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Background: Histones are basic elements of the chromatin, and are critical to controlling chromatin structure and transcription. The proteasome activator PA200 promotes the acetylation-dependent proteasomal degradation of the core histones during spermatogenesis, DNA repair, transcription and cellular aging, and maintains the stability of histone marks. Objective: The study aimed to explore whether the yeast ortholog of PA200, Blm10, promotes degradation of the core histones during transcription and regulates transcription especially during aging. Method: Protein degradation assays were performed to detect the role of Blm10 in histone degradation during transcription. mRNA profiles were compared in WT and mutant BY4741 or MDY510 yeast cells by RNA-sequencing. Results: The core histones can be degraded by the Blm10-proteasome in the non-replicating yeast, suggesting that Blm10 promotes the transcription-coupled degradation of the core histones. Blm10 preferentially regulates transcription in aged yeast, especially transcription of genes related to translation, amino acid metabolism, and carbohydrate metabolism. Mutations of Blm10 at F2125/N2126 in its putative acetyl-lysine binding region abolished the Blm10-mediated regulation of gene expression. Conclusion: Blm10 promotes degradation of the core histones during transcription and regulates transcription especially during cellular aging, further supporting the critical role of PA200 in maintaining the stability of histone marks from the evolutionary view. These results should provide meaningful insights into the mechanisms underlying aging and the related diseases.

Chinese plum (Prunus salicina Lindl.) is a stone fruit that belongs to the Prunus genus and plays an important role in the global production of plum. In this study, we report the genome sequence of the Chinese plum ‘Sanyueli’, which is known to have a low-chill requirement for flower bud break. The assembled genome size was 308.06 Mb, with a contig N50 of 815.7 kb. A total of 30,159 protein-coding genes were predicted from the genome and 56.4% (173.39 Mb) of the genome was annotated as repetitive sequence. Bud dormancy is influenced by chilling requirement in plum and partly controlled by DORMANCY ASSOCIATED MADS-box (DAM) genes. Six tandemly arrayed PsDAM genes were identified in the assembled genome. Sequence analysis of PsDAM6 in ‘Sanyueli’revealed the presence of large insertions in the intron and exon regions. Transcriptome analysis indicated that the expression of PsDAM6 in the dormant flower buds of ‘Sanyueli’ was significantly lower than that in the dormant flower buds of the high chill requiring ‘Furongli’ plum. In addition, the expression of PsDAM6 was repressed by chilling treatment. The genome sequence of ‘Sanyueli’ plum provides a valuable resource for elucidating the molecular mechanisms responsible for the regulation of chilling requirements, and is also useful for the identification of the genes involved in the control of other important agronomic traits and molecular breeding in plum.

Fluorescent carbon dots (CDs) were directly synthesized by hydrothermal treatment of medicinal mulberry leaves (Morus alba L.) residues without the need for any chemical reagent. The CDs were collected successively through filtration, centrifugation, and dialysis from the resultant solution. The as-purified CDs were almost non-cytotoxic and successfully used for the intracellular fluorescence imaging of human hepatocellular carcinoma cells (HepG2). Due to the presence of plentiful surface groups, the CDs were further used as drug carriers for the loading of Lycorine, an anti-cancer alkaloidal extracted from bulbs of Lycoris radiata L. Importantly, the Lycorine-loaded CDs were successfully applied for simultaneous intracellular imaging and drug delivery for the better anti-cancer cell activity. The present work both provides a strategy for the reuse of medicinal herb residues for the preparation of CDs and promotes a potential application of CDs in biomedicine and bioimaging.

The epigenetic inheritance relies on stability of histone marks, but various diseases, including aging-related disorders, are usually associated with alterations of histone marks. Whether and how the proteasome is responsible for maintaining the histone marks during transcription and aging remain unclear. The core histones can be degraded by the atypical proteasome, which contains the proteasome activator PA200, in an acetylation-dependent manner during somatic DNA damage response and spermiogenesis. Methods: By utilizing a substitute of methionine to label proteins metabolically, we analyzed histone degradation genome-wide by sequencing the DNA fragments following pulse-chase assays. The genome-wide RNA-sequencing analysis was performed to analyze transcription and chromatin-immunoprecipitation (ChIP)-sequencing was used for analyses of histone marks. The experimental models included gene-manipulated cells (including both mouse and yeast), mouse liver, and mice. Results: Degradation of H4 or the transcription-coupled histone variant H3.3 could be suppressed by deletion of PA200 or its yeast ortholog Blm10. The histone deacetylase inhibitor accelerated the degradation rates of H3, while the mutations of the putative acetyl-lysine-binding region of PA200 abolished histone degradation in the G1-arrested cells. Deletion of PA200 dramatically altered deposition of the active transcriptional hallmarks (H3K4me3 and H3K56ac) and transcription, especially during cellular aging. Furthermore, deletion of PA200 or Blm10 accelerated cellular aging. Notably, the PA200-deficient mice displayed a range of aging-related deteriorations, including immune malfunction, anxiety-like behavior and shorter lifespan. Conclusion: PA200 promotes the transcription-coupled degradation of the core histones, and plays an important role in maintaining the stability of histone marks during transcription and aging.

