Combining transcriptomics and metabolomics to identify key response genes for aluminum toxicity in the root system of Brassica napus L. seedlings.

KEY MESSAGE: By integrating QTL mapping, transcriptomics and metabolomics, 138 hub genes were identified in rapeseed root response to aluminum stress and mainly involved in metabolism of lipids, carbohydrates and secondary metabolites. Aluminum (Al) toxicity has become one of the important abiotic stress factors in areas with acid soil, which hinders the absorption of water and nutrients by roots, and consequently retards the growth of crops. A deeper understanding of the stress-response mechanism of Brassica napus may allow us to identify the tolerance gene(s) and use this information in breeding-resistant crop varieties. In this study, a population of 138 recombinant inbred lines (RILs) was subjected to aluminum stress, and QTL (quantitative trait locus) mapping was used to preliminarily locate quantitative trait loci related to aluminum stress. Root tissues from seedlings of an aluminum-resistant (R) line and an aluminum-sensitive (S) line from the RIL population were harvested for transcriptome sequencing and metabolome determination. By combining the data on quantitative trait genes (QTGs), differentially expressed genes (DEGs), and differentially accumulated metabolites (DAMs), key candidate genes related to aluminum tolerance in rapeseed were determined. The results showed that there were 3186 QTGs in the RIL population, 14,232 DEGs and 457 DAMs in the comparison between R and S lines. Lastly, 138 hub genes were selected to have a strong positive or negative correlation with 30 important metabolites (|R|≥ 0.95). These genes were mainly involved in the metabolism of lipids, carbohydrates and secondary metabolites in response to Al toxicity stress. In summary, this study provides an effective method for screening key genes by combining QTLs, transcriptome sequencing and metabolomic analysis, but also lists key genes for exploring the molecular mechanism of Al tolerance in rapeseed seedling roots.

Lithium-Ion Conductor Li2ZrO3-Coated Primary Particles To Optimize the Performance of Li-Rich Mn-Based Cathode Materials.

A lithium-rich manganese-based cathode material (LRMC) is currently considered as one of the most promising next-generation materials for lithium-ion batteries, which has received much attention, but the LRMC still faces some key scientific issues to break through, such as poor rate capacity, rapid voltage, capacity decay, and low first coulomb efficiency. In this work, homogeneous Li2ZrO3 (LZO) was successfully coated on the surface of Li1.2Mn0.54Ni0.13Co0.13O2 (LRO) by molten salt-assisted sintering technology. Li2ZrO3 has good chemical and electrochemical stability, which can effectively inhibit the side reaction between electrode materials and electrolytes and reduce the dissolution of transition metal ions. Thus, the as-prepared LRO@LZO composites are expected to improve the cycling performance. It can be found that the discharge specific capacity of LRO is 271 mAh g-1 at 0.1 C, and the capacity retention rate is still 93.7% after 100 cycles at 1 C. In addition, Li2ZrO3 is an excellent lithium-ion conductor, which is prone to increasing the lithium-ion transfer rate and improving the rate capacity of LRO. Therefore, this study provides a new solution to improve the structure stability and electrochemical performance of LRMCs.

Stable isotopes in tree rings record physiological trends in Larix gmelinii after fires.

Fire is an important regulator of ecosystem dynamics in boreal forests, and in particular has a complicated association with growth and physiological processes of fire-tolerant tree species. Stable isotope ratios in tree rings are used extensively in eco-physiological studies for evaluating the impact of past environmental (e.g., drought and air pollution) factors on tree growth and physiological processes. Yet, such studies based on carbon (δ13C) and oxygen (δ18O) isotope ratios in tree rings are rarely conducted on fire effect, and are especially not well explored for fire-tolerant trees. In this study, we investigated variations in basal area increment and isotopes of Larix gmelinii (Rupr.) Rupr. before and after three moderate fires (different fire years) at three sites across the Great Xing'an Mountains, Northeastern China. We found that the radial growth of L. gmelinii trees has significantly declined after the fires across study sites. Following the fires, a simultaneous increase in δ13C and δ18O has strengthened the link between the two isotopes. Further, fires have significantly enhanced the 13C-derived intrinsic water-use efficiency (iWUE) and largely altered the relationships between δ13C, δ18O, iWUE and climate (temperature and precipitation). A dual-isotope conceptual model revealed that an initial co-increase in δ13C and δ18O in the fire year can be mainly attributed to a reduction in stomatal conductance with a constant photosynthetic rate. However, this physiological response would shift to different patterns over post-fire time between sites, which might be partly related to spring temperature. This study is beneficial to better understand, from a physiological perspective, how fire-tolerant tree species adapt to a fire-prone environment. It should also be remembered that the limitation of model assumptions and constraints may challenge model applicability and further inferred physiological response.

