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Anastasia N Tikhonova, Igor Dolgalev, Hai Hu, Kishor K Sivaraj, Edlira Hoxha, Álvaro Cuesta-Domínguez, Sandra Pinho, Ilseyar Akhmetzyanova, Jie Gao, Matthew Witkowski, Maria Guillamot, Michael C Gutkin, Yutong Zhang, Christian Marier, Catherine Diefenbach, Stavroula Kousteni, Adriana Heguy, Hua Zhong, David R Fooksman, Jason M Butler, Aris Economides, Paul S Frenette, Ralf H Adams, Rahul Satija, Aristotelis Tsirigos, Iannis Aifantis
An Amendment to this paper has been published and can be accessed via a link at the top of the paper.
July 12, 2019: Nature
Marco De Cecco, Takahiro Ito, Anna P Petrashen, Amy E Elias, Nicholas J Skvir, Steven W Criscione, Alberto Caligiana, Greta Brocculi, Emily M Adney, Jef D Boeke, Oanh Le, Christian Beauséjour, Jayakrishna Ambati, Kameshwari Ambati, Matthew Simon, Andrei Seluanov, Vera Gorbunova, P Eline Slagboom, Stephen L Helfand, Nicola Neretti, John M Sedivy
An Amendment to this paper has been published and can be accessed via a link at the top of the paper.
July 12, 2019: Nature
Zhenishbek Zhakypov, Kazuaki Mori, Koh Hosoda, Jamie Paik
In ant colonies, collectivity enables division of labour and resources1-3 with great scalability. Beyond their intricate social behaviours, individuals of the genus Odontomachus4 , also known as trap-jaw ants, have developed remarkable multi-locomotion mechanisms to 'escape-jump' upwards when threatened, using the sudden snapping of their mandibles5 , and to negotiate obstacles by leaping forwards using their legs6 . Emulating such diverse insect biomechanics and studying collective behaviours in a variety of environments may lead to the development of multi-locomotion robotic collectives deployable in situations such as emergency relief, exploration and monitoring7 ; however, reproducing these abilities in small-scale robotic systems with simple design and scalability remains a key challenge...
July 10, 2019: Nature
Arnold J T M Mathijssen, Joshua Culver, M Saad Bhamla, Manu Prakash
The biophysical relationships between sensors and actuators1-5 have been fundamental to the development of complex life forms. Swimming organisms generate abundant flows that persist in aquatic environments6-13 , and responding promptly to external stimuli is key to survival14-19 . Here we present the discovery of 'hydrodynamic trigger waves' in cellular communities of the protist Spirostomum ambiguum that propagate-in a manner similar to a chain reaction20-22 -hundreds of times faster than their swimming speed...
July 10, 2019: Nature
Philip Jonsson, Chaitanya Bandlamudi, Michael L Cheng, Preethi Srinivasan, Shweta S Chavan, Noah D Friedman, Ezra Y Rosen, Allison L Richards, Nancy Bouvier, S Duygu Selcuklu, Craig M Bielski, Wassim Abida, Diana Mandelker, Ozge Birsoy, Liying Zhang, Ahmet Zehir, Mark T A Donoghue, José Baselga, Kenneth Offit, Howard I Scher, Eileen M O'Reilly, Zsofia K Stadler, Nikolaus Schultz, Nicholas D Socci, Agnes Viale, Marc Ladanyi, Mark E Robson, David M Hyman, Michael F Berger, David B Solit, Barry S Taylor
Mutations in BRCA1 and BRCA2 predispose individuals to certain cancers1-3 , and disease-specific screening and preventative strategies have reduced cancer mortality in affected patients4,5 . These classical tumour-suppressor genes have tumorigenic effects associated with somatic biallelic inactivation, although haploinsufficiency may also promote the formation and progression of tumours6,7 . Moreover, BRCA1/2-mutant tumours are often deficient in the repair of double-stranded DNA breaks by homologous recombination8-13 , and consequently exhibit increased therapeutic sensitivity to platinum-containing therapy and inhibitors of poly-(ADP-ribose)-polymerase (PARP)14,15 ...
