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Abstract The color of red-skinned pear (Pyrus spp.) is primarily attributed to accumulation of anthocyanins, which provide nutritional benefits for human health and are closely associated with the commercial value of fruits. Here, we reported the functional characterization of a R2R3-MYB repressor PyMYB107, which forms an ‘activator-repressor’ loop to control anthocyanin accumulation in the red-skinned pear. PyMYB107 overexpression inhibited anthocyanin biosynthesis in both pear calli and fruits, while virus-induced gene silencing of PyMYB107 increased anthocyanin accumulation in pear fruits. Furthermore, ectopic expression of PyMYB107 decreased anthocyanin accumulation in tomato, strawberry and tobacco. PyMYB107 can competitively bind to PybHLH3 with PyMYB10/MYB114, thereby suppressing the transcriptional activation of key anthocyanin biosynthesis genes, PyANS and PyUFGT. Site-directed mutagenesis showed that mutations within the R3 domain and EAR motif of PyMYB107 eliminated its repressive activity. Additionally, PyMYB107 exhibited a comparable expression pattern to PyMYB10/MYB114 and was transcriptionally activated by them. Our finding advanced comprehension of the repression mechanism underlying anthocyanin accumulation, providing valuable molecular insights into improving quality of pear fruits.

Abstract The mechanisms underlying the organization and evolution of the telencephalic pallium are not yet clear.. To address this issue, we first performed comparative analysis of genes critical for the development of the pallium (Emx1/2 and Pax6) and subpallium (Dlx2 and Nkx1/2) among 500 vertebrate species. We found that these genes have no obvious variations in chromosomal duplication/loss, gene locus synteny or Darwinian selection. However, there is an additional fragment of approximately 20 amino acids in mammalian Emx1 and a poly-(Ala)6–7 in Emx2. Lentiviruses expressing mouse or chick Emx2 (m-Emx2 or c-Emx2 Lv) were injected into the ventricle of the chick telencephalon at embryonic Day 3 (E3), and the embryos were allowed to develop to E12–14 or to posthatchling. After transfection with m-Emx2 Lv, the cells expressing Reelin, Vimentin or GABA increased, and neurogenesis of calbindin cells changed towards the mammalian inside-out pattern in the dorsal pallium and mesopallium. In addition, a behavior test for posthatched chicks indicated that the passive avoidance ratio increased significantly. The study suggests that the acquisition of an additional fragment in mammalian Emx2 is associated with the organization and evolution of the mammalian pallium.

Abstract Nickel-rich layered oxide cathodes promise ultrahigh energy density but is plagued by the mechanical failure of the secondary particle upon (de)lithiation. Existing approaches for alleviating the structural degradation could retard pulverization, yet fail to tune the stress distribution and root out the formation of cracks. Herein, we report a unique strategy to uniformize the stress distribution in secondary particle via Kirkendall effect to stabilize the core region during electrochemical cycling. Exotic metal/metalloid oxides (such as Al2O3 or SiO2) is introduced as the heterogeneous nucleation seeds for the preferential growth of the precursor. The calcination treatment afterwards generates a dopant-rich interior structure with central Kirkendall void, due to the different diffusivity between the exotic element and nickel atom. The resulting cathode material exhibits superior structural and electrochemical reversibility, thus contributing to a high specific energy density (based on cathode) of 660 Wh kg−1 after 500 cycles with a retention rate of 86%. This study suggests that uniformizing stress distribution represents a promising pathway to tackle the structural instability facing nickel-rich layered oxide cathodes.

Abstract Fiber-reinforced polymer (FRP) composites have gained widespread applications in many engineering fields, making it imperative to study long-term performance under service conditions. Due to their heterogeneity and multifield coupling conditions, the long-term performance of FRP composites has become a complex scientific problem that involves multiscale and multidisciplinary aspects. With advancements in nanotechnology and computational power, researchers have increasingly conducted studies on the deterioration mechanisms and durability of FRP composites using top-down experiments and bottom-up multiscale simulations. Here, we review micro- and nano-mechanics in relation to the durability of FRP composites, including progress in the use of atomic and molecular simulations. We elucidate the role of multiscale methods, particularly molecular dynamics simulations, in the study of FRP composites and outline its prospects, to illustrate how micro- and nano-mechanics contribute to research on the durability of FRP composites.

Fruit quality is dependent on various factors including flavour, texture and colour. These factors are determined by the ripening process, either climacteric or non-climacteric. In grape berry, which is non-climacteric, the process is signalled by a complex set of hormone changes. Abscisic acid (ABA) is one of the key hormones involved in ripening, while sugar availability also plays a significant role in certain ripening aspects such as anthocyanin production. To understand the relative influence of hormone and sugar signalling in situ can prove problematic due to the physiological and environmental (abiotic and biotic) factors at play in vineyards. Here we report on the use of in vitro detached berry culture to investigate the comparative significance of ABA and sugar in the regulation of Pinot noir berry anthocyanin production under controlled conditions. Using a factorial experimental design, pre-véraison berries were cultured on media with various concentrations of sucrose and ABA. After 15 days of in vitro culture, the berries were analysed for changes in metabolites, hormones and gene expression. Results illustrated a stimulatory effect of sucrose and ABA on enhancing berry colour and a corresponding increase in anthocyanins. Increased ABA concentration was able to boost anthocyanin production in berries when sucrose supply was low. The sucrose and ABA effects on berry anthocyanins were primarily manifested through the up-regulation of transcription factors and other genes in the phenylpropanoid pathway, while in other parts of the pathway a down-regulation of key proanthocyanindin transcription factors and genes corresponded to sharp reduction in berry proanthocyanidins, irrespective of sucrose supply. Similarly, increased ABA was correlated with a significant reduction in berry malic acid and associated regulatory genes. These findings suggest a predominance of berry ABA over berry sugar in coordinating the physiological and genetic regulation of anthocyanins and proanthocyanins in Pinot noir grape berries.

