Characterization of nuclear DNA diversity in an individual Leymus chinensis.

Intraorganismal genetic heterogeneity (IGH) exists when an individual organism harbors more than one genotype among its cells. In general, intercellular DNA diversity occurs at a very low frequency and cannot be directly detected by DNA sequencing from bulk tissue. In this study, based on Sanger and high-throughput sequencing, different species, different organs, different DNA segments and a single cell were employed to characterize nucleotide mutations in Leymus chinensis. The results demonstrated that 1) the nuclear DNA showed excessive genetic heterogeneity among cells of an individual leaf or seed but the chloroplast genes remained consistent; 2) a high density of SNPs was found in the variants of the unique DNA sequence, and the similar SNP profile shared between the leaf and seed suggested that nucleotide mutation followed a certain rule and was not random; and 3) the mutation rate decreased from the genomic DNA sequence to the corresponding protein sequence. Our results suggested that Leymus chinensis seemed to consist of a collection of cells with different genetic backgrounds.

Deflection of a reflected intense spatiotemporal optical vortex beam.

In this Letter, we reveal a new deflection effect in the reflection of an intense spatiotemporal optical vortex (STOV) beam. When a STOV beam with relativistic intensities (>1018 W cm-2) impacts on an overdense plasma target, the reflected beam deviates from the specular reflection direction in the incident plane. Using two-dimensional (2D) particle-in-cell simulations, we demonstrated that the typical deflection angle is of a few milliradians and can be enhanced by using a stronger STOV beam with tightly focused size and higher topological charge. Though similar to the angular Goos-Hänchen effect, however, it is worth emphasizing that the deviation induced by a STOV beam exists, even in normal incidence, revealing an essentially nonlinear effect. This novel effect is explained from the viewpoint of angular momentum conservation, as well as the Maxwell stress tensor. It is shown that an asymmetrical light pressure of the STOV beam breaks the rotational symmetry of the target surface and leads to nonspecular reflection. Unlike the shear press of an Laguerre-Gaussian beam, which only acts in oblique incidence, the deflection caused by the STOV beam exists more widely, including in normal incidence.

Protective effects of black onion polysaccharide on liver and kidney injury in T2DM rats through the synergistic impact of hypolipidemic and antioxidant abilities.

In this study, the synergistic effects of black onion on the hypolipidemic and antioxidant activities in T2DM rats induced by a high-fat-diet and alloxan were investigated. The results showed that the fasting blood glucose of diabetic rats was significantly decreased after treatment with black onion polysaccharide (p < 0.01). Blood lipid analysis indicated that black onion polysaccharide could significantly improve the abnormal metabolism of blood lipids caused by diabetes. In addition, the MDA and ROS of the diabetic rats treated with black onion polysaccharide were significantly reduced; moreover, SOD was increased, indicating the excellent antioxidant activity of black onion polysaccharide. A histological examination clearly showed that black onion polysaccharide could improve the histological morphology of the liver and kidney. Furthermore, the indices of liver and kidney function were restored. These results indicate that black onion polysaccharide can reduce blood glucose and simultaneously show synergistic effects of hypoglycemic and antioxidant activities in diabetic rats. Therefore, black onion polysaccharide may alleviate liver and kidney function injury by improving the "two-hit" mechanism and can thus be used as a potential functional food to prevent diabetes and its complications.

Distinctive in vitro ATP Hydrolysis Activity of AtVIPP1, a Chloroplastic ESCRT-III Superfamily Protein in Arabidopsis.

