bluuebunny/crossref_metadata_2025_split huggingface dataset:
A stomatal safety-efficiency trade-off constrains responses to leaf dehydration
Authors: Henry Christian , John Grace P. , Pan Ruihua , Bartlett Megan K. , Fletcher Leila R. , Scoffoni Christine , Sack Lawren 
Published: July 2019

AbstractStomata, the microvalves on leaf surfaces, exert major influences across scales, from plant growth and productivity to global carbon and water cycling. Stomatal opening enables leaf photosynthesis, and plant growth and water use, whereas plant survival of drought depends on stomatal closure. Here we report that stomatal function is constrained by a safety-efficiency trade-off, such that species with greater stomatal conductance under high water availability (gmax) show greater sensitivity to closure during leaf dehydration, i.e., a higher leaf water potential at which stomatal conductance is reduced by 50% (Ψgs50). The gmax - Ψgs50 trade-off and its mechanistic basis is supported by experiments on leaves of California woody species, and in analyses of previous studies of the responses of diverse flowering plant species around the world. Linking the two fundamental key roles of stomata—the enabling of gas exchange, and the first defense against drought—this trade-off constrains the rates of water use and the drought sensitivity of leaves, with potential impacts on ecosystems.
Stimulation of CRISPR-mediated homology-directed repair by an engineered RAD18 variant
Authors: Nambiar Tarun S. , Billon Pierre , Diedenhofen Giacomo , Hayward Samuel B. , Taglialatela Angelo , Cai Kunheng , Huang Jen-Wei , Leuzzi Giuseppe , Cuella-Martin Raquel , Palacios Andrew , Gupta Anuj , Egli Dieter , Ciccia Alberto 
Published: July 2019

AbstractPrecise editing of genomic DNA can be achieved upon repair of CRISPR-induced DNA double-stranded breaks (DSBs) by homology-directed repair (HDR). However, the efficiency of this process is limited by DSB repair pathways competing with HDR, such as non-homologous end joining (NHEJ). Here we individually express in human cells 204 open reading frames involved in the DNA damage response (DDR) and determine their impact on CRISPR-mediated HDR. From these studies, we identify RAD18 as a stimulator of CRISPR-mediated HDR. By defining the RAD18 domains required to promote HDR, we derive an enhanced RAD18 variant (e18) that stimulates CRISPR-mediated HDR in multiple human cell types, including embryonic stem cells. Mechanistically, e18 induces HDR by suppressing the localization of the NHEJ-promoting factor 53BP1 to DSBs. Altogether, this study identifies e18 as an enhancer of CRISPR-mediated HDR and highlights the promise of engineering DDR factors to augment the efficiency of precision genome editing.
MAPCap allows high-resolution detection and differential expression analysis of transcription start sites
Authors: Bhardwaj Vivek , Semplicio Giuseppe , Erdogdu Niyazi Umut , Manke Thomas , Akhtar Asifa 
Published: July 2019

AbstractThe position, shape and number of transcription start sites (TSS) are critical determinants of gene regulation. Most methods developed to detect TSSs and study promoter usage are, however, of limited use in studies that demand quantification of expression changes between two or more groups. In this study, we combine high-resolution detection of transcription start sites and differential expression analysis using a simplified TSS quantification protocol, MAPCap (Multiplexed Affinity Purification of Capped RNA) along with the software icetea. Applying MAPCap on developing Drosophila melanogaster embryos and larvae, we detected stage and sex-specific promoter and enhancer activity and quantify the effect of mutants of maleless (MLE) helicase at X-chromosomal promoters. We observe that MLE mutation leads to a median 1.9 fold drop in expression of X-chromosome promoters and affects the expression of several TSSs with a sexually dimorphic expression on autosomes. Our results provide quantitative insights into promoter activity during dosage compensation.
The role of energy storage in deep decarbonization of electricity production
Authors: Arbabzadeh Maryam , Sioshansi Ramteen , Johnson Jeremiah X. , Keoleian Gregory A. 
Published: July 2019

