Phase-matching of high-order harmonic generation in the extreme ultraviolet region with orbital angular momentum.

High-order harmonics can generate vortex beams with orbital angular momentum (OAM) in the extreme ultraviolet region. However, experimental research on their phase-matching (PM) characteristics is limited. In this study, vortex high-order harmonic generation (HHG) in the extreme ultraviolet region was generated with Ar gas. Phase-matched HHG with OAM was obtained by optimizing the focus position, laser energy, and gas pressure. The dependence of the PM characteristics on these parameters was analyzed. In addition, we conducted an experimental analysis of the dimensional properties of vortex harmonics under PM conditions. This study is a contribution towards the intense vortex high-order harmonic light sources and their applications.

Determination of Paraquat in Arabidopsis Tissues and Protoplasts by UHPLC-MS/MS.

Paraquat is a cost-effective herbicide, widely used in many countries, that can induce severe oxidative stress in photosynthetic tissues. Studying plant herbicide resistance or antioxidant stress mechanisms requires determining the cellular paraquat level when plants are treated by paraquat. The traditional isotopic labeling method has the potential risk to cause problems to both human health and the environment. For radioisotope manipulation, special operation spaces and strict environmental inspection are also required. In addition, the radiolabeled paraquat is increasingly hard to buy due to the extended production cycle. Here, we describe a nonradioactive method to determine the paraquat level in a small number of Arabidopsis tissues or protoplasts, using a high resolution ultra-high-performance liquid chromatography (UHPLC)-mass spectrometry (MS)/MS method. This method is highly selective and sensitive, and more environmentally compatible and technically feasible than the isotope detection method.

Characteristics of Gut Microbiota in Female Patients with Diabetic Microvascular Complications.

Objective: To explore the characteristics and analyze the gut microbiota in female patients with diabetic microvascular complications (DMC). Methods: Thirty-seven female patients with type 2 diabetes mellitus (T2DM) were included in the study. These patients were divided into DM group with microvascular complications (T2DM-MC, n = 17) and no microvascular complications group (T2DM-0, n = 20). Patients in the microvascular group presented with the involvement of at least one of the following: kidney, retinal, or peripheral nerves. Using real-time fluorescence quantitative polymerase chain reaction, fecal samples from the two groups were tested for Bacteroides, Prevotella, Bifidobacterium spp, Lactobacillus, Faecalibacterium prausnitzii, Enterococcus spp, Eubacterium rectale, Veillonellaceae, Clostridium leptum, and Roseburia inulinivorans. Levels of fasting and 2 h postprandial blood glucose, glycosylated hemoglobin (HbA1c), lipids, and creatinine were determined to explore the correlation between gut microbiota and blood sugar. Mann-Whitney U test was used to analyze the differences between the two groups. Spearman correlation analysis was used to determine the correlation between gut microbiota and blood glucose. Multifactor logistic regression was used to analyze the risk factors for DMC. Results: The HbA1c levels in the T2DM-MC group were higher than those in the T2DM-0 group. The abundances of Bacteroides and Enterococcus spp in the T2DM-MC group were higher than that in the T2DM-0 group. The abundances of Bacteroides and Enterococcus spp in the T2DM-MC group were lower than that in the T2DM-0 group. Spearman's correlation analysis showed that Bacteroides, Prevotella, Lactobacillus, C. leptum, and R. inulinivorans were related to the levels of HbA1c or blood glucose (p < 0.05). Logistic regression analysis showed that after adjusting for confounding factors such as age, body mass index, family history, HbA1c, hypertension, dyslipidemia, and creatinine, Bacteroides remained an independent risk factor in female patients with DMC. Conclusion: Gut microbiota is related to blood glucose levels. Female patients with DMC experience gut microbiota disorders. The abundances of Bacteroidesare related to DMC, and the abundances of intestinal flora may affect the blood sugar levels of the body.

Application of machine learning tools: Potential and useful approach for the prediction of type 2 diabetes mellitus based on the gut microbiome profile.