Vesicle-inducing protein in plastid 1 (VIPP1), characteristic to oxygenic photosynthetic organisms, is a membrane-remodeling factor that forms homo-oligomers and functions in thylakoid membrane formation and maintenance. The cyanobacterial VIPP1 structure revealed a monomeric folding pattern similar to that of endosomal sorting complex required for transport (ESCRT) III. Characteristic to VIPP1, however, is its own GTP and ATP hydrolytic activity without canonical domains. In this study, we found that histidine-tagged Arabidopsis VIPP1 (AtVIPP1) hydrolyzed GTP and ATP to produce GDP and ADP in vitro, respectively. Unexpectedly, the observed GTPase and ATPase activities were biochemically distinguishable, because the ATPase was optimized for alkaline conditions and dependent on Ca2+ as well as Mg2+, with a higher affinity for ATP than GTP. We found that a version of AtVIPP1 protein with a mutation in its nucleotide-binding site, as deduced from the cyanobacterial structure, retained its hydrolytic activity, suggesting that Arabidopsis and cyanobacterial VIPP1s have different properties. Negative staining particle analysis showed that AtVIPP1 formed particle or rod structures that differed from those of cyanobacteria and Chlamydomonas. These results suggested that the nucleotide hydrolytic activity and oligomer formation of VIPP1 are common in photosynthetic organisms, whereas their properties differ among species.

Cyclic Nucleotide-Gated Ion Channel 6 Mediates Thermotolerance in Arabidopsis Seedlings by Regulating Hydrogen Peroxide Production via Cytosolic Calcium Ions.

We previously reported the involvement of cyclic nucleotide-gated ion channel 6 (CNGC6) and hydrogen peroxide (H2O2) in plant responses to heat shock (HS). To demonstrate their relationship with plant thermotolerance, we assessed the effect of HS on several groups of Arabidopsis (Arabidopsis thaliana) seedlings: wild-type, cngc6 mutant, and its complementation line. Under exposure to HS, the level of H2O2 was lower in the cngc6 mutant seedlings than in the wild-type (WT) seedlings but obviously increased in the complementation line. The treatment of Arabidopsis seeds with calcium ions (Ca2+) increased the H2O2 levels in the seedlings under HS treatment, whereas treatment with a Ca2+ chelator (EGTA) inhibited it, indicating that CNGC6 may stimulate the accumulation of H2O2 in a manner dependent on an increase in cytosolic Ca2+ ([Ca2+]cyt). This point was verified by phenotypic observations and thermotolerance testing with transgenic plants overexpressing AtRbohB and AtRbohD (two genes involved in HS-responsive H2O2 production), respectively, in a cngc6 background. Real-time reverse transcription-polymerase chain reactions and Western blotting suggested that CNGC6 enhanced the gene transcription of HS factors (HSFs) and the accumulation of HS proteins (HSPs) via H2O2. These upon results indicate that H2O2 acts downstream of CNGC6 in the HS signaling pathway, increasing our understanding of the initiation of plants responses to high temperatures.

Polarized electron acceleration in beam-driven plasma wakefield based on density down-ramp injection.

We investigate the precession of electron spins during beam-driven plasma-wakefield acceleration based on density down-ramp injection by means of full three-dimensional (3D) particle-in-cell (PIC) simulations. A relativistic electron beam generated via, e.g., laser wakefield acceleration, serves as the driving source. It traverses the prepolarized gas target and accelerates polarized electrons via the excited wakefield. We derive the criteria for the driving beam parameters and the limitation on the injected beam flux to preserve a high degree of polarization for the accelerated electrons, which are confirmed by our 3D PIC simulations and single-particle modeling. The electron-beam driver is free of the prepulse issue associated with a laser driver, thus eliminating possible depolarization of the prepolarized gas due to ionization by the prepulse. These results provide guidance for future experiments towards generating a source of polarized electrons based on wakefield acceleration.

VIPP1 Involved in Chloroplast Membrane Integrity Has GTPase Activity in Vitro.

