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

Gene Silencing of \u3ci\u3eArgonaute5\u3c/i\u3e Negatively Affects the Establishment of the Legume-Rhizobia Symbiosis

The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, can bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance, AGO5 regulates the systemic resistance of Arabidopsis against Potato Virus X as well as the pigmentation of soybean (Glycine max) seeds. Here, we show that AGO5 is also playing a central role in legume nodulation based on its preferential expression in common bean (Phaseolus vulgaris) and soybean roots and nodules. We also report that the expression of AGO5 is induced after 1 h of inoculation with rhizobia. Down-regulation of AGO5 gene in P. vulgaris and G. max causes diminished root hair curling, reduces nodule formation and interferes with the induction of three critical symbiotic genes: Nuclear Factor Y-B (NF-YB), Nodule Inception (NIN) and Flotillin2 (FLOT2). Our findings provide evidence that the common bean and soybean AGO5 genes play an essential role in the establishment of the symbiosis with rhizobia

DESAlert: enabling real-time transient follow-up with dark energy survey data

The Dark Energy Survey is undertaking an observational programme imaging 1/4 of the southern hemisphere sky with unprecedented photometric accuracy. In the process of observing millions of faint stars and galaxies to constrain the parameters of the dark energy equation of state, the Dark Energy Survey will obtain pre-discovery images of the regions surrounding an estimated 100 gamma-ray bursts over 5 yr. Once gamma-ray bursts are detected by, e.g., the Swift satellite, the DES data will be extremely useful for follow-up observations by the transient astronomy community. We describe a recently-commissioned suite of software that listens continuously for automated notices of gamma-ray burst activity, collates information from archival DES data, and disseminates relevant data products back to the community in near-real-time. Of particular importance are the opportunities that non-public DES data provide for relative photometry of the optical counterparts of gamma-ray bursts, as well as for identifying key characteristics (e.g., photometric redshifts) of potential gamma-ray burst host galaxies. We provide the functional details of the DESAlert software, and its data products, and we show sample results from the application of DESAlert to numerous previously detected gamma-ray bursts, including the possible identification of several heretofore unknown gamma-ray burst hosts

Automated transient identification in the Dark Energy Survey

We describe an algorithm for identifying point-source transients and moving objects on reference-subtracted optical images containing artifacts of processing and instrumentation. The algorithm makes use of the supervised machine learning technique known as Random Forest. We present results from its use in the Dark Energy Survey Supernova program (DES-SN), where it was trained using a sample of 898,963 signal and background events generated by the transient detection pipeline. After reprocessing the data collected during the first DES-SN observing season (2013 September through 2014 February) using the algorithm, the number of transient candidates eligible for human scanning decreased by a factor of 13.4, while only 1.0% of the artificial Type Ia supernovae (SNe) injected into search images to monitor survey efficiency were lost, most of which were very faint events. Here we characterize the algorithm's performance in detail, and we discuss how it can inform pipeline design decisions for future time-domain imaging surveys, such as the Large Synoptic Survey Telescope and the Zwicky Transient Facility. An implementation of the algorithm and the training data used in this paper are available at at http://portal.nersc.gov/project/dessn/autoscan

