Summary
Plant protoplasts are useful for assessing the efficiency of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‐associated protein 9 (Cas9) mutagenesis. We improved the ...process of protoplast isolation and transfection of several plant species. We also developed a method to isolate and regenerate single mutagenized Nicotianna tabacum protoplasts into mature plants. Following transfection of protoplasts with constructs encoding Cas9 and sgRNAs, target gene DNA could be amplified for further analysis to determine mutagenesis efficiency. We investigated N. tabacum protoplasts and derived regenerated plants for targeted mutagenesis of the phytoene desaturase (NtPDS) gene. Genotyping of albino regenerants indicated that all four NtPDS alleles were mutated in amphidiploid tobacco, and no Cas9 DNA could be detected in most regenerated plants.
ObjectiveA comprehensive immune landscape for HBV infection is pivotal to achieve HBV cure.DesignWe performed single-cell RNA sequencing of 2 43 000 cells from 46 paired liver and blood samples of 23 ...individuals, including six immune tolerant, 5 immune active (IA), 3 acute recovery (AR), 3 chronic resolved and 6 HBV-free healthy controls (HCs). Flow cytometry and histological assays were applied in a second HBV cohort for validation.ResultsBoth IA and AR were characterised by high levels of intrahepatic exhausted CD8+ T (Tex) cells. In IA, Tex cells were mainly derived from liver-resident GZMK+ effector memory T cells and self-expansion. By contrast, peripheral CX3CR1+ effector T cells and GZMK+ effector memory T cells were the main source of Tex cells in AR. In IA but not AR, significant cell–cell interactions were observed between Tex cells and regulatory CD4+ T cells, as well as between Tex and FCGR3A+ macrophages. Such interactions were potentially mediated through human leukocyte antigen class I molecules together with their receptors CANX and LILRBs, respectively, contributing to the dysfunction of antiviral immune responses. By contrast, CX3CR1+GNLY+ central memory CD8+ T cells were concurrently expanded in both liver and blood of AR, providing a potential surrogate marker for viral resolution. In clinic, intrahepatic Tex cells were positively correlated with serum alanine aminotransferase levels and histological grading scores.ConclusionOur study dissects the coordinated immune responses for different HBV infection phases and provides a rich resource for fully understanding immunopathogenesis and developing effective therapeutic strategies.
Mare volcanics on the Moon are the key record of thermo-chemical evolution throughout most of lunar history
. Young mare basalts-mainly distributed in a region rich in potassium, rare-earth elements ...and phosphorus (KREEP) in Oceanus Procellarum, called the Procellarum KREEP Terrane (PKT)
-were thought to be formed from KREEP-rich sources at depth
. However, this hypothesis has not been tested with young basalts from the PKT. Here we present a petrological and geochemical study of the basalt clasts from the PKT returned by the Chang'e-5 mission
. These two-billion-year-old basalts are the youngest lunar samples reported so far
. Bulk rock compositions have moderate titanium and high iron contents with KREEP-like rare-earth-element and high thorium concentrations. However, strontium-neodymium isotopes indicate that these basalts were derived from a non-KREEP mantle source. To produce the high abundances of rare-earth elements and thorium, low-degree partial melting and extensive fractional crystallization are required. Our results indicate that the KREEP association may not be a prerequisite for young mare volcanism. Absolving the need to invoke heat-producing elements in their source implies a more sustained cooling history of the lunar interior to generate the Moon's youngest melts.
Summary
In eukaryotes, mechanisms such as alternative splicing (AS) and alternative translation initiation (ATI) contribute to organismal protein diversity. Specifically, splicing factors play ...crucial roles in responses to environment and development cues; however, the underlying mechanisms are not well investigated in plants. Here, we report the parallel employment of short‐read RNA sequencing, single molecule long‐read sequencing and proteomic identification to unravel AS isoforms and previously unannotated proteins in response to abscisic acid (ABA) treatment. Combining the data from the two sequencing methods, approximately 83.4% of intron‐containing genes were alternatively spliced. Two AS types, which are referred to as alternative first exon (AFE) and alternative last exon (ALE), were more abundant than intron retention (IR); however, by contrast to AS events detected under normal conditions, differentially expressed AS isoforms were more likely to be translated. ABA extensively affects the AS pattern, indicated by the increasing number of non‐conventional splicing sites. This work also identified thousands of unannotated peptides and proteins by ATI based on mass spectrometry and a virtual peptide library deduced from both strands of coding regions within the Arabidopsis genome. The results enhance our understanding of AS and alternative translation mechanisms under normal conditions, and in response to ABA treatment.
Significance Statement
In this study, a customized analytical pipeline was developed to study transcriptional and translational changes during the abscisic acid response in plants. Using single molecule long‐read sequencing and short‐read RNA sequencing, we identified numerous alternative spliced (AS) transcripts in Arabidopsis and characterized two new AS types. Proteomic identification indicates differentially expressed AS events were more likely to undergo protein translation. The entire workflow is applicable for other plant species.