VESICLE-INDUCING PROTEIN IN PLASTID1 (VIPP1) is conserved among oxygenic photosynthetic organisms and appears to have diverged from the bacterial PspA protein. VIPP1 localizes to the chloroplast envelope and thylakoid membrane, where it forms homooligomers of high molecular mass. Although multiple roles of VIPP1 have been inferred, including thylakoid membrane formation, envelope maintenance, membrane fusion, and regulation of photosynthetic activity, its precise role in chloroplast membrane quality control remains unknown. VIPP1 forms an oligomer through its amino-terminal domain and triggers membrane fusion in an Mg2+-dependent manner. We previously demonstrated that Arabidopsis (Arabidopsis thaliana) VIPP1 also exhibits dynamic complex disassembly in response to osmotic and heat stresses in vivo. These results suggest that VIPP1 mediates membrane fusion/remodeling in chloroplasts. Considering that protein machines that regulate intracellular membrane fusion/remodeling events often require a capacity for GTP binding and/or hydrolysis, we questioned whether VIPP1 has similar properties. We conducted an in vitro assay using a purified VIPP1-His fusion protein expressed in Escherichia coli cells. VIPP1-His showed GTP hydrolysis activity that was inhibited competitively by an unhydrolyzable GTP analog, GTPγS, and that depends on GTP binding. It is particularly interesting that the ancestral PspA from E. coli also possesses GTP hydrolysis activity. Although VIPP1 does not contain a canonical G domain, the amino-terminal α-helix was found to be important for both GTP binding and GTP hydrolysis as well as for oligomer formation. Collectively, our results reveal that the properties of VIPP1/PspA are similar to those of GTPases.

Terawatt-scale optical half-cycle attosecond pulses.

Extreme-ultravoilet (XUV) attosecond pulses with durations of a few tens of attosecond have been successfully applied for exploring ultrafast electron dynamics at the atomic scale. But their weak intensities limit the further application in demonstrating nonlinear responses of inner-shell electrons. Optical attosecond pulses will provide sufficient photon flux to initiate strong-field processes. Here we proposed a novel method to generate an ultra-intense isolated optical attosecond pulse through relativistic multi-cycle laser pulse interacting with a designed gas-foil target. The underdense gas target sharpens the multi-cycle laser pulse, producing a dense layer of relativistic electrons with a thickness of a few hundred nanometers. When the dense electron layer passes through an oblique foil, it emits single ultra-intense half-cycle attosecond pulse in the visible and ultraviolet spectral range. The emitted pulse has a peak intensity exceeding 1018 W/cm2 and full-width-half-maximum duration of 200 as. The peak power of this attosecond light source reaches 2 terawatt. The proposed method relaxes the single-cycle requirement on the driving pulse for isolated attosecond pulse generation and significantly boosts the peak power, thus it may open up the route to new experiments tracking the nonlinear response of inner-shell electrons as well as nonlinear attosecond phenomena investigation.

Deflection of a Reflected Intense Vortex Laser Beam.

An interesting deflection effect deviating the optical reflection law is revealed in the relativistic regime of intense vortex laser plasma interaction. When an intense vortex laser obliquely impinges onto an overdense plasma target, the reflected beam deflects out of the plane of incidence with an experimentally observable deflection angle. The mechanism is demonstrated by full three-dimensional particle-in-cell simulation as well as analytical modeling using the Maxwell stress tensor. The deflection results from the rotational symmetry breaking of the foil driven by the unsymmetrical shear stress of the vortex beam. The l-dependent shear stress, where l is the topological charge, as an intrinsic characteristic to the vortex beam, plays an important role as the ponderomotive force in relativistic vortex laser matter interaction.

Protection of Chloroplast Membranes by VIPP1 Rescues Aberrant Seedling Development in Arabidopsis nyc1 Mutant.

Chlorophylls (Chl) in photosynthetic apparatuses, along with other macromolecules in chloroplasts, are known to undergo degradation during leaf senescence. Several enzymes involved in Chl degradation, by which detoxification of Chl is safely implemented, have been identified. Chl degradation also occurs during embryogenesis and seedling development. Some genes encoding Chl degradation enzymes such as Chl b reductase (CBR) function during these developmental stages. Arabidopsis mutants lacking CBR (NYC1 and NOL) have been reported to exhibit reduced seed storability, compromised germination, and cotyledon development. In this study, we examined aberrant cotyledon development and found that NYC1 is solely responsible for this phenotype. We inferred that oxidative damage of chloroplast membranes caused the aberrant cotyledon. To test the inference, we attempted to trans-complement nyc1 mutant with overexpressing VIPP1 protein that is unrelated to Chl degradation but which supports chloroplast membrane integrity. VIPP1 expression actually complemented the aberrant cotyledon of nyc1, whereas stay-green phenotype during leaf senescence remained. The swollen chloroplasts observed in unfixed cotyledons of nyc1, which are characteristics of chloroplasts receiving envelope membrane damage, were recovered by overexpressing VIPP1. These results suggest that chloroplast membranes are a target for oxidative damage caused by the impairment in Chl degradation. Trans-complementation of nyc1 with VIPP1 also suggests that VIPP1 is useful for protecting chloroplasts against oxidative stress.

