SARS-CoV-2 impairs interferon production via NSP2-induced repression of mRNA translation.

Viruses evade the innate immune response by suppressing the production or activity of cytokines such as type I interferons (IFNs). Here we report the discovery of a mechanism by which the SARS-CoV-2 virus coopts an intrinsic cellular machinery to suppress the production of the key immunostimulatory cytokine IFN-ß. We reveal that the SARS-CoV-2 encoded nonstructural protein 2 (NSP2) directly interacts with the cellular GIGYF2 protein. This interaction enhances the binding of GIGYF2 to the mRNA cap-binding protein 4EHP, thereby repressing the translation of the Ifnb1 mRNA. Depletion of GIGYF2 or 4EHP significantly enhances IFN-ß production, which inhibits SARS-CoV-2 replication. Our findings reveal a target for rescuing the antiviral innate immune response to SARS-CoV-2 and other RNA viruses.

Theoretical characterization of two-photon fluorescent probes for nitric oxide detection: sensing mechanism, photophysical properties and protonation effects.

Nitric oxide (NO) is an important signal molecule in biological systems and is correlated with many physiological processes and pathological diseases. To date, numerous fluorescent probes based on o-diamino aromatics have been designed and synthesized for NO detection utilizing the principle of photoinduced electron transfer (PET). However, the underlying PET mechanism has rarely been validated, and a systematic computational study on the photophysical properties is urgently desired. In this study, we used a theoretical protocol to comparatively investigate the sensing mechanism, photophysical properties and protonation effects of two emblematic probes NINO and PYSNO in aqueous solution, which combines a polarizable continuum model (PCM), time-dependent density functional theory (TD-DFT) and thermal vibration correlation function formalism (TVCF). Our findings reveal that the weak emission of NINO is due to activated PET with negative driving energy and blocked fluorescence with significant charge separation. In contrast, the poor luminescence of PYSNO is caused by the facilitated non-radiative dissipation, even though the fluorescence emission remains unobstructed. Although NINO has been successfully used in two-photon microscopy for detecting NO, we suggest that PYSNO possesses a superior two-photon absorption (TPA) cross section in the near-infrared region. The protonation effects suggest that both probes can function effectively in practical acidic lysosomal environments. Our study opens a new avenue for understanding the mechanism and predicting the properties of two-photon fluorescent probes for NO detection, thus aiding the rational design of efficient fluorescent sensors.

Effects of Cd uptake, translocation and redistribution in different hybrid rice varieties on grain Cd concentration.

In order to identify the key transport process that determines the Cd concentration in brown rice, this study used 21 hybrid rice varieties as experimental materials and conducted field experiments in Qiyang (cadmium-contaminated site) and Yongding (low-cadmium site). Cd concentrations in 8 organs were measured, and bioconcentration factors and transfer factor were further calculated. The results showed that the Cd concentrations of the organs related to the xylem transport were as follows: root > node > stem > leaf sheath > leaf. In the phloem, the Cd concentrations were as follows: rachis > brown rice > rice husk. And the results of the correlation analysis found that Cd concentration between brown rice and root showed a significant positive correlation in Cd-contaminated site, but no significant correlation in low-cadmium site. Meanwhile, at both experimental sites, the Cd concentration of brown rice showed the most significant correlation with the phloem transfer factor from leaf and leaf sheath to brown rice. Principal Component Analysis (PCA) and stepwise regression analysis likewise found that Cd concentration in leaf and leaf sheath and their phloem transport of Cd to brown rice were significantly and positively correlated with Cd concentration in brown rice. The above results showed that the transport of leaf and leaf sheath to brown rice was a key process, and played a more important role in the accumulation of cadmium in brown rice than in root.

An AIE-Active Conjugated Polymer with High ROS-Generation Ability and Biocompatibility for Efficient Photodynamic Therapy of Bacterial Infections.

New, biocompatible materials with favorable antibacterial activity are highly desirable. In this work, we develop a unique conjugated polymer featuring aggregation-induced emission (AIE) for reliable bacterial eradication. Thanks to the AIE and donor-π-acceptor structure, this polymer shows a high reactive oxygen species (ROS)-generation ability compared to a low-mass model compound and the common photosensitizer Chlorin E6. Moreover, the selective binding of pathogenic microorganisms over mammalian cells was found, demonstrating its biocompatibility. The effective growth inhibition of bacteria upon polymer treatment under light irradiation was validated in vitro and in vivo. Notably, the recovery from infection after treatment with our polymer is faster than that with cefalotin. Thus, this polymer holds great promise in fighting against bacteria-related infections in practical applications.

