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  • 1
    Online Resource
    Online Resource
    Author Correction: Sparse whole-genome sequencing identifies two loci for major depressive disorder
    Springer Science and Business Media LLC ; 2023
    In:  Nature Vol. 620, No. 7976 ( 2023-08-31), p. E28-E28
    Details
    In: Nature, Springer Science and Business Media LLC, Vol. 620, No. 7976 ( 2023-08-31), p. E28-E28
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
    URL: Article
    DOI: 10.1038/s41586-023-06276-1
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
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  • 2
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    Sparse whole-genome sequencing identifies two loci for major depressive disorder
    Springer Science and Business Media LLC ; 2015
    In:  Nature Vol. 523, No. 7562 ( 2015-07-30), p. 588-591
    Details
    In: Nature, Springer Science and Business Media LLC, Vol. 523, No. 7562 ( 2015-07-30), p. 588-591
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
    URL: Article
    DOI: 10.1038/nature14659
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2015
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  • 3
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    Structural changes in bacteriophage T7 upon receptor-induced genome ejection
    Proceedings of the National Academy of Sciences ; 2021
    In:  Proceedings of the National Academy of Sciences Vol. 118, No. 37 ( 2021-09-14)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 118, No. 37 ( 2021-09-14)
    Abstract: Many tailed bacteriophages assemble ejection proteins and a portal–tail complex at a unique vertex of the capsid. The ejection proteins form a transenvelope channel extending the portal–tail channel for the delivery of genomic DNA in cell infection. Here, we report the structure of the mature bacteriophage T7, including the ejection proteins, as well as the structures of the full and empty T7 particles in complex with their cell receptor lipopolysaccharide. Our near–atomic-resolution reconstruction shows that the ejection proteins in the mature T7 assemble into a core, which comprises a fourfold gene product 16 (gp16) ring, an eightfold gp15 ring, and a putative eightfold gp14 ring. The gp15 and gp16 are mainly composed of helix bundles, and gp16 harbors a lytic transglycosylase domain for degrading the bacterial peptidoglycan layer. When interacting with the lipopolysaccharide, the T7 tail nozzle opens. Six copies of gp14 anchor to the tail nozzle, extending the nozzle across the lipopolysaccharide lipid bilayer. The structures of gp15 and gp16 in the mature T7 suggest that they should undergo remarkable conformational changes to form the transenvelope channel. Hydrophobic α-helices were observed in gp16 but not in gp15, suggesting that gp15 forms the channel in the hydrophilic periplasm and gp16 forms the channel in the cytoplasmic membrane.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2102003118
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2021
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  • 4
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    Single-atom Mo–Co catalyst with low biotoxicity for sustainable degradation of high-ionization-potential organic pollutants
    Proceedings of the National Academy of Sciences ; 2023
    In:  Proceedings of the National Academy of Sciences Vol. 120, No. 29 ( 2023-07-18)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 120, No. 29 ( 2023-07-18)
    Abstract: Single-atom catalysts (SACs) are a promising area in environmental catalysis. We report on a bimetallic Co–Mo SAC that shows excellent performance in activating peroxymonosulfate (PMS) for sustainable degradation of organic pollutants with high ionization potential (IP 〉 8.5 eV). Density Functional Theory (DFT) calculations and experimental tests demonstrate that the Mo sites in Mo – Co SACs play a critical role in conducting electrons from organic pollutants to Co sites, leading to a 19.4-fold increase in the degradation rate of phenol compared to the CoCl 2 – PMS group. The bimetallic SACs exhibit excellent catalytic performance even under extreme conditions and show long-term activation in 10-d experiments, efficiently degrading 600 mg/L of phenol. Moreover, the catalyst has negligible toxicity toward MDA-MB-231, Hela, and MCF-7 cells, making it an environmentally friendly option for sustainable water treatment. Our findings have important implications for the design of efficient SACs for environmental remediation and other applications in biology and medicine.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2305933120
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2023
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  • 5
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    Tunable assembly of amyloid-forming peptides into nanosheets as a retrovirus carrier
    Proceedings of the National Academy of Sciences ; 2015
    In:  Proceedings of the National Academy of Sciences Vol. 112, No. 10 ( 2015-03-10), p. 2996-3001
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 112, No. 10 ( 2015-03-10), p. 2996-3001