Significance It is a tenet of modern biology that species adapt through natural selection to cope with the ever-changing environment. By comparing genetic variants between the island and mainland populations of a passerine, we inferred the related age of genetic variants across its entire genome and suggest that preexisting standing variants played the predominant role in local adaptation. Our findings not only resolve a long-standing fundamental problem in biology regarding the genetic sources of adaptation, but imply that the evolutionary potential of a population is highly associated with its preexisting genetic variation., What kind of genetic variation contributes the most to adaptation is a fundamental question in evolutionary biology. By resequencing genomes of 80 individuals, we inferred the origin of genomic variants associated with a complex adaptive syndrome involving multiple quantitative traits, namely, adaptation between high and low altitudes, in the vinous-throated parrotbill (Sinosuthora webbiana) in Taiwan. By comparing these variants with those in the Asian mainland population, we revealed standing variation in 24 noncoding genomic regions to be the predominant genetic source of adaptation. Parrotbills at both high and low altitudes exhibited signatures of recent selection, suggesting that not only the front but also the trailing edges of postglacial expanding populations could be subjected to environmental stresses. This study verifies and quantifies the importance of standing variation in adaptation in a cohort of genes, illustrating that the evolutionary potential of a population depends significantly on its preexisting genetic diversity. These findings provide important context for understanding adaptation and conservation of species in the Anthropocene.

A sodium (Na) metal anode plays a pivotal role in realizing long-term cycling stability in promising Na-based batteries. However, the uncontrollable plating-stripping process and unstable solid electrolyte interphase (SEI) layer can induce electrode degradation, which hinders its potential applications. In this work, the synergy effects of a composite Na metal anode and fluorine-rich electrolyte were introduced to investigate the Na+ plating-stripping process and its potential use in Na-metal batteries (SMBs). The composite anode was fabricated via alloying and capillary action between the sodiophilic carbon matrix and molten Na metal, thus forming an integrated structure, which effectively improved the interconnection between Na and carbon scaffold to obtain uniform deposition. Combined with the fluorine-rich electrolyte, stable SEI layers consisting of ion-permeable NaF and mechanically durable organic components were obtained. When coupled with an Na3V2(PO4)3 cathode with a high mass loading of ∼9 mg cm−2, an ultra-stable cycling behaviour (capacity retention of >90% over 1000 cycles) and outstanding rate performance (capacity retention of >80% at 15C) were observed due to the improved Na deposition process and interface stability. This work demonstrates that the synergy effects of the composite metal anode and electrolyte modification can be an effective strategy to fabricate highly stable SMBs.

The epigenetic inheritance relies on stability of histone marks, but various diseases, including aging-related diseases, are usually associated with alterations of histone marks. How the stability of histone marks is maintained still remains unclear. The core histones can be degraded by the atypical proteasome, which contains the proteasome activator PA200, in an acetylation-dependent manner during somatic DNA damage response and spermiogenesis. Here we show that PA200 promotes the transcription-coupled degradation of the core histones, and plays an important role in maintaining the stability of histone marks. Degradation of the histone variant H3.3, which is incorporated into chromatin during transcription, was much faster than that of its canonical form H3.1, which is incorporated during DNA replication. This degradation of the core histones could be suppressed by the transcription inhibitor, the proteasome inhibitor or deletion of PA200. The histone deacetylase inhibitor accelerated the degradation rates of H3 in general, especially its variant H3.3, while the mutations of the putative acetyl-lysine-binding region of PA200 abolished histone degradation in the G1-arrested cells, supporting that acetylation is involved in the degradation of the core histones. Deletion of PA200 dramatically altered deposition of the active transcriptional hallmarks (H3K4me3 and H3K56ac) and transcription, especially during cellular aging. Furthermore, deletion of PA200 or its yeast ortholog Blm10 accelerated cellular aging. Notably, the PA200-deficient mice displayed a range of aging-related deteriorations, including immune malfunction, anxiety-like behaviors and shorter lifespan. Thus, the proteasome activator PA200 is critical to the maintenance of the stability of histone marks during transcription and aging.

