bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide associated study identifies NAC42-activated nitrate transporter conferring high nitrogen use efficiency in rice
Authors: Tang Weijie , Ye Jian , Yao Xiangmei , Zhao Pingzhi , Xuan Wei , Tian Yunlu , Zhang Yuanyan , Xu Shuang , An Hongzhou , Chen Gaoming , Yu Jun , Wu Wei , Ge Yuwei , Liu Xiaolan , Li Jin , Zhang Hanzhi , Zhao Yaqin , Yang Bing , Jiang Xingzhou , Peng Chao , Zhou Cong , Terzaghi William , Wang Chunming , Wan Jianmin 
Published: November 2019

AbstractOver-application of nitrogen fertilizer in fields has had a negative impact on both environment and human health. Domesticated rice varieties with high nitrogen use efficiency (NUE) reduce fertilizer for sustainable agriculture. Here, we perform genome-wide association analysis of a diverse rice population displaying extreme nitrogen-related phenotypes over three successive years in the field, and identify an elite haplotype of nitrate transporter OsNPF6.1HapB that enhances nitrate uptake and confers high NUE by increasing yield under low nitrogen supply. OsNPF6.1HapB differs in both the protein and promoter element with natural variations, which are differentially trans-activated by OsNAC42, a NUE-related transcription factor. The rare natural allele OsNPF6.1HapB, derived from variation in wild rice and selected for enhancing both NUE and yield, has been lost in 90.3% of rice varieties due to the increased application of fertilizer. Our discovery highlights this NAC42-NPF6.1 signaling cascade as a strategy for high NUE and yield breeding in rice.
Symmetry of molecular Rydberg states revealed by XUV transient absorption spectroscopy
Authors: Peng Peng , Marceau Claude , Hervé Marius , Corkum P. B. , Naumov A. Yu. , Villeneuve D. M. 
Published: November 2019

AbstractTransient absorption spectroscopy is utilized extensively for measurements of bound- and quasibound-state dynamics of atoms and molecules. The extension of this technique into the extreme ultraviolet (XUV) region with attosecond pulses has the potential to attain unprecedented time resolution. Here we apply this technique to aligned-in-space molecules. The XUV pulses are much shorter than the time during which the molecules remain aligned, typically$$<$$<100 fs. However, transient absorption is not an instantaneous probe, because long-lived coherences re-emit for picoseconds to nanoseconds. Due to dephasing of the rotational wavepacket, it is not clear if these coherences will be evident in the absorption spectrum, and whether the properties of the initial excitations will be preserved. We studied Rydberg states of N$${}_{2}$$2and O$${}_{2}$$2from 12 to 23 eV. We were able to determine the polarization direction of the electronic transitions, and hence identify the symmetry of the final states.
Global geochemical fingerprinting of plume intensity suggests coupling with the supercontinent cycle
Authors: Gamal EL Dien Hamed , Doucet Luc S. , Li Zheng-Xiang , Cox Grant , Mitchell Ross 
Published: November 2019

AbstractPlate tectonics and mantle plumes are two of the most fundamental solid-Earth processes that have operated through much of Earth history. For the past 300 million years, mantle plumes are known to derive mostly from two large low shear velocity provinces (LLSVPs) above the core-mantle boundary, referred to as the African and Pacific superplumes, but their possible connection with plate tectonics is debated. Here, we demonstrate that transition elements (Ni, Cr, and Fe/Mn) in basaltic rocks can be used to trace plume-related magmatism through Earth history. Our analysis indicates the presence of a direct relationship between the intensity of plume magmatism and the supercontinent cycle, suggesting a possible dynamic coupling between supercontinent and superplume events. In addition, our analysis shows a consistent sudden drop in MgO, Ni and Cr at ~3.2–3.0 billion years ago, possibly indicating an abrupt change in mantle temperature at the start of global plate tectonics.
Leishmania RNA virus exacerbates Leishmaniasis by subverting innate immunity via TLR3-mediated NLRP3 inflammasome inhibition
Authors: de Carvalho Renan V. H. , Lima-Junior Djalma S. , da Silva Marcus Vinícius G. , Dilucca Marisa , Rodrigues Tamara S. , Horta Catarina V. , Silva Alexandre L. N. , da Silva Patrick F. , Frantz Fabiani G. , Lorenzon Lucas B. , Souza Marcos Michel , Almeida Fausto , Cantanhêde Lilian M. , Ferreira Ricardo de Godoi M. , Cruz Angela K. , Zamboni Dario S. 
Published: November 2019

