Evidence of neutral transcriptome evolution in plants

The transcriptome of an organism is its set of gene transcripts (mRNAs) at a defined spatial and temporal locus. Because gene expression is affected markedly by environmental and developmental perturbations, it is widely assumed that transcriptome divergence among taxa represents adaptive phenotypic selection. This assumption has been challenged by neutral theories which propose that stochastic processes drive transcriptome evolution. To test for evidence of neutral transcriptome evolution in plants, we quantified 18 494 gene transcripts in nonsenescent leaves of 14 taxa of Brassicaceae using robust cross-species transcriptomics which includes a two-step physical and in silicobased normalization procedure based on DNA similarity among taxa. Transcriptome divergence correlates positively with evolutionary distance between taxa and with variation in gene expression among samples. Results are similar for pseudogenes and chloroplast genes evolving at different rates. Remarkably, variation in transcript abundance among root-cell samples correlates positively with transcriptome divergence among root tissues and among taxa. Because neutral processes affect transcriptome evolution in plants, many differences in gene expression among or within taxa may be nonfunctional, reflecting ancestral plasticity and founder effects. Appropriate null models are required when comparing transcriptomes in space and time

Sub-sampling a large physical soil archive for additional analyses to support spatial mapping; a pre-registered experiment in the Southern Nations, Nationalities, and Peoples Region (SNNPR) of Ethiopia

The value of physical archives of soil material from field sampling activities has been widely recognized. If we want to use archive material for new destructive analyses to support a task, such as spatial mapping, then an efficient sub-sampling strategy is needed, both to manage analytical costs and to conserve the archive material. In this paper we present an approach to this problem when the objective is spatial mapping by ordinary kriging. Our objective was to subsample the physical archive from the Ethiopia Soil Information System (EthioSIS) survey of the Southern Nations, Nationalities and Peoples Region (SNNPR) for spatial mapping of two variables, concentrations of particular fractions of selenium and iodine in the soil, which had not been measured there. We used data from cognate parts of surrounding regions of Ethiopia to estimate variograms of these properties, and then computed prediction error variances for maps in SNNPR based on proposed subsets of the archive of different size, selected to optimize a spatial coverage criterion (with some close sample pairs included). On this basis a subsample was selected. This is a preregistered experiment in that we have proposed criteria for evaluating the success of our approach, and are publishing that in advance of receiving analytical data on the subsampled material from the laboratories where they are being processed. A subsequent short report will publish the outcome. The use of preregistered trials is widely recommended and used in areas of science including public health, and we believe that it is a sound strategy to promote reproducible research in soil science

Faster colonoscope withdrawal time without impaired detection using EndoRings

Background and study aims:  Mucosal exposure devices on the colonoscope tip have improved detection. We evaluated detection and procedure times in colonoscopies performed with EndoRings. Patients and methods:  We had 14 endoscopists in a university practice trial EndoRings. We compared detection and procedure times to age- and indication-matched procedures by the same endoscopists. Results:  There were 137 procedures with EndoRings. The adenoma detection rate was 44 % with EndoRings vs. 39 % without ( P  = 0.39). Mean adenomas per colonoscopy (standard deviation) was 1.2 (2.3) with EndoRings vs. 0.9 (1.6) without ( P  = 0.055). Mean insertion time with EndoRings was 6.2 (3.2) minutes vs. 6.6 (6.7) minutes without ( P  = 0.81). Mean withdrawal time with EndoRings in all patients with or without polypectomy was 12.2 (5.3) minutes and 16.1 (10.3) minutes without ( P  = 0.0005). Conclusion:  EndoRings may allow faster withdrawal during colonoscopy without any reduction in detection. Prospective trials with mucosal exposure devices targeting procedure times as primary endpoints are warranted

Xenon isotopes in Archean and Proterozoic insoluble organic matter: a robust indicator of syngenecity?

Insoluble organic materials (kerogens) isolated from ancient sedimentary rocks provide unique insights into the evolution of early life. However, establishing whether these kerogens are indeed syngenetic with the deposition of associated sedimentary host rocks, or contain contribution from episodes of secondary deposition, is not straightforward. Novel geochemical criterions are therefore required to test the syngenetic origin of Archean organic materials. On one hand, the occurrence of mass-independent fractionation of sulphur isotopes (MIF-S) provides a tool to test the Archean origin of ancient sedimentary rocks. Determining the isotope composition of sulphur within kerogens whilst limiting the contribution from associated minerals (e.g., nano-pyrites) is however challenging. On the other end, the Xe isotope composition of the Archean atmosphere has been shown to present enrichments in the light isotopes relative to its modern composition, together with a mono-isotopic deficit in ¹²⁹Xe. Given that the isotopic composition of atmospheric Xe evolved through time by mass dependent fractionation (MDF) until ∼2.5-2.0 Ga, the degree of MDF of Xe isotopes trapped in kerogens could provide a time stamp for the last chemical equilibration between organic matter and the atmosphere. However, the extent to which geological processes could affect the signature of Xe trapped in ancient kerogen remains unclear. In this contribution, we present new Ar, Kr and Xe isotopic data for four kerogens isolated from 3.4 to 1.8 Gy-old cherts and confirm that Xe isotopes from the Archean atmosphere can be retained within kerogens. However, new Xe-derived model ages are lower than expected from the ages of host rocks, indicating that initially trapped Xe components were at least partially lost and/or mixed together with some Xe carried out by younger generations of organic materials, therefore complicating the Xe-based dating method. Whilst non-null Δ³³S values and ¹²⁹Xe deficits relative to modern atmosphere constitute reliable imprints from the Archean atmosphere, using Xe isotopes to provide information on the syngenetic origin of ancient organic matter appears to be a promising - but not unequivocal - tool that calls for further analytical development

