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  1. Article ; Online: The advertisement call of Leptobrachella liui Fei and Ye, 1990 (Anura: Megophryidae).

    Ding, Guo-Hua / Chen, Zhi-Qiang / Tang, Yun / Lin, Zhi-Hua

    Zootaxa

    2019  Volume 4576, Issue 3, Page(s) zootaxa.4576.3.11

    Abstract: ... from southern China: L. alpina (Fei, Ye Li, 1990), L. laui (Sung, Yang Wang, 2014), L. liui (Fei Ye, 1990), L ... yunkaiensis (Wang, Li, Lyu Wang, 2018), L. ventripunctata (Fei, Ye Li, 1990), L. pelodytoides (Boulenger, 1893 ...

    Abstract Leptobrachella (Anura: Megophryidae) is currently composed of seventy-one species distributed in China and Southeast Asia (Frost 2018). Fourteen species of Leptobrachella are currently known from southern China: L. alpina (Fei, Ye Li, 1990), L. laui (Sung, Yang Wang, 2014), L. liui (Fei Ye, 1990), L. mangshanensis (Hou, Zhang, Hu, Li, Shi, Chen, Mo Wang, 2018), L. maoershanensis (Yuan, Sun, Chen, Rowley Che, 2017), L. oshanensis (Liu, 1950), L. purpura (Yang, Zeng Wang, 2018), L. tengchongensis (Yang, Wang, Chen Rao, 2016), L. wuhuangmontis (Wang, Yang Wang, 2018), L. yingjiangensis (Yang, Zeng Wang, 2018), L. yunkaiensis (Wang, Li, Lyu Wang, 2018), L. ventripunctata (Fei, Ye Li, 1990), L. pelodytoides (Boulenger, 1893) and L. sungi (Lathrop, Murphy, Orlov Ho, 1998) and the first eleven species are endemic of this region (AmphibiaChina 2018). Many new species in this genus were discovered based on molecular, morphometric and bioacoustic data in recent years (Frost 2018). In comparison to molecular and morphological data, bioacoustics is especially useful in species identification of Leptobrachella in field surveys (Rowley et al. 2016). Although the advertisement calls of many Leptobrachella species were described along with the species descriptions (e.g., Rowley et al. 2016), the advertisement calls of only three Chinese endemic species (L. alpinus; L. laui and L. oshanensis) are known (Jiang et al. 2002; Matsui 2006; Xu et al. 2005). Here, we describe the advertisement calls of L. liui, which inhabits rocky streams in southeastern China (Fujian, Jiangxi and Zhejinag) and is morphologically diagnosed by the combination of a set of external color traits (Fig. 1).
    MeSH term(s) Animals ; Anura ; China ; Color ; Gastropoda ; Phenotype
    Language English
    Publishing date 2019-04-03
    Publishing country New Zealand
    Document type Journal Article
    ISSN 1175-5334
    ISSN (online) 1175-5334
    DOI 10.11646/zootaxa.4576.3.11
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Fungal Epithiodiketopiperazines Carrying α,β-Polysulfide Bridges from Penicillium steckii YE, and Their Chemical Interconversion.

    Jiang, Guangde / Zhang, Peilan / Ratnayake, Ranjala / Yang, Guang / Zhang, Yi / Zuo, Ran / Powell, Magan / Huguet-Tapia, José C / Abboud, Khalil A / Dang, Long H / Teplitski, Max / Paul, Valerie / Xiao, Rui / Ahammad, K H / Zaman, Uz / Hu, Zhenquan / Cao, Shugeng / Luesch, Hendrik / Ding, Yousong

    Chembiochem : a European journal of chemical biology

    2020  Volume 22, Issue 2, Page(s) 416–422

    Abstract: Some fungal epithiodiketopiperazine alkaloids display α,β-polysulfide bridges alongside diverse structural variations. However, the logic of their chemical diversity has rarely been explored. Here, we report the identification of three new (2, 3, 8) and ... ...

