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Abstract Astaxanthin (ASX) is an oxygen‐containing non‐vitamin A carotenoid pigment. However, the role of ASX in autoimmune hepatitis (AIH) remains unclear. In this study, a mouse model of AIH is established induced by concanavalin A (ConA). Mass cytometry and single‐cell RNA sequencing (scRNA‐seq) are used to analyze the potential role of ASX in regulating the immune microenvironment of AIH. ASX treatment effectively alleviated liver damage induced by ConA and downregulated pro‐inflammatory cytokines production in mice. Mass cytometry and scRNA‐seq analyses revealed a significant increase in the number of CD8+ T cells following ASX treatment. Functional markers of CD8+ T cells, such as CD69, MHC II, and PD‐1, are significantly downregulated. Additionally, specific CD8+ T cell subclusters (subclusters 4, 13, 24, and 27) are identified, each displaying distinct changes in marker gene expression after ASX treatment. This finding suggests a modulation of CD8+ T cell function by ASX. Finally, the key transcription factors for four subclusters of CD8+ T cells are predicted and constructed a cell‐to‐cell communication network based on receptor‐ligand interactions probability. In conclusion, ASX holds the potential to ameliorate liver damage by regulating the number and function of CD8+ T cells.

The pyridine alkaloid nicotine acts as one of best-studied plant resistant traits in tobacco. Previous research has shown that NtERF199 and NtERF189, acting as master regulators within the NIC1 and NIC2 locus, quantitatively contribute to nicotine accumulation levels in N. tabacum. Genome editing-created Nic1(Nterf199) and Nic2 (Nterf189) double mutant provides an ideal platform for precisely dissecting the defensive role of nicotine and the connection between the nicotine biosynthetic pathway with other putative metabolic networks. Taking this advantage, we performed a comparative transcriptomic analysis to reevaluate the potential physiological and metabolic changes in response to nicotine synthesis defect by comparing the nic1nic2 and NIC1NIC2 plants. Our findings revealed that nicotine reduction could systematically diminishes the expression intensities of genes associated with stimulus perception, signal transduction and regulation, as well as secondary metabolic flux. Consequently, this global expression reduction might compromise tobacco adaptions to environmental fitness, herbivore resistances, and plant growth and development. The up-regulation of a novel set of stress-responsive and metabolic pathway genes might signify a newly established metabolic reprogramming to tradeoff the detrimental effect of nicotine loss. These results offer additional compelling evidence regarding nicotine’s critical defensive role in nature and highlights the tight link between nicotine biosynthesis and gene expression levels of quantitative resistance-related genes for better environmental adaptation.

Abstract Mitochondrial genomes (mitogenomes) of flowering plants vary greatly in structure and size, which can lead to frequent gene mutation, rearrangement, or recombination, then result in the cytoplasmic male sterile (CMS) mutants. In tobacco (Nicotiana tabacum), suaCMS lines are widely used in heterosis breeding; however, the related genetic regulations are not very clear. In this study, the cytological observation indicated that the pollen abortion of tobacco suaCMS(HD) occurred at the very early stage of the stamen primordia differentiation. In this study, the complete mitochondrial genomes of suaCMS(HD) and its maintainer HD were sequenced using the PacBio and Illumina Hiseq technology. The total length of the assembled mitogenomes of suaCMS(HD) and HD was 494,317 bp and 430,694 bp, respectively. Comparative analysis indicated that the expanded 64 K bases in suaCMS(HD) were mainly located in noncoding regions, and 23 and 21 big syntenic blocks (>5000 bp) were found in suaCMS(HD) and HD with a series of repeats. Electron transport chain‐related genes were highly conserved in two mitogenomes, except five genes (ATP4, ATP6, COX2, CcmFC, and SDH3) with substantial substitutions. Three suaCMS(HD)‐specific genes, orf261, orf291, and orf433, were screened. Sequence analysis and RT‐PCR verification showed that they were unique to suaCMS(HD). Further gene location analysis and protein property prediction indicated that all the three genes were likely candidates for suaCMS(HD). This study provides new insight into understanding the suaCMS mechanism and is useful for improving tobacco breeding.

Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) system has been widely applied in cultivated crops, but limited in their wild relatives. Nicotiana alata is a typical wild species of genus Nicotiana that is globally distributed as a horticultural plant and well-studied as a self-incompatibility model. It also has valuable genes for disease resistance and ornamental traits. However, it lacks an efficient genetic transformation and genome editing system, which hampers its gene function and breeding research. In this study, we developed an optimized hypocotyl-mediated transformation method for CRISPR-Cas9 delivery. The genetic transformation efficiency was significantly improved from approximately 1% to over 80%. We also applied the CRISPR-Cas9 system to target the phytoene desaturase (NalaPDS) gene in N. alata and obtained edited plants with PDS mutations with over 50% editing efficiency. To generate self-compatible N. alata lines, a polycistronic tRNA-gRNA (PTG) strategy was used to target exonic regions of allelic S-RNase genes and generate targeted knockouts simultaneously. We demonstrated that our system is feasible, stable, and high-efficiency for N. alata genome editing. Our study provides a powerful tool for basic research and genetic improvement of N. alata and an example for other wild tobacco species.

