Molecular insights into the defense of Dioscorea opposita cv. 'Tiegun' callus against pathogenic and endophytic fungal infection through transcriptome analysis.

Dioscorea opposita cv. 'Tiegun' is an economically important crop with high nutritional and medicinal value. Plants can activate complex and diverse defense mechanisms after infection by pathogenic fungi. Moreover, endophytic fungi can also trigger the plant immune system to resist pathogen invasion. However, the study of the effects of endophytic fungi on plant infection lags far behind that of pathogenic fungi, and the underlying mechanism is not fully understood. Here, the black spot pathogen Alternaria alternata and the endophytic fungus Penicillium halotolerans of 'Tiegun' were identified and used to infect calli. The results showed that A. alternata could cause more severe membrane lipid peroxidation, while P. halotolerans could rapidly increase the activity of the plant antioxidant enzymes superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT); thus, the degree of damage caused by P. halotolerans to the callus was weaker than that caused by A. alternata. RNA-seq analysis revealed that various plant defense pathways, such as phenylpropanoid biosynthesis, flavonoid biosynthesis, plant hormone signal transduction, and the MAPK signaling pathway, play important roles in triggering the plant immune response during fungal infection. Furthermore, the tryptophan metabolism, betalain biosynthesis, fatty acid degradation, flavonoid biosynthesis, tyrosine metabolism and isoquinoline alkaloid biosynthesis pathways may accelerate the infection of pathogenic fungi, and the ribosome biogenesis pathway in eukaryotes may retard the damage caused by endophytic fungi. This study lays a foundation for exploring the infection mechanism of yam pathogens and endophytic fungi and provides insight for effective fungal disease control in agriculture.

IPA1 improves drought tolerance by activating SNAC1 in rice.

Drought is a major abiotic stress to rice (Oryza sativa) during growth. Ideal Plant Architecture (IPA1), the first cloned gene controlling the ideal plant type in rice, has been reported to function in both ideal rice plant architecture and biotic resistance. Here, we report that the IPA1/OsSPL14, encoding a transcriptional factor, positively regulates drought tolerance in rice. The IPA1 is constitutively expressed and regulated by H2O2, abscisic acid, NaCl and polyethylene glycol 6000 treatments in rice. Furthermore, the IPA1-knockout plants showed much greater accumulation of H2O2 as measured by 3,3'-diaminobenzidine staining in leaves compared with WT plants. Yeast one-hybrid, dual-luciferase and electrophoretic mobility shift assays indicated that the IPA1 directly activates the promoter of SNAC1. Expression of SNAC1 is significantly down-regulated in IPA1 knockout plants. Further investigation indicated that the IPA1 plays a positive role in drought-stress tolerance by inducing reactive oxygen species scavenging in rice. Together, these findings indicated that the IPA1 played important roles in drought tolerance by regulating SNAC1, thus activating the antioxidant system in rice.

The Role of Surface Termination in Halide Perovskites for Efficient Photocatalytic Synthesis.

Halide perovskites have received attention in the field of photocatalysis owing to their excellent optoelectronic properties. However, the semiconductor properties of halide perovskite surfaces and the influence on photocatalytic performance have not been systematically clarified. Now, the conversion of triose (such as 1,3-dihydroxyacetone (DHA)) is employed as a model reaction to explore the surface termination of MAPbI3 . By rational design of the surface termination for MAPbI3 , the production rate of butyl lactate is substantially improved to 7719 µg g-1 cat. h-1 under visible-light illumination. The MAI-terminated MAPbI3 surface governs the photocatalytic performance. Specially, MAI-terminated surface is susceptible to iodide oxidation, which thus promotes the exposure of PbII as active sites for this photocatalysis process. Moreover, MAI-termination induces a p-doping effect near the surface for MAPbI3 , which facilitates carrier transport and thus photosynthesis.

Numerical study of the future PM2.5 concentration under climate change and best-health-effect (BHE) scenario.

