Comparison of genes involved in brain development: insights into the organization and evolution of the telencephalic pallium.

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.

Kirkendall effect-induced uniform stress distribution stabilizes nickel-rich layered oxide cathodes.

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.

Folic acid-coupled bovine serum albumin-modified magnetic nanocomposites from quantum-sized Fe3O4 and layered double hydroxide for actively targeted delivery of 5-fluorouracil.

The development of multifunctional magnetic nanocomposites as a drug delivery system for cancer therapy is highly desirable in current nanomedicine. Herein, folic acid-bovine serum albumin conjugate (FA-BSA) was modified on nanocomposites by combining quantum-sized Fe3O4 and layered double hydroxide (LDH) to obtain a novel FA-BSA/Fe3O4@LDH for the delivery of the anticancer drug 5-Fluorouracil (5-Fu). The prepared nanocomposites showed good dispersibility, colloidal stability, magnetic property and erythrocyte compatibility. FA-BSA/Fe3O4@LDH/5-Fu showed pH responsiveness, with both the amount and duration of release of FA-BSA/Fe3O4@LDH/5-Fu being significantly higher in pH 5.0 release medium than in pH 7.4 release medium. The cellular experiments implied that no significant cytotoxicity of FA-BSA/Fe3O4@LDH, particularly due to the presence of FA-BSA, which further enhanced the biocompatibility of the nanocomposite. Furthermore, FA-BSA/Fe3O4@LDH/5-Fu could specifically target the 2D HepG2 cells model and 3D hepatoma cell microspheres model in vitro, and efficient internalization through folate receptor-mediated endocytosis, showing excellent anti-cancer cell activity in a concentration-dependent manner. Therefore, the constructed FA-BSA/Fe3O4@LDH was able to provide a potential novel multifunctional nanocomposite for magnetic-targeting drug delivery and pH-responsive release of drugs to enhance the efficiency of cancer therapy.

MkcDBGAS: a reference-free approach to identify comprehensive alternative splicing events in a transcriptome.

Alternative splicing (AS) is an essential post-transcriptional mechanism that regulates many biological processes. However, identifying comprehensive types of AS events without guidance from a reference genome is still a challenge. Here, we proposed a novel method, MkcDBGAS, to identify all seven types of AS events using transcriptome alone, without a reference genome. MkcDBGAS, modeled by full-length transcripts of human and Arabidopsis thaliana, consists of three modules. In the first module, MkcDBGAS, for the first time, uses a colored de Bruijn graph with dynamic- and mixed- kmers to identify bubbles generated by AS with precision higher than 98.17% and detect AS types overlooked by other tools. In the second module, to further classify types of AS, MkcDBGAS added the motifs of exons to construct the feature matrix followed by the XGBoost-based classifier with the accuracy of classification greater than 93.40%, which outperformed other widely used machine learning models and the state-of-the-art methods. Highly scalable, MkcDBGAS performed well when applied to Iso-Seq data of Amborella and transcriptome of mouse. In the third module, MkcDBGAS provides the analysis of differential splicing across multiple biological conditions when RNA-sequencing data is available. MkcDBGAS is the first accurate and scalable method for detecting all seven types of AS events using the transcriptome alone, which will greatly empower the studies of AS in a wider field.

Identification of clade-wide putative cis-regulatory elements from conserved non-coding sequences in Cucurbitaceae genomes.

Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms. Many conserved non-coding sequences (CNSs) function as cis-regulatory elements. They control the development of various lineages. However, predicting clade-wide cis-regulatory elements across several closely related species remains challenging. Based on the relationship between CNSs and cis-regulatory elements, we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes. Using 12-way whole-genome alignment, we first obtained 632 112 CNSs in Cucurbitaceae. Next, we identified 16 552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants. Furthermore, we predicted 3 271 potential regulatory pairs in the cucumber genome, of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages. The CNSs, Cucurbitaceae-wide cis-regulatory elements, and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/. These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.

[Spatial Distribution, Speciation, and Ecological Risk Assessment of Heavy Metals in Surface Sediments of Dongjiang Lake, Hunan Province].