The controllable synthesis of nanosized Fe3O4 (10–20 nm) encapsulated in different numbers of graphene layers (1–5 layers) (Fe3O4@DGL NPs) was realized through a facile and green hydrothermal reaction at a temperature as low as 200 °C. The competitive reduction–oxidation between reducing ethylene glycol (EG) and oxidizing H2O under hydrothermal conditions resulted in the emergence of a magnetic Fe3O4 core. Then, the pyrolytic reaction of the polyvinyl alcohol (PVA) molecules attached to the surface of the Fe3O4 core with different surface densities led to the formation of graphene with a controlled number of layers. These Fe3O4@DGL NPs exhibited fast adsorption and sensitive SERS detection for rhodamine B (RhB). A physical and mathematical model was proposed for the estimation of the enhancement factor (EF) by combining the adsorption efficiency and SERS of RhB. This approach and model are applicable for the adsorption, sensitive SERS detection and determination of SERS EF when using functional magnetic nanoparticles as the adsorbent. The Fe3O4@1G NPs were also used as a novel nano-adsorbent for the fast removal of Escherichia coli (E. coli) from an aqueous solution. The Fe3O4@1G NPs regenerated after 3 cycles also showed high efficiency in the adsorption and separation of RhB and E. coli.

BackgroundRecent studies have demonstrated that phylogenomics is an important basis for answering many fundamental evolutionary questions. With more high-quality whole genome sequences published, more efficient phylogenomics analysis workflows are required urgently.ResultsTo this end and in order to capture putative differences among evolutionary histories of gene families and species, we developed a phylogenomics workflow for gene family classification, gene family tree inference, species tree inference and duplication/loss events dating. Our analysis framework is on the basis of two guiding ideas: 1) gene trees tend to be different from species trees but they influence each other in evolution; 2) different gene families have undergone different evolutionary mechanisms. It has been applied to the genomic data from 64 vertebrates and 5 out-group species. And the results showed high accuracy on species tree inference and few false-positives in duplication events dating.ConclusionsBased on the inferred gene duplication and loss event, only 9∼16% gene families have duplication retention after a whole genome duplication (WGD) event. A large part of these families have ohnologs from two or three WGDs. Consistent with the previous study results, the gene function of these families are mainly involved in nervous system and signal transduction related biological processes. Specifically, we found that the gene families with ohnologs from the teleost-specific (TS) WGD are enriched in fat metabolism, this result implyng that the retention of such ohnologs might be associated with the environmental status of high concentration of oxygen during that period.

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.

Well-crystallized β-Sn nanoparticles with different diameters have been prepared by a wet chemical method at different reaction temperatures. Both optical characterizations and finite element simulations confirmed that higher-order resonance modes will appear when the size of nanoparticles gets bigger and the plasmon resonance absorption peaks resulting from all resonance modes will keep red-shifting with the increase in the size of nanoparticles. In addition, surface-enhanced Raman scattering measurements and corresponding calculations indicate that β-Sn nanoparticles could reveal a near-field enhancement effect and therefore could be an alternative efficient plasmonic material for the Si-based optoelectronic and/or photovoltaic devices.

Chinese narcissus (Narcissus tazetta L. var. chinensis Roem.) is a popular flower in Asia. However, flower colors are limited with all cultivars having a white perianth and yellow corona. Previous studies have shown no anthocyanin accumulation in this species. The reason for an absence of anthocyanins remains unknown, with the flavonoid biosynthetic pathway in this flower recently being investigated. In this study, a transcriptomic approach combined with gene expression and biochemical analysis was used to predict and annotate genes in the flavonoid biosynthetic pathway. Results showed that the major flavonoid metabolites are flavonols and proanthocyanidins. Proanthocyanidin biosynthesis is exclusively catechin-based, with the gene encoding leucoanthocyanidin reductase (LAR) being well expressed. We identified 16 unigenes encoding key enzymes involved in flavonoid biosynthesis. Flavonol synthase (FLS) and dihydroflavonol reductase (DFR) appear to play important roles in regulating proanthocyanidin and flavonol levels, while anthocyanidin synthase (ANS) expression is not detected. Our results suggest that the absence of anthocyanins in Chinese narcissus is due to high expression of LAR and FLS, and a lack of ANS expression.

