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Graphene-based materials (GBMs) have become potential soil pollutants due to their wide applications in agricultural environments. Although physiological mechanisms of plant responses to GBMs have been previously explored, the underlying molecular mechanisms remain unclear. In this paper, we analysed the physiological and transcriptomic changes of buckwheat (Fagopyrum spp.) roots exposed to 100 mg/L graphene oxide (GO) with different diameter. GO negatively affected root growth and higher diameters of GO caused more adverse effects on the root. In total 3 724 GO-responsive genes were identified in root by transcriptome analysis. 70 differentially expressed genes (DEGs) were involved in ROS detoxification, and 37 transporter-encoding genes were found to be involved in GO response. These transporters may regulate the uptake and transport of GO in buckwheat. The gene expression of 84 transcription factors (TFs) showed a response to GO stress in the root, which may regulate the transporters and reactive oxygen species (ROS) detoxification-related genes. Finally, the difference in the transcriptomic response of the root to the three GO materials with different diameters was investigated. 49 GO-responsive genes may be involved in the difference in the toxicity of GO with different diameters. This study provides new insights into the molecular mechanisms of plant roots to GBMs.

This study is the first to use highland barley (HB) to study the toxic effects of Cr (VI) on seedlings and the response mechanism of HELNs to Cr (VI) stress. The outcomes indicated that the germination rate of HB seeds, plant height, root length, water content, and levels of proline (PRO) and soluble sugar in both leaves and roots were all impacted by varying concentrations of Cr (VI) treatments. Differential changes in the activities of antioxidant enzymes (SOD, POD, CAT) were observed in leaves and roots of HB. We also extracted HB-derived ELNs (HELNs) and characterized and sequenced HELNs. The average particle size of CK-HELNs was 79.0 nm, and the concentration of HELNs was 4.56 E+10 (particles/mL). As the concentration of Cr (VI) increased, the particle size of HELNs in HB seedlings also increased, while the concentration decreased. A total of 29 miRNA species were identified in CK-HELNs, Cr10-HELNs, and Cr40-HELNs. Out of these, 25 were newly predicted miRNAs, and the remaining four were known miRNAs. A total of 2 known miRNAs and 11 novel miRNAs were upregulated under different concentrations of Cr (VI) stress. 1 known and 5 novel miRNAs were downregulated under different concentrations of Cr (VI) stress. Enrichment of the GO and KEGG pathways revealed that the differential gene functions were mainly focused on binding and catalytic activities. This study reveals for the first time the changes of HELNs under different concentrations of Cr (VI) stress and the toxic effects of Cr (VI) on HB seedlings. This study provides a new perspective to explore the function and utilisation of ELNs.

Tartary buckwheat is characterized by its numerous inflorescences; however, the uneven distribution of resources can lead to an overload in certain areas, significantly limiting plant productivity. Plant growth regulators effectively modulate plant growth and development. This study investigated the effects of three concentrations of brassinosteroids (EBR) on the Tartary buckwheat cultivar with high seed-setting rates, specifically Chuanqiao No. 1 (CQ1), and low seed-setting rates, namely Xiqiao No. 1 (XQ1), through field experiments. The goal was to investigate how EBR regulates buckwheat grain-filling, enhancing the seed-setting rates, and to understand the physiological mechanisms behind this improvement. The results indicated that EBR treatment followed the typical “S” type growth curve of crops, resulting in an increase in the Tartary buckwheat grain-filling rate. Varieties with high seed-setting rates demonstrated a greater capacity for grain-filling. EBR was observed to regulate hormone content, enhance the photosynthetic capacity of Tartary buckwheat, and increase yield. This was accomplished by enhancing the accumulation of photosynthetic products during the grain-filling period. Specifically, EBR elevated the activity of several key enzymes, including pre-leaf sucrose phosphate synthase (SPS), seed sucrose synthase (SS), late grain-filling acid invertase (AI), grain-filling leaf SPS, and grain SS. These changes led to an increased accumulation of sucrose and starch from photosynthetic products. In summary, the G2 concentration of EBR (0.1 mg/L) demonstrated the most significant impact on the seed-setting rates and yield enhancement of Tartary buckwheat.

Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn) is a crop of significant interest due to its nutritional value and resilience to drought conditions. However, drought, particularly following flowering, is a major factor contributing to yield reduction. This research employed two distinct Tartary buckwheat genotypes to investigate the effects of post-anthesis drought on growth and physicochemical characteristics. The study aimed to elucidate the response of Tartary buckwheat to drought stress. The findings indicated that post-anthesis drought adversely impacted the growth, morphology, and biomass accumulation of Tartary buckwheat. Drought stress enhanced the maximum photosynthetic capacity (Fv/Fm) and light protection ability (NPQ) of the ‘Xiqiao-2’ genotype. In response to drought stress, ‘Dingku-1’ and ‘Xiqiao-2’ maintained osmotic balance by accumulating soluble sugars and proline, respectively. Notably, ‘Xiqiao-2’ exhibited elevated levels of flavonoids and polyphenols in its leaves, which helped mitigate oxidative damage caused by drought. Furthermore, rewatering after a brief drought period significantly improved plant height, stem diameter, and biomass accumulation in ‘Dingku-1’. Overall, ‘Xiqiao-2’ demonstrated greater long-term tolerance to post-anthesis drought, while ‘Dingku-1’ was less adversely affected by short-term post-anthesis drought.