BackgroundFungal co-infection is prevalent in critically ill patients with COVID-19. The conventional approach applied to fungal identification has relatively low sensitivity and is time-consuming. The metagenomic next-generation sequencing (mNGS) technology can simultaneously detect a variety of microorganisms, and is increasingly being used for the rapid detection and diagnosis of pathogens.MethodsIn this single-center retrospective study, we described the clinical presentation and outcomes of COVID-19 and mNGS positive for fungi in pulmonary critically ill patients during the outbreak of Omicron infection from December 2022 to January 2023.ResultsAmong 43 COVID-19 patients with acute respiratory distress syndrome (ARDS) on a single intensive care unit (ICU), 10 were reported to be fungal positive using the mNGS test. The number of pathogenic microorganisms detected by mNGS was significantly higher than that via traditional methods, especially in the detection of fungi and viruses. Aspergillus infection was dominant, and most of these patients also had concurrent bacterial or viral infections. Probable or possible COVID-19-associated pulmonary aspergillosis (CAPA) was diagnosed in all 10 patients, and the prognosis was poor.ConclusionPatients with COVID-19 may be at increased risk of developing fungal infections as well as concurrent bacterial or viral infections, and mNGS can be a powerful tool in identifying these infections. Clinicians should be aware of the increased risk of fungal infections in COVID-19 patients, particularly those who have underlying immunocompromising conditions, and should monitor for early signs of infection.

In this work, flexible Cu2−xS films on nylon membranes are prepared by combining a simple hydrothermal synthesis and vacuum filtration followed by hot pressing. The films consist of Cu2S and Cu1.96S two phases with grain sizes from nano to submicron. Doping Se on the S site not only increases the Cu1.96S content in the Cu2−xS to increase carrier concentration but also modifies electronic structure, thereby greatly improves the electrical properties of the Cu2−xS. Specifically, an optimal composite film with a nominal composition of Cu2−xS0.98Se0.02 exhibits a high power factor of ~150.1 μW m−1 K−2 at 300 K, which increases by ~138% compared to that of the pristine Cu2−xS film. Meanwhile, the composite film shows outstanding flexibility (~97.2% of the original electrical conductivity is maintained after 1500 bending cycles with a bending radius of 4 mm). A four-leg flexible thermoelectric (TE) generator assembled with the optimal film generates a maximum power of 329.6 nW (corresponding power density of 1.70 W m−2) at a temperature difference of 31.1 K. This work provides a simple route to the preparation of high TE performance Cu2−xS-based films.

The formation of the Jinsha River drainage is a significant subject of concern in the geological and geomorphological fields. Among them, one key question is whether there was a regional paleo lake into which Lower Jinsha River drainage drained during the late Pliocene to early Pleistocene, due to massive fluvio-lacustrine sediments widely distributed in the Lower Jinsha River. Nevertheless, there has yet to be a consensus on the genesis of those fluvio-lacustrine sediments due to poor sedimentological and chronological data. In this study, to unravel the origin of those fluvio-lacustrine sediments and the formation model of the Lower Jinsha River, sedimentary characteristics, including spatial distribution, lithological composition, and stratigraphic contact relationship of those fluvio-lacustrine sediments were analyzed, and chronological determination of the fluvio-lacustrine sediments using Electron Spin Resonance and Optically stimulated luminescence method was conducted. The results show that in the Lower Jinsha River, the lacustrine sediments are mainly composed of silt and clay, with apparent horizontal bedding, stacked with fluvial cobble-gravel and sand, and are in unconformable contact with the underlying bedrock strata or paleo soil. The lacustrine sediments are spatially discontinuous and mainly distributed in the Shigu, Taoyuan, Panzhihua, and Longjie reaches. Downstream of these reaches are deeply incised gorges with an average slope >30°, and many landslide landforms and deposits can be identified here. In each reach, the lacustrine sediments were closely distributed along the trunk and tributary channels in the plane and were distributed at different altitudes, forming a sequence of lacustrine terraces. Chronological analysis shows that in different reaches, the deposition ages of lacustrine sediments are significantly different. In each reach, the deposition age of the lacustrine terraces of high altitude is older than that of low altitude. The above characteristics collectively indicate that the lacustrine sediments in the Lower Jinsha River were locally deposited by individual dammed lakes, probably induced by landslide rather than a regional paleo lake by tectonic activities. During the incision process of the river valley, landslides continuously block the river channel, forming dammed lakes, and then deposited lacustrine sediments at different elevations, forming lacustrine terraces. The lacustrine sediment of the topmost lacustrine terrace in Panzhihua reach was dated to be 1.78 Ma, combined with previous studies on the fluvial terraces, indicating the Lower Jinsha River existed and started to incise its valley before the early Pleistocene. The widespread dammed lake sediment indicates that the formation of the Jinsha River valley follows the pattern of “incision-landslide-damming-aggradation-incision”.

