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  1. Article ; Online: Corrigendum to "A microfabricated lab-on-chip with three-dimensional electrodes for microscopic observation of bioelectromagnetic effects of cells" [Bioelectrochemistry 154 (2023) 108554].

    Lu, Yingxian / Shi, Yigong

    Bioelectrochemistry (Amsterdam, Netherlands)

    2024  Volume 157, Page(s) 108641

    Language English
    Publishing date 2024-02-17
    Publishing country Netherlands
    Document type Published Erratum
    ZDB-ID 2010650-6
    ISSN 1878-562X ; 0302-4598 ; 1567-5394
    ISSN (online) 1878-562X
    ISSN 0302-4598 ; 1567-5394
    DOI 10.1016/j.bioelechem.2024.108641
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    Zs.A 1178: Show issues Location:
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  2. Article ; Online: Dark and Dronc activation in

    Tian, Lu / Li, Yini / Shi, Yigong

    Proceedings of the National Academy of Sciences of the United States of America

    2024  Volume 121, Issue 9, Page(s) e2312784121

    Abstract: The onset of apoptosis is characterized by a cascade of caspase activation, where initiator caspases are activated by a multimeric adaptor complex known as the apoptosome. ... ...

    Abstract The onset of apoptosis is characterized by a cascade of caspase activation, where initiator caspases are activated by a multimeric adaptor complex known as the apoptosome. In
    MeSH term(s) Animals ; Apoptosomes/chemistry ; Caspases/metabolism ; Drosophila/metabolism ; Drosophila melanogaster/metabolism ; Drosophila Proteins/metabolism
    Chemical Substances Apoptosomes ; Caspases (EC 3.4.22.-) ; Drosophila Proteins ; dark protein, Drosophila ; dronc protein, Drosophila (EC 3.4.22.-)
    Language English
    Publishing date 2024-02-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2312784121
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  3. Article ; Online: A microfabricated lab-on-chip with three-dimensional electrodes for microscopic observation of bioelectromagnetic effects of cells.

    Lu, Yingxian / Shi, Yigong

    Bioelectrochemistry (Amsterdam, Netherlands)

    2023  Volume 154, Page(s) 108554

    Abstract: Electromagnetic (EM) signals are widely used in electronic instruments and biomedical systems and might have affected the human bodies surrounded by them. However, the interaction mechanism of EM signals with biological structures is poorly understood. ... ...

    Abstract Electromagnetic (EM) signals are widely used in electronic instruments and biomedical systems and might have affected the human bodies surrounded by them. However, the interaction mechanism of EM signals with biological structures is poorly understood. We propose a micro-fabricated low-frequency EM stimulation lab-on-chip with three-dimensional interdigital electrodes for observation of cell lines with microscope. The field strength between the electrodes at various frequencies is estimated through simulation. An electric field strength of 4.45V
    MeSH term(s) Humans ; HEK293 Cells ; Cell Proliferation ; Cell Cycle ; Computer Simulation ; Electrodes
    Language English
    Publishing date 2023-08-28
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2010650-6
    ISSN 1878-562X ; 0302-4598 ; 1567-5394
    ISSN (online) 1878-562X
    ISSN 0302-4598 ; 1567-5394
    DOI 10.1016/j.bioelechem.2023.108554
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  4. Article ; Online: Arnold J. Levine and my career development.

    Shi, Yigong

    Journal of molecular cell biology

    2019  Volume 11, Issue 7, Page(s) 546–550

    MeSH term(s) History, 20th Century ; History, 21st Century ; Humans ; Molecular Biology/education ; Molecular Biology/history
    Language English
    Publishing date 2019-07-23
    Publishing country United States
    Document type Biography ; Historical Article ; Journal Article
    ZDB-ID 2500949-7
    ISSN 1759-4685 ; 1674-2788
    ISSN (online) 1759-4685
    ISSN 1674-2788
    DOI 10.1093/jmcb/mjz069
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  5. Article ; Online: Structural insights into CED-3 activation.

    Li, Yini / Tian, Lu / Zhang, Ying / Shi, Yigong

    Life science alliance

    2023  Volume 6, Issue 9

    Abstract: ... ...

    Abstract In
    MeSH term(s) Animals ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/metabolism ; Apoptosomes/metabolism ; Apoptosis
    Chemical Substances Caenorhabditis elegans Proteins ; Apoptosomes
    Language English
    Publishing date 2023-07-04
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2575-1077
    ISSN (online) 2575-1077
    DOI 10.26508/lsa.202302056
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  6. Article ; Online: Structure of the nuclear pore complex goes atomic.