Tea grey blight disease is one of the most destructive diseases that infects tea and is caused by the pathogen Pestalotiopsis theae (Sawada) Steyaert. L-theanine is a unique non-protein amino acid of the tea plant. Different concentrations of L-theanine exhibit significant inhibitory effects on the growth and sporulation ability of the pathogen causing tea grey blight disease. To understand the effect mechanism of L-theanine on P. theae, transcriptome profiling was performed on the pathogenic mycelium treated with three different concentrations of L-theanine: no L-theanine treatment (TH0), 20 mg/mL theanine treatment (TH2), and 40 mg/mL theanine treatment (TH4). The colony growths were significantly lower in the treatment with L-theanine than those without L-theanine. The strain cultured with a high concentration of L-theanine produced no spores or only a few spores. In total, 2344, 3263, and 1158 differentially expressed genes (DEGs) were detected by RNA-sequencing in the three comparisons, Th2 vs. Th0, Th4 vs. Th0, and Th4 vs. Th2, respectively. All DEGs were categorized into 24 distinct clusters. According to GO analysis, low concentrations of L-theanine primarily affected molecular functions, while high concentrations of L-theanine predominantly affected biological processes including external encapsulating structure organization, cell wall organization or biogenesis, and cellular amino acid metabolic process. Based on KEGG, the DEGs of Th2 vs. Th0 were primarily involved in pentose and glucuronate interconversions, histidine metabolism, and tryptophan metabolism. The DEGs of Th4 vs. Th0 were mainly involved in starch and sucrose metabolism, amino sugar, and nucleotide sugar metabolism. This study indicated that L-theanine has a significant impact on the growth and sporulation of the pathogen of tea grey blight disease and mainly affects amino acid metabolism, carbohydrate metabolism, and cellular structure-related biosynthesis processes of pathogenic fungi. This work provides insights into the direct control effect of L-theanine on pathogenic growth and also reveals the molecular mechanisms of inhibition of L-theanine to P. theae.

Abstract A stable { $$\stackrel{\mathrm{-}}{1}{\text{10}}$$ 1 - 10 } single component sharp texture was obtained during ambient temperature tube High-Pressure Shearing (t-HPS) of 99.999% purity aluminum. It is shown that the grain size and the grain aspect ratio saturate at ~ 8 μm and ~ 1.6, respectively, at an equivalent strain of ~ 30 and the high-angle grain boundary fraction continues to decrease after this saturation even to equivalent strains exceeding ~ 200. The { $$\stackrel{\mathrm{-}}{1}{\text{10}}$$ 1 - 10 } texture emerges at an equivalent strain of ~ 6 to 9 with the completion of recrystallization and develops gradually as a sole component sharp texture with increasing intensity upon further processing. This component is a stable orientation in t-HPS processing although it was not previously observed experimentally as a shear texture. Thus, t-HPS processing provides a new and effective experimental tool for simple shear testing that is distinctly different from earlier shear strain methods such as torsional processing.

Abstract Background Structural variants (SVs) play important roles in adaptation evolution and species diversification. Especially, in plants, many phenotypes of response to the environment were found to be associated with SVs. Despite the prevalence and significance of SVs, long insertions remain poorly detected and studied in all but model species. Results We used whole-genome resequencing of paired reads from 80 Asian butternuts to detect long insertions and further analyse their characteristics and potential functional effects. By combining of mapping-based and de novo assembly-based methods, we obtained a multiple related species pangenome representing higher taxonomic groups. We obtained 89,312 distinct contigs totaling 147,773,999 base pair (bp) of new sequences, of which 347 were putative long insertions placed in the reference genome. Most of the putative long insertions appeared in multiple species; in contrast, only 62 putative long insertions appeared in one species, which may be involved in the response to the environment. 65 putative long insertions fell into 61 distinct protein-coding genes involved in plant development, and 105 putative long insertions fell into upstream of 106 distinct protein-coding genes involved in cellular respiration. 3,367 genes were annotated in 2,606 contigs. We propose PLAINS ( https://github.com/CMB-BNU/PLAINS.git ), a streamlined, comprehensive pipeline for the prediction and analysis of long insertions using whole-genome resequencing. Conclusions Our study lays down an important foundation for further whole-genome long insertion studies, allowing the investigation of their effects by experiments.

CDK4/6 inhibitor resistance is common in breast cancer. Here, the authors show that p16 overexpression may be linked to reduced efficacy of CDK4/6 inhibition, and show that the combination with PI3K inhibitors may increase anti-tumour effects.

Abstract The energy density of commercial lithium (Li) ion batteries with graphite anode is reaching the limit. It is believed that directly utilizing Li metal as anode without a host could enhance the battery’s energy density to the maximum extent. However, the poor reversibility and infinite volume change of Li metal hinder the realistic implementation of Li metal in battery community. Herein, a commercially viable hybrid Li-ion/metal battery is realized by a coordinated strategy of symbiotic anode and prelithiated cathode. To be specific, a scalable template-removal method is developed to fabricate the porous graphite layer (PGL), which acts as a symbiotic host for Li ion intercalation and subsequent Li metal deposition due to the enhanced lithiophilicity and sufficient ion-conducting pathways. A continuous dissolution-deintercalation mechanism during delithiation process further ensures the elimination of dead Li. As a result, when the excess plating Li reaches 30%, the PGL could deliver an ultrahigh average Coulombic efficiency of 99.5% for 180 cycles with a capacity of 2.48 mAh cm−2 in traditional carbonate electrolyte. Meanwhile, an air-stable recrystallized lithium oxalate with high specific capacity (514.3 mAh g−1) and moderate operating potential (4.7–5.0 V) is introduced as a sacrificial cathode to compensate the initial loss and provide Li source for subsequent cycles. Based on the prelithiated cathode and initial Li-free symbiotic anode, under a practical-level 3 mAh capacity, the assembled hybrid Li-ion/metal full cell with a P/N ratio (capacity ratio of LiNi0.8Co0.1Mn0.1O2 to graphite) of 1.3 exhibits significantly improved capacity retention after 300 cycles, indicating its great potential for high-energy-density Li batteries.