    Abstract Some fungal epithiodiketopiperazine alkaloids display α,β-polysulfide bridges alongside diverse structural variations. However, the logic of their chemical diversity has rarely been explored. Here, we report the identification of three new (2, 3, 8) and five known (1, 4-7) epithiodiketopiperazines of this subtype from a marine-derived Penicillium sp. The structure elucidation was supported by multiple spectroscopic analyses. Importantly, we observed multiple nonenzymatic interconversions of these analogues in aqueous solutions and organic solvents. Furthermore, the same biosynthetic origin of these compounds was supported by one mined gene cluster. The dominant analogue (1) demonstrated selective cytotoxicity to androgen-sensitive prostate cancer cells and HIF-depleted colorectal cells and mild antiaging activities, linking the bioactivity to oxidative stress. These results provide crucial insight into the formation of fungal epithiodiketopiperazines through chemical interconversions.
    MeSH term(s) Diketopiperazines/chemistry ; Molecular Structure ; Penicillium/chemistry ; Sulfides/chemistry
    Chemical Substances Diketopiperazines ; Sulfides ; polysulfide (9080-49-3)
    Language English
    Publishing date 2020-09-30
    Publishing country Germany
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2020469-3
    ISSN 1439-7633 ; 1439-4227
    ISSN (online) 1439-7633
    ISSN 1439-4227
    DOI 10.1002/cbic.202000403
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book: Shi yong xue ye bing xue

    Ding, Xunjie

    1992  

    Title translation Practical hematology.
    Author's details zhu bian Ding Xunjie ... [deng]
    MeSH term(s) Hematologic Diseases ; Leukemia ; Lymphoma
    Language Chinese
    Size 10, 685 p. :, ill.
    Edition Di 1 ban.
    Publisher Shanghai yi ke da xue sh'u ban she
    Publishing place Shanghai Shi
    Document type Book
    ISBN 9787562701187 ; 7562701180
    Database Catalogue of the US National Library of Medicine (NLM)

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  4. Article ; Online: Supramolecular polynuclear clusters sustained cubic hydrogen bonded frameworks with octahedral cages for reversible photochromism.

    Ding, Xiaojun / Chen, Jing / Ye, Gang

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 2782

    Abstract: Developing supramolecular porous crystalline frameworks with tailor-made architectures from advanced secondary building units (SBUs) remains a pivotal challenge in reticular chemistry. Particularly for hydrogen-bonded organic frameworks (HOFs), ... ...

    Abstract Developing supramolecular porous crystalline frameworks with tailor-made architectures from advanced secondary building units (SBUs) remains a pivotal challenge in reticular chemistry. Particularly for hydrogen-bonded organic frameworks (HOFs), construction of geometrical cavities through secondary units has been rarely achieved. Herein, a body-centered cubic HOF (TCA_NH
    Language English
    Publishing date 2024-03-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-47058-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Working memory for gaze benefits from the face context.

    Ye, Shujuan / Ye, Tian / Duan, Ziyi / Ding, Xiaowei

    Psychonomic bulletin & review

    2023  

    Abstract: Retaining gaze in working memory (WM) is essential for successfully navigating through the social world. In the current study, we investigated how WM stores gaze direction by focusing on the role of face context in gaze WM. To address this question, we ... ...

    Abstract Retaining gaze in working memory (WM) is essential for successfully navigating through the social world. In the current study, we investigated how WM stores gaze direction by focusing on the role of face context in gaze WM. To address this question, we propose two competing hypotheses. The independence hypothesis predicts that eye gaze is stored independently and is not susceptible to the influence of the surrounding face context. Conversely, the embedding hypothesis claims that gaze WM involves face context and that disruption of holistic face processing would also impair memory for embedded gaze. In three experiments, we adopted different manipulations to disrupt holistic face processing and compared WM performance for gaze within and without face context. In Experiments 1 and 2, we tested WM for gaze direction with schematic upright or inverted faces. We found better performance for gaze within upright faces (vs. inverted faces) by increasing the probability of being remembered. In Experiment 3, we replaced schematic faces with photographic faces, and disrupted holistic processing by using scrambled faces. Results replicated our previous findings, showing that photographic gaze within intact faces was better remembered than gaze presented alone or gaze within scrambled faces. These findings indicate that gaze memory is face-dependent and support the embedding hypothesis.
    Language English
    Publishing date 2023-12-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2031311-1
    ISSN 1531-5320 ; 1069-9384
    ISSN (online) 1531-5320
    ISSN 1069-9384
    DOI 10.3758/s13423-023-02430-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: DP/MM: A Hybrid Model for Zinc-Protein Interactions in Molecular Dynamics.

