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Machinery that guides immunity p.442

The peptide-loading complex is key to the initiation of an immune response that raises killer T cells in vertebrates. Its structure has now been determined, and might provide information that improves immune protection.

doi: 10.1038/d41586-017-07268-8

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Thunderous nuclear reactions p.443

The discovery that thunderstorms can trigger nuclear reactions provides insight into the physics of atmospheric electricity and unveils a previously unknown natural source of radioactive isotopes on Earth.

doi: 10.1038/d41586-017-07266-w

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How T cells spot tumour cells p.444

Immunotherapy can reawaken T cells to destroy tumour cells. Modelling of tumour and T-cell interactions suggests why certain tumour cells are targeted and improves predictions of immunotherapy outcome.

doi: 10.1038/d41586-017-07267-9

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Crowdsourcing Earth's microbes p.446

A large-scale study has been assessing microbial diversity by analysing DNA sequences from samples submitted by scientists around the globe. The initial results are now being used to create an open-access resource. See Article p.457

Jeroen Raes

doi: 10.1038/nature24756

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Super-reactive catalyst for bond cleavage p.447

Carbon–hydrogen bonds in organic molecules can be cut to install other chemical groups on the carbon atom, but these reactions have been limited. A catalytic palladium complex opens up fresh opportunities.

doi: 10.1038/d41586-017-07270-0

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Layered-up regulation in the developing brain p.448

Modification of messenger RNAs through a process called m6A methylation facilitates dynamic temporal regulation of RNA levels in neural precursor cells, enabling fine-tuning of developing neuronal circuits in the brain.

doi: 10.1038/d41586-017-07269-7

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Articles

A communal catalogue reveals Earth’s multiscale microbial diversity OPEN p.457

As phase 1 of the Earth Microbiome Project, analysis of 16S ribosomal RNA sequences from more than 27,000 environmental samples delivers a global picture of the basic structure and drivers of microbial distribution.

Luke R. Thompson, Jon G. Sanders, Daniel McDonald, Amnon Amir, Joshua Ladau, Kenneth J. Locey, Robert J. Prill, Anupriya Tripathi, Sean M. Gibbons, Gail Ackermann + et al.

doi: 10.1038/nature24621

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Visualization of chemical modifications in the human 80S ribosome structure p.472

A high-resolution structure of the human ribosome determined by cryo-electron microscopy visualizes numerous RNA modifications that are concentrated at functional sites with an extended shell, and suggests the possibility of designing more specific ribosome-targeting drugs.

S. Kundhavai Natchiar, Alexander G. Myasnikov, Hanna Kratzat, Isabelle Hazemann & Bruno P. Klaholz

doi: 10.1038/nature24482

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Letters

Photonuclear reactions triggered by lightning discharge p.481

Ground-based observations during a thunderstorm provide conclusive evidence of positrons being produced after lightning, confirming that lightning can trigger photonuclear reactions.

Teruaki Enoto, Yuuki Wada, Yoshihiro Furuta, Kazuhiro Nakazawa, Takayuki Yuasa, Kazufumi Okuda, Kazuo Makishima, Mitsuteru Sato, Yousuke Sato, Toshio Nakano + et al.

doi: 10.1038/nature24630

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Photonic quantum state transfer between a cold atomic gas and a crystal p.485

In a step towards hybrid quantum networks, a quantum state can be transferred between two fundamentally different systems—a cold atomic ensemble and a solid-state crystal—by a single photon.

Nicolas Maring, Pau Farrera, Kutlu Kutluer, Margherita Mazzera, Georg Heinze & Hugues de Riedmatten

doi: 10.1038/nature24468

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Hydrogen-bearing iron peroxide and the origin of ultralow-velocity zones p.494

A reaction between iron and water at the high pressure and temperature of the lowermost mantle is described that produces hydrogen-bearing iron peroxide, which has the properties expected of the ultralow-velocity zones at Earth’s core–mantle boundary.

Jin Liu, Qingyang Hu, Duck Young Kim, Zhongqing Wu, Wenzhong Wang, Yuming Xiao, Paul Chow, Yue Meng, Vitali B. Prakapenka, Ho-Kwang Mao + et al.

doi: 10.1038/nature24461

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Genome sequence of the progenitor of the wheat D genome Aegilops tauschii OPEN p.498

Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat1 (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat2–4. The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence5. Here we use an array of advanced technologies, including orderedclone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a reference-quality genome sequence for Ae. tauschii ssp. strangulata accession AL8/78, which is closely related to the wheat D genome. We show that compared to other sequenced plant genomes, including a much larger conifer genome, the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences. Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes. The decay of colinearity with other grass genomes correlates with recombination rates along chromosomes. We propose that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution.

Ming-Cheng Luo, Yong Q. Gu, Daniela Puiu, Hao Wang, Sven O. Twardziok, Karin R. Deal, Naxin Huo, Tingting Zhu, Le Wang, Yi Wang + et al.

doi: 10.1038/nature24486

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Quantitative microbiome profiling links gut community variation to microbial load p.507

Quantitive microbiome profiling reveals that total microbial load is an important determinant of enterotypes and may be a key driver of microbiota alterations in patients with Crohn’s disease.

Doris Vandeputte, Gunter Kathagen, Kevin D’hoe, Sara Vieira-Silva, Mireia Valles-Colomer, João Sabino, Jun Wang, Raul Y. Tito, Lindsey De Commer, Youssef Darzi + et al.

doi: 10.1038/nature24460

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Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer p.512

The analysis of T-cell antigens in long-term survivors of pancreatic ductal adenocarcinoma suggests that neoantigen immunogenicity and quality, not purely quantity, correlate with survival.

Vinod P. Balachandran, Marta Łuksza, Julia N. Zhao, Vladimir Makarov, John Alec Moral, Romain Remark, Brian Herbst, Gokce Askan, Umesh Bhanot, Yasin Senbabaoglu + et al.

doi: 10.1038/nature24462

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A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy p.517

An immune fitness model for tumours under checkpoint blockade immunotherapy is proposed, through which the authors show that the presentation and recognition properties of dominant neoantigens distributed over tumour subclones are predictive of response in melanoma and lung cancer cohorts.

Marta Łuksza, Nadeem Riaz, Vladimir Makarov, Vinod P. Balachandran, Matthew D. Hellmann, Alexander Solovyov, Naiyer A. Rizvi, Taha Merghoub, Arnold J. Levine, Timothy A. Chan + et al.

doi: 10.1038/nature24473

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Structure of the human MHC-I peptide-loading complex p.525

Electron cryo-microscopy structures of the human peptide-loading complex shed light on its operation and on the onset of adaptive immune responses.

Andreas Blees, Dovile Januliene, Tommy Hofmann, Nicole Koller, Carla Schmidt, Simon Trowitzsch, Arne Moeller & Robert Tampé

doi: 10.1038/nature24627

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