Summary: Potatoes consist of flavonoids that provide health benefits for human consumers. To learn more about how potato tuber flavonoid accumulation and flesh pigmentation are controlled, we analyzed the transcriptomic and metabolomic profile of potato tubers from three colored potato clones at three developmental phases using an integrated approach. From the 72 flavonoids identified in pigmented flesh, differential abundance was noted for anthocyanins, flavonols, and flavones. Weighted gene co-expression network analysis further allowed modules and candidate genes that positively or negatively regulate flavonoid biosynthesis to be identified. Furthermore, an R2R3-MYB repressor StMYB3 and an R3-MYB repressor StMYBATV involved in the modulation of anthocyanin biosynthesis during tuber development were identified. Both StMYB3 and StMYBATV could interact with the cofactor StbHLH1 and repress anthocyanin biosynthesis. Our results indicate a feedback regulatory mechanism of a coordinated MYB activator-repressor network on fine-tuning of potato tuber pigmentation during tuber development.

How resistance to different classes of AKT inhibitors can emerge is unclear. Here, the authors show that resistance to allosteric inhibitors is mainly due to mutation of AKT1 while the ATP competitive resistance is driven by activation of PIM kinases in prostate cancer models.

The genetic link between apple red flesh (RF) coloration and the internal flesh browning disorder (FBD) is a major challenge when breeding high fruit quality RF apple cultivars. A genome-wide association study (GWAS) was conducted in a population of about 900 red-leaved seedlings to identify genomic regions and putative candidate genes using whole genome sequencing of the pools of extreme phenotypes (XP) for the RF colour coverage (using the weighted cortex index (WCI)) and FBD. This study identified novel genomic regions contributing to WCI and FBD variation in the red-leaved seedlings. The FBD-associated regions were enriched for genes regulating senescence, heat shock proteins, cytochrome P450, ascorbate metabolism and pectin methyl esterases. Although there were no significant regions in common for WCI and FBD, there were several genes (e.g. MYB85, MYB66, ethylene insensitive 3, DNAJ heat shock protein, WRKY7, and NAC42) enriched commonly between the genomic regions associated with these traits, potentially underpinning the genetic connection between WCI and FBD. Some of the differentially expressed genes between the R6:MdMYB10 and white-fleshed ‘control’ apples resided within the GWAS hotspot for WCI (e.g. chalcone synthase, UDP-Glycosyl transferase) and FBD (e.g. Rho GTPase activating protein, lipoxygenase 1, phytoene synthase) – validating the XP-GWAS findings. Paralogs of several genes resided in the trait-associated genomic regions, suggesting that whole genome duplication plays an important role in the regulation of these traits. Adverse genetic correlations between WCI and sensory traits were observed, and strategies to develop FBD-free high fruit quality RF cultivars are discussed.

Abstract Security risks of flammability and explosion represent major problems with the use of conventional lithium rechargeable batteries using a liquid electrolyte. The application of solid‐state electrolytes could effectively help to avoid these safety concerns. However, integrating the solid‐state electrolytes into the all‐solid‐state lithium batteries is still a huge challenge mainly due to the high interfacial resistance present in the entire battery, especially at the interface between the cathode and the solid‐state electrolyte pellet and the interfaces inside the cathode. Herein, recent progress made from investigations of cathode/solid‐state electrolyte interfacial behaviors including the contact problem, the interlayer diffusion issue, the space‐charge layer effect, and electrochemical compatibility is presented according to the classification of oxide‐, sulfide‐, and polymer‐based solid‐state electrolytes. We also propose strategies for the construction of ideal next‐generation cathode/solid‐state electrolyte interfaces with high room‐temperature ionic conductivity, stable interfacial contact during long cycling, free formation of the space‐charge region, and good compatibility with high‐voltage cathodes.

Summary: Alternative splicing is crucial for a wide range of biological processes. However, limited by the availability of reference genomes, genome-wide patterns of alternative splicing remain unknown in most nonmodel organisms. We present an attention-based convolutional neural network model, DeepASmRNA, for predicting alternative splicing events using only transcriptomic data. DeepASmRNA consists of two parts: identification of alternatively spliced transcripts and classification of alternative splicing events, which outperformed the state-of-the-art method, AStrap, and other deep learning models. Then, we utilize transfer learning to increase the performance in species with limited training data and use an interpretation method to decipher splicing codes. Finally, applying Amborella, DeepASmRNA can identify more AS events than AStrap while maintaining the same level of precision, suggesting that DeepASmRNA has superior sensitivity to identify alternative splicing events. In summary, DeepASmRNA is scalable and interpretable for detecting genome-wide patterns of alternative splicing in species without a reference genome.

Abstract A key challenge for solid-state-batteries development is to design electrode-electrolyte interfaces that combine (electro)chemical and mechanical stability with facile Li-ion transport. However, while the solid-electrolyte/electrode interfacial area should be maximized to facilitate the transport of high electrical currents on the one hand, on the other hand, this area should be minimized to reduce the parasitic interfacial reactions and promote the overall cell stability. To improve these aspects simultaneously, we report the use of an interfacial inorganic coating and the study of its impact on the local Li-ion transport over the grain boundaries. Via exchange-NMR measurements, we quantify the equilibrium between the various phases present at the interface between an S-based positive electrode and an inorganic solid-electrolyte. We also demonstrate the beneficial effect of the LiI coating on the all-solid-state cell performances, which leads to efficient sulfur activation and prevention of solid-electrolyte decomposition. Finally, we report 200 cycles with a stable capacity of around 600 mAh g−1 at 0.264 mA cm−2 for a full lab-scale cell comprising of LiI-coated Li2S-based cathode, Li-In alloy anode and Li6PS5Cl solid electrolyte.

Abstract Background Alternative splicing (AS) is an important mechanism of posttranscriptional modification and dynamically regulates multiple physiological processes in plants, including fruit ripening. However, little is known about alternative splicing during fruit development in fleshy fruits. Results We studied the alternative splicing at the immature and ripe stages during fruit development in cucumber, melon, papaya and peach. We found that 14.96–17.48% of multiexon genes exhibited alternative splicing. Intron retention was not always the most frequent event, indicating that the alternative splicing pattern during different developmental process differs. Alternative splicing was significantly more prevalent at the ripe stage than at the immature stage in cucumber and melon, while the opposite trend was shown in papaya and peach, implying that developmental stages adopt different alternative splicing strategies for their specific functions. Some genes involved in fruit ripening underwent stage-specific alternative splicing, indicating that alternative splicing regulates fruits ripening. Conserved alternative splicing events did not appear to be stage-specific. Clustering fruit developmental stages across the four species based on alternative splicing profiles resulted in species-specific clustering, suggesting that diversification of alternative splicing contributes to lineage-specific evolution in fleshy fruits. Conclusions We obtained high quality transcriptomes and alternative splicing events during fruit development across the four species. Dynamics and nonconserved alternative splicing were discovered. The candidate stage-specific AS genes involved in fruit ripening will provide valuable insight into the roles of alternative splicing during the developmental processes of fleshy fruits.

