bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial arrangement and biofertilizers enhance the performance of legume – millet intercropping system in rainfed areas of southern India
Authors: Singh Devesh , Mathimaran Natarajan , Sekar Jegan , Ramalingam Prabavathy Vaiyapuri , Perisamy Yuvaraj , Raju Kathiravan , Raj Rengalakshmi , King Israel Oliver , Nanjundegowda Thimmegowda Matadadoddi , Narayanswamy Manjunatha Baiyapalli , Chikkegowda Bhavitha Nayakanahalli , Siddegowda Savitha Matakere , Bagyaraj Davis Joseph , Mäder Paul , Boller Thomas , Kahmen Ansgar 
Published: November 2020

AbstractBiofertilization via the inoculation with arbuscular mycorrhizal fungi (AMF), combined with rhizobia and plant growth promoting rhizobacteria (PGPR), are beginning to become established as an effective and sustainable measure to improve yields. Biofertilization might have a particular potential to boost the yield of intercropping systems in rainfed areas because AMF can form a common mycorrhizal network (CMN) that can transfer nutrients and water between two plants and balance as such belowground competition. In this study, we tested if biofertilizers can enhance the yield of intercropping systems using a pigeon pea (PP) – finger millet (FM) intercropping system grown for two consecutive growing seasons (2016/17 and 2017/18) at two contrasting sites in Bengaluru and Kolli Hills, India. To validate the process of bioirrigation (transfer of water between rhizosphere of two plants), we tested, for the first time, if the spatial arrangement of intercropped plants using either a row-wise or a mosaic design affected yield and water relations with and without biofertilizers. Our results demonstrate that intercropping can improve the straw and grain yield in PP–FM intercropping compared to the respective monocultures but that intercropping effects vary depending on the site characteristic such as climate and soil type. Spatial arrangement of component plants affected the total, straw and grain biomass in intercropping treatments, but this effect also varied across sites. Most importantly, the results from the 2017-18 growing season clearly demonstrated a positive effect of biofertilizer on biomass yield, and this effect was irrespective of site, spatial arrangement, mixed or monoculture. Despite a yield increase in intercropping, we did not see a positive effect of biofertilization on water relations of FM possibly due to interspecific competition for soil moisture where PP dominated. In summary, our study shows the potential of biofertilizers to increase the yield of intercropping systems in rainfed dryland agriculture.
A history of previous childbirths is linked to women’s white matter brain age in midlife and older age
Authors: Voldsbekk Irene , Barth Claudia , Maximov Ivan I. , Kaufmann Tobias , Beck Dani , Richard Geneviève , Moberget Torgeir , Westlye Lars T. , de Lange Ann-Marie G. 
Published: November 2020

AbstractMaternal brain adaptations occur in response to pregnancy, but little is known about how parity impacts white matter (WM) and WM ageing trajectories later in life. Utilising global and regional brain-age prediction based on multi-shell diffusion MRI data, we investigated the association between previous childbirths and WM brain age in 8,895 women in the UK Biobank cohort (age range = 54 - 81 years). The results showed that number of previous childbirths was negatively associated with WM brain age, potentially indicating a protective effect of parity on brain WM later in life. Both global WM and grey matter brain age estimates showed unique contributions to the association with previous childbirths, suggesting partly independent processes. Corpus callosum contributed uniquely to the global WM association with previous childbirths, and showed a stronger relationship relative to several other tracts. While our findings demonstrate a link between reproductive history and brain WM characteristics later in life, longitudinal studies are required to establish causality and determine how parity may influence women’s WM trajectories across the lifespan.
Determination of the fixed oil quality of ripepistacia lentiscusfruits andOpuntia-ficus indicaseeds
Authors: Kechidi Mohamed , Chalal Mohamed Anis , Bouzenad Amel , Gherib Asma , Touahri Brahim , Mustapha Mohamed Abou , Ourihene Mohamed 
Published: November 2020