AbstractDeep decarbonization of electricity production is a societal challenge that can be achieved with high penetrations of variable renewable energy. We investigate the potential of energy storage technologies to reduce renewable curtailment and CO2 emissions in California and Texas under varying emissions taxes. We show that without energy storage, adding 60 GW of renewables to California achieves 72% CO2 reductions (relative to a zero-renewables case) with close to one third of renewables being curtailed. Some energy storage technologies, on the other hand, allow 90% CO2 reductions from the same renewable penetrations with as little as 9% renewable curtailment. In Texas, the same renewable-deployment level leads to 54% emissions reductions with close to 3% renewable curtailment. Energy storage can allow 57% emissions reductions with as little as 0.3% renewable curtailment. We also find that generator flexibility can reduce curtailment and the amount of energy storage that is needed for renewable integration.
The late stage of COPI vesicle fission requires shorter forms of phosphatidic acid and diacylglycerol
Authors: Park Seung-Yeol , Yang Jia-Shu , Li Zhen , Deng Pan , Zhu Xiaohong , Young David , Ericsson Maria , Andringa Ruben L. H. , Minnaard Adriaan J. , Zhu Chunmei , Sun Fei , Moody D. Branch , Morris Andrew J. , Fan Jun , Hsu Victor W. 
Published: July 2019

AbstractStudies on vesicle formation by the Coat Protein I (COPI) complex have contributed to a basic understanding of how vesicular transport is initiated. Phosphatidic acid (PA) and diacylglycerol (DAG) have been found previously to be required for the fission stage of COPI vesicle formation. Here, we find that PA with varying lipid geometry can all promote early fission, but only PA with shortened acyl chains promotes late fission. Moreover, diacylglycerol (DAG) acts after PA in late fission, with this role of DAG also requiring shorter acyl chains. Further highlighting the importance of the short-chain lipid geometry for late fission, we find that shorter forms of PA and DAG promote the vesiculation ability of COPI fission factors. These findings advance a general understanding of how lipid geometry contributes to membrane deformation for vesicle fission, and also how proteins and lipids coordinate their actions in driving this process.
Continuous plate subduction marked by the rise of alkali magmatism 2.1 billion years ago
Authors: Liu He , Sun Wei-dong , Zartman Robert , Tang Ming 
Published: July 2019

AbstractOver the Earth’s evolutionary history, the style of plate subduction has evolved through time due to the secular cooling of the mantle. While continuous subduction is a typical feature of modern plate tectonics, a stagnant-lid tectonic regime with localized episodic subduction likely characterized the early Earth. The timing of the transition between these two subduction styles bears important insights into Earth’s cooling history. Here we apply a statistical analysis to a large geochemical dataset of mafic rocks spanning the last 3.5 Ga, which shows an increasing magnitude of alkali basaltic magmatism beginning at ca. 2.1 Ga. We propose that the rapid rise of continental alkali basalts correlates with an abruptly decreasing degree of mantle melting resulting from the enhanced cooling of the mantle at ca. 2.1 Ga. This might be a consequence of the initiation of continuous subduction, which recycled increasing volumes of cold oceanic crust into the mantle.
A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides
Authors: Chen Zhen-Lin , Meng Jia-Ming , Cao Yong , Yin Ji-Li , Fang Run-Qian , Fan Sheng-Bo , Liu Chao , Zeng Wen-Feng , Ding Yue-He , Tan Dan , Wu Long , Zhou Wen-Jing , Chi Hao , Sun Rui-Xiang , Dong Meng-Qiu , He Si-Min 
Published: July 2019

AbstractWe describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a two-stage open search strategy facilitated by fragment indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets, 15N metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art search engines. This systematic evaluation shows that pLink 2 outperforms these methods in precision and sensitivity, especially at proteome scales. Lastly, re-analysis of four published proteome-scale cross-linking datasets with pLink 2 required only a fraction of the time used by pLink 1, with up to 27% more cross-linked residue pairs identified. pLink 2 is therefore an efficient and reliable tool for cross-linking mass spectrometry analysis, and the systematic evaluation methods described here will be useful for future software development.
Catalytic enantioselective addition of organometallics to unprotected carboxylic acids
Authors: Yan Xingchen , Harutyunyan Syuzanna R. 
Published: July 2019