VIPP1 Has a Disordered C-Terminal Tail Necessary for Protecting Photosynthetic Membranes against Stress.

Integrity of biomembranes is vital to living organisms. In bacteria, PspA is considered to act as repairing damaged membrane by forming large supercomplexes in Arabidopsis (Arabidopsis thaliana). Vulnerable to oxidative stress, photosynthetic organisms also contain a PspA ortholog called VIPP1, which has an additional C-terminal tail (Vc). In this study, Vc was shown to coincide with an intrinsically disordered region, and the role of VIPP1 in membrane protection against stress was investigated. We visualized VIPP1 by fusing it to GFP (VIPP1-GFP that fully complemented lethal vipp1 mutations), and investigated its behavior in vivo with live imaging. The intrinsically disordered nature of Vc enabled VIPP1 to form what appeared to be functional particles along envelopes, whereas the deletion of Vc caused excessive association of the VIPP1 particles, preventing their active movement for membrane protection. Expression of VIPP1 lacking Vc complemented vipp1 mutation, but exhibited sensitivity to heat shock stress. Conversely, transgenic plants over-expressing VIPP1 showed enhanced tolerance against heat shock, suggesting that Vc negatively regulates VIPP1 particle association and acts in maintaining membrane integrity. Our data thus indicate that VIPP1 is involved in the maintenance of photosynthetic membranes. During evolution, chloroplasts have acquired enhanced tolerance against membrane stress by incorporating a disordered C-terminal tail into VIPP1.

Generation of intense high-order vortex harmonics.

This Letter presents for the first time a scheme to generate intense high-order optical vortices that carry orbital angular momentum in the extreme ultraviolet region based on relativistic harmonics from the surface of a solid target. In the three-dimensional particle-in-cell simulation, the high-order harmonics of the high-order vortex mode is generated in both reflected and transmitted light beams when a linearly polarized Laguerre-Gaussian laser pulse impinges on a solid foil. The azimuthal mode of the harmonics scales with its order. The intensity of the high-order vortex harmonics is close to the relativistic region, with the pulse duration down to attosecond scale. The obtained intense vortex beam possesses the combined properties of fine transversal structure due to the high-order mode and the fine longitudinal structure due to the short wavelength of the high-order harmonics. In addition to the application in high-resolution detection in both spatial and temporal scales, it also presents new opportunities in the intense vortex required fields, such as the inner shell ionization process and high energy twisted photons generation by Thomson scattering of such an intense vortex beam off relativistic electrons.

Possible function of VIPP1 in maintaining chloroplast membranes.

A protein designated as VIPP1 is found widely in organisms performing oxygenic photosynthesis, but its precise role in chloroplasts has remained somewhat mysterious. Based on its structural similarity, it presumably has evolved from bacterial Phage shock protein A (PspA) with a C-terminal extension of approximately 40 amino acids. Both VIPP1 and PspA are membrane-associated despite the lack of transmembrane helices. They form an extremely large homo-complex that consists of an oligomeric ring unit. Although PspA is known to respond to membrane stress and although it acts in maintaining proton motive force through membrane repair, the multiple function of VIPP1, such as vesicle budding from inner envelope to deliver lipids to thylakoids, maintenance of photosynthetic complexes in thylakoid membranes, biogenesis of Photosystem I, and protective role of inner envelope against osmotic stress, has been proposed. Whatever its precise function in chloroplasts, it is an important protein because depletion of VIPP1 in mutants severely affects photoautotrophic growth. Recent reports of the relevant literature describe that VIPP1 becomes highly mobile when chloroplasts receive hypotonic stress, and that VIPP1 is tightly bound to lipids, which implies a crucial role of VIPP1 in membrane repair through lipid transfer. This review presents a summary of our current knowledge related to VIPP1, particularly addressing the dynamic behavior of complexes against stress and its property of lipid binding. Those data altogether suggest that VIPP1 acts a priori in chloroplast membrane maintenance through its activity to transfer lipids rather than in thylakoid formation through vesicles. This article is part of a Special Issue titled: Chloroplast Biogenesis.

