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BackgroundWheat is a powerful genetic model for studying polyploid evolution and crop domestication. Hexaploid bread wheat was formed by two rounds of interspecific hybridization and polyploidization, processes which are often accompanied by genetic and epigenetic changes, including DNA methylation. However, the extent and effect of such changes during wheat evolution, particularly from tetraploid-to-hexaploid wheat, are currently elusive.ResultsHere we report genome-wide DNA methylation landscapes in extracted tetraploid wheat (ETW, AABB), natural hexaploid wheat (NHW, AABBDD), resynthesized hexaploid wheat (RHW, AABBDD), natural tetraploid wheat (NTW, AABB), and diploid (DD). In the endosperm, levels of DNA methylation, especially in CHG (H=A, T, or C) context, were dramatically decreased in the ETW relative to natural hexaploid wheat; hypo-differentially methylated regions (DMRs) (850,832) were 24-fold more than hyper-DMRs (35,111). Interestingly, those demethylated regions in ETW were remethylated in the resynthesized hexaploid wheat after the addition of the D genome. In ETW, hypo-DMRs correlated with gene expression, and TEs were demethylated and activated, which could be silenced in the hexaploid wheat. In NHW, groups of TEs were dispersed in genic regions of three subgenomes, which may regulate the expression of TE-associated genes. Further, hypo-DMRs in ETW were associated with reduced H3K9me2 levels and increased expression of histone variant genes, suggesting concerted epigenetic changes after separation from the hexaploid.ConclusionGenome merger and separation provoke dynamic and reversible changes in chromatin and DNA methylation. These changes correlate with altered gene expression and TE activity, which may provide insights into polyploid genome and wheat evolution.

Legionella pneumophila promotes its survival and replication in phagocytes by actively modulating cellular processes using effectors injected into host cells by its Dot/Icm type IV secretion system. Many of these effectors function to manipulate the ubiquitin network of infected cells, thus contributing to the biogenesis of the Legionella-containing vacuole (LCV), which is permissive for bacterial replication. Among these, members of the SidE effector family (SidEs) catalyze ubiquitination of functionally diverse host proteins by a mechanism that is chemically distinct from the canonical three-enzyme cascade. The activity of SidEs is regulated by two mechanisms: reversal of the phosphoribosyl ubiquitination by DupA and DupB and direct inactivation by SidJ, which is a calmodulin-dependent glutamylase. In many L. pneumophila strains, SidJ belongs to a two-member protein family. Its homolog SdjA appears to function differently from SidJ despite the high-level similarity in their primary sequences. Here, we found that SdjA is a bifunctional enzyme that exhibits distinct activities toward members of the SidE family. It inhibits the activity of SdeB and SdeC by glutamylation. Unexpectedly, it also functions as a deglutamylase that reverses SidJ-induced glutamylation on SdeA. Our results reveal that an enzyme can catalyze two completely opposite biochemical reactions, which highlights the distinct regulation of phosphoribosyl ubiquitination by the SidJ effector family. IMPORTANCE One unique feature of L. pneumophila Dot/Icm effectors is the existence of protein families with members of high-level similarity. Whereas members of some families are functionally redundant, as suggested by their primary sequences, the relationship between SidJ and SdjA, the two members of the SidJ family, has remained mysterious. Despite their sharing 57% identity, sdjA cannot complement the defects in virulence displayed by a mutant lacking sidJ. SidJ inhibits the activity of the SidE family by a calmodulin (CaM)-dependent glutamylase activity. Here, we found that SdjA is a dual function protein: it is a CaM-dependent glutamylase against SdeB and SdeC but exhibits deglutamylase activity toward SdeA that has been modified by SidJ, indicating that SdjA functions to fine-tune the activity of SidEs. These findings have paved the way for future structural and functional analysis of SdjA, which may reveal novel mechanism for isopeptide bond cleavage and provide insights into the study of protein evolution.