To understand the heavy metal pollution status of Dongjiang Lake, the contents and species of heavy metals in the surface sediments were investigated during September 2021, and the heavy metal pollution level and potential ecological risk were evaluated. The results showed that Cd, Pb, As, Cu, Zn, Ni, and Cr contents were in the range of 0.40-34.1, 14.8-1688, 6.99-1155, 6.89-280, 26.2-1739, 6.29-55.4, and 23.3-44.8 mg·kg-1, respectively, with extremely uneven spatial distributions. The highest contents of Cd, Pb, As, Zn, Cu, and Ni were found in the site adjacent to Yaogangxian tungsten ore. The proportion of metal species with bioavailability was high, in which Cd in acid-soluble species was 46.7%-71.5% and Pb in reducible species was 46.8%-67.0%. The bioavailable species of Cu, Zn, Ni, and Cr were 35%-68%, 42%-72%, 26%-51%, and 6%-30%, respectively, although they primarily existed in residual species. According to the geo-accumulation index (Igeo), there was a moderate or extreme pollution status of Cd in all sites, moderate or extreme pollution status of Pb in 90% of sites, and moderate pollution status of As, Cu, and Zn in 30% of sites. The ecological risk factor (Eri) of Cd showed high potential ecological risk in all sites with significantly high potential ecological risk in 80% of sites. Moreover, As and Pb had significantly high potential ecological risk, and Cu had moderate potential ecological risk in S7, which was adjacent to Yaogangxian tungsten ore. There was a high total potential ecological risk in all sites and significantly high potential ecological risk in 50% of sites. Therefore, the surface sediments of Dongjiang Lake were under the combined pollution of Cd, Pb, As, Zn, and Cu with high bioavailability and high total potential ecological risk.

Solidification/stabilisation behaviours of Zn2+ in magnesium potassium phosphate cement: Experiments and density functional theory study.

The solidification/stabilisation behaviours of Zn2+ in magnesium potassium phosphate cement (MKPC) have not been thoroughly investigated. Herein, a series of experiments and a detailed density functional theory (DFT) study were conducted to investigate the solidification/stabilisation behaviours of Zn2+ in MKPC. The results showed that the compressive strength of MKPC reduced with the addition of Zn2+ because the formation of MgKPO4·6H2O (the main hydration product in MKPC) was delayed with the addition of Zn2+, as discovered by the crystal characteristics, and because Zn2+ exhibited a lower binding energy in MgKPO4·6H2O compared to Mg2+, as revealed by DFT results. Additonally, Zn2+ had little influence on the structure of MgKPO4·6H2O, and Zn2+ existed in MKPC as the formation of Zn2(OH)PO4, which was decomposed in the range of around 190-350 °C. Moreover, there were a lot of well-crystallised tabular hydration products before the addition of Zn2+, but the matrix was comprised of irregular prism crystals after adding Zn2+. Furthermore, the leaching toxicity of Zn2+ of MKPC was much smaller than the requirements of Chinese and European standards.

Metal-organic framework decorated with glycyrrhetinic acid conjugated chitosan as a pH-responsive nanocarrier for targeted drug delivery.

Stimulus-responsive nanomaterials have become a hot spot in controllable drug delivery systems researches owing to their spatiotemporal controllable properties based on the differences between tumor microenvironment and normal tissue. Herein, iron (III) carboxylate metal-organic framework nanoparticles coated with glycyrrhetinic acid-chitosan conjugate (MIL-101/GA-CS) were successfully fabricated and acted as the pH-responsive and target-selective system to deliver doxorubicin (DOX) for hepatocellular carcinoma (HCC) therapy. The prepared nanocarrier possess the advantages of uniform size, comparable drug loading efficiency (28.89%), and superior pH-dependent controlled drug release (DOX release of 2.74% and 89.18% within 72 h at pH 7.4 and 5.5, respectively). In vitro cytotoxicity assays showed that the drug-loaded nanocarriers exhibited excellent inhibitory effects on HepG2 cells due to the sustained release of DOX, while the nanocarriers showed no significant toxicity. Furthermore, cell uptake experiments demonstrated that MIL-101-DOX/GA-CS could target HepG2 cells based on receptor-dependent internalization of glycyrrhetinic acid receptors mediated. In vitro 3D hepatoma cell microspheres experiments showed that MIL-101-DOX/GA-CS had excellent penetration and tumor killing ability. Therefore, MIL-101-DOX/GA-CS nanoparticles have a prospective application in cancer therapy as a pH-responsive controlled drug delivery system.

ploidyfrost: Reference-free estimation of ploidy level from whole genome sequencing data based on de Bruijn graphs.

