Transcriptomics Reveals the Molecular Basis for Methyl Jasmonate to Promote the Synthesis of Monoterpenoids in Schizonepeta tenuifolia Briq.

BACKGROUND: Methyl jasmonate has an important effect on the synthesis of plant secondary metabolites. Schizonepeta tenuifolia Briq. has a wide range of pharmacological effects and the secondary metabolites are dominated by monoterpenes (pulegone, menthone). OBJECTIVE: It is essential to determine the changes in secondary metabolites in S. tenuifolia under methyl jasmonate treatment and to probe the molecular mechanism. This can improve the accumulation of secondary metabolites in the medicinal plant S. tenuifolia and enrich the information gene expression at different MeJA levels, which can help to elucidate the molecular mechanism of monoterpenoid synthesis in S. tenuifolia. METHODS: In this study, we determined the changes in the content of monoterpenoids in S. tenuifolia under methyl jasmonate treatment. Meanwhile, we established a transcriptome database of S. tenuifolia under methyl jasmonate level using high-throughput sequencing. RESULTS: A certain concentration of MeJA promoted the accumulation of monoterpenoids in S. tenuifolia. The transcriptome database of S. tenuifolia leaves under 0, 50, 100 and 250 µM MeJA treatment was established. We generated 88,373 unigenes with an N50 length of 2678 bp, of which 50,843 (57.53%) can be annotated in at least one database. Compared with the CK (0 µM) group, 12,557 (50 µM), 15,409 (100 µM) and 13,286 (250 µM) differentially expressed genes were identified. GO and KEGG enrichment analysis revealed that JA signal transduction and monoterpenoid synthesis were the two most significant enrichment pathways. The expression levels of related DEGs involved in JA signaling and monoterpenoid synthesis were significantly up-regulated by MeJA. In addition, our phenotypic and differentially expressed gene association analysis revealed that monoterpenoid biosynthesis in S. tenuifolia was more associated with genes involved in plant trichome branching, phytohormone signaling and transcriptional regulation. CONCLUSIONS: This study confirmed that methyl jasmonate significantly promoted monoterpenoid biosynthesis in S. tenuifolia. A large number of genes responding to methyl jasmonate were associated with JA signaling and monoterpenoid biosynthesis.

Exploration of Antimicrobial Ingredients in Psoralea corylifolia L. Seed and Related Mechanism against Methicillin-Resistant Staphylococcus aureus.

With the abuse of antibiotics, bacterial antibiotic resistance is becoming a major public healthcare issue. Natural plants, especially traditional Chinese herbal medicines, which have antibacterial activity, are important sources for discovering potential bacteriostatic agents. This study aimed to develop a fast and reliable method for screening out antimicrobial compounds targeting the MRSA membrane from Psoralea corylifolia Linn. seed. A UPLC-MS/MS method was applied to identify the prenylated flavonoids in major fractions from the extracts of Psoralea corylifolia Linn. seed. The broth microdilution method was used to determine the minimum inhibitory concentrations (MICs) of different fractions and compounds. The morphological and ultrastructural changes of MRSA were determined by scanning electron microscopy (SEM). The membrane-targeting mechanism of the active ingredients was explored by membrane integrity assays, membrane fluidity assays, membrane potential assays, ATP, and ROS determination. We identified eight prenylated flavonoids in Psoralea corylifolia Linn. seed. The antibacterial activity and mechanism studies showed that this type of compound has a unique destructive effect on MRSA cell membranes and does not result in drug resistance. The results revealed that prenylated flavonoids in Psoralea corylifolia Linn. seeds are promising candidates for the development of novel antibiotic agents to combat MRSA-associated infections.

LincRNA-EPS impairs host antiviral immunity by antagonizing viral RNA-PKR interaction.

