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Chromosome-level genome assembly of a parent species of widely cultivated azaleas.

Fu-Sheng Yang, Shuai Nie, Hui Liu, Tian-Le Shi, Xue-Chan Tian, Shan-Shan Zhou, Yu-Tao Bao, Kai-Hua Jia, Jing-Fang Guo, Wei Zhao, Na An, Ren-Gang Zhang, Quan-Zheng Yun, Xin-Zhu Wang, Chanaka Mannapperuma, Ilga Porth, Yousry Aly El-Kassaby, Nathaniel Robert Street, Xiao-Ru Wang, Yves Van de Peer, Jian-Feng Mao,

Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly for Rhododendron simsii, the primary ancestor of azalea cultivars. Genome analyses unveil the remnants of an ancient whole-genome duplication preceding the radiation of most Ericaceae, likely contributing ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5269]

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Direct C(sp2)-H alkylation of unactivated arenes enabled by photoinduced Pd catalysis.

Daeun Kim, Geun Seok Lee, Dongwook Kim, Soon Hyeok Hong,

Despite the fundamental importance of efficient and selective synthesis of widely useful alkylarenes, the direct catalytic C(sp2)-H alkylation of unactivated arenes with a readily available alkyl halide remains elusive. Here, we report the catalytic C(sp2)-H alkylation reactions of unactivated arenes with alkyl bromides via visible-light induced Pd catalysis. The reaction ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5266]

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Solution-processable integrated CMOS circuits based on colloidal CuInSe2 quantum dots.

Hyeong Jin Yun, Jaehoon Lim, Jeongkyun Roh, Darren Chi Jin Neo, Matt Law, Victor I Klimov,

The emerging technology of colloidal quantum dot electronics provides an opportunity for combining the advantages of well-understood inorganic semiconductors with the chemical processability of molecular systems. So far, most research on quantum dot electronic devices has focused on materials based on Pb- and Cd chalcogenides. In addition to environmental concerns ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5280]

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Structural basis of heterotetrameric assembly and disease mutations in the human cis-prenyltransferase complex.

Michal Lisnyansky Bar-El, Pavla Vaňková, Adva Yeheskel, Luba Simhaev, Hamutal Engel, Petr Man, Yoni Haitin, Moshe Giladi,

The human cis-prenyltransferase (hcis-PT) is an enzymatic complex essential for protein N-glycosylation. Synthesizing the precursor of the glycosyl carrier dolichol-phosphate, mutations in hcis-PT cause severe human diseases. Here, we reveal that hcis-PT exhibits a heterotetrameric assembly in solution, consisting of two catalytic dehydrodolichyl diphosphate synthase (DHDDS) and inactive Nogo-B receptor ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5273]

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The structure of a red-shifted photosystem I reveals a red site in the core antenna.

Hila Toporik, Anton Khmelnitskiy, Zachary Dobson, Reece Riddle, Dewight Williams, Su Lin, Ryszard Jankowiak, Yuval Mazor,

Photosystem I coordinates more than 90 chlorophylls in its core antenna while achieving near perfect quantum efficiency. Low energy chlorophylls (also known as red chlorophylls) residing in the antenna are important for energy transfer dynamics and yield, however, their precise location remained elusive. Here, we construct a chimeric Photosystem I ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5279]

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Automated microfluidic platform for dynamic and combinatorial drug screening of tumor organoids.

Brooke Schuster, Michael Junkin, Sara Saheb Kashaf, Isabel Romero-Calvo, Kori Kirby, Jonathan Matthews, Christopher R Weber, Andrey Rzhetsky, Kevin P White, Savaş Tay,

Three-dimensional (3D) cell culture technologies, such as organoids, are physiologically relevant models for basic and clinical applications. Automated microfluidics offers advantages in high-throughput and precision analysis of cells but is not yet compatible with organoids. Here, we present an automated, high-throughput, microfluidic 3D organoid culture and analysis system to facilitate ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5271]

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Pearl millet genomic vulnerability to climate change in West Africa highlights the need for regional collaboration.

