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https://read.qxmd.com/read/31101908/author-correction-evolutionary-history-resolves-global-organization-of-root-functional-traits
#1
Zeqing Ma, Dali Guo, Xingliang Xu, Mingzhen Lu, Richard D Bardgett, David M Eissenstat, M Luke McCormack, Lars O Hedin
We thank reader Joseph Craine for pointing out three inadvertent errors in this Letter. First, 4 of the 71 divergence dates extracted from ref. 1 of this Amendment and used in Fig. 1b of the original Letter were overestimated. The correct values are 45 million years ago (Ma) for Apocynaceae, 51 Ma for Anacardiaceae, 40 Ma for Primulaceae, and 53 Ma for Amaryllidaceae. These errors had little influence on the overall trend of Fig. 1b (r2 is now 0.48 rather than 0.54, with no change to P < 0.001) and do not change our conclusion and inferences...
May 17, 2019: Nature
https://read.qxmd.com/read/31092928/transcriptional-cofactors-display-specificity-for-distinct-types-of-core-promoters
#2
Vanja Haberle, Cosmas D Arnold, Michaela Pagani, Martina Rath, Katharina Schernhuber, Alexander Stark
Transcriptional cofactors (COFs) communicate regulatory cues from enhancers to promoters and are central effectors of transcription activation and gene expression1 . Although some COFs have been shown to prefer certain promoter types2-5 over others (for example, see refs 6,7 ), the extent to which different COFs display intrinsic specificities for distinct promoters is unclear. Here we use a high-throughput promoter-activity assay in Drosophila melanogaster S2 cells to screen 23 COFs for their ability to activate 72,000 candidate core promoters (CPs)...
May 15, 2019: Nature
https://read.qxmd.com/read/31092927/mapping-hiv-prevalence-in-sub-saharan-africa-between-2000-and-2017
#3
Laura Dwyer-Lindgren, Michael A Cork, Amber Sligar, Krista M Steuben, Kate F Wilson, Naomi R Provost, Benjamin K Mayala, John D VanderHeide, Michael L Collison, Jason B Hall, Molly H Biehl, Austin Carter, Tahvi Frank, Dirk Douwes-Schultz, Roy Burstein, Daniel C Casey, Aniruddha Deshpande, Lucas Earl, Charbel El Bcheraoui, Tamer H Farag, Nathaniel J Henry, Damaris Kinyoki, Laurie B Marczak, Molly R Nixon, Aaron Osgood-Zimmerman, David Pigott, Robert C Reiner, Jennifer M Ross, Lauren E Schaeffer, David L Smith, Nicole Davis Weaver, Kirsten E Wiens, Jeffrey W Eaton, Jessica E Justman, Alex Opio, Benn Sartorius, Frank Tanser, Njeri Wabiri, Peter Piot, Christopher J L Murray, Simon I Hay
HIV/AIDS is a leading cause of disease burden in sub-Saharan Africa. Existing evidence has demonstrated that there is substantial local variation in the prevalence of HIV; however, subnational variation has not been investigated at a high spatial resolution across the continent. Here we explore within-country variation at a 5 × 5-km resolution in sub-Saharan Africa by estimating the prevalence of HIV among adults (aged 15-49 years) and the corresponding number of people living with HIV from 2000 to 2017...
May 15, 2019: Nature
https://read.qxmd.com/read/31092926/epigenetic-evolution-and-lineage-histories-of-chronic-lymphocytic-leukaemia
#4
Federico Gaiti, Ronan Chaligne, Hongcang Gu, Ryan M Brand, Steven Kothen-Hill, Rafael C Schulman, Kirill Grigorev, Davide Risso, Kyu-Tae Kim, Alessandro Pastore, Kevin Y Huang, Alicia Alonso, Caroline Sheridan, Nathaniel D Omans, Evan Biederstedt, Kendell Clement, Lili Wang, Joshua A Felsenfeld, Erica B Bhavsar, Martin J Aryee, John N Allan, Richard Furman, Andreas Gnirke, Catherine J Wu, Alexander Meissner, Dan A Landau
Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary course of cancer1 . Chronic lymphocytic leukaemia (CLL) is a highly informative model for cancer evolution as it undergoes substantial genetic diversification and evolution after therapy2,3 . The CLL epigenome is also an important disease-defining feature4,5 , and growing populations of cells in CLL diversify by stochastic changes in DNA methylation known as epimutations6 . However, previous studies using bulk sequencing methods to analyse the patterns of DNA methylation were unable to determine whether epimutations affect CLL populations homogeneously...