AbstractConjugate addition of organometallics to carbonyl based Michael acceptors is a widely used method that allows the building of new carbon-carbon (C-C) bonds and the introduction of chirality in a single step. However, conjugate additions to the simplest Michael acceptors, namely unprotected, unsaturated carboxylic acids, are considered to be prohibited by the fact that acid-base reactions overpower any other type of reactivity, including nucleophilic addition. Here we describe a transient protecting group strategy that allows efficient catalytic asymmetric additions of organomagnesium reagents to unprotected α,β-unsaturated carboxylic acids. This unorthodox pathway is achieved by preventing the formation of unreactive carboxylate salts by means of a reactive intermediate, allowing modifications of the carbon chain to proceed unhindered, while the stereochemistry is controlled with a chiral copper catalyst. A wide variety of β-chiral carboxylic acids, obtained with excellent enantioselectivities and yields, can be further transformed into valuable molecules through for instance catalytic decarboxylative cross-coupling reactions.
Modification of messenger RNA by 2′-O-methylation regulates gene expression in vivo
Authors: Elliott Brittany A. , Ho Hsiang-Ting , Ranganathan Srivathsan V. , Vangaveti Sweta , Ilkayeva Olga , Abou Assi Hala , Choi Alex K. , Agris Paul F. , Holley Christopher L. 
Published: July 2019

AbstractEpitranscriptomic modifications of mRNA are important regulators of gene expression. While internal 2′-O-methylation (Nm) has been discovered on mRNA, questions remain about its origin and function in cells and organisms. Here, we show that internal Nm modification can be guided by small nucleolar RNAs (snoRNAs), and that these Nm sites can regulate mRNA and protein expression. Specifically, two box C/D snoRNAs (SNORDs) and the 2′-O-methyltransferase fibrillarin lead to Nm modification in the protein-coding region of peroxidasin (Pxdn). The presence of Nm modification increases Pxdn mRNA expression but inhibits its translation, regulating PXDN protein expression and enzyme activity both in vitro and in vivo. Our findings support a model in which snoRNA-guided Nm modifications of mRNA can regulate physiologic gene expression by altering mRNA levels and tuning protein translation.
Profiling host ANP32A splicing landscapes to predict influenza A virus polymerase adaptation
Authors: Domingues Patricia , Eletto Davide , Magnus Carsten , Turkington Hannah L. , Schmutz Stefan , Zagordi Osvaldo , Lenk Matthias , Beer Martin , Stertz Silke , Hale Benjamin G. 
Published: July 2019

AbstractSpecies’ differences in cellular factors limit avian influenza A virus (IAV) zoonoses and human pandemics. The IAV polymerase, vPol, harbors evolutionary sites to overcome restriction and determines virulence. Here, we establish host ANP32A as a critical driver of selection, and identify host-specific ANP32A splicing landscapes that predict viral evolution. We find that avian species differentially express three ANP32A isoforms diverging in a vPol-promoting insert. ANP32As with shorter inserts interact poorly with vPol, are compromised in supporting avian-like IAV replication, and drive selection of mammalian-adaptive vPol sequences with distinct kinetics. By integrating selection data with multi-species ANP32A splice variant profiling, we develop a mathematical model to predict avian species potentially driving (swallow, magpie) or maintaining (goose, swan) mammalian-adaptive vPol signatures. Supporting these predictions, surveillance data confirm enrichment of several mammalian-adaptive vPol substitutions in magpie IAVs. Profiling host ANP32A splicing could enhance surveillance and eradication efforts against IAVs with pandemic potential.
Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung
Authors: Kordes Adrian , Preusse Matthias , Willger Sven D. , Braubach Peter , Jonigk Danny , Haverich Axel , Warnecke Gregor , Häussler Susanne 
Published: July 2019

AbstractPrevious studies have demonstrated substantial genetic diversification ofPseudomonas aeruginosaacross sub-compartments in cystic fibrosis (CF) lungs. Here, we isolateP. aeruginosafrom five different sampling areas in the upper and lower airways of an explanted CF lung, analyze ex vivo transcriptional profiles by RNA-seq, and use colony re-sequencing and deep population sequencing to determine the genetic diversity within and across the various sub-compartments. We find that, despite genetic variation, the ex vivo transcriptional profiles ofP. aeruginosapopulations inhabiting different regions of the CF lung are similar. Although we cannot estimate the extent to which the transcriptional response recorded here actually reflects the in vivo transcriptomes, our results indicate that there may be a common in vivo transcriptional profile in the CF lung environment.
Facile access to nitroarenes and nitroheteroarenes using N-nitrosaccharin
Authors: Calvo Roxan , Zhang Kun , Passera Alessandro , Katayev Dmitry 
Published: July 2019