AbstractPistacia lentiscusandOpuntia-ficus indicaare used in several fields, this study made it possible to highlight the determination of the oil quality from the fruits ofPistacia lentiscusand that of the seeds oil ofOpuntia-ficus indica, and this, by determining its physicochemical parameters such as acid value, saponification and insaponification value, iodine index, peroxyd value, as well as refraction index, humidity and their biochemical compositions, in particular the fatty acids (by CPG) from the samples of oils collected from the region of Khemis Miliana (Ain defla) and extracted by a mechanical method. The results show a quantitative difference between the oily samples in percentage of fatty acids. The contents of Oleic Acid, Linoleic Acid and Palmitic Acid are highest in the case of lentisk oil and are respectively 58.35%, 19.65%, 19.63%. However, the content of Linoleic Acid, Oleic Acid, Palmitic Acid and Stearic Acid are highest in the case of prickly pear and are respectively 63.74%, 21.30%, 10.17%, 3.58%.
Correcting for Superficial Bias in 7T Gradient Echo fMRI
Authors: Huang Pei , Correia Marta M. , Rua Catarina , Rodgers Christopher T. , Henson Richard N. , Carlin Johan D. 
Published: November 2020

1AbstractThe arrival of submillimetre ultra high-field fMRI makes it possible to compare activation profiles across cortical layers. However, the Blood Oxygenation Level Dependent (BOLD) signal measured by Gradient-Echo fMRI is biased towards superficial layers of the cortex, which is a serious confound for laminar analysis. Several univariate and multivariate analysis methods have been proposed to correct this bias. We compare these methods using computational simulations and example human 7T fMRI data from Regions-of-Interest (ROIs) during a visual attention paradigm. The simulations show that two methods - the ratio of ROI means across conditions and a novel application of Deming regression - offer the most robust correction for superficial bias. Deming regression has the additional advantage that it does not require that the conditions differ in their mean activation over voxels within an ROI. When applied to the example dataset, these methods suggest that attentional modulation of activation is similar across cortical layers within the ventral visual stream, despite a naïve activation-based analysis producing stronger modulation in superficial layers. Our study demonstrates that accurate correction of superficial bias is crucial to avoid drawing erroneous conclusions from laminar analyses of Gradient-Echo fMRI data.
Lysine methylation shields an intracellular pathogen from ubiquitylation
Authors: Engström Patrik , Burke Thomas P. , Iavarone Anthony T. , Welch Matthew D. 
Published: November 2020

AbstractMany intracellular pathogens avoid detection by their host cells. However, it remains unknown how they avoid being tagged by ubiquitin, an initial step leading to anti-microbial autophagy. Here, we show that the intracellular bacterial pathogenRickettsia parkeriuses two protein-lysine methyltransferases (PKMTs) to modify outer membrane proteins (OMPs) and prevent their ubiquitylation. Mutants deficient in the PKMTs were avirulent in mice and failed to grow in macrophages due to ubiquitylation and autophagy. Analysis of the lysine-methylome revealed that PKMTs modify a subset of OMPs by methylation at the same sites that are recognized by host ubiquitin. These findings show that lysine methylation is an essential determinant of rickettsial pathogenesis that shields bacterial proteins from ubiquitylation to evade autophagic targeting.
VirB, a key transcriptional regulator of virulence plasmid genes inShigella flexneri, forms DNA-binding site dependent foci in the bacterial cytoplasm
Authors: Socea Jillian N. , Bowman Grant R. , Wing Helen J. 
Published: November 2020

