Petrology and geochemistry of selected nepheline syenites from Malawi and their potential as alternative potash sources

The Sub Saharan Africa agricultural sector is one of the most disadvantaged regions, partly due to high fertiliser import costs from the northern hemisphere. Malawi is one such country which faces these fertiliser challenges for the agricultural sector growth and food crop production. However, Malawi has numerous intrusive alkaline rocks, nepheline syenites, especially within the Chilwa alkaline province. This study was therefore conducted to assess these nepheline syenites for their potential as potassium sources. We used Malawi's new airborne geophysical gamma ray data acquired in 2013, coupled with satellite remote sensing, to identify nepheline syenites suitable as possible sources for alternative silicate K-fertiliser, and carried out geochemical analysis of whole rock samples. Results show that the K2O content for the nepheline syenites varies from 3.17 wt % to 9.14 wt % with an average of 5.22 wt %. The K2O/Na2O ratio for Malawi's nepheline syenites ranges from 0.41 to 1.28 withan average of 0.65 showing that the nepheline syenites are mostly sodic but with variable composition. In addition to nepheline, the calcium feldspathoid davidsmithite ((Na,Ca)AlSiO4) was identified in the syenites using scanning electron microscopy with energy dispersive analysis. Although the different intrusive complexes are not homogenous, our results show that, generally, the nepheline syenites from Malawi have similar geochemistry and mineralogical composition to those which have been used as crushed-rock fertilisers in other parts of the world

Angular reflectance of leaves with a dual-wavelength terrestrial lidar and its implications for leaf-bark separation and leaf moisture estimation

A new generation of multi-wavelength lidars offer the potential to measure the structure and biochemistry of vegetation simultaneously, using range resolved spectra indices to overcome the confounding effects in passive optical measurements. However, the reflectance of leaves depends on angle of incidence and if this dependence varies between wavelengths, the resulting spectral indices will also vary with angle of incidence, complicating their use in separating structural and biochemical effects in vegetation canopies. The SALCA dualwavelength terrestrial laser scanner (Salford Advanced Laser Canopy Analyser) was used to measure the angular dependence of reflectance for a range of leaves at the wavelengths used by the new generation of multi-wavelength lidars, 1063 nm and 1545nm, as used by SALCA, DWEL and the Optech Titan. The influence of the angle of incidence on the Normalised Difference Index of these wavelengths (NDI) was also assessed. The reflectance at both wavelengths depended on the angle of incidence, was non-Lambertian and could be well modelled as a cosine. The change in NDI with leaf angle of incidence was small compared to the observed difference in NDI between fresh and dry leaves and between leaf and bark. Therefore it is concluded that angular effects will not significantly impact leaf moisture retrievals or prevent leaf/bark separation for the wavelengths used in the new generation of 1063 nm and 1545 nm multi-wavelength lidars

Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits.

The cardiac transcription factor (TF) gene NKX2-5 has been associated with electrocardiographic (EKG) traits through genome-wide association studies (GWASs), but the extent to which differential binding of NKX2-5 at common regulatory variants contributes to these traits has not yet been studied. We analyzed transcriptomic and epigenomic data from induced pluripotent stem cell-derived cardiomyocytes from seven related individuals, and identified ~2,000 single-nucleotide variants associated with allele-specific effects (ASE-SNVs) on NKX2-5 binding. NKX2-5 ASE-SNVs were enriched for altered TF motifs, for heart-specific expression quantitative trait loci and for EKG GWAS signals. Using fine-mapping combined with epigenomic data from induced pluripotent stem cell-derived cardiomyocytes, we prioritized candidate causal variants for EKG traits, many of which were NKX2-5 ASE-SNVs. Experimentally characterizing two NKX2-5 ASE-SNVs (rs3807989 and rs590041) showed that they modulate the expression of target genes via differential protein binding in cardiac cells, indicating that they are functional variants underlying EKG GWAS signals. Our results show that differential NKX2-5 binding at numerous regulatory variants across the genome contributes to EKG phenotypes

Non-intersecting leaf insertion algorithm for tree structure models

We present an algorithm and an implementation to insert broadleaves or needleleaves to a quantitative structure model according to an arbitrary distribution, and a data structure to store the required information efficiently. A structure model contains the geometry and branching structure of a tree. The purpose of the work is to offer a tool for making more realistic simulations with tree models with leaves, particularly for tree models developed from terrestrial laser scan (TLS) measurements. We demonstrate leaf insertion using cylinder-based structure models, but the associated software implementation is written in a way that enables the easy use of other types of structure models. Distributions controlling leaf location, size and angles as well as the shape of individual leaves are user-definable, allowing any type of distribution. The leaf generation process consist of two stages, the first of which generates individual leaf geometry following the input distributions, while in the other stage intersections are prevented by doing transformations when required. Initial testing was carried out on English oak trees to demonstrate the approach and to assess the required computational resources. Depending on the size and complexity of the tree, leaf generation takes between 6 and 18 minutes. Various leaf area density distributions were defined, and the resulting leaf covers were compared to manual leaf harvesting measurements. The results are not conclusive, but they show great potential for the method. In the future, if our method is demonstrated to work well for TLS data from multiple tree types, the approach is likely to be very useful for 3D structure and radiative transfer simulation applications, including remote sensing, ecology and forestry, among others

Common DNA sequence variation influences 3-dimensional conformation of the human genome.

BACKGROUND:The 3-dimensional (3D) conformation of chromatin inside the nucleus is integral to a variety of nuclear processes including transcriptional regulation, DNA replication, and DNA damage repair. Aberrations in 3D chromatin conformation have been implicated in developmental abnormalities and cancer. Despite the importance of 3D chromatin conformation to cellular function and human health, little is known about how 3D chromatin conformation varies in the human population, or whether DNA sequence variation between individuals influences 3D chromatin conformation. RESULTS:To address these questions, we perform Hi-C on lymphoblastoid cell lines from 20 individuals. We identify thousands of regions across the genome where 3D chromatin conformation varies between individuals and find that this variation is often accompanied by variation in gene expression, histone modifications, and transcription factor binding. Moreover, we find that DNA sequence variation influences several features of 3D chromatin conformation including loop strength, contact insulation, contact directionality, and density of local cis contacts. We map hundreds of quantitative trait loci associated with 3D chromatin features and find evidence that some of these same variants are associated at modest levels with other molecular phenotypes as well as complex disease risk. CONCLUSION:Our results demonstrate that common DNA sequence variants can influence 3D chromatin conformation, pointing to a more pervasive role for 3D chromatin conformation in human phenotypic variation than previously recognized

Design of chemical space networks incorporating compound distance relationships

Networks, in which nodes represent compounds and edges pairwise similarity relationships, are used as coordinate-free representations of chemical space. So-called chemical space networks (CSNs) provide intuitive access to structural relationships within compound data sets and can be annotated with activity information. However, in such similarity-based networks, distances between compounds are typically determined for layout purposes and clarity and have no chemical meaning. By contrast, inter-compound distances as a measure of dissimilarity can be directly obtained from coordinate-based representations of chemical space. Herein, we introduce a CSN variant that incorporates compound distance relationships and thus further increases the information content of compound networks. The design was facilitated by adapting the Kamada-Kawai algorithm. Kamada-Kawai networks are the first CSNs that are based on numerical similarity measures, but do not depend on chosen similarity threshold values