Fluorescent carbon dots (CDs) with excitation-wavelength-dependent and excitation-wavelength-independent emission have been prepared with varying amounts citric acid (CA), ethylenediamin end-capped polyethylenimine (PEI-EC) and sodium borohydride (NaBH 4 ), their structure, optical and chemical sensing properties have been also systematically investigated. The varying of NaBH 4 and PEI-EC renders the structure and surface state change as well as photoluminescence (PL) properties. The results indicated that NaBH 4 made the CDs sensitive to Co 2+ ions, whilst the PEI-EC served to increase their sensitivity. The synergistic roles that both NaBH 4 and PEI-EC played on the selective and sensitive detection of Co 2+ were achieved via a simple adjustment of the mass ratios during synthesis. Furthermore, the PL intensity was gradually recovered until completely restored with the addition of chelating agent ethylenediaminetetraacetic acid (EDTA) to the Co 2+ quenched CDs solutions. This work provided quantitatively preparation and controllable synthesis of excitation-wavelength-dependent or independent CDs for the development of PL based sensors.

Both magnetic Fe3O4 nanoparticles (Fe3O4 NPs) and luminescent carbon dots (CDs) were simultaneously synthesized via a hydrothermal route at temperature as low as 200 °C. The synthesized magnetic Fe3O4 NPs and luminescent CDs were readily separated and purified from the reaction mixture, without the need for additional energy input and chemicals. The magnetic properties of purified Fe3O4 and photoluminescence (PL) behaviors of purified CDs were investigated using Squid-VSM magnetic property measurement system and fluorescence spectrophotometer, respectively. The size of Fe3O4 NPs and the luminescent properties of CDs were tunable by changing the reaction time or ratio between starting materials within a certain range. Fe3O4 NPs exhibited high saturation magnetization in the range of 36.59–68.22 emu/g and their magnetic behavior significantly depend on the size and structure of Fe3O4 NPs. This work was expected to provide a kind of green and high efficiency simultaneously synthesis of size-controllable Fe3O4 NPs and photoluminescence tunable CDs.

Anthocyanin and proanthocyanidin (PA) accumulation is regulated by both myeloblastosis (MYB) activators and repressors, but little information is available on hierarchical interactions between the positive and negative regulators. Here, we report on a R2R3-MYB repressor in peach, designated PpMYB18, which acts as a negative regulator of anthocyanin and PA accumulation. PpMYB18 can be activated by both anthocyanin- and PA-related MYB activators, and is expressed both at fruit ripening and juvenile stages when anthocyanins or PAs, respectively, are being synthesized. The PpMYB18 protein competes with MYB activators for binding to basic Helix Loop Helixes (bHLHs), which develops a fine-tuning regulatory loop to balance PA and anthocyanin accumulation. In addition, the bHLH binding motif in the R3 domain and the C1 and C2 repression motifs in the C-terminus of PpMYB18 both confer repressive activity of PpMYB18. Our study also demonstrates a modifying negative feedback loop, which prevents cells from excess accumulation of anthocyanin and PAs, and serves as a model for balancing secondary metabolite accumulation at the transcriptional level.

Improving charge carriers separation to achieve high photoconversion efficiency in heterogeneous photocatalysts is highly desirable. Herein, heterostructured ZnS@CdS double-layered porous nanotubes (PNTs), in which the spatially separated reduction and oxidation reaction sites lie on the outer and inner shell, respectively, are fabricated through a robust self-template conversion strategy. After selective photo-deposition of Ni and CoOx as dual cocatalysts, Ni nanoparticles as electron collectors and reduction reaction sites are loaded on the outer shell, while CoOx nanoparticles as hole collectors and oxidation reaction sites are loaded on the inner shells. As a result, a novel CoOx/ZnS@CdS/Ni photocatalyst is obtained and shows high visible-light-driven photocatalytic hydrogen production activity owing to the synergistic effect of self-template-derived thin mesoporous heterojunctions and photo-deposition-derived spatially separated dual cocatalysts, which can significantly provide driving force for the ordered transfer of photogenerated electrons and holes toward opposite direction and promote the surface catalytic reaction. Additionally, the facile strategy can be broadened to the preparation of CoOx/ZnSe@CdSe/Ni PNTs with enhanced photocatalytic activity.

