A Review of Classification, Biosynthesis, Biological Activities and Potential Applications of Flavonoids.

Flavonoids represent the main class of plant secondary metabolites and occur in the tissues and organs of various plant species. In plants, flavonoids are involved in many biological processes and in response to various environmental stresses. The consumption of flavonoids has been known to reduce the risk of many chronic diseases due to their antioxidant and free radical scavenging properties. In the present review, we summarize the classification, distribution, biosynthesis pathways, and regulatory mechanisms of flavonoids. Moreover, we investigated their biological activities and discuss their applications in food processing and cosmetics, as well as their pharmaceutical and medical uses. Current trends in flavonoid research are also briefly described, including the mining of new functional genes and metabolites through omics research and the engineering of flavonoids using nanotechnology. This review provides a reference for basic and applied research on flavonoid compounds.

The Glutathione S-Transferase PtGSTF1 Improves Biomass Production and Salt Tolerance through Regulating Xylem Cell Proliferation, Ion Homeostasis and Reactive Oxygen Species Scavenging in Poplar.

Glutathione S-transferases (GSTs) play an essential role in plant cell detoxification and secondary metabolism. However, their accurate functions in the growth and response to abiotic stress in woody plants are still largely unknown. In this work, a Phi class Glutathione S-transferase encoding gene PtGSTF1 was isolated from poplar (P. trichocarpa), and its biological functions in the regulation of biomass production and salt tolerance were investigated in transgenic poplar. PtGSTF1 was ubiquitously expressed in various tissues and organs, with a predominant expression in leaves and inducible expression by salt stress. Transgenic poplar overexpressing PtGSTF1 showed improved shoot growth, wood formation and improved salt tolerance, consistent with the increased xylem cell number and size under normal condition, and the optimized Na+ and K+ homeostasis and strengthened reactive oxygen species scavenging during salt stress. Further transcriptome analyses demonstrated that the expressions of genes related to hydrolase, cell wall modification, ion homeostasis and ROS scavenging were up- or down-regulated in transgenic plants. Our findings imply that PtGSTF1 improves both biomass production and salt tolerance through regulating hydrolase activity, cell wall modification, ion homeostasis and ROS scavenging in transgenic poplar, and that it can be considered as a useful gene candidate for the genetic breeding of new tree varieties with improved growth under salt stress conditions.

Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice.

BACKGROUND: Cadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity. RESULTS: In this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs. CONCLUSION: The exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.

Linkage analysis, GWAS, transcriptome analysis to identify candidate genes for rice seedlings in response to high temperature stress.

BACKGROUND: Rice plants suffer from the rising temperature which is becoming more and more prominent. Mining heat-resistant genes and applying them to rice breeding is a feasible and effective way to solve the problem. RESULT: Three main biomass traits, including shoot length, dry weight, and fresh weight, changed after abnormally high-temperature treatment in the rice seedling stage of a recombinant inbred lines and the natural indica germplasm population. Based on a comparison of the results of linkage analysis and genome-wide association analysis, two loci with lengths of 57 kb and 69 kb in qDW7 and qFW6, respectively, were associated with the rice response to abnormally high temperatures at the seedling stage. Meanwhile, based on integrated transcriptome analysis, some genes are considered as important candidate genes. Combining with known genes and analysis of homologous genes, it was found that there are eight genes in candidate intervals that need to be focused on in subsequent research. CONCLUSIONS: The results indicated several relevant loci, which would help researchers to further discover beneficial heat-resistant genes that can be applied to rice heat-resistant breeding.

Characteristic-Aroma-Component-Based Evaluation and Classification of Strawberry Varieties by Aroma Type.