AbstractVirB is a key regulator of virulence genes located on the large virulence plasmid (pINV) of the bacterial pathogenShigella flexneri.VirB is unusual in that it is not related to other transcriptional regulators, instead, it belongs to a protein family that primarily functions in plasmid and chromosome partitioning; exemplified by ParB. Despite this, VirB does not function to segregate DNA, but rather counters transcriptional silencing of virulence genes mediated by the nucleoid structuring protein, H-NS. Since ParB localizes subcellularly as discrete foci in the bacterial cytoplasm, we chose to investigate the subcellular localization of VirB to gain novel insight into how VirB functions as a transcriptional anti-silencer. To do this, a GFP-VirB fusion that retains the regulatory activity of VirB and yet, does not undergo significant protein degradation in S.flexneri,was used. Surprisingly, discrete fluorescent foci were observed in live wild-type S.flexnericells and an isogenicvirBmutant using fluorescence microscopy. In contrast, foci were rarely observed (<10%) in cells cured of pINV. Moreover, in the context of the fusion, amino acid substitutions in the DNA binding domain of VirB resulted in the fluorescent signal becoming entirely diffuse. Combined, these data demonstrate that the VirB:DNA interactions required for the transcriptional anti-silencing activity of VirB on pINV are a prerequisite for the subcellular localization of VirB in the bacterial cytoplasm. The significance of these findings, in light of the anti-silencing activity of VirB, is discussed.ImportanceThis study reveals the subcellular localization of VirB, a key transcriptional regulator of virulence genes found on the large virulence plasmid inShigella.Fluorescent signals generated by an active GFP-VirB fusion form 2, 3, or 4 discrete foci in the bacterial cytoplasm, predominantly at the quarter cell position. These signals are completely dependent upon VirB interacting with its DNA binding site found either on the virulence plasmid or an engineered surrogate. Our findings: 1) provide novel insight into VirB:pINV interactions, 2) suggest that VirB may have utility as a DNA marker, and 3) raise questions about how and why this anti-silencing protein that controls virulence gene expression on pINV ofShigellaspp. forms discrete foci/hubs within the bacterial cytoplasm.
Harmonization of whole genome sequencing for outbreak surveillance of Enterobacteriaceae and Enterococci
Authors: Jamin Casper , de Koster Sien , van Koeveringe Stefanie , de Coninck Dieter , Mensaert Klaas , de Bruyne Katrien , Selva Natascha Perales , Lammens Christine , Goossens Herman , Hoebe Christian , Savelkoul Paul , van Alphen Lieke ,   and the i-4-1-Health Study Group
Published: November 2020

AbstractWhole genome sequencing (WGS), is becoming the facto standard for bacterial typing and outbreak surveillance of resistant bacterial pathogens. We performed a three-center ring trial to assert if inter-laboratory harmonization of WGS is achievable, for this goal. To this end, a set of 30 bacterial isolates comprising of various species belonging to the Enterobacteriaceae and Enterococcus genera were selected and sequenced using the same protocol on the Illumina MiSeq platform in each individual centre. All generated sequencing data was analysed by 1 centre using BioNumerics (6.7.3) for i) genotyping origin of replications & antimicrobial resistance genes, ii) core-genome (cgMLST) forE. coliandK. pneumoniae& whole-genome multi locus sequencing typing (wgMLST) for all species. Additionally, a split k-mer analysis was performed to determine the number of SNPs between samples. A precision of 99.0% and an accuracy of 99.2% was achieved for genotyping. Based on cgMLST, only in 2/27 and 3/15 comparisons a discrepant allele was called between two genomes, forE. coliandK. pneumonia,respectively. Based on wgMLST, the number of discrepant alleles ranged from 0 to 7 (average 1.6). For SNPs, this ranged from 0-11 SNPs (average 3.4). Furthermore, we demonstrate that using differentde novoassemblers to analyse the same dataset introduces up to 150 SNPs, which surpasses most thresholds for bacterial outbreaks. This shows the importance of harmonisation of data processing surveillance of bacterial outbreaks. Summarizing, multi-center WGS for bacterial surveillance is achievable, but only if protocols are harmonized.
Automatic Analysis of Bees’ Waggle Dance
Authors: Reece Jordan , Couvillon Margaret , Grüter Christoph , Ratnieks Francis , Reyes-Aldasoro Constantino Carlos 
Published: November 2020

AbstractThis work describe an algorithm for the automatic analysis of the waggle dance of honeybees. The algorithm analyses a video of a beehive with 13,624 frames, acquired at 25 frames/second. The algorithm employs the following traditional image processing steps:conversion to grayscale, low pass filtering, background subtraction, thresholding, tracking and clusteringto detect run of bees that perform waggle dances. The algorithm detected 44,530 waggle events, i.e. one bee waggling in one time frame, which were then clustered into 511waggle runs. Most of these were concentrated in one section of the hive. The accuracy of the tracking was 90% and a series of metrics like intra-dance variation in angle and duration were found to be consistent with literature. Whilst this algorithm was tested on a single video, the ideas and steps, which are simple as compared with Machine and Deep Learning techniques, should be attractive for researchers in this field who are not specialists in more complex techniques.
N6-methyladenosine (m6A) is an endogenous A3 adenosine receptor ligand
Authors: Ogawa Akiko , Nagiri Chisae , Shihoya Wataru , Inoue Asuka , Kawakami Kouki , Hiratsuka Suzune , Aoki Junken , Ito Yasuhiro , Suzuki Takeo , Suzuki Tsutomu , Inoue Toshihiro , Nureki Osamu , Tanihara Hidenobu , Tomizawa Kazuhito , Wei Fan-Yan 
Published: November 2020