Flexible Ag2Se thermoelectric (TE) films are promising for wearable applications near room temperature (RT). Herein, a Ag2Se film on a nylon membrane with high TE performance was fabricated by a facile method. First, Ag2Se powders were prepared by a microwave-assisted synthesis method using Ag nanowires as a template. Second, the Ag2Se powders were deposited onto nylon via vacuum filtration followed by hot pressing. Through modulating the Ag/Se molar ratio for synthesizing the Ag2Se powders, an optimized Ag2Se film demonstrates a high power factor of 1577.1 μW m−1 K−2 and good flexibility at RT. The flexibility of the Ag2Se film is mainly attributed to the flexible nylon membrane. In addition, a six-leg flexible TE generator (f-TEG) fabricated with the optimized Ag2Se film exhibits a maximum power density of 18.4 W m−2 at a temperature difference of 29 K near RT. This work provides a new solution to prepare high-TE-performance flexible Ag2Se films for f-TEGs.

Dam deformation monitoring data are generally characterized by non-smooth and no-saturated S-type fluctuation. The grey Verhulst model can get better results only when the data series is non-monotonic swing development and the saturated S-shaped sequence. Due to the limitations of the grey Verhulst model, the prediction accuracy will be limited to a certain extent. Aiming at the shortages in the prediction based on the traditional Verhulst model, the optimized grey Verhulst model is proposed to improve the prediction accuracy of the dam deformation monitoring. Compared with those of the traditional GM (1,1) model, the DGM (2,1) model, and the traditional Verhulst (1,1) model, the experimental results show that the new proposed optimized Verhulst model has higher prediction accuracy than the traditional gray model. This study offers an effective model for dealing with the non-saturated fluctuation sequence to predict dam deformation under uncertain conditions.

Abstract Background Ischemia‐reperfusion injury (IRI) is considered an inherent component of organ transplantation that compromises transplant outcomes and organ availability. The ischemia‐free liver transplantation (IFLT) procedure has been developed to avoid interruption of blood supply to liver grafts. It is unknown how IFLT might change the characteristics of graft IRI. Methods Serum and liver biopsy samples were collected from IFLT and conventional liver transplantation (CLT) recipients. Pathological, metabolomics, transcriptomics, and proteomics analyses were performed to identify the characteristic changes in graft IRI in IFLT. Results Peak aspartate aminotransferase (539.59 ± 661.76 U/L versus 2622.28 ± 3291.57 U/L) and alanine aminotransferase (297.64 ± 549.50 U/L versus 1184.16 ± 1502.76 U/L) levels within the first 7 days and total bilirubin levels by day 7 (3.27 ± 2.82 mg/dl versus 8.33 ± 8.76 mg/dl) were lower in the IFLT versus CLT group (all p values

Abstract In the process of synthetic aperture radar image noise suppression by the bi‐dimensional empirical mode decomposition (BEMD) algorithm, the edge effect is a key problem in the BEMD operation. To weaken this effect, an improved BEMD‐kernel principal component analysis (BEMD‐KPCA) method of image denoising is proposed in this study. Experimental results show that the BEMDKPCA algorithm has a good capability of improving edge effects in the BEMD decomposition process and satisfying the requirement of the reliable decomposition results. Compared with the traditional BEMD method, the proposed approach has a good effect on suppressing speckle noise. Additionally, the denoised image from the decomposed components of the IMFs processed by the BEMD‐KPCA method sufficiently preserves the edge and detail information, confirming its high coherency with the original image.

Surface subsidence is a serious threat to human life, buildings and traffic in Beijing. Surface subsidence is closely related to human activities, and human activities in Beijing area showed a decreasing trend during the Corona Virus Disease 2019 (COVID-19). To study surface subsidence in Beijing before and after the COVID-19 outbreak and its causes, a total of 51 Sentinel-1A SAR images covering Beijing from January 2018 to April 2022 were selected to derive subsidence information by Time Series Interferometry Synthetic Aperture Radar (TS-InSAR). The results of surface subsidence in Beijing demonstrate that Changping, Chaoyang, Tongzhou and Daxing Districts exhibited the most serious subsidence phenomenon before the COVID-19 outbreak. The four main subsidence areas form an anti-Beijing Bay that surrounds other important urban areas. The maximum subsidence rate reached −57.0 mm/year. After the COVID-19 outbreak, the main subsidence area was separated into three giant subsidence funnels and several small subsidence funnels. During this period, the maximum subsidence rate was reduced to −43.0 mm/year. Human activity decrease with the COVID-19 outbreak. This study effectively analysed the influence of natural factors on surface subsidence after excluding most of the human factors. The following conclusions are obtained from the analysis: (1) Groundwater level changes, Beijing’s geological structure and infrastructure construction are the main reasons for surface subsidence in Beijing. (2) Seasonal changes in rainfall and temperature indirectly affect groundwater level changes, thereby affecting surface subsidence in the area. (3) The COVID-19 outbreak in early 2020 reduced the payload of Beijing’s transportation facilities. It also slowed down the progress of various infrastructure construction projects in Beijing. These scenarios affected the pressure on the soft land base in Beijing and reduced the surface subsidence trend to some extent.

