mlsa-iai-msu-lab/ru_sci_bench_zho_cite_reranking huggingface dataset:
Grafting vigour is associated with DNA de-methylation in eggplant

In horticulture, grafting is a popular technique used to combine positive traits from two different plants. This is achieved by joining the plant top part (scion) onto a rootstock which contains the stem and roots. Rootstocks can provide resistance to stress and increase plant production, but despite their wide use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype remain largely unknown. Given that epigenetics plays a relevant role during distance signalling in plants, we studied the genome-wide DNA methylation changes induced in eggplant (Solanum melongena) scion using two interspecific rootstocks to increase vigour. We found that vigour was associated with a change in scion gene expression and a genome-wide hypomethylation in the CHH context. Interestingly, this hypomethylation correlated with the downregulation of younger and potentially more active long terminal repeat retrotransposable elements (LTR-TEs), suggesting that graft-induced epigenetic modifications are associated with both physiological and molecular phenotypes in grafted plants. Our results indicate that the enhanced vigour induced by heterografting in eggplant is associated with epigenetic modifications, as also observed in some heterotic hybrids.
Frequent germplasm exchanges drive the high genetic diversity of Chinese-cultivated common apricot germplasm

The genetic diversity of germplasm is critical for exploring genetic and phenotypic resources and has important implications for crop-breeding sustainability and improvement. However, little is known about the factors that shape and maintain genetic diversity. Here, we assembled a high-quality chromosome-level reference of the Chinese common apricot ‘Yinxiangbai’, and we resequenced 180 apricot accessions that cover four major ecogeographical groups in China and other accessions from occidental countries. We concluded that Chinese-cultivated common apricot germplasms possessed much higher genetic diversity than those cultivated in Western countries. We also detected seven migration events among different apricot groups, where 27% of the genome was identified as being introgressed. Remarkably, we demonstrated that these introgressed regions drove the current high level of germplasm diversity in Chinese-cultivated common apricots by introducing different genes related to distinct phenotypes from different cultivated groups. Our results highlight the consideration that introgressed regions may provide an important reservoir of genetic resources that can be used to sustain modern breeding programs.
The CaCIPK3 gene positively regulates drought tolerance in pepper

Drought stress is a major agricultural problem restricting the growth, development, and productivity of plants. Calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs) significantly influence the plant response to different stresses. However, the molecular mechanisms of CBL-CIPK in the drought stress response of pepper are still unknown. Here, the function of CaCIPK3 in the regulation of drought stress in pepper (Capsicum annuum L.) was explored. Transcriptomic data and quantitative real-time PCR (qRT-PCR) analysis revealed that CaCIPK3 participates in the response to multiple stresses. Knockdown of CaCIPK3 in pepper increased the sensitivity to mannitol and methyl jasmonate (MeJA). Transient overexpression of CaCIPK3 improved drought tolerance by enhancing the activities of the antioxidant system and positively regulating jasmonate (JA)-related genes. Ectopic expression of CaCIPK3 in tomato also improved drought and MeJA resistance. As the CaCIPK3-interacting partner, CaCBL2 positively influenced drought resistance. Additionally, CaWRKY1 and CaWRKY41 directly bound the CaCIPK3 promoter to influence its expression. This study shows that CaCIPK3 acts as a positive regulator in drought stress resistance via the CBL-CIPK network to regulate MeJA signaling and the antioxidant defense system.
High throughput sequencing unravels tomatopathogen interactions towards a sustainable plant breeding

