2,744 research outputs found
CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping.
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
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
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
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 at BESIII
Using events collected with the BESIII detector
at the BEPCII storage rings, we observe for the first time the process
,
with a significance of ( including systematic
uncertainties). The product branching fraction of is measured to be
, where the first error is statistical and the
second is systematic. This measurement provides information on the
production near threshold coupling to and improves the understanding
of the dynamics of decays to four body processes.Comment: 8 pages, 7 figure
Search for the radiative transitions and
By using a 2.92 fb data sample taken at GeV with
the BESIII detector operating at the BEPCII collider, we search for the
radiative transitions and
through the hadronic decays . 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
and
. Combining our result with world-average
values of , we find the
branching fractions
and at a 90%
confidence level.Comment: 10 pages, 4 figure
Precision Measurement of the Mass of the Lepton
An energy scan near the pair production threshold has been performed
using the BESIII detector. About pb of data, distributed over four
scan points, was collected. This analysis is based on pair decays to
, , , , , , , and
final states, where denotes a charged or . The mass of the
lepton is measured from a maximum likelihood fit to the pair production
cross section data to be )
MeV/, which is currently the most precise value in a single measurement.Comment: 13 pages, 7 figure
Observation of an anomalous line shape of the mass spectrum near the mass threshold in
Using events collected by the BESIII experiment
in 2012, we study the
process and observe a significant abrupt change in the slope of the
invariant mass distribution at the
proton-antiproton () mass threshold. We use two models to
characterize the line shape around
: 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
with strong couplings to final states or a
narrow state just below the mass threshold. Although we cannot
distinguish between the fits, either one supports the existence of a
molecule-like state or bound state with greater than significance
Search for C-parity violation in and
Using events recorded in
collisions at 3.686 GeV with the BESIII at the BEPCII collider, we
present searches for C-parity violation in and decays via . No significant
signals are observed in either channel. Upper limits on the branching fractions
are set to be and
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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