The unique fruity aroma of strawberries, a popular fruit of high economic value, is closely related to all the volatile organic compounds (VOCs) contained within them. Despite extensive studies on the identification of VOCs in strawberries, systematic studies on fruit-aroma-related VOCs are few, resulting in a lack of effective standards for accurately distinguishing aroma types. In the present study, solid-phase micro extraction and gas chromatography-mass spectrometry were used to analyze and identify VOCs in the ripe fruit of each of the 16 strawberry varieties at home and abroad and to explore their characteristic aroma components and the classification of such varieties by aroma type. The results suggested remarkable variations in the types and contents of VOCs in different strawberry varieties, of which esters were dominant. The principal volatile components, consisting of four esters, three alcohols, one aldehyde, and one ketone, in 16 strawberry varieties were detected based on the absolute and relative contents of VOCs in the fruit. The characteristic aroma components in strawberries, containing nine esters, six aldehydes, and one alcohol, were determined based on the aroma values of different VOCs, and the characteristic aroma components were divided into five types further based on aroma descriptions. Sixteen strawberry varieties were finally divided into four aroma types, namely, peachy, pineapple, fruity, and floral, based on the contributions of different types. The results provided a basis and standard for classifying strawberries by aroma type, studying the hereditary regularity of the fruity aroma of strawberries, and improving aroma quality.

Development of Loop-Mediated Isothermal Amplification (LAMP) for Universal Detection of Enteroviruses.

Enteroviruses are found in most environments and cause several diseases in humans. Loop-mediated isothermal amplification (LAMP) was adapted and evaluated for the rapid detection of enteroviruses. Based on the highly conserved 5' untranslated region (5'-UTR) of the human enteroviruses (HEVs), particularly human enterovirus A (HEV-A) and HEV-B, a set of universal primers was designed. The LAMP amplification was carried out under isothermal conditions at 61 °C, depending on the template concentration results were obtained within 45-90 min. The detection limits were found to be 10(1) copies of cloned enterovirus 71 fragments, more sensitive than conventional PCR. Nine water samples collected from drinking water sources during three seasons and 19 stool specimens collected from HFMD patients were analyzed. By using the LAMP assay, the majority of samples was tested positive, 9/9 (100 %) and 18/19 (94.7 %), respectively. LAMP is a practical method for the rapid detection of enteroviruses in environmental and clinical samples.

[Screening and identification of key signal transduction pathways in pulmonary silicotic fibrosis].

OBJECTIVE: To investigate the differential gene expression profile of the lung tissues in experimental silicosis rats and to screen for and identify the key signal transduction pathways in pulmonary silicotic fibrosis. METHODS: A total of 80 rats were randomly divided into control group (n = 40) and silica-instilled group (n = 40). Each group was equally divided into five subgroups, and each subgroup was treated at 1, 7, 14, 21, or 28 d. Intratracheal instillation was used to give 1 ml of silica suspension (50 mg/ml) in the silica-instilled group and normal saline in the control group. Silicotic nodules and type I and III collagen were observed through hematoxylin and eosin staining and Sirius red staining, respectively. Differentially expressed genes in pulmonary silicotic fibrosis were selected by the rat whole-genome gene expression RatRef-12 BeadChip (Illumina, USA), and a fold change cutoff was applied. Quantitative real-time polymerase chain reaction (qRT-PCR) was also used to verify differentially expressed genes. Through bioinformatics databases such as Visualization and Integrated Discovery (DAVID) and Kyoto Encyclopedia of Genes and Genomes (KEGG), preliminary research was performed on the biological pathways of differential genes, key biological signal transduction pathways were identified, and key differentially expressed genes in each pathway at different time points were searched for. RESULTS: A total of 2694 genes were differentially expressed and changed dynamically. The KEGG pathway analysis showed that 141 signal transduction pathways were involved in the development and progression of pulmonary silicotic fibrosis, among which 48 pathways were more significant than others (P < 0.01), with the mitogen-activated protein kinase (MAPK) pathway exceptionally significant. The differentially expressed genes interleukin-1 receptor (IL-1R), tumor necrosis factor receptor (TNFR), and transforming growth factor beta (TGF-ß) in the MAPK pathway were up-regulated at different time points after silica instillation. The results of real-time PCR showed that granulocyte-macrophage colony-stimulating factor (GM-CSF) was over-expressed at 4 time points and under-expressed at 1 time point compared with the control group. CONCLUSION: The MAPK signal transduction pathway plays a very important role in the development of pulmonary silicotic fibrosis. Both IL-1R and TNFR may play major roles during inflammation phase through the P38/Jun N-terminal kinase (JNK) pathway, and TGF-ß may have important function through the extracellular-signal-regulated kinase (ERK) pathway in the formation of fibrosis.

