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  • 1
    Online Resource
    Online Resource
    Root-Associated Microbiomes of Panax notoginseng under the Combined Effect of Plant Development and Alpinia officinarum Hance Essential Oil
    MDPI AG ; 2022
    In:  Molecules Vol. 27, No. 18 ( 2022-09-15), p. 6014-
    Details
    In: Molecules, MDPI AG, Vol. 27, No. 18 ( 2022-09-15), p. 6014-
    Abstract: Essential oils (EOs) have been proposed as an alternative to conventional pesticides to inhibit fungal pathogens. However, the application of EOs is considerably limited due to their highly volatile nature and unpredictable effects on other microbes. In our study, the composition of bacterial and fungal communities from the rhizosphere soil of P. notoginseng under four treatment levels of Alpinia officinarum Hance EO was characterized over several growth stages. Leaf weight varied dramatically among the four EO treatment levels after four months of growth, and the disease index at a low concentration (0.14 mg/g) of EO addition was the lowest among the P. notoginseng growth stages. The content of monomeric saponins was elevated when EO was added. Bacterial and fungal diversity in the absence of plants showed a decreasing trend with increasing levels of EO. Bacterial diversity recovery was more correlated with plant growth than was fungal diversity recovery. Compared with the control (no EO addition), a low concentration of EO significantly accumulated Actinomycota, including Acidothermus, Blastococcus, Catenulispora, Conexibacter, Rhodococcus, and Sinomonas, after one month of plant-microbial interaction. Overall, the results showed that both the plant growth stage and EOs drive changes in the microbial community composition in the rhizosphere of P. notoginseng. Plant development status had a stronger influence on bacterial diversity than on fungal diversity. EO had a more significant effect on fungal community composition, increasing the dominance of Ascomycota when EO concentration was increased. Under the interaction of P. notoginseng growth and EO, a large number of bacterial genera that have been described as plant growth-promoting rhizobacteria (PGPR) responded positively to low concentrations of EO application, suggesting that EO may recruit beneficial microbes in the root zone to cope with pathogens and reduce root rot disease. These results offer novel insights into the relationship between EO application, altered microbial communities in the plant roots, plant growth stage, and disease occurrence.
    Type of Medium: Online Resource
    ISSN: 1420-3049
    URL: Article
    DOI: 10.3390/molecules27186014
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2008644-1
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  • 2
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    Identification of 15 lncRNAs Signature for Predicting Survival Benefit of Advanced Melanoma Patients Treated with Anti-PD-1 Monotherapy
    MDPI AG ; 2021
    In:  Cells Vol. 10, No. 5 ( 2021-04-22), p. 977-
    Details
    In: Cells, MDPI AG, Vol. 10, No. 5 ( 2021-04-22), p. 977-
    Abstract: The blockade of programmed cell death protein 1 (PD-1) as monotherapy has been widely used in melanoma, but to identify melanoma patients with survival benefit from anti-PD-1 monotherapy is still a big challenge. There is an urgent need for prognostic signatures improving the prediction of immunotherapy responses of these patients. We analyzed transcriptomic data of pre-treatment tumor biopsies and clinical profiles in advanced melanoma patients receiving only anti-PD-1 monotherapy (nivolumab or pembrolizumab) from the PRJNA356761 and PRJEB23709 data sets as the training and validation cohort, respectively. Weighted gene co-expression network analysis was used to identify the key module, then least absolute shrinkage and selection operator was conducted to determine prognostic-related long noncoding RNAs (lncRNAs). Subsequently, the differentially expressed genes between different clusters were identified, and their function and pathway annotation were performed. In this investigation, 92 melanoma patients with complete survival information (51 from training cohort and 41 from validation cohort) were included in our analyses. We initiallyidentified the key module (skyblue) by weighted gene co-expression network analysis, and then identified a 15 predictive lncRNAs (AC010904.2, LINC01126, AC012360.1, AC024933.1, AL442128.2, AC022211.4, AC022211.2, AC127496.5, NARF-AS1, AP000919.3, AP005329.2, AC023983.1, AC023983.2, AC139100.1, and AC012615.4) signature in melanoma patients treated with anti-PD-1 monotherapy by least absolute shrinkage and selection operator in the training cohort. These results were then validated in the validation cohort. Finally, enrichment analysis showed that the functions of differentially expressed genes between two consensus clusters were mainly related to the immune process and treatment. In summary, the 15 lncRNAs signature is a novel effective predictor for prognosis in advanced melanoma patients treated with anti-PD-1 monotherapy.
