Evaluating potential of leaf reflectance spectra to monitor plant genetic variation

Remote sensing of vegetation by spectroscopy is increasingly used to characterize trait distributions in plant communities. How leaves interact with electromagnetic radiation is determined by their structure and contents of pigments, water, and abundant dry matter constituents like lignins, phenolics, and proteins. High-resolution ("hyperspectral") spectroscopy can characterize trait variation at finer scales, and may help to reveal underlying genetic variation-information important for assessing the potential of populations to adapt to global change. Here, we use a set of 360 inbred genotypes of the wild coyote tobacco Nicotiana attenuata: wild accessions, recombinant inbred lines (RILs), and transgenic lines (TLs) with targeted changes to gene expression, to dissect genetic versus non-genetic influences on variation in leaf spectra across three experiments. We calculated leaf reflectance from hand-held field spectroradiometer measurements covering visible to short-wave infrared wavelengths of electromagnetic radiation (400-2500 nm) using a standard radiation source and backgrounds, resulting in a small and quantifiable measurement uncertainty. Plants were grown in more controlled (glasshouse) or more natural (field) environments, and leaves were measured both on- and off-plant with the measurement set-up thus also in more to less controlled environmental conditions. Entire spectra varied across genotypes and environments. We found that the greatest variance in leaf reflectance was explained by between-experiment and non-genetic between-sample differences, with subtler and more specific variation distinguishing groups of genotypes. The visible spectral region was most variable, distinguishing experimental settings as well as groups of genotypes within experiments, whereas parts of the short-wave infrared may vary more specifically with genotype. Overall, more genetically variable plant populations also showed more varied leaf spectra. We highlight key considerations for the application of field spectroscopy to assess genetic variation in plant populations

Simulated and experimental verification for a terahertz specific finite rate of innovation signal processing method

Recently, finite rate of innovation methods have been successfully applied to achieve low sampling rates in many areas, such as for ultrasound and radio signals. However, to the best of our knowledge, there are no journal publications applying this to real terahertz signals. In this work, we mathematically describe a finite rate of innovation method applied specifically to terahertz signals both experimentally and in simulation. To demonstrate our method, we applied it to randomized simulated signals with and without the presence of noise and to simple experimental measurements. We found excellent agreement between the simulated signals and those recreated based on results from our method, with this success also being replicated experimentally. These results were obtained at relatively low sampling rates, compared to standard methods, which is a key advantage to using a finite rate of innovation method as it allows for faster data acquisition and signal processing

Monitoring the terahertz response of skin beneath transdermal drug delivery patches using sparse deconvolution

Terahertz (THz) spectroscopy is a technique proving extremely useful for investigating various biomedical applications by virtue of its high sensitivity in the measurement of water content and non-ionizing nature. By combining this with sparse deconvolution, the THz response of skin directly underneath transdermal drug delivery (TDD) patches was isolated and reconstructed to determine the skin water content in vivo. Verification for this method was given by a comparison of skin measured through patches using sparse deconvolution, and skin measurements immediately following patch removal processed with standard approaches. It was found that patches with a non-permeable film backing hydrated the skin to a greater extent than permeable woven polyester fiber backed patches and that this hydration effect primarily occurs within the first 30 minutes of patch application and lasts for at least 24 hours given that the patch remains applied. We demonstrate the effectiveness of this sparse reconstruction method to track hydration levels through layers such as patches and identify scope for further applications including TDD patch development and wound healing techniques and monitoring

Pangolin genomes and the evolution of mammalian scales and immunity

Pangolins, unique mammals with scales over most of their body, no teeth, poor vision, and an acute olfactory system, comprise the only placental order (Pholidota) without a whole-genome map. To investigate pangolin biology and evolution, we developed genome assemblies of the Malayan (Manis javanica) and Chinese (M. pentadactyla) pangolins. Strikingly, we found that interferon epsilon (IFNE), exclusively expressed in epithelial cells and important in skin and mucosal immunity, is pseudogenized in all African and Asian pangolin species that we examined, perhaps impacting resistance to infection. We propose that scale development was an innovation that provided protection against injuries or stress and reduced pangolin vulnerability to infection. Further evidence of specialized adaptations was evident from positively selected genes involving immunity-related pathways, inflammation, energy storage and metabolism, muscular and nervous systems, and scale/hair development. Olfactory receptor gene families are significantly expanded in pangolins, reflecting their well-developed olfaction system. This study provides insights into mammalian adaptation and functional diversification, new research tools and questions, and perhaps a new natural IFNE-deficient animal model for studying mammalian immunity.University of Malaya and Ministry of Education, Malaysia [UM.C/HIR/MOHE/08]; UMRG grant from the University of Malaya and Ministry of Education, Malaysia [RG541-13HTM]; Russian Ministry of Science [11.G34.31.0068]; NIH-NHGRI grant [5U54HG00307907]SCI(E)[email protected]

Effect of Iron Therapy on Platelet Counts in Patients with Inflammatory Bowel Disease-Associated Anemia

Secondary thrombocytosis is a clinical feature of unknown significance. In inflammatory bowel disease (IBD), thrombocytosis is considered a marker of active disease; however, iron deficiency itself may trigger platelet generation. In this study we tested the effect of iron therapy on platelet counts in patients with IBD-associated anemia.Platelet counts were analyzed before and after iron therapy from four prospective clinical trials. Further, changes in hemoglobin, transferrin saturation, ferritin, C-reactive protein, and leukocyte counts, before and after iron therapy were compared. In a subgroup the effect of erythropoietin treatment was tested. The results were confirmed in a large independent cohort (FERGIcor).A total of 308 patient records were available for the initial analysis. A dose-depended drop in platelet counts (mean 425 G/L to 320 G/L; p<0.001) was found regardless of the type of iron preparation (iron sulphate, iron sucrose, or ferric carboxymaltose). Concomitant erythropoietin therapy as well as parameters of inflammation (leukocyte counts, C-reactive protein) had no effect on the change in platelet counts. This effect of iron therapy on platelets was confirmed in the FERGIcor study cohort (n=448, mean platelet counts before iron therapy: 383 G/L, after: 310 G/L, p<0.001).Iron therapy normalizes elevated platelet counts in patients with IBD-associated anemia. Thus, iron deficiency is an important pathogenetic mechanism of secondary thrombocytosis in IBD