The gut microbiota plays an important role in the regulation of the immune system and the metabolism of the host. The aim of the present study was to characterize the gut microbiota of patients with type 2 diabetes mellitus (T2DM). A total of 118 participants with newly diagnosed T2DM and 89 control subjects were recruited in the present study; six clinical parameters were collected and the quantity of 10 different types of bacteria was assessed in the fecal samples using quantitative PCR. Taking into consideration the six clinical variables and the quantity of the 10 different bacteria, 3 predictive models were established in the training set and test set, and evaluated using a confusion matrix, area under the receiver operating characteristic curve (AUC) values, sensitivity (recall), specificity, accuracy, positive predictive value and negative predictive value (npv). The abundance of Bacteroides, Eubacterium rectale and Roseburia inulinivorans was significantly lower in the T2DM group compared with the control group. However, the abundance of Enterococcus was significantly higher in the T2DM group compared with the control group. In addition, Faecalibacterium prausnitzii, Enterococcus and Roseburia inulinivorans were significantly associated with sex status while Bacteroides, Bifidobacterium, Enterococcus and Roseburia inulinivorans were significantly associated with older age. In the training set, among the three models, support vector machine (SVM) and XGboost models obtained AUC values of 0.72 and 0.70, respectively. In the test set, only SVM obtained an AUC value of 0.77, and the precision and specificity were both above 0.77, whereas the accuracy, recall and npv were above 0.60. Furthermore, Bifidobacterium, age and Roseburia inulinivorans played pivotal roles in the model. In conclusion, the SVM model exhibited the highest overall predictive power, thus the combined use of machine learning tools with gut microbiome profiling may be a promising approach for improving early prediction of T2DM in the near feature.

Resonance absorption of the inner shell during high-order harmonic generation.

In this work, we report the observation of resonance absorption of the inner shell during the high-order harmonic generation (HHG) from xenon (Xe) and krypton (Kr). The absorption peaks show a periodic variation with the change of carrier-envelope phase of driving laser pulses and the delay of two-color laser field, which indicates the absorption peaks come from the collective multielectron effects during the HHG. With the increase of gas pressure, the depth of absorption peak will continue to increase, while due to the phase matching effect, there will be an optimal pressure for the intensity of harmonic signal. Our experimental results pave the way to uncover the physical mechanism of the collective multielectron effects involving inner-shell electrons in the HHG process.

Changing Gly311 to an acidic amino acid in the MATE family protein DTX6 enhances Arabidopsis resistance to the dihydropyridine herbicides.

In modern agriculture, frequent application of herbicides may induce the evolution of resistance in plants, but the mechanisms underlying herbicide resistance remain largely unexplored. Here, we report the characterization of rtp1 (resistant to paraquat 1), an Arabidopsis mutant showing strong resistance to the widely used herbicides paraquat and diquat. The rtp1 mutant is semi-dominant and carries a point mutation in the gene encoding the multidrug and toxic compound extrusion family protein DTX6, leading to the change of glycine to glutamic acid at residue 311 (G311E). The wild-type DTX6 with glycine 311 conferred weak paraquat and diquat resistance when overexpressed, while mutation of glycine 311 to a negatively charged amino acid (G311E or G311D) markedly increased the paraquat and diquat resistance of plants, whereas mutation to a positively charged amino acid (G311R or G311K) compromised the resistance, suggesting that the charge property of residue 311 of DTX6 is critical for the paraquat and diquat resistance of Arabidopsis plants. DTX6 is localized in the endomembrane trafficking system and may undergo the endosomal sorting to localize to the vacuole and plasma membrane. Treatment with the V-ATPase inhibitor ConA reduced the paraquat resistance of the rtp1 mutant. Paraquat release and uptake assays demonstrated that DTX6 is involved in both exocytosis and vacuolar sequestration of paraquat. DTX6 and DTX5 show functional redundancy as the dtx5 dtx6 double mutant but not the dtx6 single mutant plants were more sensitive to paraquat and diquat than the wild-type plants. Collectively, our work reveals a potential mechanism for the evolution of herbicide resistance in weeds and provides a promising gene for the manipulation of plant herbicide resistance.

New perspectives on the plant PARP family: Arabidopsis PARP3 is inactive, and PARP1 exhibits predominant poly (ADP-ribose) polymerase activity in response to DNA damage.