This paper presents a study on all-atom molecular dynamics (MD) simulations of fibre–matrix interfaces in fibre-reinforced polymer (FRP) composites, with a focus on the effect of fibre sizing. The reactive force field ReaxFF was used in the simulations. The sizing treatment was found to significantly increase the interface toughness while has little effect on the peak stress of fibre–matrix interface. The characteristics of the fracture surfaces and the scission of C-O bonds observed in the simulations are consistent with pervious experimental observations. The developed modelling method opens up a new avenue of investigating the deterioration mechanism of FRP under combined mechanical-chemical-thermal actions.

Being the key process of a promising scalable production method, mechanical peeling is often used to construct high-quality van der Waals (vdW) heterostructures. By combining molecular dynamics (MD) studies and theoretical analysis, the investigation of the process of peeling heterostructures at different angles is reported. Taking vdW interaction into account, we present a theory that considers the effects of peeling angles on peeling forces. The theory is verified with results of MD simulations and found to describe the stable peeling stage well. Furthermore, there is a characteristic length at the initial stage of peeling, which reflects the bending and interfacial properties of the layered materials during peeling and indicates the influence of peeling angles on transition from unstable peeling to stable peeling. Our findings could help to understand the peeling mechanisms of 2D material interfaces and may give a guidance for the construction of better-quality and more complex vdW heterostructures.

Two different types sulfuric acids, i.e. the biological sulfuric acid (BSA) produced by T.t bacteria (Thiobacillus thiooxidans) and chemical sulfuric acid (CSA), were applied to simulate the corrosion. The sulphoaluminate cement (SAC) and the sea sand were mixed to made the concrete. The mass loss, compressive strength, chloride binding rate, pH value and pore structure were measured in the process of corrosion. Furthermore, X-ray diffraction (XRD) and scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS) were used to analyze the products of the reaction. It could be found that under the corrosion of sulfuric acid, the initial hydration products of SAC, including ettringite (AFt) and Friedels’ salt, were decomposed continuously and the main corrosion product was dihydrate gypsum. Under corrosion of BSA, the corrosion became more intense due to the influence of bacterial effect. Moreover, the corrosion of BSA was more severe than that of CSA, which was obvious in terms of mass loss, strength decline and pore structure. The BSA has a more negative effect on the performance of SAC concrete.

Whether species demography and diversification are driven primarily by extrinsic environmental changes such as climatic oscillations in the Quaternary or by intrinsic biological interactions like coevolution between antagonists is a matter of active debate. In fact, their relative importance can be assessed by tracking past population fluctuations over considerable time periods. We applied the pairwise sequentially Markovian coalescent approach on the genomes of 11 temperate Juglans species to estimate trajectories of changes in effective population size (Ne ) and used a Bayesian-coalescent based approach that simultaneously considers multiple genomes (G-PhoCS) to estimate divergence times between lineages. Ne curves of all study species converged 1.0 million yr ago, probably reflecting the time when the walnut genus last shared a common ancestor. This estimate was confirmed by the G-PhoCS estimates of divergence times. But all species did not react similarly to the dramatic climatic oscillations following early Pleistocene cooling, so the timing and amplitude of changes in Ne differed among species and even among conspecific lineages. The population histories of temperate walnut species were not driven by extrinsic environmental changes alone, and a key role was probably played by species-specific factors such as coevolutionary interactions with specialized pathogens.

NG (Natural gas) distribution pressure varies in a wide range in different applications and has significant effect on system exergy efficiency. RC (Rankine cycle) and DEC (direct expansion cycle) can utilize the cold and pressure exergies of LNG (liquefied natural gas), respectively. In this paper, SRC (single-stage RC), PTRC (parallel two-stage RC) and CTRC (cascade two-stage RC) with and without DEC are optimized by Particle Swarm Optimization and compared to obtain the optimal configurations for different NG distribution pressures. Propane, propylene, ethane and ethylene are adopted as the working fluids. The results show that the addition of DEC could increase the exergy efficiency by lifting the evaporation temperature of LNG. CTRC + DEC with propane/ethylene and CTRC + DEC with propane/ethane as the working fluid achieve the largest exergy efficiencies of 23.89% and 18.25% at NG distribution pressures of 1 MPa and 2 MPa, respectively. PTRC + DEC with propane/ethane is the optimal system with maximum exergy efficiencies of 15.18%, 13.24%, 11.7% and 10.4% at NG distribution pressures of 3, 4, 5 and 6 MPa, respectively. PTRC + DEC with ethane as the working fluid in both cycles is a generally suitable system for all NG distribution pressures with high efficiency and only one type of working fluid.

