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  1. Article ; Online: Alpinetin alleviates LPS-induced lung epithelial cell injury by inhibiting p38 and ERK1/2 signaling via aquaporin-1.

    Zhang, Junjie / Ma, Bin

    Tissue & cell

    2024  Volume 87, Page(s) 102305

    Abstract: Alpinetin has been reported to play a protective role in lung diseases, while its special mechanisms remain indistinct. In this study, acute lung injury (ALI) model was constructed by inducing MLE-12 cells with lipopolysaccharide (LPS). Cell activity ... ...

    Abstract Alpinetin has been reported to play a protective role in lung diseases, while its special mechanisms remain indistinct. In this study, acute lung injury (ALI) model was constructed by inducing MLE-12 cells with lipopolysaccharide (LPS). Cell activity together with apoptosis was judged employing cell counting kit-8 (CCK-8), flow cytometry along with western blot. Oxidative stress levels were measured by dichloro-dihydro-fluorescein diacetate (DCFH-DA) staining and corresponding kits. In addition, enzyme-linked immunosorbent assay (ELISA) was to examine the levels of inflammatory factors. The protein expressions of aquaporin-1 (AQP1), p38 and extracellular signal-regulated kinase (ERK) 1/2 pathway were estimated utilizing western blot. The data showed that alpinetin increased the viability, reduced the apoptosis, oxidative stress and inflammation and inactivated p38 and ERK1/2 signaling in LPS-induced MLE-12 cells. Moreover, alpinetin also increased AQP1 expression and AQP1 knockdown reversed the impacts of alpinetin on LPS-induced MLE-12 cells. Additionally, AQP1 agonist AqF026 also exerted anti-apoptotic and anti-inflammatory activities in LPS-treated MLE-12 cells. Evidently, alpinetin may exert its protective role in LPS-induced ALI by inactivation of p38 and ERK1/2 signaling through regulating AQP1.
    MeSH term(s) Humans ; Lipopolysaccharides/toxicity ; MAP Kinase Signaling System ; Acute Lung Injury/chemically induced ; Acute Lung Injury/drug therapy ; Epithelial Cells ; Aquaporins ; Lung ; Flavanones
    Chemical Substances Lipopolysaccharides ; alpinetin ; Aquaporins ; Flavanones
    Language English
    Publishing date 2024-01-08
    Publishing country Scotland
    Document type Journal Article
    ZDB-ID 204424-9
    ISSN 1532-3072 ; 0040-8166
    ISSN (online) 1532-3072
    ISSN 0040-8166
    DOI 10.1016/j.tice.2024.102305
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    Zs.A 1016: Show issues Location:
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  2. Article ; Online: OptoCRISPRi-HD: Engineering a Bacterial Green-Light-Activated CRISPRi System with a High Dynamic Range.

    Chen, Ke-Ning / Ma, Bin-Guang

    ACS synthetic biology

    2023  Volume 12, Issue 6, Page(s) 1708–1715

    Abstract: The ability to modulate gene expression is crucial for studying gene function and programming cell behaviors. Combining the reliability of CRISPRi and the precision of optogenetics, the optoCRISPRi technique is emerging as an advanced tool for live-cell ... ...

    Abstract The ability to modulate gene expression is crucial for studying gene function and programming cell behaviors. Combining the reliability of CRISPRi and the precision of optogenetics, the optoCRISPRi technique is emerging as an advanced tool for live-cell gene regulation. Since previous versions of optoCRISPRi often exhibit no more than a 10-fold dynamic range due to the leakage activity, they are not suitable for targets that are sensitive to such leakage or critical for cell growth. Here, we describe a green-light-activated CRISPRi system with a high dynamic range (40 fold) and the flexibility of changing targets in
    MeSH term(s) CRISPR-Cas Systems ; Metabolic Engineering/methods ; Reproducibility of Results ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics
    Chemical Substances Escherichia coli Proteins
    Language English
    Publishing date 2023-05-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2161-5063
    ISSN (online) 2161-5063
    DOI 10.1021/acssynbio.3c00035
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  3. Article ; Online: Down-regulation of COL1A1 inhibits tumor-associated fibroblast activation and mediates matrix remodeling in the tumor microenvironment of breast cancer

    Ma Bin / Li Fangfang / Ma Binlin

    Open Life Sciences, Vol 18, Iss 1, Pp 106535-

    2023  Volume 48

    Keywords fibroblasts ; tumor microenvironment ; matrix remodeling ; collagen type i a1 ; cav-1 ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher De Gruyter
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: SPEQ: quality assessment of peptide tandem mass spectra with deep learning.