Systems model-guided rice yield improvements based on genes controlling source, sink, and flow.

A large number of genes related to source, sink, and flow have been identified after decades of research in plant genetics. Unfortunately, these genes have not been effectively utilized in modern crop breeding. This perspective paper aims to examine the reasons behind such a phenomenon and propose a strategy to resolve this situation. Specifically, we first systematically survey the currently cloned genes related to source, sink, and flow; then we discuss three factors hindering effective application of these identified genes, which include the lack of effective methods to identify limiting or critical steps in a signaling network, the misplacement of emphasis on properties, at the leaf, instead of the whole canopy level, and the non-linear complex interaction between source, sink, and flow. Finally, we propose the development of systems models of source, sink and flow, together with a detailed simulation of interactions between them and their surrounding environments, to guide effective use of the identified elements in modern rice breeding. These systems models will contribute directly to the definition of crop ideotype and also identification of critical features and parameters that limit the yield potential in current cultivars.

Comparative genomics identifies the Magnaporthe oryzae avirulence effector AvrPi9 that triggers Pi9-mediated blast resistance in rice.

We identified the Magnaporthe oryzae avirulence effector AvrPi9 cognate to rice blast resistance gene Pi9 by comparative genomics of requisite strains derived from a sequential planting method. AvrPi9 encodes a small secreted protein that appears to localize in the biotrophic interfacial complex and is translocated to the host cell during rice infection. AvrPi9 forms a tandem gene array with its paralogue proximal to centromeric region of chromosome 7. AvrPi9 is expressed highly at early stages during initiation of blast disease. Virulent isolate strains contain Mg-SINE within the AvrPi9 coding sequence. Loss of AvrPi9 did not lead to any discernible defects during growth or pathogenesis in M. oryzae. This study reiterates the role of diverse transposable elements as off-switch agents in acquisition of gain-of-virulence in the rice blast fungus. The prevalence of AvrPi9 correlates well with the avirulence pathotype in diverse blast isolates from the Philippines and China, thus supporting the broad-spectrum resistance conferred by Pi9 in different rice growing areas. Our results revealed that Pi9 and Piz-t at the Pi2/9 locus activate race specific resistance by recognizing sequence-unrelated AvrPi9 and AvrPiz-t genes, respectively.

Comparative Analysis of Anther Transcriptome Profiles of Two Different Rice Male Sterile Lines Genotypes under Cold Stress.

Rice is highly sensitive to cold stress during reproductive developmental stages, and little is known about the mechanisms of cold responses in rice anther. Using the HiSeq™ 2000 sequencing platform, the anther transcriptome of photo thermo sensitive genic male sterile lines (PTGMS) rice Y58S and P64S (Pei'ai64S) were analyzed at the fertility sensitive stage under cold stress. Approximately 243 million clean reads were obtained from four libraries and aligned against the oryza indica genome and 1497 and 5652 differentially expressed genes (DEGs) were identified in P64S and Y58S, respectively. Both gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted for these DEGs. Functional classification of DEGs was also carried out. The DEGs common to both genotypes were mainly involved in signal transduction, metabolism, transport, and transcriptional regulation. Most of the DEGs were unique for each comparison group. We observed that there were more differentially expressed MYB (Myeloblastosis) and zinc finger family transcription factors and signal transduction components such as calmodulin/calcium dependent protein kinases in the Y58S comparison group. It was also found that ribosome-related DEGs may play key roles in cold stress signal transduction. These results presented here would be particularly useful for further studies on investigating the molecular mechanisms of rice responses to cold stress.

Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells.

The integrated stress response (ISR) is critical for cell survival under stress. In response to diverse environmental cues, eIF2α becomes phosphorylated, engendering a dramatic change in mRNA translation. The activation of ISR plays a pivotal role in the early embryogenesis, but the eIF2-dependent translational landscape in pluripotent embryonic stem cells (ESCs) is largely unexplored. We employ a multi-omics approach consisting of ribosome profiling, proteomics, and metabolomics in wild-type (eIF2α+/+) and phosphorylation-deficient mutant eIF2α (eIF2αA/A) mouse ESCs (mESCs) to investigate phosphorylated (p)-eIF2α-dependent translational control of naive pluripotency. We show a transient increase in p-eIF2α in the naive epiblast layer of E4.5 embryos. Absence of eIF2α phosphorylation engenders an exit from naive pluripotency following 2i (two chemical inhibitors of MEK1/2 and GSK3α/ß) withdrawal. p-eIF2α controls translation of mRNAs encoding proteins that govern pluripotency, chromatin organization, and glutathione synthesis. Thus, p-eIF2α acts as a key regulator of the naive pluripotency gene regulatory network.