LincRNA-EPS is an important regulator in inflammation. However, the role of lincRNA-EPS in the host response against viral infection is unexplored. Here, we show that lincRNA-EPS is downregulated in macrophages infected with different viruses including VSV, SeV, and HSV-1. Overexpression of lincRNA-EPS facilitates viral infection, while deficiency of lincRNA-EPS protects the host against viral infection in vitro and in vivo. LincRNA-EPS-/- macrophages show elevated expression of antiviral interferon-stimulated genes (ISGs) such as Mx1, Oas2, and Ifit2 at both basal and inducible levels. However, IFN-ß, the key upstream inducer of these ISGs, is downregulated in lincRNA-EPS-/- macrophages compared with control cells. RNA pulldown and mass spectrometry results indicate that lincRNA-EPS binds to PKR and antagonizes the viral RNA-PKR interaction. PKR activates STAT1 and induces antiviral ISGs independent of IFN-I induction. LincRNA-EPS inhibits PKR-STAT1-ISGs signaling and thus facilitates viral infection. Our study outlines an alternative antiviral pathway, with downregulation of lincRNA-EPS promoting the induction of PKR-STAT1-dependent ISGs, and reveals a potential therapeutic target for viral infectious diseases.

Predicting the Postmortem Interval Based on Gravesoil Microbiome Data and a Random Forest Model.

The estimation of a postmortem interval (PMI) is particularly important for forensic investigations. The aim of this study was to assess the succession of bacterial communities associated with the decomposition of mouse cadavers and determine the most important biomarker taxa for estimating PMIs. High-throughput sequencing was used to investigate the bacterial communities of gravesoil samples with different PMIs, and a random forest model was used to identify biomarker taxa. Redundancy analysis was used to determine the significance of environmental factors that were related to bacterial communities. Our data showed that the relative abundance of Proteobacteria, Bacteroidetes and Firmicutes showed an increasing trend during decomposition, but that of Acidobacteria, Actinobacteria and Chloroflexi decreased. At the genus level, Pseudomonas was the most abundant bacterial group, showing a trend similar to that of Proteobacteria. Soil temperature, total nitrogen, NH4+-N and NO3--N levels were significantly related to the relative abundance of bacterial communities. Random forest models could predict PMIs with a mean absolute error of 1.27 days within 36 days of decomposition and identified 18 important biomarker taxa, such as Sphingobacterium, Solirubrobacter and Pseudomonas. Our results highlighted that microbiome data combined with machine learning algorithms could provide accurate models for predicting PMIs in forensic science and provide a better understanding of decomposition processes.

3D reconstruction of dynamic behaviors of vacuum arcs under transverse magnetic fields via computer tomography.

The transverse magnetic field (TMF) contacts make the vacuum arcs deviate from the axisymmetric structure, so complete spatiotemporal evolution information of the plasma cannot be obtained by adopting one- or two-dimensional (2D) diagnostic methods. To address the issues, computer tomography was introduced in this paper. First, a multi-angle diagnostic imaging system based on split fiber bundles was proposed, which used a high-speed camera to simultaneously acquire eight angles of the arc image over time. In addition, a tomography algorithm called the maximum likelihood expectation maximum with Split Bregman denoising was proposed to reconstruct the dynamic spatiotemporal characteristics of the arc under complex conditions. Then, the three-dimensional (3D) distribution of Cu i and Cr i particles inside the contact gap was obtained by adopting optical filters. The 3D distribution of the vacuum arc had shown an obvious asymmetrical pattern under the TMF contacts, and there was a ring-like aggregation zone inside the arc, which can cause severe ablation on the anode contacts. According to the reconstructed 3D distribution of Cu i and Cr i, it is found that the metal vapor was mainly concentrated near the electrode surface and showed a clear distribution of non-uniform aggregates, while the concentration of particles in the gap was low. Moreover, on the cathode surface, the cathode spots moved in the form of groups driven by the TMF, while the anode surface was ablated by the electric arc, and the metal vapor existed in the form of bands.

Identification and expression analysis of the WRKY gene family in Isatis indigotica.

The WRKY proteins, which represent one of the largest families of transcriptional regulators in plants, play pivotal roles in regulating multiple processes of growth and development, particularly in diverse stress responses. Isatis indigotica is widely used in Traditional Chinese Medicine and is famous for its use as a dye for the color indigo. However, reports of the WRKY gene family in I. indigotica are limited. In this study, 64 IiWRKY genes encoding proteins with the complete WRKY domain were identified from genome of I. indigotica. Based on their structure and phylogenetic relationships of this gene family in I. indigotica, the IiWRKY genes were classified into three groups: Group I (n = 13), Group II (n = 35) and Group III (n = 16). Sequence alignment revealed that IiWRKY proteins harbored two variants, WRKYRQK and WRKYGKK, of the highly conserved WRKYGQK motif. The number of exons in IiWRKY genes varied from two to 14, with most of IiWRKY genes containing three exons. Investigation of gene duplication demonstrated that 10 and 14 IiWRKY genes were incorporated in tandem and segmental duplication events, respectively. Finally, the expression profiles derived from transcriptome data and quantitative real-time PCR analysis showed distinct expression patterns of these IiWRKY gene in five different organs or in response to four abiotic stresses. Taken together, our results will contribute to functional analysis of IiWRKY genes, and also provide a basis for further clarification of the molecular mechanism of stress responses in this important herb.

