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Single-molecule analysis of specificity and multivalency in binding of short linear substrate motifs to the APC/C.

Nairi Hartooni, Jongmin Sung, Ankur Jain, David O Morgan,

Robust regulatory signals in the cell often depend on interactions between short linear motifs (SLiMs) and globular proteins. Many of these interactions are poorly characterized because the binding proteins cannot be produced in the amounts needed for traditional methods. To address this problem, we developed a single-molecule off-rate (SMOR) assay ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):341]

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Nanobubbles explain the large slip observed on lubricant-infused surfaces.

Christopher Vega-Sánchez, Sam Peppou-Chapman, Liwen Zhu, Chiara Neto,

Lubricant-infused surfaces hold promise to reduce the huge frictional drag that slows down the flow of fluids at microscales. We show that infused Teflon wrinkled surfaces induce an effective slip length 50 times larger than expected based on the presence of the lubricant alone. This effect is particularly striking as ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):351]

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Two opposing hippocampus to prefrontal cortex pathways for the control of approach and avoidance behaviour.

Candela Sánchez-Bellot, Rawan AlSubaie, Karyna Mishchanchuk, Ryan W S Wee, Andrew F MacAskill,

The decision to either approach or avoid a potentially threatening environment is thought to rely upon the coordinated activity of heterogeneous neural populations in the hippocampus and prefrontal cortex (PFC). However, how this circuitry is organized to flexibly promote both approach or avoidance at different times has remained elusive. Here, ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):339]

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RNF43/ZNRF3 loss predisposes to hepatocellular-carcinoma by impairing liver regeneration and altering the liver lipid metabolic ground-state.

Germán Belenguer, Gianmarco Mastrogiovanni, Clare Pacini, Zoe Hall, Anna M Dowbaj, Robert Arnes-Benito, Aleksandra Sljukic, Nicole Prior, Sofia Kakava, Charles R Bradshaw, Susan Davies, Michele Vacca, Kourosh Saeb-Parsy, Bon-Kyoung Koo, Meritxell Huch,

RNF43/ZNRF3 negatively regulate WNT signalling. Both genes are mutated in several types of cancers, however, their contribution to liver disease is unknown. Here we describe that hepatocyte-specific loss of Rnf43/Znrf3 results in steatohepatitis and in increase in unsaturated lipids, in the absence of dietary fat supplementation. Upon injury, Rnf43/Znrf3 deletion ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):334]

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Abrupt conclusion of the late Miocene-early Pliocene biogenic bloom at 4.6-4.4 Ma.

B -Th Karatsolis, B C Lougheed, D De Vleeschouwer, J Henderiks,

The late Miocene-early Pliocene biogenic bloom was an extended time interval characterised by elevated ocean export productivity at numerous locations. As primary productivity is nutrient-limited at low-to-mid latitudes, this bloom has been attributed to an increase or a redistribution of available nutrients, potentially involving ocean-gateway or monsoon-related mechanisms. While the ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):353]

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Epigenetic aging of the demographically non-aging naked mole-rat.

Csaba Kerepesi, Margarita V Meer, Julia Ablaeva, Vince G Amoroso, Sang-Goo Lee, Bohan Zhang, Maxim V Gerashchenko, Alexandre Trapp, Sun Hee Yim, Ake T Lu, Morgan E Levine, Andrei Seluanov, Steve Horvath, Thomas J Park, Vera Gorbunova, Vadim N Gladyshev,

The naked mole-rat (NMR) is an exceptionally long-lived rodent that shows no increase of mortality with age, defining it as a demographically non-aging mammal. Here, we perform bisulfite sequencing of the blood of > 100 NMRs, assessing > 3 million common CpG sites. Unsupervised clustering based on sites whose methylation correlates with age reveals ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):355]

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Unprotected peptide macrocyclization and stapling via a fluorine-thiol displacement reaction.

Md Shafiqul Islam, Samuel L Junod, Si Zhang, Zakey Yusuf Buuh, Yifu Guan, Mi Zhao, Kishan H Kaneria, Parmila Kafley, Carson Cohen, Robert Maloney, Zhigang Lyu, Vincent A Voelz, Weidong Yang, Rongsheng E Wang,

We report the discovery of a facile peptide macrocyclization and stapling strategy based on a fluorine thiol displacement reaction (FTDR), which renders a class of peptide analogues with enhanced stability, affinity, cellular uptake, and inhibition of cancer cells. This approach enabled selective modification of the orthogonal fluoroacetamide side chains in ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):350]

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Uncovering the reaction mechanism behind CoO as active phase for CO2 hydrogenation.