Background: Eurotium cristatum (E. cristatum) is the probiotic fungus in Fu-brick tea, with which fermentation brings a unique flavor and taste and health-promoting effects. Tartary buckwheat leaves are rich in functional active substances such as flavonoids and phenolic compounds, yet are not effectively utilized. Methods: Tartary buckwheat leaves were processed into raw green tea first and subsequently fermented with E. cristatum to develop a novel fermented leaf tea. The tea quality was evaluated by the aspects of the sensory scores by E-tongue, the volatile compounds by HS-SPME-GC-MS, the non-volatile profile by biochemical and UPLC-MS/MS methods and the antioxidant activity by the colorimetric assay. Results: Fermented leaf tea displayed a golden yellow color, a unique “flower” aroma and a dark-tea taste, with an improved sensory acceptability. Fermentation raised the content of volatile heterocyclic and aromatic compounds, alkenes and other aromatic components, which produced a unique floral flavor. The proportion of sour, bitter and astringency accounting non-volatile compounds such as phenolic acids and amino acids decreased, while the proportion of umami and sweet accounting substances such as responsible amino acids increased. Fermented leaf tea displayed a relative stronger total antioxidant activity against ABTS. Conclusion: E. cristatum fermentation exerted positive effects on Tartary buckwheat leaf tea quality.

As we face increasing challenges of world food security and malnutrition, coarse cereals are coming into favor as an important supplement to human staple foods due to their high nutritional value. In addition, their functional components, such as flavonoids and polyphenols, make them an important food source for healthy diets. However, we lack a systematic understanding of the importance of coarse cereals for world food security and nutritional goals. This review summarizes the worldwide cultivation and distribution of coarse cereals, indicating that the global area for coarse cereal cultivation is steadily increasing. This paper also focuses on the special adaptive mechanisms of coarse cereals to drought and discusses the strategies to improve coarse cereal crop yields from the perspective of agricultural production systems. The future possibilities, challenges, and opportunities for coarse cereal production are summarized in the face of food security challenges, and new ideas for world coarse cereal production are suggested.

Abstract Background Photoperiod is an important environmental cue interacting with circadian clock pathway to optimize the local adaption and yield of crops. Quinoa (Chenopodium quinoa) in family Amaranthaceae has been known as superfood due to the nutritious elements. As quinoa was originated from the low-latitude Andes, most of the quinoa accessions are short-day type. Short-day type quinoa usually displays altered growth and yield status when introduced into higher latitude regions. Thus, deciphering the photoperiodic regulation on circadian clock pathway will help breed adaptable and high yielding quinoa cultivars. Results In this study, we conducted RNA-seq analysis of the diurnally collected leaves of quinoa plants treated by short-day (SD) and long-day conditions (LD), respectively. We identified 19,818 (44% of global genes) rhythmic genes in quinoa using HAYSTACK analysis. We identified the putative circadian clock architecture and investigated the photoperiodic regulatory effects on the expression phase and amplitude of global rhythmic genes, core clock components and transcription factors. The global rhythmic transcripts were involved in time-of-day specific biological processes. A higher percentage of rhythmic genes had advanced phases and strengthened amplitudes when switched from LD to SD. The transcription factors of CO-like, DBB, EIL, ERF, NAC, TALE and WRKY families were sensitive to the day length changes. We speculated that those transcription factors may function as key mediators for the circadian clock output in quinoa. Besides, we identified 15 novel time-of-day specific motifs that may be key cis elements for rhythm-keeping in quinoa. Conclusions Collectively, this study lays a foundation for understanding the circadian clock pathway and provides useful molecular resources for adaptable elites breeding in quinoa.

Multiple plant lineages have independently evolved sex chromosomes and variable karyotypes to maintain their sessile lifestyles through constant biological innovation. Morus notabilis, a dioecious mulberry species, has the fewest chromosomes among Morus spp., but the genetic basis of sex determination and karyotype evolution in this species has not been identified. In this study, three high-quality genome assemblies were generated for Morus spp. [including dioecious M. notabilis (male and female) and Morus yunnanensis (female)] with genome sizes of 301–329 Mb and were grouped into six pseudochromosomes. Using a combination of genomic approaches, we found that the putative ancestral karyotype of Morus species was close to 14 protochromosomes, and that several chromosome fusion events resulted in descending dysploidy (2n = 2x = 12). We also characterized a ∼ 6.2-Mb sex-determining region on chromosome 3. Four potential male-specific genes, a partially duplicated DNA helicase gene (named MSDH) and three Ty3_Gypsy long terminal repeat retrotransposons (named MSTG1/2/3), were identified in the Y-linked area and considered to be strong candidate genes for sex determination or differentiation. Population genomic analysis showed that Guangdong accessions in China were genetically similar to Japanese accessions of mulberry. In addition, genomic areas containing selective sweeps that distinguish domesticated mulberry from wild populations in terms of flowering and disease resistance were identified. Our study provides an important genetic resource for sex identification research and molecular breeding in mulberry.