[Transcriptome analysis of early interaction between rice and Magnaporthe oryzae using next-generation sequencing technology].

Magnaporthe oryzae is speculated to express and translocate a set of effector proteins to interfere with rice innate immunity and to promote its invasion. In this study, we carried out a transcriptome analysis of early interaction between rice and M. oryzae using a next generation sequencing technology to identify putative effector protein genes. We totally obtained 338 942 M. oryzae derived sequence tags from around 12.5 M gross mixed tags by referring the genome sequence of reference strain 70-15. These M. oryzae sequences were finally mapped to 779 predicted genes. Of these 799 genes, 108 were predicted to be involved in the interaction between rice and M. oryzae and 42 encoded proteins predicted to be secreted. Expression of these 42 putative secreted protein genes were further assessed using a reverse transcription polymerase chain reaction (RT-PCR) method, which revealed that 12 of them were expressed during the infection. Four of these 12 expressed genes were further confirmed to be expressed specifically during the infection. This study demonstrated an attempt to isolate M. oryzae genes, especially those putative effector protein genes, which are expressed specifically at the early interaction stage using a next-generation sequencing technology.

Effects of Salinity Stress at Reproductive Growth Stage on Rice (Oryza sativa L.) Composition, Starch Structure, and Physicochemical Properties.

This study aimed to investigate the changes in polished rice composition, starch structure, and physicochemical properties from three rice cultivars treated with medium and high salinity stress at the reproductive growth stage. The results showed that salt stress led to poor milling and appearance quality, higher total starch content, protein content, higher proportion of the medium, and long chains of amylopectin, as well as gelatinization temperature (GT) but lower amylose content and lower proportion of the short chain of amylopectin. Compared with salt-sensitive cultivars, the salt-tolerant cultivars exhibited lower GT and gelatinization enthalpy, better pasting properties, and more stable crystal structure; therefore, their eating and cooking quality (ECQ) was less affected. The above results imply that salt stress at the reproductive growth stage can degrade ECQ and can slightly increase the pasting property of starch from salt-tolerant rice cultivar.

The mTOR chromatin-bound interactome in prostate cancer.

A growing number of studies support a direct role for nuclear mTOR in gene regulation and chromatin structure. Still, the scarcity of known chromatin-bound mTOR partners limits our understanding of how nuclear mTOR controls transcription. Herein, comprehensive mapping of the mTOR chromatin-bound interactome in both androgen-dependent and -independent cellular models of prostate cancer (PCa) identifies a conserved 67-protein interaction network enriched for chromatin modifiers, transcription factors, and SUMOylation machinery. SUMO2/3 and nuclear pore protein NUP210 are among the strongest interactors, while the androgen receptor (AR) is the dominant androgen-inducible mTOR partner. Further investigation reveals that NUP210 facilitates mTOR nuclear trafficking, that mTOR and AR form a functional transcriptional module with the nucleosome remodeling and deacetylase (NuRD) complex, and that androgens specify mTOR-SUMO2/3 promoter-enhancer association. This work identifies a vast network of mTOR-associated nuclear complexes advocating innovative molecular strategies to modulate mTOR-dependent gene regulation with conceivable implications for PCa and other diseases.

Referential modification strategy based on phenolic hydroxyl-containing KSA luminogens for ER-targeting probe construction.

The endoplasmic reticulum (ER) plays essential roles in various physiological processes and is intimately connected to kinds of diseases. The development of ER-targeting theranostic agents is highly demanded for precise treatments, however, the effective and referential strategies for the construction of ER-targeting probes are limited. Herein, we developed series of ER-targeting luminogens based on keto-salicylaldehyde azine (KSA) framework by introducing phenolic hydroxyl group, which present good theranostic performance with selective enrichment in ER. Under systematical structure modulation, the key role of phenolic hydroxyl group at K-terminal in ER-targeting was experimentally confirmed. Besides, the cyanobenzyl moiety at S-terminal can enhance the luminous efficiency and improve cellular uptake ability. Moreover, the generated reactive oxygen species (ROS) of these KSA derivatives can efficiently trigger ER stress to induce the apoptosis of cancer cells, resulting in the effective inhibition of tumor cells both in vitro and in vivo. Therefore, this feasible modification strategy of inserting phenolic hydroxyl group to common multi-aryl-based luminogens provides a reliable and referential approach for ER-targeting probe establishment.