Tomato (Solanum lycopersicum) is one of the most economically important vegetables throughout the world. It is one of the best studied cultivated dicotyledonous plants, often used as a model system for plant research into classical genetics, cytogenetics, molecular genetics, and molecular biology. Tomato plants are affected by different pathogens such as viruses, viroids, fungi, oomycetes, bacteria, and nematodes, that reduce yield and affect product quality. The study of tomato as a plant-pathogen system helps to accelerate the discovery and understanding of the molecular mechanisms underlying disease resistance and offers the opportunity of improving the yield and quality of their edible products. The use of functional genomics has contributed to this purpose through both traditional and recently developed techniques, that allow the identification of plant key functional genes in susceptible and resistant responses, and the understanding of the molecular basis of compatible interactions during pathogen attack. Nextgeneration sequencing technologies (NGS), which produce massive quantities of sequencing data, have greatly accelerated research in biological sciences and offer great opportunities to better understand the molecular networks of plant-pathogen interactions. In this review, we summarize important research that used high-throughput RNA-seq technology to obtain transcriptome changes in tomato plants in response to a wide range of pathogens such as viruses, fungi, bacteria, oomycetes, and nematodes. These findings will facilitate genetic engineering efforts to incorporate new sources of resistance in tomato for protection against pathogens and are of major importance for sustainable plant-disease management, namely the ones relying on the plant’s innate immune mechanisms in view of plant breeding.
CmMLO17 and its partner CmKIC potentially support Alternaria alternata growth in Chrysanthemum morifolium

The Mildew Resistance Locus O (MLO) gene family has been investigated in many species.However,there are few studies on chrysanthemum MLO genes.We report in this study that CmMLO17 in Chrysanthemum morifolium was upregulated after Alternaria alternata infection.Silencing of CmMLO17 by artificial microRNA resulted in reduced susceptibility of chrysanthemum to A.alternata infection.Genes in the abscisic acid (ABA) and Ca~(2+) signaling pathways were upregulated in the CmMLO17-silenced line R20 compared to the wild-type plants.We speculated that CmMLO17-silenced plants had a faster and stronger defense response that was mediated by the ABA and Ca~(2+) signaling pathways,resulting in reduced susceptibility of chrysanthemum to A.alternata infection.In addition,a candidate gene,CmKIC,that may interact with CmMLO17 was discovered by the yeast two-hybrid assay.The interaction between CmMLO17 and CmKIC was confirmed using the yeast two-hybrid assay and bimolecular fluorescence complementation (BiFC) analysis.CmMLO17 and CmKIC were both located on the plasma membrane,and CmKIC was also located on the nucleus.CmKIC overexpression increased the susceptibility of chrysanthemum to A.alternata,whereas CmKIC silencing resulted in reduced susceptibility.Therefore,CmMLO17 and CmKIC may work together in C.morifolium to support the growth of A.alternata.The results of this study will provide insight into the potential function of MLO and improve the understanding of plant defense responses to necrotrophic pathogens.
PbEIL1 acts upstream of PbCysp1 to regulate ovule senescence in seedless pear

Numerous environmental and endogenous signals control the highly orchestrated and intricate process of plant senescence.Ethylene,a well-known inducer of senescence,has long been considered a key endogenous regulator of leaf and flower senescence,but the molecular mechanism of ethylene-induced ovule senescence has not yet been elucidated.In this study,we found that blockage of fertilization caused ovule abortion in the pear cultivar ‘1913'.According to transcriptome and phytohormone content data,ethylene biosynthesis was activated by pollination.At the same time,ethylene overaccumulated in ovules,where cells were sensitive to ethylene signals in the absence of fertilization.We identified a transcription factor in the ethylene signal response,ethylene-insensitive 3-like (EIL1),as a likely participant in ovule senescence.Overexpression of PbEIL1 in tomato caused precocious onset of ovule senescence.We further found that EIL1 could directly bind to the promoter of the SENESCENCE-ASSOCIATED CYSTEINE PROTEINASE 1 (PbCysp1) gene and act upstream of senescence.Yeast one-hybrid and dual-luciferase assays revealed the interaction of the transcription factor and the promoter DNA sequence and demonstrated that PbEIL1 enhanced the action of PbCysp1.Collectively,our results provide new insights into how ethylene promotes the progression of unfertilized ovule senescence.
The genome of Magnolia biondii Pamp.provides insights into the evolution of Magnoliales and biosynthesis of terpenoids