Tartary buckwheat (Fagopyrum tataricum Gaertn.) is an important pseudocereal crop with excellent edible, nutritional and medicinal values. However, the yield of Tartary buckwheat (TB) is very low due to old-fashioned cultivation techniques, particularly unreasonable application of nitrogen fertilizer. To improve the understanding on the theories of nitrogen use in TB, the effects of nitrogen application on growth, as well as chemical properties and microbial community of rhizosphere soil were investigated in this study. Nitrogen application could promote the plant height, stem diameter, nitrogen accumulation and yield of TB. The relative abundance and diversity of bacteria and fungi in the rhizosphere soil of TB were improved by nitrogen fertilizer. Nitrogen application increased the abundance of beneficial bacteria such as Lysobacter and Sphingomonas in rhizosphere soil, and decreased the abundance of pathogenic fungi such as Fusarium and Plectosphaerella. The results indicated that nitrogen application changed the distribution of microbial communities in TB rhizosphere soil. Furthermore, the specific enriched or depleted microorganisms in the rhizosphere soil of four TB varieties were analyzed at OTU level. 87 specific nitrogen-responsive genes with sequence variation were identified in four varieties by integrating genomic re-sequencing and transcriptome analysis, and these genes may involve in the recruitment of specific rhizosphere microorganisms in different TB varieties. This study provided new insights into the effects of nitrogen application on TB growth and rhizosphere microbial community, and improved the understanding on the mechanisms of TB root–microbe interactions.

Titanium has been reported to have positive effects on crop growth and production in various species. However, the impact of titanium on the Tartary buckwheat crops has not yet been studied. Therefore, an experiment was conducted to investigate the effect of spraying different concentrations of ionic titanium on the growth, photosynthesis, and uptake of mineral nutrients in Tartary buckwheat. The results showed that the application of titanium significantly improved dry matter accumulation, internode diameter, main stem node, root length, root average diameter, root surface area, root volume, grains per plant, and weight of grains per plant. Additionally, chlorophyll and photosynthetic parameters showed improvement regardless of the concentration of titanium used. The study found that titanium accumulation was mainly in leaves. The content of titanium in leaves showed a significant positive correlation with K, Ca, Mg, Mn, Cu, Zn, and B. This suggests a potential synergistic relationship between titanium and minerals in Tartary buckwheat leaves. Furthermore, the study also observed a significant increase in the total accumulation of P, K, Ca, Mg, Mn, Cu, Zn, and B in Tartary buckwheat plants. Overall, this study provides evidence for the positive effects of titanium on Tartary buckwheat and offers a theoretical foundation for practical production.

Tartary buckwheat is a cereal crop that has both medicinal and food origins. However, the underlying factors that contribute to Tartary buckwheat’s flowering and seed-setting characteristics, effective grain formation, and physiological changes are still not well understood. This study aimed to investigate the flowering and seed-setting characteristics of different parts of Tartary buckwheat, as well as the grain-filling characteristics after flowering. To achieve this, Tartary buckwheat cultivars with high (QK3) and low (XQ2) seed-setting rates were selected for pot and field experiments. The study found that Tartary buckwheat undergoes flowering and seed setting simultaneously. Many wilted flowers and grains were observed 45 and 51 d after flowering. Compared to XQ2, QK3 exhibited a higher grain formation rate and seed-setting rate by 7.42% and 26.16%, respectively. Additionally, QK3 had a significantly lower grain abortion rate by 12.03%. The 1000-grain weight and average grain-filling rate of QK3 were 11.10% and 14.81% higher than those of XQ2, respectively. QK3 exhibited a faster maximum grain-filling rate (Rmax), reaching 18.38% faster than XQ2. Additionally, the dry matter average distribution rate in the main stem and branched grains of QK3 was 13.26% and 23.07% higher than that of XQ2, respectively. The sucrose concentration, SS, and SSS enzyme activities of QK3 were all higher than those of XQ2, by 0.29–25.99%, 5.22–11.62%, and 6.64–12.47%, respectively. Correlation analysis revealed a significant positive correlation between sucrose, soluble sugar, and starch concentration during the grain formation process and SS and SSS activities. This suggests that the levels of SS, SSS, soluble sugar, and sucrose in the grain play a crucial role in grain filling.

