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"Bai, Hong"
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Network Pharmacology Databases for Traditional Chinese Medicine: Review and Assessment
The research field of systems biology has greatly advanced and, as a result, the concept of network pharmacology has been developed. This advancement, in turn, has shifted the paradigm from a \"one-target, one-drug\" mode to a \"network-target, multiple-component-therapeutics\" mode. Network pharmacology is more effective for establishing a \"compound-protein/gene-disease\" network and revealing the regulation principles of small molecules in a high-throughput manner. This approach makes it very powerful for the analysis of drug combinations, especially Traditional Chinese Medicine (TCM) preparations. In this work, we first summarized the databases and tools currently used for TCM research. Second, we focused on several representative applications of network pharmacology for TCM research, including studies on TCM compatibility, TCM target prediction, and TCM network toxicology research. Third, we compared the general statistics of several current TCM databases and evaluated and compared the search results of these databases based on 10 famous herbs. In summary, network pharmacology is a rational approach for TCM studies, and with the development of TCM research, powerful and comprehensive TCM databases have emerged but need further improvements. Additionally, given that several diseases could be treated by TCMs, with the mediation of gut microbiota, future studies should focus on both the microbiome and TCMs to better understand and treat microbiome-related diseases.
Journal Article
Changes and response mechanism of sugar and organic acids in fruits under water deficit stress
The content and the ratio of soluble sugars and organic acids in fruits are significant indicators for fruit quality. They are affected by multiple environmental factors, in which water-deficient is the most concern. Previous studies found that the content of soluble sugars and organic acids in fruit displayed great differences under varied water stress. It is important to clarify the mechanism of such difference and to provide researchers with systematic knowledge about the response to drought stress and the mechanism of sugar and acid changes in fruits, so that they can better carry out the study of fruit quality under drought stress. Therefore, the researchers studied dozens of research articles about the content of soluble sugar and organic acid, the activity of related metabolic enzymes, and the expression of related metabolic genes in fruits under water stress, and the stress response of plants to water stress. We found that after plants perceived and transmitted the signal of water deficit, the expression of genes related to the metabolism of soluble sugars and organic acids changed. It was then affected the synthesis of metabolic enzymes and changed their metabolic rate, ultimately leading to changes in soluble sugar and organic acid content. Based on the literature review, we described the pathway diagrams of sugar metabolism, organic acid metabolism, mainly malic acid, tartaric acid, and citric acid metabolism, and of the response to drought stress. From many aspects including plants’ perception of water stress signal, signal conversion and transmission, induced gene expression, the changes in soluble sugar and the enzyme activities of organic acids, as well as the final sugar and acid content in fruits, this thesis summarized previous studies on the influence of water stress on soluble sugars and the metabolism of organic acids in fruits.
Journal Article
Transcriptome sequencing and metabolome analysis reveal the molecular mechanism of Salvia miltiorrhiza in response to drought stress
Salvia miltiorrhiza
is commonly used as a Chinese herbal medicine to treat different cardiovascular and cerebrovascular illnesses due to its active ingredients. Environmental conditions, especially drought stress, can affect the yield and quality of
S. miltiorrhiza.
However, moderate drought stress could improve the quality of
S. miltiorrhiza
without significantly reducing the yield, and the mechanism of this initial drought resistance is still unclear. In our study, transcriptome and metabolome analyses of
S. miltiorrhiza
under different drought treatment groups (CK, A, B, and C groups) were conducted to reveal the basis for its drought tolerance. We discovered that the leaves of
S. miltiorrhiza
under different drought treatment groups had no obvious shrinkage, and the malondialdehyde (MDA) contents as well as superoxide dismutase (SOD) and peroxidase (POD) activities dramatically increased, indicating that our drought treatment methods were moderate, and the leaves of
S. miltiorrhiza
began to initiate drought resistance. The morphology of root tissue had no significant change under different drought treatment groups, and the contents of four tanshinones significantly enhanced. In all, 5213, 6611, and 5241 differentially expressed genes (DEGs) were shared in the A, B, and C groups compared with the CK group, respectively. The results of KEGG and co-expression analysis showed that the DEGs involved in plant-pathogen interactions, the MAPK signaling pathway, phenylpropanoid biosynthesis, flavonoid biosynthesis, and plant hormone signal transduction responded to drought stress and were strongly correlated with tanshinone biosynthesis. Furthermore, the results of metabolism analysis indicated that 67, 72, and 92 differentially accumulated metabolites (DAMs), including fumarate, ferulic acid, xanthohumol, and phytocassanes, which were primarily involved in phenylpropanoid biosynthesis, flavonoid biosynthesis, and diterpenoid biosynthesis pathways, were detected in these groups. These discoveries provide valuable information on the molecular mechanisms by which
S. miltiorrhiza
responds to drought stress and will facilitate the development of drought-resistant and high-quality
S. miltiorrhiza
production.