Effects of Supplemental Lighting on Flavonoid and Anthocyanin Biosynthesis in Strawberry Flesh Revealed via Metabolome and Transcriptome Co-Analysis.

The spectral composition of light influences the biosynthesis of flavonoids in many plants. However, the detailed composition of flavonoids and anthocyanins and the molecular basis for their biosynthesis in strawberry fruits under two light-quality treatments, red light supplemented with blue light (RB) and ultraviolet B (UVB) irradiation, remain unclear. In this study, the content of flavonoids and anthocyanins was significantly increased in strawberry fruits under RB light and UVB, respectively. The content of flavonoids and anthocyanins in strawberry fruits under UVB light was dramatically higher than that in strawberry fruits irradiated with RB light, and a total of 518 metabolites were detected by means of LC-MS/MS analysis. Among them, 18 phenolic acids, 23 flavonoids, and 8 anthocyanins were differentially accumulated in the strawberry fruits irradiated with red/blue (RB) light compared to 30 phenolic acids, 46 flavonoids, and 9 anthocyanins in fruits irradiated with UVB. The major genes associated with the biosynthesis of flavonoids and anthocyanins, including structural genes and transcription factors (TFs), were differentially expressed in the strawberry fruits under RB and UVB irradiation, as determined through RNA-seq data analysis. A correlation test of transcriptome and metabolite profiling showed that the expression patterns of most genes in the biosynthesis pathway of flavonoids and anthocyanins were closely correlated with the differential accumulation of flavonoids and anthocyanins. Two TFs, bZIP (FvH4_2g36400) and AP2 (FvH4_1g21210), induced by RB and UVB irradiation, respectively, exhibited similar expression patterns to most structural genes, which were closely correlated with six and eight flavonoids, respectively. These results indicated that these two TFs regulated the biosynthesis of flavonoids and anthocyanins in strawberry fruit under RB light and UVB, respectively. These results provide a systematic and comprehensive understanding of the accumulation of flavonoids and anthocyanins and the molecular basis for their biosynthesis in strawberry fruits under RB light and UVB.

A dual-branch selective attention capsule network for classifying kiwifruit soft rot with hyperspectral images.

Kiwifruit soft rot is highly contagious and causes serious economic loss. Therefore, early detection and elimination of soft rot are important for postharvest treatment and storage of kiwifruit. This study aims to accurately detect kiwifruit soft rot based on hyperspectral images by using a deep learning approach for image classification. A dual-branch selective attention capsule network (DBSACaps) was proposed to improve the classification accuracy. The network uses two branches to separately extract the spectral and spatial features so as to reduce their mutual interference, followed by fusion of the two features through the attention mechanism. Capsule network was used instead of convolutional neural networks to extract the features and complete the classification. Compared with existing methods, the proposed method exhibited the best classification performance on the kiwifruit soft rot dataset, with an overall accuracy of 97.08% and a 97.83% accuracy for soft rot. Our results confirm that potential soft rot of kiwifruit can be detected using hyperspectral images, which may contribute to the construction of smart agriculture.

Analysis of Ethylene Signal Regulating Sucrose Metabolism in Strawberry Fruits Based on RNA-seq.