May 15, 2019: Nature
https://read.qxmd.com/read/31092925/progenitors-from-the-central-nervous-system-drive-neurogenesis-in-cancer
#5
Philippe Mauffrey, Nicolas Tchitchek, Vilma Barroca, Alexis Bemelmans, Virginie Firlej, Yves Allory, Paul-Henri Roméo, Claire Magnon
Autonomic nerve fibres in the tumour microenvironment regulate cancer initiation and dissemination, but how nerves emerge in tumours is currently unknown. Here we show that neural progenitors from the central nervous system that express doublecortin (DCX+ ) infiltrate prostate tumours and metastases, in which they initiate neurogenesis. In mouse models of prostate cancer, oscillations of DCX+ neural progenitors in the subventricular zone-a neurogenic area of the central nervous system-are associated with disruption of the blood-brain barrier, and with the egress of DCX+ cells into the circulation...
May 15, 2019: Nature
https://read.qxmd.com/read/31092924/mitochondrial-fragmentation-drives-selective-removal-of-deleterious-mtdna-in-the-germline
#6
Toby Lieber, Swathi P Jeedigunta, Jonathan M Palozzi, Ruth Lehmann, Thomas R Hurd
Mitochondria contain their own genomes that, unlike nuclear genomes, are inherited only in the maternal line. Owing to a high mutation rate and low levels of recombination of mitrochondrial DNA (mtDNA), special selection mechanisms exist in the female germline to prevent the accumulation of deleterious mutations1-5 . However, the molecular mechanisms that underpin selection are poorly understood6 . Here we visualize germline selection in Drosophila using an allele-specific fluorescent in situ-hybridization approach to distinguish wild-type from mutant mtDNA...
May 15, 2019: Nature
https://read.qxmd.com/read/31092923/cavity-quantum-electrodynamics-with-atom-like-mirrors
#7
Mohammad Mirhosseini, Eunjong Kim, Xueyue Zhang, Alp Sipahigil, Paul B Dieterle, Andrew J Keller, Ana Asenjo-Garcia, Darrick E Chang, Oskar Painter
It has long been recognized that atomic emission of radiation is not an immutable property of an atom, but is instead dependent on the electromagnetic environment1 and, in the case of ensembles, also on the collective interactions between the atoms2-6 . In an open radiative environment, the hallmark of collective interactions is enhanced spontaneous emission-super-radiance2 -with non-dissipative dynamics largely obscured by rapid atomic decay7 . Here we observe the dynamical exchange of excitations between a single artificial atom and an entangled collective state of an atomic array9 through the precise positioning of artificial atoms realized as superconducting qubits8 along a one-dimensional waveguide...
May 15, 2019: Nature
https://read.qxmd.com/read/31092922/targeting-the-cbm-complex-causes-t-reg-cells-to-prime-tumours-for-immune-checkpoint-therapy
#8
Mauro Di Pilato, Edward Y Kim, Bruno L Cadilha, Jasper N Prüßmann, Mazen N Nasrallah, Davide Seruggia, Shariq M Usmani, Sandra Misale, Valentina Zappulli, Esteban Carrizosa, Vinidhra Mani, Matteo Ligorio, Ross D Warner, Benjamin D Medoff, Francesco Marangoni, Alexandra-Chloe Villani, Thorsten R Mempel
Solid tumours are infiltrated by effector T cells with the potential to control or reject them, as well as by regulatory T (Treg ) cells that restrict the function of effector T cells and thereby promote tumour growth1 . The anti-tumour activity of effector T cells can be therapeutically unleashed, and is now being exploited for the treatment of some forms of human cancer. However, weak tumour-associated inflammatory responses and the immune-suppressive function of Treg cells remain major hurdles to broader effectiveness of tumour immunotherapy2 ...
