Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are endogenously encoded small RNAs that post-transcriptionally regulate gene expression. MiRNAs play essential roles in almost all plant biological processes. Currently, few miRNAs have been identified in the model food legume <it>Phaseolus vulgaris </it>(common bean). Recent advances in next generation sequencing technologies have allowed the identification of conserved and novel miRNAs in many plant species. Here, we used Illumina's sequencing by synthesis (SBS) technology to identify and characterize the miRNA population of <it>Phaseolus vulgaris</it>.</p> <p>Results</p> <p>Small RNA libraries were generated from roots, flowers, leaves, and seedlings of <it>P. vulgaris</it>. Based on similarity to previously reported plant miRNAs,114 miRNAs belonging to 33 conserved miRNA families were identified. Stem-loop precursors and target gene sequences for several conserved common bean miRNAs were determined from publicly available databases. Less conserved miRNA families and species-specific common bean miRNA isoforms were also characterized. Moreover, novel miRNAs based on the small RNAs were found and their potential precursors were predicted. In addition, new target candidates for novel and conserved miRNAs were proposed. Finally, we studied organ-specific miRNA family expression levels through miRNA read frequencies.</p> <p>Conclusions</p> <p>This work represents the first massive-scale RNA sequencing study performed in <it>Phaseolus vulgaris </it>to identify and characterize its miRNA population. It significantly increases the number of miRNAs, precursors, and targets identified in this agronomically important species. The miRNA expression analysis provides a foundation for understanding common bean miRNA organ-specific expression patterns. The present study offers an expanded picture of <it>P. vulgaris </it>miRNAs in relation to those of other legumes.</p

Isolation and characterization of potent antifungal strains of the Streptomyces violaceusniger clade active against Candida albicans

Streptomyces strains were isolated from a sagebrush rhizosphere soil sample on humic acid vitamin (HV) agar and water yeast extract (WYE) agar supplemented with 1.5% (w/w) phenol as a selective medium. Acidic, neutral and alkaline pH conditions were also used in the isolation procedures. The phenol treatment reduced the numbers of both actinomycetes and non-actinomycetes on plates under all three pH conditions. From phenol-amended HV and WYE agar, 16 strains were isolated in pure culture; 14 from the HV agar and two from the WYE agar. All the isolates were tested for their antifungal activities against Pythium ultimum P8 and five yeast strains, including two antifungal drug-resistant Candida albicans strains. HV isolates that showed broad-spectrum antifungal antibiotic activities were all found to be members of the Streptomyces violaceusniger clade, while those that did not were non-clade members. The phenol treatment was not selective for S. violaceusniger clade members. Therefore, we tested the spores of both S. violaceusniger clade and non-clade members using two biocides, phenol and hydrogen peroxide, as selection agents. Spores of non-clade members, such as S. coelicolor M145 and S. lividans TK 21, survived these two biocides just as well as S. violaceusniger clade members. Thus, in our hands, biocide resistance was not S. violaceusniger clade specific as previously reported. However, isolates showing broad-spectrum antifungal and antiyeast activity were all members of the clade. We conclude that screening of isolates for broad-spectrum antifungal/antiyeast activity is the preferred method of isolating S. violaceusniger clade strains rather than biocide-based selection. Phylogenetic analysis of the phenol-resistant isolates revealed that the HV isolates that exhibited broad-spectrum antifungal antibiotic activity were all clustered and closely related to the S. violaceusniger clade, while the isolates that did not exhibit antifungal antibiotic activity were all non-clade members

Identification of actinomycetes from plant rhizospheric soils with inhibitory activity against Colletotrichum spp., the causative agent of anthracnose disease

<p>Abstract</p> <p>Background</p> <p><it>Colletotrichum </it>is one of the most widespread and important genus of plant pathogenic fungi worldwide. Various species of <it>Colletotrichum </it>are the causative agents of anthracnose disease in plants, which is a severe problem to agricultural crops particularly in Thailand. These phytopathogens are usually controlled using chemicals; however, the use of these agents can lead to environmental pollution. Potential non-chemical control strategies for anthracnose disease include the use of bacteria capable of producing anti-fungal compounds such as actinomycetes spp., that comprise a large group of filamentous, Gram positive bacteria from soil. The aim of this study was to isolate actinomycetes capable of inhibiting the growth of <it>Colletotrichum </it>spp, and to analyze the diversity of actinomycetes from plant rhizospheric soil.</p> <p>Results</p> <p>A total of 304 actinomycetes were isolated and tested for their inhibitory activity against <it>Colletotrichum gloeosporioides </it>strains DoA d0762 and DoA c1060 and <it>Colletotrichum capsici </it>strain DoA c1511 which cause anthracnose disease as well as the non-pathogenic <it>Saccharomyces cerevisiae </it>strain IFO 10217. Most isolates (222 out of 304, 73.0%) were active against at least one indicator fungus or yeast. Fifty four (17.8%) were active against three anthracnose fungi and 17 (5.6%) could inhibit the growth of all three fungi and <it>S. cerevisiae </it>used in the test. Detailed analysis on 30 selected isolates from an orchard at Chanthaburi using the comparison of 16S rRNA gene sequences revealed that most of the isolates (87%) belong to the genus <it>Streptomyces </it>sp., while one each belongs to <it>Saccharopolyspora </it>(strain SB-2) and <it>Nocardiopsis </it>(strain CM-2) and two to <it>Nocardia </it>(strains BP-3 and LK-1). Strains LC-1, LC-4, JF-1, SC-1 and MG-1 exerted high inhibitory activity against all three anthracnose fungi and yeast. In addition, the organic solvent extracts prepared from these five strains inhibited conidial growth of the three indicator fungi. Preliminary analysis of crude extracts by high performance liquid chromatography (HPLC) indicated that the sample from strain JF-1 may contain a novel compound. Phylogenetic analysis revealed that this strain is closely related to <it>Streptomyces cavurensis </it>NRRL 2740 with 99.8% DNA homology of 16S rRNA gene (500 bp).</p> <p>Conclusion</p> <p>The present study suggests that rhizospheric soil is an attractive source for the discovery of a large number of actinomycetes with activity against <it>Colletotrichum </it>spp. An interesting strain (JF-1) with high inhibitory activity has the potential to produce a new compound that may be useful in the control of <it>Colletotrichum </it>spp.</p

