Nature Communications

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ISSN / EISSN : 2041-1723 / 2041-1723
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Jayson S. Jia, , , Yijian Ning, ,
Published: 13 July 2021
Nature Communications, Volume 12, pp 1-12; doi:10.1038/s41467-021-24606-7

Abstract:
Kinship networks are a fundamental social unit in human societies, and like social networks in general, provide social support in times of need. Here, we investigate the impact of sudden environmental shock, the Ms 7.0 2013 Ya’an earthquake, on the mobile communications patterns of local families, which we operationalize using anonymized individual-level mobile telecommunications metadata from family plan subscribers of a major carrier (N = 35,565 people). We demonstrate that families’ communications dynamics after the earthquake depended on their triadic embeddedness structure, a structural metric we propose that reflects the number of dyads in a family triad that share social ties. We find that individuals in more embedded family structures were more likely to first call other family plan members and slower in calling non-family ties immediately after the earthquake; these tendencies were stronger at higher earthquake intensity. In the weeks after the event, individuals in more embedded family structures had more reciprocal communications and contacted more social ties in their broader social network. Overall, families that are structurally more embedded displayed higher levels of intra-family coordination and mobilization of non-family social connections.
Zikang Ye, Xing Lin, Na Wang, Jianhai Zhou, Meiyi Zhu, ,
Published: 13 July 2021
Nature Communications, Volume 12, pp 1-9; doi:10.1038/s41467-021-24560-4

Abstract:
Phonon-assisted up-conversion photoluminescence can boost energy of an emission photon to be higher than that of the excitation photon by absorbing vibration energy (or phonons) of the emitter. Here, up-conversion photoluminescence power-conversion efficiency (power ratio between the emission and excitation photons) for CdSe/CdS core/shell quantum dots is observed to be beyond unity. Instead of commonly known defect-assisted up-conversion photoluminescence for colloidal quantum dots, temperature-dependent measurements and single-dot spectroscopy reveal the up-conversion photoluminescence and conventional down-conversion photoluminescence share the same electron-phonon coupled electronic states. Ultrafast spectroscopy results imply the thermalized excitons for up-conversion photoluminescence form within 200 fs, which is 100,000 times faster than the radiative recombination rate of the exciton. Results suggest that colloidal quantum dots can be exploited as efficient, stable, and cost-effective emitters for up-conversion photoluminescence in various applications.
Sasha Wagner, Alysha I. Coppola, , Thorsten Dittmar, Jutta Niggemann, , , Robert G. M. Spencer, Hongyan Bao
Published: 13 July 2021
Nature Communications, Volume 12, pp 1-4; doi:10.1038/s41467-021-24477-y

, Wei Zhao, Wenxin Hu, Joshua M. L. Casan, Amit Kumar, Jori Symons, , Danielle Fong, Ilia Voskoboinik, , et al.
Published: 13 July 2021
Nature Communications, Volume 12, pp 1-16; doi:10.1038/s41467-021-24577-9

Abstract:
The recent dramatic appearance of variants of concern of SARS-coronavirus-2 (SARS-CoV-2) highlights the need for innovative approaches that simultaneously suppress viral replication and circumvent viral escape from host immunity and antiviral therapeutics. Here, we employ genome-wide computational prediction and single-nucleotide resolution screening to reprogram CRISPR-Cas13b against SARS-CoV-2 genomic and subgenomic RNAs. Reprogrammed Cas13b effectors targeting accessible regions of Spike and Nucleocapsid transcripts achieved >98% silencing efficiency in virus-free models. Further, optimized and multiplexed Cas13b CRISPR RNAs (crRNAs) suppress viral replication in mammalian cells infected with replication-competent SARS-CoV-2, including the recently emerging dominant variant of concern B.1.1.7. The comprehensive mutagenesis of guide-target interaction demonstrated that single-nucleotide mismatches does not impair the capacity of a potent single crRNA to simultaneously suppress ancestral and mutated SARS-CoV-2 strains in infected mammalian cells, including the Spike D614G mutant. The specificity, efficiency and rapid deployment properties of reprogrammed Cas13b described here provide a molecular blueprint for antiviral drug development to suppress and prevent a wide range of SARS-CoV-2 mutants, and is readily adaptable to other emerging pathogenic viruses.
Shengjun Tan, Huijing Ma, Jinbo Wang, Man Wang, Mengxia Wang, Haodong Yin, YaQiong Zhang, Xinying Zhang, Jieyu Shen, Danyang Wang, et al.
Published: 13 July 2021
Nature Communications, Volume 12, pp 1-14; doi:10.1038/s41467-021-24585-9