BACKGROUND: Poly (ADP-ribosyl) ation (PARylation) is an important posttranslational modification that regulates DNA repair, gene transcription, stress responses and developmental processes in multicellular organisms. Poly (ADP-ribose) polymerase (PARP) catalyzes PARylation by consecutively adding ADP-ribose moieties from NAD+ to the amino acid receptor residues on target proteins. Arabidopsis has three canonical PARP members, and two of these members, AtPARP1 and AtPARP2, have been demonstrated to be bona fide poly (ADP-ribose) polymerases and to regulate DNA repair and stress response processes. However, it remains unknown whether AtPARP3, a member that is highly expressed in seeds, has similar biochemical activity to that of AtPARP1 and AtPARP2. Additionally, although both the phylogenetic relationships and structural similarities indicate that AtPARP1 and AtPARP2 correspond to animal PARP1 and PARP2, respectively, two previous studies have indicated that AtPARP2, and not AtPARP1, accounts for most of the PARP activity in Arabidopsis, which is contrary to the knowledge that PARP1 is the predominant PARP in animals. RESULTS: In this study, we obtained both in vitro and in vivo evidence demonstrating that AtPARP3 does not act as a typical PARP in Arabidopsis. Domain swapping and point mutation assays indicated that AtPARP3 has lost NAD+-binding capability and is inactive. In addition, our results showed that AtPARP1 was responsible for most of the PARP enzymatic activity in response to the DNA damage-inducing agents zeocin and methyl methanesulfonate (MMS) and was more rapidly activated than AtPARP2, which supports that AtPARP1 remains the predominant PARP member in Arabidopsis. AtPARP1 might first become activated by binding to damaged sites, and AtPARP2 is then poly (ADP-ribosyl) ated by AtPARP1 in vivo. CONCLUSIONS: Collectively, our biochemical and genetic analysis results strongly support the notion that AtPARP3 has lost poly (ADP-ribose) polymerase activity in plants and performs different functions from those of AtPARP1 and AtPARP2. AtPARP1, instead of AtPARP2, plays the predominant role in PAR synthesis in both seeds and seedlings. These data bring new insights into our understanding of the physiological functions of plant PARP family members.

OsERF101, an ERF family transcription factor, regulates drought stress response in reproductive tissues.

KEY MESSAGE: An ERF transcription factor OsERF101 is predominantly expressed in rice reproductive tissues and plays an important role in improving rice seed setting rate under drought stress. Drought reduces grain yield due to the cumulative damage effects to plant vegetative and reproductive developmental processes. However, the genes involved in these processes are still not completely understood. In this study, we identified a gene named OsERF101 as an important positive regulator in the adaptive responses to dehydration stress during the reproductive and vegetative stages. This gene encodes a member of APETALA2/Ethylene-Responsive Element Binding Protein (AP2/EREBP) family. OsERF101 was predominantly expressed in flowers, particularly in the tapetum and microspores under normal growth conditions. It was induced by drought, PEG6000 and abscisic acid (ABA) in leaves. During the vegetative stage, OsERF101-overexpression plants were more resistant to osmotic stress caused by PEG6000 compared to the control plants. They also had higher survival and seed setting rates than wild type when subjected to reproductive-stage drought stress. Further physiological analysis revealed that the pollen fertility was improved in the overexpression lines, while the knockout mutant and RNAi lines showed reduced pollen fertility and compromised drought tolerance during the reproductive stage. The increased proline content and peroxidase activity in OsERF101-overexpression plants might contribute to the improved drought-tolerance of plants. In addition, OsERF101-overexpression plants displayed ABA susceptible phenotype, in which the expression levels of ABA-responsive genes RD22, LEA3, and PODs were up-regulated. Taken together, our results indicate that OsERF101 is a gene that regulates dehydration responses during the vegetative and reproductive stages.

The AWPM-19 Family Protein OsPM1 Mediates Abscisic Acid Influx and Drought Response in Rice.