Due to advances in the industrial development of light-emitting diodes (LEDs), much research has been conducted in recent years to get a better understanding of how plants respond to these light sources. This study investigated the effects of different LED-based light regimes on strawberry plant development and performance. The photosynthetic pigment content, biochemical constituents, and growth characteristics of strawberry plants were investigated using a combination of different light intensities (150, 200, and 250 μmol m−2 s−1), qualities (red, green, and blue LEDs), and photoperiods (14/10 h, 16/8 h, and 12/12 h light/dark cycles) compared to the same treatment with white fluorescent light. Plant height, root length, shoot fresh and dry weight, chlorophyll a, total chlorophyll/carotenoid content, and most plant yield parameters were highest when illuminated with LM7 [intensity (250 μmol m−2 s−1) + quality (70% red/30% blue LED light combination) + photoperiod (16/8 h light/dark cycles)]. The best results for the effective quantum yield of PSII photochemistry Y(II), photochemical quenching coefficient (qP), and electron transport ratio (ETR) were obtained with LM8 illumination [intensity (250 μmol m−2 s−1) + quality (50% red/20% green/30% blue LED light combination) + photoperiod (12 h/12 h light/dark cycles)]. We conclude that strawberry plants require prolonged and high light intensities with a high red-light component for maximum performance and biomass production.

Abstract Global navigation satellite systems (GNSSs) are increasingly used for multi‐satellite missions in space service volume (SSV). However, the performance of GNSS‐based autonomous orbit determination (AOD) for SSV users is severely constrained by limited measurement accuracy and signal availability. Relative measurement and orbital dynamic models can be used to improve the AOD performance when the estimator is prone to divergence due to the cross‐correlation of the distributed formation network. In this paper, a sequential game‐theoretic (SGT) optimization algorithm is proposed to deal with cross‐correlation issues when fusing the GNSS and relative measurements for dynamic AOD in the SSV field. A four geostationary Earth orbit satellite mission is simulated as the case study for the AOD performance analysis. The conventional sequential covariance intersection (SCI) is also presented for comparison purposes. The simulation results show that with the combination of GNSS and relative measurements with 10 m and 0.1 m precision, the SGT‐based AOD can achieve about 1.9 m three‐dimensional positioning accuracy, which is 80% better than in the GNSS‐only case. It is also demonstrated that the SGT‐based AOD is superior to the SCI‐based AOD by 50% in the fusion of GNSS and relative measurements in the range of 1–10 m and with 0.1–0.001 m accuracy.

Abstract Background With the rapid development of accurate sequencing and assembly technologies, an increasing number of high-quality chromosome-level and haplotype-resolved assemblies of genomic sequences have been derived, from which there will be great opportunities for computational pangenomics. Although genome graphs are among the most useful models for pangenome representation, their structural complexity makes it difficult to present genome information intuitively, such as the linear reference genome. Thus, efficiently and accurately analyzing the genome graph spatial structure and coordinating the information remains a substantial challenge. Results We developed a new method, a colored superbubble (cSupB), that can overcome the complexity of graphs and organize a set of species- or population-specific haplotype sequences of interest. Based on this model, we propose a tri-tuple coordinate system that combines an offset value, topological structure and sample information. Additionally, cSupB provides a novel method that utilizes complete topological information and efficiently detects small indels (

AbstractPopulation-specific, positive selection promotes the diversity of populations and drives local adaptations in the population. However, little is known about population-specific, recent positive selection in the populations of cultivated cucumber (Cucumis sativus

In recent years, lots of efforts have been applied to improve the initial Coulombic efficiency (ICE) of lithium-ion batteries (LIBs), among which prelithiation is considered to be one of the most promising schemes. Here we report a modified LixSi with high lithium reserves and great environmental adaptability as the prelithiation reagent, which can make up for the capacity loss of the negative electrode in the first cycle. Through the chemical reaction between aluminum isopropoxide and LixSi, a protective layer consisting of LixAlySiOz/Li2O is formed on the surface of LixSi particles. This synthesized material provides a new idea for the actual industrial production of prelithiation.

Abstract Background Alternative splicing (AS) plays a critical regulatory role in modulating transcriptome and proteome diversity. In particular, it increases the functional diversity of proteins. Recent genome-wide analysis of AS using RNA-Seq has revealed that AS is highly pervasive in plants. Furthermore, it has been suggested that most AS events are subject to tissue-specific regulation. Description To reveal the functional characteristics induced by AS and tissue-specific splicing events, a database for exploring these characteristics is needed, especially in plants. To address these goals, we constructed a database of annotated transcripts generated by alternative splicing in cucumbers (CuAS: http://cmb.bnu.edu.cn/alt_iso/index.php ) that integrates genomic annotations, isoform-level functions, isoform-level features, and tissue-specific AS events among multiple tissues. CuAS supports a retrieval system that identifies unique IDs (gene ID, isoform ID, UniProt ID, and gene name), chromosomal positions, and gene families, and a browser for visualization of each gene. Conclusion We believe that CuAS could be helpful for revealing the novel functional characteristics induced by AS and tissue-specific AS events in cucumbers. CuAS is freely available at http://cmb.bnu.edu.cn/alt_iso/index.php .

