Identification of two major QTLs for pod shell thickness in peanut (Arachis hypogaea L.) using BSA-seq analysis.

BACKGROUND: Pod shell thickness (PST) is an important agronomic trait of peanut because it affects the ability of shells to resist pest infestations and pathogen attacks, while also influencing the peanut shelling process. However, very few studies have explored the genetic basis of PST. RESULTS: An F2 segregating population derived from a cross between the thick-shelled cultivar Yueyou 18 (YY18) and the thin-shelled cultivar Weihua 8 (WH8) was used to identify the quantitative trait loci (QTLs) for PST. On the basis of a bulked segregant analysis sequencing (BSA-seq), four QTLs were preliminarily mapped to chromosomes 3, 8, 13, and 18. Using the genome resequencing data of YY18 and WH8, 22 kompetitive allele-specific PCR (KASP) markers were designed for the genotyping of the F2 population. Two major QTLs (qPSTA08 and qPSTA18) were identified and finely mapped, with qPSTA08 detected on chromosome 8 (0.69-Mb physical genomic region) and qPSTA18 detected on chromosome 18 (0.15-Mb physical genomic region). Moreover, qPSTA08 and qPSTA18 explained 31.1-32.3% and 16.7-16.8% of the phenotypic variation, respectively. Fifteen genes were detected in the two candidate regions, including three genes with nonsynonymous mutations in the exon region. Two molecular markers (Tif2_A08_31713024 and Tif2_A18_7198124) that were developed for the two major QTL regions effectively distinguished between thick-shelled and thin-shelled materials. Subsequently, the two markers were validated in four F2:3 lines selected. CONCLUSIONS: The QTLs identified and molecular markers developed in this study may lay the foundation for breeding cultivars with a shell thickness suitable for mechanized peanut shelling.

Potential to reduce methane production of using cultivated seaweeds supplementation to reshape the community structure of rumen microorganisms.

Methane is a short-lived greenhouse gas but has a far greater warming effect than carbon dioxide. At the same time, the livestock sector serves as a large contributor to global emissions of anthropogenic methane. Herein, this work aimed to use cultivated seaweed supplementation to reduce methane emissions and investigate the potential influencing mechanism. To evaluate the feasibility, two cultivated seaweeds, Laminaria japonica Aresch, and Porphyra tenera, along with the enzymatic hydrolysates derived from L. japonica, underwent in vitro trials, and they were both added into corn silage feed (CSF) with different concentrations (1%, 5%, and 10% of CSF) for methane reduction evaluation. The results indicated that >75% and 50% reductions in methane production were observed for the seaweeds and seaweed enzymatic hydrolysates in 9- and 30-day, respectively. Combined high-throughput sequencing and multivariate analysis revealed that supplementation with seaweed and seaweed enzymatic hydrolysates had a notable impact on the prokaryotic community structure. Mantel tests further revealed that significant correlations between the prokaryotic community and methane accumulation (P < 0.05), implying the prokaryotic community plays a role in reducing methane emissions within the rumen. Correspondingly, the networks within the prokaryotic community unveiled the crucial role of propionate/butyrate-producing bacteria in regulating methane emissions through microbial interactions. The predicted function of the prokaryotic community exhibited a significant reduction in the presence of the narB gene in seaweed-supplemented treatments. This reduction may facilitate an increased rate of electron flow toward the nitrate reduction pathway while decreasing the conversion of H2 to methane. These results indicated the supplementation of cultivated seaweeds and the enzymatic hydrolysates has the potential to reshape the community structure of rumen microbial communities, and this alteration appears to be a key factor contributing to their methane production-reduction capability.

Cytological and transcriptomic analysis to unveil the mechanism of web blotch resistance in Peanut.