In this paper, we present a linear marching scheme to recover frequency-dependent complex shear moduli in viscoelastic models utilizing two sets of single component displacement data. The proposed method is designed to provide stable and accurate estimation of the tissue viscoelastic stiffness parameters by solving a first-order complex partial differential equation. To control the exponential growth of the numerical error resulting from one of the complex coefficients in the inverse equation, a modified upwind discretization is utilized on the first-order derivative terms of the target parameter. The algorithm is fully stablized when: (1) carefully chosen multiple data-sets are combined to eliminate the remaining complex coefficient that contributes to exponential error growth; and (2) a modified Tikhonov regularization is applied to the inversion method. We obtain the stability result in the norm so that the numerical scheme is convergent at fractional 1 / 2 order. Its performance is compared wi...

Atmospheric transport of black carbon (BC) from surrounding areas has been shown to impact the Tibetan environment, and clarifying the geographical source and receptor regions is crucial for providing guidance for mitigation actions. In this study, 10 trace volatile organic compounds (VOCs) sampled across Tibet are chosen as proxies to diagnose source regions and related transport of pollutants to Tibet. The levels of these VOCs in Tibet are higher than those in the Arctic and Antarctic regions but much lower than those observed at many remote and background sites in Asia. The highest VOC level is observed in the eastern region, followed by the southern region and the northern region. A positive matrix factorization (PMF) model found that three factors—industry, biomass burning, and traffic—present different spatial distributions, which indicates that different zones of Tibet are influenced by different VOC sources. The average age of the air masses in the northern and eastern regions is estimated to be 3.5 and 2.8 days using the ratio of toluene to benzene, respectively, which indicates the foreign transport of VOC species to those regions. Back-trajectory analyses show that the Afghanistan-Pakistan-Tajikistan region, Indo-Gangetic Plain (IGP), and Meghalaya-Myanmar region could transport industrial VOCs to different zones of Tibet from west to east. The agricultural bases in northern India could transport biomass burning-related VOCs to the middle-northern and eastern zones of Tibet. High traffic along the unique national roads in Tibet is associated with emissions from local sources and neighboring areas. Our study proposes international joint-control efforts and targeted actions to mitigate the climatic changes and effects associated with VOCs in Tibet, which is a climate sensitive region and an important source of global water.

The overuse of antibiotics in animal agriculture and medicine has caused a series of potential threats to public health. Macleaya cordata is a medicinal plant species from the Papaveraceae family, providing a safe resource for the manufacture of antimicrobial feed additive for livestock. The active constituents from M. cordata are known to include benzylisoquinoline alkaloids (BIAs) such as sanguinarine (SAN) and chelerythrine (CHE), but their metabolic pathways have yet to be studied in this non-model plant. The active biosynthesis of SAN and CHE in M. cordata was first examined and confirmed by feeding 13 C-labeled tyrosine. To gain further insights, we de novo sequenced the whole genome of M . cordata , the first to be sequenced from the Papaveraceae family. The M. cordata genome covering 378 Mb encodes 22,328 predicted protein-coding genes with 43.5% being transposable elements. As a member of basal eudicot, M. cordata genome lacks the paleohexaploidy event that occurred in almost all eudicots. From the genomics data, a complete set of 16 metabolic genes for SAN and CHE biosynthesis was retrieved, and 14 of their biochemical activities were validated. These genomics and metabolic data show the conserved BIA metabolic pathways in M. cordata and provide the knowledge foundation for future productions of SAN and CHE by crop improvement or microbial pathway reconstruction.

In this paper, we explored material similarity between graphene and shale for methane (CH 4 ) adsorption in the shale gas recovery simulations. The reasons of choosing graphene to model shale have been clarified. Through theoretical analysis, we obtained the attenuation law of interaction potential between CH 4 and multilayer graphene. It indicates the adsorption energy of CH 4 on monolayer graphene is closest to that on shale. The limiting heat of adsorption of CH 4 on graphene was calculated by molecular dynamics (MD) simulation. The adsorption isotherms and adsorption heats on the monolayer graphene, whose width of the slit pore ranges from 2 nm to 11 nm, were calculated by using grand canonical Monte Carlo (GCMC) simulations at different temperatures. The computed adsorption heat is validated by experimental data, which indicates that the adsorption properties of CH 4 on shale are quite similar with that of CH 4 on graphene. Our study may provide a direct evidence of using graphene in modeling shale in simulating the shale gas adsorption/desorption.