Polyploidy is ubiquitous and its consequences are complex and variable. A change of ploidy level generally influences genetic diversity and results in morphological, physiological and ecological differences between cells or organisms with different ploidy levels. To avoid cumbersome experiments and take advantage of the less biased information provided by the vast amounts of genome sequencing data, computational tools for ploidy estimation are urgently needed. Until now, although a few such tools have been developed, many aspects of this estimation, such as the requirement of a reference genome, the lack of informative results and objective inferences, and the influence of false positives from errors and repeats, need further improvement. We have developed ploidyfrost, a de Bruijn graph-based method, to estimate ploidy levels from whole genome sequencing data sets without a reference genome. ploidyfrost provides a visual representation of allele frequency distribution generated using the ggplot2 package as well as quantitative results using the Gaussian mixture model. In addition, it takes advantage of colouring information encoded in coloured de Bruijn graphs to analyse multiple samples simultaneously and to flexibly filter putative false positives. We evaluated the performance of ploidyfrost by analysing highly heterozygous or repetitive samples of Cyclocarya paliurus and a complex allooctoploid sample of Fragaria × ananassa. Moreover, we demonstrated that the accuracy of analysis results can be improved by constraining a threshold such as Cramér's V coefficient on variant features, which may significantly reduce the side effects of sequencing errors and annoying repeats on the graphical structure constructed.

Construction of pH-responsive polydopamine coated magnetic layered hydroxide nanostructure for intracellular drug delivery.

In recent years, using magnetic nanocomposites for controlled release of drugs and target-specific drug delivery has great potential in exploring a new method for cancer chemotherapy. Nevertheless, the low loading rate of insoluble drugs greatly restricts their efficacy and clinical application. Here, an efficient magnetic nanostructure combining Fe3O4 nanoparticles and layered double hydroxide (LDH) was developed and used for tumor cell inhibition. LDH was first deposited on Fe3O4 nanoparticles (Fe3O4@LDH), curcumin (Cur) was then loaded and polydopamine (PDA) eventually formed a PDA-coating on Fe3O4@Cur-LDH via self-polymerization. The Fe3O4@Cur-LDH/PDA nanostructure showed a suitable nano-meter size, excellent magnetic property, and high drug loading rate (up to 38 %). In vitro release results implied that Fe3O4@Cur-LDH/PDA nanostructure had good pH-responsive performance and excellent controlled-release behaviors due to the introduction of PDA. The cellular experiments demonstrated that Fe3O4@Cur-LDH/PDA nanostructure had good biocompatibility. In addition, Fe3O4@Cur-LDH/PDA entered into the cells mainly through endocytosis and had excellent inhibition on HepG2 cell viability in a concentration-dependent manner. Therefore, Fe3O4@Cur-LDH/PDA nanostructure has a prospective application in cancer therapy as a controlled drug delivery system.

DeepASmRNA: Reference-free prediction of alternative splicing events with a scalable and interpretable deep learning model.

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.

Evidence for a stable single component sharp texture in high purity aluminum during tube high-pressure shearing at room temperature.

A stable {[Formula: see text]} <110> 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 {[Formula: see text]} <110> 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.

Characteristics and potential functional effects of long insertions in Asian butternuts.

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.

PEGylation of Phosphatidylglycerol/Docosahexaenoic Acid Hexosomes with d-α-Tocopheryl Succinate Poly(ethylene glycol)2000 Induces Morphological Transformation into Vesicles with Prolonged Circulation Times.