Background: Early allograft dysfunction (EAD) is correlated with poor patient or graft survival in liver transplantation. However, the power of distinct definitions of EAD in prediction of graft survival is unclear.Methods: This retrospective, single-center study reviewed data of 677 recipients undergoing orthotopic liver transplant between July 2015 and June 2020. The following EAD definitions were compared: liver graft assessment following transplantation (L-GrAFT) risk score model, early allograft failure simplified estimation score (EASE), model for early allograft function (MEAF) scoring, and Olthoff criteria. Risk factors for L-GrAFT7 high risk group were evaluated with univariate and multivariable logistic regression analysis.Results: L-GrAFT7 had a satisfied C-statistic of 0.87 in predicting a 3-month graft survival which significantly outperformed MEAF (C-statistic = 0.78, P = 0.01) and EAD (C-statistic = 0.75, P < 0.001), respectively. L-GrAFT10, EASE was similar to L-GrAFT7, and they had no statistical significance in predicting survival. Laboratory model for end-stage liver disease score and cold ischemia time are risk factors of L-GrAFT7 high-risk group.Conclusion: L-GrAFT7 risk score is capable for better predicting the 3-month graft survival than the MEAF and EAD in a Chinese cohort, which might standardize assessment of early graft function and serve as a surrogate endpoint in clinical trial.

Summary: Background Ischaemia-reperfusion injury is considered an inevitable component of organ transplantation, compromising organ quality and outcomes. Although several treatments have been proposed, none has avoided graft ischaemia and its detrimental consequences.Methods Ischaemia-free liver transplantation (IFLT) comprises surgical techniques enabling continuous oxygenated blood supply to the liver of brain-dead donor during procurement, preservation, and implantation using normothermic machine perfusion technology. In this non-randomised study, 38 donor livers were transplanted using IFLT and compared to 130 conventional liver transplants (CLT).Findings Two recipients (5•3%) in the IFLT group experienced early allograft dysfunction, compared to 50•0% in patients receiving conventional transplants (absolute risk difference, 44•8%; 95% confidence interval, 33•6-55•9%). Recipients of IFLT had significantly reduced median (IQR) peak aspartate aminotransferase levels within the first week compared to CLT recipients (365, 238-697 vs 1445, 791-3244 U/L, p

Background: Ischemia injury affects the recovery of liver allograft function. We propose a novel technique aimed at avoiding a second ischemic injury: transplanting an extended criteria donor (ECD) liver directly under normothermic machine perfusion (NMP) without recooling. We studied two cases to evaluate the efficacy and safety of this technique.Methods: The perioperative characteristics and postoperative outcomes of two recipients of ECD livers were analyzed. Both transplantations were performed with continuous normothermic machine perfusion without recooling.Result: In case 1, the cause of donor death was anoxia, and the donor liver had hypernatremia before procurement. The recipient was diagnosed with decompensated cirrhosis. His model for end-stage liver disease (MELD) score was 38. In case 2, the donor liver was from a donor after cardiac death (DCD), and the donor had elevated aspartate aminotransferase (AST) and alanine aminotransferase (ALT) levels. The recipient was diagnosed with acute hepatic failure. His MELD score was 35. Both donor livers were maintained under NMP and then transplanted without recooling. The peak ALT and AST levels after surgery were 452 and 770 U/L in case 1 and 100 and 592 U/L in case 2. Neither early allograft dysfunction (EAD) nor primary graft non-function (PNF) was present in these two cases.Conclusion: In conclusion, our results demonstrate that continuous NMP without recooling is efficacious and safe for LT with extended criteria donor livers. Further investigations of this technique will be performed to confirm these promising results.