LincRNA-EPS alleviates severe acute pancreatitis by suppressing HMGB1-triggered inflammation in pancreatic macrophages.

Acute pancreatitis (AP), an inflammatory disorder of the pancreas with a high hospitalization rate, frequently leads to systemic inflammatory response syndrome (SIRS) and multiple organ dysfunction syndrome (MODS). However, therapeutic targets for effective treatment and early intervention of AP are still urgently required to be identified. Here, we have observed that the expression of pancreatic lincRNA-EPS, a long intergenic non-coding RNA, is dynamically changed during both caerulein-induced AP (Cer-AP) and sodium taurocholate-induced severe AP (NaTc-SAP). The expression pattern of lincRNA-EPS is negatively correlated with the typical inflammatory genes such as IL-6, IL-1ß, CXCL1, and CXCL2. Further studies indicate that knockout of lincRNA-EPS aggravates the pathological symptoms of AP including more induction of serum amylase and lipase, severe edema, inflammatory cells infiltration and acinar necrosis in both experimental AP mouse models. Besides these intrapancreatic effects, lincRNA-EPS also protects against tissue damages in the extra-pancreatic organs such as lung, liver, and gut in the NaTc-SAP mouse model. In addition, we have observed more serum pro-inflammatory cytokines TNF-α and IL-6 in the lincRNA-EPS-/- NaTc-SAP mice and more extracellular HMGB1 around injured acinar cells in the pancreas from lincRNA-EPS-/- NaTc-SAP mice, compared with their respective controls. Pharmacological inhibition of NF- κ B activity by BAY11-7082 significantly abolishes the suppressive effect of lincRNA-EPS on TLR4 ligand-induced inflammatory genes in macrophages. Our study has described a protective role of lincRNA-EPS in alleviating AP and SAP, outlined a novel pathway that lincRNA-EPS suppresses HMGB1-NF- κ B-dependent inflammatory response in pancreatic macrophages and provided a potential therapeutic target for SAP.

An improved deep learning-based algorithm for 3D reconstruction of vacuum arcs.

Extensive attempts have been made to enable the application of deep learning to 3D plasma reconstruction. However, due to the limitation on the number of available training samples, deep learning-based methods have insufficient generalization ability compared to the traditional iterative methods. This paper proposes an improved algorithm named convolutional neural network-maximum likelihood expectation maximization-split-Bergman (CNN-MLEM-SB) based on the combination of the deep learning CNN and an iterative algorithm known as MLEM-SB. This method uses the prediction result of a CNN as the initial value and then corrects it using the MLEM-SB to obtain the final results. The proposed method is verified experimentally by reconstructing two types of vacuum arcs with and without transverse magnetic field (TMF) control. In addition, the CNN and the proposed algorithm are compared with respect to accuracy and generalization ability. The results show that the CNN can effectively reconstruct the arcs between a pair of disk contacts, which has specific distribution patterns: its structural similarity index measurement (SSIM) can reach 0.952. However, the SSIM decreases to 0.868 for the arc between a pair of TMF contacts, which is controlled by the TMF and has complex distribution patterns. Compared with the CNN reconstruction method, the proposed algorithm can achieve a higher reconstruction accuracy for any arc shape. Compared with the iterative algorithm, the proposed algorithm's reconstruction efficiency is higher by 38.24% and 35.36% for the vacuum arc between the disk and the TMF contacts, respectively.

Acid vacuolar invertase 1 (PbrAc-Inv1) and invertase inhibitor 5 (PbrII5) were involved in sucrose hydrolysis during postharvest pear storage.