SUMMARYAbout 150 post-transcriptional RNA modifications have been identified in all kingdoms of life. During RNA catabolism, most modified nucleosides are resistant to degradation and are released into the extracellular space. In this study, we explored the physiological role of these extracellular modified nucleosides and found thatN6-methyladenosine (m6A), widely known as an epigenetic mark in RNA, acts as a ligand for the adenosine A3 receptor, for which it has greater affinity than unmodified adenosine. Structural modeling defined the amino acids required for specific binding of m6A to the A3 receptor. m6A is dynamically released in response to cytotoxic stimuli and facilitates type I allergy. Our findings shed light on m6A as a signaling molecule with the ability to activate GPCRs, a previously unreported property of RNA modifications.
Public LC-Orbitrap-MS/MS Spectral Library for Metabolite Identification
Authors: Phapale Prasad , Palmer Andrew , Gathungu Rose Muthoni , Kale Dipali , Brügger Britta , Alexandrov Theodore 
Published: November 2020

ABSTRACTLiquid chromatography-mass spectrometry(LC-MS)-based untargeted metabolomics studies require high-quality spectral libraries for reliable metabolite identification. We have constructed EMBL-MCF, an open LC-MS/MS spectral library that currently contains over 1600 fragmentation spectra from 435 authentic standards of endogenous metabolites and lipids. The unique features of the library are presence of chromatographic profiles acquired with different LC-MS methods and coverage of different adduct ions. The library covers many biologically important metabolites with some unique metabolites and lipids as compared to other public libraries. The EMBL-MCF spectral library is created and shared using anin-housedeveloped web-application athttps://curatr.mcf.embl.de/. The library is freely available online and also integrated with other mass spectral repositories.
Lipidomic analysis of roseobacters of the pelagic RCA cluster and their response to phosphorus limitation
Authors: Silvano Eleonora , Yang Mingyu , Wolterink Mathias , Giebel Helge-Ansgar , Simon Meinhard , Scanlan David J , Zhao Yanlin , Chen Yin 
Published: November 2020

AbstractThe marine roseobacter-clade Affiliated cluster (RCA) represents one of the most abundant groups of bacterioplankton in the global oceans, particularly in temperate and sub-polar regions. They play a key role in the biogeochemical cycling of various elements and are important players in oceanic climate-active trace gas metabolism. In contrast to copiotrophic roseobacter counterparts such asRuegeria pomeroyiDSS-3 andPhaeobactersp. MED193, RCA bacteria are truly pelagic and have smaller genomes. We have previously shown that RCA bacteria do not appear to encode the PlcP-mediated lipid remodelling pathway, whereby marine heterotrophic bacteria remodel their membrane lipid composition in response to phosphorus (P) stress by substituting membrane glycerophospholipids with alternative glycolipids or betaine lipids. In this study, we report lipidomic analysis of six RCA isolates. In addition to the commonly found glycerophospholipids such as phosphatidylglycerol and phosphatidylethanolamine, RCA bacteria synthesise a relatively uncommon phospholipid, acylphosphatidylglycerol, which is not found in copiotrophic roseobacters. Instead, like the abundant SAR11 clade, RCA bacteria upregulate ornithine lipid biosynthesis in response to P stress, suggesting a key role of this aminolipid in the adaptation of marine heterotrophs to oceanic nutrient limitation.
Broadband Tuning the Voltage Dependence of a Sodium Channel
Authors: McCord Eedann , Wisedchaisri Goragot , Catterall William A. 
Published: November 2020