BACKGROUND: Peanut is an important oil crop worldwide. Peanut web blotch is a fungal disease that often occurs at the same time as other leaf spot diseases, resulting in substantial leaf drop, which seriously affects the peanut yield and quality. However, the molecular mechanism underlying peanut resistance to web blotch is unknown. RESULTS: The cytological examination revealed no differences in the conidium germination rate between the web blotch-resistant variety ZH and the web blotch-susceptible variety PI at 12-48 hpi. The appressorium formation rate was significantly higher for PI than for ZH at 24 hpi. The papilla formation rate at 36 hpi and the hypersensitive response rate at 60 and 84 hpi were significantly higher for ZH than for PI. We also compared the transcriptional profiles of web blotch-infected ZH and PI plants at 0, 12, 24, 36, 48, 60, and 84 hpi using an RNA-seq technique. There were more differentially expressed genes (DEGs) in ZH and PI at 12, 36, 60, and 84 hpi than at 24 and 48 hpi. Moreover, there were more DEGs in PI than in ZH at each time-point. The analysis of metabolic pathways indicated that pantothenate and CoA biosynthesis; monobactam biosynthesis; cutin, suberine and wax biosynthesis; and ether lipid metabolism are specific to the active defense of ZH against YY187, whereas porphyrin metabolism as well as taurine and hypotaurine metabolism are pathways specifically involved in the passive defense of ZH against YY187. In the protein-protein interaction (PPI) network, most of the interacting proteins were serine acetyltransferases and cysteine synthases, which are involved in the cysteine synthesis pathway. The qRT-PCR data confirmed the reliability of the transcriptome analysis. CONCLUSION: On the basis of the PPI network for the significantly enriched genes in the pathways which were specifically enriched at different time points in ZH, we hypothesize that serine acetyltransferases and cysteine synthases are crucial for the cysteine-related resistance of peanut to web blotch. The study results provide reference material for future research on the mechanism mediating peanut web blotch resistance.

Person re-identification via semi-supervised adaptive graph embedding.

Video surveillance is an indispensable part of the smart city for public safety and security. Person Re-Identification (Re-ID), as one of elementary learning tasks for video surveillance, is to track and identify a given pedestrian in a multi-camera scene. In general, most existing methods has firstly adopted a CNN based detector to obtain the cropped pedestrian image, it then aims to learn a specific distance metric for retrieval. However, unlabeled gallery images are generally overlooked and not utilized in the training. On the other hands, Manifold Embedding (ME) has well been applied to Person Re-ID as it is good to characterize the geometry of database associated with the query data. However, ME has its limitation to be scalable to large-scale data due to the huge computational complexity for graph construction and ranking. To handle this problem, we in this paper propose a novel scalable manifold embedding approach for Person Re-ID task. The new method is to incorporate both graph weight construction and manifold regularized term in the same framework. The graph we developed is discriminative and doubly-stochastic so that the side information has been considered so that it can enhance the clustering performances. The doubly-stochastic property can also guarantee the graph is highly robust and less sensitive to the parameters. Meriting from such a graph, we then incorporate the graph construction, the subspace learning method in the unified loss term. Therefore, the subspace results can be utilized into the graph construction, and the updated graph can in turn incorporate discriminative information for graph embedding. Extensive simulations is conducted based on three benchmark Person Re-ID datasets and the results verify that the proposed method can achieve better ranking performance compared with other state-of-the-art graph-based methods.

Evaluation of the effects of notoginseng total saponins (NS), safflower total flavonoids (SF), and the combination of NS and SF (CNS) on the activities of cytochrome P450 enzymes using a cocktail method in rats.

Notoginseng total saponins (NS), safflower total flavonoids (SF), and the combination of NS and SF, namely CNS, are used for the treatment of cardiovascular diseases in clinic. This study developed a cocktail assay involving seven cytochrome P450 (CYP) enzymes to elucidate the effect of NS, SF, and CNS on CYP enzymes and to explore the synergistic effect of CNS in terms of CYP enzymes. Ultra-performance liquid chromatography-MS and reverse-transcription polymerase chain reaction were applied to detect the activities and mRNA expression levels of CYP enzymes. SF exhibited inhibitory effects on CYP1A2, 2B1, 2E1, and 2C11 and induction effects on CYP2C19 and 2D4. NS exhibited induction effects on CYP1A2, 2B1, 2E1, 2C11, 2C19, and 2D4. CNS exhibited induction effects on CYP1A2, 2B1, 2E1, 2C19, and 2D4 and inhibitory effects on CYP3A1 in vivo. Moreover, mRNA expression results were consistent with pharmacokinetic results. Potential herb-drug interactions should be studied closely when SF, NS, or CNS with clinical drugs are metabolized by CYP1A2, 2B1, 2E1, 2C11, 2C19, 2D4, and 3A1. CNS could change the inhibition or induction effects of CYP compared to the NS group, which might be one of the causes for the synergistic effects of the combination of NS and SF.

A new prenylated coumarin diglycoside with insulin-release promoting activity from Clausena dunniana.

A new prenylated coumarin diglycoside, 6-prenylcoumarin-7-O-ß-D-apiofuranosyl-(1→6)-ß-D-glucopyranoside (1) and five known flavonoid glycosides (2-6) were isolated from the leaves and stems of Clausena dunniana. The structures of these isolates were elucidated based on comprehensive MS, UV, IR, and NMR spectroscopic data analysis and comparison with the data reported in literature. Compounds 2-6 are obtained from the title plant for the first time. All these isolates were evaluated for their insulin-release promoting effects, and compounds 1, 2, and 4 exhibited significant activities (2.0 to 3.3-fold higher in comparison with the control, p < 0.01) at 40 µM.[Formula: see text].