Hollow screw-like drill in plasma using an intense Laguerre-Gaussian laser.

With the development of ultra-intense laser technology, MeV ions can be obtained from laser-foil interactions in the laboratory. These energetic ion beams can be applied in fast ignition for inertial confinement fusion, medical therapy, and proton imaging. However, these ions are mainly accelerated in the laser propagation direction. Ion acceleration in an azimuthal orientation was scarcely studied. In this research, a doughnut Laguerre-Gaussian (LG) laser is used for the first time to examine laser-plasma interaction in the relativistic intensity regime in three-dimensional particle-in-cell simulations. Studies have shown that a novel rotation of the plasma is produced from the hollow screw-like drill of an mode laser. The angular momentum of particles in the longitudinal direction produced by the LG laser is enhanced compared with that produced by the usual laser pulses, such as linearly and circularly polarized Gaussian pulses. Moreover, the particles (including electrons and ions) can be trapped and uniformly compressed in the dark central minimum of the doughnut LG pulse. The hollow-structured LG laser has potential applications in the generation of x-rays with orbital angular momentum, plasma accelerators, fast ignition for inertial confinement fusion, and pulsars in the astrophysical environment.

Light fan driven by a relativistic laser pulse.

When a relativistic laser pulse with a high photon density interacts with a specially tailored thin foil target, a strong torque is exerted on the resulting spiral-shaped foil plasma, or "light fan." Because of its structure, the latter can gain significant orbital angular momentum (OAM), and the opposite OAM is imparted to the reflected light, creating a twisted relativistic light pulse. Such an interaction scenario is demonstrated by particle-in-cell simulation as well as analytical modeling, and should be easily verifiable in the laboratory. As an important characteristic, the twisted relativistic light pulse has a strong torque and ultrahigh OAM density.

Positron acceleration in a hollow plasma channel up to TeV regime.

Nowadays, human's understanding of the fundamental physics is somehow limited by the energy that our high energy accelerators can afford. Up to 4 TeV protons are realized in the Large Hadron Collider (LHC). Leptons, such as electrons and positrons, however gained energies of about 100 GeV or less. Multi-TeV lepton accelerators are still lacking due to the relatively low acceleration gradient of conventional methods, which may induce unbearable cost. On the other hand, plasmas have shown extraordinary potential in accelerating electrons and ions, providing orders of magnitude higher acceleration fields of 10-100 GV/m. In such context, we propose a plasma-based high-energy lepton accelerator, in which a weakly focusing plasma structure is formed near the beam axis. The structure preserves the emittance of the accelerated beam and produces low radiation losses. Moreover, the structure allows for a considerable decrease of the witness energy spread at the driver depletion stage.

Arabidopsis thylakoid formation 1 is a critical regulator for dynamics of PSII-LHCII complexes in leaf senescence and excess light.

In higher plants, photosystem II (PSII) is a large pigment-protein supramolecular complex composed of the PSII core complex and the plant-specific peripheral light-harvesting complexes (LHCII). PSII-LHCII complexes are highly dynamic in their quantity and macro-organization to various environmental conditions. In this study, we reported a critical factor, the Arabidopsis Thylakoid Formation 1 (THF1) protein, which controls PSII-LHCII dynamics during dark-induced senescence and light acclimation. Loss-of-function mutations in THF1 lead to a stay-green phenotype in pathogen-infected and senescent leaves. Both LHCII and PSII core subunits are retained in dark-induced senescent leaves of thf1, indicative of the presence of PSII-LHCII complexes. Blue native (BN)-polyacrylamide gel electrophoresis (PAGE) and immunoblot analysis showed that, in dark- and high-light-treated thf1 leaves, a type of PSII-LHCII megacomplex is selectively retained while the stability of PSII-LHCII supercomplexes significantly decreased, suggesting a dual role of THF1 in dynamics of PSII-LHCII complexes. We showed further that THF1 interacts with Lhcb proteins in a pH-dependent manner and that the stay-green phenotype of thf1 relies on the presence of LHCII complexes. Taken together, the data suggest that THF1 is required for dynamics of PSII-LHCII supramolecular organization in higher plants.