Enhanced kinetic behaviors of hollow MoO2/MoS2 nanospheres for sodium-ion-based energy storage.

Mo-based heterostructures offer a new strategy to improve the electronics/ion transport and diffusion kinetics of the anode materials for sodium-ion batteries (SIBs). MoO2/MoS2 hollow nanospheres have been successfully designed via in-situ ion exchange technology with the spherical coordination compound Mo-glycerates (MoG). The structural evolution processes of pure MoO2, MoO2/MoS2, and pure MoS2 materials have been investigated, illustrating that the structureofthenanospherecan be maintained by introducing the S-Mo-S bond. Based on the high conductivity of MoO2, the layered structure of MoS2 and the synergistic effect between components, as-obtained MoO2/MoS2 hollow nanospheres display enhanced electrochemical kinetic behaviors for SIBs. The MoO2/MoS2 hollow nanospheres achieve a rate performance with 72% capacity retention at a current of 3200 mA g-1 compared to 100 mA g-1. The capacity can be restored to the initial capacity after a current returns to 100 mA g-1, while the capacity fading of pure MoS2 is up to 24%. Moreover, the MoO2/MoS2 hollow nanospheres also exhibit cycling stability, maintaining a stable capacity of 455.4 mAh g-1 after 100 cycles at a current of 100 mA g-1. In this work, the design strategy for the hollow composite structure provides insight into the preparation of energy storage materials.

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Betula platyphylla is a pioneer tree species after fire disturbance in forest communities in the Daxing'an Mountains of China. Bark, as an external structure of vascular cambium, plays an important role in protection and transport. To understand the survival strategy of B. platyphylla under fire disturbance, we analyzed the functional traits of inner and outer bark of B. platyphylla at different heights (0.3, 0.8 and 1.3 m) in natural secondary forest of the Daxing'an Mountains. We further quantified the explanation of three environmental factors (stand, topography and soil) and identified the key factors driving the changes in those traits. The results showed that the relative inner bark thickness of B. platyphylla in burned plot followed an order of 0.3 m (4.7%) > 0.8 m (3.8%) > 1.3 m (3.3%), which was 28.6%, 14.4% and 3.1% higher than that in the unburned plot (30-35 years without fire disturbance), respectively. The relative outer bark thickness and the relative total bark thickness showed similar pattern with tree height. Fire had different effects on other bark functional traits of B. platyphylla. The inner bark density of B. platyphylla in burned plot was significantly decreased by 3.8%-5.6% and water content was significantly increased by 11.0%-12.2%, compared with that in unburned plot across the three heights. However, the contents of carbon, nitrogen, and phosphorus in inner (or outer) bark were not significantly affected by fire. Further, the mean inner bark nitrogen content at 0.3 m in burned plot (5.24 g·kg-1) was significantly higher than that at the other two heights (4.56-4.76 g·kg-1). Environmental factors explained 49.6% and 28.1% of the total variation in inner and outer bark functional traits, respectively, with the highest single explanation (18.9% or 9.9%) of soil factors. Diameter at breast height was the most important factor affecting the growth of inner and outer barks. In summary, fire affected survival strategies of B. platyphylla (e.g., increased the resource allocation to the base bark) via changing the environment factors, which would help improve their defense ability under fire disturbance.

Exploring the physicochemical role of Pd dopant in promoting Li-ion diffusion dynamics and storage performance of NbS2 at the atomic scale.

