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Nature Communications

Bert Wuyts, Alan R Champneys, Joanna I House
This corrects the article DOI: 10.1038/ncomms15519.
February 21, 2018: Nature Communications
Jack Rivers-Auty, Michael J D Daniels, Isaac Colliver, David L Robertson, David Brough
The interleukin-1 (IL-1) receptor and ligand families are components of the immune system. Knowledge of their evolutionary history is essential to understand their function. Using chromosomal anatomy and sequence similarity, we show that IL-1 receptor family members are related and nine members are likely formed from duplication and modification of a proto-IL-1R1 receptor. The IL-1 ligands have a different evolutionary history. The first proto-IL-1β gene coincided with proto-IL-1R1 and duplication events resulted in the majority of IL-1 ligand family members...
March 20, 2018: Nature Communications
Nazmul Haque, Ryota Ouda, Chao Chen, Keiko Ozato, J Robert Hogg
Control of type I interferon production is crucial to combat infection while preventing deleterious inflammatory responses, but the extent of the contribution of post-transcriptional mechanisms to innate immune regulation is unclear. Here, we show that human zinc finger RNA-binding protein (ZFR) represses the interferon response by regulating alternative pre-mRNA splicing. ZFR expression is tightly controlled during macrophage development; monocytes express truncated ZFR isoforms, while macrophages induce full-length ZFR to modulate macrophage-specific alternative splicing...
March 20, 2018: Nature Communications
Sean D Workman, Liam J Worrall, Natalie C J Strynadka
Undecaprenyl pyrophosphate phosphatase (UppP) is an integral membrane protein that recycles the lipid carrier essential to the ongoing biosynthesis of the bacterial cell wall. Individual building blocks of peptidoglycan are assembled in the cytoplasm on undecaprenyl phosphate (C55-P) before being flipped to the periplasmic face, where they are polymerized and transferred to the existing cell wall sacculus, resulting in the side product undecaprenyl pyrophosphate (C55-PP). Interruption of UppP's regeneration of C55-P from C55-PP leads to the buildup of cell wall intermediates and cell lysis...
March 20, 2018: Nature Communications
Charles M Denby, Rachel A Li, Van T Vu, Zak Costello, Weiyin Lin, Leanne Jade G Chan, Joseph Williams, Bryan Donaldson, Charles W Bamforth, Christopher J Petzold, Henrik V Scheller, Hector Garcia Martin, Jay D Keasling
Flowers of the hop plant provide both bitterness and "hoppy" flavor to beer. Hops are, however, both a water and energy intensive crop and vary considerably in essential oil content, making it challenging to achieve a consistent hoppy taste in beer. Here, we report that brewer's yeast can be engineered to biosynthesize aromatic monoterpene molecules that impart hoppy flavor to beer by incorporating recombinant DNA derived from yeast, mint, and basil. Whereas metabolic engineering of biosynthetic pathways is commonly enlisted to maximize product titers, tuning expression of pathway enzymes to affect target production levels of multiple commercially important metabolites without major collateral metabolic changes represents a unique challenge...
March 20, 2018: Nature Communications
Andrea Castelli, Joost de Graaf, Sergio Marras, Rosaria Brescia, Luca Goldoni, Liberato Manna, Milena P Arciniegas
Colloidal nanocrystals can self-assemble into highly ordered superlattices. Recent studies have focused on changing their morphology by tuning the nanocrystal interactions via ligand-based surface modification for simple particle shapes. Here we demonstrate that this principle is transferable to and even enriched in the case of a class of branched nanocrystals made of a CdSe core and eight CdS pods, so-called octapods. Through careful experimental analysis, we show that the octapods have a heterogeneous ligand distribution, resembling a cone wrapping the individual pods...
March 20, 2018: Nature Communications
Jeffrey S Mugridge, Ryan W Tibble, Marcin Ziemniak, Jacek Jemielity, John D Gross
The conserved decapping enzyme Dcp2 recognizes and removes the 5' eukaryotic cap from mRNA transcripts in a critical step of many cellular RNA decay pathways. Dcp2 is a dynamic enzyme that functions in concert with the essential activator Dcp1 and a diverse set of coactivators to selectively and efficiently decap target mRNAs in the cell. Here we present a 2.84 Å crystal structure of K. lactis Dcp1-Dcp2 in complex with coactivators Edc1 and Edc3, and with substrate analog bound to the Dcp2 active site. Our structure shows how Dcp2 recognizes cap substrate in the catalytically active conformation of the enzyme, and how coactivator Edc1 forms a three-way interface that bridges the domains of Dcp2 to consolidate the active conformation...