AbstractLeishmania RNA virus (LRV) is an important virulence factor associated with the development of mucocutaneous Leishmaniasis, a severe form of the disease. LRV-mediated disease exacerbation relies on TLR3 activation, but downstream mechanisms remain largely unexplored. Here, we combine human and mouse data to demonstrate that LRV triggers TLR3 and TRIF to induce type I IFN production, which induces autophagy. This process results in ATG5-mediated degradation of NLRP3 and ASC, thereby limiting NLRP3 inflammasome activation in macrophages. Consistent with the known restricting role of NLRP3 for Leishmania replication, the signaling pathway triggered by LRV results in increased parasite survival and disease progression. In support of this data, we find that lesions in patients infected with LRV+ Leishmania are associated with reduced inflammasome activation and the development of mucocutaneous disease. Our findings reveal the mechanisms triggered by LRV that contribute to the development of the debilitating mucocutaneous form of Leishmaniasis.
Deep ocean seascape and Pseudotanaidae (Crustacea: Tanaidacea) diversity at the Clarion-Clipperton Fracture Zone
Authors: Jakiel Aleksandra , Palero Ferran , Błażewicz Magdalena 
Published: November 2019

AbstractUnderstanding the diversity and spatial distribution of benthic species is fundamental to properly assess the impact of deep sea mining. Tanaidacea provide an exceptional opportunity for assessing spatial patterns in the deep-sea, given their low mobility and limited dispersal potential. The diversity and distribution of pseudotanaid species is characterized here for the Clarion and Clipperton Fractures Zone (CCZ), which is the most extensive deposit field of metallic nodules. Samples were taken from the Belgian, German and French license areas, but also from the APEI 3 (Area of Particular Environmental Interest 3) of the Interoceanmetal consortium associates. The combination of morphological and genetic data uncovered one new pseudotanaid genus (Beksitanais n. gen.) and 14 new species of Pseudotanais (2 of them virtual taxa). Moreover, our results suggest that spatial structuring of pseudotanaid diversity is correlated with deep-sea features, particularly the presence of fractures and seamount chains crossing the CCZ. The presence of geographical barriers delimiting species distributions has important implications for the establishment of protected areas, and the APEI3 protected area contains only one third of the total pseudotanaid species in CCZ. The specimen collection studied here is extremely valuable and represents an important first step in characterizing the diversity and distribution of pseudotanaids within the Tropical Eastern Pacific.
Methodological aspects of testing vestibular evoked myogenic potentials in infants at universal hearing screening program
Authors: Verrecchia Luca , Karpeta Niki , Westin Magnus , Johansson Ann , Aldenklint Sonny , Brantberg Krister , Duan Maoli 
Published: November 2019

AbstractMotor development in infants is dependent upon the function of the inner ear balance organ (vestibular organ). Vestibular failure causes motor delays in early infancy and suboptimal motor skills later on. A vestibular test for newborns and infants that is applicable on a large scale, safe and cost effective is in demand in various contexts: in the differential diagnosis of early onset hearing loss to determine forms associated with vestibular failure; in early hearing habilitation with cochlear implant, indicating the vestibular predominant side; and in the habilitation of children affected by motor skill disorders, revealing the contribution of a vestibular failure. This work explored the feasibility of cervical vestibular evoked myogenic potentials (VEMP) in conjunction with newborn universal hearing screening program. VEMP was measured after the hearing tests and was evoked by bone-conducted stimuli. Moreover, stimulus delivery was regulated by neck muscle activity, with infants rested unconstrained in their parents´ arms and with the head supported by the operator´s hand. This VEMP protocol showed a high level of feasibility in terms of test viability and result reproducibility. VEMP integrated into the newborn hearing screening program may represent a practical method for large-scale assessment of balance function in infants.
Serine substitutions are linked to codon usage and differ for variable and conserved protein regions
Authors: Schwartz Gregory W. , Shauli Tair , Linial Michal , Hershberg Uri 
Published: November 2019