    Type of Medium: Online Resource
    ISSN: 2073-4409
    URL: Article
    DOI: 10.3390/cells10050977
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2661518-6
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  • 3
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    Online Resource
    Structural and Functional Characterization of a New Bacterial Dipeptidyl Peptidase III Involved in Fruiting Body Formation in Myxobacteria
    MDPI AG ; 2022
    In:  International Journal of Molecular Sciences Vol. 24, No. 1 ( 2022-12-30), p. 631-
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 24, No. 1 ( 2022-12-30), p. 631-
    Abstract: Dipeptidyl peptidase III (DPP III) is a zinc-dependent enzyme that specifically hydrolyzes dipeptides from the N-terminal of different-length peptides, and it is involved in a number of physiological processes. Here, DPP III with an atypical pentapeptide zinc binding motif (HELMH) was identified from Corallococcus sp. EGB. It was shown that the activity of recombined CoDPP III was optimal at 50 °C and pH 7.0 with high thermostability up to 60 °C. Unique to CoDPP III, the crystal structure of the ligand-free enzyme was determined as a dimeric and closed form. The relatively small inter-domain cleft creates a narrower entrance to the substrate binding site and the unfavorable binding of the bulky naphthalene ring. The ectopic expression of CoDPP III in M. xanthus DK1622 resulted in a 12 h head start in fruiting body development compared with the wild type. Additionally, the A-signal prepared from the starving DK1622-CoDPP III rescued the developmental defect of the asgA mutant, and the fruiting bodies were more numerous and closely packed. Our data suggested that CoDPP III played a role in the fruiting body development of myxobacteria through the accumulation of peptides and amino acids to act as the A-signal.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms24010631
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2019364-6
    SSG: 12
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  • 4
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    Online Resource
    Adsorption of Reactive Brilliant Red X-3B in Aqueous Solutions on Clay–Biochar Composites from Bagasse and Natural Attapulgite
    MDPI AG ; 2018
    In:  Water Vol. 10, No. 6 ( 2018-05-29), p. 703-
    Details
    In: Water, MDPI AG, Vol. 10, No. 6 ( 2018-05-29), p. 703-
    Type of Medium: Online Resource
    ISSN: 2073-4441
    URL: Article
    DOI: 10.3390/w10060703
    Language: English
    Publisher: MDPI AG
    Publication Date: 2018
    detail.hit.zdb_id: 2521238-2
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  • 5
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    Online Resource
    Bioactive Phenolic and Isocoumarin Glycosides from the Stems of Homalium paniculiflorum
    MDPI AG ; 2018
    In:  Molecules Vol. 23, No. 2 ( 2018-02-22), p. 472-
    Details
    In: Molecules, MDPI AG, Vol. 23, No. 2 ( 2018-02-22), p. 472-
    Type of Medium: Online Resource
    ISSN: 1420-3049
    URL: Article
    DOI: 10.3390/molecules23020472
    Language: English
    Publisher: MDPI AG
    Publication Date: 2018
    detail.hit.zdb_id: 2008644-1
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  • 6
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    Online Resource
    Antibody–Drug Conjugate to Treat Meningiomas
    MDPI AG ; 2021
    In:  Pharmaceuticals Vol. 14, No. 5 ( 2021-05-02), p. 427-
    Details
    In: Pharmaceuticals, MDPI AG, Vol. 14, No. 5 ( 2021-05-02), p. 427-
    Abstract: Meningiomas are primary tumors of the central nervous system with high recurrence. It has been reported that somatostatin receptor 2 (SSTR2) is highly expressed in most meningiomas, but there is no effective targeted therapy approved to control meningiomas. This study aimed to develop and evaluate an anti-SSTR2 antibody–drug conjugate (ADC) to target and treat meningiomas. The meningioma targeting, circulation stability, toxicity, and anti-tumor efficacy of SSTR2 ADC were evaluated using cell lines and/or an intracranial xenograft mouse model. The flow cytometry analysis showed that the anti-SSTR2 mAb had a high binding rate of 〉 98% to meningioma CH157-MN cells but a low binding rate of 〈 5% to the normal arachnoidal AC07 cells. The In Vivo Imaging System (IVIS) imaging demonstrated that the Cy5.5-labeled ADC targeted and accumulated in meningioma xenograft but not in normal organs. The pharmacokinetics study and histological analysis confirmed the stability and minimal toxicity. In vitro anti-cancer cytotoxicity indicated a high potency of ADC with an IC50 value of 〈 10 nM. In vivo anti-tumor efficacy showed that the anti-SSTR2 ADC with doses of 8 and 16 mg/kg body weight effectively inhibited tumor growth. This study demonstrated that the anti-SSTR2 ADC can target meningioma and reduce the tumor growth.