Bénédicte Rhoné, Dimitri Defrance, Cécile Berthouly-Salazar, Cédric Mariac, Philippe Cubry, Marie Couderc, Anaïs Dequincey, Aichatou Assoumanne, Ndjido Ardo Kane, Benjamin Sultan, Adeline Barnaud, Yves Vigouroux,

Climate change is already affecting agro-ecosystems and threatening food security by reducing crop productivity and increasing harvest uncertainty. Mobilizing crop diversity could be an efficient way to mitigate its impact. We test this hypothesis in pearl millet, a nutritious staple cereal cultivated in arid and low-fertility soils in sub-Saharan Africa. ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5274]

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Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA.

Gulfem D Guler, Yuhong Ning, Chin-Jen Ku, Tierney Phillips, Erin McCarthy, Christopher K Ellison, Anna Bergamaschi, Francois Collin, Paul Lloyd, Aaron Scott, Michael Antoine, Wendy Wang, Kim Chau, Alan Ashworth, Stephen R Quake, Samuel Levy,

Pancreatic cancer is often detected late, when curative therapies are no longer possible. Here, we present non-invasive detection of pancreatic ductal adenocarcinoma (PDAC) by 5-hydroxymethylcytosine (5hmC) changes in circulating cell free DNA from a PDAC cohort (n = 64) in comparison with a non-cancer cohort (n = 243). Differential hydroxymethylation is found in thousands ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5270]

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Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance.

Malte Herold, Susana Martínez Arbas, Shaman Narayanasamy, Abdul R Sheik, Luise A K Kleine-Borgmann, Laura A Lebrun, Benoît J Kunath, Hugo Roume, Irina Bessarab, Rohan B H Williams, John D Gillece, James M Schupp, Paul S Keim, Christian Jäger, Michael R Hoopmann, Robert L Moritz, Yuzhen Ye, Sujun Li, Haixu Tang, Anna Heintz-Buschart, Patrick May, Emilie E L Muller, Cedric C Laczny, Paul Wilmes,

The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5281]

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A pyridinic Fe-N4 macrocycle models the active sites in Fe/N-doped carbon electrocatalysts.

Travis Marshall-Roth, Nicole J Libretto, Alexandra T Wrobel, Kevin J Anderton, Michael L Pegis, Nathan D Ricke, Troy Van Voorhis, Jeffrey T Miller, Yogesh Surendranath,

Iron- and nitrogen-doped carbon (Fe-N-C) materials are leading candidates to replace platinum catalysts for the oxygen reduction reaction (ORR) in fuel cells; however, their active site structures remain poorly understood. A leading postulate is that the iron-containing active sites exist primarily in a pyridinic Fe-N4 ligation environment, yet, molecular model ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5283]

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The ultrafast onset of exciton formation in 2D semiconductors.

Chiara Trovatello, Florian Katsch, Nicholas J Borys, Malte Selig, Kaiyuan Yao, Rocio Borrego-Varillas, Francesco Scotognella, Ilka Kriegel, Aiming Yan, Alex Zettl, P James Schuck, Andreas Knorr, Giulio Cerullo, Stefano Dal Conte,

The equilibrium and non-equilibrium optical properties of single-layer transition metal dichalcogenides (TMDs) are determined by strongly bound excitons. Exciton relaxation dynamics in TMDs have been extensively studied by time-domain optical spectroscopies. However, the formation dynamics of excitons following non-resonant photoexcitation of free electron-hole pairs have been challenging to directly probe ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5277]

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Hsc70/Stub1 promotes the removal of individual oxidatively stressed peroxisomes.

Bo-Hua Chen, Yao-Jen Chang, Steven Lin, Wei Yuan Yang,

Peroxisomes perform beta-oxidation of branched and very-long chain fatty acids, which leads to the formation of reactive oxygen species (ROS) within the peroxisomal lumen. Peroxisomes are therefore prone to ROS-mediated damages. Here, using light to specifically and acutely induce ROS formation within the peroxisomal lumen, we find that cells individually ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5267]

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Whole blood immunophenotyping uncovers immature neutrophil-to-VD2 T-cell ratio as an early marker for severe COVID-19.