Magnolia biondii Pamp.(Magnoliaceae,magnoliids) is a phylogenetically,economically,and medicinally important ornamental tree species widely grown and cultivated in the north-temperate regions of China.Determining the genome sequence of M.biondii would help resolve the phylogenetic uncertainty of magnoliids and improve the understanding of individual trait evolution within the Magnolia genus.We assembled a chromosome-level reference genome of M.biondii using ~67,~175,and ~154 Gb of raw DNA sequences generated via Pacific Biosciences singlemolecule real-time sequencing,10X Genomics Chromium,and Hi-C scaffolding strategies,respectively.The final genome assembly was ~2.22 Gb,with a contig N50 value of 269.11 kb and a BUSCO complete gene percentage of 91.90%.Approximately 89.17% of the genome was organized into 19 chromosomes,resulting in a scaffold N50 of 92.86 Mb.The genome contained 47,547 protein-coding genes,accounting for 23.47% of the genome length,whereas 66.48% of the genome length consisted of repetitive elements.We confirmed a WGD event that occurred very close to the time of the split between the Magnoliales and Laurales.Functional enrichment of the Magnolia-specific and expanded gene families highlighted genes involved in the biosynthesis of secondary metabolites,plant-pathogen interactions,and responses to stimuli,which may improve the ecological fitness and biological adaptability of the lineage.Phylogenomic analyses revealed a sister relationship of magnoliids and Chloranthaceae,which are sister to a clade comprising monocots and eudicots.The genome sequence of M.biondii could lead to trait improvement,germplasm conservation,and evolutionary studies on the rapid radiation of early angiosperms.
Special Issue on Soil Microbial Ecology

Soils would not exist without the activity and diversity of residential microorganisms. Soil microbes are fundamental to maintaining key soil processes associated with organic matter decomposition, nutrient cycling, and plant productivity and are thus integral to human wellbeing. Recent technological advances have exponentially increased our knowledge concerning soil microbial composition, diversity, distribution, and ecological functions. The special issue on soil microbial ecology focuses on various aspects of soil microbiology, including soil microbial spatial distribution, microbial succession, community assembly processes, microbial biogeochemical cycles, the associations between microbial communities and plant health, and the identification and isolation of benefiting microbes for crop growth. The call for papers was widely recognized within the community, reflected by 12 research papers now published in the issue.
Soil phyllosilicate and iron oxide inhibit the quorum sensing of Chromobacterium violaceum

Microorganisms respond to various adverse environmental conditions and regulate different physiological functions by secreting and sensing signal molecules through quorum sensing (QS) systems. Phyllosilicates and iron oxides present in soils and sediments may have substantial impact on bacterial activity and QS due to their unique reactivity and close association with microorganisms. This research explored the effect of goethite, montmorillonite and kaolinite (0.05-2 g L~(-1)) on the growth and QS of a bacterial model, Chromobacterium violaceum. The results showed that kaolinite and goethite caused cellular damage at low mineral concentrations. The capacity for violacein production and biofilm formation of C. violaceum were inhibited by the minerals in the order of kaolinite > goethite > montmorillonite. The possible underlying mechanisms for QS inhibition by different minerals were investigated. Specifically, kaolinite repressed QS function through downregulation the expression of signal molecules synthesis gene cviI. Goethite and montmorillonite interfered with QS by adsorption of extracellular signal molecules. This work provides a better understanding of the interactions between bacteria and minerals and proposed that the inhibition of QS system is an ignored mechanism for bacterial toxicity by phyllosilicates and iron oxides.
Hydrogen peroxide enabled two-dimensional molybdenum trioxide nanosheet clusters for enhanced surface Li-ion storage