Abstract Background MicroRNAs (miRNAs) play a pivotal role in hepatocellular carcinoma (HCC) progression and have been confirmed to participate in the carcinogenesis and development of HCC. However, the relationship between miR-497-5p and HCC remains unclear. Methods Kaplan–Meier curve analysis and the log-rank test were used to investigate the efficacy of miR-497-5p on overall survival (OS) and disease-free survival (DFS) in patients with HCC. According to in vitro experiments, programmed cell death 4 (PDCD4) was a target of miR-497-5p by the dual-luciferase activity assay. The efficacy of PDCD4 on cell proliferation and metastasis in HCC was examined by transwell assays, CCK-8 assays and reverse transcription quantitative PCR (RT-qPCR). Additionally, we conducted a luciferase activity reporter assay to confirm the interaction between lncRNA XIST and miR-49-5p. Then, to evaluate the relationship between lncRNA XIST and miR-497-5p, several mechanistic experiments, including qRT-PCR, Western blotting, transwell assays and tumor xenograft assays, were performed. Results miR-497-5p was upregulated in HCC tissues, and high expression of miR-497-5p resulted in increases in tumor size and tumor number and a higher tumor-node-metastasis (TNM) stage and Edmondson grade in patients with HCC. Silencing miR-497-5p inhibited the proliferation and migration of HCC cells. PDCD4, which was downregulated in HCC tissues, was shown to be a target of miR-497-5p and was negatively correlated with the expression of miR-497-5p. lncRNA XIST was found to act as a miR-497-5p sponge and to regulate the level of PDCD4, which is targeted by miR-497-5p. lncRNA XIST was observed to be downregulated in the HCC tissues and positively correlated with the expression of PDCD4. Conclusions Our findings reveal that the XIST/miR-497-5p/PDCD4 axis participates in HCC development and that XIST could be used as a biomarker of HCC.

It is difficult to get robust deformation results using conventional differential interferometric synthetic aperture radar (D-InSAR) method, due to the limitation of the phase measurement error, baseline error, and atmospheric delay in synthetic aperture radar (SAR) interferometry. Persistent scatterer interferometry (PSI) represents a powerful tool to measure mining subsidence, as it offers a synoptic view that can be repeated at different time intervals and at various scales. In many cases, PSI data are integrated with in situ monitoring instrumentation, since the joint use of satellite and ground-based data facilitates the geological interpretation of mining subsidence and allows a better understanding of mining subsidence geometry and kinematics. In this paper, PSI interferometry and conventional ground-based monitoring techniques have been used to characterize and to monitor Ge-Ting mining located in Shandong, China. The PSI technique used in this paper overcomes most of the limitations of conventional interferometric approaches by identifying, within the area of interest, a set of “radar benchmarks” (PS), where very precise displacement measurements can be carried out. More than 78000 PS were identified by processing SAR images acquired from 2004 to 2009 by the ENVISAT. The PSInSAR application at a sub-regional scale detected slow ground deformations ranging from 0 to -58 cm/year and resulting from various processes (swelling/shrinkage of clay soils and water pumping). The results reveal the evolution process of “bowl” in mining subsidence and are helpful to the early warning of the mine disaster.

Genetic linkage maps representing the tobacco genome have been an important tool for breeding programs because of the elucidation of polygenic traits. We constructed a genetic linkage map of cigar tobacco (Nicotiana tabacum L.) based on an inter-type backcross population of 213 individuals and performed a comparative analysis with other published maps of dark tobacco and flue-cured tobacco. The map consisted of 562 SSR loci distributed on 24 tentative linkage groups and spanned a total length of 1341.18 cM with an average distance of 2.39 cM between adjacent markers. The comparative analysis revealed a Spearman correlation index of 0.93 for marker order conservation with the previously published maps constructed for different tobacco types. Approximately 91% of the SSR markers common to other inter-type maps were located in the same positions as in previous maps. The three maps exhibit good synteny in terms of the shared markers, which suggests that there might be no translocation variations between the genomes of the cigar, dark and flue-cured tobaccos. These results indicate the feasibility of generating a unique genetic map of preferred traits in cigar tobacco and that such mapping may be helpful for breeding programs because plants derived from different inter-type populations can be rapidly scanned using the markers associated with useful cigar traits

In present study, we report the complete chloroplast genome of Nicotiana debneyi, a species endemic to eastern coast of Australia. The total genome size of N.debneyi is 156,073 bp in length, containing a large single-copy region of 86,672 bp, a small single-copy region of 18,581 bp, and two inverted repeat regions of 25,410 bp. The all GC content of N.debneyi chloroplast genome is 38.4%. It encodes a total of 129 unique genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes, of which seven tRNA, four rRNA and seven protein-coding genes are duplicated in the IR. Sixteen genes contain a single intron, and only two genes have two introns. Phylogenetic analysis results strongly supported that N.debneyi was closely related to Nicotiana sylvestris and Nicotiana tabacum.