Journal Article
Composition Operators on Weighted Zygmund Spaces of the First Loo-keng Hua Domain
Let HEI denote the first Loo-keng Hua domain. In this paper, we obtain many elementary results on HEI by the continuous and careful discussions. In some applications, we obtain some necessary conditions or sufficient conditions for the boundedness and compactness of the composition operators on weighted Zygmund space defined on HEI.
Journal Article
TCM-Mesh: The database and analytical system for network pharmacology analysis for TCM preparations
With the advancement of systems biology research, we have already seen great progress in pharmacology studies, especially in network pharmacology. Network pharmacology has been proven to be effective for establishing the “compounds-proteins/genes-diseases” network, and revealing the regulation principles of small molecules in a high-throughput manner, thus would be very effective for the analysis of drug combinations, especially for TCM preparations. In this work, we have proposed the TCM-Mesh system, which records TCM-related information collected from various resources and could serve for network pharmacology analysis for TCM preparations in a high-throughput manner (http://mesh.tcm.microbioinformatics.org/). Currently, the database contains 6,235 herbs, 383,840 compounds, 14,298 genes, 6,204 diseases, 144,723 gene-disease associations, 3,440,231 pairs of gene interactions, 163,221 side effect records and 71 toxic records, and web-based software construct a network between herbs and treated diseases, which will help to understand the underlying mechanisms for TCM preparations at molecular levels. We have used 1,293 FDA-approved drugs, as well as compounds from an herbal material
Panax ginseng
and a patented drug Liuwei Dihuang Wan (LDW) for evaluating our database. By comparison of different databases, as well as checking against literature, we have demonstrated the completeness, effectiveness, and accuracy of our database.
Journal Article
Whole-genome DNA methylation patterns and complex associations with gene expression associated with anthocyanin biosynthesis in apple fruit skin
DNA methylation is a common feature of epigenetic regulation and is associated with various biological processes. Anthocyanins are among the secondary metabolites that contribute to fruit colour, which is a key appearance and nutrition quality attribute of apple fruit. Although few studies reported that DNA methylation in the promoter of MYB transcription factor was associated with fruit skin color, there is a general lack of understanding of the dynamics of global and genic DNA methylation in apple fruit. Here, whole-genome bisulfite sequencing was carried out in fruit skin of apple (Malus domestica Borkh.) cv. ‘Red Delicious’ (G0) and its four-generation bud sport mutants, including ‘Starking Red’ (G1), ‘Starkrimson’ (G2), ‘Campbell Redchief’ (G3) and ‘Vallee spur’ (G4) at color break stage. Correlation and linear-regression analysis between DNA methylation level and anthocyanin content, as well as the transcription levels of genes related to anthocyanin biosynthesis were carried out. The results showed that the number of differentially methylated regions (DMRs) and differentially methylated genes (DMGs) was considerably increased from G1 to G4 versus the number observed in G0. The mCHH context was dominant in apple, but the levels of mCG and mCHG of DMGs were significantly higher than that of the mCHH. Genetic variation of bud sport mutants from ‘Red Delicious’ was associated with differential DNA methylation. Additionally, hypomethylation of mCG and mCHG contexts in flavonoid biosynthesis pathway genes (PAL, 4CL, CYP98A, PER, CCOAOMT, CHS, and F3'H), mCHG context in MYB10 at upstream, led to transcriptional activation and was conductive to anthocyanin accumulation. However, hypermethylation of mCG context in bHLH74 at upstream led to transcriptional inhibition, inhibiting anthocyanin accumulation.