Iris C Ten Have, Josepha J G Kromwijk, Matteo Monai, Davide Ferri, Ellen B Sterk, Florian Meirer, Bert M Weckhuysen,

Transforming carbon dioxide into valuable chemicals and fuels, is a promising tool for environmental and industrial purposes. Here, we present catalysts comprising of cobalt (oxide) nanoparticles stabilized on various support oxides for hydrocarbon production from carbon dioxide. We demonstrate that the activity and selectivity can be tuned by selection of ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):324]

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Structure and function of a family of tick-derived complement inhibitors targeting properdin.

Katharina Braunger, Jiyoon Ahn, Matthijs M Jore, Steven Johnson, Terence T L Tang, Dennis V Pedersen, Gregers R Andersen, Susan M Lea,

Activation of the serum-resident complement system begins a cascade that leads to activation of membrane-resident complement receptors on immune cells, thus coordinating serum and cellular immune responses. Whilst many molecules act to control inappropriate activation, Properdin is the only known positive regulator of the human complement system. By stabilising the ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):317]

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Model-based evaluation of alternative reactive class closure strategies against COVID-19.

Quan-Hui Liu, Juanjuan Zhang, Cheng Peng, Maria Litvinova, Shudong Huang, Piero Poletti, Filippo Trentini, Giorgio Guzzetta, Valentina Marziano, Tao Zhou, Cecile Viboud, Ana I Bento, Jiancheng Lv, Alessandro Vespignani, Stefano Merler, Hongjie Yu, Marco Ajelli,

There are contrasting results concerning the effect of reactive school closure on SARS-CoV-2 transmission. To shed light on this controversy, we developed a data-driven computational model of SARS-CoV-2 transmission. We found that by reactively closing classes based on syndromic surveillance, SARS-CoV-2 infections are reduced by no more than 17.3% (95%CI: ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):322]

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Modeling uniquely human gene regulatory function via targeted humanization of the mouse genome.

Emily V Dutrow, Deena Emera, Kristina Yim, Severin Uebbing, Acadia A Kocher, Martina Krenzer, Timothy Nottoli, Daniel B Burkhardt, Smita Krishnaswamy, Angeliki Louvi, James P Noonan,

The evolution of uniquely human traits likely entailed changes in developmental gene regulation. Human Accelerated Regions (HARs), which include transcriptional enhancers harboring a significant excess of human-specific sequence changes, are leading candidates for driving gene regulatory modifications in human development. However, insight into whether HARs alter the level, distribution, and ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):304]

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4polar-STORM polarized super-resolution imaging of actin filament organization in cells.

Caio Vaz Rimoli, Cesar Augusto Valades-Cruz, Valentina Curcio, Manos Mavrakis, Sophie Brasselet,

Single-molecule localization microscopy provides insights into the nanometer-scale spatial organization of proteins in cells, however it does not provide information on their conformation and orientation, which are key functional signatures. Detecting single molecules' orientation in addition to their localization in cells is still a challenging task, in particular in dense ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):301]

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Eliminating chronic myeloid leukemia stem cells by IRAK1/4 inhibitors.

Yosuke Tanaka, Reina Takeda, Tsuyoshi Fukushima, Keiko Mikami, Shun Tsuchiya, Moe Tamura, Keito Adachi, Terumasa Umemoto, Shuhei Asada, Naoki Watanabe, Soji Morishita, Misa Imai, Masayoshi Nagata, Marito Araki, Hitoshi Takizawa, Tomofusa Fukuyama, Chrystelle Lamagna, Esteban S Masuda, Ryoji Ito, Susumu Goyama, Norio Komatsu, Tomoiku Takaku, Toshio Kitamura,

Leukemia stem cells (LSCs) in chronic myeloid leukemia (CML) are quiescent, insensitive to BCR-ABL1 tyrosine kinase inhibitors (TKIs) and responsible for CML relapse. Therefore, eradicating quiescent CML LSCs is a major goal in CML therapy. Here, using a G<sub>0</sub> marker (G<sub>0</sub>M), we narrow down CML LSCs as G<sub>0</sub>M- and CD27- ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):271]

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Electronic nature of charge density wave and electron-phonon coupling in kagome superconductor KV3Sb5.