    Type of Medium: Online Resource
    ISSN: 1424-8247
    URL: Article
    DOI: 10.3390/ph14050427
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2193542-7
    SSG: 15,3
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  • 7
    Online Resource
    Online Resource
    LGCCT: A Light Gated and Crossed Complementation Transformer for Multimodal Speech Emotion Recognition
    MDPI AG ; 2022
    In:  Entropy Vol. 24, No. 7 ( 2022-07-21), p. 1010-
    Details
    In: Entropy, MDPI AG, Vol. 24, No. 7 ( 2022-07-21), p. 1010-
    Abstract: Semantic-rich speech emotion recognition has a high degree of popularity in a range of areas. Speech emotion recognition aims to recognize human emotional states from utterances containing both acoustic and linguistic information. Since both textual and audio patterns play essential roles in speech emotion recognition (SER) tasks, various works have proposed novel modality fusing methods to exploit text and audio signals effectively. However, most of the high performance of existing models is dependent on a great number of learnable parameters, and they can only work well on data with fixed length. Therefore, minimizing computational overhead and improving generalization to unseen data with various lengths while maintaining a certain level of recognition accuracy is an urgent application problem. In this paper, we propose LGCCT, a light gated and crossed complementation transformer for multimodal speech emotion recognition. First, our model is capable of fusing modality information efficiently. Specifically, the acoustic features are extracted by CNN-BiLSTM while the textual features are extracted by BiLSTM. The modality-fused representation is then generated by the cross-attention module. We apply the gate-control mechanism to achieve the balanced integration of the original modality representation and the modality-fused representation. Second, the degree of attention focus can be considered, as the uncertainty and the entropy of the same token should converge to the same value independent of the length. To improve the generalization of the model to various testing-sequence lengths, we adopt the length-scaled dot product to calculate the attention score, which can be interpreted from a theoretical view of entropy. The operation of the length-scaled dot product is cheap but effective. Experiments are conducted on the benchmark dataset CMU-MOSEI. Compared to the baseline models, our model achieves an 81.0% F1 score with only 0.432 M parameters, showing an improvement in the balance between performance and the number of parameters. Moreover, the ablation study signifies the effectiveness of our model and its scalability to various input-sequence lengths, wherein the relative improvement is almost 20% of the baseline without a length-scaled dot product.