Agronomic biofortification increases grain zinc concentration of maize grown under contrasting soil types in Malawi

Zinc (Zn) deficiency remains a public health problem in Malawi, especially among poor and marginalized rural populations, linked with low dietary intake of Zn due to consumption of staple foods that are low in Zn content. The concentration of Zn in staple cereal grain can be increased through application of Zn-enriched fertilizers, a process called agronomic biofortification or agro-fortification. Field experiments were conducted at three Agricultural Research Station sites to assess the potential of agronomic biofortification to improve Zn concentration in maize grain in Malawi as described in registered report published previously. The hypotheses of the study were (i) that application of Zn-enriched fertilizers would increase in the concentration of Zn in maize grain to benefit dietary requirements of Zn and (ii) that Zn concentration in maize grain and the effectiveness of agronomic biofortification would be different between soil types. At each site two different subsites were used, each corresponding to one of two agriculturally important soil types of Malawi, Lixisols and Vertisols. Within each subsite, three Zn fertilizer rates (1, 30, and 90 kg ha−1) were applied to experimental plots, using standard soil application methods, in a randomized complete block design. The experiment had 10 replicates at each of the three sites as informed by a power analysis from a pilot study, published in the registered report for this experiment, designed to detect a 10% increase in grain Zn concentration at 90 kg ha−1, relative to the concentration at 1 kg ha−1. At harvest, maize grain yield and Zn concentration in grain were measured, and Zn uptake by maize grain and Zn harvest index were calculated. At 30 kg ha−1, Zn fertilizer increased maize grain yields by 11% compared with nationally recommended application rate of 1 kg ha−1. Grain Zn concentration increased by 15% and uptake by 23% at the application rate of 30 kg ha−1 relative to the national recommendation rate. The effects of Zn fertilizer application rate on the response variables were not dependent on soil type. The current study demonstrates the importance of increasing the national recommendation rate of Zn fertilizer to improve maize yield and increase the Zn nutritional value of the staple crop

Sub-sampling a large physical soil archive for additional analyses to support spatial mapping; a pre-registered experiment in the Southern Nations, Nationalities, and Peoples Region (SNNPR) of Ethiopia

The value of physical archives of soil material from field sampling activities has been widely recognized. If we want to use archive material for new destructive analyses to support a task, such as spatial mapping, then an efficient sub-sampling strategy is needed, both to manage analytical costs and to conserve the archive material. In this paper we present an approach to this problem when the objective is spatial mapping by ordinary kriging. Our objective was to subsample the physical archive from the Ethiopia Soil Information System (EthioSIS) survey of the Southern Nations, Nationalities and Peoples Region (SNNPR) for spatial mapping of two variables, concentrations of particular fractions of selenium and iodine in the soil, which had not been measured there. We used data from cognate parts of surrounding regions of Ethiopia to estimate variograms of these properties, and then computed prediction error variances for maps in SNNPR based on proposed subsets of the archive of different size, selected to optimize a spatial coverage criterion (with some close sample pairs included). On this basis a subsample was selected. This is a preregistered experiment in that we have proposed criteria for evaluating the success of our approach, and are publishing that in advance of receiving analytical data on the subsampled material from the laboratories where they are being processed. A subsequent short report will publish the outcome. The use of preregistered trials is widely recommended and used in areas of science including public health, and we believe that it is a sound strategy to promote reproducible research in soil science

High-definition colonoscopy versus Endocuff versus EndoRings versus Full-Spectrum Endoscopy for adenoma detection at colonoscopy: a multicenter randomized trial

Background Devices used to improve polyp detection during colonoscopy have seldom been compared with each other. Methods We performed a 3-center prospective randomized trial comparing high-definition (HD) forward-viewing colonoscopy alone to HD with Endocuff to HD with EndoRings to the Full Spectrum Endoscopy (FUSE) system. Patients were age ≥50 years and had routine indications and intact colons. The study colonoscopists were all proven high-level detectors. The primary endpoint was adenomas per colonoscopy (APC) Results Among 1,188 patients who completed the study, APC with Endocuff (APC Mean ± SD 1.82 ± 2.58), EndoRings (1.55 ± 2.42), and standard HD colonoscopy (1.53 ± 2.33) were all higher than FUSE (1.30 ± 1.96,) (p<0.001 for APC). Endocuff was higher than standard HD colonoscopy for APC (p=0.014) . Mean cecal insertion times with FUSE (468 ± 311 seconds) and EndoRings (403 ± 263 seconds) were both longer than with Endocuff (354 ± 216 seconds) (p=0.006 and 0.018, respectively). Conclusions For high-level detectors at colonoscopy, forward-viewing HD instruments dominate the FUSE system, indicating that for these examiners image resolution trumps angle of view. Further, Endocuff is a dominant strategy over EndoRings and no mucosal exposure device on a forward-viewing HD colonoscope