Ethylene is a key hormone that regulates the maturation and quality formation of horticultural crops, but its effects on non-respiratory climacteric fruits such as strawberries are not yet clear. In this study, strawberry fruits were treated with exogenous ethephon (ETH) and 1-methylcyclopropene (1-MCP). It was found that ETH treatment increased the soluble solids and anthocyanin content of the fruits, reduced hardness, and decreased organic acid content, while 1-MCP treatment inhibited these processes. Transcriptome analysis revealed that differentially expressed genes (DEGs) were enriched in the starch-sucrose metabolism pathway. qRT-PCR results further showed significant changes in the expression levels of sucrose metabolism genes, confirming the influence of ethylene signals on soluble sugar accumulation during strawberry fruit development. This study elucidates the quality changes and molecular mechanisms of ethylene signal in the development of strawberry fruits, providing some key targets and theoretical support for guiding strawberry cultivation and variety improvement.

[Significance of apolipoprotein A1 as biomarker for early diagnosis and classification of bladder urothelial carcinoma].

OBJECTIVE: To investigate the significance of apolipoprotein (Apo)-A1 in urine as a biomarker for early diagnosis and classification of bladder urothelial carcinoma (BUC). METHODS: Urine samples were divided into four groups: normal control group, benign bladder disease group, low-grade malignant BUC group, and high-grade malignant BUC group. Apo-A1, which showed significantly different expression among the four groups, was selected according to the two-dimensional electrophoresis (2-DE) images of the four groups, and enzyme-linked immunosorbent assay (ELISA) was used to quantify Apo-A1 in the four groups. A receiver operating characteristic (ROC) curve was generated, and the optimal operating points on the ROC curve were found to determine the critical concentrations of Apo-A1 for early diagnosis of BUC and differentiation of low-grade and high-grade malignant BUC. The results were verified clinically, and the specificity and sensitivity were calculated. RESULTS: The 2-DE images showed that that the level of Apo-A1 increased from the normal control grouP to high-grade malignant BUC group. The ELISA showed that there was no significant difference in Apo-A1 level between the normal control grouP and benign bladder disease group, but the Apo-A1 level was significantly higher in the BUC groups than in the normal control grouP and benign bladder disease grouP (P < 0.01); the high-grade BUC grouP had a significantly higher Apo-A1 level than the low-grade BUC grouP (P < 0.01). The BUC patients and those without BUC could be differentiated with an Apo-A1 concentration of 18.22 ng/ml, while the low-grade and high-grade malignant BUC could be differentiated with an Apo-A1 concentration of 29.86 ng/ml. When used as a biomarker, Apo-A1 had a sensitivity of 91.6% (98/107) and a specificity of 85.7% (42/49) for diagnosis of BUC and had a sensitivity of 83.7% (41/49) and a specificity of 89.7% (52/58) for BUC classification. CONCLUSION: Apo-A1 may be a biomarker for early diagnosis and classification of BUC and shows promise for clinical application.

Arbuscular mycorrhizal fungi influence the uptake of cadmium in industrial hemp (Cannabis sativa L.).

Phytoremediation is currently a more environmentally friendly and economical measure for the remediation of cadmium (Cd) contaminated soil. Heavy metal-resistant plant species, Cannabis sativa L. was inoculated with Rhizophagus irregularis to investigate the mechanisms of mycorrhizal in improving the Cd remediation ability of C. sativa. The results showed that after inoculation with R. irregularis, C. sativa root Cd contents increased significantly, and leaf Cd enrichment decreased significantly. At the transcriptional level, R. irregularis down-regulated the expression of the ABC transporter family but up-regulated differentially expressed genes regulating low molecular weight organic acids. The levels of malic acid, citric acid, and lactic acid were significantly increased in the rhizosphere soil, and they were significantly and strongly related to oxidizable Cd concentrations. Then citric acid levels were considerably and positively connected to exchangeable Cd concentrations. Our findings revealed that through regulating the movement of root molecules, arbuscular mycorrhizal fungus enhanced the heavy metal tolerance of C. sativa even more, meanwhile, they changed the Cd chemical forms by altering the composition of low molecular weight organic acids, which in turn affected soil Cd bioavailability.

