Plant microbiomes play an important role in agricultural productivity, but there is still much to learn about their provenance, diversity, and organization. In order to study the role of vertical ...transmission in establishing the bacterial and fungal populations of juvenile plants, we used high-throughput sequencing to survey the microbiomes of seeds, spermospheres, rhizospheres, roots, and shoots of the monocot crops maize (B73), rice (Nipponbare), switchgrass (Alamo),
Brachiaria decumbens
, wheat, sugarcane, barley, and sorghum; the dicot crops tomato (Heinz 1706), coffee (Geisha), common bean (G19833), cassava, soybean, pea, and sunflower; and the model plants
Arabidopsis thaliana
(Columbia-0) and
Brachypodium distachyon
(Bd21). Unsterilized seeds were planted in either sterile sand or farm soil inside hermetically sealed jars, and after as much as 60 days of growth, DNA was extracted to allow for amplicon sequence-based profiling of the bacterial and fungal populations that developed. Seeds of most plants were dominated by Proteobacteria and Ascomycetes, with all containing operational taxonomic units (OTUs) belonging to
Pantoea
and
Enterobacter
. All spermospheres also contained DNA belonging to
Pseudomonas
,
Bacillus
, and
Fusarium
. Despite having only seeds as a source of inoculum, all plants grown on sterile sand in sealed jars nevertheless developed rhizospheres, endospheres, and phyllospheres dominated by shared Proteobacteria and diverse fungi. Compared to sterile sand-grown seedlings, growth on soil added new microbial diversity to the plant, especially to rhizospheres; however, all 63 seed-transmitted bacterial OTUs were still present, and the most abundant bacteria (
Pantoea
,
Enterobacter
,
Pseudomonas
,
Klebsiella
, and
Massilia
) were the same dominant seed-transmitted microbes observed in sterile sand-grown plants. While most plant mycobiome diversity was observed to come from soil, judging by read abundance, the dominant fungi (
Fusarium
and
Alternaria
) were also vertically transmitted. Seed-transmitted fungi and bacteria appear to make up the majority of juvenile crop plant microbial populations by abundance, and based on occupancy, there seems to be a pan-angiosperm seed-transmitted core bacterial microbiome. Further study of these seed-transmitted microbes will be important to understand their role in plant growth and health, as well as their fate during the plant life cycle and may lead to innovations for agricultural inoculant development.
High levels of cytokines, such as interleukin (IL)-1β, tumor necrosis factor (TNF)-α and IL-6, are associated with chronic diseases like rheumatoid arthritis, asthma, atherosclerosis, Alzheimer's ...disease and cancer; therefore cytokine inhibition might be an important target for the treatment of these diseases. Most drugs used to alleviate some inflammation-related symptoms act by inhibiting cyclooxygenases activity or by blocking cytokine receptors. Nevertheless, these drugs have secondary effects when used on a long-term basis. It has been mentioned that flavonoids, namely quercetin, apigenin and luteolin, reduce cytokine expression and secretion. In this regard, flavonoids may have therapeutical potential in the treatment of inflammation-related diseases as cytokine modulators. This review is focused on current research about the effect of flavonoids on cytokine modulation and the description of the way these compounds exert their effect.
PURPOSETo validate MRI Analyzer Quality Control (MA-QC), a free and open-source online software designed to facilitate MR data acquisition quality control and PI-QUAL score calculation. MATERIAL AND ...METHODSMA-QC is a web-based software, designed for analysing DICOM data related to MR acquisition parameters. The software allows automatic extraction of 18 technical criteria, and manual input of 12 visual criteria, to calculate the PI-QUAL score. We collected 100 prostate MRI datasets from four MR device manufacturers to test data compatibility, automatic sequence recognition, and robustness of technical criteria extraction from DICOM data. The main issue was to determine the spatial resolution in the phase and frequency directions, due to variable encoding of the DICOM datasets. RESULTSAcquisition data could be extracted from all sample examinations (100%), with a median analysis speed of 15.2 ± 4.4 images per second and mean processing time of 96 11-326 seconds per examination. MA-CQ automatically detected the optimal T2-w, DWI and DCE sequences in 71 out of 100 (71%) cases, and required manual selection of at least one sequence in 29 out of 100 (29%) cases to get the best parameters. Display of technical criteria for the 3 sequences was instantaneous. PI-QUAL score could be calculated in all cases. CONCLUSIONThis software brings substantial help in the quality assessment of prostate MRI examinations, by providing fast extraction of series data and the 18 technical parameters of PI-QUAL. PI-QUAL scoring can be performed in less than two minutes, helping to focus on the visual criteria, allowing use of this software in the clinical workflow in the aim of improving overall image quality in prostate MR imaging.
