Nature Communications

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ISSN / EISSN : 2041-1723 / 2041-1723
Current Publisher: Springer Science and Business Media LLC (10.1038)
Former Publisher: Wiley (10.1111)
Total articles ≅ 35,341
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Keito Okazaki, Hayato Anzawa, Zun Liu, Nao Ota, Hiroshi Kitamura, Yoshiaki Onodera, Morshedul Alam, Daisuke Matsumaru, Takuma Suzuki, Fumiki Katsuoka, et al.
Nature Communications, Volume 12, pp 1-1; doi:10.1038/s41467-021-20927-9

Abstract:
A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-20927-9.
Shuangyi Linghu, Zhaoqi Gu, Jinsheng Lu, Wei Fang , Zongyin Yang, Huakang Yu, Zhiyuan Li, Runlin Zhu, Jian Peng, Qiwen Zhan , et al.
Nature Communications, Volume 12, pp 1-8; doi:10.1038/s41467-020-20683-2

Abstract:
Chemically synthesized metal nanowires are promising building blocks for next-generation photonic integrated circuits, but technological implementation in monolithic integration will be severely hampered by the lack of controllable and precise manipulation approaches, due to the strong adhesion of nanowires to substrates in non-liquid environments. Here, we demonstrate this obstacle can be removed by our proposed earthworm-like peristaltic crawling motion mechanism, based on the synergistic expansion, friction, and contraction in plasmon-driven metal nanowires in non-liquid environments. The evanescently excited surface plasmon greatly enhances the heating effect in metal nanowires, thereby generating surface acoustic waves to drive the nanowires crawling along silica microfibres. Advantages include sub-nanometer positioning accuracy, low actuation power, and self-parallel parking. We further demonstrate on-chip manipulations including transporting, positioning, orientation, and sorting, with on-situ operation, high selectivity, and great versatility. Our work paves the way to realize full co-integration of various functionalized photonic components on single chips.
Anna Maria Lena , Valerio Rossi, Susanne Osterburg, Artem Smirnov , Christian Osterburg, Marcel Tuppi, Angela Cappello, Ivano Amelio , Volker Dötsch , Massimo De Felici, et al.
Nature Communications, Volume 12, pp 1-14; doi:10.1038/s41467-020-20669-0

Abstract:
The transcription factor p63 mediates distinct cellular responses, primarily regulating epithelial and oocyte biology. In addition to the two amino terminal isoforms, TAp63 and ΔNp63, the 3’-end of p63 mRNA undergoes tissue-specific alternative splicing that leads to several isoforms, including p63α, p63β and p63γ. To investigate in vivo how the different isoforms fulfil distinct functions at the cellular and developmental levels, we developed a mouse model replacing the p63α with p63β by deletion of exon 13 in the Trp63 gene. Here, we report that whereas in two organs physiologically expressing p63α, such as thymus and skin, no abnormalities are detected, total infertility is evident in heterozygous female mice. A sharp reduction in the number of primary oocytes during the first week after birth occurs as a consequence of the enhanced expression of the pro-apoptotic transcriptional targets Puma and Noxa by the tetrameric, constitutively active, TAp63β isoform. Hence, these mice show a condition of ovary dysfunction, resembling human primary ovary insufficiency. Our results show that the p63 C-terminus is essential in TAp63α-expressing primary oocytes to control cell death in vivo, expanding the current understanding of human primary ovarian insufficiency.
K. Mukasa, K. Matsuura, M. Qiu, M. Saito, Y. Sugimura, K. Ishida, M. Otani, Y. Onishi, Y. Mizukami, K. Hashimoto , et al.
Nature Communications, Volume 12, pp 1-7; doi:10.1038/s41467-020-20621-2

Abstract:
The interplay among magnetism, electronic nematicity, and superconductivity is the key issue in strongly correlated materials including iron-based, cuprate, and heavy-fermion superconductors. Magnetic fluctuations have been widely discussed as a pairing mechanism of unconventional superconductivity, but recent theory predicts that quantum fluctuations of nematic order may also promote high-temperature superconductivity. This has been studied in FeSe1−xSx superconductors exhibiting nonmagnetic nematic and pressure-induced antiferromagnetic orders, but its abrupt suppression of superconductivity at the nematic end point leaves the nematic-fluctuation driven superconductivity unconfirmed. Here we report on systematic studies of high-pressure phase diagrams up to 8 GPa in high-quality single crystals of FeSe1−xTex. When Te composition x(Te) becomes larger than 0.1, the high-pressure magnetic order disappears, whereas the pressure-induced superconducting dome near the nematic end point is continuously found up to x(Te) ≈ 0.5. In contrast to FeSe1−xSx, enhanced superconductivity in FeSe1−xTex does not correlate with magnetism but with the suppression of nematicity, highlighting the paramount role of nonmagnetic nematic fluctuations for high-temperature superconductivity in this system.
Gloria Gamiz-Arco, Luis I. Gutierrez-Rus, Valeria A. Risso, Beatriz Ibarra-Molero , Yosuke Hoshino, Dušan Petrović, Jose Justicia, Juan Manuel Cuerva , Adrian Romero-Rivera, Burckhard Seelig , et al.
Nature Communications, Volume 12, pp 1-16; doi:10.1038/s41467-020-20630-1