    Ding, Ye / Huang, Jing

    The journal of physical chemistry letters

    2024  Volume 15, Issue 2, Page(s) 616–627

    Abstract: Zinc-containing proteins are vital for many biological processes, yet accurately modeling them using classical force fields is hindered by complicated polarization and charge transfer effects. This study introduces DP/MM, a hybrid force field scheme that ...

    Abstract Zinc-containing proteins are vital for many biological processes, yet accurately modeling them using classical force fields is hindered by complicated polarization and charge transfer effects. This study introduces DP/MM, a hybrid force field scheme that utilizes a deep potential model to correct the atomic forces of zinc ions and their coordinated atoms, elevating them from MM to QM levels of accuracy. Trained on the difference between MM and QM atomic forces across diverse zinc coordination groups, the DP/MM model faithfully reproduces structural characteristics of zinc coordination during simulations, such as the tetrahedral coordination of
    MeSH term(s) Molecular Dynamics Simulation ; Zinc/chemistry
    Chemical Substances Zinc (J41CSQ7QDS)
    Language English
    Publishing date 2024-01-10
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.3c03158
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Recent advances in producing food additive L-malate: Chassis, substrate, pathway, fermentation regulation and application.

    Ding, Qiang / Ye, Chao

    Microbial biotechnology

    2023  Volume 16, Issue 4, Page(s) 709–725

    Abstract: In addition to being an important intermediate in the TCA cycle, L-malate is also widely used in the chemical and beverage industries. Due to the resulting high demand, numerous studies investigated chemical methods to synthesize L-malate from ... ...

    Abstract In addition to being an important intermediate in the TCA cycle, L-malate is also widely used in the chemical and beverage industries. Due to the resulting high demand, numerous studies investigated chemical methods to synthesize L-malate from petrochemical resources, but such approaches are hampered by complex downstream processing and environmental pollution. Accordingly, there is an urgent need to develop microbial methods for environmentally-friendly and economical L-malate biosynthesis. The rapid progress and understanding of DNA manipulation, cell physiology, and cell metabolism can improve industrial L-malate biosynthesis by applying intelligent biochemical strategies and advanced synthetic biology tools. In this paper, we mainly focused on biotechnological approaches for enhancing L-malate synthesis, encompassing the microbial chassis, substrate utilization, synthesis pathway, fermentation regulation, and industrial application. This review emphasizes the application of novel metabolic engineering strategies and synthetic biology tools combined with a deep understanding of microbial physiology to improve industrial L-malate biosynthesis in the future.
    MeSH term(s) Fermentation ; Malates/metabolism ; Biosynthetic Pathways/genetics ; Biotechnology ; Metabolic Engineering/methods ; Synthetic Biology/methods
    Chemical Substances malic acid (817L1N4CKP) ; Malates
    Language English
    Publishing date 2023-01-05
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2406063-X
    ISSN 1751-7915 ; 1751-7915
    ISSN (online) 1751-7915
    ISSN 1751-7915
    DOI 10.1111/1751-7915.14206
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Microbial engineering for shikimate biosynthesis.

    Ding, Qiang / Ye, Chao

    Enzyme and microbial technology

    2023  Volume 170, Page(s) 110306

    Abstract: Shikimate, a precursor to the antiviral drug oseltamivir (Tamiflu®), can influence aromatic metabolites and finds extensive use in antimicrobial, antitumor, and cardiovascular applications. Consequently, various strategies have been developed for ... ...