The Beijing-Tianjin-Hebei (BTH) is one of the key areas with PM2.5 air pollution in China. Driven by the PM2.5 target accessibility of the Interim Target-1 (IT-1) by World Health Organization (WHO) and China's carbon neutrality, this study explored and quantified the contribution of climate change and anthropogenic emission to future PM2.5 in the region. The experiments considered future climate change scenarios RCP8.5, RCP4.5, and RCP2.6 with the baseline (Base) and reduced emission (EIT1) inventories in 2030, and RCP4.5 climate scenario with 3 emission inventories in 2050, the additional strong control emission scenario called Best-Health-Effect (BHE). Under various climate scenarios, the future air quality research modelling system projected annual PM2.5 concentrations nearing 35 µg/m3 in 2030. However, considering only the effect of emission reduction, the annual PM2.5 concentrations under EIT1 emission scenario is about 35% less than under Base scenario in different key years. The future PM2.5 concentrations are highly related to anthropogenic emission from human activities, while climate change by 2030 or 2050 has little impact on future air quality over the BTH region. The BHE emission reduction is significantly required for China to meet the new PM2.5 guideline value of WHO in the future.

OsBBP1, a newly identified protein containing DUF630 and DUF632 domains confers drought tolerance in rice.

Domain of unknown function (DUF) protein families, which are uncharacterized and numerous within the Pfam database. Recently, studies have demonstrated that DUFs played crucial roles in plant development, but whether, or how, they function in drought resistance remain unclear. In this study, we identified the Os03g0321500 gene, encoding OsbZIP72 binding protein 1 (OsBBP1), as a target of OsbZIP72 using chromatin immunoprecipitation sequencing in rice. OsBBP1 is a novel member of DUFs, which localize both in the nuclei and cytoplasm of rice protoplasts. Furthermore, yeast one-hybrid and electrophoretic mobility shift assays confirmed the specific binding between OsbZIP72 and OsBBP1. Additionally, a luciferase reporter analysis illustrated that OsbZIP72 activated the expression of OsBBP1. Drought tolerance experiments demonstrate that the OsBBP1 CRISPER-CAS9 transgenic mutants were sensitive to drought stress, but the transgenic OsBBP1 over-expressing rice plants showed enhanced drought resistance. Moreover, drought tolerance experiments in a paddy field suggested that OsBBP1 contributed to less yield or yield-related losses under drought conditions. Mechanistically, OsBBP1 might confer drought resistance by inducing more efficient reactive oxygen species (ROS) scavenging. Several ROS scavenging-related genes showed increased expression levels in OsBBP1 overexpression lines and decreased expression levels in OsBBP1 CRISPER-CAS9 mutants under drought conditions. Thus, OsBBP1, acting downstream of OsbZIP72, contributes to drought resistance and causes less yield or yield-related losses under drought conditions.

Viability and transcriptional responses of multidrug resistant E. coli to chromium stress.

The viability of multidrug resistant (MDR) bacteria in environment is critical for the spread of antimicrobial resistance. In this study, two Escherichia coli strains, MDR LM13 and susceptible ATCC25922, were used to elucidate differences in their viability and transcriptional responses to hexavalent chromium (Cr(VI)) stress. The results show that the viability of LM13 was notably higher than that of ATCC25922 under 2-20 mg/L Cr(VI) exposure with bacteriostatic rates of 3.1%-57%, respectively, for LM13 and 0.9%-93.1%, respectively, for ATCC25922. The levels of reactive oxygen species and superoxide dismutase in ATCC25922 were much higher than those in LM13 under Cr(VI) exposure. Additionally, 514 and 765 differentially expressed genes were identified from the transcriptomes of the two strains (log2|FC| > 1, p < 0.05). Among them, 134 up-regulated genes were enriched in LM13 in response to external pressure, but only 48 genes were annotated in ATCC25922. Furthermore, the expression levels of antibiotic resistance genes, insertion sequences, DNA and RNA methyltransferases, and toxin-antitoxin systems were generally higher in LM13 than in ATCC25922. This work shows that MDR LM13 has a stronger viability under Cr(VI) stress, and therefore may promote the dissemination of MDR bacteria in environment.