July 10, 2019: Nature
Chen Cao, Laurence A Lemaire, Wei Wang, Peter H Yoon, Yoolim A Choi, Lance R Parsons, John C Matese, Wei Wang, Michael Levine, Kai Chen
Ascidian embryos highlight the importance of cell lineages in animal development. As simple proto-vertebrates, they also provide insights into the evolutionary origins of cell types such as cranial placodes and neural crest cells. Here we have determined single-cell transcriptomes for more than 90,000 cells that span the entirety of development-from the onset of gastrulation to swimming tadpoles-in Ciona intestinalis. Owing to the small numbers of cells in ascidian embryos, this represents an average of over 12-fold coverage for every cell at every stage of development...
July 10, 2019: Nature
Nalle Pentinmikko, Sharif Iqbal, Miyeko Mana, Simon Andersson, Armand B Cognetta, Radu M Suciu, Jatin Roper, Kalle Luopajärvi, Eino Markelin, Swetha Gopalakrishnan, Olli-Pekka Smolander, Santiago Naranjo, Tuure Saarinen, Anne Juuti, Kirsi Pietiläinen, Petri Auvinen, Ari Ristimäki, Nitin Gupta, Tuomas Tammela, Tyler Jacks, David M Sabatini, Benjamin F Cravatt, Ömer H Yilmaz, Pekka Katajisto
A decline in stem cell function impairs tissue regeneration during ageing, but the role of the stem-cell-supporting niche in ageing is not well understood. The small intestine is maintained by actively cycling intestinal stem cells that are regulated by the Paneth cell niche1,2 . Here we show that the regenerative potential of human and mouse intestinal epithelium diminishes with age owing to defects in both stem cells and their niche. The functional decline was caused by a decrease in stemness-maintaining Wnt signalling due to production of Notum, an extracellular Wnt inhibitor, in aged Paneth cells...
July 10, 2019: Nature
Katja Faelber, Lea Dietrich, Jeffrey K Noel, Florian Wollweber, Anna-Katharina Pfitzner, Alexander Mühleip, Ricardo Sánchez, Misha Kudryashev, Nicolas Chiaruttini, Hauke Lilie, Jeanette Schlegel, Eva Rosenbaum, Manuel Hessenberger, Claudia Matthaeus, Séverine Kunz, Alexander von der Malsburg, Frank Noé, Aurélien Roux, Martin van der Laan, Werner Kühlbrandt, Oliver Daumke
Balanced fusion and fission are key for the proper function and physiology of mitochondria1,2 . Remodelling of the mitochondrial inner membrane is mediated by the dynamin-like protein mitochondrial genome maintenance 1 (Mgm1) in fungi or the related protein optic atrophy 1 (OPA1) in animals3-5 . Mgm1 is required for the preservation of mitochondrial DNA in yeast6 , whereas mutations in the OPA1 gene in humans are a common cause of autosomal dominant optic atrophy-a genetic disorder that affects the optic nerve7,8 ...
July 10, 2019: Nature
Katerina Harvati, Carolin Röding, Abel M Bosman, Fotios A Karakostis, Rainer Grün, Chris Stringer, Panagiotis Karkanas, Nicholas C Thompson, Vassilis Koutoulidis, Lia A Moulopoulos, Vassilis G Gorgoulis, Mirsini Kouloukoussa
Two fossilized human crania (Apidima 1 and Apidima 2) from Apidima Cave, southern Greece, were discovered in the late 1970s but have remained enigmatic owing to their incomplete nature, taphonomic distortion and lack of archaeological context and chronology. Here we virtually reconstruct both crania, provide detailed comparative descriptions and analyses, and date them using U-series radiometric methods. Apidima 2 dates to more than 170 thousand years ago and has a Neanderthal-like morphological pattern...