PDB-1 is a new C-27-carboxylated-lupane-triterpenoid derivative isolated from Potentilla discolor Bunge. In our previous research, PDB-1 was suggested to have an obvious selectivity for tumor cells. This study focused on clarifying PDB-1’s anticancer mechanism in the inhibition of proliferation and in the induction of apoptosis and autophagy in A549 cells. In general, A549 cells were treated with PDB-1 for different times, and cell survival was assessed by a CCK8 assay. The assessment of intracellular reactive oxygen species, a mitochondrial membrane potential assay, a cell cycle assay, an annexin V-FITC/PI assay, and MDC staining were performed in A549 cells treated with PDB-1. Moreover, the mRNA and protein expression of cell cycle-, apoptosis- and autophagy-related factors were detected by RT-qPCR and western blotting. The results showed that PDB-1 inhibited A549 cell proliferation and colony formation in a dose- and time-dependent manner. The decrease in the viability of A549 cells was due to a G2/M cell cycle arrest. Moreover, PDB-1 induced cell apoptosis, accompanied by an increase in the Bax/Bcl-2 ratio and an increase in the expression levels of cleaved caspase-3/caspase-9. We also found that PDB-1 induced autophagy by increasing the conversion of LC3-I to LC3-II and elevating Beclin-1. In addition, further studies indicated that pretreatment with a specific PI3K inhibitor (LY294002) enhanced the effects of PDB-1 on the expression of proteins associated with apoptosis and autophagy, demonstrating that the PI3K/Akt/mTOR pathway was related to PDB-1-induced apoptosis and autophagy. These results indicated that PDB-1 may be considered a potential candidate for the future treatment of lung adenocarcinoma. These findings should benefit the development of the C14-COOH type of pentacyclic triterpenoids.

Objective Alkaline phosphatase (ALP) serves as a biomarker for diagnosing several types of diseases in adults; nonetheless, its use is restricted in children because of changes in ALP activity during different physiological phases. The present study aimed to investigate ALP activity and its dynamics in children of different ages to establish the reference values for ALP activity in children. Methods Total 167,625 samples of children aged 0–18 years were enrolled in this study. ALP activity was measured using the 4-nitrophenyl-1-phosphate disodium salt (4-NPP)–2-amino-2-methyl-1-propanol (AMP) method with an automatic biochemical analyzer. Patients with known diagnoses that may affect ALP activity were excluded. A percentile curve was plotted using MATLAB software, and the curve was fitted using the skewness–median–coefficient of variation (LMS) method. Results ALP activity reached the highest peak at 12–13 years of age and then gradually decreased to the lowest peak at 18–19 years of age in boys, whereas it reached the highest at 10–11 years and then gradually reduced to the lowest at 17–18 years in girls. Furthermore, the highest peak of ALP activity appeared substantially earlier in children of either sex in China than in those in Germany. Conclusions We showed the dynamics of ALP activity in both boys and girls between the ages of 0 and 18 years in China and compared the difference in ALP activity between children in China and Germany. Our findings provide a reference for clinicians.

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.

To gain insight into how anthocyanin biosynthesis is controlled by light in fruit, transcriptome and metabolome analyses were performed in the Chinese sand pear cultivar “Mantianhong” (Pyrus pyrifolia) after bagging and bag removal. We investigated transcriptional and metabolic changes and gene-metabolite correlation networks. Correlation tests of anthocyanin content and transcriptional changes revealed that 1,530 transcripts were strongly correlated with 15 anthocyanin derivatives (R2 > 0.9, P-value PybZIPa, that might play an important role during light-induced anthocyanin accumulation. The overexpression of PybZIPa promoted anthocyanin accumulation in pear and strawberry fruit as well as tobacco leaves. Dual luciferase and Y1H assays further verified that PybZIPa directly activated the expression of PyUFGT by binding to tandem G-box motifs in the promoter, which was key to differential anthocyanin accumulation in debagged pear skin, and the number of G-box motifs affected the transcriptional activation of PyUFGT by PybZIPa. The results indicate that the light-induced anthocyanin biosynthesis regulatory mechanism in pear differs from that described in previous reports suggesting that a bZIP family member co-regulates anthocyanin biosynthesis with other transcription factors in apple and Arabidopsis. It was found that, in response to light, PybZIPa promoted anthocyanin biosynthesis by regulating important transcription factors (PyMYB114, PyMYB10, and PyBBX22) as well as structural genes (PyUFGT) via binding to G-boxes within promoters. This activation was amplified by the self-binding of PybZIPa to activate its own promoter. Overall, we demonstrate the utility of a multiomics integrative approach for discovering new functional genes and pathways underlying light-induced anthocyanin biosynthesis.