Journal Article
Numerical analysis for the vertical bearing capacity of composite pile foundation system in liquefiable soil under sine wave vibration
Composite pile foundation has been widely used in ground engineering. This composite pile foundation system has complex pile-soil interactions under seismic loading. The calculation of vertical bearing capacity of composite pile foundation is still an unsolved problem if the soil around piles is partially or completely liquefied under seismic loading. We have completed indoor shaking table model tests to measure the vertical bearing capacity in a liquefiable soil foundation under seismic loading. This paper will use a numerical approach to analyze the change of this vertical bearing capacity under seismic loading. Firstly, the Goodman contact element is improved to include the Rayleigh damping. Such an improvement can well describe the reflection and absorption of seismic waves at the interface of soil and piles. Secondly, the Biot’s dynamic consolidation theory incorporated an elastoplastic model is applied to simulate the soil deformation and the generation and accumulation of pore water pressure under seismic loading. Thirdly, after verification with our indoor shaking table test data, this approach is used to investigate the effects of pile spacing on liquefaction resistance of the composite pile foundation in liquefiable soil. The time histories of pore water pressure ratio ( PPR ′) are calculated for the liquefiable soil and the vertical bearing capacity in partially liquefied soil is calculated and compared with our indoor shaking table test data at the 3D, 3.5D, 4D, 5D and 6D cases (D is the pile diameter). It is found that the pile spacing has some influence on the extent of soil liquefaction between piles. The vertical bearing capacity varies with liquefaction extent of inter-pile soil. The optimization of pile spacing varies with liquefaction extent. These results may provide some reference for the design of composite pile foundation under seismic loading.
Journal Article
Localization of matter fields on flat fermion brane
In this paper, we investigate the localization of matter fields on a flat fermion thick brane. To localize scalar and fermion fields within a five-dimensional spacetime, we introduce the Yukawa coupling mechanism. Based on this framework, we study the localization and evolution of the scalar field, as well as the localization of the fermion field on the brane. For scalar fields, various effective potentials can be derived from the variation of the scalar field function
F
(
Φ
)
in the coupling function. The flat brane can exhibit an effective potential resembling either a volcano or an infinitely deep potential well. By choosing the appropriate coupling parameters, we can find the localized zero mode and some resonance states. This result is similar to the localization of the fermion field on a background scalar field. Additionally, we employ various resonance states as initial values to further explore the evolution on the brane. For the fermion field, we find that the fermion zero mode cannot be localized on the brane. However, by varying the coupling parameters, we obtain an asymmetric infinitely deep potential well. As the coupling parameters increase, the asymmetry become more pronounced.
Journal Article
Siglec-9 acts as an immune-checkpoint molecule on macrophages in glioblastoma, restricting T-cell priming and immunotherapy response
Neoadjuvant immune-checkpoint blockade therapy only benefits a limited fraction of patients with glioblastoma multiforme (GBM). Thus, targeting other immunomodulators on myeloid cells is an attractive therapeutic option. Here, we performed single-cell RNA sequencing and spatial transcriptomics of patients with GBM treated with neoadjuvant anti-PD-1 therapy. We identified unique monocyte-derived tumor-associated macrophage subpopulations with functional plasticity that highly expressed the immunosuppressive SIGLEC9 gene and preferentially accumulated in the nonresponders to anti-PD-1 treatment. Deletion of Siglece (murine homolog) resulted in dramatically restrained tumor development and prolonged survival in mouse models. Mechanistically, targeting Siglece directly activated both CD4
T cells and CD8
T cells through antigen presentation, secreted chemokines and co-stimulatory factor interactions. Furthermore, Siglece deletion synergized with anti-PD-1/PD-L1 treatment to improve antitumor efficacy. Our data demonstrated that Siglec-9 is an immune-checkpoint molecule on macrophages that can be targeted to enhance anti-PD-1/PD-L1 therapeutic efficacy for GBM treatment.
Journal Article