July 10, 2019: Nature
Florian Erhard, Marisa A P Baptista, Tobias Krammer, Thomas Hennig, Marius Lange, Panagiota Arampatzi, Christopher S Jürges, Fabian J Theis, Antoine-Emmanuel Saliba, Lars Dölken
Single-cell RNA sequencing (scRNA-seq) has highlighted the important role of intercellular heterogeneity in phenotype variability in both health and disease1 . However, current scRNA-seq approaches provide only a snapshot of gene expression and convey little information on the true temporal dynamics and stochastic nature of transcription. A further key limitation of scRNA-seq analysis is that the RNA profile of each individual cell can be analysed only once. Here we introduce single-cell, thiol-(SH)-linked alkylation of RNA for metabolic labelling sequencing (scSLAM-seq), which integrates metabolic RNA labelling2 , biochemical nucleoside conversion3 and scRNA-seq to record transcriptional activity directly by differentiating between new and old RNA for thousands of genes per single cell...
July 10, 2019: Nature
Ryan J Ries, Sara Zaccara, Pierre Klein, Anthony Olarerin-George, Sim Namkoong, Brian F Pickering, Deepak P Patil, Hojoong Kwak, Jun Hee Lee, Samie R Jaffrey
N6 -methyladenosine (m6 A) is the most prevalent modified nucleotide in mRNA1,2 , with around 25% of mRNAs containing at least one m6 A. Methylation of mRNA to form m6 A is required for diverse cellular and physiological processes3 . Although the presence of m6 A in an mRNA can affect its fate in different ways, it is unclear how m6 A directs this process and why the effects of m6 A can vary in different cellular contexts. Here we show that the cytosolic m6 A-binding proteins-YTHDF1, YTHDF2 and YTHDF3-undergo liquid-liquid phase separation in vitro and in cells...
July 10, 2019: Nature
Nadim Aizarani, Antonio Saviano, Sagar, Laurent Mailly, Sarah Durand, Josip S Herman, Patrick Pessaux, Thomas F Baumert, Dominic Grün
The human liver is an essential multifunctional organ. The incidence of liver diseases is rising and there are limited treatment options. However, the cellular composition of the liver remains poorly understood. Here we performed single-cell RNA sequencing of about 10,000 cells from normal liver tissue from nine human donors to construct a human liver cell atlas. Our analysis identified previously unknown subtypes of endothelial cells, Kupffer cells, and hepatocytes, with transcriptome-wide zonation of some of these populations...
July 10, 2019: Nature
Pierre Canavelli, Saidul Islam, Matthew W Powner
Amide bond formation is one of the most important reactions in both chemistry and biology1-4 , but there is currently no chemical method of achieving α-peptide ligation in water that tolerates all of the 20 proteinogenic amino acids at the peptide ligation site. The universal genetic code establishes that the biological role of peptides predates life's last universal common ancestor and that peptides played an essential part in the origins of life5-9 . The essential role of sulfur in the citric acid cycle, non-ribosomal peptide synthesis and polyketide biosynthesis point towards thioester-dependent peptide ligations preceding RNA-dependent protein synthesis during the evolution of life5,9-13 ...
July 10, 2019: Nature
Yu Xiao, Martin Stegmann, Zhifu Han, Thomas A DeFalco, Katarzyna Parys, Li Xu, Youssef Belkhadir, Cyril Zipfel, Jijie Chai
Receptor kinases (RKs) of the Catharanthus roseus RLK1-like (CrRLK1L) family have emerged as important regulators of plant reproduction, growth and responses to the environment1 . Endogenous RAPID ALKALINIZATION FACTOR (RALF) peptides2 have been proposed as ligands for several CrRLK1L members1 . The mechanistic basis of this perception, however, is unknown. Here, we report that RALF23 induces a complex between the CrRLK1L FERONIA (FER) and LORELEI (LRE)-LIKE GLYCOSYLPHOSPHATIDYLINOSITOL (GPI)-ANCHORED PROTEIN 1 (LLG1) to regulate immune signalling...