Highly selective inhibition of IMPDH2 provides the basis of antineuroinflammation therapy.

Inosine monophosphate dehydrogenase (IMPDH) of human is an attractive target for immunosuppressive agents. Currently, small-molecule inhibitors do not show good selectivity for different IMPDH isoforms (IMPDH1 and IMPDH2), resulting in some adverse effects, which limit their use. Herein, we used a small-molecule probe specifically targeting IMPDH2 and identified Cysteine residue 140 (Cys140) as a selective druggable site. On covalently binding to Cys140, the probe exerts an allosteric regulation to block the catalytic pocket of IMPDH2 and further induces IMPDH2 inactivation, leading to an effective suppression of neuroinflammatory responses. However, the probe does not covalently bind to IMPDH1. Taken together, our study shows Cys140 as a druggable site for selectively inhibiting IMPDH2, which provides great potential for development of therapy agents for autoimmune and neuroinflammatory diseases with less unfavorable tolerability profile.

Three new compounds from Dictamnus dasycarpus and their anti-inflammatory activities.

Three new compounds (1-3), named dasycarine G (1), dasycarether (2), and dasycarester (3), along with seven known compounds (4-10) obtained from the genus Dictamnus for the first time, were isolated from the root bark of Dictamnus dasycarpus. Their structures were elucidated on the basis of spectroscopic data (UV, IR, HR-ESI-MS, 1D and 2D NMR, and CD). In the in vitro assay, compounds 1, 5, 6, 9, and 10 exhibited NO inhibitory effects of LPS-induced BV-2 cells with IC50 values in the range of 10.4 µM to 27.2 µM.

Cucurbitacin E Inhibits Huh7 Hepatoma Carcinoma Cell Proliferation and Metastasis via Suppressing MAPKs and JAK/STAT3 Pathways.

Cucurbitacin E (CuE), a highly oxygenated tetracyclic triterpene from Cucurbitaceae, has shown to exhibit potent cytotoxic and anti-proliferative properties against several human cancer cells. However, the underlying effects and mechanisms of CuE regarding hepatocellular carcinoma (HCC) have not been well understood. In the current study, unbiased RNA-sequencing (RNA-seq) and bioinformatics analysis was applied to elucidate the underlying molecular mechanism. CuE could significantly inhibit cell proliferation and migration of Huh7 cells, meanwhile CuE exhibited potent anti-angiogenic activity. RNA-seq analysis revealed that CuE negatively regulated 241 differentially expressed genes (DEGs) involved in multiple processes including cytoskeleton formation, angiogenesis and focal adhesion. Further analysis revealed that CuE effectually regulated diversified pharmacological signaling pathways such as MAPKs and JAK-STAT3. Our findings demonstrated the role of CuE in inhibiting proliferation and migration, providing an insight into the regulation of multiple signaling pathways as a new paradigm for anti-cancer treatment strategy.

Identification of potential crucial genes associated with carcinogenesis of clear cell renal cell carcinoma.

Clear cell renal cell carcinoma (ccRCC) is a common genitourinary malignancy with high mortality. However, the molecular pathogenesis of ccRCC remains unclear and effective biomarkers for daily practice are still limited. Thus, we aimed to identify the potential crucial genes and pathways associated with carcinogenesis of ccRCC and further analyze the molecular mechanisms implicated in tumorigenesis. In the present study, expression profiles GSE 66270, GSE 53757, GSE 36895, and GSE 76351 were downloaded from GEO database, including 244 matched primary and adjacent normal tissues, furthermore, the level 3 RNAseq dataset (RNAseqV2 RSEM) of KIRC was also downloaded from The Cancer Genome Atlas (TCGA), which consist of 529 ccRCC tumors and 72 normal tissues. Then, differentially expressed genes (DEGs) and pathway enrichment were analyzed by using R software. A total of 129 up- and 123 down-regulated genes were identified, which were aberrantly expressed both in GEO and TCGA data. Second, Gene ontology (GO) analyses revealed that most of the DEGs were significantly enriched in integral component of membrane, extracellular exosome, plasma membrane, cell adhesion, and receptor binding. Signaling pathway analyses indicated that DEGs had common pathways in signal transduction, metabolism, and immune system. Third, hub genes were identified with protein-protein interaction (PPI) network, including PTPRC, TGFB1, EGF, MYC, ITGB2, CTSS, FN1, CCL5, KNG1, and CD86. Additionally, sub-networks analyse was also performed by using MCODE plugin. In conclusion, the novel DEGs and pathways in ccRCC identified in this study may provide new insight into the underlying molecular mechanisms that facilitates RCC carcinogenesis.

