Over-expression of miR172 causes loss of spikelet determinacy and floral organ abnormalities in rice (Oryza sativa)

<p>Abstract</p> <p>Background</p> <p>Regulation of gene expression by microRNAs (miRNAs) plays a crucial role in many developmental and physiological processes in plants. miRNAs act to repress expression of their target genes via mRNA cleavage or translational repression. Dozens of miRNA families have been identified in rice, 21 of which are conserved between rice and Arabidopsis. miR172 is a conserved miRNA family which has been shown to regulate expression of <it>APETALA2 </it>(<it>AP2</it>)-like transcription factors in Arabidopsis and maize. The rice genome encodes five <it>AP2</it>-like genes predicted to be targets of miR172. To determine whether these rice <it>AP2</it>-like genes are regulated by miR172 and investigate the function of the target genes, we studied the effect of over-expressing two members of the miR172 family on rice plant development.</p> <p>Results</p> <p>Analysis of miR172 expression showed that it is most highly expressed in late vegetative stages and developing panicles. Analyses of expression of three miR172 targets showed that <it>SUPERNUMERARY BRACT </it>(<it>SNB</it>) and <it>Os03g60430 </it>have high expression in developing panicles. Expression of miR172 was not inversely correlated with expression of its targets although miR172-mediated cleavage of <it>SNB </it>was detected by 5' rapid amplification of cDNA ends (RACE). Over-expression of miR172b in rice delayed the transition from spikelet meristem to floral meristem, and resulted in floral and seed developmental defects, including changes to the number and identity of floral organs, lower fertility and reduced seed weight. Plants over-expressing miR172b not only phenocopied the T-DNA insertion mutant of <it>SNB </it>but showed additional defects in floret development not seen in the <it>snb </it>mutant. However <it>SNB </it>expression was not reduced in the miR172b over-expression plants.</p> <p>Conclusions</p> <p>The phenotypes resulting from over-expression of miR172b suggests it represses <it>SNB </it>and at least one of the other miR172 targets, most likely <it>Os03g60430</it>, indicating roles for other <it>AP2</it>-like genes in rice floret development. miR172 and the <it>AP2</it>-like genes had overlapping expression patterns in rice and their expression did not show an obvious negative correlation. There was not a uniform decrease in the expression of the <it>AP2</it>-like miR172 target mRNAs in the miR172b over-expression plants. These observations are consistent with miR172 functioning via translational repression or with expression of the <it>AP2</it>-like genes being regulated by a negative feedback loop.</p

ALTERED MERISTEM PROGRAM 1 Is involved in Development of Seed Dormancy in Arabidopsis

Mutants in the rice PLASTOCHRON 3 and maize VIVIPAROUS 8 genes have been shown to have reduced dormancy and ABA levels. In this study we used several mutants in the orthologous gene ALTERED MERISTEM PROGRAM 1 (AMP1) to determine its role in seed dormancy in Arabidopsis. Here we report that there are accession-specific effects of mutations in AMP1. In one accession, amp1 mutants produce seeds with higher dormancy, while those in two other accessions produce seeds of lower dormancy. These accession-specific effects of mutating AMP1 were shown to extend to ABA levels. We assayed global gene transcription differences in seeds of wild-type and mutant from two accessions demonstrating opposing phenotypes. The transcript changes observed indicate that the amp1 mutation shifts the seed transcriptome from a dormant into an after-ripened state. Specific changes in gene expression in the mutants give insight into the direct and indirect effects that may be contributing to the opposing dormancy phenotypes observed, and reveal a role for AMP1 in the acquisition and/or maintenance of seed dormancy in Arabidopsis

Vernalization-Repression of Arabidopsis FLC Requires Promoter Sequences but Not Antisense Transcripts

The repression of Arabidopsis FLC expression by vernalization (extended cold) has become a model for understanding polycomb-associated epigenetic regulation in plants. Antisense and sense non-coding RNAs have been respectively implicated in initiation and maintenance of FLC repression by vernalization. We show that the promoter and first exon of the FLC gene are sufficient to initiate repression during vernalization; this initial repression of FLC does not require antisense transcription. Long-term maintenance of FLC repression requires additional regions of the gene body, including those encoding sense non-coding transcripts

Longitudinal clusters of pain and stiffness in polymyalgia rheumatica: 2-year results from the PMR Cohort study