Quinoa (Chenopodium quinoa) is a prospective orphan crop that needs yield improvement. Previous studies indicate PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN (PEBP) family genes are highly associated with the key agronomic traits of crops. Characterizing the pivotal PEBP genes will speed up the domestication and yield improvement of quinoa. Previous investigations on PEBP genes of Chenopodium species indicated that, the PEBP genes, despite in the same subclade, may have experienced functional diversification. Especially, the allotetraploidy (AABB) and numerous segmental duplications and chromosomal rearrangements in quinoa make it more difficult to understand the functions of PEBP genes. More recently, 6 quinoa FT subfamily genes were predicted to be related to flowering of quinoa. However, investigation on the whole PEBP family members is still lacking. In this study, we obtained 23 PEBP genes, including 5 MFT, 11 FTL and 7 TFL genes. We found 7 orthologous gene pairs, from sub-genome A and sub-genome B, respectively, showing collinearities with sugar beet. Evolution analysis on PEBP genes of two quinoa sub-genomes, sugar beet and relatives of diploid ancestors indicated that, the reasons for gene duplication events varied and 4 tandem duplications are the major reason for PEBP family expansion. Tissue-specific expression analysis suggested that expression patterns are mostly differing between orthologous gene pairs. Analysis on gene expressions at 6 stages suggested the possible positive roles of CqFTL1/CqFTL2, CqFTL5, CqFTL8, CqFTL6/CqFTL9 and CqTFL6/CqTFL7, and negative roles of CqTFL1/CqTFL2/CqTFL3, CqTFL4/CqTFL5 in inflorescence branching. Expression analysis in ABA-treated seed, in combination with the cis-acting element distribution analysis, indicated that CqMFT2, CqMFT3 and CqMFT4 may regulate seed germination via ABA signaling. Observations on responses to night break and photoperiod changes highlighted the roles of CqFTL5 and CqFTL8 under short day, and CqFTL6 under long day for quinoa flowering. Further, co-expression network analysis indicated that 64 transcription factors may act upstream of CqFTL5 and CqFTL8 to regulate flowering. Together, this study will help us identify the pivotal PEBP genes that may be utilized for quinoa breeding in future.

Abstract Background Type II diabetes mellitus (T2DM) is an important risk factor for osseointegration of implants. The aim of this study was to explore key genes of T2DM affecting bone metabolism through bioinformatic analysis of published RNA sequencing data, identify potential biomarkers, and provide a reference for finding the molecular mechanism of abnormal osseointegration caused by T2DM. Methods We identified differentially expressed mRNAs and miRNAs from the Gene Expression Omnibus database using the R package ‘limma’ and analysed the predicted target genes using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis and Gene Ontology analysis. At the same time, miRNA–mRNA interactions were explored using miRWalk 2.0. Results We constructed an miRNA-gene regulatory network and a protein–protein interaction network. The enrichment pathways of differentially expressed mRNAs included extracellular matrix receptor interactions, protein digestion and absorption, the PI3K-Akt signalling pathway, cytokine–cytokine receptor interactions, chemokine signalling pathways, and haematopoietic cell lineage functions. We analysed the expression of these differentially expressed mRNAs and miRNAs in T2DM rats and normal rats with bone implants and identified Smpd3, Itga10, and rno-mir-207 as possible key players in osseointegration in T2DM. Conclusion Smpd3, Itga10, and rno-mir-207 are possible biomarkers of osseointegration in T2DM. This study sheds light on the possible molecular mechanism of abnormal osseointegration caused by bone metabolism disorder in T2DM.

Objective: By using bioinformatics analysis, abnormal methylated differentially expressed genes (MDEGs) in Kawasaki disease (KD) were identified and a random forest diagnostic model for KD was established. Methods: The expression (GSE18606, GSE68004, GSE73461) and methylation (GSE109430) profiles was retrieved and download from Gene Expression Omnibus (GEO). We conducted enrichment analyses by using R software. In addition, we constructed a protein interaction network, and obtained 6 hub genes. We used expression profiles GSE100154 from GEO to verify the hub genes. Finally, we constructed a diagnostic model based on random forest. Results: We got a total of 55 MDEGs (43 hyper-methylated, low-expressing genes and 12 hypo-methylated, high-expressed genes). Six hub genes (CD2, IL2RB, IL7R, CD177, IL1RN, and MYL9) were identified by Cytoscape software. The area under curve (AUC) of the six hub genes was from 0.745 to 0.898, and the combined AUC was 0.967. The random forest diagnostic model showed that AUC was 0.901. Conclusion: The identification of 6 new hub genes improves our understanding of the molecular mechanism of KD, and the established model can be employed for accurate diagnosis and provide evidence for clinical diagnosis.