May 15, 2019: Nature
https://read.qxmd.com/read/31092921/tracing-the-origin-of-adult-intestinal-stem-cells
#9
Jordi Guiu, Edouard Hannezo, Shiro Yui, Samuel Demharter, Svetlana Ulyanchenko, Martti Maimets, Anne Jørgensen, Signe Perlman, Lene Lundvall, Linn Salto Mamsen, Agnete Larsen, Rasmus H Olesen, Claus Yding Andersen, Lea Langhoff Thuesen, Kristine Juul Hare, Tune H Pers, Konstantin Khodosevich, Benjamin D Simons, Kim B Jensen
Adult intestinal stem cells are located at the bottom of crypts of Lieberkühn, where they express markers such as LGR51,2 and fuel the constant replenishment of the intestinal epithelium1 . Although fetal LGR5-expressing cells can give rise to adult intestinal stem cells3,4 , it remains unclear whether this population in the patterned epithelium represents unique intestinal stem-cell precursors. Here we show, using unbiased quantitative lineage-tracing approaches, biophysical modelling and intestinal transplantation, that all cells of the mouse intestinal epithelium-irrespective of their location and pattern of LGR5 expression in the fetal gut tube-contribute actively to the adult intestinal stem cell pool...
May 15, 2019: Nature
https://read.qxmd.com/read/31092920/distinct-modes-of-cell-competition-shape-mammalian-tissue-morphogenesis
#10
Stephanie J Ellis, Nicholas C Gomez, John Levorse, Aaron F Mertz, Yejing Ge, Elaine Fuchs
Cell competition-the sensing and elimination of less fit 'loser' cells by neighbouring 'winner' cells-was first described in Drosophila. Although cell competition has been proposed as a selection mechanism to optimize tissue and organ development, its evolutionary generality remains unclear. Here, by using live imaging, lineage tracing, single-cell transcriptomics and genetics, we identify two cell competition mechanisms that sequentially shape and maintain the architecture of stratified tissue during skin development in mice...
May 15, 2019: Nature
https://read.qxmd.com/read/31092919/an-apical-hypoxic-niche-sets-the-pace-of-shoot-meristem-activity
#11
Daan A Weits, Alicja B Kunkowska, Nicholas C W Kamps, Katharina M S Portz, Niko K Packbier, Zoe Nemec Venza, Christophe Gaillochet, Jan U Lohmann, Ole Pedersen, Joost T van Dongen, Francesco Licausi
Complex multicellular organisms evolved on Earth in an oxygen-rich atmosphere1 ; their tissues, including stem-cell niches, require continuous oxygen provision for efficient energy metabolism2 . Notably, the maintenance of the pluripotent state of animal stem cells requires hypoxic conditions, whereas higher oxygen tension promotes cell differentiation3 . Here we demonstrate, using a combination of genetic reporters and in vivo oxygen measurements, that plant shoot meristems develop embedded in a low-oxygen niche, and that hypoxic conditions are required to regulate the production of new leaves...
May 15, 2019: Nature
https://read.qxmd.com/read/31092918/total-synthesis-of-escherichia-coli-with-a-recoded-genome
#12
Julius Fredens, Kaihang Wang, Daniel de la Torre, Louise F H Funke, Wesley E Robertson, Yonka Christova, Tiongsun Chia, Wolfgang H Schmied, Daniel L Dunkelmann, Václav Beránek, Chayasith Uttamapinant, Andres Gonzalez Llamazares, Thomas S Elliott, Jason W Chin
Nature uses 64 codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon-out of up to 6 synonyms-to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis...
May 15, 2019: Nature
https://read.qxmd.com/read/31089213/author-correction-photoredox-catalysis-using-infrared-light-via-triplet-fusion-upconversion
#13
Benjamin D Ravetz, Andrew B Pun, Emily M Churchill, Daniel N Congreve, Tomislav Rovis, Luis M Campos
In Fig. 1c of this Letter, the orange axis label of the graph should have read 'FDPP upconversion photoluminescence (AU)' instead of 'TTBP upconversion photoluminescence (AU)'. This has been corrected online.
May 15, 2019: Nature
https://read.qxmd.com/read/31089212/author-correction-metabolic-reprogramming-by-the-s-nitroso-coa-reductase-system-protects-against-kidney-injury
#14
Hua-Lin Zhou, Rongli Zhang, Puneet Anand, Colin T Stomberski, Zhaoxia Qian, Alfred Hausladen, Liwen Wang, Eugene P Rhee, Samir M Parikh, S Ananth Karumanchi, Jonathan S Stamler
Change history: In Fig. 1j of this Letter, one data point was inadvertently omitted from the graph for the acute kidney injury (AKI), double knockout (-/-), S-nitrosothiol (SNO) condition at a nitrosylation level of 25.9 pmol mg-1 and the statistical significance given of P = 0.0221 was determined by Fisher's test instead of P = 0.0032 determined by Tukey's test (with normalization for test-day instrument baseline). Figure 1 and its Source Data have been corrected online.
