Genomic and phenotypic characterization of finger millet indicates a complex diversification history

Advances in sequencing technologies mean that insights into crop diversification can now be explored in crops beyond major staples. We use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the whole and sub‐genome level. A set of 8778 SNPs and 13 agronomic traits was used to characterize a diverse panel of 423 landraces from Africa and Asia. Through principal component analysis (PCA) and discriminant analysis of principal components, four distinct groups of accessions were identified that coincided with the primary geographic regions of finger millet cultivation. Notably, East Africa, presumed to be the crop's origin, exhibited the lowest genetic diversity. The PCA of phenotypic data also revealed geographic differentiation, albeit with differing relationships among geographic areas than indicated with genomic data. Further exploration of the sub‐genomes A and B using neighbor‐joining trees revealed distinct features that provide supporting evidence for the complex evolutionary history of finger millet. Although genome‐wide association study found only a limited number of significant marker‐trait associations, a clustering approach based on the distribution of marker effects obtained from a ridge regression genomic model was employed to investigate trait complexity. This analysis uncovered two distinct clusters. Overall, the findings suggest that finger millet has undergone complex and context‐specific diversification, indicative of a lengthy domestication history. These analyses provide insights for the future development of finger millet

Corticotrophin releasing factor increases ascending colon volume after a fructose test meal in healthy humans: a randomised control trial

Background: Poorly absorbed, fermentable carbohydrates can provoke irritable bowel syndrome (IBS) symptoms by escaping absorption in the small bowel and being rapidly fermented in the colon in some susceptible subjects. IBS patients are often anxious and stressed and stress accelerates small bowel transit which may exacerbate malabsorption. Objective: In this study we investigated the effect of intravenous injection of corticotrophin releasing factor (CRF) on fructose malabsorption and the resulting volume of water in the small bowel. Design: We performed a randomised, placebo controlled, cross-over study of CRF versus saline injection in 11 male and 10 female healthy subjects, examining the effect on the malabsorption of a 40 g fructose test meal and its transit through the gut which was assessed by serial Magnetic Resonance imaging (MRI) and breath hydrogen measurement. Orocaecal transit was assessed using the lactose-ureide C13 breath test and the adrenal response to CRF assessed by serial salivary cortisol measurements. Results: (Mean ± SD) CRF injection caused a significant rise in salivary cortisol which lasted 135 minutes. Small bowel water content (SBWC) rose from baseline, peaking at 45 minutes after fructose ingestion while breath hydrogen peaked later at 75 minutes. The area under the curve (AUC) for SBWC from -15 - 135 minutes was significantly lower after CRF versus saline (mean difference [95% CI] 7433 [275, 14591] mL.min, P = 0.04). Ascending colon volume rose after CRF, significantly more for male volunteers than female (P = 0.025). Conclusions: CRF constricts the small bowel and increases fructose malabsorption as shown by increased ascending colon volumes. This mechanism may help to explain the increased sensitivity of some stressed individuals to fructose malabsorption. This trial was registered at ClinicalTrials.gov as NCT0176328

The value of Sentinel-2 spectral bands for the assessment of winter wheat growth and development

Leaf Area Index (LAI) and chlorophyll content are strongly related to plant development and productivity. Spatial and temporal estimates of these variables are essential for efficient and precise crop management. The availability of open-access data from the European Space Agency’s (ESA) Sentinel-2 satellite—delivering global coverage with an average 5-day revisit frequency at a spatial resolution of up to 10 metres—could provide estimates of these variables at unprecedented (i.e., sub-field) resolution. Using synthetic data, past research has demonstrated the potential of Sentinel-2 for estimating crop variables. Nonetheless, research involving a robust analysis of the Sentinel-2 bands for supporting agricultural applications is limited. We evaluated the potential of Sentinel-2 data for retrieving winter wheat LAI, leaf chlorophyll content (LCC) and canopy chlorophyll content (CCC). In coordination with destructive and non-destructive ground measurements, we acquired multispectral data from an Unmanned Aerial Vehicle (UAV)-mounted sensor measuring key Sentinel-2 spectral bands (443 to 865 nm). We applied Gaussian processes regression (GPR) machine learning to determine the most informative Sentinel-2 bands for retrieving each of the variables. We further evaluated the GPR model performance when propagating observation uncertainty. When applying the best-performing GPR models without propagating uncertainty, the retrievals had a high agreement with ground measurements—the mean R2 and normalised root-mean-square error (NRMSE) were 0.89 and 8.8%, respectively. When propagating uncertainty, the mean R2 and NRMSE were 0.82 and 11.9%, respectively. When accounting for measurement uncertainty in the estimation of LAI and CCC, the number of most informative Sentinel-2 bands was reduced from four to only two—the red-edge (705 nm) and near-infrared (865 nm) bands. This research demonstrates the value of the Sentinel-2 spectral characteristics for retrieving critical variables that can support more sustainable crop management practices

Increased fasting small-bowel water content in untreated coeliac disease and scleroderma as assessed by magnetic resonance imaging