Abscisic acid (ABA) regulates plant stress responses and development. However, how the ABA signal is transmitted in response to stresses remains largely unclear, especially in monocots. In this study, we found that rice (Oryza sativa) OsPM1 (PLASMA MEMBRANE PROTEIN1), encoded by a gene of AWPM-19 like family, mediates ABA influx through the plasma membrane. OsPM1 is predominantly expressed in vascular tissues, guard cells, and mature embryos. Phenotypic analysis of overexpression, RNA interference (RNAi), and knockout (KO) lines showed that OsPM1 is involved in drought responses and seed germination regulation. 3H-(±)ABA transport activity and fluorescence resonance energy transfer assays both demonstrated that OsPM1 facilitates ABA uptake into cells. The physiological isomer of ABA, (+)-ABA, is the preferred substrate of OsPM1. Higher ABA accumulation and faster stomatal closure in response to ABA treatment were observed in the overexpression lines compared with the wild-type control. Many ABA-responsive genes were upregulated more in the OsPM1-overexpression lines but less in the RNAi lines compared with wild-type plants. Further investigation revealed that OsPM1 expression is regulated by the AREB/ABF family transcription factor OsbZIP46. Our results thus revealed that OsPM1 is an ABA influx carrier that plays an important role in drought responses.

Overexpressing Exogenous 5-Enolpyruvylshikimate-3-Phosphate Synthase (EPSPS) Genes Increases Fecundity and Auxin Content of Transgenic Arabidopsis Plants.

Transgenic glyphosate-tolerant plants overproducing EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) may exhibit enhanced fitness in glyphosate-free environments. If so, introgression of transgenes overexpressing EPSPS into wild relative species may lead to increased competitiveness of crop-wild hybrids, resulting in unpredicted environmental impact. Assessing fitness effects of transgenes overexpressing EPSPS in a model plant species can help address this question, while elucidating how overproducing EPSPS affects the fitness-related traits of plants. We produced segregating T2 and T3Arabidopsis thaliana lineages with or without a transgene overexpressing EPSPS isolated from rice or Agrobacterium (CP4). For each of the three transgenes, we compared glyphosate tolerance, some fitness-related traits, and auxin (indole-3-acetic acid) content in transgene-present, transgene-absent, empty vector (EV), and parental lineages in a common-garden experiment. We detected substantially increased glyphosate tolerance in T2 plants of transgene-present lineages that overproduced EPSPS. We also documented significant increases in fecundity, which was associated with increased auxin content in T3 transgene-present lineages containing rice EPSPS genes, compared with their segregating transgene-absent lineages, EV, and parental controls. Our results from Arabidopsis with nine transgenic events provide a strong support to the hypothesis that transgenic plants overproducing EPSPS can benefit from a fecundity advantage in glyphosate-free environments. Stimulated biosynthesis of auxin, an important plant growth hormone, by overproducing EPSPS may play a role in enhanced fecundity of the transgenic Arabidopsis plants. The obtained knowledge is useful for assessing environmental impact caused by introgression of transgenes overproducing EPSPS from any GE crop into populations of its wild relatives.

Poly(ADP-ribose) polymerases regulate cell division and development in Arabidopsis roots.

Root organogenesis involves cell division, differentiation and expansion. The molecular mechanisms regulating root development are not fully understood. In this study, we identified poly(adenosine diphosphate (ADP)-ribose) polymerases (PARPs) as new players in root development. PARP catalyzes poly(ADP-ribosyl)ation of proteins by repeatedly adding ADP-ribose units onto proteins using nicotinamide adenine dinucleotide (NAD+ ) as the donor. We found that inhibition of PARP activities by 3-aminobenzomide (3-AB) increased the growth rates of both primary and lateral roots, leading to a more developed root system. The double mutant of Arabidopsis PARPs, parp1parp2, showed more rapid primary and lateral root growth. Cyclin genes regulating G1-to-S and G2-to-M transition were up-regulated upon treatment by 3-AB. The proportion of 2C cells increased while cells with higher DNA ploidy declined in the roots of treated plants, resulting in an enlarged root meristematic zone. The expression level of PARP2 was very low in the meristematic zone but high in the maturation zone, consistent with a role of PARP in inhibiting mitosis and promoting cell differentiation. Our results suggest that PARPs play an important role in root development by negatively regulating root cell division.

