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90
result(s) for
"Ma, Sheng-jie"
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Genome-wide identification of Brassicaceae B-BOX genes and molecular characterization of their transcriptional responses to various nutrient stresses in allotetraploid rapeseed
Background
B-box
(
BBX
) genes play important roles in plant growth regulation and responses to abiotic stresses. The plant growth and yield production of allotetraploid rapeseed is usually hindered by diverse nutrient stresses. However, no systematic analysis of Brassicaceae
BBXs
and the roles of
BBXs
in the regulation of nutrient stress responses have not been identified and characterized previously.
Results
In this study, a total of 536
BBXs
were identified from nine brassicaceae species, including 32
AtBBXs
, 66
BnaBBXs
, 41
BoBBXs
, 43
BrBBXs
, 26
CrBBXs
, 81
CsBBXs
, 52
BnBBXs
, 93
BjBBXs
, and 102
BcBBXs
. Syntenic analysis showed that great differences in the gene number of Brassicaceae
BBXs
might be caused by genome duplication. The
BBXs
were respectively divided into five subclasses according to their phylogenetic relationships and conserved domains, indicating their diversified functions. Promoter
cis
-element analysis showed that
BBXs
probably participated in diverse stress responses. Protein-protein interactions between BnaBBXs indicated their functions in flower induction. The expression profiles of
BnaBBXs
were investigated in rapeseed plants under boron deficiency, boron toxicity, nitrate limitation, phosphate shortage, potassium starvation, ammonium excess, cadmium toxicity, and salt stress conditions using RNA-seq data. The results showed that different
BnaBBXs
showed differential transcriptional responses to nutrient stresses, and some of them were simultaneously responsive to diverse nutrient stresses.
Conclusions
Taken together, the findings investigated in this study provided rich resources for studying Brassicaceae
BBX
gene family and enriched potential clues in the genetic improvement of crop stress resistance.
Journal Article
Genome-wide identification of Brassicaceae histone modification genes and their responses to abiotic stresses in allotetraploid rapeseed
Background
Histone modification is an important epigenetic regulatory mechanism and essential for stress adaptation in plants. However, systematic analysis of histone modification genes (
HMs
) in Brassicaceae species is lacking, and their roles in response to abiotic stress have not yet been identified.
Results
In this study, we identified 102
AtHMs
, 280
BnaHMs
, 251
BcHMs
, 251
BjHMs
, 144
BnHMs
, 155
BoHMs
, 137
BrHMs
, 122
CrHMs
, and 356
CsHMs
in nine Brassicaceae species, respectively. Their chromosomal locations, protein/gene structures, phylogenetic trees, and syntenies were determined. Specific domains were identified in several Brassicaceae
HMs
, indicating an association with diverse functions. Syntenic analysis showed that the expansion of Brassicaceae
HMs
may be due to segmental and whole-genome duplications. Nine key
BnaHMs
in allotetraploid rapeseed may be responsible for ammonium, salt, boron, cadmium, nitrate, and potassium stress based on co-expression network analysis. According to weighted gene co-expression network analysis (WGCNA), 12
BnaHMs
were associated with stress adaptation. Among the above genes,
BnaPRMT11
simultaneously responded to four different stresses based on differential expression analysis, while
BnaSDG46
,
BnaHDT10
, and
BnaHDA1
participated in five stresses.
BnaSDG46
was also involved in four different stresses based on WGCNA, while
BnaSDG10
and
BnaJMJ58
were differentially expressed in response to six different stresses. In summary, six candidate genes for stress resistance (
BnaPRMT11
,
BnaSDG46
,
BnaSDG10
,
BnaJMJ58
,
BnaHDT10
, and
BnaHDA1
) were identified.
Conclusions
Taken together, these findings help clarify the biological roles of Brassicaceae
HMs
. The identified candidate genes provide an important reference for the potential development of stress-tolerant oilseed plants.