Abstract
Magnetohydrodynamic (MHD) turbulence is an important agent of energetic particle acceleration. Focusing on the compressible properties of magnetic turbulence, we adopt the test particle ...method to study the particle acceleration from Alfvén, slow, and fast modes in four turbulence regimes that may appear in a realistic astrophysical environment. Our studies show that (1) the second-order Fermi mechanism drives the acceleration of particles in the cascade processes of three modes by particle-turbulence interactions, regardless of whether the shock wave appears; (2) not only can the power spectra of maximum-acceleration rates reveal the inertial range of compressible turbulence, but also recover the scaling and energy ratio relationship between the modes; (3) fast mode dominates the acceleration of particles, especially in the case of super-Alfvénic and supersonic turbulence, slow mode dominates the acceleration for sub-Alfvénic turbulence in the very-high-energy range, and the acceleration of Alfvén mode is significant at the early stage of the acceleration; (4) particle acceleration from three modes results in a power-law distribution in the certain range of evolution time. From the perspective of particle-wave mode interaction, this paper promotes the understanding for both the properties of turbulence and the behavior of particle acceleration, which will help provide insight into astrophysical processes involved in MHD turbulence.
The genetic links among rift magmatism, crustal growth and water–rock interaction are an important issue about mass and heat transfer between mantle and crust during supercontinent breakup. A ...combined study of Hf and O isotopes in zircons from Neoproterozoic granitoids in South China provides evidence for growth and reworking of juvenile and ancient crusts with different styles of water–rock interactions along rift tectonic zones. Two generations of the granitoids show contrasting features in both zircon Hf and O isotope compositions, indicating their distinct petrogenesis. The ∼
825 Ma granitoids exhibit negative
ε
Hf(
t) values of −
3.4
±
0.8 to −
1.6
±
0.8 with old model Hf ages of 1.81
±
0.07 to 1.92
±
0.10 Ga, and high
δ
18O values of 8.7 to 10.4‰. These indicate that the source material of granitoid magmas was derived from melting of Paleoproterozoic basement that has the Hf isotope signature similar to the enriched mantle but experienced chemical weathering process before anatexis. Reworking of ancient crust is demonstrated to occur at ∼
825 Ma in the orogenic collapse zone, with overprinting of subsolidus hydrothermal alteration during magma emplacement. In contrast, the 760–750 Ma bimodal intrusives are characterized by positive
ε
Hf(
t) values of 3.5
±
0.8 to 9.9
±
0.8 with young model Hf ages of 0.94
±
0.06 to 1.18
±
0.06 Ga, and both low and high
δ
18O values of 4.2 to 6.2‰ relative to 5.3
±
0.3‰ for the normal mantle zircon. Prompt reworking of juvenile crust is suggested to occur at ∼
750 Ma in the rifted tectonic zone, with occurrence of supersolidus hydrothermal alteration and local low-
18O magmatism during supercontinent breakup. Contributions of the depleted mantle to their magma sources are contrasting in the two episodes of magmatism in association with breakup of the supercontinent Rodinia. While the change in melt source from the crust to the mantle keeps pace with the advance from continental rifting to supercontinent breakup, significant transport of both heat and material from the depleted mantle to the continental crust only occurred along the active rifting zone. In either case, the growth and reworking of continental crust are episodically associated with rift magmatism.
Four populations of zircons are recognized by U–Pb analyses of the Neoproterozoic Liantuo Formation in the northern part of the Yangtze Block, South China. They are grains of detrital zircon older ...than 3.0 Ga, ca. 2.95 Ga, ca. 1.95 Ga and 820–750 Ma, respectively. The oldest zircon has a U–Pb age of 3802±8 Ma with a εHf(t) value of −0.8 and model Hf ages of 3.96 Ga (TDM1) and 4.00 Ga (TDM2). This demonstrates the existence of 3.8 Ga old crustal remnants in South China, with possible crustal growth as early as 4.0 Ga. A series of 3.3 Ga zircons have positive εHf(t) values as high as 4.2, providing compelling evidence for growth of juvenile crust from a depleted mantle reservoir at Paleoarchean. All the zircons have Archean Hf model ages, with prominent peaks at 3.2 to 3.6 Ga, indicating an important period of crustal growth in this period. The other three zircon populations at ∼2.95 Ga, ∼1.95 Ga and 820–750 Ma have negative εHf(t) values and consistent Archean Hf model ages, suggesting multi-stage episodic reworking of Archean crustal materials. The youngest zircons have U–Pb ages of ∼750 Ma, very close to the deposition time of the Liantuo Formation. This indicates rapid recycling of supracrustal materials in a rift basin, possibly in association with breakup of the supercontinent Rodinia at that time.