In the plant immune system, according to the ‘gene-for-gene’ model, a resistance (R) gene product in the plant specifically surveils a corresponding effector protein functioning as an avirulence (Avr) gene product. This system differs from other plant–pathogen interaction systems, in which plant R genes recognize a single type of gene or gene family because almost all virus genes with distinct structures and functions can also interact with R genes as Avr determinants. Thus, research conducted on viral Avr-R systems can provide a novel understanding of Avr and R gene product interactions and identify mechanisms that enable rapid co-evolution of plants and phytopathogens. In this review, we intend to provide a brief overview of virus-encoded proteins and their roles in triggering plant resistance, and we also summarize current progress in understanding plant resistance against virus Avr genes. Moreover, we present applications of Avr gene-mediated phenotyping in R gene identification and screening of segregating populations during breeding processes.

Abstract Background Tomato zonate spot virus (TZSV), a dominant species of thrips-transmitted orthotospoviruses in Yunnan and Guangxi provinces in China, causes significant loss of yield in lots of crops and is a major threat to incomes of rural families. However, the detailed molecular mechanism of crop disease caused by TZSV remains obscure. Methods Next-generation sequencing (NGS)-based transcriptome analysis (RNA-seq) was performed to investigate and compare the gene expression changes in systemic leaves of tobacco upon infection with TZSV and mock-inoculated plants as a control. Results De novo assembly and analysis of tobacco transcriptome data by RNA-Seq identified 135,395 unigenes. 2102 differentially expressed genes (DEGs) were obtained in tobacco with TZSV infection, among which 1518 DEGs were induced and 584 were repressed. Gene Ontology enrichment analysis revealed that these DEGs were associated with multiple biological functions, including metabolic process, oxidation-reduction process, photosynthesis process, protein kinase activity. The KEGG pathway analysis of these DEGs indicated that pathogenesis caused by TZSV may affect multiple processes including primary and secondary metabolism, photosynthesis and plant-pathogen interactions. Conclusion Our global survey of transcriptional changes in TZSV infected tobacco provides crucial information into the precise molecular mechanisms underlying pathogenesis and symptom development. This is the first report on the relationships in the TZSV-plant interaction using transcriptome analysis. Findings of present study will significantly help enhance our understanding of the complicated mechanisms of plant responses to orthotospoviral infection.

Plant viruses have evolved multiple strategies to overcome host defense to establish an infection. Here, we identified two components of a host mitogen-activated protein kinase (MAPK) cascade, MKK2 and MPK4, as bona fide targets of the βC1 protein encoded by the betasatellite of tomato yellow leaf curl China virus (TYLCCNV). βC1 interacts with the kinase domain of MKK2 and inhibits its activity. In vivo, βC1 suppresses flagellin-induced MAPK activation and downstream responses by targeting MKK2. Furthermore, βC1 also interacts with MPK4 and inhibits its kinase activity. TYLCCNV infection induces the activation of the MAPK cascade, mutation in MKK2 or MPK4 renders the plant more susceptible to TYLCCNV, and can complement the lack of βC1. This work shows for the first time that a plant virus both activates and suppresses a MAPK cascade, and the discovery of the ability of βC1 to selectively interfere with the host MAPK activation illustrates a novel virulence function and counter-host defense mechanism of geminiviruses.

The whitefly-transmitted geminiviruses induce severe developmental abnormalities in plants. Geminivirus-encoded C4 protein functions as one of viral symptom determinants that could induce abnormal cell division. However, the molecular mechanism by which C4 contributes to cell division induction remains unclear. Here we report that tomato leaf curl Yunnan virus (TLCYnV) C4 interacts with a glycogen synthase kinase 3 (GSK3)/SHAGGY-like kinase, designed NbSKη, in Nicotiana benthamiana. Pro32, Asn34 and Thr35 of TLCYnV C4 are critical for its interaction with NbSKη and required for C4-induced typical symptoms. Interestingly, TLCYnV C4 directs NbSKη to the membrane and reduces the nuclear-accumulation of NbSKη. The relocalization of NbSKη impairs phosphorylation dependent degradation on its substrate-Cyclin D1.1 (NbCycD1;1), thereby increasing the accumulation level of NbCycD1;1 and inducing the cell division. Moreover, NbSKη-RNAi, 35S::NbCycD1;1 transgenic N. benthamiana plants have the similar phenotype as 35S::C4 transgenic N. benthamiana plants on callus-like tissue formation resulted from abnormal cell division induction. Thus, this study provides new insights into mechanism of how a viral protein hijacks NbSKη to induce abnormal cell division in plants.