Molybdenum trioxide (MoO 3) is regarded as a promising electrode material for lithium (Li)-ion batteries because of its unique layered structure with a high theoretical capacity (~ 1117 mAh·g~(–1)). Till now, numerous researches have focused on tuning MoO 3 morphology to improve its electrochemical performance. However, the fabrication of MoO 3 with a two-dimensional (2D) nanosheet clusters structure has yet been achieved. Here, we report a facile one-step solvothermal method to prepare MoO 3 nanosheets, of which the morphology can be facilely tuned via the dose of hydrogen peroxide. Both the experimental results and theoretical calculation suggest that the resultant 2D nanosheets structure could reduce the diffusion paths, which is beneficial for the intercalation of Li-ion. As a result, the nanosheets assembled Li-ion battery has a reversible specific capacity of 756.1 mAh·g~(–1) at 0.5 A·g~(–1), and maintained at 214.7 mAh·g~(–1) after 600 cycles at a current density of 1 A·g~(–1) with the Coulombic efficiency as high as 97.17%.
Changes in the soil microbial communities of different soil aggregations after vegetation restoration in a semiarid grassland, China

Soil aggregate fractions can regulate microbial community composition and structure after vegetation restoration. However, there has been less focus on the effects of soil aggregate fractions on the distributions of microbial communities. Here, we used phospholipid fatty acid (PLFA) analysis to explore the effects of different years of vegetation restoration (a 35-year-old Thymus mongolicus community (Re-35yrs) and a 2-year-old nongrazing grassland (Ug-2yrs)) on microbial communities within different soil aggregate sizes ( < 0.25 mm, 0.25-1 mm, 1-2 mm, 2-3 mm, 3-5 mm and >5 mm). The results indicated that the amount of total PLFA in Re-35yrs was 10 times greater than that in Ug-2yrs. The soil aggregate stability increased with increasing duration of vegetation restoration. In Re-35yrs, the total PLFA shown an increase as the soil aggregate size increased, and the highest values were observed in 3-5 mm. Ug-2yrs differed from Re-35yrs, the soil microbial diversity was higher in medium particle sizes (1-2 mm and 2-3 mm) and lower in microaggregates ( < 0.25 mm and 0.25-1 mm) and macroaggregates (3-5 mm and >5 mm). Soil microbial diversity was highest in large particle size aggregates, which resulted in low environmental stress and strong stability. The same tendency was observed in the high values of cyc/prec, S/M and soil organic matter, which indicated a lower turnover speed (F/B) of fungal energy utilization and a higher fixation rate. After years of natural restoration, the soil microbial community generally transformed from nutrient-rich to heterotrophdominant, especially in microaggregates (reflected in the G+/G -ratio).
Preface to the special issue on advanced materials for nuclear energy applications

Nuclear energy is playing an essential role in modern human society. Because of renewed public concern with regard to energy generation and climate change, worldwide interest in nuclear energy and technology is increasing. According to Director General Rafael Mariano Grossi from International Atomic Energy Agency (IAEA), nuclear energy contributes to ~ 10% global energy. The development of advanced nuclear energy systems, including both fusion and fission, is significantly accelerated. The largest fusion device under construction, ITER, is now preparing to install the first coil pair. The Joint European Torus (JET) has recently started fusion experiments using tritium, a radioactive isotope of hydrogen which is very rare and expensive. In China, Hualong One, the Chinese Generation III + pressurized water nuclear reactor, enters commercial service at the beginning of 2021. As the power capability keeps increasing in these advanced nuclear energy systems, the materials in these nuclear systems are exposed to aggressive environmental conditions and damage from high-temperature radiation, which results in mechanical degradation and life reduction. As a highly active field, both challenges and opportunities are present, and thus, we encourage the youth and talents to join the field, contributing to the development of advanced nuclear materials.
The role of tungsten-related elements for improving the electrochemical performances of cathode materials in lithium ion batteries