Abstract:
Despite long being considered as “junk”, transposable elements (TEs) are now accepted as catalysts of evolution. One example is Mutator-like elements (MULEs, one type of terminal inverted repeat DNA TEs, or TIR TEs) capturing sequences as Pack-MULEs in plants. However, their origination mechanism remains perplexing, and whether TIR TEs mediate duplication in animals is almost unexplored. Here we identify 370 Pack-TIRs in 100 animal reference genomes and one Pack-TIR (Ssk-FB4) family in fly populations. We find that single-copy Pack-TIRs are mostly generated via transposition-independent gap filling, and multicopy Pack-TIRs are likely generated by transposition after replication fork switching. We show that a proportion of Pack-TIRs are transcribed and often form chimeras with hosts. We also find that Ssk-FB4s represent a young protein family, as supported by proteomics and signatures of positive selection. Thus, TIR TEs catalyze new gene structures and new genes in animals via both transposition-independent and -dependent mechanisms.
Olivia J. James, Maud Vandereyken, , Francois Singh, Susan E. Bray, Jamie Wilson, Andrew G. Love,
Published: 13 July 2021
Nature Communications, Volume 12, pp 1-16; doi:10.1038/s41467-021-24473-2

Abstract:
Intestinal intraepithelial lymphocytes (IEL) are an abundant population of tissue-resident T cells that protect and maintain the intestinal barrier. IEL respond to epithelial cell-derived IL-15, which is complexed to the IL-15 receptor α chain (IL-15/Rα). IL-15 is essential both for maintaining IEL homeostasis and inducing IEL responses to epithelial stress, which has been associated with Coeliac disease. Here, we apply quantitative mass spectrometry to IL-15/Rα-stimulated IEL to investigate how IL-15 directly regulates inflammatory functions of IEL. IL-15/Rα drives IEL activation through cell cycle regulation, upregulation of metabolic machinery and expression of a select repertoire of cell surface receptors. IL-15/Rα selectively upregulates the Ser/Thr kinases PIM1 and PIM2, which are essential for IEL to proliferate, grow and upregulate granzyme B in response to inflammatory IL-15. Notably, IEL from patients with Coeliac disease have high PIM expression. Together, these data indicate PIM kinases as important effectors of IEL responses to inflammatory IL-15.
Quoc Vo,
Published: 13 July 2021
Nature Communications, Volume 12, pp 1-7; doi:10.1038/s41467-021-24534-6

Abstract:
A stone thrown in a lake captures air as it collides with water and sinks; likewise a rain drop falling on a flat surface traps air bubbles underneath and creates a spectacular splash. These natural occurrences, from bubble entrapment to liquid ejection, happen as air fails to escape from the closing gap between liquid and solid surfaces. Trapping of air is devastating for casting, coating, painting, and printing industries, or those intolerant of water entry noise. Attempts to eliminate the interfering air rely on either reducing the ambient pressure or modifying the solid surfaces. The former approach is inflexible in its implementation, while the latter one is inherently limited by the wetting speed of liquid or the draining capacity of air passages created on the solid. Here, we present a “divide and conquer” approach to split the thin air gap into tunnels and subsequently squeeze air out from the tunnels against its viscous resistance using spatially periodic dielectrophoretic force. We confirm the working principles by demonstrating suppression of both bubble entrapment and splash upon impacts of droplets on solid surfaces.
Wei-Ching Chen, Minh D. To, Peter M. K. Westcott, Reyno Delrosario, Il-Jin Kim, , Quan Tran, Saumya R. Bollam, , Nora Bayani, et al.
Published: 13 July 2021
Nature Communications, Volume 12, pp 1-14; doi:10.1038/s41467-021-24498-7