Rapid industrialization and urbanization have caused serious cadmium (Cd) pollution in soil. Tartary buckwheat is an important pseudocereal crop with the potential ability to tolerate various stresses. However, the responses to Cd stress in this species are unclear. In this study, we assessed the phenotypic, cytological, physiological, and transcriptomic characteristics of Tartary buckwheat under the various concentrations of Cd treatments to investigate the responses and their regulatory pathways for the first time. The results showed Tartary buckwheat could tolerate the high Cd concentration of 50 mg/L under Cd stress. The average root diameters increased as a result of more cell layers of the endodermis and the bigger size of the pericycle. Cd primarily accumulated in roots and relatively less transferred to leaves. Antioxidant activities and malondialdehyde (MDA) accumulation varied in different tissues and different Cd concentrations of treatments. Meanwhile, Cd stress led to the formation of Casparian strips in roots and damaged the cytoderm and organelles. The weighted gene co-expression and interaction network analyses revealed that 9 core genes induced by Cd stress were involved in metal ion binding, Ca signal transduction, cell wall organization, antioxidant activities, carbohydrate metabolic process, DNA catabolic process, and plant senescence, which regulated a series of phenotypic, cytological, and physiological changes above. These results laid the foundation for a deep understanding of the responses to Cd toxicity in Tartary buckwheat. It’s also a critical reference for the functional characterization of genes for Cd tolerance.

Tartary buckwheat is highly attractive for the richness of nutrients and quality, yet post-embryonic seed abortion greatly halts the yield. Seed development is crucial for determining grain yield, whereas the molecular basis and regulatory network of Tartary buckwheat seed development and filling is not well understood at present. Here, we assessed the transcriptional dynamics of filling stage Tartary buckwheat seeds at three developmental stages by RNA sequencing. Among the 4249 differentially expressed genes (DEGs), genes related to seed development were identified. Specifically, 88 phytohormone biosynthesis signaling genes, 309 TFs, and 16 expansin genes participating in cell enlargement, 37 structural genes involved in starch biosynthesis represented significant variation and were candidate key seed development genes. Cis-element enrichment analysis indicated that the promoters of differentially expressed expansin genes and starch biosynthesis genes are rich of hormone-responsive (ABA-, AUX-, ET-, and JA-), and seed growth-related (MYB, MYC and WRKY) binding sites. The expansin DEGs showed strong correlations with DEGs in phytohormone pathways and transcription factors (TFs). In total, phytohormone ABA, AUX, ET, BR and CTK, and related TFs could substantially regulate seed development in Tartary buckwheat through targeting downstream expansin genes and structural starch biosynthetic genes. This transcriptome data could provide a theoretical basis for improving yield of Tartary buckwheat.

Abstract Background Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Results In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes. Conclusions Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

In close-range photogrammetry, circular-coded targets (CCTs) are a reliable method to solve the issue of image correspondence. Currently, the identification methods for CCTs are very mature, but complex illumination conditions are still a key factor restricting identification. This article proposes an adaptive homomorphic filtering (AHF) algorithm to solve this issue, utilizing homomorphic filtering (HF) to eliminate the influence of uneven illumination. However, HF parameters vary with different lighting types. We use a genetic algorithm (GA) to carry out global optimization and take the identification result as the objective function to realize automatic parameter adjustment. This is different from the optimization strategy of traditional adaptive image enhancement methods, so the most significant advantage of the proposed algorithm lies in its automation and universality, i.e., users only need to input photos without considering the type of lighting conditions. As a preprocessing algorithm, we conducted experiments combining advanced commercial photogrammetric software and traditional identification methods, respectively. We cast stripe- and lattice-structured light to create complex lighting conditions, including uneven lighting, dense shadow areas, and elliptical light spots. Experiments showed that our algorithm significantly improves the robustness and accuracy of CCT identification methods under complex lighting conditions. Given the perfect performance under stripe-structured light, this algorithm can provide a new idea for the fusion of close-range photogrammetry and structured light. This algorithm helps to improve the quality and accuracy of photogrammetry and even helps to improve the decision making and planning process of photogrammetry.

Ciboria shiraiana causes hypertrophy sorosis scleroteniosis in mulberry trees, resulting in huge economic losses, and exploring its pathogenic mechanism at a genomic level is important for developing new control methods. Here, genome sequencing of C. shiraiana based on PacBio RSII and Illumina HiSeq 2500 platform as well as manual gap filling was performed. Synteny analysis with Sclerotinia sclerotiorum revealed 16 putative chromosomes corresponding to 16 chromosomes of C. shiraiana. Screening of rapid-evolution genes revealed that 97 and 2.4% of genes had undergone purifying selection and positive selection, respectively. When compared with S. sclerotiorum, fewer secreted effector proteins were found in C. shiraiana. The number of genes involved in pathogenicity, including secondary metabolites, carbohydrate active enzymes, and P450s, in the C. shiraiana genome was comparable with that of other necrotrophs but higher than that of biotrophs and saprotrophs. The growth-related genes and plant cell-wall-degradation-related genes in C. shiraiana were expressed in different developmental and infection stages, and may be potential targets for prevention and control of this pathogen. These results provide new insights into C. shiraiana pathogenic mechanisms, especially host range and necrotrophy features, and lay the foundation for further study of the underlying molecular mechanisms.