    Type of Medium: Online Resource
    ISSN: 1099-4300
    URL: Article
    DOI: 10.3390/e24071010
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2014734-X
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  • 8
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    Integrated Proteomics and Lipidomics Investigation of the Mechanism Underlying the Neuroprotective Effect of N-benzylhexadecanamide
    MDPI AG ; 2018
    In:  Molecules Vol. 23, No. 11 ( 2018-11-09), p. 2929-
    Details
    In: Molecules, MDPI AG, Vol. 23, No. 11 ( 2018-11-09), p. 2929-
    Abstract: Macamides are very important secondary metabolites produced by Lepidium meyenii Walp, which possess multiple bioactivities, especially in the neuronal system. In a previous study, we observed that macamides exhibited excellent effects in the recovery of injured nerves after 1-methyl-4-phenylpyridinium (MPP+)-induced dopaminergic neuronal damage in zebrafish. However, the mechanism underlying this effect remains unclear. In the present study, we observed that N-benzylhexadecanamide (XA), which is a typical constituent of macamides, improved the survival rate of neurons in vitro. We determined the concentration of neurotransmitters in MN9D cells and used it in conjunction with an integrated proteomics and lipidomics approach to investigate the mechanism underlying the neuroprotective effects of XA in an MPP+-induced neurodegeneration cell model using QqQ MS, Q-TOF MS, and Orbitrap MS. The statistical analysis of the results led to the identification of differentially-expressed biomarkers, including 11 proteins and 22 lipids, which may be responsible for the neuron-related activities of XA. All these potential biomarkers were closely related to the pathogenesis of neurodegenerative diseases, and their levels approached those in the normal group after treatment with XA. Furthermore, seven lipids, including five phosphatidylcholines, one lysophosphatidylcholine, and one phosphatidylethanolamine, were verified by a relative quantitative approach. Moreover, four proteins (Scarb2, Csnk2a2, Vti1b, and Bnip2) were validated by ELISA. The neurotransmitters taurine and norepinephrine, and the cholinergic constituents, correlated closely with the neuroprotective effects of XA. Finally, the protein–lipid interaction network was analyzed. Based on our results, the regulation of sphingolipid metabolism and mitochondrial function were determined to be the main mechanisms underlying the neuroprotective effect of XA. The present study should help us to better understand the multiple effects of macamides and their use in neurodegenerative diseases.
    Type of Medium: Online Resource
    ISSN: 1420-3049
    URL: Article
    DOI: 10.3390/molecules23112929
    Language: English
    Publisher: MDPI AG
    Publication Date: 2018
    detail.hit.zdb_id: 2008644-1
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  • 9
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    Synthesis and In Vitro Anti-Influenza Virus Evaluation of Novel Sialic Acid (C-5 and C-9)-Pentacyclic Triterpene Derivatives
    MDPI AG ; 2017
    In:  Molecules Vol. 22, No. 7 ( 2017-06-22), p. 1018-
    Details
    In: Molecules, MDPI AG, Vol. 22, No. 7 ( 2017-06-22), p. 1018-
    Type of Medium: Online Resource
    ISSN: 1420-3049
    URL: Article
    DOI: 10.3390/molecules22071018
    Language: English
    Publisher: MDPI AG
    Publication Date: 2017
    detail.hit.zdb_id: 2008644-1
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  • 10
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    Lignin Structure and Solvent Effects on the Selective Removal of Condensed Units and Enrichment of S-Type Lignin
    MDPI AG ; 2018
    In:  Polymers Vol. 10, No. 9 ( 2018-09-01), p. 967-
    Details
    In: Polymers, MDPI AG, Vol. 10, No. 9 ( 2018-09-01), p. 967-
    Abstract: This study focused on the structural differences of lignin after pyridine–acetic acid–water (PAW) and dioxane–acidic water (DAW) purification processes. These structural differences included the S/G ratio, condensed structure, weight-average (MW) molecular weights, β-O-4 linkages and sugar content. The chemical structure of the isolated crude lignin (CL), PAW purified lignin (PPL) and DAW purified lignin (DPL) was elucidated using quantitative 13C NMR, 2D-HSQC NMR spectra, thermogravimetric analysis (TGA), gel permeation chromatography (GPC) and Fourier transform infrared spectroscopy (FTIR). The results showed that the PPL fractions contain fewer condensed structures, higher S/G ratios, more β-O-4 linkages, higher average MW and lower thermal degradation properties compared to the CL and DPL fractions. Furthermore, the PAW process was more selective in removing condensed units and enriching S-type lignin from CL compared to the DAW process. These results provide valuable information for understanding which purification process is more suitable to be applied for lignin.
    Type of Medium: Online Resource
    ISSN: 2073-4360
    URL: Article
    DOI: 10.3390/polym10090967
    Language: English
    Publisher: MDPI AG
    Publication Date: 2018
    detail.hit.zdb_id: 2527146-5
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