Monitoring, a regulation of cognition component of metacognition, is an essential aspect of self-regulated learning. Monitoring is recognized as learners' ability to successfully understand what they ...are learning, and typically involves metacognitive activities such as questioning, reflection, drawing inferences, and self-generating feedback. However, while extant research converges on the notion that monitoring is a malleable and trainable skill, no investigation to date has systematically explored differences in monitoring accuracy effects. Therefore, a meta-analysis was conducted on research that examined the effect of learning strategy instruction on monitoring compared with a control. The meta-analysis explored how weighted effect sizes varied as a function of learning strategies used, study characteristics, and other potential moderators. A systematic search of major databases ultimately produced 56 independent effect sizes involving 7,667 participants, which were subsequently extracted and analyzed. Across the 56 studies, learning strategy instruction interventions yielded a moderate unbiased grand mean effect size (g = -.565; 95% confidence interval -.639, -.491), indicating improved monitoring accuracy compared to a control. Moderator analysis results revealed that the weighted mean effect size was larger for studies conducted in laboratories with adult-only samples (ranging in size from 101 to 200 participants) that used deep learning strategies, prediction and postdiction confidence judgments, the difference between prediction-postdiction judgments to calculate monitoring accuracy, and multiple-choice response options for the performance test. Weighted mean effect sizes for the type of monitoring measure, research design, learning strategy instruction duration, and geographic location did not vary significantly among studies.
Educational Impact and Implications StatementThe present meta-analysis included 56 independent studies examining the influence of learning strategy instruction interventions on metacognitive monitoring accuracy. This meta-analysis supports the conclusion that learning strategy instruction interventions lead to appreciable gains in metacognitive monitoring accuracy, even after accounting for key moderators such as the learning strategies trained. Thus, research on the observed effects of learning strategy interventions aimed at improving metacognitive monitoring accuracy should continue in hopes of uncovering the most effective learning strategies to improve learning outcomes.
The Asian vinegar fly Drosophila suzukii (spotted wing Drosophila SWD) has emerged as a major invasive insect pest of small and stone fruits in both the Americas and Europe since the late 2000s. ...While research efforts have rapidly progressed in Asia, North America, and Europe over the past 5 years, important new insights may be gained in comparing and contrasting findings across the regions affected by SWD. In this review, we explore common themes in the invasion biology of SWD by examining (1) its biology and current pest status in endemic and recently invaded regions; (2) current efforts and future research needs for the development of predictive models for its geographic expansion; and (3) prospects for both natural and classical (=importation) biological control of SWD in invaded habitats, with emphasis on the role of hymenopteran parasitoids. We conclude that particularly fruitful areas of research should include fundamental studies of its overwintering, host-use, and dispersal capabilities; as well as applied studies of alternative, cost-effective management techniques to complement insecticide use within the integrated pest management framework. Finally, we emphasize that outreach efforts are critical to effective SWD management by highlighting successful strategies and insights gained from various geographic regions.
Pacific oysters are a key aquaculture species globally, and genetic improvement via selective breeding is a major target. Genomic selection has the potential to expedite genetic gain for key target ...traits of a breeding program, but has not yet been evaluated in oyster. The recent development of SNP arrays for Pacific oyster (
) raises the opportunity to test genomic selection strategies for polygenic traits. In this study, a population of 820 oysters (comprising 23 full-sibling families) were genotyped using a medium density SNP array (23 K informative SNPs), and the genetic architecture of growth-related traits shell height (SH), shell length (SL), and wet weight (WW) was evaluated. Heritability was estimated to be moderate for the three traits (0.26 ± 0.06 for SH, 0.23 ± 0.06 for SL and 0.35 ± 0.05 for WW), and results of a GWAS indicated that the underlying genetic architecture was polygenic. Genomic prediction approaches were used to estimate breeding values for growth, and compared to pedigree based approaches. The accuracy of the genomic prediction models (GBLUP) outperformed the traditional pedigree approach (PBLUP) by ∼25% for SL and WW, and ∼30% for SH. Further, reduction in SNP marker density had little impact on prediction accuracy, even when density was reduced to a few hundred SNPs. These results suggest that the use of genomic selection in oyster breeding could offer benefits for the selection of breeding candidates to improve complex economic traits at relatively modest cost.