AbstractSerine is the only amino acid that is encoded by two disjoint codon sets (TCN & AGY) so that a tandem substitution of two nucleotides is required to switch between the two sets. We show that these codon sets underlie distinct substitution patterns at positions subject to purifying and diversifying selections. We found that in humans, positions that are conserved among ~100 vertebrates, and thus subjected to purifying selection, are enriched for substitutions involving serine (TCN, denoted S′), proline, and alanine, (S′PA). In contrast, the less conserved positions are enriched for serine encoded with AGY codons (denoted S″), glycine and asparagine, (GS″N). We tested this phenomenon in the HIV envelope glycoprotein (gp120), and the V-gene that encodes B-cell receptors/antibodies. These fast evolving proteins both have hypervariable positions, which are under diversifying selection, closely adjacent to highly conserved structural regions. In both instances, we identified an opposite abundance of two groups of serine substitutions, with enrichment of S′PA in the conserved positions, and GS″N in the hypervariable regions. Finally, we analyzed the substitutions across 60,000 individual human exomes to show that, when serine has a specific functional constraint of phosphorylation capability, S′ codons are 32-folds less prone than S″ to substitutions to Threonine or Tyrosine that could potentially retain the phosphorylation site capacity. Combined, our results, that cover evolutionary signals at different temporal scales, demonstrate that through its encoding by two codon sets, serine allows for the existence of alternating substitution patterns within positions of functional maintenance versus sites of rapid diversification.
Treatment with etanercept and low monocyte concentration contribute to the risk of invasive aspergillosis in patients post allogeneic stem cell transplantation
Authors: Zoran Tamara , Weber Michael , Springer Jan , White P. Lewis , Bauer Joachim , Schober Annika , Löffler Claudia , Seelbinder Bastian , Hünniger Kerstin , Kurzai Oliver , Scherag André , Schäuble Sascha , Morton C. Oliver , Einsele Hermann , Linde Jörg , Löffler Jürgen 
Published: November 2019

AbstractInvasive aspergillosis (IA) is a life-threatening complication among allogeneic hematopoietic stem cell transplant (alloSCT) recipients. Despite well known risk factors and different available assays, diagnosis of invasive aspergillosis remains challenging. 103 clinical variables from patients with hematological malignancies and subsequent alloSCT were collected. Associations between collected variables and patients with (n = 36) and without IA (n = 36) were investigated by applying univariate and multivariable logistic regression. The predictive power of the final model was tested in an independent patient cohort (23 IA cases and 25 control patients). Findings were investigated further byin vitrostudies, which analysed the effect of etanercept onA. fumigatus-stimulated macrophages at the gene expression and cytokine secretion. Additionally, the release of C-X-C motif chemokine ligand 10 (CXCL10) in patient sera was studied. Low monocyte concentration (p = 4.8 × 10−06), severe GvHD of the gut (grade 2–4) (p = 1.08 × 10−02) and etanercept treatment of GvHD (p = 3.5 × 10−03) were significantly associated with IA. Our studies showed that etanercept lowers CXCL10 concentrationsin vitroandex vivoand down-regulates genes involved in immune responses and TNF-alpha signaling. Our study offers clinicians new information regarding risk factors for IA including low monocyte counts and administration of etanercept. After necessary validation, such information may be used for decision making regarding antifungal prophylaxis or closely monitoring patients at risk.
The SMYD3 methyltransferase promotes myogenesis by activating the myogenin regulatory network
Authors: Codato Roberta , Perichon Martine , Divol Arnaud , Fung Ella , Sotiropoulos Athanassia , Bigot Anne , Weitzman Jonathan B. , Medjkane Souhila 
Published: November 2019

AbstractThe coordinated expression of myogenic regulatory factors, including MyoD and myogenin, orchestrates the steps of skeletal muscle development, from myoblast proliferation and cell-cycle exit, to myoblast fusion and myotubes maturation. Yet, it remains unclear how key transcription factors and epigenetic enzymes cooperate to guide myogenic differentiation. Proteins of the SMYD (SET and MYND domain-containing) methyltransferase family participate in cardiac and skeletal myogenesis during development in zebrafish, Drosophila and mice. Here, we show that the mammalian SMYD3 methyltransferase coordinates skeletal muscle differentiation in vitro. Overexpression of SMYD3 in myoblasts promoted muscle differentiation and myoblasts fusion. Conversely, silencing of endogenous SMYD3 or its pharmacological inhibition impaired muscle differentiation. Genome-wide transcriptomic analysis of murine myoblasts, with silenced or overexpressed SMYD3, revealed that SMYD3 impacts skeletal muscle differentiation by targeting the key muscle regulatory factor myogenin. The role of SMYD3 in the regulation of skeletal muscle differentiation and myotube formation, partially via the myogenin transcriptional network, highlights the importance of methyltransferases in mammalian myogenesis.
Effective CRISPR interference of an endogenous gene via a single transgene in mice
Authors: MacLeod Ryan S. , Cawley Keisha M. , Gubrij Igor , Nookaew Intawat , Onal Melda , O’Brien Charles A. 
Published: November 2019