In pear, sucrose was mainly distributed in vacuole; and the alternation of sucrose abundance was associated the change of vacuolar invertase (VI) activity during fruit storage. However, the molecular mechanism beneath such phenomenon has not been clarified until recently. For this, a combination of metabolite, enzyme activity, transcriptome, quantitative real-time PCR (qRT-PCR), bioinformation, subcellular localization, and transient overexpression assay was conducted in this study to identify the acid invertase 1 (PbrAc-Inv1) and invertase inhibitor 5 (PbrII5) involved in sucrose degradation during 'Housui' pear storage. Both PbrAc-Inv1 and PbrII5 were located in vacuolar membrane. PbrAc-Inv1 could accelerate sucrose degradation; on the other hand, PbrII5 could bind with PbrAc-Inv1 to form a inactive complex, downregulate the VI activity, and suppressed sucrose decomposition. Based on Bio-layer interferometry (BLI) result after domain substitution, the domain on the left of catalytic 'WEC-P/V-D' box in PbrAc-Inv1 might played a key role in its interaction with PbrII5.

Characterization and Quantification of Polyphenols and Triterpenoids in Thinned Young Fruits of Ten Pear Varieties by UPLC-Q TRAP-MS/MS.

Large quantities of thinned young pears, a natural source of bioactive compounds, are abandoned as agricultural by-products in many orchards. Hence, ten thinned young pear varieties were systematically investigated in terms of their chemical composition and antioxidant potential. Through ultra-performance liquid chromatography coupled with electrospray ionization triple quadrupole mass spectrometry (UPLC-Q TRAP-MS/MS), 102 polyphenols and 16 triterpenoids were identified and individually quantified within a short time using multiple reaction monitoring (MRM). Subsequently, the antioxidant capacities of these pears were determined with DPPH assays, and the correlation between total antioxidant activity and each component was analyzed. The results indicated that the bioactive compound content and antioxidant capacity in thinned pears were considerably high. Regarding chemical composition, chlorogenic acid, quinic acid and arbutin were the primary polyphenols and ursolic acid was the predominant triterpenoid, whereas 27 polyphenolic compounds, especially chlorogenic acid and most of the flavan-3-ols, were the main antioxidants in young pears. These findings should provide a scientific basis for the further use of pear fruit by-products.

An integrated antioxidant activity fingerprint for commercial teas based on their capacities to scavenge reactive oxygen species.

An integrated antioxidant activity fingerprint, based on on-line screening methods for three reactive oxygen species (ROS: superoxide anion radical, hydrogen peroxide, and hydroxyl radical) was developed to comprehensively evaluate the quality of 12 batches of commercial tea. High-performance liquid chromatography (HPLC) coupled with a chemiluminescent detector was used to determine the antioxidant characteristics of a selection of teas as bioactivity fingerprints. An HPLC-electrospray ionization-mass spectrometry analysis was used to determine the chemical profiles of the teas in the chromatographic fingerprints. All of the green teas (S01-S08) were better scavengers of the three ROS compared to the oolong teas (S09-S12). The main scavengers of the three ROS in green tea were 5-galloylquinic acid, (-)-epigallocatechin-3-O-gallate, and (-)-epicatechin-3-O-gallate, whereas in oolong tea, they were (-)-epigallocatechin-3-O-gallate and (-)-epigallocatechin. This study demonstrates that comprehensive fingerprinting is a potentially meaningful method for evaluating the quality of food products.

A novel multi-hyphenated analytical method to simultaneously determine xanthine oxidase inhibitors and superoxide anion scavengers in natural products.

Natural products, such as rosmarinic acid and apigenin, can act as xanthine oxidase inhibitors (XOIs) as well as superoxide anion scavengers, and have potential for treatment of diseases associated with high uric acid levels and oxidative stress. However, efficient simultaneous screening of these two bioactivities in natural products has been challenging. We have developed a novel method by assembling a multi-hyphenated high performance liquid chromatography (HPLC) system that combines a photo-diode array, chemiluminescence detector and a HPLC system with a variable wavelength detector, to simultaneously detect components that act as both XOIs and superoxide anion scavengers in natural products. Superoxide anion scavenging activity in the analyte was measured by on-line chemiluminescence chromatography based on pyrogallol-luminol oxidation, while xanthine oxidase inhibitory activity was determined by semi-on-line HPLC analysis. After optimizing multiple elements, including chromatographic conditions (e.g., organic solvent concentration and mobile phase pH), concentrations of xanthine/xanthine oxidase and reaction temperature, our validated analytical method was capable of mixed sample analysis. The final results from our method are presented in an easily understood visual format including comprehensive bioactivity data of natural products.

