2,744 research outputs found

    CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping.

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    Broad-scale protein-protein interaction mapping is a major challenge given the cost, time, and sensitivity constraints of existing technologies. Here, we present a massively multiplexed yeast two-hybrid method, CrY2H-seq, which uses a Cre recombinase interaction reporter to intracellularly fuse the coding sequences of two interacting proteins and next-generation DNA sequencing to identify these interactions en masse. We applied CrY2H-seq to investigate sparsely annotated Arabidopsis thaliana transcription factors interactions. By performing ten independent screens testing a total of 36 million binary interaction combinations, and uncovering a network of 8,577 interactions among 1,453 transcription factors, we demonstrate CrY2H-seq's improved screening capacity, efficiency, and sensitivity over those of existing technologies. The deep-coverage network resource we call AtTFIN-1 recapitulates one-third of previously reported interactions derived from diverse methods, expands the number of known plant transcription factor interactions by three-fold, and reveals previously unknown family-specific interaction module associations with plant reproductive development, root architecture, and circadian coordination

    Orchestration of the stilbene synthase gene family and their regulators by subgroup 2 MYB genes

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    The control of plant specialised metabolism is exerted by transcription factors and co-regulators acting on cis-regulatory DNA sequences of pathway-structural genes, determining when, where, and how metabolites are accumulated. A particularly interesting case for studying the transcriptional control of metabolism is represented by stilbenoids, produced within the phenylpropanoid pathway, as their ability to inhibit infection by coronaviruses MERS-CoV and SARS-CoV has been recently demonstrated in vitro. Integrative omic studies in grapevine (Vitis vinifera L.), including gene co-expression networks, have previously highlighted several transcription factors (TFs) from different gene families as potential modulators of stilbenoid accumulation, offering an ideal framework for gene function characterisation using genome-wide approaches. In the context of non-model plant species, DNA affinity purification sequencing (DAP-Seq) results a novel and potentially powerful tool for the analysis of novel uncharacterised regulators, however, it has not yet been applied in fruit crops. Accordingly, we tested as a proof-of-concept the binding of two previously characterised R2R3-MYB TFs to their known targets of the stilbene pathway, MYB14 and MYB15, obtaining 5,222 and 4,502 binding events assigned to 4,038 and 3,645 genes for each TF, respectively. Bound genes (putative targets) were overlapped with aggregated gene centred co-expression networks resulting in shared and exclusive High Confidence Targets (HCTs) suggesting a high, but not complete, redundancy. Our results show that in addition to the previously known but few STS targets, these regulators bind to almost half of the complete STS family in addition to other phenylpropanoid- and stilbenoid-related genes. We also suggest they are potentially involved in other processes such as the circadian rhythm or the synthesis of biotin. We searched the activated transcriptomes of transiently MYB15-overexpressing grapevine plants and observed a large activation of its high confidence targets, validating our methodological approach. Our results also show that MYB15 seems to play a role in regulating other stilbenoid-related TFs such as WRKY03.This work was supported by Grant PGC2018-099449-A-I00 and by the Ramón y Cajal program grant RYC-2017-23645, both awarded to J.T.M. and to the FPI scholarship PRE2019-088044 granted to L.O. from the Ministerio de Ciencia, Innovaci´on y Universidades (MCIU, Spain), Agencia Estatal de Investigaci´on (AEI, Spain), and Fondo Europeo de Desarrollo Regional (FEDER, European Union). C.Z. is supported by China Scholarship Council (CSC) no. 201906300087. This article is based upon work from COST Action CA 17111 INTEGRAPE, supported by COST (European Cooperation in Science and Technology). Data has been treated and uploaded in public repositories according to the FAIR principles.N

    Application of photoreflectance to advanced multilayer structures for photovoltaics

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    Photoreflectance (PR) is a convenient characterization tool able to reveal optoelectronic properties of semiconductor materials and structures. It is a simple non-destructive and contactless technique which can be used in air at room temperature. We will present experimental results of the characterization carried out by means of PR on different types of advanced photovoltaic (PV) structures, including quantum-dot-based prototypes of intermediate band solar cells, quantum-well structures, highly mismatched alloys, and III?V-based multi-junction devices, thereby demonstrating the suitability of PR as a powerful diagnostic tool. Examples will be given to illustrate the value of this spectroscopic technique for PV including (i) the analysis of the PR spectra in search of critical points associated to absorption onsets; (ii) distinguishing signatures related to quantum confinement from those originating from delocalized band states; (iii) determining the intensity of the electric field related to built-in potentials at interfaces according to the Franz?Keldysh (FK) theory; and (v) determining the nature of different oscillatory PR signals among those ascribed to FK-oscillations, interferometric and photorefractive effects. The aim is to attract the interest of researchers in the field of PV to modulation spectroscopies, as they can be helpful in the analysis of their devices