    Abstract: Using and engineering amyloid as nanomaterials are blossoming trends in bionanotechnology. Here, we show our discovery of an amyloid structure, termed “amyloid-like nanosheet,” formed by a key amyloid-forming segment of Alzheimer’s Aβ. Combining multiple biophysical and computational approaches, we proposed a structural model for the nanosheet that is formed by stacking the amyloid fibril spines perpendicular to the fibril axis. We further used the nanosheet for laboratorial retroviral transduction enhancement and directly visualized the presence of virus on the nanosheet surface by electron microscopy. Furthermore, based on our structural model, we designed nanosheet-forming peptides with different functionalities, elucidating the potential of rational design for amyloid-based materials with novel architecture and function.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1416690112
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2015
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  • 6
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    Cryo-EM structure of a herpesvirus capsid at 3.1 Å
    American Association for the Advancement of Science (AAAS) ; 2018
    In:  Science Vol. 360, No. 6384 ( 2018-04-06)
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 360, No. 6384 ( 2018-04-06)
    Abstract: Structurally and genetically, human herpesviruses are among the largest and most complex of viruses. Using cryo–electron microscopy (cryo-EM) with an optimized image reconstruction strategy, we report the herpes simplex virus type 2 (HSV-2) capsid structure at 3.1 angstroms, which is built up of about 3000 proteins organized into three types of hexons (central, peripentonal, and edge), pentons, and triplexes. Both hexons and pentons contain the major capsid protein, VP5; hexons also contain a small capsid protein, VP26; and triplexes comprise VP23 and VP19C. Acting as core organizers, VP5 proteins form extensive intermolecular networks, involving multiple disulfide bonds (about 1500 in total) and noncovalent interactions, with VP26 proteins and triplexes that underpin capsid stability and assembly. Conformational adaptations of these proteins induced by their microenvironments lead to 46 different conformers that assemble into a massive quasisymmetric shell, exemplifying the structural and functional complexity of HSV.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.aao7283
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2018
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    detail.hit.zdb_id: 2066996-3
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  • 7
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    Indirect influence in social networks as an induced percolation phenomenon
    Proceedings of the National Academy of Sciences ; 2022
    In:  Proceedings of the National Academy of Sciences Vol. 119, No. 9 ( 2022-03)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 119, No. 9 ( 2022-03)
    Abstract: Percolation theory has been widely used to study phase transitions in network systems. It has also successfully explained various macroscopic spreading phenomena across different fields. Yet, the theoretical frameworks have been focusing on direct interactions among nodes, while recent empirical observations have shown that indirect interactions are common in many network systems like social and ecological networks, among others. By investigating the detailed mechanism of both direct and indirect influence on scientific collaboration networks, here we show that indirect influence can play the dominant role in behavioral influence. To address the lack of theoretical understanding of such indirect influence on the macroscopic behavior of the system, we propose a percolation mechanism of indirect interactions called induced percolation. Surprisingly, our model exhibits a unique anisotropy property. Specifically, directed networks show first-order abrupt transitions as opposed to the second-order continuous transition in the same network structure but with undirected links. A mix of directed and undirected links leads to rich hybrid phase transitions. Furthermore, a unique feature of the nonmonotonic pattern is observed in network connectivities near the critical point. We also present an analytical framework to characterize the proposed induced percolation, paving the way to further understanding network dynamics with indirect interactions.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2100151119
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2022
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  • 8
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    Rice SPX1 and SPX2 inhibit phosphate starvation responses through interacting with PHR2 in a phosphate-dependent manner
    Proceedings of the National Academy of Sciences ; 2014
    In:  Proceedings of the National Academy of Sciences Vol. 111, No. 41 ( 2014-10-14), p. 14953-14958
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 111, No. 41 ( 2014-10-14), p. 14953-14958