July 10, 2019: Nature
Adam C Wilkinson, Reiko Ishida, Misako Kikuchi, Kazuhiro Sudo, Maiko Morita, Ralph Valentine Crisostomo, Ryo Yamamoto, Kyle M Loh, Yukio Nakamura, Motoo Watanabe, Hiromitsu Nakauchi, Satoshi Yamazaki
An Amendment to this paper has been published and can be accessed via a link at the top of the paper.
July 9, 2019: Nature
Patrick Knüppel, Sylvain Ravets, Martin Kroner, Stefan Fält, Werner Wegscheider, Atac Imamoglu
Engineering strong interactions between optical photons is a challenge for quantum science. Polaritonics, which is based on the strong coupling of photons to atomic or electronic excitations in an optical resonator, has emerged as a promising approach to address this challenge, paving the way for applications such as photonic gates for quantum information processing1 and photonic quantum materials for the investigation of strongly correlated driven-dissipative systems2,3 . Recent experiments have demonstrated the onset of quantum correlations in exciton-polariton systems4,5 , showing that strong polariton blockade6 -the prevention of resonant injection of additional polaritons in a well delimited region by the presence of a single polariton-could be achieved if interactions were an order of magnitude stronger...
July 8, 2019: Nature
Deshun Gong, Ximin Chi, Jinhong Wei, Gewei Zhou, Gaoxingyu Huang, Lin Zhang, Ruiwu Wang, Jianlin Lei, S R Wayne Chen, Nieng Yan
The high-conductance intracellular calcium (Ca2+ ) channel RyR2 is essential for the coupling of excitation and contraction in cardiac muscle. Among various modulators, calmodulin (CaM) regulates RyR2 in a Ca2+ -dependent manner. Here we reveal the regulatory mechanism by which porcine RyR2 is modulated by human CaM through the structural determination of RyR2 under eight conditions. Apo-CaM and Ca2+ -CaM bind to distinct but overlapping sites in an elongated cleft formed by the handle, helical and central domains...
July 5, 2019: Nature
Corentin C Loron, Camille François, Robert H Rainbird, Elizabeth C Turner, Stephan Borensztajn, Emmanuelle J Javaux
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
July 4, 2019: Nature
Ritika Dusad, Franziska K K Kirschner, Jesse C Hoke, Benjamin R Roberts, Anna Eyal, Felix Flicker, Graeme M Luke, Stephen J Blundell, J C Séamus Davis
Magnetic monopoles1-3 are hypothetical elementary particles with quantized magnetic charge. In principle, a magnetic monopole can be detected by the quantized jump in magnetic flux that it generates upon passage through a superconducting quantum interference device (SQUID)4 . Following the theoretical prediction that emergent magnetic monopoles should exist in several lanthanide pyrochlore magnetic insulators5,6 , including Dy2 Ti2 O7 , the SQUID technique has been proposed for their direct detection6 . However, this approach has been hindered by the high number density and the generation-recombination fluctuations expected of such thermally generated monopoles...
July 3, 2019: Nature
Logan W Clark, Ningyuan Jia, Nathan Schine, Claire Baum, Alexandros Georgakopoulos, Jonathan Simon
Ordinarily, photons do not interact with one another. However, atoms can be used to mediate photonic interactions1,2 , raising the prospect of forming synthetic materials3 and quantum information systems4-7 from photons. One promising approach combines highly excited Rydberg atoms8-12 with the enhanced light-matter coupling of an optical cavity to convert photons into strongly interacting polaritons13-15 . However, quantum materials made of optical photons have not yet been realized, because the experimental challenge of coupling a suitable atomic sample with a degenerate cavity has constrained cavity polaritons to a single spatial mode that is resonant with an atomic transition...
July 3, 2019: Nature
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