DES13S2cmm: the first superluminous supernova from the Dark Energy Survey

We present DES13S2cmm, the first spectroscopically-confirmed superluminous supernova (SLSN) from the Dark Energy Survey (DES). We briefly discuss the data and search algorithm used to find this event in the first year of DES operations, and outline the spectroscopic data obtained from the European Southern Observatory (ESO) Very Large Telescope to confirm its redshift (z = 0.663 +/- 0.001 based on the host-galaxy emission lines) and likely spectral type (type I). Using this redshift, we find M_U_peak = -21.05 +0.10 -0.09 for the peak, rest-frame U-band absolute magnitude, and find DES13S2cmm to be located in a faint, low metallicity (sub-solar), low stellar-mass host galaxy (log(M/M_sun) = 9.3 +/- 0.3); consistent with what is seen for other SLSNe-I. We compare the bolometric light curve of DES13S2cmm to fourteen similarly well-observed SLSNe-I in the literature and find it possesses one of the slowest declining tails (beyond +30 days rest frame past peak), and is the faintest at peak. Moreover, we find the bolometric light curves of all SLSNe-I studied herein possess a dispersion of only 0.2-0.3 magnitudes between +25 and +30 days after peak (rest frame) depending on redshift range studied; this could be important for 'standardising' such supernovae, as is done with the more common type Ia. We fit the bolometric light curve of DES13S2cmm with two competing models for SLSNe-I - the radioactive decay of 56Ni, and a magnetar - and find that while the magnetar is formally a better fit, neither model provides a compelling match to the data. Although we are unable to conclusively differentiate between these two physical models for this particular SLSN-I, further DES observations of more SLSNe-I should break this degeneracy, especially if the light curves of SLSNe-I can be observed beyond 100 days in the rest frame of the supernova.Comment: Accepted by MNRAS (2015 January 23), 13 pages, 6 figures, 2 table

Search for gamma-ray emission from DES dwarf spheroidal galaxy candidates with Fermi-LAT data

Due to their proximity, high dark-matter (DM) content, and apparent absence of non-thermal processes, Milky Way dwarf spheroidal satellite galaxies (dSphs) are excellent targets for the indirect detection of DM. Recently, eight new dSph candidates were discovered using the first year of data from the Dark Energy Survey (DES). We searched for gamma-ray emission coincident with the positions of these new objects in six years of Fermi Large Area Telescope data. We found no significant excesses of gamma-ray emission. Under the assumption that the DES candidates are dSphs with DM halo properties similar to the known dSphs, we computed individual and combined limits on the velocity-averaged DM annihilation cross section for these new targets. If the estimated DM content of these dSph candidates is confirmed, they will constrain the annihilation cross section to lie below the thermal relic cross section for DM particles with masses ≲ 20 {GeV} annihilating via the b\bar{b} or tau+tau- channels

The transverse momentum dependence of charged kaon Bose-Einstein correlations in the SELEX experiment

CNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOWe report the measurement of the one-dimensional charged kaon correlation functions using 600GeV/c σ-, π- and 540GeV/c p beams from the SELEX (E781) experiment at the Fermilab Tevatron. K±K± correlation functions are studied for three transverse pair momentum, kT, ranges and parameterized by a Gaussian form. The emission source radii, R, and the correlation strength, λ, are extracted. The analysis shows a decrease of the source radii with increasing kaon transverse pair momentum for all beam types. © 2015 The Authors.We report the measurement of the one-dimensional charged kaon correlation functions using 600GeV/c σ-, π- and 540GeV/c p beams from the SELEX (E781) experiment at the Fermilab Tevatron. K±K± correlation functions are studied for three transverse pair momentum, kT, ranges and parameterized by a Gaussian form. The emission source radii, R, and the correlation strength, λ, are extracted. The analysis shows a decrease of the source radii with increasing kaon transverse pair momentum for all beam types.753458464CNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOSem informaçãoSem informaçãoRuss, J.S., Akchurin, N., Andreev, V.A., First charm hadroproduction results from SELEX (1998) ICHEP'98 Proc. Int. Conf. on High Energy Physics II, p. 1259. , arxiv:hep-ex/9812031Goldhaber, G., Fowler, W.B., Goldhaber, S., Hoang, T.F., Kalogeropoulos, T.E., Powell, W.M., Pion-pion correlations in antiproton annihilation events (1959) Phys. Rev. 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C, 52, pp. 787-803. , arxiv:0708.1122Achard, P., Test of the τ-model of Bose-Einstein correlations and reconstruction of the source function in hadronic Z-boson decay at LEP (2011) Eur. Phys. J. C, 71, p. 1648. , arxiv:1105.4788Aamodt, K., Femtoscopy of pp collisions at s = 0.9 and 7 TeV at the LHC with two-pion Bose-Einstein correlations (2011) Phys. Rev. D, 84. , arxiv:1101.3665Wiedemann, U.A., Heinz, U.W., Resonance contributions to Hanbury-Brown-Twiss correlation radii (1997) Phys. Rev. C, 56, pp. 3265-3286. , arxiv:nucl-th/9611031Werner, K., Karpenko, I., Pierog, T., Bleicher, M., Mikhailov, K., Evidence for hydrodynamic evolution in proton-proton scattering at 900 GeV (2011) Phys. Rev. C, 83. , arxiv:1010.0400Humanic, T.J., Predictions for two-pion correlations for s=14TeV proton-proton collisions (2007) Phys. Rev. C, 76. , arxiv:nucl-th/0612098Alexopoulos, T., Study of source size in pp- collisions at s=1.8TeV using pion interferometry (1993) Phys. Rev. D, 48, pp. 1931-1942Csorgo, T., Kittel, W., Metzger, W.J., Novák, T., Parametrization of Bose-Einstein correlations and reconstruction of the space-time evolution of pion production in e+e- annihilation (2008) Phys. Lett. B, 663, pp. 214-216. , arxiv:0803.3528Bialas, A., Kucharczyk, M., Palka, H., Zalewski, K., Mass dependence of HBT correlations in e+e- annihilation (2000) Phys. Rev. D, 62. , arxiv:hep-ph/0006290Alexander, G., Open questions related to Bose-Einstein correlations in e+e- → hadrons (2004) Acta Phys. Pol. B, 35, pp. 69-76. , arxiv:hep-ph/0311114Alexander, G., Mass and transverse mass effects on the hadron emitter size (2001) Phys. Lett. B, 506, pp. 45-51. , arxiv:hep-ph/0101319The authors are indebted to the staff of Fermi National Accelerator Laboratory and for invaluable technical support from the staffs of collaborating institutions. This project was supported in part by Bundesministerium für Bildung, Wissenschaft, Forschung und Technologie, Consejo Nacional de Ciencia y Tecnología (CONACyT), Conselho Nacional de Desenvolvimento Científico e Tecnológico, Fondo de Apoyo a la Investigación (UASLP), Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), the Israel Science Foundation founded by the Israel Academy of Sciences and Humanities, Istituto Nazionale di Fisica Nucleare (INFN), the International Science Foundation (ISF), the National Science Foundation, NATO, the Russian Academy of Sciences, the Russian Ministry of Science and Technology, the Russian Foundation for Basic Research (research project No. 11-02-01302-a), the Secretaría de Educación Pública (Mexico), the Turkish Scientific and Technological Research Board (TÜBİTAK), and the U.S. Department of Energy. We thank ITEP and National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) for providing computing powers and support for data analysis and simulations. The authors also would like to thank Prof. Michael Lisa and Prof. Richard Lednický for helpful comments and fruitful discussions

The restorative role of annexin A1 at the blood–brain barrier

Annexin A1 is a potent anti-inflammatory molecule that has been extensively studied in the peripheral immune system, but has not as yet been exploited as a therapeutic target/agent. In the last decade, we have undertaken the study of this molecule in the central nervous system (CNS), focusing particularly on the primary interface between the peripheral body and CNS: the blood–brain barrier. In this review, we provide an overview of the role of this molecule in the brain, with a particular emphasis on its functions in the endothelium of the blood–brain barrier, and the protective actions the molecule may exert in neuroinflammatory, neurovascular and metabolic disease. We focus on the possible new therapeutic avenues opened up by an increased understanding of the role of annexin A1 in the CNS vasculature, and its potential for repairing blood–brain barrier damage in disease and aging

Elective Cancer Surgery in COVID-19-Free Surgical Pathways During the SARS-CoV-2 Pandemic: An International, Multicenter, Comparative Cohort Study.