More is less: Creation of pathogenic microbe-related theranostic oriented AIEgens.

Theranostic agents based on photo-dynamic therapy exhibited the properties of the noninvasive feature, spatial-temporal control and be free of drug resistance. Herein, based on the principle of "More is Less", a multifunctional nanoprobe for selective lighting-up of fungi and targeted anti-microbes was designed and achieved. The introducing of the hydroxyl groups and alkaline diethylamino moiety facilitate the probe with well aggregation-induced emission feature, good selectivity towards fungi and acid responsiveness. This probe could only light-up fungi with bright fluorescence, and exhibited diversity anti-microbe behavior towards different microbes. Moreover, the in vitro and in vivo eradication of the supergerm of methicillin resistant staphylococcus aureus was achieved by the treatment of the probe. Confidently, this well-designed nanoprobe is anticipated to have great potential in infective theranostic applications in clinic.

Architectural and Physiological Features to Gain High Yield in an Elite Rice Line YLY1.

Identification of traits strongly associated with high yield can help future gene engineering towards improvements of productivity. Here we systematically determine the major architectural and physiological features associated with high yield in two elite historical hybrid rice cultivars, i.e., YLY1 and LYP9. Data from a six-year experiment show that high yield of YLY1 are related to a number of architectural and physiological parameters. Compared to LYP9, YLY1 had 5.5% and 47.3% higher canopy photosynthesis under high and low photosynthetic photon flux densities, respectively, during the grain filling stage, an average 1.5% higher proportion of biomass allocation to above-ground tissues, a 4.5%-10.5% higher photosynthate reserve in leaf sheath before grain filling, and a more efficient photosynthate translocation during grain filling and finally an average 25.2% higher number of productive tillers. These features differ dramatically from features associated with high yield in YLY900 and Yongyou12#, two other high-yielding rice cultivars in China. These identified features and their combinations can support designing new strategies in the future high-yield rice breeding.

Influence of high natural field temperature during grain filling stage on the morphological structure and physicochemical properties of rice (Oryza sativa L.) starch.

This study investigated the effects of natural high temperature in the field during grain filling stage on the morphological structure and physicochemical properties of rice starch. High natural field temperature during rice grain filling stage resulted in poor processing and appearance quality, higher gelatinization properties including gelatinization temperature, gelatinization enthalpy, swelling power, and water solubility due to the reduction of amylose content. High temperature decreased the setback and trough viscosities, and increased breakdown, implying that the pasting properties were slightly better. High temperature did not change the starch crystalline type, while it significantly affected relative crystallinity, as well as pitting and unevenness on the surface of the starch granules with lower granule size. The above results imply that high temperature can degrade cooking and eating quality, and increase pasting properties of starch slightly.

Relationship between grain yield and leaf photosynthetic rate in super hybrid rice.

In order to explore the relationship between grain yield and photosynthesis, the yield composition and leaf photosynthetic rate in some super hybrid rices and ordinary hybrid rice 'Shanyou 63' as control were measured in 2000-2005. The results were as follows. (1) The yield levels of the four super hybrid rices, 'Pei'ai 64S/E32', 'P88S/0293', 'Jin23A/611' and 'GD-1S/RB207', were significantly higher, being 108%-120% of 'Shanyou 63'. (2) These super hybrid rices had a better plant type with more erect upper layer leaves and bigger panicles or more spikelets per panicle, being 125%-177% of spikelets Shanyou 63 spikelets. (3) Net photosynthetic rates of these super hybrid rices were significantly higher in the second leaf but not necessarily in the first leaf or flag leaf than those of spikelets Shanyou 63 spikelets. (4) The removal of half flag leaf led to a decline in the seed-setting rate, while the removal of half panicle induced its increase in spikelets GD-1S/RB207 spikelets. Hence, higher yield in these super hybrid rices can be attributed to their bigger panicles, better plant type and higher light use efficiency of their canopies. Raising the photosynthetic capacity of each leaf, especially flag leaf, is the key to overcome the photosynthate-source restriction on grain yield and to make a new breakthrough of yield potential in future breeding of super hybrid rice.

Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies.

Asian cultivated rice (Oryza sativa L.) consists of two main subspecies, indica and japonica. Indica has higher nitrate-absorption activity than japonica, but the molecular mechanisms underlying that activity remain elusive. Here we show that variation in a nitrate-transporter gene, NRT1.1B (OsNPF6.5), may contribute to this divergence in nitrate use. Phylogenetic analysis revealed that NRT1.1B diverges between indica and japonica. NRT1.1B-indica variation was associated with enhanced nitrate uptake and root-to-shoot transport and upregulated expression of nitrate-responsive genes. The selection signature of NRT1.1B-indica suggests that nitrate-use divergence occurred during rice domestication. Notably, field tests with near-isogenic and transgenic lines confirmed that the japonica variety carrying the NRT1.1B-indica allele had significantly improved grain yield and nitrogen-use efficiency (NUE) compared to the variety without that allele. Our results show that variation in NRT1.1B largely explains nitrate-use divergence between indica and japonica and that NRT1.1B-indica can potentially improve the NUE of japonica.

[Fertility alteration of male sterile rice line annong S-1 and the expression of fertility related aprt gene].

The thermo-sensitive point and the thermo-sensitive stage for fertility alteration in the thermo-sensitive genic male sterile (TGMS) line Annong S-1 were studied. In nature environment and green house,the leaf, root and young panicle were treated by low and high temperature respectively. In total, 8 treatments were carried out. Results indicated that during the thermo-sensitive stage of fertility alteration, in high temperature environmental conditions, the low temperature treatment in the root did not significantly induce Annong S-1 to be fertile, while the low temperature treatment in young panicle obviously induced Annong S-1 to be fertile. Therefore, the thermo-sensitive point of Annong S-1 is the young panicle. The stage of fertility alteration was also investigated. Results indicated that alteration occurred in the phase from the formation of pollen mother cell to the tetrad of miosis. aprt gene is related the male sterility. The expression of aprt gene in root,young panicle and leaf were investigated by RT-PCR respectively. In young panicle, the expression of aprt gene was greatly down regulated by high temperature, while in root and leaf the expressions have no great changes. These data show that the young panicle is sensitive to temperature change. The result also supported that the young panicle is the thermo-sensitive point of Annong S-1 in the fertility alteration. These conclusions can be used to direct in hybrid rice seed production.

RNase Z(S1) processes UbL40 mRNAs and controls thermosensitive genic male sterility in rice.

Thermosensitive genic male-sterile (TGMS) lines, which are male-sterile at restrictive (high) temperatures but male-fertile at permissive (low) temperatures, have been widely used in breeding two-line hybrid rice (Oryza sativa L.). Here we find that mutation of thermosensitive genic male sterile 5 (tms5) in rice causes the TGMS trait through a loss of RNase Z(S1) function. We show that RNase Z(S1) processes the mRNAs of three ubiquitin fusion ribosomal protein L40 (UbL40) genes into multiple fragments in vitro and in vivo. In tms5 mutants, high temperature results in increased levels of UbL40 mRNAs. Overaccumulation of UbL40 mRNAs causes defective pollen production and male sterility. Our results uncover a novel mechanism of RNase Z(S1)-mediated UbL40 mRNA regulation and shows that loss of this regulation produces TGMS in rice, a finding with potential applications in hybrid crop breeding.

Comparison of architecture among different cultivars of hybrid rice using a spatial light model based on 3-D digitising.

Modification of plant types (i.e. plant architecture) is an important strategy to enhance the yield potential of crops. The aims of this study were to specify rice plant types using 3-D modelling methodology. The architecture of three typical hybrid rice cultivars were measured in situ in a paddy field using a 3-D digitiser at four development stages from the panicle initiation to the filling stage. The structural parameters of the rice canopies were calculated and their light capture and potential carbon gain were simulated based on a 3-D light model. The results confirmed that a plant type with steeper leaf angles let light penetrate more deeply with relatively uniform light distribution in the canopy at higher sun elevation angles, although this result was related to leaf area index. The variations of plant types, however, did not convert into differences of light distribution across rice varieties at lower sun elevation angles. Light use efficiency at the higher leaf area index could be enhanced by reducing mutual-shading. These results indicate that a promising approach to quantify the rice architecture in situ is to combine 3-D digitising and a 3-D light model to evaluate light interception and photosynthesis of rice plant types.