Lithium ion batteries using Ni–Co–Mn ternary oxide materials (NCMs) and Ni–Co–Al materials (NCAs) as the cathode materials are dominantly employed to power the electric vehicles (EVs). Increasing the driving range of EVs necessitates an increase of Ni content to improve the energy densities, which, however, degrades the cycle stability. Here we review the doping/coating of tungsten and related elements to improve the electrochemical performance of these cathodes especially the cycle stability. The selection of tungsten and related elements is based on their special properties including the high valence state, strong bonding with oxygen and the large ionic radius. The improvement of cycle stability mainly results from two features: (1) the enhancement of bulk structure stability upon doping (Mo, W, Ta, Nb) and (2) the resistance of side reactions of electrode/electrolyte by the surficial layer induced by direct coating (V, W, Nb) or bulk doping. For the recent high Ni materials, the formation of Ni 2+ and its migration to the Li layer induced by these doped/coated tungsten-related elements, and the presence of spinel or rock-salt phase before cycling contributes to improving the cycle stability. The key challenges are the selection of an optimized additive concentration and the fundamental understanding of the reaction mechanism, which will provide insightful guidance for maximizing the electrochemical performance of the state-of-the-art lithium-ion batteries at minimal additional process costs.
Defect inspection technologies for additive manufacturing

Additive manufacturing (AM) technology is considered one of the most promising manufacturing technologies in the aerospace and defense industries. However, AM components are known to have various internal defects, such as powder agglomeration, balling, porosity, internal cracks and thermal/internal stress, which can significantly affect the quality, mechanical properties and safety of final parts. Therefore, defect inspection methods are important for reducing manufactured defects and improving the surface quality and mechanical properties of AM components. This paper describes defect inspection technologies and their applications in AM processes. The architecture of defects in AM processes is reviewed. Traditional defect detection technology and the surface defect detection methods based on deep learning are summarized, and future aspects are suggested.
The transcriptome of circulating cells indicates potential biomarkers and therapeutic targets in the course of hypertension-related myocardial infarction

Hypertension (HT) is the most common public-health challenge and shows a high incidence around the world. Cardiovascular diseases are the leading cause of mortality and morbidity among the elderly (age >65 years) in the United States. Now, there is widespread acceptance of the causal link between HT and acute myocardial infarction (MI). This is the first data-mining study to identify co-expressed differentially expressed genes (co-DEGs) between HTand MI (relative to normal control) and to uncover potential biomarkers and therapeutic targets of HTrelated MI. In this manuscript, HT-specific DEGs and MI-specific DEGs and differentially expressed microRNAs (DE-miRNAs) were identified in Gene Expression Omnibus (GEO) datasets GSE24752, GSE60993, GSE62646, and GSE24548 after data consolidation and batch correction. Subsequently, enrichment in Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways as well as proteineprotein interaction networks were identified, and singlegene gene set enrichment analysis was performed to determine the affected biological categories and networks. Cross-matching of the results on co-DE-miRNAs and predicted miRNAs targeting the co-DEGs was conducted and discussed as well.We found that MYC and HIST1H2BO may be associated with HT, whereas FCGR1A, FYN, KLRD1, KLRB1, and FOLR3 may be implicated in MI. Moreover, co-DEGs FOLR3 and NFE2 with predicted miRNAs and DE-miRNAs, especially miR-7 and miR-548, may be significantly associated and show huge potential as a new set of novel biomarkers and important molecular targets in the course of HT-related MI.
Mowing weakens the positive effects of nitrogen deposition on fundamental ecosystem service of grassland

Forage yield is the fundamental ecosystem service of grasslands. While the quantitative responses of forage yield to nitrogen (N) enrichment are well known, its qualitative responses remain unclear. Even less known is the relative contribution of changes in community composition to the quality of the yield at the community level. We examined the quantitative and qualitative responses of forage yield at both plant functional group and community levels with factorial treatments of N addition and mowing in a temperate steppe. Nitrogen addition significantly enhanced the community-level yield by favoring the growth of rhizomatous grass. Mowing tended to mediate the impacts of N addition on the yield. Nitrogen addition increased the concentrations of crude protein and crude fat in forage at the community level. Neither the main effects of mowing nor its interactive effects with N addition affected forage quality. The N-induced shifts in plant species composition significantly contributed to the effects of N addition on forage quality at the community level. Our results suggest that mowing wound weaken the positive effects of N deposition on the quantity but not the quality of forage yield. Changes in plant community composition are important in driving the qualitative responses of yield to N deposition.