    Direct regulation of shikimate, early phenylpropanoid, and stilbenoid pathways by subgroup 2 R2R3-MYBs in grapevine

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    The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors (TFs) have been identified as regulators of this pathway but the extent of this control has not been deeply studied. Here we show how DNA affinity purification sequencing (DAP-Seq) allows for the genome-wide TF-binding site interrogation in grape. We obtained 5190 and 4443 binding events assigned to 4041 and 3626 genes for MYB14 and MYB15, respectively (approximately 40% of peaks located within −10 kb of transcription start sites). DAP-Seq of MYB14/MYB15 was combined with aggregate gene co-expression networks (GCNs) built from more than 1400 transcriptomic datasets from leaves, fruits, and flowers to narrow down bound genes to a set of high confidence targets. The analysis of MYB14, MYB15, and MYB13, a third uncharacterized member of Subgroup 2 (S2), showed that in addition to the few previously known stilbene synthase (STS) targets, these regulators bind to 30 of 47 STS family genes. Moreover, all three MYBs bind to several PAL, C4H, and 4CL genes, in addition to shikimate pathway genes, the WRKY03 stilbenoid co-regulator and resveratrol-modifying gene candidates among which ROMT2-3 were validated enzymatically. A high proportion of DAP-Seq bound genes were induced in the activated transcriptomes of transient MYB15-overexpressing grapevine leaves, validating our methodological approach for delimiting TF targets. Overall, Subgroup 2 R2R3-MYBs appear to play a key role in binding and directly regulating several primary and secondary metabolic steps leading to an increased flux towards stilbenoid production. The integration of DAP-Seq and reciprocal GCNs offers a rapid framework for gene function characterization using genome-wide approaches in the context of non-model plant species and stands up as a valid first approach for identifying gene regulatory networks of specialized metabolism.This work was supported by Grant PGC2018-099449-A-I00 and by the Ramón y Cajal program (grant RYC-2017-23 645), both awarded to JTM, and to the FPI scholarship (PRE2019-088044) granted to LO from the Ministerio de Ciencia, Innovación y Universidades (MCIU, Spain), Agencia Estatal de Investigación (AEI, Spain), and Fondo Europeo de Desarrollo Regional (FEDER, European Union). CZ is supported by China Scholarship Council (CSC; no. 201906300087). KG and ZR were supported by the Slovenian Research Agency (grants P4-0165 and Z7-1888). SCH is partially supported by the National Science Foundation (grant PGRP IOS-1916804). This article is based upon work from COST Action CA 17111 INTEGRAPE, supported by COST (European Cooperation in Science and Technology).Peer reviewe

    Observation of J/ψppˉa0(980)J/\psi \rightarrow p\bar{p}a_{0}(980) at BESIII

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    Using 2.25×1082.25\times10^{8} J/ψJ/\psi events collected with the BESIII detector at the BEPCII storage rings, we observe for the first time the process J/ψppˉa0(980)J/\psi\rightarrow p\bar{p}a_{0}(980), a0(980)π0ηa_{0}(980)\rightarrow \pi^{0}\eta with a significance of 6.5σ6.5\sigma (3.2σ3.2\sigma including systematic uncertainties). The product branching fraction of J/ψppˉa0(980)ppˉπ0ηJ/\psi\rightarrow p\bar{p}a_{0}(980)\rightarrow p\bar{p}\pi^{0}\eta is measured to be (6.8±1.2±1.3)×105(6.8\pm1.2\pm1.3)\times 10^{-5}, where the first error is statistical and the second is systematic. This measurement provides information on the a0a_{0} production near threshold coupling to ppˉp\bar{p} and improves the understanding of the dynamics of J/ψJ/\psi decays to four body processes.Comment: 8 pages, 7 figure

    Search for the radiative transitions ψ(3770)γηc\psi(3770)\to\gamma\eta_c and γηc(2S)\gamma\eta_c(2S)