The use of avidin or streptavidin in the purification of biotinylated proteins has been highly restricted due to the harsh and denaturing elution conditions. Here, we use biotinylated bovine serum albumin as a working model to demonstrate a simple and rapid method for biotin-tagged protein purification under non-denaturing conditions. The biotinylated bovine serum albumin is specifically bound to the anti-biotin antibody agarose beads and competitively eluted with free biotin under near-neutral conditions. The optimized elution conditions include using 4 mg/ml biotin (pH 8.5) as the elution buffer and allowing the buffer to incubate with agarose beads for 30 min prior to elution. The elution recovery rate is over 85% without apparent protein denaturation. The method is applicable for both immunoprecipitation and column chromatography.

Wufanshu (Vaccinium bracteatum Thunb.), which is a wild member of the genus Vaccinium, accumulates high concentration of anthocyanin in its berries. In this study, the accumulated anthocyanins and their derivatives in Wufanshu berries were identified through UHPLC–MS/MS analysis. Candidate anthocyanin biosynthetic genes were identified from the transcriptome of Wufanshu berries. qRT-PCR analyses showed that the expression of anthocyanin structural genes correlated with anthocyanin accumulation in berries. The R2R3-MYB, VbMYBA, which is a homolog of anthocyanin promoting R2R3-MYBs from other Vaccinium species, was also identified. Transient expression of VbMYBA in Nicotiana tabacum leaves confirmed its role as an anthocyanin regulator, and produced a higher anthocyanin concentration when compared with blueberry VcMYBA expression. Dual-luciferase assays further showed that VbMYBA can activate the DFR and UFGT promoters from other Vaccinium species. VbMYBA has an additional 23 aa at the N terminus compared with blueberry VcMYBA, but this was shown not to affect the ability to regulate anthocyanins. Taken together, our results provide important information on the molecular mechanisms responsible for the high anthocyanin content in Wufanshu berries.

Plum is one of the most important stone fruits in the world and anthocyanin-rich plums are increasingly popular due to their health-promoting potential. In this study, we investigated the mechanisms of anthocyanin accumulation in the flesh of the red-fleshed mutant of the yellow-fleshed plum ‘Sanyueli’. RNA-Seq and qRT-PCR showed that anthocyanin biosynthetic genes and the transcription factor PsMYB10.2 were upregulated in the flesh of the mutant. Functional testing in tobacco leaves indicated that PsMYB10.2 was an anthocyanin pathway activator and can activate the promoter of the anthocyanin biosynthetic genes PsUFGT and PsGST. The role of PsMYB10.2 in anthocyanin accumulation in the flesh of plum was further confirmed by virus-induced gene silencing. These results provide information for further elucidating the underlying mechanisms of anthocyanin accumulation in the flesh of plum and for the breeding of new red-fleshed plum cultivars.

Anthocyanins: Coloring Kiwifruit The genetic processes that determine the colors in purple kiwifruit have been revealed by researchers in New Zealand. Anthocyanin pigments are not only essential for plant growth and development, but also provide color to make fruit attractive to pollinators and indicate ripeness for the food industry. Andrew Allan and co-workers at the University of Auckland and The New Zealand Institute for Plant and Food Research Limited examined several different kiwifruit species, and found that their color was determined by the ratio of red cyanidin-based to blue delphinidin-based anthocyanins. The team identified four biosynthetic genes that are crucial for accumulating anthocyanins, and showed that two of those genes control the red-to-blue pigment ratio. This new understanding of the anthocyanin profile could allow metabolic engineering of novel fruit colors, possibly with greater health benefits for humans.

Red coloration contributes to fruit quality and is determined by anthocyanin content in peach (Prunus persica). Our previous study illustrated that anthocyanin accumulation is strongly regulated by light, and the effect of induction differs according to light quality. Here we showed that both ultraviolet-A (UVA) and ultraviolet-B (UVB) irradiation promoted anthocyanin biosynthesis in “Hujingmilu” peach fruit, and a combination of UVA and UVB had additional effects. The expression of anthocyanin biosynthesis and light signaling related genes, including transcription factor genes and light signaling elements, were induced following UV irradiation as early as 6 h post-treatment, earlier than apparent change in coloration which occurred at 72 h. To investigate the molecular mechanisms for UVA- and UVB-induced anthocyanin accumulation, the genes encoding ELONGATED HYPOCOTYL 5 (HY5), CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), Cryptochrome (CRY), and UV RESISTANCE LOCUS 8 (UVR8) in peach were isolated and characterized through functional complementation in corresponding Arabidopsis (Arabidopsis thaliana) mutants. PpHY5 and PpCOP1.1 restored hypocotyl length and anthocyanin content in Arabidopsis mutants under white light; while PpCRY1 and PpUVR8.1 restored AtHY5 expression in Arabidopsis mutants in response to UV irradiation. Arabidopsis PpHY5/hy5 transgenic lines accumulated higher amounts of anthocyanin under UV supplementation (compared with weak white light only), especially when UVA and UVB were applied together. These data indicated that PpHY5, acting as AtHY5 counterpart, was a vital regulator in UVA and UVB signaling pathway. In peach, the expression of PpHY5 was up-regulated by UVA and UVB, and PpHY5 positively regulated both its own transcription by interacting with an E-box in its own promoter, and the transcription of the downstream anthocyanin biosynthetic genes chalcone synthase 1 (PpCHS1), chalcone synthase 2 (PpCHS2), and dihydroflavonol 4-reductase (PpDFR1) as well as the transcription factor gene PpMYB10.1. In summary, functional evidence supports the role of PpHY5 in UVA and UVB light transduction pathway controlling anthocyanin biosynthesis. In peach this is via up-regulation of expression of genes encoding biosynthetic enzymes, as well as the transcription factor PpMYB10.1 and PpHY5 itself.