Legionella pneumophila promotes its survival and replication in phagocytes by actively modulating cellular processes using effectors injected into host cells by its Dot/Icm type IV secretion system. Many of these effectors function to manipulate the ubiquitin network of infected cells, thus contributing to the biogenesis of the Legionella-containing vacuole (LCV), which is permissive for bacterial replication. Among these, members of the SidE effector family (SidEs) catalyze ubiquitination of functionally diverse host proteins by a mechanism that is chemically distinct from the canonical three-enzyme cascade. The activity of SidEs is regulated by two mechanisms: reversal of the phosphoribosyl ubiquitination by DupA and DupB and direct inactivation by SidJ, which is a calmodulin-dependent glutamylase. In many L. pneumophila strains, SidJ belongs to a two-member protein family. Its homolog SdjA appears to function differently from SidJ despite the high-level similarity in their primary sequences. Here, we found that SdjA is a bifunctional enzyme that exhibits distinct activities toward members of the SidE family. It inhibits the activity of SdeB and SdeC by glutamylation. Unexpectedly, it also functions as a deglutamylase that reverses SidJ-induced glutamylation on SdeA. Our results reveal that an enzyme can catalyze two completely opposite biochemical reactions, which highlights the distinct regulation of phosphoribosyl ubiquitination by the SidJ effector family.

Reports in recent years have shown that pancreatic β-cell pyroptosis represents a critical mechanism involved with the progressive failure of pancreatic function. Previous research from our laboratory has indicated that artemether can increase the number of cells in pancreatic islets of db/db mice. In this study, we further examined whether artesunate (ART) protects pancreatic β-cells from the damage of streptozotocin (STZ) by inhibiting pyroptosis.In vitro, MIN6 cells exposed to 1 mM STZ were treated with ART (0.8 or 1.6 μM). The effects of ART on STZ-treated cells were evaluated through CCK-8 assay, flow cytometry and western blot, and further compared the effects of ART with the NLRP3 inhibitor, Mcc950 upon pyroptosis pathway proteins using western blot. In vivo, Male C57 mice were administered with a single intraperitoneal injection of STZ, and those with confirmed diabetes mellitus were given ART (0.5 or 1.0 mg/ml in drinking water) for 18 days. The effects of ART on STZ-induced diabetes were assessed by the observation of the general situation, glucose tolerance test, hematoxylin-eosin (HE) staining and immunohistochemistry.In MIN6 cells treated with STZ, we found that ART increased cell viability, decreased the number of late apoptotic cells (including pyroptosis cells) and inhibited the expression of proteins associated with the pyroptosis pathway. In STZ-induced animal model, the administration of ART reduced blood glucose levels, improved the consumption status within this diabetic mouse model and inhibited the expression of proteins include in the pyroptosis pathway in mice pancreats.Inhibition of pyroptosis may be a critical mechanism through which artesunate exerts protective effects upon pancreatic β cells.

Diabetic kidney disease(DKD) has become the leading cause of end-stage renal disease and the main cause of death of chronic kidney disease. Renal interstitial fibrosis is an important pathological change of DKD, and chronic microinflammation also plays a key role in the occurrence and development of Diabetic Nephropathy(DN). Macrophages are one of the main regulatory cells of inflammation and infiltrate in the kidney tissue of early DN. In addition to producing injury mediators, activated macrophages can also affect the kidney through other mechanisms. Interestingly, there are a large amount of exosomes generated by macrophage under hyperglycemia condition and it is not clear whether the exosomes has any effect on glomerular mesangial cell fibrosis in patients with diabetes. Here, we use a diabetic nephropathy db/db mouse model to determine the effect of macrophage-produced exosomes by miR-146a-5p overexpression or down-regulation on mesangial cell fibrosis. with high glucose, Macrophage proliferation is promoted in mice and miR-146a-5p expression is downregulated in both macrophages and glomerular mesangial cells. we confirmed that Smad4 is the target gene of miR-146a-5p through Luciferase reporter gene system. Fibrosis-associated col I, α-SMA, and Smad4 are upregulated in glomerular mesangial cells. In exosomes, we observed miR-146a-5p is downregulated in high glucose than low glucose. We use the exosomes from the macrophages that are transfected with miR-146a-5p mimics or inhibitor to culture the glomerular mesangial cells. Exosomes from miR-146a-5p mimics significantly downregulated glomerular Mesangial cell fibrosis-related factor α-SMA, col I protein, and Smad4. Exosomes from miR-146a-5p inhibition upregulated these factors. Finally, we found macrophage exosomes from miR-146a-5p overexpression can inhibit glomerular mesangial cell fibrosis, which could provide a potential treatment strategy for DKD. Disclosure W. Zhang: None. H. Jiang: None. Y. Ma: None. H. Peng: None. J. Liu: None. J. Yuan: None. K. Hu: None. B. Zhao: None. H. Wu: None.