March 20, 2018: Nature Communications
Jenna M Reinen, Oliver Y Chén, R Matthew Hutchison, B T Thomas Yeo, Kevin M Anderson, Mert R Sabuncu, Dost Öngür, Joshua L Roffman, Jordan W Smoller, Justin T Baker, Avram J Holmes
Higher-order cognition emerges through the flexible interactions of large-scale brain networks, an aspect of temporal coordination that may be impaired in psychosis. Here, we map the dynamic functional architecture of the cerebral cortex in healthy young adults, leveraging this atlas of transient network configurations (states), to identify state- and network-specific disruptions in patients with schizophrenia and psychotic bipolar disorder. We demonstrate that dynamic connectivity profiles are reliable within participants, and can act as a fingerprint, identifying specific individuals within a larger group...
March 20, 2018: Nature Communications
Masayuki Kondo, Kazuhito Ichii, Prabir K Patra, Joseph G Canadell, Benjamin Poulter, Stephen Sitch, Leonardo Calle, Yi Y Liu, Albert I J M van Dijk, Tazu Saeki, Nobuko Saigusa, Pierre Friedlingstein, Almut Arneth, Anna Harper, Atul K Jain, Etsushi Kato, Charles Koven, Fang Li, Thomas A M Pugh, Sönke Zaehle, Andy Wiltshire, Frederic Chevallier, Takashi Maki, Takashi Nakamura, Yosuke Niwa, Christian Rödenbeck
An integrated understanding of the biogeochemical consequences of climate extremes and land use changes is needed to constrain land-surface feedbacks to atmospheric CO2 from associated climate change. Past assessments of the global carbon balance have shown particularly high uncertainty in Southeast Asia. Here, we use a combination of model ensembles to show that intensified land use change made Southeast Asia a strong source of CO2 from the 1980s to 1990s, whereas the region was close to carbon neutral in the 2000s due to an enhanced CO2 fertilization effect and absence of moderate-to-strong El Niño events...
March 20, 2018: Nature Communications
Keith S Jennings, Taylor S Winchell, Ben Livneh, Noah P Molotch
Despite the importance of precipitation phase to global hydroclimate simulations, many land surface models use spatially uniform air temperature thresholds to partition rain and snow. Here we show, through the analysis of a 29-year observational dataset (n = 17.8 million), that the air temperature at which rain and snow fall in equal frequency varies significantly across the Northern Hemisphere, averaging 1.0 °C and ranging from -0.4 to 2.4 °C for 95% of the stations. Continental climates generally exhibit the warmest rain-snow thresholds and maritime the coolest...
March 20, 2018: Nature Communications
Honghai Zhang, Thomas L Delworth
Precipitation is characterized by substantial natural variability, including on regional and decadal scales. This relatively large variability poses a grand challenge in assessing the significance of anthropogenically forced precipitation changes. Here we use multiple large ensembles of climate change experiments to evaluate whether, on regional scales, anthropogenic changes in decadal precipitation mean state are distinguishable. Here, distinguishable means the anthropogenic change is outside the range expected from natural variability...
March 20, 2018: Nature Communications
Maxim Karpov, Martin H P Pfeiffer, Junqiu Liu, Anton Lukashchuk, Tobias J Kippenberg
Dissipative Kerr solitons (DKS) in optical microresonators provide a highly miniaturised, chip-integrated frequency comb source with unprecedentedly high repetition rates and spectral bandwidth. To date, such frequency comb sources have been successfully applied in the optical telecommunication band for dual-comb spectroscopy, coherent telecommunications, counting of optical frequencies and distance measurements. Yet, the range of applications could be significantly extended by operating in the near-infrared spectral domain, which is a prerequisite for biomedical and Raman imaging applications, and hosts commonly used optical atomic transitions...
March 20, 2018: Nature Communications
S E de Graaf, L Faoro, J Burnett, A A Adamyan, A Ya Tzalenchuk, S E Kubatkin, T Lindström, A V Danilov
Noise and decoherence due to spurious two-level systems located at material interfaces are long-standing issues for solid-state quantum devices. Efforts to mitigate the effects of two-level systems have been hampered by a lack of knowledge about their chemical and physical nature. Here, by combining dielectric loss, frequency noise and on-chip electron spin resonance measurements in superconducting resonators, we demonstrate that desorption of surface spins is accompanied by an almost tenfold reduction in the charge-induced frequency noise in the resonators...