    Abstract Shikimate, a precursor to the antiviral drug oseltamivir (Tamiflu®), can influence aromatic metabolites and finds extensive use in antimicrobial, antitumor, and cardiovascular applications. Consequently, various strategies have been developed for chemical synthesis and plant extraction to enhance shikimate biosynthesis, potentially impacting environmental conditions, economic sustainability, and separation and purification processes. Microbial engineering has been developed as an environmentally friendly approach for shikimate biosynthesis. In this review, we provide a comprehensive summary of microbial strategies for shikimate biosynthesis. These strategies primarily include chassis construction, biochemical optimization, pathway remodelling, and global regulation. Furthermore, we discuss future perspectives on shikimate biosynthesis and emphasize the importance of utilizing advanced metabolic engineering tools to regulate microbial networks for constructing robust microbial cell factories.
    MeSH term(s) Antiviral Agents ; Metabolic Engineering ; Microbial Consortia ; Oseltamivir
    Chemical Substances shikimate ; Antiviral Agents ; Oseltamivir (20O93L6F9H)
    Language English
    Publishing date 2023-08-15
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 423729-8
    ISSN 1879-0909 ; 0141-0229
    ISSN (online) 1879-0909
    ISSN 0141-0229
    DOI 10.1016/j.enzmictec.2023.110306
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: DNA methylation modulates epigenetic regulation in colorectal cancer diagnosis, prognosis and precision medicine.

    Ye, Jingxin / Zhang, Jianfeng / Ding, Weifeng

    Exploration of targeted anti-tumor therapy

    2024  Volume 5, Issue 1, Page(s) 34–53

    Abstract: Colorectal cancer (CRC) is a multifaceted disease influenced by the interplay of genetic and environmental factors. The clinical heterogeneity of CRC cannot be attributed exclusively to genetic diversity and environmental exposures, and epigenetic ... ...

    Abstract Colorectal cancer (CRC) is a multifaceted disease influenced by the interplay of genetic and environmental factors. The clinical heterogeneity of CRC cannot be attributed exclusively to genetic diversity and environmental exposures, and epigenetic markers, especially DNA methylation, play a critical role as key molecular markers of cancer. This review compiles a comprehensive body of evidence underscoring the significant involvement of DNA methylation modifications in the pathogenesis of CRC. Moreover, this review explores the potential utility of DNA methylation in cancer diagnosis, prognostics, assessment of disease activity, and prediction of drug responses. Recognizing the impact of DNA methylation will enhance the ability to identify distinct CRC subtypes, paving the way for personalized treatment strategies and advancing precision medicine in the management of CRC.
    Language English
    Publishing date 2024-01-28
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2692-3114
    ISSN (online) 2692-3114
    DOI 10.37349/etat.2024.00203
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Implementation and Validation of an OpenMM Plugin for the Deep Potential Representation of Potential Energy.

    Ding, Ye / Huang, Jing

    International journal of molecular sciences

    2024  Volume 25, Issue 3

    Abstract: Machine learning potentials, particularly the deep potential (DP) model, have revolutionized molecular dynamics (MD) simulations, striking a balance between accuracy and computational efficiency. To facilitate the DP model's integration with the popular ... ...

    Abstract Machine learning potentials, particularly the deep potential (DP) model, have revolutionized molecular dynamics (MD) simulations, striking a balance between accuracy and computational efficiency. To facilitate the DP model's integration with the popular MD engine OpenMM, we have developed a versatile OpenMM plugin. This plugin supports a range of applications, from conventional MD simulations to alchemical free energy calculations and hybrid DP/MM simulations. Our extensive validation tests encompassed energy conservation in microcanonical ensemble simulations, fidelity in canonical ensemble generation, and the evaluation of the structural, transport, and thermodynamic properties of bulk water. The introduction of this plugin is expected to significantly expand the application scope of DP models within the MD simulation community, representing a major advancement in the field.
    MeSH term(s) Molecular Dynamics Simulation ; Water/chemistry ; Thermodynamics
    Chemical Substances Water (059QF0KO0R)
    Language English
    Publishing date 2024-01-24
    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/ijms25031448
    Database MEDical Literature Analysis and Retrieval System OnLINE

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