Based on the results of single factor experiments, response surface methodology was used to optimize the extraction conditions of flavonoids from Penthorum chinense Pursh (PCF). The optimal extraction conditions were the ratio of liquid to material 22 mL/g, ethanol concentration 68%, extraction temperature 82 °C, and extraction time 2.2 h, respectively. Under these optimized conditions, the PCF yield was 10.72%, which closely agreed with the predicted value (10.75%). In addition, PCF significantly scavenged DPPH radical, hydroxyl radical and superoxide radical in vitro. In the in vivo assays, PCF enhanced the resistance of Caenorhabditis elegans against heat stress, which might be attributed to PCF increased the activities of catalase (CAT) and superoxide dismutase (SOD), and decreased the level of malondialdehyde (MDA). In summary, these results suggested that the optimized extraction was a very effective method to extract PCF and the PCF could be explored as a potential antioxidant for medicine and function food.

Plants have evolved genetic and physiological mechanisms to mitigate the adverse effects of high temperature. CARBOXYL TERMINUS OF THE HSC70-INTERACTING PROTEINS (CHIP) is a conserved chaperone-dependent ubiquitin E3 ligase that targets misfolded proteins. Here, we report functional analysis of the SlCHIP gene from tomato (Solanum lycopersicum) in heat tolerance. SlCHIP encodes a CHIP protein with three tandem tetracopeptide repeat (TPR) motifs and a C-terminal U box domain. Phylogenetic analysis of CHIP homologs from animals, spore-bearing and seed plants revealed a tree topology similar to the evolutionary tree of the organisms. Expression of SlCHIP was induced under high temperature and was also responsive to plant stress hormones. Silencing of SlCHIP in tomato reduced heat tolerance based on increased heat stress symptoms, reduced photosynthetic activity, elevated electrolyte leakage and accumulation of insoluble protein aggregates. The accumulated protein aggregates in SlCHIP-silenced plants were still highly ubiquitinated, suggesting involvement of other E3 ligases in ubiquitination. SlCHIP restored the heat tolerance of Arabidopsis chip mutant to the wild type levels. These results indicate that tomato SlCHIP plays a critical role in heat stress responses most likely by targeting degradation of misfolded proteins that are generated during heat stress.

Protecting Information Systems (IS) relies traditionally on security risk analysis methods. Designed for well-perimetrised environments, these methods rely on a systematic identification of threats and vulnerabilities to identify efficient control-centered protection countermeasures. Unfortunately, this does not fit security challenges carried out by the opened and agile organizations provided by the Social, Mobile, big data Analytics, Cloud and Internet of Things (SMACIT) environment. Due to their inherently collaborative and distributed organization, such multi-tenancy systems require the integration of contextual vulnerabilities, depending on the a priori unknown way of using, storing and exchanging data in opened cloud environment. Moreover, as data can be associated to multiple copies, different protection requirements can be set for each of these copies, which may lead the initial data owner lose control on the data protection. To overcome these limits, we propose a Data centered Usage based Protection model relying on an IS description model to set a consistent protection for data assets. Protection means are defined according to both organizational and technical risks. To this end, we propose a GDPR compliant security and extended usage ontology which is used to define usage-control assertions coupling usage rights to security countermeasures so that data assets can be efficiently protected according to both organizational and technical dimensions. Thanks to a Blockchain-based usage control, our Data centered and Usage based Protection architecture also allows tracking the way assets are used so their life-long protection can be checked.; Protecting Information Systems (IS) relies traditionally on security risk analysis methods. Designed for well-perimetrised environments, these methods rely on a systematic identification of threats and vulnerabilities to identify efficient control-centered protection countermeasures. Unfortunately, this does not fit security challenges carried out by the opened and agile organizations provided by the Social, Mobile, big data Analytics, Cloud and Internet of Things (SMACIT) environment. Due to their inherently collaborative and distributed organization, such multi-tenancy systems require the integration of contextual vulnerabilities, depending on the a priori unknown way of using, storing and exchanging data in opened cloud environment. Moreover, as data can be associated to multiple copies, different protection requirements can be set for each of these copies, which may lead the initial data owner lose control on the data protection. To overcome these limits, we propose a Data centered Usage based Protection model relying on an IS description model to set a consistent protection for data assets. Protection means are defined according to both organizational and technical risks. To this end, we propose a GDPR compliant security and extended usage ontology which is used to define usage-control assertions coupling usage rights to security countermeasures so that data assets can be efficiently protected according to both organizational and technical dimensions. Thanks to a Blockchain-based usage control, our Data centered and Usage based Protection architecture also allows tracking the way assets are used so their life-long protection can be checked.