The two-dimensional layered niobium disulfide (NbS2), as a kind of anode material for Li-ion batteries, has received great attention because of its excellent electronic conductivity and structural stability. However, its ionic conductivity is far from desirable. Herein, we have proposed an effective way to acquire the rapid promotion of its Li-ion diffusion dynamics from the palladium doping effect. By first-principle calculations, we firstly investigated quantitative relations among lattice constants, mechanical properties, and Pd-doped concentration (x) for Pd doped NbS2 (PdxNbS2). It is found that the interlayer spacing of PdxNbS2 undergoes dramatic expansion, which contributes to affording its large space for Li-ion storage. And Pd0.25NbS2 has the best ductility, exhibiting its excellent destruction-resistant properties. Among PdxNbS2 (x = 0, 0.083, 0.167, 0.250, 0.333, and 0.417), it is also proved that Pd0.25NbS2 is the easiest to be prepared with the introduction of NbPd3 as the raw material for the Pd-dopant and it also exhibits excellent thermal stability at room temperature (300 K). Most importantly, by analysis with the climbing-image nudged elastic band method (CI-NEB), it is revealed that Pd0.25NbS2 shows the lowest Li-ion diffusion energy barrier of 0.26 eV, which is also much lower than that of NbS2 (0.43 eV). This is attributed to the inductive effect of the Pd-dopant in its layered structure, trying to maintain the Li-S six-coordinated structure at the initial state when Li-ions transfer to the saddle point. Accordingly, it induces a small structural difference in coordinate structures between initial states and transition states. Moreover, Pd0.25NbS2 undergoes a less obvious oxidation and reduction reaction, maintaining its excellent structural stability during Li intercalation/deintercalation. Additionally, the theoretical average voltage of Pd0.25NbS2 (1.75 V for Li0.75Pd0.25NbS2vs. Li/Li+) is also much lower than that of NbS2 (2.41 V vs. Li/Li+), implying that it can provide a higher power density. Therefore, our theoretical results pave a distinctive way to develop an ultrahigh-rate and long-life anode material for Li-ion batteries.

Unveiling the Role and Mechanism of Nb Doping and In Situ Carbon Coating on Improving Lithium-Ion Storage Characteristics of Rod-Like Morphology FeF3 ·0.33H2 O.

Given the inherent characteristics of transition metal fluorides and open tunnel-type frameworks, intercalation-conversion-type FeF3 ·0.33H2 O has attracted widespread attention as a promising lithium-ion battery cathode material with high operating voltage and high energy density. However, its low electronic conductivity and poor structural stability impede its practical application in high-rate capacity and long-lifetime batteries. Herein, rod-like Nb-substituted FeF3 ·0.33H2 O (Nb-FeF3 ·0.33H2 O@C) nanocrystals with a carbon coating derived from in situ carbonization in an ionic liquid are deliberately designed and prepared. Based on first-principles calculations and electrochemical analysis, it is shown that substitution of Nb into a proportion of Fe sites can dramatically reduce the total energy of the system and the bandgap, thus boosting the structural stability and electronic conductivity of FeF3 ·0.33H2 O. Simultaneously, the combination of a surface conductive carbon coating and assembly of the nanoparticles into a rod-like mesoporous architecture can produce an omni-directional ion/electron transmission network and a robust 3D composite structure. The Nb-FeF3 ·0.33H2 O@C composite with 3% Nb-doping displays high capacity (583.2 mAh g-1 at 0.2 C), good rate capacity (187.8 mAh g-1 at a high rate of 5.0 C), and excellent long-term cycle stability (160.4 mAh g-1 after 300 long cycles).

Protein-DNA Binding Residue Prediction via Bagging Strategy and Sequence-Based Cube-Format Feature.

Protein-DNA interactions play an important role in diverse biological processes. Accurately identifying protein-DNA binding residues is a critical but challenging task for protein function annotations and drug design. Although wet-lab experimental methods are the most accurate way to identify protein-DNA binding residues, they are time consuming and labor intensive. There is an urgent need to develop computational methods to rapidly and accurately predict protein-DNA binding residues. In this study, we propose a novel sequence-based method, named PredDBR, for predicting DNA-binding residues. In PredDBR, for each query protein, its position-specific frequency matrix (PSFM), predicted secondary structure (PSS), and predicted probabilities of ligand-binding residues (PPLBR) are first generated as three feature sources. Secondly, for each feature source, the sliding window technique is employed to extract the matrix-format feature of each residue. Then, we design two strategies, i.e., square root (SR) and average (AVE), to separately transform PSFM-based and two predicted feature source-based, i.e., PSS-based and PPLBR-based, matrix-format features of each residue into three corresponding cube-format features. Finally, after serially combining the three cube-format features, the ensemble classifier is generated via applying bagging strategy to multiple base classifiers built by the framework of 2D convolutional neural network. The computational experimental results demonstrate that the proposed PredDBR achieves an average overall accuracy of 93.7% and a Mathew's correlation coefficient of 0.405 on two independent validation datasets and outperforms several state-of-the-art sequenced-based protein-DNA binding residue predictors. The PredDBR web-server is available at https://jun-csbio.github.io/PredDBR/.

Accurate prediction of protein-ATP binding residues using position-specific frequency matrix.