Tomato spotted wilt virus (TSWV) is one of the most destructive viral pathogens of plants. Recently, a single dominant gene conferring complete resistance to TSWV (RTSW) was identified in Nicotina alata and introgressed into cultivated tobacco (N. tabacum). However, whether the TSWV carries an avirulence (Avr) factor directed against RTSW remains obscure. In the present study, we identified the non-structural protein (NSm), the movement protein of TSWV, which is an RTSW-specific Avr factor, by using two different transient expression systems. Using amino acid (aa) substitution mutants, we demonstrated the ability to induce RTSW-mediated hypersensitive response (HR) of NSm is independent of its movement function. Moreover, key substitutions (C118Y and T120N), a 21-aa viral effector epitope, and different truncated versions of NSm, which are responsible for the recognition of the Sw-5b resistance gene of tomato, were tested for their ability to trigger HR to TSWV in tobacco. Together, our results demonstrated that RTSW-mediated resistance is triggered by NSm in the same way as by Sw-5b, however, via different elicitor active sites. Finally, an Avr gene-based diagnostic approach was established and used to determine the presence and effectiveness of resistance genes in tobacco.

Monopartite begomoviruses and their associated satellites form unique disease complexes that have emerged as a serious threat to agriculture worldwide. It is well known that frequent recombination contributes to the diversification and evolution of geminiviruses. In this study, we identified a novel defective satellite molecule (RecSat) in association with Tobacco leaf curl Yunnan virus (TbLCYNV) in a naturally infected tobacco plant. Sequence analysis showed that Recsat comprises 754 nucleotides in size and is a chimera involving alphasatellite and betasatellite sequences, containing both betasatellite-conserved region and alphasatellite stem-loop structure. Recombination analysis revealed that RecSat has arisen from three independent recombination events likely involving Tomato yellow leaf curl China betasatellite, Ageratum yellow vein China betasatellite and Tobacco curly shoot alphasatellite. Co-inoculation of RecSat with TbLCYNV induced symptoms indistinguishable from those induced by TbLCYNV alone in Nicotiana benthamiana. Southern blot hybridization showed that RecSat could be trans-replicated stably in N. benthamiana plants by TbLCYNV, and impaired the accumulation of helper virus and co-inoculated alphasatellite. Our results provide the first evidence for recombination between two distinct types of satellites among geminivirus complex and highlight recombination as a driving force for geminivirus evolution.

We investigated the influence of particle size on the microstructure and magnetocaloric effect of Fe-based alloy powders (11 μm to 100 μm in diameter). The degree of structure order varies with the powder size. The 11 μm to 18 μm powders show the largest peak magnetic entropy change (MEC). Increasing the degree of structure order tends to decrease the maximum MEC. Nevertheless, enhancement of refrigerant capacity and MEC (above 70 K) is achieved when the crystalline phase content is ∼50% (above 75 μm) in the 75 μm to 100 μm powders. Exponent n of the field dependence of MEC increases with the decrease in powder size above 22.5 K. The size dependence of the structure and properties is associated with the fact that a larger particle has a slower cooling rate and takes a longer time to form medium-to-long range ordered structures.

The availability of infectious full-length clone is indispensable for reverse genetics studies of virus biology, pathology and construction of viral vectors. However, for RNA viruses with large genome sizes or those exhibiting inherent cloning difficulties, procedure to generate biologically active complementary DNA (cDNA) clones can be time-consuming or technically challenging. Here we have constructed a yeast-Escherichia coli-Agrobacterium shuttle vector that enables highly efficient homologous recombination in yeast for assembly of Agrobacterium compatible plant virus clones. Using this vector, we show that infectious cDNA clones of a plant negative-stranded RNA virus, sonchus yellow net rhabdovirus, can be rapidly assembled. In addition, one-step assembly of infectious clones of potato virus Y in yeast, either with or without intron, was readily achieved from as many as eight overlapping DNA fragments. More importantly, the recovered yeast plasmids can be transformed directly into Agrobacterium for inoculation, thereby obviating the E. coli cloning steps and associated toxicity issues. This method is rapid, highly efficient and cost-effective and should be readily applicable to a broad range of plant viruses.

Transcriptional gene silencing (TGS) can serve as an innate immunity against invading DNA viruses throughout Eukaryotes. Geminivirus code for TrAP protein to suppress the TGS pathway. Here, we identified an Arabidopsis H3K9me2 histone methyltransferase, Su(var)3-9 homolog 4/Kryptonite (SUVH4/KYP), as a bona fide cellular target of TrAP. TrAP interacts with the catalytic domain of KYP and inhibits its activity in vitro. TrAP elicits developmental anomalies phenocopying several TGS mutants, reduces the repressive H3K9me2 mark and CHH DNA methylation, and reactivates numerous endogenous KYP-repressed loci in vivo. Moreover, KYP binds to the viral chromatin and controls its methylation to combat virus infection. Notably, kyp mutants support systemic infection of TrAP-deficient Geminivirus. We conclude that TrAP attenuates the TGS of the viral chromatin by inhibiting KYP activity to evade host surveillance. These findings provide new insight on the molecular arms race between host antiviral defense and virus counter defense at an epigenetic level.