Abstract:
Glycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ∼5500 reported crystallographic structures of ∼1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when sampling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed.
Robert Zimmermann, Michael Seidling, Peter Hommelhoff
Nature Communications, Volume 12, pp 1-6; doi:10.1038/s41467-020-20592-4

Abstract:
Electron and ion beams are indispensable tools in numerous fields of science and technology, ranging from radiation therapy to microscopy and lithography. Advanced beam control facilitates new functionalities. Here, we report the guiding and splitting of charged particle beams using ponderomotive forces created by the motion of charged particles through electrostatic optics printed on planar substrates. Shape and strength of the potential can be locally tailored by the lithographically produced electrodes’ layout and the applied voltages, enabling the control of charged particle beams within precisely engineered effective potentials. We demonstrate guiding of electrons and ions for a large range of energies (from 20 to 5000 eV) and masses (from 5 · 10−4 to 131 atomic mass units) as well as electron beam splitting for energies up to the keV regime as a proof-of-concept for more complex beam manipulation.
Wenhan Cao, Nourin Alsharif, Zhongjie Huang, Alice E. White, Yuhuang Wang , Keith A. Brown
Nature Communications, Volume 12, pp 1-7; doi:10.1038/s41467-020-20612-3

Abstract:
Resolution and field-of-view often represent a fundamental tradeoff in microscopy. Atomic force microscopy (AFM), in which a cantilevered probe deflects under the influence of local forces as it scans across a substrate, is a key example of this tradeoff with high resolution imaging being largely limited to small areas. Despite the tremendous impact of AFM in fields including materials science, biology, and surface science, the limitation in imaging area has remained a key barrier to studying samples with intricate hierarchical structure. Here, we show that massively parallel AFM with >1000 probes is possible through the combination of a cantilever-free probe architecture and a scalable optical method for detecting probe–sample contact. Specifically, optically reflective conical probes on a comparatively compliant film are found to comprise a distributed optical lever that translates probe motion into an optical signal that provides sub-10 nm vertical precision. The scalability of this approach makes it well suited for imaging applications that require high resolution over large areas.
Tsz Wai Ko, Jonas A. Finkler , Stefan Goedecker, Jörg Behler
Nature Communications, Volume 12, pp 1-11; doi:10.1038/s41467-020-20427-2

Abstract:
Machine learning potentials have become an important tool for atomistic simulations in many fields, from chemistry via molecular biology to materials science. Most of the established methods, however, rely on local properties and are thus unable to take global changes in the electronic structure into account, which result from long-range charge transfer or different charge states. In this work we overcome this limitation by introducing a fourth-generation high-dimensional neural network potential that combines a charge equilibration scheme employing environment-dependent atomic electronegativities with accurate atomic energies. The method, which is able to correctly describe global charge distributions in arbitrary systems, yields much improved energies and substantially extends the applicability of modern machine learning potentials. This is demonstrated for a series of systems representing typical scenarios in chemistry and materials science that are incorrectly described by current methods, while the fourth-generation neural network potential is in excellent agreement with electronic structure calculations.
Amit Rai , Hideki Hirakawa, Ryo Nakabayashi, Shinji Kikuchi, Koki Hayashi, Megha Rai, Hiroshi Tsugawa , Taiki Nakaya, Tetsuya Mori, Hideki Nagasaki, et al.
Nature Communications, Volume 12, pp 1-19; doi:10.1038/s41467-020-20508-2

Abstract:
Plant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes’ evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.
Sebastian Contreras , Jonas Dehning, Matthias Loidolt , Johannes Zierenberg , F. Paul Spitzner, Jorge H. Urrea-Quintero, Sebastian B. Mohr , Michael Wilczek , Michael Wibral, Viola Priesemann
Nature Communications, Volume 12, pp 1-13; doi:10.1038/s41467-020-20699-8

Abstract:
Without a cure, vaccine, or proven long-term immunity against SARS-CoV-2, test-trace-and-isolate (TTI) strategies present a promising tool to contain its spread. For any TTI strategy, however, mitigation is challenged by pre- and asymptomatic transmission, TTI-avoiders, and undetected spreaders, which strongly contribute to ”hidden" infection chains. Here, we study a semi-analytical model and identify two tipping points between controlled and uncontrolled spread: (1) the behavior-driven reproduction number $${R}_{t}^{H}$$ R t H of the hidden chains becomes too large to be compensated by the TTI capabilities, and (2) the number of new infections exceeds the tracing capacity. Both trigger a self-accelerating spread. We investigate how these tipping points depend on challenges like limited cooperation, missing contacts, and imperfect isolation. Our results suggest that TTI alone is insufficient to contain an otherwise unhindered spread of SARS-CoV-2, implying that complementary measures like social distancing and improved hygiene remain necessary.
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