Knowledge of protein-ATP interaction can help for protein functional annotation and drug discovery. Accurately identifying protein-ATP binding residues is an important but challenging task to gain the knowledge of protein-ATP interactions, especially for the case where only protein sequence information is given. In this study, we propose a novel method, named DeepATPseq, to predict protein-ATP binding residues without using any information about protein three-dimension structure or sequence-derived structural information. In DeepATPseq, the HHBlits-generated position-specific frequency matrix (PSFM) profile is first employed to extract the feature information of each residue. Then, for each residue, the PSFM-based feature is fed into two prediction models, which are generated by the algorithms of deep convolutional neural network (DCNN) and support vector machine (SVM) separately. The final ATP-binding probability of the corresponding residue is calculated by the weighted sum of the outputted values of DCNN-based and SVM-based models. Experimental results on the independent validation data set demonstrate that DeepATPseq could achieve an accuracy of 77.71%, covering 57.42% of all ATP-binding residues, while achieving a Matthew's correlation coefficient value (0.655) that is significantly higher than that of existing sequence-based methods and comparable to that of the state-of-the-art structure-based predictors. Detailed data analysis show that the major advantage of DeepATPseq lies at the combination utilization of DCNN and SVM that helps dig out more discriminative information from the PSFM profiles. The online server and standalone package of DeepATPseq are freely available at: https://jun-csbio.github.io/DeepATPseq/for academic use.

Superior Na-Storage Properties of Nickel-Substituted Na2FeSiO4@C Microspheres Encapsulated with the In Situ-Synthesized Alveolation-like Carbon Matrix.

The poor electronic conductivity of Na2FeSiO4 always limits its electrochemical reactivities and no effective solution has been found to date. Herein, the novel Ni-substituted Na2Fe1-xNixSiO4@C nanospheres (50-100 nm) encapsulated with a 3D hierarchical porous skeleton (named as alveolation-like configuration) constructed using in situ carbon are first synthesized via a facile sol-gel method, and the effects of Ni substitution combined with the design of a unique carbon network on Na-storage properties are assessed systematically, focusing on alleviating the inherent defects of the Na2FeSiO4 cathode material. A series of characterization technologies such as X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy and so forth, coupled with the electrochemical measurements and first-principles calculations, are used to explore the structure, morphology and electrochemical behaviors of the as-prepared materials. The results show that the synergism between Ni substitution and the special alveolation-like configuration enables fast Na ions mobility (from 10-14 to 10-12 cm2 s-1), reduces band gap energy (from 2.82 to 1.79 eV) and lowers Na-ion diffusion barriers, finally reciprocating the vigorous electrochemical kinetics of the electrode. Especially, the elaborately designed material-Na2Fe0.97Ni0.03SiO4@C-displays superior Na-storage properties of around 197.51 mA h g-1 (corresponding to 1.43 Na+ intercalation) at 0.1 C within 1.5-4.5 V along with desirable capacity retention (84.44% after 100 cycles), and the rate capability is also markedly enhanced (a capacity of 133.62 mA h g-1 at 2 C). Such the effective methodology employed in this work opens a potential pathway to synthesize the silicate cathode material with excellent electrochemical properties.

Studies on the Kinetic Behaviors of Na Ions Insertion/Extraction in Na2FeSiO4/C Cathode Material at Various Desodiation States.

Na2FeSiO4, as one of the promising cathode materials in sodium-ion batteries, has attracted great interests. However, studies on the kinetic behaviors of Na ions insertion/extraction in Na2FeSiO4 composite electrode have been barely considered, until now. Importantly, the specific capacity and rate capability of Na2FeSiO4 cathode materials are greatly correlated with the kinetics of Na+ transfer in the host material. Herein, on the basis of the characterizations of microstructure and morphologies (i.e., Rietveld refinement, FESEM, HRTEM, etc.), the electrochemical kinetics of Na ions extraction in Na2FeSiO4/C electrode are first studied in detail via two electrochemical techniques (EIS and GITT), establishing the rate-controlling steps of Na+ transport in Na2FeSiO4/C, evaluating series of kinetic parameters, as well as calculating the Na+ diffusion coefficient at various state-of-desodiation. Changes of impedance response of Na2FeSiO4/C electrode depending on the different levels of desodiation show that a serial features of electrode process for Na ions migration have tremendous discrepancies, indicating that the kinetics of Na+ extraction from Na2FeSiO4/C electrode are largely influenced by different electrode reaction processes. These results provide useful insight into the inner properties of Na2FeSiO4/C electrode, and it is significant to optimize the electrochemical performance of Na2FeSiO4/C. Moreover, two models of equivalent circuits are also constructed to simulate the electrode processes and describe the behaviors of Na ions transfer in Na2FeSiO4/C.