Hailan Luo, Qiang Gao, Hongxiong Liu, Yuhao Gu, Dingsong Wu, Changjiang Yi, Junjie Jia, Shilong Wu, Xiangyu Luo, Yu Xu, Lin Zhao, Qingyan Wang, Hanqing Mao, Guodong Liu, Zhihai Zhu, Youguo Shi, Kun Jiang, Jiangping Hu, Zuyan Xu, X J Zhou,

The Kagome superconductors AV<sub>3</sub>Sb<sub>5</sub> (A = K, Rb, Cs) have received enormous attention due to their nontrivial topological electronic structure, anomalous physical properties and superconductivity. Unconventional charge density wave (CDW) has been detected in AV<sub>3</sub>Sb<sub>5</sub>. High-precision electronic structure determination is essential to understand its origin. Here we unveil electronic nature ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):273]

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Genetic alterations of the SUMO isopeptidase SENP6 drive lymphomagenesis and genetic instability in diffuse large B-cell lymphoma.

Markus Schick, Le Zhang, Sabine Maurer, Hans Carlo Maurer, Konstandina Isaakaidis, Lara Schneider, Upayan Patra, Kathrin Schunck, Elena Rohleder, Julia Hofstetter, Apoorva Baluapuri, Anna Katharina Scherger, Julia Slotta-Huspenina, Franziska Hettler, Julia Weber, Thomas Engleitner, Roman Maresch, Jolanta Slawska, Richard Lewis, Rouzanna Istvanffy, Stefan Habringer, Katja Steiger, Armin Baiker, Robert A J Oostendorp, Cornelius Miething, Hans-Peter Lenhof, Florian Bassermann, Björn Chapuy, Matthias Wirth, Elmar Wolf, Roland Rad, Stefan Müller, Ulrich Keller,

SUMOylation is a post-translational modification of proteins that regulates these proteins' localization, turnover or function. Aberrant SUMOylation is frequently found in cancers but its origin remains elusive. Using a genome-wide transposon mutagenesis screen in a MYC-driven B-cell lymphoma model, we here identify the SUMO isopeptidase (or deconjugase) SENP6 as a ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):281]

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Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing.

Till L V Bornemann, Panagiotis S Adam, Victoria Turzynski, Ulrich Schreiber, Perla Abigail Figueroa-Gonzalez, Janina Rahlff, Daniel Köster, Torsten C Schmidt, Ralf Schunk, Bernhard Krauthausen, Alexander J Probst,

Earth's mantle releases 38.7 ± 2.9 Tg/yr CO<sub>2</sub> along with other reduced and oxidized gases to the atmosphere shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we perform comparative metagenomics coupled to geochemical measurements of deep subsurface ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):284]

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Obligate mutualistic cooperation limits evolvability.

Benedikt Pauli, Leonardo Oña, Marita Hermann, Christian Kost,

Cooperative mutualisms are widespread and play fundamental roles in many ecosystems. Given that these interactions are often obligate, the Darwinian fitness of the participating individuals is not only determined by the information encoded in their own genomes, but also the traits and capabilities of their corresponding interaction partners. Thus, a ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):337]

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Contribution of the medial eye field network to the voluntary deployment of visuospatial attention.

Guillaume Herbet, Hugues Duffau,

Historically, the study of patients with spatial neglect has provided fundamental insights into the neural basis of spatial attention. However, lesion mapping studies have been unsuccessful in establishing the potential role of associative networks spreading on the dorsal-medial axis, mainly because they are uncommonly targeted by vascular injuries. Here we ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):328]

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Impact of bulk-edge coupling on observation of anyonic braiding statistics in quantum Hall interferometers.

J Nakamura, S Liang, G C Gardner, M J Manfra,

Quantum Hall interferometers have been used to probe fractional charge and statistics of quasiparticles. We present measurements of a small Fabry-Perot interferometer in which the electrostatic coupling constants which affect interferometer behavior can be determined experimentally. Near the center of the ν = 1/3 state this device exhibits Aharonov-Bohm interference interrupted by ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):344]

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Distinct kinetics of antibodies to 111 Plasmodium falciparum proteins identifies markers of recent malaria exposure.