March 20, 2018: Nature Communications
Sheng Li, Shiming Zhu, Qiangqiang Jia, Dongwei Yuan, Chonghua Ren, Kang Li, Suning Liu, Yingying Cui, Haigang Zhao, Yanghui Cao, Gangqi Fang, Daqi Li, Xiaoming Zhao, Jianzhen Zhang, Qiaoyun Yue, Yongliang Fan, Xiaoqiang Yu, Qili Feng, Shuai Zhan
Many cockroach species have adapted to urban environments, and some have been serious pests of public health in the tropics and subtropics. Here, we present the 3.38-Gb genome and a consensus gene set of the American cockroach, Periplaneta americana. We report insights from both genomic and functional investigations into the underlying basis of its adaptation to urban environments and developmental plasticity. In comparison with other insects, expansions of gene families in P. americana exist for most core gene families likely associated with environmental adaptation, such as chemoreception and detoxification...
March 20, 2018: Nature Communications
Andreas Fichtner, Werner Härdtle, Helge Bruelheide, Matthias Kunz, Ying Li, Goddert von Oheimb
Theory suggests that plant interactions at the neighbourhood scale play a fundamental role in regulating biodiversity-productivity relationships (BPRs) in tree communities. However, empirical evidence of this prediction is rare, as little is known about how neighbourhood interactions scale up to influence community BPRs. Here, using a biodiversity-ecosystem functioning experiment, we provide insights into processes underlying BPRs by demonstrating that diversity-mediated interactions among local neighbours are a strong regulator of productivity in species mixtures...
March 20, 2018: Nature Communications
Xiao-Lin Chou, Xiyue Wang, Zheng-Gang Zhang, Li Shen, Brian Zingg, Junxiang Huang, Wen Zhong, Lukas Mesik, Li I Zhang, Huizhong Whit Tao
Zona incerta (ZI) is a functionally mysterious subthalamic nucleus containing mostly inhibitory neurons. Here, we discover that GABAergic neurons in the rostral sector of ZI (ZIr) directly innervate excitatory but not inhibitory neurons in the dorsolateral and ventrolateral compartments of periaqueductal gray (PAG), which can drive flight and freezing behaviors respectively. Optogenetic activation of ZIr neurons or their projections to PAG reduces both sound-induced innate flight response and conditioned freezing response, while optogenetic suppression of these neurons enhances these defensive behaviors, likely through a mechanism of gain modulation...
March 20, 2018: Nature Communications
Daniel Maticzka, Ibrahim Avsar Ilik, Tugce Aktas, Rolf Backofen, Asifa Akhtar
RNA-binding proteins (RBPs) play important and essential roles in eukaryotic gene expression regulating splicing, localization, translation, and stability of mRNAs. We describe ultraviolet crosslinking and affinity purification (uvCLAP), an easy-to-use, robust, reproducible, and high-throughput method to determine in vivo targets of RBPs. uvCLAP is fast and does not rely on radioactive labeling of RNA. We investigate binding of 15 RBPs from fly, mouse, and human cells to test the method's performance and applicability...
March 20, 2018: Nature Communications
Shilpa N Raja, Xingchen Ye, Matthew R Jones, Liwei Lin, Sanjay Govindjee, Robert O Ritchie
Nanoscale stress sensing is of crucial importance to biomechanics and other fields. An ideal stress sensor would have a large dynamic range to function in a variety of materials spanning orders of magnitude of local stresses. Here we show that tetrapod quantum dots (tQDs) exhibit excellent sensing versatility with stress-correlated signatures in a multitude of polymers. We further show that tQDs exhibit pressure coefficients, which increase with decreasing polymer stiffness, and vary >3 orders of magnitude...
March 20, 2018: Nature Communications
Xuejuan Wang, Salar Ahmad, Zhihui Zhang, Jacques Côté, Gang Cai
The NuA4/TIP60 acetyltransferase complex is required for gene regulation, DNA repair and cell cycle progression. The limited structural information impeded understanding of NuA4/TIP60 assembly and regulatory mechanism. Here, we report the 4.7 Å cryo-electron microscopy (cryo-EM) structure of a NuA4/TIP60 TEEAA assembly (Tra1, Eaf1, Eaf5, actin and Arp4) and the 7.6 Å cryo-EM structure of a TEEAA-piccolo assembly (Esa1, Epl1, Yng2 and Eaf6). The Tra1 and Eaf1 constitute the assembly scaffold. The Eaf1 SANT domain tightly binds to the LBE and FATC domains of Tra1 by ionic interactions...
March 20, 2018: Nature Communications
David Elkouss, David Pérez-García
Most communication channels are subjected to noise. One of the goals of information theory is to add redundancy in the transmission of information so that the information is transmitted reliably and the amount of information transmitted through the channel is as large as possible. The maximum rate at which reliable transmission is possible is called the capacity. If the channel does not keep memory of its past, the capacity is given by a simple optimization problem and can be efficiently computed. The situation of channels with memory is less clear...
March 20, 2018: Nature Communications
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