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Additional file 1: Figure S1. Extracted tetraploid wheat (ETW) shows decreased starch content, smaller starch granule, and reduced fertility. (a) Images showing pollen fertility by iodine staining (top panel) and starch structure by scanning electron microscopy (bottom panel). S refers to starch granules. Materials are T. durum (AABB), Ae. Tauschii (DD), natural hexaploid wheat (NHW, AABBDD), ETW (AABB), and resynthesized hexaploid wheat (RHW, AABBDD). Scale bars = 100 μm (top images) and 15 μm (bottom images). (b) Developing seed morphology at 6 days after pollination (DAP) in the same set of lines as in (a). Scale bar = 0.5 cm for all images. (c, d) Total starch content (mg/100 mg) (c) and thousand-kernel weight (grams) (d) of the same set of lines as in (a). Error bars indicate standard deviation of three biological replicates with three asterisk showing a statistical significance level of P

Polyploidy occurs in some animals and all flowering plants, including important crops such as wheat. The consequences of polyploidy in crops remain elusive, partly because their progenitors are unknown. Using two resynthesized wheat allotetraploids Sl Sl AA and AADD with known diploid progenitors, we analyzed mRNA and small RNA transcriptomes in the endosperm, compared transcriptomes between endosperm and root in AADD, and examined chromatin changes in the allotetraploids. In the endosperm, there were more non-additively expressed genes in Sl Sl AA than in AADD. In AADD, non-additively expressed genes were developmentally regulated, and the majority (62-70%) were repressed. The repressed genes in AADD included a group of histone methyltransferase gene homologs, which correlated with reduced histone H3K9me2 levels and activation of various transposable elements in AADD. In Sl Sl AA, there was a tendency for expression dominance of Sl over A homoeologs, but the histone methyltransferase gene homologs were additively expressed, correlating with insignificant changes in histone H3K9me2 levels. Moreover, more 24-nucleotide small inferring RNAs (siRNAs) in the A subgenome were disrupted in AADD than in Sl Sl AA, which were associated with expression changes of siRNA-associated genes. Our results indicate that asymmetrical changes in siRNAs, chromatin modifications, transposons and gene expression coincide with unstable AADD genomes and stable Sl Sl AA genomes, which could help explain the evolutionary trajectories of wheat allotetraploids formed by different progenitors.

With high kinetic energy and excellent penetration performance, metal jets have been widely used in the defence industry. When a thin plate is impacted by a metal jet with a velocity higher than 3 km/s, debris clouds will be generated at both sides of the plates. However, compared with the debris clouds generated by hypervelocity impact of projectiles, debris clouds generated by hypervelocity jets is rarely observed. In this paper, the utility of ultrahigh-speed simultaneous framing and streak photography technology is applied in the experiment of copper jets impact thin aluminum plates at hypervelocity. Debris clouds and front edges of shock waves are clearly observed and recognized after using newly developed technology to effectively restrain excessive exposure caused by intensive self-illumination in the experiment. From framing and streak pictures, the process of jets impact targets is comprehensively and completely recorded and the velocities of the jet and the debris cloud are obtained using the methods of data processing developed in present paper.

We consider the problem of nearly optimal energy efficiency in massive (Multiinput Multi-output) MIMO systems. Considering the correlated channel in practice, we derive the ergodic expression with zero-forcing precoding and analyze the simplified antennas selection method. Aiming at optimizing the energy efficiency, the closed form expressions of the nearly optimal number of transmit antennas and transmit power are given under the circuit consumption model. The joint solution of the number of transmit antennas and transmit power was replaced to only solve transmit power. Based on the expression only related with transmit power, we give an energy efficiency optimization algorithm. The simulation results show that the proposed algorithm can achieve nearly optimal energy efficiency with fast convergence speed.