Background and aims: The regular overnight migrating motor complex (MMC) ensures that the normal fasting small bowel water content (SBWC) is minimised. We have applied our recently validated non-invasive magnetic resonance technique to assess SBWC in newly diagnosed coeliac disease (CD), scleroderma (SCD) and irritable bowel syndrome (IBS) conditions, possibly associated with small intestinal bacterial overgrowth (SIBO). Methods: 20 CD and 15 SCD patients with gastrointestinal symptoms were compared to 20 healthy volunteers (HV) and 26 IBS with diarrhoea (IBS-D) patients as previously reported. All underwent a fasting, magnetic resonance imaging (MRI) scan on a 1.5 T Philips Achieva MRI scanner to assess fasting SBWC and colonic volumes. Stool and symptom diaries were completed for 1 week. Results: Median (Interquartile range, IQR) Compared to healthy volunteers, all the patients had significantly increased stool frequency and Bristol stool form score. SBWC was significantly increased in CD 109(53-224) vs. 53(31-98) mL in HV, p [less than] 0.01 and 42 (28-67) in IBS-D, p [less than] 0.01. Variable increase in SBWC was also found in SCD, median 77(39-158) but this was not significant, p=0.2. Colonic volumes were similar for all groups being 547 (442-786) for CD, 511 (453-789) for SCD, 612 (445-746) for HV and 521 (428-757) mL for IBS-D. When CD patients were subdivided according to the Marsh classification, the higher grades had larger colonic volumes.Conclusion: Fasting SBWC as assessed by MRI is significantly increased in newly diagnosed CD and SCD but decreased in IBS-D. Future studies should test whether increased resting fluid predisposes to SIBO

Petabyte-scale innovations at the European Nucleotide Archive

Dramatic increases in the throughput of nucleotide sequencing machines, and the promise of ever greater performance, have thrust bioinformatics into the era of petabyte-scale data sets. Sequence repositories, which provide the feed for these data sets into the worldwide computational infrastructure, are challenged by the impact of these data volumes. The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/embl), comprising the EMBL Nucleotide Sequence Database and the Ensembl Trace Archive, has identified challenges in the storage, movement, analysis, interpretation and visualization of petabyte-scale data sets. We present here our new repository for next generation sequence data, a brief summary of contents of the ENA and provide details of major developments to submission pipelines, high-throughput rule-based validation infrastructure and data integration approaches

Comparing magnetic resonance liver fat fraction measurements with histology in fibrosis: the difference between proton density fat fraction and tissue mass fat fraction

Magnetic resonance spectroscopy (MRS) provides a powerful method of measuring fat fraction. However, previous studies have shown that MRS results give lower values compared with visual estimates from biopsies in fibrotic livers. This study investigated these discrepancies and considered whether a tissue water content correction, as assessed by MRI relaxometry, could provide better agreement. 110 patients were scanned in a 1.5 T Philips scanner and biopsies were obtained. Multiple echo MRS (30 × 30 ×  30 mm volume) was used to determine Proton Density Fat Fraction (PDFF). Biopsies were assessed by visual assessment for fibrosis and steatosis grading. Digital image analysis (DIA) was also used to quantify fat fraction within tissue samples. T relaxation times were then used to estimate tissue water content to correct PDFF for confounding factors. PDFF values across the four visually assessed steatosis grades were significantly less in the higher fibrosis group (F3-F4) compared to the lower fibrosis group (F0-F2). The slope of the linear regression of PDFF vs DIA fat fraction was ~ 1 in the low fibrosis group and 0.77 in the high fibrosis group. Correcting for water content based on T increased the gradient but it did not reach unity. In fibrotic livers, PDFF underestimated fat fraction compared to DIA methods. Values were improved by applying a water content correction, but fat fractions were still underestimated

Homosexuality, politics and Pentecostal nationalism in Zambia

Building upon debates about the politics of nationalism and sexuality in post-colonial Africa, this article highlights the role of religion in shaping nationalist ideologies that seek to regulate homosexuality. It specifically focuses on Pentecostal Christianity in Zambia, where the constitutional declaration of Zambia as a Christian nation has given rise to a form of ‘Pentecostal nationalism’ in which homosexuality is considered to be a threat to the purity of the nation and is associated with the Devil. The article offers an analysis of recent Zambian public debates about homosexuality, focusing on the ways in which the ‘Christian nation’ argument is deployed, primarily in a discourse of anti-homonationalism, but also by a few recent dissident voices. The latter prevent Zambia, and Christianity, from accruing a monolithic depiction as homophobic. Showing that the Zambian case presents a mobilisation against homosexuality that is profoundly shaped by the local configuration in which Christianity defines national identity – and in which Pentecostal-Christian moral concerns and theo-political imaginations shape public debates and politics – the article nuances arguments that explain African controversies regarding homosexuality in terms of exported American culture wars, proposing an alternative reading of these controversies as emerging from conflicting visions of modernity in Africa

Gay Rights, the Devil and the End Times: Public Religion and the Enchantment of the Homosexuality Debate in Zambia

This article contributes to the understanding of the role of religion in the public and political controversies about homosexuality in Africa. As a case study it investigates the heated public debate in Zambia following a February 2012 visit by United Nations Secretary General Ban Ki-moon, who emphasised the need for the country to recognise the human rights of homosexuals. The focus is on a particular Christian discourse in this debate, in which the international pressure to recognise gay rights is considered a sign of the end times, and Ban Ki-moon, the UN and other international organisations are associated with the Antichrist and the Devil. Here, the debate about homosexuality becomes eschatologically enchanted through millennialist thought. Building on discussions about public religion and religion and politics in Africa, this article avoids popular explanations in terms of fundamentalist religion and African homophobia, but rather highlights the political significance of this discourse in a postcolonial African context