RCMs. Our work uses experiments which mirror those found in the Coupled Model Intercomparison Project (CMIP), which focuses on complex Earth system and atmosphere–ocean general circulation models. Using both scenario-based and idealised experiments, we examine RCMs' global-mean temperature response under a range of forcings. We find that the RCMs can all reproduce the approximately 1 ∘C of warming since pre-industrial times, with varying representations of natural variability, volcanic eruptions and aerosols. We also find that RCMs can emulate the global-mean temperature response of CMIP models to within a root-mean-square error of 0.2 ∘C over a range of experiments. Furthermore, we find that, for the Representative Concentration Pathway (RCP) and Shared Socioeconomic Pathway (SSP)-based scenario pairs that share the same IPCC Fifth Assessment Report (AR5)-consistent stratospheric-adjusted radiative forcing, the RCMs indicate higher effective radiative forcings for the SSP-based scenarios and correspondingly higher temperatures when run with the same climate settings. In our idealised setup of RCMs with a climate sensitivity of 3 ∘C, the difference for the ssp585–rcp85 pair by 2100 is around 0.23∘C(±0.12 ∘C) due to a difference in effective radiative forcings between the two scenarios. Phase 1 demonstrates the utility of RCMIP's open-source infrastructure, paving the way for further phases of RCMIP to build on the research presented here and deepen our understanding of RCMs

RUNX1 is a driver of renal cell carcinoma correlating with clinical outcome

The recurring association of specific genetic lesions with particular types of cancer is a fascinating, and largely unexplained area of cancer biology. This is particularly true of clear cell renal cell carcinoma (ccRCC) where although key mutations such as loss of VHL is an almost ubiquitous finding, there remains a conspicuous lack of targetable genetic drivers. In this study, we have identified a previously unknown pro-tumorigenic role for the RUNX genes in this disease setting. Analysis of patient tumor biopsies together with loss of function studies in preclinical models established the importance of RUNX1 and RUNX2 in ccRCC. Patients with high RUNX1 (and RUNX2) expression exhibited significantly poorer clinical survival compared to patients with low expression. This was functionally relevant as deletion of RUNX1 in ccRCC cell lines reduced tumor cell growth and viability in vitro and in vivo. Transcriptional profiling of RUNX1-CRISPR-deleted cells revealed a gene signature dominated by extracellular matrix remodelling, notably affecting STMN3, SERPINH1, and EPHRIN signaling. Finally, RUNX1 deletion in a genetic mouse model of kidney cancer improved overall survival and reduced tumor cell proliferation. In summary, these data attest to the validity of targeting a RUNX1-transcriptional program in ccRCC. [Abstract copyright: Copyright ©2020, American Association for Cancer Research.

Sputum is a surrogate for bronchoalveolar lavage for monitoring Mycobacterium tuberculosis transcriptional profiles in TB patients

SummaryPathogen-targeted transcriptional profiling in human sputum may elucidate the physiologic state of Mycobacterium tuberculosis (M. tuberculosis) during infection and treatment. However, whether M. tuberculosis transcription in sputum recapitulates transcription in the lung is uncertain. We therefore compared M. tuberculosis transcription in human sputum and bronchoalveolar lavage (BAL) samples from 11 HIV-negative South African patients with pulmonary tuberculosis. We additionally compared these clinical samples with in vitro log phase aerobic growth and hypoxic non-replicating persistence (NRP-2). Of 2179 M. tuberculosis transcripts assayed in sputum and BAL via multiplex RT-PCR, 194 (8.9%) had a p-value <0.05, but none were significant after correction for multiple testing. Categorical enrichment analysis indicated that expression of the hypoxia-responsive DosR regulon was higher in BAL than in sputum. M. tuberculosis transcription in BAL and sputum was distinct from both aerobic growth and NRP-2, with a range of 396–1020 transcripts significantly differentially expressed after multiple testing correction. Collectively, our results indicate that M. tuberculosis transcription in sputum approximates M. tuberculosis transcription in the lung. Minor differences between M. tuberculosis transcription in BAL and sputum suggested lower oxygen concentrations or higher nitric oxide concentrations in BAL. M. tuberculosis-targeted transcriptional profiling of sputa may be a powerful tool for understanding M. tuberculosis pathogenesis and monitoring treatment responses in vivo