Impact of parameter fluctuations on the performance of ethanol precipitation in production of Re Du Ning Injections, based on HPLC fingerprints and principal component analysis.

The present study was designed to determine the relationships between the performance of ethanol precipitation and seven process parameters in the ethanol precipitation process of Re Du Ning Injections, including concentrate density, concentrate temperature, ethanol content, flow rate and stir rate in the addition of ethanol, precipitation time, and precipitation temperature. Under the experimental and simulated production conditions, a series of precipitated resultants were prepared by changing these variables one by one, and then examined by HPLC fingerprint analyses. Different from the traditional evaluation model based on single or a few constituents, the fingerprint data of every parameter fluctuation test was processed with Principal Component Analysis (PCA) to comprehensively assess the performance of ethanol precipitation. Our results showed that concentrate density, ethanol content, and precipitation time were the most important parameters that influence the recovery of active compounds in precipitation resultants. The present study would provide some reference for pharmaceutical scientists engaged in research on pharmaceutical process optimization and help pharmaceutical enterprises adapt a scientific and reasonable cost-effective approach to ensure the batch-to-batch quality consistency of the final products.

The integrated quality assessment of Chinese commercial dry red wine based on a method of online HPLC-DAD-CL combined with HPLC-ESI-MS.

AIM: To apply an integrated quality assessment strategy to investigate the quality of multiple Chinese commercial dry red wine samples. METHOD: A comprehensive method was developed by combining a high performance liquid chromatography-diode array detector-chemiluminescence (HPLC-DAD-CL) online hyphenated system with an HPLC-ESI-MS technique. RESULTS: Chromatographic and H2O2-scavenging active fingerprints of thirteen batches of different, commercially available Chinese dry red wine samples were obtained and analyzed. Twenty-five compounds, including eighteen antioxidants were identified and evaluated. The dominant and characteristic antioxidants in the samples were identified. The relationships between antioxidant potency and the cultivated variety of grape, producing area, cellaring period, and trade mark are also discussed. CONCLUSION: The results provide the feasibility for an integrated quality assessment strategy to be efficiently and objectively used in quality (especially antioxidant activity) assessment and identification of dry red wine.

The Spectrum-Effect integrated fingerprint of Polygonum cuspidatum based on HPLC-diode array detection-flow injection-chemiluminescence.

AIM: To establish the Spectrum-Effect integrated fingerprint of Polygonum cuspidatum to evaluate the quality of P. cuspidatum. METHODS: An on-line HPLC-DAD-flow injection chemiluminescence (FICL) method was developed to investigate the quality of P. cuspidatum from different habitats based on the established Spectrum-Effect integrated fingerprint. RESULTS: Nineteen batches of samples of P. cuspidatum were evaluated for the similarity of their chromatographic and free radical scavenging fingerprints, and the results compared. Main antioxidants were estimated by regression analysis between peak areas of thirteen compounds and their activities. Some active compounds were identified by HPLC-ESI-MS. CONSULSIONS: The results indicated that main antioxidants in P. cuspidatum could be rapidly screened by the established Spectrum-Effect integrated fingerprint based on on-line HPLC-DAD-FICL, and would be more efficient and objective method to evaluate the quality of P. cuspidatum.

Neuroprotective effects of total saponins from Rubus parvifolius L. on cerebral ischemia/reperfusion injury in rats.

This study examines the neuroprotective effects and mechanisms of action of total saponins from Rubus parvifolius L. (TSRP) on focal cerebral ischemia and reperfusion injury in rats. Focal cerebral ischemia and reperfusion injury was performed in rats using the suture method. The results indicate that intragastric injection of TSRP, at 5, 10 and 20 mg/kg, could decrease neurological impairment, reduce cerebral infarct volume, diminish pathological changes, and significantly inhibit the apoptosis of neurons surrounding the ischemic area. In addition, TSRP upregulated the expression of the anti-apoptotic factor Bcl-2, at the protein and mRNA levels, and it downregulated the expression of the pro-apoptotic factor Bax, at the protein and mRNA levels. These findings indicate that TSRP protects against cerebral ischemia/reperfusion injury, and that it may do so by regulating the expression of Bcl-2 and Bax.