Abstract:
The commonly mutated human KRAS oncogene encodes two distinct KRAS4A and KRAS4B proteins generated by differential splicing. We demonstrate here that coordinated regulation of both isoforms through control of splicing is essential for development of Kras mutant tumors. The minor KRAS4A isoform is enriched in cancer stem-like cells, where it responds to hypoxia, while the major KRAS4B is induced by ER stress. KRAS4A splicing is controlled by the DCAF15/RBM39 pathway, and deletion of KRAS4A or pharmacological inhibition of RBM39 using Indisulam leads to inhibition of cancer stem cells. Our data identify existing clinical drugs that target KRAS4A splicing, and suggest that levels of the minor KRAS4A isoform in human tumors can be a biomarker of sensitivity to some existing cancer therapeutics.
, , Scott L. Delp, Steven H. Collins
Published: 13 July 2021
Nature Communications, Volume 12, pp 1-11; doi:10.1038/s41467-021-24173-x

Abstract:
Physical inactivity is the fourth leading cause of global mortality. Health organizations have requested a tool to objectively measure physical activity. Respirometry and doubly labeled water accurately estimate energy expenditure, but are infeasible for everyday use. Smartwatches are portable, but have significant errors. Existing wearable methods poorly estimate time-varying activity, which comprises 40% of daily steps. Here, we present a Wearable System that estimates metabolic energy expenditure in real-time during common steady-state and time-varying activities with substantially lower error than state-of-the-art methods. We perform experiments to select sensors, collect training data, and validate the Wearable System with new subjects and new conditions for walking, running, stair climbing, and biking. The Wearable System uses inertial measurement units worn on the shank and thigh as they distinguish lower-limb activity better than wrist or trunk kinematics and converge more quickly than physiological signals. When evaluated with a diverse group of new subjects, the Wearable System has a cumulative error of 13% across common activities, significantly less than 42% for a smartwatch and 44% for an activity-specific smartwatch. This approach enables accurate physical activity monitoring which could enable new energy balance systems for weight management or large-scale activity monitoring.
Dexin Yang, Guoling Zhang, Runchen Lai, Yao Cheng, Yaxiao Lian, Min Rao, Dexuan Huo, , Baodan Zhao,
Published: 13 July 2021
Nature Communications, Volume 12, pp 1-7; doi:10.1038/s41467-021-24616-5

Abstract:
Reducing environmental impact is a key challenge for perovskite optoelectronics, as most high-performance devices are based on potentially toxic lead-halide perovskites. For photovoltaic solar cells, tin-lead (Sn–Pb) perovskite materials provide a promising solution for reducing toxicity. However, Sn–Pb perovskites typically exhibit low luminescence efficiencies, and are not ideal for light-emitting applications. Here we demonstrate highly luminescent germanium-lead (Ge–Pb) perovskite films with photoluminescence quantum efficiencies (PLQEs) of up to ~71%, showing a considerable relative improvement of ~34% over similarly prepared Ge-free, Pb-based perovskite films. In our initial demonstration of Ge–Pb perovskite LEDs, we achieve external quantum efficiencies (EQEs) of up to ~13.1% at high brightness (~1900 cd m−2), a step forward for reduced-toxicity perovskite LEDs. Our findings offer a new solution for developing eco-friendly light-emitting technologies based on perovskite semiconductors.
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