Seed development in angiosperms requires a 2:1 maternal-to-paternal genome ratio (2m:1p) in the endosperm. When the ratio is disrupted, the seed development is impaired. Rice interploidy crosses result in endosperm failures, but the underlying molecular mechanisms remain unclear. Here, we report that the defective endosperm in rice interploidy crosses was associated with nonadditive expression of small RNAs and protein-coding genes. Interestingly, 24-nt small interfering RNAs were enriched in the 5′ and 3′ flanking sequences of nonadditively expressed genes in the interploidy crosses and were negatively associated with the expression of imprinted genes. Furthermore, some PRC2 family genes and DNA methylation-related genes including OsMET1b and OsCMT3a were upregulated in the 2×4 cross (pollinating a diploid "mother" with a tetraploid "father") but repressed in the reciprocal cross. These different epigenetic effects could lead to precocious or delayed cellularization during endosperm development. Notably, many endosperm-preferred genes, including starch metabolic and storage protein genes during grain filling, were found to be associated with DNA methylation or H3K27me3, which are repressed in both 2×4 and 4×2 crosses. WUSCHEL homeobox2 ( WOX2 ) -like ( WOX2L ), an endosperm-preferred gene, was expressed specifically in the rice endosperm, in contrast to WOX2 expression in the Arabidopsis embryo. Disruption of WOX2L in transgenic rice by CRISPR/Cas9-mediated gene editing blocked starch and protein accumulation, resulting in seed abortion. In addition to gene repression, disrupting epigenetic process in the interploidy crosses also induced expression of stress-responsive genes. Thus, maintaining the 2m:1p genome ratio in the endosperm is essential for normal grain development in rice and other cereal crops.

Genetic imprinting refers to the unequal expression of paternal and maternal alleles of a gene in sexually reproducing organisms, including mammals and flowering plants. Although many imprinted genes have been identified in plants, the functions of these imprinted genes have remained largely uninvestigated. We report genome-wide analysis of gene expression, DNA methylation and small RNAs in the rice endosperm and functional tests of five imprinted genes during seed development using Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated gene9 (CRISPR/Cas9) gene editing technology. In the rice endosperm, we identified 162 maternally expressed genes (MEGs) and 95 paternally expressed genes (PEGs), which were associated with miniature inverted-repeat transposable elements, imprinted differentially methylated loci and some 21-22 small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs). Remarkably, one-third of MEGs and nearly one-half of PEGs were associated with grain yield quantitative trait loci. Most MEGs and some PEGs were expressed specifically in the endosperm. Disruption of two MEGs increased the amount of small starch granules and reduced grain and embryo size, whereas mutation of three PEGs reduced starch content and seed fertility. Our data indicate that both MEGs and PEGs in rice regulate nutrient metabolism and endosperm development, which optimize seed development and offspring fitness to facilitate parental-offspring coadaptation. These imprinted genes and mechanisms could be used to improve the grain yield of rice and other cereal crops.

Hordeum californicum (2n = 2x = 14, HH) is resistant to several wheat diseases and tolerant to lower nitrogen. In this study, a molecular karyotype of H. californicum chromosomes in the Triticum aestivum L. cv. Chinese Spring (CS)-H. californicum amphidiploid (2n = 6x = 56, AABBDDHH) was established. By genomic in situ hybridization (GISH) and multicolor fluorescent in situ hybridization (FISH) using repetitive DNA clones (pTa71, pTa794 and pSc119.2) as probes, the H. californicum chromosomes could be differentiated from each other and from the wheat chromosomes unequivocally. Based on molecular karyotype and marker analyses, 12 wheat-alien chromosome lines, including four disomic addition lines (DAH1, DAH3, DAH5 and DAH6), five telosomic addition lines (MtH7L, MtH1S, MtH1L, DtH6S and DtH6L), one multiple addition line involving H. californicum chromosome H2, one disomic substitution line (DSH4) and one translocation line (TH7S/1BL), were identified from the progenies derived from the crosses of CS-H. californicum amphidiploid with common wheat varieties. A total of 482 EST (expressed sequence tag) or SSR (simple sequence repeat) markers specific for individual H. californicum chromosomes were identified, and 47, 50, 45, 49, 21, 51 and 40 markers were assigned to chromosomes H1, H2, H3, H4, H5, H6 and H7, respectively. According to the chromosome allocation of these markers, chromosomes H2, H3, H4, H5, and H7 of H. californicum have relationship with wheat homoeologous groups 5, 2, 6, 3, and 1, and hence could be designated as 5H(c), 2H(c), 6H(c), 3H(c) and 1H(c), respectively. The chromosomes H1 and H6 were designated as 7H(c) and 4H(c), respectively, by referring to SSR markers located on rye chromosomes.