    Huang, Gaoxingyu / Zeng, Chao / Shi, Yigong

    Current opinion in structural biology

    2023  Volume 78, Page(s) 102523

    Abstract: The nuclear pore complex (NPC) is a supra-molecular assembly that mediates substance and information flow across the nuclear envelope (NE). Due to its extraordinary size and complexity, the NPC remains one of the most challenging tasks in structural ... ...

    Abstract The nuclear pore complex (NPC) is a supra-molecular assembly that mediates substance and information flow across the nuclear envelope (NE). Due to its extraordinary size and complexity, the NPC remains one of the most challenging tasks in structural elucidation at atomic resolution. Recent breakthroughs in cryo-electron microscopy (cryo-EM) reconstruction, Machine Learning empowered structure prediction and biochemical reconstitution have combined to yield molecular models of the NPC at unprecedented accuracy. Furthermore, in cellulo cryo-electron tomography (cryo-ET) structures reveal substantial structural dynamics of the NPC. These advances shed light on the organizational principles and functions of the NPC.
    MeSH term(s) Nuclear Pore/chemistry ; Cryoelectron Microscopy ; Nuclear Envelope ; Nuclear Pore Complex Proteins/chemistry ; Models, Molecular
    Chemical Substances Nuclear Pore Complex Proteins
    Language English
    Publishing date 2023-01-13
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2022.102523
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    Zs.A 3206: Show issues Location:
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  7. Article ; Online: Interactions between electromagnetic radiation and biological systems.

    Liu, Lingyu / Huang, Bing / Lu, Yingxian / Zhao, Yanyu / Tang, Xiaping / Shi, Yigong

    iScience

    2024  Volume 27, Issue 3, Page(s) 109201

    Abstract: Even though the bioeffects of electromagnetic radiation (EMR) have been extensively investigated during the past several decades, our understandings of the bioeffects of EMR and the mechanisms of the interactions between the biological systems and the ... ...

    Abstract Even though the bioeffects of electromagnetic radiation (EMR) have been extensively investigated during the past several decades, our understandings of the bioeffects of EMR and the mechanisms of the interactions between the biological systems and the EMRs are still far from satisfactory. In this article, we introduce and summarize the consensus, controversy, limitations, and unsolved issues. The published works have investigated the EMR effects on different biological systems including humans, animals, cells, and biochemical reactions. Alternative methodologies also include dielectric spectroscopy, detection of bioelectromagnetic emissions, and theoretical predictions. In many studies, the thermal effects of the EMR are not properly controlled or considered. The frequency of the EMR investigated is limited to the commonly used bands, particularly the frequencies of the power line and the wireless communications; far fewer studies were performed for other EMR frequencies. In addition, the bioeffects of the complex EM environment were rarely discussed. In summary, our understanding of the bioeffects of the EMR is quite restrictive and further investigations are needed to answer the unsolved questions.
    Language English
    Publishing date 2024-02-10
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2024.109201
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  8. Article ; Online: Impact of specific electromagnetic radiation on wakefulness in mice.

    Deng, Hu / Liu, Lingyu / Tang, Xiaping / Lu, Yingxian / Wang, Xiaofei / Zhao, Yanyu / Shi, Yigong

    Proceedings of the National Academy of Sciences of the United States of America

    2024  Volume 121, Issue 15, Page(s) e2313903121

    Abstract: Electromagnetic radiation (EMR) in the environment, particularly in the microwave range, may constitute a public health concern. Exposure to 2.4 GHz EMR modulated by 100 Hz square pulses was recently reported to markedly increase wakefulness in mice. ... ...