AbstractNitroaromatics and nitroheteroaromatics serve as key building blocks and intermediates in synthesis, and form the core scaffold of a vast number of materials, dyes, explosives, agrochemicals and pharmaceuticals. However, their synthesis relies on harsh methodologies involving excess mineral acids, which present a number of critical drawbacks in terms of functional group compatibility and environmental impact. Modern, alternative strategies still suffer from significant limitations in terms of practicality, and a general protocol amenable to the direct C-H functionalization of a broad range of aromatics has remained elusive. Herein we introduce a bench-stable, inexpensive, easy to synthesize and recyclable nitrating reagent based on saccharin. This reagent acts as a controllable source of the nitronium ion, allowing mild and practical nitration of both arenes and heteroarenes displaying an exceptional functional group tolerance.
Impacts of air pollutants from rural Chinese households under the rapid residential energy transition
Authors: Shen Guofeng , Ru Muye , Du Wei , Zhu Xi , Zhong Qirui , Chen Yilin , Shen Huizhong , Yun Xiao , Meng Wenjun , Liu Junfeng , Cheng Hefa , Hu Jianying , Guan Dabo , Tao Shu 
Published: July 2019

AbstractRural residential energy consumption in China is experiencing a rapid transition towards clean energy, nevertheless, solid fuel combustion remains an important emission source. Here we quantitatively evaluate the contribution of rural residential emissions to PM2.5 (particulate matter with an aerodynamic diameter less than 2.5 μm) and the impacts on health and climate. The clean energy transitions result in remarkable reductions in the contributions to ambient PM2.5, avoiding 130,000 (90,000–160,000) premature deaths associated with PM2.5 exposure. The climate forcing associated with this sector declines from 0.057 ± 0.016 W/m2 in 1992 to 0.031 ± 0.008 W/m2 in 2012. Despite this, the large remaining quantities of solid fuels still contributed 14 ± 10 μg/m3 to population-weighted PM2.5 in 2012, which comprises 21 ± 14% of the overall population-weighted PM2.5 from all sources. Rural residential emissions affect not only rural but urban air quality, and the impacts are highly seasonal and location dependent.
Genomic Features of High-Priority Salmonella enterica Serovars Circulating in the Food Production Chain, Brazil, 2000–2016
Authors: Monte Daniel F. , Lincopan Nilton , Berman Hanna , Cerdeira Louise , Keelara Shivaramu , Thakur Siddhartha , Fedorka-Cray Paula J. , Landgraf Mariza 
Published: July 2019

AbstractMultidrug-resistant (MDR) Salmonella enterica has been deemed a high-priority pathogen by the World Health Organization. Two hundred and sixty-four Salmonella enterica isolates recovered over a 16-year period (2000 to 2016) from the poultry and swine production chains, in Brazil, were investigated by whole-genome sequencing (WGS). Most international lineages belonging to 28 serovars, including, S. enterica serovars S. Schwarzengrund ST96, S. Typhimurium ST19, S. Minnesota ST548, S. Infantis ST32, S. Heidelberg ST15, S. Newport ST45, S. Brandenburg ST65 and S. Kentucky ST198 displayed MDR and virulent genetic backgrounds. In this regard, resistome analysis revealed presence of qnrE1 (identified for the first time in S. Typhimurium from food chain), qnrB19, qnrS1, blaCTX-M-8, blaCTX-M-2 and blaCMY-2 genes, as well as gyrA mutations; whereas ColpVC, IncHI2A, IncHI2, IncFIA, Incl1, IncA/C2, IncR, IncX1 and po111 plasmids were detected. In addition, phylogenetic analysis revealed multiple independent lineages such as S. enterica serovars S. Infantis, S. Schwarzengrund, S. Minnesota, S. Kentucky and S. Brandenburg. In brief, ocurrence and persistence of international lineages of S. enterica serovars in food production chain is supported by conserved genomes and wide virulome and resistome.
Cooperative and distinct functions of MK2 and MK3 in the regulation of the macrophage transcriptional response to lipopolysaccharide
Authors: Ehlting Christian , Rex Julia , Albrecht Ute , Deenen René , Tiedje Christopher , Köhrer Karl , Sawodny Oliver , Gaestel Matthias , Häussinger Dieter , Bode Johannes Georg 
Published: July 2019