AbstractDrawbacks of conditional gene deletion in mice include the need for extensive breeding and, often, a lack of cell type-specificity. CRISPR interference (CRISPRi) is an alternative approach for loss-of-function studies that inhibits expression by guiding a transcriptional repressor to the transcription start-site of target genes. However, there has been limited exploration of CRISPRi in mice. We tested the effectiveness of a single CRISPRi transgene broadly expressing a single guide RNA and a catalytically dead Cas9 fused to the KRAB repressor domain to suppress a well-characterized target gene, Tnfsf11. The phenotype of CRISPRi transgenic mice was compared to mice with germline deletion of Tnfsf11, which are osteopetrotic and do not form lymph nodes. High transgene expression mimicked gene deletion, with failure of lymph node development and classic signs of osteopetrosis such as high bone mass and failure of tooth eruption. Mice with low transgene expression were normal and mice with medium expression displayed an intermediate phenotype. Transgene expression in tissues from these mice correlated inversely with Tnfsf11 mRNA levels. These results demonstrate that a single CRISPRi transgene can effectively suppress a target gene in mice and suggest that this approach may be useful for cell type-specific loss-of-function studies.
Effect of electric field on optoelectronic properties of indiene monolayer for photoelectric nanodevices
Authors: Singh Deobrat , Gupta Sanjeev K. , Lukačević Igor , Mužević Matko , Sonvane Yogesh , Ahuja Rajeev 
Published: November 2019

AbstractIn recent years, layered materials display interesting properties and the quest for new sorts of two-dimensional (2D) structures is a significance for future device manufacture. In this paper, we study electronic and optical properties of 2D indiene allotropes with planar and buckled structures. The optical properties calculations are based on density functional theory (DFT) simulations including in-plane and out-of-plane directions of light polarization. We indicate that the optical properties such as complex refractive index, absorption spectrum, electron energy loss function (EELS), reflectivity and optical conductivity spectra are strongly dependent on the direction of light’s polarization. High values and narrow peaks in optical spectra introduce indiene to the field of ultra-thin optical systems. The effect of external static electric field on electronic and optical properties of indiene is also observed and discussed. We show that the band gap in buckled indiene can be effectively changed by applying the external electric field. The discoveries here expand the group of 2D materials beyond graphene and transition metal dichalcogenides (TMDs) and give valuable data for future experimental realization of new mono-elemental materials with conceivable applications in optical devices.
Breakthrough in Marine Invertebrate Cell Culture: Sponge Cells Divide Rapidly in Improved Nutrient Medium
Authors: Conkling Megan , Hesp Kylie , Munroe Stephanie , Sandoval Kenneth , Martens Dirk E. , Sipkema Detmer , Wijffels Rene H. , Pomponi Shirley A. 
Published: November 2019

AbstractSponges (Phylum Porifera) are among the oldest Metazoa and considered critical to understanding animal evolution and development. They are also the most prolific source of marine-derived chemicals with pharmaceutical relevance. Cell lines are important tools for research in many disciplines, and have been established for many organisms, including freshwater and terrestrial invertebrates. Despite many efforts over multiple decades, there are still no cell lines for marine invertebrates. In this study, we report a breakthrough: we demonstrate that an amino acid-optimized nutrient medium stimulates rapid cell division in 9 sponge species. The fastest dividing cells doubled in less than 1 hour. Cultures of 3 species were subcultured from 3 to 5 times, with an average of 5.99 population doublings after subculturing, and a lifespan from 21 to 35 days. Our results form the basis for developing marine invertebrate cell models to better understand early animal evolution, determine the role of secondary metabolites, and predict the impact of climate change to coral reef community ecology. Furthermore, sponge cell lines can be used to scale-up production of sponge-derived chemicals for clinical trials and develop new drugs to combat cancer and other diseases.
Dissection of major cancer gene variants in subsets of circulating tumor cells in advanced breast cancer
Authors: D’Oronzo Stella , Lovero Domenica , Palmirotta Raffaele , Stucci Luigia Stefania , Tucci Marco , Felici Claudia , Cascardi Eliano , Giardina Carmela , Cafforio Paola , Silvestris Franco 
Published: November 2019