Ectopic Expression of MADS-Box Transcription Factor VvAGL12 from Grape Promotes Early Flowering, Plant Growth, and Production by Regulating Cell-Wall Architecture in Arabidopsis.

The MADS-box family, a substantial group of plant transcription factors, crucially regulates plant growth and development. Although the functions of AGL12-like subgroups have been elucidated in Arabidopsis, rice, and walnut, their roles in grapes remain unexplored. In this study, we isolated VvAGL12, a member of the grape MADS-box group, and investigated its impact on plant growth and biomass production. VvAGL12 was found to localize in the nucleus and exhibit expression in both vegetative and reproductive organs. We introduced VvAGL12 into Arabidopsis thaliana ecotype Columbia-0 and an agl12 mutant. The resulting phenotypes in the agl12 mutant, complementary line, and overexpressed line underscored VvAGL12's ability to promote early flowering, augment plant growth, and enhance production. This was evident from the improved fresh weight, root length, plant height, and seed production, as well as the reduced flowering time. Subsequent transcriptome analysis revealed significant alterations in the expression of genes associated with cell-wall modification and flowering in the transgenic plants. In summary, the findings highlight VvAGL12's pivotal role in the regulation of flowering timing, overall plant growth, and development. This study offers valuable insights, serving as a reference for understanding the influence of the VvAGL12 gene in other plant species and addressing yield-related challenges.

Identification of MYB Transcription Factors Involving in Fruit Quality Regulation of Fragaria × ananassa Duch.

The cultivated strawberry (Fragaria × ananassa Duch.) is an important horticultural crop. The economic values of strawberry cultivars are decided by their fruit qualities including taste, color and aroma. The important role of MYB transcription factors in fruit quality regulation is recognized increasingly with the identification of MYB genes involved in metabolism. A total of 407 MYB genes of F. × ananassa (FaMYBs) were identified in the genome-wide scale and named according to subgenome locations. The 407 FaMYBs were clustered into 36 groups based on phylogenetic analysis. According to synteny analysis, whole genome duplication and segmental duplication contributed over 90% of the expansion of the FaMYBs family. A total of 101 FaMYB loci with 1-6 alleles were identified by the homologous gene groups on homologous chromosomes. The differentially expressed FaMYB profiles of three cultivars with different fruit quality and fruit ripe processes provided the 8 candidate loci involved in fruit quality regulation. In this experiment, 7, 5, and 4 FaMYBs were screeded as candidate genes involved in the regulation of metabolism/transportation of anthocyanins, sugars or organic acids and 4-hydroxy-2, 5-dimethyl-3(2H)-furanone, respectively. These results pointed out the key FaMYBs for further functional analysis of gene regulation of strawberry fruit quality and would be helpful in the clarification on ofe roles of MYBs in the metabolism of fruit crops.

A super pan-genomic landscape of rice.

Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. Our pan-genome reveals extensive structural variations (SVs) and gene presence/absence variations. Additionally, our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter- and intraspecific diversity. Moreover, we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes. We characterized genetic variants associated with submergence tolerance, seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice. This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species.

Cross-talk of the related bioactivity mediators in serum after injection of soluble TNF-α receptor on silicosis model of rats.