In plants, RNA silencing plays a key role in antiviral defense. To counteract host defense, plant viruses encode viral suppressors of RNA silencing (VSRs) that target different effector molecules in the RNA silencing pathway. Evidence has shown that plants also encode endogenous suppressors of RNA silencing (ESRs) that function in proper regulation of RNA silencing. The possibility that these cellular proteins can be subverted by viruses to thwart host defense is intriguing but has not been fully explored. Here we report that the Nicotiana benthamiana calmodulin-like protein Nbrgs-CaM is required for the functions of the VSR βC1, the sole protein encoded by the DNA satellite associated with the geminivirus Tomato yellow leaf curl China virus (TYLCCNV). Nbrgs-CaM expression is up-regulated by the βC1. Transgenic plants over-expressing Nbrgs-CaM displayed developmental abnormities reminiscent of βC1-associated morphological alterations. Nbrgs-CaM suppressed RNA silencing in an Agrobacterium infiltration assay and, when over-expressed, blocked TYLCCNV-induced gene silencing. Genetic evidence showed that Nbrgs-CaM mediated the βC1 functions in silencing suppression and symptom modulation, and was required for efficient virus infection. Moreover, the tobacco and tomato orthologs of Nbrgs-CaM also possessed ESR activity, and were induced by betasatellite to promote virus infection in these Solanaceae hosts. We further demonstrated that βC1-induced Nbrgs-CaM suppressed the production of secondary siRNAs, likely through repressing RNA-DEPENDENT RNA POLYMERASE 6 (RDR6) expression. RDR6-deficient N. benthamiana plants were defective in antiviral response and were hypersensitive to TYLCCNV infection. More significantly, TYLCCNV could overcome host range restrictions to infect Arabidopsis thaliana when the plants carried a RDR6 mutation. These findings demonstrate a distinct mechanism of VSR for suppressing PTGS through usurpation of a host ESR, and highlight an essential role for RDR6 in RNA silencing defense response against geminivirus infection.

Growing evidence has linked autophagy to a protective role of preconditioning in liver ischemia/reperfusion (IR). Heme oxygenase-1 (HO-1) is essential in limiting inflammation and preventing the apoptotic response to IR. We previously demonstrated that HO-1 is up-regulated in liver graft after remote ischemic preconditioning (RIPC). The aim of this study was to confirm that RIPC protects against IR via HO-1-mediated autophagy.RIPC was performed with regional ischemia of limbs before liver ischemia, and HO-1 activity was inhibited pre-operation. Autophagy was assessed by the expression of light chain 3-II (LC3-II). The HO-1/extracellular signal-related kinase (ERK)/p38/mitogen-activated protein kinase (MAPK) pathway was detected in an autophagy model and mineral oil-induced IR in vitro.In liver IR, the expression of LC3-II peaked 12-24 h after IR, and the ultrastructure revealed abundant autophagosomes in hepatocytes after IR. Autophagy was inhibited when HO-1 was inactivated, which we believe resulted in the aggravation of liver IR injury (IRI) in vivo. Hemin-induced autophagy also protected rat hepatocytes from IRI in vitro, which was abrogated by HO-1 siRNA. Phosphorylation of p38-MAPK and ERK1/2 was up-regulated in hemin-pretreated liver cells and down-regulated after treatment with HO-1 siRNA.RIPC may protect the liver from IRI by induction of HO-1/p38-MAPK-dependent autophagy.

Plant intracellular nucleotide- binding domain, leucine-rich repeat- containing recep- tors (NLRs) activate a robust immune response upon detection of pathogen effectors. How NLRs induce downstream immune defense genes remains poorly understood. The Mediator complex plays a central role in transducing signals from gene-specific transcription factors to the transcription machinery for gene transcription/activation. In this study, we demonstrate that MED10b and MED7 of the Mediator complex mediate jasmonate-dependent transcription repression, and coiled-coil NLRs (CNLs) in Solanaceae modulate MED10b/MED7 to activate immunity. Using the tomato CNL Sw-5b, which confers resistance to tospovirus, as a model, we found that the CC domain of Sw-5b directly interacts with MED10b. Knockout/down of MED10b and other subunits including MED7 of the middle module of Mediator activates plant defense against tospovirus. MED10b was found to directly interact with MED7, and MED7 directly interacts with JAZ proteins, which function as transcriptional repressors of jasmonic acid (JA) signaling. MED10b–MED7–JAZ together can strongly repress the expression of JA-responsive genes. The activated Sw-5b CC interferes with the interac- tion between MED10b and MED7, leading to the activation of JA-dependent defense signaling against tospovirus. Furthermore, we found that CC domains of various other CNLs including helper NLR NRCs from Solanaceae modulate MED10b/MED7 to activate defense against different pathogens. Together, our findings reveal that MED10b/ MED7 serve as a previously unknown repressor of jasmonate-dependent transcription repression and are modulated by diverse CNLs in Solanaceae to activate the JA-specific defense pathways. [ABSTRACT FROM AUTHOR]