Possible function of VIPP1 in thylakoids: protection but not formation?

VIPP1 protein in photosynthetic organisms is homologous to bacterial PspA, which protects plasma membrane integrity upon stresses. Despite the proposed role of VIPP1 in thylakoid biogenesis, its precise function remains unclear. Recently, our in-depth analysis of Arabidopsis vipp1 mutants revealed VIPP1's involvement in the maintenance of chloroplast envelopes. Chloroplasts in intact vipp1 leaves exhibited spherical balloon-like morphology, which resulted from osmotic stress across envelopes. In fact, observation of VIPP1 fused to green fluorescence protein in vivo revealed that most VIPP1 is localized as a lattice-like macro complex attached along with the envelope. Because of the proposed function in thylakoids, we examined whether vipp1 also exhibited altered morphologies in thylakoids. Results show that thylakoid morphologies were detected irregularly, but vipp1 chloroplasts retained normal-appearing grana stacks. We infer that VIPP1 might influence thylakoids as well as envelopes, but that it is not involved directly in thylakoid membrane formation.

Essential role of VIPP1 in chloroplast envelope maintenance in Arabidopsis.

VESICLE-INDUCING PROTEIN IN PLASTIDS1 (VIPP1), proposed to play a role in thylakoid biogenesis, is conserved in photosynthetic organisms and is closely related to Phage Shock Protein A (PspA), which is involved in plasma membrane integrity in Escherichia coli. This study showed that chloroplasts/plastids in Arabidopsis thaliana vipp1 knockdown and knockout mutants exhibit a unique morphology, forming balloon-like structures. This altered morphology, as well as lethality of vipp1, was complemented by expression of VIPP1 fused to green fluorescent protein (VIPP1-GFP). Several lines of evidence show that the balloon chloroplasts result from chloroplast swelling related to osmotic stress, implicating VIPP1 in the maintenance of plastid envelopes. In support of this, Arabidopsis VIPP1 rescued defective proton leakage in an E. coli pspA mutant. Microscopy observation of VIPP1-GFP in transgenic Arabidopsis revealed that VIPP1 forms large macrostructures that are integrated into various morphologies along the envelopes. Furthermore, live imaging revealed that VIPP1-GFP is highly mobile when chloroplasts are subjected to osmotic stress. VIPP1-GFP showed dynamic movement in the transparent area of spherical chloroplasts, as the fluorescent molecules formed filament-like structures likely derived from disassembly of the large VIPP1 complex. Collectively, our data demonstrate that VIPP1 is a multifunctional protein in chloroplasts that is critically important for envelope maintenance.

Defective etioplasts observed in variegation mutants may reveal the light-independent regulation of white/yellow sectors of Arabidopsis leaves.

Leaf variegation resulting from nuclear gene mutations has been used as a model system to elucidate the molecular mechanisms of chloroplast development. Since most variegation genes also function in photosynthesis, it remains unknown whether their roles in photosynthesis and chloroplast development are distinct. Here, using the variegation mutant thylakoid formation1 (thf1) we show that variegation formation is light independent. It was found that slow and uneven chloroplast development in thf1 can be attributed to defects in etioplast development in darkness. Ultrastructural analysis showed the coexistence of plastids with or without prolamellar bodies (PLB) in cells of thf1, but not of WT. Although THF1 mutation leads to significant decreases in the levels of Pchlide and Pchllide oxidoreductase (POR) expression, genetic and 5-aminolevulinic acid (ALA)-feeding analysis did not reveal Pchlide or POR to be critical factors for etioplast formation in thf1. Northern blot analysis showed that plastid gene expression is dramatically reduced in thf1 compared with that in WT, particularly in the dark. Our results also indicate that chlorophyll biosynthesis and expression of plastidic genes are coordinately suppressed in thf1. Based on these results, we propose a model to explain leaf variegation formation from the plastid development perspective.