Fruit with stripes, which are generally longitudinal, can occur naturally, but the bioprocesses underlying this phenomenon are unclear. Previously, we observed an atypical anthocyanin distribution that caused red-striped fruit on the spontaneous pear bud sport “Red Zaosu” (Pyrus bretschneideri Rehd.). In this study, comparative transcriptome analysis of the sport and wild-type “Zaosu” revealed that this atypical anthocyanin accumulation was tightly correlated with abnormal overexpression of the gene-encoding gibberellin (GA) 2-beta-dioxygenase 8, PbGA2ox8. Consistently, decreased methylation was also observed in the promoter region of PbGA2ox8 from “Red Zaosu” compared with “Zaosu”. Moreover, the GA levels in “Red Zaosu” seedlings were lower than those in “Zaosu” seedlings, and the application of exogenous GA4 reduced abnormal anthocyanin accumulation in “Red Zaosu”. Transient overexpression of PbGA2ox8 reduced the GA4 level and caused anthocyanin accumulation in pear fruit skin. Moreover, the presence of red stripes indicated anthocyanin accumulation in the hypanthial epidermal layer near vascular branches (VBs) in “Red Zaosu”. Transient overexpression of PbGA2ox8 resulting from vacuum infiltration induced anthocyanin accumulation preferentially in calcium-enriched areas near the vascular bundles in pear leaves. We propose a fruit-striping mechanism, in which the abnormal overexpression of PbGA2ox8 in “Red Zaosu” induces the formation of a longitudinal array of anthocyanin stripes near vascular bundles in fruit.

MYB transcription factors comprise one of the largest families in plant kingdom, which play a variety of functions in plant developmental processes and defence responses, the R2R3-MYB members are the predominant form found in higher plants. In the present study, a total of 111 StR2R3-MYB transcription factors were identified and further phylogenetically classified into 31 subfamilies, as supported by highly conserved gene structures and motifs. Collinearity analysis showed that the segmental duplication events played a crucial role in the expansion of StR2R3-MYB gene family. Synteny analysis indicated that 37 and 13 StR2R3-MYB genes were orthologous to Arabidopsis and wheat (Triticum aestivum), respectively, and these gene pairs have evolved under strong purifying selection. RNA-seq data from different tissues and abiotic stresses revealed tissue-preferential and abiotic stress-responsive StR2R3-MYB genes. We further analyzed StR2R3-MYB genes might be involved in anthocyanin biosynthesis and drought stress by using RNA-seq data of pigmented tetraploid potato cultivars and drought-sensitive and -tolerant tetraploid potato cultivars under drought stress, respectively. Moreover, EAR motifs were found in 21 StR2R3-MYB proteins and 446 pairs of proteins were predicted to interact with 21 EAR motif-containing StR2R3-MYB proteins by constructing the interaction network with medium confidence (0.4). Additionally, Gene Ontology (GO) analysis of the 21 EAR motif-containing StR2R3-MYB proteins was performed to further investigate their functions. This work will facilitate future biologically functional studies of potato StR2R3-MYB transcription factors and enrich the knowledge of MYB superfamily genes in plant species.

Hierarchical classification approaches have been shown to be effective for protein function prediction problem. Traditionally, a set of simple classifiers are used for each hierarchical level separately. In this paper, we introduce a deep neural network (DNN) model with multiple heads and multiple ends to realize the whole set of classifiers. The DNN model consists of three parts: the body part, the multi-end part and the multi-head part. The body part is a deep multilayer perceptron (MLP) shared by different classifiers for feature mapping. The multi-end part performs feature fusion transforming the input vectors of different classifiers to feature vectors with the same length so as to share the feature mapping part. The multi-head part is a set of linear multi-label classifiers. By sharing a deep MLP with multiple classifiers, we are able to construct more powerful classifiers for each level with limited training samples, and expecting to have better classification performance. Experiment results on benchmark datasets show that the proposed method significantly outperforms these traditional methods.