In recent years, much effort has been devoted to understanding the response of plants to various light sources, largely due to advances in industry light-emitting diodes (LEDs). In this study, the effect of different light modes on rocket (Eruca sativa. Mill.) photosynthetic performance and other physiological traits was evaluated using an orthogonal design based on a combination between light intensity, quality, and photoperiod factors. Some morphological and biochemical parameters and photosynthetic efficiency of the plants were analyzed. Plants grew in a closed chamber where three light intensities (160, 190, and 220 μmol m-2 s-1) provided by LEDs with a combination of different ratios of red, green, and blue (R:G:B- 7:0:3, 3:0:7, and 5:2:3) and three different photoperiods (light/dark -10/14 h, 12/12 h, and 14/10 h) were used and compared with white fluorescent light (control). This experimental setup allowed us to study the effect of 9 light modes (LM) compared to white light. The analyzes performed showed that the highest levels of chlorophyll a, chlorophyll b, and carotenoids occurred under LM4, LM3, and LM1, respectively. Chlorophyll a fluorescence measurement showed that the best effective quantum yield of PSII photochemistry Y(II), non-photochemical quenching (NPQ), photochemical quenching coefficient (qP), and electron transport ratio (ETR) were obtained under LM2. The data showed that the application of R7:G0:B3 light mode with a shorter photoperiod than 14/10 h (light/dark), regardless of the light intensity used, resulted in a significant increase in growth as well as higher photosynthetic capacity of rocket plants. Since, a clear correlation between the studied traits under the applied light modes was not found, more features should be studied in future experiments.

Sodium–sulfur batteries operating at a high temperature between 300 and 350°C have been used commercially, but the safety issue hinders their wider adoption. Here the authors report a “cocktail optimized” electrolyte system that enables higher electrochemical performance and room-temperature operation.

Abstract Background Temperature is a major determinant of spontaneous mutation, but the precise mode, and the underlying mechanisms, of the temperature influences remain less clear. Here we used a mutation accumulation approach combined with whole-genome sequencing to investigate the temperature dependence of spontaneous mutation in an Escherichia coli strain. Experiments were performed under aerobic conditions at 25, 28 and 37 °C, three temperatures that were non-stressful for the bacterium but caused significantly different bacterial growth rates. Results Mutation rate did not differ between 25 and 28 °C, but was higher at 37 °C. Detailed analyses of the molecular spectrum of mutations were performed; and a particularly interesting finding is that higher temperature led to a bias of mutation to coding, relative to noncoding, DNA. Furthermore, the temperature response of mutation rate was extremely similar to that of metabolic rate, consistent with an idea that metabolic rate predicts mutation rate. Conclusions Temperature affects mutation rate and the types of mutation supply, both being crucial for the opportunity of natural selection. Our results help understand how temperature drives evolutionary speed of organisms and thus the global patterns of biodiversity. This study also lend support to the metabolic theory of ecology for linking metabolic rate and molecular evolution rate.

Abstract Background Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) ‘Hongyang’ draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. Results A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within ‘Hongyang’ The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned ‘Hort16A’ cDNAs and comparing with the predicted protein models for Red5 and both the original ‘Hongyang’ assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised ‘Hongyang’ annotation, respectively, compared with 90.9% to the Red5 models. Conclusions Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis.

Abstract Background Alternative splicing (AS) is an important post-transcriptional process. It has been suggested that most AS events are subject to tissue-specific regulation. However, the global dynamics of AS in different tissues are poorly explored. Results To analyse global changes in AS in multiple tissues, we identified the AS events and constructed a comprehensive catalogue of AS events within each tissue based on the genome-wide RNA-seq reads from ten tissues in cucumber. First, we found that 58% of the multi-exon genes underwent AS. We further obtained 565 genes with significantly more AS events compared with random genes. These genes were found significant enrichment in biological processes related to the regulation of actin filament length. Second, significantly different AS event profiles among ten tissues were found. The tissues with the same origin of development are more likely to have a relatively similar AS profile. Moreover, 7370 genes showed tissue-specific AS events and were highly enriched in biological processes related to the positive regulation of cellular component organization. Root-specificity AS genes were related to the cellular response to DNA damage stimulus. Third, the genes with different intron retention (IR) patterns among the ten tissues showed significant difference in GC percentages of the retained intron, and the number of exons and FPKM of the major transcripts. Conclusions Our study provided a comprehensive view of AS in multiple tissues. We revealed novel insights into the patterns of AS in multiple tissues and the tissue-specific AS in cucumber.

Abstract Background Because phylogenetic inference is an important basis for answering many evolutionary problems, a large number of algorithms have been developed. Some of these algorithms have been improved by integrating gene evolution models with the expectation of accommodating the hierarchy of evolutionary processes. To the best of our knowledge, however, there still is no single unifying model or algorithm that can take all evolutionary processes into account through a stepwise or simultaneous method. Results On the basis of three existing phylogenetic inference algorithms, we built an integrated pipeline for inferring the evolutionary history of a given gene family; this pipeline can model gene sequence evolution, gene duplication-loss, gene transfer and multispecies coalescent processes. As a case study, we applied this pipeline to the STIMATE (TMEM110) gene family, which has recently been reported to play an important role in store-operated Ca2+ entry (SOCE) mediated by ORAI and STIM proteins. We inferred their phylogenetic trees in 69 sequenced chordate genomes. Conclusions By integrating three tree reconstruction algorithms with diverse evolutionary models, a pipeline for inferring the evolutionary history of a gene family was developed, and its application was demonstrated.

The Hippo tumor suppressor pathway is essential for development and tissue growth control. Here the authors employ a multi-disciplinary approach to characterize the interactions of the three Hippo kinases with the signaling adaptor MOB1 and show how they differently affect development, tissue growth and tumor suppression.

Abstract Kerogens are extracted from deep shales to study pyrolysis of deep shale samples. The 2D molecular models of kerogens are obtained by a series of physical and chemical experiments by which the macromolecular models of kerogens are constructed. Then, the reasonable 3D macromolecular models are established by molecular mechanics and global energy minimization. The effects of temperature and heating rate on the chemical kinetics of kerogen pyrolysis are studied using reactive force field (ReaxFF). The hybrid molecular dynamics/force‐biased Monte Carlo (MD/fbMC) approach is used to simulate the pyrolytic process at the experimental temperature, which is lower than the conventional one. The gaseous products and residues obtained by the simulations agree with the experimental results, which means a reliable simulation method for pyrolysis at experimental temperature is provided. This study constructs the rational macromolecular models of kerogen by experiments, and proposes the mechanisms of typical reactions of kerogen pyrolysis, which may help in understanding the formation of shale oil and gas.