May 15, 2019: Nature
https://read.qxmd.com/read/31086338/publisher-correction-p53-regulation-of-ammonia-metabolism-through-urea-cycle-controls-polyamine-biosynthesis
#15
Le Li, Youxiang Mao, Lina Zhao, Lijia Li, Jinjun Wu, Mengjia Zhao, Wenjing Du, Li Yu, Peng Jiang
In Fig. 1c of this Letter, the labels p53+/+ and p53-/- were inadvertently swapped. The original figure has been corrected online.
May 14, 2019: Nature
https://read.qxmd.com/read/31086337/fidelity-benchmarks-for-two-qubit-gates-in-silicon
#16
W Huang, C H Yang, K W Chan, T Tanttu, B Hensen, R C C Leon, M A Fogarty, J C C Hwang, F E Hudson, K M Itoh, A Morello, A Laucht, A S Dzurak
Universal quantum computation will require qubit technology based on a scalable platform1 , together with quantum error correction protocols that place strict limits on the maximum infidelities for one- and two-qubit gate operations2,3 . Although various qubit systems have shown high fidelities at the one-qubit level4-10 , the only solid-state qubits manufactured using standard lithographic techniques that have demonstrated two-qubit fidelities near the fault-tolerance threshold6 have been in superconductor systems...
May 13, 2019: Nature
https://read.qxmd.com/read/31086336/molecular-recording-of-mammalian-embryogenesis
#17
Michelle M Chan, Zachary D Smith, Stefanie Grosswendt, Helene Kretzmer, Thomas M Norman, Britt Adamson, Marco Jost, Jeffrey J Quinn, Dian Yang, Matthew G Jones, Alex Khodaverdian, Nir Yosef, Alexander Meissner, Jonathan S Weissman
Ontogeny describes the emergence of complex multicellular organisms from single totipotent cells. This field is particularly challenging in mammals, owing to the indeterminate relationship between self-renewal and differentiation, variation in progenitor field sizes, and internal gestation in these animals. Here we present a flexible, high-information, multi-channel molecular recorder with a single-cell readout and apply it as an evolving lineage tracer to assemble mouse cell-fate maps from fertilization through gastrulation...
May 13, 2019: Nature
https://read.qxmd.com/read/31081500/publisher-correction-viral-and-metazoan-poxins-are-cgamp-specific-nucleases-that-restrict-cgas-sting-signalling
#18
James B Eaglesham, Youdong Pan, Thomas S Kupper, Philip J Kranzusch
In this Letter, Supplementary Fig. 1 was missing. This error has been corrected online.
May 13, 2019: Nature
https://read.qxmd.com/read/31073228/publisher-correction-resonant-electro-optic-frequency-comb
#19
Alfredo Rueda, Florian Sedlmeir, Madhuri Kumari, Gerd Leuchs, Harald G L Schwefel
Change history: In the Methods section of this Letter, there were formatting errors to the equations of motion using the Heisenberg picture; see accompanying Amendment for further details. This has been corrected online.
May 10, 2019: Nature
https://read.qxmd.com/read/31073227/publisher-correction-electron-magnetic-reconnection-without-ion-coupling-in-earth-s-turbulent-magnetosheath
#20
T D Phan, J P Eastwood, M A Shay, J F Drake, B U Ö Sonnerup, M Fujimoto, P A Cassak, M Øieroset, J L Burch, R B Torbert, A C Rager, J C Dorelli, D J Gershman, C Pollock, P S Pyakurel, C C Haggerty, Y Khotyaintsev, B Lavraud, Y Saito, M Oka, R E Ergun, A Retino, O Le Contel, M R Argall, B L Giles, T E Moore, F D Wilder, R J Strangeway, C T Russell, P A Lindqvist, W Magnes
Change history: In this Letter, the y-axis values in Fig. 3f should go from 4 to -8 (rather than from 4 to -4), the y-axis values in Fig. 3h should appear next to the major tick marks (rather than the minor ticks), and in Fig. 1b, the arrows at the top and bottom of the electron-scale current sheet were going in the wrong direction; these errors have been corrected online.
May 10, 2019: Nature
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