Fibroblast Growth Factors: Biology, Function, and Application for Tissue Regeneration

Fibroblast growth factors (FGFs) that signal through FGF receptors (FGFRs) regulate a broad spectrum of biological functions, including cellular proliferation, survival, migration, and differentiation. The FGF signal pathways are the RAS/MAP kinase pathway, PI3 kinase/AKT pathway, and PLCγ pathway, among which the RAS/MAP kinase pathway is known to be predominant. Several studies have recently implicated the in vitro biological functions of FGFs for tissue regeneration. However, to obtain optimal outcomes in vivo, it is important to enhance the half-life of FGFs and their biological stability. Future applications of FGFs are expected when the biological functions of FGFs are potentiated through the appropriate use of delivery systems and scaffolds. This review will introduce the biology and cellular functions of FGFs and deal with the biomaterials based delivery systems and their current applications for the regeneration of tissues, including skin, blood vessel, muscle, adipose, tendon/ligament, cartilage, bone, tooth, and nerve tissues

SIC-8000 versus hetastarch as a submucosal injection fluid for endoscopic mucosal resection: a randomized controlled trial

Background and Aims Viscous solutions provide a superior submucosal cushion for endoscopic mucosal resection (EMR). SIC-8000 (Eleview, Aries Pharmaceuticals, La Jolla, Calif) is a commercially available FDA approved solution but hetastarch is also advocated. We performed a randomized trial comparing SIC-8000 to hetastarch as submucosal injection agents for colorectal EMR. Methods This was a single-center double-blinded randomized controlled trial performed at a tertiary referral center. Patients were referred to our center with flat or sessile lesions measuring ≥15 mm in size. The primary outcome measures were the Sydney Resection Quotient (SRQ) and the rate of en bloc resections. Secondary outcomes were total volume needed for a sufficient lift, number of resected pieces, and adverse events. Results There were 158 patients with 159 adenomas (84 SIC-8000 and 75 hetastarch) and 57 serrated lesions (30 SIC-8000 and 27 hetastarch). SRQ was significantly better in the SIC-8000 group compared with hetastarch group (9.3 vs 8.1, p=0.001). There was no difference in the proportion of lesions with en bloc resections. The total volume of injectate was significantly lower with SIC-8000 (14.8 mL vs 20.6 mL, p=0.038) Conclusions SIC-8000 is superior to hetastarch for use during EMR in terms of SRQ and total volume needed, although the absolute differences were small

Mehlich 3 as an indicator of grain nutrient concentration for five cereals in sub-Saharan Africa

Context or Problem: Soil testing for available nutrients is an important tool to determine fertilizer rates, however many standard methods test the availability of a single nutrient only. In contrast, Mehlich 3 (M3) is a multi-element test for predicting crop yield responses to the addition of macro and micronutrients. However, the M3 test has rarely been validated against crop nutrient concentrations, which limits its application for dietary improvement studies in sub-Saharan Africa. Objective or Research Question: The primary objective was to test how well the M3 nutrient concentrations corresponds to grain nutrient concentrations as an indicator of plant nutrient status and grain quality. A secondary objective was to compare the performance of the M3 test with other extraction tests. Methods: This study used 1096 paired soil and crop samples of five cereals: maize, rice, sorghum, teff and wheat, covering a broad range of soil types and soil properties in Ethiopia and Malawi (e.g., pH 4.5 - 8.8; Olsen P < 1 - 280 ppm). The samples were selected from a larger collection based on “high” or “low” grain nutrient concentrations in the crop, and the respective soil available nutrients were measured with M3 and other extraction tests: CaCl2 (P, K, Mg, Mn), Ca(NO3)2 (K and Mg), Olsen P, sequential extraction (S), and DTPA (Mn, Fe and Zn). Results: The M3 concentrations followed the trend of the “high” and “low” grain concentrations in nearly all nutrients and crops, and this was statistically significant in teff and wheat for all nutrients. The results were best for macronutrients, and slightly less good for micronutrients, probably because the concentration of micronutrients in the selected soil samples was generally quite low. Compared to the other multi-element extractant (CaCl2), the M3 test corresponded better to grain concentrations of K and Mg, and equally well to Olsen P, sequential extraction (S), and DTPA predictions of P, S, Zn and Fe, respectively. M3 extracted much greater concentrations than the other tests, and this was more pronounced in alkaline soils. Conclusions: Given that the M3 test corresponded well to grain nutrient concentrations across a range of soils and crops in sub-Saharan Africa (SSA), we conclude that it can be considered a universal test for plant nutrients. We also proposed thresholds for M3 values, defining below optimum, optimum and above optimum soil fertility status. Implications or Significance: These results validate the use of the M3 test to assess soil fertility and develop fertilizer recommendations for improved produce quality to enhance diets in SSA