Guillaume Carissimo, Weili Xu, Immanuel Kwok, Mohammad Yazid Abdad, Yi-Hao Chan, Siew-Wai Fong, Kia Joo Puan, Cheryl Yi-Pin Lee, Nicholas Kim-Wah Yeo, Siti Naqiah Amrun, Rhonda Sin-Ling Chee, Wilson How, Stephrene Chan, Bingwen Eugene Fan, Anand Kumar Andiappan, Bernett Lee, Olaf Rötzschke, Barnaby Edward Young, Yee-Sin Leo, David Chien Lye, Laurent Renia, Lai Guan Ng, Anis Larbi, Lisa Fp Ng,

SARS-CoV-2 is the novel coronavirus responsible for the current COVID-19 pandemic. Severe complications are observed only in a small proportion of infected patients but the cellular mechanisms underlying this progression are still unknown. Comprehensive flow cytometry of whole blood samples from 54 COVID-19 patients reveals a dramatic increase in the ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5243]

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ATP hydrolysis by yeast Hsp104 determines protein aggregate dissolution and size in vivo.

Udhayabhaskar Sathyanarayanan, Marina Musa, Peter Bou Dib, Nuno Raimundo, Ira Milosevic, Anita Krisko,

Signs of proteostasis failure often entwine with those of metabolic stress at the cellular level. Here, we study protein sequestration during glucose deprivation-induced ATP decline in Saccharomyces cerevisiae. Using live-cell imaging, we find that sequestration of misfolded proteins and nascent polypeptides into two distinct compartments, stress granules, and Q-bodies, is ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5226]

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Genome-wide screens identify Toxoplasma gondii determinants of parasite fitness in IFNγ-activated murine macrophages.

Yifan Wang, Lamba Omar Sangaré, Tatiana C Paredes-Santos, Musa A Hassan, Shruthi Krishnamurthy, Anna M Furuta, Benedikt M Markus, Sebastian Lourido, Jeroen P J Saeij,

Macrophages play an essential role in the early immune response against Toxoplasma and are the cell type preferentially infected by the parasite in vivo. Interferon gamma (IFNγ) elicits a variety of anti-Toxoplasma activities in macrophages. Using a genome-wide CRISPR screen we identify 353 Toxoplasma genes that determine parasite fitness in ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5258]

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Defining the impact of dietary macronutrient balance on PCOS traits.

Valentina Rodriguez Paris, Samantha M Solon-Biet, Alistair M Senior, Melissa C Edwards, Reena Desai, Nicodemus Tedla, Madeleine J Cox, William L Ledger, Robert B Gilchrist, Stephen J Simpson, David J Handelsman, Kirsty A Walters,

Lifestyle, mainly dietary, interventions are first-line treatment for women with polycystic ovary syndrome (PCOS), but the optimal diet remains undefined. We combined a hyperandrogenized PCOS mouse model with a systematic macronutrient approach, to elucidate the impact of dietary macronutrients on the development of PCOS. We identify that an optimum dietary macronutrient balance ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5262]

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16.8% Monolithic all-perovskite triple-junction solar cells via a universal two-step solution process.

Junke Wang, Valerio Zardetto, Kunal Datta, Dong Zhang, Martijn M Wienk, René A J Janssen,

Perovskite semiconductors hold a unique promise in developing multijunction solar cells with high-efficiency and low-cost. Besides design constraints to reduce optical and electrical losses, integrating several very different perovskite absorber layers in a multijunction cell imposes a great processing challenge. Here, we report a versatile two-step solution process for high-quality ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5254]

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Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2.

Xue Huang, Wei Sun, Zhi Cheng, Minxuan Chen, Xueyan Li, Jiuyu Wang, Gang Sheng, Weimin Gong, Yanli Wang,

To understand how the RuvC catalytic domain of Class 2 Cas proteins cleaves DNA, it will be necessary to elucidate the structures of RuvC-containing Cas complexes in their catalytically competent states. Cas12i2 is a Class 2 type V-I CRISPR-Cas endonuclease that cleaves target dsDNA by an unknown mechanism. Here, we ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5241]

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Single-shot stereo-polarimetric compressed ultrafast photography for light-speed observation of high-dimensional optical transients with picosecond resolution.

Jinyang Liang, Peng Wang, Liren Zhu, Lihong V Wang,

Simultaneous and efficient ultrafast recording of multiple photon tags contributes to high-dimensional optical imaging and characterization in numerous fields. Existing high-dimensional optical imaging techniques that record space and polarization cannot detect the photon's time of arrival owing to the limited speeds of the state-of-the-art electronic sensors. Here, we overcome this ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5252]

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A bacterial endophyte exploits chemotropism of a fungal pathogen for plant colonization.