Overexpression of a GIPC glycosyltransferase gene, OsGMT1, suppresses plant immunity and delays heading time in rice.

Glycosylinositol phosphorylceramides (GIPCs) are the major sphingolipids in the plant plasma membrane. In Arabidopsis, mutations of genes involved in the synthesis of GIPCs affect many physiological aspects of plants, including growth, pollen fertility, defense, and stress signaling. Loss of function of the GIPC MANNOSYL-TRANSFERASE1 (AtGMT1) results in GIPC misglycosylation and induces plant immune responses accompanied by a severely dwarfed phenotype, thus indicating that GIPCs play important roles in plant immunity. Here, we investigated the enzymatic activity and phenotypes of transgenic lines of OsGMT1, the ortholog of AtGMT1. Sphingolipidomic analysis indicated that OsGMT1 retained the enzymatic activity of GIPC hexose (Hex) glycosylation, but the knockout lines did not accumulate H2O2. In contrast, the OsGMT1 overexpression lines showed significant down-regulation of several defense-associated or cell wall synthesis-associated genes, and enhanced sensitivity to rice blast. Furthermore, we first demonstrated the sensitivity of rice cells to MoNLP1 protein through calcein AM release assays using rice protoplasts, thus legitimizing the presence of MoNLPs in rice blast fungus. In addition, yeast two-hybrid screens using OsGMT1 as bait revealed that OsGMT1 may regulate heading time through the OsHAP5C signaling pathway. Together, our findings suggested clear physiological functional differentiation of GMT1 orthologs between rice and Arabidopsis.

SH3P2, an SH3 domain-containing protein that interacts with both Pib and AvrPib, suppresses effector-triggered, Pib-mediated immunity in rice.

Plants usually keep resistance (R) proteins in a static state under normal conditions to avoid autoimmunity and save energy for growth, but R proteins can be rapidly activated upon perceiving pathogen invasion. Pib, the first cloned blast disease R gene in rice, encoding a nucleotide-binding leucine-rich repeat (NLR) protein, mediates resistance to the blast fungal (Magnaporthe oryzae) isolates carrying the avirulence gene AvrPib. However, the molecular mechanisms about how Pib recognizes AvrPib and how it is inactivated and activated remain largely unclear. In this study, through map-based cloning and CRISPR-Cas9 gene editing, we proved that Pib contributes to the blast disease resistance of rice cultivar Yunyin (YY). Furthermore, an SH3 domain-containing protein, SH3P2, was found to associate with Pib mainly at clathrin-coated vesicles in rice cells, via direct binding with the coiled-coil (CC) domain of Pib. Interestingly, overexpression of SH3P2 in YY compromised Pib-mediated resistance to M. oryzae isolates carrying AvrPib and Pib-AvrPib recognition-induced cell death. SH3P2 competitively inhibits the self-association of the Pib CC domain in vitro, suggesting that binding of SH3P2 with Pib undermines its homodimerization. Moreover, SH3P2 can also interact with AvrPib and displays higher affinity to AvrPib than to Pib, which leads to dissociation of SH3P2 from Pib in the presence of AvrPib. Taken together, our results suggest that SH3P2 functions as a "protector" to keep Pib in a static state by direct interaction during normal growth but could be triggered off by the invasion of AvrPib-carrying M. oryzae isolates. Our study reveals a new mechanism about how an NLR protein is inactivated under normal conditions but is activated upon pathogen infection.

Recent Progress in Designing Halide-Perovskite-Based System for the Photocatalytic Applications.