LC-MS-Guided Isolation of Insulin-Secretion-Promoting Monoterpenoid Carbazole Alkaloids from Murraya microphylla.

Fifteen new structurally unique monoterpenoid carbazole alkaloids, including two pairs of epimers (1/2 and 3/4), three pairs of enantiomers (6a/6b, 7a/7b, and 8a/8b), and five optically pure analogues (5, 9-12), were obtained from a 95% aqueous EtOH extract of Murraya microphylla by a combination of bioassay- and LC-MS-guided fractionation procedures. Their structures were established based on NMR and HRESIMS data interpretation. The absolute configuration of compound 1 was determined via X-ray crystallographic data analysis and for all compounds by comparison of experimental and calculated ECD data. Compounds 1-5 were assigned as five new thujane-carbazole alkaloids, and compounds 6-12 as 10 new menthene-carbazole alkaloids linked through an ether or carbon-carbon bond. Compounds 1-12 promoted insulin secretion in the HIT-T15 cell line, 1.9-3.1-fold higher than the gliclazide control at 100 µM.

Nitric Oxide Inhibitory Sesquiterpenoids and Its Dimers from Artemisia freyniana.

Two new disesquiterpenoids (1 and 2) and 11 new (3-13) and 10 known (14-23) sesquiterpenoids were isolated from the whole plants of Artemisia freyniana. Their structures were elucidated by spectroscopic data analysis and comparison with published NMR data. The absolute configurations of the new isolates (1-13) were assigned based on single-crystal X-ray diffraction data and comparison of the experimental and calculated ECD data. The eremophilane derivatives 8 and 9 possess an unprecedented 2-isopropyl-3,7,7a-trimethyl-2,4,5,6,7,7a-hexahydro-1 H-indene scaffold, and a putative biosynthetic pathway for these compounds is proposed. Compounds 4, 5, and 9 exhibited inhibitory effects against LPS-stimulated nitric oxide (NO) production in RAW 264.7 macrophage cells with IC50 values of 10.8, 12.6, and 11.7 µM, respectively.

Anti-Inflammatory Prenylated Phenylpropenols and Coumarin Derivatives from Murraya exotica.

Three new prenylated phenylpropenols, exotiacetals A-C (1-3), 10 new coumarin derivatives, exotimarins A-I (4-13), and 35 known analogues (14-48) were isolated from the roots of Murraya exotica. The absolute configurations of the new compounds were assigned via comparison of their specific rotations, single-crystal X-ray diffraction data, Mosher's method, the ECD exciton coupling method, comparison of experimental and calculated ECD data, and the ECD data of the in situ formed transition metal complexes. Compounds 1-3, which possess an unprecedented hexahydro-1H-isochromen-1-ol system, are presumably biosynthesized from two prenylated p-coumaryl alcohol moieties via Diels-Alder [4+2] cycloaddition and cyclic hemiacetal formation reactions. Compounds 1, 28, 33, and 35 demonstrated inhibition against LPS-induced NO production in BV-2 microglial cells with IC50 values of 8.6 ± 0.3, 11.8 ± 0.9, 15.5 ± 0.9, and 16.9 ± 1.0 µM, respectively.

Pyrrolo[2,1-a]isoquinoline and pyrrole alkaloids from Sinomenium acutum.

Two pyrrolo[2,1-a]isoquinolines (1 and 2) and three pyrrole alkaloids (3-5), including three new ones, named sinopyrines A-C (1-3), were isolated from the 95% EtOH extract of the stems and rhizomes of Sinomenium acutum (Thumb.) Rehd. et Wils. The structures of the new compounds were elucidated on the basis of spectroscopic data. This is the first report of pyrrole-bearing natural compounds from the family Menispermaceae.

Three new indole alkaloid derivatives from the roots of Murraya paniculata.

Three new indole alkaloid derivatives, named paniculidines D‒F (1‒3), and six known analogs (4‒9) were isolated from the roots of Murraya paniculata. The structures were elucidated on the basis of comprehensive HRESIMS, UV, IR, and NMR spectroscopic data analysis and comparison with the data reported in literature. The absolute configurations of new compounds were assigned via the determination of specific optical rotation, Mosher's method, and ECD spectra. Compound 3 is the first heterodimer of C-N linked indole and coumarin derivatives.

Azukisapogenol Triterpene Glycosides from Oxytropis chiliophylla Royle.