Smoothing the multi-scale textures with strong gradient while maintaining the weak structures is still a challenging work for the existing texture filtering methods. In this paper, we propose a variant of the bilateral filter to address this issue. Unlike the classical bilateral filter, which usually uses a fixed range kernel for texture filtering, the variant uses an adaptive range kernel, that is, if a pixel is located near a structure, the range kernel assigned to the pixel is small, otherwise, the range kernel is large. This mechanism ensures the preservation of sharp edges. In order to perform structure measurement, we propose a local histogram operator, which can identify structures from textures by comparing the difference in color distribution between the left and right half neighboring windows centered on the pixel of interest. In addition, after once bilateral filtering, instead of multiple iterations, a novel anisotropic filter is designed to remove residual textures, which can avoid edge blurring to some extent. Experimental results demonstrate the effectiveness of our method by comparing it with the state-of-the-art methods in preserving weak structures as well as suppressing textures with strong gradient or varying scales.

The concurrent collection of surface electromyography (sEMG) and strain signals is important for many applications, such as human–machine interaction, sign language recognition, and clinical evaluation of muscle function. Nevertheless, the conventional sensor systems made of rigid, bulky components cannot provide a reliable, conformal interface for accurate, continuous measurements of the epidermal physiological signals. Herein, a skin‐interfaced, multifunctional epidermal sensor patch with characteristics of mechanical softness, large stretchability, and wearable conformability for multimodal measurements of sEMG signals and associated skin deformations from various muscle activities and joint motions is reported. The sensor patch features two pairs of stretchable sEMG electrodes and two thin, miniaturized strain sensors, which are connected by stretchable filamentary serpentine interconnects in an open‐meshed structure. Experimental and computational studies reveal the design and operation of the sensor patch, which exhibit stable and repetitive performance even under a 30% stretching strain level. Demonstrations of the sensor patch on the wrist for simple sign language recognition and on the lower back for the flexion‐relaxation phenomenon illustrate its potential for the comprehensive assessment of the muscle activities and related motions of muscle joints.

Mulberry (Morus alba L.) leaves and fruit are traditional Chinese medicinal materials with anti-inflammatory, immune regulatory, antiviral and anti-diabetic properties. Melatonin performs important roles in the regulation of circadian rhythms and immune activities. We detected, identified and quantitatively analyzed the melatonin contents in leaves and mature fruit from different mulberry varieties. Melatonin and three novel isoforms were found in the Morus plants. Therefore, we conducted an expression analysis of melatonin and its isomer biosynthetic genes and in vitro enzymatic synthesis of melatonin and its isomer to clarify their biosynthetic pathway in mulberry leaves. MaASMT4 and MaASMT20, belonging to class II of the ASMT gene family, were expressed selectively in mulberry leaves, and two recombinant proteins that they expressed catalyzed the conversion of N-acetylserotonin to melatonin and one of three isomers in vitro. Unlike the ASMTs of Arabidopsis and rice, members of the three ASMT gene families in mulberry can catalyze the conversion of N-acetylserotonin to melatonin. This study provides new insights into the molecular mechanisms underlying melatonin and its isomers biosynthesis and expands our knowledge of melatonin isomer biosynthesis.

Tartary buckwheat microgreens (TBM) are popular worldwide products but display an extremely short shelf life. Thus, the effects of storage temperature, packaging material, and wash treatment on the quality and shelf life were analyzed. Headspace composition, weight loss, electrolyte leakage, microbial population and sensory quality were investigated during storage. Results showed that shelf life and quality of TBM decreased with the increment of storage temperature when stored at 5–25 °C. During 5 °C storage, LDPE bags were the best packaging materials for preserving the quality of LDPE, PE and HDPE bags. On the basis of 5 °C and LDPE packages, ClO2 + citric acid wash treatment could further inhibit quality deterioration and extend the shelf life. The results demonstrated bioactive constituents and antioxidant capacity were significantly affected by storage time. The study provides insights into developing optimal packaging and storage conditions for TBM.

Umami is an important widely-used taste component of food seasoning. Umami peptides are specific structural peptides endowing foods with a favorable umami taste. Laboratory approaches used to identify umami peptides are time-consuming and labor-intensive, which are not feasible for rapid screening. Here, we developed a novel peptide sequence-based umami peptide predictor, namely iUP-BERT, which was based on the deep learning pretrained neural network feature extraction method. After optimization, a single deep representation learning feature encoding method (BERT: bidirectional encoder representations from transformer) in conjugation with the synthetic minority over-sampling technique (SMOTE) and support vector machine (SVM) methods was adopted for model creation to generate predicted probabilistic scores of potential umami peptides. Further extensive empirical experiments on cross-validation and an independent test showed that iUP-BERT outperformed the existing methods with improvements, highlighting its effectiveness and robustness. Finally, an open-access iUP-BERT web server was built. To our knowledge, this is the first efficient sequence-based umami predictor created based on a single deep-learning pretrained neural network feature extraction method. By predicting umami peptides, iUP-BERT can help in further research to improve the palatability of dietary supplements in the future.