Background & aimsBreast regression protein 39 (BRP39) (Chi3L1) and its human homolog YKL-40, is an established biomarker of liver fibrosis in nonalcoholic steatohepatitis (NASH) patients, but its role in NASH pathogenesis remains unclear. We recently identified Chi3L1 as one of the top up-regulated genes in mice with inducible gain-of-function NOD-like receptor protein 3 (NLRP3) activation that mimics several liver features of NASH. This study aimed to investigate the effects of BRP39 deficiency on NLRP3-induced liver inflammation using tamoxifen-inducible Nlrp3 knockin mice sufficient (Nlrp3A350V CRT) and deficient for BRP39 (Nlrp3A350V/BRP-/- CRT).MethodsUsing Nlrp3A350V CRT mice and Nlrp3A350V BRP-/- CRT, we investigated the consequences of BRP39 deficiency influencing NLRP3-induced liver inflammation.ResultsOur results showed that BRP39 deficiency in NLRP3-induced inflammation improved body weight and liver weight. Moreover, liver inflammation, fibrosis, and hepatic stellate cell activation were reduced significantly, corresponding to significantly decreased Ly6C+ infiltrating macrophages, CD68+ osteopontin-positive hepatic lipid-associated macrophages, and activated Lymphocyte antigen 6 complex locus G6D positive (Ly6G+) and citrullinated histone H3 postivie (H3Cit+) neutrophil accumulation in the liver. Further investigation showed that circulatory neutrophils from NLRP3-induced BRP39-deficient mice have impaired chemotaxis and migration ability, and this was confirmed by RNA bulk sequencing showing reduced immune activation, migration, and signaling responses in neutrophils.ConclusionsThese data showcase the importance of BRP39 in regulating the NLRP3 inflammasome during liver inflammation and fibrotic NASH by altering cellular activation, recruitment, and infiltration during disease progression, and revealing BRP39 to be a potential therapeutic target for future treatment of inflammatory NASH and its associated diseases.

Background: Although the cucumber reference genome and its annotation were published several years ago, the functional annotation of predicted genes, particularly protein-coding genes, still requires further improvement. In general, accurately determining orthologous relationships between genes allows for better and more robust functional assignments of predicted genes. As one of the most reliable strategies, the determination of collinearity information may facilitate reliable orthology inferences among genes from multiple related genomes. Currently, the identification of collinear segments has mainly been based on conservation of gene order and orientation. Over the course of plant genome evolution, various evolutionary events have disrupted or distorted the order of genes along chromosomes, making it difficult to use those genes as genome-wide markers for plant genome comparisons.Results: Using the localized LASTZ/MULTIZ analysis pipeline, we aligned 15 genomes, including cucumber and other related angiosperm plants, and identified a set of genomic segments that are short in length, stable in structure, uniform in distribution and highly conserved across all 15 plants. Compared with protein-coding genes, these conserved segments were more suitable for use as genomic markers for detecting collinear segments among distantly divergent plants. Guided by this set of identified collinear genomic segments, we inferred 94,486 orthologous protein-coding gene pairs (OPPs) between cucumber and 14 other angiosperm species, which were used as proxies for transferring functional terms to cucumber genes from the annotations of the other 14 genomes. In total, 10,885 protein-coding genes were assigned Gene Ontology (GO) terms which was nearly 1,300 more than results collected in Uniprot-proteomic database. Our results showed that annotation accuracy would been improved compared with other existing approaches.Conclusions: In this study, we provided an alternative resource for the functional annotation of predicted cucumber protein-coding genes, which we expect will be beneficial for the cucumber's biological study, accessible from http://cmb.bnu.edu.cn/functional_annotation. Meanwhile, using the cucumber reference genome as a case study, we presented an efficient strategy for transferring gene functional information from previously well-characterized protein-coding genes in model species to newly sequenced or “non-model” plant species.

In apple, the MYB transcription factor MYB10 controls the accumulation of anthocyanins. MYB10 is able to auto-activate its expression by binding its own promoter at a specific motif, the R1 motif. In some apple accessions a natural mutation, termed R6, has more copies of this motif within the MYB10 promoter resulting in stronger auto-activation and elevated anthocyanins. Here we show that other anthocyanin-related MYBs selected from apple, pear, strawberry, petunia, kiwifruit and Arabidopsis are able to activate promoters containing the R6 motif. To examine the specificity of this motif, members of the R2R3 MYB family were screened against a promoter harboring the R6 mutation. Only MYBs from subgroups 5 and 6 activate expression by binding the R6 motif, with these MYBs sharing conserved residues in their R2R3 DNA binding domains. Insertion of the apple R6 motif into orthologous promoters of MYB10 in pear (PcMYB10) and Arabidopsis (AtMY75) elevated anthocyanin levels. Introduction of the R6 motif into the promoter region of an anthocyanin biosynthetic enzyme F3′5′H of kiwifruit imparts regulation by MYB10. This results in elevated levels of delphinidin in both tobacco and kiwifruit. Finally, an R6 motif inserted into the promoter the vitamin C biosynthesis gene GDP-L-Gal phosphorylase increases vitamin C content in a MYB10-dependent manner. This motif therefore provides a tool to re-engineer novel MYB-regulated responses in plants.

Anthocyanins provide nutritional benefits and are responsible for red coloration in many fruits. Light affects anthocyanin biosynthesis in peach (Prunus persica). However, some cultivars show differential sensitivity to light. In the present study, ‘Hujingmilu (HJ),’ a naturally deeply colored cultivar, and ‘Yulu (YL),’ showing low pigmentation, were used to study the mechanism underlying UV-light-induced anthocyanin biosynthesis. Both UVA and UVB induced fruit pigmentation of ‘HJ,’ but ‘YL’ was only sensitive to UVB. Transcriptomic analyses showed over 5000 genes were differentially expressed by pairwise comparisons of RNA libraries isolated from tissue of each cultivar treated with darkness, UVA and UVB. Twenty-three genes related to anthocyanin biosynthesis were identified from the transcriptome data, which were coordinately up-regulated during accumulation of anthocyanins, and down-regulated in the dark. Altered expression of several light receptors, as well as CONSTITUTIVE PHOTOMORPHOGENIC10 (COP10) and ELONGATED HYPOCOTYL 5 homolog (HYH), and a specific anthocyanin transporter glutathione S-transferase (GST), in ‘YL’ fruit appears to be responsible for the insensitivity to UVA of this cultivar. Expression profiles of several transcription factors of the families MYB, bHLH, bZIP and NAC were highly correlated with those of the anthocyanin biosynthesis genes. The study provides a valuable overview of the underlying molecular mechanisms of UV-light induced anthocyanin response using peach cultivars with differing light sensitivities.