The halide perovskite material has attracted vast attention as a versatile semiconductor in the past decade. With the unique advantages in physical and chemical properties, they have also shown great potential in photocatalytic applications. This review aims at the specific design principles triggered by the unique properties when employing halide-perovskite-based photocatalytic systems from the following perspectives: (I) Design of photoelectrocatalytic device structures including the n-i-p/p-i-n structure, photoelectrode device encapsulation, and electrolyte engineering. (II) The design of heterogeneous photocatalytic systems toward the hydrogen evolution reaction (HER) and CO2 reduction reaction, including the light management, surface/interface engineering, stability improvement, product selectivity engineering, and reaction system engineering. (III) The photocatalysts for the environmental application and organic synthesis. Based on the analyses, the review also suggests the prospective research for the future development of halide-perovskite-based photocatalytic systems.

Numerical study of air pollution over a typical basin topography: Source appointment of fine particulate matter during one severe haze in the megacity Xi'an.

Many cities are located in lands with typical basin topographies, which are not conducive to the spread of air pollutants. In the winter of 2016/2017, a severe haze happened in Xi'an, the main city in the Guanzhong Basin in central China. When the peak daily concentration of fine particulate matter (PM2.5) reaches 499 µg/m3, the source of the atmospheric pollution needs to be found urgently in order to take countermeasures. The comprehensive air quality model with extensions, coupled with the tracer tagging particulate source apportionment technology (PSAT) module, and an improved emission inventory, higher grid resolution, and bigger inner domain area, have been applied to quantify the contributions of local and regional emissions to the PM2.5 pollutions. The model performed well in time period considered in this study. The correlation of the simulated daily PM2.5 concentration data reaches 0.82, and the fraction of predictions within a factor of two of observations approaches 84%. With the PSAT module, the PM2.5 contributions from local and regional sources to the urban centre and rural areas during the severe winter haze event are analysed in detail. The PM2.5 concentrations in the urban centre in Xi'an is mainly originating from local emissions (60%), and Xianyang City is the largest contributor among the surrounding source regions (11.6%), while the transportation sector outside the Shaanxi Province (5.1%) also contributes significantly. Comparatively, the rural areas have lower local contributions and higher transport contributions. In particular, in the northern rural area Yanliang, the contribution from surrounding source regions approaches 82%. The results of this study suggest that to improve the air quality in a typical basin city, a regional-scale coordinated emissions control should be used, focusing on the emissions from both local and surrounding areas.

Solving global shallow water equations on heterogeneous supercomputers.

The scientific demand for more accurate modeling of the climate system calls for more computing power to support higher resolutions, inclusion of more component models, more complicated physics schemes, and larger ensembles. As the recent improvements in computing power mostly come from the increasing number of nodes in a system and the integration of heterogeneous accelerators, how to scale the computing problems onto more nodes and various kinds of accelerators has become a challenge for the model development. This paper describes our efforts on developing a highly scalable framework for performing global atmospheric modeling on heterogeneous supercomputers equipped with various accelerators, such as GPU (Graphic Processing Unit), MIC (Many Integrated Core), and FPGA (Field Programmable Gate Arrays) cards. We propose a generalized partition scheme of the problem domain, so as to keep a balanced utilization of both CPU resources and accelerator resources. With optimizations on both computing and memory access patterns, we manage to achieve around 8 to 20 times speedup when comparing one hybrid GPU or MIC node with one CPU node with 12 cores. Using a customized FPGA-based data-flow engines, we see the potential to gain another 5 to 8 times improvement on performance. On heterogeneous supercomputers, such as Tianhe-1A and Tianhe-2, our framework is capable of achieving ideally linear scaling efficiency, and sustained double-precision performances of 581 Tflops on Tianhe-1A (using 3750 nodes) and 3.74 Pflops on Tianhe-2 (using 8644 nodes). Our study also provides an evaluation on the programming paradigm of various accelerator architectures (GPU, MIC, FPGA) for performing global atmospheric simulation, to form a picture about both the potential performance benefits and the programming efforts involved.