In this paper, we propose a novel color-texture image segmentation method based on local histograms. Starting with clustering-based color quantization, we extract a sufficient number of representative colors. For each pixel, through counting the number of pixels with each representative color within a circular neighborhood, a local histogram is obtained. After the circular neighborhood is extended to several scales, a local histogram with an appropriate scale is adopted as a color-texture descriptor at the corresponding pixel for image segmentation. Further, we correct the color-texture features near boundaries and obtain a initial segmentation by a clustering method with the color-texture descriptors. Finally, in order to obtain a better segmentation result, we merge the over segmented regions guided by the obtained boundaries. Experiments are performed on both synthetic and natural color-texture images, and the results show that our proposed method performs much better compared with state-of-the-art methods on image segmentation, particularly in textured areas.

As a non-essential heavy metal, cadmium (Cd) is toxic to plants. In the last 15 years, over 70 transcriptome studies have been published to decipher the molecular response mechanism against Cd stress in different plants. To extract generalization results from transcriptomic data across different plants and obtain some hub genes that respond to Cd stress, we carried out a meta-analysis of 32 published datasets. Cluster analysis revealed that plant species played a more decisive role than the media used and exposure time in the transcriptome patterns of plant roots response to Cd. The datasets from a Gramineae-like (GL) group were closer in clustering. 838 DEGs were commonly Cd-regulated in at least nine of 18 GL datasets. Gene ontology and KEGG pathway analyses revealed that oxidative stress-related terms and lignin synthesis-related terms were significantly enriched. Mapman analysis revealed that these common DEGs were mainly involved in regulation, cellular response, secondary metabolism, transport, cell wall and lipid metabolism. In Oryza sativa, 15 DEGs were up-regulated in at least four of five HM (As, Cr, Cd, Hg and Pb) groups, such as Os10g0517500 (methionine gamma-lyase) and Os01g0159800 (bHLH107). Moreover, our datasets can be used to retrieve log2FC value of specific genes across 29 studies (48 datasets), which provides data reference for the subsequent selection of HM-related genes. Our results provide the basis for further understanding of Cd tolerance mechanisms in plants.

Hypertrophy sorosis scleroteniosis caused by Ciboria shiraiana is the most devastating disease of mulberry fruit. However, few mulberry lines show any resistance to C. shiraiana. An increasing amount of research has shown that host-induced gene silencing (HIGS) is an effective strategy for enhancing plant tolerance to pathogens by silencing genes required for their pathogenicity. In this study, two G protein α subunit genes, CsGPA1 and CsGPA2, were identified from C. shiraiana. Silencing CsGPA1 and CsGPA2 had no effect on hyphal growth but reduced the number of sclerotia and increased the single sclerotium weight. Moreover, silencing CsGpa1 resulted in increased fungal resistance to osmotic and oxidative stresses. Compared with wild-type and empty vector strains, the number of appressoria was clearly lower in CsGPA1-silenced strains. Importantly, infection assays revealed that the virulence of CsGPA1-silenced strains was significantly reduced, which was accompanied by formation of fewer appressoria and decreased expression of several cAMP/PKA- or mitogen-activated protein-kinase-related genes. Additionally, transgenic Nicotiana benthamiana expressing double-stranded RNA targeted to CsGpa1 through the HIGS method significantly improved resistance to C. shiraiana. Our results indicate that CsGpa1 is an important regulator in appressoria formation and the pathogenicity of C. shiraiana. CsGpa1 is an efficient target to improve tolerance to C. shiraiana using HIGS technology.

Abstract This study explored the role of fibulin-3 in osteosarcoma progression and the possible signaling pathway involved. Fibulin-3 mRNA and protein expression in normal tissue, benign fibrous dysplasia, osteosarcoma, osteosarcoma cell lines (HOS and U-2OS), the normal osteoblastic cell line hFOB, and different invasive subclones was evaluated by immunohistochemistry (IHC) or immunocytochemistry (ICC) and real time reverse transcriptase-polymerase chain reaction (real time qRT-PCR). To assess the role of fibulin-3 in the invasion and metastasis of osteosarcoma cells, lentiviral vectors with fibulin-3 small hairpin RNA (shRNA) and pLVX-fibulin-3 were constructed and used to infect the highly invasive and low invasive subclones. The effects of fibulin-3 knockdown and upregulation on the biological behavior of osteosarcoma cells were investigated by functional in vitro and in vivo assays. The results revealed that fibulin-3 expression was upregulated in osteosarcoma, and was positively correlated with low differentiation, lymph node metastasis, and poor prognosis. Fibulin-3 could promote osteosarcoma cell invasion and metastasis by inducing EMT and activating the Wnt/β-catenin signaling pathway. Collectively, our findings demonstrate that fibulin-3 is a promoter of osteosarcoma development and progression, and suggest a novel therapeutic target for future studies.