ABSTRACTVoltage-gated sodium channels initiate action potentials in prokaryotes and in many eukaryotic cells, including vertebrate nerve and muscle. Their activation is steeply voltage-dependent, but it is unclear how the voltage sensitivity is set or whether it can be broadly shifted to positive voltages. Here we show that the voltage dependence of activation (VA) of the ancestral bacterial sodium channel NaVAb can be progressively shifted from −118 mV to +35 mV in chimeras with increasing numbers of amino acid residues from the extracellular half of the voltage sensor of human NaV1.7 channels. In a minimal chimera in which only 32 residues were transferred, we analyzed the effects of six additional mutations of conserved amino acid residues singly, in pairs, and as triple mutations. The resulting chimeric mutants exhibited a broad range of voltage sensitivity from VA=−118 mV to VA=+120 mV. Three mutations (N48K, L112A, and M119V) shifted VAto +61 mV when substituted in NaVAb itself, and substitution of two additional Cys residues in the Cys-free background of NaVAb further shifted VAto +105 mV. In these mutants, measurement of gating currents revealed that the voltage dependence of gating charge movement (VQ) shifted to positive membrane potentials as much or more than VA, confirming that the gating charges are trapped in their resting positions by these VA-shifting mutations. Our results demonstrate broadband shifting of VAand VQof a sodium channel across a range of 240 mV and provide a toolbox of methods and constructs to analyze sodium channel structure and function in the resting state at 0 mV and in activated states at positive membrane potentials.GRAPHICAL ABSTRACTThe complete range of broadband tuning of voltage-dependent activation of a sodium channel.
Three-dimensional ATUM-SEM reconstruction and analysis of hepatic endoplasmic reticulum-organelle interactions
Authors: Jiang Yi , Li Linlin , Chen Xi , Liu Jiazheng , Yuan Jingbin , Xie Qiwei , Han Hua 
Published: November 2020

AbstractThe endoplasmic reticulum (ER) is a contiguous and complicated membrane network in eukaryotic cells, and membrane contact sites (MCSs) between the ER and other organelles perform vital cellular functions, including lipid homeostasis, metabolite exchange, calcium level regulation, and organelle division. Here, we establish a whole pipeline to reconstruct all ER, mitochondria, lipid droplets, lysosomes, peroxisomes, and nuclei by automated tape-collecting ultramicrotome scanning electron microscopy (ATUM-SEM) and deep-learning techniques, which generates an unprecedented 3D model for mapping liver samples. Furthermore, the morphology of various organelles is systematically analyzed. We found that the ER presents with predominantly flat cisternae and is knitted tightly all throughout the intracellular space and around other organelles. In addition, the ER has a smaller volume-to-membrane surface area ratio than other organelles, which suggests that the ER could be more suited for functions that require a large membrane surface area. Moreover, the MCSs between the ER and other organelles are explored. Our data indicate that ER-mitochondrial contacts are particularly abundant, especially for branched mitochondria. In addition, ER contacts with lipid droplets, lysosomes, and peroxisomes are also plentiful. In summary, we design an efficient method for obtaining a 3D reconstruction of biological structures at a nanometer resolution. Our study also provides the first 3D reconstruction of various organelles in liver samples together with important information fundamental for biochemical and functional studies in the liver.
In vivostabilization of endogenous chloroplast RNAs by customized artificial pentatricopeptide repeat proteins
Authors: Manavski Nikolay , Meteignier Louis-Valentin , Rojas Margarita , Brachmann Andreas , Barkan Alice , Hammani Kamel 
Published: November 2020

ABSTRACTPentatricopeptide repeat (PPR) proteins are helical repeat-proteins that bind RNA in a modular fashion with a sequence-specificity that can be manipulated by the use of an amino acid code. As such, PPR repeats are promising scaffolds for the design of RNA binding proteins for synthetic biology applications. However, thein vivofunctional capabilities of artificial PPR proteins built from consensus PPR motifs are just starting to be explored. Here, we reportin vivofunctions of an artificial PPR protein, dPPRrbcL, made of consensus PPR motifs that were designed to bind a sequence near the 5’ end ofrbcLtranscripts in Arabidopsis chloroplasts. We used a functional complementation assay to demonstrate that this protein bound its intended RNA target with specificityin vivoand that it substituted for a natural PPR protein by stabilizing processedrbcLmRNA. We targeted a second protein of analogous design to thepetL5’ UTR, where it substituted for the native stabilizing PPR protein PGR3, albeit inefficiently. These results showed that artificial PPRs can be engineered to functionally mimic the class of native PPR proteins that serve as physical barriers against exoribonucleases.