Victor Yman, James Tuju, Michael T White, Gathoni Kamuyu, Kennedy Mwai, Nelson Kibinge, Muhammad Asghar, Christopher Sundling, Klara Sondén, Linda Murungi, Daniel Kiboi, Rinter Kimathi, Timothy Chege, Emily Chepsat, Patience Kiyuka, Lydia Nyamako, Faith H A Osier, Anna Färnert,

Strengthening malaria surveillance is a key intervention needed to reduce the global disease burden. Reliable serological markers of recent malaria exposure could improve current surveillance methods by allowing for accurate estimates of infection incidence from limited data. We studied the IgG antibody response to 111 Plasmodium falciparum proteins in 65 ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):331]

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Au-activated N motifs in non-coherent cupric porphyrin metal organic frameworks for promoting and stabilizing ethylene production.

Xulan Xie, Xiang Zhang, Miao Xie, Likun Xiong, Hao Sun, Yongtao Lu, Qiaoqiao Mu, Mark H Rummeli, Jiabin Xu, Shuo Li, Jun Zhong, Zhao Deng, Bingyun Ma, Tao Cheng, William A Goddard, Yang Peng,

Direct implementation of metal-organic frameworks as the catalyst for CO<sub>2</sub> electroreduction has been challenging due to issues such as poor conductivity, stability, and limited > 2e<sup>-</sup> products. In this study, Au nanoneedles are impregnated into a cupric porphyrin-based metal-organic framework by exploiting ligand carboxylates as the Au<sup>3+</sup> -reducing agent, simultaneously cleaving the ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):63]

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Completely aqueous processable stimulus responsive organic room temperature phosphorescence materials with tunable afterglow color.

Dan Li, Yujie Yang, Jie Yang, Manman Fang, Ben Zhong Tang, Zhen Li,

Many luminescent stimuli responsive materials are based on fluorescence emission, while stimuli-responsive room temperature phosphorescent materials are less explored. Here, we show a kind of stimulus-responsive room temperature phosphorescence materials by the covalent linkage of phosphorescent chromophore of arylboronic acid and polymer matrix of poly(vinylalcohol). Attributed to the rigid environment ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):347]

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Pre-configuring chromatin architecture with histone modifications guides hematopoietic stem cell formation in mouse embryos.

Chen C Li, Guangyu Zhang, Junjie Du, Di Liu, Zongcheng Li, Yanli Ni, Jie Zhou, Yunqiao Li, Siyuan Hou, Xiaona Zheng, Yu Lan, Bing Liu, Aibin He,

The gene activity underlying cell differentiation is regulated by a diverse set of transcription factors (TFs), histone modifications, chromatin structures and more. Although definitive hematopoietic stem cells (HSCs) are known to emerge via endothelial-to-hematopoietic transition (EHT), how the multi-layered epigenome is sequentially unfolded in a small portion of endothelial cells ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):346]

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Fault rock heterogeneity can produce fault weakness and reduce fault stability.

John D Bedford, Daniel R Faulkner, Nadia Lapusta,

Geological heterogeneity is abundant in crustal fault zones; however, its role in controlling the mechanical behaviour of faults is poorly constrained. Here, we present laboratory friction experiments on laterally heterogeneous faults, with patches of strong, rate-weakening quartz gouge and weak, rate-strengthening clay gouge. The experiments show that the heterogeneity leads ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):326]

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Giant room temperature compression and bending in ferroelectric oxide pillars.

Ying Liu, Xiangyuan Cui, Ranming Niu, Shujun Zhang, Xiaozhou Liao, Scott D Moss, Peter Finkel, Magnus Garbrecht, Simon P Ringer, Julie M Cairney,

Plastic deformation in ceramic materials is normally only observed in nanometre-sized samples. However, we have observed high levels of plasticity (>50% plastic strain) and excellent elasticity (6% elastic strain) in perovskite oxide Pb(In<sub>1/2</sub>Nb<sub>1/2</sub>)O<sub>3</sub>-Pb(Mg<sub>1/3</sub>Nb<sub>2/3</sub>)O<sub>3</sub>-PbTiO<sub>3</sub>, under compression along <100><sub>pc</sub> pillars up to 2.1 μm in diameter. The extent of this deformation is ... Read more >>

Nat Commun (Nature communications)
[2022, 13(1):335]

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