Ethylene regulates plant abiotic stress responses and tolerances, and ethylene-insensitive3 (EIN3)/EIN3-like (EIL) proteins are the key components of ethylene signal transduction. Although the functions of EIN3/EIL proteins in response to abiotic stresses have been investigated in model plants, little is known in non-model plants, including mulberry (Morus L.), which is an economically important perennial woody plant. We functionally characterized a gene encoding an EIN3-like protein from mulberry, designated as MnEIL3. A quantitative real-time PCR analysis demonstrated that the expression of MnEIL3 could be induced in roots and shoot by salt and drought stresses. Arabidopsis overexpressing MnEIL3 exhibited an enhanced tolerance to salt and drought stresses. MnEIL3 overexpression in Arabidopsis significantly upregulated the transcript abundances of ethylene biosynthetic genes. Furthermore, MnEIL3 enhanced the activities of the MnACO1 and MnACS1 promoters, which respond to salt and drought stresses. Thus, MnEIL3 may play important roles in tolerance to abiotic stresses and the expression of ethylene biosynthetic genes.

The zinc-regulated transporters, iron-regulated transporter-like proteins (ZIPs), the natural resistance and macrophage proteins (NRAMP), the heavy metal ATPases (HMAs) and the metal tolerance or transporter proteins (MTPs) families are involved in cadmium (Cd) uptake, translocation and sequestration in plants. Mulberry (Morus L.), one of the most ecologically and economically important (as a food plant for silkworm production) genera of perennial trees, exhibits excellent potential for remediating Cd-contaminated soils. However, there is no detailed information about the genes involved in Cd2+ transport in mulberry. In this study, we identified 31 genes based on a genome-wide analysis of the Morus notabilis genome database. According to bioinformatics analysis, the four transporter gene families in Morus were distributed in each group of the phylogenetic tree, and the gene exon/intron structure and protein motif structure were similar among members of the same group. Subcellular localization software predicted that these transporters were mainly distributed in the plasma membrane and the vacuolar membrane, with members of the same group exhibiting similar subcellular locations. Most of the gene promoters contained abiotic stress-related cis-elements. The expression patterns of these genes in different organs were determined, and the patterns identified, allowing the categorization of these genes into four groups. Under low or high-Cd2+ concentrations (30 μM or 100 μM, respectively), the transcriptional regulation of the 31 genes in root, stem and leaf tissues of M. alba seedlings differed with regard to tissue and time of peak expression. Heterologous expression of MaNRAMP1, MaHMA3, MaZIP4, and MaIRT1 in Saccharomyces cerevisiae increased the sensitivity of yeast to Cd, suggested that these transporters had Cd transport activity. Subcellular localization experiment showed that the four transporters were localized to the plasma membrane of yeast and tobacco. These results provide the basis for further understanding of the Cd tolerance mechanism in Morus, which can be exploited in Cd phytoremediation.

Although ethylene is well known as an essential regulator of fruit development, little work has examined the role ethylene plays in the development and maturation of mulberry (Morus L.) fruit. To study the mechanism of ethylene action during fruit development in this species, we measured the ethylene production, fruit firmness, and soluble solids content (SSC) during fruit development and harvest. By comparing the results with those from other climacteric fruit, we concluded that Morus fruit are probably climacteric. Genes associated with the ethylene signal transduction pathway of Morus were characterized from M. notabilis Genome Database, including four ethylene receptor genes, a EIN2-like gene, a CTR1-like gene, four EIN3-like genes, and a RTE1-like gene. The expression patterns of these genes were analyzed in the fruit of M. atropurpurea cv. Jialing No.40. During fruit development, transcript levels of MaETR2, MaERS, MaEIN4, MaRTE, and MaCTR1 were lower at the early stages and higher after 26 days after full bloom (DAF), while MaETR1, MaEIL1, MaEIL2, and MaEIL3 remained constant. In ripening fruit, the transcripts of MaACO1 and MaACS3 increased, while MaACS1 and MaACO2 decreased after harvest. The transcripts of MaACO1, MaACO2, and MaACS3 were inhibited by ethylene, and 1-MCP (1-methylcyclopropene) upregulated MaACS3. The transcripts of the MaETR-like genes, MaRTE, and MaCTR1 were inhibited by ethylene and 1-MCP, suggesting that ethylene may accelerate the decline of MaETRs transcripts. No significant changes in the expression of MaEIN2, MaEIL1, and MaEIL3 were observed during ripening or in response to ethylene, while the expressions of MaEIL2 and MaEIL4 increased rapidly after 24 h after harvest (HAH) and were upregulated by ethylene. The present study provides insights into ethylene biosynthesis and signal transduction in Morus plants and lays a foundation for the further understanding of the mechanisms underlying Morus fruit development and ripening.

In order to systematically explore and understand the structure–activity relationship (SAR) of a lesinurad-based hit (1c) derived from the replacement of the S atom in lesinurad with CH2, 18 compounds (1a–1r) were designed, synthesized and subjected to in vitro URAT1 inhibitory assay. The SAR exploration led to the discovery of a highly potent flexible URAT1 inhibitor, 1q, which was 31-fold more potent than parent lesinurad (IC50 = 0.23 μM against human URAT1 for 1q vs 7.18 μM for lesinurad). The present study discovered a flexible molecular scaffold, as represented by 1q, which might serve as a promising prototype scaffold for further development of potent URAT1 inhibitors, and also demonstrated that the S atom in lesinurad was not indispensable for its URAT1 inhibitory activity.