    Abstract: In plants, sensing the levels of external and internal nutrients is essential for reprogramming the transcriptome and adapting to the fluctuating environment. Phosphate (Pi) is a key plant nutrient, and a large proportion of Pi starvation-responsive genes are under the control of PHOSPHATE STARVATION RESPONSE REGULATOR 1 (PHR1) in Arabidopsis (AtPHR1) and its homologs, such as Oryza sativa (Os)PHR2 in rice. AtPHR1 and OsPHR2 expression is not very responsive to Pi starvation, raising the question as to how plants sense changes in cellular Pi levels to activate the central regulator. SPX [named after SYG1 (suppressor of yeast gpa1 ), Pho81 (CDK inhibitor in yeast PHO pathway), and XPR1 (xenotropic and polytropic retrovirus receptor)] proteins that harbor only the SPX domain are reported to be involved in the negative regulation of Pi starvation responses. Here, we show that the nuclear localized SPX proteins SPX1 and SPX2 are Pi-dependent inhibitors of the activity of OsPHR2 in rice. Indeed, SPX1 and SPX2 proteins interact with PHR2 through their SPX domain, inhibiting its binding to P1BS (the PHR1-binding sequence: GNATATNC). In vivo data, as well as results from in vitro experiments using purified SPX1, SPX2, and OsPHR2 proteins, showed that SPX1 and SPX2 inhibition of OsPHR2 activity is Pi-dependent. These data provide evidence to support the involvement of SPX1 and SPX2 in the Pi-sensing mechanism in plants.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1404680111
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2014
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  • 9
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    Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring
    Proceedings of the National Academy of Sciences ; 2023
    In:  Proceedings of the National Academy of Sciences Vol. 120, No. 28 ( 2023-07-11)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 120, No. 28 ( 2023-07-11)
    Abstract: Plasma cell-free DNA (cfDNA) is a noninvasive biomarker for cell death of all organs. Deciphering the tissue origin of cfDNA can reveal abnormal cell death because of diseases, which has great clinical potential in disease detection and monitoring. Despite the great promise, the sensitive and accurate quantification of tissue-derived cfDNA remains challenging to existing methods due to the limited characterization of tissue methylation and the reliance on unsupervised methods. To fully exploit the clinical potential of tissue-derived cfDNA, here we present one of the largest comprehensive and high-resolution methylation atlas based on 521 noncancer tissue samples spanning 29 major types of human tissues. We systematically identified fragment-level tissue-specific methylation patterns and extensively validated them in orthogonal datasets. Based on the rich tissue methylation atlas, we develop the first supervised tissue deconvolution approach, a deep-learning-powered model, cfSort , for sensitive and accurate tissue deconvolution in cfDNA. On the benchmarking data, cfSort showed superior sensitivity and accuracy compared to the existing methods. We further demonstrated the clinical utilities of cfSort with two potential applications: aiding disease diagnosis and monitoring treatment side effects. The tissue-derived cfDNA fraction estimated from cfSort reflected the clinical outcomes of the patients. In summary, the tissue methylation atlas and cfSort enhanced the performance of tissue deconvolution in cfDNA, thus facilitating cfDNA-based disease detection and longitudinal treatment monitoring.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2305236120
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2023
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  • 10
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    Efficient hydrogen production from wastewater remediation by piezoelectricity coupling advanced oxidation processes
    Proceedings of the National Academy of Sciences ; 2023
    In:  Proceedings of the National Academy of Sciences Vol. 120, No. 7 ( 2023-02-14)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 120, No. 7 ( 2023-02-14)
    Abstract: Efficient H 2 harvesting from wastewater instead of pure water can minimize fresh water consumption, which is expected to solve the problem of water shortage in H 2 production process and contribute to carbon neutrality in the environmental remediation, but the inevitable electron depletion caused by electron-consuming pollutants will result in an exhausted H 2 evolution reaction (HER) performance. In this paper, by coupling piezocatalysis and advanced oxidation processes (AOPs) by a MoS 2 /Fe 0 /peroxymonosulfate (PMS) ternary system, extensive types of wastewater achieved considerable H 2 generation, which exceeded the yield in pure water with synchronous advanced degradation of organic pollutants. In addition, profiting from the crucial bridging role of PMS, the H 2 yield in nitrobenzene wastewater after the introduction of PMS-based AOPs increased 3.37-fold from 267.7 μmol·g −1 ·h −1 to 901.0 μmol·g −1 ·h −1 because the presence of PMS both thermodynamically benefited MoS 2 piezocatalytic H 2 evolution and eliminated the electron depletion caused by organic pollutants. By this way, the original repressed H 2 evolution performance in substrate of wastewater not only was regained but even showed a significant enhancement than that in pure water (505.7 μmol·g −1 ·h −1 ). Additionally, the cyclonic piezoelectric reactor was preliminarily designed for future industrialization. This strategy provided a valuable path for the recycling of actual wastewater by fuel production and synchronous advanced treatment.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2218813120
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2023
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