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    By using a 2.92 fb1^{-1} data sample taken at s=3.773\sqrt{s} = 3.773 GeV with the BESIII detector operating at the BEPCII collider, we search for the radiative transitions ψ(3770)γηc\psi(3770)\to\gamma\eta_c and γηc(2S)\gamma\eta_c(2S) through the hadronic decays ηc(ηc(2S))KS0K±π\eta_c(\eta_c(2S))\to K^0_SK^\pm\pi^\mp. No significant excess of signal events above background is observed. We set upper limits at a 90% confidence level for the product branching fractions to be B(ψ(3770)γηc)×B(ηcKS0K±π)<1.6×105\mathcal{B}(\psi(3770)\to\gamma\eta_c)\times \mathcal{B}(\eta_c\to K^0_SK^\pm\pi^\mp) < 1.6\times10^{-5} and B(ψ(3770)γηc(2S))×B(ηc(2S)KS0K±π)<5.6×106\mathcal{B}(\psi(3770)\to\gamma\eta_c(2S))\times \mathcal{B}(\eta_c(2S)\to K^0_SK^\pm\pi^\mp) < 5.6\times10^{-6}. Combining our result with world-average values of B(ηc(ηc(2S))KS0K±π)\mathcal{B}(\eta_c(\eta_c(2S))\to K^0_SK^\pm\pi^\mp), we find the branching fractions B(ψ(3770)γηc)<6.8×104\mathcal{B}(\psi(3770)\to\gamma\eta_c) < 6.8\times10^{-4} and B(ψ(3770)γηc(2S))<2.0×103\mathcal{B}(\psi(3770)\to\gamma\eta_c(2S)) < 2.0\times10^{-3} at a 90% confidence level.Comment: 10 pages, 4 figure

    Precision Measurement of the Mass of the τ\tau Lepton

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    An energy scan near the τ\tau pair production threshold has been performed using the BESIII detector. About 2424 pb1^{-1} of data, distributed over four scan points, was collected. This analysis is based on τ\tau pair decays to eeee, eμe\mu, eheh, μμ\mu\mu, μh\mu h, hhhh, eρe\rho, μρ\mu\rho and πρ\pi\rho final states, where hh denotes a charged π\pi or KK. The mass of the τ\tau lepton is measured from a maximum likelihood fit to the τ\tau pair production cross section data to be mτ=(1776.91±0.120.13+0.10m_{\tau} = (1776.91\pm0.12 ^{+0.10}_{-0.13}) MeV/c2c^2, which is currently the most precise value in a single measurement.Comment: 13 pages, 7 figure

    Observation of an anomalous line shape of the ηπ+π\eta^{\prime}\pi^{+}\pi^{-} mass spectrum near the ppˉp\bar{p} mass threshold in J/ψγηπ+πJ/\psi\rightarrow\gamma\eta^{\prime}\pi^{+}\pi^{-}

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    Using 1.09×1091.09\times10^{9} J/ψJ/\psi events collected by the BESIII experiment in 2012, we study the J/ψγηπ+πJ/\psi\rightarrow\gamma\eta^{\prime}\pi^{+}\pi^{-} process and observe a significant abrupt change in the slope of the ηπ+π\eta^{\prime}\pi^{+}\pi^{-} invariant mass distribution at the proton-antiproton (ppˉp\bar{p}) mass threshold. We use two models to characterize the ηπ+π\eta^{\prime}\pi^{+}\pi^{-} line shape around 1.85 GeV/c21.85~\text{GeV}/c^{2}: one which explicitly incorporates the opening of a decay threshold in the mass spectrum (Flatt\'{e} formula), and another which is the coherent sum of two resonant amplitudes. Both fits show almost equally good agreement with data, and suggest the existence of either a broad state around 1.85 GeV/c21.85~\text{GeV}/c^{2} with strong couplings to ppˉp\bar{p} final states or a narrow state just below the ppˉp\bar{p} mass threshold. Although we cannot distinguish between the fits, either one supports the existence of a ppˉp\bar{p} molecule-like state or bound state with greater than 7σ7\sigma significance

    Search for C-parity violation in J/ψγγJ/ \psi \to \gamma\gamma and γϕ \gamma \phi

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    Using 1.06×1081.06\times10^8 ψ(3686)\psi(3686) events recorded in e+ee^{+}e^{-} collisions at s=\sqrt{s}= 3.686 GeV with the BESIII at the BEPCII collider, we present searches for C-parity violation in J/ψγγJ/\psi \to \gamma\gamma and γϕ \gamma \phi decays via ψ(3686)J/ψπ+π\psi(3686) \to J/\psi \pi^+\pi^-. No significant signals are observed in either channel. Upper limits on the branching fractions are set to be B(J/ψγγ)<2.7×107\mathcal{B}(J/\psi \to \gamma\gamma) < 2.7 \times 10^{-7} and B(J/ψγϕ)<1.4×106\mathcal{B}(J/\psi \to \gamma\phi) < 1.4 \times 10^{-6} at the 90\% confidence level. The former is one order of magnitude more stringent than the previous upper limit, and the latter represents the first limit on this decay channel.Comment: 7 pages, 2 figure
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