AbstractEnumeration of circulating tumor cells (CTCs) may reflect the metastatic potential of breast cancer (BC). By using the DEPArray, we investigated CTCs with respect to their epithelial-to-mesenchymal transition phenotype and compared their genomic heterogeneity with tissue biopsies. Seventeen stage IV BC patients were enrolled. Pre-enriched CTC suspensions were stained with fluorescent-labeled antibodies to epithelial (E) and mesenchymal (M) markers. CTC samples were processed by DEPArray system and clustered in relation to their markers. DNA from CTCs, as well as from primary tumor samples, was sequenced by next generation sequencing to assess the mutational state of 50 major cancer-related genes. We identified four different CTC subsets that harbored different gene variants. The most heterogenous CTC subsets included the M+/E− phenotype, which, however, expressed only 7 repeatedly mutated genes, while in the M−/E+ subset multiple mutations affected only 2 out of 50 genes. When matching all gene variants among CTC subsets, a small number of mutations was shared by only 4 genes, namely ATM, FGFR3, PIK3CA, and TP53 that, however, were absent in primary tumors. Our results postulate that the detected mutations in all CTC subsets may be considered as genomic markers of metastatic dissemination to be investigated during early stages of BC.
Untargeted histone profiling during naive conversion uncovers conserved modification markers between mouse and human
Authors: De Clerck Laura , Taelman Jasin , Popovic Mina , Willems Sander , Van der Jeught Margot , Heindryckx Björn , De Sutter Petra , Marks Hendrik , Deforce Dieter , Dhaenens Maarten 
Published: November 2019

AbstractRecent progress has enabled the conversion of primed human embryonic stem cells (hESCs) to the naive state of pluripotency, resembling the well-characterized naive mouse ESCs (mESCs). However, a thorough histone epigenetic characterization of this conversion process is currently lacking, while its likeness to the mouse model has not been clearly established. Here, we profile the histone epigenome of hESCs during conversion in a time-resolved experimental design, using an untargeted mass spectrometry-based approach. In total, 23 histone post-translational modifications (hPTMs) changed significantly over time. H3K27Me3 was the most prominently increasing marker hPTM in naive hESCs. This is in line with previous reports in mouse, prompting us to compare all the shared hPTM fold changes between mouse and human, revealing a set of conserved hPTM markers for the naive state. Principally, we present the first roadmap of the changing human histone epigenome during the conversion of hESCs from the primed to the naive state. This further revealed similarities with mouse, which hint at a conserved mammalian epigenetic signature of the ground state of pluripotency.
New insight into the mechanisms of ectopic fat deposition improvement after bariatric surgery
Authors: Angelini Giulia , Castagneto Gissey Lidia , Del Corpo Giulia , Giordano Carla , Cerbelli Bruna , Severino Anna , Manco Melania , Basso Nicola , Birkenfeld Andreas L. , Bornstein Stefan R. , Genco Alfredo , Mingrone Geltrude , Casella Giovanni 
Published: November 2019

AbstractNon-alcoholic fatty-liver disease (NAFLD) is frequent in obese patients and represents a major risk factor for the development of diabetes and its complications. Bariatric surgery reverses the hepatic features of NAFLD. However, its mechanism of action remains elusive. We performed a comprehensive analysis of the mechanism leading to the improvement of NAFLD and insulin resistance in both obese rodents and humans following sleeve-gastrectomy (SG). SG improved insulin sensitivity and reduced hepatic and monocyte fat accumulation. Importantly, fat accumulation in monocytes was well comparable to that in hepatocytes, suggesting that Plin2 levels in monocytes might be a non-invasive marker for the diagnosis of NAFLD. Both in vitro and in vivo studies demonstrated an effective metabolic regeneration of liver function and insulin sensitivity. Specifically, SG improved NAFLD significantly by enhancing AMP-activated protein kinase (AMPK) phosphorylation and chaperone-mediated autophagy (CMA) that translate into the removal of Plin2 coating lipid droplets. This led to an increase in lipolysis and specific amelioration of hepatic insulin resistance. Elucidating the mechanism of impaired liver metabolism in obese subjects will help to design new strategies for the prevention and treatment of NAFLD.