Eight azukisapogenol triterpene glycosides, including five new compounds, oxychiliotriterpenosides A⁻E (1⁻5), two new methyl glucuronide derivatives that proved to be artifacts, oxychiliotriterpenoside E-glucuronic acid methyl ester (6) and myrioside B-glucuronic acid methyl ester (7), and a known one, myrioside B (8), was isolated from the aerial part of Oxytropis chiliophylla Royle. Their structures were elucidated based on extensive spectroscopic analyses and chemical methods. Triterpene glycosides were first obtained from O. chiliophylla, and those containing a galactose unit (1, 2, 5 and 6) and diglucosidic or triglucosidic linkage at C-29 (1⁻4), were reported from Oxytropis species for the first time, which might be recognized as a chemotaxonomic feature of O. chiliophylla. All isolated compounds were evaluated for their anti-inflammatory activities against NO production using lipopolysaccharide (LPS)-induced RAW 264.7 cells, but no compounds showed potent inhibition on NO production.

[Four new cis-phenylethanoid glycosides from stems of Cistanche deserticola cultured in Tarim desert].

In order to clarify the chemical constituents of Cistanche deserticola cultured in Tarim desert, a systematically phytochemical investigation was carried out. The chemical constituents were isolated by column chromatography, such as silica gel, Sephadex LH-20, MCI gel, ODS and semi-preparative HPLC, and their structures were determined on the basis of MS, NMR spectroscopic analysis, and comparison with literature data. Four compounds were isolated from the 85% ethanol extract of the stems of C. cultured in Tarim desert. Their structures were identified as cis-tubuloside (1), cis-cistanoside (2), cis-cistanoside J (3), and cis-isocistanoside C(4). Compounds 1-4 were four new cis-phenylethanoid glycosides. Herein, we firstly report the ¹H, ¹³C-NMR data of the new compounds(1-4) for the first time. This study will provide the scientific evidence for comprehensively analyzing the chemical constituents of C. deserticola cultured in Tarim desert.

New terpenoids and thiophene derivatives from the aerial parts of Artemisia sieversiana.

One new highly oxygenated nortriterpene, named sieverlactone (1), one new sesquiterpene, 1ß,10ß-epoxy-8α-acetoxyachillin (2), one new natural product, 5-propinyl-thiophene-2-carboxylic acid (3), and one new thiophene, 3-hydroxy-5-propinyl-2-acetyl-thiophene (4), together with 10 other known compounds (5-14), were isolated from the dried aerial parts of Artemisia sieversiana. Their structures were elucidated by a combination of extensive spectroscopic analysis, including 1D, 2D NMR spectroscopic and mass spectrometric data. Meanwhile, the stereochemistry of 1 and 2 was confirmed by single-crystal X-ray diffraction technique using Cu radiation. All the isolates were evaluated for their anti-neuroinflammatory effects on the lipopolysaccharide-induced nitric oxide production in BV-2 murine microglial cells. Compounds 2, 5, and 6 exhibited the significant activities with IC50 values of 6.5 ±â€¯0.5, 11.9 ±â€¯0.7, and 10.1 ±â€¯0.3 µM, respectively, comparable to the positive control, quercetin, with an IC50 value of 16.3 ±â€¯0.4 µM.

Non-Convex Sparse and Low-Rank Based Robust Subspace Segmentation for Data Mining.

Parsimony, including sparsity and low-rank, has shown great importance for data mining in social networks, particularly in tasks such as segmentation and recognition. Traditionally, such modeling approaches rely on an iterative algorithm that minimizes an objective function with convex l1-norm or nuclear norm constraints. However, the obtained results by convex optimization are usually suboptimal to solutions of original sparse or low-rank problems. In this paper, a novel robust subspace segmentation algorithm has been proposed by integrating lp-norm and Schatten p-norm constraints. Our so-obtained affinity graph can better capture local geometrical structure and the global information of the data. As a consequence, our algorithm is more generative, discriminative and robust. An efficient linearized alternating direction method is derived to realize our model. Extensive segmentation experiments are conducted on public datasets. The proposed algorithm is revealed to be more effective and robust compared to five existing algorithms.

Ruticarpsides A-C, three new ester glycosides from the fruits of Tetradium ruticarpum.

In the course of our ongoing phytochemical investigation on the n-butanol extract of the fruits of Tetradium ruticarpum (Rutaceae), three new compounds, ruticarpsides A-C (1-3), were obtained and their structures were elucidated by a comprehensive analysis of NMR and MS data. Compound 3 showed a weak inhibition effect on nitric oxide production in BV-2 microglial cells stimulated with lipopolysaccharide.