RPC upgrade project for CMS Phase II

The Muon Upgrade Phase II of the Compact Muon Solenoid (CMS) aims to guarantee the optimal conditions of the present system and extend the eta coverage to ensure a reliable system for the High Luminosity Large Hadron Collider (HL-LHC) period. The Resistive Plate Chambers (RPCs) system will upgrade the off-detector electronics (called link system) of the chambers currently installed chambers and place improved RPCs (iRPCs) to cover the high pseudo-rapidity region, a challenging region for muon reconstruction in terms of background and momentum resolution. In order to find the best option for the iRPCs, an R&D program for new detectors was performed and real size prototypes have been tested in the Gamma Irradiation Facility (GIF++) at CERN. The results indicated that the technology suitable for the high background conditions is based on High Pressure Laminate (HPL) double-gap RPC. The RPC Upgrade Phase II program is planned to be ready after the Long Shutdown 3 (LS3)

High voltage calibration method for the CMS RPC detector

The Resistive Plate Chambers (RPC) are used for muon triggers in the CMS experiment. To calibrate the high voltage working-points (WP) and identify degraded detectors due to radiation or chemical damage, a high voltage scan has been performed using 2017 data from pp collisions at a center-of-mass energy of 13 TeV. In this paper, we present the calibration method and the latest results obtained for the 2017 data. A comparison with all scans taken since 2011 is considered to investigate the stability of the detector performance in time

RPC radiation background simulations for the high luminosity phase in the CMS experiment

The high luminosity expected from the HL-LHC will be a challenge for the CMS detector. The increased rate of particles coming from the collisions and the radioactivity induced in the detector material could cause significant damage and result in a progressive degradation of its performance. Simulation studies are very useful in these scenarios as they allow one to study the radiation environment and the impact on detector performance. Results are presented for CMS RPC stations considering the operating conditions expected at the HL-LHC

The CMS RPC detector performance and stability during LHC RUN-2

The CMS experiment, located at the Large Hadron Collider (LHC) in CERN, has a redundant muon system composed by three different gaseous detector technologies: Cathode Strip Chambers (in the forward regions), Drift Tubes (in the central region), and Resistive Plate Chambers (both its central and forward regions). All three are used for muon reconstruction and triggering. The CMS RPC system confers robustness and redundancy to the muon trigger. The RPC system operation in the challenging background and pileup conditions of the LHC environment is presented. The RPC system provides information to all muon track finders and thus contributing to both muon trigger and reconstruction. The summary of the detector performance results obtained with proton-proton collision at root s = 13 TeV during 2016 and 2017 data taking have been presented. The stability of the system is presented in terms of efficiency and cluster size vs time and increasing instantaneous luminosity. Data-driven predictions about the expected performance during High Luminosity LHC (HL-LHC) stage have been reported

CMSRPC efficiency measurement using the tag-and-probe method

We measure the efficiency of CMS Resistive Plate Chamber (RPC) detectors in proton-proton collisions at the centre-of-mass energy of 13 TeV using the tag-and-probe method. A muon from a Z(0) boson decay is selected as a probe of efficiency measurement, reconstructed using the CMS inner tracker and the rest of CMS muon systems. The overall efficiency of CMS RPC chambers during the 2016-2017 collision runs is measured to be more than 96% for the nominal RPC chambers

Search for resonances in the mass spectrum of muon pairs produced in association with b quark jets in proton-proton collisions at root 8 and 13 TeV

A search for resonances in the mass range 12-70 GeV produced in association with a b quark jet and a second jet, and decaying to a muon pair, is reported. The analysis is based on data from proton-proton collisions at center-of-mass energies of 8 and 13 TeV, collected with the CMS detector at the LHC and corresponding to integrated luminosities of 19.7 and 35.9 fb(-1), respectively. The search is carried out in two mutually exclusive event categories. Events in the first category are required to have a b quark jet in the central region (|| 2.4) and at least one jet in the forward region (|| > 2.4). Events in the second category are required to have two jets in the central region, at least one of which is identified as a b quark jet, no jets in the forward region, and low missing transverse momentum. An excess of events above the background near a dimuon mass of 28 GeV is observed in the 8 TeV data, corresponding to local significances of 4.2 and 2.9 standard deviations for the first and second event categories, respectively. A similar analysis conducted with the 13 TeV data results in a mild excess over the background in the first event category corresponding to a local significance of 2.0 standard deviations, while the second category results in a 1.4 standard deviation deficit. The fiducial cross section measurements and 95% confidence level upper limits on those for a resonance consistent with the 8 TeV excess are provided at both collision energies