    Abstract Electromagnetic radiation (EMR) in the environment, particularly in the microwave range, may constitute a public health concern. Exposure to 2.4 GHz EMR modulated by 100 Hz square pulses was recently reported to markedly increase wakefulness in mice. Here, we demonstrate that a similar wakefulness increase can be induced by the modulation frequency of 1,000 Hz, but not 10 Hz. In contrast to the carrier frequency of 2.4 GHz, 935 MHz EMR of the same power density has little impact on wakefulness irrespective of modulation frequency. Notably, the replacement of the 100 Hz square-pulsed modulation by sinusoidal-pulsed modulation of 2.4 GHz EMR still allows a marked increase of wakefulness. In contrast, continuous sinusoidal amplitude modulation of 100 Hz with the same time-averaged power output fails to trigger any detectable change of wakefulness. Therefore, alteration of sleep behavior by EMR depends upon not just carrier frequency but also frequency and mode of the modulation. These results implicate biological sensing mechanisms for specific EMR in animals.
    MeSH term(s) Mice ; Animals ; Wakefulness ; Electromagnetic Radiation ; Electromagnetic Fields
    Language English
    Publishing date 2024-04-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2313903121
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  9. Article ; Online: Structural insights into human exon-defined spliceosome prior to activation.

    Zhang, Wenyu / Zhang, Xiaofeng / Zhan, Xiechao / Bai, Rui / Lei, Jianlin / Yan, Chuangye / Shi, Yigong

    Cell research

    2024  

    Abstract: Spliceosome is often assembled across an exon and undergoes rearrangement to span a neighboring intron. Most states of the intron-defined spliceosome have been structurally characterized. However, the structure of a fully assembled exon-defined ... ...

    Abstract Spliceosome is often assembled across an exon and undergoes rearrangement to span a neighboring intron. Most states of the intron-defined spliceosome have been structurally characterized. However, the structure of a fully assembled exon-defined spliceosome remains at large. During spliceosome assembly, the pre-catalytic state (B complex) is converted from its precursor (pre-B complex). Here we report atomic structures of the exon-defined human spliceosome in four sequential states: mature pre-B, late pre-B, early B, and mature B. In the previously unknown late pre-B state, U1 snRNP is already released but the remaining proteins are still in the pre-B state; unexpectedly, the RNAs are in the B state, with U6 snRNA forming a duplex with 5'-splice site and U5 snRNA recognizing the 3'-end of the exon. In the early and mature B complexes, the B-specific factors are stepwise recruited and specifically recognize the exon 3'-region. Our study reveals key insights into the assembly of the exon-defined spliceosomes and identifies mechanistic steps of the pre-B-to-B transition.
    Language English
    Publishing date 2024-04-24
    Publishing country England
    Document type Journal Article
    ZDB-ID 1319303-x
    ISSN 1748-7838 ; 1001-0602
    ISSN (online) 1748-7838
    ISSN 1001-0602
    DOI 10.1038/s41422-024-00949-w
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  10. Article ; Online: Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome.

    Bai, Rui / Yuan, Meng / Zhang, Pu / Luo, Ting / Shi, Yigong / Wan, Ruixue

    Science (New York, N.Y.)

    2024  Volume 383, Issue 6688, Page(s) 1245–1252

    Abstract: The minor spliceosome, which is responsible for the splicing of U12-type introns, comprises five small nuclear RNAs (snRNAs), of which only one is shared with the major spliceosome. In this work, we report the 3.3-angstrom cryo-electron microscopy ... ...

    Abstract The minor spliceosome, which is responsible for the splicing of U12-type introns, comprises five small nuclear RNAs (snRNAs), of which only one is shared with the major spliceosome. In this work, we report the 3.3-angstrom cryo-electron microscopy structure of the fully assembled human minor spliceosome pre-B complex. The atomic model includes U11 small nuclear ribonucleoprotein (snRNP), U12 snRNP, and U4atac/U6atac.U5 tri-snRNP. U11 snRNA is recognized by five U11-specific proteins (20K, 25K, 35K, 48K, and 59K) and the heptameric Sm ring. The 3' half of the 5'-splice site forms a duplex with U11 snRNA; the 5' half is recognized by U11-35K, U11-48K, and U11 snRNA. Two proteins, CENATAC and DIM2/TXNL4B, specifically associate with the minor tri-snRNP. A structural analysis uncovered how two conformationally similar tri-snRNPs are differentiated by the minor and major prespliceosomes for assembly.
    MeSH term(s) Humans ; Cryoelectron Microscopy ; Introns ; Ribonucleoproteins, Small Nuclear/chemistry ; RNA Splice Sites ; RNA Splicing ; RNA, Small Nuclear/chemistry ; Spliceosomes/chemistry ; Nucleic Acid Conformation
    Chemical Substances Ribonucleoproteins, Small Nuclear ; RNA Splice Sites ; RNA, Small Nuclear ; U12 small nuclear RNA
    Language English
    Publishing date 2024-03-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.adn7272
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