Davide Palmieri, Stefania Vitale, Giuseppe Lima, Antonio Di Pietro, David Turrà,

Soil-inhabiting fungal pathogens use chemical signals released by roots to direct hyphal growth towards the host plant. Whether other soil microorganisms exploit this capacity for their own benefit is currently unknown. Here we show that the endophytic rhizobacterium Rahnella aquatilis locates hyphae of the root-infecting fungal pathogen Fusarium oxysporum through ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5264]

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The protein translation machinery is expressed for maximal efficiency in Escherichia coli.

Xiao-Pan Hu, Hugo Dourado, Peter Schubert, Martin J Lercher,

Protein synthesis is the most expensive process in fast-growing bacteria. Experimentally observed growth rate dependencies of the translation machinery form the basis of powerful phenomenological growth laws; however, a quantitative theory on the basis of biochemical and biophysical constraints is lacking. Here, we show that the growth rate-dependence of the ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5260]

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Mutations associated with neuropsychiatric conditions delineate functional brain connectivity dimensions contributing to autism and schizophrenia.

Clara A Moreau, Sebastian G W Urchs, Kumar Kuldeep, Pierre Orban, Catherine Schramm, Guillaume Dumas, Aurélie Labbe, Guillaume Huguet, Elise Douard, Pierre-Olivier Quirion, Amy Lin, Leila Kushan, Stephanie Grot, David Luck, Adrianna Mendrek, Stephane Potvin, Emmanuel Stip, Thomas Bourgeron, Alan C Evans, Carrie E Bearden, Pierre Bellec, Sebastien Jacquemont,

16p11.2 and 22q11.2 Copy Number Variants (CNVs) confer high risk for Autism Spectrum Disorder (ASD), schizophrenia (SZ), and Attention-Deficit-Hyperactivity-Disorder (ADHD), but their impact on functional connectivity (FC) remains unclear. Here we report an analysis of resting-state FC using magnetic resonance imaging data from 101 CNV carriers, 755 individuals with idiopathic ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5272]

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Single-cell transcriptomics identifies divergent developmental lineage trajectories during human pituitary development.

Shu Zhang, Yueli Cui, Xinyi Ma, Jun Yong, Liying Yan, Ming Yang, Jie Ren, Fuchou Tang, Lu Wen, Jie Qiao,

The anterior pituitary gland plays a central role in regulating various physiological processes, including body growth, reproduction, metabolism and stress response. Here, we perform single-cell RNA-sequencing (scRNA-seq) of 4113 individual cells from human fetal pituitaries. We characterize divergent developmental trajectories with distinct transitional intermediate states in five hormone-producing cell lineages. ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5275]

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Author Correction: Loss of MTX2 causes mandibuloacral dysplasia and links mitochondrial dysfunction to altered nuclear morphology.

Sahar Elouej, Karim Harhouri, Morgane Le Mao, Genevieve Baujat, Sheela Nampoothiri, Hϋlya Kayserili, Nihal Al Menabawy, Laila Selim, Arianne Llamos Paneque, Christian Kubisch, Davor Lessel, Robert Rubinsztajn, Chayki Charar, Catherine Bartoli, Coraline Airault, Jean-François Deleuze, Agnes Rötig, Peter Bauer, Catarina Pereira, Abigail Loh, Nathalie Escande-Beillard, Antoine Muchir, Lisa Martino, Yosef Gruenbaum, Song-Hua Lee, Philippe Manivet, Guy Lenaers, Bruno Reversade, Nicolas Lévy, Annachiara De Sandre-Giovannoli,

An amendment to this paper has been published and can be accessed via a link at the top of the paper. ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5349]

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A streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics.

Pan Fang, Yanlong Ji, Ivan Silbern, Carmen Doebele, Momchil Ninov, Christof Lenz, Thomas Oellerich, Kuan-Ting Pan, Henning Urlaub,

Regulation of protein N-glycosylation is essential in human cells. However, large-scale, accurate, and site-specific quantification of glycosylation is still technically challenging. We here introduce SugarQuant, an integrated mass spectrometry-based pipeline comprising protein aggregation capture (PAC)-based sample preparation, multi-notch MS3 acquisition (Glyco-SPS-MS3) and a data-processing tool (GlycoBinder) that enables confident identification ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5268]

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