Frequency modulation of high-order harmonic generation in an orthogonally polarized two-color laser field.

We have experimentally investigated the frequency modulation of high-order harmonics in an orthogonally polarized two-color laser field consisting of a mid-infrared 1800nm fundamental pulse and its second harmonic pulse. It is demonstrated that the high harmonic spectra can be fine-tuned as we slightly change the relative delay of the two-color laser pulses. By analyzing the relative frequency shift of each harmonic at different two-color delays, the nonadiabatic spectral shift induced by the rapid variation of the intensity-dependent intrinsic dipole phase can be distinguished from the blueshift induced by the change of the refractive index during self-phase modulation (SPM). Our comprehensive analysis shows that the frequency modulation pattern is a reflection of the average emission time of high-order harmonic generation (HHG), thus offering a simple method to fine-tune the spectra of the harmonics on a sub-cycle time scale.

MID1 plays an important role in response to drought stress during reproductive development.

Drought during rice reproductive development results in yield loss. It is important to understand the functions of drought-responsive genes in reproductive tissues for improving rice yield under water-deficit conditions. We show here that MID1 (MYB Important for Drought Response1), encoding a putative R-R-type MYB-like transcription factor, can improve rice yield under drought. MID1 was primarily expressed in root and leaf vascular tissues, with low level in the tapetum, and was induced by drought and other abiotic stresses. Compared with wild type, MID1-overexpressing plants were more tolerant to drought at both vegetative and reproductive stages and produced more grains under water stress. MID1-overexpressing plants exhibited less severe anther defects such as deformed anther locules, abnormal tapetum, degenerated microspores and expanded middle layer, with improved pollen fertility and higher seed setting rate. MID1 was localized to the nucleus and could activate gene expression in yeast, and its homologs were identified in many other plants with high levels sequence similarity. In addition, candidate MID1-regulated genes were analyzed using RNA-seq and qRT-PCR, including genes crucial for stress responses and anther development, with altered expressions in the florets of MID1-overexpressing plants and RNAi lines. Furthermore, MID1 could bind to the promoters of two drought-related genes (Hsp17.0 and CYP707A5) and one anther developmental gene (KAR) according to ChIP-qPCR data. Our findings suggest that MID1 is a transcriptional regulator that promotes rice male development under drought by modulating the expressions of drought-related and anther developmental genes and provide valuable information for crop improvement.

Effect of nuclear motion on spectral broadening of high-order harmonic generation.

High-order harmonic generation (HHG) in molecular targets is experimentally investigated in order to reveal the role of the nuclear motion played in the harmonic generation process. An obvious broadening in the harmonic spectrum from the H2 molecule is observed in comparison with the harmonic spectrum generated from other molecules with relatively heavy nuclei. We also find that the harmonic yield from the H2 molecule is much weaker than the yield from those gas targets with the similar ionization potentials, such as Ar atom and N2 molecule. The yield suppression and the spectrum broadening of HHG can be attributed to the vibrational motion of nuclear induced by the driving laser pulse. Moreover, the one-dimensional (1D) time-dependent Schrödinger equation (TDSE) with the non-Born-Oppenheimer (NBO) treatment is numerically solved to provide a theoretical support to our explanation.

Ultrafast Excitation of an Inner-Shell Electron by Laser-Induced Electron Recollision.

Extreme ultraviolet attosecond pulses, generated by a process known as laser-induced electron recollision, are a key ingredient for attosecond metrology, providing a tool to precisely initiate and probe subfemtosecond dynamics in atoms, molecules, and solids. However, extending attosecond metrology to scrutinize the dynamics of the inner-shell electrons is a challenge, that is because of the lower efficiency in generating the required soft x-ray (ℏω>300 eV) attosecond bursts. A way around this problem is to use the recolliding electron to directly initiate the desired inner-shell process, instead of using the currently low flux x-ray attosecond sources. Such an excitation process occurs in a subfemtosecond time scale, and may provide the necessary "pump" step in a pump-probe experiment. Here we used a few cycle infrared (λ_{0}≈1800 nm) source and observed direct evidence for inner-shell excitations through the laser-induced electron recollision process. It is the first step toward time-resolved core-hole studies in the keV energy range with subfemtosecond time resolution.