    Gholamizoj, Soroosh / Ma, Bin

    Bioinformatics (Oxford, England)

    2022  Volume 38, Issue 6, Page(s) 1568–1574

    Abstract: Motivation: In proteomics, database search programs are routinely used for peptide identification from tandem mass spectrometry data. However, many low-quality spectra cannot be interpreted by any programs. Meanwhile, certain high-quality spectra may ... ...

    Abstract Motivation: In proteomics, database search programs are routinely used for peptide identification from tandem mass spectrometry data. However, many low-quality spectra cannot be interpreted by any programs. Meanwhile, certain high-quality spectra may not be identified due to incompleteness of the database or failure of the software. Thus, spectrum quality (SPEQ) assessment tools are helpful programs that can eliminate poor-quality spectra before the database search and highlight the high-quality spectra that are not identified in the initial search. These spectra may be valuable candidates for further analyses.
    Results: We propose SPEQ: a spectrum quality assessment tool that uses a deep neural network to classify spectra into high-quality, which are worthy candidates for interpretation, and low-quality, which lack sufficient information for identification. SPEQ was compared with a few other prediction models and demonstrated improved prediction accuracy.
    Availability and implementation: Source code and scripts are freely available at github.com/sor8sh/SPEQ, implemented in Python.
    MeSH term(s) Tandem Mass Spectrometry ; Algorithms ; Deep Learning ; Peptides/chemistry ; Software
    Chemical Substances Peptides
    Language English
    Publishing date 2022-01-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btab874
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  5. Article ; Online: Reply - Letter to the editor: Comment on "Global prevalence of sarcopenic obesity in older adults: A systematic review and meta-analysis".

    Gao, Qianqian / Ma, Bin

    Clinical nutrition (Edinburgh, Scotland)

    2022  Volume 41, Issue 6, Page(s) 1454–1456

    MeSH term(s) Aged ; Humans ; Obesity/epidemiology ; Prevalence ; Sarcopenia/epidemiology
    Language English
    Publishing date 2022-04-14
    Publishing country England
    Document type Letter ; Meta-Analysis ; Systematic Review ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 604812-2
    ISSN 1532-1983 ; 0261-5614
    ISSN (online) 1532-1983
    ISSN 0261-5614
    DOI 10.1016/j.clnu.2022.04.013
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    Zs.A 1774: Show issues Location:
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  6. Article ; Online: Chromosome structure modeling tools and their evaluation in bacteria.

    Liu, Tong / Qiu, Qin-Tian / Hua, Kang-Jian / Ma, Bin-Guang

    Briefings in bioinformatics

    2024  Volume 25, Issue 2

    Abstract: The three-dimensional (3D) structure of bacterial chromosomes is crucial for understanding chromosome function. With the growing availability of high-throughput chromosome conformation capture (3C/Hi-C) data, the 3D structure reconstruction algorithms ... ...

    Abstract The three-dimensional (3D) structure of bacterial chromosomes is crucial for understanding chromosome function. With the growing availability of high-throughput chromosome conformation capture (3C/Hi-C) data, the 3D structure reconstruction algorithms have become powerful tools to study bacterial chromosome structure and function. It is highly desired to have a recommendation on the chromosome structure reconstruction tools to facilitate the prokaryotic 3D genomics. In this work, we review existing chromosome 3D structure reconstruction algorithms and classify them based on their underlying computational models into two categories: constraint-based modeling and thermodynamics-based modeling. We briefly compare these algorithms utilizing 3C/Hi-C datasets and fluorescence microscopy data obtained from Escherichia coli and Caulobacter crescentus, as well as simulated datasets. We discuss current challenges in the 3D reconstruction algorithms for bacterial chromosomes, primarily focusing on software usability. Finally, we briefly prospect future research directions for bacterial chromosome structure reconstruction algorithms.
    MeSH term(s) Chromosome Structures ; Bacteria ; Prokaryotic Cells ; Chromosomes, Bacterial/genetics ; Algorithms ; Escherichia coli/genetics
    Language English
    Publishing date 2024-02-22
    Publishing country England
    Document type Review ; Journal Article
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbae044
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  7. Article ; Online: Explore the prognostic influence of the treatment sequence of TURBT-chemotherapy combination for patients with localized muscle-invasive bladder cancer.