Objectives. To investigate potential subgroups of primary care diagnosed patients with polymyalgia rheumatica (PMR) based on self-reported pain and stiffness severity over time.Methods. 652 people with an incident PMR diagnosis were recruited from English general practices and completed a baseline postal questionnaire. They were followed-up with a further six questionnaires over a two-year period. 446 people completed 2-year follow-up. Pain and stiffness were reported on 0-10 numerical rating scales. Latent class growth analysis was used to estimate the joint trajectories of pain and stiffness overtime. A combination ofstatistical and clinical considerations was used to choose the number of clusters. Characteristics of the classes were described. Results. Five clusters were identified. One cluster represented the profile of ‘classical’ PMR symptoms and one represented sustained symptoms that may not be PMR. The other three clusters displayed a partial recovery, a recovery followed by worsening and a slow, but sustained recovery. Those displaying classical PMR symptoms were in better overall health at diagnosis than the other groups.Conclusions. PMR is a heterogeneous condition, with a number of phenotypes. The spectrum of presentation, as well as varying responses to treatment, may be related to underlying health status at diagnosis. Future research should seek to stratify patients at diagnosis to identify those likely to have a poor recovery and in need of an alternative treatment pathway. Clinicians should be aware of the different experiences of patients and monitor symptoms closely, even where there is initial improvement

The histone modification H3 lysine 27 tri-methylation has conserved gene regulatory roles in the triplicated genome of Brassica rapa L

© The Author(s) 2019. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. Brassica rapa L. is an important vegetable and oilseed crop. We investigated the distribution of the histone mark tri-methylation of H3K27 (H3K27me3) in B. rapa and its role in the control of gene expression at two stages of development (2-day cotyledons and 14-day leaves) and among paralogs in the triplicated genome. H3K27me3 has a similar distribution in two inbred lines, while there was variation of H3K27me3 sites between tissues. Sites that are specific to 2-day cotyledons have increased transcriptional activity, and low levels of H3K27me3 in the gene body region. In 14-day leaves, levels of H3K27me3 were associated with decreased gene expression. In the triplicated genome, H3K27me3 is associated with paralogs that have tissue-specific expression. Even though B. rapa and Arabidopsis thaliana are not closely related within the Brassicaceae, there is conservation of H3K27me3-marked sites in the two species. Both B. rapa and A. thaliana require vernalization for floral initiation with FLC being the major controlling locus. In all four BrFLC paralogs, low-temperature treatment increases H3K27me3 at the proximal nucleation site reducing BrFLC expression. Following return to normal temperature growth conditions, H3K27me3 spreads along all four BrFLC paralogs providing stable repression of the gene

ChIPseqR: analysis of ChIP-seq experiments

<p>Abstract</p> <p>Background</p> <p>The use of high-throughput sequencing in combination with chromatin immunoprecipitation (ChIP-seq) has enabled the study of genome-wide protein binding at high resolution. While the amount of data generated from such experiments is steadily increasing, the methods available for their analysis remain limited. Although several algorithms for the analysis of ChIP-seq data have been published they focus almost exclusively on transcription factor studies and are usually not well suited for the analysis of other types of experiments.</p> <p>Results</p> <p>Here we present ChIPseqR, an algorithm for the analysis of nucleosome positioning and histone modification ChIP-seq experiments. The performance of this novel method is studied on short read sequencing data of <it>Arabidopsis thaliana </it>mononucleosomes as well as on simulated data.</p> <p>Conclusions</p> <p>ChIPseqR is shown to improve sensitivity and spatial resolution over existing methods while maintaining high specificity. Further analysis of predicted nucleosomes reveals characteristic patterns in nucleosome sequences and placement.</p

Antimicrobial resistance in dairy slurry tanks: A critical point for measurement and control

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Strengthening and stretching for rheumatoid arthritis of the hand (SARAH):Design of a randomised controlled trial of a hand and upper limb exercise intervention-ISRCTN89936343

Background: Rheumatoid Arthritis (RA) commonly affects the hands and wrists with inflammation, deformity, pain, weakness and restricted mobility leading to reduced function. The effectiveness of exercise for RA hands is uncertain, although evidence from small scale studies is promising. The Strengthening And Stretching for Rheumatoid Arthritis of the Hand (SARAH) trial is a pragmatic, multi-centre randomised controlled trial evaluating the clinical and cost effectiveness of adding an optimised exercise programme for hands and upper limbs to best practice usual care for patients with RA.Methods/design: 480 participants with problematic RA hands will be recruited through 17 NHS trusts. Treatments will be provided by physiotherapists and occupational therapists. Participants will be individually randomised to receive either best practice usual care (joint protection advice, general exercise advice, functional splinting and assistive devices) or best practice usual care supplemented with an individualised exercise programme of strengthening and stretching exercises. The study assessors will be blinded to treatment allocation and will follow participants up at four and 12 months. The primary outcome measure is the Hand function subscale of the Michigan Hand Outcome Questionnaire, and secondary outcomes include hand and wrist impairment measures, quality of life, and resource use. Economic and qualitative studies will also be carried out in parallel.Discussion: This paper describes the design and development of a trial protocol of a complex intervention study based in therapy out-patient departments. The findings will provide evidence to support or refute the use of an optimised exercise programme for RA of the hand in addition to best practice usual care.Trial registration: Current Controlled Trials ISRCTN89936343Keywords: Randomised controlled trial, Rheumatoid arthritis, Exercise, Hand, Rehabilitatio