Journal Article
Cooperative autoinhibition and multi-level activation mechanisms of calcineurin
The Ca2＋/calmodulin-dependent protein phosphatase calcineurin （CN）, a heterodimer composed of a catalytic subunit A and an essential regulatory subunit B, plays critical functions in various cellular processes such as cardiac hypertrophy and T cell activation. It is the target of the most widely used immunosuppressants for transplantation, tacrolimus （FKS06） and cyclosporin A. However, the structure of a large part of the CNA regulatory region remains to be determined, and there has been considerable debate concerning the regulation of CN activity. Here, we report the crystal structure of full-length CN （β isoform）, which revealed a novel autoinhibitory segment （AIS） in addition to the well-known autoinhibitory domain （AID）. The AIS nestles in a hydrophobic intersubunit groove, which over- laps the recognition site for substrates and immunosuppressant-immunophilin complexes. Indeed, disruption of this AIS interaction results in partial stimulation of CN activity. More importantly, our biochemical studies demonstrate that calmodulin does not remove AID from the active site, but only regulates the orientation of AID with respect to the catalytic core, causing incomplete activation of CN. Our findings challenge the current model for CN activation, and provide a better understanding of molecular mechanisms of CN activity regulation.
Journal Article
Implementation of quantum key distribution surpassing the linear rate-transmittance bound
Quantum key distribution (QKD)1,2 offers a long-term solution to secure key exchange. Due to photon loss in transmission, it was believed that the repeaterless key rate is bounded by a linear function of the transmittance, O(η) (refs. 3,4), limiting the maximal secure transmission distance5,6. Recently, a novel type of QKD scheme has been shown to beat the linear bound and achieve a key rate performance of O(η) (refs. 7–9). Here, by employing the laser injection technique and the phase post-compensation method, we match the modes of two independent lasers and overcome the phase fluctuation. As a result, the key rate surpasses the linear bound via 302 km and 402 km commercial-fibre channels, over four orders of magnitude higher than existing results5. Furthermore, our system yields a secret key rate of 0.118 bps with a 502 km ultralow-loss fibre. This new type of QKD pushes forward long-distance quantum communication for the future quantum internet.Phase-matching quantum key distribution is implemented with a 502 km ultralow-loss optical fibre. The fluctuations of the laser initial phases and frequencies are suppressed by the laser injection technique and the phase post-compensation method.
Journal Article
Associated production of neutrino and dark fermion at future lepton colliders
A
bstract
Fermionic dark matter can be pairly produced and hence searched with missing energy at colliders. We extend such probe to the associated production of a neutrino and a dark sector fermion at the future
e
+
e
−
colliders such as CEPC, FCC-ee, ILC, and CLIC. Two typical processes, the mono-photon and electron-positron pair productions associated with missing energy, can serve the purpose. While the mono-photon search prevails at CEPC, FCC-ee, and ILC, the
channel has more significant contributions at CLIC with much higher collision energy
s
. The beam polarizations can help further suppressing the SM backgrounds to enhance the signal significance while differential cross sections can distinguish the Lorentz structure of various effective operators. The combined sensitivity can reach well above 1 TeV at CEPC/FCC-ee and ILC while it further touches 30 TeV at CLIC. Comparing with the updated results from the direct detection experiments (XENON1T, PandaX-II, PandaX-4T, LZ, and XENONnT), astrophysical
X/γ
-ray observations, and cosmological constraints for the sub-MeV absorption dark matter, the collider searches are actually more sensitive and hence can provide a complementary approach to addressing the dark fermions.