Accurate identification of orthologous genomic regions (OGRs) between two closely related genomes is crucial for the reliable detection of genomic changes, which range from small-scale changes (e.g., single nucleotide or small nucleotides) to large-scale structural changes. Although diverse OGRs inferred at different levels have been successfully applied to address various biological questions, a limited number of studies have simultaneously integrated OGRs from different levels. Here, we report on a new approach to construct a hierarchical map of OGRs. Using different types of genomic markers, this approach was applied to two very closely related cucumber genomes [ L. var. and L. var. (Royle) Alef.]. We identified two different levels of OGRs using Mugsy (denoted as dnaOGRs) and i-ADHoRe (denoted as proOGRs). Using information regarding the anchored chromosomes of the two genomes, a third level of OGRs (denoted chrOGRs) could be built at the chromosomal level. Together, these OGRs could be organized into a hierarchical map that represented the parent–child relationships (chrOGR:proOGRs:dnaOGRs) between the two genomes. For this case study, the map consisted of seven chrOGRs, 540 proOGRs, and 22,321 dnaOGRs. Based on this map, we designed different methods to detect both small-scale and large-scale genomic changes. Surprisingly, many genomic changes were detected at each OGR level despite the very short divergence time between the two subspecies. Together, our results show that a hierarchical map of OGRs and their related genomic changes are useful resources for elucidating the diversity and evolution of cucumber genomes and phenotypes.

The Finite-element method (FEM) and experiments were used to investigate the geometric factors and material parameter on the strain distribution during tube high-pressure shearing (t-HPS). The results show that t-HPS could be realized successfully either by pressurizing on both ends of the tube, or by pressurizing using the wedge effect; and in both cases, the “dead metal zone” could be found at both ends of the tube. The grain size distribution from the experiment confirmed this strain distribution feature. In the case of t-HPS pressurized using the wedge effect, the half cone angle has little effect on the strain distribution. Decreasing the strain-hardening exponent leads to increased deformation inhomogeneity in both the ideal t-HPS described by theoretical equations and the close to practical t-HPS described by FEM. This feature of t-HPS stands out from other SPD processes like HPT, and makes practical t-HPS behavior more predictable using the analytical formation than any other SPD processes, and places it an advantageous position in understanding the basics of deformation physics through the coupling between practical experiments and theoretical approaches.

Chitinase-3-like 1 protein (CHI3L1) is a secreted glycoprotein, strongly correlated with fibrosis severity in chronic liver diseases including non-alcoholic steatohepatitis (NASH). However, the mechanisms by which CHI3L1 contributes to fibrogenesis remain undefined. Here, we showed that infiltrating monocyte-derived liver macrophages represent the main source of CHI3L1 in murine NASH. We developed a floxed CHI3L1 knock-out (KO) mouse to further study the cell-specific role of CHI3L1 ablation. Wildtype (WT) and myeloid cell-specific CHI3L1 KO mice (CreLyz) were challenged with a highly inflammatory and fibrotic dietary model of NASH by administering choline-deficient high-fat diet for 10 weeks. Macrophage accumulation and inflammatory cell recruitment were significantly ameliorated in the CreLyz group compared to WT (F4/80 IHC p

STAT6 (signal transducer and activator of transcription 6) is a transcription factor that plays a central role in the pathophysiology of allergic inflammation. We have identified 16 patients from 10 families spanning three continents with a profound phenotype of early-life onset allergic immune dysregulation, widespread treatment-resistant atopic dermatitis, hypereosinophilia with esosinophilic gastrointestinal disease, asthma, elevated serum IgE, IgE-mediated food allergies, and anaphylaxis. The cases were either sporadic (seven kindreds) or followed an autosomal dominant inheritance pattern (three kindreds). All patients carried monoallelic rare variants in STAT6 and functional studies established their gain-of-function (GOF) phenotype with sustained STAT6 phosphorylation, increased STAT6 target gene expression, and TH2 skewing. Precision treatment with the anti-IL-4Rα antibody, dupilumab, was highly effective improving both clinical manifestations and immunological biomarkers. This study identifies heterozygous GOF variants in STAT6 as a novel autosomal dominant allergic disorder. We anticipate that our discovery of multiple kindreds with germline STAT6 GOF variants will facilitate the recognition of more affected individuals and the full definition of this new primary atopic disorder.

INTRODUCTION:The potato (Solanum tuberosum) cultivar 'Xin Daping' is tetraploid with white skin and white flesh, while the cultivar 'Hei Meiren' is also tetraploid with purple skin and purple flesh. Comparative transcriptome analysis of white and purple cultivars was carried out using high-throughput RNA sequencing in order to further understand the mechanism of anthocyanin biosynthesis in potato. METHODS AND RESULTS:By aligning transcript reads to the recently published diploid potato genome and de novo assembly, 209 million paired-end Illumina RNA-seq reads from these tetraploid cultivars were assembled on to 60,930 transcripts, of which 27,754 (45.55%) are novel transcripts and 9393 alternative transcripts. Using a comparison of the RNA-sequence datasets, multiple versions of the genes encoding anthocyanin biosynthetic steps and regulatory transcription factors were identified. Other novel genes potentially involved in anthocyanin biosynthesis in potato tubers were also discovered. Real-time qPCR validation of candidate genes revealed good correlation with the transcriptome data. SNPs (Single Nucleotide Polymorphism) and indels were predicted and validated for the transcription factors MYB AN1 and bHLH1 and the biosynthetic gene anthocyanidin 3-O-glucosyltransferase (UFGT). CONCLUSIONS:These results contribute to our understanding of the molecular mechanism of white and purple potato development, by identifying differential responses of biosynthetic gene family members together with the variation in structural genes and transcription factors in this highly heterozygous crop. This provides an excellent platform and resource for future genetic and functional genomic research.