We investigate how to recover the spectral properties of underlying magnetohydrodynamic (MHD) turbulence using fluctuation statistics of synchrotron polarization radiation, based on the synthetic ...observations. Taking spatially coincident, separated, and compounded synchrotron emission and Faraday rotation regions into account, we extract the power spectrum of synchrotron polarization intensities integrated along the line of sight. Our results demonstrate that in the short wavelength range, the power spectra reflect fluctuation statistics of the perpendicular component of turbulent magnetic fields, and the spectra at long wavelengths reveal the fluctuation of the Faraday rotation density, which is a product of the parallel component of magnetic field and thermal electron density. We find that our numerical results (in the case of spatially coincident regions) are in agreement with the analytical prediction in Lazarian & Pogosyan, and this theoretical prediction is applicable to more complicated settings, i.e., the spatially separated and compounded regions. We simulate telescopic observations that incorporate the effects of telescope angular resolution and noise, and find that statistics of underlying MHD turbulence can be recovered successfully. We expect that the technique can be applied to a variety of astrophysical environments, with existing synchrotron data cubes and a large number of forthcoming data sets from such as the LOw Frequency Array for Radio astronomy, the Square Kilometer Array, and the Five-hundred-meter Aperture Spherical radio Telescope.
SUMMARY
Intron‐containing genes have the ability to generate multiple transcript isoforms by splicing, thereby greatly expanding the eukaryotic transcriptome and proteome. In eukaryotic cells, ...precursor mRNA (pre‐mRNA) splicing is performed by a mega‐macromolecular complex defined as a spliceosome. Among its splicing components, U1 small nuclear ribonucleoprotein (U1 snRNP) is the smallest subcomplex involved in early spliceosome assembly and 5′‐splice site recognition. Its central component, named U1‐70K, has been extensively characterized in animals and yeast. Very few investigations on U1‐70K genes have been conducted in plants, however. To this end, we performed a comprehensive study to systematically identify 115 U1‐70K genes from 67 plant species, ranging from algae to angiosperms. Phylogenetic analysis suggested that the expansion of the plant U1‐70K gene family was likely to have been driven by whole‐genome duplications. Subsequent comparisons of gene structures, protein domains, promoter regions and conserved splicing patterns indicated that plant U1‐70Ks are likely to preserve their conserved molecular function across plant lineages and play an important functional role in response to environmental stresses. Furthermore, genetic analysis using T‐DNA insertion mutants suggested that Arabidopsis U1‐70K may be involved in response to osmotic stress. Our results provide a general overview of this gene family in Viridiplantae and will act as a reference source for future mechanistic studies on this U1 snRNP‐specific splicing factor.
Significance Statement
This study describes a comprehensive analysis to systematically name and identify 115 U1‐70K genes from 67 plant species, ranging from algae to angiosperms.
•UHT metamorphism is reported for the first time in the Himalaya.•The heat source was an over-thickened crust associated with lithospheric thinning.•Cold vs. granulitized eclogites formed during ...infant vs. mature collisional stages.•2.0–1.8 Ga eclogites have formed by a Himalaya-type global collisional network.
Modern-style plate tectonics, often characterised by subduction, is a fundamental dynamic process for planet Earth. Subduction related eclogites are widely used to indicate initiation of plate tectonics or whether different tectonic regimes dominated Earth history. However, such markers are commonly overprinted in ancient metamorphic terranes and rarely preserved even in most Phanerozoic mountain belts. This study tries to reveal the detailed burial and exhumation processes that formed granulitized eclogites in the Everest east region, central Himalaya, so as to explore the tectonic regimes recorded by similar rocks on early Earth. Robust Pressure-Temperature-time paths were achieved by studying the mineral relicts (Omp, Jd ∼29%), high-temperature mineral textures (Sil-Crd-Qz-Spl-Mesoperthite assemblage, rutile exsolution in biotite), and multiple thermobarometry and petrochronology of eclogites and metapelites. Results show that these eclogites underwent eclogitization at conditions of 730–770°C and ∼20 kbar (∼11°C/km) at ∼30 Ma and were overprinted by a heating and decompression path to ultrahigh temperature (UHT) conditions of 6–11 kbar and 900–970°C (∼40°C/km) during 25–15 Ma. The resulting exhumation rate (2–3 mm/yr) is slow and prolonged (10–15 Myr) (U)HT favoured re-equilibration of the eclogitic mineral assemblage and textures. The obtained UHT conditions, the first time ever reported for the Himalaya, were induced by combined effects of over-thickened (∼60 km) radioactive felsic crust and thinning of lithosphere to <90 km. This case study provides a critical example to understand the heat sources and timescale of UHT condition during continental collision. By comparing with the western Himalaya eclogites, we suggest that formation of cold vs. granulitized continental eclogites during the Himalayan orogeny is caused by different crustal thickness (normal ∼30 km vs. over-thickened ∼60 km) due to different collisional stages (infant vs. mature). In a wider perspective, ancient eclogites were commonly granulitized by stacking into the over-thickened orogenic crust during mature continental collision. According to similar granulitized eclogites preserved on early Earth, Himalaya-type continental subduction/collision should have become a global pattern during the Paleoproterozoic (2.0–1.8 Ga).
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