AbstractThe p38MAPK downstream targets MAPKAP kinases (MK) 2 and 3 are critical for the regulation of the macrophage response to LPS. The extents to which these two kinases act cooperatively and distinctly in regulating LPS-induced inflammatory cytokine expression are still unclear. To address this uncertainty, whole transcriptome analyses were performed using bone marrow-derived macrophages (BMDM) generated from MK2−/− or MK2/3−/− animals and their wild-type littermates. The results suggest that in BMDM, MK2 and MK3 not only cooperatively regulate the transcript expression of signaling intermediates, including IL-10, IL-19, CXCL2 and the IL-4 receptor (IL-4R)α subunit, they also exert distinct regulatory effects on the expression of specific transcripts. Based on the differential regulation of gene expression by MK2 and MK3, at least six regulatory patterns were identified. Importantly, we confirmed our previous finding, which showed that in the absence of MK2, MK3 negatively regulates IFN-β. Moreover, this genome-wide analysis identified the regulation of Cr1A, NOD1 and Serpina3f as similar to that of IFN-β. In the absence of MK2, MK3 also delayed the nuclear translocation of NFκB by delaying the ubiquitination and subsequent degradation of IκBβ, reflecting the substantial plasticity of the response of BMDM to LPS.
Fast long-term denudation rate of steep alpine headwalls inferred from cosmogenic 36Cl depth profiles
Authors: Mair David , Lechmann Alessandro , Yesilyurt Serdar , Tikhomirov Dmitry , Delunel Romain , Vockenhuber Christof , Akçar Naki , Schlunegger Fritz 
Published: July 2019

AbstractQuantifications of in-situ denudation rates on vertical headwalls, averaged over millennia, have been thwarted because of inaccessibility. Here, we benefit from a tunnel crossing a large and vertical headwall in the European Alps (Eiger), where we measured concentrations of in-situ cosmogenic 36Cl along five depth profiles linking the tunnel with the headwall surface. Isotopic concentrations of 36Cl are low in surface samples, but high at depth relative to expectance for their position. The results of Monte-Carlo modelling attribute this pattern to inherited nuclides, young minimum exposure ages and to fast average denudation rates during the last exposure. These rates are consistently high across the Eiger and range from 45 ± 9 cm kyr−1 to 356 ± 137 cm kyr−1 (1σ) for the last centuries to millennia. These high rates together with the large inheritance point to a mechanism where denudation has been accomplished by frequent, cm-scale rock fall paired with chemical dissolution of limestone.
Systemic arterial hypertension leads to decreased semen quality and alterations in the testicular microcirculation in rats
Authors: Colli Lucas Giglio , Belardin Larissa Berloffa , Echem Cinthya , Akamine Eliana Hiromi , Antoniassi Mariana Pereira , Andretta Rhayza Roberta , Mathias Lucas Solla , Rodrigues Stephen Fernandes de Paula , Bertolla Ricardo Pimenta , de Carvalho Maria Helena Catelli 
Published: July 2019

AbstractArterial hypertension is a cardiovascular disease that leads to important systemic alterations and drastically impairs normal organ function over time. Hypertension affects around 700 million men of reproductive age and hypertensive men present increased risk for reproductive disorders, such as erectile dysfunction. However, the link between arterial hypertension and male reproductive disorders is associative at best. Moreover, many studies have reported associations between decreased male fertility and/or semen quality and alterations to general male health. In this study we aim to investigate the effect of systemic high blood pressure in sperm quality, sperm functional characteristics and testicular physiology in a rat model. Hypertensive rats presented altered testicular morphology – mainly vascular alterations and impaired testicular vasomotion. Hypertensive rats also presented decrease in sperm concentration, DNA integrity and increased percentages of sperm with dysfunctional mitochondria, intracellular superoxide anion activity and abnormal morphology. This study provides mechanistic insights by which arterial hypertension affects the testes, evidencing the testes as another target organ for hypertension as well as its impact on sperm quality.