Considering the broad therapeutic potential of omega-3 polyunsaturated fatty acids such as docosahexaenoic acid (DHA), here we study the effect of PEGylation of DHA-incorporated hexosomes on their physicochemical characteristics and biodistribution following intravenous injection into mice. Hexosomes were formed from phosphatidylglycerol and DHA with a weight ratio of 3:2. PEGylation was achieved through the incorporation of either d-α-tocopheryl succinate poly(ethylene glycol)2000 (TPGS-mPEG2000) or 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-methoxy-poly(ethylene glycol)2000 (DSPE-mPEG2000) at a concentration of 1.5 wt %. Nanoparticle tracking analysis, synchrotron small-angle scattering, and cryo-transmission electron microscopy were employed to characterize the nanodispersions. The results show that PEGylated lipids induce a structural transition from an inverse hexagonal (H2) phase inside the nanoparticles (hexosomes) to a lamellar (Lα) phase (vesicles). We also followed the effect of mouse plasma on the nanodispersion size distribution, number, and morphology because changes brought by plasma constituents could regulate the in vivo performance of intravenously injected nanodispersions. For comparative biodistribution studies, fluorescently labeled nanodispersions of equivalent quantum yields were injected intravenously into healthy mice. TPGS-mPEG2000-induced vesicles were most effective in avoiding hepatosplenic clearance at early time points. In an orthotopic xenograft murine model of glioblastoma, TPGS-mPEG2000-induced vesicles also showed improved localization to the brain compared with native hexosomes. We discuss these observations and their implications for the future design of injectable lyotropic nonlamellar liquid crystalline drug delivery nanosystems for therapeutic interventions of brain and liver diseases.

Free-Standing Stable Silicon-Based Anode with Exceptional Flexibility Realized by a Multifunctional Structure Design in Multiple Dimensions.

Cyclized polyacrylonitrile (cPAN) with decently flexible, elastic, and conductive properties is a promising substrate or binder material for flexible devices. However, it is infeasible to accommodate the large volume expansion and contribute the exceptional rate capability of silicon anodes in lithium-ion batteries only counting on the limited elasticity and conductivity of cPAN. Herein, we report a robust silicon/carbon-cPAN-graphene (SC-CP-G) composite membrane with excellent flexibility based on a multifunctional structure design in multiple dimensions, which can be used as a free-standing integrated anode for lithium ion batteries. In this integrated electrode, silicon nanoparticles are encapsulated in porous carbon with in situ formed confined space, and the silicon/carbon particles are further embedded in cPAN nanofibers, which are inextricably interwoven with a reduced graphene oxide film, forming an interpenetrating network architecture. The unique hierarchical and functional structure design greatly improves the mechanical performance, cycling stability, and capacity accessibility of silicon electrodes, delivering a specific capacity of 1847 mA h g-1 at 2 A g-1 and a capacity retention of 87% after 150 cycles.

High p16 expression and heterozygous RB1 loss are biomarkers for CDK4/6 inhibitor resistance in ER+ breast cancer.

CDK4/6 inhibitors combined with endocrine therapy have demonstrated higher antitumor activity than endocrine therapy alone for the treatment of advanced estrogen receptor-positive breast cancer. Some of these tumors are de novo resistant to CDK4/6 inhibitors and others develop acquired resistance. Here, we show that p16 overexpression is associated with reduced antitumor activity of CDK4/6 inhibitors in patient-derived xenografts (n = 37) and estrogen receptor-positive breast cancer cell lines, as well as reduced response of early and advanced breast cancer patients to CDK4/6 inhibitors (n = 89). We also identified heterozygous RB1 loss as biomarker of acquired resistance and poor clinical outcome. Combination of the CDK4/6 inhibitor ribociclib with the PI3K inhibitor alpelisib showed antitumor activity in estrogen receptor-positive non-basal-like breast cancer patient-derived xenografts, independently of PIK3CA, ESR1 or RB1 mutation, also in drug de-escalation experiments or omitting endocrine therapy. Our results offer insights into predicting primary/acquired resistance to CDK4/6 inhibitors and post-progression therapeutic strategies.

Enhancement of photosynthesis efficiency and yield of strawberry (Fragaria ananassa Duch.) plants via LED systems.

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.

Commercially Viable Hybrid Li-Ion/Metal Batteries with High Energy Density Realized by Symbiotic Anode and Prelithiated Cathode.

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.