Arabidopsis PARG1 is the key factor promoting cell survival among the enzymes regulating post-translational poly(ADP-ribosyl)ation.

Poly(ADP-ribosyl)ation is a reversible post-translational modification of proteins, characterized by the addition of poly(ADP-ribose) (PAR) to proteins by poly(ADP-ribose) polymerase (PARP), and removal of PAR by poly(ADP-ribose) glycohydrolase (PARG). Three PARPs and two PARGs have been found in Arabidopsis, but their respective roles are not fully understood. In this study, the functions of each PARP and PARG in DNA repair were analyzed based on their mutant phenotypes under genotoxic stresses. Double or triple mutant analysis revealed that PARP1 and PARP2, but not PARP3, play a similar but not critical role in DNA repair in Arabidopsis seedlings. PARG1 and PARG2 play an essential and a minor role, respectively under the same conditions. Mutation of PARG1 results in increased DNA damage level and enhanced cell death in plants after bleomycin treatment. PARG1 expression is induced primarily in root and shoot meristems by bleomycin and induction of PARG1 is dependent on ATM and ATR kinases. PARG1 also antagonistically modulates the DNA repair process by preventing the over-induction of DNA repair genes. Our study determined the contribution of each PARP and PARG member in DNA repair and indicated that PARG1 plays a critical role in this process.

Enhanced high-order harmonic generation from spatially prepared filamentation in argon.

We experimentally demonstrate enhanced high-order harmonic generation (HHG) from spatially prepared filamentation in Argon. Upon shifting the focus position of an elliptically polarized laser pulse over the filament induced by a linearly polarized laser pulse, an obvious enhancement of harmonic yield by nearly one order of magnitude is observed. The result could be interpreted in terms of the double contributions from both the excited states of target atom and the phase-matching effect of harmonic beam. In contrast to the enhancement phenomena, an obvious suppression of harmonic yield is also presented, which could be attributed to both the ground-state depletion and the plasma effect.

CEP-controlled supercontinuum generation during filamentation with mid-infrared laser pulse.

With carrier-envelope phase (CEP) stabilized mid-infrared (MIR) laser pulse, the CEP-controlled supercontinuum generation can be distinctly observed in a very small distance range when the focus of the laser pulse closes to the exit surface of the fused silica (FS). This CEP effect will be gradually weakened and finally disappears if the laser focus moves out of this range. With numerical simulation, we find that although the CEP effect starts from the tunneling ionization of the electron, it can be observed only when the supercontinuum mainly comes from the self-phase modulation (SPM) and self-steepening of the laser pulse and too much electrons will make it ambiguous.

Carrier-envelope phase effects on the spatial coherence of high-order harmonics.

In this work, we report the Carrier-Envelope Phase Effects on the Spatial Coherence of High-order Harmonics driven by phase-stabilized few-cycle mid-infrared laser pulses. The degree of coherence varies with carrier-envelope phase periodically with a period of π. At the same time, as the harmonic orders increase, the extreme points on the curve of coherence degree vs. carrier-envelope phase shift toward the direction of carrier-envelope phase increasing. Through theoretical analysis, we find that the ionization induced frequency chirp plays an important role in the Carrier-Envelope Phase Effects on the Spatial Coherence. This effect suggests a possible method to optimize the spatial coherence of harmonics by tuning the carrier-envelope phase of the driving field.

Spatially and spectrally resolved quantum-path tracing in high-order harmonic generation.

We experimentally demonstrate the macroscopic evolution of quantum-path distributions in harmonic emission with spatial and spectral resolution from an argon gas jet, and obviously observe that the spatial profiles of harmonics are gradually split into two components (the red and blue shifts) when the driving laser intensity is increased. Moreover, the red and blue shifts in quantum-path distributions are experimentally traced and clarified in the spatial and spectral domain by choosing the focal position. These results give a more comprehensive understanding and therefore a better control of harmonic emission.