Abstract
We present 888 visual-wavelength spectra of 122 nearby type II supernovae (SNe II) obtained between 1986 and 2009, and ranging between 3 and 363 days post-explosion. In this first paper, we ...outline our observations and data reduction techniques, together with a characterization based on the spectral diversity of SNe II. A statistical analysis of the spectral matching technique is discussed as an alternative to nondetection constraints for estimating SN explosion epochs. The time evolution of spectral lines is presented and analyzed in terms of how this differs for SNe of different photometric, spectral, and environmental properties: velocities, pseudo-equivalent widths, decline rates, magnitudes, time durations, and environment metallicity. Our sample displays a large range in ejecta expansion velocities, from ∼9600 to ∼1500 km s
−1
at 50 days post-explosion with a median
value of 7300 km s
−1
. This is most likely explained through differing explosion energies. Significant diversity is also observed in the absolute strength of spectral lines, characterized through their pseudo-equivalent widths. This implies significant diversity in both temperature evolution (linked to progenitor radius) and progenitor metallicity between different SNe II. Around 60% of our sample shows an extra absorption component on the blue side of the
P-Cygni profile (“Cachito” feature) between 7 and 120 days since explosion. Studying the nature of Cachito, we conclude that these features at early times (before ∼35 days) are associated with Si
ii
, while past the middle of the plateau phase they are related to high velocity (HV) features of hydrogen lines.
Abstract
Background
The Pacific oyster (Crassostrea gigas) is a bivalve mollusc with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. ...gigas, highly contiguous reference genomes are required to support both fundamental and applied research. Herein we report the creation and annotation of a chromosome-level assembly for C. gigas.
Findings
High-coverage long- and short-read sequence data generated on Pacific Biosciences and Illumina platforms were used to generate an initial assembly, which was then scaffolded into 10 pseudo-chromosomes using both Hi-C sequencing and a high-density linkage map. The assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously published C. gigas assembly. Annotation based on Pacific Biosciences Iso-Seq and Illumina RNA-Seq resulted in identification of ∼30,000 putative protein-coding genes. Annotation of putative repeat elements highlighted an enrichment of Helitron rolling-circle transposable elements, suggesting their potential role in shaping the evolution of the C. gigas genome.
Conclusions
This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for selective breeding of C. gigas in aquaculture.
Context Type 2 diabetes, prediabetes, and metabolic syndrome are highly prevalent in Hispanic individuals in the U.S. Cultural adaptations of traditional lifestyle interventions have been recommended ...to better reach this high-risk population. This systematic review examined the effectiveness of diabetes prevention programs for Hispanics in lowering risk for Type 2 diabetes, as evidenced by a reduction in weight or improvement in glucose regulation. Evidence acquisition PubMed/MEDLINE, Cochrane Central Register of Controlled Trials, Web of Science, and PsycINFO were searched from database inception to June 2016 for studies that evaluated diabetes prevention trials targeting U.S. Hispanic populations. Twelve publications met criteria for inclusion. Evidence synthesis Interventions varied substantially in length, rigor, and tailoring strategies. Five of 12 studies were RCTs. Eight studies included entirely or largely (>70%) female samples. All studies were delivered in Spanish and took place in community settings. Nine studies reported significant reductions in weight, and two in glucose regulation, post-intervention or when compared with controls. Effect sizes were small to moderate, study quality was moderate, and attrition was high in most trials. Interventions with the largest effect sizes included one or more of the following adaptations: literacy modification, Hispanic foods/recipes, cultural diabetes beliefs, family/friend participation, structured community input, and innovative experiential learning. Conclusions Culturally tailored lifestyle interventions for diabetes prevention appear to be modestly effective in reducing risk for diabetes in Hispanics in the U.S. More studies are needed that utilize randomized controlled designs, recruit Hispanic men, report intervention content and tailoring strategies systematically, and publish participant evaluation and feedback.
SNP arrays are enabling tools for high-resolution studies of the genetic basis of complex traits in farmed and wild animals. Oysters are of critical importance in many regions from both an ecological ...and economic perspective, and oyster aquaculture forms a key component of global food security. The aim of our study was to design a combined-species, medium density SNP array for Pacific oyster (
) and European flat oyster (
), and to test the performance of this array on farmed and wild populations from multiple locations, with a focus on European populations. SNP discovery was carried out by whole-genome sequencing (WGS) of pooled genomic DNA samples from eight
populations, and restriction site-associated DNA sequencing (RAD-Seq) of 11 geographically diverse
populations. Nearly 12 million candidate SNPs were discovered and filtered based on several criteria, including preference for SNPs segregating in multiple populations and SNPs with monomorphic flanking regions. An Affymetrix Axiom Custom Array was created and tested on a diverse set of samples (
= 219) showing ∼27 K high quality SNPs for
and ∼11 K high quality SNPs for
segregating in these populations. A high proportion of SNPs were segregating in each of the populations, and the array was used to detect population structure and levels of linkage disequilibrium (LD). Further testing of the array on three
nuclear families (
= 165) revealed that the array can be used to clearly distinguish between both families based on identity-by-state (IBS) clustering parental assignment software. This medium density, combined-species array will be publicly available through Affymetrix, and will be applied for genome-wide association and evolutionary genetic studies, and for genomic selection in oyster breeding programs.
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