    Xia, Yu / Ma, Bin-Bin / Liu, Xi / Xu, Dan-Feng

    Asian journal of surgery

    2024  Volume 47, Issue 4, Page(s) 1986–1987

    MeSH term(s) Humans ; Prognosis ; Urinary Bladder Neoplasms/drug therapy ; Urinary Bladder Neoplasms/surgery ; Cystectomy ; Drug Therapy, Combination ; Muscles ; Neoplasm Invasiveness ; Neoplasm Recurrence, Local
    Language English
    Publishing date 2024-01-11
    Publishing country Netherlands
    Document type Letter
    ZDB-ID 1068461-x
    ISSN 0219-3108 ; 1015-9584
    ISSN (online) 0219-3108
    ISSN 1015-9584
    DOI 10.1016/j.asjsur.2023.12.198
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  8. Article ; Online: Light Intensity Modulates the Functional Composition of Leaf Metabolite Groups and Phyllosphere Prokaryotic Community in Garden Lettuce (

    Kong, Dedong / Ye, Ziran / Dai, Mengdi / Ma, Bin / Tan, Xiangfeng

    International journal of molecular sciences

    2024  Volume 25, Issue 3

    Abstract: Light intensity primarily drives plant growth and morphogenesis, whereas the ecological impact of light intensity on the phyllosphere (leaf surface and endosphere) microbiome is poorly understood. In this study, garden lettuce ( ...

    Abstract Light intensity primarily drives plant growth and morphogenesis, whereas the ecological impact of light intensity on the phyllosphere (leaf surface and endosphere) microbiome is poorly understood. In this study, garden lettuce (
    MeSH term(s) Lactuca/genetics ; Nitrates/metabolism ; Gardens ; Chlorophyll/metabolism ; Plant Leaves/metabolism
    Chemical Substances Nitrates ; Chlorophyll (1406-65-1)
    Language English
    Publishing date 2024-01-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms25031451
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  9. Article ; Online: Screening of the effective sites of Cichorium glandulosum against hyperuricemia combined with hyperlipidemia and its network pharmacology analysis.

    Yang, Zhiguo / Lyu, Bo / Ma, Bin / Gao, Yuefeng / Qin, Dongmei

    Computational biology and chemistry

    2024  Volume 110, Page(s) 108088

    Abstract: Cichorium glandulosum, a common traditional Chinese medicine used by Uyghur and Mongolian ethnic groups, is recognized for its potential to ameliorate metabolic disorders. However, the specific efficacy and mechanisms of Cichorium glandulosum in treating ...

    Abstract Cichorium glandulosum, a common traditional Chinese medicine used by Uyghur and Mongolian ethnic groups, is recognized for its potential to ameliorate metabolic disorders. However, the specific efficacy and mechanisms of Cichorium glandulosum in treating the comorbidity of hyperuricaemia and hyperlipidaemia remain unexplored. This study aims to explore the pharmacological effects and mechanisms of Cichorium glandulosum on this comorbidity through a combination of animal experiments, network pharmacology, and molecular docking techniques. A rat model of hyperuricaemia combined with hyperlipidaemia was established through a high-fat and high-purine diet, and the effective parts of the aqueous extract of Cichorium glandulosum to reduce uric acid and lipid levels were screened and the components of the parts were analysed by LC-MS/MS. The active components, core targets, and key pathways were analysed using network pharmacology and validated by molecular docking. Animal experimental results indicated that the n-butanol extract of Cichorium glandulosum showed a significant therapeutic effect on this comorbidity. Analysis of the n-butanol extract yielded 35 active ingredients and 138 intersecting targets related to diseases. Key targets identified through compound-target-pathway (C-T-P) and Protein-Protein Interaction (PPI) analyses included RELA, CASP3, PTGS2, TNF, and ESR1. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed 2515 functional items and 164 pathways, respectively. Molecular docking demonstrated that isochlorogenic acid A, baicalin, chicoric acid, and lactucopicrin showed the highest binding affinity to RELA and PTGS2. The n-butanol fraction from the aqueous extract of Cichorium glandulosum was found to reduce uric acid and lipid levels effectively. In summary, Cichorium glandulosum has a therapeutic effect on hyperuricaemia combined with hyperlipidaemia through its multi-component, multi-target, and multi-pathway characteristics.
    Language English
    Publishing date 2024-04-26
    Publishing country England
    Document type Journal Article
    ISSN 1476-928X
    ISSN (online) 1476-928X
    DOI 10.1016/j.compbiolchem.2024.108088
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  10. Article ; Online: Prognostic risk factors and nomogram for Chinese American patients with prostate cancer.

    Xia, Yu / Ma, Bin-Bin / Liu, Xi / Huang, Tao

    Asian journal of surgery

    2024  

    Language English
    Publishing date 2024-05-14
    Publishing country Netherlands
    Document type Letter
    ZDB-ID 1068461-x
    ISSN 0219-3108 ; 1015-9584
    ISSN (online) 0219-3108
    ISSN 1015-9584
    DOI 10.1016/j.asjsur.2024.05.036
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