Journal Article
Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation
Doc number: 67 Abstract Background: Nitrogen limitation can induce neutral lipid accumulation in microalgae, as well as inhibiting their growth. Therefore, to obtain cultures with both high biomass and high lipid contents, and explore the lipid accumulation mechanisms, we implemented nitrogen deprivation in a model diatom Phaeodactylum tricornutum at late exponential phase. Results: Neutral lipid contents per cell subsequently increased 2.4-fold, both the number and total volume of oil bodies increased markedly, and cell density rose slightly. Transcriptional profile analyzed by RNA-Seq showed that expression levels of 1213 genes (including key carbon fixation, TCA cycle, glycerolipid metabolism and nitrogen assimilation genes) increased, with a false discovery rate cut-off of 0.001, under N deprivation. However, most light harvesting complex genes were down-regulated, extensive degradation of chloroplast membranes was observed under an electron microscope, and photosynthetic efficiency declined. Further identification of lipid classes showed that levels of MGDG and DGDG, the main lipid components of chloroplast membranes, dramatically decreased and triacylglycerol (TAG) levels significantly rose, indicating that intracellular membrane remodeling substantially contributed to the neutral lipid accumulation. Conclusions: Our findings shed light on the molecular mechanisms of neutral lipid accumulation and the key genes involved in lipid metabolism in diatoms. They also provide indications of possible strategies for improving microalgal biodiesel production.
Journal Article
Revisiting the fermionic dark matter absorption on electron target
A
bstract
We perform a systematic study of the fermionic DM absorption interactions on electron target in the context of effective field theory. The fermionic DM absorption is not just sensitive to sub-MeV DM with efficient energy release, but also gives a unique signature with clear peak in the electron recoil spectrum whose shape is largely determined by the atomic effects. Fitting with the Xenon1T and PandaX-II data prefers DM mass at
m
χ
= 59 keV and 105 keV, respectively, while the cut-off scale is probed up to around 1 TeV. The DM overproduction in the early Universe, the invisible decay effect on the cosmological evolution, and the visible decay signal collected by the astrophysical X(gamma)-ray observations (Insight-HXMT, NuSTAR, HEAO-1, and INTEGRAL) are thoroughly explored to constrain the DM absorption interactions. With stringent bounds on the tensor and pseudo-scalar operators, the other fermionic DM operators are of particular interest at tonne-scale direct detection experiments such as PandaX-4T, XENONnT, and LZ.
Journal Article
Shuttle-run synchronization in mobile ad hoc networks
In this work, we study the collective dynamics of phase oscillators in a mobile ad hoc network whose topology changes dynamically. As the network size or the communication radius of individual oscillators increases, the topology of the ad hoc network first undergoes percolation, forming a giant cluster, and then gradually achieves global connectivity. It is shown that oscillator mobility generally enhances the coherence in such networks. Interestingly, we find a new type of phase synchronization/clustering, in which the phases of the oscillators are distributed in a certain narrow range, while the instantaneous frequencies change signs frequently, leading to shuttle-run-like motion of the oscillators in phase space. We conduct a theoretical analysis to explain the mechanism of this synchronization and obtain the critical transition point.
Journal Article
PGLYRP2 drives hepatocyte-intrinsic innate immunity by trapping and clearing hepatitis B virus
Spontaneous clearance of hepatitis B virus (HBV) is frequent in adults (95%) but rare in infants (5%), emphasizing the critical role of age-related hepatic immunocompetence. However, the underlying mechanisms of hepatocyte-specific immunosurveillance and age-dependent HBV clearance remain unclear. Here, we identified PGLYRP2 as a hepatocyte-specific pattern recognition receptor with age-dependent expression, and demonstrated that phase separation of PGLYRP2 was a critical driver of spontaneous HBV clearance in hepatocytes. Mechanistically, PGLYRP2 recognized and potentially eliminated covalently closed circular DNA via phase separation, coordinated by its intrinsically disordered region and HBV DNA-binding domain (PGLYRP2IDR/209-377) in the nucleus. Additionally, PGLYRP2 suppressed HBV capsid assembly by directly interacting with the viral capsid, mediated by its PGRP domain. This interaction promoted the nucleocytoplasmic translocation of PGLYRP2 and subsequent secretion of the PGLYRP2/HBV capsid complex, thereby bolstering the hepatic antiviral response. Pathogenic variants or deletions in PGLYRP2 impaired its ability to inhibit HBV replication, highlighting its essential role in hepatocyte-intrinsic immunity. These findings suggest that targeting the PGLYRP2-mediated host-virus interaction may offer a potential therapeutic strategy for the development of anti-HBV treatments, representing a promising avenue for achieving a functional cure for HBV infection.
Journal Article