PURPOSE: As cancer surgery restarts after the first COVID-19 wave, health care providers urgently require data to determine where elective surgery is best performed. This study aimed to determine whether COVID-19-free surgical pathways were associated with lower postoperative pulmonary complication rates compared with hospitals with no defined pathway. PATIENTS AND METHODS: This international, multicenter cohort study included patients who underwent elective surgery for 10 solid cancer types without preoperative suspicion of SARS-CoV-2. Participating hospitals included patients from local emergence of SARS-CoV-2 until April 19, 2020. At the time of surgery, hospitals were defined as having a COVID-19-free surgical pathway (complete segregation of the operating theater, critical care, and inpatient ward areas) or no defined pathway (incomplete or no segregation, areas shared with patients with COVID-19). The primary outcome was 30-day postoperative pulmonary complications (pneumonia, acute respiratory distress syndrome, unexpected ventilation). RESULTS: Of 9,171 patients from 447 hospitals in 55 countries, 2,481 were operated on in COVID-19-free surgical pathways. Patients who underwent surgery within COVID-19-free surgical pathways were younger with fewer comorbidities than those in hospitals with no defined pathway but with similar proportions of major surgery. After adjustment, pulmonary complication rates were lower with COVID-19-free surgical pathways (2.2% v 4.9%; adjusted odds ratio [aOR], 0.62; 95% CI, 0.44 to 0.86). This was consistent in sensitivity analyses for low-risk patients (American Society of Anesthesiologists grade 1/2), propensity score-matched models, and patients with negative SARS-CoV-2 preoperative tests. The postoperative SARS-CoV-2 infection rate was also lower in COVID-19-free surgical pathways (2.1% v 3.6%; aOR, 0.53; 95% CI, 0.36 to 0.76). CONCLUSION: Within available resources, dedicated COVID-19-free surgical pathways should be established to provide safe elective cancer surgery during current and before future SARS-CoV-2 outbreaks

Elective cancer surgery in COVID-19-free surgical pathways during the SARS-CoV-2 pandemic: An international, multicenter, comparative cohort study

PURPOSE As cancer surgery restarts after the first COVID-19 wave, health care providers urgently require data to determine where elective surgery is best performed. This study aimed to determine whether COVID-19–free surgical pathways were associated with lower postoperative pulmonary complication rates compared with hospitals with no defined pathway. PATIENTS AND METHODS This international, multicenter cohort study included patients who underwent elective surgery for 10 solid cancer types without preoperative suspicion of SARS-CoV-2. Participating hospitals included patients from local emergence of SARS-CoV-2 until April 19, 2020. At the time of surgery, hospitals were defined as having a COVID-19–free surgical pathway (complete segregation of the operating theater, critical care, and inpatient ward areas) or no defined pathway (incomplete or no segregation, areas shared with patients with COVID-19). The primary outcome was 30-day postoperative pulmonary complications (pneumonia, acute respiratory distress syndrome, unexpected ventilation). RESULTS Of 9,171 patients from 447 hospitals in 55 countries, 2,481 were operated on in COVID-19–free surgical pathways. Patients who underwent surgery within COVID-19–free surgical pathways were younger with fewer comorbidities than those in hospitals with no defined pathway but with similar proportions of major surgery. After adjustment, pulmonary complication rates were lower with COVID-19–free surgical pathways (2.2% v 4.9%; adjusted odds ratio [aOR], 0.62; 95% CI, 0.44 to 0.86). This was consistent in sensitivity analyses for low-risk patients (American Society of Anesthesiologists grade 1/2), propensity score–matched models, and patients with negative SARS-CoV-2 preoperative tests. The postoperative SARS-CoV-2 infection rate was also lower in COVID-19–free surgical pathways (2.1% v 3.6%; aOR, 0.53; 95% CI, 0.36 to 0.76). CONCLUSION Within available resources, dedicated COVID-19–free surgical pathways should be established to provide safe elective cancer surgery during current and before future SARS-CoV-2 outbreaks