This study investigates cross-talk of the related bioactivity mediators in silica-induced pulmonary inflammatory and fibrosis on rats, which contributes to the preventive and therapeutic effect of soluble TNF-α receptor. Wistar rats received saline or 50 mg of quartz by intratracheal instillation. Rats in drug-treated groups were given soluble tumor necrosis factor-α (TNF-α) receptor (500 µg) by hypodermic injection on days 1, 5 and 8 after operation. At 7 days or 14 days after instillation, rats were killed to observe the degree of injury and expression of the related bioactivity mediators including nuclear factor KB (NF-KB), nitric oxide, interleukin-1ß, interleukin-10, transforming growth factor beta 1 (TGF-ß1), TNF-α, interferon-Y (IFN-Y) and granulocyte macrophage colony-stimulating factor (GM-CSF). The area percentages of type I and III collagens in intervention group were lower than those in silica group. The expression of NF-κB, TGF-ß1, and COL I were lower in intervention group than in silica group(p < 0.05) and GM-CSF was significantly higher (p < 0.05) at 7 days after instillation, however, NF-κB, TGF-ß1, and COL I were identically lower in intervention group than in silica group, and TNF-α, IFN-γ, and GM-CSF were higher at 14 days after instillation. It may be concluded that soluble TNF-α receptor upregulating or downregulating the expression of the related bioactivity mediators results in decreasing lung injury induced by silica.

(7R,8S,9S,12S)-1-Benz-yloxy-13,14-didehydro-12-hy-droxy-2,13-dimeth-oxy-N-methyl-morphinane.

In the title compound, C(26)H(31)NO(4), a sinomenine derivative, the angle between the two aromatic rings is 53.34 (4)°. The N-containing ring is in a chair conformation, while the other two non-planar rings are in a half-boat conformation. In the crystal, mol-ecules are linked by O-H⋯N inter-actions into a C(8) chain along [100].

(7R,8S,9S,12S)-1-(4-Chloro-benz-yloxy)-13,14-didehydro-12-hy-droxy-2,13-dimeth-oxy-N-methyl-morphinane.

The title compound, C(26)H(30)ClNO(4), a sinomenine derivative, has five six-membered rings, two of which are aromatic, with a dihedral angle of 34.13 (20)° between these. The N-containing ring and the fourth ring exhibit chair conformations, while the fifth ring approximates an envelope conformation. A single inter-molecular O-H⋯N hydrogen-bonding inter-action gives a one-dimensional chain structure which extends along the a axis. The absolute configuration for the mol-ecule has been determined.

(9S,13R,14S)-7,8-Didehydro-4-(4-fluoro-benz-yloxy)-3,7-dimeth-oxy-17-methyl-morphinan-6-one sesquihydrate.

In the title sinomenine derivative, C(26)H(28)FNO(4)·1.5H(2)O, the dihedral angle between the two aromatic rings is 55.32 (6)°. The N-containing ring has an approximate chair conformation, while other two rings have approximate envelope and half-chair conformations. One water mol-ecule is located on a twofold symmetry axis. In the crystal, the water mol-ecules form O-H⋯O and O-H⋯N hydrogen bonds, bridging symmetry-related main mol-ecules.

[Differential analysis of two-dimensional gel electrophoresis profiles in the protective effects of resveratrol on HaCaT cells induced by UVB irradiation].

OBJECTIVE: To analysis the differences of protein expression and possible protective mechanisms of resveratrol (Res) on human keratinocytes (HaCaT cells) irradiated by ultraviolet B (UVB). METHODS: MTT test was used to assay the effects of Res on the proliferation of HaCaT cells. The tested objects were divided into four groups, the control, UVB irradiation, Res intervention and UVB + Res intervention (r-u) groups. Then the protein of cells in the four groups was separated by a two-dimensional gel electrophoresis (2-DE) and the differentially expressed protein spots were identified by MALDI-TOF-MS. RESULTS: Ten differential expressed protein spots were analyzed, and eight kinds of protein were identified. Except for four kinds of uncharacterized protein, the level of Histone H1.2 was up-regulated in UVB group (P < 0.05), the levels of TFIIE-beta and zinc finger were down-regulated in both UVB and r-u groups, and the level of MAGOH was down-regulated significantly in UVB group (P < 0.05). CONCLUSION: The differentially expressed protein spots related to the protection of Res on HaCaT cells irradiated by UVB were found with the two-dimensional gel electrophoresis.